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The potential energy surface of the glycine dimer is examined by using the dynamics/quenching technique. It is observed that the most steady structure of the glycine dimer ascertained with the empirical potential does not agree with the planar cyclic structure with two O - H(hellip)O hydrogen bonds but with the stacked arrangement.

The nuclear magnetic resonance (NMR) spectroscopy was used to investigate the (super 13)C, (super 15)N-labeled DNA hairpin molecule of the sequence d(GCGAAGC) = d(G1C2G3A4A5G6C7), and to determine the one-bond and two-bond NMR spin-spin coupling constants. The result shows that one-bond and two-bond coupling constants are very sensitive to the position of the C and N nucleus in the pyrimidine or purine rings.

Free energy perturbation molecular dynamics simulations of the relative binding free energies of three spherands and alkali metal ions are presented. It was found that relative free energies of binding calculated in water are in better agreement with experiment than those calculated in chloroform.

A study was conducted to examine the counterion effects and the bilinear Eyring plot exhibited by the pyridine edge interchange reaction. The results revealed that the ordinary reaction mechanism, rotation around the Pt-N bond, proceeds after association of the counterion with Pt atom at its fifth ligand.

The coordination-driven self-assembly of four different trigonal prisms from 3 equiv of one of four different tetrapyridyl star connectors and 6 equiv of a platinum linker dication in nitromethane is presented. The use of a conformationally chiral star connector leads to a conformationally chiral prism when connector arm ends attached to a vertex have a strongly correlated twist sense and chirality is communicated across polyhedral faces, edges, and vertices.

Theoretical study of the acetic acid dimer, its microhydration and its behavior in water and chloroform solution was performed. The results concluded that acetic acid does not form any dimer structure in water solution.

AMBER empirical stabilization energies were verified by comparing them with correlated ab initio stabilization energies. The constant energy NVE ensemble MD simulations gave largest populations for stacked structures and all planar hydrogen-bonded structures were polluted negligibly.

Research was conducted to examine the constant energy molecular dynamics simulations of nuclear dynamics of benzene-Ar and benzene-Ar(sub n) clusters using the ab initio intermolecular potential of benzene-Ar. The mode selectivity of the intracluster vibrational energy redistribution and its linear dependence on the excess vibrational energy were established. Results indicate the bottleneck effect for intracluster vibrational energy flow due to the considerable frequency mismatch between the high-frequency vibrational modes of benzene.

Friction in molecular rotors is examined by classical molecular dynamics simulations for grid-mounted azimuthal dipolar molecular rotors, whose rotation is either allowed to decay freely or is driven at GHz frequencies by a flow of rare gas or by a rotating electric field. The rotating parts (rotators) are propeller-shaped. Their two to six blades consist of condensed aromatic rings and are attached to a deltahedral carborane hub, whose antipodal carbons carry [n]staffane axles mounted on a square molecular grid. The dynamic friction constant η has been derived in several independent ways with similar results. Analysis of free rotation decay yields η as a continuous exponentially decreasing function of rotor frequency. The calculated dependence of friction torque on frequency resembles the classical macroscopic Stribeck curve. Its relation to rotational potential energy barriers and the key role of the rate of intramolecular vibrational redistribution (IVR) of energy and angular momentum from rotator rotation to other modes are considered in two limiting regimes. (i) In the strongly overdamped regime, rotation is much slower than IVR, and effective friction can be expressed through potential barriers to rotation. (ii) In the strongly underdamped regime, rotation is much faster than IVR, whose rate then determines friction., (© 2012 American Chemical Society)