Home

G A M E S S - U K USER'S GUIDE Version 8.0 June 2008 MOPAC

1. is the unipositive sparkle The charge on the system would then be zero A water molecule polarized by a positive sparkle would have the formula H3O and the charge on the system would be 4 1 At first sight a sparkle would appear to be too ionic to be a point charge and would combine with the first charge of opposite sign it encountered This representation is faulty and a better description would be of an ion of diameter 1 4 and the charge delocalized over its surface Computationally a sparkle is an integer charge at the center of a repulsion sphere of form exp ar The hardness of the sphere is such that other atoms or sparkles can approach within about 2 quite easily but only with great difficulty come closer than 1 4 6 13 Mechanism of the frame in FORCE calculation Uses of Sparkles 1 They can be used as counterions e g for acid anions or for cations Thus if the ionic form of an acid is wanted then the moieties H X H and X could be examined 2 Two sparkles of equal and opposite sign can form a dipole for mimicking solvation effects Thus water could be surrounded by six dipoles to simulate the solvent cage A dipole of value D can be made by using the two sparkles and or using and If and are used the inter sparkle separation would be D 4 803A If and are used the separation would be D 9 606A If the inter sparkle separation is less than 1 0A a situation that cannot oc
2. sign TRIPLET C The triplet state is defined If the system has an odd number of electrons an error message will be printed Keywords UHF interpretation The number of alpha electrons exceeds that of the beta electrons by 2 If TRIPLET is not specified then the numbers of alpha and beta electrons are set equal This does not necessarily correspond to a singlet RHF interpretation An RHF MECI calculation is performed to calculate the triplet state If no other C I keywords are used then only one state is calculated by default The occupancy of the M O s in the SCF calculation is defined as 2 1 1 0 that is one electron is put in each of the two highest occupied M O s See keywords C I 2n and OPEN n1 n2 TS C Within the Eigenvector Following routine the option exists to optimize a transition state To do this use TS Preliminary indications are that the TS method is much faster and more reliable than either SIGMA or NLLSQ TS appears to work well with cartesian coordinates In the event that TS does not converge on a stationary point try adding RECALC 5 to the keyword line UHF C The unrestricted Hartree Fock Hamiltonian is to be used VECTORS 0 The eigenvectors are to be printed In UHF calculations both alpha and beta eigenvectors are printed in all cases the full set occupied and virtual are output The eigenvectors are normalized to unity that is the sum of the squares of t
3. 0 76725 0 00000 0 62774 0 00000 0 00000 0 54204 00000 0 23848 31495 00000 23848 31495 00000 o Oooo0 o0 Testdata VIBRATION FREQ T DIPOLE TRAVEL RED MASS VIBRATION FREQ T DIPOLE TRAVEL RED MASS VIBRATION FREQ T DIPOLE TRAVEL RED MASS VIBRATION FREQ T DIPOLE TRAVEL RED MASS VIBRATION FREQ T DIPOLE TRAVEL RED MASS VIBRATION FREQ T DIPOLE TRAVEL RED MASS DESCRIPTION OF VIBRATIONS 1 1209 90 0 8545 0 1199 1 9377 2 1214 67 0 1275 0 1360 1 5004 3 1490 53 0 3445 0 1846 0 6639 4 2114 54 3 3662 0 0484 6 7922 5 3255 94 0 7829 0 1174 0 7508 6 3302 12 0 3478 0 1240 0 6644 ATOM PAIR C2 H3 C2 H4 1 072 ATOM PAIR C2 H3 C2 H4 01 C2 ATOM PAIR C225 H4 C2 H3 01 C2 ATOM PAIR d C2 62 9 Hi C2 H3 ATOM PAIR C2 H3 C2 H4 Otis 602 ATOM PAIR C2 H4 C2 H3 Oot ES C2 SYSTEM IS A GROUND STATE ENERGY ENERGY ENERGY ENERGY ENERGY ENERGY CONTRIBUTION 42 7 79 4 40 79 14 6 CONTRIBUTION 45 1 62 3 45 1 9 8 CONTRIBUTION 49 6 61 5 49 6 0 9 CONTRIBUTION 60 1 100 5 20 0 20 0 CONTRIBUTION 49 5 72 2 49 5 1 0 CONTRIBUTION 49 3 69 8 49 3 1 4 FORMALDEHYDE MNDO ENERGY 32 8819 See Manual DEMONSTRATION OF MOPAC FORCE AND THERMODYNAMICS CALCULATION MOLECULE IS NOT LINEAR THERE ARE 6 GENUINE VIBRATIONS IN
4. 2 3 Definitions of keywords POINT n C The number of points to be calculated on a reaction path is specified by POINT n Used only with STEP in a path calculation POINT1 n C In a grid calculation the number of points to be calculated in the first direction is given by POINT1 n n should be less than 24 default 11 POINT2 n C In a grid calculation the number of points to be calculated in the second direction is given by POINT2 n n should be less than 24 default 11 POTWRT W In an ESP calculation write out surface points and electrostatic potential values to UNIT 21 POLAR C The polarizability and first and second hyperpolarizabilities are to be calculated At present this calculation does not work for polymers but should work for all other systems Two different options are implemented the older finite field method and a new time dependent Hartree Fock method Time Dependent Hartree Fock This procedure is based on the detailed description given by M Dupuis and S Karna J Comp Chem 12 487 1991 The program is capable of calculating Frequency Dependent Polarizability alpha w w Second Harmonic Generation beta 2w w w Electrooptic Pockels Effect beta w 0 w Optical Rectification beta 0 w w Third Harmonic Generation gamma 3w w w w DC EFISH gamma 2w 0 w w Optical Kerr Effect gamma w 0 0 w Intensity Dependent Index of Refraction gamma w w w w The input is given
5. 6 12 Sparkles Four extra elements have been put into MOPAC These represent pure ionic charges roughly equivalent to the following chemical entities Chemical Symbol Equivalent to Tetramethyl ammonium radical Potassium atom or Cesium atom Barium atom Borohydride radical Halogen or Nitrate radical gt Sulfate oxalate For the purposes of discussion these entities are called sparkles the name arises from consideration of their behavior Behavior of sparkles in MOPAC Sparkles have the following properties 1 Their nuclear charge is integer and is 1 2 1 or 2 there are an equivalent number of electrons to maintain electroneutrality 1 2 1 and 2 respectively For example a sparkle consists of a unipositive nucleus and an electron The electron is donated to the quantum mechanics calculation 2 They all have an ionic radius of 0 7 A Any two sparkles of opposite sign will form an ion pair with a interatomic separation of 1 4 A 3 They have a zero heat of atomization no orbitals and no ionization potential They can be regarded as unpolarizable ions of diameter 1 4A They do not contribute to the orbital count and cannot accept or donate electrons Since they appear as uncharged species which immediately ionize attention should be given to the charge on the whole system For example if the alkaline metal salt of formic acid was run the formula would be HC00 where
6. This section is aimed at the complete novice someone who knows nothing at all about the structure of a MOPAC data file First of all there are at most four possible types of data files for MOPAC but the simplest data file is the most commonly used Rather than define it two examples are shown below An explanation of the geometry definitions shown in the examples is given in the chapter GEOMETRY SPECIFICATION 1 6 1 Example of data for ethylene Line 1 UHF PULAY MINDO3 VECTORS DENSITY LOCAL T 300 Line 2 3 EXAMPLE OF DATA FOR MOPAC Line 3 4 MINDO 3 UHF CLOSED SHELL D2D ETHYLENE Line 4a C Line 4b C 1 400118 1 Line 4c H 1 098326 1 123 572063 1 Line 4d H 1 098326 1 123 572063 1 180 000000 0 2 1 Line 4e H 1 098326 1 123 572063 1 90 000000 0 1 2 Line 4f H 1 098326 1 123 572063 1 270 000000 0 1 2 Line bu As can be seen the first three lines are textual The first line consists of keywords here seven keywords are shown These control the calculation The next two lines are comments or titles The user might want to put the name of the molecule and why it is being run on these two lines These three lines are obligatory If no name or comment is wanted leave blank lines If no keywords are specified leave a blank line A common error is to have a blank line before the keyword line this error is quite tricky to find so be careful not to have four lines before the start of the geometric data lines 4a 4f in the exampl
7. 3 2 Rin E SE oro ean Background Crot 3 2 R 6 17 Translation M is Molecular weight ABBAS e EET 6 18 Eq 3 2 RT Sia R S 5m gt inet Sm mr inp 5 2 RInT 3 2 Rln M Rn p 2 31482 Cu 5 2 R or Hira 5 2 RT due to the pV term cf H U pV The internal energy U at T is U Eeq at Evib T Erot E Erral 6 23 or U Eeq ag Ezero Evin 0 Z gt T T Exot a Erra 6 24 Enthalpy H for one mole of gas is defined as H U pV 6 25 Assumption of an ideal gas i e pV RT leads to H U pV U RT 6 26 Thus Gibbs free energy G can be calculated as G H TS 0 T 6 27 Thermochemistry in MOPAC It should be noted that MO parameters for MINDO 3 MNDO AM1 and PM3 are op timized so as to reproduce the experimental heat of formation i e standard enthalpy of formation or the enthalpy change to form a mole of compound at 25 degrees C from its elements in their standard state as well as observed geometries mostly at 25 degrees C and not to reproduce the Eq and equilibrium geometry at 0 K In this sense Esef defined as Heat of formation force constants normal vibration Ezero calculated in FORCE is not the true Ezero Its use as Ezero should be made at your own risk bearing in mind the situation discussed above Since E is standard enthalpy of formation at 25 degree C Eset Eeq Ezero Evip 0 gt 298 15 Erot Etra pV _ Ege at
8. Odd electron systems given in parentheses CHARGE n C When the system being studied is an ion the charge n on the ion must be supplied by CHARGE n For cations n can be 1 2 3 etc for anions 1 or 2 or 3 etc Examples 2 3 Definitions of keywords ION KEYWORD ION KEYWORD NH4 CHARGE 1 CH3C00 CHARGE 1 C2H5 CHARGE 1 COO CHARGE 2 04 CHARGE 2 P04 3 CHARGE 3 HS04 CHARGE 1 H2P04 CHARGE 1 DCART O The cartesian derivatives which are calculated in DCART for variationally optimized systems are printed if the keyword DCART is present The derivatives are in units of kcals Angstrom and the coordinates are displacements in x y and z DEBUG 0 Certain keywords have specific output control meanings such as FOCK VECTORS and DENSITY If they are used only the final arrays of the relevant type are printed If DEBUG is supplied then all arrays are printed This is useful in debugging ITER DEBUG can also increase the amount of output produced when certain output keywords are used e g COMPFG DENOUT 0 The density matrix at the end of the calculation is to be output in a form suitable for input in another job If an automatic dump due to the time being exceeded occurs during the current run then DENOUT is invoked automatically see RESTART DENSITY O At the end of a job when the results are being printed the density matrix is also printed For RHF the normal density mat
9. all things to all atoms On bonding to hydrogen it behaves similar to a hydrogen atom On bonding to fluorine it behaves like a very electronegative atom If several capped bond atoms are used each will behave independently Thus if the two hydrogen atoms in formic acid were replaced by Cb s then each Cb would independently become electroneutral Capped bonds internal coordinates should not be optimized A fixed bond length of 1 7 A is recommended if two Cb are on one atom a contained angle of 109 471221 degrees is suggested and if three Cb are on one atom a contained dihedral of 120 degrees note sign should be used Element 99 X or XX is known as a dummy atom and is used in the definition of the geometry it is deleted automatically from any cartesian coordinate geometry files Dummy atoms are pure mathematic points and are useful in defining geometries for example in ammonia the definition of C3v symmetry is facilitated by using one dummy atom and symmetry relating the three hydrogens to it Output normally only gives chemical symbols Isotopes are used in conjunction with chemical symbols If no isotope is specified the average isotopic mass is used thus chlorine is 35 453 This is different from some earlier versions of MOPAC in which the most abundant isotope was used by default This change was justified by the removal of any ambiguity in the choice of isotope Also the experimental vibrational spectra involve a mixture of i
10. 1988 On Half Electron Ground States of Conjugated Molecules IX Hydrocarbon Radicals and Radical Ions M J S Dewar J A Hashmall C G Venier J A C S 90 1953 1968 Triplet States of Aromatic Hydrocarbons M J S Dewar N Trinajstic Chem Comm 646 1970 Semiempirical SCF MO Treatment of Excited States of Aromatic Compounds M J S Dewar N Trinajstic J Chem Soc A 1220 1971 On Pulay s Converger Convergence Acceleration of Iterative Sequences The Case of SCF Iteration Pulay P Chem Phys Lett 73 393 1980 On Pseudodiagonalization Fast Semiempirical Calculations Stewart J J P Csaszar P Pulay P J Comp Chem 3 227 1982 On Localization A New Rapid Method for Orbital Localization P G Perkins and J J P Stewart J C S Faraday II 11 000 1981 On Diagonalization Beppu Y Computers and Chemistry Vol 6 1982 References On MECI Molecular Orbital Theory for the Excited States of Transition Metal Complexes D R Armstrong R Fortune P G Perkins and J J P Stewart J Chem Soc Faraday IT 68 1839 1846 1972 On Broyden Fletcher Goldfarb Shanno Method Broyden C G Journal of the Institute for Mathematics and Applications Vol 6 pp 222 231 1970 Fletcher R Computer Journal Vol 13 pp 317 322 1970 Goldfarb D Mathematics of Computation Vol 24 pp 23 26 1970 Shanno D F Mathematics of Compu
11. C 1 551261 1 0 000000 0 0 000000 0 1 00 Line 4c 0 1 401861 1 108 919034 1 0 000000 0 2 1 0 Line 4d C 1 401958 1 119 302489 1 179 392581 1 3 2 1 Line 4e C 1 551074 1 108 956238 1 179 014664 1 4 3 2 Line 4f C 1 541928 1 113 074843 1 179 724877 1 5 4 3 Line 4g C 1 551502 1 113 039652 1 179 525806 1 6 5 4 Line 4h 0 1 402677 1 108 663575 1 179 855864 1 T 6 5 Line 4i C 1 402671 1 119 250433 1 179 637345 1 8 7T 6 Line 4j C 1 552020 1 108 665746 1 179 161900 1 9 8 7 Line 4k XX 1 552507 1 112 659354 1 178 914985 1 10 9 8 Line 41 XX 1 547723 1 113 375266 1 179 924995 1 11 10 9 Line 4m H 1 114250 1 89 824605 1 126 911018 1 1 3 2 Line 4n H 1 114708 1 89 909148 1 126 650667 1 1 3 2 Line 4o H 1 123297 1 93 602831 1 127 182594 1 2 4 3 1 6 The data file Line Line Line Line Line Line Line Line Line Line Line Line Line Line Line Polytetrahydrofuran has a repeat unit of C4HgO o i e twice the monomer unit This is necessary in order to allow the lattice to repeat after a translation through 12 3 A See the section on Solid State Capability for further details Note the two dummy atoms on lines 4k and 4l These are useful but not essential for defining the geometry The atoms on lines 4y to 4B use these dummy atoms as does the translation vector on line 4C The translation vector has only the length marked for 4p 4q 4r 4s 4t 4u 4v 4w 4x 4y 4z 4A 4B AC 5 3 Hi oH Hj HS Hd dio di Hi Hj Hd Hd d
12. MNDO MINDO 3 AMI or PM3 Hamiltonian here the default MNDO Hamiltonian is used Note 2 The Version number is a constant for any release of MOPAC and refers to the program not to the Hamiltonians used The version number should be cited in any correspondence regarding MOPAC Users own in house modified versions of MOPAC will have a final digit different from zero e g 6 01 All the keywords used along with a brief explanation should be printed at this time If a keyword is not printed it has not been recognized by the program Keywords can be in upper or lower case letters or any mixture The cryptic message at the right end of the lower line of asterisks indicates the number of heavy and light atoms this version of MOPAC is configured for Note 3 Symmetry information is output to allow the user to verify that the requested symmetry functions have in fact been recognized and used Note 4 The data for this example used a mixture of atomic numbers and chemical symbols but the internal coordinate output is consistently in chemical symbols The atoms in the system are in order e Atom 1 an oxygen atom this is defined as being at the origin e Atom 2 the carbon atom Defined as being 1 2 Angstroms from the oxygen atom it is located in the x direction This distance is marked for optimiza tion e Atom 3 a hydrogen atom It is defined as being 1 1 Angstroms from the carbon atom and making an angle of 120 degrees with th
13. The pure NR step can be skipped by giving the keyword NONR An alternative to the QA step is to simply scale the P RFO step down to the trust radius by a multiplicative constant this can be accomplished by specifying RSCAL Background 2 Using the step determined from 1 the new energy and gradient are evaluated If it is a TS search two criteria are used in determining whether the step is appropriate The ratio between the actual and predicted energy change should ideally be 1 If it deviates substantially from this value the second order Taylor expansion is no longer accurate RMIN and RMAX default values 0 and 4 determine the limits on how far from 1 the ratio can be before the step is rejected If the ratio is outside the RMIN and RMAX limits the step is rejected the trust radius reduced by a factor of two and a new step is determined The second criteria is that the eigenvector along which the energy is being maximized should not change substantially between iterations The minimum overlap of the TS eigenvector with that of the previous iteration should be larger than OMIN otherwise the step is rejected Such a step rejection can be recognized in the output by the presence of possibly more lines with the same CYCLE number The default OMIN value is 0 8 which allows fairly large changes to occur and should be suitable for most uncomplicated systems See below for a discussion of how to use RMIN RMAX and OMIN for difficult c
14. calling GRAPH GRAPH first calls MULLIK in order to generate the inverse square root of the overlap matrix which is required for the re normalization of the eigenvectors All data essential for the graphics package DENSITY are then output HESS n W When the Eigenvector Following routine is used for geometry optimization it frequently works faster if the Hessian is constructed first If HESS 1 is specified the Hessian matrix will be constructed before the geometry is optimized There are other less common options e g HESS 2 See comments in subroutine EF for details H PRIORITY O In a DRC calculation results will be printed whenever the calculated heat of formation changes by 0 1 kcal mole Abbreviation H PRIO H PRIORITY n nn O In a DRC calculation results will be printed whenever the calculated heat of formation changes by n nn kcal mole IRC C An Intrinsic Reaction Coordinate calculation is to be run All kinetic energy is shed at every point in the calculation See Background IRC n C An Intrinsic Reaction Coordinate calculation to be run an initial perturbation in the direction of normal coordinate n to be applied If n is negative then perturbation is reversed i e initial motion is in the opposite direction to the normal coordinate This keyword cannot be written with spaces around the sign 2 3 Definitions of keywords ISOTOPE O Generation of the FORCE matrix is very time consuming and
15. contribution of the pair to the mode calculated according to the formula described below Formula for energy contribution The total vibrational energy T carried by all pairs of bonded atoms in a molecule is first calculated For any given pair of atoms A and B the relative contribution R A B as a percentage is given by the energy of the pair P A B times 100 divided by T i e r A B 100 HE As an example for formaldehyde the energy carried by the pair of atoms C O is added to the energy of the two C H pairs to give a total T Note that this total cannot be related to anything which is physically meaningful there is obvious double counting but it is a convenient artifice For mode 4 the C O stretch the relative contribution of the carbon oxygen pair is 60 196 It might be expected to be about 100 after all we envision the C O bond as absorbing the photon however the fact that the carbon atom is vibrating implies that it is changing its position relative to the two hydrogen atoms If the total vibrational energy E the actual energy of the absorbed photon as distinct from T were carried equally by the carbon and oxygen atoms then the relative contributions to the mode would be C O 50 C H 25 C H 25 respectively This leads to the next entry which is given in parentheses For the pair with the highest relative contribution in mode 4 the C O stretch the energy of that pair divided by the t
16. information read the comments in subroutine EF K n nn n C Used in band structure calculations K n nn n specifies the step size in the Brillouin zone and the number of atoms in the monomeric unit Two band structure calculations are supported electronic and phonon Both require a polymer to be used If FORCE is used a phonon spectrum is assumed otherwise an electronic band structure is assumed For both calculations a density of states is also done The band structure calculation is very fast so a small step size will not use much time The output is designed to be fed into a graphics package and is not elegant For polyethylene a suitable keyword would be K 0 01 6 KINETIC n nnn C In a DRC calculation n nnn kcals mole of excess kinetic energy is added to the system as soon as the kinetic energy builds up to 0 2 kcal mole The excess energy is added to the velocity vector without change of direction LARGE O Most of the time the output invoked by keywords is sufficient LARGE will cause less commonly wanted but still useful output to be printed 1 To save space DRC and IRC outputs will by default only print the line with the percent sign Other output can be obtained by use of the keyword LARGE according to the following rules Keywords LARGE Print all internal and cartesian coordinates and cartesian velocities LARGE 1 Print all internal coordinates LARGE 1 Print all internal and cartesian
17. one two or three arguments Possible options are MOPAC MYDATAFILE 120 4 MOPAC MYDATAFILE 120 MOPAC MYDATAFILE In the latter case it is assumed that the shortest queue will be adequate The COM file to run the MOPAC can be accessed using the command MOPAC followed by none one or two arguments Possible options are MOPAC MYDATAFILE 120 MOPAC MYDATAFILE In the latter case it is assumed that the default time 15 seconds will be adequate MOPAC In this case you will be prompted for the datafile and then for the queue Restarts should be user transparent If MOPAC does make any restart files do not change them It would be hard to do anyhow as they re in machine code as they will be used when you run a RESTART job The files used by MOPAC are File Description Logical name lt filename gt DAT Data FOROO5 filename OUT Results FOROO6 lt filename gt RES Restart FOROO9 lt filename gt DEN Density matrix in binary FORO10 SYS 0UTPUT LOG file FORO11 lt filename gt ARC Archive or summary FORO12 lt filename gt GPT Data for program DENSITY FORO13 lt filename gt SYB SYBYL data FORO16 SETUP DAT SETUP data SETUP Short version For various reasons it might not be practical to assemble the entire MOPAC program For example your computer may have memory limitations or you may have very large systems to be run or some options may never be wanted For whatever reason if using the entire program is undesirable an
18. research work of Prof Dewar s group The new AMPAC 2 1 thus has functionalities not present in MOPAC In publications users should cite not only the program name but also the version number Commercial concerns have optimized both MOPAC and AMPAC for use on super computers The quality of optimization and the degree to which the parent algorithm has been preserved differs between MOPAC and AMPAC and also between some machine specific versions Different users may prefer one program to the other based on consider ations such as speed Some modifications of AMPAC run faster than some modifications of MOPAC and vice versa but if these are modified versions of MOPAC 3 0 or AMPAC 1 0 they represent the programming prowess of the companies doing the conversion and not any intrinsic difference between the two programs Testing of these large algorithms is difficult and several times users have reported bugs in MOPAC or AMPAC which were introduced after they were supplied by QCPE Cooperative Development of MOPAC MOPAC has developed and hopefully will continue to develop by the addition of con tributed code As a policy any supplied code which is incorporated into MOPAC will be described in the next release of the Manual and the author or supplier acknowledged In the following release only journal references will be retained T he objective is to produce a good program This is obviously not a one person undertaking if it was then the prod
19. s or the McIver Komornicki methods For any further results to be printed the second message must be as shown when no SCF is obtained no results will be printed Note 13 Again the results are headed with either MNDO or MINDO 3 banners and the version number The date has been moved to below the version number for convenience Note 14 The total energy of the system is the addition of the electronic and nuclear terms The heat of formation is relative to the elements in their standard state The I P is the negative of the energy level of the highest occupied or highest partially occupied molecular orbital in accordance with Koopmans theorem Note 15 Advice on time required for the calculation This is obviously useful in esti mating the times required for other systems Note 16 The fully optimized geometry is printed here If a parameter is not marked for optimization it will not be changed unless it is a symmetry related parameter Note 17 The roots are the eigenvalues or energy levels in electron volts of the molecular orbitals There are six filled levels therefore the HOMO has an energy of 11 041eV analysis of the corresponding eigenvector not given here shows that it is mainly lone pair on oxygen The eigenvectors form an orthonormal set Note 18 The charge on an atom is the sum of the positive core charge for hydrogen carbon and oxygen these numbers are 1 0 4 0 and 6 0 respectively and the nega tive of t
20. uct would be poor indeed Instead as we are in a time of rapid change in computational chemistry a time characterized by a very free exchange of ideas and code MOPAC has been evolving by accretion T he unstinting and generous donation of intellectual effort speaks highly of the donors However with the rapid commercialization of computational Description of MOPAC chemistry software in the past few years it is unfortunate but it seems unlikely that this idyllic state will continue 1 5 Programs recommended for use with MOPAC MOPAC is the core program of a series of programs for the theoretical study of chemical phenomena This version is the sixth in an on going development and efforts are being made to continue its further evolution In order to make using MOPAC easier five other programs have also been written Users of MOPAC are recommended to use all four programs Efforts will be made to continue the development of these programs HELP HELP is a stand alone program which mimics the VAX HELP function It is intended for users on UNIX computers HELP comes with the basic MOPAC 6 00 and is recommended for general use DRAW DRAW written by Maj Donn Storch USAF and available through QCPE is a pow erful editing program specifically written to interface with MOPAC Among the various facilities it offers are 1 The on line editing and analysis of a data file starting from scratch or from an existing data file an archi
21. 000000 0 1 2 3 0 0 000000 0 0 000000 0 0 0000000 0 0 O0 3 1 4 5 6 T 8 3 2 4 5 6 T 8 Here atom 3 a hydrogen is used to define the bond lengths symmetry relation 1 of atoms 4 5 6 7 and 8 with the atoms they are specified to bond with in the NA column of the data file similarly its angle symmetry relation 2 is used to define the bond angle of atoms 4 5 6 7 and 8 with the two atoms specified in the NA and NB columns of the data file The other angles are point group symmetry defined as a multiple of 60 degrees Keywords Spaces tabs or commas can be used to separate data Note that only three parameters are marked to be optimized The symmetry data can be the last line of the data file unless more data follows in which case a blank line must be inserted after the symmetry data The full list of available symmetry relations is as follows lt Symmetry SYMMETRY FUNCTIONS relation gt 1 BOND LENGTH IS SET EQUAL TO THE REFERENCE BOND LENGTH 2 BOND ANGLE IS SET EQUAL TO THE REFERENCE BOND ANGLE 3 DIHEDRAL ANGLE IS SET EQUAL TO THE REFERENCE DIHEDRAL ANGLE 4 DIHEDRAL ANGLE VARIES AS 90 DEGREES REFERENCE DIHEDRAL 5 DIHEDRAL ANGLE VARIES AS 90 DEGREES REFERENCE DIHEDRAL 6 DIHEDRAL ANGLE VARIES AS 120 DEGREES REFERENCE DIHEDRAL 7 DIHEDRAL ANGLE VARIES AS 120 DEGREES REFERENCE DIHEDRAL 8 DIHEDRAL ANGLE VARIES AS 180 DEGREES REFERENCE DIHEDRAL 9 DIHEDRAL ANGLE VARIES AS 180 DEGREES REFERENCE DIHEDRAL 10 DIHEDRAL AN
22. 08893 0 39806 8 0 27166 0 00003 0 38524 0 15510 0 53641 9 0 00007 0 60187 0 00001 0 00000 0 00000 10 0 53307 0 00006 0 55757 0 08893 0 39803 11 0 27165 0 00003 0 38524 0 15509 0 53637 12 0 00007 0 60187 0 00001 0 00000 0 00000 ROOT NO 7 8 9 10 11 0 00019 0 00044 0 00016 3 38368 2 03661 1 0 25401 0 00000 0 00000 0 00000 0 00000 1974 54 1972 29 1969 14 Note 4 Note 5 3302 Oo o0 o OO OOO 0o 12319 00067 00000 00000 06298 00000 00000 36994 57206 00000 36997 57209 00000 12 76725 00000 5 2 Results file for the force calculation 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0 10 0 11 0 12 0 ROOT NO 1209 1 0 2 0 3 0 4 0 5 0 6 0 7 0 8 0 9 0 10 0 11 0 12 0 ROOT NO 0 1 0 2 0 3 0 4 0 5 0 6 0 T 0 8 0 9 0 10 0 11 0 12 0 00000 00000 25401 00000 00000 25401 00000 00000 25401 00000 00000 MASS WEIGHTED COORDINATE ANALYSIS 90331 00000 26985 00002 00000 46798 00006 53018 27018 00007 53018 27018 00007 00025 72996 00000 00000 63247 00000 00000 18321 00000 00000 18321 00000 00000 1214 25401 00000 00000 25401 00000 00000 25401 00000 00000 25401 00000 67040 00000 00003 15005 00000 00005 51814 00005 00003 59541 00006 00003 59541 00022 00000 72996 00000 00000 6
23. 1 114434 1 90 189506 1 126 759550 1 4 6 5 H 1 114534 1 88 522263 1 127 041363 1 5 T 6 Geometry specification md Tv 1 114557 1 114734 1 115150 7 746928 0 000000 Orrrre 88 707407 90 638631 91 747016 0 000000 0 000000 1 126 716355 1 127 793055 1 126 187496 0 0 000000 0 0 000000 oorRnRrRE O H 0 0 O ON ON o00 Oo Chapter 4 Examples In this chapter various examples of data files are described With MOPAC comes two sets of data for running calculations One of these is called MNRSD1 DAT and this will now be described 4 1 MNRSDI test data file for formaldehyde The following file is suitable for generating the results described in the next section and would be suitable for debugging data SYMMETRY Formaldehyde for Demonstration Purposes Line Line Line Line 0 Line C 1 2 1 Line H 1 1 1 120 1 Line H 1 10 1200 18002 13 Line o co 10014 0 lNH w 14 24 Line Line 10 Line 11 w These data could be more neatly written as Line 1 SYMMETRY Line 2 Formaldehyde for Demonstration Purposes Line 3 Line 4 0 Line 5 C 1 20 1 1 Line 6 H 1 10 1 120 00 1 2 1 Line 7 H 1 10 0 120 00 0 180 00 0 2 1 3 Line 8 Line 9 3 1 4 Line 10 3 2 4 Line 11 These two data files will produce identical results files In all geometric specifications care must be taken in defining the internal coordinates to ensure that no three atoms being used to define a fourth atom
24. 6 43 Background Non linear molecule NE T 1 2 44 Qrot a c ascen 6 Ey ORT 6 45 R T kT 3 Stot P cana 3c s n 0 5R3In kT he 2ino n az z 3 6 46 0 5R 31In Ci 2ino In 7 3 Gra 3 2 R 6 47 Translation VORMETINSN 1 660540 x 7 x20 MKT V Qn e eec S 6 48 h h Bug CERT 6 49 Hea 3 2 RT pV 5 2 RT cf pV RT 6 50 Stra R 2 5 nT 31n M 2 31482 cf p latm 0 993608 5 In T 31n M 2 31482 6 51 In MOPAC Hyib Eyib 0 T 6 52 Note Ezero is not included in Hy w is not derived from force constants at 0 K and for T Hr Hvip T Hrot F Hira 6 53 while for T 298 15 K H298 Hvib Hrot Hira 6 54 Note that Hr and H 98 is equivalent to Eyib Ezero Erot Etra pV 6 55 except that the normal frequencies are those obtained from force constants at 25 degree C or at least not at 0 K Thus Standard Enthalpy of Formation AH can be calculated according to Eqs 6 24 6 25 and 6 28 as shown in Eq 6 29 AH Est Hr Hogs 6 56 Note that Ezero is already counted in Eger see Eq 6 28 By using Eq 6 26 Standard Internal Energy of Formation AU can be calculated as AU AH R T 298 15 6 57 Standard Gibbs Free Energy of Formation AG can be calculated by taking the dif ference from that for the isomer or that at different temperature AG AH TS for the state under co
25. ElectroStatic Potentials ESP Atomic Charges Derived from Semiempirical Methods B H Besler K M Merz Jr P A Kollman J Comp Chem 11 431 439 1990 On MNDO Ground States of Molecules 38 The MNDO Method Approximations and Parame ters M J S Dewar W Thiel J Am Chem Soc 99 4899 1977 Original References for Elements Parameterized in MNDO H M J S Dewar W Thiel J Am Chem Soc 99 4907 1977 Li Parameters taken from the MNDOC program written by Walter Thiel Quant Chem Prog Exch No 436 2 63 1982 Be M J S Dewar H S Rzepa J Am Chem Soc 100 777 1978 B M J S Dewar M L McKee J Am Chem Soc 99 5231 1977 C M J S Dewar W Thiel J Am Chem Soc 99 4907 1977 N M J S Dewar W Thiel J Am Chem Soc 99 4907 1977 O M J S Dewar W Thiel J Am Chem Soc 99 4907 1977 F M J S Dewar H S Rzepa J Am Chem Soc 100 58 1978 Al L P Davis R M Guidry J R Williams M J S Dewar H S Rzepa J Comp Chem 2 433 1981 References Si a M J S Dewar M L McKee H S Rzepa J Am Chem Soc 100 3607 1978 1 c M J S Dewar J Friedheim G Grady E F Healy J J P Stewart Organometallics 5 375 1986 P M J S Dewar M L McKee H S Rzepa J Am Chem Soc 100 3607 1978 S a M J S Dewar M L McKee H S Rzepa J Am Chem Soc 100 3607 1978 1 b M J S Dewar C H Reynolds J Comp Chem 7 140 19
26. FOCK Every Fock matrix Note 1 HCORE The one electron matrix and two electron integrals ITER Values of variables and constants in ITER LARGE Increases amount of output generated by other keywords LINMIN Details of line minimization LINMIN LOCMIN SEARCH MOLDAT Molecular data number of orbitals U values etc MECI C I matrices M Q indices etc PL Differences between density matrix elements Note 4 in ITER LINMIN Function values step sizes at all points in the Debugging line minimization LINMIN or SEARCH TIMES Times of stages within ITER VECTORS All eigenvectors on every iteration Note 1 Notes 1 These keywords are activated by the keyword DEBUG Thus if DEBUG and FOCK are both specified every Fock matrix on every iteration will be printed 2 DEBUG is not intended to increase the output but does allow other keywords to have a special meaning 3 PULAY is already a keyword so DEBUGPULAY was an obvious alternative 4 PL initiates the output of the value of the largest difference between any two density matrix elements on two consecutive iterations This is very useful when investigating options for increasing the rate of convergence of the SCF calculation Suggested procedure for locating bugs Users are supplied with the source code for MOPAC and while the original code is fairly bug free after it has been modified there is a possibility that bugs may have been introduced In these circumstances
27. FORCE calculation where the geometry needs to be known quite precisely then PRECISE is recommended for small systems the extra cost in CPU time is minimal PRECISE is not recommended for experienced users instead GNORM n nn and SCFCRT n nn are suggested PRECISE should only very rarely be necessary in a FORCE calculation all it does is remove quartic contamination which only affects the trivial modes significantly and is very expensive in CPU time PULAY W The default converger in the SCF calculation is to be replaced by Pulay s procedure as soon as the density matrix is sufficiently stable A considerable improvement in speed can be achieved by the use of PULAY If a large number of SCF calculations are envisaged a sample calculation using 1SCF and PULAY should be compared with using 1SCF on its own and if a saving in time results then PULAY should be used in the full calculation 2 3 Definitions of keywords PULAY should be used with care in that its use will prevent the combined package of convergers SHIFT PULAY and the CAMP KING convergers from automatically being used in the event that the system fails to go SCF in ITRY 10 iterations The combined set of convergers very seldom fails QUARTET C RHF interpretation The desired spin state is a quartet i e the state with component of spin 1 2 and spin 3 2 When a configuration interaction calculation is done all spin states of spin equal to or greater tha
28. IRC RESTART and IRC 7 Restarting a DRC RESTART and DRC or DRC n nn 8 Restarting a DRC starting from a transition state RESTART and DRC or DRC n nn Other keywords such as T nnn or GEO OK can be used anytime Examples of DRC IRC data Use of the IRC DRC facility is quite complicated In the following examples various reasonable options are illustrated for a calculation on water It is assumed that an optimized transition state geometry is available Example 1 A Dynamic Reaction Coordinate starting at the transition state for water inverting initial motion opposite to the transition normal mode with 6kcal of excess kinetic energy added in Every point calculated is to be printed Note all coordinates are marked with a zero and T PRIO H PRIO and X PRIO are all absent The results of an earlier calculation using the same keywords is assumed to exist The earlier calculation would have constructed the force matrix While the total cpu time is specified it is in fact redundant in that the calculation will run to completion in less than 600 seconds KINETIC 6 RESTART IRC 1 DRC T 600 WATER H 0 000000 0 0 000000 0 0 000000 0 0 0 0 0 0 911574 0 0 000000 0 0 000000 0 100 H 0 911574 0 180 000000 0 0 000000 0 2 1 0 0 0 000000 0 0 000000 0 0 000000 0 0 0 0 Example 2 An Intrinsic Reaction Coordinate calculation Here the restart is from a previous IRC calculation which was stopped before the minimum was reached Recall that RES
29. M 22J 5 j K i j x O x O j lt i Formation of microstate configuration Microstates are particular electron configurations Thus if there are 5 electrons in 5 levels then various microstates could be as follows Microstates for 5 electrons in 5 M 0 s Electron Configuration Electron Configuration Alpha Beta M s Alpha Beta M s 12345 12345 12345 12345 1 1 1 1 0 0 1 1 0 0 0 1 2 4 1 1 1 1 1 0 0 0 0 0 5 2 2 1 1 0 0 0 1 1 1 0 0 1 2 5 1 1 0 1 0 1 1 0 0 0 1 2 3 1 1 1 0 0 0 0 0 1 1 1 2 6 1 1 0 1 0 1 0 1 0 0 1 2 For 5 electrons in 5 M O s there are 252 microstates 10 5 5 but as states of different spin do not mix we can use a smaller number If doublet states are needed then 100 states 5 2 3 5 3 2 are needed If only quartet states are of interest then 25 states 5 1 4 5 4 1 are needed and if the sextet state is required then only one state is calculated In the microstates listed state 1 is the ground state configuration This can be written as 2 2 1 0 0 meaning that M O s 1 and 2 are doubly occupied M O 3 is singly occupied by an alpha electron and M O s 4 and 5 are empty Microstate 1 has a component of spin of 1 2 and is a pure doublet By Kramer s degeneracy sometimes called time inversion symmetry microstate 2 is also a doublet and has a spin of 1 2 and a component of spin of 1 2 Microstate 3 while it has a component of spin of 1 2 is not a doublet but is in fact a comp
30. RMOPAC When a long job ends RMOPAC will also send a mail message to the user giving a brief description of the job You may want to change the default definition of a long job currently it is 12 hours This feature was written by Dr James Petts of Kodak Ltd Research Labs A recommended sequence of operations to get MOPAC up and running would be 1 Modify the file DIMSIZES DAT The default sizes are 40 heavy atoms and 40 light atoms Do not make the size less than 7 by 7 2 Read through the COMMAND files to familiarize yourself with what is being done 3 Edit the file MOPAC COM to use the local queue names 4 Edit the ile RMOPAC COM if the default file names are not acceptable 5 Edit MOPACCOM COM to assign MOPACDIRECTORY to the disk and directory which will hold MOPAC 6 Edit the individual LOGIN COM files to insert the following line 0 lt Mopac directory gt MOPACCOM Note that MOPACDIRECTORY cannot be used as the definition of MOPACDI RECTORY is made in MOPACCOM COM 7 Execute the modified LOGIN command so that the new commands are effective 8 Run COMPILE COM This takes about 8 minutes to execute Installing MOPAC 9 Enter the command MOPAC You will receive the message What file to which the reply should be the actual data file name For example MNRSD1 the file is assumed to end in DAT e g MNRSD1 DAT You will then be prompted for the queue What queue Any queue defined in MOPAC C
31. SCF calculation does not distinguish between OPEN 2 2 and TRIPLET since both keywords define the same starting configuration This can be verified by monitoring the convergence using PL for which both keywords give the same SCF energy Removal of electrons from starting configuration For a starting configuration of alpha M O occupancies O i O i being in the range 0 0 to 1 0 the energies of the M O s involved in the MECI can be calculated from E i 2 2J 3 KG DOG J where J i j and K i j are the coulomb and exchange integrals between M O s i and j The M O index j runs over those M O s involved in the MECI only Most MECI calculations will involve between 1 and 5 M O s so a system with about 30 filled or partly filled M O s could have M O s 25 30 involved The resulting eigenvalues correspond to those of the cationic system resulting from removal of n electrons where n is twice the sum of the orbital occupancies of those M O s involved in the C I The arbitrary zero of energy in a MECI calculation is the starting ground state without any correction for errors introduced by the use of fractional occupancies In order to calculate the energy of the various configurations the energy of the vacuum 6 14 Configuration interaction state i e the state resulting from removal of the electrons used in the C I needs to be evaluated This energy is defined by GSE 2 E i O i J i i x O i x O i
