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Agilent Vnmrj 4.2 Spectroscopy Agilent VnmrJ 4.2 Spectroscopy User Guide Agilent Technologies Notices © Agilent Technologies, Inc. 2014 Warranty (June 1987) or DFAR 252.227-7015 (b)(2) (November 1995), as applicable in any No part of this manual may be reproduced The material contained in this docu- technical data. in any form or by any means (including ment is provided “as is,” and is sub- electronic storage and retrieval or transla- ject to being changed, without notice, tion into a foreign language) without prior Safety Notices agreement and written consent from in future editions. Further, to the max- Agilent Technologies, Inc. as governed by imum extent permitted by applicable United States and international copyright law, Agilent disclaims all warranties, CAUTION laws. either express or implied, with regard to this manual and any information A CAUTION notice denotes a haz- Manual Part Number contained herein, including but not ard. It calls attention to an operat- limited to the implied warranties of ing procedure, practice, or the like G7446-90573 merchantability and fitness for a par- that, if not correctly performed or ticular purpose. Agilent shall not be adhered to, could result in damage Edition liable for errors or for incidental or to the product or loss of important Revision B, June 2015 consequential damages in connection data. Do not proceed beyond a with the furnishing, use, or perfor- CAUTION notice until the indicated mance of this document or of any Revision log conditions are fully understood and information contained herein. Should met. Agilent and the user have a separate Revision Changes written agreement with warranty Rev A, May 2014 Initial revision for terms covering the material in this VnmrJ 4.2 document that conflict with these WARNING terms, the warranty terms in the sep- Rev B, June 2015 Minor corrections A WARNING notice denotes a arate agreement shall control. based on Spisights hazard. It calls attention to an feedback: fixed operating procedure, practice, or capitalization in Technology Licenses table on pg 96; cor- the like that, if not correctly per- The hardware and/or software described in rected to 48.5mM formed or adhered to, could result this document are furnished under a on pg 464. in personal injury or death. Do not license and may be used or copied only in accordance with the terms of such license. proceed beyond a WARNING notice until the indicated condi- This guide is valid for 4.2 revision of the tions are fully understood and met. Agilent VnmrJ software, until superseded. Restricted Rights Legend Printed in USA If software is for use in the performance of a U.S. Government prime contract or sub- Agilent Technologies, Inc. contract, Software is delivered and 5301 Stevens Creek Boulevard licensed as “Commercial computer soft- Santa Clara, CA 95051 USA ware” as defined in DFAR 252.227-7014 (June 1995), or as a “commercial item” as defined in FAR 2.101(a) or as “Restricted computer software” as defined in FAR 52.227-19 (June 1987) or any equivalent agency regulation or contract clause. Use, duplication or disclosure of Software is subject to Agilent Technologies’ standard commercial license terms, and non-DOD Departments and Agencies of the U.S. Gov- ernment will receive no greater than Restricted Rights as defined in FAR 52.227-19(c)(1-2) (June 1987). U.S. Govern- ment users will receive no greater than Limited Rights as defined in FAR 52.227-14 Contents 1 Running Liquids NMR Experiments NMR Experiment Tasks 18 Prepare for an experiment 18 Select an experiment 18 Set up an experiment 18 Acquire a spectrum 20 Process the data 20 Display the data 20 Print or plot the data 22 Saving NMR Data (Optional) 23 Stopping an Experiment 24 2 Preparing for an Experiment Starting VnmrJ 26 Preparing the Sample 27 Selecting a solvent 27 Setting the sample height 27 Sample position using the depth gauge 28 Sample tubes 29 Sample changes and probe tuning 29 Ejecting and Inserting the Sample 30 Ejecting a sample 30 Inserting a sample 30 Loading a Probe File 32 Tuning Probes on Systems with ProTune 33 Configuring for operation with automated sample handlers 33 Running ProTune on systems without automated sample handlers 33 Remote tuning from the ProTune window 34 Tuning Probes on Standard Systems 37 Selecting correct quarter-wavelength 37 Tuning using Mtune 37 Tuning using TUNE INTERFACE remote 39 3 Experiment Setup Selecting an Experiment 44 Protocols vertical tab 44 Main menu selections 44 Agilent VnmrJ 4 Spectroscopy User Guide 3 Spinning the Sample 46 Liquids spinner 46 MAS spinner 47 Setting the Sample Temperature 51 Handling Spin and Temperature Error 54 Working with the Lock and Shim Pages 55 Mouse control of buttons and sliders 55 Lock buttons and controls 55 Shim buttons and controls 56 