Fast Decorrelating Monte Carlo Moves for Efficient Path Sampling

Many relevant processes in chemistry, physics, and biology are rare events from a computational perspective as they take place beyond the accessible time scale of molecular dynamics (MD). Examples are chemical reactions, nucleation, and conformational changes of biomolecules. Path sampling is an approach to break this time scale limit via a Monte Carlo (MC) sampling of MD trajectories. Still, many trajectories are needed for accurately predicting rate constants. To improve the speed of convergence, we propose two new MC moves, stone skipping and web throwing. In these moves, trajectories are constructed via a sequence of subpaths obeying superdetailed balance. By a reweighting procedure, almost all paths can be accepted. Whereas the generation of a single trajectory becomes more expensive, the reduced correlation results in a significant speedup. For a study on DNA denaturation, the increase was found to be a factor 12

Enantiomeric Adsorption of Lactic Acid Mixtures in Achiral Zeolites

We studied the adsorption of chiral mixtures of lactic acid in several zeolites. All zeolite systems showed either no selectivity or heteroselectivity in which the minority enantiomer is adsorbed by a higher fraction than its fraction in the reservoir. Analysis of the mechanism showed that none of the previously identified origins of enantioselective adsorption of scalemic mixtures apply to lactic acid. However, on the basis of the lack of any ordered distribution in the adsorbed phase, we postulate a new mechanism that is likely to be very generic for chiral adsorption processes that proceed via chaotic packing of the adsorbate molecules. The new mechanism can explain several characteristics of the adsorption data and hints at new prospective separation methods with a high potential for pharmaceutical applications

Effective Monte Carlo Scheme for Multicomponent Gas Adsorption and Enantioselectivity in Nanoporous Materials

We devise an efficient Monte Carlo scheme to study the adsorption of a multicomponent gas in a nanoporous material. The configurational bias move is extended by a novel replica exchange procedure where the configurations of the different simulations describing one particular gas content are being swapped. For chiral mixtures, the efficiency can be further improved using the chiral inversion move. The method is demonstrated for an Ising-type model and a complicated realistic zeolite system

Density Functional Theory Study on the Interactions of Metal Ions with Long Chain Deprotonated Carboxylic Acids

In this work, interactions between carboxylate ions and calcium or sodium ions are investigated via density functional theory (DFT). Despite the ubiquitous presence of these interactions in natural and industrial chemical processes, few DFT studies on these systems exist in the literature. Special focus has been placed on determining the influence of the multibody interactions (with up to 4 carboxylates and one metal ion) on an effective pair-interaction potential, such as those used in molecular mechanics (MM). Specifically, DFT calculations are employed to quantify an effective pair-potential that implicitly includes multibody interactions to construct potential energy curves for carboxylate–metal ion pairs. The DFT calculated potential curves are compared to a widely used molecular mechanics force field (OPLS-AA). The calculations indicate that multibody effects do influence the energetic behavior of these ionic pairs and the extent of this influence is determined by a balance between (a) charge transfer from the carboxylate to the metal ions which stabilizes the complex and (b) repulsion between carboxylates, which destabilizes the complex. Additionally, the potential curves of the complexes with 1 and 2 carboxylates and one counterion have been examined to higher separation distance (20 Å) by the use of relaxed scan optimization and constrained density functional theory (CDFT). The results from the relaxed scan optimization indicate that near the equilibrium distance, the charge transfer between the metal ion and the deprotonated carboxylic acid group is significant and leads to non-negligible differences between the DFT and MM potential curves, especially for calcium. However, at longer separation distances the MM calculated interaction potential functions converge to those calculated with CDFT, effectively indicating the approximate domain of the separation distance coordinate where charge transfer between the ions is occurring