Home

- University of Mississippi

1. This calculated frequency matches exactly the shifted peak seen in the spectrum of 50 mole fraction This 1s reasonable because there should be one methanol molecule for each pyrimidine molecule in this mixture meaning the shifted peak should be due to the species for which the calculation was performed Frequencies were also calculated and scaled for the system of pyrimidine hydrogen bonded to two methanol molecules The calculated v 44 frequency of this system was 1001 cm The experimentally observed shifted peak only shifts to a frequency of 997 cm for a mole fraction of 90 methanol We can conclude from these data that even with a 9 1 ratio of methanol molecules to pyrimidine molecules the doubly hydrogen bonded pyrimidine is not the prevalent species v still shifts however with mole fractions of water greater than 0 50 The average number of methanol molecules hydrogen bonded to one pyrimidine molecule must between one and two Benzyl Alcohol 1 Hexanol and Hexylamine To investigate further the shifting of the v peak or pyrimidine with hydrogen bonding and the cause of the continuous shifting benzyl alcohol 1 hexanol and hexylamine were also investigated similarly to methanol and water above These molecules are only capable of forming hydrogen bonds at one location Therefore their spectra were expected to exhibit similar properties as the spectrum of methanol The spectra are shown in Figure 3 14 The spectra of
2. for our setup The plane of With Homemade Half Wave Plate Without Homemade Half Wave Plate polarization of light can be rotated ninety degrees by means of a half Raman Intensity wave plate We constructed our own half wave plate using a 900 950 1000 1050 1100 1150 1200 1250 l l Energy cm microscope slide and glossy Fi igure 2 10 The effect of a half wave plate on two cellophane tape as suggested in an benzene peaks The half wave plate rotates the plane of polarization of the laser ninety degrees optics textbook The results are 29 shown in Figure 2 10 The totally symmetric mode at 990 cm decreases greatly in intensity when the laser polarization is not rotated to be vertical Notice the mode at higher energy is not changed as much because it is not totally symmetric A commercial grade half wave plate was purchased for use in the final version of the experimental setup 2 4 References 1 Armstrong D P Fletcher W H Trimble D S Data Acquisition and Control of a Raman Spectrometer Using A DEC PDP 11 34 Computer Oak Ridge Gaseous Diffusion Plant 1987 2 Hecht E Optics Second ed Addison 1987 30 3 Raman Spectroscopic Investigations of Intermolecular Interactions Involving Pyrimidine Presented here is an investigation of intermolecular interactions involving pyrimidine 1 3 Diazabenzene using Raman spectroscopy Room temperature Raman vibrational spectra of py
3. s front panel is a plot of data collected when a scan is being executed For a single scan the chart displays the spectrum as it is being collected For multiple scans the chart displays the current scan in addition to the average of all other spectra collected in previous scans 2 3 The New Experimental Setup Danaher Motion 3 Stepping Motor PUAN pping Labview Controller Jobin Yvon Ramanor HG2 S Macro Sample Compartment Pe a a are r or NIM Bin Figure 2 8 Block diagram of ts the updated Raman 4 Housing T spectroscopy setup Ortec 9302 pa ifi Ortec 770 C31034 Amplifier Discriminator Photon Counter PMT I II 1 Hage it ae Fisher Scientific Circulating Bath Ortec 779 Interface Controller T u M u _ 26 On June 23 2008 the first spectra were collected using the new experimental setup A block diagram is shown in Figure 2 8 The first spectra collected were of carbon tetrachloride CCl4 one of the original compounds studied by Raman himself and a classic example in any spectroscopy or physical chemistry course The spectrum is shown in Figure 2 9a Compare this spectrum to one taken using a CCD camera and microscope as part of the physical chemistry laboratory course at the University of Mississippi Figure 2 9b Notice the tremendous difference in resolution The full width at half of the maximum of the three leftmost peaks shows how much higher
4. acquired the Raman spectrometer and all pieces of equipment that the senders thought to be relevant including the Spectra Link In addition the Hammer group was able to acquire copies of the original owner s manuals for the spectrometer itself from and the Spectra Link interface from Jobin Yvon In late 2007 our group began our attempt to restore the spectrometer to working order and update it once again with a modern computer controlled system for running the spectrometer and taking data The first step was to see if the spectrometer was still in working order starting with the stepping motor that controls the monochromators Included in a NIM for Nuclear Instrumentation Module a standard in electronics bins bin filled with electronic equipment was the original rack that controlled slit width on the spectrometer in addition to an optional method for turning the diffraction gratings inside the Ramanor The rack was still capable of controlling slit width but not grating position We next turned to the Spectra 19 Link manual and tried to see what was necessary to connect the Spectra Link to the spectrometer and also to control the spectrometer Dismantling of the Spectra Link revealed that the original modules discussed in the owner s manual were no longer present Essentially the Spectra Link was a box full of electronics which would not be useful as their function and operating instructions could not be known It is unclear whether or n
5. controlling the Ramanor and PMT The spectrum being recorded is of CCl a destination In addition the final version contains the necessary elements to record multiple spectra and average them The user selects the number of scans and the spectrometer scans as normal except it rewinds after each scan to being a new scan All data is saved to a text file formatted in columns with one column for wavenumber position and one column for each scan A screenshot of the final version is shown in Figure 2 7 The top right portion reads data from the photon counter every 0 5s and plots it on the chart displays each value on the 25 circular gauge and displays this number in the box labeled Counts To the left of this wavenumber position in absolute and relative wavenumbers is displayed along with the time elapsed and time remaining for each scan The top left portion of the screen contains knobs and buttons for laser line selection and recalibration of the computer s wavenumber position with the number displayed on the spectrometer itself The bottom left portion contains a slider for grating speed selection and number of scans Here the user selects the destination in units of relative or absolute wavenumbers and whether or not to collect data to save it Scan or simply move the gratings Go To Also included here is the option to save spectral data collected even if an entire scan has not been completed The bottom right portion of the program
6. 11 Three possible combinations of pyrimidine water hydrogen bonds Note the ability of water to hydrogen bond with itself as well Figure 3 12 One and two methanol molecules hydrogen bonding with pyrimidine 43 Figure 3 13 Raman spectra of mixtures of pyrimidine with the indicated mole fractions of methanol monitoring the position of v The broad peak at 1030cm in the spectrum corresponding to a mole fraction of 0 90 methanol is due to methanol itself de i oe ee ee E 970 980 990 1000 1010 i 1020 1030 Raman Shift cm Figure 3 13 shows that v is blue shifted when the hydrogen bond donor is methanol just as when the hydrogen bond donor is water The shift of 9 cm is however less than the shift seen with water Furthermore the shift is very little after the first aliquot of methanol is added This indicates that whatever species is responsible for the shifted peak is present as soon as any methanol is added This differs from water in that addition of water caused continuously further shifting indicating that new hydrogen bonded species were being formed as more water was added Frequency calculations were performed on both hydrogen bonded species of pyrimidine and methanol and the pyrimidine monomer Frequencies were scaled such that the v peak of the monomer matched the experimental spectrum The calculated and scaled frequency for v for the pyrimidine hydrogen bonded with one methanol system was 994 cm
7. Daniels M C Strain O Farkas D K M A D Rabuck K Raghavachari J B Foresman J V O Q Cui A G Baboul S Clifford J Cioslowski B B S G Liu A Liashenko P Piskorz I Komaromi R L M D J Fox T Keith M A Al Laham C Y Peng A N M Challacombe P M W Gill B Johnson W C M W Wong C Gonzalez and J A Pople Revision E 01 ed Gaussian Inc Wallingford CT 2004 22 Bokobza Sebagh L Zarembowitch J Spectrochimica Acta 1976 324 797 805 23 Wheatley P J Acta Crystallographica 1960 13 80 85 52
8. EJ Perpendicular to the laser polarization Perpendicular refers to spectra collected by rotating the same polarizer film ninety degrees A drastic reduction in intensity indicates a peak corresponding to a mode of a symmetry 1100 1150 1200 1250 1530 1560 1590 1620 1 Raman Shift cm According to Schlucker s calculations the hydrogen bond strength present in the pyrimidine water system is found to increase predictably only for new water molecules hydrogen bonding to water already hydrogen bonded with pyrimidine Optimized structures for several configurations of water hydrogen bonding with pyrimidine are shown in Figure 3 11 Notice the network of hydrogen bonds that results when more water molecules are included as opposed to hydrogen bonds occurring only between water molecules and pyrimidine 42 Methanol To investigate whether or not this continuous shift of the v peak was indeed due to the hydrogen bond network formed by water molecules we performed the same experiment with methanol as the hydrogen bond donor Although there are a myriad of possibilities for combinations of water molecules hydrogen bonding with each other and with pyrimidine there are only two combinations possible with a molecule such as methanol because it lacks the ability to form a network as water does The two possible combinations are shown in Figure 3 12 Raman spectra for the methanol experiment are shown in Figure 3 13 Figure 3
