Luigi Delle Site

Adaptive resolution molecular-dynamics simulation: Changing the degrees of freedom on the fly

We present a new adaptive resolution technique for efficient particle-based multiscale molecular-dynamics simulations. The presented approach is tailor-made for molecular systems where atomistic resolution is required only in spatially localized domains whereas a lower mesoscopic level of detail is sufficient for the rest of the system. Our method allows an on-the-fly interchange between a given molecules atomic and coarse-grained levels of description, enabling us to reach large length and time scales while spatially retaining atomistic details of the system. The new approach is tested on a model system of a liquid of tetrahedral molecules. The simulation box is divided into two regions: one containing only atomistically resolved tetrahedral molecules, and the other containing only one-particle coarse-grained spherical molecules. The molecules can freely move between the two regions while changing their level of resolution accordingly. The hybrid and the atomistically resolved systems have the same statistical properties at the same physical conditions.

Force Fields for Studying the Structure and Dynamics of Ionic Liquids: A Critical Review of Recent Developments

Classical molecular dynamics simulations are a valuable tool to study the mechanisms that dominate the properties of ionic liquids (ILs) on the atomistic and molecular level. However, the basis for any molecular dynamics simulation is an accurate force field describing the effective interactions between all atoms in the IL. Normally this is done by empirical potentials which can be partially derived from quantum mechanical calculations on simple subunits or have been fitted to experimental data. Unfortunately, the number of accurate classical non-polarizable models for ILs that allow a reasonable description of both dynamical and statical properties is still low. However, the strongly increasing computational power allows one to apply computationally more expensive methods, and even polarizable-force-field-based models on time and length scales long enough to ensure a proper sampling of the phase space. This review attempts to summarize recent achievements and methods in the development of classical force fields for ionic liquids. As this class of salts covers a large number of compounds, we focus our review on imidazolium-based ionic liquids, but show that the main conclusions are valid for non-imidazolium salts, too. Insight obtained from recent electronic density functional results into the parametrization of partial charges and on the influence of polarization effects in bulk ILs is highlighted. An overview is given of different available force fields, ranging from the atomistic to the coarse-grained level, covering implicit as well as explicit modeling of polarization. We show that the recently popular usage of the ion charge as fit parameter can looked upon as treating polarization effects in a mean-field matter.

Adaptive resolution simulation of liquid water

Water plays a central role in biological systems and processes, and is equally relevant in a large range of industrial and technological applications. Being the most important natural solvent, its presence uniquely influences biological function as well as technical processes. Because of their importance, aqueous solutions are among the most experimentally and theoretically studied systems. However, many questions still remain open. Both experiments and theoretical models are usually restricted to specific cases. In particular all-atom simulations of biomolecules and materials in water are computationally very expensive and often not possible, mainly due to the computational effort to obtain water–water interactions in regions not relevant for the problem under consideration. In this paper we present a coarse-grained model that can reproduce the behaviour of liquid water at a standard temperature and pressure remarkably well. The model is then used in a multiscale simulation of liquid water, where a spatially adaptive molecular resolution procedure allows one to change from a coarse-grained to an all-atom representation on-the-fly. We show that this approach leads to the correct description of essential thermodynamic and structural properties of liquid water. Our adaptive multiscale scheme allows for significantly greater extensive simulations than existing approaches by taking explicit water into account only in the regions where the atomistic details are physically relevant.

Effect of Anions on Static Orientational Correlations, Hydrogen Bonds, and Dynamics in Ionic Liquids: A Simulational Study

Three different ionic liquids are investigated via atomistic molecular dynamics simulations using the force field of Lopes and PAdua (J. Phys. Chem. B 2006, 110, 19586). In particular, the 1-ethyl-3-methylimidazolium cation EMIM+ is studied in the presence of three different anions, namely, chloride Cl-, tetrafluoroborate BF(4)(-), and bis((trifluoromethyl)sulfonyly)imide TF2N-. In the focus of the present study are the static distributions of anions and cations around a cation as a function of anion size. It is found that the preferred positions of the anions change from being close to the imidazolium hydrogens to being above and below the imidazolium rings. Lifetimes of hydrogen bonds are calculated and found to be of the same order of magnitude as those of pure liquid water and of some small primary alcohols. Three kinds of short-range cation-cation orderings are studied, among which the offset stacking dominates in all of the investigated ionic liquids. The offset stacking becomes weaker from [EMIM][Cl] to [EMIM][BF4] to [EMIM][TF2N]. Further investigation of the dynamical behavior reveals that cations in [EMIM][TF2N] have a slower tumbling motion compared with those in [EMIM][Cl] and [EMIM][BF4] and that pure diffusive behavior can be observed after 1.5 ns for all three systems at temperatures 90 K above the corresponding melting temperatures.