32. THE SYSTEM IS A TRANSITION STATE USED IN THERMODYNAMICS CALCULATION TRIPLET TRIPLET STATE REQUIRED TS USING EF ROUTINE FOR TS SEARCH UHF UNRESTRICTED HARTREE FOCK CALCULATION VECTORS PRINT FINAL EIGENVECTORS VELOCITY SUPPLY THE INITIAL VELOCITY VECTOR IN A DRC CALCULATION WILLIAMS USE WILLIAMS SURFACE X PRIO GEOMETRY CHANGES TAKE PRIORITY IN DRC XYZ DO ALL GEOMETRIC OPERATIONS IN CARTESIAN COORDINATES 2 3 Definitions of keywords The definitions below are given with some technical expressions which are not further defined Interested users are referred to Appendix E of this manual to locate appropriate references which will provide further clarification There are three classes of keywords 1 those which CONTROL substantial aspects of the calculation i e those which affect the final heat of formation 2 those which determine which OUTPUT will be calculated and printed and 3 those which dictate the WORKING of the calculation but which do not affect the heat of formation The assignment to one of these classes is designated by a C O or W respectively following each keyword in the list below amp C An 4j amp means turn the next line into keywords Note the space before the amp sign Since amp is a keyword it must be preceeded by a space A amp on line 1 would mean that a second line of keywords should be read in If that second line contained a amp then a
33. a check on the input data All obvious errors are trapped and warning messages printed A second use is to convert from one format to another The input geometry is printed in various formats at the end of a OSCF calculation If NOINTER is absent carte sian coordinates are printed Unconditionally MOPAC Z matrix internal coordinates are printed and if AIGOUT is present Gaussian Z matrix internal coordinates are printed OSCF should now be used in place of DDUM 1ELECTRON O The final one electron matrix is printed out This matrix is composed of atomic orbitals the array element between orbitals and j on different atoms is given by H i j 0 5 x B Bj x overlap i j The matrix elements between orbitals i and j on the same atom are calculated from the electron nuclear attraction energy and also from the U i value if i j The one electron matrix is unaffected by a the charge and b the electron density It is only a function of the geometry Abbreviation 1ELEC 1SCF C When users want to examine the results of a single SCF calculation of a geometry 1SCF should be used 1SCF can be used in conjunction with RESTART in which case a single SCF calculation will be done and the results printed When 1SCF is used on its own that is RESTART is not also used then derivatives will only be calculated if GRAD is also specified 1SCF is helpful in a learning situation MOPAC normally performs many SCF calcula tions an
34. a series of 2 x 2 rotations which maximize 74 Called by WRITE e LOCMIN Main sequence In a gradient minimization LOCMIN does a line search to find the gradient norm minimum Main arguments current geometry search direction step current gradient norm on exit optimized geometry gradient norm e MAMULT Utility Matrix multiplication Two matrices stored as lower half trian gular packed arrays are multiplied together and the result stored in a third array as the lower half triangular array Called from PULAY e MATOUT Utility Matrix printer Prints a square matrix and a row vector usually eigenvectors and eigenvalues The indices printed depend on the size of the matrix they can be either over orbitals atoms or simply numbers thus M O s are over orbitals vibrational modes are over numbers Called by WRITE FORCE e ME08A MEO8B Utilities Part of the complex diagonalizer and called by CDIAG e MECI Main sequence Main function for Configuration Interaction MECI con structs the appropriate C I matrix and evaluates the roots which correspond to the electronic energy of the states of the system The appropriate root is then returned Called by ITER only e MECID Utility Constructs the differential C I secular determinant e MECIH Utility Constructs the normal C I secular determinant e MECIP Utility Reforms the density matrix after a MECI calculation e MINV Utility Called by DIIS MINV inverts the Hessian ma
35. an attempt is made to modify any other parameters then an error message is printed and the calculation terminated NUMBER OF PARTICLES nn GREATER THAN When user defined microstates are not used the MECI will calculate all possible mi crostates that satisfy the space and spin constraints imposed This is done in PERM which permutes N electrons in M levels If N is greater than M then no possible permu tation is valid This is not a fatal error the program will continue to run but no C I will be done NUMBER OF PERMUTATIONS TOO GREAT LIMIT 60 The number of permutations of alpha or beta microstates is limited to 60 Thus if 3 alpha electrons are permuted among 5 M O s that will generate 10 5 3 2 alpha mi crostates which is an allowed number However if 4 alpha electrons are permuted among Error messages produced by MOPAC 8 M O s then 70 alpha microstates result and the arrays defined will be insufficient Note that 60 alpha and 60 beta microstates will permit 3600 microstates in all which should be more than sufficient for most purposes An exception would be for excited radical icosohedral systems SYMMETRY SPECIFIED BUT CANNOT BE USED IN DRC This is self explanatory The DRC requires all geometric constraints to be lifted Any symmetry constraints will first be applied to symmetrize the geometry and then removed to allow the calculation to proceed SYSTEM DOES NOT APPEAR TO BE OPTIMIZABLE This
36. at the end of the MOPAC deck and consists of two lines of free field input followed by a list energies The variables on the first line are Keywords Nfreq How many energies will be used to calculate the desired quantities Iwflb Type of beta calculation to be performed This valiable is only important if iterative beta calculations are chosen 0 static 1 SHG 2 EOPE 3 OR Ibet Type of beta calculation 0 beta 0 0 static 1 iterative calculation with type of beta chosen by Iwflb 1 Noniterative calculation of SHG 2 Noniterative calculation of EOPE 3 Noniterative calculation of OR Igam Type of gamma calculation 0 No gamma calculation 1 THG 2 DC EFISH 3 IDRI 4 OKE The vaiables on the second line are Atol Cutoff tolerance for alpha calculations 1 0e 4 seems reasonable Maxitu Maximum number of iteractions for beta calculations Maxita Maximum number of iterations for alpha calculations Btol Cutoff tolerance for beta calculations Nfreq lines follow each with an energy value in eV s at which the hyperpolarizabilites are to be calculated POWSQ C Details of the working of POWSQ are printed out This is only useful in debugging PRECISE W The criteria for terminating all optimizations electronic and geometric are to be increased by a factor normally 100 This can be used where more precise results are wanted If the results are going to be used in a
37. bound of mmm Kelvin the step size being calculated in order to give approximately 20 points and a reasonable value for the step The size of the step in Kelvin degrees will be 1 2 or 5 or a power of 10 times these numbers THERMO nnn mmm ll O Same as for THERMO nnn mmm only now the user can explicitly define the step size The step size cannot be less than 1K T PRIORITY O In a DRC calculation results will be printed whenever the calculated time changes by 0 1 femtoseconds Abbreviation T PRIO T PRIORITY n nn O In a DRC calculation results will be printed whenever the calculated time changes by n nn femtoseconds TRANS C The imaginary frequency due to the reaction vector in a transition state calculation must not be included in the thermochemical calculation The number of genuine vibrations considered can be 3N 5 for a linear ground state system 3N 6 for a non linear ground state system or 3N 6 for a linear transition state complex 3N 7 for a non linear transition state complex This keyword must be used in conjunction with THERMO if a transition state is being calculated TRANS n C The facility exists to allow the THERMO calculation to handle systems with internal rota tions TRANS n will remove the n lowest vibrations Note that TRANS 1 is equivalent to TRANS on its own For xylene for example TRANS 2 would be suitable This keyword cannot be written with spaces around the
38. contribution to the Fock matrix element arising from the exchange integral between an atomic orbital and its equivalent in the adjacent unit cells is ignored This is necessitated by the fact that the density matrix element involved is invariably large The unit cell must be large enough that an atomic orbital in the center of the unit cell has an insignificant overlap with the atomic orbitals at the ends of the unit cell In practice a translation vector of more that about 7 or 8A is sufficient For one rare group of compounds a larger translation vector is needed Polymers with delocalized 7 systems and polymers with very small band gaps will require a larger translation vector in order to accurately sample k space For these systems a translation vector in the order of 15 20 Angstroms is needed Background Chapter 7 Program The logic within MOPAC is best understood by use of flow diagrams There are two main sequences geometric and electronic These join only at one common subroutine COMPFG It is possible therefore to understand the geometric or electronic sections in isolation without having studied the other section 7 1 Main geometric sequence MAIN CHIRON m ei aaa OED nece re eng BERN aum c LT esu eed EEEE OEN IIRC DRCI FORCE REACT1 PATHS or EF je ts Pea E l besas l or POLAR MN het OE lex Jl eat d
39. derivatives are normally calculated using Liotard s analytical C I method If this method is NOT to be used specify NOANCI NO ANalytical Configuration Inter action derivatives NODIIS W In the event that the G DIIS option is not wanted NODIIS can be used The G DIIS normally accelerates the geometry optimization but there is no guarantee that it will do so If the heat of formation rises unexpectedly i e rises during a geometry optimization while the GNORM is larger than about 0 3 then try NODIIS NOINTER O The interatomic distances are printed by default If you do not want them to be printed specify NOINTER For big jobs this reduces the output file considerably NOLOG O Normally a copy of the archive file will be directed to the LOG file along with a synopsis of the job If this is not wanted it can be suppressed completely by NOLOG NOMM C All four semi empirical methods underestimate the barrier to rotation of a peptide bond A Molecular Mechanics correction has been added which increases the barrier in N methyl acetamide to 14 kcal mole If you do not want this correction specify NOMM NO Molecular Mechanics NONR W Not recommended for normal use Used with the EF routine See source code for more details NOTHIEL W In a normal geometry optimization using the BFGS routine Thiel s FSTMIN technique is used If normal line searches are wanted specify NOTHIEL NOXYZ O The cartesian coordinates a
40. description will be given here The main steps in the saddle calculation are as follows 1 The heats of formation of both systems are calculated 2 A vector R of length 3N 6 defining the difference between the two geometries is calculated 3 The scalar P of the difference vector is reduced by some fraction normally about 5 to 15 percent 4 Identify the geometry of lower energy call this G 5 Optimize G subject to the constraint that it maintains a constant distance P from the other geometry 6 If the newly optimized geometry is higher in energy then the other geometry then go to 1 If it is higher and the last two steps involved the same geometry moving make the other geometry G without modifying P and go to 5 7 Otherwise go back to 2 The mechanism of 5 involves the coordinates of the moving geometry being perturbed by an amount equal to the product of the discrepancy between the calculated and required P and the vector R As the specification of the geometries is quite difficult in that the difference vector depends on angles which are of necessity ill defined by 360 degrees SADDLE can be made to run in cartesian coordinates using the keyword XYZ If this option is chosen then the initial steps of the calculation are as follows 1 Both geometries are converted into cartesian coordinates 2 Both geometries are centered about the origin of cartesian space 3 One geometry is rotated until the difference
41. domain and can be used by anyone for any purpose To help developers the donated code is packaged into files each file representing one donation In addition some notes have been added to the Manual These may be useful in understanding the donations If you want to use MOPAC 7 for production work you should get the copyrighted copy from the Quantum Chemistry Program Exchange That copy has been carefully written and allows the donors contributions to be used in a full production quality program Contents 01 GAMESS UK MOPAC Interface leen 0 1 1 Running MOPAC from GAMESS UK 0 1 2 Using MOPAC together with GAMESS UK Description of MOPAC 11 Summary of MOPAC capabilities ss 1 2 Copyright status of MOPAC len 1 3 Porting MOPAC to other machines e 1 4 Relationship of AMPAC and MOPAC 1 5 Programs recommended for use with MOPAC 1 6 Vhe datafile i o we ede rpm em Tender Yi rm Rep AT PEE eS 1 6 1 Example of data for ethylene 204 1 6 2 Example of data for polytetrahydrofur n Keywords 2 1 Specification of keywords A 2 2 Full list of keywords used in MOPAC 2 3 Definitions of keywords serice greri ai pepe a ie ia p a a i a pta R 2 4 Keywords that go together 222A Geometry specification 3 1 Internal coordinate definition o aoo a e e a a a aa Sled COn TA Sa
42. errors appear in the thermodynamic quantities The 0 4 gradient norm is only a suggestion WARNING INTERNAL COORDINATES Triatomics are by definition defined in terms of internal coordinates This warning is only a reminder For diatomics cartesian and internal coordinates are the same For tetra atomics and higher the presence or absence of a connectivity table distinguishes internal and cartesian coordinates but for triatomics there is an ambiguity To resolve this cartesian coordinates are not allowed for the data input for triatomics Error messages produced by MOPAC Chapter 9 Criteria MOPAC uses various criteria which control the precision of its stages These criteria are chosen as the best compromise between speed and acceptable errors in the results The user can override the default settings by use of keywords however care should be exercised as increasing a criterion can introduce the potential for infinite loops and decreasing a criterion can result in unacceptably imprecise results These are usually characterized by noise in a reaction path or large values for the trivial vibrations in a force calculation 9 1 SCF criterion Name Defined in Default value Basic Test Exceptions SCFCRT ITER 0 0001 kcal mole Change in energy in kcal mole on successive iterations is less than SCFCRT If PRECISE is specified SCFCRT 0 000001 If a polarization calculation SCFCRT 1 D 11 If a FORCE calcul
43. fatal error message is printed and the calculation stopped ATOMIC NUMBER nn IS NOT AVAILABLE An element has been used for which parameters are not available Only if a typographic error has been made can this be rectified This check is not exhaustive in that even if the elements are acceptable there are some combinations of elements within MINDO 3 that are not allowed This is a fatal error message ATOMIC NUMBER OF nn An atom has been specified with a negative or zero atomic number This is normally caused by forgetting to specify an atomic number or symbol This is a fatal error message Error messages produced by MOPAC ATOMS nn AND nn ARE SEPARATED BY nn nnnn ANGSTROMS Two genuine atoms not dummies are separated by a very small distance This can occur when a complicated geometry is being optimized in which case the user may wish to continue This can be done by using the keyword GEO OK More often however this message indicates a mistake and the calculation is by default stopped ATTEMPT TO GO DOWNHILL IS UNSUCCESSFUL A quite rare message produced by Bartel s gradient norm minimization Bartel s method attempts to minimize the gradient norm by searching the gradient space for a minimum Apparently a minimum has been found but not recognized as such The program has searched in all 3 N 6 directions and found no way down but the criteria for a minimum have not been satisfied No advice is availabl
44. for SIGMA calculation Called by POWSQ e POWSQ Main sequence The McIver Komornicki gradient minimization routine Constructs a full Hessian matrix and proceeds by line searches Called from MAIN when SIGMA is specified e PRTDRC Utility Prints DRC and IRC results according to instructions Output can be a every point calculated default b in constant steps in time space or energy e PULAY Utility A new converger Uses a powerful mathematical non iterative method for obtaining the SCF Fock matrix Principle is that at SCF the eigenvectors of the Fock and density matrices are identical so F P is a measure of the non self consistency While very powerful PULAY is not universally applicable Used by ITER e QUADR Utility Used in printing the IRC DRC results Sets up a quadratic in time of calculated quantities so that PRTDRC can select specific reaction times for printing e REACT1 Main sequence Uses reactants and products to find the transition state A hypersphere of N dimensions is centered on each moiety and the radius steadily reduced The entity of lower energy is moved and when the radius vanishes the transition state is reached Called by MNDO only e READ Main sequence Almost all the data are read in through READ There is a lot of data checking in READ but very little calculation Called by MNDO e READA Utility General purpose character number reader Used to enter numerical data in the control line as l
45. iat E ec cq y SE ES NLLSQ pr etree arene ree and FMAT FLEPO POWSQ aoe eal PEA Sao ty Wee or aene ces l SEARCH or LINMIN LOCMIN Program 7 2 Main electronic flow COMPFG See GEOMETRIC SEQUENCE HCORE _______ DERIV ____ GMETRY Pane CERE SYMTRY een Pee ee ae ae RD DCART Io PARTIEN alienen 0 Io S oe edune E EEE DHC ITER RSP espe ees NERO EEA l __ un fa E n reser ie Jd DENSIT ROTATE FOCK1 CNVG PULAY H1ELEC FOCK2 Rear ate sso rons MN oS 2 E E MECI DIAT o iuc ios ne colles ss 7 3 Control within MOPAC Almost all the control information is passed via the single datum KEYWRD a string of 80 characters which is read in at the start of the job Each subroutine is made independent as far as possible even at the expense of extra code or calculation Thus for example the SCF criterion is set in subroutine ITER and nowhere else Similarly subroutine DERIV has exclusive control of the step size in the 7 3 Control within MOPAC finite difference calculation of the energy de
46. if any are not recognised WRTKEY can stop the job if any errors are found e WRITXT Main Sequence Writes out KEYWRD KOMENT and TITLE The inverse of GETTXT e XXX Utility Forms a unique logical name for a Gaussian Z matrix logical Called by GEOUTG only e XYZINT Utility Converts from cartesian coordinates into internal e XYZGEO XYZINT sets up its own numbering system so no connectivity is needed Description of subroutines Appendix D Heats of formation Test MNDO PM3 and AM1 compounds In order to verify that MOPAC is working correctly a large number of tests need to be done These take about 45 minutes on a VAX 11 780 and even then many potential bugs remain undetected It is obviously impractical to ask users to test MOPAC However users must be able to verify the basic working of MOPAC and to do this the following tests for the elements have been provided Each element can be tested by making up a data file using estimated geometries and running that file using MOPAC The optimized geometries should give rise to heats of formation as shown Any difference greater than 0 1 kcal mole indicates a serious error in the program Caveats 1 Geometry definitions must be correct 2 Heats of formation may be too high for certain compounds This is due to a poor starting geometry trapping the system in an excited state Affects IC at times Element Test Compound Heat of Formation MINDO 3 MNDO AM1 PM3 Hydrogen CH
47. in isotopic substitution studies several vibrational calculations may be needed To allow the frequencies to be calculated from the constant force matrix ISOTOPE is used When a FORCE cal culation is completed ISOTOPE will cause the force matrix to be stored regardless of whether or not any intervening restarts have been made To re calculate the frequencies etc starting at the end of the force matrix calculation specify RESTART The two keywords RESTART and ISOTOPE can be used together For example if a normal FORCE calculation runs for a long time the user may want to divide it up into stages and save the final force matrix Once ISOTOPE has been used it does not need to be used on subsequent RESTART runs ISOTOPE can also be used with FORCE to set up a RESTART file for an IRC n calculation ITRY NN W The default maximum number of SCF iterations is 200 When this limit presents difficulty ITRY nn can be used to re define it For example if ITRY 400 is used the maximum number of iterations will be set to 400 ITRY should normally not be changed until all other means of obtaining a SCF have been exhausted e g PULAY CAMP KING etc IUPD n W IUPD is used only in the EF routine IUPD should very rarely be touched IUPD 1 can be used in minimum searches if the message HEREDITARY POSITIVE DEFINITENESS ENDANGERED UPDATE SKIPPED THIS CYCLE occurs every cycle for 10 20 iterations Never use IUPD 2 for a TS search For more
48. in lines 4a to 4f line 5 terminates both the geometry and the data file Any additional data for example symmetry data would follow line 5 Summarizing then the structure for a MOPAC data file is Line 1 Keywords See chapter 2 on definitions of keywords Line 2 Title of the calculation e g the name of the molecule or ion Line 3 Other information describing the calculation Lines 4 Internal or cartesian coordinates See chapter on specification of geometry Line 5 Blank line to terminate the geometry definition Other layouts for data files involve additions to the simple layout These additions occur at the end of the data file after line 5 The three most common additions are e Symmetry data This follows the geometric data and is ended by a blank line e Reaction path After all geometry and symmetry data if any are read in points on the reaction coordinate are defined e Saddle data A complete second geometry is input The second geometry follows the first geometry and symmetry data if any 1 6 2 Example of data for polytetrahydrofuran The following example illustrates the data file for a four hour polytetrahydrofuran calcu lation As you can see the layout of the data is almost the same as that for a molecule the main difference is in the presence of the translation vector atom Tv Line 1 T 4H Line 2 POLY TETRAHYDROFURAN C4 H8 0 2 Line 3 Line 4a C 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 4b
49. internal coordinates in ARCHIVE file 0 0 000000 0 0 000000 0 0 000000 209615 1 0 000000 0 0 000000 313679 1 116 886168 1 0 000000 964468 1 115 553316 1 0 000000 108040 1 128 726078 1 180 000000 000000 0 0 000000 0 omumdmuoso OrRrOrRF Oooo000 ONWNFHO OrRPFNF OO Oc0n 000 0 000000 Polymers are defined by the presence of a translation vector In the following example polyethylene the translation vector spans three monomeric units and is 7 7 Angstroms long Note in this example the presence of two dummy atoms These not only make the geometry definition easier but also allow the translation vector to be specified in terms of distance only rather than both distance and angles Example of polymer coordinates from ARCHIVE file T 20000 POLYETHYLENE CLUSTER UNIT C6H12 C 0 000000 0 0 000000 0 0 000000 0 0 0 0 C 1 540714 1 0 000000 0 0 000000 0 1 0 0 C 1 542585 1 113 532306 1 0 000000 0 2 1 0 C 1 542988 1 113 373490 1 179 823613 1 3 2 1 C 1 545151 1 113 447508 1 179 811764 1 4 3 2 C 1 541777 1 113 859804 1 179 862648 1 5 4 3 XX 1 542344 1 108 897076 1 179 732346 1 6 5 4 XX 1 540749 1 108 360151 1 178 950271 1 T 6 5 H 1 114786 1 90 070026 1 126 747447 1 1 3 2 H 1 114512 1 90 053136 1 127 134856 1 1 3 2 H 1 114687 1 90 032722 1 126 717889 1 2 4 3 H 1 114748 1 89 975504 1 127 034513 1 2 4 3 H 1 114474 1 90 063308 1 126 681098 1 3 5 4 H 1 114433 1 89 915262 1 126 931090 1 3 5 4 H 1 114308 1 90 028131 1 127 007845 1 4 6 5 H
50. is a gradient norm minimization message These routines will only work if the nearest minimum to the supplied geometry in gradient norm space is a transition state or a ground state Gradient norm space can be visualized as the space of the scalar of the derivative of the energy space with respect to geometry To a first approximation there are twice as many minima in gradient norm space as there are in energy space It is unlikely that there exists any simple way to refine a geometry that results in this message While it is appreciated that a large amount of effort has probably already been expended in getting to this point users should steel themselves to writing off the whole geometry It is not recommended that a minor change be made to the geometry and the job re submitted Try using SIGMA instead of POWSQ TEMPERATURE RANGE STARTS TOO LOW The thermodynamics calculation assumes that the statistical summations can be replaced by integrals This assumption is only valid above 100K so the lower temperature bound is set to 100 and the calculation continued THERE IS A RISK OF INFINITE LOOPING The SCF criterion has been reset by the user and the new value is so small that the SCF test may never be satisfied This is a case of user beware THIS MESSAGE SHOULD NEVER APPEAR CONSULT A PROGRAMMER This message should never appear a fault has been introduced into MOPAC most prob ably as a result of a programming error If this messa
51. large reduced mass For the trivial vibrations the reduced mass is ill defined and where this happens the reduced mass is set to zero 6 16 Use of SADDLE calculation A SADDLE calculation uses two complete geometries as shown on the following data file for the ethyl radical hydrogen migration from one methyl group to the other Line 1 UHF SADDLE Line 2 ETHYL RADICAL HYDROGEN MIGRATION Line 3 Line 4 C 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 5 C 1 479146 1 0 000000 0 0 000000 0 100 Line 6 H 1 109475 1 111 328433 1 0 000000 0 2 1 0 Line 7 H 1 109470 1 111 753160 1 120 288410 1 2 1 3 Line 8 H 1 109843 1 110 103163 1 240 205278 1 2 1 3 Line 9 H 1 082055 1 121 214083 1 38 110989 1 1 2 3 Line 10 H 1 081797 1 121 521232 1 217 450268 1 1 2 3 Line 11 0 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 12 C 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 13 C 1 479146 1 0 000000 0 0 000000 0 1 00 6 16 Use of SADDLE calculation Line 14 H 1 109475 1 111 328433 1 0 000000 0 2 1 0 Line 15 H 1 109470 1 111 753160 1 120 288410 1 2 1 3 Line 16 H 2 109843 1 30 103163 1 240 205278 1 2 1 3 Line 17 H 1 082055 1 121 214083 1 38 110989 1 1 2 3 Line 18 H 1 081797 1 121 521232 1 217 450268 1 1 2 3 Line 19 0 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 20 Details of the mathematics of SADDLE appeared in print in 1984 M J S Dewar E F Healy J J P Stewart J Chem Soc Faraday Trans II 3 227 1984 so only a superficial
52. might be for N H stretch rather than inversion In that case the IRC will relax the geometry to the optimized planar structure 2 Do anormal FORCE calculation specifying ISOTOPE in order to save the FORCE matrices Do not attempt to run the IRC directly unless you have confidence that the FORCE calculation will work as expected If the IRC calculation is run directly 6 11 Reaction coordinates specify ISOTOPE anyway that will save the FORCE matrix and if the calculation has to be re done then RESTART will work correctly 3 Using IRC n and RESTART run the IRC calculation If RESTART is specified with IRC n then the restart is assumed to be from the FORCE calculation If RESTART is specified without IRC n say with IRC on its own then the restart is assumed to be from an earlier IRC calculation that was shut down before going to completion A DRC calculation is simpler in that a force calculation is not a prerequisite however most calculations of interest normally involve use of an internal coordinate For this reason IRC n can be combined with DRC to give a calculation in which the initial motion 0 3kcal worth of kinetic energy is supplied by the IRC and all subsequent motion obeys conservation of energy The DRC motion can be modified in three ways 1 It is possible to calculate the reaction path followed by a system in which the gener ated kinetic energy decays with a finite half life This can be defined by DRC n nnn where
53. nuclear charges DIPX C Similar to DIPOLE except the fit will be for the X component only DIPY C Similar to DIPOLE except the fit will be for the Y component only DIPZ C Similar to DIPOLE except the fit will be for the Z component only DMA X n nn W In the EF routine the maximum step size is 0 2 Angstroms or radians by default This can be changed by specifying DMAX n nn Increasing DMAX can lead to faster convergence but can also make the optimization go bad very fast Furthermore the Hessian updating may deteriorate when using large stepsizes Reducing the stepsize to 0 10 or 0 05 is recommended when encountering convergence problems DOUBLET C When a configuration interaction calculation is done all spin states are calculated si multaneously either for component of spin 0 or 1 2 When only doublet states are of interest then DOUBLET can be specified and all other spin states while calculated are ignored in the choice of root to be used Note that while almost every odd electron system will have a doublet ground state DOUBLET should still be specified if the desired state must be a doublet DOUBLET has no meaning in a UHF calculation DRC C A Dynamic Reaction Coordinate calculation is to be run By default total energy is conserved so that as the reaction proceeds in time energy is transferred between kinetic and potential forms DRC n nnn C In a DRC calculation the half l
54. s dihedral angle ever fall into a straight line This can happen in the course of a geometry optimization in a SADDLE calculation or in following a reaction coordinate If such a condition should develop then the position of the dependent atom would become ill defined Examples 4 2 MOPAC output for test data file MNRSD1 FKK KK KK K K FK FK FK FK K ok ok K 2 K FK FK FK ok 3K K K K K ok ok ook FK FK FK ok oko K 2 ok oe oe oe ok ok ok oe K K K o oe FK FK FK FK o eoe K 2K oko FK FK FK FK K K K K K K gt K gt K gt K FRANK J SEILER RES LAB U S AIR FORCE ACADEMY COLO SPGS CO 80840 KK kk ok ak ak ak k k 2K 2k ok ok oke K K ok ke ke 2k 2k ke oko oj ok ok ke aK K kk 2k ok oj ok ke ke ok 3K 3K 2K 2K gt K gt K ke ok ke ke 2K 2k aK koe ke ke 2K gt K K 2K 2K 2K 2K K K K gt K 2K 2K MNDO CALCULATION RESULTS Note 1 FKK akak k 3k ak aK 3K aK aK 3K 3K aK 3K RIA 3K 3K aK 3K 3K RAK I A 3K aK 3K I aK K 21 2K gt K 3K 2121 3K 3K 21 21 3K Fk 21 K K 3K K K 3K K K FK 3K K 2K 3K K K FK K K Ek 2k FK MOPAC VERSION 6 00 CALC D 4 0CT 90 Note 2 SYMMETRY SYMMETRY CONDITIONS TO BE IMPOSED T A TIME OF 3600 0 SECONDS REQUESTED DUMP N RESTART FILE WRITTEN EVERY 3600 0 SECONDS FKK kk k 3k ak aK OO 2K 3K 3K K K FKK K ROI KKK 3K KK 2K KK K KK K RK KKK O43BY043 PARAMETER DEPENDENCE DATA REFERENCE ATOM FUNCTION NO DEPENDENT ATOM S 3 1 4 3 2 4 DESCRIPTIONS OF THE FUNCTIONS USED 1 BOND LENGTH IS SET EQUAL TO THE REFER
55. selected in order to preserve tetrahedral symmetry to avoid the Jahn Teller effects 3 Illustration of the use of the amp in the keyword line and of the new optional definition of atoms 2 and 3 4 Illustration of Gaussian Z matrix input 5 An example of Eigenvector Following to locate a transition state 6 Use of SETUP Normally SETUP would point to a special file which would contain keywords only Here the only file we can guarantee exists is the file being run so that is the one used 7 Example of labelling atoms 8 This part of the test writes the density matrix to disk for later use 9 A simple calculation on water 10 The previous optimized geometry is to be used to start this calculation 11 The density matrix written out earlier is now used as input to start an SCF This example is taken from the first data file in TESTDATA DAT and illustrates the working of a FORCE calculation 5 1 Data file for a force calculation Line 1 nointer noxyz mndo dump 8 Line 2 t 2000 thermo 298 298 force isotope Line 3 ROT 2 Line 4 DEMONSTRATION OF MOPAC FORCE AND THERMODYNAMICS CALCULATION 5 Line FORMALDEHYDE MNDO ENERGY 32 8819 See Manual Testdata Line Line Line O ON 0o Line Line 10 ommoo 1 216487 1 1 0 0 1 106109 1 123 513310 1 2 1 0 1 106109 1 123 513310 1 180 000000 1 2 1 3 0 000000 0 0 000000 0 0 000000 0 0 0 0 5 2 Results file for the force calculation FKK KK K kK kK 2 FK oko FK K
56. should not be used if either the HOMO or LUMO is degenerate in this case the full manifold of HOMO x LUMO should be included in the C I using MECI options The user should be aware of this situation When the biradical calculation is performed correctly the result is normally a net stabilization However if the first singlet excited state is much higher in energy than the closed shell ground state BIRADICAL can lead to a destabilization Abbreviation BIRAD See also MECI C I OPEN SINGLET BONDS 0 The rotationally invariant bond order between all pairs of atoms is printed In this context a bond is defined as the sum of the squares of the density matrix elements connecting any two atoms For ethane ethylene and acetylene the carbon carbon bond orders are roughly 1 00 2 00 and 3 00 respectively The diagonal terms are the valencies calculated from the atomic terms only and are defined as the sum of the bonds the atom makes with other atoms In UHF and non variationally optimized wavefunctions the calculated valency will be incorrect the degree of error being proportional to the non duodempotency of the density matrix For an RHF wavefunction the square of the density matrix is equal to twice the density matrix The bonding contributions of all M O s in the system are printed immediately before the bonds matrix The idea of molecular orbital valency was developed by Gopinathan Siddarth and Ravimohan Just as an atomic orbital has
57. than the original parameters these have not been adopted within MOPAC because to do so at this time would prevent earlier calculations from being duplicated Parameters for P O and P F have been added these were abstracted from Frenking s 1980 paper No inconsistency is involved as MINDO 3 historically did not have P O or P F parameters Extra entities available to MNDO MINDO 3 AMI and PM3 A 100 ionic alkali metal A 100 ionic alkaline earth metal A 100 ionic halogen like atom A 100 ionic group VI like atom Cb A special type of monovalent atom Elements 103 104 105 and 106 are the sparkles elements 11 and 19 are sparkles tailored to look like the alkaline metal ions Tv is the translation vector for polymer calculations See Full description of sparkles in Chapter 6 Element 102 symbol Cb is designed to satisfy valency requirements of atoms for which some bonds are not completed Thus in solid diamond the usual way to complete the normal valency in a cluster model is to use hydrogen atoms This approach has the defect that the electronegativity of hydrogen is different from that of carbon The capped bond atom Cb is designed to satisfy these valency requirements without acquiring a net charge Cb behaves like a monovalent atom with the exception that it can alter its electroneg ativity to achieve an exactly zero charge in whatever environment it finds itself It is thus Geometry specification
58. the SIGMA and NLLSQ gradient minimizations The line search subroutine SEARCH locates the gradient minimum and calculates the second derivative of the energy in the search direction Called by POWSQ and NLLSQ SECOND Utility Contains VAX specific code Function SECOND returns the number of CPU seconds elapsed since an arbitrary starting time If the SHUT DOWN command has been issued the CPU time is in error by exactly 1 000 000 seconds and the job usually terminates with the message time exceeded SET Utility Called by DIAT2 evaluates some terms used in overlap calculation SETUP3 Utility Sets up the Gaussian expansion of Slater orbitals using a STO 3G basis set SETUPG Utility Sets up the Gaussian expansion of Slater orbitals using a STO 6G basis set SOLROT Utility For Cluster systems adds all the two electron integrals of the same type between different unit cells and stores them in a single array Has no effect on molecules SORT Utility Part of CDIAG the complex diagonalizer SPACE Utility Called by DIIS only SPCG Written out of Version 6 00 SPLINE Utility Part of Camp King converger SS Utility An almost general Slater orbital overlap calculation Called by DIAT SUPDOT Utility Matrix mutiplication A B C SURFAC Utility Part of the ESP SWAP Utility Used with FILL SWAP ensures that a specified M O is filled Called by ITER only SYMTRY Utility Calculates values for geometric parameters from k
59. the change in position is equal to the integral over the time interval of the velocity The velocity vector is accurate to the extent that it takes into account the previous velocity the current acceleration the predicted acceleration and the change in predicted acceleration over the time interval Very little error is introduced due to higher order contributions to the velocity those that do occur are absorbed in a re normalization of the magnitude of the velocity vector after each time interval The magnitude of Dt the time interval is determined mainly by the factor needed to re normalize the velocity vector If it is significantly different from unity Dt will be reduced if it is very close to unity Dt will be increased Even with all this errors creep in and a system started at the transition state is un likely to return precisely to the transition state unless an excess kinetic energy is supplied for example 0 2kcal mole The calculation is carried out in cartesian coordinates and converted into internal coordinates for display All cartesian coordinates must be allowed to vary in order to conserve angular and translational momentum IRC The Intrinsic Reaction Coordinate is the path followed by all the atoms in a system assuming all kinetic energy is completely lost at every point i e as the potential energy changes the kinetic energy generated is annihilated so that the total energy kinetic plus potential is always equal
60. the code involve programming concepts or constructions which while not of sufficient importance to warrant publication are described here in order to facilitate understanding 6 2 AIDER AIDER will allow gradients to be defined for a system MOPAC will calculate gradients as usual and will then use the supplied gradients to form an error function This error function is supplied gradients initial calculated gradients which is then added to the computed gradients so that for the initial SCF the apparent gradients will equal the supplied gradients A typical data set using AIDER would look like this PM3 AIDER AIGOUT GNORM 0 01 EF Cyclohexane 1 0 CX CX CX CX CX CX H1C H1C H1C H1C H1C H1C H2C H2C H2C H2C H2C o o ciu uwrrrrrr rrr 1 Hi Hd Hd Hd Hd Hd Hd Hd Hd Hd Hd O0 2 20 P4 P4 2 0 Q B4 K o oon ss 0 PRPrRPRPRrPRPRRPrFP RP RFP RFP NNN ONNN M CXX CXX CXX 90 0 90 0 CXX CXX CXX H1CX H1CX H1CX H1CX H1CX H1CX H2CX H2CX H2CX H2CX H2CX 3 120 3 120 0 180 w o NONNNNNNNNNNNWWW It 180 60 60 180 180 180 180 180 180 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 000000 Background H 10 H2C 1 H2CX 2 0 000000 CX 1 46613 H1C 1 10826 H2C 1 10684 CXX 80 83255 H1CX 103 17316 H2CX 150 96100 AIDER 0 0000 13 7589 1 7383 1
61. to be the easiest way of describing what are often complicated vibrations Note 8 In order the thermodynamic quantities calculated are The vibrational contribution The rotational contribution The sum of 1 and 2 this gives the internal contribution Aa WwW N Lm The translational contribution For partition functions the various contributions are multiplied together A new quantity is the heat of formation at the defined temperature This is intended for use in calculating heats of reaction Because of a limitation in the data available the H o F at T Kelvin is defined as The heat of formation of the compound at T Kelvin from it s elements in their standard state at 298 Kelvin Obviously this definition of heat of formation is incorrect but should be useful in calculating heats of reaction where the elements in their standard state at 298 Kelvin drop out 5 3 Example of reaction path with symmetry In this example one methyl group in ethane is rotated relative to the other and the geometry is optimized at each point As the reaction coordinate involves three hydrogen atoms moving symmetry is imposed to ensure equivalence of all hydrogens Line 1 SYMMETRY T 600 Line 2 ROTATION OF METHYL GROUP IN ETHANE Line 3 EXAMPLE OF A REACTION PATH CALCULATION Line 4 C Line 5 C 1 479146 1 Line 6 H 1 109475 1 111 328433 1 Line 7 H 1 109470 0 111 7531600 120 000000 0 2 1 3 Testdata Line 8 H 1 1
62. up to 6 and angular quantum numbers up to 2 are allowed Main arguments Atomic numbers and cartesian coordinates in Angstroms of the two atoms Diatomic overlaps on exit Called by HIELEC DIAT2 Utility Calculates reduced overlap integrals between atoms of principal quantum numbers 1 2 and 3 for s and p orbitals Faster than the SS in DIAT This is a dedicated subroutine and is unable to stand alone without considerable backup Called by DIAT DIGIT Utility Part of READA DIGIT assembles numbers given a character string DIHED Utility Calculates the dihedral angle between four atoms Used in convert ing from cartesian to internal coordinates DIIS Utility Pulay s Geometric Direct Inversion of the Iterative Subspace G DIIS accelerates the rate at which the BFGS locates an energy minimum In MOPAC 6 00 the DIIS is only partially installed several capabilities of the DIIS are not used DIJKL1 Utility Part of the analytical C I derivative package Called by DERI DIJKL1 calculates the two electron integrals over M O bases e g lt i j 1r k l DIJKL2 Utility Part of the analytical C I derivative package Called by DERI2 DIJKL2 calculates the derivatives of the two electron integrals over M O bases e g lt i j ir kl wrt cartesian coordinates DIPIND Utility Similar to DIPOLE but used by the POLAR calculation only DIPOLE Utility Evaluates and if requested prints dipole components and dipole for th
