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It has been reported that beta amyloid induces production of radical oxygen species and oxidative stress in neuronal cells, which in turn upregulates β-secretase (BACE-1) expression and beta amyloid levels, thereby propagating oxidative... more
It has been reported that beta amyloid induces production of radical oxygen species and oxidative stress in neuronal cells, which in turn upregulates β-secretase (BACE-1) expression and beta amyloid levels, thereby propagating oxidative stress and increasing neuronal injury. A series of resveratrol derivatives, known to be inhibitors of oxidative stress-induced neuronal cell death (oxytosis) were biologically evaluated against BACE-1 using homogeneous time-resolved fluorescence (TRF) assay. Correlation between oxytosis inhibitory and BACE-1 inhibitory activity of resveratrol derivatives was statistically significant, supporting the notion that BACE-1 may act as pivotal mediator of neuronal cell oxytosis. Four of the biologically evaluated resveratrol analogs demonstrated considerably higher activity than resveratrol in either assay. The discovery of some "hits" led us to initiate detailed docking studies associated with Molecular Dynamics in order to provide a plausible explanation for the experimental results and understand their molecular basis of action.
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Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for... more
Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for state points along a near-critical isotherm (1.02 T(c)) over a wide range of densities, using new developed optimized potential models for both isomers. The similarities and differences in the solvation structures around each isomer have been presented and discussed. The local density augmentation and enhancement factors of CO(2) around the isomers have been found significantly larger than the corresponding values for pure supercritical CO(2). The dynamic local density reorganization has been investigated and related to previously proposed relaxation mechanisms. The density dependence of the calculated self-diffusion coefficients has revealed the existence of a plateau in the region of 0.7-1.1 ρ(c), where the local density augmentation exhibits the maximum value. The reorientational dynamics of the C═C bond vector have been also studied, exhibiting significant differences between the two isomers in the case of the second-order Legendre time correlation functions.
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In this paper we describe the development of a code that implements a coarse grained dynamics for the large<br> scale modeleling of 3 dimensional athermal yielding and flow of disordered systems under externally applied<br>... more
In this paper we describe the development of a code that implements a coarse grained dynamics for the large<br> scale modeleling of 3 dimensional athermal yielding and flow of disordered systems under externally applied<br> steady shear. The stochastic lattice model for the heterogeneous flow response involves long range elastic<br> interactions, that are resolved using fast Fourier techniques, implemented in parallel in an efficient and well<br> scaling MPI algorithm.
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The work produced within this task is an extension of the UEABS (Unified European Applications Benchmark Suite) for accelerators. As a first version of the extension, this document will present a full definition of a suite for... more
The work produced within this task is an extension of the UEABS (Unified European Applications Benchmark Suite) for accelerators. As a first version of the extension, this document will present a full definition of a suite for accelerators. This will cover each code, presenting the code in itself as well as the test cases defined for the benchmarks and the problems that could occur during the next months. As the UEABS, this suite aims to present results for many scientific fields that can use HPC accelerated resources. Hence, it will help the European scientific communities to make a decision in terms of infrastructures they could buy in a near future. We focus on Intel Xeon Phi coprocessors and NVidia GPU cards for benchmarking as they are the two most important accelerated resources available at the moment. The following table lists the codes that will be presented in the next sections as well as their implementations available. It should be noted that OpenMP can be used with the ...
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Summary ChemBioServer 2.0 is the advanced sequel of a web server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse... more
Summary ChemBioServer 2.0 is the advanced sequel of a web server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a refere...
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ChemBioServer 2.0 is the advanced sequel of a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and... more
ChemBioServer 2.0 is the advanced sequel of a web-server for filtering, clustering and networking of chemical compound libraries facilitating both drug discovery and repurposing. It provides researchers the ability to (i) browse and visualize compounds along with their physicochemical and toxicity properties, (ii) perform property-based filtering of chemical compounds, (iii) explore compound libraries for lead optimization based on perfect match substructure search, (iv) re-rank virtual screening results to achieve selectivity for a protein of interest against different protein members of the same family, selecting only those compounds that score high for the protein of interest, (v) perform clustering among the compounds based on their physicochemical properties providing representative compounds for each cluster, (vi) construct and visualize a structural similarity network of compounds providing a set of network analysis metrics, (vii) combine a given set of compounds with a refer...
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Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug... more
Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of sufficiently high quality are available.
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Force fields for Sulfur Hexafluoride (SF6) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve... more
Force fields for Sulfur Hexafluoride (SF6) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve as well as supercritical states. Experimental data include numerous PVT state points, corresponding structural properties in terms of radial distribution functions, diffusion coefficient and shear viscosity. The existing force fields were extensively examined in the framework of molecular dynamics simulations and it is found that they do not accurately reproduce the macroscopic properties of the fluid, especially at high densities. To overcome this problem with the aim to obtain improved potential parameters that better reproduce experimental data, a multi-variable optimization of the force field parameters procedure has been systematically applied based on the “Simplex” method. Finally, it is found that for some common functional forms of these force fields, the new optimized parameters predict better the experimental properties of SF6 under investigation compared to the original ones.
