Generic force fields for ionic liquids Dommert, Florian; Wendler, Katharina; Qiao, Baofu ...
Journal of molecular liquids,
04/2014, Volume:
192
Journal Article
Peer reviewed
Ionic liquids have been intensively studied during the last decade, but many questions still remain unresolved. From the computational side there is the lack of good transferable force fields for ...molecular simulations that would allow accurate theoretical predictions and interpretations of the properties of ionic liquids. Within this article a method is described that allows for the derivation of partial charges for ionic liquids since they play a particular important role, particularly for a liquid that consists entirely of ions. Our partial charges are carefully determined in such a way that they incorporate in an average way the influence of polarization effects of the neighboring ions in a bulk situation thereby reducing the total ionic charge to values less than one. When combined with our recently introduced method for the optimization of the short-range interactions 1 we have a well described route to develop generic force fields for ionic liquids. In this article we describe our results for the partial charges for the three imidazolium based liquids MMIM+, EMIM+, and BMIM+ for three different anions.
•A method to derive classical force fields for ionic liquids is introduced.•Electronic structure information from DFT is mapped to partial charges.•Classical MD results for slightly varying sets of partial charges are presented.•A workflow is introduced to construct a set of generic partial charges.
In this review, we provide a short overview of the Molecular Dynamics (MD) method and how it can be used to model the water splitting process in photoelectrochemical hydrogen production. We cover ...classical non-reactive and reactive MD techniques as well as multiscale extensions combining classical MD with quantum chemical and continuum methods. Selected examples of MD investigations of various aqueous semiconductor interfaces with a special focus on TiO2 are discussed. Finally, we identify gaps in the current state-of-the-art where further developments will be needed for better utilization of MD techniques in the field of water splitting.
For over a century the definitions of mass and derivations of its relation with energy continue to be elaborated, demonstrating that the concept of mass is still not satisfactorily understood. The ...aim of this study is to show that, starting from the properties of Minkowski spacetime and from the principle of least action, energy expresses the property of inertia of a body. This implies that inertial mass can only be the object of a definition—the so called mass-energy relation—aimed at measuring energy in different units, more suitable to describe the huge amount of it enclosed in what we call the “rest-energy” of a body. Likewise, the concept of gravitational mass becomes unnecessary, being replaceable by energy, thus making the weak equivalence principle intrinsically verified. In dealing with mass, a new unit of measurement is foretold for it, which relies on the de Broglie frequency of atoms, the value of which can today be measured with an accuracy of a few parts in 10
9
.
The objective of the project was to give an overview and hands-on insight into modern biotechnological modeling in and across several scales (and dimensions), from Quantum Mechanics to Classical ...Mechanics, from Molecular Mechanics to Molecular Dynamics, and from Single Molecules to Biological Systems. Here we give a starting tour of using the classical Molecular Dynamics software package AMBER 1, and the quantum mechanical Car-Parrinello package CPMD (www. cpmd.org) 2. Introductions to some useful visualization software software specialised for biological systems was also given (Visual Molecular Dynamics) 3.
The main focus of this project is to apply multi-scale, here the so-called QM/MM molecular dynamics, methods to a biological system. In current biophysical modeling two main branches exist; classical force-field MD and static QM calculations. Though both methods are regularly and successfully applied to biological systems, many intrinsic restrictions exist, some of which are greatly reduced or solved by using multi-scale QM/MM MD. In classical MD, the by-far most common approach, the potential energy surface is parametrized through a fitting to empirical and/or theoretical data. They are therefore intrinsically restricted to situations where no significant changes of the electronic structure occur, but for example chemical reactions can only be treated adequately by a quantum mechanical description. Further restrictions include that the force field parameters are pre-defined and do not change when the system changes, either from conformational changes or from changes in the local environment. Secondly, if one wishes to model e.g. metallic centers or more uncommon organic molecules, no parameters may be available and a sometimes arduous and non-trivial parametrization is necessary.