63. written with spaces around the sign THERMO 0 The thermodynamic quantities internal energy heat capacity partition function and entropy can be calculated for translation rotation and vibrational degrees of freedom for a single temperature or a range of temperatures Special situations such as linear systems and transition states are accommodated The approximations used in the THERMO calculation are invalid below 100K and checking of the lower bound of the temperature range is done to prevent temperatures of less than 100K being used 2 3 Definitions of keywords Another limitation for which no checking is done is that there should be no internal rotations If any exist they will not be recognized as such and the calculated quantities will be too low as a result In order to use THERMO the keyword FORCE must also be specified as well as the value for the symmetry number this is given by ROT n If THERMO is specified on its own then the default values of the temperature range are assumed This starts at 200K and increases in steps of 10 degrees to 400K Three options exist for overriding the default temperature range These are THERMO nnn O The thermodynamic quantities for a 200 degree range of temperatures starting at nnnK and with an interval of 10 degrees are to be calculated THERMO nnn mmm O The thermodynamic quantities for the temperature range limited by a lower bound of nnn Kelvin and an upper
64. yne etc If the exceptions are used care must be taken to ensure that the program does not violate these constraints during any optimizations or during any calculations of derivatives see also FORCE Conversion to Cartesian Coordinates By definition atom 1 is at the origin of cartesian coordinate space be careful however if atom 1 is a dummy atom Atom 2 is defined as lying on the positive X axis for atom 2 Y 0 and Z 0 Atom 3 is in the X Y plane unless the angle 3 2 1 is exactly 0 or 180 degrees Atom 4 5 6 etc can lie anywhere in 3 D space 3 2 Gaussian Z matrices With certain limitations geometries can now be specified within MOPAC using the Gaus sian Z matrix format Exceptions to the full Gaussian standard 1 The option of defining an atom s position by one distance and two angles is not allowed In other words the N4 variable described in the Gaussian manual must either be zero or not specified MOPAC requires the geometry of atoms to be defined in terms of at most one distance one angle and one dihedral 2 Gaussian cartesian coordinates are not supported 3 Chemical symbols must not be followed by an integer identifying the atom Numbers after a symbol are used by MOPAC to indicate isotopic mass If labels are desired they should be enclosed in parentheses thus Cl on C5 34 96885 4 The connectivity N1 N2 N3 must be integers Labels are not allowed Specification of Gaussian Z matrices T
65. 0 1 GAMESS UK MOPAC Interface Page 1 GAMESS UK USER S GUIDE Version 8 0 June 2008 MOPAC Interface J M H Thomas 0 1 GAMESS UK MOPAC Interface This document is the original MOPAC 7 0 Manual written by Dr James J P Stewart with a section pre pended to it that serves to document the directives that allow users of GAMESS UK to drive MOPAC from within GAMESS UK The original MOPAC manual is freely available for download on the web at http ccl osc edu cca software SOURCES FORTRAN mopac7_sources mopac uncompressed manuals mopac man latex source index shtml No changes have been made to the manual itself bar the inclusion of this section The MOPAC interface within GAMESS UK allows MOPAC to be run from a standard GAMESS UK input file The MOPAC version that is supplied with GAMESS UK is version 7 0 The interface between GAMESS UK and MOPAC currently permits geometries from a MOPAC run to be imported into GAMESS UK for incorporation in a standard GAMESS UK calculation This permits users to run for example a quick optimisation with the AM1 semi emprical method before importing the optimised geometry into GAMESS UK to run a full ab inito calculation There are example input files for running MOPAC from within GAMESS UK in the directory GAMESS UK examples mopac 0 1 1 Running MOPAC from GAMESS UK The MOPAC directives should be included in a standard GAMESS UK input file and must appear before any GAMESS UK directives The
66. 09843 0 110 103163 0 240 000000 0 2 1 3 Line 9 H 1 082055 0 121 214083 0 60 000000 1 1 2 3 Line 10 H 1 081797 0 121 521232 0 180 000000 0 1 2 3 Line 11 H 1 081797 O 121 521232 O 60 000000 0 1 2 3 Line 12 0 0 000000 0 0 000000 0 0 000000 0 0 0 0 Line 13 3145678 Line 14 3245678 Line 15 67 7 Line 16 6 11 8 Line 17 Line 18 70 80 90 100 110 120 130 140 150 Points to note 1 The dihedrals of the second and third hydrogens are not marked for optimization the dihedrals follow from point group symmetry All six C H bond lengths and H C C angles are related by symmetry see lines 13 and 14 The dihedral on line 9 is the reaction coordinate while the dihedrals on lines 10 and 11 are related to it by symmetry functions on lines 15 and 16 The symmetry functions are defined by the second number on lines 13 to 16 see SYMMETRY for definitions of functions 1 2 7 and 11 Symmetry data are ended by a blank line The reaction coordinate data are ended by the end of file Several lines of data are allowed Whenever symmetry is used in addition to other data below the geometry definition it will always follow the blank line immediately following the geometry definition The other data will always follow the symmetry data Chapter 6 Background 6 1 Introduction While all the theory used in MOPAC is in the literature so that in principle one could read and understand the algorithm many parts of
67. 10 dyn cm Definition Moment of inertia J 1 amu angstrom 1 660540 x 107 g cm Rotational constants A B and C e g A h 877J With J in amu angstroms then A in MHz 5 053791 x 10 I A in em 5 053791 x 10 cI 16 85763 1 6 10 2 Thermochemistry from ab initio MO methods Ab initio MO methods provide total energies Eg as the sum of electronic and nuclear nuclear repulsion energies for molecules isolated in vacuum without vibration at 0 K Eeq m Ea ale Epnuclear nuclear 6 1 From the 0 K potential surface and using the harmonic oscillator approximation we can calculate the vibrational frequencies v of the normal modes of vibration Using these we can calculate vibrational rotational and translational contributions to the thermodynamic quantities such as the partition function and heat capacity which arise from heating the system from 0 to T K Q partition function E energy S entropy and C heat capacity Vibration 1 Qvib 25 1 exp hy kT i FEyib for a molecule at the temperature T as oe 2 hvi hy exp hvj kT 6 3 2 1 exp hu kT where h is the Planck constant v the i th normal vibration frequency and k the Boltz mann constant For 1 mole of molecules Ej should be multiplied by the Avogadro number N R k Thus M hvi hwjexp hvi kT Ew Na gt gO NL Tan 02 6 10 A note on thermochemistry Note that
68. 3 7589 1 7383 0 0000 13 7589 1 7383 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 0 0000 13 7589 1 7383 0 0000 13 7589 1 7383 0 0000 13 7589 1 7383 0 0000 17 8599 2 1083 0 0000 17 8599 2 1083 0 0000 17 8599 2 1083 0 0000 17 8599 2 1083 0 0000 17 8599 2 1083 0 0000 17 8599 2 1083 0 0000 17 5612 0 6001 0 0000 17 5612 0 6001 0 0000 17 5612 0 6001 0 0000 17 5612 0 6001 0 0000 17 5612 0 6001 0 0000 17 5612 0 6001 0 0000 Each supplied gradient goes with the corresponding internal coordinate In the exam ple given the gradients came from a 3 21G calculation on the geometry shown Symmetry will be taken into account automatically Gaussian prints out gradients in atomic units these need to be converted into kcal mol Angstrom or kcal mol radian for MOPAC to use The resulting geometry from the MOPAC run will be nearer to the optimized 3 21G geometry than if the normal geometry optimizers in Gaussian had been used 6 3 Correction to the peptide linkage The residues in peptides are joined together by peptide linkages HNCO These linkages are almost flat and normally adopt a trans configuration the hydrogen and oxygen atoms being on opposite sides of the C N bond Experimentally the barrier to interconversion in N methyl acetamide is about 14 kcal mole but all four methods within MOPAC predict a significantly lower barrier PM3 giving the lowest value The low barrier can be traced to the tendency of semiempirical
69. 3247 00000 00000 18321 00000 00000 18321 00000 ooo o0 00000 25401 00000 00000 25401 00000 00000 25401 00000 00000 25401 52685 2114 16877 00000 00000 13432 00000 00000 56805 39249 00001 56806 39249 00001 00047 00000 00000 72996 00000 00000 63247 00000 00000 18321 00000 00000 18321 OOo oo o0o0o0o000 l o l O OO OO OO On One l O O O OR OO OO On On OO l O 00000 00000 00000 00000 00000 00000 00000 70572 00000 00000 70572 53841 66231 00000 00000 73040 00000 00000 05871 10238 00000 05871 10238 00000 10 38368 00000 00000 00000 00000 00000 00000 00000 00000 TOT11 00000 00000 TOT11 o o OOo oo0o0o0000 ooo OOo oo0oo0o0o000 00000 19832 00000 00000 19764 00000 00000 39642 00000 00000 39642 93651 00000 01649 00000 00001 29524 00000 40255 54246 00000 40252 54242 00000 11 03661 00000 00000 66681 00000 00000 57578 00000 00000 33455 00000 00000 33455 0 17792 0 00000 0 00000 0 17731 0 00000 0 26930 0 35565 0 00000 0 26930 0 35565 0 00000 Note 6 3302 12319 0 00271 0 00000 0 00000 0 22013 0 00001 0 00000 0 37455 0 57918 0 00000 0 37457 0 57922 0 00000 Note 7 12
70. 4 6 3 11 9 8 8 13 0 Lithium LiH 23 2 Beryllium BeO 38 6 53 0 Boron BF3 270 2 261 0 272 1 Carbon CH4 6 3 11 9 8 8 13 0 Nitrogen NH3 9 1 6 4 13 c3 24 Oxygen C02 95 7 75 1 T9 8 85 0 Fluorine CF4 223 9 214 2 225 7 225 1 Magnesium MgF2 160 7 Aluminium AlF 83 6 TT 9 50 1 Silicon SiH 82 9 90 2 84 5 94 6 Phosphorus PH3 2 5 3 9 10 2 0 2 Sulfur H28 2 6 3 8 1 2 0 9 Chlorine HCl 21 1 15 3 24 6 20 5 Zinc ZnMe2 19 9 19 8 8 2 Gallium GaC13 79 7 Germanium GeF 16 4 19 7 3 3 Arsenic AsH3 12 7 Selenium SeC12 38 0 Bromine HBr 3 6 10 5 5 3 Heats of formation Cadmium CdC12 48 6 Indium InC13 72 8 Tin SnF 20 4 17 5 Antimony SbC13 72 4 Tellurium TeH2 23 8 Iodine ICl 6 7 4 6 10 8 Mercury HgC12 36 9 44 8 32 7 Thallium T1C1 13 4 Lead PbF 22 6 21 0 Bismuth BiCl3 42 6 x Not an exhaustive test of AM1 boron Appendix E References On G DIIS Computational Strategies for the Optimization of Equilibrium Geometry and Transition State Structures at the Semiempirical Level Peter L Cummings Jill E Gready J Comp Chem 10 939 950 1989 On Analytical C I Derivatives An Efficient Procedure for Calculating the Molecular Gradient using SCF CI Semiem pirical Wavefunctions with a Limited Number of Configurations M J S Dewar D A Liotard J Mol Struct Theochem 206 123 133 1990 On Eigenvector Following J Baker J Comp Chem 1 385 1986 On
71. 86 Cl a M J S Dewar M L McKee H S Rzepa J Am Chem Soc 100 3607 1978 t b M J S Dewar H S Rzepa J Comp Chem 4 158 1983 Zn M J S Dewar K M Merz Organometallics 5 1494 1986 Ge M J S Dewar G L Grady E F Healy Organometallics 6 186 1987 Br M J S Dewar E F Healy J Comp Chem 4 542 1983 I M J S Dewar E F Healy J J P Stewart J Comp Chem 5 358 1984 Sn M J S Dewar G L Grady J J P Stewart J Am Chem Soc 106 6771 1984 Hg M J S Dewar G L Grady K Merz J J P Stewart Organometallics 4 1964 1985 Pb M J S Dewar M Holloway G L Grady J J P Stewart Organometallics 4 1973 1985 N B t Parameters defined here are obsolete On MINDO 3 Part XXVI Bingham R C Dewar M J S Lo D H J Am Chem Soc 97 1975 On AM1 AM1 A New General Purpose Quantum Mechanical Molecular Model M J S Dewar E G Zoebisch E F Healy J J P Stewart J Am Chem Soc 107 3902 3909 1985 On PM3 Optimization of Parameters for Semi Empirical Methods I Method J J P Stewart J Comp Chem 10 221 1989 Optimization of Parameters for Semi Empirical Methods II Applications J J P Stewart J Comp Chem 10 221 1989 These two references refer to H C N O F Al Si P S Cl Br and I Optimization of Parameters for Semi Empirical Methods III Extension of PM3 to Be Mg Zn Ga Ge As Se Cd In Sn Sb Te Hg Tl Pb
72. 9 Version 3 10 0 00557 0 00049 0 00194 87 02506 11 18157 10 65295 Version 4 00 0 00044 0 00052 0 00041 12 99014 3 08110 3 15427 Version 5 00 0 00040 0 00044 0 00062 21 05654 2 80744 3 83712 Version 6 00 0 00025 0 00022 0 00047 3 38368 2 03661 0 76725 Note 6 Normal modes are not of much use in assigning relative importance to atoms in a mode Thus in iodomethane it is not obvious from an examination of the normal modes which mode represents the C I stretch A more useful description is provided by the energy or mass weighted coordinate analysis Each set of three coefficients now represents the relative energy carried by an atom This is not strictly accurate as a definition but is believed by JJPS to be more useful than the stricter definition Note 7 The following description of the coordinate analysis is given without rigorous justification Again the analysis although difficult to understand has been found to be more useful than previous descriptions On the left hand side are printed the frequencies and transition dipoles Underneath these are the reduced masses and idealized distances traveled which represent the simple harmonic motion of the vibration The mass is assumed to be attached by a spring to an infinite mass Its displacement is the travel The next column is a list of all pairs of atoms that contribute significantly to the energy of the mode Across from each pair next column is the percentage energy
73. A general subroutine of which ITER is a good example handles three kinds of data First data which the subroutine is going to work on for example the one and two electron matrices second data necessary to manipulate the first set of data such as the number of atomic orbitals third the calculated quantities here the electronic energy and the density and Fock matrices Reference data are entered into a subroutine by way of the common blocks This is to emphasize their peripheral role Thus the number of orbitals while essential to ITER is not central to the task it has to perform and is passed through a common block Data the subroutine is going to work on are passed via the argument list Thus the one and two electron matrices which are the main reason for ITER s existence are entered as two of the four arguments As ITER does not own these matrices it can use them but may not change their contents The other argument is EE the electronic energy EE is owned by ITER even though it first appears before ITER is called Sometimes common block data should more correctly appear in an argument list This is usually not done in order to prevent obscuring the main role the subroutine has to perform Thus ITER calculates the density and Fock matrices but these are not represented in the argument list as the calling subroutine never needs to know them instead they are stored in common 7 3 1 Subroutine GMETRY Description for programmers G
74. ALS 2 2 Full list of keywords used in MOPAC MAX MECI MICROS MINDO 3 MMOK MODE N MOLDAT MS N MULLIK NLLSQ NOANCI NODIIS NOINTER NOLOG NOMM NONR NOTHIEL NSURF N NOXYZ NSURF OLDENS OLDGEO OPEN ORIDE PARASOK PI PL PM3 POINT N POINT1 N POINT2 N POLAR POTWRT POWSQ PRECISE PULAY QUARTET QUINTET RECALC N RESTART ROOT n ROT n SADDLE SCALE SCFCRT n SCINCR SETUP SEXTET SHIFT n SIGMA SINGLET SLOPE SPIN STEP PRINTS MAXIMUM GRID SIZE 23 23 PRINT DETAILS OF MECI CALCULATION USE SPECIFIC MICROSTATES IN THE C I USE THE MINDO 3 HAMILTONIAN USE MOLECULAR MECHANICS CORRECTION TO CONH BONDS IN EF FOLLOW HESSIAN MODE NO N PRINT DETAILS OF WORKING IN MOLDAT IN MECI MAGNETIC COMPONENT OF SPIN PRINT THE MULLIKEN POPULATION ANALYSIS MINIMIZE GRADIENTS USING NLLSQ DO NOT USE ANALYTICAL C I DERIVATIVES DO NOT USE DIIS GEOMETRY OPTIMIZER DO NOT PRINT INTERATOMIC DISTANCES SUPPRESS LOG FILE TRAIL WHERE POSSIBLE DO NOT USE MOLECULAR MECHANICS CORRECTION TO CONH BONDS DO NOT USE THIEL S FSTMIN TECHNIQUE NUMBER OF SURFACES IN AN ESP CALCULATION DO NOT PRINT CARTESIAN COORDINATES NUMBER OF LAYERS USED IN ELECTROSTATIC POTENTIAL READ INITIAL DENSITY MATRIX OFF DISK PREVIOUS GEOMETRY TO BE USED OPEN SHELL RHF CALCULATION REQUESTED IN AM1 CALCULATIONS SOME MNDO PARAMETERS ARE TO BE USED RESOLVE DENSITY MATRIX INTO SIGMA AND PI BONDS MONITOR CONVERGENCE OF DENSITY MATRIX IN ITER U
75. Beta C I 1 1 1 1 1 0 1 C I 2 1 1 4 1 0 2 C I 3 2 2 9 2 1 9 C I 4 2 2 36 2 1 24 C I 5 3 3 100 3 2 100 C I 26 3 3 400 3 2 300 C I 7 4 4 1225 4 3 1225 C I 8 Do not use unless other keywords also used see below If a change of spin is defined then larger numbers of M O s can be used up to a maximum of 10 The C I matrix is of size 100 x 100 For calculations involving up to 100 configurations the spin states are exact eigenstates of the spin operators For systems with more than 100 configurations the 100 configurations of lowest energy are used See also MICROS and the keywords defining spin states Note that for any system use of C I 5 or higher normally implies the diagonalization of a 100 by 100 matrix As a geometry optimization using a C I requires the derivatives to be calculated using derivatives of the C I matrix geometry optimization with large C I s will require more time than smaller C I s Associated keywords MECI ROOT MICROS SINGLET DOUBLET etc C I n m In addition to specifying the number of M O s in the active space the number of electrons can also be defined In C I n m n is the number of M O s in the active space and m is the number of doubly filled levels to be used Examples Keywords Number of M O0 s No Electrons C I 2 2 2 1 C I 2 1 2 2 3 C I 2 3 1 3 2 3 C I 2 3 2 3 4 5 C I 3 0 OPEN 2 3 3 2 N A C I 3 1 OPEN 2 3 4 N A C I 3 1 OPEN 1 2 3 N A 3
76. CE Main sequence Performs a force constant and vibrational frequency cal culation on a given system If the starting gradients are large the geometry is optimized to reduce the gradient norm unless LET is specified in the keywords Isotopic substitution is allowed Thermochemical quantities are calculated Called by MAIN e FORMD Main Sequence Called by EF FORMD constructs the next step in the geometry optimization or transition state location e FORMXY Utility Part of DIJKL1 FORMXY constructs part of the two electron integral over M O s e FORSAV Utility Saves and restores data used in FMAT in FORCE calculation Called by FMAT Description of subroutines FRAME Utility Applies a very rigid constraint on the translations and rotations of the system Used to separate the trivial vibrations in a FORCE calculation FREQCY Main sequence Final stage of a FORCE calculation Evaluates and prints the vibrational frequencies and modes FSUB Utility Part of ESP GENUN Utility Part of ESP Generates unit vectors over a sphere called by SURFAC only GEOUT Utility Prints out the current geometry Can be called at any time Does not change any data GEOUTG Utility Prints out the current geometry in Gaussian Z matrix format GETDAT Utility Reads in all the data and puts it in a scratch file on channel 5 GETGEG Utility Reads in Gaussian Z matrix geometry Equivalent to GETGEO and GETSYM combined GETGEO Utility Read
77. CORE SOLROT FORCE FREQCY DERI23 FLEPO EF ESP GRID ITER PATHS POWSQ DERI2 DERI22 EF JCARIN DERI1 DERITR SOLROT MULLIK FLEPO MNDO REACT 1 FLEPO REACT1 Subroutine calls in MOPAC TQLRAT TRBAK3 TRED3 UPCASE UPDATE UPDHES VECPRT WRITE WRTKEY WRTTXT XXX XYZGEO XYZINT RSP RSP RSP GETTXT DATIN EF BONDS ITER WRITE FORCE READ GEOUT GEOUTG XYZINT DFPSAV POWSAV DIIS FFHPOL MECI MOLDAT ITER MNDO GRID PATHK FORCE GEOUT PRTDRC FORCE MULLIK PATHS READ GETGEO HCORE POWSQ REACT1 WRITE PARSAV Appendix C Description of subroutines e AABABC Utility Calculates the configuration interaction matrix element between two configurations differing by exactly one alpha M O Called by MECI only e AABACD Utility Calculates the configuration interaction matrix element between two configurations differing by exactly two alpha M O s Called by MECI only e AABBCD Utility Calculates the configuration interaction matrix element between two configurations differing by exactly two M O s one configuration has alpha M O A and beta M O C while the other configuration has alpha M O B and beta M O D Called by MECI only e AINTGS Utility Within the overlap integrals calculates the A integrals Dedicated to function SS within DIAT e ANALYT Main Sequence Calculates the analytical derivatives of the energy with respect to cartesian coordinates for
78. DAT DATIN REACT1 GRID PATHS FORCE DRC NLLSQ COMPFG POWSQ EF WRITE POLAR PERM MECIH VECPRT HQRII MATOUT GMETRY VECPRT GMETRY MULT DENSIT VECPRT COMPFG GEOUT LOCMIN PARSAV GEOUT FLEPO GEOUT WRTTXT FLEPO WRITE AXIS COMPFG FFHPOL GEOUT COMPFG VECPRT RSP SEARCH XYZINT QUADR OSINV SYMTRY GEOUT GMETRY FLEPO COMPFG WRITE GETGEG GETGEO DATE GEOUT WRTKEY GETSYM NUCHAR WRITXT GMETRY Subroutine calls in MOPAC REFER REPP ROTAT ROTATE RSP SAXPY SCHMIB SCHMIT SCOPY SEARCH SECOND SET SETUPG SOLROT SORT SPACE SPLINE SUPDOT SWAP SYMTRY THERMO TIMCLK TIMER TIMOUT TQL2 TQLRAT TRBAK3 TRED3 UPCASE UPDATE UPDHES VECPRT WRITE WRTKEY WRTTXT XXX XYZGEO XYZINT REPP EPSETA TRED3 COMPFG AINTGS BINTGS ROTATE BFN HADDON DATE WRTTXT VECPRT MATOUT LOCAL ENPART BANGLE DIHED DIHED BANGLE TQLRAT TQL2 TRBAK3 GEOUT DERIV TIMOUT SYMTRY GMETRY GEOUT CHRGE BRLZON MPCSYB DENROT MOLVAL BONDS MULLIK MPCPOP GEOUTG XYZGEO A list of subroutines called by various segments the inverse of the first list Subroutine AABABC AABACD AABBCD AINTGS ANALYT ANAVIB AXIS BABBBC BABBCD BANGLE BFN Called by MECIH MECIH MECIH SET DCART FORCE FORCE FRAME MECIH MECIH XYZGEO XYZINT SPLINE POLAR Subroutine calls in MOPAC BINTGS BKRSAV BONDS BRLZON CALPAR CAPCOR CDIAG CHRGE CNVG COE COMPFG DANG DATIN DCART DELMOL DELRI DENROT DENSIT DEPVAR DE
79. DIM SIZES DAT these should be modified before COMPILE is run If for whatever rea son DIMSIZES DAT needs to be changed then COMPILE should be re run as modules compiled with different DIMSIZES DAT will be incompatible The parameters within DIMSIZES DAT that the user can modify are MAXLIT MAX HEV MAXTIM and MAXDMP MAXLIT is assigned a value equal to the largest number of hydrogen atoms that a MOPAC job is expected to run MAXHEV is assigned the cor responding number of heavy non hydrogen atoms The ratio of light to heavy atoms should not be less than 1 2 Do not set MAXHEV or MAXLIT less than 7 If you do some subroutines will not compile correctly Some molecular orbital eigenvector arrays are overlapped with Hessian arrays and to prevent compilation time error messages the number of allowed A O s must be greater than or equal to three times the number of allowed real atoms MAXTIM is the default maximum time in seconds a job is allowed to run before either completion or a restart file being written MAXDMP is the default time in seconds for the automatic writing of the restart files If your computer is very reliable and disk space is at a premium you might want to set MAXDMP as MAXDMP 999999 If SYBYL output is wanted set ISYBYL to 1 otherwise set it to zero If you want NMECI can be changed Setting it to 1 will save some space but will prevent all C I calculations except simple radicals If you want NPULAY can be set
80. EAD DIAT MNDO DHC DHCORE SYMTRY COMPFG DERITR DCART DERI2 EF INTERP MECI ITER COMPFG DERITR DFOCK2 FOCK2 DERITR DFOCK2 FOCK2 FLEPO WRITE NLLSQ main segment PULAY FFHPOL FORCE WRITE CDIAG MEO8A COMPFG DERI1 DERI1 DERI2 COMPFG DIIS DATIN MNDO WRITE BONDS WRITE MNDO ITER DFPSAV NLLSQ READ DERITR MOLDAT WRITE HCORE ITER ITER ITER DERI2 MECI PATHK FLEPO PARSAV DIPIND MULLIK MECI LOCAL MECI PATHS GETGEO PATHK DRC POLAR MECI Subroutine calls in MOPAC MPCSYB MTXM MTXMC MULLIK MULT MXM MXMT NLLSQ NUCHAR OSINV OVERLP PARSAV PARTXY PATHK PATHS PERM POLAR POWSAV POWSQ PRTDRC PULAY QUADR REACT1 READ REFER REPP ROTAT ROTATE RSP SCHMIB SCHMIT SCOPY SEARCH SECOND SET SETUPG SOLROT SORT SPACE SPLINE SUPDOT SWAP SYMTRY THERMO TIMCLK TIMER TIMOUT TQL2 WRITE DERI1 DERI21 WRITE MULLIK DERI1 MECIP DERI22 FORCE GETGEO DERI2 FORMD NLLSQ IJKL MNDO MNDO MECI MNDO POWSQ MNDO DRC ITER PRTDRC MNDO MNDO MOLDAT ROTATE DELMOL DHC AXIS POWSQ INTERP INTERP DERI1 POWSQ DERI2 FMAT NLLSQ TIMER COMPFG COMPFG DHC CDIAG DIIS INTERP DERI1 ITER COMPFG READ FORCE SECOND COMPFG WRITE RSP DERI2 DERI2 MTXMC MNDO READ PULAY DHC DHCORE FFHPOL DERI2 DRC FORCE PATHK WRITE DIAT2 HCORE DERI1 DERITR WRITE DERI1 DERI21 DERI21 DERI22 DHCORE HCORE H
81. ENCE BOND LENGTH 2 BOND ANGLE IS SET EQUAL TO THE REFERENCE BOND ANGLE SYMMETRY Note 3 Formaldehyde for Demonstration Purposes ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE NUMBER SYMBOL ANGSTROMS DEGREES DEGREES I NA I NB NA I NC NB NA I NA NB NC 1 0 Note 4 2 C 1 20000 x 1 3 H 1 10000 x 120 00000 x 2 1 4 H 1 10000 120 00000 180 00000 2 1 3 CARTESIAN COORDINATES NO ATOM X Y Z 1 0 0 0000 0 0000 0 0000 2 C 1 2000 0 0000 0 0000 Note 5 3 H 1 7500 0 9526 0 0000 4 H 1 7500 0 9526 0 0000 H MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 O MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 RHF CALCULATION NO OF DOUBLY OCCUPIED LEVELS 6 INTERATOMIC DISTANCES Q 0 1 C 2 H 3 H 4 0 1 0 000000 C 2 1 200000 0 000000 H 3 1 992486 1 100000 0 000000 Note 6 H 4 1 992486 1 100000 1 905256 0 000000 CYCLE 1 TIME 0 75 TIME LEFT 3598 2 GRAD 6 349 HEAT 32 840147 CYCLE 2 TIME 0 37 TIME LEFT 3597 8 GRAD 2 541 HEAT 32 880103 HEAT OF FORMATION TEST SATISFIED Note 7 PETERS TEST SATISFIED Note 8 SYMMETRY Note 9 Formaldehyde for Demonstration Purposes Note 10 4 2 MOPAC output for test data file MNRSD1 PETERS TEST WAS SATISFIED IN BFGS 0 SCF FIELD WAS ACHIEVED MNDO CALCULATION FINAL HEAT OF FORMATION 32 8817 TOTAL ENERGY 478 1191 ELECTRONIC ENERGY 870 6964 CORE CORE REPULSION x 392 5773 IONIZATION POTE
82. ENGTH BOND ANGLE TWIST ANGLE NUMBER SYMBOL ANGSTROMS DEGREES DEGREES I NA I NB NA I NC NB NA I NA NB NC ATOM CHEMICAL BOND LENGTH BOND ANGLE TWIST ANGLE 1 0 2 C 1 21649 1 3 H 1 10611 123 51331 2 1 4 H 1 10611 123 51331 180 00000 2 1 3 H MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 C MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 O MNDO M J S DEWAR W THIEL J AM CHEM SOC 99 4899 1977 RHF CALCULATION NO OF DOUBLY OCCUPIED LEVELS 6 HEAT OF FORMATION 32 881900 KCALS MOLE 5 2 Results file for the force calculation INTERNAL COORDINATE DERIVATIVES ATOM AT NO BOND ANGLE DIHEDRAL 1 0 2 C 0 000604 3 H 0 000110 0 000054 4 H 0 000110 0 000054 0 000000 GRADIENT NORM 0 00063 Note 2 TIME FOR SCF CALCULATION 0 45 TIME FOR DERIVATIVES 0 32 Note 3 MOLECULAR WEIGHT 30 03 PRINCIPAL MOMENTS OF INERTIA IN CM 1 9 832732 B 1 261998 1 118449 PRINCIPAL MOMENTS OF INERTIA IN UNITS OF 10 40 GRAM CM 2 A 2 846883 B 22 181200 C ORIENTATION OF MOLECULE IN FORCE CALCULATION NO ATOM X Y Z 1 8 0 6093 0 0000 0 0000 2 6 0 6072 0 0000 0 0000 3 1 1 2179 0 9222 0 0000 4 1 1 2179 0 9222 0 0000 FIRST DERIVATIVES WILL BE USED IN THE CALCULATION ESTIMATED TIME TO COMPLETE CALCULATION 25 028083 OF SECOND DERIVATIVES 36 96 SECONDS STEP 1 TIME 2 15 SECS INTEGRAL 2 15 STEP 2 TIME 2 49 SECS INTEGRAL 4 64 STE
83. F SHIFT PULAY ITRY CAMP SCFCRT 1SCF PL In C I work SINGLET DOUBLET etc OPEN n m C I 2 n m LARGE MECI MS n VECTORS ESR ROOT n MICROS In excited states UHF with TRIPLET QUARTET etc C I 2n C I 2 n m In geometry optimization a Using BFGS GNORM n n XYZ PRECISE b Using EF GNORM n n XYZ PRECISE c Using NLLSQ GNORM n n XYZ PRECISE d Using SIGMA GNORM n n XYZ PRECISE In Gaussian work AIGIN AIGOUT AIDER In SADDLE XYZ BAR n n Chapter 3 Geometry specification FORMAT The geometry is read in using essentially Free Format of FORTRAN 77 In fact a character input is used in order to accommodate the chemical symbols but the numeric data can be regarded as free format indexdata free format This means that integers and real numbers can be interspersed numbers can be separated by one or more spaces a tab and or by one comma If a number is not specified its value is set to zero The geometry can be defined in terms of either internal or cartesian coordinates 3 1 Internal coordinate definition For any one atom i this consists of an interatomic distance in Angstroms from an already defined atom j an interatomic angle in degrees between atoms i and j and an already defined k k and j must be different atoms and finally a torsional angle in degrees between atoms i j k and an already defined atom 1 cannot be the same as k or j See also dihedral angle coherenc
84. FER REPP ROTAT ROTATE RSP SEARCH SECOND SETUPG SOLROT SWAP SYMTRY THERMO TIMER UPDATE VECPRT WRITE WRTKEY WRITXT XYZINT Names of FORTRAN 7 files Appendix B Subroutine calls in MOPAC A list of the program segments which call various subroutines SUBROUTINE AABABC AABACD AABBCD AINTGS ANALYT ANAVIB AXIS BABBBC BABBCD BANGLE BFN BINTGS BKRSAV BONDS BRLZON CALPAR CAPCOR CDIAG CHRGE CNVG COE COMPFG DANG DATIN DCART DELMOL DELRI DENROT DENSIT DEPVAR DERIO DERI1 DERI2 DERI21 CALLS DERS DELRI DELMOL RSP GEOUT VECPRT MPCBDS CDIAG DOFS MEO8A ECO8C SORT SETUPG SYMTRY GMETRY TIMER HCORE ITER DIHED DERIV MECIP UPDATE MOLDAT CALPAR ANALYT DHC DIHED ROTAT GMETRY COE TIMER DHCORE SCOPY DFOCK2 SUPDOT MTXM MXM DIJKL1 MECID MECIH SUPDOT TIMER DERI21 DERI22 MXM OSINV MTXM SCOPY DERI23 DIJKL2 MECID MECIH SUPDOT MTXMC HORII MXM Subroutine calls in MOPAC DERI22 DERI23 DERITR DERNVO DERS DFOCK2 DFPSAV DHC DHCORE DIAG DIAGI DIAT DIAT2 DIHED DIIS DIJKL1 DIJKL2 DIPIND DIPOLE DOFS DRC DRCOUT EAO8C EAO9C ECOSC EF ENPART EPSETA EXCHNG FFHPOL FLEPO FMAT FOCK2 FOCK2D FORCE FORMD FORMXY FORSAV FRAME FREQCY GEOUT GEOUTG GETDAT GETGEG GETGEO GETSYM GETTXT GMETRY GOVER GRID HiELEC MXM SCOPY SYMTRY JCARIN DERIO JAB XYZINT H1ELEC H1ELEC EPSETA COE SET DANG SPACE FORMXY CHRGE GMETRY EAO9C EAO8C BKRSAV COMPFG DF
85. GECNT CURRENT 40768 VIRTUALPAGECNT MAX 600000 are sufficient for the default MOPAC values of 43 heavy and 43 light atoms In order for users to have access to MOPAC they must insert in their individual LOGIN COM files the line 0 Mopac directory MOPACCOM Installing MOPAC where lt Mopac directory gt is the name of the disk and directory which holds all the MOPAC files For example DRAO MOPAC thus DRAO MOPAC MOPAC MOPACCOM COM should be modified once to accommodate local definitions of the directory which is to hold MOPAC This change must also be made to RMOPAC COM and to MOPAC COM MOPAC This command file submits a MOPAC job to a queue Before use MOPAC COM should be modified to suit local conditions The user s VAX is assumed to run three queues called QUEUES3 QUEUE2 and QUEUE1 The user should substitute the actual names of the VAX queues for these symbolic names Thus for example if the local names of the queues are TWELVEHOUR for jobs of length up to 12 hours ONEHOUR for jobs of less than one hour and 30MINS for quick jobs then in place of QUEUE3 QUEUE2 and QUEUET the words TWELVEHOUR ONEHOUR and 30MINS should be inserted RMOPAC RMOPAC is the command file for running MOPAC It assigns all the data files that MOPAC uses to the channels If the user wants to use other file name endings than those supplied the modifications should be made to
86. GLE VARIES AS 240 DEGREES REFERENCE DIHEDRAL 11 DIHEDRAL ANGLE VARIES AS 240 DEGREES REFERENCE DIHEDRAL 12 DIHEDRAL ANGLE VARIES AS 270 DEGREES REFERENCE DIHEDRAL 13 DIHEDRAL ANGLE VARIES AS 270 DEGREES REFERENCE DIHEDRAL 14 DIHEDRAL ANGLE VARIES AS THE NEGATIVE OF THE REFERENCE DIHEDRAL 15 BOND LENGTH VARIES AS HALF THE REFERENCE BOND LENGTH 16 BOND ANGLE VARIES AS HALF THE REFERENCE BOND ANGLE 17 BOND ANGLE VARIES AS 180 DEGREES REFERENCE BOND ANGLE 18 BOND LENGTH IS A MULTIPLE OF REFERENCE BOND LENGTH Function 18 is intended for use in polymers in which the translation vector may be a multiple of some bond length 1 2 3 and 14 are most commonly used Abbreviation SYM SYMMETRY is not available for use with cartesian coordinates T W This is a facility to allow the program to shut down in an orderly manner on computers with execution time cpu limits The total cpu time allowed for the current job is limited to nn nn seconds by default this is one hour i e 3600 seconds If the next cycle of the calculation cannot be completed without running a risk of exceeding the assigned time the calculation will write a restart file and then stop The safety margin is 100 percent that is to do another cycle enough time to do at least two full cycles must remain Alternative specifications of the time are T nn nnM this defines the time in minutes T nn nnH in hours and T nn nnD in days for very long jobs This keyword cannot be
87. MATRIX 18CF DO ONE SCF AND THEN STOP AIDER READ IN AB INITIO DERIVATIVES AIGIN GEOMETRY MUST BE IN GAUSSIAN FORMAT AIGOUT IN ARC FILE INCLUDE AB INITIO GEOMETRY ANALYT USE ANALYTICAL DERIVATIVES OF ENERGY WRT GEOMETRY AM1 USE THE AM1 HAMILTONIAN BAR n n REDUCE BAR LENGTH BY A MAXIMUM OF n n BIRADICAL SYSTEM HAS TWO UNPAIRED ELECTRONS BONDS PRINT FINAL BOND ORDER MATRIX CT A MULTI ELECTRON CONFIGURATION INTERACTION SPECIFIED Keywords CHARGE n COMPFG CONNOLLY DEBUG DENOUT DENSITY DEP DEPVAR n DERIV DFORCE DFP DIPOLE DIPX DIPY DIPZ DMAX DOUBLET DRC DUMP n ECHO EF EIGINV EIGS ENPART ESP ESPRST i ESR EXCITED EXTERNAL FILL n FLEPO FMAT R FOCK FORCE GEO OK GNORM n n GRADIENTS GRAPH x HCORE HESS N H PRIO HYPERFINE IRC ISOTOPE ITER ITRY N IUPD K N N KINETIC LINMIN LARGE LET B LOCALIZE CHARGE ON SYSTEM n e g NH4 gt CHARGE 1 PRINT HEAT OF FORMATION CALCULATED IN COMPFG USE CONNOLLY SURFACE DEBUG OPTION TURNED ON DENSITY MATRIX OUTPUT CHANNEL 10 PRINT FINAL DENSITY MATRIX GENERATE FORTRAN CODE FOR PARAMETERS FOR NEW ELEMENTS TRANSLATION VECTOR IS A MULTIPLE OF BOND LENGTH PRINT PART OF WORKING IN DERIV FORCE CALCULATION SPECIFIED ALSO PRINT FORCE MATRIX USE DAVIDON FLETCHER POWELL METHOD TO OPTIMIZE GEOMETRIES FIT THE ESP TO THE CALCULATED DIPOLE X COMP
88. METRY has two arguments GEO and COORD On input GEO contains either a internal coordinates or b cartesian coordinates On exit COORD contains the cartesian coordinates The normal mode of usage is to supply the internal coordinates in which case the connectivity relations are found in common block GEOKST If the contents of NA 1 is zero as required for any normal system then the normal internal to cartesian conversion is carried out If the contents of NA 1 is 99 then the coordinates found in GEO are assumed to be cartesian and no conversion is made This is the situation in a FORCE calculation A further option exists within the internal to cartesian conversion If STEP stored in common block REACTN is non zero then a reaction path is assumed and the internal coordinates are adjusted radially in order that the distance in internal coordinate space Program from the geometry specified in GEO is STEPP away from the geometry stored in GEOA stored in REACTN During the internal to cartesian conversion the angle between the three atoms used in defining a fourth atom is checked to ensure that it is not near to 0 or 180 degrees If it is near to these angles then there is a high probability that a faulty geometry will be generated and to prevent this the calculation is stopped and an error message printed Note 1 If the angle is exactly 0 or 180 degrees then the calculation is not terminated This is the normal situatio
89. MOPAC calls function SECOND the presence of a readable file called SHUTDOWN logically identified with lt filename gt END is checked for and if it exists the apparent elapsed CPU time is increased by 1 000 000 seconds and a warning message issued No further action is taken until the elapsed time is checked to see if enough time remains to do another cycle Since an apparently very long time has been used there is not enough time left to do another cycle and the restart files are generated and the run stopped SHUTDOWN is completely machine independent Specific instructions for mounting MOPAC on other computers have been left out due to limitations of space in the Manual however the following points may prove useful 11 1 ESP calculation 1 Function SECOND is machine specific SECOND is double precision and should return the CPU time in seconds from an arbitary zero of time If the SHUT command has been issued the value returned by SECOND should be increased by 1 000 000 2 On UNIX based and other machines on line help can be provided by using help f Documentation on help f is in help f 3 OPEN and CLOSE statements are a fruitful source of problems If MOPAC does not work most likely the trouble lies in these statements 4 RMOPAC COM should be read to see what files are attached to what logical chan nel How to use MOPAC The COM file to run the MOPAC can be accessed using the command MOPAC followed by none
90. NDO 3 AM1 and PM3 are used in the electronic part of the calculation to obtain molecular orbitals the heat of formation and its derivative with respect to molecular geometry Using these results MOPAC calculates the vibrational spectra thermodynamic quantities isotopic substitution effects and force constants for molecules radicals ions and polymers For studying chemical reactions a transition state location routine and two transition state optimizing routines are available For users to get the most out of the program they must understand how the program works how to enter data how to interpret the results and what to do when things go wrong While MOPAC calls upon many concepts in quantum theory and thermodynamics and uses some fairly advanced mathematics the user need not be familiar with these specialized topics MOPAC is written with the non theoretician in mind The input data are kept as simple as possible so users can give their attention to the chemistry involved and not concern themselves with quantum and thermodynamic exotica The simplest description of how MOPAC works is that the user creates a data file which describes a molecular system and specifies what kind of calculations and output are desired The user then commands MOPAC to carry out the calculation using that data file Finally the user extracts the desired output on the system from the output files created by MOPAC 1 This is the sixth edition MOPAC has under
91. NTIAL 11 0419 NO OF FILLED LEVELS 6 MOLECULAR WEIGHT 30 026 SCF CALCULATIONS 15 COMPUTATION TIME 2 740 SECONDS ATOM CHEMICAL BOND LENGTH BOND ANGLE NUMBER SYMBOL ANGSTROMS DEGREES I NA I NB NA I 1 0 2 C 1 21678 3 H 1 10590 123 50259 4 H 1 10590 123 50259 INTERATOMIC DISTANCES 0 1 Cx 32 H 3 0 1 0 000000 C 2 1 216777 0 000000 H 3 2 046722 1 105900 0 000000 H 4 2 046722 1 105900 1 844333 0 00 EIGENVALUES PTIMIZATION Note 11 Note 12 Note 13 VERSION 6 00 4 0CT 90 6 KCAL Note 14 7 EV 9 EV 3 EV 8 Note 15 TWIST ANGLE DEGREES NC NB NA I NA NB NC 1 Note 16 2 1 180 00000 2 1 3 H 4 0000 42 98352 25 12201 16 95327 16 29819 14 17549 11 04198 0 85804 3 6768 3 84990 7 12408 Note 17 NET ATOMIC CHARGES AND DIPOLE CONTRIBUTIONS ATOM NO TYPE CHARGE ATO 1 0 0 2903 6 2 C 0 2921 3 3 H 0 0009 1 4 H 0 0009 1 DIPOLE X Y Z TOTAL POINT CRG 1 692 0 000 0 000 1 692 HYBRID 0 475 0 000 0 000 0 475 SUM 2 166 0 000 0 000 2 166 CARTESIAN COORDINATES NO ATOM X Y al 0 0 0000 0 0000 2 C 1 2168 0 0000 3 H 1 8272 0 9222 4 H 1 8272 0 9222 ATOMIC ORBITAL ELECTRON POPULATIONS 1 88270 1 21586 1 89126 1 30050 1 25532 0 1 00087 1 00087 TOTAL CPU TIME MOPAC DONE 3 11 SECONDS M ELECTRON DENSITY 2903 TOT9 Note 18 0009 0009 Note 19 Z 0 0000 0 0000 0 0000 0 0000 86217 0 89095 0 69950 Note 20 Examples Note 1 The banner indicates whether the calculation uses
92. OM will suffice SYS BATCH Finally the priority will be requested What priority 5 To which any value between 1 and 5 will suffice Note that the maximum priority is limited by the system manager 11 1 ESP calculation As supplied MOPAC will not do the ESP calculation because of the large memory re quirement of the ESP To install the ESP make the following changes 1 Rename ESP ROF to ESP FOR 2 Add to the first line of MOPAC OPT the string ESP without the quotation marks 3 Edit MNDO FOR to uncomment the line C CALL ESP 4 Compile ESP and MNDO and relink MOPAC using e g COMPILE ESP MNDO 5 If the resulting executable is too large modify DIMSIZES DAT to reduce MAXHEV and MAXLIT then recompile everything and relink MOPAC with COMPILE To familiarize yourself with the system the following operations might be useful 1 Run the supplied test molecules and verify that MOPAC is producing accept able results 2 Make some simple modifications to the datafiles supplied in order to test your un derstanding of the data format 3 When satisfied that MOPAC is working and that data files can be made begin production runs Working of SHUTDOWN command If for whatever reason a run needs to be stopped prematurely the command SHUT lt jobname gt can be issued This will execute a small command language file which copies the data file to form a new file called filename END The next time
93. ONENT OF DIPOLE TO BE FITTED Y COMPONENT OF DIPOLE TO BE FITTED Z COMPONENT OF DIPOLE TO BE FITTED MAXIMUM STEPSIZE IN EIGENVECTOR FOLLOWING DOUBLET STATE REQUIRED DYNAMIC REACTION COORDINATE CALCULATION WRITE RESTART FILES EVERY n SECONDS DATA ARE ECHOED BACK BEFORE CALCULATION STARTS USE EF ROUTINE FOR MINIMUM SEARCH PRINT ALL EIGENVALUES IN ITER PARTITION ENERGY INTO COMPONENTS ELECTROSTATIC POTENTIAL CALCULATION RESTART OF ELECTROSTATIC POTENTIAL CALCULATE RHF UNPAIRED SPIN DENSITY OPTIMIZE FIRST EXCITED SINGLET STATE READ PARAMETERS OFF DISK IN RHF OPEN AND CLOSED SHELL FORCE M O n TO BE FILLED PRINT DETAILS OF GEOMETRY OPTIMIZATION PRINT DETAILS OF WORKING IN FMAT PRINT LAST FOCK MATRIX FORCE CALCULATION SPECIFIED OVERRIDE INTERATOMIC DISTANCE CHECK EXIT WHEN GRADIENT NORM DROPS BELOW n n PRINT ALL GRADIENTS GENERATE FILE FOR GRAPHICS PRINT DETAILS OF WORKING IN HCORE OPTIONS FOR CALCULATING HESSIAN MATRICES IN EF HEAT OF FORMATION TAKES PRIORITY IN DRC HYPERFINE COUPLING CONSTANTS TO BE CALCULATED INTRINSIC REACTION COORDINATE CALCULATION FORCE MATRIX WRITTEN TO DISK CHANNEL 9 PRINT DETAILS OF WORKING IN ITER SET LIMIT OF NUMBER OF SCF ITERATIONS TO N MODE OF HESSIAN UPDATE IN EIGENVECTOR FOLLOWING BRILLOUIN ZONE STRUCTURE TO BE CALCULATED EXCESS KINETIC ENERGY ADDED TO DRC CALCULATION PRINT DETAILS OF LINE MINIMIZATION PRINT EXPANDED OUTPUT OVERRIDE CERTAIN SAFETY CHECKS PRINT LOCALIZED ORBIT
94. ORITY is used then turning points cannot be monitored Currently H PRIORITY and X PRIORITY are not implemented but will be as soon as practical To monitor geometry turning points put a T in place of the geometry optimization flag for the relevant geometric variable To monitor the potential energy turning points put a I for the flag for atom 1 bond length Do not forget to put in a bond length zero will do The effect of these flags together is as follows 1 No options All calculated points will be printed No turning points will be calcu lated 2 Atom 1 bond length flagged with a I If T PRIO etc are NOT specified then potential energy turning points will be printed 3 Internal coordinate flags set to T If T PRIO etc are NOT specified then ge ometry extrema will be printed If only one coordinate is flagged then the turning point will be displayed in chronologic order if several are flagged then all turning points occuring in a given time interval will be printed as they are detected In other Background words some may be out of chronologic order Note that each coordinate flagged will give rise to a different geometry minimize flagged coordinates to minimize output 4 Potential and geometric flags set The effect is equivalent to the sum of the first two options 5 T PRIO set No turning points will be printed but constant time slices by default 0 1 fs will be used to control the print
