NMR Facility User Guide Analytical Instrumentation Center School of Pharmacy University of Wisconsin–Madison F2 (ppm) 1.5 2.0 2.5 3.0 3.5 4.0 4.5 75 70 65 60 55 50 45 40 35 30 F1 (ppm) Thomas C. Stringfellow Sixth Edition Version 2019-05-01 Table of Contents 1 Introduction 1 1.1 NMR Spectrometers .................................... 1 1.1.1 AV-400 Spectrometer ................................ 2 1.1.2 UI-500 Spectrometer ................................ 2 1.2 Supporting Computers and Software ............................ 5 1.3 NMR Facility Policies ................................... 6 1.3.1 Access and Use ................................... 6 1.3.2 User Training .................................... 6 1.3.3 Fees and Services .................................. 6 1.3.4 Reserving Instrument Time ............................. 6 1.3.5 Laboratory Safety and Health Issues ........................ 7 1.3.6 AV-400 Sample-Management Policies ....................... 9 1.3.7 Incident Report Form ................................ 10 2 Computers and Software 12 2.1 Information for Bruker Users ................................ 12 2.1.1 IconNMR Web View ................................ 13 2.2 Information for Varian Users ................................ 13 2.2.1 VNMR 6.1C Users Take Note! ........................... 13 2.2.2 Sun Desktop Environments: CDE versus OWD .................. 14 2.3 NMR Facility Computer Network ............................. 15 2.4 Samba Server Connections to NMR Facility Disk Shares ................. 15 2.4.1 Connection to Samba Shares from Microsoft Windows Clients .......... 16 2.4.2 Connection to Samba Shares from Mac OS X Clients ............... 17 2.5 X-Win32 Connectivity to Sun Computers ......................... 17 2.5.1 Installing X-Win32 ................................. 18 2.5.2 Configuring X-Win32 ............................... 19 2.5.3 Configuring the PC Monitor Resolution ...................... 20 2.5.4 X-Win32 License Configuration .......................... 21 2.5.5 Using X-Win32 ................................... 21 2.6 Data Archiving ....................................... 22 2.6.1 Using the UNIX tar Command .......................... 23 2.6.2 File Compression .................................. 24 2.6.3 Writing to a CD/DVD Drive ............................ 25 2.7 NMR Facility PC ...................................... 25 2.8 Mnova Notes ........................................ 25 3 NMR Sample Preparation 27 3.1 Sample Tube Selection and Care .............................. 27 3.2 Sample Preparation Guidelines ............................... 29 4 Guide to TopSpin and IconNMR 31 4.1 TopSpin Experiment Codes ................................. 31 4.2 TopSpin and IconNMR Directory Structure ........................ 36 5 Guide to VNMR 6.1C 39 5.1 VNMR User Interfaces ................................... 39 5.1.1 CustomQ ...................................... 39 5.2 Basic VNMR Parameters and Commands .......................... 40 5.3 Data Processing Tips .................................... 41 5.4 Spectral Display and the VNMR Graphics Window .................... 42 5.5 Plotting 2D Spectra ..................................... 43 5.5.1 The plcosy Macro ................................ 44 5.5.2 The plhxcor Macro ............................... 45 5.5.3 The plot2D Macro ................................ 45 5.6 Using Other Networked Printers .............................. 45 5.6.1 Customizing the Default Printer and Plotter .................... 46 5.7 Suppressing Automatic Printing .............................. 46 5.8 Advanced Graphics Handling Techniques ......................... 46 5.8.1 Introduction to Graphics Images .......................... 46 5.8.2 Setting Colors Under VNMR ............................ 47 5.8.3 Setting Up the Page Layout ............................ 48 5.8.4 Plotting to a File from VNMR ........................... 48 5.8.5 Copying from VNMR and Pasting into Other Applications ............ 49 5.9 Custom VNMR Menu Items ................................. 51 5.9.1 From the Main Menu Custom Macros Menu Level ............... 51 ! 5.9.2 From the Main Menu File Set Directory Menu Level ............ 51 ! ! 5.9.3 From the Main Menu Display Plot Menu Level ............... 52 ! ! 5.9.4 From the Main Menu Display Plot to File Menu Level ........... 52 ! ! 5.10 Custom VNMR Macros ................................... 52 5.11 Miscellaneous Considerations ............................... 57 5.11.1 Recovering After Locking Yourself out of VNMR ................. 57 5.11.2 Communication Between the Host and Acquisition Computers .......... 59 6 Sensitivity Issues in NMR 62 6.1 Introductory Definitions and Principles ........................... 62 6.1.1 Fundamental Constants ............................... 