Marco Masia

On the performance of molecular polarization methods. II. Water and carbon tetrachloride close to a cation

Our initial study on the performance of molecular polarization methods close to a positive point charge [M. Masia, M. Probst, and R. Rey, J. Chem. Phys. 121, 7362 (2004)] is extended to the case in which a molecule interacts with a real cation. Two different methods (point dipoles and shell model) are applied to both the ion and the molecule. The results are tested against high-level ab initio calculations for a molecule (water or carbon tetrachloride) close to Li+, Na+, Mg2+, and Ca2+. The monitored observable is in all cases the dimer electric dipole as a function of the ion-molecule distance for selected molecular orientations. The moderate disagreement previously obtained for point charges at intermediate distances, and attributed to the linearity of current polarization methods (as opposed to the nonlinear effects evident in ab initio calculations), is confirmed for real cations as well. More importantly, it is found that at short separations the phenomenological polarization methods studied here substantially overestimate the dipole moment induced if the ion is described quantum chemically as well, in contrast to the dipole moment induced by a point-charge ion, for which they show a better degree of accord with ab initio results. Such behavior can be understood in terms of a decrease of atomic polarizabilities due to the repulsion between electronic charge distributions at contact separations. It is shown that a reparametrization of the Thole method for damping of the electric field, used in conjunction with any polarization scheme, allows to satisfactorily reproduce the dimer dipole at short distances. In contrast with the original approach (developed for intramolecular interactions), the present reparametrization is ion and method dependent, and corresponding parameters are given for each case.

Influence of Site-Dependent Pigment−Protein Interactions on Excitation Energy Transfer in Photosynthetic Light Harvesting

A site-dependent spectral density system-bath model of the Fenna-Matthews-Olsen (FMO) pigment-protein complex is developed using results from ground-state molecular mechanics simulations together with a partial charge difference model for how the long-range contributions to the chromophore excitation energies fluctuate with environmental configuration. A discussion of how best to consistently process the chromophore excitation energy fluctuation correlation functions calculated in these classical simulations to obtain reliable site-dependent spectral densities is presented. The calculations reveal that chromophores that are close to the protein-water interface can experience strongly dissipative environmental interactions characterized by reorganization energies that can be as much as 2-3 times those of chromophores that are buried deep in the hydrophobic protein scaffolding. Using a linearized density matrix quantum propagation method, we demonstrate that the inhomogeneous system-bath model obtained from our site-dependent spectral density calculations gives results consistent with experimental dissipation and dephasing rates. Moreover, we show that this model can simultaneously enhance the energy-transfer rate and extend the decoherence time. Finally, we explore the influence of initially exciting different chromophores and mutating local environments on energy transfer through the network. These studies suggest that different pathways, selected by varying initial photoexcitation, can exhibit significantly different relaxation times depending on whether the energy-transfer path involves chromophores at the protein-solvent interface or if all chromophores in the pathway are buried in the protein.

The polarizable point dipoles method with electrostatic damping: Implementation on a model system

Recently, the use of polarizable force fields in Molecular Dynamics simulations has been gaining importance, since they allow a better description of heterogeneous systems compared to simple point charges force fields. Among the various techniques developed in the last years the one based on polarizable point dipoles represents one of the most used. In this paper, we review the basic technical issues of the method, illustrating the way to implement intramolecular and intermolecular damping of the electrostatic interactions, either with and without the Ewald summation method. We also show how to reduce the computational overhead for evaluating the dipoles, introducing to the state-of-the-art methods: the extended Lagrangian method and the always stable predictor corrector method. Finally we discuss the importance of screening the electrostatic interactions at short range, defending this technique against simpler approximations usually made. We compare results of density functional theory and classical force field-based Molecular Dynamics simulations of chloride in water.

On the coupling between molecular diffusion and solvation shell exchange

The connection between diffusion and solvent exchanges between first and second solvation shells is studied by means of molecular dynamics simulations and analytic calculations, with detailed illustrations for water exchange for the Li(+) and Na(+) ions, and for liquid argon. First, two methods are proposed which allow, by means of simulation, to extract the quantitative speed-up in diffusion induced by the exchange events. Second, it is shown by simple kinematic considerations that the instantaneous velocity of the solute conditions to a considerable extent the character of the exchanges. Analytic formulas are derived which quantitatively estimate this effect, and which are of general applicability to molecular diffusion in any thermal fluid. Despite the simplicity of the kinematic considerations, they are shown to well describe many aspects of solvent exchange/diffusion coupling features for nontrivial systems.

Dynamical Properties of Confined Water Nanoclusters: Simulation Study of Hydrated Zeolite NaA: Structural and Vibrational Properties

Water nanoclusters confined to zeolitic cavities have been extensively investigated by various experimental techniques. We report a series of molecular dynamics simulations at different temperatures and for water nanoclusters of different sizes in order to attempt an atomistic interpretation of the properties of these systems. The cavities of zeolite NaA are spherical in shape and about 1 nm in diameter and can host nanoclusters of water containing nearly up to 24 water molecules. A modified interaction potential, yielding a better reproduction of experimental hydration energy and water diffusivity across a number of different zeolites, is proposed. Molecular dynamics simulations reproduce the known experimental structural features obtained by X-ray diffraction. Variations of simulated vibrational IR and IINS spectra with temperature and size of nanoclusters are in good agreement with experiment. The simulated water nanoclusters in zeolite NaA are found to be too small to crystallize and, at low temperature, behave as amorphous ice, in agreement with recent experimental results for similar water nanoclusters in reverse micelles.

