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MERCURYplus Calibration, Demonstration, and

1. External hard disk Mbytes Serial no Tape drive size Serial no CD ROM drive model Serial no Printer model Serial no Plotter model Serial no Terminal model Serial no Other peripheral Serial no Computer function NMR host Workstation running VnmrJ on site or off site Workstation running other NMR software on site or off site Workstation running VnmrJ and other NMR software on site or off site VnmrJ version Operating system The above computer audit was performed during installation of the system Varian Representative Date I certify that the information on this form is accurate and that all computers to be used to run VnmrJ software including variants VnmrS VnmrX Vnmrl VnmrSGI and VnmrV or to run other software to process data obtained on this spectrometer have been included in the audit including those previously registered as part of purchases of other Varian NUR spectrometers Customer Representative Date 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 61 Chapter 5 Acceptance Test Results Use these forms for additional computers If more forms are needed copy this page Attach all copies to the Computer Audit Information on computer Manufacturer Computer S N Memory Mbytes Peripherals Internal hard disk Mbytes External hard disk Mbytes Tape drive size CD ROM drive model Printer model Plotter model Terminal model O
2. You can reload the 1D data but if you do that in the current workspace it will replace the COSY data so you may want to use another workspace instead 1 Select Create a Workspace under the Utilities menu Utilities gt Create a Workspace A list of experiments appears in the locator 2 Double click exp2 in the locator 3 Click the Home button above the file browser The easiest but not the only way to retrieve your data is from the Locator 40 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 4 5 Basic Spectrometer Operation Click on the Locator Statements icon and select Sort NMR Data The search statement appears next to the Locator Statements icon Show all Data Run by everyone on any date Right click everyone and select me Click the square underneath the time_run to sort the data by time Drag your proton 1D experiment into the graphics window It is automatically processed Selecting Sort Workspaces from the Locator Statements will once again list exp1 exp2 etc in the locator Switch between workspaces by double clicking on the Show all Data Run byeveryone on any date Sort Workspaces All by group Sort automation by Autodir Name Sort Studies by project by notebook and page Sort NMR Data by type by group by pulse sequence by user defined attributes Sort Shimsets by probe and shims by user defined attributes suwe s pem
3. CAUTION The use of air as the VT gas for temperatures above 100 C is not recommended Such use destructively oxidizes the heater element and the thermocouple Demonstration Limitations If dry nitrogen gas and liquid nitrogen are unavailable at the time of installation the range of VT demonstration is limited to temperatures between 30 C and 100 C Sample No sample is used Probe and Hardware Requirements Any VT probe is used Procedure 1 Click the Utilities menu and select Systems Settings 2 Click the System config button and verify the VT Controller is set to Present 3 Set N2 gas flow to 9 5 to 10 0 LPM for temperatures below 100 C increase N2 flow to 12 LPM 4 Click the Start tab and select the Spin Temperature page a Enter a value in the temperature field or use the slider bar to set a value The heat exchanger must be in place for values below room temperature b Click the Regulate Temp button Maintain the temperature for 5 minutes 5 Operate the VT unit within the specifications of the probe Test the temperature at set points that correspond to the following 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 25 Chapter 2 Console and Magnet Test Procedures e Maximum minimum and midpoint of the allowed temperature 95 80 60 if air is used 120 30 20 if dry nitrogen is used or 120 100 40 if a heat exchanger is used Ambient temperature The software lim
4. Phone Spectrometer type Fax Console S N Sales Order No Magnet S N Magnet Familiarization Done Topic Reference Overall magnet familiarization Oxford Magnet Reference Manual LHe and LN top off procedures Oxford Magnet Reference Manual and Lhe refill video Use of flow meters Oxford Magnet Reference Manual Antivibration system operation Antivibration Accessory Installation Manual Posting of magnetic field warning signs Appendix A Posting Requirements for Magnetic Field Warning Signs Probes Done Topic Reference Probe installation Choose a specific probe manual removal tuning and filter setup for ID AutoSwitchable probes and TR experiments Broadband probes Indirect Detection probes Nano probes Dual and DualBB probes Flow probes VT system installation Variable Temperature Unit Installation VT system operation User Guide Liquids NMR Console Done Topic Reference Major component overview System Overview OS Shut down procedures Solaris Installation and Administration Host console connection and overview VnmrJ Installation and Administration 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 63 Chapter 5 Acceptance Test Results Host Computer Done Topic Reference Host computer setup VunmrJ installation Directory structure overview Using acqproc and makeuser commands Storage devices and acces
5. Building a Composite Protocol page 21 e Customizing the Parameters and Starting Data Acquisition page 22 e Acquiring Data Using a Composite Protocol page 22 These experiments demonstrate the capabilities of the spectrometer the correct calibration of the instrument and validate the correct functioning of the instrument These experiments do not use the sample changer If a sample changer is present set traymax 0 The following is part of the ATP and training session Set up and use Walkup interface e Use the application type selection drop down menu to select the application type Std1D Hetero 2D and Homo 2D Set up 1D 2D gradient if appropriate hardware is installed and non gradient protocols by selecting from the list of protocols the experimental protocols for proton and carbon 1D homonuclear 2D and heteronuclear 2D experiments e Create run save data and plot the results obtained a composite protocol Use the VnmrJ Walkup interface for these experiments it is a required part of the ATP These experiments can be run using either the Walkup Account Owner or Walkup Operator interface Refer to the VamrJ Software Installation and Administration manual for instructions on setting the user interface both the walkup administrator and walkup operator and the Walkup VnmrJ manual for working with the VnmrJ Walkup interface Sample for Automated Data Acquisition Sample Sample Size mm Sample Part Num
6. Dept hcemult varian Dqcosy homo2d varian 5 Fill out sample information select solvent 8605 homaza vaan Jad add eke Po 6 Click the Find z0 button The system acquires data and writes out a message with the z0 value 7 Click on the Gradient Shim button 8 After the system finishes gradient shimming select the Lock page and click the Lock On button 9 Click the Acquire tab Set the following as appropriate although the default values are good for this example Number of Transients e Spectral Width Relaxation Delay 10 Click on the Acquire button to start the acquisition The spectrum is displayed but not saved First we will save the data and then demonstrate integration and custom plotting Save the Data 1 Click the Acquire tab and select the Future Actions page 2 Click the Save FID Now button The FID is be saved in your local data directory Alternatively you can select Automatic FID save before you start your experiment and the FID will automatically be saved in your local data directory when the experiment is done 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 43 Chapter 4 Customer Training Integration l 2 3 Cursor or box Expand or full display Set integrals _ gt Display scale Integral resets Grab and move Integral LvI TIt Threshold Phase Refresh Return to gt pe Li To reset the integral regions by hand click the Se
7. Provides information about the walkup NMR interfaces available in VnmrJ step by step instruction on setting up experiments instructions for automated sample changer operation VamrJ Liquids NMR Provides an overview of VnmrJ and instrument operations instructions for locking shimming and probe tuning explanations of data acquisition parameters and digital signal processing data processing display and plotting instructions for setting up all the standard experiments provided with VnmrJ Not every experiment listed can be run on every system The type and configuration of the instrument will determine which experiments can be run This is the manual to go to when you have very specialized experimental requirements and will most likely be running the experiments from the command line Installations Installation Planning Guide Provides site planning information and site requirements Acceptance Test Procedures Provides installation test procedures and specifications for spectrometer and magnet Included in this manual is the information used by the installation engineer for the introductory training at the end of the installation This manual does not cover the probe test procedures but refers to them VamrJ Installation and Administration Provides instructions for the installation VnmrJ software instructions for setting up various plotters and printers
8. The calibration will follow the same pattern as the calibration of the proton pw90 and the carbon pwx90 using default values for target values if no target specification is given A reference carbon spectrum is obtained first The Ill l full reference spectrum contains three il Luuli sets of resonances at the far right Figure 7 Gradient Calibrations approximately 22 ppm is the HE resonance from methyl iodide the doublet at 10 ppm is from the 13C resonance from the phosponate methylester and the 1 1 1 triplet far left at 78 ppm is the 13C resonance of chloroform d HCCI The carbon pw90 calibration is analogous to the proton calibration The reference carbon spectrum shown in Figure 8 is saved as C13 ref W 5 10 15 20 25 30 35 40 45 ppm Figure 8 Proton Coupled e Spectrum of 3C Methyl Iodide 48 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 4 6 Interpreting the Calibration and Indanone Spectra The carbon observe pw90 is determined using a pw array see Figure 9 and saved as C13pw90 TUL Figure 9 13C Observe pw Array of Proton Coupled Spectra a a The final calibration is of the proton decoupler The first calibration step determines the value of yH at a decoupler power of 40 the default value This measurement is made usin
9. is created and the VnmrJ administration interface is run from this user account Each user account is assigned to an interface type Experimental Walkup or Imaging During the training process both the Experimental and Walkup interfaces are used 2 oe a The calibration procedures are run by the VnmrJ administrator typically vnmr1 using the Experimental interface The automated data acquisition procedures are run by either the walkup account owner or by an operator that does not have UNIX system privileges but has NMR operating privileges by way of the Walkup Operator interface Login as the VnmrJ Administrator typically vnmr1 Open a terminal window Enter vnmrj adm the VnmrJ Administration interface starts Set the VnmrJ Administrator account to use the Experimental interface as follows a Click on the VnmrJ administrator login in the user panel b Click on the radio button next to Experimental in the user profile panel if this button is not already selected 36 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 5 Basic Spectrometer Operation c Click on Save User in the menu bar 5 Seta user for the Walkup interface as follows a Click on the user s login in the users panel b Click on the radio button next to Walkup in the user profile panel if this button is not already selected c Click on Save User in the menu bar 6 Exit the VnmrJ Administration interface a Click on Manageme
10. or use the slider bar to set a value b Click the Regulate Temp button Wait a minimum of 10 minutes for the temperature reach regulation 6 Repeat the procedure in Data Acquisition page 27 7 After finishing the low temperature test a Click the Start tab and select the Spin Temperature page b Click the Temp Off button c Click the Reset VT button d Keep the dry nitrogen gas flowing to the probe and upper barrel e Remove the polystyrene VT dewar containing liquid nitrogen f Continue the flow of dry nitrogen gas to the probe to prevent condensation inside the probe Allow the dry nitrogen gas to flow through the probe and upper barrel for at least 15 minutes while the probe warms up to room temperature 28 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 4 Optional Tests Data Analysis Plot a graph of the VT controller reading horizontal axis as compared with the calculated VT reading from the chemical shift differences between the two peaks vertical axis Draw a straight line through the points Stability Calibration for High Stability VT Optional Test This optional test is for high stability VT units only Part No 00 992953 00 The test demonstrates that the VT unit can hold the temperature with 0 1 C The test requires preconditioning of the laboratory air and restricts the room temperature fluctuations Table 4 Samples for Optional High Stability VT Test Sample Tub
11. the HSQC experiment has the advantage that the H H homonuclear coupling do not evolve As a result the resolution in the 2D plane is higher in the HSQC experiment The higher resolution has the added advantage of improving the signal to noise The version of the HSQC experiment supplied with VnmrJ has the added benefit that it will distinguish CH CH and CH 3 groups In this case phase is indicated by whether the crosspeak is filled in with multiple contours above the plane or is a single contour below the plane By contrast to the gHSQC experiment the gHMBC and HMBC experiment shows long range mostly 2 and 3 bond H 3C correlations This shows connectivity between the non protonated carbonyl and the protons on C 2 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 53 Chapter 4 Customer Training 10 D So lt O B bd e t8 2 pa 3 4 3 2 3 0 2 8 2 6 2 4 2 2 2 0 1 8 1 6 1 4 1 2 1 0 F1 ppm Figure 19 TOCSY of 2 Ethyl 1 Indanone Correlations of Protons on C11 C10 C3 to Aa 3 E A cf pai d a ee 4 S J E E 77 p 3 a T T T T T T T T 8 7 6 5 4 3 2 1 Figure 20 NOESY Spectrum of 2 Ethyl 1 Indanone 54 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 4 6 Interpreting the Calibration and Indanone Spectra TTT TL TTT TET TTT TTT 130 110 90 80 70 60 50 40 3
12. Files from under the Sort NMR Parameter Files category 3 Click the title above the right most column and select Directory from the lists that is displayed Select shmd2o and drag it to the VnmrJ graphics canvas Insert the doped 2 Hz H 0 D 0 sample 01 901855 01 Go to the Lock page Start tab gt Lock page Click Lock Scan and set Lock to Off SP Oy a Adjust Z0 to be on resonance Adjust this as close as possible the shimmap depends on accuracy 8 Adjust Power Gain and Phase for a steady lock level of about 80 9 Click Lock Scan to stop the lock update Click Standard to go to the Study page Setting Up the Probe Calibration File Before you calibrate a probe for the first time you must set up the probe calibration file You must be logged in as the VnmrJ administrator for this procedure 1 Select Utilities gt Standard Calibration Experiments gt Calibrate Probe or click the Probe button on the hardware bar see Figure 1 2 Click the Edit Probe box editing options appear in the Probe window From the Utilities menu do this From the hardware bar do this OR m Standard Calibration Experiments Calibrate Probe Study Options zl Submit Save data Start Autotest Time Display options Autotest settings TSIEN ESHA BEE Pro Aaima o l HCN_123 Select LL 123 Sj Click AE Grayed if the probe is a system level probe and active for us
