We analysed the length distributions of different types of beta-strand in a high resolution, non-homologous set of 500 protein structures, finding differences in their mean lengths. Antiparallel edge strands in strand-turn-strand motifs show a preference for an even number of residues. This propensity is enhanced if the length is corrected for beta-bulges, which insert an extra residue into the...

Hydrogen bond interactions between acetone and supercritical water are investigated using a combined and sequential Monte Carlo/quantum mechanics (S-MC/QM) approach. Simulation results show a dominant presence of configurations with one hydrogen bond for different supercritical states, indicating that this specific interaction plays an important role on the solvation properties of acetone in su...

The basic retention mechanisms of reversed-phase and hydrophilic-interaction liquid chromatography (HILIC) were quantitatively analyzed using simple molecular mechanics (MM) calculations. The model bonded phases were composed of an alkyl chain bonded to siloxane-like molecules. The head of the alkyl chain was a hydroxyl group, used to study retention mechanisms of HILIC. The standard analytes w...

The structures of 2-acetamido-4-tolyl-1,3-thiazole, C(12)H(12)N(2)OS, (I), and 2-amino-4-tolyl-1,3-thiazolium chloride dihydrate, C(10)H(11)N(2)S(+).Cl(-).2H(2)O, (II), reveal that both molecules are essentially planar, with the respective dihedral angles between the benzene and thiazole rings being 2.9 (1) and 10.39 (7) degrees . Compound (I) associates via a single N-H...O interaction to form...

A search of the Cambridge Structural Database (CSD) was carried out for phosphine-water and arsine-water complexes in which water is either the proton donor in hydrogen-bonded complexes, or the electron-pair donor in pnicogen-bonded complexes. The range of experimental P-O distances in the phosphine complexes is consistent with the results of ab initio MP2/aug’-cc-pVTZ calculations carried out ...

We use ab initio molecular dynamics simulation to calculate the dipole moment of water molecules in one-dimensional hydrogen bonded chains in narrow pores. The electronic charges are partitioned among the water molecules using maximally localized Wannier functions. For water molecules confined to the interior of a carbon nanotube we find an average dipole moment of about 2.7 D, almost 10 % lowe...

2-Acylamino-6-pyridones (acyl = RCO, where R = Me, Et, i-Pr, t-Bu, and 1-adamantyl) were previously characterized by X-ray diffractometry and solid-state NMR techniques by us. One of these compounds was used recently in organocatalysis. The series is now studied in solution and by computational methods recommended for noncovalent interactions (DFT/M05). These compounds showed interesting behavi...

DFT study of hydrogen-bonded dimers and tetramer of glyoxilic acid oxime (GAO) has been performed at B3LYP/ 6-31G* and B3LYP/6-31++G** levels of the theory. The N HAO and O HAO hydrogen bondings in the selfassembling structures studied have been estimated from intermolecular distances, enthalpy of stabilization, hydrogenbonding energies and AIM electron density at the hydrogen bond critical poi...

The structural and energetic characteristics of O3–H2O complexes have been investigated by means of B3LYP, MP2, MP4(SDTQ), CCSD(T) and QCISD(T) methods in conjunction with the AUG-cc-pVDZ and AUG-cc-pVTZ basis sets. Six conformers were found for the O3–H2O complex. Two different intermolecular interactions were expected to participate in the formation of complexes, namely conventional O∙∙∙H hyd...