Empirical criteria for identification of hydrogen bonds were analyzed to produce a set of geometrically consistent criteria. For a data set of 30 structures, application of a set of purely geometrical criteria, along with exclusion of abnormal backbone conformations, also excluded a common interaction of Ser/Thr side chains with Asp/Glu side chains ([ST]/[DE] pairs). These interactions were ter...

Recent evidence has shown a correlation between the heat diffusion pathways and the known allosteric communication pathways in proteins. Allosteric communication in proteins is a central, yet unsolved, problem in biochemistry, and the study and characterization of the structural determinants that mediate energy transfer among different parts of proteins is of major importance. In this work, we ...

in this paper, we consider rna structures with arc-length 4 . first, we represent thesestructures as matrix models and zero-one linearprogramming problems. then, we obtain anoptimal solution for this problemusing an implicit enumeration method. the optimal solutioncorresponds toan rna structure with the maximum number of hydrogen bonds.

an azobenzene bridge was introduced into the lower (or smaller) rim of p-tert-butylcalix[8]arene to form 1,5-singly bridged calix[8]arene derivatives, respectively. bridged calix[8]arene of conformationally rigid wereisolated. the stability of the two structures of bridged calix[8]arenes have been compared.the study of organicstructure to form nanoporous structures is a well known in chemistry ...

Buried solvent molecules are common in the core of globular proteins and contribute to structural stability. Folding necessitates the burial of polar backbone atoms in the protein core, whose hydrogen-bonding capacities should be satisfied on average. Whereas the residues in alpha-helices and beta-sheets form systematic main-chain hydrogen bonds, the residues in turns, coils and loops often con...

The transition from α-helical to β-hairpin conformations of α-syn12 peptide is characterized here using long timescale, unbiased molecular dynamics (MD) simulations in explicit solvent models at physiological and acidic pH values. Four independent normal MD trajectories, each 2500 ns, are performed at 300 K using the GROMOS 43A1 force field and SPC water model. The most clustered structures at ...

In the crystal structure of the title compound, C(4)H(12)N(+)·H(2)PO(4) (-)·0.5H(2)O, the anions form an infinite hydrogen-bonded chain along the [10] direction. The anion chains are connected by water mol-ecules, which lie on crystallographic twofold rotation axes, through O-H⋯O hydrogen bonds. These hydrogen bonds are almost perpendicular to the other hydrogen bonds which create an assembled ...

A charge-assisted hydrogen-bonding network involving N-H⋯O and O-H⋯O hydrogen bonds stabilizes the crystal of the title salt, C5H8N3 (+)·H2PO4 (-). The dihydrogen phosphate anions form one-dimensional chains along [100], via O-H⋯O hydrogen bonds. The 2-amino-4-methyl-pyrimidinium cations are linked to these chains by means of two different kinds of N-H⋯O hydrogen bonds. Neighbouring chains are ...

in this research, this possibility was investigated the relative stablilty geometry and bindingenergies of the hydrogen bonds of molybdate-phosphonic acid (mpa) complex in gas phase onthe basis of result of ab initio and dft calculations. three dft methods have been applied forcalculations are b3lyp, bp86 and b3pw91 that have been studied in two series of basis sets:d95** and 6-31+g(d,p) for hy...

It has long been recognized that hydrogen bonds formed by protein backbone amides with cysteinyl S(γ) atoms play important roles in modulating the functional and structural properties of the iron-sulfur centers in proteins. Here we use single molecule atomic force microscopy, cyclic voltammetry, and protein engineering techniques to investigate directly how the strength of N-H···S(γ) hydrogen b...