13. High The samples required for acceptance testing of any individual probe are supplied with the probe Typical samples required for probe acceptance tests are chloroform in acetone d ethyl benzene in chloroform d and ASTM 40 p dioxane in 60 benzene d6 Other samples might be required depending upon the type of probe The specific sample requirements and test procedures are specified in the manual for each probe 1 4 General Testing and Specification Requirements 12 The MERCURYplus performance specifications in effect at the time of your order are used to evaluate the system The appropriate quarter wavelength cable must be used for each nucleus except AutoSwitchable probes operated in 4 nucleus mode The 31p quarter wavelength cable is used in this case Homogeneity settings must be optimized for each sample manual shimming may be required in any or all cases The shim parameters for resolution tests on each probe should be recorded in a log book and in a separate file name in the directory vnmr shims for each probe For example for a 5 mm switchable probe the shim parameters can be saved with the command svs sw5res These values can then MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 1 4 General Testing and Specification Requirements be used as a starting point when adjusting the homogeneity on unknown samples by the command rts sw5res The probe must be tuned to the approp
14. Presat Carbon Phosphorus Dept Study Options zl i Lenath experiment Exercise 3 1D Proton HSQC and More The purpose of this exercise is to e introduce the Hetero 2D experiments in Walkup select multiple experiments remove experiments Queue Experiments VnmrJ runs the experiments in the order they appear in the queue Also if 1D spectra are available the spectra are plotted on the edge of the 2D plot If no 3C 1D spectrum is available an F1 projection will be plotted instead 1 Select the Hetero 2D tab 2 Click once on the Ghsqe button or Hsqc if your system does not have gradients Notice as before a Proton 1D is also queued 3 Click the Ghmbc button or Hmbc if your system does not have gradients The Ghmbc is added to the queue 4 Select the Std1D tab Click Carbon and drag it into the Study Queue between the Proton and Ghsqc The Carbon experiment will be run before the HSQC Remove an Experiment Removing experiments from the locator is just as easy 1 Click the Ghmbce the larger blue letters A yellow box appears around the Ghmbc 2 Drag it to the trash can Run the Hetero 2D Experiments 1 Double click 1 min Proton and as before select the Start tab then the Study page 2 Enter sample and text information if desired Also if your sample is already locked and shimmed deselect the Find z0 and gradient shimming boxes Make sure the solvent is set t
15. Start page 16 e Setting Up the Probe Calibration File page 16 e Calibrating ZO and Make LOCK gmap page 17 e Calibrating Probe and System Files page 18 Lineshape and resolution tests described in the probe manual shipped with your probe must be run before these procedures are run The probe calibration procedures create probe calibration files that are used for some of the console procedures The probe calibration data written to these probe files will meet or exceed the specifications for the probe Probe performance tests and calibrations that are executed during AutoCalibration will not be repeated manually Probe Calibration Samples The following samples are required for probe calibration Sample i le Tube Nuclei Part No 13C enriched 1 methyl iodide 1 trimethyl 5 IH Bcand 00 968120 96 phosphite and 0 2 Cr AcAc in chloroform d 31p doped 4 Hz H O D 0 0 1 mg ml GdCl in 5 1H 01 901855 01 1 H O in D70 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 1 5 Chapter 2 Console and Magnet Test Procedures Before You Start Before beginning the probe calibration you should already have the following e defined a printer and plotter see VnmrJ Installation and Administrator for details obtained the lineshape specifications see the appropriate probe manual for details 1 Log in as the VnmrJ administrator 2 Click the Locator Statements menu P and select System Param
16. Std 1D tab and click the following experimental protocols in this order a Proton b Carbon c Dept d Apt 2D Nongradient Protocols 1 Click the Homo 2D tab and click the following experimental protocols in this order a Tocsy b Noesy c Cosy click only if the system does not have gradients 2 Continue with 2D Gradient Protocols page 21 if the system has gradients go to Customizing the Parameters and Starting Data Acquisition page 22 if the system does not have gradients 2D Gradient Protocols 1 From the Homo 2D tab click Gcosy 2 Click the Hetero 2D tab and click the following experimental protocols in this order a Ghsqe b Ghmbc 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 21 Chapter 2 Console and Magnet Test Procedures Customizing the Parameters and Starting Data Acquisition The study queue contains the protocols in the order each one was selected and should look similar to the study queue shown below e Customize the Noesy Parameters page 22 e Customize the Carbon Parameters page 22 Customize the Noesy Parameters os tnew sample Proton amp Presat Protocol L120 sec Presat B Tocsy ay Node L 22 min 38 sec Tocsy SE Acquire Process M Show Tire Time__ Pulse Sequence NOESY Display Sequence Fourier Number in F2 amp Ft 2kx2k v Scans per increment 16 Linear Prediction in tt Tni z vcr ti crement
17. be run 1D Experiments IH Bog APT and DEPT e 2D Non gradient experiments NOESY and TOCSY for non gradient system or probe COSY is also run e 2D Gradient experiments gCOSY gHSQC gHMBC will be demonstrated if gradients are present Walk through the demonstration spectra and the Interpreting the Calibration and Indanone Spectra page 46 Demonstration of gradient shimming using PFG gradients if present or homospoil Review how to use the manuals online and hard copy and where to find information Review the post installation 30 day check list Detailed specifications and circuit descriptions are not covered Formal training in the operation and maintenance of the spectrometer is conducted by Varian Inc at periodically scheduled training seminars held in most Varian Inc NMR Application Laboratories Installation engineers are responsible for guiding you through the acquisition of the spectra as provided in the manual The installation engineer is not responsible for interpretation of the results beyond what is provided in this manual On site training is available in some geographic locations Contact your sales representative 4 9 Warranty and Who to Call for Assistance page 57 for further information on availability and pricing for these courses To make the system demonstration most beneficial the customer should review Varian Inc and OEM manuals before viewing the demonstration 01 999255
18. checked after the magnet is installed Only qualified maintenance personnel shall remove equipment covers or make internal adjustments Dangerous high voltages that can kill or injure exist inside the instrument Before working inside a cabinet turn off the main system power switch located on the back of the console Do not substitute parts or modify the instrument Any unauthorized modification could injure personnel or damage equipment and potentially terminate the warranty agreements and or service contract Written authorization approved by a Varian Inc product manager is required to implement any changes to the hardware of a Varian NMR spectrometer Maintain safety features by referring system service to a Varian service office Do not operate in the presence of flammable gases or fumes Operation with flammable gases or fumes present creates the risk of injury or death from toxic fumes explosion or fire Leave area immediately in the event of a magnet quench If the magnet should quench sudden appearance of gasses from the top of the dewar leave the area immediately Sudden release of helium or nitrogen gases can rapidly displace oxygen in an enclosed space creating a possibility of asphyxiation Helium will displace air from the top of a room and cold nitrogen can displace air from the lower levels of a room Do not return until the oxygen level returns to normal Avoid helium or nitrogen contact with any part of the bod
19. installation engineer 9 Installation Planning Guide 34 installation planning guide 12 L lineshape determination digital 13 from a plot 13 linewidth measurement 14 liquid nitrogen 25 32 loading programs 11 Low Temperature Calibrations Test optional 28 M magnet acceptance tests 15 magnet demonstration 11 magnet drift test procedure 23 sample and part number 23 magnet quench warning 6 magnet refilling 11 magnetic media caution 7 metal objects warning 5 methanol 26 modifying the instrument 6 N nitrogen contact with body 6 nitrogen gas 25 31 nitrogen gas flowmeters caution 8 noise region 14 O OEM manuals 10 P pacemaker warning 5 policies for acceptance test specifications 10 preinstallation checklist 65 Probe Acceptance Test Procedures and Specifications Manuals 34 Probe calibration setup 16 Z0 and Make LOCK gmap 17 MERCURYplus Console Acceptance Tests for VamrJ 73 Index probe demonstration 11 prosthetic parts warning 5 pw parameter 13 Q quarter wavelength cable 12 R radio frequency emission regulations 8 relief valves warning 7 removable quench tubes warning 7 rts command 13 S safety precautions 5 7 samples required for acceptance testing 12 sensitivity tests 13 shim parameters 12 shipment damage 65 signal to noise measurement 13 skin damage from helium and nitrogen 56 Software Installation 34 Software Object Code License Agree
20. ppm that arise from C outer pair of doublets and 12C inner doublet of the methyl ester The analysis of this sample is fully discussed in an article by Paul Keifer in Magnetic Moments Keifer P A Magnetic Moments 1996 8 2 18 20 The reaction results in a sample is partially enriched to give approximately 60 abundance of carbon 13 in methyl iodide The natural abundance of carbon 13 is 1 1 so this level of enrichment is more then adequate for the purposes of calibration The next spectrum shown in Figure 4 is an array of increasing H pulse widths based on the H pulse you specified in the Acquire window If you did not enter a value for the pulse width it is set to the default targets pw90 is set to 15 us and tpwr of 51 adl Figure 4 IH pw Array The observe transmitter power is set to the value you specified and reduce by 3 for the first test If the resulting pw90 is shorter then the value you specified or the default if you did not specify a pw90 target the next test is started If the pw90 is longer then the target the observe power is increased Two attempts are made If the calibration fails to achieve a pw90 that is less than the specified pw90 the AutoCalibration exits If either attempt yields a pw90 that is less then the specified value the AutoCalibration routine adjusts the observe power the remaining tests are aborted If the pw90 is less then the specified value the AutoCalibration then adjusts the power unti
21. 0 20 F1 ppm Figure 21 HSQC Spectrum of 2 Ethyl 1 Indanone 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 55 Chapter 4 Customer Training 4 7 Magnet Maintenance Magnet maintenance is described in the VamrJ Installation and Administration manual Before undertaking any work with the magnet read the warnings below and in the SAFETY PRECAUTIONS page 5 of this manual Also be sure to review the documentation provided by the magnet vendor WARNING The extremely low temperature of liquefied helium and nitrogen can cause skin damage similar to high temperature burns Contact with the cold gas evolving from the liquid may produce the same effect Delicate body tissues such as the eyes are easily damaged by exposure to cold gas or liquid Skin can stick to metal that is refrigerated by liquid helium and can tear when pulled away Immediately flood with large quantities of unheated water any area of the body that is burned by liquid or cold gas and then apply cold compresses If the skin is blistered or there is any chance the eyes are affected immediately seek medical treatment WARNING Wear goggles and loose fitting protective gloves while working with cyrogens Magnet maintenance consists of three basic elements e Periodic checks of the cryogen levels and boil off rates Liquid nitrogen fill Liquid helium fill All cryogens should be delivered in nonmagnetic dewars Consult the manual supp
22. 0 55 or 4 95 cm from the baseline If the noise is significant at the 0 55 and 0 11 levels the linewidth should be measured horizontally to the center of the noise e Use the dsnmax macro to determine signal to noise sensitivity You can also choose a noise region free of any anomalous features with the cursors Neither cursor should be placed any closer to an edge of the spectrum than 10 percent of the value of sw This should produce the best possible signal to noise that is representative of the spectrum The results of all tests should be plotted to create a permanent record Include a descriptive label and a list of parameters These plots can then be saved as part of the acceptance tests documentation 14 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 Chapter 2 Console and Magnet Test Procedures Sections in this chapter e 2 1 Calibrating a Probe page 15 e 2 2 Automated Data Acquisition page 19 2 3 Magnet Drift Test page 23 e 2 4 Optional Tests page 25 This chapter contains the procedures for testing and demonstrate the operation of the NMR consoles and magnets Refer to Chapter 3 Consoles and Magnets Specifications and record results in Chapter 5 Acceptance Test Results using the provided forms 2 1 Calibrating a Probe This procedure uses the AutoCalibration features of the VnmrJ Experimental interface e Probe Calibration Samples page 15 e Before You
23. 0 and makes a gradient map for gradient shimming for systems with gradients and gradient probes Gradient shimming will be done for non gradient systems by using homospoil 1 Click the Select Calibration button in the Probe window 2 Set AutoLOCK and AutoSHIM to NO 3 Right click the Experiment drop eee ee ak Calibrate Proton CEtBz down menu and select autoLock Ca ibrate Proton es Lock gmap and z0 4 Hz D20 AutoSHIM Calibrate Fluorine 19F S N A i Calibrate Phosphorus 31P S N from the list of calibration options calibrate H C Ind Det Grad CH3I Ok Calibrate H Ind Det Grad Cautotest 4 Click Ok 10CK gmap and zo 2Hz 020 5 Click Exit 6 The message Set z0 exactly on resonance before starting acquisition is displayed Refer to the VamrJ Liquids NMR manual for more information on setting the lock 7 Click Confirm in the popup prompt window 4 Hz DO lock set on resonance 8 Click Start Calibration 9 Click Confirm in the popup prompt window if a PFG probe is in the magnet At the end of the calibration routine the calibrations are automatically incorporated into the probe file 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 17 Chapter 2 Console and Magnet Test Procedures Calibrating Probe and System Files k O E ey 10 11 12 13 Eject the sample from the magnet and insert the 1 13C enriched methyl iodide 1 trimet