Adaptive resolution molecular dynamics simulation through coupling to an internal particle reservoir.

For simulation studies of (macro) molecular liquids it would be of significant interest to be able to adjust or increase the level of resolution within one region of space, while allowing for the free exchange of molecules between open regions of different resolution or representation. We generalize the adaptive resolution idea and suggest an interpretation in terms of an effective generalized grand canonical approach. The method is applied to liquid water at ambient conditions.

Ionic Charge Reduction and Atomic Partial Charges from First-Principles Calculations of 1,3-Dimethylimidazolium Chloride

We present a detailed calculation of partial charges for the 1,3-dimethylimidazolium chloride ionic liquid. We first analyze MP2 electronic structure calculations and DFT results on isolated ion pairs with various methods of assigning partial charges to the atomic centers. In a second run we analyze the trajectory of a 25 ps long Car-Parrinello MD run of 30 ion pairs under bulk conditions using a charge fitting procedure due to Blöchl. Both, the single ion pair and the bulk system, provide us with a similar total ionic charge considerably less than unity. Especially the liquid state DFT results give convincing evidence for a reduced ionic charge on the ions. The similarity of both results suggest that the delocalization of the Cl charge is due only to local interactions. The relevance of our results is 2-fold; on the one hand they shed light on the basic property of the liquid and its reduced ionic character, and on the other hand, the ab initio derived partial charges provide a fundamental theoretical basis for the recent attempts to use the total ionic charge as an adjustable parameter. Furthermore, all our partial charges are subject to large fluctuations, hinting to the importance of polarization effects.

Coupling different levels of resolution in molecular simulations

Simulation schemes for liquids or strongly fluctuating systems that allow to change the molecular representation in a subvolume of the simulation box while preserving the equilibrium with the surroundings introduce conceptual problems of thermodynamic consistency. In this work we present a general scheme based on thermodynamic arguments which ensures a thermodynamic equilibrium among molecules of different representations. The robustness of the algorithm is tested for two examples, namely, an adaptive resolution simulation, atomistic/coarse grained, for a liquid of tetrahedral molecules, and an adaptive resolution simulation of a binary mixture of tetrahedral molecules and spherical solutes.

Modeling diffusive dynamics in adaptive resolution simulation of liquid water

We present a dual-resolution molecular dynamics (MD) simulation of liquid water employing a recently introduced Adaptive Resolution Scheme (AdResS). The spatially adaptive molecular resolution procedure allows for changing from a coarse-grained to an all-atom representation and vice versa on-the-fly. In order to find the most appropriate coarse-grained water model to be employed with AdResS, we first study the accuracy of different coarse-grained water models in reproducing the structural properties of the all-atom system. Typically, coarse-grained molecular models have a higher diffusion constant than the corresponding all-atom models due to the reduction in degrees of freedom (DOFs) upon coarse-graining that eliminates the fluctuating forces associated with those integrated-out molecular DOFs. Here, we introduce the methodology to obtain the same diffusional dynamics across different resolutions. We show that this approach leads to the correct description of the here relevant structural, thermodynamical, and dynamical properties, i.e., radial distribution functions, pressure, temperature, and diffusion, of liquid water at ambient conditions.

A comparative study of two classical force fields on statics and dynamics of [EMIM][BF4] investigated via molecular dynamics simulations

The influences of two different commonly employed force fields on statical and dynamical properties of ionic liquids are investigated for [EMIM][BF(4)]. The force fields compared in this work are the one of Canongia Lopes and Padua [J. Phys. Chem. B 110, 19586 (2006)] and that of Liu et al. [J. Phys. Chem. B 108, 12978 (2004)]. Differences in the strengths of hydrogen bonds are found, which are also reflected in the static ion distributions around the cation. Moreover, due to the stronger hydrogen bonding in the force field of Liu et al., the diffusive motions of cations and anions and the rotational behavior of the cations are slower compared with those obtained with the force field of Canongia Lopes and Padua. Both force fields underestimate the zero-field electrical conductivity, while the experimental dielectric constant can be reproduced within the expected statistical error boundaries.

A macromolecule in a solvent: Adaptive resolution molecular dynamics simulation

The authors report adaptive resolution molecular dynamics simulations of a flexible linear polymer in solution. The solvent, i.e., a liquid of tetrahedral molecules, is represented within a certain radius from the polymers center of mass with a high level of detail, while a lower coarse-grained resolution is used for the more distant solvent. The high resolution sphere moves with the polymer and freely exchanges molecules with the low resolution region through a transition regime. The solvent molecules change their resolution and number of degrees of freedom on the fly. The authors show that their approach correctly reproduces the static and dynamic properties of the polymer chain and surrounding solvent.