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Synthesis of graphene with reduced use of chemical reagents is essential for manufacturing scale-up and to control its structure and properties. In this paper, we report the mechanism for exfoliating graphene from graphite slabs using laser impulse. We set up a molecular dynamics model that accounts for the charge-mediated inter-atomic potential along with the forces from electromagnetic fields of a laser pulse. The role of different laser fluences on the exfoliation process of graphene quantified in terms of the interlayer energy transition, inter-layer displacement jump, and thermal shock propagation in graphene-graphite system. The simulation results confirm the exfoliation of a single layer graphene sheet for the laser power ranging from 100 × 10 − 14 to 2000 × 10 − 14 J/nm2. With an increase of laser fluence from 2000 × 10 − 14 to 4000 × 10 − 14 J/nm2, there is an increase in the graphene yield via the layer-after-layer exfoliation. The bridging bond dynamics between the successive graphene layers govern the exfoliation of the second layer. The results indicate promises for producing chemical-free graphene on a large scale for industrial applications. [ABSTRACT FROM AUTHOR]

The ability to automatically extend and improve molecular force fields to accurately describe an ever wider range of compounds is a key enabler for the application of molecular modelling of chemicals and materials in industry. In this work we have developed a set of tools to process structural data available in well-known databases, to find deficiencies in the force field, and where necessary, automatically fit force- field parameters to on-the-fly calculated quantum data based on Density Functional Theory, supplemented by experimental data. The protocols have been applied to structures from the Maybridge, PoLyInfo and ILThermo databases, covering drug-like molecules, polymers and ionic liquids respectively. We demonstrate that the new version of the force field can type all structures in the extended data set without missing parameters, with a similar high-quality prediction of geometry (bonds, angles, torsions), energy and forces of earlier versions. [ABSTRACT FROM AUTHOR]

Actual CTAB and SB3-12 surfactant force field models fail to reproduce one of the most important thermodynamic property of those molecules, the surface tension. Molecular dynamics simulations were conducted to construct new force fields of the cationic surfactant, Cetyl Trimethyl Ammonium Bromide (CTAB), and the non-ionic, cocoamidopropyl betaine, surfactants using united atom models. By scaling the Lennard Jones parameters, the well depth potential (ε) and the intermolecular distance (σ), we constructed an united atom model of the cationic and the betaine surfactants. The new models were tested with actual experiments reported in the literature. With the correct parameters, surface tensions of both surfactants were calculated at different temperatures and different areas per molecule. Electrostatic properties and micelle structures were also calculated with the new set of parameters and radius of gyrations, i.e. micelle radius, were evaluated showing good affinity with experimental data. The new force fields were proved with two different water models, TIP4P/ε and SPC/E, having good agreement with actual experiments [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations are more frequently being utilised to predict macroscale mechanical properties as a result of atomistic defects. However, the interatomic force field can significantly affect the resulting mechanical properties. While several studies exist which demonstrate the ability of various force fields to predict mechanical properties, the investigation into which is most accurate for the investigation of vacancies is limited. To obtain meaningful predictions of mechanical properties, a clear understanding of force field parameterisation is required. As such, the current study evaluates various many-body force fields to demonstrate the reduction in mechanical properties of iron and iron–chromium due to the presence of vacancies while undergoing room temperature atomistic uniaxial tension. Reduction was normalised in each case with the zero-vacancy elastic modulus, removing the need to predict an accurate nominal elastic modulus. Comparisons were made to experimental data and an empirical model from literature. It was demonstrated that accurate fitting to vacancy formation and migration energy allowed for accurate predictions. In addition, bond-order based force fields showed enhanced predictions regardless of fitting procedure. Overall, these findings highlight the need to understand capabilities and limitations of available force fields, as well as the need for enhanced parameterisation of force fields. [ABSTRACT FROM AUTHOR]