24. 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 11 Chapter 1 Introduction 1 2 General Acceptance Testing Requirements Each MERCURYplus spectrometer is designed to provide high resolution performance when operated in an environment as specified in the nstallation Planning Guide Unless both the specific requirements of this manual and the general requirements specified in the MERCURYplus Installation Planning Guide are met Varian Inc cannot warrant that the NMR spectrometer system will meet the published specifications 1 3 Samples Required for Acceptance Tests The MERCURYplus spectrometer is supplied with the samples listed in Table 1 Table 1 Samples Required for Console Acceptance Tests Test Sample rs le Tube Nucleus aks i imber autotest sample 0 1 13C enriched methanol in 5 IH and C 00 968120 68 1 H 0 99 DO 13C enriched 1 methyl iodide 1 trimethyl 5 IH Bcand 00 968120 96 phosphite and 0 2 Cr AcAc in chloroform d 31p doped 4 Hz H O D 0 0 1 mg ml GdCl in 5 IH 01 901855 01 1 H O in D20 2 2 ethyl 1 indanone in chloroform d gt Hand C 01 901855 03 0 1 ethylbenzene 0 01 TMS 5 IH 00 968120 70 99 89 deuterochloroform CDC1 0 1 ethylbenzene 0 01 TMS 10 IH 00 968123 70 99 89 deuterochloroform CDC1 chloroform in acetone d lineshape 5 IH 00 968 120 xx 100 methanol reagent grade 50 to 25 Low 5 IH 00 968 120 80 100 ethylene glycol reagent grade 25 to 100 5 IH 00 968 120 79
25. 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 35 Chapter 4 Customer Training 4 3 Initial System Settings System settings are used to enable or disable installed hardware and define the events that will occur upon completion of data acquisition System settings do not replace the system configuration Keep the defaults except as described below l 2 U 1O EGOS AD Oy M Click the Utilities menu and select System Settings Click the System tab Enable the Z gradient Select on from the drop down menu next to the Z to the right of Gradient amplifier Set Type of digital signal processing to Realtime Do not enable Frequency shifted quadrature detection no check in the box Set Hardware Z1 shimming to None Do not enable Probe protection or Solids VT System no check in the boxes Set VT cutoff 0 50 to 25 Enable Process data after acquisition and Autosave data after acquisition check in the box 10 Click the Display Plot tab 11 Enable Process data on drag and drop check in the box 12 Set Spectrum updating during phasing 0 100 to 100 13 Do not enable Display only matching items in locator no check in the box 14 Enable Show current operator studies only check in the box 4 4 Set Up Experimental and Walkup Users Creating a new user account is described in the VnmrJ Installation and Administration manual During the VnmrJ installation process the VnmrJ administrator typically vamr1
26. 58 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 Chapter 5 Acceptance Test Results This chapter contains the following forms for recording system information and acceptance test results e 5 1 Computer Audit page 61 5 2 Installation Customer Training Checklist page 63 e 5 3 System Installation Checklist page 65 e 5 4 Supercon Shim Values page 67 e 5 5 Console and Magnet Test Results page 69 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 59 Chapter 5 Acceptance Test Results Notes 60 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 5 1 Computer Audit 5 1 Computer Audit Information about your site please print Company University Address Principal User Phone Spectrometer type Fax Console S N Sales Order No Delivery month day Information on each computer additional forms are on the back of this page Include computers directly attached to the spectrometer computers networked or non networked on site or off site used to process NMR data using Varian s VnmrJ software and computers on site and off site used to process data collected on this spectrometer with software from other vendors Information on computer __ of ___ e g 1 Of 3 Manufacturer Model no Computer S N Purchased from Memory Mbytes Screen size in Peripherals Internal hard disk Mbytes
27. Console Acceptance Tests MERCURYplus NMR Spectrometer Systems with VamrJ Pub No 01 999255 00 Rev B 0904 ave TAN VA AJ IAN Console Acceptance Tests 0904 MERCURYplus NMR Spectrometer Systems with VamrJ Pub No 01 999255 00 Rev B ave TAY VARIAN AJ Console Acceptance Tests MERCURYplus NMR Spectrometer Systems with VnmrJ Pub No 01 999255 00 Rev B0904 Applicability of manual MERCURYplus NMR spectrometer systems running VnmrJ Technical contributors Frits Vosman and Christine Hofstetter Revision history A0604 Initial release with VnmrJ 1 1D A0804 Corrections and updates B0904 Shipping kit correction ECO Copyright 2004 by Varian Inc 1 800 356 4437 3120 Hansen Way Palo Alto California 94304 http www varianinc com All rights reserved Printed in the United States The information in this document has been carefully checked and is believed to be entirely reliable However no responsibility is assumed for inaccuracies Statements in this document are not intended to create any warranty expressed or implied Specifications and performance characteristics of the software described in this manual may be changed at any time without notice Varian reserves the right to make changes in any products herein to improve reliability function or design Varian does not assume any liability arising out of the application or use of any product or circuit described herein nei
28. alibration and Indanone Spectra The assignment of H7 to the signal at 7 72 ppm is confirmed by the gHMBC data TOCSY is a phase sensitive experiment The cross peaks are narrower than in the COSY giving higher resolution Correlations among all protons in a spin system are observed in the TOCSY spectrum see Figure 18 The critical parameter is mix In this case mix is 0 08 seconds which is sufficient to show correlations throughout the entire spin system Shorter mix times will reveal fewer correlations Hy CHs Ili iit ta H H Hy ae e ss va J e M e o zorr pak ee F1 ppm Figure 18 TOCSY of 2 Ethyl 1 Indanone shows Correlations Among All Protons The expansion shows the completely defined spin system starting with the CH3 group and ending with protons on C10 Figure 19 A total of 5 crosspeaks are seen in the row The indanone sample does not have any significant NOE crosspeaks Figure 20 The main area of interest in this spectrum is to note that the diagonal will be negative and the NOESY crosspeaks will be positive Crosspeaks which appear to have both positive and negative components are actually not NOE correlations but coupling artifacts In the gHSQC and HSQC experiment see Figure 21 the protons correlate with the carbons to which they are attached The detected nucleus is H and this results in a higher signal to noise then the 5C detected hetcor experiment When compared to the HMQC experiment
29. ant manual for the information referred to i This symbol might be used on warning labels attached to the equipment When by the warning label WARNING CAUTION Warnings are used when failure to observe instructions or precautions could result in injury or death to humans or animals or significant property damage Cautions are used when failure to observe instructions could result in serious damage to equipment or loss of data Warning Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these warnings or with specific warnings elsewhere in Varian manuals violates safety standards of design manufacture and intended use of the instrument Varian assumes no liability for customer failure to comply with these precautions WARNING WARNING 01 999255 00 Persons with implanted or attached medical devices such as pacemakers and prosthetic parts must remain outside the 5 gauss perimeter from the centerline of the magnet The superconducting magnet system generates strong magnetic fields that can affect operation of some cardiac pacemakers or harm implanted or attached devices such as prosthetic parts and metal blood vessel clips and clamps Pacemaker wearers should consult the user manual provided by the pacemaker manufacturer or contact the pacemaker manufacturer to determine the effect on a specific pacemaker Pacemaker wearers should a
30. as a condition of sale are detailed in the sales contract and will not be covered by the installation engineer Online Customer Support and Information Service and Technical Support Applications Support Sales Support Product Information Webb Addresses http www varianinc com nmr service http www varianinc com nmr apps http www varianinc com nmr contact http Awww varianinc com nmr products In warranty Service Location Phone Number United States and North America Palo Alto California 1 800 356 4437 Europe Local Sales Office See Varian Sales Offices Other International Local Sales Office See Varian Sales Offices Technical Support Location Phone Number United States and North America Palo Alto California 1 800 356 4437 Europe Oxford UK 44 1865 388 800 Other International Local Sales Office See Varian Sales Offices Post Warranty Support Location Phone Number United States and North America Palo Alto California 1 800 356 4437 Europe Local Sales Office See Varian Sales Offices Other International Local Sales Office See Varian Sales Offices Applications Support Location Phone Number United States and North America Palo Alto California 650 424 4526 Columbia Maryland 410 381 7229 Europe Darmstadt Germany 49 6152 703 253 Japan Tokyo Japan 81 3 5232 1211 Other International Local Sales Office See Varian Sales Offices Varian Sales Offices For product sales and service
31. as flow and cooling air flow levels are between 9 5 to 10 LPM and gas flow to the probe is not restricted in any way 6 Setup the parameters Acquire a normal spectrum and shim the water signal to about 3 to 4 Hz linewidth at 50 7 Click the Start tab and select the Study page a Eject the doped 4 Hz H O D 0 sample b Insert the appropriate sample High Temperature 100 ethylene glycol 00 968120 79 Low Temperature 100 methanol 00 968 120 80 c Click the drop down menu next to Autolock and select Unlocked 26 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 4 Optional Tests 8 Select the Lock page and click the lock OFF button 9 Click the Acquire tab a Select the Acquisition page b Set the following parameters Observe Pulse to 2 Receiver Gain to 5 or some value that doesn t overload the receiver Spectral width to 10000 Acquisition time to 2 and Scans Requested to 1 by entering these values in the fields next to the parameters c Select the Future Actions page d Remove any entries in the Zf an Error Occurs field The test is run unlocked because the sample has no deuterated solvent to lock on 10 Click the Start tab and click Setup Hardware Check the probe tuning for the ethylene glycol sample 11 Click the Acquire button to acquire the spectrum 12 Place the single cursor between the two peaks 13 Click the Process tab and select the Cursor Integration page 14 C
32. ber 2 2 ethyl 1 indanone in chloroform d 5 01 901855 03 Protocols for Automated Data Acquisition The following protocols will be combined into a single composite protocol The composite protocol is submitted to the study queue and the 1D and 2D experiments specified by the protocol are run on the study sample This demonstrates the ease with which a study protocol can be created and run on a given sample 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 1 9 Chapter 2 Console and Magnet Test Procedures System console and probe configuration determines the experiment selection as follows Protocol Gradient Nongradient Systems Systems 1 D Protocols Acquisition of a proton spectrum E n Acquisition of a proton decoupled carbon observe spectrum E E Dept distortionless enhancement by polarization transfer QO m Apt attached proton test n O Non gradient 2D Protocols Tocsy total correlation spectroscopy E QO Noesy nuclear overhauser spectroscopy E QO Gradient 2D Protocols requires PFG option and gradient probe Gcosy gradient correlation spectroscopy E Ghsqc gradient heteronuclear single quantum correlation E Ghmbc gradient heteronuclear multiple bond correlation QO Non gradient Protocols Cosy correlation spectroscopy UO Login to Walkup Interface 1 Log on using the UNIX VnmrJ Walkup Account Owner 2 Select the Walkup account owner from the Operato
33. ce Tests for VamrJ 71 72 3 Magnet area danger signs Figure 24 Post at each entrance to the magnet area Be sure each sign is outside the 5 gauss perimeter A A10 GAUSS A UAINE 7 STRONG MAGNETIC FIELD Tools and Equipment Strong magnetic fields are present that can make magnetic items suddenly fly towards the magnet which could cause personal injury or serious damage Do not take tools equipment or personal items containing steel iron or other magnetic materials closer to the magnet than this sign Dewars The stray field of the magnet can pull a magnetic dewar into the magnet body causing serious damage Use only nonmagnetic stainless steel dewars Do not use iron or steel A STRONG MAGNETIC FIELD Pacemaker Metallic Implant Hazard Strong magnetic and rf fields are present that can cause serious injury or death to persons with implanted or attached medical devices such as pacemakers and prosthetic parts Such persons must not go closer to the magnet than this sign until safety at a closer distance is identified by a physician or device Magnetic Media ATM Credit Cards Strong magnetic fields are present that can erase magnetic media disable ATM and credit cards and damage some watches Do not take such objects closer to the magnet than this sign dewars during servicing Eg Eg AK ARIAN Pub No 87 250909 00 B0604 Gauss Warming Sign VARIAN Pub No 67 250902 00 80604 10 Gauss War
34. ceseceeeecereseaeees 12 Chapter 2 Console and Magnet Test Procedures cccccececeeeeeeeeeeeeees 15 2A Calibrating aPLODe 4 scncsteseegevianyohisiis chitosan ERE RER ERE erations anton eee 15 Probe Calibration Samples sirier etna niicbi kei EEES EE 15 WC LOR Ee VOU SPARE ER E ET 16 Setting Up the Probe Calibration File cic cc c cccccsccncercsnsdiesstadiatartesceateents 16 Calibrating ZO and Make LOCK gmap ou eceeccescesseesseeseesseeecsecseecaeenseseeneens 17 Calibrating Probe and System Piles 5 0 c scccccisesccinaesssadasieniiiecesnars 18 2 2 Automated Data Acquisition oo cceececsecssecsecsseeeceeceeeeeceseeeeeeeeeseecsecseecaecasenaeeeenaeens 19 Sample for Automated Data Acquisition 2 c c ccccccescecsecscessscacncesssensisceseceeade 19 Protocols for Automated Data Acquisition ti eeseeeseesseseeseceeeecesenseeeterenecneres 19 Lopin to Walkup WSEAS chcchecadsieeatsetessi acs lpiss x2 abeesesdhcesinassehceetsusnueestasiastessen 20 Setting Up the Study and Lock Solvent oo cece cesesesessecesescnneseeersneersevenensenes 20 Buldme a Composite Protocol sssrinin neriie essek EE EVERE REE 21 Customizing the Parameters and Starting Data Acquisition sssssessesseseeeesseeee 22 Acquiring Data Using a Composite Protocol sseesessesessssssssrerssessesersesersereeeseees 22 23 Magnet Drift Test cis aise iiiivenial nis aineinnieiinn diagdn diet E aR 23 Samples for Magnet Drift Test oo ccccccssssecseesseesec
35. csseeeeeseecesenereesseeneees 50 4 7 Magnet Maintenance ececceccecssescessecscecsecscesecsecaeceeeeseeeenaeeseeeaeeseecsecaaeeaeenseeaeeneees 56 4 8 30 Day System Maintenance oo cecceeccessssseesceseeeecesceseecaeesaeeecaeeaeceeeeeseseeseenseeaeeaaes 56 4 9 Warranty and Who to Call for Assistance ceeesessseceeeceecseeeesseeseceteecaecaeeeceeenaeaeees 57 Varan Sales OCES seerne ira eieae nei ea EEEE EEE TEEPEE RE EEE S ESR EREE ERER 57 Chapter 5 Acceptance Test ReSuIts ccccccssssssssseeeeeeeeeseasessseeeeeeeeseeeaenens 59 Sl Computer ANdit sere na nnr EEE a E ETE teeans 61 5 2 Installation Customer Training Checklist eeeseeeeeeeeeseseeierersrsressrrererersrrersrrrerseneee 63 5 3 System Installation Checklist ciscicccscccscccccseeccaccccutectecnccveceaacsscsseess esadacsacsceadacnteseaces 65 5 4 Supercon Shim Values ccccccceccsssssscesceseeeeceeeeeeceseeeeecseecsecseeaeeeceeeeeeeeeseeseeeeeeeneeenes 67 5 5 Console and Magnet Test Results snsscsciseisssirisrcesisiisesesissireriiisssseseisisieeessessisers 69 Appendix A Posting Requirements for Magnetic Field Warning Signs 71 WANTS SIENS esner eas cadtsadedd a e E R R EE a 71 4 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 SAFETY PRECAUTIONS The following warning and caution notices illustrate the style used in Varian manuals for safety precaution notices and explain when each type is used you see this symbol refer to the relev