9. Ortec 556 high voltage power supply at the cathode and an amplifier discriminator Ortec 9302 at the anode The original amplifier discriminator in Figure 2 4 was in our possession but appeared to have been replaced by the Ortec model and consequently was not used in the new setup The output of this amplifier discriminator is fed to a photon counter Ortec 770 that was also included in our package of old electronics Initial tests of the photomultiplier tube connected as mentioned above using brief exposures to room light showed that the photon counter and photomultiplier tube were in working order The Ortec 770 photon counter has no output that can be read with a computer directly Research indicated that in the past scientists using the Ortec 770 counter also used an Ortec 779 interface controller At my request Ortec provided the user s manual for this device which showed that the interface controller could be used to read the photon counter data with a computer s serial port We were able to buy the interface controller and test it out in the NIM bin Using the correct Amphenol fourteen pin cables a loop is created between the photon counter and the interface controller The interface controller 1s capable of resetting the counter to zero and reading the number of counts from it The interface controller is connected to a PC via serial cable and commands are sent from the Labview program similarly as they are to the stepping motor cont
10. an amount equal to the frequency of vibration An energy level diagram for each situation is shown in Figure 1 1 Figure 1 1 An energy Virtual State z 4 ce ieee eae diagram showing the vibrational transitions h w 4 w resulting a Rayleigh Excited hw scattered light and Vibrational State Raman scattered light of the b Stokes and c Vibrational anti Stokes lines Ground State a b c When light is Rayleigh scattered the molecule is excited to a virtual excited state and relaxes creating a photon of the same frequency Light may also be Raman scattered as shown in Figure 1 1b and Figure 1 lc Figure 1 1b represents the Stokes line The molecule is excited to a virtual state of energy hw The molecule then relaxes to a vibrational excited state of energy hw The photon created in this case has energy less than the exciting radiation by an amount hw This is the property that makes Raman spectroscopy such a valuable tool By measuring the intensity of scattered light over a range of frequencies the frequencies observed to have intense emissions correspond to h w wyp Thus the frequency of the monochromatic exciting radiation can be used to find vibrational frequencies of the molecule The transition producing the anti Stokes line corresponds to a molecule in a vibrational excited state being excited to a virtual state and relaxing to the vibrational ground state The frequency of this scattered radiation 1s
11. as they have the ability to participate in both hydrogen bonding through the nitrogen atom and m stacking through the delocalized a system Vibrational spectroscopy both infrared IR and Raman lends itself to studies of these interactions Changes in a vibrational spectrum allow us to ascertain exactly which atoms and bonds are being affected in the intermolecular interactions taking place and to what extent these interactions are occurring Hydrogen bonds have been investigated with Raman spectroscopy as far back as the 1950s when Puranik investigated hydrogen bonds between donors and carbonyl acceptors and found the first evidence in a Raman spectrum for hydrogen bonds to nitrogen Vibrational spectroscopy has also been used to investigate hydrogen bonding in terms of thermodynamic properties including se 10 11 ee association constants rate constants and formation enthalpies In this study we investigate the Raman spectrum of pyrimidine under different conditions Pyrimidine from which the nucleobases known as pyrimidines are derived 1s shown in Figure 3 1 along with the pyrimidine nucleobases cytosine thymine and uracil Also shown in Figure 3 1 are the remaining nucleobases prevalent in nucleic acids known as the purines Notice that these molecules also contain six membered 32 rings consisting of two nitrogen atoms It should be apparent then that pyrimidine can participate in similar non covalent interactions as the
12. elsewhere in the CH stretching region of the spectrum but that discussed above can be seen to be the most pronounced presumably because this interaction 1s forced to occur strongly as pyrimidine is crystallized Strong Hydrogen Bonds in Pyrimidine Binary Mixtures Water Our first step in this study was to repeat the experiment by Schlucker and compare the results We prepared mixtures of pyrimidine with varying mole fractions of water and collected the Raman spectrum of each The results are shown in Figure 3 8 We were v4 a 7 0 90 ei Figure 3 8 Raman spectra of mixtures of pyrimidine with the indicated mole ia fractions of water monitoring the position of v 7 0 30 x 0 15 X 0 00 se oe oS Ue le 980 990 1000 1010 1020 Raman Shift cm able to replicate the previous results The peak v was found to shift by 13cm from 990 cm to 1003 cm as the amount of water present was increased It is important to note that the peak continues to increase while more water is added Our group also found 40 other shifts in the Raman spectrum of pyrimidine to occur Shown in Figure 3 9 are four other regions of the spectrum where similar albeit smaller blue shifts of pyrimidine peaks occur as more water is added Vibrations corresponding to visa and vie were discussed above and shown in Figure 3 5 v6 and ve correspond to in plane ring modes Voa V15 and v3 are due to in plane CH wagging modes There has bee
13. first with a description of light scattering and then with a description of the Raman Effect and its relationship to the vibrational energy of molecules This background information precedes a short history of Raman instrumentation containing pertinent technical details 1 1 Light Matter Interaction When light is incident on an atom or molecule there are two possibilities for interaction First a photon with an energy exactly matching that of a vibrational electronic or rotational energy level transition can be absorbed by the atom or molecule This absorption promotes the system to a higher energy level For photons not of the correct energy to be absorbed scattering can occur The elastic scattering of photons was described in the 19 century an effect now known as Rayleigh scattering Lord Rayleigh showed the relationship between scattering power and wavelength and why this causes the blue color of the sky Rayleigh scattering occurs by a process in which the oscillating electric field of light incident on a molecule induces a dipole moment in the molecule by separating positive and negative charge density Because the electric field oscillates sinusoidally the induced dipole moment oscillates with the same frequency Since electric dipoles produce electric fields this dipole oscillation produces a new electric field oscillating with the same frequency as the incident light Oscillating electric fields induce oscillating magnetic field
14. greater than that of the excited radiation and can give similar information about vibrational frequencies In practice Raman spectroscopy measures Stokes lines more often because of the fact that at room temperature the vast majority of molecules will be in the vibrational ground state With more molecules to produce them the Stokes lines will be more intense It 1s worth noting that Stokes and anti Stokes lines are terms originating in fluorescence spectroscopy A fluorescence peak is predicted to be at a lower energy than the exciting radiation producing the fluorescence and is said to have Stokes shifted This process is wholly unrelated to the Stokes lines produced by the Raman Effect and the use of these terms has simply carried over from fluorescence Spectroscopy This above situation was described for a homonuclear diatomic molecule for simplicity For a general polyatomic molecule the case becomes more complicated The vibrations are not just stretching or contraction of one bond but can be any linear combination of what are known as normal modes The term normal mode when applied to molecular vibrations is characterized by the fact that each atom executes simple harmonic motion with the same frequency and the atoms generally move in phase Normal refers to the fact that the displacements of one atom during any two different normal modes are orthogonal 1 e have an inner product of zero For a molecule of N atoms there exist 3N 6 nor
15. purines and pyrimidines present in nucleic acids Futhermore three of the twenty essential amino acids tryptophan tyrosine and phenylalanine contain aromatic groups The study of non covalent interactions of pyrimidine could then lead to a better understanding of intermolecular interactions occurring in DNA RNA and proteins all of which contain molecules with structural and chemical similarities to pyrimidine NH2 O O A N Cr ONH D J Figure 3 1 The N A N A N A N pyrimidine class of H H H nucleic acids and a b c d pyrimidine a Cytosine b Thymine c Uracil d HN O a e Guanine NH N i N q D NH q 2 N N N N H H e o Pyrimidine and other nitrogen containing heterocycles are well studied molecules with the first Raman spectrum of pyrimidine being published in 1957 In this study we investigate specifically spectral shifts of the v peak corresponding to the ring breathing mode in which all bonds of the ring lengthen or contract simultaneously In 1963 Fratiello found that the ring breathing peak in the Raman spectrum of pyridine shifted to higher frequencies with higher concentrations of water In 1966 Takahashi carried out a thorough investigation of the IR spectra of the azabenzenes pyridine pyrimidine 33 pyrazine and pyridazine in various hydrogen bond donor and non donor solvents Takahashi also found the v peaks of the various azabenzenes investigated to shift to higher frequen