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The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local... more
The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.
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ABSTRACT The intermolecular interactions of the catalyst tris(1,2-ethylenedithiolate-S,S′)tungsten, W(S2C2H2)3, with the molecules of a 25:75 water–acetone mixed solvent, are examined by statistical mechanical methods, and specifically by... more
ABSTRACT The intermolecular interactions of the catalyst tris(1,2-ethylenedithiolate-S,S′)tungsten, W(S2C2H2)3, with the molecules of a 25:75 water–acetone mixed solvent, are examined by statistical mechanical methods, and specifically by a molecular dynamics (MD) technique, using charge distributions obtained by extended Hückel calculations. The results are presented in the form of pair correlation functions (PCF), and show that an average of up to three water molecules come close to the sites of the catalyst, whereas the acetone molecules form an open cage at a somewhat longer distance. The supramolecular structure around the catalyst is asymmetric, and is examined in the two characteristic geometries corresponding to the D3h and C2v symmetries which the ‘tris(dithiolene)’ molecule transiently assumes during its fluxional metamorphoses in solution. At large distance (large values of the correlation parameter r) the system is homogeneous. Yet, at nanometer distances the symmetry breaks down, and the system becomes highly asymmetric with differentiation (selectivity) in space. The mobility of the water and acetone molecules, close to the catalyst, was also studied by estimating the translational self-diffusion coefficients Dwat and Dacet from the center of mass linear velocity correlation functions. The results show that the water molecules are more mobile than the acetone molecules, which is the opposite of what happens without the catalyst.
The development of new effective intermolecular potential models of benzene and hexafluororbenzene, capable in reproducing the thermodynamic and structural properties of molecular systems in a wide range of thermodynamic state points has... more
The development of new effective intermolecular potential models of benzene and hexafluororbenzene, capable in reproducing the thermodynamic and structural properties of molecular systems in a wide range of thermodynamic state points has been presented and discussed. Subsequently, the properties of the fluids have been investigated by employing molecular dynamics and Monte Carlo simulation techniques. The main purpose of this study
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The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD)... more
The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD) simulation techniques. The simulations were performed at state points along an isotherm close to the critical temperature of each system (T(r) = T/T(c) = 1.03). The molecular fluids under study have been chosen on the basis of the electrostatic character of their intermolecular interactions as follows: monatomic, dipolar and hydrogen bonding (HB), quadrupolar, and octupolar. In the case of dipolar scfs, their HB nature when present was systematically explored and related to the behavior of the created local density inhomogeneities at all densities. The results obtained reveal strong influence of the dipolar and HB interactions of the investigated systems upon the local density augmentation. We found that this effect is fairly larger in the case of the dipolar and HB fluids (H2O, CH3OH, and NH3) compared to those for the non-dipolar ones (Xe, CH4, CO2, and N2). In the case of sc CO2, the dependence of the local density augmentation on the bulk density is in agreement with available experimental data as also reported previously. The estimated average number of hydrogen bonds per molecule (nHB) in these HB fluids shows an analogue nonlinear trend compared to the behavior of the average coordination numbers Nco(rho) of a particle with bulk density. The local density dynamics of the first and second solvation shell of each fluid were further analyzed and related to our previously proposed [Skarmoutsos, I.; Samios, J. J. Chem. Phys. 2007, 126, 044503] different time-scale relaxation mechanisms. Finally, the effect of the different strength of the molecular interactions corresponding to these fluids upon the local density dynamics has also been revealed in the behavior of the predicted appropriate time correlation functions and their corresponding correlation times.
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ABSTRACT The intermolecular interactions of the catalyst tris(1,2-ethylenedithiolate-S,S′)tungsten, W(S2C2H2)3, with the molecules of a 25:75 water–acetone mixed solvent, are examined by statistical mechanical methods, and specifically by... more
ABSTRACT The intermolecular interactions of the catalyst tris(1,2-ethylenedithiolate-S,S′)tungsten, W(S2C2H2)3, with the molecules of a 25:75 water–acetone mixed solvent, are examined by statistical mechanical methods, and specifically by a molecular dynamics (MD) technique, using charge distributions obtained by extended Hückel calculations. The results are presented in the form of pair correlation functions (PCF), and show that an average of up to three water molecules come close to the sites of the catalyst, whereas the acetone molecules form an open cage at a somewhat longer distance. The supramolecular structure around the catalyst is asymmetric, and is examined in the two characteristic geometries corresponding to the D3h and C2v symmetries which the ‘tris(dithiolene)’ molecule transiently assumes during its fluxional metamorphoses in solution. At large distance (large values of the correlation parameter r) the system is homogeneous. Yet, at nanometer distances the symmetry breaks down, and the system becomes highly asymmetric with differentiation (selectivity) in space. The mobility of the water and acetone molecules, close to the catalyst, was also studied by estimating the translational self-diffusion coefficients Dwat and Dacet from the center of mass linear velocity correlation functions. The results show that the water molecules are more mobile than the acetone molecules, which is the opposite of what happens without the catalyst.
