Molecular Simulation

Four common pure fluids were chosen to elucidate the reliability of reactive force fields in estimating bulk properties of selected molecular systems: CH4, H2O, CO2 and H2. The pure fluids are not expected to undergo chemical reactions at the conditions chosen for these simulations. The 'combustion' ReaxFF was chosen as reactive force field. In the case of water, we also considered the 'aqueous' ReaxFF model. The results were compared to data obtained implementing popular classic force fields. In the gas phase it was found that simulations conducted using the 'combustion' ReaxFF formalism yield structural properties in reasonable good agreement with classic simulations for CO2 and H2, but not for CH4 and H2O. In the liquid phase 'combustion' ReaxFF simulations reproduce reasonably well the structure obtained from classic simulations for CH4, degrade for CO2 and H2, and are rather poor for H2O. In the gas phase the simulation results are compared to experimental second virial coefficient data. The 'combustion' ReaxFF simulations yield second virial coefficients that are not sufficiently negative for both CH4 and CO2, and slightly too negative for H2. The 'combustion' ReaxFF parameterization induces too strong an effective attraction between water molecules, while the 'aqueous' ReaxFF yields a second virial coefficient for water that is in reasonable agreement with experiments. The 'combustion' ReaxFF parameterization yields acceptable self-diffusion coefficients for gas-phase properties of CH4, CO2 and H2. In the liquid phase the results are good for CO2, while the self-diffusion coefficient predicted for liquid CH4 is slower, and that predicted for liquid H2 is about 9 times faster than those expected based on classic simulations. The 'aqueous' ReaxFF parameterization yields good results for both the structure and the diffusion of both bulk liquid and bulk vapour water.

An accurate gravimetric method was used to explore water adsorption/desorption isotherms between 105 and to 250°C for a number of synthetic and natural porous solids including controlled pore glass, activated carbon fiber monoliths, natural zeolites, pillared clay, and geothermal reservoir rocks. The main goal of this work was to evaluate water adsorption results, in particular temperature dependence of hysteresis, for relatively uniform, nano-structured solids, in the context of other state-of-the-art experimental and modeling methods including nitrogen adsorption, spectroscopy, neutron scattering, and molecular simulation. Since no single method is able to provide a complete characterization of porous materials, a combination of approaches is needed to achieve progress in understanding the fluid-solid interactions on the way to developing a predictive capability.

Quantum mechanical, molecular mechanics and molecular dynamics (MD) methods were used to investigate initial steps of 2 0 -deoxyuridine-5 0 -monophosphate (dUMP) methylation catalysed by the thymidylate synthase (TS) enzyme. The amino acid residues surrounding the active site within a 10 A ˚radius sphere were modelled with the combined quantum mechanical (B3LYP/LANL2DZ) and molecular mechanics ONIOM double-layer method. The results indicated the initial nucleophilic attack of Cys146 on dUMP to be concerted with formation of a hydrogen bond to the oxygen O4 of dUMP. Moreover, the proton in the vicinity of the O4 atom appears to act as a 'proton switch': if a proton is present near O4, it stabilises the S(Cys146)ZC6(dUMP) sulphur-carbon bond, but if it is absent, the sulphur-carbon bond does not form. If the O4 oxygen is replaced by sulphur atom, the 'switch effect' does not occur. The suggested correlation between the strength of hydrogen bond involving O4 oxygen and the ability of dUMP to form bonds at C6 corresponds well to the crystal structures of TS complexes available in the Protein Data Bank. In the vast majority of crystal structures, the presence of the S(Cys146)ZC6(dUMP) bond was coupled with the presence of hydrogen bond between the dUMP O4 atom and the conserved Asn177. The 'proton switch' hypothesis is supported also by the results of MD studies of TS binary complexes, suggesting that average distance separating S(Cys146) and C6(dUMP) becomes distinctly shorter in the presence of hydrogen bonding between Asn177 and O4.

Quantum mechanical, molecular mechanics and molecular dynamics (MD) methods were used to investigate initial steps of 2 0 -deoxyuridine-5 0 -monophosphate (dUMP) methylation catalysed by the thymidylate synthase (TS) enzyme. The amino acid residues surrounding the active site within a 10 A ˚radius sphere were modelled with the combined quantum mechanical (B3LYP/LANL2DZ) and molecular mechanics ONIOM double-layer method. The results indicated the initial nucleophilic attack of Cys146 on dUMP to be concerted with formation of a hydrogen bond to the oxygen O4 of dUMP. Moreover, the proton in the vicinity of the O4 atom appears to act as a 'proton switch': if a proton is present near O4, it stabilises the S(Cys146)ZC6(dUMP) sulphur-carbon bond, but if it is absent, the sulphur-carbon bond does not form. If the O4 oxygen is replaced by sulphur atom, the 'switch effect' does not occur. The suggested correlation between the strength of hydrogen bond involving O4 oxygen and the ability of dUMP to form bonds at C6 corresponds well to the crystal structures of TS complexes available in the Protein Data Bank. In the vast majority of crystal structures, the presence of the S(Cys146)ZC6(dUMP) bond was coupled with the presence of hydrogen bond between the dUMP O4 atom and the conserved Asn177. The 'proton switch' hypothesis is supported also by the results of MD studies of TS binary complexes, suggesting that average distance separating S(Cys146) and C6(dUMP) becomes distinctly shorter in the presence of hydrogen bonding between Asn177 and O4.