16. 4 Amplifier Discriminator VT105 PMT Terminal i I Neslab Refrigerated Ortec HP 7470A Circulating Bath 456 Plotter HV Power Supply interface was a scan and data acquisition system that used different modules programmed and called by means of DIP switches on each module Many modules were available so that experimental setups could be customized to fit any experimental needs This setup used the motor driver module MDR to drive the stepping motor controlling the monochromators the recorder shutter module RSXY to block the laser from entering the sample compartment the pulse count module DCNT to read pulses from the amplifier discriminator thus counting photons and the interface module INT to link the 18 other modules to the computer Their report on updating the spectrometer goes into great detail regarding the intricacies involved in interfacing the software and hardware of this setup and in the routines this setup can execute to automate spectral acquisition The result of their work was a more reliable more flexible larger easier to use system compatible with laboratory equipment and independent from restrictive operating systems 2 2 The Restoration By 2007 the spectrometer described above had been placed in storage at the University of Tennessee along with many of the components from the experimental setup described in Figure 2 4 In the fall of 2007 the Hammer group at the University of Mississippi
17. UPGRADE OF A RAMAN SPECTROMETER WITH MODERN COMPUTER CONTROL AND DATA ACQUISITION FOR STUDIES OF HYDROGEN BONDING IN PYRIMIDINE by Austin Archie Howard A thesis submitted to the faculty of the University of Mississippi in partial fulfillment of the requirements of the Sally McDonnell Barksdale Honors College Oxford May 2009 Approved by Advisor Professor Nathan Hammer Reader Professor Gregory Tschumper Reader Professor Susan Pedigo ACKNOWLEDGEMENTS Many people in the Department of Chemistry and Biochemistry here at the University of Mississippi were of great assistance during the work presented in this manuscript I would like to thank the members of the Keith Hollis Daniell Mattern Walter Cleland Takashi Tomioka and Susan Pedigo research groups for the donation of some of the chemicals used in these experiments I would like to thank Dr Susan Pedigo for the extended loan of a circulating water bath without which the Raman spectrometer could acquire no data I would like to thank Dr Maurice Eftink for taking the time to teach me how to use his high pressure apparatus I would like to thank the research group of Dr Gregory Tschumper for assisting in matters of computations I would also like to thank the members of my research group for always being of assistance Lastly I would like to thank my advisor Dr Nathan Hammer for allowing me a position in his laboratory as well as a worthwhile project to fulfill this thesis
18. al polyatomic case the induced dipole and the electric field must be represented as three dimensional vectors The polarizability in this case must be represented as a rank two tensor in three dimensions Only one component of the polarizability tensor must change during a normal mode for this mode to be Raman active Typically modes are determined to be Raman active or inactive using symmetry considerations of the mode and of the polarizability tensor for a certain point group One advantage of Raman spectroscopy is that some vibrational modes that are not infrared active may be Raman active 1 3 Instrumentation Raman first used sunlight focused by a telescope as the exciting source in his experiments along with colored filters and the human eye for detection of the effect now bearing his name Raman first collected spectra using a mercury lamp as the source a prism to disperse the scattered radiation and photographic plates as the detectors The Raman Effect as noted above is very weak and as a result collection spectra using mercury lamps and photographic plates required long exposure times on the order of 180 hours for vapor samples for example In these early days however Raman spectroscopy was still relatively easier than infrared spectroscopy and was therefore a field with much activity Raman spectroscopy still presented many challenges however The weak signal resulting from inelastically scattered light was difficult t
19. an C V Nature 1928 619 Raman C V Nature 1928 501 Herzberg G Infrared and Raman Spectra Van Nostrand Reinhold New York 1945 Adar F Delhaye M DaSilva E In Waters Symposium Pittcon 2003 In Laser Electro Optics Technology Series Bateman G Ed 1997 Palmer C Diffraction Grating Handbook 6th ed 2005 Skoog D A Holler F J Crouch S R Principles of Instrumental Analysis Sixth ed Thomson 2007 13 2 Upgrade of a High Resolution Cold War Era Raman Spectrometer for Modern Data Acquisition and Control In Chapter 1 the theory history and instrumentation of Raman spectroscopy were presented Following below are the details of the implementation of a Raman spectroscopy experimental setup using a high resolution spectrometer manufactured during the 1970 s updated with modern computer control and data acquisition 2 1 Ramanor HG2 S Raman Spectrometer By 1972 Jobin Yvon a French photonics company that had produced the first commercially available holographic diffraction gratings was offering Raman spectrometers equipped with a double monochromator and a photomultiplier tube detector The user s manual accompanying this instrument billed the Ramanor HG2 S as the first to take full advantage of the unique properties of holographic gratings Their monochromator design was reduced to a single dispersing element the Concave Aberration Corrected Holographic Grating This differs from othe
20. and read by a computer Calibration of the photodiode array allows regions of the spectrum to be assigned to the individual photodiodes so that the charge accumulated on the photodiodes can produce a spectrum Charge coupled devices CCD another type of modern Raman detector have a two dimensional array of photosensitive elements that work similarly to photodiode arrays Multichannel detectors offer high acquisition speed and thus the ability to perform many scans in a short amount of time drastically reducing the signal to noise ratio of the spectrum Multichannel detectors also allow time resolved studies Since the time required to acquire one Raman spectrum is so short many can be collected over a period of time and used to study how a system evolves Despite the advantages of CCD and PDA detectors photomultiplier tubes still offer much higher sensitivity than their more modern counterparts Because of the size of the array of photosensitive elements limits the amount to which light can be dispersed and still detected over a suitable range photomultiplier tubes are also capable of acquiring spectra with higher resolution 12 1 4 References 1 2 3 4 5 6 7 8 9 10 11 12 McHale J L Molecular Spectroscopy 1999 Hecht E Optics Second ed Addison 1987 Chodos A In APS News 2009 Vol 18 Singh R Physics in Perspective 2002 399 Raman C V Indian Journal of Physics 1928 2 388 Ram
21. at hydrogen bond to other water molecules and not to pyrimidine Their conclusions seem to indicate the large role of a hydrogen bonded network versus single hydrogen bonds to pyrimidine in wavenumber position of the ring breathing mode of pyrimidine In our study we wished to investigate further the 34 hydrogen bonding in pyrimidine We monitored the position of v in the Raman spectrum of pyrimidine in mixtures of pyrimidine and various concentrations of water methanol benzyl alcohol 1 hexanol acetic acid hexylamine CH3 CH2 sNH 2 acetonitrile CH3CN ethylene glycol HOCH2 CH2OH and 2 mercaptoethanol HOCH2CH2SH In addition we monitored the position of other vibrational modes and we acquired Raman spectra of pyrimidine under high pressure to investigate the weak hydrogen bonding in neat pyrimidine as the liquid crystallizes Below we also clear up a few discrepancies present in the literature regarding the symmetry of certain normal modes 3 2 Experimental Commercially obtained pyrimidine Sigma Aldrich was used in all experiments without further purification All Raman spectra were recorded using a Jobin Yvon HG2 S Raman spectrometer with a double grating monochromator and photomultiplier tube detector as described in Chapter 2 of this manuscript Data were collected using a custom Labview program written for control of the spectrometer and data collection The exciting source used throughout the experiment was the 514nm li
22. cy upon hydrogen bond formation Takahashi mentions briefly the possibility that the blue shift must be due to a considerable shift in electron density citing a comparison of his spectra to the vibrational spectrum of the pyridinium cation published by Cook More recently hydrogen bonding in pyridine mixtures has been investigated by monitoring the shift of the v peak in mixtures of ethanol and water and in terms of the shift of water s peaks in a vibrational spectrum Pyrimidine was most recently investigated in 2007 when Schlucker and coworkers investigated theoretically and experimentally the shift of the v peak of the Raman spectrum in mixtures of varying amounts of water Their calculations showed that the wavenumber shift which should be indicative of the degree of hydrogen bonding taking place showed a perfect negative correlation with the bond distance between nitrogen and the hydrogen on water molecules and the wavenumber position of v This correlation however only exists within certain subgroups of pyrimidine and water clusters Within these subgroups increasing water concentration leads to increased wavenumber position of v The water concentration in their calculations was increased by adding more water molecules in positions to hydrogen bond with pyrimidine or with water molecules already present The subgroups in which the negative correlation holds are those in which water molecules are added th