The behaviour of water confined in zeolites: molecular dynamics simulations versus experiment

In order to study the behaviour of water adsorbed in zeolites, which are microporous crystalline aluminosilicates, whose channels and cavities of nanometric dimensions can host many different molecules, we developed a sophisticated empirical potential for water, including the full flexibility of the molecule and the correct response to the electric field generated by the cations and by the charged atoms of the aluminosilicate framework. The reproduction of experimental data by our potential model is similar or even better than that obtained from the first principles methods. The results of molecular dynamics simulations of water confined in a variety of zeolites (worm-like clusters in silicalite, spherical nanoclusters in zeolite A and ice-like nanotubes in AlPO(4)-5 and SSZ-24) at different temperatures and coverage (loading) are discussed in connection with the experimental data, whose overall good reproduction encourages the attempt of an atomic-scale description of structural and dynamical phenomena occurring in confined water, in particular in the supercooled regime. The results are also compared with simulations and experimental data on bulk water.

Ab initio based polarizable force field parametrization

Experimental and simulation studies of anion-water systems have pointed out the importance of molecular polarization for many phenomena ranging from hydrogen-bond dynamics to water interfaces structure. The study of such systems at molecular level is usually made with classical molecular dynamics simulations. Structural and dynamical features are deeply influenced by molecular and ionic polarizability, which parametrization in classical force field has been an object of long-standing efforts. Although when classical models are compared to ab initio calculations at condensed phase, it is found that the water dipole moments are underestimated by approximately 30%, while the anion shows an overpolarization at short distances. A model for chloride-water polarizable interaction is parametrized here, making use of Car-Parrinello simulations at condensed phase. The results hint to an innovative approach in polarizable force fields development, based on ab initio simulations, which do not suffer for the mentioned drawbacks. The method is general and can be applied to the modeling of different systems ranging from biomolecular to solid state simulations.

On the performance of molecular polarization methods. I. Water and carbon tetrachloride close to a point charge

The three main methods to implement molecular polarization (point dipoles, fluctuating charges, and shell model) are tested against high level ab initio calculations for a molecule (water, carbon tetrachloride) close to a point charge (at the distance of a lithium or magnesium ion). The goal is to check whether an approximation (linear polarization) strictly valid at large intermolecular distances is sufficiently accurate for liquid state molecular dynamics simulations, where strong polarization effects are to be expected at short separations. The monitored observable is the molecular dipole moment as a function of the charge-molecule distance for selected molecular orientations. Analytic formulas are derived for the components of the molecular polarization tensor, facilitating the optimization of the performance for each polarization method as a function of its underlying parameters. Overall, the methods studied provide a remarkably good representation of the induced dipole, with no divergences appearing even at the shortest distances. For water close to a monovalent point charge the point dipole model, implemented with one or three dipoles, accurately reproduces the water dipole moment at all distances. Deficiencies appear as the molecular polarizability and/or charge increase: basically, the ab initio induced moments grow faster at intermediate distances than the linear increase characteristic of the phenomenological polarization methods, suggesting that nonlinear effects (hyperpolarizability) cannot be neglected in these cases. Regarding the capabilities of each method, the point dipole method is the one that performs best overall, with the shell model achieving acceptable results in most instances. The fluctuating charge method shows some noticeable limitations for implementations of comparable complexity (in terms of the number of sites required).

Effect of temperature in a closed unstirred Belousov–Zhabotinsky system

Complex periodic and aperiodic behaviours are reported in an unstirred Belousov-Zhabotinsky oscillatory reaction performed at temperatures varying between 0°C and 8°C. A route to chaos following a Ruelle-Takens-Newhouse (RTN) scenario is identified. Thus, temperature effects on the coupling between chemical kinetics, diffusion and convection, seem to be responsible for the observed RTN scenario. In this Letter we demonstrate that the temperature is a bifurcation parameter for the sequence period-1 → quasiperiodicity → chaos.

Estimation of Partial Charges in Small Zeolite Imidazolate Frameworks from Density Functional Theory Calculations

Zeolitic Imidazolate Frameworks (ZIFs) are the new frontier in the field of metal-organic materials. They incorporate the confining properties of the more traditional aluminosilicate zeolites together with the catalytic activity provided by transition metal ions and organic links. Computation of atomic point charges for these hybrid materials is important in the field of molecular simulations for substantial prediction of experimental results. However, due to the structural complexity of advanced materials in general, studies involving derivation of point charges for these materials are truly scarce. In this article, we have derived the atomic point charges of ZIF-8 through fitting of the quantum electrostatic potential obtained systematically from density functional theory (DFT) calculations both on finite clusters of increasing size and on the periodic system. For the periodic system, fluctuations on the atomic charges have been studied through ab initio molecular dynamics simulations. Using the latter approach, we have extended the study to ZIF-2 and ZIF-3, where it has been found that charge fluctuations are, as well as for ZIF-8, very narrow, therefore justifying the use of the point charge approximation for these materials.