95. P 3 TIME 2 53 SECS INTEGRAL 7 17 STEP 4 TIME 2 31 SECS INTEGRAL 9 48 STEP 5 RESTART FILE WRITTEN INTEGRAL 11 97 STEP 6 TIME 2 43 SECS INTEGRAL 14 40 STEP 7 TIME 2 32 SECS INTEGRAL 16 72 STEP 8 TIME 2 30 SECS INTEGRAL 19 02 STEP 9 RESTART FILE WRITTEN INTEGRAL 22 17 TIME LEFT 1997 08 TIME LEFT 1994 59 TIME LEFT 1992 06 TIME LEFT 1989 75 TIME LEFT 1987 26 TIME LEFT 1984 83 TIME LEFT 1982 51 TIME LEFT 1980 21 TIME LEFT 1977 06 Testdata STEP 10 TIME 2 52 SECS INTEGRAL 24 69 TIME LEFT STEP 11 TIME 2 25 SECS INTEGRAL 26 94 TIME LEFT STEP 12 TIME 3 15 SECS INTEGRAL 30 09 TIME LEFT FORCE MATRIX IN MILLIDYNES ANGSTROM 0 0 1 Cc 2 H 3 H 4 0 1 9 557495 C 2 8 682982 11 426823 H 3 0 598857 2 553336 3 034881 H 4 0 598862 2 553344 0 304463 3 034886 HEAT OF FORMATION ZERO POINT ENERGY 32 881900 KCALS MOLE 18 002 KILOCALORIES PER MOLE THE LAST 6 VIBRATIONS ARE THE TRANSLATION AND ROTATION MODES THE FIRST THREE OF THESE BEING TRANSLATIONS IN X Y AND Z RESPECTIVELY NORMAL COORDINATE ANALYSIS ROOT NO 1 2 3 4 5 1209 90331 1214 67040 1490 52685 2114 53841 3255 93651 1 0 00000 0 00000 0 04158 0 25182 0 00000 2 0 06810 0 00001 0 00000 0 00000 0 00409 3 0 00000 0 03807 0 00000 0 00000 0 00000 4 0 00000 0 00000 0 03819 0 32052 0 00000 5 0 13631 0 00002 0 00000 0 00000 0 08457 6 0 00002 0 15172 0 00000 0 00000 0 00000 7 0 53308 0 00005 0 55756 0
96. PSAV FORSAV JAB GMETRY FMAT DRC OVERLP AXIS BRLZON XYZINT XXX GETVAL GEOUT UPCASE GEOUT DFPSAV DIAT MXMT GMETRY MXM DERI1 KAB GEOUT ROTATE ROTATE GOVER VECPRT GMETRY COMPFG COMPFG DIPIND COMPFG COMPFG KAB COMPFG VECPRT ANAVIB FRAME WRTTXT GETVAL NUCHAR FLEPO FOCK2 FOCK1 SUPDOT HCORE ITER DERIV DERNVO DCART GEOUT DERITR DERI2 SOLROT FOCK2 DIAT2 MINV PRTDRC BKRSAV UPDHES HQRII FORMD SYMTRY VECPRT RSP MATOUT SCOPY GEOUT SUPDOT LINMIN DIIS CHRGE NLLSQ FLEPO WRITE XYZINT AXIS FRAME RSP MATOUT FREQCY MATOUT THERMO RSP CHRGE GETVAL XYZINT GEOUT WRTTXT Subroutine calls in MOPAC HADDON HCORE HELECT HQRII IJKL INTERP ITER JAB JCARIN KAB LINMIN LOCAL LOCMIN MNDO MAMULT MATOUT MEO8A MEO8B MECI MECIH MECIP MINV MOLDAT MOLVAL MPCBDS MPCPOP MPCSYB MTXM MTXMC MULLIK MULT MXM MXMT NLLSQ NUCHAR OSINV OVERLP PARSAV PARTXY PATHK PATHS PERM POLAR POWSAV POWSQ PRTDRC PULAY QUADR REACT1 READ DEPVAR H1ELEC PARTXY HQRII EPSETA HQRII SYMTRY COMPFG MATOUT COMPFG GETDAT PATHK FLEPO MEOSB IJKL MXM REFER MXM RSP PARSAV XYZINT FORMXY DFPSAV DFPSAV GMETRY XYZINT POWSAV CHRGE MAMULT GETGEO GETTXT SYMTRY ROTATE SOLROT VECPRT SCHMIT SCHMIB SPLINE VECPRT J FOCK2 FOCK1 WRITE INTERP PULAY DIAG MATOUT SWAP DENSIT CNVG GMETRY EXCHNG EXCHNG READ MOL
97. RCE calculation is a prerequisite for a THERMO calculation Before a FORCE calculation is started a check is made to ensure that a stationary point is being used This check involves calculating the gradient norm GNORM and if it is significant the GNORM will be reduced using BFGS All internal coordinates are optimized and any symmetry constraints are ignored at this point An implication of this is that if the specification of the geometry relies on any angles being exactly 180 or zero degrees the calculation may fail The geometric definition supplied to FORCE should not rely on angles or dihedrals assuming exact values The test of exact linearity is sufficiently slack that most molecules that are linear such as acetylene and but 2 yne should not be stopped See also THERMO LET TRANS ISOTOPE In a FORCE calculation PRECISE will eliminate quartic contamination part of the anharmonicity This is normally not important therefore PRECISE should not routinely be used In a FORCE calculation the SCF criterion is automatically made more stringent this is the main cause of the SCF failing in a FORCE calculation GEO OK W Normally the program will stop with a warning message if two atoms are within 0 8 Angstroms of each other or more rarely the BFGS routine has difficulty optimizing the geometry GEO OK will over ride the job termination sequence and allow the calculation to proceed In practice most jobs that terminate due to th
98. RIO DERI1 DERI2 DERI21 DERI22 DERI23 DERITR DERNVO DERS DFOCK2 DFPSAV DHC DHCORE DIAG DIAGI DIAT DIAT2 DIHED DIIS DIJKL1 DIJKL2 DIPIND DIPOLE DOFS DRC DRCOUT EA08C EAO9C ECO8C EF ENPART EPSETA EXCHNG SET EF WRITE FREQCY DATIN ITER BRLZON DIPIND ITER DENROT DRC FORCE POLAR DIHED MNDO DERITR ANALYT ANALYT WRITE ITER HADDON DERNVO DERNVO DERI2 DERI2 DERI2 DERI2 DERITR DERITR ANALYT DERI1 FLEPO DCART DERI1 DERI21 DERI21 DIAT DIAT COMPFG FLEPO DERI1 DERI2 FFHPOL FMAT BRLZON FORCE PRTDRC ECO8C EAO8C CDIAG MNDO WRITE DIAG LINMIN WRITE FMAT GEOUT PRTDRC WRITE DIAT EF FFHPOL FLEPO FMAT LINMIN LOCMIN MNDO NLLSQ POWSQ REACT1 SEARCH MULLIK DERNVO GRID PATHK PATHS DERI1 ITER H1ELEC DCART XYZGEO XYZINT WRITE MNDO ITER RSP LOCMIN Subroutine calls in MOPAC FFHPOL FLEPO FMAT FOCK2 FORCE FORMD FORMXY FORSAV FRAME FREQCY GEOUT WRITE GEOUTG GETDAT GETGEG GETGEO GETSYM GETTXT GMETRY GOVER GRID H1ELEC HADDON HCORE HELECT HQRII IJKL INTERP ITER JAB JCARIN KAB LINMIN LOCAL LOCMIN MNDO MAMULT MATOUT MEO8A MEO8B MECI MECIH MECIP MINV MOLDAT MOLVAL MPCBDS MPCPOP POLAR FORCE GRID REACT1 FORCE DERI22 DHC MNDO EF DIJKL1 PARTXY FMAT FORCE FREQCY FORCE BKRSAV DERITR GMETRY GRID POWSAV REACT 1 WRITE WRITE MNDO READ REACT 1 READ READ READ COMPFG DENROT FORCE JCARIN REACT1 R
99. SE THE MNDO PM3 HAMILTONIAN NUMBER OF POINTS IN REACTION PATH NUMBER OF POINTS IN FIRST DIRECTION IN GRID CALCULATION NUMBER OF POINTS IN SECOND DIRECTION IN GRID CALCULATION CALCULATE FIRST SECOND AND THIRD ORDER POLARIZABILITIES IN ESP WRITE OUT ELECTROSTATIC POTENTIAL TO UNIT 21 PRINT DETAILS OF WORKING IN POWSQ CRITERIA TO BE INCREASED BY 100 TIMES USE PULAY S CONVERGER TO OBTAIN A SCF QUARTET STATE REQUIRED QUINTET STATE REQUIRED IN EF RECALCULATE HESSIAN EVERY N STEPS CALCULATION RESTARTED ROOT n TO BE OPTIMIZED IN A C I CALCULATION THE SYMMETRY NUMBER OF THE SYSTEM IS n OPTIMIZE TRANSITION STATE SCALING FACTOR FOR VAN DER WAALS DISTANCE IN ESP DEFAULT SCF CRITERION REPLACED BY THE VALUE SUPPLIED INCREMENT BETWEEN LAYERS IN ESP EXTRA KEYWORDS TO BE READ OF SETUP FILE SEXTET STATE REQUIRED A DAMPING FACTOR OF n DEFINED TO START SCF MINIMIZE GRADIENTS USING SIGMA SINGLET STATE REQUIRED MULTIPLIER USED TO SCALE MNDO CHARGES PRINT FINAL UHF SPIN MATRIX STEP SIZE IN PATH Keywords STEPi n STEP SIZE n FOR FIRST COORDINATE IN GRID CALCULATION STEP2 n STEP SIZE n FOR SECOND COORDINATE IN GRID CALCULATION STO 3G DEORTHOGONALIZE ORBITALS IN STO 3G BASIS SYMAVG AVERAGE SYMMETRY EQUIVALENT ESP CHARGES SYMMETRY IMPOSE SYMMETRY CONDITIONS T n A TIME OF n SECONDS REQUESTED THERMO PERFORM A THERMODYNAMICS CALCULATION TIMES PRINT TIMES OF VARIOUS STAGES T PRIO TIME TAKES PRIORITY IN DRC TRANS
100. TART with IRC n implies a restart from the FORCE calculation Since this is a restart from within an IRC calculation the keyword IRC n has been replaced by IRC IRC on its own without the n implies an IRC calculation from the starting position here the RESTART position without initial displacement RESTART IRC T 600 WATER H 0 000000 0 0 000000 0 0 000000 0 0 0 0 0 0 911574 0 0 000000 0 0 000000 0 100 H 0 911574 0 180 000000 0 0 000000 0 2 1 0 0 0 000000 0 0 000000 0 0 000000 0 0 0 O 6 11 Reaction coordinates Output format for IRC and DRC The IRC and DRC can produce several different forms of output Because of the large size of these outputs users are recommended to use search functions to extract information To facilitate this specific lines have specific characters Thus a search for the symbol will summarize the energy profile while a search for AA will yield the coordinates of atom 1 whenever it is printed The main flags to use in searches are SEARCH FOR YIELDS 2E Energies for all points calculated excluding extrema XM Energies for all turning points VMAX Energies for all maxima AMINO Energies for all minima ay Aad Energies for all points calculated gt AA Internal coordinates for atom 1 for every point gt AR Internal coordinates for atom 5 for every point 7 123AB Internal coordinates for atom 5 for point 123 As the keywords for the IRC DRC are interdependent the following list
101. THIS SYSTEM THIS THERMODYNAMICS CALCULATION IS LIMITED TO MOLECULES WHICH HAVE NO INTERNAL ROTATIONS RADIAL 12 6 12 6 0 0 RADIAL 0 0 0 0 0 0 RADIAL 0 6 0 6 100 0 RADIAL 100 0 17 7 ir RADIAL 98 1 98 1 0 0 RADIAL 95 57 95 5 100 0 Note 8 5 2 Results file for the force calculation CALCULATED THERMODYNAMIC PROPERTIES TEMP K PARTITION FUNCTION H O F ENTHALPY HEAT CAPACITY ENTROPY KCAL MOL CAL MOLE CAL K MOL CAL K MOL 298 VIB 1 007 23 39484 0 47839 0 09151 ROT 709 888 305 2 981 16 026 INT 714 911 700 3 459 16 117 TRA 0 159E 27 1480 509 4 968 36 113 TOT 32 882 2392 2088 8 4274 52 2300 NOTE HEATS OF FORMATION ARE RELATIVE TO THE ELEMENTS IN THEIR STANDARD STATE AT 298K TOTAL CPU TIME 32 26 SECONDS MOPAC DONE Note 1 All three words ROT FORCE and THERMO are necessary in order to obtain thermodynamic properties In order to obtain results for only one temperature THERMO has the first and second arguments identical The symmetry number for the C point group is 2 Note 2 Internal coordinate derivatives are in kcal Angstrom or kcal radian Values of less than about 0 2 are quite acceptable Note 3 In larger calculations the time estimates are useful In practice they are pes simistic and only about 7096 of the time estimated will be used usually The principal moments of inertia can be directly related to the microwave spectrum of the molecule They a
102. The numbering of the M O s used in the MECI is standard and follows the Aufbau principle The order of filling is in order of energy and alpha before beta This point is critically important in deciding the sign of matrix elements For a 5 M O system then the order of filling is 1 1 2 2 3 3 4 4 5 5 A triplet state arising from two microstates each with a component of spin 0 will thus be the positive combination 1 2 02 This is in variance with the sign convention used in earlier programs for running MNDO This standard sign convention was chosen in order to allow the signs of the microstate coefficients to conform to those resulting from the spin step down operator Matrix elements between all pairs of microstates are calculated in order to form the secular determinant Many elements will be identically zero due to the interacting deter minants differing by more than two M O s For the remaining interactions the following types can be identified 1 The two determinants are identical No permutations are necessary in order to calculate the sign of the matrix element E p p is given simply by where O i p is the occupancy of a M O i in microstate p and Og i p is the occupancy of 8 M O i in microstate p 2 Determinants differing by exactly one M O The differing M O can be of type o or B It is sufficient to evaluate the case in which both M O s are of alpha type the beta form is obtained in like
103. a valency so has a molecular orbital This leads to the following relations The sum of the bonding contributions of all occupied M O s is the same as the sum of all valencies which in turn is equal to two times the sum of all bonds The sum of the bonding contributions of all M O s is zero C I n C Normally configuration interaction is invoked if any of the keywords which imply a C I calculation are used such as BIRADICAL TRIPLET or QUARTET Note that ROOT does not imply a C I calculation ROOT is only used when a C I calculation is done However as these implied C I s involve the minimum number of configurations practical Keywords the user may want to define a larger than minimum C I in which case the keyword C I n can be used When C I n is specified the n M O s which bracket the occupied virtual energy levels will be used Thus C I 22 will include both the HOMO and the LUMO while C I 21 implied for odd electron systems will only include the HOMO This will do nothing for a closed shell system and leads to Dewar s half electron correction for odd electron systems Users should be aware of the rapid increase in the size of the C I with increasing numbers of M O s being used Numbers of microstates implied by the use of the keyword C I n on its own are as follows Keyword Even electron systems Odd electron systems No of electrons configs No of electrons configs Alpha Beta Alpha
104. abbreviated version which lacks the full range of options of the whole program can be specified at compile time Installing MOPAC At the bottom of the DIMSIZES DAT file the programmer is asked for various options to be used in compiling These options allow arrays of MECI PULAY and ESP to assume their correct size As long as no attempt is made to use the reduced subroutines the program will function normally If an attempt is made to use an option which has been excluded then the program will error Size of MOPAC The amount of storage required by MOPAC depends mainly on the number of heavy and light atoms As it is useful for programmers to have an idea of how large various MOPACs are the following data are presented as a guide Sizes of various MOPAC Version 6 00 executables in which the number of heavy atoms is equal to the number of light atoms assembled on a VAX computer are No of heavy atoms Size of Executable Kbytes MOPAC 5 00 MOPAC 6 00 AMPAC 2 00 10 1 653 2 054 N A 20 3 442 4 689 4 590 30 6 356 8 990 9 150 40 10 400 14 955 15 588 50 15 572 22 586 23 944 60 21 872 31 880 34 145 100 58 361 87 519 200 228 602 336 867 300 511 723 754 540 The size S of any given MOPAC executable in Kbytes may be estimated for MOPAC 5 00 as S 9939 N 9 57 N N 5 64 and for MOPAC 6 00 as S 1091 N 13 40 N N 8 33 The large increase in size of MOPAC was caused mainly by the inclusion of the ana ly
105. alculation is completely precise in the group theoretic sense but the accuracy of the calculation is limited by the Hamiltonian used a space dependent function Choice of state to be optimized MECI can calculate a large number of states of various total spin Two schemes are provided to allow a given state to be selected First ROOT n will when used on its own select the n th state irrespective of its total spin By default n 1 If ROOT n is used in conjunction with a keyword from the set SINGLET DOUBLET TRIPLET QUARTET QUINTET or SEXTET then the n th root of that spin state will be used For example ROOT 4 and SINGLET will select the 4th singlet state If there are two triplet states below the fourth singlet state then this will mean that the sixth state will be selected Calculation of unpaired spin density Starting with the state functions as linear combinations of configurations the unpaired spin density corresponding to the alpha spin density minus the beta spin density will be calculated for the first few states This calculation is straightforward for diagonal terms and only those terms are used 6 15 Reduced masses in a force calculation Reduced masses for a diatomic are given by T X Tm my cmo For a Hydrogen molecule the reduced mass is thus 0 5 for heavily hydrogenated systems e g methane the reduced mass can be very low A vibration involving only heavy atoms e g a C N in cyanide should give a
106. all atoms Use only if the mantissa is short less than 52 bits or out of interest Should not be used for routine work on a VAX e ANAVIB Utility Gives a brief interpretation of the modes of vibration of the molecule The principal pairs of atoms involved in each vibration are identified and the mode of motion tangential or radial is output e AXIS Utility Works out the three principal moments of inertia of a molecule If the system is linear one moment of inertia is zero Prints moments in units of cm and 10 9 g cm e BABBBC Utility Calculates the configuration interaction matrix element between two configurations differing by exactly one beta M O Called by MECI only e BABBCD Utility Calculates the configuration interaction matrix element between two configurations differing by exactly two beta M O s Called by MECI only e BANGLE Utility Given a set of coordinates BANGLE will calculate the angle between any three atoms e BFN Utility Calculates the B functions in the Slater overlap e BINTGS Utility Calculates the B functions in the Slater overlap e BKRSAV Utility Saves and restores data used by the eigenvector following subrou tine Called by EF only e BONDS Utility Evaluates and prints the valencies of atoms and bond orders be tween atoms Main argument density matrix No results are passed to the calcu lation and no data are changed Called by WRITE only Description of subroutines BRLZON Main S
107. alled by ESP NAICAP Utility Called by ESP NLLSQ Main sequence Used in the gradient norm minimization NUCHAR Takes a character string and reads all the numbers in it and stores these in an array OSINV Utility Inverts a square matrix Called by PULAY only OVERLP Utility Part of EF OVERLP decides which normal mode to follow OVLP Utility Called by ESP only OVLP calculates the overlap over Gaussian STO s PARSAV Utility Stores and restores data used in the gradient norm minimization calculation PARTXY Utility Called by IJKL only PART XY calculates the partial product lt i j ir in jij 1 r kl PATHK Main sequence Calculates a reaction coordinate which uses a constant step size Invoked by keywords STEP and POINTS PATHS Main sequence Given a reaction coordinate as a row vector PATHS per forms a FLEPO geometry optimization for each point the later geometries being initially guessed from a knowledge of the already optimized geometries and the current step Called by MNDO only PDGRID Utility Part of ESP Calculates the Williams surface PERM Utility Permutes n1 electrons of alpha or beta spin among n2 M O s Description of subroutines e POLAR Utility Calculates the polarizability volumes for a molecule or ion Uses 19 SCF calculations so appears after WRITE has finished Cannot be used with FORCE but can be used anywhere else Called by WRITE e POWSAV Utility Calculation store and restart
108. and Bi J J P Stewart J Comp Chem In press expected date of publication Feb 1991 Original References for Elements Parameterized in AM1 H M J S Dewar E G Zoebisch E F Healy J J P Stewart J Am Chem Soc 107 3902 3909 1985 B M J S Dewar C Jie E G Zoebisch Organometallics 7 513 521 1988 C M J S Dewar E G Zoebisch E F Healy J J P Stewart J Am Chem Soc 107 3902 3909 1985 N M J S Dewar E G Zoebisch E F Healy J J P Stewart J Am Chem Soc 107 3902 3909 1985 References O M J S Dewar E G Zoebisch E F Healy J J P Stewart J Am Chem Soc 107 3902 3909 1985 F M J S Dewar E G Zoebisch Theochem 180 1 1988 Al M J S Dewar A J Holder Organometallics 9 508 1990 Si M J S Dewar C Jie Organometallics 6 1486 1490 1987 P M J S Dewar C Jie Theochem 187 1 1989 S No reference Cl M J S Dewar E G Zoebisch Theochem 180 1 1988 Zn M J S Dewar K M Merz Jr Organometallics 7 522 1988 Ga M J S Dewar C Jie Organometallics 8 1544 1989 Br M J S Dewar E G Zoebisch Theochem 180 1 1988 I M J S Dewar E G Zoebisch Theochem 180 1 1988 Hg M J S Dewar C Jie Organometallics 8 1547 1989 see also PARASOK for the use of MNDO parameters for other elements On Shift The Dynamic Level Shift Method for Improving the Convergence of the SCF Proce dure A V Mitin J Comp Chem 9 107 110
109. artesian coordinates will not be reflected in the internal coordinates For example if the Y coordinates of atoms 5 and 6 are equal it does not follow that the internal coordinate angles these atoms make are equal This is a fatal error ELEMENT NOT FOUND When an external file is used to redefine MNDO AM1 or PM3 parameters the chemical symbols used must correspond to known elements Any that do not will trigger this fatal message ERROR DURING READ AT ATOM NUMBER Something is wrong with the geometry data In order to help find the error the geometry already read in is printed The error lies either on the last line of the geometry printed or on the next unprinted line This is a fatal error FAILED IN SEARCH SEARCH CONTINUING Not a fatal error The McIver Komornicki gradient minimization involves use of a line search to find the lowest gradient This message is merely advice However if SIGMA takes a long time consider doing something else such as using NLLSQ or refining the geometry a bit before resubmitting it to SIGMA lt lt lt lt FAILED TO ACHIEVE SCF gt gt gt gt The SCF calculation failed to go to completion an unwanted and depressing message that unfortunately appears every so often To date three unconditional convergers have appeared in the literature the SHIFT technique Pulay s method and the Camp King converger It would not be fair to the authors to condemn their meth
110. ases The selection of which eigenvector to follow towards the TS is given by MODE n where n is the number of the Hessian eigenvector to follow The default is MODE 1 These features can be turned off by giving suitable values as keywords e g RMIN 100 RMAX 100 effectively inhibits step rejection Similarly setting OMIN 0 disables step rejection based on large changes in the structure of the TS mode The default is to use mode following even if the TS mode is the lowest eigenvector This means that the TS mode may change to some higher mode during the optimization To turn of mode following and thus always follow the mode with lowest eigenvalue set MODE O If it is a minimum search the new energy should be lower than the previous The acceptance criteria used is that the actual predicted ratio should be larger than RMIN which for the default value of RMIN 0 is equivalent to a lower energy If the ratio is below RMIN the step is rejected the trust radius reduced by a factor of two and a new step is predicted The RMIN RMAX and OMIN features has been introduced in the current version of EF to improve the stability of TS optimizations Setting RMIN and RMAX close to one will give a very stable but also very slow optimization Wide limits on RMIN and RMAX may in some cases give a faster convergence but there is always the risk that very poor steps are accepted causing the optimization to diverge The default values of 0 and 4 rarely rejects st
111. at 1204 5 cm the in plane C H asymmetric bend is the most unsymmetric vibration and is chosen to demonstrate conservation of vibrational purity Mode 1 has a frequency corresponding to 3 44 kcal mole and a predicted vibrational time of 27 69 fs By direct calculation using the DRC the cycle time is 27 55 fs The rate of decay of this mode has an estimated half life of a few thousands femtoseconds Rate of decay of starting mode For trajectories initiated by an IR C n calculation whenever the potential energy is a minimum the current velocity is compared with the supplied velocity The square of the cosine of the angle between the two velocity vectors is a measure of the intensity of the original mode in the current vibration Half Life for decay of initial mode Vibrational purity is assumed to decay according to zero th order kinetics The half life is thus 0 6931472t log w fs where 7 is the square of the overlap integral of the original vibration with the current vibration Due to the very slow rate of decay of the starting mode several half life calculations should be examined Only when successive half lives are similar should any confidence be placed in their value DRC print options The amount of output in the DRC is controlled by three sets of options These sets are e Equivalent Keywords H PRIORITY T PRIORITY and X PRIORITY e Potential Energy Turning Point option e Geometry Maxima Turning Point options If T PRI
112. ated geometry changes by 0 05 A The geometry change is defined as the linear sum of the translation vectors of motion for all atoms in the system Abbreviation X PRIO X PRIORITY n nn O In a DRC calculation results will be printed whenever the calculated geometry changes by n nn A XYZ W The SADDLE calculation quite often fails due to faulty definition of the second geometry because the dihedrals give a lot of difficulty To make this option easier to use XYZ was developed A calculation using XYZ runs entirely in cartesian coordinates thus eliminating the problems associated with dihedrals The connectivity of the two systems can be different but the numbering must be the same Dummy atoms can be used these will be removed at the start of the run A new numbering system will be generated by the program when necessary XYZ is also useful for removing dummy atoms from an internal coordinate file use XYZ and OSCF If a large ring system is being optimized sometimes the closure is difficult in which case XYZ will normally work Except for SADDLE do not use XYZ by default use it only when something goes wrong In order for XYZ to be used the supplied geometry must either be in cartesian coordi nates or if internal coordinates are used symmetry must not be used and all coordinates must be flagged for optimization If dummy atoms are present only 3N 6 coordinates need to be flagged for optimization If at all possible th
113. ation SCFCRT 0 0000001 If SCFCRT n nnn is specified SCFCRT n nnn If a BFGS optimization SCFCRT becomes a function of the difference between the current energy and the lowest energy of previous SCFs Secondary tests 1 Change in density matrix elements on two successive iterations must be less than 0 001 2 Change in energy in eV on three successive iterations must be less than 10 x SCFCRT 9 2 Geometric optimization criteria Name Defined in Default value Basic Test Exceptions Name Defined in Default value TOLERX Test on X Satisfied FLEPO 0 0001 Angstroms The projected change in geometry is less than TOLERX Angstroms If GNORM is specified the TOLERX test is not used DELHOF Herbert s Test Satisfied FLEPO 0 001 Criteria Basic Test Exceptions Name Defined in Default value Basic Test Exceptions Name Defined in Default value Basic Test Exceptions Secondary Tests Other Tests Exceptions Name Defined in Default value Basic Test Exceptions Name Defined in The projected decrease in energy is less than DELHOF kcals mole If GNORM is specified the DELHOF test is not used TOLERG FLEPO 1 0 The gradient norm in kcals mole Angstrom is less than TOLERG multiplied by the square root of the number of coordinates to be optimized Test on Gradient Satisfied If GNORM n nnn is specified TOLERG n nnn divided by the square root of the number of coord
114. atoms including atoms 1 2 and 3 can be optimized Dummy atoms should not be used for obvious reasons 3 4 Conversion between various formats MOPAC can accept any of the following formats cartesian MOPAC internal coordinates and Gaussian internal coordinates Both MOPAC and Gaussian Z matrices can also contain dummy atoms Internally MOPAC works with either a cartesian coordinate set if XYZ is specified or internal coordinates the default If the OSCF option is requested the geometry defined on input will be printed in MOPAC Z matrix format along with other optional formats The type s of geometry printed at the end of a OSCF calculation depend only on the keywords XYZ AIGOUT and NOX YZ The geometry printed is independent of the type of input geometry and therefore makes a convenient conversion mechanism If XYZ is present all dummy atoms are removed and the internal coordinate definition remade All symmetry relations are lost if XYZ is used Geometry specification If NOXYZ is present cartesian coordinates will not be printed If AIGOUT is present a data set using Gaussian Z matrix format is printed Note 1 Only if the keyword XYZ is absent and the keyword SYMMETRY present in a MOPAC internal coordinate geometry or two or more internal coordinates in a Gaussian Z matrix have the same symbolic will symmetry be present in the MOPAC or Gaussian geometries output 2 This expanded use of 0SCF replaces the program DDUM
115. be performed A controlled termination of the run would follow this message The job may terminate earlier than expected this is ordinarily due to one of the recently completed cycles taking unusually long and the safety margin has been increased to allow for the possibility that the next cycle might also run for much longer than expected TRIPLET SPECIFIED WITH ODD NUMBER OF ELECTRONS If TRIPLET has been specified the number of electrons must be even Check the charge on the system the empirical formula and whether TRIPLET was intended unnnnnuunnn n UNABLE TO ACHIEVE SELF CONSISTENCY See the error message lt lt lt lt FAILED TO ACHIEVE SCF gt gt gt gt UNDEFINED SYMMETRY FUNCTION USED Symmetry operations are restricted to those defined i e in the range 1 18 Any other symmetry operations will trip this fatal message UNRECOGNIZED ELEMENT NAME In the geometric specification a chemical symbol which does not correspond to any known element has been used The error lies in the first datum on a line of geometric data k WARNING Don t pay too much attention to this message Thermodynamics calculations require a higher precision than vibrational frequency calculations In particular the gradient norm should be very small However it is frequently not practical to reduce the gradient norm further and to date no one has determined just how slack the gradient criterion can be before unacceptable
116. ber Research Center for Molecular Dynamics The Hebrew University of Jerusalem 91904 Jerusalem Israel The OVGF technique was used with the self energy part extended to include third order perturbation corrections The higher order contributions were estimated by the renormalization procedure The actual expression used to calculate the self energy 6 19 COSMO Conductor like Screening Model part gt p w chosen in the diagonal form is given in equation 6 59 where YO w and Y w are the second and third order corrections and A is the screening factor accounting for all the contributions of higher orders 3 Y w 2 Mw 1 A Vw 6 59 pp Pp The particular expression which was used for the second order corrections is given in equation 6 60 2 Y w ES Sy 2Vpaij Vpaji V paij pl 2Vpiab m Vpiba Vpiab 6 60 pp a dj i W a i j W Ei eg ep where Vars GOROUD dndn In equation 6 60 i and j denote occupied orbitals a and b denote virtual orbitals p denotes orbitals of unspecified occupancy and e denotes an orbital energy The equations are solved by an iterative procedure represented in equation 6 61 wit ep X C u 6 61 pp The SCF energies and the corresponding integrals which were calculated by one of the semiempirical methods MNDO AMI or PM3 were taken as the zero th approximation and all M O s may be included in the active spa
117. can be used instead of explicitly specifying each point The number of steps is given by POINT If the reaction coordinate is an interatomic distance only positive STEPs are allowed STEP1 n nnn C In a grid calculation the step size in degrees or Angstroms for the first of the two pa rameters is given by n nnn By default an 11 by 11 grid is generated See POINT1 and POINT2 on how to adjust this number The first point calculated is the supplied geometry and is in the upper left hand corner This is a change from Version 5 00 where the supplied geometry was the central point STEP2 n nnn C In a grid calculation the step size in degrees or Angstroms for the second of the two parameters is given by n nnn 2 3 Definitions of keywords STO3G W In an ESP calculation STO3G means Use the STO 3G basis set to de orthogonalize the semiempirical orbitals SYMAVG W Used by the ESP SYMAVG will average charges which should have the same value by symmetry SYMMETRY C Symmetry data defining related bond lengths angles and dihedrals can be included by supplying additional data after the geometry has been entered If there are any other data such as values for the reaction coordinates or a second geometry as required by SADDLE then it would follow the symmetry data Symmetry data are terminated by one blank line For non variationally optimized systems symmetry constraints can save a lot of time because many derivative
118. ce for the OVGF calculations The expressions used for Yo and A are given in The OVGF method itself is described in detail in 6 18 1 Example of OVGF calculation Because Danovich s OVGF method is new to MOPAC users will want to see how well it works The data set test green dat will calculate the first 8 I P s for dimethoxy s tetrazine This calculation is discussed in detail in The experimental and calculated I P s are shown in Table 6 1 Table 6 1 OVGF Calculation Comparison with Experiment M O Expt PM3 Error OVGF PM3 Error n 9 05 10 15 1 10 9 46 0 41 71 9 6 10 01 0 41 9 65 0 05 na 11 2 11 96 0 76 11 13 0 07 T2 11 8 12 27 0 47 11 43 0 37 R Gleiter V Schehlmann J Spanget Larsen H Fischer and F A Neugebauer J Org Chem 53 5756 1988 From this we see that for PM3 the average error is 0 69eV but after OVGF correction the error drops to 0 22eV This is typical of nitrogen heterocycle calculations 6 19 COSMO Conductor like Screening Model This section was written based on material provided by Background Andreas Klamt Bayer AG Q18 D 5090 Leverkusen Bayerwerk Germany Unlike the Self Consistent Reaction Field model the Conductor like Screening Model COSMO is a new continuum approach which while more complicated is com putationally quite efficient The expression for the total screening energy is simple enough to allow the first derivatives of the energy with respe
119. ch would be the next time the timer routine is accessed Xxx MAX NUMBER OF ATOMS ALLOWED At compile time the maximum sizes of the arrays in MOPAC are fixed The system being run exceeds the maximum number of atoms allowed To rectify this modify the file DIM SIZES DAT to increase the number of heavy and light atoms allowed If DIMSIZES DAT is altered then the whole of MOPAC should be re compiled and re linked Xxx MAX NUMBER OF ORBITALS At compile time the maximum sizes of the arrays in MOPAC are fixed The system being run exceeds the maximum number of orbitals allowed To rectify this modify the file DIMSIZES DAT to change the number of heavy and light atoms allowed If DIMSIZES DAT is altered then the whole of MOPAC should be re compiled and re linked Xxx MAX NUMBER OF TWO ELECTRON INTEGRALS At compile time the maximum sizes of the arrays in MOPAC are fixed The system being run exceeds the maximum number of two electron integrals allowed To rectify this modify the file DIMSIZES DAT to modify the number of heavy and light atoms allowed If DIMSIZES DAT is altered then the whole of MOPAC should be re compiled and re linked NAME NOT FOUND Various atomic parameters can be modified in MOPAC by use of EXTERNAL These comprise Uss Betas Gp2 GSD Upp Betap Hsp GPD Udd Betad AM1 GDD Zs Gss Expc FN1 Zp Gsp Gaus FN2 Zd Gpp Alp FN3 Thus to change the Uss of hydrogen to 13 6 the line USS H 13 6 could be used If
120. ck the DERIV finite difference calculation If the wavefunction is non variationally optimized check DERNVO If the geometric calculation is faulty use FLEPO to monitor the optimization DE RIV may also be useful here For the FORCE calculation DCART or DERIV are useful for variationally opti mized functions COMPFG for non variationally optimized functions For reaction paths verify that FLEPO is working correctly if so then PATHS is faulty For saddle point calculations verify that FLEPO is working correctly if so then REACT1 is faulty Keep in mind the fact that MOPAC is a large calculation and while intended to be versatile many combinations of options have not been tested If a bug is found in the original code please communicate details to the Academy to Dr James J P Stewart Frank J Seiler Research Laboratory U S Air Force Academy Colorado Springs CO 80840 6528 Debugging Chapter 11 Installing MOPAC MOPAC is distributed on a magnetic tape as a set of FORTRAN 77 files along with ancillary documents such as command help data and results files The format of the tape is that of DIGITAL S VAX computers The following instructions apply only to users with VAX computers users with other machines should use the following instructions as a guide to getting MOPAC up and running 1 2 3 4 5 Put the magnetic tape on the tape drive write protected Allocate the tape drive with a comma
121. contributions in turn are divided into nuclear and one and two electron terms ESP C This is the ElectroStatic Potential calculation of K M Merz and B H Besler ESP calculates the expectation values of the electrostatic potential of a molecule on a uniform distribution of points The resultant ESP surface is then fitted to atom centered charges that best reproduce the distribution in a least squares sense ESPRST W ESPRST restarts a stopped ESP calculation Do not use with RESTART ESR O The unpaired spin density arising from an odd electron system can be calculated both RHF and UHF In UHF calculation the alpha and beta M O s have different spatial forms so unpaired spin density can naturally be present on in plane hydrogen atoms such as in the phenoxy radical In the RHF formalism a MECI calculation is performed If the keywords OPEN and C L are both absent then only a single state is calculated The unpaired spin density is then calculated from the state function In order to have unpaired spin density on the hydrogens in for example the phenoxy radical several states should be mixed Keywords EXCITED C The state to be calculated is the first excited open shell singlet state If the ground state is a singlet then the state calculated will be S 1 if the ground state is a triplet then S 2 This state would normally be the state resulting from a one electron excitation from the HOMO to the LUMO Except
122. coordinates and cartesian velocities LARGE n Print every n th set of internal coordinates LARGE n Print every n th set of internal and cartesian coordinates and cartesian velocities If LARGE 1 is used the output will be the same as that of Version 5 0 when LARGE was not used If LARGE is used the output will be the same as that of Version 5 0 when LARGE was used To save disk space do not use LARGE LINMIN O There are two line minimization routines in MOPAC an energy minimization and a gra dient norm minimization LINMIN will output details of the line minimization used in a given job LET W As MOPAC evolves the meaning of LET is changing Now LET means essentially I know what I m doing override safety checks Currently LET has the following meanings 1 Ina FORCE calculation it means that the supplied geometry is to be used even if the gradients are large 2 In a geometry optimization the specified GNORM is to be used even if it is less than 0 01 3 Ina POLAR calculation the molecule is to be orientated along its principal moments of inertia before the calculation starts LET will prevent this step being done LOCALIZE O The occupied eigenvectors are transformed into a localized set of M O s by a series of 2 by 2 rotations which maximize w The value of 1 w is a direct measure of the number of centers involved in the MO Thus the value of 1 1 4 is 2 0 for H2 3 0 for a three cent
123. ct to atomic coordinates to be easily evaluated Details of the procedure have been submitted for publication A Klamt and G Schu urmann COSMO A New Approach to Dielectric Screening in Solvents with Explicit Ex pressions for the Screening Energy and its Gradient J Chem Soc Perkin Trans 2 1993 in press The COSMO procedure generates a conducting polygonal surface around the system ion or molecule at the van der Waals distance By introducing a dependent correction factor e 1 e i into the expressions for the screening energy and its gradient the theory can be extended to finite dielectric constants with only a small error The accuracy of the method can be judged by how well it reproduces known quantities such as the heat of solution in water water has a dielectric constant of 78 4 at 25 C Table 6 2 Here the keywords used were NSPA 60 GRADIENTS 1SCF EPS 78 4 AM1 CHARGE 1 From the Table we see that the glycine zwitterion becomes the stable form in water while the neutral species is the stable gas phase form The COSMO method is easy to use and the derivative calculation is of sufficient precision to allow gradients of 0 1 to be readily achieved fle Table 6 2 Calculated and Observed Hydration Energies Compound Method AH kcal mol Hydration gas phase solution phase AH calc Enthalpy exp 1 NH AMI 150 6 59 5 91 1 88 0 N Me AMI 1574 101 1 56 0 59 9 N Et i AMI 1321 84 2 47 9 57 0 Gl
124. cur naturally then the energy due to the dipole on its own is subtracted from the total energy 3 They can operate as polarization functions A controlled shaped electric field can easily be made from two or more sparkles The polarizability in cubic Angstroms of a molecule in any particular orientation can then easily be calculated 6 13 Mechanism of the frame in FORCE calculation The FORCE calculation uses cartesian coordinates and all 3N modes are calculated where N is the number of atoms in the system Clearly there will be 5 or 6 trivial vibrations which represent the three translations and two or three rotations If the molecule is exactly at a stationary point then these vibrations will have a force constant and frequency of precisely zero If the force calculation was done correctly and the molecule was not exactly at a stationary point then the three translations should be exactly zero but the rotations would be non zero The extent to which the rotations are non zero is a measure of the error in the geometry If the distortions are non zero the trivial vibrations can interact with the low lying genuine vibrations or rotations and with the transition vibration if present To prevent this the analytic form of the rotations and vibrations is calculated and arbi trary eigenvalues assigned these are 500 600 700 800 900 and 1000 millidynes angstrom for Tx Ty Tz Rx Ry and Rz if present respectively The rota