36. e a Enter 50 in the temperature field or use the slider bar to set a value b Click the Regulate Temp button Wait a minimum of 10 minutes for the temperature reach regulation 4 Repeat the procedure in Data Acquisition page 27 5 Click the Start tab and select the Spin Temperature page a Enter 100 in the temperature field or use the slider bar to set a value b Click the Regulate Temp button Wait a minimum of 10 minutes for the temperature reach regulation 6 Repeat the procedure in Data Acquisition page 27 Low Temperature Calibrations Test CAUTION For low temperature calibrations fill the VT dewar with liquid nitrogen If a chemical mixture is used instead of liquid nitrogen for low temperature calibrations choose the chemical slurry carefully A mixture of crushed dry ice and acetone is not recommended because it will dissolve the polystyrene VT dewar 1 Follow the procedure in Set up page 26 2 Acquire a spectrum at room temperature follow the procedure in Data Acquisition page 27 3 Click the Start tab and select the Spin Temperature page a Enter 20 in the temperature field or use the slider bar to set a value b Click the Regulate Temp button Wait a minimum of 10 minutes for the temperature reach regulation 4 Repeat the procedure in Data Acquisition page 27 5 Click the Start tab and select the Spin Temperature page a Enter 80 in the temperature field
37. e Test Sample Nucleus Foie 10 mM DSS in D O sample volume H 5 Customer of 0 6 ml in a S mm NMR tube supplied DSS 3 trimethylsilyl 1 propanesulfonic acid The customer must make this sample using DSS and deuterium oxide 99 8 or 99 9 atom D Upon request Varian can make this sample if DSS is not available at the customer site Probe and Hardware Requirements High stability variable temperature accessory and a 5 mm probe capable of H direct observe are required Test Procedure 1 Click the Locator Statements menu B and select System Param Files from under the Sort NMR Parameter Files category 2 Click the title above the right most column and select Directory from the lists that is displayed 3 Select shmd2o and drag it to the VnmrJ graphics canvas 4 Insert the doped 4 Hz H O D 0 sample 01 901855 01 5 Click the Acquire tab a Select the Acquisition page b Set the following parameters Observe Pulse to 90 degree pulse width for the probe gain to a value that doesn t overload the receiver Spectral width to 10000 Acquisition time to 10 and Scans Requested to 1 by entering these values in the fields next to the parameters c Select the Future Actions page d Remove any entries in the fan Error Occurs field 6 Click the Start tab and select the Spin Temperature page a Enter 40 in the temperature field or use the slider bar to set a value b Click the Regulate Temp button Wait a minimum of 10 m
38. e HDO signal to 4 to 5 Hz linewidth at 50 4 Click the Start tab and select the Lock page a Adjust Z0 to be on resonance 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 23 Chapter 2 Console and Magnet Test Procedures b Adjust Power Gain and Phase for a steady lock level of about 80 5 Select the Spin Temp page and do the following a Click the Ignore spinner error radio button b Click the Ignore temperature error button c Enter 0 in the spin spinner speed field and click the Spin Off button 6 Click the Acquire tab and select the Acquisition page 7 Enter 1 in the Scans Requested field 8 Click the Arrays button and fill in the array form as follows a Enter d1 in the cell under Param Name The row will be highlighted and the cell descriptions and values will be filled in for the remaining cells If this did not happen you did not press return after entering d1 in the cell under Param Name b Enter 11 in the Array Size field c Enter 3600 in the First Value field d Enter 0 in the Increment field e Highlight the first value for the first position and enter 60 f Click Close 9 Click the Acquire button The test takes approximately 10 to 11 hours to finish At the conclusion of the experiment the data are automatically processed and displayed The data can be processed manually if desired a Click the Process tab and select the Process page b Click Transform All then Autophase Zero b
39. e that the VT unit and probe go to the desired temperature as registered on the window of the VT controller If the system is equipped with a VT unit the system user should read through the VT operation instructions before the demonstration Dry nitrogen is required as the VT gas if the requested temperature is over 100 C or below 10 C Otherwise air can be used For temperatures below 40 C dry nitrogen gas is recommended for cooling the bearing spinner and decoupler This prevents moisture condensation in the probe and spinner housing CAUTION The use of air as the VT gas for temperatures above 100 C is not recommended Such use destructively oxidizes the heater element and the thermocouple CAUTION Extreme temperatures can damage the probe The high and low temperature must be within the specified range of the probe 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 31 Chapter 3 Consoles and Magnets Specifications Demonstration Limitations If dry nitrogen gas and liquid nitrogen are not available at the time of installation the range of VT demonstration is limited to temperatures between 30 C and 100 C Basic Specifications The specifications for variable temperature ranges are listed with each probe 3 3 Temperature Accuracy for VT Accessories The temperature reading displayed on the VT unit display panel should be within 1 C of the actual temperature reading as measured from the chemical s
40. e the basic operation of the system to the laboratory staff The objective of the demonstration is to familiarize the customer with system features and safety requirements as well as to assure that all mechanical and electrical functions are operating properly MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 1 1 Overview of the Acceptance Testing Process The system demonstration includes the following items Magnet Demonstration The following are demonstrated Posting requirements for magnetic field warning signs Cryogenics handling procedures and safety precautions e Magnet refilling Flowmeters Homogeneity disturbances Console and Probe Demonstration The following are demonstrated e Loading programs VnmrJ Optional VnmrJ packages operating system OS Experiment setup including installing the probe in the magnet Basic instrument operation to obtain typical spectra including probe tuning magnet homogeneity shimming and printer plotter operation Note that Varian Inc installation engineers are not responsible for or trained to run any spectra not described in this manual e AutoCalibration of key probe parameters such as H pw90 Bc pwx90 decoupler field gradient strength if gradients are present and other probe specific parameters Demonstration of automated data acquisition Using the 2 Ethyl 1 indanone sample provided with the console the following experiments will
41. ear Correlation Experiments gt Gcosy or Cosy if you do not have gradients 7 Click the Acquire tab and select the Defaults page Change the Number of Scans and Relaxation Delay as appropriate or keep the defaults which are fine for this example 8 Click the Acquire button to start the acquisition 9 After the acquisition has finished click the Process tab and select the Plot page Click the Automatic Plot Page button Observations How does this plot compare to that produced using Study Queue Exercise 1 Notice that the spectra plotted along the sides of the contour plot are NOT the high resolution 1D proton spectrum but are instead the projections of the 2D data and are therefore of much lower resolution though probably still useful The automatic plotting routine does not know where to find the 1D spectrum so it uses the projections instead You can process the 2D data using the pages under the Process tab 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 45 Chapter 4 Customer Training 4 6 Interpreting the Calibration and Indanone Spectra 46 In this section the data obtained from the automated probe calibration and 2 2 ethyl 1 indanone sample are interpreted e Calibration When is it Necessary on this page e Interpretation of the Calibration Data on this page Interpretation of 2 Ethyl 1 Indanone Spectra page 50 Calibration When is it Necessary Before acquiring s
42. er Select Probe hex789 System zl Open the Probe window aS Tune gain 50 level probe Place a check in this box as shown _MEditProbe Hi v Probe name entry field Calibration availability level Probe name hex7e9 Parameters Standard xl Level System zl 4 Add probe Delete probe Click here to start the selected calibration Click here to select a calibration Select Calibration Start Calibration Close sandr Figure 1 Calibrating a Probe 1 6 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 2 1 Calibrating a Probe 3 Enter the name of the probe in the Probe name field e g asw_Smm 4 Select System from the Level drop down menu The System selection writes the calibrations into vnmr probes probe_ name and makes all calibration available to all users The User selection writes the calibrations into vnmrsys probes probe_ name and are available only to the logged in user creating the calibration file 5 Leave Parameters at zero 6 Click the Add probe 7 From the menu next to Edit Probe select Probe Enter the correct value for rfsize click Save Exit Refer to the probe manual for the correct value Probe ATB JE Probe Parameters gradient n gcal 00 Ikmap n H1 map n hsmap n tuneflg n rfsize 16 TEB date 00 00 0000 Save Clear Calibrating Z0 and Make LOCK gmap This procedure calibrates Z
43. esceeeesceeeeseeseesseeseeseeensenaes 23 Probe and Hardware Requirements ei cc c cccvecesccctscsccaciessevacscscstvasscesdeceeseeescecseee 23 Be EE vs ceceeceese aces TE E E TT 23 PEE ao r e E ace A O E E E 23 2A Optional Tests s sccviccninadsaneitad tam Eaa EEE E E nE Enar EKE Ea onea taraia 25 Variable Temperature Operation Optional Hardware ssssesecesseneeereseeeeees 25 Temperature Accuracy for VT Systems Optional Test esseseeeeeeeeseeeeesseseee 26 Stability Calibration for High Stability VT Optional Test oe eeeeseeseeeeeees 29 Chapter 3 Consoles and Magnets Specifications ccccceeeeeeeeeeeeees 31 3A Mapnet Drift soroan adios EE EEEE EEEE EE EAE E E Ea 31 3 2 Variable Temperature Operation essesessesesseesesersesersseessstsrsstesestesrsrrsrenessesensesesessete 31 3 3 Temperature Accuracy for VT Accessories sseeeseseseseseesseeesseeessreresesseserseeeesresese 32 3 4 Stability Calibration for High Stability VT Accessory ccecesseeseeeeceseeeseeeeeseeneeenes 32 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 3 Table of Contents Chapter 4 Customer Training scsciiccicerieseieicecccccarsisdeetadesdnerienssanscucnieasersncaesunsins 33 4 1 Where to Look for Answers esssessesssssessesssssisrsesesestsssstssststseesstsestsssstersenesteesseseses 33 Vime Online Help serres isio iei eRe E E E E ERE ER E 33 OEA e ATE E E E T 34 stala enS iei e E T ea ees ee AKR 34 Teck
44. g continuous wave cw decoupling The pulse sequence is the same as in the previous experiment carbon observe with proton decoupling except pw is now set to a fixed value decoupler modulation mode dmm is set to c decoupler mode dm is set to yyy and the decoupler offset dof is arrayed to produce the spectra shown in Figure 10 le ole Figure 10 Proton Decoupler dof Array From these spectra the first estimate of the proton decouple pw90 is 1 made Using the relationship between the pulse width and the decoupler YH2 4 pw90 field strength yH gt shown in the equation below the decoupler pw90 is determined The sequence is now set to ppcal and the proton decoupler 90 pulse pp is determined These spectra shown in Figure 11 are saved as Hdec_ dept These parameters and calibrations are used to setup WALTZ decoupling This completes the calibrations During the calibration procedure spectra and the array values are plotted to provide a permanent record of the calibrations Figure 11 Calibration of the Decoupler 90 Pulse Width pp 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 49 Chapter 4 Customer Training Interpretation of 2 Ethyl 1 Indanone Spectra The proton NMR shows several distinct features First there are some impurities in the sample These impurities shown in Figure 12 are at the 2 level and some crosspeaks will show up in the 2D The very la
45. g your local Varian office in other countries MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 Numerics 180 pulse 13 2 Ethyl 1 indanone in chloroform d automated data acquisition 20 90 pulse 13 A Acceptance Test Procedures and Specifications 34 acceptance test specifications overview 10 acceptance tests documentation 14 acceptance tests objectives 9 Accessory Manuals 34 APT demonstration 20 Attached Proton Test 20 AutoCalibration ZO and Make LOCK gmap 17 automated data acquisition 19 1D homo2D and hetero2D 19 automatic teller machine ATM cards caution 7 B basic system operation 11 broadband operation 11 C Calibration training 46 calibrations 49 cautions defined 5 computer audit form 10 61 console acceptance tests 15 console demonstration 11 credit cards caution 7 cryogenics handling procedures 11 D decoupling 11 demonstration of system 10 DEPT demonstration 20 Distortionless Enhancement by Polarization Transfer 20 E ethylene glycol 26 experiment setup 11 F flammable gases warning 6 flowmeters 11 G gamma H2 pw90 relationship 49 01 999255 00 B0904 Index H helium contact with body 6 helium gas flowmeters caution 8 high power amplifiers cautions 8 high stability VT units optional test 29 High Temperature Calibrations Test optional 23 26 27 homogeneity settings 12 I installation checklist 63 65
46. hift 3 4 Stability Calibration for High Stability VT Accessory The high stability VT accessory holds the set temperature to within 0 1 C 0 1 C 0 001 ppm or in field dependent terms 0 2 Hz at 200 MHz 0 3 Hz at 300 MHz and 0 4 Hz at 400 MHz 32 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 Chapter 4 Customer Training Sections in this chapter 4 1 Where to Look for Answers this page e 4 2 VnmrJ Directory Structure page 35 4 3 Initial System Settings page 36 4 4 Set Up Experimental and Walkup Users page 36 e 4 5 Basic Spectrometer Operation page 37 e 4 6 Interpreting the Calibration and Indanone Spectra page 46 4 7 Magnet Maintenance page 56 4 8 30 Day System Maintenance gt page 56 4 9 Warranty and Who to Call for Assistance page 57 This chapter describes training provided by the installer This training is intended as a general overview of the instrument basic maintenance requirements software features data acquisition and storage file maintenance and other routine tasks Comprehensive training classes are offered at various Varian Inc Applications Laboratories around the world Call your sales representative or contact the Varian Inc NMR systems office nearest you for class offerings schedules and cost 4 1 Where to Look for Answers Knowing where to look is the first step to an
