Spectrum Research, LLC.

 

 

 

 

SAMS: (Structure Assembly Made Simple)

Computer-Assisted Structure Elucidation of Oleanderol

 

 

 

 

 

 

Table of Contents

 

Overview: 3

I-1. Getting Started with SAMS. 4

I-2. Opening a New Working Data Set 4

I-3. Generation of Building Blocks. 5

I-4.  User-Defined Building Blocks. 7

I-5.  Setting up Bond Constraints. 8

I-6.  User-Defined Bond Constraints. 8

I-7.  Parameters for Structure Generation. 11

I-8.  Structure Generation. 12

I-9.  Exporting Structures. 14

II-1.  Structure Elucidation of Compounds based on MS Data. 14

                                               

 

 

 

Copyright Notice

Copyright © 2001 through 2002 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.

 

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

 

Trademarks

SAMS is a trademark of Spectrum Research, LLC.

 

 

 

 

Computer-Assisted Structure Elucidation of Oleanderol
Using SAMS

Overview:

The following document provides step-by-step instructions that lead the user through the process of computer-assisted structure elucidation of oleanderol using MS data.  It is assumed that the users of this document will have a good understanding of general Mass Spec techniques and their application to structure elucidation problems.  The MS data of oleanderol (Fig. 1) is adapted from the publication of S. Siddiqui et al., J. Nat. Products  51, 229 (1988). 

 

Figure 1. Two-dimensional structure of oleanderol with dashed lines showing some of the fragmentation used in this example. For detail please refer to S. Siddiqui et al., J. Nat. Prod.   51, 229 (1988).

I:  Structural Analysis of Oleanderol with SAMS

I-1. Getting Started with SAMS

From the Program Manager or the Start Menu, click the SAMS icon in the Spectrum2001 group to launch the SAMS program.  Once the program has been initiated, the main SAMS window appears, as well as a ‘Status Window’ that lists the current status of the structure elucidation process and also suggests the next possible steps for the user to take. 

I-2. Opening a New Working Data Set

Select ‘New’ from the File menu, and an ‘Open File’ dialog box will appear.  Input a new root name for the working data set (for example oleanderol.mdf), as shown below:

 

 

Then, click ‘OK’ and SAMS will create the following files in the current directory:

 

oleanderol.mdf –     master data file.  Stores all of the intermediate and final results.

oleanderol.par –     default parameter file.  Stores all of the control parameters used for data interpretation and structure generation.  SAMS uses a set of default control parameters, but also provides the user the option of changing these control parameters under the Edit Menu. (‘Parameters’ with the pull right options: 'Setting up ACMX' and '2D Structure Generation').  

oleanderol.nmr –     A dummy file not used for this analysis because it is assumed that there is no NMR data available.  If NMR data is available, then the NMR-SAMS program is recommended instead of SAMS. 

oleanderol.log –      log file.  Stores all of the warning and error messages produced during the analysis.  The user can view the log file by selecting ‘Log File’ from the Edit menu. 

oleanderol.str –       Stores the connection table of the generated structures.

oleanderol.lock –  Prevents the data set from being opened simultaneously by more than one user.

 

Next, enter the molecular formula of Oleanderol (C30H48O3) into the ‘Input Molecular Formula’ dialog box as shown below:  

 

 

Then click, ‘OK’ and the molecular formula is automatically interpreted for element composition and common valences.  This information is written into the oleanderol.mdf file after the keyword, ‘Atoms’.  If an atom has an unusual valence, specify the valence after the element symbol (C47H51N(V)O14 where N(V) indicates a nitrogen atom with a valence of 5).  Otherwise, the common valence will be adopted. 

I-3. Generation of Building Blocks

In this step, the Building Blocks (based on the molecular formula) are determined and displayed.  To do this, select ‘Building Blocks’ from the Analysis menu and the following will appear:

 

 

At this stage, SAMS generates all possible building block sets based on the elemental composition defined in the molecular formula.  The upper limit defined in the parameters is 500 building block sets, so the program displays the message 'the maximum number of building block sets (500) has been reached.  The remaining ones, if any, were ignored.'

Select 'OK' and the first Building Block set will be displayed along with a Building Block Browser and a Connection Table:

 

The Connection Table can be closed by selecting 'Display Options - Connection Table' from the 'Display' menu.  Selecting ‘Status Window’ from the Display menu will close the Status Window. 

 

The first set of Building Blocks is displayed below:

 

 

To view the different building block sets, use the slider in the Building Block Browser.  For each building block set, SAMS can generate candidate structures.  In this case, known fragments observed in the MS data of Oleanderol will be input to restrict the search space for the structure elucidation, so any Building Block set can be used as the starting set.  Set the Building Block Browser to number 1, and click 'Select'.  The program will display the following message:

 

 

Select 'Yes' and the Building Block Browser will disappear and only the selected Building Block set will be retained:

 

 

Atoms with unsatisfied valences are marked by an asterisk (*) and are displayed in a different color (by default, blue).  To modify the appearance of the building blocks, the user can select ‘Display Options’ with the following pull-right choices: Balls, Carbon Symbols, Numbers, Chemical Shifts, Protons, Molecular Formula, etc. from the Display menu.