125. d in order to minimize output when following the working of the SCF calculation 1SCF is very useful AIDER C AIDER allows MOPAC to optimize an ab initio geometry To use it calculate the ab initio gradients using e g Gaussian Supply MOPAC with these gradients after converting them into kcal mol The geometry resulting from a MOPAC run will be nearer to the optimized ab initio geometry than if the geometry optimizer in Gaussian had been used Keywords AIGIN C If the geometry Z matrix is specified using the Gaussian 8X then normally this will be read in without difficulty In the event that it is mistaken for a normal MOPAC type Z matrix the keyword AIGIN is provided AIGIN will force the data set to be read in assuming Gaussian format This is necessary if more than one system is being studied in one run AIGOUT 0 The ARCHIVE file contains a data set suitable for submission to MOPAC If in addition to this data set the Z matrix for Gaussian input is wanted then AIGOUT ab initio geometry output should be used The Z matrix is in full Gaussian form Symmetry where present will be correctly de fined Names of symbolics will be those used if the original geometry was in Gaussian for mat otherwise logical names will be used Logical names are of form lt t gt lt a gt lt b gt lt c gt lt a gt where lt t gt is r for bond length a for angle or d for dihedral lt a gt is the atom n
126. data are read in data defining each microstate is read in using format 20I1 one microstate per line The microstate data is preceded by the word MICROS on a line by itself There is at present no mechanism for using MICROS with a reaction path For a system with n M O s in the C I use OPEN n1 n or C I n to do this the populations of the n alpha M O s are defined followed by the n beta M O s Allowed occupancies are zero and one For n 6 the closed shell ground state would be defined as 111000111000 meaning one electron in each of the first three alpha M O s and one electron in each of the first three beta M O s Users are warned that they are responsible for completing any spin manifolds Thus while the state 111100110000 is a triplet state with component of spin 1 the state 111000110100 while having a component of spin 0 is neither a singlet nor a triplet In order to complete the spin manifold the microstate 110100111000 must also be included If a manifold of spin states is not complete then the eigenstates of the spin operator will not be quantized When and only when 100 or fewer microstates are supplied can spin quantization be conserved There are two other limitations on possible microstates First the number of electrons in every microstate should be the same If they differ a warning message will be printed and the calculation continued but the results will almost certainly be nonsense Second th
127. ded if at all possible when non variationally optimized calcula tions are being done If the Hessian is suspected to be corrupt within SIGMA it will be automatically recalculated This frequently speeds up the rate at which the transition state is located If you do not want the Hessian to be reinitialized it is costly in CPU time specify LET on the keyword line SINGLET C When a configuration interaction calculation is done all spin states are calculated si multaneously either for component of spin 0 or 1 2 When only singlet states are of interest then SINGLET can be specified and all other spin states while calculated are ignored in the choice of root to be used Note that while almost every even electron system will have a singlet ground state SINGLET should still be specified if the desired state must be a singlet SINGLET has no meaning in a UHF calculation but see also TRIPLET SLOPE C In an ESP calculation SLOPE n nn specifies the scale factor for MNDO charges de fault 1 422 SPIN O The spin matrix defined as the difference between the alpha and beta density matrices is to be printed If the system has a closed shell ground state e g methane run UHF the spin matrix will be null If SPIN is not requested in a UHF calculation then the diagonal of the spin matrix that is the spin density on the atomic orbitals will be printed STEP C In a reaction path if the path step is constant STEP
128. des FORCE ISOTOPE At this point copy all the files to a second filename for use later 3 Given vibrational frequencies of 654 123 234 and 456 identify via DRAW 2 the normal coordinate mode let s say that is the 654 mode Eliminate the second mode by IRC 2 DRC T 30M RESTART LARGE 6 17 How to escape from a hilltop Use is made of the FORCE restart file 4 Identify the minimum in the potential energy surface by inspection or using the VAX SEARCH command of form SEARCH lt Filename gt OUT 5 Edit out of the output file the data file corresponding to the lowest point and refine the geometry using SIGMA 6 Repeat the last three steps but for the negative of the normal mode using the copied files The keywords for the first of the two jobs are IRC 2 DRC T 30M RESTART LARGE 7 Repeat the last four steps as often as there are spurious modes 8 Finally carry out a DRC to confirm that the transition state does in fact connect the reactants and products The drop in potential energy should be monotonic If you are unsure whether this last operation will work successfully do it at any time you have a stationary point If it fails at the very start then we are back where we were last year give up and go home 6 17 1 EigenFollowing Description of the EF and TS function by Dr Frank Jensen Department of Chemistry Odense University 5230 Odense Denmark The current version of the EF optimization routin
129. during a geometry optimization or gradient minimization If they do and if the angle made by the atom being defined is not zero or 180 degrees then its position becomes ill defined This is not desirable and the calculation will stop in order to allow corrective action to be taken Note that if the three atoms are in an exactly straight line this message will not be triggered The good news is that the criterion used to trigger this message was set too coarsely The criterion has been tightened so that this message now does not often appear Geometric integrity does not appear to be compromized CARTESIAN COORDINATES READ IN AND CALCULATION If cartesian coordinates are read in but the calculation is to be carried out using internal coordinates then either all possible geometric variables must be optimized or none can be optimized If only some are marked for optimization then ambiguity exists For example if the X coordinate of atom 6 is marked for optimization but the Y is not then when the conversion to internal coordinates takes place the first coordinate becomes a bond length and the second an angle These bear no relationship to the X or Y coordinates This is a fatal error Error messages produced by MOPAC CARTESIAN COORDINATES READ IN AND SYMMETRY If cartesian coordinates are read in but the calculation is to be carried out using internal coordinates then any symmetry relationships between the c
130. e Whatever is decided the three lines blank or otherwise are obligatory In the example given one line of keywords and two of documentation are shown By use of keywords these defaults can be changed Modifying keywords are amp and SETUP These are defined in the KEYWORDS chapter The following table illustrates the allowed combinations Line 1 Line 2 Line 3 Line 4 Line 5 Setup used Keys Text Text Z matrix Z matrix not used Keys Keys Text Text Z matrix not used Keys Keys Keys Text Text not used Keys amp Keys Text Z matrix Z matrix not used Keys amp Keys amp Keys Z matrix Z matrix not used Keys SETUP Text Text Z matrix Z matrix 1 or 2 lines used Keys Keys SETUP Text Text Z matrix 1 line used Keys amp Keys SETUP Text Z matrix Z matrix 1 line used No other combinations are allowed The proposed use of the SETUP option is to allow a frequently used set of keywords to be defined by a single keyword For example if the default criteria are not suitable SETUP might contain SCFCRT 1 D 8 SHIFT 30 ITRY 600 GNORM 0 02 ANALYT Ww Ww Description of MOPAC The order of usage of a keyword is Line 1 gt Line 2 gt Line 3 Line 1 gt SETUP Line 2 gt SETUP SETUP gt built in default values The next set of lines defines the geometry In the example the numbers are all neatly lined up this is not necessary but does make it easier when looking for errors in the data The geometry is defined
131. e component of spin for every microstate must be the same except for teaching purposes Two microstates of different components of spin will have a zero matrix element connecting them No warning will be given as this is a reasonable operation in a teaching situation For example if all states arising from two electrons in two levels are to be calculated say for teaching Russel Saunders coupling then the following microstates would be used Microstate No of alpha beta electrons Ms State 1100 2 0 1 Triplet 1010 1 1 O Singlet 1001 1 1 O Mixed 0110 1 1 O Mixed 0101 1 1 0 Singlet 0011 0 2 1 Triplet Constraints on the space manifold are just as rigorous but much easier to satisfy If the energy levels are degenerate then all components of a manifold of degenerate M O s should be either included or excluded If only some but not all components are used the required degeneracy of the states will be missing As an example for the tetrahedral methane cation if the user supplies the microstates corresponding to a component of spin 3 2 neglecting Jahn Teller distortion the mini mum number of states that can be supplied is 90 6 1 5 6 4 2 Keywords While the total number of electrons should be the same for all microstates this number does not need to be the same as the number of electrons supplied to the C I thus in the example above a cationic state could be 110000111000 The format is defined as 20I1 so that spac
132. e first 3 atoms should be real Except in SADDLE XYZ will still work if one or more dummy atoms occur before the fourth real atom in which case more than 3N 6 coordinates will be flagged for optimization This could cause difficulties with the EF method which is why dummy atoms at the start of the geometry specification should be avoided The coordinates to be optimized depend on the internal coordinate definition of real atoms 1 2 and 3 If the position of any of these atoms depends on dummy atoms then the optimization flags will be different from the case where the first three atoms defined are all real The geometry is first converted to cartesian coordinates and dummy atoms excluded The cartesian coordinates to be optimized are Atoms RRR RRX RXR XRR RXX XRX XXR KKK XYZ XYZ XYZ XYZ XYZ XYZ XYZ XYZ Atom 1 2 3 tet t Feet 4 on Ft Where R and X apply to real and dummy atoms in the internal coordinate Z matrix and atoms 1 2 3 and 4 are the real atoms in cartesian coordinates A means that Keywords the relevant coordinate is flagged for optimization Note that the number of flagged coordinates varies from 3N 6 to 3N 3 atom 1 is never optimized 2 4 Keywords that go together Normally only a subset of keywords are used in any given piece of research Keywords which are related to each other in this way are 1 2 In getting an SC
133. e for getting round this error BOTH SYSTEMS ARE ON THE SAME SIDE A non fatal message but still cause for concern During a SADDLE calculation the two geometries involved are on opposite sides of the transition state This situation is verified at every point by calculating the cosine of the angle between the two gradient vectors For as long as it is negative then the two geometries are on opposite sides of the T S If however the cosine becomes positive then the assumption is made that one moiety has fallen over the T S and is now below the other geometry That is it is now further from the T S than the other temporarily fixed geometry To correct this identify geometries corresponding to points on each side of the T S Two geometries on the output separated by the message SWAPPING and make up a new data file using these geometries This corresponds to points on the reaction path near to the T S Run a new job using these two geometries but with BAR set to a third or a quarter of its original value e g BAR 0 05 This normally allows the T S to be located C I NOT ALLOWED WITH UHF There is no UHF configuration interaction calculation in MOPAC Either remove the keyword that implies C I or the word UHF CALCULATION ABANDONED AT THIS POINT A particularly annoying message In order to define an atom s position the three atoms used in the connectivity table must not accidentally fall into a straight line This can happen
134. e is a combination of the original EF algorithm of Simons et al J Phys Chem 89 52 as implemented by Baker J Comp Chem 7 385 and the QA algorithm of Culot et al Theo Chim Acta 82 189 with some added features for improving stability The geometry optimization is based on a second order Taylor expansion of the energy around the current point At this point the energy the gradient and some estimate of the Hessian are available There are three fundamental steps in determining the next geometry based on this information e finding the best step within or on the hypersphere with the current trust radius e possibly reject this step based on various criteria e update the trust radius 1 For a minimum search the correct Hessian has only positive eigenvalues For a Transition State TS search the correct Hessian should have exactly one negative eigenvalue and the corresponding eigenvector should be in the direction of the desired reaction coordinate The geometry step is parameterized as g s H where s is a shift factor which ensure that the step length is within or on the hypersphere If the Hessian has the correct structure a pure Newton Raphson step is attempted This corresponds to setting the shift factor to zero If this step is longer than the trust radius a P RFO step is attempted If this is also too long then the best step on the hypersphere is made via the QA formula This three step procedure is the default
135. e m arzt ge dutem MP ape deu des uper ads 3 2 Gaussian Z matrices 2l ll ls 3 3 Cartesian coordinate definition 2s 3 4 Conversion between various formats ll 3 5 Definition of elements and isotopes llle 3 6 Examples of coordinate definitions ls Examples 4 1 MNRSDI test data file for formaldehyde lees 4 2 MOPAC output for test data ile MNRSD1 Testdata 5 1 Data file for a force calculation lr 5 2 Results file for the force calculation 2l 5 3 Example of reaction path with symmetry Background 6 L Introduction ux 3 2 RR boxeo ee kh wp OO Eo xeb0b onm 625 SAT ERs destro tem er ie cet tremit SiY T rie ENS 6 3 Correction to the peptide linkage lees 6 4 Level of precision within MOPAC llle 6 5 Convergence tests in subroutine ITER 2s 6 6 Convergence in SCF calculation es aow bkpwwnNnr LE N wow 40 Al Al Al 42 43 43 44 46 49 49 50 55 55 56 63 CONTENTS 6 7 Causes of failure to achieve an SCF aoaaa aa 70 6 8 Torsion or dihedral angle coherency 02 020005 71 6 9 Vibrational analysis 4 lh 71 6 10 A note on thermochemistry pee eee 71 6 10 1 Basic Physical Constants 2 2 20 0 0 02 eee ee 72 6 10 2 Thermochemistry from ab initio MO methods 72 6 11 Reaction coordinates a
136. e molecule or ion Arguments Density matrix Charges on every atom coor dinates dipoles on exit Called by WRITE and FMAT DIST2 Utility Called by ESP only DIST2 works out the distance between two points in 3D space DOFS Main Sequence Calculates the density of states within a Brillouin zone Used in polymer work only DOT Utility Given two vectors X and Y of length N function DOT returns with the dot product X Y I e if X Y then DOT the square of X Called by FLEPO DRC Main Sequence The dynamic and intrinsic reaction coordinates are calculated by following the mass weighted trajectories DRCOUT Utility Sets up DRC and IRC data in quadratic form preparatory to being printed EAO08C Part of the diagonalizer RSP EAO9C Part of the diagonalizer RSP ECOSC Part of the diagonalizer RSP EF Main Sequence EF is the Eigenvector Following routine EF implements the keywords EF and TS ELESP Utility Within the ESP ELESP calculates the electronic contribution to the electrostatic potential Description of subroutines e ENPART Utility Partitions the energy of a molecule into its monatomic and di atomic components Called by WRITE when the keyword ENPART is specified No data are changed by this call e EPSETA Utility Calculates the machine precision and dynamic range for use by the two diagonalizers e ESP Main Sequence ESP is not present in the default copy of MOPAC ESP calculates the atomic charges which
137. e oxygen atom The asterisks indicate that the bond length and angle are both to be optimized e Atom 4 a hydrogen atom The bond length supplied has been overwritten with the symmetry defined C H bond length Atom 4 is defined as being 1 1 from atom 2 making a bond angle of 120 degrees with atom 1 and a dihedral angle of 180 degrees with atom 3 None of the coordinates of atom 4 are marked for optimization The bond length and angle are symmetry defined by atom 3 and the dihedral is group theory symmetry defined as being 180 degrees The molecule is flat Note 5 The cartesian coordinates are calculated as follows Stage 1 The coordinate of the first atom is defined as being at the origin of cartesian space while the coordinate of the second atom is defined as being displaced by its defined bond length along the positive x axis The coordinate of the third atom is defined as being displaced by its bond length in the x y plane from either atom 1 or 2 as defined in the data or from atom 2 if no numbering is given The angle it makes with atoms 1 and 2 is that given by its bond angle The dihedral which first appears in the fourth atom is defined according to the IUPAC convention Note This is different from previous versions of MNDO and MINDO 3 where the dihedral had the opposite chirality to that defined by the IUPAC convention Stage 2 Any dummy atoms are removed As this particular system contains no dummy atoms nothing
138. e so marked a warning is given but the calculation will continue In cartesian coordinates all parameters can be optimized 3 6 Examples of coordinate definitions Two examples will be given The first is formic acid HCOOH and is presented in the normal style with internal coordinates This is followed by formaldehyde presented in such a manner as to demonstrate as many different features of the geometry definition as possible MINDO 3 Formic acid 3 6 Examples of coordinate definitions Example of normal geometry definition 0 Atom 1 needs no coordinates C 1 20 1 Atom 2 bonds to atom 1 0 1 321 116 8 1 2 1 Atom 3 bonds to atom 2 and makes an angle with atom 1 H 0 98 1 123 9 1 0 00 3 2 1 Atom 4 has a dihedral of 0 0 with atoms 3 2 and 1 2 1 3 H 1 11 1 127 0 0 0 0 180 0 0 00 0 0 31 0 0 00 00 Atom 2 a carbon is bonded to oxygen by a bond length of 1 20 Angstroms and to atom 3 an oxygen by a bond length of 1 32 Angstroms The O C O angle is 116 8 degrees The first hydrogen is bonded to the hydroxyl oxygen and the second hydrogen is bonded to the carbon atom The H C O O dihedral angle is 180 degrees MOPAC can generate data files both in the Archive files and at the end of the normal output file when a job ends prematurely due to time restrictions Note that the data are all neatly lined up This is of course characteristic of machine generated data but is useful when checking for errors Format of
139. ed In some cases the FORCE calculation may be run only to decide if a state is a ground state or a transition state in which case the results have only two interpretations Under these circumstances LET may be warranted GRADIENT IS VERY LARGE In a calculation of the thermodynamic properties of the system if the rotation and trans lation vibrations are non zero as would be the case if the gradient norm was significant then these vibrations would interfere with the low lying genuine vibrations The crite ria for THERMO are much more stringent than for a vibrational frequency calculation as it is the lowest few genuine vibrations that determine the internal vibrational energy entropy etc ILLEGAL ATOMIC NUMBER An element has been specified by an atomic number which is not in the range 1 to 107 Check the data the first datum on one of the lines is faulty Most likely line 4 is faulty IMPOSSIBLE NUMBER OF OPEN SHELL ELECTRONS The keyword OPEN n1 n2 has been used but for an even electron system n1 was speci fied as odd or for an odd electron system n1 was specified as even Either way there is a conflict which the user must resolve IMPOSSIBLE OPTION REQUESTED A general catch all This message will be printed if two incompatible options are used such as both MINDO 3 and AMI being specified Check the keywords and resolve the conflict INTERNAL COORDINATES READ IN AND CALCULATION If internal coordinates a
140. ed by that M O This is necessitated by the fact that in a reaction a particular M O may change its character considerably A useful procedure is to run 15CF and DENOUT first in order to identify the M O s the complete job is then run with OLDENS and FILL nn so that the eigenvectors at the first iteration are fully known As FILL is known to give difficulty at times consider also using C I 2n and ROOT m FLEPO O The predicted and actual changes in the geometry the derivatives and search direction for each geometry optimization cycle are printed This is useful if there is any question regarding the efficiency of the geometry optimizer FMAT Details of the construction of the Hessian matrix for the force calculation are to be printed FORCE C A force calculation is to be run The Hessian that is the matrix in millidynes per Angstrom of second derivatives of the energy with respect to displacements of all pairs of atoms in x y and z directions is calculated On diagonalization this gives the force constants for the molecule The force matrix weighted for isotopic masses is then used for calculating the vibrational frequencies The system can be characterized as a ground state or a transition state by the presence of five for a linear system or six eigenvalues which are very small less than about 30 reciprocal centimeters A transition state is further characterized by one and exactly one negative force constant A FO
141. ely increased Superficially requesting a GNORM of zero might seem excessively stringent but as soon as the run starts it will be cut back to 0 01 Even that might seem too stringent The geometry optimization will continue to lower the energy and hopefully the GNORM but frequently it will not prove possible to lower the GNORM to 0 01 If after 10 cycles the energy does not drop then the job will be stopped At this point you have the best geometry that MOPAC in its current form can give If a slightly less than highest precision is needed such as for normal publication quality work set the GNORM to the limit wanted For example for a flexible system a GNORM of 0 1 to 0 5 will normally be good enough for all but the most demanding work If higher than the default but still not very high precision is wanted then use the keyword PRECISE This will tighten up various criteria so that higher than routine precision will be given If high precision is used so that the printed GNORM is 0 000 and the resulting geometry resubmitted for one SCF and gradients calculation then normally a GNORM higher than 0 000 will result This is NOT an error in MOPAC the geometry printed is only precise to six figures after the decimal point Geometries need to be specified to more than six decimals in order to drive the GNORM to less than 0 000 If you want to test MOPAC or use it for teaching purposes the GNORM lower limit of 0 01 can be overridden b
142. ema to be output In the geometry specification if an internal coordinate is marked for optimization then when that internal coordinate passes through an extremum a message will be printed and the geometry output Difficulties can arise from the way internal coordinates are processed The internal coordinates are generated from the cartesian coordinates so an internal coordinate sup plied may have an entirely different meaning on output In particular the connectivity may have changed For obvious reasons dummy atoms should not be used in the supplied geometry specification If there is any doubt about the internal coordinates or if the start ing geometry contains dummy atoms then run a 1SCF calculation specifying XYZ This will produce an ARC file with the ideal numbering the internal numbering system used by MOPAC Use this ARC file to construct a data file suitable for the DRC or IRC Notes Background 1 Any coordinates marked for optimization will result in only extrema being printed 2 If extrema are being printed then kinetic energy extrema will also be printed Keywords for use with the IRC and DRC 1 Setting up the transition state NLLSQ SIGMA TS 2 Constructing the FORCE matrix FORCE or IRC n ISOTOPE LET 3 Starting an IRC RESTART and IRC n T PRIO X PRIO H PRIO 4 Starting a DRC DRC or DRC n nn KINETIC n nn 5 Starting a DRC from a transition state DRC or DRC n and IRC n KINETIC n 6 Restarting an
143. ems e g formaldehyde and benzene For systems with low barriers to rotation or flat potential surfaces e g aniline or water dimer quite large HoF errors can result Background Various precision levels In normal non publication quality work the default precision of MOPAC is recom mended This will allow reasonably precise results to be obtained in a reasonable time Unless this precision proves unsatisfactory use this default for all routine work The best way of controlling the precision of the geometry optimization and gradient minimization is by specifying a gradient norm which must be satisfied This is done via the keyword GNORM Altering the GNORM automatically disables the other termination tests resulting in the gradient norm dominating the calculation This works both ways a GNORM of 20 will give a very crude optimization while a GNORM of 0 01 will give a very precise optimization The default GNORM is 1 0 When the highest precision is needed such as in exacting geometry work or when you want results which cannot be improved then use the combination keywords GNORM 0 0 and SCFCRT 1 D NN NN should be in the range 2 15 Increasing the SCF criterion the default is SCFCRT 1 D 4 helps the line search routines by increasing the precision of the heat of formation calculation however it can lead to excessive run times so take care Also there is an increased chance of not achieving an SCF when the SCF criterion is excessiv
144. ena which can be studied are Photoexcitation If the purpose of a calculation is to predict the energy of photoexcita tion then the ground state should first be optimized Once this is done then a C I calculation can be carried out using 1SCF With the appropriate keywords MECI C I n etc the energy of photoexcitation to the various states can be predicted A more expensive but more rigorous calculation would be to optimize the geometry using all the C I keywords This is unlikely to change the results significantly however Background Fluorescence If the excited state has a sufficiently long lifetime so that the geometry can relax then if the system returns to the ground state by emission of a photon the energy of the emitted photon will be less it will be red shifted than that of the exciting photon To do such a calculation proceed as follows e Optimize the ground state geometry using all the keywords for the later steps but specify the ground state e g C I 23 EF GNORM 0 01 MECI Optimize the excited state e g C I c3 ROOT 2 EF GNORM 0 01 MECI Calculate the Franck Condon excitation energy using the results of the ground state calculation only Calculate the Franck Condon emission energy using the results of the excited state calculation only If indirect emission energies are wanted these can be obtained from the A Hy of the optimized excited and optimized ground state calculations In order for
145. endent non linear optical calculations can be performed Prakashan Korambath dissertation research Frank Jensen Department of Chemistry Odense Universitet Campusvej 55 DK 5230 Odense M Denmark The efficiency of Baker s EF routine has been improved John M Simmie Chemistry Department University College Galway Ire land The MOPAC Manual has been completely re formatted in the LaTeX document preparation system Equations are now much easier to read and to understand Jorge A Medrano 5428 Falcon Ln West Chester OH 45069 and Roberto Bochicchio Universidad de Buenos Aires The BONDS function has been extended to allow free valence and other quan tities to be calculated George Purvis III CAChe Scientific P O Box 500 Delivery Station 13 400 Beaverton OR 97077 The STO 6G Gaussian expansion of the Slater orbitals has been expanded to Principal Quantum Number 6 These expansions are used in analytical derivative calculations e Bug reports bug fixes Victor I Danilov Department of Quantum Biophysics Academy of Sci ences of the Ukraine Kiev 143 Ukraine Several faults in the multi electron configuration interaction were identified and recommendations made regarding their correction CONTENTS Chapter 1 Description of MOPAC MOPAC is a general purpose semi empirical molecular orbital package for the study of chemical structures and reactions The semi empirical Hamiltonians MNDO MI
146. eps which would lead to faster convergence but may occasionally accept poor steps If TS searches are found to cause problems the first try should be to lower the limits to 0 5 and 2 Tighter limits like 0 8 and 1 2 or even 0 9 and 1 1 will almost always slow the optimization down significantly but may be necessary in some cases In minimum searches it is usually desirable that the energy decreases in each iter ation In certain very rigid systems however the initial diagonal Hessian may be so poor that the algorithm cannot find an acceptable step larger than DDMIN and the optimization terminates after only a few cycles with the TRUST RADIUS BE LOW DDMIN warning long before the stationary point is reached In such cases the user can specify RMIN to some negative value say 10 thereby allowing steps which increases the energy The algorithm has the capability of following Hessian eigenvectors other than the one with the lowest eigenvalue toward a TS Such higher mode following are always much more difficult to make converge Ideally as the optimization progresses the TS mode should at some point become the lowest eigenvector Care must be taken during the optimization however that the nature of the mode does not change all of a sudden leading to optimization to a different TS than the one desired OMIN has been designed for ensuring that the nature of the TS mode only changes 6 17 How to escape from a hilltop gradually specif
147. equence BRLZON generates a band structure or phonon struc ture for high polymers Called by WRITE and FREQCY CALPAR Utility When external parameters are read in via EXTERNAL the derived parameters are worked out using CALPAR Note that all derived parameters are calculated for all parameterized elements at the same time CAPCOR Utility Capping atoms of type Cb should not contribute to the energy of a system CAPCOR calculates the energy contribution due to the Cb and subtracts it from the electronic energy CDIAG Utility Complex diagonalization Used in generating eigenvalues of com plex Hermitian secular determinant for band structures Called by BRLZON only CHRGE Utility Calculates the total number of valence electrons on each atom Main arguments density matrix array of atom charges empty on input Called by ITER only CNVG Utility Used in SCF cycle CNVG does a three point interpolation of the last three density matrices Arguments Last three density matrices Number of iterations measure of self consistency empty on input Called by ITER only COE Utility Within the general overlap routine COE calculates the angular coeffi cients for the s p and d real atomic orbitals given the axis and returns the rotation matrix COMPFG Main Sequence Evaluates the total heat of formation of the supplied geometry and the derivatives if requested This is the nodal point connecting the electronic and geometric parts of the
148. er bond and 1 0 for a lone pair Higher degeneracies than allowed by point group theory are readily obtained For example benzene would give rise to a 6 fold degenerate C H bond a 6 fold degenerate C C sigma bond and a three fold degenerate C C pi bond In principle there is no single step method to unambiguously obtain the most localized set of M O s in systems where several canonical structures are possible just as no simple method exists for finding the most stable conformer of some large compound However the localized bonds generated will normally be quite acceptable for routine applications Abbreviation LOCAL MAX In a grid calculation the maximum number of points 23 in each direction is to be used The default is 11 The number of points in each direction can be set with POINTS1 and POINTS2 2 3 Definitions of keywords MECI 0 At the end of the calculation details of the Multi Electron Configuration Interaction calculation are printed if MECI is specified The state vectors can be printed by specifying VECTORS The MECI calculation is either invoked automatically or explicitly invoked by the use of the C I 2n keyword MICROS n C The microstates used by MECI are normally generated by use of a permutation operator When individually defined microstates are desired then MICROS n can be used where n defines the number of microstates to be read in Format for Microstates After the geometry data plus any symmetry
149. eration use BAR 0 03 BIRADICAL C Note BIRADICAL is a redundant keyword and represents a particular configuration interaction calculation Experienced users of MECI q v can duplicate the effect of the keyword BIRADICAL by using the MECI keywords OPEN 2 2 and SINGLET For molecules which are believed to have biradicaloid character the option exists to optimize the lowest singlet energy state which results from the mixing of three states These states are in order 1 the micro state arising from a one electron excitation from the HOMO to the LUMO which is combined with the microstate resulting from the time reversal operator acting on the parent microstate the result being a full singlet state 2 the state resulting from de excitation from the formal LUMO to the HOMO 2 3 Definitions of keywords and 3 the state resulting from the single electron in the formal HOMO being excited into the LUMO Microstate 1 Microstate 2 Microstate 3 Alpha Beta Alpha Beta Alpha Beta Alpha Beta LUMO HOMO A configuration interaction calculation is involved here A biradical calculation done without C I at the RHF level would be meaningless Either rotational invariance would be lost as in the D2d form of ethylene or very artificial barriers to rotations would be found such as in a methane molecule orbiting a D2d ethylene In both cases the inclusion of limited configuration interaction corrects the error BIRADICAL
150. eria Chapter 10 Debugging There are three potential sources of difficulty in using MOPAC each of which requires special attention There can be problems with data due to errors in the data or MOPAC may be called upon to do calculations for which it was not designed There are intrinsic errors in MOPAC which extensive testing has not yet revealed but which a user s novel calculation uncovers Finally there can be bugs introduced by the user modifying MOPAC either to make it compatible with the host computer or to implement local features For whatever reason the user may need to have access to more information than the normal keywords can provide and a second set specifically for debugging is provided These keywords give information about the working of individual subroutines and do not affect the course of the calculation 10 1 Debugging keywords A full list of keywords for debugging subroutines 1ELEC the one electron matrix Note 1 COMPFG Heat of Formation DCART Cartesian derivatives DEBUG Note 2 DEBUGPULAY Pulay matrix vector and error function Note 3 DENSITY Every density matrix Note 1 DERI1 Details of DERI1 calculation DERI2 Details of DERI2 calculation DERITR Details of DERITR calculation DERIV All gradients and other data in DERIV DERNVO Details of DERNVO calculation DFORCE Print Force Matrix DIIS Details of DIIS calculation EIGS All eigenvalues FLEPO Details of BFGS minimization FMAT
151. es can be used for empty M O s MINDO 3 C The default Hamiltonian within MOPAC is MNDO with the alternatives of AM1 and MINDO 3 To use the MINDO 3 Hamiltonian the keyword MINDO 3 should be used Acceptable alternatives to the keyword MINDO 3 are MINDO and MINDO3 MMOK C If the system contains a peptide linkage then MMOK will allow a molecular mechanics correction to be applied so that the barrier to rotation is increased to 14 00 kcal mole in N methyl acetamide MODE C MODE is used in the EF routine Normally the default MODE 1 is used to locate a transition state but if this is incorrect explicitly define the vector to be followed by using MODE n MODE is not a recommended keyword If you use the FORCE option when deciding which mode to follow set all isotopic masses to 1 0 The normal modes from FORCE are normally mass weighted this can mislead Alternatively use LARGE with FORCE this gives the force constants and vectors in addition to the mass weighted normal modes Only the mass weighted modes can be drawn with DRAW MS n Useful for checking the MECI calculation and for teaching MS n overrides the normal choice of magnetic component of spin Normally if a triplet is requested an MS of 1 will be used this excludes all singlets If MS 0 is also given then singlets will also be calculated The use of MS should not affect the values of the results at all MULLIK 0 A full Mulliken Population analysis is t
152. ese checks contain errors in data so caution should be exercised if GEO OK is used An important exception to this warning is when the system contains or may give rise to a Hydrogen molecule GEO OK Keywords will override other geometric safety checks such as the unstable gradient in a geometry optimization preventing reliable optimization See also the message GRADIENTS OF OLD GEOMETRY GNORM nn nnnn GNORM n nn W The geometry optimization termination criteria in both gradient minimization and energy minimization can be over ridden by specifying a gradient norm requirement For example GNORM 20 would allow the geometry optimization to exit as soon as the gradient norm dropped below 20 0 the default being 1 0 For high precision work GNORM 0 0 is recommended Unless LET is also used the GNORM will be set to the larger of 0 01 and the specified GNORM Results from GNORM 0 01 are easily good enough for all high precision work GRADIENTS 0 In a 1SCF calculation gradients are not calculated by default in non variationally opti mized systems this would take an excessive time GRADIENTS allows the gradients to be calculated Normally gradients will not be printed if the gradient norm is less than 2 0 However if GRADIENTS is present then the gradient norm and the gradients will unconditionally be printed Abbreviation GRAD GRAPH 0 Information needed to generate electron density contour maps can be written to a file by
153. f BIRADICAL is specified exactly one electron will end up on hydrogen A similar result can be obtained by specifying TRIPLET in a UHF calculation 6 8 Torsion or dihedral angle coherency MOPAC calculations do not distinguish between enantiomers consequently the sign of the dihedrals can be multiplied by 1 and the calculations will be unaffected However if chirality is important a user should be aware of the sign convention used The dihedral angle convention used in MOPAC is that defined by Klyne and Prelog in Experientia 16 521 1960 In this convention four atoms AXYB with a dihedral angle of 90 degrees will have atom B rotated by 90 degrees clockwise relative to A when X and Y are lined up in the direction of sight X being nearer to the eye In their words To distinguish between enantiomeric types the angle tau is considered as positive when it is measured clockwise from the front substituent A to the rear substituent B and negative when it is measured anticlockwise The alternative convention was used in all earlier programs including QCPE 353 6 9 Vibrational analysis Analyzing normal coordinates is very tedious Users are normally familiar with the in ternal coordinates of the system they are studying but not familiar with the cartesian coordinates To help characterize the normal coordinates a very simple analysis is done automatically and users are strongly encouraged to use this analysis first and then t
154. f the super matrix Description of subroutines DERII Utility Part of the analytical C I derivative package Calculates the frozen density contribution to the derivative of the energy wrt cartesian coordinates and the derivatives of the frozen Fock matrix in M O basis It s partner is DERI2 DERI2 Utility Part of the analytical C I derivative package Calculates the relax ing density contribution to the derivative of the energy wrt cartesian coordinates Uses the results of DERII DERI21 Utility Part of the analytical C I derivative package Called by DERI2 only DERI22 Utility Part of the analytical C I derivative package Called by DERI2 only DERI23 Utility Part of the analytical C I derivative package Called by DERI2 only DERITR Utility Calculates derivatives of the energy wrt internal coordinates using full SCF s Used as a foolproof way of calculating derivatives Not recommended for normal use DERIV Main Sequence Calculates the derivatives of the energy with respect to the geometric variables This is done either by using initially cartesian derivatives normal mode by analytical C I RHF derivatives or by full SCF calculations NOANCI in half electron and C I mode Arguments on input geometry on output derivatives Called by COMPFG DERNVO Analytical C I Derivative main subroutine Calculates the derivative of the energy wrt geometry for a non variationally optimized wavefunction a SCF CI
155. first line of the input file should consist of the single keyword MOPAC in A format A standard MOPAC input as described in the rest of this manual should then follow terminated by a single blank line With an input of this format all that will happen is that GAMESS UK will drive MOPAC and the output produced will be a standard MOPAC output prepended with the some minimal output generated by the GAMESS UK input processor An example of a such a simple MOPAC job is below which shows a MNDO calcula tion on water run for a single SCF cycle The input for this example is the file mopac 1 in mopac mndo iscf h o11 h 1 1 111 1 Page 2 0 1 2 Using MOPAC together with GAMESS UK As described above GAMESS UK serves as little more than a wrapper for running MOPAC Of greater interest is the use of the results generated by MOPAC in a GAMESS UK run Currently the only data that can be exported from MOPAC for use by GAMESS UK are the atomic coordinates allowing MOPAC to serve as a quick optimiser for GAMESS UK For this to work the directive out gamess must be included on the MOPAC keyword line the first line of the MOPAC directives This instructs MOPAC to create an archive file that stores the coordinates for retrieval by GAMESS UK Following the MOPAC directives there should be a blank line followed the keyword GAMESS in A format indicating the start of the GAMESS UK directives From this line onwards the directives sh