The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD)... more
The effect of intermolecular interactions of different strength on the local density inhomogeneities in pure supercritical fluids (scfs), with different intramolecular structure, was investigated by employing molecular dynamics (MD) simulation techniques. The simulations were performed at state points along an isotherm close to the critical temperature of each system (T(r) = T/T(c) = 1.03). The molecular fluids under study have been chosen on the basis of the electrostatic character of their intermolecular interactions as follows: monatomic, dipolar and hydrogen bonding (HB), quadrupolar, and octupolar. In the case of dipolar scfs, their HB nature when present was systematically explored and related to the behavior of the created local density inhomogeneities at all densities. The results obtained reveal strong influence of the dipolar and HB interactions of the investigated systems upon the local density augmentation. We found that this effect is fairly larger in the case of the dipolar and HB fluids (H2O, CH3OH, and NH3) compared to those for the non-dipolar ones (Xe, CH4, CO2, and N2). In the case of sc CO2, the dependence of the local density augmentation on the bulk density is in agreement with available experimental data as also reported previously. The estimated average number of hydrogen bonds per molecule (nHB) in these HB fluids shows an analogue nonlinear trend compared to the behavior of the average coordination numbers Nco(rho) of a particle with bulk density. The local density dynamics of the first and second solvation shell of each fluid were further analyzed and related to our previously proposed [Skarmoutsos, I.; Samios, J. J. Chem. Phys. 2007, 126, 044503] different time-scale relaxation mechanisms. Finally, the effect of the different strength of the molecular interactions corresponding to these fluids upon the local density dynamics has also been revealed in the behavior of the predicted appropriate time correlation functions and their corresponding correlation times.
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Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for... more
Molecular dynamics simulation techniques have been employed to investigate the solvation structure and dynamics in dilute mixtures of cis- and trans-1,2-dichloroethene in supercritical carbon dioxide. The calculations were performed for state points along a near-critical isotherm (1.02 T(c)) over a wide range of densities, using new developed optimized potential models for both isomers. The similarities and differences in the solvation structures around each isomer have been presented and discussed. The local density augmentation and enhancement factors of CO(2) around the isomers have been found significantly larger than the corresponding values for pure supercritical CO(2). The dynamic local density reorganization has been investigated and related to previously proposed relaxation mechanisms. The density dependence of the calculated self-diffusion coefficients has revealed the existence of a plateau in the region of 0.7-1.1 ρ(c), where the local density augmentation exhibits the maximum value. The reorientational dynamics of the C═C bond vector have been also studied, exhibiting significant differences between the two isomers in the case of the second-order Legendre time correlation functions.
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Structure-activity relationship studies, regarding the influence of side chains of phosphinic pseudotripeptidic inhibitors on matrix metalloproteinases (MMPs), provided potent and selective inhibitors for this family of structurally and... more
Structure-activity relationship studies, regarding the influence of side chains of phosphinic pseudotripeptidic inhibitors on matrix metalloproteinases (MMPs), provided potent and selective inhibitors for this family of structurally and functionally related proteases. Among them, phosphinic pseudopeptide CbzPhepsi[P(O)(OH)CH(2)] phenylpropyl TrpNH(2), known as RXP03, has been extensively used for in vivo and in vitro studies so far. The large quantities of RXP03 required for in vivo studies, as well as the necessity for diastereoisomeric purity, motivated us to further explore and develop an efficient synthetic methodology, which allows separation of the four diastereoisomers of RXP03 based on the astonishing observed differences in solubility of the four isomers in various solvents. This fact prompted us to examine theoretically the conformational differences of these four isomers via computer simulations in the solvents used experimentally. Given the fact that the four examined diastereoisomeric forms of the phosphinic peptides exhibit different behavior in terms of potency and selectivity profiles toward zinc-metalloproteases, this theoretical study provides valuable information on the conformation of phosphinic inhibitors and therefore improves the design and synthesis of active structures. The differences in solubility of RXP03 diastereoisomers in the used solvents were examined in terms of intra- and intermolecular structure. It is found that the different solubility of the RRS and RSS diastereoisomers in EtOH is a result of the different number of hydrogen bonds formed by each isomer with EtOH molecules. In the case of SRS and SSS in Et(2)O, their different solubility might be attributed to the different intramolecular hydrogen bonds formed on these diastereoisomers.
