Liquid methanol Monte Carlo simulations with a refined potential which includes polarizability, nonadditivity, and intramolecular relaxation

Size of the hydrogen bond network in liquid methanol: a quantum cluster equilibrium model with extensive structure search

Studies have debated what is a favorable cluster size in liquid methanol. Applications of the quantum cluster equilibrium (QCE) model on a limited set of cluster structures have demonstrated the dominance of cyclic hexamers in liquid methanol. In this study, we examined the aforementioned question by integrating our implementation of QCE with a molecular-dynamics-based structural searching scheme. QCE simulations were performed using a database comprising extensively searched stable conformers of (MeOH)n for n = 2-14, which were optimized by B3LYP/6-31+G(d,p) with and without the dispersion correction. Our analysis indicated that an octamer structure can contribute significantly to cluster probability. By reoptimizing selected conformers with high probability at the MP2 level, we found that the aforementioned octamer became the dominant species due to favorable vibrational free energy, which was attributed to modes of intermolecular vibration.

A refined potential for hydroxylamine clusters and the liquid phase

A detailed study including ab initio calculations and classic Monte-Carlo simulations of hydroxylamine in the gas and liquid phases is presented. A classical interaction potential for hydroxylamine, which includes polarizability, many-body effects, and intramolecular relaxation, was constructed. The results of the simulation were compared to the available experimental data in order to validate the model. We conclude that liquid hydroxylamine has a multitude of hydrogen bonds leading to a large density where the existence of cis conformers and clusters of these conformers is possible. This explains the occurrence of the classical [R. Nast and I. Z. Foppl, Z. Anorg. Allg. Chem. 263, 310 (1950)] scheme for the molecule's decomposition at room temperature and its large exothermicity and instability.

Biological physics in México: Review and new challenges

Biological and physical sciences possess a long-standing tradition of cooperativity as separate but related subfields of science. For some time, this cooperativity has been limited by their obvious differences in methods and views. Biological physics has recently experienced a kind of revival (or better a rebirth) due to the growth of molecular research on animate matter. New avenues for research have been opened for both theoretical and experimental physicists. Nevertheless, in order to better travel for such paths, the contemporary biological physicist should be armed with a set of specialized tools and methods but also with a new attitude toward multidisciplinarity. In this review article, we intend to somehow summarize what has been done in the past (in particular, as an example we will take a closer look at the Mexican case), to show some examples of fruitful investigations in the biological physics area and also to set a proposal of new curricula for physics students and professionals interested in applying their science to get a better understanding of the physical basis of biological function.

A wave-function based approach for polarizable charge model: Systematic comparison of polarization effects on protic, aprotic, and ionic liquids

We first describe a wave-function based formalism of polarizable charge model by starting from the Hartree product ansatz for the total wave function and making the second-order expansion of individual molecular energies with the use of partial charge operators. The resulting model is shown to be formally equivalent to the charge response kernel model that starts from the linear-response approximation to partial charges, and also closely related to a family of fluctuating charge models that are based on the electronegativity equalization principle. We then apply the above model to a systematic comparison of polarization effects on qualitatively different liquids, namely, protic solvents (water and methanol), an aprotic polar solvent (acetonitrile), and imidazolium-based ionic liquids. Electronic polarization is known to decelerate molecular motions in conventional solvents while it accelerates them in ionic liquids. To obtain more insights into these phenomena, we consider an effective decomposition of total polarization energy into molecular contributions, and show that their statistical distribution is well-correlated with the acceleration/deceleration of molecular motions. In addition, we perform effective nonpolarizable simulations based on mean polarized charges, and compare them with fully polarizable simulations. The result shows that the former can reproduce structural properties of conventional solvents rather accurately, while they fail qualitatively to reproduce acceleration of molecular motions in ionic liquids.

Molecular modeling and dynamics studies with explicit inclusion of electronic polarizability. Theory and applications

A current emphasis in empirical force fields is on the development of potential functions that explicitly treat electronic polarizability. In the present article, the commonly used methodologies for modelling electronic polarization are presented along with an overview of selected application studies. Models presented include induced point-dipoles, classical Drude oscillators, and fluctuating charge methods. The theoretical background of each method is followed by an introduction to extended Langrangian integrators required for computationally tractable molecular dynamics simulations using polarizable force fields. The remainder of the review focuses on application studies using these methods. Emphasis is placed on water models, for which numerous examples exist, with a more thorough discussion presented on the recently published models associated with the Drude-based CHARMM and the AMOEBA force fields. The utility of polarizable models for the study of ion solvation is then presented followed by an overview of studies of small molecules (e.g. CCl(4), alkanes, etc) and macromolecule (proteins, nucleic acids and lipid bilayers) application studies. The review is written with the goal of providing a general overview of the current status of the field and to facilitate future application and developments.