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Idealized Molecular Geometry Library


Molecular Structure Laboratory / Idealized Molecular Geometry Library / About the IMGL Updated: October 26, 2015


About the Library


How to use the Library

Submit a new geometry

References and contributors

Contact me

About the Library

The purpose of the library is to provide facile access to idealized geometries of some molecules that may cause problems during crystallographic structural refinement. The library was populated over the years with geometries optimized theoretically. However, in several cases interatomic distances obtained by averaging many relevant bond lengths from the Cambridge Structural Database are also supplied. The optimizations were performed with Gaussian03 at various levels of theory.

How to use the Library

A prerequisite to using the database is basic understanding of the FRAG command of program XL from the SHELX package. The SHELX manual is available online; sections 4.5 and 7.3 (pages 7-14 and 7-16 are particularly relevant) will explain what the FRAG constraint can do and how to incorporate it into your instruction file.

A good example is proved in Guzei, I. A. (2014). J. Appl. Crystallogr. 47, 806-809.

The FRAG commands are easiest to use as described in section "Constraining the molecular geometry" of Ilia Guzei's Notes on OLEX.

The coordinates in the Library are orthogonal. Thus, no unit cell parameters on the FRAG line are required. An example for an acetone molecule is provided.

 

Submit a new geometry

If you wish to share your geometry you can e-mail Ilia Guzei with a labeled molecular drawing and FRAG card. The geometry may be based on a good experimental structure or optimized theoretically. Include a brief description of the structure, your affiliation, and proper reference.

 

References and contributors

You are welcome to use any of the geometries provided in the library. The only condition is you must reference the library: Guzei, I. A. (2014). J. Appl. Crystallogr. 47, 806-809.

Program Gaussian03 may be referenced as
Michael J Frisch, Alice B Nielsen, Gaussian 03 Programmer's Reference, Gaussian, Inc.

Cambridge Structural Database. Allen, F.H. (2002). Acta Cryst. B58, 380-388.

 

Contact me

If you have questions, suggestions, or comments feel free to send Ilia Guzei a message.




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