Hydrogen-bond patterns

The nature of solute-solute and solute-solvent interactions is dependent on the solvent environment. Solvent influences the hydrogen-bonding pattern, solute surface area, and hydrophilic and hydrophobic group exposures. 

Fig. 1. The two principal elements of secondary stmcture in proteins, (a) The a-helix stabilized by hydrogen bonds between the backbone of residue i and i + 4. There are 3.6 residues per turn of helix and an axial translation of 150 pm per residue. represents the carbon connected to the amino acid side chain, R. (b) The P sheet showing the hydrogen bonding pattern between neighboring extended -strands. Successive residues along the chain point...

Figure 2.5 Schematic illustrations of antiparallel (3 sheets. Beta sheets are the second major element of secondary structure in proteins. The (3 strands are either all antiparallel as in this figure or all parallel or mixed as illustrated in following figures, (a) The extended conformation of a (3 strand. Side chains are shown as purple circles. The orientation of the (3 strand is at right angles to those of (b) and (c). A p strand is schematically illustrated as an arrow, from N to C terminus, (bj Schematic illustration of the hydrogen bond pattern in an antiparallel p sheet. Main-chain NH and O atoms within a p sheet are hydrogen bonded to each other.

Figure 2.6 Parallel p sheet, (a) Schematic diagram showing the hydrogen bond pattern in a parallel p sheet, (b) Ball-and-stlck version of (a). The same color scheme is used as in Figure 2.5c. (c) Schematic diagram illustrating the pleat of a parallel p sheet.

FIGURE 10.41 (a) Gramicidin forms a double helix in organic solvents a helical dimer is the preferred strnctnre in lipid bilayers. The strnctnre is a head-to-head, left-handed helix, with the carboxy-termini of the two monomers at the ends of the strnctnre. (b) The hydrogen-bonding pattern resembles that of a parallel /3-sheet. 

Examine the structure of a strand of Nylon 6 in which all amide bonds are E. Describe how this differs from the strand in which the amide linkages are Z. In particular, are the same hydrogen-bond patterns found ... 

Fig. II. Hydrogen bond pattern in the crystalline 1 1 complex (R7 = i-Bu, R" = CH2Ph) 3S>. The thin lines indicate hydrogen bonds...

A 6 positional state that is stabilized by the interaction of His 161 with a molecule of the inhibitor stigmatellin bound in the quinone binding pocket (41), which is supposed to mimic the hydrogen bonding pattern of the reaction intermediate, semiqui-none (43)... 

An important step is to validate the structure, that is, to compare features of the structure to features in known protein structures. This includes localized fit to density, hydrogen bonding patterns, divergence from standard geometry, and much more [12]. Such calculations can highlight where the model requires further improvement. 

Instead, including the protein environment in a QM MM description gives a correct and stable hydrogen-bond pattern at a low computational cost. 

Figure 2-14. Illustration of the different hydrogen bonding patterns for an iron-bound peroxide in IPNS using an active-site model (left) and an ONIOM QM MM model (right)...

Fig. 32a and b. Schematic illustration of intermolecular arrangements in the crystalline complexes of host 25 (taken from Ref.25>) a the two-dimensional hydrogen bonding pattern parallel to the ab plane (the shaded area represents the 1,1-diphenylcyclohexane framework) b the van der Waals type packing of the hydrogen bonded layers along the c axis (R represents the cyclohexyl ends of the host species)... 

Murray, J. S., M. E. Grice, P. Politzer, and M. C. Etter. 1991a. A Computational Analysis of Some Diaryl Ureas in Relation to Their Observed Crystalline Hydrogen Bonding Patterns. Mol. Eng. 1, 95. 

Among the wealth of issues relevant to hydrogen bonding in alcohol clusters, this review will focus on aspects related to hydrogen bond patterns and on the dynamical implications over a wide range of time scales. Some key questions connected to these aspects will be formulated. 

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