23. distinguished this effect from fluorescence The effect was very weak approximately 1 in 10 photons are scattered this way but using long exposure times Raman was able to collect the spectra on photographic plates in those days of sixty different liquids and vapors These spectra first appeared in the Indian Journal of Physics along with his articles Because Nature had not published Raman s spectra with his articles he sent copies of the Indian Journal of Physics paper to two thousand scientists in France Germany Russian Canada and the United States Raman realized as others did that the spacing of the lines in spectra he collected was equal to the infrared frequencies of the molecules represented by the spectra The terms Raman Effect and Raman lines were coined by 1929 and physicists and chemists all over the world began to collect Raman spectra to investigate the vibration and rotation of molecules and verify 3 quantum theories 1 2 The Raman Effect A simplified explanation of the Raman Effect and its relation to molecular vibrations follows According to Equation 2 above the induced dipole moment in a molecule is equal to the product of the polarizability and the applied electric field Molecules are constantly vibrating at any temperature above 0 K For a homonuclear diatomic molecule we can write the nuclear displacement from the equilibrium position as Equation 4 q qo COS Wyt 4 Equation 4 is a resu
24. e peak at 352 cm reduces in intensity and disappears into the baseline as pyrimidine is crystallized This peak corresponds to an out of plane 37 bending of the atoms of the ring The peak at 401 cm splits into two peaks as pyrimidine crystallizes This peak corresponds to another out of plane bending of the atoms of the ring These two modes are pictured in Figure 3 5 The changes in these peaks reflect the changes in pyrimidine as it crystallizes The mode at 352 cm must 30000 psi 20000 is I J 10000 psi a b 400 500 600 700 800 Raman Shift cm Figure 3 5 Two normal modes of pyrimidine at their maximum amplitudes corresponding to Figure 3 4 Enlarged version of Figure 3 3 4 Raman peaks at a 352 cm and b 402 cm cease to occur or only occur less as pyrimidine crystallizes Furthermore the mode at 401 cm must split into two peaks because of two different environments in which the mode occurs That is in the crystal structure of pyrimidine a fraction of the pyrimidine molecules must exist in an environment where the vibration pictured in Figure 3 5b cannot occur as it does elsewhere in the crystal The unit cell of the actual crystal structure of pyrimidine is pictured in Figure 3 6 The intermolecular interactions Figure 3 6 Unit cell of the crystal structure of pyrimidine Dotted lines indicate intermolecular interactions or weak hydrogen bonds 38 occurring in the crystal s
25. ectrometer were first successfully turned on 20 March 27 2008 using the command line prompt of the MCPI While finding the monochromators to be in working order was a success the overall goal of updating the REAL revs spd 8 spectrometer with computer control was to be accomplished using begin _ INPUT 1 revs spd Labview software which would allow for easy communication If revs 0 the goto endp between the computer and the various components of the endif PEET spectrometer The next step was to control the motor using accel 50 decel 50 Labview This was accomplished by writing an MC BASIC movei revs l waitdon program and downloading it into the controller The program r olowmegin used is shown in Figure 2 5 This program is downloaded directly endp l l END Into the controller When executing the program shown the command INPUT 1 causes the program to pause and wait for Figure 2 5 MC BASIC program allowing user a input via the serial port Numbers as hexadecimal strings are sent control via serial port via serial port and read into the controller as the variables revs and spd Before movement is executed by the controller the speed acceleration and deceleration required by the user are set The desired speed is set from the variable read from the serial port The command movei number of revolutions executes movement the desired number of revolutions of the motor The c
26. ed the programs accordingly to implement them in their own experimental setup A block diagram of their experimental setup is shown below Figure 2 4 The diagram shows the Ramanor spectrometer equipped with a sample compartment an optional feature provided by Jobin Yvon and a microscope for acquiring Raman spectra of microscopic samples The diagram also shows their photomultiplier tube detector and its housing cooled by water bath at 10 C and cooled further thermoelectrically to temperatures in the range between 20 C and 30 C The cathode of the photomultiplier tube is held at 1500V by an Ortec high voltage power 17 supply The output of the photomultiplier tube at the anode is passed through an amplifier discriminator which amplifies only pulses above a certain threshold to reduce spectra noise The slit control pictured is the same electronic rack from the original setup mentioned above The spectrometer with the exception of the slits is controlled by the computer through the Spectra Link interface The Spectra Link Figure 2 4 The experimental setup Shutter used by the authors of Reference 1 showing the spectrometer detector computer and Slit the modular interface of rm the computer and the Jobin Yvon spectrometer Ramanor HG2 S Macro Motor RSXY INT Sample Drive DCNT Compartment Spectra Link Nachet 4 TE Cooled Interface DEC RLO2 NS 400 PMT PDP 11 34 Microscope Housing RLO2 i Pacific RCA 3103
27. effects similar in magnitude with water Acetic acid however did not cause the gradual shift caused by water Furthermore ethylene glycol caused the appearance of a third peak at very high concentrations 3 5 References 1 Hobza P Havlas Z Chemical Reviews 2000 4253 4264 2 Jeffrey G A An Introduction to Hydrogen Bonding Oxford University Press New York 1997 3 Pauling L Journal of the American Chemical Society 1931 53 1367 1400 4 Bates D M Anderson J A Oloyede P Tschumper G S Physical Chemistry Chemical Physics 2008 10 2775 2779 5 Schlucker S Koster J Singh R K Asthana B P Journal of Physical Chemistry A 2007 111 5185 5191 6 Puranik P G Proceedings Indian Academy of Sciences Section A 1953 374 499 503 7 Puranik P G Proceedings Indian Academy of Sciences Section A 1953 338A 233 238 50 8 9 10 11 12 13 14 15 16 17 18 19 20 21 Puranik P G Journal of Chemical Physics 1957 26 601 603 Puranik P G Proceedings Indian Academy of Sciences Section A 1957 45A 51 a Kasende O Zeegers Huyskens T Spectroscopy Letters 1980 13 493 502 Cabaco M I Besnard M Molecular Physics 1992 75 157 172 Kim J H Lee H J Eun Jung Kim Jung H J Choi Y S Park J Yoon C J Journal of Physical Chemistry A 2004 108 921 927 Lord R C Marston A L Miller F A Spectroch
28. er to control destination and scan speed and was able to keep track of the wavenumber position It should be noted that there is no electronic output of the spectrometer itself for current wavenumber position In the past devices kept up with wavenumber position by being calibrated once and controlling each speed and change in position after that The Labview program had to keep up with position using a system of timing The timer has variable input and can adapt to different scanning speeds The current wavenumber position is calculated constantly during a scan using the starting position time elapsed since the command to move was executed and the scan speed This position is stored in a global variable and displayed on the user interface screen of the program The position is stored into a text file after the motor has finished turning each time so that the program knows the wavenumber position of the spectrometer even when it has been closed and reopened This version of the program also contained the option to recalibrate 22 wavenumber position if the computer s wavenumber position did not match the true position This happens for example if the motor has been turned using the MCPI terminal and the necessary text file not rewritten A screenshot of the front panel of this program is shown in Figure 2 6 This program looks quite simple but the graphical code in this version is the same that continues to run the monochromators on the Ramano
29. esults are shown in Figure 3 17 As we can see v does not shift at all with addition of acetonitrile 48 These results show that the shifts are due to hydrogen bonding and not due to a solvent polarity effect 1 0 90 Figure 3 17 Raman spectrum of pyrimidine and varying mole fractions of acetonitrile 980 985 990 995 1000 Raman Shift cm 3 4 Conclusion Hydrogen bonding between pyrimidine and various donors and acceptors was investigated using Raman spectroscopy to measure the positions of bands in the spectra Previous studies have shown the band v to be a suitable marker for the degree of hydrogen bonding in pyrimidine We found that other bands shift as well in mixtures of pyrimidine and water We also found different behaviors of the shifts of pyrimidine in mixtures of hydrogen donors other than water Methanol was found to cause a shift that was smaller in magnitude and less continuous than the shift caused by water Our calculations showed this to be due to the formation of pyrimidine molecules hydrogen bonding with an average of between one and two methanol molecules This difference in shift may also be due to the inability of methanol to hydrogen bond with itself and with pyrimidine Benzyl alcohol and l hexanol were found to exhibit similar effects Hexylamine was found to cause no shift in pyrimidine s peak presumably because the hydrogen bonds exhibited are weaker Acetic acid and ethylene glycol showed