Valence Shell Electron Pair Repulsion (VSEPR) theory, commonly taught in introductory chemistry courses, provides a basis for understanding the molecular structures of molecules of the type XY , where X is a central atom surrounded by m Y ligands. While VSEPR is generally thought of only as a qualitative theory, Bartell and coworkers constructed a semi-quantitative model potential to address the physical underpinnings of VSEPR by introducing a points-on-a-sphere (POS) potential such that all X-Y bonds are of fixed length and all atoms Y repel each other. More than forty years ago, this simple model was shown to be effective in reproducing relative quadratic and cubic bending force constants for a variety of binary XY compounds when compared to values computed with semi-empirical and fairly primitive methods. The work presented here endeavours to go beyond the model used in the early investigations by Bartell and coworkers. Specifically, stretching force constants are clearly omitted from any POS model with a fixed radius, and are (primitively) included here by treating all X-Y bonds as simple (and equivalent) Morse oscillators. With the additional degrees of freedom in the parametrization that come from the Morse potential, the resulting model was investigated. The degree to which this simple mechanical model can reproduce quadratic and cubic force fields for PF is studied here, as well as how it works for a more difficult problem – the energetics and transition state properties for the intermediate in the (Berry) pseudorotation process that interchanges axial and equatorial fluorines in this prototype molecule. The five parameter Morse-POS model is shown to be do quite well in describing the quadratic and cubic force fields, as well as the pseudorotation process, a fairly impressive feat given the naivete of the model. [ABSTRACT FROM AUTHOR]

A potential able to capture the properties and interactions of curved polycyclic aromatic hydrocarbons (cPAHs) was developed and used to investigate the nucleation behavior and structure of nascent soot particles. The flexoelectric charge polarization of cPAHs caused by pentagon integration was included through the introduction of off-site virtual atoms, and enhanced dispersion interaction parameters were fitted. The electric polarization and intermolecular interactions of cPAHs were accurately reproduced compared to ab initio calculations. This potential was used within molecular dynamics simulations to examine the homogeneous and heterogeneous nucleation behavior of the cPAH corannulene and planar PAH coronene across a range of temperatures relevant to combustion. The enhanced interactions between cPAHs and potassium ions resulted in significant and rapid nucleation of stable clusters compared to all other systems, highlighting their importance in soot nucleation. In addition, the resulting cPAH clusters present morphologies distinct from the stacked planar PAH clusters. [ABSTRACT FROM AUTHOR]

Valence Shell Electron Pair Repulsion (VSEPR) theory, commonly taught in introductory chemistry courses, provides a basis for understanding the molecular structures of molecules of the type XY , where X is a central atom surrounded by m Y ligands. While VSEPR is generally thought of only as a qualitative theory, Bartell and coworkers constructed a semi-quantitative model potential to address the physical underpinnings of VSEPR by introducing a points-on-a-sphere (POS) potential such that all X-Y bonds are of fixed length and all atoms Y repel each other. More than forty years ago, this simple model was shown to be effective in reproducing relative quadratic and cubic bending force constants for a variety of binary XY compounds when compared to values computed with semi-empirical and fairly primitive methods. The work presented here endeavours to go beyond the model used in the early investigations by Bartell and coworkers. Specifically, stretching force constants are clearly omitted from any POS model with a fixed radius, and are (primitively) included here by treating all X-Y bonds as simple (and equivalent) Morse oscillators. With the additional degrees of freedom in the parametrization that come from the Morse potential, the resulting model was investigated. The degree to which this simple mechanical model can reproduce quadratic and cubic force fields for PF is studied here, as well as how it works for a more difficult problem – the energetics and transition state properties for the intermediate in the (Berry) pseudorotation process that interchanges axial and equatorial fluorines in this prototype molecule. The five parameter Morse-POS model is shown to be do quite well in describing the quadratic and cubic force fields, as well as the pseudorotation process, a fairly impressive feat given the naivete of the model. [ABSTRACT FROM AUTHOR]

Molecular dynamics simulations, which take place on the atomistic scale, are now being used to predict the influence of atomistic processes on macro-scale mechanical properties. However, there is a lack of clear understanding on which potential should be used when attempting to obtain these properties. Moreover, many MD studies that do test mechanical properties do not actually simulate the macro-scale laboratory tension tests used to obtain them. As such, the purpose of the current study was to evaluate the various types of potentials for their accuracy in predicting the mechanical properties of iron from an atomistic uniaxial tension test at room temperature. Results demonstrated that while EAM and MEAM potentials all under predicted the elastic modulus at room temperature, the Tersoff and ReaxFF potentials were significantly more accurate. Unlike EAM and MEAM, both the Tersoff and ReaxFF potentials are bond order based. Therefore, these results demonstrate the importance of considering bonding between atoms when modelling tensile tests. In addition, the ReaxFF potential also accurately predicted the Poisson's ratio, allowing for complete characterisation of the material's behaviour. Overall, these findings highlight the need to understand the capabilities and limitations of each potential before application to a problem outside of the initial intended use. [ABSTRACT FROM AUTHOR]