 

At this stage information regarding the current building block set will be written into the *.mdf file after the keyword ‘Atoms.’  To view the .mdf file, select 'Master Data File (MDF)' from the 'Edit' menu and the .mdf file will be displayed in a notepad editor.  Please note that for each step, SAMS keeps only one copy of the results in the master data file (*.mdf).  When any step is repeated, the previous results of that step and any previous steps will be overwritten. 

I-4.  User-Defined Building Blocks

In order to begin the process of entering known structural fragments derived from MS data into SAMS, select 'User-Defined Building Blocks' from the 'Analysis' menu and the following will appear:

 

 

Using the 'User-Defined Building Blocks' palette, the user can Add, Modify, and Delete the basic building blocks  (C, CH, CH2, CH3, N, O etc.) according to the known MS fragment data.  For building the known fragments of Oleanderol, it is necessary to have 7 C, 6 CH, 12 CH2, 5 CH3 and 3 OH.  To begin modifying the building blocks, select 'Modify', 'C' for the Element and '1' for Proton Count and then click in the SAMS window to modify Building Block #8 from a 'C' into a 'CH', as shown below:

 

 

In this manner, continue to 'Add', 'Modify' and 'Delete' the building blocks until all necessary basic building blocks (7 C, 6 CH, 12 CH2, 5 CH3 and 3 OH) are present.  The modified Building Blocks set is displayed below:

 

I-5.  Setting up Bond Constraints

To continue the process of entering structural fragments derived from MS data into SAMS, select 'Bond Constraints' from the 'Analysis' menu. 

 

Atoms with unsatisfied valences are marked by an asterisk (*), and are displayed in a different color (blue, by default).  Fixed bonds with unknown bond types are displayed as dashed lines, and can become single, double, or triple bonds in the structure generation process. 

I-6.  User-Defined Bond Constraints

The structural fragments derived from MS data are referred to as known substructures.  Please note that SAMS requires the known substructures to be non-overlapping, otherwise the correct structure will not be generated.  There is no requirement on the size and number of the known substructures, though the closer the substructures are to the real structure, the better the final result.

 

In order to enter the structural fragments into SAMS, select 'User-Defined Bond Constraints' from the 'Analysis' menu and the following will appear:

 

For the Oleanderol sample, the following substructures are known:

 

 

To create the first fragment,

 

Select 'Add' and 'Single' for the bond type and then click on 1 and 26: 

 

 

Next, click on 1 and 27: 

 

Next, click on 1 and 8: 

 

Next, click on 8 and 31:

 

At any time during the building of fragments, the user can refine the display of the fragments by selecting 'Display Options - Refine' from the 'Display' menu (or click the ‘Refine’ icon in the tool bar).  Continue in a similar manner to create the remaining fragments.  To delete a bond, select 'Delete' and then click on the two elements to delete the bond between.  To modify an existing bond, select 'Add' and the bond type and then click on the two elements sharing the existing bond.  If a mistake is made during the process of creating fragments, use the delete option along with other bond type options, or select 'Cancel' and all fragments will be cleared.  

Note: During structure generation, bonds will be formed only between unsaturated atoms. 

I-7.  Parameters for Structure Generation

It is important to ensure that the right set of parameters is used for structure generation, so select 'Edit Parameters - 2D Structure Generation' from the 'Edit' menu.  The following will appear: 

 

 

For this example, edit the following entries:

Search Criteria for Structure Generation - Exhaustive

Ring Size (0 for Unlimited) -            Min: 0              Max: 6

Maximum Candidate Structures to Store (0 for Unlimited) - 1,000

Store Partially Completed Structures (PACS): unchecked

 

 

I-8.  Structure Generation

Once the user has given SAMS all the necessary information (plus any user-defined information) for structure generation, select ‘Generate 2D Structures’ from the Analysis menu.  The structure generation process will be initiated, and the following dialog box will be displayed:

 

 

This dialog box shows the progress of the structure generation process.  At any time the user can abort the structure generation process by clicking ‘Stop’ (it will take a few seconds to stop the structure generation). 

 

In less than one minute, the following dialog box will appear to announce that 24 complete structures have been generated:

 

 

Click ‘OK’ and the first of the 24 structures will be displayed:

 

 

The first structure is displayed along with a Structure Browser so that the user can look through the remaining 23 structures.  Structure 3 matches the structure of Oleanderol reported in the literature: 

 

 

I-9.  Exporting Structures

SAMS enables the user to export the final structures into a structure file (*.mol, *.mdl or *.sdf), select ‘Export – Structures’ from the File menu.  This will bring up the following dialog box:

 

 

Click ‘OK’ and the current structure will be saved into the ‘oleanderol001.mol’ file. 

 

 

II:  Application of SAMS

 

II-1.  Structure Elucidation of Compounds based on MS Data  

 

SAMS is an excellent tool for structure elucidation of compounds for which only molecular formula and substructure information is available.  Based on the molecular formula, SAMS generates all possible connectivity isomers.  Inclusion of substructure information obtained from UV, IR and MS spectral data can further restrict structure generation of possible isomers.  Structures generated by SAMS can be exported into *.sdf or *.mol files for searching through third party spectral and chemical databases.  SAMS-generated structures can be used with NMR-SCAPE for the prediction of carbon NMR spectra.