47. hyl phosphite and 0 2 Cr AcAc in chloroform d sample Tune the probe if needed Click Select Calibration in the Probe window Set AutoLOCK and AutoSHIM to YES Right click the Experiment drop down menu and select Calibrate H C Ind Det Grad CH3D Click Ok Click Exit Click Confirm to confirm that the correct sample is in the magnet Click Start Calibration Select the following H1 Observe C13 Decouple C13 Observe H1 Decouple If the probe is equipped with gradients also select gradient G cm dac C H gradient ratio These are typical calibration for autoswitchable indirect detection and triple resonance probes Enter target values for 1H obs pw90 13C obs pw90 1H dec pp90 and 13C dec pwx90 calibrations The values are usually the pulse specifications for the probe For Plot Results select Yes Click Ok Click Exit At the end of the calibration routine the power and pulse width values are automatically incorporated into the probe file 18 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 2 Automated Data Acquisition 2 2 Automated Data Acquisition The automated data acquisition procedures outline several 1D and 2D experiments using the ethyl indanone sample e Sample for Automated Data Acquisition page 19 e Protocols for Automated Data Acquisition page 19 e Login to Walkup Interface page 20 e Setting Up the Study and Lock Solvent page 20 e
48. information contact one of the Varian sales offices e Argentina Buenos Aires 114 783 5306 e Australia Mulgrave Victoria 3 9566 1138 e Austria V sendorf 1 699 96 69 Belgium Brussels 02 721 51 51 e Brazil Sao Paulo 11 829 5444 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 57 Chapter 4 Customer Training e Canada Ottawa Ontario 613 260 0331 China Beijing 10 6846 3640 Denmark Herlev 42 84 6166 France Orsay 1 69 86 38 38 e Germany Darmstadt 6151 70 30 e Italy Milan 39 02 9273401 Japan Tokyo 3 5232 1211 Korea Seoul 2 3452 2452 e Mexico Mexico City 5 523 9465 Netherlands Houten 0118 61 71 56 Norway Oslo 9 86 74 70 Russian Federation Moscow 95 241 7014 Spain Madrid 91 472 7612 Sweden Solna 8 445 1601 Switzerland Zug 41 749 88 44 Taiwan Taipei 2 2698 9555 United Kingdom Walton on Thames England 1932 898 000 United Kingdom Oxford England Sales and Service 44 1865 388 883 E mail technical support varianinc com NMR Service Manager Europe and Pacific Rim e United States Palo Alto California Varian Inc NMR Systems Customer Sales Support 650 424 5434 Service Support Palo Alto California 1 800 356 4437 E mail nmr customersupport varianinc com North American Service Manager 9017 Mendenhall Ct Ste D Columbia MD 21045 410 381 7229 e Venezuela Valencia 41 257608
49. ings could result in extensive equipment damage CAUTION Never operate solids high power amplifiers with liquids probes On systems with solids high power amplifiers never operate the amplifiers with a liquids probe The high power available from these amplifiers will destroy liquids probes Use the appropriate high power probe with the high power amplifier CAUTION Take electrostatic discharge ESD precautions to avoid damage to sensitive electronic components Wear grounded antistatic wristband or equivalent before touching any parts inside the doors and covers of the spectrometer system Also take ESD precautions when working near the exposed cable connectors on the back of the console Radio Frequency Emission Regulations The covers on the instrument form a barrier to radio frequency rf energy Removing any of the covers or modifying the instrument may lead to increased susceptibility to rf interference within the instrument and may increase the rf energy transmitted by the instrument in violation of regulations covering rf emissions It is the operator s responsibility to maintain the instrument in a condition that does not violate rf emission requirements 8 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 Chapter 1 Introduction Sections in this chapter 1 1 Overview of the Acceptance Testing Process this page 1 2 General Acceptance Testing Requirements page 12 1 3 Samples Req
50. instructions for various VnmrJ related administration tasks e Solaris Installation and Administration Provides instructions for the installation Solaris software instructions for various Solaris related administration tasks Linux Software Installation Provides instructions for the installation Linux software e Probe installation testing and specifications manuals Each type of probe has its own installation test and specifications manual In these manuals are the detailed instructions for installing tuning testing the probe e Accessory manuals Each accessory is covered in an independent manual which contains installation testing and sometimes operation instructions 34 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 2 VnmrJ Directory Structure Technical References System Schematics Provides schematic and technical drawings Technical Reference Provides technical details of the spectrometer systems and electronics System Description Provides an overview of the spectrometer system and hardware User Programming Provides details about the VnmrJ macro programming language Magical II instructions for writing custom macros and editing existing macro Command and Parameter Reference Provides Alphabetical reference for commands parameters and macros 4 2 VnmrJ Directory Structure The VamrJ Installation and Adminis
51. inutes for the temperature reach regulation 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 29 Chapter 2 Console and Magnet Test Procedures c Set spin to 0 Allow the VT controller to regulate to 40 C which should be about 10 higher than the room temperature Check that the probe is tuned 7 Click the Acquire button to acquire the spectrum 8 Place the single cursor between the DSS signal right most peak 9 Click the Process tab and select the Cursor Integration page 10 Click the Move transmitter button 11 Click the Acquire tab a Select the Acquisition page b Set Spectral width to 1000 12 Click the Acquire button to acquire the spectrum Shim the DSS signal to about 0 6 Hz or less linewidth at 50 The sample of DSS in DO should equilibrate at 40 C for at least 2 hours before the next step 13 Click the Arrays button and fill in the array form as follows a Enter d1 in the cell under Param Name The row is highlighted and the cell descriptions and values are filled in for the remaining cells b Enter 73 in the Array Size field c Enter 600 in the First Value field d Enter 0 in the Increment field e Highlight the first value for the first position and enter 0 f Click Close This sets up an array of d1 values with the first spectrum collected at time 0 minutes and subsequent spectra collected at 10 minute intervals for up to 12 hours 14 Click Acquire The test take
52. its the ramp rate to 12 C per minute up or down Wait for the temperature to equilibrate Temperature Accuracy for VT Systems Optional Test The optional tests in this section check temperature accuracy calibrations for high and low temperatures using ethylene glycol and or methanol respectively Table 3 lists the samples for low temperature and high temperature tests Table 3 Samples for Optional VT Accuracy Test Temperature Range Sample Tube Sample Part Sampie CC mm Number 100 methanol reagent grade 50 to 25 Low 5 00 968 120 80 100 ethylene glycol reagent grade 25 to 100 High 5 00 968120 79 Probe and Hardware Requirements The variable temperature accessory and a VT probe are required Run VT tests with a 5 mm probe capable of H direct observe from 150 C to 200 C For probes that have a more limited temperature range particularly PFG probes run the test at two or three temperatures that fall within the VT range of the probe These tests can also be run using the H decoupling coil of the 5 mm broadband probe as H direct observe Set up 1 Click the Locator Statements menu Pr and select System Param Files from under the Sort NMR Parameter Files category 2 Click the title above the right most column and select Directory from the lists that is displayed 3 Select shmd2o and drag it to the VnmrJ graphics area 4 Insert the doped 4 Hz H O D 0 sample 5 Make sure that the VT g
53. l Hardware page 25 From Temperature Accuracy for VT Systems Optional Test page 26 From Stability Calibration for High Stability VT Optional Test page 29 Varian Representative Date Customer Representative Date 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 69 Chapter 5 Acceptance Test Results Notes 70 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 Appendix A Posting Requirements for Magnetic Field Warning Signs The strong magnetic fields that surround a superconducting magnet are capable of causing death or serious injury to individuals with implanted or attached medical devices such as pacemakers or prosthetic parts Such fields can also suddenly pull nearby magnetic tools equipment and dewars into the magnet body with considerable force which could cause personal injury or serious damage Moreover strong magnetic fields can erase magnetic media such as tapes and floppy disks disable the information stored on the magnetic strip of automated teller machine ATM and credit cards and damage some watches To warn of the presence and hazard of strong magnetic fields the customer is responsible for posting clearly visible signs warning of magnetic field hazards This responsibility includes measuring stray fields with a gaussmeter Radio frequency emissions may also pose a danger to some individuals The rf emission levels from Varian NMR equi
54. l the measured pw90 is no greater then the specified value but not more then 0 5 us less than this value The spectra from a successful calibration are saved as H1pw90 The carbon pwx90 calibration is the next experiment The pulse sequence changes from s2pul to PWXCAL The specification for the carbon pw90 and of 51 are used as the target values Just as with the proton pw90 calibration the AutoCalibration makes two attempts to achieve the specification and exits the AutoCalibration if the target specification is not reached after the Figure 5 1 C pwx Array second attempt The data from the PWXCAL are saved as C13pwx and shown in Figure 5 tpwr are used as the target values If no values were specified the default values of 15 us at power in this case pwxlv1 a 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 47 Chapter 4 Customer Training The next two experiments are run only if you have gradients The first experiment calibrates the Z gradient strength produces the profile shown in Figure 6 and stores this information in the parameter gcal The next experiment calculates the ratios of the gradients to be used in various H 3C indirect detection experiments and stores this information in the parameter Cgrad for only 830 Figure 7 Figure 6 Gradient Profile The next calibration is carbon observe pulse width and the pulse sequence is changed to s2pul for direct observation of the carbon
55. lick the Move transmitter button 15 Make sure the VT gas flow and cooling air flow levels are between 9 5 and 10 LPM Data Acquisition 1 Acquire a spectrum record the temperature and record the chemical shift a Click the Acquire button to acquire another spectrum b Select the icon from the graphics control bar c Position the right and left cursors on the right and left peaks 2 Pull down the command line and do either of the following High Temperature Enter tempcal glycol Low Temperature Enter tempcal methanol 3 Record the temperature reading on the VT controller Temperature is displayed on the face of the VT controller remote status unit if ordered and on the hardware bar 4 Record the chemical shift frequencies of the two peaks 5 Follow the procedure for either the high or low temperature test e High Temperature Calibrations Test page 27 Low Temperature Calibrations Test page 28 High Temperature Calibrations Test CAUTION Extreme temperatures can damage the probe The high and low temperatues must be within the specified range of the probe 1 Follow the procedure in Set up page 26 2 Acquire a spectrum at room temperature follow the procedure in Data Acquisition page 27 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 27 Chapter 2 Console and Magnet Test Procedures 3 Click the Start tab and select the Spin Temperature pag
56. lied by Oxford complete instructions and for more detailed information on cyrogen fill intervals and capacities CAUTION Failure to maintain the correct liquid nitrogen levels will lead to excessive liquid helium boil off which in turn may lead to a quench of the magnet CAUTION Failure to maintain the correct liquid helium levels may lead to a quench of the magnet 4 8 30 Day System Maintenance The following procedures must be performed while logged in as vnmr1 1 Updating Solvent Shims Reshim lineshape and then save shims to vnmr shims acetone 2 Check Calibration of pw90 and tpwr as described in Calibrating a Probe page 13 3 Perform hard drive maintenance delete unused files directories old FIDs macros shims or users 4 Check magnet drift as described in 2 3 Magnet Drift Test page 23 If necessary when ZO is high or close to maximum 2047 reset ZO by adjusting the lockfreq parameter as follows a Load H1sn par 56 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 9 Warranty and Who to Call for Assistance b Set pw 1 gain 2 d1 0 in n at 1 sw 100 c Set Z0 to 0 d Insert a pure water sample and acquire a spectrum e Enterf full apho rh Place a cursor on the water peak and enternl movetof setlockfreq 4 9 Warranty and Who to Call for Assistance The installation engineer will explain the standard warranty terms Non standard warranty terms if included
57. loor Refer to the Installation Planning Manual for details Do not remove the relief valves on the vent tubes The relief valves prevent air from entering the nitrogen and helium vent tubes Air that enters the magnet contains moisture that can freeze causing blockage of the vent tubes and possibly extensive damage to the magnet It could also cause a sudden dangerous release of nitrogen and helium gases from the dewar Except when transferring nitrogen or helium be certain that the relief valves are secured on the vent tubes On magnets with removable quench tubes keep the tubes in place except during helium servicing On Varian 200 and 300 MHz 54 mm magnets only the dewar includes removable helium vent tubes If the magnet dewar should quench sudden appearance of gases from the top of the dewar and the vent tubes are not in place the helium gas would be partially vented sideways possibly injuring the skin and eyes of personnel beside the magnet During helium servicing when the tubes must be removed follow carefully the instructions and safety precautions given in the manual supplied with the magnet Caution Notices Observe the following precautions during installation operation maintenance and repair of the instrument Failure to comply with these cautions or with specific cautions elsewhere in Varian manuals violates safety standards of design manufacture and intended use of the instrument Varian assumes no liability fo
58. lso always notify their physician and discuss the health risks of being in proximity to magnetic fields Wearers of metal prosthetics and implants should contact their physician to determine if a danger exists Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed Keep metal objects outside the 10 gauss perimeter from the centerline of the magnet The strong magnetic field surrounding the magnet attracts objects containing steel iron or other ferromagnetic materials which includes most ordinary tools electronic equipment compressed gas cylinders steel chairs and steel carts Unless restrained such objects can suddenly fly towards the magnet causing possible personal injury and extensive damage to the probe dewar and superconducting solenoid The greater the mass of the object the more the magnet attracts the object Only non ferromagnetic materials plastics aluminum wood nonmagnetic stainless steel etc should be used in the area around the magnet If an object B0904 MERCURYplus Console Acceptance Tests for VnmrJ 5 WARNING WARNING WARNING WARNING WARNING WARNING WARNING is stuck to the magnet surface and cannot easily be removed by hand contact Varian service for assistance Refer to the manuals supplied with the magnet for the size of a typical 10 gauss stray field This gauss level should be