156. fluorescence to occur the photoemission probability must be quite large therefore only transitions of the same spin are allowed For example if the ground state is So then the fluorescing state would be Sj Phosphorescence If the photoemission probability is very low then the lifetime of the excited state can be very long sometimes minutes Such states can become popu lated by S T intersystem crossing Of course the geometry of the system will relax before the photoemission occurs Indirect emission If the system relaxes from the excited electronic ground vibrational state to the ground electronic ground vibrational state then a more complicated calculation is called for The steps of such a calculation are e Optimize the geometry of the excited state e Using the same keywords except that the ground state is specified optimize the geometry of the ground state e Take the difference in AH of the optimized excited and optimized ground state calculations e Convert this difference into the appropriate units Excimers An excimer is a pair of molecules one of which is in an electronic excited state Such systems are usually stabilized relative to the isolated systems Optimization of the geometries of such systems is difficult Suggestions on how to improve this type of calculation would be appreciated 6 18 Outer Valence Green s Function This section is based on materials supplied by Dr David Danovich The Fritz Ha
157. g the potential and kinetic energy at various times Two extreme conditions can be identified a gas phase in which the total energy is a constant through time there being no damping of the kinetic energy allowed and b liquid phase in which kinetic energy is always set to zero the motion of the atoms being infinitely damped All possible degrees of damping are allowed In addition the facility exists to dump energy into the system appearing as kinetic energy As kinetic energy is a function of velocity a vector quantity the energy appears as energy of motion in the direction in which the molecule would naturally move If the system is a transition state then the excess kinetic energy is added after the intrinsic kinetic energy has built up to at least 0 2 kcal mole For ground state systems the excess energy sometimes may not be added if the intrinsic kinetic energy never rises above 0 2kcal mole then the excess energy will not be added Equations used Force acting on any atom Me H s dE dE DE 9 gt vg 1 oer quay Acceleration due to force acting on each atom ali xi CO Ote OP New velocity V o DO Dtg i 1 2 DE2g 1 3 DE g or V i V i V i t V V OB Background That is the change in velocity is equal to the integral over the time interval of the acceleration New position of atoms X i X o V o t 1 2 VV 1 3 Vt 1 4 V 1 That is
158. ge appears in the vanilla version of MOPAC a version ending in 00 please contact JJPS as I would be most interested in how this was achieved THREE ATOMS BEING USED TO DEFINE If the cartesian coordinates of an atom depend on the dihedral angle it makes with three other atoms and those three atoms fall in an almost straight line then a small change in the cartesian coordinates of one of those three atoms can cause a large change in its position This is a potential source of trouble and the data should be changed to make the geometric specification of the atom in question less ambiguous This message can appear at any time particularly in reaction path and saddle point calculations An exception to this rule is if the three atoms fall into an exactly straight line For example if in propyne the hydrogens are defined in terms of the three carbon atoms then no error will be flagged In such a system the three atoms in the straight line must Error messages produced by MOPAC not have the angle between them optimized as the finite step in the derivative calculation would displace one atom off the straight line and the error trap would take effect Correction involves re defining the connectivity LET and GEO OK will not allow the calculation to proceed TIME UP The time defined on the keywords line or 3 600 seconds if no time was specified is likely to be exceeded if another cycle of calculation were to
159. gone a steady expansion since its first release and users of the earlier editions are recommended to familiarize themselves with the changes which are described in this manual If any errors are found or if MOPAC does not perform as described please contact Dr James J P Stewart Frank J Seiler Research Laboratory U S Air Force Academy Colorado Springs CO 80840 6528 2 MOPAC runs successfully on normal CDC Data General Gould and DEC com puters and also on the CDC 205 and CRAY XMP supercomputers The CRAY version has been partly optimized to take advantage of the CRAY architecture Several versions exist for microcomputers such as the IBM PC AT and XT Zenith etc 1 1 Summary of MOPAC capabilities 1 MNDO MINDO 3 AMI and PM3 Hamiltonians 2 Restricted Hartree Fock RHF and Unrestricted Hartree Fock UHF methods 3 Extensive Configuration Interaction Description of MOPAC a b c d 100 configurations Singlets Doublets Triplets Quartets Quintets and Sextets Excited states amr RES KE RE Geometry optimizations etc on specified states 4 Single SCF calculation 5 Geometry optimization 6 Gradient minimization 7 Transition state location 8 Reaction path coordinate calculation 9 Force constant calculation 10 Normal coordinate analysis 11 Transition dipole calculation 12 Thermodynamic properties calculation 13 Localized orbitals 14 Covalent bond orders 15 Bond analysis into sigma a
160. hat the pi system involves only pz on oxygen and carbon Note that numerical values are not checked but only relative values If an error is found use MOLDAT to verify the orbital character etc If faulty the error lies in READ GETGEO or MOLDAT Otherwise the error lies in HCORE HIELEC or ROTATE If the starting matrices are correct go on to step 2 2 Check the density or Fock matrix on every iteration with the words FOCK or DENSITY Check the equivalence of the two hydrogen atoms and the pi system as in 1 10 1 Debugging keywords If an error is found check the first Fock matrix If faulty the bug lies in ITER probably in the Fock subroutines FOCK1 or FOCK2 or in the guessed density matrix MOLDAT An exception is in the UHF closed shell calculation where a small asymmetry is introduced to initiate the separation of the alpha and beta UHF wavefunctions If no error is found check the second Fock matrix If faulty the error lies in the density matrix DENSIT or the diagonalization RSP If the Fock matrix is acceptable check all the Fock matrices If the error starts in iterations 2 to 4 the error probably lies in CNVG if after that in PULAY if used If SCF is achieved and the heat of formation is faulty check HELECT If C I was used check MECI If the derivatives are faulty use DCART to verify the cartesian derivatives If these are faulty check DCART and DHC If they are correct or not calculated che
161. he behavior of such systems is not well investigated users are cautioned to exercise unusual care To alert users to this situation the keyword PARASOK is defined For PM3 acceptable symbols are Elements Dummy atom sparkles and Translation Vector Be x C N 0 F 3 5 Definition of elements and isotopes Na Mg Al Si P S Cl o K Zn Ga Ge As Se Br XX Cb FS Tv Rb Cd In Sn Sb Te I 99 102 103 104 105 106 107 Hg TLl Pb Bi Diatomics Parameterized within the MINDO 3 Formalism H B C N 0 F Si P S Cl A star indicates A eT Bee ATT Pe ES that the atom pair is H parameterized within B x MINDO 3 C x N x O F x Si P x S Cl x Note MINDO 3 should now be regarded as being of historical interest only MOPAC contains the original parameters These do not reproduce the original reported results in the case of P Si or S The original work was faulty see G Frenking H Goetz and F Marschner J Am Chem Soc 100 5295 1978 Re optimized parameters for P C and P CI were derived later which gave better results These are e Alpha P CO 0 8700 G Frenking H Goetz F Marschner e Beta P C 0 5000 J Am Chem Soc 100 5295 5296 1978 e Alpha P Cl 1 5400 G Frenking F Marschner H Goetz e Deta P Cl 0 2800 Phosphorus and Sulfur 8 337 342 1980 Although better
162. he coefficients is exactly one If DEBUG is specified then ALL eigenvectors on every iteration of every SCF calculation will be printed This is useful in a learning context but would normally be very undesirable VELOCITY C The user can supply the initial velocity vector to start a DRC calculation Limitations have to be imposed on the geometry in order for this keyword to work These are a the input geometry must be in cartesian coordinates b the first three atoms must not be coaxial c triatomic systems are not allowed See geometry specification triatomic systems are in internal coordinates by definition Put the velocity vector after the geometry as three data per line representing the x y and z components of velocity for each atom The units of velocity are centimeters per second The velocity vector will be rotated so as to suit the final cartesian coordinate orienta tion of the molecule If KINETIC n n is also specified the velocity vector will be scaled to equal the velocity corresponding to n n kcal mole This allows the user to define the direction of the velocity vector the magnitude is given by KINETIC n n 2 3 Definitions of keywords WILLIAMS C Within the ESP calculation the Connolly surface is used as the default If the surface generation procedure of Donald Williams is wanted the keyword WILLIAMS should be used X PRIORITY O In a DRC calculation results will be printed whenever the calcul
163. he information contained in the Gaussian Z matrix is identical to that in a MOPAC Z matrix The order of presentation is different Atom N real or dummy is specified in the format Element N1 Length N2 Alpha N3 Beta where Element is the same as for the MOPAC Z matrix N1 N2 and N3 are the connec tivity the same as the MOPAC Z matrix NA NB and NC bond lengths are between N and N1 angles are between N N1 and N2 and dihedrals are between N N1 N2 and N3 The same rules apply to N1 N2 and N3 as to NA NB and NC Length Alpha and Beta are the bond lengths the angle and dihedral They can be real e g 1 45 109 4 180 0 or symbolic A symbolic is an alphanumeric string of up to 8 characters e g R51 A512 D5213 CH CHO CHOC etc Two or more symbolics can be the same Dihedral symbolics can optionally be preceeded by a minus sign in which case the value of the dihedral is the negative of the value of the symbolic This is the equivalent of the normal MOPAC SYMMETRY operations 1 2 3 and 14 If an internal coordinate is real it will not be optimized This is the equivalent of the MOPAC optimization flag 0 If an internal coordinate is symbolic it can be optimized The Z matrix is terminated by a blank line after which comes the starting values of the symbolics one per line If there is a blank line in this set then all symbolics after 3 3 Cartesian coordinate definition the blank line are conside
164. he number of valence electrons or atom electron density on the atom here 1 0010 3 7079 and 6 2902 respectively Note 19 The dipole is the scalar of the dipole vector in cartesian coordinates The com ponents of the vector coefficients are the point charge dipole and the hybridization dipole In formaldehyde there is no z dipole since the molecule is flat Note 20 MNDO AMI PM3 and MINDO 3 all use the Coulson density matrix Only the diagonal elements of the matrix representing the valence orbital electron pop ulations will be printed unless the keyword DENSITY is specified Extra lines are added as a result of user requests Examples 1 The total CPU time for the job excluding loading of the executable is printed 2 In order to know that MOPAC has ended the message MOPAC DONE is printed Chapter 5 Testdata TESTDATA DAT supplied with MOPAC 6 00 is a single large job consisting of several small systems which are run one after the other In order the calculations run are 1 A FORCE calculation on formaldehyde The extra keywords at the start are to be used later when TESTDATA DAT acts as a SETUP file This unusual usage of a data set was made necessary by the need to ensure that a SETUP file existed If the first two lines are removed the data set used in the example given below is generated 2 The vibrational frequencies of a highly excited dication of methane are calculated A non degenerate state was
165. he transition state in a simple chemical reaction is to be optimized Extra data are required After the first geometry specifying the reactants and any symmetry functions have been defined the second geometry specifying the products is defined using the same format as that of the first geometry SADDLE often fails to work successfully Frequently this is due to equivalent dihedral angles in the reactant and product differing by about 360 degrees rather than zero degrees As the choice of dihedral can be difficult users should consider running this calculation with the keyword XYZ There is normally no ambiguity in the definition of cartesian coordinates See also BAR Many of the bugs in SADDLE have been removed in this version Use of the XYZ option is strongly recommended SCALE C SCALE n n specifies the scaling factor for Van der Waals radii for the initial layer of the Connolly surface in the ESP calculation 2 3 Definitions of keywords SCFCRT n nn W The default SCF criterion is to be replaced by that defined by SCFCRT The SCF criterion is the change in energy in kcal mol on two successive iterations Other minor criteria may make the requirements for an SCF slightly more stringent The SCF criterion can be varied from about 0 001 to 1 D 25 although numbers in the range 0 0001 to 1 D 9 will suffice for most applications An overly tight criterion can lead to failure to achieve a SCF and consequent failure of the r
166. ically the overlap between to successive TS modes should be higher than OMIN While this concept at first appears very promising it is not without problems when the Hessian is updated As the updated Hessian in each step is only approximately correct there is a upper limit on how large the TS mode overlap between steps can be To understand this consider a series of steps made from the same geometry e g at some point in the optimization but with steadily smaller step sizes The update adds corrections to the Hessian to make it a better approximation to the exact Hessian As the step size become small the updated Hessian converges toward the exact Hessian at least in the direction of the step The old Hessian is constant thus the overlap between TS modes thus does not converge toward 1 but rather to a constant value which indicate how well the old approximate Hessian resembles the exact Hessian Test calculations suggest a typical upper limit around 0 9 although cases have been seen where the limit is more like 0 7 It appears that an updated Hessian in general is not of sufficient accuracy for reliably rejecting steps with TS overlaps much greater than 0 80 The default OMIN of 0 80 reflects the typical use of an updated Hessian If the Hessian is recalculated in each step however the TS mode overlap does converge toward 1 as the step size goes toward zero and in this cases there is no problems following high lying modes Unfortunately se
167. ife for loss of kinetic energy is defined as n nnn fem toseconds If n nnn is set to zero infinite damping simulating a very condensed phase is obtained This keyword cannot be written with spaces around the sign 2 3 Definitions of keywords DUMP W Restart files are written automatically at one hour cpu time intervals to allow a long job to be restarted if the job is terminated catastrophically To change the frequency of dump set DUMP nn to request a dump every nn seconds Alternative forms DUMP nnM DUMP nnH DUMP nnD for a dump every nn minutes hours or days respectively DUMP only works with geometry optimization gradient minimization path and FORCE calculations It does not yet work with a SADDLE calculation ECHO 0 Data are echoed back if ECHO is specified Only useful if data are suspected to be corrupt EF C The Eigenvector Following routine is an alternative to the BFGS and appears to be much faster To invoke the Eigenvector Following routine specify EF EF is particularly good in the end game when the gradient is small See also HESS DMAX EIGINV EIGINV W Not recommended for normal use Used with the EF routine See source code for more details ENPART 0 This is a very useful tool for analyzing the energy terms within a system The total energy in eV obtained by the addition of the electronic and nuclear terms is partitioned into mono and bi centric contributions and these
168. ill have equal energy this is normally a consequence of both trajectories leading to the same point or symmetry equivalent points After all spurious negative modes have been eliminated the remaining normal mode corresponds to the reaction coordinate and the transition state has been located This technique is relatively rapid and relies on starting from a stationary point to begin each trajectory If any other point is used the trajectory will not be even roughly simple harmonic If by mistake the reaction coordinate is selected then the potential energy will drop to that of either the reactants or products which incidentally forms a handy criterion for selecting the spurious modes if the potential energy only drops by a small amount and the time evolution is roughly simple harmonic then the mode is one of the spurious modes If there is any doubt as to whether a minimum is in the vicinity of a stationary point allow the trajectory to continue until one complete cycle is executed At that point the geometry should be near to the initial geometry Superficially a line search might appear more attractive than the relatively expensive DRC However a line search in cartesian space will normally not locate the minimum in a mode An obvious example is the mode corresponding to a methyl rotation Keyword Sequences to be Used 1 To locate the starting stationary point given an approximate transition state SIGMA 2 To define the normal mo
169. inates to be optimized and the secondary tests are not done If LET is not specified n nnn is reset to 0 01 if it was smaller than O 01 If PRECISE is specified TOLERG 0 2 If a SADDLE calculation TOLERG is made a function of the last gradient norm TOLERF Heat of Formation Test Satisfied FLEPO 0 002 kcal mole The calculated heats of formation on two successive cycles differ by less than TOLERF If GNORM is specified the TOLERF test is not used For the TOLERG TOLERF and TOLERX tests a second test in which no individual component of the gradient should be larger than TOLERG must be satisfied If after the TOLERG TOLERF or TOLERX test has been satisfied three consecutive times the heat of formation has dropped by less than 0 3kcal mole then the optimization is stopped If GNORM is specified then this test is not performed TOL2 POWSQ 0 4 The absolute value of the largest component of the gradient is less than TOL2 If PRECISE is specified TOL2 0 01 If GNORM n nn is specified TOL2 n nn If LET is not specified TOL2 is reset to 0 01 if n nn was smaller than 0 01 TOLS1 NLLSQ 9 2 Geometric optimization criteria Default Value Basic Test Name Defined in Default Value Basic Test 0 000 000 000 001 The square of the ratio of the projected change in the geometry to the actual geometry is less than TOLS1 none NLLSQ 0 2 Every component of the gradient is less than 0 2 Crit
170. io di od PRPrPrRPRPP PRP RPRP PRB S pB ars ON 123640 123549 123417 114352 114462 114340 114433 123126 123225 123328 123227 113970 114347 299490 000000 OrRPRRPRPRP RP RP BP BBP RP RP BP BB 93 90 90 90 89 89 89 93 93 90 91 90 90 0 0 853406 682924 679889 239157 842852 831790 753913 644744 880969 261019 051403 374545 255788 000000 000000 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 126 126 127 126 127 126 126 127 126 127 125 126 126 0 0 320187 763659 033695 447043 140168 653999 926618 030541 380511 815464 914234 799259 709810 000000 000000 1 1 1 1 1 1 1 1 1 1 1 1 1 0 0 o OAWANN DD A COON NDAD H MH W m e DOO ONN DOO TH AAD BPR eR Nere Pree e O O urs o 12 11 o 0 0 e e are p o optimization The reason for this is also explained in the Background chapter Description of MOPAC Chapter 2 Keywords 2 1 Specification of keywords All control data are entered in the form of keywords which form the first line of a data file A description of what each keyword does is given in Section 2 3 The order in which keywords appear is not important although they must be separated by a space Some keywords can be abbreviated allowed abbreviations are noted in Section 2 3 for example ELECTRON can be entered as 1ELECT However the full keyword is prefer
171. ion when OPEN n1 n2 is used ORIDE W Do not use this keyword until you have read Simons article ORIDE is part of the EF routine and means Use whatever A s are produced even if they would normally be unacceptable J Simons P Jorgensen H Taylor J Ozment J Phys Chem 87 2745 1983 PARASOK W Use this keyword with extreme caution The AM1 method has been parameterized for only a few elements less than the number available to MNDO or PM3 If any elements which are not parameterized at the AMI level are specified the MNDO parameters if available will be used The resulting mixture of methods AM1 with MNDO has not been studied to see how good the results are and users are strictly on their own as far as accuracy and compatibility with other methods is concerned In particular while all parameter sets are referenced in the output other programs may not cite the parameter sets used and thus compatibility with other MNDO programs is not guaranteed PI O The normal density matrix is composed of atomic orbitals that is s px py and pz PI allows the user to see how each atom atom interaction is split into c and m bonds The resulting density matrix is composed of the following basis functions s c p o p m d c d r d The on diagonal terms give the hybridization state so that an sp hybridized system would be represented as s o 1 0 p o 2 0 p r 1 0 PM3 C The PM3 method is to be used
172. ions would be if the lowest singlet state were a biradical in which case the EXCITED state could be a closed shell The EXCITED state will be calculated from a BIRADICAL calculation in which the second root of the C I matrix is selected Note that the eigenvector of the C I matrix is not used in the current formalism Abbreviation EXCI Note EXCITED is a redundant keyword and represents a particular configuration interaction calculation Experienced users of MECI can duplicate the effect of the keyword EXCITED by using the MECI keywords OPEN 2 2 SINGLET and ROOT 2 EXTERNAL name C Normally PM3 AM1 and MNDO parameters are taken from the BLOCK DATA files within MOPAC When the supplied parameters are not suitable as in an element recently parameterized and the parameters have not yet installed in the user s copy of MOPAC then the new parameters can be inserted at run time by use of EXTERNAL lt filename gt where filename is the name of the file which contains the new parameters filename consists of a series of parameter definitions in the format Parameter Element Value of parameter where the possible parameters are USS UPP UDD ZS ZP ZD BETAS BETAP BE TAD GSS GSP GPP GP2 HSP ALP FNnm n 1 2 or 3 and m 1 to 10 and the elements are defined by their chemical symbols such as Si or SI When new parameters for elements are published they can be typed in as shown This file is ended by a blan
173. is done Note 6 The interatomic distances are output for the user s advice and a simple check made to insure that the smallest interatomic distance is greater than 0 8 A 4 2 MOPAC output for test data file MNRSD1 Note 7 The geometry is optimized in a series of cycles each cycle consisting of a line search and calculation of the gradients The time given is the cpu time for the cycle time left is the total time requested here 100 seconds less the cpu time since the start of the calculation which is earlier than the start of the first cycle These times can vary slightly from cycle to cycle due to different options being used for example whether or not two or more SCF calculations need to be done to ensure that the heat of formation is lowered The gradient is the scalar length in kcal mole Angstrom of the gradient vector Note 8 At the end of the BFGS geometry optimization a message is given which in dicates how the optimization ended All normal termination messages contain the word satisfied other terminations may give acceptable results but more care should be taken particularly regarding the gradient vector Notes 9 10 The keywords used titles and comments are reproduced here to remind the user of the name of the calculation Notes 11 12 Two messages are given here The first is a reminder of how the geometry was obtained whether from the Broyden Fletcher Goldfarb Shanno Eigenvector Following Bartel
174. job has been stopped for whatever reason and intermediate results have been stored then the calculation can be restarted at the point where it stopped by specifying RESTART The most common cause of a job stopping before completion is its exceeding the time allocated A saddle point calculation has no restart but the output file contains information which can easily be used to start the calculation from a point near to where it stopped It is not necessary to change the geometric data to reflect the new geometry As a result the geometry printed at the start of a restarted job will be that of the original data not that of the restarted file A convenient way to monitor a long run is to specify 1SCF and RESTART this will give a normal output file at very little cost Note 1 In the FORCE calculation two restarts are possible These are a a restart in FLEPO if the geometry was not optimized fully before FORCE was called and b the normal restart in the construction of the force matrix If the restart is in FLEPO within FORCE then the keyword FORCE should be deleted and the keyword RESTART used on its own Forgetting this point is a frequent cause of failed jobs Keywords Note 2 Two restarts also exist in the IRC calculation If an IRC calculation stops while in the FORCE calculation then a normal restart can be done If the job stops while doing the IRC calculation itself then the keyword IRC n should be changed to IRC or it can be o
175. k line the word END or nothing i e no end of file delimiter An example of a parameter data file would be put at least 2 spaces before and after parameter name Line 1 USS Si 34 08201495 Line 2 UPP Si 28 03211675 Line 3 BETAS Si 5 01104521 Line 4 BETAP Si 2 23153969 Line 5 ZS Si 1 28184511 Line 6 ZP Si 1 84073175 Line 7 ALP Si 2 18688712 Line 8 GSS Si 9 82 Line 9 GPP Si 7 31 Line 10 GSP Si 8 36 Line 11 GP2 Si 6 54 Line 12 HSP Si 1 32 Derived parameters do no need to be entered they will be calculated from the op timized parameters All constants such as the experimental heat of atomization are already inserted for all elements NOTE EXTERNAL can only be used to input parameters for MNDO AMI or PM3 It is unlikely however that any more MINDO 3 parameters will be published See also DEP to make a permanent change FILL n C The n th M O in an RHF calculation is constrained to be filled It has no effect on a UHF calculation After the first iteration NOTE not after the first SCF calculation but 2 3 Definitions of keywords after the first iteration within the first SCF calculation the n th M O is stored and if occupied no further action is taken at that time If unoccupied then the HOMO and the n th M O s are swapped around so that the n th M O is now filled On all subsequent iterations the M O nearest in character to the stored M O is forced to be filled and the stored M O replac
176. lates the one and two electron matrices and the nuclear energy Called by COMPFG HELECT Utility Given the density matrix and the one electron and Fock matrices calculates the electronic energy No data are changed by a call of HELECT Called by ITER and DERIV Description of subroutines e HQRI Utility Rapid diagonalization routine Accepts a secular determinant and produces a set of eigenvectors and eigenvalues The secular determinant is destroyed e IJKL Utility Fills the large two electron array over a M O basis set Called by MECI e INTERP Utility Runs the Camp King converger q v e ITER Main sequence Given the one and two electron matrices ITER calculates the Fock and density matrices and the electronic energy Called by COMPFG e JAB Utility Calculates the coulomb contribution to the Fock matrix in NDDO formalism Called by FOCK2 e JCARIN Utility Calculates the difference vector in cartesian coordinates corre sponding to a small change in internal coordinates e KAB Utility Calculates the exchange contribution to the Fock matrix in NDDO formalism Called by FOCK2 e LINMIN Main sequence Called by the BFGS geometry optimized FLEPO LINMIN takes a step in the search direction and if the energy drops returns Otherwise it takes more steps until if finds one which causes the energy to drop e LOCAL Utility Given a set of occupied eigenvectors produces a canonical set of localized bonding orbitals by
177. le maximum to the desired transition state The technique used will now be described If a multiple maximum is identified most likely one negative force constant corre sponds to the reaction coordinate in which case the objective is to render the other force constants positive The associated normal mode eigenvalues are complex but in the out put are printed as negative frequencies and for the sake of simplicity will be described as negative vibrations Use DRAW 2 to display the negative vibrations and identify which mode corresponds to the reaction coordinate This is the one we need to retain Hitherto simple motion in the direction of the other modes has proved difficult How ever the DRC provides a convenient mechanism for automatically following a normal coordinate Pick the largest of the negative modes to be annihilated and run the DRC along that mode until a minimum is reached At that point refine the geometry once more using SIGMA and repeat the procedure until only one negative mode exists To be on the safe side after each DRC SIGMA sequence do the DRC SIGMA oper ation again but use the negative of the initial normal coordinate to start the trajectory After both stationary points are reached choose the lower point as the starting point for the next elimination The lower point is chosen because the transition state wanted is the highest point on the lowest energy path connecting reactants to products Sometimes the two points w
178. lities Michael B Coolidge The Frank J Seiler Research Laboratory U S Air Force Academy CO 80840 and James J P Stewart Stewart Computational Chemistry 15210 Paddington Circle Colorado Springs CO 80921 2512 The Air Force code was obtained under the Freedom of Information Act Symmetry is used to speed up FORCE calculations and to facilitate the anal ysis of molecular vibrations David Danovich The Fritz Haber Research Center for Molecular Dynamics The Hebrew University of Jerusalem 91904 Jerusalem Israel Ionization potentials are corrected using Green s Function techniques The resulting I P s are generally more accurate than the conventional I P s The point group of the system is identified and molecular orbitals are charac terized by irreducible representation Andreas Klamt Bayer AG Q18 D 5090 Leverkusen Beyerwerk Germany A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient has been added e Existing Functionalities Victor I Danilov Department of Quantum Biophysics Academy of Sci ences of the Ukraine Kiev 143 Ukraine Edited the MOPAC 7 Manual and provided the basis for Section 6 17 2 on excited states Henry Kurtz and Prakashan Korambath Department of Chemistry Memphis State University Memphis TN 38152 The Hyperpolarizability calculation originally written by Prof Kurtz has been improved so that frequency dep
179. locities to simple harmonic motion a much better fit is ob tained Calculated Simple Harmonic Diff Time Velocity 25316 Sin 0 529t 0 000 0 0 0 0 0 0 0 100 1338 6 1338 6 0 0 0 200 2673 9 2673 4 0 5 0 300 4001 0 4000 8 0 2 0 400 5317 3 5317 0 0 3 0 500 6618 5 6618 3 0 2 0 600 7900 8 7901 0 0 2 The repeat time required for this motion is 11 88 fs in good agreement with the three values calculated using static models The repeat time should not be calculated from the time required to go from a minimum to a maximum and then back to a minimum only half a cycle For all real systems the potential energy is a skewed parabola so that the potential energy slopes are different for both sides a compression as in this case normally leads to a higher force constant and shorter apparent repeat time as in this case Only the addition of the two half cycles is meaningful 6 11 Reaction coordinates Conservation of normal coordinate So far this analysis has only considered a homonuclear diatomic A detailed analysis of a large polyatomic is impractical and for simplicity a molecule of formaldehyde will be studied In polyatomics energy can transfer between modes This is a result of the non parabolic nature of the potential surface For small displacements the surface can be considered as parabolic This means that for small displacements interconversion between modes should occur only very slowly Of the six normal modes mode 1
180. manner E p a gt lk Gk jk Occa K Occg K ij kk Occb k Oceg k k E p q may need to be multiplied by 1 if the number of two electron permutations required to bring M O s 4 and j into coincidence is odd Where Occa k is the alpha molecular orbital occupancy in the configuration inter action 6 14 Configuration interaction 3 Determinants differing by exactly two M O s The two M O s can have the same or opposite spins Three cases can be identified a Both M O s have alpha spin For the first microstate having M O s i and j and the second microstate having M O s k and l the matrix element connecting the two microstates is given by Q p q ikl jl ill pk E p q may need to be multiplied by 1 if the number of two electron per mutations required to bring M O i into coincidence with M O k and M O j into coincidence with M O l is odd b Both M O s have beta spin The matrix element is calculated in the same manner as in the previous case c One M O has alpha spin and one beta spin For the first microstate having M O s alpha i and beta j and the second microstate having M O s alpha k and beta l the matrix element connecting the two microstates is given by Q p q ikl jl E p q may need to be multiplied by 1 if the number of two electron per mutations required to bring M O i into coincidence with M O k and M O j into coi
181. methods to give pyra midal nitrogens The degree to which pyramidalization of the nitrogen atom is preferred can be seen in the following series of compounds Compound MINDO 3 MNDO AM1 PM3 Exp Ammonia Py Py Py Py Py Aniline Py Py Py Py Py Formamide Py Py Flat Py Py 6 4 Level of precision within MOPAC Acetamide Flat Py Flat Py Flat N methyl formamide Flat Py Flat Py Flat N methyl acetamide Flat Flat Flat Py Flat To correct this a molecular mechanics correction has been applied This consists of identifying the R HNCO unit and adding a torsion potential of form k x sin 6 where 0 is the X N C O angle X R or H and k varies from method to method This has two effects there is a force constraining the nitrogen to be planar and HNCO barrier in N methyl acetamide is raised to 14 00 kcal mole When the MM correction is in place the nitrogen atom for all methods for the last three compounds shown above is planar The correction should be user transparent Cautions 1 This correction will lead to errors of 0 5 1 5 kcal mole if the peptide linkage is made or broken in a reaction calculation 2 If the correction is applied to formamide the nitrogen will be flat contrary to ex periment 3 When calculating rotation barriers take into account the rapid rehybridization which occurs When the dihedral is 0 or 180 degrees the nitrogen will be pla nar sp2 but at 90 degrees the nitrogen should be pyramidal as the partial do
182. ming and therefore should only be invoked as a last resort It evaluates that linear combination of old and current eigenvectors which minimize the total energy One of its strengths is that systems which otherwise oscillate due to charge surges e g CHO H the C H distance being very large will converge using this very sophisticated converger 6 7 Causes of failure to achieve an SCF In a system where a biradical can form such as ethane decomposing into two CH3 units the normal RHF procedure can fail to go self consistent If the system has marked birad 6 8 Torsion or dihedral angle coherency icaloid character then BIRADICAL or UHF and TRIPLET can often prove successful These options rely on the assumption that two unpaired electrons can represent the open shell part of the wave function Consider H Cl with the interatomic distance being steadily increased At first the covalent bond will be strong and a self consistent field is readily obtained Gradually the bond will become more ionic and eventually the charge on chlorine will become very large The hydrogen meanwhile will become very electropositive and there will be an increased energy advantage to any one electron to transfer from chlorine to hydrogen If this in fact occurred the hydrogen would suddenly become very electron rich and would on the next iteration lose its extra electron to the chlorine A sustained oscillation would then be initiated To prevent this i
183. mitted if DRC is also specified The absence of the string IRC is used to indicate that the FORCE calculation was completed before the restart files were written ROOT n C The n th root of a C I calculation is to be used in the calculation If a keyword specifying the spin state is also present e g SINGLET or TRIPLET then the n th root of that state will be selected Thus ROOT and SINGLET will select the third singlet root If ROOT 3 is used on its own then the third root will be used which may be a triplet the third singlet or the second singlet the second root might be a triplet In normal use this keyword would not be used It is retained for educational and research purposes Unusual care should be exercised when ROOT is specified ROT n C In the calculation of the rotational contributions to the thermodynamic quantities the symmetry number of the molecule must be supplied The symmetry number of a point group is the number of equivalent positions attainable by pure rotations No reflections or improper rotations are allowed This number cannot be assumed by default and may be affected by subtle modifications to the molecule such as isotopic substitution A list of the most important symmetry numbers follows mum TABLE OF SYMMETRY NUMBERS TUS C1 CI CS 1 D2 D2D D2H 4 CCINF V 1 C2 C2V C2H 2 D3 D3D D3H 6 D INF H 2 C3 C3V C3H 3 D4 DAD D4H 8 T TD 12 C4 CAV CAH 4 D6 D6D D6H 12 OH 24 C6 C6V C6H 6 S6 3 SADDLE C T
184. monic oscillator the period r is given by m 9 SN T 247 L where m is the reduced mass and k is the force constant The reduced mass in amu of a nitrogen molecule is 14 0067 2 7 00335 and the force constant can be calculated from E c 1 2 k R Ro Given Ro 1 1038 R 1 092 c 8 276655 and E 8 593407 kcal mol then 4548 2 kcal mole A 4545 x 4 184 x 10 x 107 x 1018 ergs cm 1 9029 x 10 ergs cm Therefore r 2x 3 14159 x E Ee seconds 12 054 x 10715 s 12 054 fs 1 9029 x 1030 2 From the gradient curve The force constant is the derivative of the gradient wrt distance dG k dx Since we are using discrete points the force constant is best obtained from finite differences p G2 61 z2 21 For z2 1 1100 G2 27 163 and for z 1 0980 G4 26 244 giving rise to k 4450 kcal mole A and a period of 12 186 fs 3 From the vibrational frequency Given a frequency wavenumber of vibration of No of v 2739 6 cm the period of oscillation in seconds is given directly by 1 1 cv 2739 6 x 2 998 x 1010 or as 12 175 femtoseconds Summarizing by three different methods the period of oscillation of N is calculated to be 12 054 12 186 and 12 175 fs average 12 138 fs Background Initial dynamics of Nj with N N distance 1 094 A A useful check on the dynamics of N is to calculate the initial acceleration of the two nitrogen at
185. n 1 2 are calculated simultaneously for component of spin 1 2 From these states the quartet states are selected when QUARTET is specified and all other spin states while calculated are ignored in the choice of root to be used If QUARTET is used on its own then a single state corresponding to an alpha electron in each of three M O s is calculated UHF interpretation The system will have three more alpha electrons than beta elec trons QUINTET C RHF interpretation The desired spin state is a quintet that is the state with component of spin 0 and spin 2 When a configuration interaction calculation is done all spin states of spin equal to or greater than 0 are calculated simultaneously for component of spin 0 From these states the quintet states are selected when QUINTET is specified and the septet states while calculated will be ignored in the choice of root to be used If QUINTET is used on its own then a single state corresponding to an alpha electron in each of four M O s is calculated UHF interpretation The system will have three more alpha electrons than beta elec trons RECALC n RECALC n calculates the Hessian every n steps in the EF optimization For small n this is costly but is also very effective in terms of convergence RECALC 10 and DMAX 0 10 can be useful for difficult cases In extreme cases RECALC 1 and DMAX 0 05 will always find a stationary point if it exists RESTART W When a