30. imica Acta 1957 9 113 125 Fratiello A Journal of the American Chemical Society 1963 85 3072 3075 Takahashi H Mamola K Plyler E K Journal of Molecular Spectroscopy 1966 27 217 230 Cook D Canadian Journal of Chemistry 1961 38 2009 2024 Deckert V Asthana B P Mishra P C Kiefer W Journal of Raman Specroscopy 1996 27 907 913 Schlucker S Singh R K Asthana B P Popp J Kiefer W Journal of Physical Chemistry B 2001 105 25A 25A Schlucker S Heid M Singh R K Asthana B P Popp J Kiefer W Zeitschrift Fur Physikalische Chemie International Journal of Research in Physical Chemistry amp Chemical Physics 2002 216 267 278 Maes G Smets J Adamowicz L McCarthy W VanBael M K Houben L Schoone K Elsevier Science Bv 1997 p 315 322 M J Frisch G W T H B Schlegel G E Scuseria M A Robb J R C J A Montgomery Jr T Vreven K N Kudin J C B J M Millam S S Iyengar 51 J Tomasi V Barone B M M Cossi G Scalmani N Rega G A Petersson H N M Hada M Ehara K Toyota R Fukuda J H M Ishida T Nakajima Y Honda O Kitao H Nakai M K X Li J E Knox H P Hratchian J B Cross V Bakken C A J Jaramillo R Gomperts R E Stratmann O Yazyev A J A R Cammi C Pomelli J W Ochterski P Y Ayala K M G A Voth P Salvador J J Dannenberg V G Zakrzewski S D A D
31. ings offer several advantages to prisms as dispersive elements Prisms are more expensive to produce than gratings and must be made of different materials depending on the wavelength region in which they are to be used Gratings on the other hand can be used to disperse any wavelength of light Also gratings 10 disperse light linearly unlike prisms In the 1960s interference or holographic gratings were first developed These gratings are produced by an interference pattern of an intense light source varying sinusoidally in intensity along the surface of a photosensitive material The degraded portion of the material is then dissolved producing grooves in a sinusoidal pattern on the grating Holographic gratings began to be produced commercially in 1972 and hold many advantages over mechanically ruled gratings in Raman spectroscopy Flaws in the rulings of a mechanical grating resulting from carving one groove at a time are virtually nonexistent in holographic gratings in which all the grooves are formed simultaneously Holographic gratings also reduce the amount of stray light resulting from scattering by the grating itself By the 1970s Raman spectrometers were commercially sold with multiple holographic gratings that could record spectra within 5 cm of the Rayleigh scattered light of the laser The next major advances in Raman spectroscopy instrumentation were in the form of detectors The photomultiplier tube offered advantages
32. ital display of current wavenumber position and offered different scanning or recording modes In 1987 a group of scientists from the Oak Ridge Gaseous Diffusion Plant in Oak Ridge 16 Tennessee and the University of Tennessee in Knoxville Tennessee found it necessary to update the computer control system in place on a Ramanor HG2 S While spectra were originally obtained from the Ramanor by means of a line printer reading the amplified photomultiplier tube signal the computer control system being updated by these scientists was already capable of controlling the monochromator and of data collection and storage According to the introduction of Ref 1 the authors sought to update the computer control system of this spectrometer because of the disappointing performance of the vendor supplied computer They found that their experimental setup was not optimized to their needs because of unreliable operation and unsuitable software They set out to acquire a set of basic operating programs that they could edit themselves to fit their specific needs They reasoned that this would allow them sufficient customization of their setup without the amount of time and effort required to compose their own software entirely The authors found a set of programs on a Digital Equipment Corporation PDP 11 23 computer running the Raman spectrometer at the University of Tennessee Chemistry Department The authors acquired their own DEC computer and modifi
33. lly Compton found that X rays were shifted to longer wavelengths in collisions with electrons In 1923 while investigating theoretically the dispersion of electromagnetic radiation using a quantum model of light Adolf Smekal showed that scattered monochromatic light would have components at higher and lower frequencies in addition to the elastically scattered component thus theoretically predicting inelastic scattering However this and other contributions to the discussion of dispersion at the time did not influence C V Raman in his work Raman had been investigating the scattering of light since the early 1920 s in order to disprove Rayleigh s idea that the blue appearance of the sea was due only to the reflection of the sky Raman was also led by similar interests to experimentally investigate how light is scattered in liquids and crystals Raman s discovery of the effect now bearing his name took place during his attempts to find the optical analog of the Compton scattering of X rays Raman s setup used a telescope to focus sunlight onto various samples A colored filter was used to illuminate the samples with monochromatic light and a spectroscope was used to visually detect a change in the color of the scattered radiation The effect was first termed by Raman and his assistants a feeble fluorescence referring to an optical process resulting from electronic relaxation but a change in polarization of the scattered light
34. lt of modeling the two atoms as two masses connected by a spring That is the atoms are subject to a restoring force directly proportional to displacement from equilibrium Here w is the angular frequency of the vibration These vibrations cause a change in electron density and as a result the polarizability 1s not accurately represented by a static variable but as a function of nuclear position Equation 5 0a a ao 5 do 5 O This series can be truncated at the term linear in g for small amplitudes of vibration Now Equation 3 can be written with Equation 5 substituted for the polarizability 0a p o Eo cos wt 57 qE coswt 6 O Now we substitute the expression for g Equation 4 0a p dE cos wt G do Eo COS Wt COS Wyt 7 O Lastly applying the trigonometric identity cos a cos b cos a b cos a b we obtain a classical theory describing Raman scattered light a a doEo cos w a Wy t 2 aI 8 cos w w t 1 0 p Qo Eo cos wt 5 We can see from the above equation that the dipole induced by light interacting with the vibrating diatomic molecule is oscillating with frequency w the frequency of the incident radiation corresponding to the Rayleigh scattered light Also the dipole contains components oscillating with frequencies w qa and The result is that the induced dipole is emitting light with frequencies greater than or less than the incident light by
35. lycol and pyrimidine shown in Figure 3 15b contain some interesting features as well Mixtures up to the 50 mole fraction of ethylene glycol show a blue shifting of v as expected Comparison with Figure 3 15a shows this shift is not as a great as for acetic acid The 70 and 90 mole fraction mixtures show something not seen in other systems studied thus far There is the clear appearance of a third peak shifted a full 13 cm from the original pyrimidine peak At high concentrations of ethylene glycol there must exist three distinct species of ethylene glycol hydrogen bonding with pyrimidine These species could be any of a number of configurations of ethylene glycol and pyrimidine since ethylene glycol has two sites capable of hydrogen bonding What is interesting is that this third new species only appears to be present in appreciable concentrations when the ethylene glycol makes up a 90 mole fraction of the entire mixture Acetonitrile Our final investigation was to repeat the experiment yet again with acetonitrile as the molecule mixed with pyrimidine Acetonitrile is not capable of donating hydrogen atoms for hydrogen bonding It would not be expected therefore to cause the shift attributed to hydrogen bonding in the above cases However we wished to make sure that the effect seen was not one due to polarity of the solvent Since acetonitrile is highly polar while not being able to hydrogen bond this molecule was ideal for this purpose The r
36. mal modes or 3N 5 for a linear molecule This number corresponds to three degrees of freedom of motion for each atom i e in the x y and z directions with the number of motions corresponding to rotation and translation of the molecule subtracted As noted above any motion of the atoms of a molecule can be represented by an equation of motion that is nothing more than a linear combination of the normal mode equations of motion Each normal mode has an energy associated with it although the energy may be the same for two normal modes The predicted energy for a normal mode and often its symmetry properties are used to assign the peaks in a Raman spectrum to particular normal modes Not every normal mode will have a peak present in the Raman spectrum however As noted two normal modes may have the same energy and then are said to be degenerate These normal modes will not be distinguishable in a Raman spectrum In addition certain normal modes are not Raman active Notice the l nE N second term in Equation 8 containing the derivative 5 as a coefficient If this O derivative is zero the dipole will not have components oscillating at either of the Raman shifted frequencies at least to first order Thus no Raman scattered light will appear Physically we interpret this as a change in polarization with a normal mode being a requirement for that mode s Raman activity In moving from the homonuclear diatomic case to the gener
37. mixtures of pyrimidine and alcohols exhibit similar behavior to the spectra of methanol above In Figure 3 17a the blue shifted peak can be found between the ring breathing peak v of pyrimidine at 990 cm and the ring l As with methanol the blue shifted peak breathing peak of benzyl alcohol at 1000 cm has an immediate appearance with the 15 mole fraction mixture and the shift in subsequent mixtures 1s very little Again the peak does not shift as much as the peak due to hydrogen bonds with water The spectrum of 1 hexanol in Figure 3 14b shows similar behavior to the methanol spectra also The spectra of mixtures of hexylamine do not exhibit the same behavior as the alcohols however Figure 3 14c shows that the position 45 te 7 0 90 a i arn r er a ae a Toe 2 oe hah Sh CO es 980 990 1000 1010 970 980 990 1000 1010 1020 1030 Raman Shift cm Raman Shift cm a b Figure 3 14 Raman spectra of mixtures of pyrimidine and varying mole fractions of a benzyl alcohol b 1 hexanol and c hexylamine ee 970 980 990 1000 1010 ai Raman Shift cm c of v does not change appreciably with any amount of hexylamine added We would expect that hexylamine participates in hydrogen bonding with pyrimidine However due to the lower electronegativity of nitrogen compared to oxygen the hydrogen bonds formed may be weaker and therefore unable to cause a measurable shift 46 Acetic Acid a