59. mand line which is not normally displayed To display it simply click on the small dot at the top center of the graphics area and drag it down e To enable the sample changer after finishing the exercises reset traymax to its proper value or exit from and restart VnmrJ to automatically resets traymax 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 37 Chapter 4 Customer Training 38 Walkup Interface Refer the VnmrJ Walkup manual and review the description of the Walkup interface Prepare and Insert the Sample 1 Put the NMR sample tube into the turbine sometimes called the spinner Use the sample depth gauge to center the sample volume Refer to section 2 3 Preparing the Sample of the VamrJ Liquids NMR User Guide manual 2 Click the Start tab and select the Study page Click the Eject button and then place the sample turbine into the top of the upper barrel Click the Insert button to lower the sample turbine into the probe Exercise 1 1D Proton Using the Study Queue The purpose of this first exercise is to acquaint you with one of the standard ways to set up routine experiments and with the things that normally have to be done with most experiments Before you begin e you must be logged in as a walkup user the sample must be prepared and inserted as described above Set Up and Acquire 1D Proton 1 Select the Std 1D tab and click once on Proton You will see a new sample entry i
60. ment 10 Solaris software Installation 34 solids high power amplifiers caution 8 spectra 13C observe pw array 49 spinning speed 13 streaming magnetic tape unit 11 svs command 12 System Demonstration 10 system demonstration 10 system documentation review 10 system installation checklist 65 System Maintenance 30 day check list 56 T Technical References Command and Parameter Ref 35 System Description 35 System Schematics 35 Technical Reference 35 User Programming 35 temperature accuracy for VT systems 26 test conditions 12 test parameters 13 training 2 ethyl 1 indanone spectra 50 53 training seminars 11 U upper barrel warning 6 V variable temperature control demonstration 25 74 MERCURYplus Console Acceptance Tests for VamrJ temperature accuracy optional 26 Varian manuals 10 Varian Sales Offices 57 VNMR directory and file structure 35 VnmrJ Liquids manual 34 VnmrJ Walkup NMR manual 34 vortexing 13 VT experiment warning 6 W warnings defined 5 warranty coverage 10 where to look for answers 33 Installations 34 Operations 34 Technical References 35 Varian Sales Offices 57 Who to Call for Assistance 57 Who to Call for Assistance 57 Z ZO and Make LOCK gmap calibration 17 01 999255 00 B0904
61. n the Study queue area the lower left portion of the window 2 Double click 1 min Proton to load the experimental parameters 3 Select the Study page and set Solvent to CDCI3 4 Enter whatever you like or nothing at all for Sample Notebook Page and Comment 5 Under Prescans select Find z0 and Gradient Shim You can choose the Plot all data option or not as you wish The first study is now ready for acquisition 6 Click the Submit button to start the acquisition The Submit button is under the Study Queue Observations The first thing you should see happening after some overhead during which the study status changes from Queued to Active is a 1 scan spectrum the Find z0 scan which sets z0 for later autolocking After the Find z0 scan is completed gradient shimming is set up and started during both the Find z0 scan and gradient shimming the Proton node shown in the Study queue area will be highlighted in yellow The shimming will probably take 2 or 3 iterations and should be completed in 3 4 minutes after which the actual experiment starts The highlight color changes from yellow to turquoise showing the currently active experiment When the experiment is complete the data is automatically loaded into the MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 5 Basic Spectrometer Operation current workspace where it can be viewed For a description of the interactive display see the VamrJ Liq
62. na BPE V OTIS minteeneiyi aia i aie ae EN E EEEa iaeei 35 42 Vir Directory StUCtUTE c c ceccsesesnneessescssennosssissnvestesssneansbinseuasesbesdeonsesutoessusnnsens 35 4 3 Initial System Settings oo es seessesceseseesessseseesecesessesecoesasscensesasetsesnesseeassesenvenenes 36 4 4 Set Up Experimental and Walkup Users cccececcssssessssecseeeeeeceseeeeaeeeeenecaeeeeeaeeaeenees 36 4 5 Basic Spectrometer Operation sssrinin siiri iri sristi assisi 37 Sample for EXG0G1SS eeir pestise inai nerien eiie ne iaeiae iE eeii e 37 Disable the Sample Changer v c 0cicsiseeessasiiaie duets ie i a 37 Walkup IMEraCE siieireriis iisisti nieren rie ENE N E ER rN 38 Prepare and Insert the Sample sinnene nnne n is 38 Exercise 1 1D Proton Using the Study Queue sssesessssseseeeesesessersresessesessesessee 38 Exercise 2 1D Proton and COSY Using the Study Queue sseeessssesesersesseeeesee 39 Exercise 3 1D Proton HSQC and More 50 c scccccciceccssetessesesassencesonceeetsvsetevers 41 Exercise 4 1D Spectra Using the Experimental Interface ote eeeeeeeeteees 42 Exercise S Ru nmine MUSH COSY socair owns 45 4 6 Interpreting the Calibration and Indanone Spectra e sessssseeseserersterereersrererrrereeses 46 Calibration When isit Necessary 5 0 cies cicin alice adarieiieseait 46 Interpretation of the Calibration Data cscesccescesseeseessessseeecseceecsessseeeesens 46 Interpretation of 2 Ethyl 1 Indanone Spectra oo eeescsse
63. ning Sian Figure 22 10 Gauss Warning Sign Figure 23 5 Gauss Warning Sign Amma A STRONG MAGNETIC AND RADIO FREQUENCY FIELDS ARE PRESENT Tools and Equipment Magnetic Media and ATM Credit Cards Strong magnetic fields are present that could erase magnetic media such as floppies and tapes disable ATM Flute KL e EAE B ETET GI some watches Strong magnetic fields are present that could make some magnetic items suddenly fly towards the magnet body which could cause personal injury or serious damage Do not take tools equipment or personal items containing steel iron or other magnetic materials closer to the magnet than the 10 GAUSS WARNING signs Do not take such objects closer to the magnet than the 5 GAUSS WARNING signs ow Pub No 87 250801 00 80694 Magnet Area Entrance Danger Sign VARIAN Figure 24 Magnet Area Danger Sign Stray magnetic fields can reach beyond the published distances when two or more magnetic fields intersect or when the field extends over large ferromagnetic masses or structures steel doors steel construction beams etc In this case the customer must measure the stray field using a gaussmeter to determine how the 5 and 10 gauss fields are altered contact a scientific instrumentation supplier for information on acquiring a gaussmeter You can request additional signs from Varian by telephoning 1 800 356 4437 in the United States or by contactin
64. nt in the menu bar b Click on Exit the interface closes 4 5 Basic Spectrometer Operation This section contains exercises that are designed to acquaint you with basic spectrometer operations using the walkup and experimental interfaces in VnmrJ These exercises should take no longer that 2 hours to complete Before proceeding the system must be set up and calibrated as described in Chapter 2 Console and Magnet Test Procedures of this manual The first 3 exercises will use the Walkup mode so be sure you are logged in as the walkup user for these e Sample for Exercises on this page e Disable the Sample Changer on this page e Walkup Interface page 38 Prepare and Insert the Sample page 38 e Exercise 1 1D Proton Using the Study Queue page 38 e Exercise 2 1D Proton and COSY Using the Study Queue page 39 e Exercise 3 1D Proton HSQC and More page 41 Exercise 4 1D Spectra Using the Experimental Interface page 42 e Exercise 5 Running Just a COSY page 45 Sample for Exercises Sample Sample Size mm Sample Part Number 2 2 ethyl 1 indanone in chloroform d 5 01 901855 03 Disable the Sample Changer It is easier to run the exercises without using a sample changer so if your system has a sample changer disable it You can reenable it after the finishing the exercises e To disable the sample changer enter traymax 0 You will need the com
65. nt in the spectrum which actually arise from the impurities shown in Figure 15 An example of this is the cross peak at 3 5 ppm ilk oda kW F2 ppm ao oF 4 J a x 24 t S z Impurities 4 w a r a 3 4 Bw Pe 54 g 74 3 es 5 78 84 a a S LE LL S S 8 7 6 5 4 3 2 1 F1 ppm Figure 15 Gradient COSY of 2 Ethyl 1 Indanone 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VamrJ 51 Chapter 4 Customer Training The methyl triplet in Figure 16 shows major cross peaks to the H10 protons The multiplicity of the H10 and H2 protons cross peaks show that they are weakly coupled the J value is small Aa r2 4 amp om no 3 1 24 a 1 44 2 3 3 D 3 1 64 1 84 3 f ex 2 04 E iE 2 24 2 44 2 64 1e q 3 2 83 3 04 3 24 3 q amp 3 44 3 64 3 Bree Te EM ATA 3 8 3 4 3 0 2 6 2 2 1 8 1 4 1 0 F1 ppm Figure 16 Gradient COSY gCOSY of Aliphatic Region of 2 Ethyl 1 Indanone Assignment of the aliphatic region begins with H7 the most deshielded proton Figure 17 From H7 direct connectivity is apparent to H6 The rest of the assignment is H6 to H5 the other triplet and then to H4 CHCl3 A T9 Fa J Jk 7S IA TA F1 ppm Figure 17 Gradient COSY gCOSY of the Aromatic Region of 2 Ethyl 1 Indanone 52 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 4 6 Interpreting the C
66. o CDCl 01 999255 00 B0904 41 MERCURYplus Console Acceptance Tests for VamrJ Chapter 4 Customer Training 3 Select the Acquire tab and click on the Prescan button Make sure Proton and MinSW are selected 4 Double click the Carbon node 10 min Carbon 5 Select the Acquire tab You can change the spectral width either by choosing one of the values from the pull down menu or by specifying the upfield and downfield values For example change the 15 Upfield value to 5 Notice the spectral width ppm menu is now blank You can also change the number of transients and relaxation delay An option to test for signal to noise test at the completion of each block is also available If this option is chosen the acquisition will stop when the specified signal to noise is reached 6 Double click Ghsqe 7 Select the Acquire tab Here you can change the number of transients and the number of t1 increments You can also turn off multiplicity edit from here 8 Select the Acquisition page Change the relaxation delay to 1 second 9 Click on the Submit button Exercise 4 1D Spectra Using the Experimental Interface This exercise demonstrates using the Experimental interface Before you begin make sure of the following auser account is set up to use the Experimental interface as described in 4 4 Set Up Experimental and Walkup Users page 36 e printers are set up and gradients are turned on for the user acc
67. om the results of the Minsw prescan 9 From the Fourier number in F2 amp F1 menu select not used 10 Click Show Time to update the time estimate for this experiment 11 Click Submit to acquire data Observations The actual 1D proton acquisition is started immediately using the standard wide spectral width When it is complete e data is processed the spectral window adjusted to just the region of the spectrum containing signals e anda second 1D proton spectrum is acquired processed plotted and saved Finally the Gcosy or Cosy parameters are set up and that spectrum acquired processed plotted and saved On the plot the high resolution 1D proton spectrum should be plotted along the sides of the 2D contour plot You should also see that while the 1D spectra are being acquired it is the Proton node in the Study Queue that is highlighted in turquoise with the highlight on Gcosy during that experiment View the Proton Data To view the Proton strictly the Proton _Minsw data while the Gcosy data is being acquired double click the Proton experiment The data is recalled processed and displayed Create a New Workspace As in the first exercise everything is done automatically You are left with the COSY data in the current experiment But what if you want to look at the 1D spectrum It was saved after being acquired but the data is no longer present in the current workspace now being used for the COSY data
68. ount e the name of the probe is the system probe Change to the Experimental Interface 1 Ifyou are logged in as a Walkup user exit VnmrJ Select Utilities gt Exit VnmrJ 2 Log out of Solaris by clicking Exit on the CDE menu bar 3 After the Solaris login window appears log in as the experimental user 4 Start VnmrJ by entering vnmrj in a Terminal window Setup and Acquire 1D Proton As a first example we will rerun the 1D proton spectrum assuming in this case that the sample has just been put into the magnet and so needs to be locked and shimmed You will be selecting the experiment from the locator 1 Check to see that the upper level directory in the File Browser is export home If not click Home and then click the up arrow until only export home shows 42 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 5 Basic Spectrometer Operation 2 Click the Locator Statement menu and 2 Show ste experiments created byvarian 1 select Sort Protocols and me on any date D lt gt A list of standard experiments should s i qrame apptype author appear in the locator Carbon std1d varian 3 Double click on the Proton experiment Fluorine std1d vanan f 7 Phosphorus std1d varian or drag the icon from the Locator into Presat std1d varian VnmrJ graphics window Wet1d std1d varian Apt hemult varian 4 Clickthe Start tab and select the Standard Cigar2j3j hetero2d varian Cosy homo2d varian page
69. pectra of a sample the spectrometer must first be calibrated if one of the following is true The probe has been changed Anew probe has been installed The experiments are to be run at a different temperature than the last calibrations Solvent changes significantly i e an organic lock solvent vs deuterium oxide lock solvent The calibration has not been run for several weeks in this case it is simply a matter of good laboratory practice to check the calibration Interpretation of the Calibration Data The first of the spectra shown in Figure 3 is a H observe with CDCl as the lock solvent This data is saved as H1ref This spectrum contains three BCHGI resonances centered at about 2 2 ppm The center resonance is from the protons attached to carbon 12 and the two outer resonances are from the protons attached to carbon 13 The other resonances in the sample are from trimethylphosphite that has reacted with the methyl iodide Perper Pea Pe pp eee ep ape 5 5 5 0 4 5 4 0 3 5 3 0 2 5 2 0 1 5 1 0 0 5 ppm Figure 3 H Spectrum of 13C Methy1 Iodide MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 6 Interpreting the Calibration and Indanone Spectra All trimethylphosphite has reacted to form a phosponate ester CH3 P O OCH3 This phosponate ester has a doublet at about 1 5 ppm methyl group attached directly to 31P and a triplet of doublets centered around 4
70. pment have been measured and compared to the IEEE ANSI C95 1 1991 standard For further information refer to the RF Environment section of the Installation Planning Guide Warning Signs Varian provides signs to help customers meet this posting responsibility These signs must be posted according to the following requirements before the magnet is energized 1 10 gauss warning signs Figure 22 Post along the 10 gauss perimeter of the magnet so that a sign can be easily seen by any person about to enter the 10 gauss field from any direction Refer to the manuals supplied with the magnet for the size of a typical 10 gauss stray field Check this gauss level after the magnet is installed Note that the stray field may extend vertically to adjacent floors and additional signs may be needed there A sign is not required if the 10 gauss field extends less than 30 cm 12 in beyond a permanent wall or less than 61 cm 24 in beyond the floor above the magnet 2 5 gauss warning signs Figure 23 Post along the 5 gauss perimeter of the magnet so that a sign can be easily seen by any person about to enter the 5 gauss field from any direction Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field Check this gauss level after the magnet is installed Note that the stray field may extend vertically to adjacent floors and additional signs may be needed there 01 999255 00 B0904 MERCURYplus Console Acceptan