The analysis of remote sensing (RS) images, which is often accomplished using unsupervised image classification techniques, requires an effective method to determine an appropriate number of classification clusters. This paper proposes a preliminary analytical method to evaluate the input parameters for unsupervised RS image classification. Our approach involves first analysing the colour spaces of RS images based on the human visual perception theory. This enables the initial number of clusters and their corresponding centres to be automatically established based on the interaction of different forces in our supposed force field. The proposed approach can automatically determine the appropriate initial number of clusters and their corresponding centres for unsupervised image classification. A comparison of the experimental results with those of existing methods showed that the proposed method can considerably facilitate unsupervised image classification for acquiring accurate results efficiently and effectively without any prior knowledge. [ABSTRACT FROM AUTHOR]

The optimisation of a peptide-capped glycine using the novel force field FFLUX is presented. FFLUX is a force field based on the machine-learning method kriging and the topological energy partitioning method called Interacting Quantum Atoms. FFLUX has a completely different architecture to that of traditional force fields, avoiding (harmonic) potentials for bonded, valence and torsion angles. In this study, FFLUX performs an optimisation on a glycine molecule and successfully recovers the target density-functional-theory energy with an error of 0.89 ± 0.03 kJ mol−1. It also recovers the structure of the global minimum with a root-mean-squared deviation of 0.05 Å (excluding hydrogen atoms). We also show that the geometry of the intra-molecular hydrogen bond in glycine is recovered accurately. [ABSTRACT FROM AUTHOR]

By combining the bottom-up and top-down approaches, we have developed a new all-atom (AA) force field from quantum mechanics and experimental data and a new coarse grained (CG) force field from AA simulation and experimental data, for polydimethylsiloxane (PDMS). The AA force field is developed based on the TEAM force field database. The CG force field uses a mapping rule that splits the connecting oxygen into neighbouring CG beads to maintain the charge neutrality of the beads, analytical functional forms including anharmonic terms in the valence terms, and the temperature-dependent free-energy functional form to describe the inter-bead interactions. Broad range of thermodynamic properties of PDMS including density, surface tension, solubility parameter, radius of gyration and glass transition temperature are calculated to validate the force fields, and good agreements with the experimental data are obtained. [ABSTRACT FROM PUBLISHER]

The paper deals with the methodology of film growth simulations using classical molecular dynamics and an empirical interaction potential. We focus on the effect of the cut-off distance (rC) of the short-range part of the potential. On the one hand, we find thatrCdoes not affect the qualitative conclusions of the simulations and that its quantitative effect is in the logical direction (better crystallinity at higherrC). On the other hand, we show that the aforementioned quantitative effect is very strong, and clearly underestimated in the literature. The film crystallinity is affected by (non-)neglecting of as seemingly low energies as several meV per bond. The results are important for the design of growth simulations of crystalline films and for the correct interpretation of their results. [ABSTRACT FROM AUTHOR]

A transferable united-atom force field, based on Mie potentials, is presented for alkynes. The performance of the optimised Mie potential parameters is assessed for 1-alkynes and 2-alkynes using grand canonical histogram-reweighting Monte Carlo simulations. For each compound, vapour–liquid coexistence curves, vapour pressures, heats of vapourisation, critical properties and normal boiling points are predicted and compared to experiment. Experimental saturated liquid densities are reproduced to within 2% average absolute deviation (AAD), except for 1-hexyne, which are reproduced with 3% AAD. Experimental saturated vapour pressures are reproduced to within 3% AAD, except for 1-pentyne, 2-pentyne and 2-hexyne, where deviations from experiment of up to 20% AAD were observed. Binary phase diagrams, predicted from Gibbs ensemble Monte Carlo simulations, for propane + propyne, propene + propyne and propadiene + propyne, are in close agreement with experiment. [ABSTRACT FROM PUBLISHER]