The effects of the electric field on the vapor-liquid equilibria of methanol and ethanol confined in a graphitic slit pore of width 4 nm using molecular dynamics simulations are reported. The vapor-liquid critical temperature of methanol gets suppressed under confinement. The external electrical field further decreases the critical temperature with increasing electric field strength up to E = 1.5 V•nm -1 . Surprisingly, a further increase in the electric field strength reverses the critical temperature behavior and is seen to increase with increasing electric field. The reversible behavior of the critical temperature with the electric field is also seen for nanoconfined ethanol at approximately 1.5 V•nm -1 . The critical density, on the other hand, is found to continuously decrease with increasing electric field strength. Application of an external electric field results in the decrease in vapor and liquid densities. The coordination number in the liquid phase is found to decrease first with increasing electric field until E = 1.5 V•nm -1 and then increases with a further increase in the electric field, confirming the observed trend in the critical temperature according to the mean field theory. Orientational order of nanoconfined methanol and ethanol, on the other hand, is found to increase with increasing electric field.

Multiscale modeling approach is proposed to characterize interfacial behavior of crosslinked epoxy nanocomposites. In this study, crosslinked epoxy composed of epoxy resin EPON 862 and curing agent TETA with varying crosslink densities are considered and silica (SiO2) nanoparticulates having different radii are used as a filler material. The variations of interfacial characteristics are investigated using molecular dynamics (MD) and molecular mechanics (MM) simulations. The reduction of interfacial adhesion with increasing crosslinking is observed which is attributed to the changes of nonbond interaction characteristics between the filler and epoxy chains. The continuum model based on micromechanics regime is introduced to reflect the interfacial behavior depending on crosslinking densities and embedded filler sizes.

Processes using supercritical fluids constitute another special separation process option other than the membrane processes which have been presented in one of the previous issues as alternative to conventional separation processes. Separation processes that ...

A peptide mimotope of the CD52 antigen with the sequence T 1 SSPSAD 7 has been co-crystallised with the CAMPATH-1H antibody. Molecular dynamics (MD) simulations in explicit water of the T 1 SSPSAD 7 peptide in both antibody free and bound states showed that the peptide's b-turn remained stable in the bound state but it was eliminated in the free state. Based on the observation that Thr 1 and Ala 6 residues made close contacts through their side chain, a new peptide mimotope is proposed: (S,S)-C 1 SSPSCD 7 . Thr 1 and Ala 6 residues have been mutated in Cys residues and a disulphide bond has been imposed. The new analogue has been simulated in both antibody bound and free states with MD in explicit water. It was found that the peptide remained in the stable b-turn conformation, both in complexed and free states. The difference in configurational entropy was estimated to be 0.15 kJ/K/mol. However, despite the structural similarity, the cyclic analogue lost more than 25% of its buried surface area contact with the antibody and a couple of critical hydrogen bond interactions were broken. It is concluded that design of cyclic analogues that mimic the bound conformation of peptides should be carefully performed and conformational 'freezing' does not necessarily guarantee better binding.

Incorrect folding of proteins in living cells may lead to malfunctioning of the cell machinery. To prevent such cellular disasters from happening, all cells contain molecular chaperones that assist nonnative proteins in folding into the correct native structure. One of the most studied chaperone complexes is the GroEL-GroES complex. The GroEL part has a ''double-barrel'' structure, which consists of two cylindrical chambers joined at the bottom in a symmetrical fashion. The hydrophobic rim of one of the GroEL chambers captures nonnative proteins. The GroES part acts as a lid that temporarily closes the filled chamber during the folding process. Several capture-folding-release cycles are required before the nonnative protein reaches its native state. Here we report molecular simulations that suggest that translocation of the nonnative protein through the equatorial plane of the complex boosts the efficiency of the chaperonin action. If the target protein is correctly folded after translocation, it is released. However, if it is still nonnative, it is likely to remain trapped in the second chamber, which then closes to start a reverse translocation process. This shuttling back and forth continues until the protein is correctly folded. Our model provides a natural explanation for the prevalence of double-barreled chaperonins. Moreover, we argue that internal folding is both more efficient and safer than a scenario where partially refolded proteins escape from the complex before being recaptured.