38. n discrepancy in the literature in the past over the proper assignment and symmetry of the peaks shown in the bottom two spectra of Figure 3 9 Refs 13 15 17 and 22 e g To make definitive assignments Figure 3 10 shows polarized Raman spectra collected showing the modes V46a 82 Vea 84 V46b P1 2080 Vep P2 x 0 90 aa 7 0 70 0 50 1 0 50 0 30 7 0 30 Figure 3 9 Other eae blue shifting peaks in the Raman spectrum X yo 0 00 X no 0 00 of pyrimidine Vgq and ee TS ee V were fitted to 340 360 380 400 420 440 600 630 660 690 720 750 a j l N 4 Gaussian curves to Raman Shift cm Raman Shift cm clearly show their Voa 81 Vga 34 positions even when b Vap P2 the two could be not be fully resolved Each mode is described in x 0 70 the text T T T T 1100 1150 1200 1250 1520 1540 1560 1580 1600 1620 1 Raman Shift cm 1 Raman Shift cm 41 in question The drastic reduction in intensity of the peaks we have assigned to vg and Voa Shows that they do possess a symmetry and thus have been assigned correctly Interestingly Figure 3 10 indicates that peaks corresponding to vg and v15 shift noticeably while the neighboring peaks shift very little if at all Figure 3 10 Polarized Raman spectra Parallel refers to the fact that polarizer film was employed to collect only Raman scattered light that was polarized parallel O Parallel
39. nd Ethylene Glycol We continued the investigation with hydrogen bond donors that have the ability to hydrogen bond with pyrimidine and with each other These molecules would be expected to exhibit hydrogen bonding properties resembling water more than the alcohols investigated above The data are shown in Figure 3 15 7 0 90 7 0 90 71 0 70 7 0 50 7 0 30 1 0 15 7 0 00 va We E ae e S T T 970 980 990 1000 1010 1020 1030 970 980 990 1000 Nes 1020 Raman Shift cm Raman Shift cm a b Figure 3 15 Raman spectra for mixtures of pyrimidine and varying mole fractions of a acetic acid and b ethylene glycol Figure 3 15a shows the Raman spectrum for mixtures of pyrimidine and acetic acid The highest energy peak high mole fraction of acetic acid mixtures is due to acetic acid The peak between v and this peak due to acetic acid is the blue shifted peak of interest The shift of this peak to 13 cm higher energy shows that the strength of this hydrogen bond is probably more comparable that of pyrimidine with water However the gradual and continuous shift seen with water is not seen with acetic acid This 47 indicates that despite the fact that acetic acid can form hydrogen bonds with itself and thus forms the network that seems important in the position of v pyrimidine water hydrogen bonds this network does not seem to have the same effect when it is formed by acetic acid The spectra of mixtures of ethylene g
40. ne of a Coherent Innova 200 Ar laser with 1W of power A laser line filter was used to ensure the sample was only being excited with 514nm line A half wave plate Thor Labs was used to rotate the laser polarization so that the sample was illuminated with vertically polarized light Mixtures were prepared using Fisher finnipipettes Pressure studies were carried out using a custom pressure cell with quartz windows attached to a 10 cm piston press High Pressure Equipment Company Pyrimidine was placed in a glass bottle capped with a 35 small section of polyethylene tubing sealed at one end The piston and cell were filled with ethanol and the bottle was placed in the proper position inside the cell The entire system was sealed and the press was used to change the height of the piston and thereby the pressure inside the system Pressure was monitored by means of a gauge attached to the piston Geometry optimizations and frequency calculations were performed using the Gaussian 03 software package All calculations used the B3LYP hybrid functional with a 6 311G d p basis set 3 3 Results and Discussion Weak Hydrogen Bond in Crystalline Pyrimidine Shown in Figure 3 2 is the Raman spectrum of liquid pyrimidine at 20 C An exhaustive literature search showed that only one other Raman spectrum of pyrimidine ever published shows the same level of detail 1 e resolution of peaks and presence of Figure 3 2 Raman spectrum of neat py
41. o detect over the elastically scattered light from the source Problems A w With fluorescence and stray light were avoided by extensively purifying liquid samples for example with PHOTOELECTRONS multiple distillations that required as much as three months preparation time Problems of stray light and fluorescence became insurmountable obstacles to Raman Ay it ah hig af igri wig gf hg spectroscopy of polycrystalline materials Advances in P Paa an m LOAD GROU ND technology through the 1950s 1960s and 1970s Figure 1 2 Principles of a removed the challenges presented by collecting high photomultiplier tube quality Raman spectra The photomultiplier tube Figure 1 2 was invented for astronomers to detect low intensity light and by the 1950s had been incorporated into Raman spectroscopy setups The photomultiplier tube 1s capable of detecting single photons Photons strike a photosensitive material held at high negative voltage 1500V e g and cause the emission of electrons via the photoelectric effect The photomultiplier 1s made up of a number of other dynodes which are conducting plates each held at increasing positive voltage by means of a voltage divider circuit Electrons emitted at the photocathode are accelerated toward the first dynode because of the increasing potential The impact of these electrons then causes emission of even more electrons from the dynode and the cascade of electr
42. ommand waitdone tells the controller to wait until the motor has finished turning before executing any more of the program The parts of the program collecting user input and turning the motor are all contained within a loop that ends once the user enters a value of zero for the number revolutions The significance of this program is that it can be run without the MCPI software Once the program has been downloaded into the controller 1t waits for the run command from the serial port that will begin execution This enables the user to send the command to 21 run the program as well as the required user input via one of Labview s serial communication modules rather than the MCPI The program can even be ended in the manner mentioned above without the MCPI By May 9 2008 a Labview program had been written with the capability to begin execution of the MC BASIC program and turn the stepping motor a user specified number of revolutions The relationship between the number of motor revolutions and a wavenumber value of the grating position was determined using the analog display of the spectrometer itself and later versions of the program allowed the user to turn the motor by entering a wavenumber destination and to choose a speed in wavenumbers per second which would eventually allow for slower or faster scans By May 15 the motion control program had all the necessary qualities of the one required for Raman spectroscopy This program allowed the us
43. ons continues until at the last dynode the number of electrons corresponding to a single photon is greatly increased Electrons strike the anode and create electrical pulses that are amplified and sent to a counter The number of counts is directly proportional to the intensity of the light striking the photocathode and is therefore a measure of signal intensity So called dark counts resulting from emission of electrons without any incident light are minimized by cooling the photomultiplier tube There were other technological advances that improved Raman sources and optics The laser was first used as a Raman source in 1964 to study materials in the gas phase Lasers were ideal for Raman excitations because they were both very intense and monochromatic Diffraction gratings began to replace prisms as the dispersive elements in Raman spectroscopy as they became commercially available by the 1950s Gratings disperse light using destructive interference Each wavelength of light constructively interferes at a certain angle relative to the normal of the grating with all the others interfering destructively Therefore by turning the grating while keeping Raman scattered light incident at a constant angle or alternatively by moving the detection slit the intensity of light can be measured at different wavelengths with very high resolution The first gratings were produced by machines carving slits into the surface of the grating Ruled diffraction grat
44. ot the Spectra Link had these modules removed after it was no longer in use or if the modules had been replaced since the initial computer control upgrade discussed above In any case a stepper motor controller had to be purchased if any attempts to turn the gratings were to be made Sales representatives at Danaher Motion assured us that one of their controllers could be used and connected easily as their parent company Superior Electric had invented stepping motors The SLO SYN WARPDRIVE SS2000D61 is a programmable motor controller and therefore best fit our needs The motor controller 1s controlled by the user via included computer software the motion controller programming interface MCPI The MCPI allows the user to write a routine for the stepping motor in a language based on BASIC MC BASIC for Motion Control BASIC or to type the necessary commands directly into a terminal prompt Connecting the motor to the controller presented no real challenges as Superior Electric had not changed the color codes or pin assignments for their motors or controllers in the last thirty years The controller was connected to the stepping motor via the same RS 232 serial cable that had connected the motor to its previous controller whenever it had last been used The controller is connected to the computer via a homemade RS 232 serial cable with only three of the nine pins connected The controller receives its power from a 100V wall socket The gratings in the sp