The main goal of this work is the generation of a new force field data set to the interaction of several gases such as H2, O2, N2, CO, H2O, and H2S with alkali cation-doped carbon nanotubes (CNTs) usingab initiocalculations at the MP2(full)/6-311++G(d,p) level of theory. Different alkali cations including Li+, Na+,K+and Cs+were used to dope in the CNT. The calculated potential energy curve for the interaction of each gas molecule with each alkali cation-doped CNTs was fitted to an analytical potential function to obtain the parameters of the potential function. A modified Morse potential function was selected for the fitting in which the electrostatic interactions has been accounted by adding the β/rterm to the Morse potential. The accuracy of the calculated force field was checked via Grand Canonical Monte Carlo (GCMC) simulation of the H2adsorption on Li-doped graphite and Li-doped CNT. The results of these simulations were compared with the experimental measurements and the closeness of the simulation results with the experimental data indicated the accuracy of the proposed force field. The main merit of this work is the derivation of a specific force field for interaction of each of six gases with four alkali cation-doped CNT, which can be used in molecular simulation of these 24 of systems. The simulation results showed the increase of the H2adsorption capacity of nanotube and graphite up to 50% and 10%, respectively, due to the insertion of Li ions. [ABSTRACT FROM PUBLISHER]

Quantifying an atom's transferability, in a force field context, demands a quantitative understanding of how an atom ‘experiences’ the surrounding environment both intra-atomically and inter-atomically. Here we investigate the intra-atomic (EintraA) viewpoint through the study of the atoms Cα, Hα, N, O, and S in a series of ‘mono’-, tri- and penta-peptides. The remaining inter-atomic viewpoint consists of an electrostatic (via multipole moments), exchange and correlation components respectively, of which the electrostatic component has been previously reported. Together these four energy components, as calculated from the Interacting Quantum Atoms (IQA) partitioning approach, express the foundation of the Quantum Chemical Topological Force Field (QCTFF). In order to have transferability within a force field, smaller sample systems must be calculated and developed as representative of larger target systems. The Cα, Hα, N, O and S atoms in a tri-peptide are energetically comparable to those in their penta-peptide configurations, within 2.1 kJ/mol in absolute value (1 exception). Across all five elements, this energy difference ison average∼0.3 kJ/mol. On average, the tri-peptide sample systems represent a ∼8.2 Å atomic horizon around the central atoms of interest. Thus, both the previous knowledge of the ∼10.3 Å horizon sphere and ∼0.4 kJ/mol error required by the electrostatic multipole moments, determine how two of the four key QCTFF energy components are affected by an atom's molecular environment. [ABSTRACT FROM PUBLISHER]

Molecular dynamics simulations are performed to develop new parameters for acetamide using a systematic procedure proposed by Salaset al., where the atomic charges were fitted to reproduce the experimental dielectric constant and the Lennard-Jones parameters to match the surface tension and density. The parameters for formamide recently calculated by Pérezet al.were used to obtain the new parameters of acetamide where atoms of the amine group and carbon kept the same intermolecular parameter values in both molecules. The parameters of the methyl group, taken as united atom, and the oxygen atom were fitted to reproduce the dielectric constant, surface tension and density at 358.15 K. The new set of parameters, based on the optimised potential for liquids simulations with all atoms, was able to predict results of the target properties as a function of temperature as a pure component and the dielectric constant and density of binary mixtures with water and formamide as a function of acetamide concentration at 298.15 K. The polymer chains formed by hydrogen bond interactions were analysed to understand the maximum of dielectric constant in acetamide–water mixtures. [ABSTRACT FROM PUBLISHER]

Aqueous ethanol mixtures are studied through molecular dynamics simulations with the focus on exploring how various force field models reproduce the association and its influence on selected thermo-physical properties of these mixtures. The most important conclusion seems to be the inadequacy of all classical force fields to reproduce the very peculiar shape of the excess enthalpy of these mixtures, as a function of the ethanol concentration, neither quantitatively nor qualitatively. The Kirkwood–Buff (KB) integrals calculated using the simulation data follow the same trends as the experimental ones. This suggests complicated correlation of the excess enthalpy with the concentration fluctuation and clustering in these mixtures. The KB force field shows better overall agreement with experimental results than the other studied models. [ABSTRACT FROM PUBLISHER]