Liquid crystals are synthetic and biological viscoelastic anisotropic soft matter materials that combine liquid fluidity with crystal anisotropy and find use in optical devices, sensor/actuators, lubrication, super-fibers. Frequently mesogens are mixed with colloidal and nanoparticles, other mesogens, isotropic solvents, thermoplastic polymers, crosslinkable monomers, among others. This comprehensive review present recent progress on meso and macro scale thermodynamic modelling, highlighting the (i) novelties in spinodal and binodal lines in the various phase diagrams, (ii) the growth laws under phase transitions and phase separation, (iii) the ubiquitous role of metastability and its manifestation in complex droplet interfaces, (iv) the various spinodal decompositions due to composition and order fluctuations, (v) the formation of novel material architectures such as colloidal crystals, (vi) the particle rich phase behaviour in liquid crystal nanocomposites, (vii) the use of topological defects to absorb and organize nanoparticles,

We propose a concept for a homogenous computational model in carrying out cross-scale numerical experiments on liquids. The model employs the particle paradigm and comprises three types of simulation techniques: molecular dynamics (MD), dissipative particle dynamics (DPD) and smoothed particle hydrodynamics (SPH). With respect to the definition of the collision operator, this model may work in different hierarchical spatial and time scales as: MD in the atomistic scale, DPD in the mesoscale and SPH in the macroscale. The optimal computational efficiency of the three types of cross-scale experiments are estimated in dependence on: the system size N -where N is the number of particles -and the number of processors P employed for computer simulation. For the three-hierarchical-stage, as embodied in the MD-DPD-SPH model, the efficiency is proportional to N 8/7 but its dependence on P is different for each of the three types of cross-scale experiments. The problem of matching the different scales is discussed.

In the paper we make a short overview of computer models based on particle approach, which can be suitable for the simulation of fluid flow through porous media. We concentrate on Molecular Dynamics (MD) and Dissipative Particle Dynamics (DPD) methods. We describe main features of our simulation programs, and present and discuss preliminary results of MD and DPD simulations of 2D fluid flow through a simple model rigid porous media. The paper aims at the evaluation of the applicability of MD and DPD methods for simulations of liquid flows in media of complicated geometry.

We examine the utility of the virial equation of state (VEOS) for the prediction of the solubility of hexane in supercritical carbon dioxide. We computed virial coefficients up to fourth-order for this mixture at 353.15 K, using Mayer-sampling Monte Carlo applied to established molecular models for carbon dioxide and hexane. At this temperature, neither the third-nor fourth-order VEOS indicate the presence of a critical point for the mixture. However, the VEOS coupled with an ideal-solution treatment for the coexisting subcritical fluid phase (with parameters determined from coexistence data at one pressure) reproduces much of the solubility curve as previously established by Gibbs-ensemble molecular simulation. Comparison of the third-and fourth-order VEOS indicate that the virial treatment is converged at the conditions where it is applied.

Although recent experimental studies have demonstrated that doping of nanoporous carbons with nitrogen is an effective strategy for highly diluted formaldehyde capture, the impact of carbon surface chemistry and the pore size on formaldehyde capture at ~ppm concentrations is still poorly understood and controversial. This work presents a combined theoretical and experimental study on dynamic formaldehyde adsorption on pure and oxidized nanocarbons. We find using Monte Carlo simulations and confirm experimentally that cooperative effects of pore size and oxygen surface chemistry have profound impacts on the breakthrough time of formaldehyde. Molecular modeling of formaldehyde adsorption on pure and oxidized model nanoporous carbons at ~ppm pressures reveals that high adsorption of formaldehyde ppm concentrations in narrow ultramicropores <6 Å decorated with phenolic and carboxylic groups is correlated with long formaldehyde breakthrough times measured in the columns packed with specially prepared oxidized activated carbon fiber adsorbents with the pore size of ~5 Å.

Introduction 495 II. Methods of molecular modelling of proteins 495 III. Molecular modelling of different types of biological receptors 502 { This review completes the series of publications illustrating the main avenues of medicinal chemistry research [see Russ. Chem. Rev. 78 (5) (2009)].

Se analizó la marcha usando datos de posiciones (x, y) de marcadores en cadera, rodilla y tobillo. Se calcularon ángulos articulares para evaluar la movilidad y coordinación del movimiento. La velocidad y aceleración angular se estimaron con diferencias angulares en Python, aplicando un filtro de suavizado. Se graficaron las fases de la marcha, identificando valores extremos y duración de cada paso. Este estudio es clave para evaluar la eficiencia del movimiento y tiene aplicaciones en clínica y rehabilitación.

Ion channels are gated, i.e. they can switch conformation between a closed and an open state. Molecular dynamics simulations may be used to study the conformational dynamics of ion channels and of simple channel models. Simulations on model nanopores reveal that a narrow (&lt;4 Å) hydrophobic region can form a functionally closed gate in the channel and can be opened by either a small (∼1 Å) increase in pore radius or an increase in polarity. Modelling and simulation studies confirm the importance of hydrophobic gating in K channels, and support a model in which hinge‐bending of the pore‐lining M2 (or S6 in Kv channels) helices underlies channel gating. Simulations of a simple outer membrane protein, OmpA, indicate that a gate may also be formed by interactions of charged side chains within a pore, as is also the case in ClC channels.

Despite the complexity of ion-channels, MD simulations based on realistic all-atom models have become a powerful technique for providing accurate descriptions of the structure and dynamics of these systems, complementing and reinforcing experimental work. Successful multidisciplinary collaborations, progress in the experimental determination of three-dimensional structures of membrane proteins together with new algorithms for molecular simulations and the increasing speed and availability of supercomputers, have made possible a considerable progress in this area of biophysics. This review aims at highlighting some of the work in the area of potassium channels and molecular dynamics simulations where numerous fundamental questions about the structure, function, folding and dynamics of these systems remain as yet unresolved challenges.

