Application of static charge transfer within an ionic-liquid force field and its effect on structure and dynamics

The effects of linear scaling of the atomic charges of a reference potential on the structure, dynamics, and energetics of the ionic liquid 1,3-dimethylimidazolium chloride are investigated. Diffusion coefficients that span over four orders of magnitude are observed between the original model and a scaled model in which the ionic charges are +/- 0.5 e. While the three-dimensional structure of the liquid is less affected, the partial radial distribution functions change markedly-with the positive result that for ionic charges of +/- 0.7 e, an excellent agreement is observed with ab initio molecular dynamics data. Cohesive energy densities calculated from these partial-charge models are also in better agreement with those calculated from the ab initio data. We postulate that ionic-liquid models in which the ionic charges are assumed to be +/- 1 e overestimate the intermolecular attractions between ions, which results in overstructuring, slow dynamics, and increased cohesive energy densities. The use of scaled-charge sets may be of benefit in the simulation of these systems-especially when looking at properties beyond liquid structure-thus providing on alternative to computationally expensive polarisable force fields.

Atomistic Insights into Rhodopsin Activation from a Dynamic Model

Rhodopsin, the light sensitive receptor responsible for blue-green vision, serves as a prototypical G protein-coupled receptor (GPCR). Upon light absorption, it undergoes a series of conformational changes that lead to the active form, metarhodopsin II (META II), initiating a signaling cascade through binding to the G protein transducin (G(t)). Here, we first develop a structural model of META II by applying experimental distance restraints to the structure of lumi-rhodopsin (LUMI), an earlier intermediate. The restraints are imposed by using a combination of biased molecular dynamics simulations and perturbations to an elastic network model. We characterize the motions of the transmembrane helices in the LUMI-to-META II transition and the rearrangement of interhelical hydrogen bonds. We then simulate rhodopsin activation in a dynamic model to study the path leading from LUMI to our META II model for wild-type rhodopsin and a series of mutants. The simulations show a strong correlation between the transition dynamics and the pharmacological phenotypes of the mutants. These results help identify the molecular mechanisms of activation in both wild type and mutant rhodopsin. While static models can provide insights into the mechanisms of ligand recognition and predict ligand affinity, a dynamic model of activation could be applicable to study the pharmacology of other GPCRs and their ligands, offering a key to predictions of basal activity and ligand efficacy.

Computational Verification of Two Universal Relations for Simple Ionic Liquids. Kinetic Properties of a Model 2:1 Molten Salt

Two semianalytical relations [Nature, 1996, 381, 137 and Phys. Rev. Lett. 2001, 87, 245901] predicting dynamical coefficients of simple liquids on the basis of structural properties have been tested by extensive molecular dynamics simulations for an idealized 2:1 model molten salt. In agreement with previous simulation studies, our results support the validity of the relation expressing the self-diffusion coefficient as a Function of the radial distribution functions for all thermodynamic conditions such that the system is in the ionic (ie., fully dissociated) liquid state. Deviations are apparent for high-density samples in the amorphous state and in the low-density, low-temperature range, when ions condense into AB(2) molecules. A similar relation predicting the ionic conductivity is only partially validated by our data. The simulation results, covering 210 distinct thermodynamic states, represent an extended database to tune and validate semianalytical theories of dynamical properties and provide a baseline for the interpretation of properties of more complex systems such as the room-temperature ionic liquids.

On transition rates in surface hopping

Trajectory surface hopping (TSH) is one of the most widely used quantum-classical algorithms for nonadiabatic molecular dynamics. Despite its empirical effectiveness and popularity, a rigorous derivation of TSH as the classical limit of a combined quantum electron-nuclear dynamics is still missing. In this work, we aim to elucidate the theoretical basis for the widely used hopping rules. Naturally, we concentrate thereby on the formal aspects of the TSH. Using a Gaussian wave packet limit, we derive the transition rates governing the hopping process at a simple avoided level crossing. In this derivation, which gives insight into the physics underlying the hopping process, some essential features of the standard TSH algorithm are retrieved, namely (i) non-zero electronic transition rate ("hopping probability") at avoided crossings; (ii) rescaling of the nuclear velocities to conserve total energy; (iii) electronic transition rates linear in the nonadiabatic coupling vectors. The well-known Landau-Zener model is then used for illustration. (C) 2012 American Institute of Physics. [http://dx.doi.org/10.1063/1.4770280]

Universal tight binding model for chemical reactions in solution and at surfaces. III. Stoichiometric and reduced surfaces of titania and the adsorption of water

