NMR-SCAPE:

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

Trademarks

NMR-SCAPE is a trademark of Spectrum Research, LLC.

Acknowledgments

NMR-SCAPE has been developed by the Shanghai Institute of Organic Chemistry, Chinese Academy of Sciences Laboratory of Computer Chemistry, Chinese Academy of Sciences, P.R. China, and is licensed exclusively to Spectrum Research, LLC.

System Requirements

NMR-SCAPE runs on Windows 98 or higher, and the minimum platform requirements are a CPU with an Intel Pentium 100 with 16Mb of memory and 30Mb of hard disk space.

Part I: Introduction to NMR-SCAPE

The following document provides step-by-step instructions to lead the user through the process of carbon assignment prediction. This document is intended as an introduction to NMR-SCAPE and we assume that the users of this document will have a good understanding of general NMR techniques and their applications.

NMR-SCAPE performs spectral simulation and prediction of ¹³C NMR chemical shifts. It allows the user to sketch a molecule, or import a structure as a *.mol file from third-party chemical structure drawing programs. NMR-SCAPE also performs batch predictions on multiple structures and enables the user to open the predicted spectra into SpecMan for comparison and validation with experimental data. In addition, NMR-SCAPE also permits the user to add compounds to NMR-SCAPE's knowledge base in order to enhance predictions, and it works in conjunction with NMR-SAMS to provide the best solution for automated structure elucidation.

Part II: NMR-SCAPE Tutorial

I: Prediction of a *.mol File

Start NMR-SCAPE, by double-clicking on the NMR-SCAPE icon and the following screen will appear:

Once the program has been initiated, the first step is to import a molecule by selecting ‘Open’ from the File Menu. We will use the q-2mf001.mol that is found in the following: C:\Spectrum2000\Data\NMRSCAPE, so select this file and then click, ‘Open.’

The Q-2 molecule will de displayed as shown below:

Next, select ‘C-nmr’ from the Simulate Menu or click on the following toolbar button to perform the prediction:

The predicted spectra will appear as follows:

The spectrum is displayed as a stick figure spectrum. By moving the mouse over a peak, its chemical shift and chemical shift range are displayed. In addition, the corresponding atom in the structure will be highlighted as shown below:

The reliability of the predicted chemical shifts are indicated by the following three colors:

Blue Excellent

Green Good

Red Not Bad

The predicted spectrum can then be saved by clicking on the following ‘Export Chemical Shift’ icon:

The user will be prompted to save the file as a text file (*.txt), so save the prediction as ‘Q-2.txt’:

This Q-2.txt file can then be opened up into SpecMan 2.4 for display of the predicted spectrum. To import the predicted spectrum into SpecMan, activate SpecMan, and select, ‘Import NMR-SCAPE database’ from the File Menu:

Then select the Q-2.txt file that was created with NMR-SCAPE:

The user will then be prompted to save the Q-2.txt file with a *.jdx extension:

Once the Q-2.txt file has been saved as q-2.jdx file, select, ‘Open Spectrum’ from the File Menu and select the q-2.jdx file:

Remember to select the file type as Chemical Concepts *.jdx, and click, ‘Open’ to display the predicted spectrum:

II: Batch Prediction of Multiple *.mol Files

This feature enables the user to perform spectral predictions on several compounds all with one command. To do so, click on the following ‘Batch Simulate’ toolbar icon:

An ‘Open File’ dialog box will de displayed as shown below:

Next, hold down the shift key and select as many *.mol files as desired:

Once the *mol files have been selected, click, ‘Open’ and the following ‘Save as a Database File’ dialog box will be displayed:

Enter a name for the batch prediction spectra and click, ‘Save.’ A *.mba file (batch.mba) will be created. This batch.mba file can then be opened up into SpecMan 2.4 for display of the predicted spectra.

To import the predicted spectra into SpecMan, activate SpecMan, and select, ‘Import NMR-SCAPE database’ from the File Menu:

Then select the batch.mba file that was created with NMR-SCAPE:

The user will then be prompted to save the batch.mba with a *.jdx extension:

Once batch.mba has been saved as ‘batch.jdx,’ select, ‘Open Spectrum’ from the File Menu and select ‘batch.jdx.’ Remember to select the file type as Chemical Concepts *.jdx, and then click ‘Open’ as shown below:

The predicted spectrum will be displayed in SpecMan, and the user can browse through the various structures and their corresponding spectra by using the ‘Database Browser’ as shown below:

III: Prediction of a User-Created Structure File

This feature enables the user to draw a target-structure and then predict its ¹³C spectra. To do so, click on ‘New’ from the File Menu and the screen will be cleared of any previous structures or predictions. In order to draw single bonds, click on the following:

Then, left-click with the mouse to draw a single bond:

During the process, a carbon molecule is the default atom in a drawn molecule. In order to connect one atom to another atom with a single bond, make sure that there is a black box surrounding the end of the bond that the user wants to connect to as shown below:

Then, left-click with the mouse to attach single bonds as shown below:

In order to draw double bonds, click on the following:

And attach a double bond to one side of the chain:

NMR-SCAPE allows the user to create structures from general templates. Select the following, ‘Draw from Template’ toolbar icon:

This will bring up a ‘Select Template’ box, and the user can select many functional groups, including a benzene as shown below:

And a Benzene ring is attached as a side chain:

To draw a stereo bond (out), select the following icon:

And a stereo bond (out) is displayed as shown below:

To draw a stereo bond (in), select the following icon:

And a stereo bond (in) is displayed as shown below:

To change a heteroatom, click on the following ‘Atom Properties’ toolbar icon:

This will bring up the following pull-down list:

Select the atom that the user wants to put into the structure (for example, Br) and click on the old atom (C) to replace it as shown below:

To delete bonds, select the following ‘Erase’ toolbar icon and click on an atom or a bond:

Once the desired structure has been drawn, the user can save the structure (as a *.txt file) by selecting the following toolbar icon:

Once the structure has been saved, the user can predict its ¹³C NMR spectra (please refer to directions on how to predict spectra starting on Page 6):

IV: Modification of Predicted Results

This feature enables the user to update NMR-SCAPE’s knowledge base for a predicted chemical shift that is inaccurate (due to the lack of the appropriate chemical environment for the atom). When the correct value is known, this new substructure/sub-spectrum should be added into the database correlated with the correct chemical shift. To do so, the user can either select ‘Modify Simulate’ from the Simulate menu, or click on the following ‘Modify Simulate’ toolbar icon:

The following modification window will appear:

For example, modify the chemical shift of atom #1 from 33.26 to 43.26 and select ‘Update.’ Then, reselect ‘Modify Simulate’ and the new chemical shift will be listed for atom #1 as shown below:

In addition, the modified chemical shift list can also be saved by selecting ‘Save’ from the modify simulate dialog box.

Part III: NMR-SCAPE Menu Items

I. The File Menu

NMR-SCAPE allows the user to sketch a structure or import a structure file from a third-party chemical structure drawing program (*.mol file). The options under the File Menu are ‘New,’ ‘Open,’ ‘Save,’ ‘Save As,’ and ‘Exit’ as shown below: