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Method Article
Patrick Willoughby
Ripon College
Corresponding Author
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
This protocol describes an approach to preparing a series of Gaussian 09 computational input files for an ensemble of conformers generated in Spartan’14. The resulting input files are necessary for computing optimum geometries, relative conformer energies, and NMR shielding tensors using Gaussian. Using the conformational search feature within Spartan’14, an ensemble of conformational isomers was obtained. To convert the structures into a format that is readable by Gaussian 09, the conformers were first exported to a single “.sdf” file. A Python script was used to (i) read the structural information of each conformer within the “.sdf” file and (ii) write the corresponding atomic coordinates into a series Gaussian 09 input files. This approach decreases the amount of active effort required to compute NMR chemical shifts of a structure that populates an ensemble of conformers.
Keywords
NMR Computational Chemistry Organic Chemistry
The authors declare no competing financial interests.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.zip
Supplementary Data 1 Python Scripts A collection of Python scripts necessary for completion of the protocol.
- supplement0.zip
Supplementary Data 2 Representative Spartan Conformational Search Files The ".spardir" and ".spartan" files resulting from a conformational search of _cis_-3-methylcyclohexanol in Spartan.
- supplement0.pdf
Supplementary Table Troubleshooting Table
- supplement0.zip
Supplementary Data 3 Representative ".sdf" File The ".sdf" file obtained after exporting conformers of _cis_-3-methylcyclohexanol in Spartan.
- supplement0.zip
Supplementary Data 4 Representative Gaussian 09 Input Files The Gaussian 09 input files resulting from use of the Python script in *Supplementary Data 1* with the ".sdf" file in *Supplementary Data 3*.
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Subject Areas
Chemistry
Mathematics and computing
Chemical biology
Biological techniques
Synthetic chemistry
Associated Publications
A guide to small-molecule structure assignment through computation of (1H and 13C) NMR chemical shifts
by Patrick H Willoughby, Matthew J Jansma, and Thomas R Hoye
Nature Protocols (22 April, 2014)
Analysis of Seven-Membered Lactones by Computational NMR Methods: Proton NMR Chemical Shift Data are More Discriminating than Carbon
by Daniel J. Marell, Susanna J. Emond, Aman Kulshrestha, +1
The Journal Of Organic Chemistry (22 April, 2014)
Case Study of Empirical and Computational Chemical Shift Analyses: Reassignment of the Relative Configuration of Phomopsichalasin to That of Diaporthichalasin
by Susan G. Brown, Matthew J. Jansma, and Thomas R. Hoye
Journal Of Natural Products (07 March, 2014)
An open repository of community-contributed protocols sponsored by Nature Research.
Learn more about Protocol Exchange
Method Article
Patrick Willoughby
Ripon College
Corresponding Author
Version History
CURRENT STATUS: Published
View the published article at Protocol Exchange.
No community comments so far
Version 1
Posted 28 Apr, 2014
No comments provided
Metrics
Comments: 0
HTML Views: ...
License:
This work is licensed under a CC BY-NC 3.0 License. Read Full License
View the published article at Protocol Exchange.
This protocol describes an approach to preparing a series of Gaussian 09 computational input files for an ensemble of conformers generated in Spartan’14. The resulting input files are necessary for computing optimum geometries, relative conformer energies, and NMR shielding tensors using Gaussian. Using the conformational search feature within Spartan’14, an ensemble of conformational isomers was obtained. To convert the structures into a format that is readable by Gaussian 09, the conformers were first exported to a single “.sdf” file. A Python script was used to (i) read the structural information of each conformer within the “.sdf” file and (ii) write the corresponding atomic coordinates into a series Gaussian 09 input files. This approach decreases the amount of active effort required to compute NMR chemical shifts of a structure that populates an ensemble of conformers.
The authors declare no competing financial interests.
This is a list of supplementary files associated with this preprint. Click to download.
- supplement0.zip
Supplementary Data 1 Python Scripts A collection of Python scripts necessary for completion of the protocol.
- supplement0.zip
Supplementary Data 2 Representative Spartan Conformational Search Files The ".spardir" and ".spartan" files resulting from a conformational search of _cis_-3-methylcyclohexanol in Spartan.
- supplement0.pdf
Supplementary Table Troubleshooting Table
- supplement0.zip
Supplementary Data 3 Representative ".sdf" File The ".sdf" file obtained after exporting conformers of _cis_-3-methylcyclohexanol in Spartan.
- supplement0.zip
Supplementary Data 4 Representative Gaussian 09 Input Files The Gaussian 09 input files resulting from use of the Python script in *Supplementary Data 1* with the ".sdf" file in *Supplementary Data 3*.
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Associated Publications
A guide to small-molecule structure assignment through computation of (1H and 13C) NMR chemical shifts
by Patrick H Willoughby, Matthew J Jansma, and Thomas R Hoye
Nature Protocols (22 April, 2014)
Analysis of Seven-Membered Lactones by Computational NMR Methods: Proton NMR Chemical Shift Data are More Discriminating than Carbon
by Daniel J. Marell, Susanna J. Emond, Aman Kulshrestha, +1
The Journal Of Organic Chemistry (22 April, 2014)
Case Study of Empirical and Computational Chemical Shift Analyses: Reassignment of the Relative Configuration of Phomopsichalasin to That of Diaporthichalasin
by Susan G. Brown, Matthew J. Jansma, and Thomas R. Hoye
Journal Of Natural Products (07 March, 2014)