Hydrogen molecule crystal structure

The Problems of Measuring Hydrogen-Bond Lengths and Angles in Small Molecule Crystal Structures... 

The alditol crystal structures are conformationally homogeneous. The cocrystallization of different conformers of the same molecule is not common, but sufficient examples are known, especially in hydrogen-bonded crystal structures, for it to be a phenomenon with which crystallographers are familiar. It occurs when there is a population of conformers in solution, all of which have similar energies. A classical example is that of 2,3-dimethyl-2,3-butanediol (pinacol)... 

This procedure is comparable to that used to analyze the N-H 0=C interactions in small molecule crystal structures described in Part I A, Chapter 2.3 [75]. For those groups with rotational freedom such as the -OH in serine, threonine, and tyrosine, the S-H in cysteine, and the - +NH3 in lysine and at the amino terminus, it is more difficult to guess the likely position of the hydrogen atoms. In these instances, the assumptions are made that the hydrogen bonds are of the two-center type when the R-X - A angle is close to 110°. The bonds are assumed to be linear with X-ft A angles of 180° (a better approximation would be to take the most commonly observed angle of —160°). 

Because internal water molecules are in mostly apolar environments, their hydrogen bonds are often strong and well defined. The average O- -O distance is 2.89 0.21 A for the internal water molecules in lysozyme, carboxypeptidase, cytochrome c, actinidin, and penicillopepsin. As with the small molecule crystal structures, the water molecules are involved in three or four hydrogen bonds, with 48% engaged in three and 37% in four interactions. 

An alternate interpretation is that hydrogen bonding is dynamic and that the water molecule is satisfying all acceptor sites by rotating into two positions [596]. A distinction between these two hypotheses is difficult for small molecule crystal structures, and impossible for proteins. 

In protein X-ray structure determinations hydrogen atoms cannot be located, and their positions have to be calculated from the known coordinates of the C, N, O atoms. Their positions are an order of magnitude less well defined than with small molecule crystal structures. Nevertheless, general trends can be derived and yield valuable information. 

As we have seen in the previous Section 19.6, secondary-structure hydrogen-bonding geometry in the a-helices, / -pleated sheets and / -turns is constrained by the requirements of polypeptide chain folding. When the hydrogen bonds which are not involved in secondary-structure interactions are examined, their geometry is in better agreement to that observed in the small molecule crystal structures discussed in Part IB, Chapter 7. In most cases, therefore, the discussion can be limited to situations where deviations occur [596]. 

As observed for the N- H O interactions between main-chain and side-chain groups, the N-ft Ow angles are almost linear, 156(15)°, if the all-a-helix proteins are omitted from the sampling, see Ihble 19.6d. The distribution of these angles is 140° to 180° for 90% of the data, and consistent also with small molecule crystal structures [75, 382, 475]. The spread of hydrogen-bond distances is broad, and wider for C=0 than for N-H, probably because the C=0 oxygen is more readily accessible and multiple C=0- -HOw interactions are frequently observed. 

In contrast to small molecule crystal structures, where the variation in most H A distances falls within 0.3 A, hydrogen-bonding distances involving side-... 

If distances between main-chain C=0 and N-H groups and hydrogen-bonded water molecules are compared (Thble 23.5 and Fig. 23.5 a), it is apparent that the distribution is narrower about the N-H groups. The reason is that the C=0 groups are more exposed and, in most cases, accessible to more than one or two hydrogen-bond donors. Where this results in overcrowding the C=0 0W distances may be beyond the 3.5 A cut-off limit used in the analysis [596]. In the major parts of both C=0 Ow and N-H ow distribution, the peaks in Fig. 23.5a are at 2.89 A (2.94 A in Thble 23.5a) and 2.97 A respectively, as expected from the data for the hydrogen bonds in small molecule crystal structures. 

Fig. 13.8. Stereo-diagram of the preferred spatial location of hydrogen-bond donors about N in a pyridine ring, determined by mapping the composite crystal-field environment data taken from small molecule crystal structures containing this fragment. The data were expanded according to the C2v-symmetry of the pyridine ring...

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