45. our chlorine atoms should be the less naturally occurring isotope the most intense peak in the spectrum corresponds to CCl with one Cl and three Cl atoms Just as masses oscillating on a spring have a frequency of vibration inversely proportional to their reduced mass the frequency of the totally symmetric stretch will increase as the reduced mass is decreased As a result we know that the peak at higher frequency than the most intense peak is due to CCly with four C atoms The other two peaks shown correspond to CCl di substituted and tri substituted with Cl atoms The peak corresponding to CCl with four Cl atoms could not be resolved The rarity of this combination means the peak produced 1s too weak to detect CCI liquid 514 nm 8000 CCI liquid 632 8 nm 1W 1pm slits 3 scans 3 0 mW 6000 6 23 08 oy N Na 4000 Counts per 500ms 2000 Raman Intensity arbitrary units 200 400 600 800 1000 440 450 460 470 480 Energy cm Energy cm a c CCI liquid Figure 2 9 a First Raman spectrum 514 5 nm 2 1 mW P 2 26 08 acquired with the new and improved experimental setup b Raman spectrum acquired using CCD camera and Intensity arbitrary units microscope c Raman spectrum showing resolved isotopic peaks 200 400 600 800 1000 Energy cm The last major obstacle in putting a Raman spectroscopy experimental setup into place came shortly after the first spectr
46. r The next step in the restoration of this Raman spectrometer was to see if the detector and associated equipment were still in working order and to alter the Labview program to collect and record data in addition to controlling the diffraction gratings We received from the University of Tennessee the skaleris bake photomultiplier tube housing and the photomultiplier i o m tube itself We also received a NIM bin holding END many of the electronic components needed to use the Scanning speed wavenumbers s 10 0 Recast 8 fo photomultiplier tube The photomultiplier tube oe Recalibrate 8 0 housing is cooled by a water bath in addition to gareni Poston s0 being thermoelectrically cooled The NIM bin 0 included the power source for thermoelectric cooling and the power supply for a no dew feature for the window of the photomultiplier tube housing The 0 0 iw no dew feature did not appear to function any longer Figure 2 6 Labview program with the capability to control the l A but the thermoelectric cooling of the housing was in Ramanor s monochromators with user selected wavenumber positions and display the current wavenumber Perfect working order The photomultiplier tube was outfitted with an IsoTemp circulating bath from Fisher Scientific graciously donated by Dr Susan Pedigo at the University of Mississippi The cooled photomultiplier tube is 23 connected to a newly purchased
47. r instruments that use prisms and gratings in tandem more dispersing elements tend to produce more stray radiation According to the user s manual the HG2 S contains a monochromator 14 comparable in efficiency to a triple grating instrument being able to record Raman lines within 4 cm of the laser line An optical diagram of the instrument reproduced from the original user s manual is shown below in Figure 2 1 Scattered light is emitted from the sample and is focused onto the first mirror M1 M1 directs light through the first slit All R1 R2 Concave Holographic Gratings 2000 groovesimm F1 F2 F3 F4 Slits 0um 20um M1 M2 M3 M5 M6 Plane Mirrors ETI M4 Concave Mirror 01 Entrance Lens 02 Exit Lens L1 Lens PMT Photomultiplier Tube Sample Figure 2 1 Optical diagram of Ramanor HG2 S Raman spectrometer with explanations Note that additional optics allowing a single monochromator option have been omitted four slits in the Ramanor are stepping motor controlled and can be set to widths between Oum and 20um in steps of 0 0lum The light from slit one is dispersed by the first concave holographic grating and directed through F2 The light then passes through the second monochromator equipped as the first with two slits and a concave holographic grating The two monochromators are joined by a concave mirror labeled M4 in the diagram The dispersed Raman scattered light 1s foc
48. requirement ABSTRACT AUSTIN ARCHIE HOWARD Upgrade of a Raman Spectrometer with Modern Computer Control and Data Acquisition for Studies of Hydrogen Bonding in Pyrimidine Under the direction of Dr Nathan Hammer The restoration of a Cold War era high resolution Raman spectrometer to working order as well as its control and data acquisition upgrade using a Labview program authored for this purpose are discussed The restored Raman spectrometer was used in an investigation of intermolecular interactions involving pyrimidine Following in this manuscript are three chapters The first chapter 1s a brief description of the history and theory of Raman spectroscopy as well as some details of the instrumentation used in Raman spectroscopy The second chapter contains technical details of the restoration and upgrade of the high resolution Raman spectrometer The third chapter contains data and analysis for the investigation of intermolecular interactions involving pyrimidine including the investigation of weak hydrogen bonds by Raman spectroscopy of liquid and crystalline pyrimidine at varying pressures up to 30000 psi and strong hydrogen bonds in binary mixtures of pyrimidine and seven different molecules The position of the v peak in the Raman spectrum corresponding to pyrimidine s ring breathing mode was used as the marker to monitor the degree of hydrogen bonding and species involved For mixtures of water other peaks in the Raman spectrum were fo
49. resolution a Raman spectrum can be using the Ramanor instead of more modern instruments and detectors Also notice that the spectrum acquired with the Ramanor shows the resolution of both peaks of the Fermi resonance just below 800 cm whereas the Fermi resonance appears as just one broad peak in the second spectrum The first spectrum also contains several small peaks that probably correspond to other HeNe lines The high resolution of this first attempt at a spectrum was a victory in perfecting the Raman spectroscopy setup However the Ramanor can record spectra with much higher laser power than the 3 0 mW used in the first spectrum which improves the resolution further With higher power the slit width can be closed more and slower scan speeds can be executed both of which will also increase resolution Figure 2 9c shows the Raman spectrum of carbon tetrachloride collected around the peak at 459 cm in the Figures 2 9a and 2 9b The spectrum shown is the average of three scans collected with 1 W of laser power with a 1 um slit width The mode corresponding to this peak is the totally symmetric stretch wherein all carbon chlorine bonds lengthen or contract at the same time Chlorine s most abundant isotopes are Cl and Cl These occur in a ratio of 27 roughly 3 1 This ratio is high enough that modes corresponding to different combinations of chlorine isotopes in CCl can be resolved in the Raman spectrum Since one out of every f
50. rimidine 500 1000 1500 2000 2500 3000 3500 Raman Shift cm combination bands The most intense peak in the spectrum corresponds to v To ensure local heating effects were not influencing spectra because of the high laser power 36 spectra of pyrimidine were collected at lower power and showed no difference in the position or relative intensity of peaks The high power was used merely to achieve the highest signal to noise ratio in the Raman spectrum Shown in Figure 3 3 are the Raman spectra of pyrimidine at pressures 10000 psi 20000 psi and 30000 psi in addition to the spectrum at atmospheric pressure 14 7 psi all of which were acquired in the high pressure cell filled with ethanol Regions of interest are shown in greater detail and discussed below From comparison of the spectra at 30000 psi and solid pyrimidine 30000 psi Figure 3 3 Raman spectra of l pyrimidine at elevated pressures 20000 psi ee Pyrimidine crystallizes between 20000 psi and 30000 psi 10000 psi Atmospheric Pressure 500 1000 1500 2000 2500 3000 3500 1 Raman Shift cm 3 C atmospheric pressure it was determined that pyrimidine crystallizes at some pressure between 20000 psi and 30000 psi The conclusion is that intermolecular interactions of the liquid molecules are maximized somewhere between these two pressures just before the solid is formed Figure 3 4 shows the 400 800 cm region of Figure 3 3 enlarged Notice th
51. rimidine were obtained at atmospheric pressure and at elevated pressures up to 30000 psi to probe the effects of weak hydrogen bonds in crystalline pyrimidine Additionally Raman spectra of binary mixtures of pyrimidine and varying concentrations of seven other molecules were acquired to investigate strong hydrogen bonds in terms of the evolution of the Raman spectrum with changing compositions of the mixtures 3 1 Introduction Hydrogen bonding a weak intermolecular interaction is an extensively investigated phenomenon due to its importance in the chemical and physical properties of water the compound most essential to life on earth as well as its importance in the structure and function of biomolecules including amino acids nucleotides monosaccharides and the polymers formed from these molecules Hydrogen bonding has been 31 investigated since the 19 century even before the term hydrogen bond was coined by Linus Pauling in a 1931 paper on the nature of the chemical bond Typically hydrogen bonding occurs between an electron deficient hydrogen atom covalently bonded to an electronegative atom and another electronegative element with lone electron pairs Another weak intermolecular interaction important in biological systems is the so called m stacking interactions between the delocalized a systems of aromatic molecules Nitrogen containing aromatic heterocycles are suitable prototype molecules for studying these interactions