Interfacial layers of both vapour/liquid and crystal/liquid aqueous solutions of sodium and caesium halides have been analysed in detail using four different methods for the identification of interfacial molecules and layers, and both non-polarisable and polarisable models. It is found that each of the methods yields a somewhat different result with the best mutual agreement found between the ITIM (Identification of Truly Interfacial Molecules) and α-shape-based USTI (Universal Scheme for Triangulated Interfaces) methods. Concerning the water models, the commonly used JC [I. S. Joung, T. E. Cheatham, J. Phys. Chem. 112 ( ) 9020] model predicts the structural properties of the vapor/ liquid interface different from both the non-polarisable MADRID and polarisable AH/BK3 models, and also from experiment. The same applies also to the structural properties of the solid-liquid interface; although the AH/BK3 and JC models yield a surplus of chlorine ions, a segregation of Na + and Cl -ions in the interfacial layers predicted by the JC model is not observed in the polarisable model.

Taylor & Francis makes every effort to ensure the accuracy of all the information (the "Content") contained in the publications on our platform. However, Taylor & Francis, our agents, and our licensors make no representations or warranties whatsoever as to the accuracy, completeness, or suitability for any purpose of the Content. Any opinions and views expressed in this publication are the opinions and views of the authors, and are not the views of or endorsed by Taylor & Francis. The accuracy of the Content should not be relied upon and should be independently verified with primary sources of information. Taylor and Francis shall not be liable for any losses, actions, claims, proceedings, demands, costs, expenses, damages, and other liabilities whatsoever or howsoever caused arising directly or indirectly in connection with, in relation to or arising out of the use of the Content.

An algorithm is developed that finds the optimal orientation of a rigid molecular structure, represented by Nreference sites, with respect to the same number of sites in an observed structure. The optimal orientation is found by minimizing the weighted sum of squared deviations of the rotated reference site positions from the observed site positions. The rotation is parametrized by a quaternion whose components, written as a column vector, are shown to be an eigenvector of a characteristic matrix which is defined in terms of the coordinate sets to be superimposed. The presented algorithm is particularly useful with respect to the calculation of orientational correlations of molecular structures.

An extension of Wertheim’s first-order thermodynamic perturbation theory is proposed to describe the global phase behavior of linear rigid tangent hard sphere chains. The extension is based on a scaling proposed recently by Vega and McBride [Phys. Rev. E 65, 052501 (2002)] for the equation of state of linear chains in the solid phase. We have used the Einstein-crystal methodology, the Rahman–Parrinello technique, and the thermodynamic integration method for calculating the free energy and equation of state of linear rigid hard sphere chains with different chain lengths, including the solid–fluid phase equilibria. Agreement between the simulation data and theoretical predictions is excellent in all cases. Once it is confirmed that the proposed theory can be used to describe correctly the equation of state, free energy, and solid–fluid phase transitions of linear rigid molecules, a simple mean-field approximation at the level of van der Waals is included to account for segment–segment...

Purpose. Cyclodextrins are known to be good solubility enhancers for several drugs, improving bioavailability when incorporated in pharmaceutical formulations. In this work we intend to assess and characterize the formation of inclusion complexes between omeprazole (OME) and a methylated derivative of "-cyclodextrin, methyl-"-cyclodextrin (M"CD). A comparison with results obtained from the most commonly used natural cyclodextrin, "-cyclodextrin ("CD) is also presented in most cases. Materials and Methods. The interaction of OME with the mentioned cyclodextrins in aqueous solutions was studied by phase solubility studies, 1D 1 H and 2D rotating frame nuclear overhauser effect NMR spectroscopy (ROESY) and Molecular Dynamics. Results. The solubility of OME was significantly increased by formation of inclusion complexes with each cyclodextrin. Phase solubility studies and continuous variation plots revealed that OME forms an inclusion complex in a stoichiometry of 1:1 with both cyclodextrins. 1 H NMR and ROESY spectra of the inclusion complexes indicated that the benzimidazole moiety is included within the cyclodextrins cavities. Molecular dynamics showed that OME is more deeply included in the M"CD than in "CD cavity, in agreement with a larger apparent stability constant (K S ) obtained for the inclusion complex with M"CD. Conclusions. M"CD proved to be an efficient enhancer of OME solubility, thus possessing characteristics for being an useful excipient in pharmaceutical formulations of this drug.

We present a 250ns simulation of the wild-type, biotin-liganded streptavidin tetramer in the solution phase and compare the trajectory to two previously published simulations of the protein in its crystal lattice. By performing both types of simulations, we are able to interpret the protein's behavior in solution in the context of its X-ray structure. We find that the rate of conformational sampling is increased in solution over the lattice environment, although the relevant conformational space in solution is also much larger, as indicated by overall fluctuations in the positions of backbone atoms. We also compare the distributions of χ 1 angles sampled by side chains exposed to solvent in the lattice and in the solution phase, obtaining overall good agreement between the distributions obtained in our most rigorous lattice simulation and the crystallographic χ 1 angles. We observe changes in the χ 1 distributions in the solution phase, and note an apparent progression of the distributions as the environment changes from a tightly packed lattice filled with crystallization media to a bath of pure water. Finally, we examine the interaction of biotin and streptavidin in each simulation, uncovering a possible alternate conformation of the biotin carboxylate tail. We also note that a hydrogen bond observed to break transiently in previous solution phase simulations is predominantly broken in this much longer solution phase trajectory; in the lattice simulations, the lattice environment appears to help maintain the hydrogen bond, but more sampling will be needed to confirm whether the simulation model truly gives good agreement with the X-ray data in the lattice simulations. We expect that pairing solution phase biomolecular simulations with crystal lattice simulations will help to validate simulation models and improve the interpretation of experimentally determined structures.