We demonstrate a model for stoichiometric and reduced titanium dioxide intended for use in molecular dynamics and other atomistic simulations and based in the polarizable ion tight binding theory. This extends the model introduced in two previous papers from molecular and liquid applications into the solid state, thus completing the task of providing a comprehensive and unified scheme for studying chemical reactions, particularly aimed at problems in catalysis and electrochemistry. As before, experimental results are given priority over theoretical ones in selecting targets for model fitting, for which we used crystal parameters and band gaps of titania bulk polymorphs, rutile and anatase. The model is applied to six low index titania surfaces, with and without oxygen vacancies and adsorbed water molecules, both in dissociated and non-dissociated states. Finally, we present the results of molecular dynamics simulation of an anatase cluster with a number of adsorbed water molecules and discuss the role of edge and corner atoms of the cluster. (C) 2014 AIP Publishing LLC.

Ultrafast charge dynamics in an amino acid induced by attosecond pulses

In the past few years, attosecond techniques have been implemented for the investigation of ultrafast dynamics in molecules. The generation of isolated attosecond pulses characterized by a relatively high photon flux has opened up new possibilities in the study of molecular dynamics. In this paper, we report on experimental and theoretical results of ultrafast charge dynamics in a biochemically relevant molecule, namely, the amino acid phenylalanine. The data represent the first experimental demonstration of the generation and observation of a charge migration process in a complexmolecule, where electron dynamics precede nuclear motion. The application of attosecond technology to the investigation of electron dynamics in biologically relevant molecules represents a multidisciplinary work, which can open new research frontiers: those in which few-femtosecond and even subfemtosecond electron processes determine the fate of biomolecules. It can also open new perspectives for the development of new technologies, for example, in molecular electronics, where electron processes on an ultrafast temporal scale are essential to trigger and control the electron current on the scale of the molecule.

Equilibrium polymerization of cyclic carbonate oligomers

A model of the polymerization of ring oligomers of bisphenol A polycarbonate (BPA-PC) is used to investigate the influence of dimensionality (2D or 3D), density and temperature on the size distribution of the polymer chains. The polymerization step is catalyzed by a single active particle, conserves the number and type of the chemical bonds, and occurs without a significant gain in either potential energy or configurational entropy. Monte Carlo and molecular dynamics simulations show that polymerization of cyclic oligomers occurs readily at high density and is driven by the entropy associated with the distribution of interparticle bonds. Polymerization competes at lower densities with long range diffusion, which favors small molecular species, and is prevented if the system is sufficiently dilute. Polymerization occurs in 2D via a weakly first order transition as a function of density and is characterized by low hysteresis and large fluctuations in the size of polymer chains. Polymerization occurs more readily in 3D than in 2D, and is favored by increasing temperature, as expected for an entropy-driven process. (C) 2001 American Institute of Physics.

On the structure and dynamics of ionic liquids

The structure and dynamics of the ionic liquid 1-ethyl-3-methylimidazolium nitrate is studied by molecular dynamics simulations. We find long-range spatial correlations between the ions and a three-dimensional local structure that reflects the asymmetry of the cations. The main contribution to the configurational energy comes from the electrostatic interactions which leads to charge-ordering effects. Radial screening and threedimensional distribution of charge are also analyzed. The motion of a single ion is studied via velocity and reorientational correlation functions. It is found that ions "rattle" in a long-lived cage, while the orientational structure relaxes on a time scale longer than 200 ps. As in a supercooled liquid, the mean square displacements reveal a subdiffusive dynamics. In addition, the presence of dynamic heterogeneities can be detected by analyzing the non-Gaussian behavior of the van Hove correlation function and the spatial arrangement of the most mobile ions. The short-time collective dynamics is also studied through the electric current time correlation function.

Evidence of Short-Range Screening in Shock-Compressed Aluminum Plasma

We have investigated the angular variation in elastic x-ray scattering from a dense, laser-shock-compressed aluminum foil. A comparison of the experiment with simulations using an embedded atom potential in a molecular dynamics simulation shows a significantly better agreement than simulations based on an unscreened one-component plasma model. These data illustrate, experimentally, the importance of screening for the dense plasma static structure factor.

Salt-bridge dynamics control substrate-induced conformational change in the membrane transporter GlpT.

