To understand the underlying mechanisms of significant differences in dissociation rate constant among different inhibitors for HIV-1 protease, we performed steered molecular dynamics (SMD) simulations to analyze the entire dissociation processes of inhibitors from the binding pocket of protease at atomistic details. We found that the strength of hydrogen bond network between inhibitor and the ...

Three N-substituted 5-chlorosalicylamides (4-chlorophenyl, 2a; benzyl, 2b; phenethyl 2c) differing in the length of the 'linker' between the benzene ring and the amide moiety were prepared in order to compare their supramolecular architecture. The intramolecular NH··O(H) hydrogen bond and the intermolecular C=O··H–O hydrogen bond were found in the crystal structure of 2a and 2c thus forming an ...

Yamaguchi et al. have recently identified positions of hydrogen and deuterium atoms in photoactive yellow protein (PYP) using high-resolution neutron scattering. They reported that the hydrogen bond between the PYP chromophore and Glu46 was not a short ionic hydrogen bond (SIHB) but a low barrier hydrogen bond (LBHB). Furthermore, it was suggested that Arg52 close to the chromophore was deproto...

The motion of the atoms in the small protein bovine pancreatic trypsin inhibitor has been simulated for about 60 picoseconds using two different potential energy functions. In one known as HHL the hydrogen bond is purely electrostatic, in the other, known as L79, the hydrogen bond is a directional O . . . H interaction. The energy parameters and techniques used to obtain an accurate, well-equil...

Catalytic fields illustrate topology of the optimal charge distribution of a molecular environment reducing the activation energy for any process involving barrier crossing, like chemical reaction, bond rotation etc. Until now, this technique has been successfully applied to predict catalytic effects resulting from intermolecular interactions with individual water molecules constituting the fir...

The title compound, C18H18NOP, was obtained during a search for new P,N-containing ligands with the potential to generate precatalysts with chromium(III) for selective ethyl-ene oligomerization. In the crystal, mutual pairs of N-H⋯O=P hydrogen bonds link two mol-ecules into a dimer with individual mol-ecules related by a twofold rotation axis. The P=O bond length of 1.4740 (15) Å is not elongat...

The title compound, C10H13N3O3, adopts an E conformation with respect to the azomethine bond and crystallizes in the amide form. A classical intra-molecular O-H⋯N hydrogen bond is present. The two N atoms of the hydrazinecarboxamide unit are also involved in inter-molecular N-H⋯O hydrogen bonds, with the O atom of the hydrazinecarboxamide group acting as the acceptor. Pairs of N-H⋯O hydrogen bo...

We study the dynamics of the formation of multiple hydrogen bonds between ionic liquid anions and cellulose using molecular dynamics simulations. We examine fifteen different ionic liquids composed of 1-alkyl-3-methylimidazolium cations ([Cnmim], n = 1, 2, 3, 4, 5) paired with either chloride, acetate or dimethylphosphate. We map the transitions of anions hydrogen bonded to cellulose into diffe...

The molecular interactions between the component networks in poly(methacrylic acid)/poly(N-isopropyl acrylamide) (PMAA/PNIPAAm) interpenetrating polymer networks (IPNs) were investigated using attenuated total reflectance (ATR)Fourier transform IR (FTIR) spectroscopy. Hydrogen-bond formation was noted between the carboxyl groups of PMAA and the amide groups of PNIPAAm. The ATR-FTIR results show...