Hydrogen bonds torsional dynamics

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

The structural modeling of PG and PLV with the anti-parallel p-sheet form is carried out by the hybrid distance geometry-dynamic simulated annealing method115 as contained in the X-PLOR 3.1 program.116 For structural calculations, the proton-proton distance restraints and the torsion angle restraints ( =—139° and v /=135°) are derived from reference data by Wiithrich et al.ni Hydrogen-bond distance restraints are used for the N and atoms (2.7-3.3 A) in the secondary structure.118 120 The reference data of intra- and intermolecular proton-proton distances are shown in Fig. 19. 

Tonami et al.179) studied atactic-PMAA (at-PMAA)-PEO complex membranes by means of infrared spectroscopy, stress relaxation measurement and torsional analysis of dynamic-mechanical properties. They pointed out that the polymer complex was formed through hydrogen bonds between the ether... 

Acetanilide, and some of its isotopomers, have been studied by INS spectroscopy [56-58]. The dispersion curves of the fully deuterated material have been measured by coherent INS [59]. A comprehensive analysis of acetanilide in the solid state was carried out with molecular dynamics simulations [57]. This includes all the lattice modes, as shown in Fig. 10.27 The simulations suggested that the barrier to the methyl torsion was enhanced when the peptide group is hydrogen-bonded and that this was a through-bond polarization effect. The methyl torsion was... 

Neutron inelastic scattering techniques have been widely applied to the study of vibrational and rotational dynamics in hydrogenous molecular systems.1 The bulk of this research has been concerned with the study of intermolecular and interionic motions in solids, but a limited yet significant amount of effort has been directed toward the study of large-amplitude intramolecular vibrations, most notably torsional vibrations and hydrogen-bond modes.2 The present paper is restricted primarily to a discussion of the application of neutron scattering to the study of torsional vibrations and barriers to rotation of methyl groups in molecules. We will present several examples in which neutron spectra have provided information complementary to that obtained by the more widely available and applicable infrared and Raman techniques. We will also discuss in simple terms some limitations and pitfalls of the neutron technique and the interpretation of neutron spectral results. 

The combination of analytical pyrolysis, molecular modeling, and computational chemistry has also been stressed in investigating the structure of HS. It was reported that computational chemistry which allows to draw, construct and optimize in 3D space biomacromolecules, e.g., aquatic and terrestrial humic substances, with precise bond distances, bond angles, torsion angles, nonbonded distances, hydrogen bonds, charges, and chirality is a powerful tool, and molecular visualization and simulation can also be used to further understand the structure and dynamics of humic and dissolved organic matter. 

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