52. roller The instruction manual for the interface controller contained the form of each command that can be read and understood by the device These commands take the form of four different control characters members of character sets that do not correspond to written symbols Labview is capable of sending control characters via serial port as their hexadecimal equivalents The Raman program 24 was modified then to send through the serial port connected to the interface controller a Control T followed by a Control R hexadecimal 14 and 18 respectively each time a data point was to be read These commands cause the interface controller to read a number of counts from the photon counter and send it to the computer resetting the counter to zero immediately afterward In the final version of the program this data collection cycle takes place every 0 02s The data collection was successfully implemented into the program capable of turning the diffraction gratings and a few more features were added before the program was finalized The final version allows selection OIREET of different laser lines so Relative 510 187 Absolute 18926 1 O z Bee wavenumber data can be that the relative Recalibrate read correctly The final version also includes the option for the user to move the gratings to an absolute or relative wavenumber Figure 2 7 The front panel of the final version of the Labview program
53. s and thus new light of the same frequency as the incident light has been produced emanating in all directions from the molecule This scattering process is termed elastic because the energy of the incident light is equal to the energy of the scattered light following from the fact that energy is related to frequency by Planck s constant Eqn 1 e hf 1 We can imagine this process with a classical picture of the oscillating dipole described above In a linear dielectric material the magnitude of an induced dipole is given by Equation 2 p ak 2 In Equation 2 p represents the magnitude of the induced dipole a is the polarizability of the material and E is the magnitude of the electric field responsible for the induced dipole For electromagnetic radiation we know that the electric field has the form E E cos wt where E is the magnitude of the electric field is the angular frequency the frequency f in hertz multiplied by 27 and is the time It is trivial then to substitute the correct form of the electric field in an incident light wave into Equation 2 to obtain Equation 3 an expression for the frequency of the oscillating dipole when light undergoes Rayleigh scattering p aE cos wt 3 When a photon is inelastically scattered Raman scattered the scattered radiation has a different energy and thus frequency than the incident radiation Inelastic scattering of photons was first discovered in 1923 when Arthur Ho
54. tructure are indicated by the broken lines Note that these are not the strong hydrogen bonds between electronegative elements and hydrogen atoms bonded other electronegative elements These are weak interactions forced when pressure is increased or when the temperature is decreased causing crystallization The location of these interactions shows clearly how the modes pictured in Figure 3 5 are perturbed as pressure is increased An enlargement of the 2900 3200 cm region of Figure 3 3 is shown in Figure 3 7 Here we see similar changes occurring but in the CH stretching region of the spectrum Note the appearance 30000 psi 20000 psi l Figure 3 7 Raman spectra of pyrimidine at the indicated pressures Note the change in the mode at 3079cm discussed in the text 10000 psi Atmospheric Pressure 2900 3000 3100 3200 Raman Shift cm of the peak at 3079 cm This peak is present at all pressures but becomes much sharper and more pronounced as the pressure is increased This peak corresponds to the CH stretch for the CH group not connected to any nitrogen atoms Note in the crystal 39 structure that the shortest intermolecular distance is between the hydrogen atom in this CH group and a nitrogen atom on a neighboring pyrimidine molecule The crystal structure would lead us to believe that this is a relatively strong interaction and the Raman spectrum indicates that this is indeed the case Similar changes can be seen
55. um was collected in switching from a HeNe laser to an Ar laser An Ar laser emits light that is polarized while a HeNe laser s light is 28 generally not As noted in the first section of this manuscript Raman scattered light is polarized This effect is most noticeable when the source illumination is polarized Imagine a totally symmetric mode as described above The polarizability change during this vibration changes the same way in all directions The electric field of plane polarized light then will induce a dipole moment in a direction parallel to the electric field Most of the Raman scattered light will be polarized in the same direction as the incident light and scattered at all angles perpendicular to this polarization Collecting light perpendicularly to the laser as with the Ramanor requires vertically polarized light Otherwise totally symmetric modes appear with much lower intensity Other modes may also be affected but since their interaction with the electric field 1s more complicated they may not always exhibit peaks at a greatly reduced intensity Our setup used horizontally polarized Ar laser light In switching from the HeNe to the Ar laser the intensity of the totally symmetric mode of benzene at 990 cm was being monitored for signal optimization purposes and was found to be drastically reduced in intensity with the new laser despite higher power From this it was determined that the laser light was polarized incorrectly
56. und to shift as well when the concentration of water 1s increased TABLE OF CONTENTS 1 History Theory and Instrumentation ccccccscccsccccccccccccccccccccsssssscccccsceecces Id bight Matter Mra Osnon n AAEE R2 The Raman ECCT arrere a a A A E EN E EAN 4 Boa ea O A E N AOR LCL CNC CS iiot EEE EERE EEE UEIT E EEE E IEE EET 12 2 Upgrade of a High Resolution Cold War Era Raman Spectrometer for Modern Data Acquisition and COmntrol cccccccccssccccccccssccsssccsccccceccccessees 14 2 1 Ramanor HG2 S Raman Spectrometer oarenien e ATENT 14 22 ISRO Oena a r a aE a Sem ahaeieest 19 2 5 Th New Experimental SCM Pacicxcace des irises Ernim EEan ERARE EEEE EAN een une 26 Diet INC LCLCNCCS oreren raea Ta EEE ETAETA EATR EEEN 30 3 Raman Spectroscopic Investigations of Intermolecular Interactions Involving Pyrimidine E E E E E INDU Odc Oeren E E E O r aa a 31 I2 EXPE Mena leaner ET E ERE T EEEE EEEN EEG 35 3o IRESUITS and DISCUSSION cerkes iieiaeie e a a E S 36 P REE E yarns E E E E EE EERI IE EE E E A ETE 49 IR TOCOS aeren E E AS 50 1 History Theory and Instrumentation Spectroscopy is the study of the interaction of light and matter The measurement of this interaction can reveal a wide range of chemical and physical behavior in systems being studied Raman spectroscopy exploits the Raman Effect the inelastic scattering of light by molecules Following is a brief introduction to the interaction of light and matter
57. used onto the photomultiplier tube by two lenses Scans are carried out by rotating the two gratings about an axis parallel to the page via a stepping motor The opening of the slits 1s parallel to the rotation axis of the gratings This arrangement of slits and gratings is known as the Littrow 15 configuration The Ramanor is equipped with optics on a platform that can be lowered into position to divert the light between M5 and M6 directly to the photomultiplier tube This option allows the Ramanor to be used as if it were equipped with a single monochromator These optics are not shown in the optical diagram in Figure 2 1 Photographs of the optics pictured in Figure 2 1 are shown in Figure 2 2 and Figure 2 3 below Figure 2 2 The plane mirrors of the Figure 2 3 The monochromators of the Ramanor A sample is placed outside the Ramanor The camera s flash is being dispersed outlet on the left in the photograph The concave mirror is between the two gratings The monochromator was originally controlled by an electronic rack that allowed users to control wavenumber position scan speed and slit width Spectra were acquired manually or using a device that allowed automation of spectral acquisition known as the Ramandigit 03 The original operations manual contains serial connection pin assignments and necessary commands to fully automate scanning using a computer either with or without the Ramandigit 03 The Ramandigit 03 provided a dig
58. with its high signal to noise ratio and high sensitivity However acquiring spectra was still a lengthy process A Raman spectrometer employing diffraction gratings and a photomultiplier tube has to collect one data point at time That is the photon counter must record data with the diffraction grating at one position and then turn the grating by a small amount before acquiring more data Slow scans over a range of 3000 cm or more would take hours In addition the time required must be multiplied if multiple spectra are to be collected and averaged for signal to noise enhancement This meant that any system stable for only short amounts of time could not be studied directly by Raman spectroscopy Furthermore Raman spectroscopy could not be used as a way to monitor a system s 11 evolution in time because of the scanning time required These problems were addressed when multichannel detectors the digital analog of photographic plates were invented Although photographic plates measure an entire spectrum simultaneously the process is not quick as plates must be exposed for long amounts of time and then developed Modern multichannel detectors use an array of photosensitive elements containing electronic circuitry to detect light In a photodiode array PDA photodiodes are arranged linearly and are placed in the plane of dispersed light The light incident on an individual photodiode causes a buildup of charge that can be measured

- University of Mississippi

Contents

Download Pdf Manuals

Related Search

Related Contents