Here, we report the 1.53-Å crystal structure of the enzyme 7-cyano-7-deazaguanine reductase (QueF) from Vibrio cholerae, which is responsible for the complete reduction of a nitrile (C≡N) bond to a primary amine (H 2 C-NH 2 ). At present, this is the only example of a biological pathway that includes reduction of a nitrile bond, establishing QueF as particularly noteworthy. The structure of the QueF monomer resembles two connected ferrodoxin-like domains that assemble into dimers. Ligands identified in the crystal structure suggest the likely binding conformation of the native substrates NADPH and 7-cyano-7-deazaguanine. We also report on a series of numerical simulations that have shed light on the mechanism by which this enzyme affects the transfer of four protons (and electrons) to the 7-cyano-7-deazaguanine substrate. In particular, the simulations suggest that the initial step of the catalytic process is the formation of a covalent adduct with the residue Cys194, in agreement with previous studies. The crystal structure also suggests that two conserved residues (His233 and Asp102) play an important role in the delivery of a fourth proton to the substrate.

The main purpose of this work is to present a free-volume combinatorial term in predicting vapor-liquid equilibrium (VLE) and solid-liquid equilibrium (SLE) of polymer/solvent and light and heavy hydrocarbon/hydrocarbon mixtures. The proposed term is based on a modification of the original Freed Flory-Huggins model, replacing the molar volume with a free-volume (FV) term. Using an extensive database for athermal polymer solutions at finite dilution, the single parameter of the model has been well adjusted. The results obtained from the model proposed in this work were favorably compared with those obtained from the well-established entropic-FV based models, i.e., the original entropic-FV (EFV) and the modified entropic-FV (MEFV) models. The results were also compared with those of the original UNIFAC-FV model as well as a modified UNIFAC-FV model, Kannan-FV, recently proposed model by Kannan et al. The results obtained from the proposed model showed that better improvement can be attained for the polymer systems with energetic interactions as well as for VLE and SLE study of heavy alkane solutes in light alkane solvents. This observation can be further verified by comparison of the results obtained from the proposed model with those of the molecular simulation data.

We present a joint Molecular Dynamics (MD) / Kinetic Monte-Carlo (KMC) study aiming at the atomistic description of charge transport in stacks of liquid-crystalline tetra alkoxy-substituted metal-free phthalocyanines. The molecular dynamics simulations reproduce the major structural features of the mesophases, in particular a phase transition around 340 K between the rectangular and hexagonal phases. Charge transport simulations based on a Monte-Carlo algorithm show an increase by two orders of magnitude in the hole mobility when accounting for the rotational and translational dynamics. The results point to the formation of dynamical structural defects along the columns.

The success of process design in chemical engineering and energy technology depends on the availability and accuracy of thermodynamic properties. In recent years, molecular modeling and simulation has become a promising tool to accurately predict thermodynamic properties of fluids. Thermodynamic data can accurately be predicted with molecular models that are based on quantum chemical calculations and are optimized to vapor-liquid equilibrium (VLE) data only. This approach is applied to ammonia here, studying a wide range of properties and thermodynamic conditions. In addition to static properties, the self-diffusion coefficient, shear viscosity and the thermal conductivity are determined. The employed molecular model is based on one Lennard-Jones site and four point charges. Furthermore, the influence of the intramolecular degrees of freedom on the VLE is studied, showing that angle bending plays an unexpectedly large role in the liquid state, because of a significantly enhanced dip...

Density, self-diffusion coefficient, and shear viscosity of pure liquid water are predicted for temperatures between 280 and 373 K by molecular dynamics simulation and the Green–Kubo method. Four different rigid nonpolarizable water models are assessed: SPC, SPC/E, TIP4P, and TIP4P/2005. The pressure dependence of the self-diffusion coefficient and the shear viscosity for pure liquid water is also calculated and the anomalous behavior of these properties is qualitatively well predicted. Furthermore, transport properties as well as excess volume and excess enthalpy of aqueous binary mixtures containing methanol or ethanol, based on the SPC/E and TIP4P/2005 water models, are calculated. Under the tested conditions, the TIP4P/2005 model gives the best quantitative and qualitative agreement with experiments for the regarded transport properties. The deviations from experimental data are of 5% to 15% for pure liquid water and 5% to 20% for the water + alcohol mixtures. Moreover, the cent...