71. r customer failure to comply with these precautions CAUTION CAUTION 01 999255 00 Keep magnetic media ATM and credit cards and watches outside the 5 gauss perimeter from the centerline of the magnet The strong magnetic field surrounding a superconducting magnet can erase magnetic media such as floppy disks and tapes The field can also damage the strip of magnetic media found on credit cards automatic teller machine ATM cards and similar plastic cards Many wrist and pocket watches are also susceptible to damage from intense magnetism Refer to the manuals supplied with the magnet for the size of a typical 5 gauss stray field This gauss level should be checked after the magnet is installed Keep the PCs including the LC STAR workstation beyond the 5 gauss perimeter of the magnet Avoid equipment damage or data loss by keeping PCs including the LC workstation PC well away from the magnet Generally keep the PC beyond B0904 MERCURYplus Console Acceptance Tests for VamrJ 7 the 5 gauss perimeter of the magnet Refer to the nstallation Planning Guide for magnet field plots CAUTION Check helium and nitrogen gas flow meters daily Record the readings to establish the operating level The readings will vary somewhat because of changes in barometric pressure from weather fronts If the readings for either gas should change abruptly contact qualified maintenance personnel Failure to correct the cause of abnormal read
72. r menu enter the password and click OK 3 Select Utilities gt New automation run 4 Ifasample changer is present set traymax 0 5 Make sure the printer plotter is set up p gon is set properly and shim map that was made in 2 1 Calibrating a Probe page 15 has been copied into vamr shimmaps Setting Up the Study and Lock Solvent 1 Insert the indanone sample 01 901855 03 2 Click the Start tab Study Study Info Operator donald Insert Eject Lock peda Prescans Eest Shim Not Page WW Findzo SPIVTEMD sovent epcis W Gradient Shim comment F Plot all data STANDARD 1H OBSERVE Email to 3 Select the Study page 4 Enter sample information in the Comment field 20 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 2 Automated Data Acquisition 2 ethyl 1 indanone Enter information Optional in the Notebook Page and Sample fields Select CDCI3 from the Solvent drop down menu Place a check in box to enable Plot all data option Make sure the Find Z0 and Gradient shim boxes are checked Oe GO MON oN Do not place a check in check boxes for Email when study complete or Email when fid complete If a check appears in either box click the box to remove the check Building a Composite Protocol e ID Protocols on this page e 2D Nongradient Protocols page 21 e 2D Gradient Protocols page 21 1D Protocols 1 Click the
73. review Software Object Code License Agreement acceptance of product constitutes acceptance of __ object code license regardless of whether agreement is signed or not ___ Varian and OEM manuals ___ Explanation of warranty and where to telephone for information 3 Installation Training 4 Installation Customer Training Check list 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 65 Chapter 5 Acceptance Test Results Notes 66 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 5 4 Supercon Shim Values 5 4 Supercon Shim Values Fill in the following information Magnet Frequency and Serial Number Magnet Frequency Serial Number Measurement in Helipot Amps Measurements Measurement ZY XY X2 Y2 Drift Boiloff N2 He Spacers Main Field Current Customer Signature Varian Representative Signature 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 67 Chapter 5 Acceptance Test Results Notes 68 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 5 5 Console and Magnet Test Results 5 5 Console and Magnet Test Results Fill in the following information From 2 1 Calibrating a Probe page 15 From 2 2 Automated Data Acquisition page 19 From 2 3 Magnet Drift Test page 23 From Variable Temperature Operation Optiona
74. rge triplet for the methyl group has 3C satellites at J 125 Hz The CHCl singlet at 7 24 ppm is the Ia Au Adak 5 4 3 2 1 ppm residual CHCl in the CDCl solvent The protons are assigned Figure 12 Proton Spectrum of 2 Ethyl 1 Indanone in the two expansions The assignments are based upon the 2D data for the compound The protons of the two CH3 groups in the molecule shown in Figure 13 are magnetically nonequivalent and show up as individual multiplets The signals at 1 9 ppm and 1 55 ppm belong to protons on carbon 10 The two double doublets at 2 8 ppm and 3 26 ppm belong to protons on carbon 3 A complex multiplet at 2 6 ppm is the single proton on carbon 2 The protons of the aromatic ring shown in Figure 14 are assigned based on the gHMBC and gCOSY data Some minor impurities can be seen as well as the residual CHCl signal If the sample is shimmed very well there may be some truncation artifact on the CHCl signal 3 4 3 2 3 0 2 8 2 6 2 4 2 2 2 0 1 8 1 6 1 4 1 2 1 0 ppm Figure 13 Aliphatic Region of the 2 Ethyl 1 Indanone Spectrum 50 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 6 Interpreting the Calibration and Indanone Spectra 7 9 3 7 2 ppm Figure 14 Aromatic Region of the 2 Ethyl 1 Indanone Spectrum The gradient COSY shows cross peaks describing the coupling pathways Some smaller cross peaks are also prese
75. riate frequency Spinning speed must be set to the following Sample mm Nuclei Speed Hz 5 all 20 26 10 all 15 Spinning 10 mm tubes faster than 15 Hz can cause vortexing in samples severely degrading the resolution Some test parameters are stored in the disk library vnmr tests To see the parameter sets available for the standard tests use the VnmrJ File Browser Other sets come from vnmr stdpar Many of the probe parameters and performance specifications will be determined automatically and the corresponding manual tests will NOT be run by the installer Certain tests such as signal to noise and lineshape will be run manually Tests corresponding to the automatic performance tests are provided should you want to run them at a later time For all sensitivity tests the value of pw must be changed to the value of the 90 pulse found in the pulse width test on the same probe and nucleus During calibration VnmrJ creates an appropriate pw array to determine the 90 pulse width For manually run observe pulse width tests an appropriate array of pw values must be entered to determine the 360 pulse The 360 pulse is the second non zero pulse that gives minimum intensity of the spectrum The 360 pulse is usually determined by interpolation between a value that gives a positive signal and a value that gives a negative signal The 90 pulse width is one quarter the 360 pulse 360 4 Signal to noi
76. s 256 zl Window functions iaj 300 z asa S A FZ Plotwhen done EET Plot 10 Top id xj Spectral Width ppr KEU Bide 10 Stat 20 End 140 Parameters Basic Top Left z Study Queue Customized NOESY Parameter 1 Click the for the Noesy protocol if the protocol time is not visible 2 Double click the protocol time to retrieve the parameters 3 Click the Acquire tab select the Defaults page if more than one page is available The parameter panel and the pulse sequence are displayed 4 Modify the acquisition parameter as follows for both Gradient and Non Gradient systems or non Gradient Probe 5 Change the following acquisition parameters a Click the Scans per increment drop down menu and select 4 b Click the Mixing time ms drop down menu and select 1000 Customize the Carbon Parameters 1 Click the for the Carbon protocol if the protocol time is not visible 2 Double click the protocol time to retrieve the parameters 3 Click the Acquire tab and select the Defaults page if more than one page is available 4 Select 1000 from the Number of Scans drop down menu 5 Uncheck Test for S N at every block size Acquiring Data Using a Composite Protocol 1 Click the Submit button 2 All the protocols are locked automatically 3 Acquisition starts Continue with 2 3 Magnet Drift Test page 23 22 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 3 Magnet Drif
77. s about 12 hours to complete 15 After the data acquisition is completed the data is processed and the spectra are displayed as a stacked display 16 The data can be processed manually as follows Click the Process tab and select the Process page s Click Transform All then Autophase Zero buttons Select the Display page Set Display Mode to Phased Set Axis to Hertz a p Set Amplitude scaling to Absolute Click Position button Full h Click Display Array buttons Vertical and Label m h o 17 Measure the difference between the left most peak and the right most peak in Hz 30 MERCURYplus Console Acceptance Tests for VamrJ 01 999255 00 B0904 Chapter 3 Consoles and Magnets Specifications This section contains the following specifications e 3 1 Magnet Drift page 31 3 2 Variable Temperature Operation this page 3 3 Temperature Accuracy for VT Accessories page 32 3 4 Stability Calibration for High Stability VT Accessory page 32 3 1 Magnet Drift Table 5 lists the drift specifications for magnets Specifications for nominal field decay rate are less than or equal to the values listed in the table Table 5 Magnet Drift Specifications System Field Strength Nominal Field Decay Rate MHz mm T Hz hr 200 54 4 70 2 300 54 7 05 3 400 54 9 40 8 3 2 Variable Temperature Operation For basic variable temperature VT accessories Varian Part No 00 992957 00 demonstrat
78. s designed for indirect detection applications are tested for indirect detection performance only Indirect detection acceptance tests are performed only if an indirect detection probe was purchased for use with the MERCURYplus e Sample Tubes Policy Tests are performed in 5 mm sample tubes with 0 38 mm wall thickness Wilmad 528 PP or equivalent and 10 mm sample tubes with 0 46 mm wall thickness Wilmad 513 7PP or equivalent Using sample tubes with thinner walls Wilmad 5 mm 545 PPT or equivalent Wilmad 10 mm 513 7PPT or equivalent increases signal to noise Computer Audit A computer audit form is included in Computer Audit page 61 The information from this form will help Varian Inc assist you better in distributing future software upgrades and avoiding hardware compatibility problems You are asked for information about all computers directly connected to the spectrometer or else used to process NMR data Installation Checklist An installation checklist form is included in System Installation Checklist page 65 System Documentation Review Following the completion of the acceptance tests and computer audit the installation engineer will review the following system documentation with the customer Software Object Code License Agreement e Varian Inc and OEM manuals e Warranty coverage and where to telephone for information Basic System Demonstration The installation engineer will also demonstrat
79. se S N is measured by the computer as follows S N maximum amplitude of peak 2 x root mean square of noise region Lineshape should be measured digitally with the aid of the system software The properly scaled spectra should also be plotted and the plot retained Digital determination of lineshape 1 Display and expand the desired peak 2 Enter nm then dce for drift correction to ensure a flat baseline Set vs 10000 Click icon to display the horizontal threshold cursor Set th 55 the 0 55 level 3 Clickthe icon two vertical cursors are displayed Align the cursors on the intersections of the horizontal cursor and the peak Enter delta to see the difference in Hz between the cursors Set th 11 the 0 11 level and repeat You can also use the macro res Place the cursor on the resonance of interest and type res on the command line Determination of lineshape from a plot 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 1 3 Chapter 1 Introduction 1 Use a large enough plot width to allow accurate determination of the baseline The baseline should be drawn through the center of the noise in a region of the spectrum with no peaks 2 The 0 55 and 0 11 levels are then measured from the baseline and calculated from the height of the peak and the value of vs For example ifa peak is 9 0 cm high with vs 2 00 then the 0 55 level ona 100 fold vertical expansion vs 20000 is 9 x
80. sories Solaris or Linux Vnmr J Installation and Administration Vnmr J Installation and Administration Vnmr J Installation and Administration Solaris Administration Spectrometer Operation Done Topic Reference Standard parameter and probe calibration Walkup NMR Creating a composite protocol Walkup NMR Interpretation of Indanone spectra Walkup NMR Manual lock and shim demonstration VnmrJ Liquids NMR Basic spectral display procedures VnmrJ Liquids NMR Gradient shimming demonstration VnmrJ Liquids NMR Miscellaneous ATP signoff and Walkup NMR demo if applicable Hallmark of Quality Customer contacts for service applications etc Accessory training as required Varian Representative Date Customer Representative 64 MERCURYplus Console Acceptance Tests for VnmrJ Date 01 999255 00 B0904 5 3 System Installation Checklist 5 3 System Installation Checklist Company University Address Principal User Phone Spectrometer type Fax Console S N Sales Order No Magnet S N Shipment Damage Preinstallation Preparation Line voltage measured Vac console accessory Line pressure air N2 Air conditioning Cryogens liters LHe LN Testing 1 Acceptance tests and computer audit ___ Acceptance tests procedures finished Test results form completed and signed ___ Computer audit completed and signed 2 System documentation
81. swering a question VnmrJ provides two libraries of information e VnmrJ Online Help on this page e Online Manuals on this page VnmrJ Online Help VnmrJ provides online help click Help on the VnmrJ main menu and select VnmrJ Help An internet browser is started Navigate the help system using the available browser tools 01 999255 00 B0904 LDprrcury m NMR Spectrometer Systems Online Manuals Menu Operation Getting Started User Guide Liquids NMR Walkup NMR Using GLIDE VNMA Command and Parameter Reference VNMR User Programming System Administration Probes and Accessories Probes amp Accessories Help File List installation Customer Training Checklist Installation Planning Quick installation and Release Notes VNMR and Solaris Software Installation Acceptance Test Procedures Specifications Sample Management Systems VAST Technical References System Overview Hardware Technical Reference System Schematics ap VARIAN gt lt Figure 2 Example Online Manual Menu MERCURYplus Console Acceptance Tests for VnmrJ 33 Chapter 4 Customer Training Online Manuals The complete library of manuals related to the system software and available accessories is accessible as PDF files Figure 2 shows an example menu for the online manuals After the installation has been finished you will find many of your routine questions answered in the following manuals VnmrJ Walkup NMR
82. t Test 2 3 Magnet Drift Test The magnet drift test is an overnight test e Samples for Magnet Drift Test page 23 Probe and Hardware Requirements page 23 e Test Procedure page 23 Samples for Magnet Drift Test Use the sample that provides a signal with good signal to noise ratio in most cases the 1 H20 99 DO samples will a good signal see Table 2 Table 2 Sample for Magnet Drift Test Sample Sample Tube mm Sample Part Number Doped 4 Hz H 0 D 0 5 01 901855 01 0 1 mg ml GdCl in 1 H O in D20 Doped 2 Hz H 0 D 0 5 01 901855 02 0 1 mg ml GdCl in 2 H O in D20 autotest sample 0 1 3C enriched 5 01 968120 68 methanol in 1 H 0 99 D0 Probe and Hardware Requirements A 5 mm probe capable of H direct observe is recommended Set up 1 Click the Locator Statements menu p and select System Param Files from under the Sort NMR Parameter Files category 2 Click the title above the right most column and select Directory from the lists that is displayed Select shmd2o and drag it to the VnmrJ graphics canvas Insert the 4 Hz H O D 0 sample Tune the probe ON ON a a Establish lock and adjust the field homogeneity Test Procedure 1 Select the Future Actions page 2 The only option active on this page is w t in the When Experiment Finishes field All other options should be disabled or the field blank 3 Click the Acquire button and obtain a normal spectrum and shim th
