Patterns in Hydrogen Bonding: Functionality and Graph Set Analysis in Crystals
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From the Introduction to “The Guide of the Perplexed” by the medieval Jewish philosopher/physician Rabbi Moshe ben Maimon also known as the Rambam or Maimonides.
J.Bernstein M. C.Etter J. C.MacDonald J. Chem. Soc. Perkin Trans. 21990 695.
C.Glidewell G.Ferguson A. J.Lough C. M.Zakaria J. Chem. Soc. Dalton Trans.1994 1971;
Genkina E. A., 1994, Kristallografiya, 39, 641
P.Lightfoot M.Tremayne C.Glidewell K. D. M.Harris P. G.Bruce J. Chem. Soc. Perkin Trans. 21993 1625;
Note that a hydrogen bond from a cation to an anion or from a molecule to a cocrystallized solvent molecule must be denoted in the first level asD. A‐discrete set that involves more than one hydrogen bond (binary or higher level) would necessarily have more than one donor and/or acceptor and more than two atoms in the pattern so the subscript superscript and parenthetic notation of degree would all be required.
This would correspond to a differentlevelof the graph set assignment (see Section 3).
The appearance of these more complex ring notations in some automatic fashion for example in a computerized graph set assignment procedure would be an indication of such an extended ring pattern. The ring system shown here is a pervasive feature in crystal structures of the amino acids.
Pauling L., 1960, The Nature of the Chemical Bond, 6
Donohue J., 1968, Structural Chemistry and Molecular Biology
Bernstein J., 1974, Chemistry of the Quinones, 37
J.Bernstein E.Harlev unpublished results.
The following discussion is based on the assumption of the availability of rather primitive software for calculating geometry and plotting crystal structures. Surprisingly very few of the currently available molecular modeling software packages have convenient means for displaying and analyzingcrystalstructures as opposed tomolecularstructures.
One of the problems in developing the graph sets stems from the necessity in most cases to generate rather extended descriptions of thecrystal structure including the hydrogen bonding rather than simply themolecularstructure or the “view of the packing” that are sometimes automatically generated. The latter generally does not include sufficient numbers of molecules to portray all the specific intermolecular interactions. In many cases a single view of the crystal structure even in stereo is difficult to interpret. Software for readily generating and rotating crystal structures with a number of unit cells considerably facilitates this task and will make the examination of crystal structures and the assignment of their hydrogen‐bonding graph sets a much more common practice.
Kitaigorodsky A. I., 1955, Organic Chemical Crystallography
L.Shimoni M. Sc. Thesis Ben‐Gurion University of the Negev Beer Sheva Israel 1992.
In this admonition the word “all” must be taken in the light of the infinite number of increasingly larger ring systems that appear in a mesh such as that discussed earlier for α‐glycine.
(b) The two hydrogen bonds are crystallographically distinct and should be treated separately as discussed in Section 5.
Martuscelli E., 1967, Ric. Sci., 37, 102
Ganis P., 1968, J. Phys. Chem., 23, 747
The nomenclature for distinguishing polymorphs has never really been standardized [41]. To avoid even further confusion than already exists in the literature we have chosen in the following discussion to use the names of the polymorphs as they appear in the original literature that is cited here. This has been done at the expense of consistency in style in this paper.
Moore J. C., 1978, Acta Crystallogr. Sect. A, 34, 97
The relative orientation of the two independent molecules in Form 3 suggested to us the possibility of a previously unrecognized element of symmetry (inversion center or twofold axis); a careful check of relationships among the coordinates revealed that no such relationship exists.
The original graph set specifications [3] prescribed the degree of aDmotif as “the number of atoms in the entire length of the hydrogen‐bonded set starting with the proton of the first hydrogen bond proceeding along the shortest pathway and ending with the acceptor atom in the last hydrogen bond of the set”. Following those instructions would lead to degree 12 for the binary pattern shown in Fig. 14c; that description would mislead as it does not encompass all the hydrogen bonds that link the discrete cluster. The guideline should be amended so that the degreenincludes counting through all hydrogen bonds that is including all donors and acceptors. The same conclusion was reached by J. C. MacDonald (Ph.D. Dissertation University of Minnesota 1993).
R. E.Davis H.Robb V.Cody unpublished.
H.Nakai M.Takasuka M.Shiro J. Chem. Soc. Perkin Trans. 21984 1459.
R. S.Rowland Cambridge Crystallographic Data Centre (UK) personal communication.