Working with Proshim 57 Current method 58 Method editor 59 Manage shim method files 62 FID-shim parameters 63 Shim Menu Editor 64 Proshim in Automation 66 Using Proshim with Study Clone 66 Scheduling Shim Maintenance 67 Optimizing Lock 69 Finding Z0 and establishing lock 69 Lock power, gain, and phase 72 Lock control methods 72 Adjusting Field Homogeneity 75 Loading shim values 75 Loading a shim file 75 Saving a shim file 75 Shim gradients 75 Shimming on the Lock Signal Manually 77 Routine shimming 77 Setting low-order (routine) shims 79 Removing spinning sidebands (non-routine) 79 Setting the high-order axial shims (non-routine) 81 Setting high-order radial shims (non-routine) 81 Shimming PFG Systems 83 Performa I and Performa II 83 Performa XYZ 83 Calibrating the Probe 84 4 Agilent VnmrJ 4 Spectroscopy User Guide 4 Gradient Shimming Introduction to Gradient Shimming 86 Deuterium Gradient Shimming 87 Homospoil Gradient Shimming 88 Homospoil gradient type 88 Homospoil gradient shimming for 1H or 2H 89 Configuring Gradients and Hardware Control 90 Mapping Shims and Gradient Shimming 91 Recommended samples for gradient shimming 91 Manually calibrating the 90 degree pulse for 1H and 2H 91 Mapping the Shims 93 Starting gradient shimming 95 Quitting gradient shimming 95 Gradient shim commands and parameters 95 How making a shimmap works 96 How automated shimming works 97 Shimmap Display, Loading, and Sharing 98 Displaying the shimmap 98 Loading a shimmap 98 Sharing a shimmap 99 Shimmap files and parameter sets 100 Gradient Shimming for the General User 101 Deuterium Gradient Shimming Procedure for Lineshape 102 Setting up 102 Making the ShimMap 102 Starting Z gradient shimming 103 Optimizing non-spinning shims 103 Evaluating homogeneity 103 Calibrating gzwin 104 Automatic calibration of gzwin 104 Manual calibration of gzwin 105 Varying the Number of Shims 106 Changing the number of shims used for gradient shimming 106 Selecting optimization of Z1 through Z4 shims first 106 Variable Temperature Gradient Compensation 107 Spinning During Gradient Shimming 108 Suggestions for Improving Results 110 Gradient Shimming Using Selective Excitation 112 Agilent VnmrJ 4 Spectroscopy User Guide 5 Gradient Shimming Pulse Sequence and Processing 115 Gradient Shimming References 117 5 Study Queue and Studies Introduction to Studies 120 Study Clusters 121 To create a study cluster 122 To edit the last viewed cluster 124 To show the cluster library 124 To define cluster attributes 124 Operations Using a Robot Sample Changer 127 Study Queue controls-Review mode 127 Study Queue controls-Submit mode 130 Using the Study Queue-full automation 131 Day Queue, Night Queue, and Priority Queue 132 Editing experiments in a pending study 132 Extending an existing study 133 Deleting a sample from the queue 133 Operations Without a Robot Sample Changer 134 Study Queue Controls-Review mode 134 Study Queue Controls-Submit mode 135 Using the Study Queue-full automation 135 Creating a Study Queue from data acquired manually 136 Editing experiments in an active study 137 Extending a completed study 137 Data Acquisition Using a Spreadsheet 138 Study Mimic 140 Using Study Mimic 140 Study Mimic-multiple submissions 141 6 Data Acquisition Acquiring a Spectrum 144 Acquisition Settings 145 Acquisition and post acquisition actions 145 Nucleus-specific frequency settings 147 Transmitter and decoupler positioning 147 Spectral window 147 Pulse sequence settings (standard two-pulse) 148 Pulse Sequences 150 Display the pulse sequence 150 6 Agilent VnmrJ 4 Spectroscopy User Guide Standard two-pulse parameters 151 The status concept 152 Observe transmitter and decoupling settings 153 Decoupler modes 154 Parameter Arrays 155 Array definition 155 Stopping and Resuming Acquisition 158 Automatic Processing 159 Acquisition Status Window 161 7 Processing Data Introduction to Data Processing 164 Weighting Function 165 Interactive Weighting 167 Fourier Transformation 169 Phasing 170 Phase parameters 170 Autophase algorithm 171 Spectrum display 172 Advanced Data Processing 173 FID manipulation 173 Data processing methods 174 Linear prediction 174 Solvent subtraction filtering 176 Downsample 177 Interleave FIDs 178 8 Displaying FIDs and Spectra Displaying a FID or 1D Spectrum 180 FID display 180 1D spectrum display 180 Display Tools 182 Interactive display tools 182 Display parameters 183 Controlling cursors and vertical scale 185 Display limits 185 Display parameters files 185 Save Current Process / Display Parameters 187 Spectrum Annotations 188 Agilent VnmrJ 4 Spectroscopy User Guide 7 To create an annotation 188 Select and modify annotations 189 To show or hide annotations 191 To delete an annotation 191 To copy and paste annotations 192 To save or load annotations 192 To print an annotated
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