An efficient Monte Carlo method for calculating ab initio transition state theory reaction rates in solution

In this article, we propose an efficient method for sampling the relevant state space in condensed phase reactions. In the present method, the reaction is described by solving the electronic Schr\"{o}dinger equation for the solute atoms in the presence of explicit solvent molecules. The sampling algorithm uses a molecular mechanics guiding potential in combination with simulated tempering ideas and allows thorough exploration of the solvent state space in the context of an ab initio calculation even when the dielectric relaxation time of the solvent is long. The method is applied to the study of the double proton transfer reaction that takes place between a molecule of acetic acid and a molecule of methanol in tetrahydrofuran. It is demonstrated that calculations of rates of chemical transformations occurring in solvents of medium polarity can be performed with an increase in the cpu time of factors ranging from 4 to 15 with respect to gas-phase calculations.Comment: 15 pages, 9 figures. To appear in J. Chem. Phy

Molecular modeling for physical property prediction

Multiscale modeling is becoming the standard approach for process study in a broader framework that promotes computer aided integrated product and process design. In addition to usual purity requirements, end products must meet new constraints in terms of environmental impact, safety of goods and people, specific properties. This chapter adresses the use of molecular modeling tools for the prediction of physical property usefull for chemical engineering practice

Self-referential Monte Carlo method for calculating the free energy of crystalline solids

A self-referential Monte Carlo method is described for calculating the free energy of crystalline solids. All Monte Carlo methods for the free energy of classical crystalline solids calculate the free-energy difference between a state whose free energy can be calculated relatively easily and the state of interest. Previously published methods employ either a simple model crystal, such as the Einstein crystal, or a fluid as the reference state. The self-referential method employs a radically different reference state; it is the crystalline solid of interest but with a different number of unit cells. So it calculates the free-energy difference between two crystals, differing only in their size. The aim of this work is to demonstrate this approach by application to some simple systems, namely, the face centered cubic hard sphere and Lennard-Jones crystals. However, it can potentially be applied to arbitrary crystals in both bulk and confined environments, and ultimately it could also be very efficient

Improvements to the APBS biomolecular solvation software suite

The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve the equations of continuum electrostatics for large biomolecular assemblages that has provided impact in the study of a broad range of chemical, biological, and biomedical applications. APBS addresses three key technology challenges for understanding solvation and electrostatics in biomedical applications: accurate and efficient models for biomolecular solvation and electrostatics, robust and scalable software for applying those theories to biomolecular systems, and mechanisms for sharing and analyzing biomolecular electrostatics data in the scientific community. To address new research applications and advancing computational capabilities, we have continually updated APBS and its suite of accompanying software since its release in 2001. In this manuscript, we discuss the models and capabilities that have recently been implemented within the APBS software package including: a Poisson-Boltzmann analytical and a semi-analytical solver, an optimized boundary element solver, a geometry-based geometric flow solvation model, a graph theory based algorithm for determining p$K_a$ values, and an improved web-based visualization tool for viewing electrostatics

Simulating fluid-solid equilibrium with the Gibbs ensemble

The Gibbs ensemble is employed to simulate fluid-solid equilibrium for a shifted-force Lennard-Jones system. This is achieved by generating an accurate canonical Helmholtz free-energy model of the (defect-free) solid phase. This free-energy model is easily generated, with accuracy limited only by finite-size effects, by a single isothermal-isobaric simulation at a pressure not too far from coexistence for which the chemical potential is known. We choose to illustrate this method at the known triple-point because the chemical potential is easily calculated from the coexisting gas. Alternatively, our methods can be used to locate fluid-solid coexistence and the triple-point of pure systems if the chemical potential of the solid phase can be efficiently calculated at a pressure not too far from the actual coexistence pressure. Efficient calculation of the chemical potential of solids would also enable the Gibbs ensemble simulation of bulk solid-solid equilibrium and the grand-canonical ensemble simulation of bulk solids