186. n in a high symmetry molecule such as propyne 2 The check is only made if the fourth atom has a bond angle which is not zero or 180 degrees Chapter 8 Error messages produced by MOPAC MOPAC produces several hundred messages all of which are intended to be self explanatory However when an error occurs it is useful to have more information than is given in the standard messages The following alphabetical list gives more complete definitions of the messages printed AN UNOPTIMIZABLE GEOMETRIC PARAMETER When internal coordinates are supplied six coordinates cannot be optimized These are the three coordinates of atom 1 the angle and dihedral on atom 2 and the dihedral on atom 3 An attempt has been made to optimize one of these This is usually indicative of a typographic error but might simply be an oversight Either way the error will be corrected and the calculation will not be stopped here ATOM NUMBER nn IS ILLDEFINED The rules for definition of atom connectivity are 1 Atom 2 must be connected to atom 1 default no override 2 Atom 3 must be connected to atom 1 or 2 and make an angle with 2 or 1 3 All other atoms must be defined in terms of already defined atoms these atoms must all be different Thus atom 9 might be connected to atom 5 make an angle with atom 6 and have a dihedral with atom 7 If the dihedral was with atom 5 then the geometry definition would be faulty If any of these rules is broken a
187. n nnn is the half life in femtoseconds If n nn is 0 0 this corresponds to infi nite damping simulating the IRC A limitation of the program is that time only has meaning when DRC is specified without a half life 2 Excess kinetic energy can be added to the calculation by use of KINETIC n nn After the kinetic energy has built up to 0 2kcal mole or if IRC n is used then n nn kcal mole of kinetic energy is added to the system The excess kinetic energy appears as a velocity vector in the same direction as the initial motion 3 The RESTART file filename RES can be edited to allow the user to modify the velocity vector or starting geometry This file is formatted Frequently DRC leads to a periodic repeating orbit One special type the orbit in which the direction of motion is reversed so that the system retraces its own path is sensed for and if detected the calculation is stopped after exactly one cycle If the calculation is to be continued the keyword GEO OK will allow this check to be by passed Due to the potentially very large output files that the DRC can generate extra key words are provided to allow selected points to be printed After the system has changed by a preset amount the following keywords can be used to invoke a print of the geometry KeyWord Default User Specification X PRIO 0 05 Angstroms X PRIORITY n nn T PRIO 0 10 Femtoseconds T PRIORITY n nn H PRIO 0 10 kcal mole H PRIORITY n nn Option to allow only extr
188. nani deai a r a a a A A e a a 77 6 12 Sparkles i294 ace Gs Ada Ba X psp ba ee NO ee E v EU 86 6 13 Mechanism of the frame in FORCE calculation 87 6 14 Configuration interaction 2 2 87 6 15 Reduced masses in a force calculation 92 6 16 Use of SADDLE calculation 0 eA 92 6 17 How to escape froma hilltop 2 020200004 94 6 17 1 BEigenFollewing su s ja a ba eae nb ae we ee RO 95 6 17 2 Franck Condon considerations 0 0 0 00002 ee 97 6 18 Outer Valence Green s Function s osoa e le 98 6 18 1 Example of OVGF calculation 000 99 6 19 COSMO Conductor like Screening Model 0 99 6 20 Solid state capability 2 ee ee 100 7 Program 103 7 1 Main geometric sequence eA 103 7 2 Main electronic flow 0 0 ee 104 7 3 Control within MOPAC 0 0 000 eee ee ees 104 7 3 1 Subroutine GMETRY 105 8 Error messages produced by MOPAC 107 9 Criteria 115 QT ZSORAGBUOBIOI ena Bede uoo Lee Naren ON Batu egg deret tes Bs 115 9 2 Geometric optimization criteria e e e 115 10 Debugging 119 10 1 Debugging keywords ss 119 11 Installing MOPAC 123 Lid ESP calculation 2 anno IE wat qe DI Gn AUS ey RO ROS 126 A Names of FORTRAN 77 files 129 B Subroutine calls in MOPAC 131 C Description of subroutines 139 D Heats of formation 151 E References 153 CONTENTS e New Functiona
189. ncidence with M O l is odd States arising from various calculations Each MECI calculation invoked by use of the keyword C I n normally gives rise to states of quantized spins When C I is used without any other modifying keywords the following states will be obtained No of M O s States Arising States Arising From From Odd Electron Systems Even Electron Systems in MECI Doublets Singlets Triplets 1 1 1 2 1 3 8 1 6 3 4 20 4 20 15 1 5 75 24 1 50 45 These numbers of spin states will be obtained irrespective of the chemical nature of the system Calculation of spin states In order to calculate the spin state the expectation value of S2 is calculated where Ne is the no of electrons in C I C i k is the coefficient of microstate i in State k N4 i is the number of alpha electrons in microstate i Ng i is the number of beta electrons in microstate 4 O4 l k is the occupancy of alpha M O l in microstate k Og l k is the occupancy of beta M O l in microstate k S is the spin shift up or step up operator S is the spin shift down or step down operator the Kroneker delta is 1 if the two terms in brackets following it are identical The spin state is calculated from S a 2 4 4S2 11 Background In practice S is calculated to be exactly integer or half integer That is there is insignif icant error due to approximations used This does not mean however that the method is accurate The spin c
190. nd pi contributions 16 One dimensional polymer calculation 17 Dynamic Reaction Coordinate calculation 18 Intrinsic Reaction Coordinate calculation 1 2 Copyright status of MOPAC At the request of the Air Force Academy Law Department the following notice has been placed in MOPAC Notice of Public Domain nature of MOPAC This computer program is a work of the United States Government and as such is not subject to protection by copyright 17 U S C 105 Any person who fraudulently places a copyright notice or does any other act contrary to the provisions of 17 U S Code 506 c shall be subject to the penalties provided therein This notice shall not be altered or removed from this software and is to be on all reproductions I recommend that a user obtain a copy by either copying it from an existing site or ordering an official copy from the Quantum Chemistry Program Exchange QCPE Department of Chemistry Indiana University Bloomington Indiana 47405 The cost covers handling only Contact the Editor Richard Counts at 812 855 4784 for further details 1 3 Porting MOPAC to other machines 1 3 Porting MOPAC to other machines MOPAC is written for the DIGITAL VAX computer However the program has been written with the idea that it will be ported to other machines After such a port has been done the new program should be given the version number 6 10 or if two or more versions are generated 6 20 6 30 etc T
191. nd such as ALLOCATE MTAO Go into an empty directory which is to hold MOPAC Mount the magnetic tape with the command MOUNT MTAO MOPAC Copy all the files from the tape with the command COPY MTAO A useful operation after this would be to make a hard copy of the directory You should now have the following sets of files in the directory 1 2 A file AAAINVOICE TXT summarizing this list A set of FORTRAN 77 files see Appendix A The command files COMPILE MOPACCOM MOPAC RMOPAC and SHUT A file MOPAC OPT which lists all the object modules used by MOPAC Help files MOPAC HLP and HELP FOR A text file MOPAC MAN manual summarizing the updates called UPDATE MAN Two test data files TESTDATA DAT and MNRSDI DAT and corresponding re sults files TESTDATA OUT and MNRSD1 OUT Structure of command files COMPILE The parameter file DIMSIZES DAT should be read and if necessary modified before COMPILE is run DO NOT RUN COMPILE AT THIS TIME Installing MOPAC COMPILE should be run once only It assigns DIMSIZES DAT the block of FOR TRAN which contains the PARAMETERS for the dimension sizes to the logical name SIZES This is a temporary assignment but the user is strongly recommended to make it permanent by suitably modifying LOGIN file s COMPILE is a modified version of Maj Donn Storch s COMPILE for DRAW 2 All the FORTRAN files are then compiled using the array sizes given in
192. nown geometric parameters and symmetry data Called whenever GMETRY is called THERMO Main sequence After the vibrational frequencies have been calculated THERMO calculates thermodynamic quantities such as internal energy heat capac ity entropy etc for translational vibrational and rotational degrees of freedom TIMCLK Utility Vax specific code for determining CPU time TIMER Utility Prints times of various steps TIMOUT Utility Prints total CPU time in elegant format TQL2 Utility Part of the RSP Description of subroutines e TQLRAT Utility Part of the RSP e TRBAK3 Utility Part of the RSP e TRED3 Utility Part of the RSP e UPDATE Utility Given a set of new parameters stores these in their appropriate arrays Invoked by EXTERNAL e UPDHES Utility Called by EF UPDHES updates the Hessian matrix e VECPRT Utility Prints out a packed lower half triangular matrix The labeling of the sides of the matrix depend on the matrix s size if it is equal to the number of orbitals atoms or other Arguments The matrix to be printed size of matrix No data are changed by a call of VECPRT e WRITE Main sequence Most of the results are printed here All relevant arrays are assumed to be filled A call of WRITE only changes the number of SCF calls made this is reset to zero No other data are changed Called by MAIN FLEPO FORCE e WRTKEY Main Sequence Prints all keywords and checks for compatability and to see
193. nsideration AH T S for reference state 6 58 Taking the difference is necessary to cancel the unknown values of standard entropy of formation for the constituent elements 6 11 Reaction coordinates 6 11 Reaction coordinates The Intrinsic Reaction Coordinate method pioneered and developed by Mark Gordon has been incorporated in a modified form into MOPAC As this facility is quite complicated all the keywords associated with the IRC have been grouped together in this section DRC The Dynamic Reaction Coordinate is the path followed by all the atoms in a system assuming conservation of energy i e as the potential energy changes the kinetic energy of the system changes in exactly the opposite way so that the total energy kinetic plus potential is a constant If started at a ground state geometry no significant motion should be seen Similarly starting at a transition state geometry should not produce any motion after all it is a stationary point and during the lifetime of a calculation it is unlikely to accumulate enough momentum to travel far from the starting position In order to calculate the DRC path from a transition state either an initial deflection is necessary or some initial momentum must be supplied Because of the time dependent nature of the DRC the time elapsed since the start of the reaction is meaningful and is printed Description The course of a molecular vibration can be followed by calculatin
194. o look at the normal coordinate eigenvectors In the analysis each pair of bonded atoms is examined to see if there is a large relative motion between them By bonded is meant within the Van der Waals distance If there is such a motion the indices of the atoms the relative distance in Angstroms and the percentage radial motion are printed Radial plus tangential motion adds to 100 but as there are two orthogonal tangential motions and only one radial the radial component is printed 6 10 A note on thermochemistry By Tsuneo Hirano Department of Synthetic Chemistry Faculty of Engineering University of Tokyo Hongo Bunkyo ku Tokyo Japan Background 6 10 1 Basic Physical Constants Taken from Quantities Units and Symbols in Physical Chemistry Blackwell Scientific Publications Ltd Oxford OX2 OEL UK 1987 IUPAC based on CODATA of ICSU 1986 pp 81 82 Speed of light c 2 99792458 x 10 cm s Definition Boltzmann constant k R Na 1 380658 x 107 J K 1 380658 x 10719 erg K Planck constant h 6 6260755 x 10 94 J s 6 6260755 x 107 erg s Gas constant R 8 314510 J mol K 1 987216 cal mol K Avogadro number N 6 0221367 x 10 mol Volume of 1 mol of gas Vo 22 41410 1 mol at 1 atm 25 C lJTsdoxd0 eng 1 kcal 4 184 kJ Definition 1 eV 23 0606 kcal mol 1 a u 27 21135 eV mol 627 509 6 kcal mol 1 cm7 2 859144 cal mol Nahc 4 184 1 atm 1 01325 x 10 Pa 1 01325 x
195. o T then all kinetic energy turning points are printed If the flag for any other internal co ordinate is set to T then when that coordinate passes through an extremum that point Background will be printed As with the PRIORITYs the point will be calculated via a quadratic to minimize non linear errors N B Quadratics are unstable in the regions of inflection points in these circumstances linear interpolation will be used A result of this is that points printed in the region of an inflection may not correspond exactly to those requested This is not an error and should not affect the quality of the results Test of DRC verification of trajectory path Introduction Unlike a single geometry calculation or even a geometry optimization ver ification of a DRC trajectory is not a simple task In this section a rigorous proof of the DRC trajectory is presented it can be used both as a test of the DRC algorithm and as a teaching exercise Users of the DRC are asked to follow through this proof in order to convince themselves that the DRC works as it should Part 1 The nitrogen molecule For the nitrogen molecule and using MNDO the equilibrium distance is 1 103802 A the heat of formation is 8 276655 kcal mole and the vibrational frequency is 2739 6 cm For small displacements the energy curve versus distance is parabolic and the gradient curve is approximately linear as is shown in the following table A nitrogen molecule is th
196. o be done on the final RHF wavefunction This involves the following steps 1 The eigenvector matrix is divided by the square root of the overlap matrix S 2 The Coulson type density matrix P is formed 3 The overlap population is formed from P i j S 1 j 4 Half the off diagonals are added onto the diagonals NLLSQ C The gradient norm is to be minimized by Bartel s method This is a Non Linear Least Squares gradient minimization routine Gradient minimization will locate one of three possible points a A minimum in the energy surface The gradient norm will go to zero and the lowest five or six eigenvalues resulting from a FORCE calculation will be approximately zero b A transition state The gradient norm will vanish as in a but in this case the system is characterized by one and only one negative force constant 2 3 Definitions of keywords c A local minimum in the gradient norm space In this normally unwanted case the gradient norm is minimized but does not go to zero A FORCE calculation will not give the five or six zero eigenvalues characteristic of a stationary point While normally undesirable this is sometimes the only way to obtain a geometry For instance if a system is formed which cannot be characterized as an intermediate and at the same time is not a transition state but nonetheless has some chemical significance then that state can be refined using NLLSQ NOANCI W RHF open shell
197. o import the geometry then it will crash with the following error message 0 GAMESS UK Error requested archive file missing or empty It is possible to tell GAMESS UK which archive file to look for by setting the envirn ment variable archive to the name of the file before the job is run This shown below for the Bourne BASH shells archive myarchive export archive 0 1 GAMESS UK MOPAC Interface Page 3 This also allows one to use geometries stored in MOPAC archive files from previous runs by setting the archive environment variable to point to the relevant file and then inserting the GEOMETRY MOPAC directive in a standard GAMESS UK input file Page 4 MOPAC Manual Seventh Edition Dr James J P Stewart PUBLIC DOMAIN COPY NOT SUITABLE FOR PRODUCTION WORK January 1993 0 1 GAMESS UK MOPAC Interface This document is intended for use by developers of semiempirical programs and soft ware It is not intended for use as a guide to MOPAC All the new functionalities which have been donated to the MOPAC project during the period 1989 1993 are included in the program Only minimal checking has been done to ensure conformance with the donors wishes As a result this program should not be used to judge the quality of programming of the donors This version of MOPAC T is not supported and no attempt has been made to ensure reliable performance This program and documentation have been placed entirely in the public
198. o validate the new copy QCPE has a test suite of calculations If all tests are passed within the tolerances given in the tests then the new program can be called a valid version of MOPAC 6 Insofar as is practical the mode of submission of a MOPAC job should be preserved e g prompt MOPAC lt data set gt lt queue options gt Any changes which do not violate the FORTRAN 77 conventions and which users believe would be generally desirable can be sent to the author 1 4 Relationship of AMPAC and MOPAC In 1985 MOPAC 3 0 and AMPAC 1 0 were submitted to QCPE for distribution At that time AMPAC differed from MOPAC in that it had the AMI algorithm Additionally changes in some MNDO parameters in AMPAC made AMPAC results incompatable with MOPAC Versions 1 3 Subsequent versions of MOPAC in addition to being more highly debugged than Version 3 0 also had the AM1 method Such versions were compatible with AMPAC and with versions 1 3 of MOPAC In order to avoid confusion all versions of MOPAC after 3 0 include journal references so that the user knows unambiguously which parameter sets were used in any given job Since 1985 AMPAC and MOPAC have evolved along different lines In MOPAC I have endeavoured to provide a highly robust program one with only a few new features but which is easily portable and which can be relied upon to give precise if not very exciting answers At Austin the functionality of AMPAC has been enhanced by the
199. ods In MOPAC all sorts of weird and wonderful systems are calculated systems the authors of the convergers never dreamed of MOPAC uses a combination of all three convergers at times Normally only a quadratic damper is used If this message appears suspect first that the calculation might be faulty then if you feel confident use PL to monitor a single SCF Based on the SCF results either increase the number of allowed iterations default 200 or use PULAY or Camp King or a mixture If nothing works then consider slackening the SCF criterion This will allow heats of formation to be calculated with reasonable precision but the gradients are likely to be imprecise GEOMETRY TOO UNSTABLE FOR EXTRAPOLATION In a reaction path calculation the initial geometry for a point is calculated by quadratic extrapolation using the previous three points If a quadratic fit is likely to lead to an inferior geometry then the geometry of the last point calculated will be used The total effect is to slow down the calculation but no user action is recommended GRADIENT IS TOO LARGE TO ALLOW Before a FORCE calculation can be performed the gradient norm must be so small that the third and higher order components of energy in the force field are negligible If in Error messages produced by MOPAC the system under examination the gradient norm is too large the gradient norm will first be reduced using FLEPO unless LET has been specifi
200. of damping oscillations and intrinsically divergent equations can often be changed to intrinsically convergent form With slowly convergent systems the virtual M O energy levels can be moved to a more negative value The precise value of the shift used depends on the behavior of the iteration energy If it is dropping then the HOMO LUMO gap is reduced if the iteration energy rises the gap is increased rapidly 5 Pulay s method If requested when the largest change in density matrix elements on two consecutive iterations has dropped below 0 1 then routine CNVG is aban doned in favor of a multi Fock matrix interpolation This relies on the fact that the eigenvectors of the density and Fock matrices are identical at self consistency so P F 0 at SCF The extent to which this condition does not occur is a measure of the deviance from self consistency Pulay s method uses this relationship to calcu late that linear combination of Fock matrices which minimize P F This new Fock matrix is then used in the SCF calculation Under certain circumstances Pulay s method can cause very slow convergence but sometimes it is the only way to achieve a self consistent field At other times the procedure gives a ten fold increase in speed so care must be exercised in its use invoked by the keyword PULAY 6 The Camp King converger If all else fails the Camp King converger is just about guaranteed to work every time However it is time consu
201. of keywords illustrates various options KEYWORD DRC DRC 0 5 DRC 1 0 IRC IRC 4 IRC 1 KINETIC 1 DRC KINETIC 5 IRC 1 DRC KINETIC 4 DRC VELOCITY KINETIC 10 RESULTING ACTION The Dynamic Reaction Coordinate is calculated Energy is conserved and no initial impetus In the DRC kinetic energy is lost with a half life of 0 5 femtoseconds Energy is put into a DRC with an half life of 1 0 femtoseconds i e the system gains energy The Intrinsic Reaction Coordinate is calculated No initial impetus is given Energy not conserved The IRC is run starting with an impetus in the negative of the 4th normal mode direction The impetus is one quantum of vibrational energy The first normal mode is used in an IRC with the initial impetus being 1 0kcal mole In a DRC after the velocity is defined 5 kcal of kinetic energy is added in the direction of the initial velocity After starting with a 4 kcal impetus in the direction of the first normal mode energy is conserved Follow a DRC trajectory which starts with an initial velocity read in normalized to a kinetic energy of 10 kcal mol Instead of every point being printed the option exists to print specific points deter mined by the keywords T PRIORITY X PRIORITY and H PRIORITY If any one of these words is specified then the calculated points are used to define quadratics in time for all variables normally printed In addition if the flag for the first atom is set t
202. ok ok ok ok 2 FK FK FK ok K K ok K K ok ok oe oe FK FK FK K oko K 2 ok oe oe oe ok ok ok oe K K K oko oe FK FK FK ok oe oe K 2 eoe FK FK FK K K K K K K K gt K gt K gt K FRANK J SEILER RES LAB U S AIR FORCE ACADEMY COLO SPGS CO 80840 Kk kk k k ak k k oko ok ok ak K K ke ke ke 2k 2k koe 2K oj ok ok ke aK 2K K 2K 2K 2k ok oj ok K ke ok oko ok aK gt K ok ok ke ke 2K 2K ok jeje ke ke 2K K K 2K 2K 2K 2K 2K K K gt K 2K gt K MNDO CALCULATION RESULTS FEAR RIA RAI 3K aK aK 3K I ROK I A RIK I K aK 2K 21 aK 2K 3K 21 K a Fk 3K 2K gt K 3K 3K K K 3K K K FK 3K K 2K 2K K K FK K K 3K K K A K K 2K MOPAC VERSION 6 00 CALC D 12 0CT 90 T DUMP N FORCE PRECISE NOINTER ISOTOPE NOXYZ THERMO ROT o X X A TIME OF 2000 0 SECONDS REQUESTED RESTART FILE WRITTEN EVERY 8 0 SECONDS FORCE CALCULATION SPECIFTED CRITERIA TO BE INCREASED BY 100 TIMES INTERATOMIC DISTANCES NOT TO BE PRINTED Note 1 FORCE MATRIX WRITTEN TO DISK CHAN 9 CARTESIAN COORDINATES NOT TO BE PRINTED THERMODYNAMIC QUANTITIES TO BE CALCULATED SYMMETRY NUMBER OF 2 SPECIFIED KK KK KK K K K KK K K K FK FK FK K K FK FK K K FK FK FK K ok FK FK RAR FK ok K FK FK K K ARR FK FK FK K K FK FK K K K KK K K K K K K AOZOBYO40 NOINTER NOXYZ MNDO DUMP 8 T 2000 THERMO 298 298 FORCE ISOTOPE ROT 2 PRECISE DEMONSTRATION OF MOPAC FORCE AND THERMODYNAMICS CALCULATION FORMALDEHYDE MNDO ENERGY 32 8819 See Manual ATOM CHEMICAL BOND L
203. om Ay atom 6 28 To avoid the complication arising from the definition of Eset within the thermodynamics calculation the Standard Enthalpy of Formation AH is calculated by AH Est Hr Hogs 6 29 Here Es is the heat of formation at 25 degree C given in the output list and Hr and Hog are the enthalpy contributions for the increase of the temperature from 0 K to T and 298 15 respectively In other words the enthalpy of formation is corrected for the 6 10 A note on thermochemistry difference in temperature from 298 15 K to T The method of calculation for T and Ho9g will be given below In MOPAC the variables defined below are used Ci ne 6 30 The wavenumber w in cm7 Vi WiC 6 31 Ew exp hvi kT exp wihc kT exp w C1 6 32 The rotational constants A B and C in cm7 Gus 6 33 Energy and Enthalpy in cal mol and Entropy in cal mol K Thus eqs 6 2 6 27 can be written as follows Vibration Qib te EG 6 34 0 5Nahc Eo 184x107 zu 1099 E 142952 os 6 36 u ui EWJ E WiEws Evin 0 T Nahe 1 Ew Raica fa eae Ewy 6 37 wi hwy Sup R he kT ees RX h 1 E ROM TER RM In 1 Ewy 6 38 2p E kT MEETS Cab R hc A 1 m Ewj 2 Ew Odo NC pa 6 39 Xa Res ios Rotation Linear molecule 1 Qiu 1 o 1 AY kT hc AC 6 40 Et 2 2 RT 6 41 kT 1 kT Spore Rin h x R Rin m R Rin R 6 42 Crot 2 2 R
204. oms after releasing them from a starting interatomic separation of 1 094 A At R N N 1 094 A G 44 810 kcal mole or 18 749 x 101 erg cm Therefore acceleration f 18 749 x 10 9 14 0067 cm sec sec or 13 386 x 1018 cm s which is 13 386 x 1015x Earth surface gravity Distance from equilibrium 0 00980 A After 0 1 fs velocity is 0 110 5 13 38610 8 cm sec or 1338 6 cm s In the DRC the time interval between points calculated is a complicated function of the curvature of the local surface By default the first time interval is 0 105fs so the calculated velocity at this time should be 0 105 x 1338 6 1405 6 cm s in the DRC calculation the predicted velocity is 1405 6 cm s The option is provided to allow sampling of the system at constant time intervals the default being 0 1 fs For the first few points the calculated velocities are as follows TIME CALCULATED LINEAR DIFF VELOCITY VELOCITY VELOCITY 0 000 0 0 0 0 0 0 0 100 1338 6 1338 6 0 0 0 200 2673 9 2677 2 3 3 0 300 4001 0 4015 8 14 8 0 400 5317 3 5354 4 37 1 0 500 6618 5 6693 0 74 5 0 600 7900 8 8031 6 130 8 As the calculated velocity is a fourth order polynomial of the acceleration and the acceleration its first second and third derivatives are all changing the predicted velocity rapidly becomes a poor guide to future velocities For simple harmonic motion the velocity at any time is given by v vo sin 2rt r By fitting the computed ve
205. onent of a doublet a quartet and a sextet The coefficients of these states can be calculated from the Clebsch Gordon 3 J symbol For example the coefficient in the sextet is 1 4 5 Microstate 4 is a pure sextet If all 100 microstates of component of spin 1 2 were used in a C I one of the resulting states would have the same energy as the state resulting from microstate 4 Microstate 5 is an excited doublet and microstate 6 is an excited state of the system but not a pure spin state By default if n M O s are included in the MECI then all possible microstates which give rise to a component of spin 0 for even electron systems or 1 2 for odd electron systems will be used Permutations of Electrons among Molecular Orbitals 0 1 0 2 4 1100 3 5 11100 2 5 11000 1010 11010 10100 um a i 1001 11001 10010 0110 10110 10001 0 2 0 0101 10101 01100 0011 10011 01010 1 2 10 01110 01001 Background 01 1 4 1000 01101 00110 0100 01011 00101 1 3 100 0010 00111 00011 010 0001 001 2 3 110 101 011 Sets of Microstates for Various MECI Calculations Odd Electron Systems Even Electron Systems Alpha Beta No of Alpha Beta No of Configs Configs C I 1 1 1 0 1 1 1 1 1 1 1 2 1 2 0 2 2 1 2 1 2 4 3 2 3 1 3 9 2 3 2 3 9 4 2 4 1 4 24 2 4 2 4 36 5 3 5 2 5 100 3 5 3 5 100 Multi electron configuration interaction
206. otal energy of the mode E is calculated 5 3 Example of reaction path with symmetry as a percentage This is the absolute contribution A as a percentage to the total energy of the mode 100 x P A B Now the C O is seen to contribute 100 5 percent of the energy For this sort of partitioning only the sum of all A s must add to 100 each pair can contribute more or less than 100 In the case of a free rotator e g ethane the A of any specific bonded pair to the total energy can be very high several hundred percent It may be easier to view P F as a contribution to the total energy of the mode E In this case the fact that P E can be greater than unity can be explained by the fact that there are other relative motions within the molecule which make a negative contribution to Ey From the s an idea can be obtained of where the energy of the mode is going from the A value the significance of the highest contribution can be inferred Thus in mode 4 all three bonds are excited but because the C O bond carries about 100 of the energy it is clear that this is really a C O bond stretch mode and that the hydrogens are only going along for the ride In the last column the percentage radial motion is printed This is useful in assigning the mode as stretching or bending Any non radial motion is de facto tangential or bending To summarize The new analysis is more difficult to understand but is considered by the author JJPS
207. ould just be standard GAMESS UK directives To use the geometry from a MOPAC run in a GAMESS UK job the flag MOPAC should be appended to the GAMESS UK GEOMETRY keyword as demonstrated in the example below The input for this example is the file mopac 2 in mopac prec density local vect mullik pi bonds xyz graph pm3 out gamess acetone dat 0008 1 2166 0001 0 0214 0001 0 0000 0001 0000 0000 0000 0006 0 0028 0001 0 0032 0001 0 0000 0001 0000 0000 0000 0006 0 7539 0001 1 3084 0001 0 0000 0001 0000 0000 0000 0006 0 7915 0001 1 2794 0001 0 0000 0001 0000 0000 0000 0001 0 5285 0001 1 8623 0001 0 8951 0001 0000 0000 0000 0001 0 5285 0001 1 8623 0001 0 8951 0001 0000 0000 0000 0001 1 8767 0001 1 0977 0001 0 0000 0001 0000 0000 0000 0001 1 3862 0001 1 3756 0001 0 8976 0001 0000 0000 0000 0001 1 3862 0001 1 3756 0001 0 8976 0001 0000 0000 0000 0001 0 0485 0001 2 1532 0001 0 0000 0001 0000 0000 0000 gamess title acetone 6 31g geometry optimisation from mopac starup nosym geometry mopac basis 6 31g runtype optxyz xtol 0 003 enter Specifying the archive file to use By default MOPAC will create an archive file called archive containing the coordinates and this is what GAMESS UK will expect to find If however a file named archive already exists in the directory MOPAC will create one called archiveaa or if this exists one called archiveab etc If an archive file called archive cannot be found when GAMESS UK attempts t
208. program Main arguments on input geometry on output heat of formation gradients DANG Utility Called by XYZINT DANG computes the angle between a point the origin and a second point DATIN Utility Reads in external parameters for use within MOPAC Originally used for the testing of new parameters DATIN is now a general purpose reader for parameters Invoked by the keyword EXTERNAL DCART Utility Called by DERIV DCART sets up a list of cartesian derivatives of the energy wrt coordinates which DERIV can then use to construct the internal coordinate derivatives DELMOL Utility Part of analytical derivates Two electron DELRI Utility Part of analytical derivates Two electron DENROT Utility Converts the ordinary density matrix into a condensed density matrix over basis functions s sigma p sigma and p pi i e three basis functions Useful in hybridization studies Has capability to handling d functions if present DENSIT Utility Constructs the Coulson electron density matrix from the eigen vectors Main arguments Eigenvectors No of singly and doubly occupied levels density matrix empty on input Called by ITER DEPVAR Utility A symmetry defined bond length is related to another bond length by a multiple This special symmetry function is intended for use in Cluster calculations Called by HADDON DERIO Utility Part of the analytical C I derivative package Calculates the diag onal dominant part o
209. re printed by default If you do not want them to be printed specify NOXYZ For big jobs this reduces the output file considerably NSURE C In an ESP calculation NSURF n specifies the number of surface layers for the Connolly surface Keywords OLDENS W A density matrix produced by an earlier run of MOPAC is to be used to start the current calculation This can be used in attempts to obtain an SCF when a previous calculation ended successfully but a subsequent run failed to go SCF OLDGEO C If multiple geometries are to be run and the final geometry from one calculation is to be used to start the next calculation OLDGEO should be specified Example If a MNDO AM1 and PMS3 calculation were to be done on one system for which only a rough geometry was available then after the MNDO calculation the AMI calculation could be done using the optimized MNDO geometry as the starting geometry by specifying OLDGEO OPEN n1 n2 C The M O occupancy during the SCF calculation can be defined in terms of doubly occ upied empty and fractionally occupied M O s The fractionally occupied M O s are defined by OPEN n1 n2 where nl number of electrons in the open shell manifold and n2 number of open shell M O s n1 n2 must be in the range 0 to 2 OPEN 1 1 will be assumed for odd electron systems unless an OPEN keyword is used Errors introduced by use of fractional occupancy are automatically corrected in a MECI calculat
210. re read in but the calculation is to be carried out using cartesian coordinates then either all possible geometric variables must be optimized or none can be optimized If only some are marked for optimization then ambiguity exists For example if the bond length of atom 6 is marked for optimization but the angle is not then when the conversion to cartesian coordinates takes place the first coordinate becomes the X coordinate and the second the Y coordinate These bear no relationship to the bond length or angle This is a fatal error INTERNAL COORDINATES READ IN AND SYMMETRY If internal coordinates are read in but the calculation is to be carried out using cartesian coordinates then any symmetry relationships between the internal coordinates will not be reflected in the cartesian coordinates For example if the bond lengths of atoms 5 and 6 are equal it does not follow that these atoms have equal values for their X coordinates This is a fatal error JOB STOPPED BY OPERATOR Any MOPAC calculation for which the SHUTDOWN command works can be stopped by a user who issues the command SHUT filename from the directory which contains filename DAT Error messages produced by MOPAC MOPAC will then stop the calculation at the first convenient point usually after the current cycle has finished A restart file will be written and the job ended The message will be printed as soon as it is detected whi
211. re simple functions of the geometry of the system and are usually predicted with very high accuracy Note 4 Zero point energy is already factored into the MNDO parameterization Force constant data are not printed by default If you want this output specify LARGE in the keywords Note 5 Normal coordinate analysis has been extensively changed The first set of eigen vectors represent the normalized motions of the atoms The sum of the speeds not the velocities of the atoms adds to unity This is verified by looking at the motion in the z direction of the atoms in vibration 2 Simple addition of these terms unsigned adds to 1 0 whereas to get the same result for mode 1 the scalar of the motion of each atom needs to be calculated first Users might be concerned about reproducibility As can be seen from the vibrational frequencies from Version 3 00 to 6 00 given below the main difference over earlier FORCE calculations is in the trivial frequencies Real Frequencies of Formaldehyde Version 3 00 1209 96 1214 96 1490 60 2114 57 3255 36 3301 57 Version 3 10 1209 99 1215 04 1490 59 2114 57 3255 36 3301 58 Version 4 00 1209 88 1214 67 1490 52 2114 52 3255 92 3302 10 Version 5 00 1209 89 1214 69 1490 53 2114 53 3255 93 3302 10 Testdata Version 6 00 1209 90 1214 67 1490 53 2114 54 3255 94 3302 12 Trivial Frequencies of Formaldehyde T x T T z R x RCy R z Version 3 00 0 00517 0 00054 0 00285 57 31498 11 59518 9 0161
212. red in order to more clearly document the calculation and to obviate the possibility that an abbreviated keyword might not be recognized If there is insufficient space in the first line for all the keywords needed then consider abbreviating the longer words One type of keyword those with an equal sign such as BAR 0 05 may not be abbreviated and the full word needs to be supplied Most keywords which involve an equal sign such as SCFCRT 1 D 12 can at the user s discretion be written with spaces before and after the equal sign Thus all permuta tions of SCFCRT 1 D 12 such as SCFCRT 1 D 12 SCFCRT 1 D 12 SCFCRT 1 D 12 SCFCRT 1 D 12 etc are allowed Exceptions to this are T T PRIORITY H PRIORITY X PRIORITY IRC DRC and TRANS T cannot be abbre viated to T as many keywords start or end with a I for the other keywords the associated abbreviated keywords have specific meanings If two keywords which are incompatible like UHF and C I are supplied or a keyword which is incompatible with the species supplied for instance TRIPLET and a methyl radical then error trapping will normally occur and an error message will be printed This usually takes an insignificant time so data are quickly checked for obvious errors 2 2 Full list of keywords used in MOPAC amp TURN NEXT LINE INTO KEYWORDS ADD ANOTHER LINE OF KEYWORDS OSCF READ IN DATA THEN STOP 1ELECTRON PRINT FINAL ONE ELECTRON
213. red fixed that is they will not be optimized The set before the blank line will be optimized Example of Gaussian Z matrix geometry specification Line 1 AM1 Line 2 Ethane Line 3 Line 4 C Line 5 C 1 r21 Line 6 H 2 r32 1 a321 Line 7 H 2 r32 1 a321 3 d4213 Line 8 H 2 r32 1 a321 3 d4213 Line 9 H 1 r32 2 a321 3 60 Line 10 H 1 r32 2 a321 3 180 Line 11 H 1 r32 2 a321 3 d300 Line 12 Line 13 r21 1 5 Line 14 r32 1 1 Line 15 a321 109 5 Line 16 d4313 120 0 Line 17 Line 18 d300 300 0 Line 19 3 3 Cartesian coordinate definition A definition of geometry in cartesian coordinates consists of the chemical symbol or atomic number followed by the cartesian coordinates and optimization flags but no connectivity MOPAC uses the lack of connectivity to indicate that cartesian coordinates are to be used A unique case is the triatomics for which only internal coordinates are allowed This is to avoid conflict of definitions the user does not need to define the connectivity of atom 2 and can elect to use the default connectivity for atom 3 As a result a triatomic may have no explicit connectivity defined the user thus taking advantage of the default connectivity Since internal coordinates are more commonly used than cartesian the above choice was made If the keyword XYZ is absent every coordinate must be marked for optimization If any coordinates are not to be optimized the keyword XYZ must be present The coordinates of all
214. rivatives If the default values are to be reset then the new value is supplied in KEYWRD and extracted via INDEX and READA The flow of control is decided by the presence of various keywords in KEYWRD When a subroutine is called it assumes that all data required for its operation are available in either common blocks or arguments Normally no check is made as to the validity of the data received All data are owned by one and only one subroutine Ownership means the implied permission and ability to change the data Thus MOLDAT owns the number of atomic orbitals in that it calculates this number and stores it in the variable NORBS Many subroutines use NORBS but none of them is allowed to change it For obvious reasons no exceptions should be made to this rule To illustrate the usefulness of this convention consider the eigenvectors C and CBETA These are owned by ITER Before ITER is called C and CBETA are not calculated after ITER has been called C and CBETA are known so any subroutine which needs to use the eigenvectors can do so in the certain knowledge that they exist Any variables which are only used within a subroutine are not passed outside the subroutine unless an overriding reason exists This is found in PULAY and CNVG among others where arrays used to hold spin dependent data are used and these cannot conveniently be defined within the subroutines In these examples the relevant arrays are owned by ITER
215. rix is printed For UHF the sum of the alpha and beta density matrices is printed If density is not requested then the diagonal of the density matrix i e the electron density on the atomic orbitals will be printed DEP O For use only with EXTERNAL When new parameters are published they can be entered at run time by using EXTERNAL but as this is somewhat clumsy a permanent change can be made by use of DEP If DEP is invoked a complete block of FORTRAN code will be generated and this can be inserted directly into the BLOCK DATA file Note that the output is designed for use with PM3 By modifying the names the output can be used with MNDO or AMI DEPVAR n nn C In polymers the translation vector is frequently a multiple of some internal distance For example in polythene it is the C1 C3 distance If a cluster unit cell of C6H12 is used then symmetry can be used to tie together all the carbon atom coordinates and the translation vector distance In this example DEPVAR 3 0 would be suitable Keywords DFP W By default the Broyden Fletcher Goldfarb Shanno method will be used to optimize ge ometries The older Davidon Fletcher Powell method can be invoked by specifying DFP This is intended to be used for comparison of the two methods DIPOLE C Used in the ESP calculation DIPOLE will constrain the calculated charges to reproduce the cartesian dipole moment components calculated from the density matrix and
216. s do not need to be calculated At the same time there is a risk that the geometry may be wrongly specified e g if methane radical cation is defined as being tetrahedral no indication that this is faulty will be given until a FORCE calculation is run This system undergoes spontaneous Jahn Teller distortion Usually a lower heat of formation can be obtained when SYMMETRY is specified To see why consider the geometry of benzene If no assumptions are made regarding the geometry then all the C C bond lengths will be very slightly different and the angles will be almost but not quite 120 degrees Fixing all angles at 120 degrees dihedrals at 180 or 0 degrees and only optimizing one C C and one C H bond length will result in a 2 D optimization and exact Dg symmetry Any deformation from this symmetry must involve error so by imposing symmetry some error is removed The layout of the symmetry data is defining atom symmetry relation defined atom defined atom gt where the numerical code for symmetry relation is given in the table of symmetry functions below For example ethane with three independent variables can be defined as SYMMETRY ETHANE D3D NA NB NC C C 1 528853 1 1 H 1 105161 1 110 240079 1 2 1 H 1 105161 0 110 240079 0 120 000000 0 2 1 3 H 1 105161 0 110 240079 0 240 000000 0 2 1 3 H 1 105161 O 110 240079 O 60 000000 0 1 2 3 H 1 105161 0 110 240079 0 180 000000 0 1 2 3 H 1 105161 0 110 240079 0 300
