Graph sets: motifs

In the enol desmotrope, phase II, which is also the commercially available form, each molecule associates with the neighboring ones through O-H- -O hydrogen bonds, thus forming infinite zig-zag chains with Ci (6) graph-set motif (Scheme... 

Water motifs have been classified systematically using a system of nomenclature somewhat analogous to graph set analysis (Section 8.3.1).43 in this scheme water structures are discussed in terms of particular classes, listed below. 

CSD with greater than 12 occurrences, ranked in decreasing order of probability of occurrence and (b) percentage probability of formation of ring motifs 1-37 (Pm = number of motifs observed / number that could have possibly occurred) along with their graph set descriptors (reproduced with permission from The Royal Society of Chemistry). 

Some examples of graph-set descriptors of hydrogen-bonded structural motifs. 

Fig. 2.17 Examples of the use of graph set descriptors to define motifs and first and second level graph sets for schematic representations of the hydrogen-bond patterns in the crystal structure of benzamide. (From Bernstein and Davis 1999, with permission.)...

Fig. 2.19 First level graph sets for the three polymorphs of anthranrhc acid 2-V. The two molecules in the asymmetric unit of Form 1 are shown in their true crystallographic relationship to each other (see text). In (d) and (e) the third ammoniacal hydrogen, which does not participate in a hydrogen bond, is hidden hy the nitrogen to which it is attached, (a) Form II (b) Form ni (c) Form I, C(6) of A type molecnles (d) Form I, C(6) of B type molecules (e) Form I, intramolecular motifs S(6) for molecules A and B and the dimer D relationship connecting them. (Adapted from Bernstein et al. 1995, with permission.)...

Table 2.3 Unitary motifs (diagonal) and binary graph sets (off-diagonal) for anthranilic acid 2-Va, Form IP...

Bernstein, J. and Davis, R. E. (1999) Graph set analysis of hydrogen bond motifs. In Implications of molecular and materials structure for new technologies, NATO Science Series E Applied Science (ed. J. A. K. Howard and F. H. Allen and G. P. Shields), Kluwer Academic Publishers, Dordrecht, Vol. 360 275-290 [57f, 58f, 81]. 

Abstract The different C-H- X interactions are analyzed in this chapter. They are compared with the other types of hydrogen bonds, especially O-H- O ones. Theoretical tools are presented, among them the atoms in molecules theory (AIM). The H-bond motifs existing in crystals are presented. The evidences that C-H- -X interactions may be often classified as H-bonds are discussed. Etter s graph set analysis is also used to describe the structure of complex aggregates. 

The list of all motifs found in a crystal constitutes the first-level or unitary graph set of that crystal, and is a sort of fingerprint of a crystal that can help to distinguish between different polymorphs of the same crystal (for instance Form 2 of the iminodiacetic acid crystal contains six motifs and its first-level graph set is Ni = DDC(5)C(5)C(8)C(8), while Form 1 has only three motifs and its first-level graph set is Ni = C(5)C(8)R2(10). 

Figure 8. Basic types of motifs in Etter s graph set analysis [43,44], Represented from left to right is a C(4), Rj (8), S and D motif...

Figure 1.2.14 Examples of the four basic motifs in graph set analysis. From left to right we represent the C(4), R22(8), S and D motifs.

Fig. 5. Graph set notation for hydrogen bonded ring motifs in a polymorph of thalidomide...

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