The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood-Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the inverse of the size of these subvolumes, estimates for KB integrals in the thermodynamic limit are obtained. Two system size effects are observed in MD simulations: (1) effects due to the size of the simulation box and the size of the finite subvolume embedded in the simulation box, and (2) effects due to computing radial distribution functions (RDF) from a closed and finite system. In this study, we investigate the two effects in detail by computing KB integrals using the following methods: (1) Monte Carlo simulations of finite subvolumes of a liquid with an analytic RDF and (2) MD simulations of a WCA mixture for various simulation box sizes, but at the same thermodynamic state. We investigate the effect of the size of the simulation box and quantify the differences compared to KB integrals computed in the thermodynamic limit. We demonstrate that calculations of KB integrals should not be extended beyond half the size of the simulation box. For finite-size effects related to the RDF, we find that the Van der Vegt correction (J Chem Theory Comput. 2013;9:1347) yields the most accurate results.

We study the dissociation of hydrogen from molecule to atoms and show how we can compute thermodynamic and transport properties of both species in a mixture under non-ideal conditions. The small system method can be used to sample fluctuations of a few atoms or molecules in a small volume element, and gives fast access to accurate thermodynamic data of mixtures that are non-ideal. From the results of equilibrium and non-equilibrium molecular dynamics simulations of the dissociation of hydrogen in a thermal field, we compute coefficients for transport of heat and mass for the gas mixture (0.0052 g cm -3 ) at average temperature 10400 K. We show that the interdiffusion coefficient, the thermal conductivity and the Dufour effect are significantly affected by the presence of the reaction.

The modelling of thermodynamic properties of liquids from local density fluctuations is relevant to many chemical and biological processes. The Kirkwood-Buff (KB) theory connects the microscopic structure of isotropic liquids with macroscopic properties such as partial derivatives of activity coefficients, partial molar volumes and compressibilities. Originally, KB integrals were formulated for open and infinite systems which are difficult to access with standard Molecular Dynamics (MD) simulations. Recently, KB integrals for finite and open systems were formulated (J Phys Chem Lett. 2013;4:235). From the scaling of KB integrals for finite subvolumes, embedded in larger reservoirs, with the inverse of the size of these subvolumes, estimates for KB integrals in the thermodynamic limit are obtained. Two system size effects are observed in MD simulations: (1) effects due to the size of the simulation box and the size of the finite subvolume embedded in the simulation box, and (2) effects due to computing radial distribution functions (RDF) from a closed and finite system. In this study, we investigate the two effects in detail by computing KB integrals using the following methods: (1) Monte Carlo simulations of finite subvolumes of a liquid with an analytic RDF and (2) MD simulations of a WCA mixture for various simulation box sizes, but at the same thermodynamic state. We investigate the effect of the size of the simulation box and quantify the differences compared to KB integrals computed in the thermodynamic limit. We demonstrate that calculations of KB integrals should not be extended beyond half the size of the simulation box. For finite-size effects related to the RDF, we find that the Van der Vegt correction (J Chem Theory Comput. 2013;9:1347) yields the most accurate results.

We study the dissociation of hydrogen from molecule to atoms and show how we can compute thermodynamic and transport properties of both species in a mixture under non-ideal conditions. The small system method can be used to sample fluctuations of a few atoms or molecules in a small volume element, and gives fast access to accurate thermodynamic data of mixtures that are non-ideal. From the results of equilibrium and non-equilibrium molecular dynamics simulations of the dissociation of hydrogen in a thermal field, we compute coefficients for transport of heat and mass for the gas mixture (0.0052 g cm -3 ) at average temperature 10400 K. We show that the interdiffusion coefficient, the thermal conductivity and the Dufour effect are significantly affected by the presence of the reaction.

In this study, the adsorption capacity of single-wall carbon nanotubes (SWCNTs) bundles with regard to the pure CH 4 , N 2 , CO and CO 2 gases at 298 K and pressure range from 0.01 up to 2.0 MPa has been investigated experimentally and computationally. Experimental work refers to gravimetric surface excess adsorption measurements of each gas studied in this nanomaterial. Commercial samples of pristine SWC-NTs, systematically prepared and characterized at first, were used for the evaluation of their adsorption capacity. A Langmuir type equation was adopted to estimate the total adsorption isotherm based on the experimental surface excess adsorption data for each system studied. Computational work refers to Monte Carlo (MC) simulation of each adsorbed gas on a SWCNTs model of the type (9, 9) in the grand canonical (GC) ensemble at the same conditions with experiment using Scienomics' MAPS platform software simulation packages such as Towhee. The GCMC simulation technique was employed to obtain the uptake wt% of each adsorbed gas by considering a SWCNTs model of arrays with parallel tubes exhibiting open-ended cylindrical structures as in experiment. Both experimental and simulation adsorption data concerning these gases within the examined carbon material are presented and discussed in terms of the adsorbate fluid molecular characteristics and corresponding interactions among adsorbate species and adsorbent material. The adsorption isotherms obtained exhibited type I (Langmuir) behavior, providing enhanced gas-substrate interactions. We found that both the experimental as well as the simulated adsorption uptake of the examined SWCNTs at these conditions with regard to the aforementioned fluids and in comparison with adsorbate H 2 on the same material increase similarly and in the following order: H 2 N 2 ≈ CH 4 < CO CO 2 . Furthermore, for each adsorbate fluid the calculations exhibit somewhat greater gas uptake with pressure compared to the corresponding experiment. The difference in the absolute uptake values between experiment and simulation has been discussed and ascribed to the following implicit factors: (i) to the employed model calculations, (ii) to the remained carbonaceous impurities in the sample, and (iii) to a proportion of close ended tubes, contained in the experimental sample even after preparation.