217. s in geometry in character mode from specified channel and stores parameters in arrays Some error checking is done Called by READ and REACTI GETSYM Utility Reads in symmetry data Used by READ GETTXT Utility Reads in KEYWRD KOMENT and TITLE GETVAL Utility Called by GETGEG GETVAL either gets an internal coordinate or a logical name for that coordinate GMETRY Utility Fills the cartesian coordinates array Data are supplied from the array GEO GEO can be a in internal coordinates or b in cartesian coordinates If STEP is non zero then the coordinates are modified in light of the other geometry and STEP Called by HCORE DERIV READ WRITE MOLDAT etc GOVER Utility Calculates the overlap of two Slater orbitals which have been expanded into six gaussians Calculates the STP 6G overlap integrals GRID Main Sequence Calculates a grid of points for a 2 D search in coordinate space Useful when more information is needed about a reaction surface HIELEC Utility Given any two atoms in cartesian space HIELEC calculates the one electron energies of the off diagonal elements of the atomic orbital matrix H i j S i 3 8 i 8 3 2 Called by HCORE and DERIV HADDON Utility The symmetry operation subroutine HADDON relates two ge ometric variables by making one a dependent function of the other Called by SYMTRY only HCORE Main sequence Sets up the energy terms used in calculating the SCF heat of formation Calcu
218. sotopes If a user wishes to specify any specific isotope it should immediately follow the chemical symbol no space e g H2 H2 0140 C meta 13 or C13 00335 The sparkles and have no mass if they are to be used in a force calculation then appropriate masses should be used Each internal coordinate is followed by an integer to indicate the action to be taken Integer Action 1 Optimize the internal coordinate 0 Do not optimize the internal coordinate zl Reaction coordinate or grid index Remarks Only one reaction coordinate is allowed but this can be made more versatile by the use of SYMMETRY If a reaction coordinate is used the values of the reaction coordinate should follow immediately after the geometry and any symmetry data No terminator is required and free format type input is acceptable If two reaction coordinates are used then MOPAC assumes that the two dimensional space in the region of the supplied geometry is to be mapped The two dimensions to be mapped are in the plane defined by the 1 labels Step sizes in the two directions must be supplied using STEP1 and STEP2 on the keyword line Using internal coordinates the first atom has three unoptimizable coordinates the second atom two the bond length can be optimized and the third atom has one un optimizable coordinate None of these six unoptimizable coordinates at the start of the geometry should be marked for optimization If any ar
219. specifying PRECISE or FORCE It can be over ridden by explicitly defining the SCF criterion via SCFCRT 1 D 12 SELCON is further modified by the value of the gradient norm if known If GNORM is large then a more lax SCF criterion is acceptable and SCFCRT can be relaxed up to 50 times it s default value As the gradient norm drops the SCF criterion returns to its default value The SCF test is performed using the energy calculated from the Fock matrix which arises from a density matrix and not from the density matrix which arises from a Fock In the limit the two energies would be identical but the first converges faster than the second without loss of precision 6 6 Convergence in SCF calculation A brief description of the convergence techniques used in subroutine ITER follows ITER the SCF calculation employs six methods to achieve a self consistent field In order of usage these are 1 Intrinsic convergence by virtue of the way the calculation is carried out Thus a trial Fock gives rise to a trial density matrix which in turn is used to generate a better Fock matrix This is normally convergent but many exceptions are known The main situations when the intrinsic convergence does not work are a A bad starting density matrix This normally occurs when the default starting density matrix is used This is a very crude approximation and is only used to Background get the calculation started A large charge is genera
220. supplied with earlier copies of MOPAC 3 5 Definition of elements and isotopes Elements are defined in terms of their atomic numbers or their chemical symbols case insensitive Thus chlorine could be specified as 17 or Cl In Version 6 only main group elements and transition metals for which the d shell is full are available Acceptable symbols for MNDO are Elements Dummy atom sparkles and Translation Vector H Li B C N 0 F Na Al Si P SCl o K Zn Ge Br XX Cb Tv Rb Sn I 99 102 103 104 105 106 107 Ox Hg Pb These symbols refer to elements which lack a basis set This is the dummy atom for assisting with geometry specification Element not parameterized This is the translation vector for use with polymers O Old parameters for some elements are available These are provided to allow com patibility with earlier copies of MOPAC To use these older parameters use a keyword composed of the chemical symbol followed by the year of publication of the parameters Keywords currently available 811978 1978 For AM1 acceptable symbols are Elements Dummy atom sparkles and Translation Vector H B C N 0 F Na Al Si P SCl o K Zn Ge Br XX Cb Tv Rb Sn I 99 102 103 104 105 106 107 Ox Hg If users need to use other elements such as beryllium or lead they can be specified in which case MNDO type atoms will be used As t
221. t variable gt n nnn where variable is a mnemonic such as SCFCRT or CHARGE Called by READ FLEPO ITER FORCE and many other subroutines e REFER Utility Prints the original references for atomic data If an atom does not have a reference i e it has not been parameterized then a warning message will be printed and the calculation stopped e REPP Utility Calculates the 22 two electron reduced repulsion integrals and the 8 electron nuclear attraction integrals These are in a local coordinate system Arguments atomic numbers of the two atoms interatomic distance and arrays to hold the calculated integrals Called by ROTATE only e ROTAT Utility Rotates analytical two electron derivatives from atomic to molec ular frame e ROTATE Utility All the two electron repulsion integrals the electron nuclear attraction integrals and the nuclear nuclear repulsion term between two atoms are calculated here Typically 100 two electron integrals are evaluated e RSP Utility Rapid diagonalization routine Accepts a secular determinant and produces a set of eigenvectors and eigenvalues The secular determinant is destroyed e SAXPY Utility Called by the utility SUPDOT only Description of subroutines SCHMIB Utility Part of Camp King converger SCHMIT Utility Part of Camp King converger SCOPY Utility Copies an array into another array SDOT Utility Forms the scalar of the product of two vectors SEARCH Utility Part of
222. tation Vol 24 pp 647 656 1970 See also summary in Shanno D F J of Optimization Theory and Applications Vol 46 No 1 pp 87 94 1985 On Polarizability Calculation of Nonlinear Optical Properties of Molecules H A Kurtz J J P Stewart K M Dieter J Comp Chem 11 82 1990 See also Semiempirical Calculation of the Hyperpolarizability of Polyenes H A Kurtz I J Quant Chem Symp 24 xxx 1990 On Thermodynamics Ground States of Molecules 44 MINDO 3 Calculations of Absolute Heat Capacities and Entropies of Molecules without Internal Rotations Dewar M J S Ford G P J Am Chem Soc 99 7822 1977 On SIGMA Method Komornicki A McIver J W Chem Phys Lett 10 303 1971 Komornicki A McIver J W J Am Chem Soc 94 2625 1971 On Molecular Orbital Valency Valency and Molecular Structure Gopinathan M S Siddarth P Ravimohan C Theor Chim Acta 70 303 1986 On Bonds Bond Indices and Valency Armstrong D R Perkins P G Stewart J J P J Chem Soc Dalton 838 1973 For a second equivalent description see also Gopinathan M S and Jug K Theor Chim Acta 63 497 1983 On Locating Transition States Location of Transition States in Reaction Mechanisms M J S Dewar E F Healy J J P Stewart J Chem Soc Faraday Trans II 3 227 1984 On Dipole Moments for Ions Molecular Quadrupole Moments A D Buckingham Quar
223. ted on an atom in the first iteration the second iteration overcompensates and an oscillation is generated b The equations are only very slowly convergent This can be due to a long lived oscillation or to a slow transfer of charge 2 Oscillation damping If on any two consecutive iterations a density matrix element changes by more than 0 05 then the density matrix element is set equal to the old element shifted by 0 05 in the direction of the calculated element Thus if on iterations 3 and 4 a certain density matrix element was 0 55 and 0 78 respectively then the element would be set to 0 60 0 55 0 05 on iteration 4 The density matrix from iteration 4 would then be used in the construction of the next Fock matrix The arrays which hold the old density matrices are not filled until after iteration 2 For this reason they are not used in the damping before iteration 3 3 Three point interpolation of the density matrix Subroutine CNVG monitors the number of iterations and if this is exactly divisible by three and certain other conditions relating to the density matrices are satisfied a three point interpolation is performed This is the default converger and is very effective with normally convergent calculations It fails in certain systems usually those where significant charge build up is present 4 Energy level shift technique The virtual M O energy levels are normally shifted to more positive energy This has the effect
224. terly Reviews 182 1958 or 1959 References On Polymers MNDO Cluster Model Calculations on Organic Polymers J J P Stewart New Poly meric Materials 1 53 61 1987 Calculation of Elastic Moduli using Semiempirical Methods H E Klei J J P Stewart Int J Quant Chem 20 529 540 1986
225. the author of the changes is obviously responsible for removing the offending bug and the following ideas might prove useful in this context First of all and most important before any modifications are done a back up copy of the standard MOPAC should be made This will prove invaluable in pinpointing deviations from the standard working This point cannot be over emphasized make a back up before modifying MOPAC Clearly a bug can occur almost anywhere and a logical search sequence is necessary in order to minimize the time taken to locate it If possible perform the debugging with a small molecule in order to save time de bugging is of necessity time consuming and to minimize output The two sets of subroutines in MOPAC those involved with the electronics and those involved in the geometrics are kept strictly separate so the first question to be answered is which set contains the bug If the heats of formation derivatives I P s and charges etc are correct the bug lies in the geometrics if faulty in the electronics Bug in the Electronics Subroutines Use formaldehyde for this test The supplied data file MNRSD1 DAT could be used as a template for this operation Use keywords 1SCF DEBUG and any others necessary The main steps are 1 Check the starting one electron matrix and two electron integral string using the keyword HCORE It is normally sufficient to verify that the two hydrogen atoms are equivalent and t
226. the first term in equation 6 4 is the Zero point vibration energy Hence the second term in eq 6 4 is the additional vibrational contribution due to the temperature increase from 0 K to T K Namely Eyib Ezero Eyib 0 T T 6 5 hvi Ezero Na 2 3 Eu 0 T Ng 2 6 6 hv exp hvi kT 1 exp hvi KkT on The value of Eyip from GAUSSIAN 82 and 86 includes Ezero as defined by Eqs 6 4 6 7 RY hvj KT exp hinj kT 1 exp hvii kT 3 hy kT exp hv KT ea n 1 exp hvj KT At temperature T gt 0 K a molecule rotates about the x y and z axes and translates in x y and z directions By assuming the equipartition of energy energies for rotation and translation Erot and Es are calculated S vib In 1 exp hwfkr 6 8 6 9 Rotation c is symmetry number J is moment of inertia I4 Ig and Ic are moments of inertia about A B and C axes Linear molecule 8r IkT Tro wl Q t ch2 6 0 Et 2 2 RT 6 11 87 IkT Srot Rin or R 6 12 RinI Rln T Rlno 4 349203 where 4 349203 R1n 8 x 10 l z k N4h2 R Crot 2 2 R 6 13 Non linear molecule 3 2 8r kT Qrot 4 E v IAIplc e f Sy2erAY 87 cIp 85201 V t T B c h h h hc Ert 3 2 RT 6 15 So ain 3 a mee 3 2 R 6 16 R 2 In I4IpIc 3 2 RIn T Rino 5 3863921 Here 5 3863921 is calculated as
227. the virtual M O s are changed in energy relative to the occupied set then the polarizability of the occupied M O s will change pro rata Normally oscillations are due to autoregenerative charge fluctuations The SHIFT method has been re written so that the value of SHIFT changes automat ically to give a critically damped system This can result in a positive or negative shift of the virtual M O energy levels If a non zero SHIFT is specified it will be used to start the SHIFT technique rather than the default 15eV If SHIFT O is specified the SHIFT technique will not be used unless normal convergence techniques fail and the automatic ALL CONVERGERS message is produced SIGMA C The McIver Komornicki gradient norm minimization routines POWSQ and SEARCH are to be used These are very rapid routines but do not work for all species If the gradient Keywords norm is low i e less than about 5 units then SIGMA will probably work in most cases NLLSQ is recommended SIGMA first calculates a quite accurate Hessian matrix a slow step then works out the direction of fastest decent and searches along that direction until the gradient norm is minimized The Hessian is then partially updated in light of the new gradients and a fresh search direction found Clearly if the Hessian changes markedly as a result of the line search the update done will be inaccurate and the new search direction will be faulty SIGMA should be avoi
228. third line of keywords would be read in If the first line has a amp then the first description line is omitted if the second line has a amp then both description lines are omitted Examples Use of one amp VECTORS DENSITY RESTART amp NLLSQ T 1H SCFCRT 1 D 8 DUMP 30M ITRY 300 PM3 FOCK OPEN 2 2 ROOT 3 SINGLET SHIFT 30 Test on a totally weird system Use of two amp s LARGE 10 amp DRC 4 0 T 1H SCFCRT 1 D 8 DUMP 30M ITRY 300 SHIFT 30 PM3 OPEN 2 2 ROOT 3 SINGLET NOANCI ANALYT T PRIORITY 0 5 amp LET GEO OK VELOCITY KINETIC 5 0 2 3 Definitions of keywords C A sign means read another line of keywords Note the space before the sign Since is a keyword it must be preceeded by a space A on line 1 would mean that a second line of keywords should be read in If that second line contains a u then a third line of keywords will be read in Regardless of whether a second or a third line of keywords is read in the next two lines would be description lines Example of u option RESTART T 4D FORCE OPEN 2 2 SHIFT 20 PM3 SCFCRT 1 D 8 DEBUG ISOTOPE FMAT ECHO singlet ROOT 3 THERMO 300 400 1 ROT 3 Example of data set with three lines of keywords Note There are two lines of description this and the previous line OSCF O The data can be read in and output but no actual calculation is performed when this keyword is used This is useful as
229. tical C I derivatives Because they are so much more efficient and accurate than finite differences and because computer memory is becoming more available this increase was accepted as the lesser of two evils The size of MOPAC executables will vary from machine to machine due to the different sizes of the code For a VAX this amounts to approximately 0 1Mb Most machines use a 64 bit or 8 byte double precision real number so the multipliers of N and N N should apply to them For large jobs 0 1Mb is negligible therefore the above expression should be applicable to most computers No of lines in program in Version 5 00 22 084 17 718 code 4 366 comment Version 6 00 31 857 22 526 code 9 331 comment Appendix A Names of FORTRAN 77 files AABABC ANALYT ANAVIB AXIS BLOCK BONDS BRLZON CALPAR CAPCOR CDIAG CHRGE CNVG COMPFG DATIN DCART DELMOL DELRI DENROT DENSIT DEPVAR DERIO DERI1 DERI2 DERI21 DERI22 DERI23 DERITR DERIV DERNVO DERS DFOCK2 DFPSAV DIAG DIAT DIAT2 DIIS DIJKL1 DIJKL2 DIPIND DIPOLE DOFS DOT DRC DRCOUT EF ENPART EXCHNG FFHPOL FLEPO FMAT FOCK1 FOCK2 FORCE FORMXY FORSAV FRAME FREQCY GEOUT GEOUTG GETGEG GETGEO GETSYM GETTXT GMETRY GOVER GRID HiELEC HADDON JHCORE HELECT HQRII IJKL INTERP ITER JCARIN LINMIN LOCAL LOCMIN MAMULT MATOUT MATPAK MECI MECID MECIH MECIP MNDO MOLDAT MOLVAL MULLIK MULT NLLSQ NUCHAR PARSAV PARTXY PATHK PATHS PERM POLAR POWSAV POWSQ PRTDRC QUADR REACT1 READ READA RE
230. tions are about the principal axes of inertia for the system taking into account isotopic masses The force matrix for these trivial vibrations is determined and added on to the calculated force matrix After diagonalization the arbitrary eigenvalues are subtracted off the trivial vi brations and the resulting numbers are the true values Interference with genuine vibrations is thus avoided 6 14 Configuration interaction MOPAC contains a very large Multi Electron Configuration Interaction calculation MECI which allows almost any configuration interaction calculation to be performed Because of its complexity two distinct levels of input are supported the default values will be of use to the novice while an expert has available an exhaustive set of keywords from which a specific C I can be tailored A MECI calculation involves the interaction of microstates representing specific per mutations of electrons in a set of M O s Starting with a set electronic configuration either closed shell or open shell but unconditionally restricted Hartree Fock the first step in a MECI calculation is the removal from the M O s of the electrons to be used in the C I Each microstate is then constructed from these empty M O s by adding in electrons according to a prescription The energy of the configuration is evaluated as is the energy of interaction with all previously defined configurations Diagonalization then results in Backgro
231. to 1 This saves memory but also disables the PULAY converger If you want MESP can be varied This is only meaningful if ESP is installed Compile MOPAC This operation takes about 7 minutes and should be run on line as a question and answer session is involved When everything is successfully compiled the object files will then be assembled into an executable image called MOPAC EXE Once the image exists there is no reason to keep the object files and if space is at a premium these can be deleted at this time If you need to make any changes to any of the files COMPILE followed by the names of the changed files will reconstruct MOPAC provided all the other OBJ files exist For example if you change the version number in DIMSIZES DAT then READ FOR and WRITE FOR are affected and will need to be recompiled This can be done using the command COMPILE WRITE READ In the unlikely event that you want to link only use the command COMPILE LINK Sometimes the link stage will fail and give the message UALINK E INSVIRMEM insufficient virtual memory for 2614711 pages LINK E NOIMGFIL image file not created or your MOPAC will not run due to the size of the image In these cases you should ask the system manager to alter your PGFLQUO and WSEXTENT limits Possibly the system limits VIRTUALPAGECNT CURRENT and MAX will need to be changed As an example on a Microvax 3600 with 16Mb of memory PGFLQUO0 50000 WSEXTENT 16000 VIRTUALPA
232. to about 0 000001 A If ANALYT is also used the results obtained will be slightly different Chemically this change is meaningless and no significance should be attached to such numbers In addition any minor change to the algorithm such as porting it to a new machine will give rise to small changes in the optimized geometry Even the small changes involved in going from MOPAC 5 00 to MOPAC 6 00 caused small changes in the optimized geometry of test molecules As a guide GNORM of 0 1 is sufficient for all heat of formation work and GNORM of 0 01 for most geometry work If the system is large you may need to settle for a GNORM of 1 0 0 5 This whole topic was raised by Dr Donald B Boyd of Lilly Research Laboratories who provided unequivocal evidence for a failure of MOPAC and convinced me of the importance of increasing precision in certain circumstances 6 5 Convergence tests in subroutine ITER Self consistency test The SCF iterations are stopped when two tests are satisfied These are 1 when the difference in electronic energy in eV between any two consecutive iterations drops below the adjustable parameter SELCON and the difference between any three consecutive it erations drops below ten times SELCON and 2 the difference in density matrix elements on two successive iterations falls below a preset limit which is a multiple of SELCON SELCON is set initially to 0 0001 kcal mole this can be made 100 times smaller by
233. to the potential energy only The IRC is intended for use starting with the transition state geometry A normal coordinate is chosen usually the reaction coordinate and the system is displaced in either the positive or negative direction along this coordinate The internal modes are obtained by calculating the mass weighted Hessian matrix in a force calculation and translating the resulting cartesian normal mode eigenvectors to conserve momentum That is the initial cartesian coordinates are displaced by a small amount proportional to the eigenvector coefficients plus a translational constant the constant is required to ensure that the total translational momentum of the system is conserved as zero At the present time there may be small residual rotational components which are not annihilated these are considered unimportant General description of the DRC and IRC As the IRC usually requires a normal coordinate a force constant calculation normally has to be done first If IRC is specified on its own a normal coordinate is not used and the IRC calculation is performed on the supplied geometry A recommended sequence of operations to start an IRC calculation is as follows 1 Calculate the transition state geometry If the T S is not first optimized then the IRC calculation may give very misleading results For example if NH3 inversion is defined as the planar system but without the N H bond length being optimized the first normal coordinate
234. trix e MNDO Main sequence MAIN program MNDO first reads in data using READ then calls either FLEPO to do geometry optimization FORCE to do a FORCE calculation PATHS for a reaction with a supplied coordinate NLLSQ for a gradient minimization or REACT 1 for locating the transition state Starts the timer Description of subroutines MOLDAT Main Sequence Sets up all the invariant parameters used during the calculation e g number of electrons initial atomic orbital populations number of open shells etc Called once by MNDO only MOLVAL Utility Calculates the contribution from each M O to the total valency in the molecule Empty M O s normally have a negative molecular valency MTXM Utility Part of the matrix package Multiplies together two rectangular packed arrays i e C A B MTXMC Utility Part of the matrix package Similar to MTXM MULLIK Utility Constructs and prints the Mulliken Population Analysis Avail able only for RHF calculations Called by WRITE MULT Utility Used by MULLIK only MULT multiplies two square matrices to gether MXM Utility Part of the matrix package Similar to MTXM MXMT Utility Part of the matrix package Similar to MTXM MYWORD Utility Called in WRTKEY MYWORD checks for the existance of a specific string If it is found MYWORD is set true and the all occurances of string are deleted Any words not recognised will be flagged and the job stopped NAICAP Utility C
235. tting RECALC 1 is very expensive in terms of computer time but used in conjecture with OMIN 0 90 or possibly higher and maybe also tighter limits on RMIN and RMAX it represents an option of locating transitions structures that otherwise might not be possible If problems are encountered with many step rejections due to small TS mode overlaps try reducing OMIN maybe all the way down to 0 This most likely will work if the TS mode is the lowest Hessian eigenvector but it is doubtful that it will produce any useful results if a high lying mode is followed Finally following modes other than the lowest toward a TS indicates that the starting geometry is not close to the desired TS In most cases it is thus much better to further refined the starting geometry than to try following high lying modes There are cases however where it is very difficult to locate a starting geometry which has the correct Hessian and mode following may be of some use here 6 17 2 Franck Condon considerations This section was written based on discussions with Victor I Danilov Department of Quantum Biophysics Academy of Sciences of the Ukraine Kiev 143 Ukraine The Frank Condon principle states that electronic transitions take place in times that are very short compared to the time required for the nuclei to move significantly Because of this care must be taken to ensure that the calculations actually do reflect what is wanted Examples of various phenom
236. uble bond is broken At that geometry the true transition state involves motion of the nitrogen substituent so that the nitrogen in the transition state is more nearly sp2 In other words a simple rotation of the HNCO dihedral will not yield the activation barrier however it will be within 2 kcal mole of the correct answer The 14 kcal barrier mentioned earlier refers to the true transition state 4 Any job involving a CONH group will require either the keyword NOMM or MMOK If you do not want the correction to be applied use the keyword NOMM NO Molecular Mechanics 6 4 Level of precision within MOPAC Several users have criticised the tolerances within MOPAC The point made is that signif icantly different results have been obtained when different starting conditions have been used even when the same conformer should have resulted Of course different results must be expected there will always be small differences nonetheless any differences should be small e g heats of formation HoF differences should be less than about 0 1 kcal mole MOPAC has been modified to allow users to specify a much higher precision than the default when circumstances warrant it Reasons for low precision There are several reasons for obtaining low quality results The most obvious cause of such errors is that for general work the default criteria will result in a difference in HoF of less than 0 1 kcal mole This is only true for fairly rigid syst
237. umber lt b gt is the atom to which lt a gt is related lt c gt if present is the atom number to which lt a gt makes an angle and lt d gt if present is the atom number to which lt a gt makes a dihedral ANALYT W By default finite difference derivatives of energy with respect to geometry are used If ANALYT is specified then analytical derivatives are used instead Since the analytical derivatives are over Gaussian functions a STO 6G basis set is used the overlaps are also over Gaussian functions This will result in a very small less than 0 1 kcal mole change in heat of formation Use analytical derivatives a when the mantissa used is less than about 51 53 bits or b when comparison with finite difference is desired Finite difference derivatives are still used when non variationally optimized wavefunctions are present AMA C The AM1 method is to be used By default MNDO is run BAR n nn W In the SADDLE calculation the distance between the two geometries is steadily reduced until the transition state is located Sometimes however the user may want to alter the maximum rate at which the distance between the two geometries reduces BAR is a ratio normally 0 15 or 15 percent This represents a maximum rate of reduction of the bar of 15 percent per step Alternative values that might be considered are BAR 0 05 or BAR 0 10 although other values may be used See also SADDLE If CPU time is not a major consid
238. un SCINCHR n nn In an ESP calculation SCINCR n nn specifies the increment between layers of the surface in the Connolly surface default 0 20 SETUP C If on the keyword line the word SETUP is specified then one or two lines of keywords will be read from a file with the logical name SETUP The logical file SETUP must exist and must contain at least one line If the second line is defined by the first line as a keyword line and the second line contains the word SETUP then one line of keywords will be read from a file with the logical name SETUP SETUP name C Same as SETUP only the logical or actual name of the SETUP file is name SEXTET C RHF interpretation The desired spin state is a sextet the state with component of spin 1 2 and spin 5 2 The sextet states are the highest spin states normally calculable using MOPAC in its unmodified form If SEXTET is used on its own then a single state corresponding to one alpha electron in each of five M O s is calculated If several sextets are to be calculated say the second or third then OPEN n1 n2 should be used UHF interpretation The system will have five more alpha electrons than beta elec trons SHIFT n nn W In an attempt to obtain an SCF by damping oscillations which slow down the convergence or prevent an SCF being achieved the virtual M O energy levels are shifted up or down in energy by a shift technique The principle is that if
239. und state functions From the eigenvectors the expectation value of s is calculated and the spin states of the state functions calculated General overview of keywords Keywords associated with the operations of MECI are SINGLET DOUBLET EXCITED TRIPLET QUARTET BIRADICAL QUINTET SEXTET ESR OPEN n1 n2 C I n MECI ROOT n Each keyword may imply others thus TRIPLET implies an open shell system there fore OPEN 2 2 and C I 2 are implied if not user specified Starting electronic configuration MECI is restricted to RHF calculations but with that single restriction any starting configuration will be supported Examples of starting configurations would be System KeyWords used Starting Configuration Methane lt none gt 2 00 2 00 2 00 2 00 2 00 Methyl Radical lt none gt 2 00 2 00 2 00 2 00 1 00 Twisted Ethylene TRIPLET 2 00 2 00 2 00 1 00 1 00 Twisted Ethylene OPEN 2 2 2 00 2 00 2 00 1 00 1 00 Twisted Ethylene Cation OPEN 1 2 2 00 2 00 2 00 0 50 0 50 Methane Cation CHARGE 1 OPEN 5 3 2 00 2 00 1 67 1 67 1 67 Choice of starting configuration is important For example if twisted ethylene a ground state triplet is not defined using TRIPLET or OPEN 2 2 then the closed shell ground state structure will be calculated Obviously this configuration is a legitimate microstate but from the symmetry of the system a better choice would be to define one electron in each of the two formally degenerate pi type M O s The initial
240. us a good approximation to a harmonic oscillator STRETCHING CURVE FOR NITROGEN MOLECULE N N DIST HoF GRADIENT Angstroms kcal mole kcal mole Angstrom 1 1180 8 714564 60 909301 1 1170 8 655723 56 770564 1 1160 8 601031 52 609237 1 1150 8 550512 48 425249 1 1140 8 504188 44 218525 1 1130 8 462082 39 988986 1 1120 8 424218 35 736557 1 1110 8 390617 31 461161 1 1100 8 361303 27 162720 1 1090 8 336299 22 841156 1 1080 8 315628 18 496393 1 1070 8 299314 14 128353 1 1060 8 287379 9 736959 1 1050 8 279848 5 322132 1 1040 8 276743 0 883795 1 1030 8 278088 3 578130 1 1020 8 283907 8 063720 1 1010 8 294224 12 573055 1 1000 8 309061 17 106213 1 0990 8 328444 21 663271 1 0980 8 352396 26 244309 1 0970 8 380941 30 849404 1 0960 8 414103 35 478636 1 0950 8 451906 40 132083 1 0940 8 494375 44 809824 1 0930 8 541534 49 511939 1 0920 8 593407 54 238505 6 11 Reaction coordinates 1 0910 8 650019 58 989621 1 0900 8 711394 63 765330 Period of vibration The period of vibration time taken for the oscillator to undertake one complete vibration returning to its original position and velocity can be calculated in three ways Most direct is the calculation from the energy curve using the gradient constitutes a faster albeit less direct method while calculating it from the vibrational frequency is very fast but assumes that the vibrational spectrum has already been calculated 1 From the energy curve For a simple har
241. ve file or from a results file 2 The option of continuous graphical representation of the system being studied Several types of terminals are supported including DIGITAL TEKTRONIX and TERAK terminals 3 The drawing of electron density contour maps generated by DENSITY on graphical devices 4 The drawing of solid state band structures generated by MOSOL 5 The sketching of molecular vibrations generated by a normal coordinate analysis DENSITY DENSITY written by Dr James J P Stewart and available through QCPE is an electron density plotting program It accepts data files directly from MOPAC and is intended to be used for the graphical representation of electron density distribution in dividual M O s and difference maps MOHELP MOHELP also available through QCPE is an on line help facility written by Maj Donn Storch and Dr James J P Stewart to allow non VAX users access to the VAX HELP libraries for MOPAC DRAW and DENSITY MOSOL MOSOL Distributed by QCPE is a full solid state MNDO program written by Dr James J P Stewart In comparison with MOPAC MOSOL is extremely slow As a result while geometry optimization force constants and other functions can be carried out by MOSOL these slow calculations are best done using the solid state facility within MOPAC MOSOL should be used for two or three dimensional solids only a task that MOPAC cannot perform 1 6 The data file 1 6 The data file
242. vector is a minimum this minimum is within 1 degree of the absolute bottom 4 The SADDLE calculation then proceeds as described above Limitations The two geometries must be related by a continuous deformation of the coordinates By default internal coordinates are used in specifying geometries and while bond lengths and bond angles are unambiguously defined being both positive the dihedral angles can be positive or negative Clearly 300 degrees could equally well be specified as 60 degrees A wrong choice of dihedral would mean that instead of the desired reaction vector being used a completely incorrect vector was used with disastrous results To correct this ensure that one geometry can be obtained from the other by a con tinuous deformation or use the XYZ option Background 6 17 How to escape from a hilltop A particularly irritating phenomenon sometimes occurs when a transition state is being refined A rough estimate of the geometry of the transition state has been obtained by either a SADDLE or reaction path or by good guesswork This geometry is then refined by SIGMA or by NLLSQ and the system characterized by a force calculation It is at this point that things often go wrong Instead of only one negative force constant two or more are found In the past the recommendation has been to abandon the work and to go on to something less masochistic It is possible however to systematically progress from a multip
243. wavefunction DERS Utility Called by ANALYT DERS calculates the analytical derivatives of the overlap matrix within the molecular frame DEX2 Utility A function called by ESP DFOCK2 Utility Part of the analytical C I derivative package Called by DERII DFOCK2 calculates the frozen density contribution to the derivative of the energy wrt cartesian coordinates DFPSAV Utility Saves and restores data used by the BFGS geometry optimization Main arguments parameters being optimized gradients of parameters last heat of formation integer and real control data Called by FLEPO DHC Utility Called by DCART and calculates the energy of a pair of atoms using the SCF density matrix Used in the finite difference derivatve calculation DHCORE Utility Part of the analytical C I derivative package Called by DERII DHCORE calculates the derivatives of the 1 and 2 electron integrals wrt cartesian coordinates DIAG Utility Rapid pseudo diagonalization Given a set of vectors which almost block diagonalize a secular determinant DIAG modifies the vectors so that the block diagonalization is more exact Main arguments Old vectors Secular Deter minant New vectors on output Called by ITER DIAGI Utility Calculates the electronic energy arising from a given configuration Called by MECI Description of subroutines DIAT Utility Calculates overlap integrals between two atoms in general cartesian space Principal quantum numbers
244. would reproduce the electrostatic potential of the nuclii and electronic wavefunction e ESPBLO Block Data Used by the ESP calculation ESPBLO fills two small arrays e ESPFIT Utility Part of the ESP ESP fits the quantum mechanical potential to a classical point charge model e EXCHNG Utility Dedicated procedure for storing 3 parameters and one array in a store Used by SEARCH e FFHPOL Utility Part of the POLAR calculation Evaluates the effect of an electric field on a molecule e FLEPO Main Sequence Optimizes a geometry by minimizing the energy Makes use of the first and estimated second derivatives to achieve this end Arguments Parameters to be optimized overwritten on exit with the optimized parameters Number of parameters final optimized heat of formation Called by MAIN RE ACTI and FORCE e FMO06AS Utility Part of CDIAG e FMO06BS Utility part of CDIAG e FMAT Main sequence Calculates the exact Hessian matrix for a system This is done by either using differences of first derivatives normal mode or by four full SCF calculations half electron or C I mode Called by FORCE e FOCKI Utility Adds on to Fock matrix the one center two electron terms Called by ITER only e FOCK2 Utility Adds on to Fock matrix the two center two electron terms Called by ITER and DERIV In ITER the entire Fock matrix is filled in DERIV only diatomic Fock matrices are constructed e FOCK2D Written out of MOPAC 6 00 e FOR
245. y Exceptions 1 Atom 1 has no coordinates at all this is the origin 2 Atom 2 must be connected to atom 1 by an interatomic distance only 3 Atom 3 can be connected to atom 1 or 2 and must make an angle with atom 2 or 1 thus 3 2 1 or 3 1 2 no dihedral is possible for atom 3 By default atom 3 is connected to atom 2 3 1 1 Constraints 1 Interatomic distances must be greater than zero Zero Angstroms is acceptable only if the parameter is symmetry related to another atom and is the dependent function 2 Angles must be in the range 0 0 to 180 0 inclusive This constraint is for the benefit of the user only negative angles are the result of errors in the construction of the geometry and angles greater than 180 degrees are fruitful sources of errors in the dihedrals 3 Dihedrals angles must be definable If atom i makes a dihedral with atoms j k and l and the three atoms j k and are in a straight line then the dihedral has no definable angle During the calculation this constraint is checked continuously and if atoms j k and lie within 0 02 Angstroms of a straight line the calculation will output an error message and then stop Two exceptions to this constraint are a if the angle is zero or 180 degrees in which case the dihedral is not used Geometry specification b if atoms j k and 1 lie in an exactly straight line usually the result of a symmetry constraint as in acetylene acetonitrile but 2
246. y specifying LET in which case you can specify any limit for GNORM However if it is too low the job may finish due to an irreducible minimum in the heat of formation being encountered If this happens the STATIONARY POINT message will be printed Finally there is a full analytical derivative function within MOPAC These use STO 6G Gaussian wavefunctions because the derivatives of the overlap integral are easier to calculate in Gaussians than in STO s Consequently there will be a small difference in the calculated HoFs when analytical derivatives are used If there is any doubt about the accuracy of the finite derivatives try using the analytical derivatives They are a bit slower than finite derivatives but are more precise a rough estimate is 12 figures for finite difference 14 for analytical Some calculations mainly open shell RHF or closed shell RHF with C I have untracked errors which prevent very high precision For these systems GNORM should be in the range 1 0 to 0 1 6 5 Convergence tests in subroutine ITER How large can a gradient be and still be acceptable A common source of confusion is the limit to which the GNORM should be reduced in order to obtain acceptable results There is no easy answer however a few guidelines can be given First of all reducing the GNORM to an arbitarily small number is not sensible If the keywords GNORM 0 000001 LET and EF are used a geometry con be obtained which is precise
247. ycine neutral AMI 101 6 117 3 15 7 zwitterion AMI 59 2 125 6 66 4 x 1 Y Nagano M Sakiyama T Fujiwara Y Kondo J Phys Chem 92 5823 1988 6 20 Solid state capability Currently MOPAC can only handle up to one dimensional extended systems As the solid state method used is unusual details are given at this point If a polymer unit cell is large enough then a single point in k space the Gamma point is sufficient to specify the entire Brillouin zone The secular determinant for this point can be constructed by adding together the Fock matrix for the central unit cell plus those for the adjacent unit cells The Born von Karman cyclic boundary conditions are satisfied and diagonalization yields the correct density matrix for the Gamma point At this point in the calculation conventionally the density matrix for each unit cell is constructed Instead the Gamma point density and one electron density matrices are 6 20 Solid state capability combined with a Gamma point like Coulomb and exchange integral strings to produce a new Fock matrix The calculation can be visualized as being done entirely in reciprocal space at the Gamma point Most solid state calculations take a very long time These calculations called Clus ter calculations after the original publication require between 1 3 and 2 times the equiv alent molecular calculation A minor fudge is necessary to make this method work The

G A M E S S - U K USER'S GUIDE Version 8.0 June 2008 MOPAC

Contents

Download Pdf Manuals

Related Search

Related Contents