Low-lying structures of HCl (H2O) n (n = 3, 4) clusters have been studied by ab initio Monte Carlo simulated annealing (MCSA), a procedure which efficiently samples minima on a potential energy surface. In the Monte Carlo simulated annealing procedure, energies were computed ab initio at each Monte Carlo step by the B3-LYP density functional method with 6-31G* basis sets. All geometries of the isomers found for each cluster were refined in full conventional geometry optimizations, and frequency analyses were performed at both the B3-LYP and MP2 levels with 6-311+G** basis sets. The stability of the B3-LYP and MP2 energy orderings was tested in single point QCISD(T) calculations performed at the MP2 optimized geometries. Only isomers with strong H−Cl interaction were found for HCl(H2O)3. However, both associated- and dissociated-HCl structures of HCl(H2O)4 were found.

No abstract

The structures and energies of Be(n)Si(n) and Be(2n)Si(n) (n = 1-4) clusters have been examined in ab initio theoretical electronic structure calculations. Cluster geometries have been established in B3LYP/6-31G(2df) calculations and accurate relative energies determined by the G3XMP2 method. The two atoms readily bond to each other and to other atoms of their own kind. The result is a great variety of low-energy clusters in a variety of structural types.

No abstract

A number of significant structures of NH3(H2O) n (n = 3, 4) clusters have been identified by ab initio Monte Carlo simulated annealing, a procedure that efficiently samples minima on a potential energy surface. In this procedure, energies were computed ab initio at each Monte Carlo step by the B3-LYP density functional method with the 6-31G* basis set. All geometries of the isomers found for each cluster were refined in full conventional geometry optimizations, and frequency analyses were performed at both the B3-LYP and MP2 levels with the 6-311+G(d,p) basis set. The B3-LYP and MP2 energy orders were confirmed with single point QCISD(T) calculations with the 6-311+G(d,p) basis set performed on the MP2 optimized geometries. Only associated isomers were found for NH3(H2O)3. However, for NH3(H2O)4 both associated and dissociated structures were found.

The dynamics of Hemoglobin I (HbI) from the clam Lucina pectinata, from wild-type sperm whale (SW) myoglobin, and from the L29F/H64Q/V68F triple mutant of SW, both unligated and bound to hydrogen sulfide (H2S), have been studied in molecular dynamics simulations. Features that account for differences in H2S affinity among the three have been examined. Our results verify the existence of an unusual heme rocking motion in unligated HbI that can promote the entrance of large ligands such as H2S. The FQF-mutant partially reproduces the amplitude and relative orientation of the motion of HbI's heme group. Therefore, besides introducing favorable electrostatic interactions with H2S, the three mutations in the distal pocket change the dynamic properties of the heme group. The active-site residues Gln-64(E7), Phe-43(CD1), and His-93(F8) are also shown to be more flexible in unligated HbI than in FQF-mutant and SW. Further contributions to H2S affinity come from differences in hydrogen bonding between the heme propionate groups and nearby amino acid residues.

No abstract

The global minimum-energy and other significant structures of HCl(NH3)n (n=1–4) clusters have been identified by ab initio Monte Carlo simulated annealing. Geometries of the isomers were refined in density functional theoretical and Hartree–Fock plus second-order Møller–Plesset perturbation theoretical calculations. The energy orderings were confirmed in single-point higher-level calculations. While for HCl(NH3) only one hydrogen-bonded structure was found, for the larger clusters both ionic and molecular structures exist. Stabilization by hydrogen bonding is found to be less important in the ammonia clusters than in water clusters of similar size.