A novel multibinding species has been obtained by attaching four aliphatic polyamine chains to an iron(II)-polyimine centre, derived from 2,6-diacetylpyridine. Molecular simulations for the complex corroborate the evidence from 1H NMR spectroscopy of a symmetric structure, with the four polyamines displaying a tetrahedral arrangement around the metal centre. The protonated polyamine complex interacts with hexacyanoferrate(II) ions, leading to an inclusion compound which has been characterized based on vibrational and Mössbauer spectroscopy, and on cyclic voltammetry.

Defect production and amorphization due to energetic uranium recoils in zircon (ZrSiO 4 ), which is a promising ceramic nuclear waste form, is studied using molecular dynamics simulations with a partial charge model. An algorithm that distinguishes between undamaged crystal, crystalline defects and amorphous regions is used to develop a fundamental understanding of the primary damage state. The damage consists of under-coordinated Zr and polymerised Si leading to amorphization and phase separation on a nanometer scale into Zr-and Si-rich regions. This separation could play an important role in the experimentally observed formation of nanoscale ZrO 2 in ZrSiO 4 irradiated at elevated temperatures. The observed amorphisation and the associated volume expansion have the potential to enhance leaching of cations by providing diffusion pathways for cations and water molecules.

We performed all-atom molecular dynamics simulations for bulk cyclohexane and analysed the short-and medium-range structures in supercooled and glassy states by using the Voronoi tessellation technique. From the analyses of both the potential energy of the system and the radial distribution function of molecules, cyclohexane was found to be vitrified as the temperature decreased. Furthermore, the icosahedral-like structures are dominant at all temperatures and grow in a supercooled liquid, whereas the face-centred cubic structures do not grow when the temperature decreases. It was also ascertained that the icosahedral-like structure is more dominant than the full-icosahedral one. The network of the distorted icosahedron spreads throughout the system at low temperatures. Our simulation demonstrates the stability of the icosahedral structure even in a non-spherical molecule such as cyclohexane.

Nucleation of vanillin (VAN) in 2-propanol/water in the presence of additives, viz., acetovanillone (AVA), ethyl vanillin (EVA), guaiacol (GUA), guaethol (GUE), 4-hydroxyacetophenone (HAP), 4-hydroxybenzaldehyde (HBA), and vanillic acid (VAC) is investigated experimentally and by molecular simulations. In the experimental work, the induction time for nucleation is measured at different temperatures and levels of supersaturation using a multicell apparatus. A large variation in the experimental data is observed, and this variation is analyzed by statistical methods. By classical nucleation theory, the induction time data are used to estimate the solid-liquid interfacial energy of vanillin for each VAN-additive system. At 1 mol %, the interfacial energy becomes lower in the presence of AVA, EVA, HAP, and VAC, while it becomes higher in the presence of the other additives. As the additive concentration increases from 1 to 10 mol %, the interfacial energy also increases. The interfacial energy ranges from 6.9 to 10.1 mJ m -2 . Molecular modeling, implemented in the program Cerius2, is used to simulate and examine the surface chemistry of the likely crystal growth faces of VAN (i.e., {0 0 1} and {1 0 0}). To evaluate the additivecrystal face interaction energy, two approaches are used: the surface adsorption method and the lattice integration method. Both experimental and molecular simulation results indicate that the additives studied are potential modifiers of the nucleation of VAN. However, a simple and clear relationship between the experimental values of interfacial energy and the calculated interaction energies for the most important crystal faces of VAN cannot be identified. The modeling does not concern the actual nucleation but rather the conditions of a growing surface and are based on several severe simplifications. Obviously, this simplistic approach does not sufficiently capture the influence of additives on the nucleation of vanillin.

Nucleation of vanillin (VAN) in 2-propanol/water in the presence of additives, viz., acetovanillone (AVA), ethyl vanillin (EVA), guaiacol (GUA), guaethol (GUE), 4-hydroxyacetophenone (HAP), 4-hydroxybenzaldehyde (HBA), and vanillic acid (VAC) is investigated experimentally and by molecular simulations. In the experimental work, the induction time for nucleation is measured at different temperatures and levels of supersaturation using a multicell apparatus. A large variation in the experimental data is observed, and this variation is analyzed by statistical methods. By classical nucleation theory, the induction time data are used to estimate the solid-liquid interfacial energy of vanillin for each VAN-additive system. At 1 mol %, the interfacial energy becomes lower in the presence of AVA, EVA, HAP, and VAC, while it becomes higher in the presence of the other additives. As the additive concentration increases from 1 to 10 mol %, the interfacial energy also increases. The interfacial energy ranges from 6.9 to 10.1 mJ m -2 . Molecular modeling, implemented in the program Cerius2, is used to simulate and examine the surface chemistry of the likely crystal growth faces of VAN (i.e., {0 0 1} and {1 0 0}). To evaluate the additivecrystal face interaction energy, two approaches are used: the surface adsorption method and the lattice integration method. Both experimental and molecular simulation results indicate that the additives studied are potential modifiers of the nucleation of VAN. However, a simple and clear relationship between the experimental values of interfacial energy and the calculated interaction energies for the most important crystal faces of VAN cannot be identified. The modeling does not concern the actual nucleation but rather the conditions of a growing surface and are based on several severe simplifications. Obviously, this simplistic approach does not sufficiently capture the influence of additives on the nucleation of vanillin.

