Idealized Molecular Geometry Library Features

About the Library

The purpose of the Idealized Molecular Geometry Library (IMGL) is to provide facile access to idealized geometries of molecules, ions, and molecular fragments that may cause problems during crystallographic structural refinement. The IMGL is populated with theoretically optimized geometries or good geometries from actual structures. 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 the Gaussian software package at various levels of theory. New geometries are added as necessary and upon request. There are 91 geometries as of April 1, 2022.

How to use the Library

A prerequisite to using the IMGL 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 provided 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 OLEX2.

The coordinates in the Library are orthogonal. Thus, no unit cell parameters on the FRAG line are required.

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 and your affiliation.

References and contributors

You are welcome to freely use any of the geometries provided in the IMGL. The only condition is that 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.

Contact me

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