The aggregation behaviors of two trisiloxane-tailed surface active ionic liquids in water have been investigated by coarse-grained (CG) molecular dynamics simulation on the basis of MARTINI force field. The new CG model is developed from the optimized molecule computed by using density functional theory. Direct comparison of angles and bonds obtained from all-atom (AA) simulations with those calculated from the CG model has been conducted to validate the latter model. Excellent agreement between AA and CG demonstrates that the potential of the new CG model can represent the complex system well. The long time CG simulation has been performed to understand the formation process of micelles when dissolving ionic liquids in water. Vesicles were observed at the final stage of the simulation and their partially truncated views and density profiles were obtained to describe the structure in detail. [ABSTRACT FROM AUTHOR]

One of the challenges in the area of molecular simulation of biointerfaces is to ensure that the interatomic potentials used to describe such interfaces capture the essential chemistry and physics of the system. Here, we report the conformational testing of the inter-operability of the CHARMM and SPC/Fw force fields, the compatibility of which is essential for successful incorporation of a description of biomolecules into current biomineralisation force fields. The effect of the new water model, SPC/Fw, on the conformational equilibrium of two contrasting exemplar tripeptide sequences, RGD and SPT, as described by the CHARMM force field, has been probed by the analysis of results generated from replica-exchange molecular dynamics simulations. We compare the ensemble of conformational states generated from the CHARMM-SPC/Fw force fields with those obtained from the more typical CHARMM-TIPS3P combination. Analysis shows that the findings from the two force field combinations compare very favourably for equilibrium structure determination for both peptides. [ABSTRACT FROM AUTHOR]

A molecular mechanics method with COMPASS and Dreiding force fields was used to predict molecular packings for the three title compounds among seven possible space groups (P21/c, P212121, P-1, Pbca, C2/c, Pna21, and P21). Then, periodic band calculations were performed on the predicted crystals using the density functional theory generalized gradient approximation with revised Perdew-Burke-Ernzerhof (DFT-GGA-RPBE) functional method. The obtained density of state (DOS) showed that the C-N3bonds are possibly the trigger bond during thermolysis. The band gaps (ΔEg) were slightly different and hexaazidobenzene was more sensitive than the two others. Periodic calculation results on DOS were consistent with those obtained from bond dissociation energy calculations on gas molecules. [ABSTRACT FROM PUBLISHER]

In this investigation, the interaction of Calixarene with amino acid (alanine) with double-walled carbon nanotubes (DWNTs) are examined, with OPLS, Amber and MM+ force field in molecular mechanic (MM) method. The calculations achieved by methods of Monte Carlo simulation in different temperatures. The calculations were carried out using HyperChem professional release 7.01 package of program. We investigate effects of gas phase (ϵ = 1) and in various solvent media with dielectric constants of water (ϵ = 78.39), DMSO (ϵ = 46.8), methanol (ϵ = 32.63), ethanol (ϵ = 24.55), CH2Cl2(ϵ = 8.93) at seven temperatures on interaction of Calixarene with DWNTs, utilizing these force fields. The interaction of Calixarene with DWNTs in gas phase and five solvents such as water, DMSO, methanol, ethanol and dichloromethane has been processed applying the ab initio calculations. The calculations have been done with the GAUSSIAN 98 program according to Hartree-Fock (HF) theory at the HF/3-21G level. Thus, by utilizing a Hartree-Fock method, we studied the effects of different solvents on interaction of Calixarene with DWNTs within the Onsager self-consistent reaction field (SCRF) model, as well as the temperature effects on the stability of the interaction between Calixarene with DWNTs in various solvents. [ABSTRACT FROM AUTHOR]

We present a transferable force field able to model the structure of zeolites when different cation types are considered. Based on simple functional forms and interactions, it can be easily implemented in most common molecular simulation codes. The optimised force field is validated on structural properties (lattice parameters and Si–O–Al angles) for a large variety of zeolites, including faujasites of different Si/Al ratio and different extra-framework cation types (Li+, Na+, K+, Mg2+, Ca2+and Co2+). The transferability of the force field was successfully tested on zeolites of different topologies such as FAU, LTA, MFI, FER and TON. The predictive capabilities of the potential were tested on structural deformations of alkaline earth Na, Co-X faujasites with different ion-exchange ratios. [ABSTRACT FROM PUBLISHER]