With a wide range of applications, from energy and environmental engineering, such as in gas separations and water purification, to biomedical engineering and packaging, glassy polymeric materials remain in the core of novel membrane and state-of the art barrier technologies. This review focuses on molecular simulation methodologies implemented for the study of sorption and diffusion of small molecules in dense glassy polymeric systems. Basic concepts are introduced and systematic methods for the generation of realistic polymer configurations are briefly presented. Challenges related to the long length and time scale phenomena that govern the permeation process in the glassy polymer matrix are described and molecular simulation approaches developed to address the multiscale problem at hand are discussed.

Prokofiev for their time and effort in serving in my dissertation committee. I thank Prof. Maroudas for the opportunity to attend his group meetings which have always been a valuable learning experience. I would like to thank Prof. Prokofiev for his thoughtful criticism that provoked improvements in this work. I would also like to thank group members JoungMo Cho, Tracy Heckler, Jun Wang, Bing Mei and the recent members of the group for their company and help. I am thankful for having met some wonderful colleagues and friends in the department and outside. I am thankful for the company and help during my stay to Tejinder Singh, Mayur Valipa, Anurag Verma, Kedarnath Kolluri, Vivek Tomar, and George Sfyris. I would like to thank Prof. Yannis Kevrekidis who helped refine these ideas and gave useful suggestions and criticism which were invaluable to this work. I would like to acknowledge my thesis advisor Prof. Mountziaris, for being with me in this long journey. His company, always pleasant, also ensured that I kept on in this long journey and his patient attitude always kept me in good spirit. Thank you very much. My parents' love and many sacrifices afforded me this opportunity. I do not think I would ever be able to thank them, but I do hope to give them joy in the future. Thank you very much Amma and Accha.

Prokofiev for their time and effort in serving in my dissertation committee. I thank Prof. Maroudas for the opportunity to attend his group meetings which have always been a valuable learning experience. I would like to thank Prof. Prokofiev for his thoughtful criticism that provoked improvements in this work. I would also like to thank group members JoungMo Cho, Tracy Heckler, Jun Wang, Bing Mei and the recent members of the group for their company and help. I am thankful for having met some wonderful colleagues and friends in the department and outside. I am thankful for the company and help during my stay to Tejinder Singh, Mayur Valipa, Anurag Verma, Kedarnath Kolluri, Vivek Tomar, and George Sfyris. I would like to thank Prof. Yannis Kevrekidis who helped refine these ideas and gave useful suggestions and criticism which were invaluable to this work. I would like to acknowledge my thesis advisor Prof. Mountziaris, for being with me in this long journey. His company, always pleasant, also ensured that I kept on in this long journey and his patient attitude always kept me in good spirit. Thank you very much. My parents' love and many sacrifices afforded me this opportunity. I do not think I would ever be able to thank them, but I do hope to give them joy in the future. Thank you very much Amma and Accha.

Prokofiev for their time and effort in serving in my dissertation committee. I thank Prof. Maroudas for the opportunity to attend his group meetings which have always been a valuable learning experience. I would like to thank Prof. Prokofiev for his thoughtful criticism that provoked improvements in this work. I would also like to thank group members JoungMo Cho, Tracy Heckler, Jun Wang, Bing Mei and the recent members of the group for their company and help. I am thankful for having met some wonderful colleagues and friends in the department and outside. I am thankful for the company and help during my stay to Tejinder Singh, Mayur Valipa, Anurag Verma, Kedarnath Kolluri, Vivek Tomar, and George Sfyris. I would like to thank Prof. Yannis Kevrekidis who helped refine these ideas and gave useful suggestions and criticism which were invaluable to this work. I would like to acknowledge my thesis advisor Prof. Mountziaris, for being with me in this long journey. His company, always pleasant, also ensured that I kept on in this long journey and his patient attitude always kept me in good spirit. Thank you very much. My parents' love and many sacrifices afforded me this opportunity. I do not think I would ever be able to thank them, but I do hope to give them joy in the future. Thank you very much Amma and Accha.

Being HIV-1-PR an essential enzyme in the viral life cycle, its inhibition can control AIDS. Because the folding of single domain proteins, like HIV-1-PR is controlled by local elementary structures (LES, folding units stabilized by strongly interacting, highly conserved amino acids) which have evolved over myriads of generations to recognize and strongly attract each other so as to make the protein fold fast, we suggest a novel type of HIV-1-PR inhibitors which interfere with the folding of the protein: short peptides displaying the same amino acid sequence of that of LES. Theoretical and experimental evidence for the specificity and efficiency of such inhibitors are presented.