83. t integrals icon in the graphics controls bar to the left of the spectrum This will put you into partial integral mode and it is from here you can reintegrate the spectrum by hand You will now see three integral buttons The middle button is the button used to select the regions to be integrated You can click on the baseline or the integral itself to pick the regions With the H 1D spectrum of the ethyl indanone displayed select each peak as a region You can expand the spectrum to pick regions if you wish After you are happy with the selected regions click on the Process tab and then choose the Cursors Integration page Process Display Spectrum Clear Screen 4 Cursor s Integration For One Cursor on Screen For Two Cursors on Screen Scale to fit Add Reset at Cursor Move transmitter Show signal to noise AutoRegion Remove Reset at Cursor Place on nearest line Move spectral width Integral Values Clear Integrals Show linewidth Inset spectrum Normalized Values Setintegral Value Normalization value 100 000 You can use this page to set the integral value for a region For example a Click on the methyl peak 1 ppm with the left mouse button so that the cursor is under the integral b Change the Normalization Value to 3 000 c Click the Set Integral Value button The integral values will be displayed below the spectrum If you wish to start over the Clear Integrals buttons will remo
84. ther does it convey any license under its patent rights nor the rights of others Inclusion in this document does not imply that any particular feature is standard on the instrument MERCURY is a registered trademark of Varian Inc VxWORKS and VxWORKS POWERED are registered trademarks of WindRiver Systems Inc Sun is a registered trademark of Sun Microsystems Inc Ultra SPARC and SPARCstation are registered trademarks of SPARC International Inc Ethernet is a registered trademark of Xerox Corporation Other product names are trademarks of their respective holders Table of Contents Chapter 1 Introduction ic tes teeccecteeseeeeseesesenesiecseenseceeeeesweneevenssenecescenceseteeese 9 1 1 Overview of the Acceptance Testing Process cc cccescesseessessecsseeteceecesecesceseeeeeeseeseeeaes 9 PAGE PUAN CS TESIS sorrat Kae E ER Ei EE a EE ete E EERE AEE 9 Acceptance Specilicatiens once n R RE EE aE 10 Computer Audit eiiiai i R aeei aoii ineeie 10 Installation Checkiist ennie d ie iea aE aAa EES 10 System Documentation Review essssssesseseeseeeeseeeesseseeseseesessesesseeteseteeseeseeressese 10 Basic System Demonstration seia Re nE E ERS i a 10 1 2 General Acceptance Testing Requirements ccceseseesceeseeeceseeeeecseeseceeeeeeeaeensees 12 1 3 Samples Required for Acceptance Tests cceccesceesseescesceseeeseeseecsecseecseceeeeaeenseeaeens 12 1 4 General Testing and Specification Requirements 0 0 0 eceseeseseecseceeee
85. ther peripheral Computer function NMR host Workstation running VnmrJ of e g 2 of 3 Model no Purchased from Screen size in Serial no Serial no Serial no Serial no Serial no Serial no Serial no on site or off site VnmrJ version Workstation running other NMR software Workstation running VnmrJ and other NMR software Operating system on site or off site on site or off site Information on computer Manufacturer Computer S N Memory Mbytes Peripherals Internal hard disk Mbytes of e g 3 of 3 Model no Purchased from Screen size in Computer function VnmrJ version External hard disk Mbytes Tape drive size CD ROM drive model Printer model Plotter model Terminal model Other peripheral NMR host Workstation running VnmrJ Workstation running other NMR software Workstation running VnmrJ and other NMR software Operating system 62 MERCURYplus Console Acceptance Tests for VnmrJ Serial no Serial no Serial no Serial no Serial no Serial no Serial no on site or off site on site or off site on site or off site 01 999255 00 B0904 5 2 Installation Customer Training Checklist 5 2 Installation Customer Training Checklist Customer Information Company University Address Principal User
86. tion The node is the actual entry showing the time e g 1 min Proton not the bold Proton shown just above it 4 Click the Start tab and select the Study page 5 As before you can enter sample information and a comment this time you want to make sure that both the Find z0 and Gradient Shim are not checked In two dimensional 2D experiments using the entire standard H1 spectral window 2 to 14 PPM is usually efficient when running the 2D experiment Therefore in addition to an initial wide window 1D spectrum we would like to acquire a second 1D spectrum with the window reduced to just the relevant portion of the spectrum 6 Click the Acquire tab select the Prescan page and select the Minsw option It is also inefficient to acquire too many or too few increments in 2 dimensional experiments so we would like to set the number explicitly It is not that the experiment would not be run well even without this step but rather that the point is to learn what can be done and how to do it 7 Double click or drag and drop the 4 min Gcosy node 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnamrJ 39 Chapter 4 Customer Training 8 After the Gcosy pulse sequence is displayed click the Acquire tab and select the Defaults page From the Number of increments menu select 128 Do not worry about the spectral width shown as the standard full window the value used in the actual experiment will be taken fr
87. to use state Acceptance Tests Acceptance test procedures are arranged by the type of specification These procedures cover the basic specifications of the instrument signal to noise resolution and lineshape and are not intended to reflect the full range of operating capabilities or features of a MERCURYplus NMR spectrometer The order in which the tests are performed is determined by the installation engineer Some procedures use results from other procedures 01 999255 00 B0904 MERCURYplus Console Acceptance Tests for VnmrJ 9 Chapter 1 Introduction 10 Performance of additional tests beyond those described in this manual must be agreed upon in writing as part of the customer contract Acceptance Specifications All specifications are subject to change without notice The specifications published in this manual shall prevail unless negotiation or customer contract determines otherwise Refer to the text in each chapter for other conditions Request for additional specifications beyond those listed in this manual must be agreed upon in writing as part of the customer contract The following policies are in effect at installation Specifications Policy for Probes Used in Systems other than MERCUR Yplus No guarantee is given that probes purchased for use in systems other than MERCUR Yplus will meet current specifications Testing Policy for Indirect Detection Probes used for Direct Observe Broadband Performance Probe
88. tration manual contains detailed information about the VnmrJ directory structure The VnmrJ directory and file structure is set up with both global files and directories and user accounts with user level files and directories Directories and permission levels for UNIX logins other than root are as follows Read Write and Directory Deseripti n Execute Permission export home vnmr System or global directories and files VnmrJ administrator typically vnmr1 vnmr Symbolic link to VnmrJ administrator export home vnmr typically vnmr1 export home lt user gt User directory and files UNIX log in account owner export home lt user gt vnmrsys User VnmrJ directories and files UNIX log in account owner The VnmrJ administrator rather than root should make changes to VnmrJ files and directories The global files and directories contain macros pulse sequences binary files optional VnmrJ software and other files that have a common usage to all users When a command or instruction is executed in VnmrJ by a user VnmrJ first searches the vnmrsys directory for the command pulse sequence etc and then searches the global files in vnmr When creating custom macros pulse sequences menus etc it is necessary to give these files different names from the similar files in vnmr If you want the customized macros pulse sequences etc to be available to all users place them in the appropriate directory in vnmr 01 999255
89. uids NMR manual Summary Locking shimming acquisition processing plotting and saving the data was done automatically requiring only what you selected in the Study parameter panel The flow of events was e select the experiment e select experimental options acquire data including Find z0 gradient shimming and the actual acquisition e process plot and save data In the coming exercises we will learn more about doing these things by hand Exercise 2 1D Proton and COSY Using the Study Queue The purpose of this exercise is to further explore the Study Queue introducing a simple 2D experiment to see how a series of experiments can be run on a single sample You will also learn about using multiple workspaces to view several sets of data Setup and Acquire the COSY 1 Select New sample from the Study Options menu 2 Select the Homo 2D tab and click once on Gcosy just Cosy if your system does not have gradients Notice that the new sample entry in the Study Queue area shows both Proton and Gcosy nodes Since the sample is already in the magnet there is no need to eject or insert it and for that matter no need to lock and shim again assuming this exercise is being done immediately after completing Exercise 1 if not then you might need to do all these things Therefore we will need to customize this acquisition to turn off those choices among other things 3 Double click 1 min Proton to initiate customiza
90. uired for Acceptance Tests page 12 1 4 General Testing and Specification Requirements page 12 Following each installation of a Varian Inc MERCUR Yplus NMR spectrometer system an installation engineer tests and demonstrates the instrument s operation using the procedures in this manual The following is an overview of the chapters in this manual e Chapter 2 Console and Magnet Test Procedures provides the acceptance test procedures Chapter 3 Consoles and Magnets Specifications provides the acceptance test specifications Chapter 4 Customer Training provides basic spectrometer maintenance and operation training e Chapter 5 Acceptance Test Results contains forms for recording test results The acceptance test procedures and specifications for each probe are contained in a separate probe family manual for example procedures and specifications for AutoSwitchable probes are contained in the AutoSwitchable NMR Probes manual Only the lineshape and signal to noise tests are preformed manually All other probe calibrations are performed by the instrument during the AutoCalibration procedures 1 1 Overview of the Acceptance Testing Process The objectives of the acceptance tests procedures are threefold To identify the tests to be performed during system installation To identify the precise methods by which these tests are performed e To leave the instrument in a calibrated ready
91. uttons c Select the Display page d Set Display Mode to Phased e Set Axis to Hertz f Set Amplitude scaling to Absolute g Click Full button Screen Position h Click Display Array buttons Vertical and Label 10 Compare the frequency shift of the HDO peak of the arrayed spectra to the frequency of the first spectrum in the array 11 Write the results on the form in Console and Magnet Test Results page 69 24 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 2 4 Optional Tests 2 4 Optional Tests The following optional tests will be run if they are specified in contract and the hardware is present e Variable Temperature Operation Optional Hardware on this page e Temperature Accuracy for VT Systems Optional Test page 26 e Stability Calibration for High Stability VT Optional Test page 29 Variable Temperature Operation Optional Hardware This demonstration shows that the basic variable temperature VT unit and probe changes to the desired temperature and displays on the VT controller If the system is equipped with a VT unit read through the VT operation instructions before this demonstration Dry nitrogen is required as the VT gas if the requested temperature is over 100 C or below 10 C Otherwise air can be used Dry nitrogen gas is recommended for cooling the bearing spinner and decoupler This prevents moisture condensation in the probe and spinner housing
92. ve all the resets Note that the integrals in the aromatic region will not correlate well because the aromatic protons have much longer 71s than the aliphatic protons 44 MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 4 5 Basic Spectrometer Operation Plotting 1 Click the Process tab and select the Plot page setup Acquire Process Display Spectrum Clear Screen Process Plot Setup Plot Peak Frequencies FIDs Display Automatic Plot Page Plot Spectrum _ On Peaks Plot FID Linear Prediction PippSpecturm Stray Asa List PIOHeIDIana Cursorsiintegration Sereen Position Plot Spectrum Scale G None Plot FID Scale Full Center L Plot Parameter Template Left Right i Basic Parameters Integrals Clear Plot _Full Parameters Plot Integrals Autoscale _ Boxed Parameters Integral Values Hz to mm 25 0 None Plot Scaled mora Plot Pulse Sequence Plot Text Plot Normalized g 2 Click Automatic Plot Page Refer to the VamrJ Liquids NMR manual for information on customizing the plot Exercise 5 Running Just a COSY Setup and Acquire the COSY 1 Redisplay the spectrum 2 Click on the Process tab and select the Process page 3 Click the Transform all button 4 Place the cursors around the H spectrum to select the desired spectral width 5 Click the Cursors Integration page and click the Move spectral width button 6 From the Experiments menu select Homonucl
93. y Cold gasses or liquids helium and nitrogen contacting the body can cause an injury similar to a burn Never place your head over the helium and nitrogen exit tubes on top of the magnet If cold gasses or liquids contact the body seek immediate medical attention especially if the skin is blistered or the eyes are affected Do not look down the upper barrel Unless the probe is removed from the magnet never look down the upper barrel You could be injured by the sample tube as it ejects pneumatically from the probe Do not exceed the boiling or freezing point of a sample during variable temperature experiments A sample tube subjected to a change in temperature can build up excessive pressure which can break the sample tube glass and cause injury by flying glass and toxic materials To avoid this hazard establish the freezing and boiling point of a sample before doing a variable temperature experiment MERCURYplus Console Acceptance Tests for VnmrJ 01 999255 00 B0904 WARNING WARNING WARNING Support the magnet and prevent it from tipping over The magnet dewar has a high center of gravity and could tip over in an earthquake or after being struck by a large object injuring personnel and causing sudden dangerous release of nitrogen and helium gasses from the dewar Therefore the magnet must be supported by at least one of two methods with ropes suspended from the ceiling or with the antivibration legs bolted to the f

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