Abstract
On the basis of a series of practical examples, the importance of molecular modeling in structure analysis is illustrated. The situations presented prove usefulness of modeling procedures in (1) solving difficult crystal structures, with orientational, partial disordering in particular; (2) explaining erroneously determined molecular structures and deriving the correct solutions; (3) determining long range order–disorder phenomena, for example, polytypism of intercalated layered structures; and (4) dealing with multicomponent guest species absorbed in porous crystal structures. It is believed that molecular modeling will soon become an intrinsic part of structure determination procedures using diffraction data.
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Notes
- 1.
The term semi-clathrate refers to solid inclusion compounds where, in addition to non-bonded, clathrate interactions, there is a contribution of chemical bonding. In the example used above, this “chemical” contribution is of ionic nature: fluoride anion from the ammonium salt is incorporated into the water host framework linked via hydrogen bonds. Thus, the host has anionic character and guest-host interactions have ionic component.
- 2.
The host structures are similar.
- 3.
The paper was accepted for publication in Acta Crystallographica which is known for high criticism toward the methodological part of experimental and computational content. Differences in molecular geometry between the two guests have been discussed in the paper, though no clear reason could be found.
- 4.
Standard deviation calculated from experimental data.
- 5.
Site occupation factor.
- 6.
For instance, every fifth layer might contain guest molecules in orientation B.
- 7.
The option B surrounded by A is ignored in view of their relative occupancies in the structure.
- 8.
Hydrogen atoms are not included in such calculations as contributing very little to the overall diffraction.
- 9.
Ortho-bromonitrobenzene as well as ortho- and meta-dinitrobenzenes form isostructural compounds of this type, Zn(NCS)2(4-methylpyridine)4 and Cu(NCS)2(4-methylpyridine)4 (host) complexes with a variety of guest molecules are known as well.
- 10.
“Low” and “high” are relative to the guest species. meta-bromonitrobenzene shows the transition at about 60°C, while meta-dinitrobenzene shows transition of this sort at about 95°C.
- 11.
Description is somewhat simplified here. The “ordered” guest molecules shown on the picture still have some 10–15 % of disordering over two different orientations. This, however, is qualitatively different from the symmetric disordering around the threefold axis.
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Lipkowski, J., Suwińska, K. (2009). Molecular Modeling as an Auxiliary Method in Solving Crystal Structures Based on Diffraction Techniques. In: Leszczynski, J., Shukla, M. (eds) Practical Aspects of Computational Chemistry. Springer, Dordrecht. https://doi.org/10.1007/978-90-481-2687-3_11
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