Active transport of substrates across cytoplasmic membranes is of great physiological, medical and pharmaceutical importance. The glycerol-3-phosphate (G3P) transporter (GlpT) of the E. coli inner membrane is a secondary active antiporter from the ubiquitous major facilitator superfamily that couples the import of G3P to the efflux of inorganic phosphate (Pi) down its concentration gradient. Integrating information from a novel combination of structural, molecular dynamics simulations and biochemical studies, we identify the residues involved directly in binding of substrate to the inward-facing conformation of GlpT, thus defining the structural basis for the substrate-specificity of this transporter. The substrate binding mechanism involves protonation of a histidine residue at the binding site. Furthermore, our data suggest that the formation and breaking of inter- and intradomain salt bridges control the conformational change of the transporter that accompanies substrate translocation across the membrane. The mechanism we propose may be a paradigm for organophosphate:phosphate antiporters.

Interaction of Room Temperature Ionic Liquid Solutions with a Cholesterol Bilayer

Water solutions of representative (IC(4)mim][Cl] and [C(4)mim][Tf2N] room temperature ionic liquids (ILs) in contact with a neutral lipid bilayer made of cholesterol molecules has been investigated by molecular dynamics simulations based on an empirical force field model. The results show that both ILs display selective adsorption at the water-cholesterol interface, with partial inclusion of ions into the bilayer. In the case Of [C(4)mim][Cl], the adsorption of ions at the water-cholesterol interface is limited by a sizable bulk solubility of the IL, driven by the high water affinity of [Cl](-). The relatively low Solubility Of [C(4)mim][Tf2N], instead, gives rise to a nearly complete segregation of the IL component on the bilayer, altering its volume, compressibility, and electrostatic environment. The computational results display important similarities to the results of recent experimental measurements for ILs in contact with phospholipid model membranes (see Evans, K. O. Int. J. Mol. Sci. 2008, 9, 498-511 and references therein).

Structural motifs of cholesterol nanoparticles

The growth sequence of gas-phase cholesterol clusters (Ch(N)) with up to N=36 molecules has been investigated by atomistic simulation based on an empirical force field model. The results of long annealings from high temperature show that the geometric motifs characterizing the structure of pure cholesterol crystals already appear in nanometric aggregates. In all clusters molecules tend to align along a common direction. For cluster sizes above the smallest ones, dispersion interactions among the hydrocarbon body and tails of cholesterol cooperate with hydrogen bonding to give rise to a bilayer structure. Analysis of snapshots from the annealing shows that the condensation of hydrogen bonds into a connected network of rings and chains is an important step in the self-organization of cholesterol clusters. The effect of solvation on the equilibrium properties of medium-size aggregates is investigated by short molecular dynamics simulations for the N=30 and N=40 clusters in water at near ambient conditions and in supercritical carbon dioxide at T=400 K.

Structure of warm dense matter via angularly resolved x-ray scatter

In this paper we describe experimental results on angularly resolved x-ray scatter from a sample of warm dense aluminium that has been created by double sided laser-driven shock compression. The experiment was carried out on the Central Laser Facility of the Rutherford Appleton Laboratory, using the VULCAN laser. The form of the angularly resolved scatter cross-section was compared with predictions based on a series of molecular dynamics simulations with an embedded atom potential, a Yukakwa potential and a bare Coulomb potential. The importance of screening is evident from the comparison and the embedded atom model seems to match experiment better than the Yukawa potential.

Correlated electron-ion dynamics in metallic systems

In this paper we briefly discuss the problem of simulating non-adiabatic processes in systems that are usefully modelled using molecular dynamics. In particular we address the problems associated with metals, and describe two methods that can be applied: the Ehrenfest approximation and correlated electron-ion dynamics (CEID). The Ehrenfest approximation is used to successfully describe the friction force experienced by an energetic particle passing through a crystal, but is unable to describe the heating of a wire by an electric current. CEID restores the proper heating.

Liquid Structure and Dynamics of Aqueous Isopropanol over gamma-Alumina

The liquid structures of thin films of aqueous solutions of 0, 7, 19, 50, and 100 mol % isopropanol above O/Al-terminated gamma-alumina surfaces have been investigated by means of classical molecular dynamics simulations. The structuring effect of the oxide oil the liquid mixtures is strong and heavily dependent on the local structure of the oxide. Two distinct re-ions are found oil the oxide Surface characterized by the degree of coordination of Al atoms. Above octahedral Al atoms, water and isopropanol molecules adsorb via the oxygen atoms to maximize the electrostatic interaction, whereas above tetrahedral Al sites the solvent molecules adsorb via hydrogen atoms with the oxygen atoms away front the surface. More mobility is found in the second layer compared with the first; however, its structure is still influenced significantly by the orientation of molecules in the first adsorbed layer. Qualitatively, the displacement of water from the surface by the adsorption of isopropanol occurs with 2.6 Water molecules lost for every alcohol molecule present based on the effective surface areas of the two species calculated from the pure simulations.