63 6.1.2 Sample-Dependent Terms ............................. 64 6.1.3 Instrument-Specific Terms ............................. 65 6.1.4 Acquisition Parameters ............................... 65 6.1.5 Understanding the Relationships .......................... 66 ii 6.2 Magnetic Susceptibility Matched NMR Tubes and Inserts ................. 68 7 VNMR Experiment Guide 72 7.1 Which Spectrometer or Probe Should I Use? ........................ 72 7.1.1 Spectrometer Smackdown ............................. 72 7.1.2 The Role of the Probe ............................... 73 7.1.3 Direct versus Indirect Detection .......................... 73 7.1.4 Directly Detected Experiments ........................... 74 7.1.5 Indirectly Detected Experiments .......................... 75 7.2 Probe Tuning ........................................ 76 7.2.1 Tuning the hcx4765 Probe ............................. 77 7.3 Temperature Control .................................... 79 7.3.1 FTS Systems Preconditioner ............................ 79 7.3.2 Temperature Control from VNMR ......................... 79 7.3.3 Measuring the Sample Temperature ........................ 80 7.3.4 VT Checklist .................................... 81 7.4 Detection of Other X Nuclides ............................... 82 7.4.1 11B Acquisition ................................... 82 7.4.2 15N Acquisition .................................. 83 7.5 Chemical Shift Referencing ................................. 85 7.5.1 Absolute Referencing via the Unified Scale () Method ............. 85 7.5.2 Referencing 11B .................................. 89 7.5.3 Referencing 15N .................................. 89 7.5.4 Referencing 19F .................................. 89 7.5.5 Referencing 31P .................................. 90 7.6 Spin Relaxation Measurements: The T1, T2 and T1 Suite ................ 90 7.6.1 General Considerations and Preparation ...................... 91 7.6.2 Experiment Setup and Data Acquisition ...................... 91 7.6.3 Data Processing and Analysis ........................... 94 7.7 The DEPT and INEPT Family of Experiments ....................... 95 7.8 Phase-Cycled versus Gradient Experiments ........................ 95 7.9 The COSY Family of Experiments ............................. 96 7.9.1 General Considerations ............................... 96 7.9.2 Preliminary Preparations .............................. 97 7.9.3 Experiment Setup and Data Acquisition ...................... 97 7.9.4 Data Processing ................................... 98 7.9.5 ECOSY Setup, Acquisition and Processing .................... 98 7.10 TOCSY and TOCSY1D ................................... 98 7.10.1 General Considerations ............................... 98 7.10.2 Preliminary Preparations .............................. 99 7.10.3 TOCSY ....................................... 99 7.10.4 TOCSY1D ..................................... 99 7.11 The NOE Family of Experiments .............................. 100 7.11.1 General Considerations ............................... 101 7.11.2 Preliminary Preparations .............................. 101 7.11.3 NOESY ....................................... 101 iii 7.11.4 NOESY1D ..................................... 102 7.12 The ROE Family of Experiments .............................. 103 7.13 1H-detected Heteronuclear Family of Experiments .................... 103 7.13.1 General Considerations ............................... 103 7.13.2 Preliminary Preparations .............................. 103 7.13.3 Experiment Setup and Data Acquisition ...................... 103 7.13.4 Data Processing ................................... 105 7.14 The HETLOC Experiment ................................. 105 7.14.1 General Considerations ............................... 105 7.14.2 Preliminary Preparations .............................. 105 7.14.3 Experiment Setup and Data Acquisition ...................... 106 7.14.4 Data Processing ................................... 106 7.15 Combination Experiments ................................. 109 7.15.1 General Considerations ............................... 109 7.15.2 Preliminary Preparations .............................. 109 7.15.3 Experiment Setup and Data Acquisition ...................... 109 7.15.4 Data Processing ................................... 109 7.16 The 1H,19F Experiment Suite ................................ 109 7.16.1 General Considerations ............................... 110 7.16.2 Notes on Naming Conventions ........................... 111 7.16.3 Preliminary Preparations .............................. 111 7.16.4 Experiment Setup and Data Acquisition ...................... 112 7.16.5 Data Processing ................................... 113 7.17 The 1H,31P Experiment Suite ...............................