Search results for "Molecular simulation"

The Coordination of Uranyl in Water: A Combined Quantum Chemical and Molecular Simulation Study

2005

The coordination environment of uranyl in water has been studied using a combined quantum mechanical and molecular dynamics approach. Multiconfigurational wave function calculations have been performed to generate pair potentials between uranyl and water. The quantum chemically determined energies have been used to fit parameters in a polarizable force field with an added charge transfer term. Molecular dynamics simulations have been performed for the uranyl ion and up to 400 water molecules. The results show a uranyl ion with five water molecules coordinated in the equatorial plane. The U-O(H(2)O) distance is 2.40 A, which is close to the experimental estimates. A second coordination shell…

Erratum: “Computing absolute free energies of disordered structures by molecular simulation” [J. Chem. Phys. 131, 231102 (2009)]

2011

An omics perspective to the molecular mechanisms of anticancer metallo-drugs in the computational microscope era

2017

Introduction: Metallo-drugs have attracted enormous interest for cancer treatment. The achievements of this drug-type are summarized by the success story of cisplatin. That being said, there have been many drawbacks with its clinical use, which prompted decades worth of research efforts to move towards safer and more effective agents, either containing platinum or different metals. Areas covered: In this review, the authors provide an atomistic picture of the molecular mechanisms involving selected metallo-drugs from structural and molecular simulation studies. They also provide an omics perspective, pointing out many unsettled aspects of the most relevant families of metallo-drugs at an ep…

Direct experimental observation of mesoscopic fluorous domains in fluorinated room temperature ionic liquids

2017

Fluorinated room temperature ionic liquids (FRTILs) represent a class of solvent media that are attracting great attention due to their IL-specific properties as well as features stemming from their fluorous nature. Medium-to-long fluorous tails constitute a well-defined apolar moiety in the otherwise polar environment. Similarly to the case of alkyl tails, such chains are expected to result in the formation of self-assembled fluorous domains. So far, however, no direct experimental observation has been made of the existence of such structural heterogeneities on the nm scale. We report here the first experimental evidence of the existence of mesoscopic spatial segregation of fluorinated dom…

Frontiers in molecular simulation of solvated ions, molecules and interfaces.

2020

This themed collection is a collection of articles on frontiers in molecular simulation of solvated ions, molecules and interfaces.

Fick diffusion coefficients of liquid mixtures directly obtained from equilibrium molecular dynamics.

2011

A methodology for computing Fick diffusivities directly from equilibrium molecular dynamics (MD) simulations is presented and validated for acetone-methanol and acetone-tetrachloromethane liquid mixtures. Fick diffusivities are obtained from Maxwell-Stefan (MS) diffusivities and the so-called thermodynamic factor. MS diffusivities describe the friction between different components, while the thermodynamic factor is the concentration derivative of the activity describing the deviation from ideal mixing behavior. It is important to note that all mutual diffusion experiments measure Fick diffusion coefficients, while molecular simulation provides MS diffusivities. The required thermodynamic fa…

Partial molar enthalpies and reaction enthalpies from equilibrium molecular dynamics simulation

2014

We present a new molecular simulation technique for determining partial molar enthalpies in mixtures of gases and liquids from single simulations, without relying on particle insertions, deletions, or identity changes. The method can also be applied to systems with chemical reactions. We demonstrate our method for binary mixtures of Weeks-Chandler-Anderson particles by comparing with conventional simulation techniques, as well as for a simple model that mimics a chemical reaction. The method considers small subsystems inside a large reservoir (i.e., the simulation box), and uses the construction of Hill to compute properties in the thermodynamic limit from small-scale fluctuations. Results …

Molecular simulation of mixed gas hydrates in astrophysical conditions

2020

In this PhD work, numerical simulation methods have been used in order to model clathrate hydrates at the molecular scale, in thermodynamic conditions typical of astrophysical contexts. The aim was to characterize the trapping abilities of those peculiar structures of water, by means of the tools used in adsorption studies. The results presented in the present thesis are focused on a couple of chemical species which are found to be abundant in our astrophysical vicinity and are quite similar: carbon monoxide, CO, and nitrogen, N2. Thus, the single-component clathrates of CO and N2, and the mixed hydrate CO-N2 have been studied, mainly using grand canonical Monte Carlo simulations. First, th…

Computing absolute free energies of disordered structures by molecular simulation

2009

We present a Monte Carlo simulation technique by which the free energy of disordered systems can be computed directly. It is based on thermodynamic integration. The central idea is to construct an analytically solvable reference system from a configuration which is representative for the state of interest. The method can be applied to lattice models (e.g., the Ising model) as well as off-lattice molecular models. We focus mainly on the more challenging off-lattice case. We propose a Monte Carlo algorithm, by which the thermodynamic integration path can be sampled efficiently. At the examples of the hard sphere liquid and a hard disk solid with a defect, we discuss several properties of the …

New QM/MM implementation of the DFTB3 method in the gromacs package.

2015

The approximate density-functional tight-binding theory method DFTB3 has been implemented in the quantum mechanics/molecular mechanics (QM/MM) framework of the Gromacs molecular simulation package. We show that the efficient smooth particle–mesh Ewald implementation of Gromacs extends to the calculation of QM/MM electrostatic interactions. Further, we make use of the various free-energy functionalities provided by Gromacs and the PLUMED plugin. We exploit the versatility and performance of the current framework in three typical applications of QM/MM methods to solve biophysical problems: (i) ultrafast proton transfer in malonaldehyde, (ii) conformation of the alanine dipeptide, and (iii) el…