User’s Guide of

NMR-SAMS

An expert system for computer-assisted structure elucidation of organic and natural product compounds based on multidimensional spectroscopy

NMR-SAMS^TM User's Guide, April 1998.

This manual describes release 2.0 of the Windows 95/NT version of the NMR-SAMS^TM Software.

Copyright Notice

Copyright © 1996 through 2001 Spectrum Research, LLC. All rights reserved.

No part of this document may be reproduced, transmitted, transcribed, stored in a retrieval system, or translated into any language in any form by any means without the written permission of Spectrum Research, LLC.

All possible care has been taken in the preparation of this document but Spectrum Research accepts no liability for any errors/omissions that may be found.

Spectrum Research, LLC. reserves the right to change the information in this document without prior notice.

Trademarks

SpecMan^TM and NMR-SAMS^TM are trademarks of Spectrum Research, LLC.

Acknowledgments

NMR-SAMS^TM (originally known as CISOC-SES) has been developed by Dr. Shengang Yuan, Dr. Chen Peng and Prof. Chongzhi Zheng at the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences in 1988-1994. It has been further improved by Dr. Chen Peng in the group of Dr. Geoffrey Bodenhausen in the National High Magnetic Field Laboratory in 1995-1996. Portions of NMR-SAMS^TM are copyright © 1988 through 1995, Shanghai Institute of Organic Chemistry and Florida State University, and are exclusively licensed to Spectrum Research, LLC. Title and full ownership rights to the converted/modified NMR-SAMS^TM will remain solely with Spectrum Research, LLC, and NMR-SAMS^TM is asserted to be Spectrum’s proprietary information and trade secret.

Credits

If the results (figures and/or data) obtained by NMR-SAMS^TM application is used for publication purpose, please refer to it in the following manner or any other equivalent form:

"NMR-SAMS^TM software, developed by Spectrum Research, LLC., was used to compute the results in this publication".

Contents

Contents...............................................................................................................................

Abbreviations And Acronyms...............................................................................................

Introduction........................................................................................................................

1.1 General................................................................................................................................................................

1.2 Application Limitations....................................................................................................................................

1.3 System Requirement.........................................................................................................................................

1.4 Help Facility........................................................................................................................................................

1.5 Typographical Conventions..............................................................................................................................

Getting Started with NMR-SAMS.......................................................................................

2.1 Installation of the Program..............................................................................................................................

2.2 Spectrum Research Licensing........................................................................................................................

2.3 Starting NMR-SAMS........................................................................................................................................

2.4 Brief Introduction to Microsoft Windows.....................................................................................................

2.5 Description of the Main Menus.......................................................................................................................

2.6 The NMR-SAMS Toolbar.................................................................................................................................

Understanding NMR-SAMS...............................................................................................

3.1 Overview..............................................................................................................................................................

3.2 General Procedure of Structure Elucidation with NMR-SAMS...............................................................

3.3 What Spectral Data Does NMR-SAMS Use?..............................................................................................

3.4 Use of 2D NMR Connectivities: Bond Constraints...................................................................................

3.5 Use of Chemical Shifts And Peak Multiplicities.......................................................................................

3.6 Structure Generation....................................................................................................................................

3.7 User Intervention.............................................................................................................................................

3.8 Control Parameters........................................................................................................................................

Working Data Set.............................................................................................................

4.1 Overview............................................................................................................................................................

4.2 Opening An Existing Working Data Set....................................................................................................

4.3 Opening A New Working Data Set..............................................................................................................

4.4 Input Molecular Formula...............................................................................................................................

4.5 Save A Working Data Set..............................................................................................................................

4.6 Save A Working Data Set as Different Name............................................................................................

4.7 Exiting NMR-SAMS........................................................................................................................................

Input of NMR Spectral Data............................................................................................

5.1 Overview............................................................................................................................................................

5.2 Conversion of SpecMan ¹H Peak List..........................................................................................................

5.3 Conversion of SpecMan ¹³C Peak List.........................................................................................................

5.4 Conversion of SpecMan DQF-COSY Peaks Table....................................................................................

5.5 Conversion of SpecMan HMQC/HETCOR Peaks Table..........................................................................

5.6 Conversion of SpecMan HMBC/COLOC Peaks Table............................................................................

5.7 Conversion of SpecMan NOESY Peaks Table............................................................................................

5.8 Conversion of SpecMan INADEQUATE Data.............................................................................................

5.9 Manual Peak Picking.....................................................................................................................................

Spectral Interpretation.....................................................................................................

6.1 Overview............................................................................................................................................................

6.2 Interpretation of MF, ¹H, ¹³C and HMQC Data as Building Blocks.......................................................

6.2.1 Interpretation of Molecular Formula...................................................................................................

6.2.1......................................................................................................................................................................

6.2.2. Interpretation of 1D ¹H Data.................................................................................................................

6.2.2......................................................................................................................................................................

6.2.3 Interpretation of 1D ¹³C Data.................................................................................................................

6.2.4 Interpretation of HMQC/HETCOR Connectivities...........................................................................

6.2.5 Generation of Building Blocks............................................................................................................

6.3 User-Defined Building Blocks......................................................................................................................

6.4 Interpretation of 2D Spectral Data as Bond Constraints.........................................................................

6.4.1 Interpretation of COSY Connectivities...............................................................................................

6.4.2 Interpretation of HMBC/COLOC Connectivities..............................................................................

6.4.3 Interpretation of NOESY Connectivities.............................................................................................

6.4.4 Interpretation of INADEQUATE Connectivities...............................................................................

6.4.5 Transformation of Bond Constraints...................................................................................................

6.4.6 Setting up Atom-Atom Connection Matrix (ACMX).........................................................................

2D Structure Generation..................................................................................................

7.1 Overview............................................................................................................................................................

7.2 User-Defined Bond Constraints...................................................................................................................

7.2.1. Interactive Structure Generation........................................................................................................

7.3 User-Defined Atom Environment Constraints..........................................................................................

7.4 Structure Generation....................................................................................................................................

Resonance Assignment.....................................................................................................

8.1 Overview............................................................................................................................................................

8.2 Input of the Target Structure.......................................................................................................................

8.2.1. Inputting the Target Structure Interactively....................................................................................

8.2.2. Inputting the Target Structure via MDL File....................................................................................

8.2.3. Setting up the Assignment Matrix......................................................................................................

8.3 User-Defined Resonance Assignment........................................................................................................

8.4 Resonance Assignment.................................................................................................................................

Isomer Enumeration/Quick Elucidation...........................................................................

9.1 Overview............................................................................................................................................................

9.2 MF-based Isomer Enumeration.....................................................................................................................

9.3 Quick Structure Elucidation.........................................................................................................................

Graphical Display of Results............................................................................................

10.1 Overview..........................................................................................................................................................

10.2 Display of Structural Building Blocks.....................................................................................................

10.3 Display of Target Structure........................................................................................................................

10.4 Display of Generated Structures/Assignments......................................................................................

10.5 Status Window..............................................................................................................................................

10.6 Display Options.............................................................................................................................................

10.7