The potential of mean force of interacting aromatic amino acids is calculated using molecular dynamics simulations. The free energy surface is determined in order to study stacking and T-shape competition for phenylalanine-phenylalanine (Phe-Phe), phenylalanine-tyrosine (Phe-Tyr), and tyrosine-tyrosine (Tyr-Tyr) complexes in vacuo, water, carbon tetrachloride, and methanol. Stacked structures are favored in all solvents with the exception of the Tyr-Tyr complex in carbon tetrachloride, where T-shaped structures are also important. The effect of anchoring the two alpha-carbons (C(alpha)) at selected distances is investigated. We find that short and large C(alpha)-C(alpha) distances favor stacked and T-shaped structures, respectively. We analyze a set of 2396 protein structures resolved experimentally. Comparison of theoretical free energies for the complexes to the experimental analogue shows that Tyr-Tyr interaction occurs mainly at the protein surface, while Phe-Tyr and Phe-Phe interactions are more frequent in the hydrophobic protein core. This is confirmed by the Voronoi polyhedron analysis on the database protein structures. As found from the free energy calculation, analysis of the protein database has shown that proximal and distal interacting aromatic residues are predominantly stacked and T-shaped, respectively.

In this paper we compare the polarization response given by two different chemical potential equalization schemes to be applied to molecular dynamics simulations: the standard fluctuating point charge model (FQ) and the atom–atom charge transfer model (AACT). We have tested the transferability of FQ and AACT parameters, fitted to the polarizability of small size alkanes and polyenes, to large size homologues. We show that the FQ scheme is not adequate for the n-alkanes as it strongly overestimates the polarizability tensor components as the number of carbon atoms increases. The FQ approach has been found more predictive for highly conjugated systems like polyenes, although still unsatisfactory. The AACT parameters tuned on ethane are instead perfectly transferable to alkanes of any length and conformation. The AACT scheme satisfactorily reproduces the polarization response also for highly conjugated systems.

We propose a new approach for the umbrella sampling method in molecular dynamics simulations of complex systems. An accelerated sampling of the slow degrees of freedom is achieved by generating a single self-adaptive trajectory that tends to span uniformly the reaction coordinate using a time dependent bias potential derived from the preceding history of the system. To show the convergent behavior and the efficiency of the method, we present the free energy surface of alanine dipeptide in water as a function of the backbone dihedral angles.

An analysis of the conformational properties and hydrogen bonding in the condensed phases of glycerol is reported using the same model as adopted in Part I (Phys. Chem. Chem. Phys., 1999, 1, 871). Structural properties of the liquid and glassy states are analyzed in relation to the molecular backbone conformation of the glycerol molecule. The e †ects of hydrogen bonding and of temperature on the conformational distribution are analyzed. The structural and dynamical properties of hydrogen bonding in glycerol are also investigated. The results are consistent with available experimental observations and clarify many important and interrelated aspects of the microscopic structure of liquid, glassy and crystalline phases of glycerol.

Using a model potential function we have performed a molecular dynamics simulation of several static and dynamical properties of glycerol in the crystal, glass and liquid phases. Comparison with available experimental data shows an excellent agreeent and proves the validity of the potential model used. For the calculation of the molar speciÐc heat of the liquid and of the glass we have developed a theoretical approach which takes into account the contributions of the conformational structure energy and of the vibrational energy computed using the BoseÈEinstein statistics.