Structure and transport properties at grain boundaries in polycrystalline olivine have been investigated at the atomic scale by molecular dynamics simulation (MD) using an empirical ionocovalent ...interaction potential. On the time scale of the simulation (a few tens of nanoseconds for a system size of ∼650,000 atoms) grain boundaries and grain interior were identified by mapping the atomic displacements along the simulation run. In the investigated temperature range (1300–1700K) the mean thickness of the grain boundary phase is evaluated between 0.5 and 2nm, a value which depends on temperature and grain size. The structure of the grain boundary phase is found to be disordered (amorphous-like) and is different from the one exhibited by the supercooled liquid. The self-diffusion coefficients of major elements in the intergranular region range from ∼10−13 to 10−10m2/s between 1300 and 1700K (with DSigb<DOgb<DFegb<DMggb) and are only one order of magnitude smaller than those evaluated in the supercooled melt. In using a newly derived expression for the bulk self-diffusion coefficient it is concluded that the latter one is driven by the grain boundary contribution as long as the grain size is smaller than a centimeter. In assuming that the electrical conduction at grain boundaries is purely ionic, the macroscopic grain boundary conductivity is found to be two orders of magnitude lower than in molten olivine, and one order of magnitude higher than the lattice conductivity. A consequence is that the conductivity of the olivine polycrystal is dominated by the grain interior contribution as soon as the grain size is larger than a micrometer or so. The grain boundary viscosity has been evaluated from the Green-Kubo relation expressing the viscosity as function of the stress tensor time correlation function. In spite of a slow convergence of the calculation by MD, the grain boundary viscosity was estimated about ∼105Pas at 1500K, a value in agreement with high-temperature viscoelastic relaxation data. An interesting information gained from MD is that sliding at grain boundaries is essentially controlled by the internal friction between the intergranular phase and the grain edges.
We study the π-stacking interaction between the chromophore and Tyr203 in the Yellow Fluorescent Protein (YFP) in order to (i) evaluate the contribution of the internal interaction energy of the ...isolated Chromophore-Tyrosine complex (Eint) to the 26nm red shift observed from GFP to YFP, (ii) compare the effects of Eint and of the proteic environment. To that end, we perform quantum mechanical and force field (ff) calculations of the isolated complex in S0 and S1 states on a large sample of geometries, together with molecular dynamics simulations and potential of mean force analysis. The calculated absorption wavelengths are found red shifted with respect to the isolated chromophore by 12–19nm, that represents a large part of the GFP-YFP shift. We find that the effect of the protein is determinant on the dynamics of the complex while the error that results from using a classicalff is of limited effect.
Adsorption of a methane molecule (CH4) onto a defected and rippled graphene sheet is studied using ab initio and molecular mechanics calculations. The optimal adsorption position and orientation of ...this molecule on the graphene surface (motivated by the recent realization of graphene sensors to detect individual gas molecules) is determined and the adsorption energies are calculated. In light of the density of states, we used the SIESTA code. It is found that (i) classical force field yields adsorption energy comparable with experimental result and ab initio calculation; (ii) the periodic nature of the van der Waals potential energy stored between methane and perfect sheet is altered due to the insertion vacancies and sinusoidal ripples; (iii) the van der Waals potential energy is found to be sensitive to the presence of the vacancies and the ripples so that the added molecule avoids to be around vacant cites and on top of the peaks.
► The estimated binding energy is in good agreement with ab initio and experimental. ► Both defects and ripples alter the periodicity of the vdW energy surfaces. ► CH4 avoids to be located around the defective cites and the peaks of the ripples. ► CH4 molecule prefers to be inside the valleys of the ripples.
A fitting procedure is presented to use a valence force field model to generate the phonon spectrum of large nanostructures. This approach uses a relatively large number of parameters (∼50) in order ...to generate the accurate ab initio phonon spectrum. Since the emphasis is in the accuracy rather than the transferability, it can only be used in similar bonding environments. Because of this, a reliable and automatic fitting procedure is essential. We discuss the detailed aspects of the fitting procedure, including the stages of fitting, the type of ab initio values used for the fitting, the weighting factors for different quantities, the number of ab initio data points needed, as well as the uniqueness of the parameters. We found that the parameters cannot be determined uniquely, indicating interdependence of the parameters. Nevertheless, the different parameters resulted from different fits all give accurate phonon spectrum compared to ab initio results. We have used the fitted valence force field model to study the phonon spectra of CdSe nanowires.
PDF