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The development of new effective intermolecular potential models of benzene and hexafluororbenzene, capable in reproducing the thermodynamic and structural properties of molecular systems in a wide range of thermodynamic state points has... more
The development of new effective intermolecular potential models of benzene and hexafluororbenzene, capable in reproducing the thermodynamic and structural properties of molecular systems in a wide range of thermodynamic state points has been presented and discussed. Subsequently, the properties of the fluids have been investigated by employing molecular dynamics and Monte Carlo simulation techniques. The main purpose of this study
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ABSTRACT We report a study of the intermolecular structure and translational diffusion of Carbonyl Sulphide (OCS) dissolved in Ne and Kr, using Molecular Dynamics (MD) simulation. The mixtures have been investigated at different... more
ABSTRACT We report a study of the intermolecular structure and translational diffusion of Carbonyl Sulphide (OCS) dissolved in Ne and Kr, using Molecular Dynamics (MD) simulation. The mixtures have been investigated at different thermodynamic points corresponding to the pressures between 5 and 300 bar and at temperature of 293 K. The computations were carried out with effective site-site Lennard-Jones (LJ) potential model. We found that the proposed model predicts a non-linear T-shaped dimer structure of Ne-OCS and Kr-OCS in accordance with experiment. The study of the local structure of the solute-solvents was based upon the calculated relevant pair distribution functions. The self-diffusion coefficients of both components in the mixtures were calculated and compared. The results show a non-linear dependence in the density range under study. In the case of Kr as solvent and at the whole density range under study, the diffusion coefficient of Kr appears to be larger than that of OCS. This unusual result on the solute-solvent diffusivities (mOCS &lt; mKr, DOCS &lt; DKr) has been further discussed in terms of the microscopic dynamics of the species.
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The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local... more
The supercritical mixture ethanol-carbon dioxide (EtOH-CO2) with mole fraction of ethanol X(EtOH) congruent with 0.1 was investigated at 348 K, by employing the molecular dynamics simulation technique in the canonical ensemble. The local intermolecular structure of the fluid was studied in terms of the calculated appropriate pair radial distribution functions. The estimated average local coordination numbers and mole fractions around the species in the mixture reveal the existence of local composition enhancement of ethanol around the ethanol molecules. This finding indicates the nonideal mixing behavior of the mixture due to the existence of aggregation between the ethanol molecules. Furthermore, the local environment redistribution dynamics have been explored by analyzing the time correlation functions (TCFs) of the total local coordination number (solvent, cosolvent) around the cosolvent molecules in appropriate parts. The analysis of these total TCFs in the auto-(solvent-solvent, cosolvent-cosolvent) and cross-(solvent-cosolvent, cosolvent-solvent) TCFs has shown that the time dependent redistribution process of the first solvation shell of ethanol is mainly determined by the redistribution of the CO2 solvent molecules. These results might be explained on the basis of the CO2-CO2 and EtOH-CO2 intermolecular forces, which are sufficiently weaker in comparison to the EtOH-EtOH hydrogen bonding interactions, creating in this way a significantly faster redistribution of the CO2 molecules in comparison with EtOH. Finally, the self-diffusion coefficients and the single reorientational dynamics of both the cosolvent and solvent species in the mixture have been predicted and discussed in relationship with the local environment around the species, which in the case of the EtOH molecules seem to be strongly affected.
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Force fields for Sulfur Hexafluoride (SF6) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve... more
Force fields for Sulfur Hexafluoride (SF6) from the literature, were investigated by means of their ability to reproduce experimental data in a wide range of thermodynamic conditions, including liquid, gas, vapor–liquid coexistence curve as well as supercritical states. Experimental data include numerous PVT state points, corresponding structural properties in terms of radial distribution functions, diffusion coefficient and shear viscosity. The existing force fields were extensively examined in the framework of molecular dynamics simulations and it is found that they do not accurately reproduce the macroscopic properties of the fluid, especially at high densities. To overcome this problem with the aim to obtain improved potential parameters that better reproduce experimental data, a multi-variable optimization of the force field parameters procedure has been systematically applied based on the “Simplex” method. Finally, it is found that for some common functional forms of these force fields, the new optimized parameters predict better the experimental properties of SF6 under investigation compared to the original ones.
Research Interests:
The influences of an elevated temperature on the structure and dynamics of the Jahn-Teller distorted [Cr(H(2)O)(6)](2+) complex have been studied using an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics... more
The influences of an elevated temperature on the structure and dynamics of the Jahn-Teller distorted [Cr(H(2)O)(6)](2+) complex have been studied using an ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics simulation, showing that the increased temperature affects the lifetime distortions of the hydrated Cr(2+) ion by decreasing the inversion time to 0.5-2 ps.