Hydrogen bond distance distribution

Fig. 2.5. Distribution of hydrogen-bond distances observed by neutron diffraction crystal structure analyses of the amino acids [60]...

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. 

Einally, structural properties that depend directly neither on the data nor on the energy parameters can be checked by comparing the structures to statistics derived from a database of solved protein structures. PROCHECK-NMR and WHAT IE [94] use, e.g., statistics on backbone and side chain dihedral angles and on hydrogen bonds. PROSA [95] uses potentials of mean force derived from distributions of amino acid-amino acid distances. 

The alkaloid Nigellicine proved to be the pyridazino[l,2-u]indazolium-l 1-carboxylate (234) and forms yellow crystals (Scheme 77). It was isolated from the widely distributed herbaceous plant Nigella saliva L., which is used as a spice and for the treatment of various diseases (85TL2759). The structure was determined by an X-ray crystal structure analysis. The carboxylate bond distances are essentially equal (123.3 and 125.6 pm). An intramolecular hydrogen bond was found between the carboxylate oxygen atom and the hydroxy group. In mass spectrometry, the molecular peak was found at mjz —246 (20) and the base peak at mjz —202 which corresponds... 

The intensity curves I, II, III, and IV of Fig. 4 are calculated for coplanar trans models with C-H = 1.06 A., the angle H - C=C = 115°, and the angle H—C—H = 109.5°. Although these hydrogen parameters are so chosen as to agree as well as possible with minor peaks of the radial distribution function, no great reliance can be placed on them, and indeed it is likely that for this molecule the C-H bond distance is 1.09 A. The models have the following additional parameters... 

Another property relevant to the current discussion is the distribution of water in the active site. Specifically, we characterize the population of various water wires connecting the zinc-bound water/hydroxide and His 64 found in the SCC-DFTB/MM simulations. These wires were identified following a definition of hydrogen-bond in terms of both distance (O—O < 3.5 A) and angle (O—H—O > 140°) and care... 

This was averaged over the total distribution of ionic and dipolar spheres in the solution phase. Parameters in the calculations were chosen to simulate the Hg/DMSO and Ga/DMSO interfaces, since the mean-spherical approximation, used for the charge and dipole distributions in the solution, is not suited to describe hydrogen-bonded solvents. Some parameters still had to be chosen arbitrarily. It was found that the calculated capacitance depended crucially on d, the metal-solution distance. However, the capacitance was always greater for Ga than for Hg, partly because of the different electron densities on the two metals and partly because d depends on the crystallographic radius. The importance of d is specific to these models, because the solution is supposed (perhaps incorrectly see above) to begin at some distance away from the jellium edge. 

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