The simple six-site intermolecular potential functions have been derived to reproduce the results from density functional theory calculations of the interaction energy for rigid SbF5and SbCl5. These adjusted intermolecular potential parameters (force field parameters) were used in the molecular dynamics (MD) simulations of the liquids SbF5and SbCl5to obtain density, internal energy, enthalpy and radial distribution function (RDF) using Lennard–Jones potential at 1 atm. There is a good agreement between the values of density, heat capacity and RDF obtained from MD and those of experimental. [ABSTRACT FROM AUTHOR]

Secondary structures of antimicrobial peptides (AMPs) play an important role in their activity. The AMP cecropin P1, like most other anti-microbial peptides, is known to form a helix at the interface of bacterial cell membranes. This structure is fundamental to its activity and its ability to destroy the membrane. In contrast, as reported in experimental measurements, this peptide unfolds in bulk water. We analysed this behaviour using two different force fields, CHARMM22/CMAP and AMBER ff99SB. Although these two force fields are commonly used in molecular dynamics (MD) and have been extensively validated, we observed two sharply different results. A sodium dodecyl sulphate (SDS) micelle was used to model the bacterial membrane using MD simulations. CHARMM22 resulted in a peptide that stays mostly folded in both environments (bulk water and SDS), while AMBER correctly predicted the unfolding in bulk water and produced results that closely match the available experimental data. We further computed the free energy of folding and unfolding, using the adaptive biasing force method, to get a complete picture of the energy barriers and the different metastable states. To get further insights into the interaction of the peptide with its environment, we computed the average number of hydrogen bonds between different components versus the folding reaction coordinate. [ABSTRACT FROM PUBLISHER]

Conformational search using force field methods on complex biomolecular systems is a key factor in understanding molecular and structural properties. The reliability of such investigations strongly depends on the efficiency of the conformational search algorithm as well as the accuracy of the employed force field. In the present work we compared the performance of two different approaches: the Monte-Carlo multiple minimum/low mode sampling (MCMM/LM), in combination with the OPLS2005 (MCMM/LM//OPLS2005), and Tabu-Search combined with Basin Hopping (TS/BH), employing the original OPLS-AA implementation proposed by Jorgensen (TS/BH//OPLS-AA). We investigated their performance in locating energetically low-lying structures and the efficiency in scanning the conformational phase space of non-covalently bonded complexes. As test systems we employed complexes of the artificial peptide receptor CBS-KKF with four different tetrapeptide ligands. The reliability and the accuracy of both approaches were examined by re-optimising all low-energy structures employing density functional theory with empirical dispersion correction in combination with triple zeta basis sets. Solvent effects were mimicked by a continuum solvent model. In all the four-test systems, the TS/BH//OPLS-AA approach yielded structures that are much lower in energy after the DFT optimisation. Additionally, it provided many low-lying structures that were not identified by the MCMM/LM//OPLS2005 approach. [ABSTRACT FROM PUBLISHER]

One-step perturbation is an efficient technique to explore the relation between force-field or model parameters and properties of a molecular system in the condensed phase from a single simulation of the latter using a particular set of model parameters. The accuracy of the prediction of different properties as a function of the extent of perturbation of different model parameters is evaluated using liquid water at ambient temperature and pressure as the test system. The accuracy of predicted changes in free enthalpy, energy, radial distribution functions and dielectric permittivity due to variations in geometric, van der Waals or electrostatic interaction parameters is strongly dependent on the type of property analysed and the type of parameter varied. This is illustrated by the application of one-step perturbation to predict the properties of four models of liquid water from the four ensembles generated for these models. [ABSTRACT FROM AUTHOR]

Force fields for engineering applications are often parameterised using strategies based on quantum mechanicalab initiocalculations and thermodynamic properties from experiment. An automated procedure for adjusting molecular model parameters to experimental thermodynamic property data is introduced. The process accelerates the development of molecular models by an efficient use of parallel computing power and an autonomous progress of the model development without any user interaction. As a case study, the procedure is applied to the parameterisation of a molecular model for acetonitrile. The resulting model reproduces vapour–liquid equilibrium data of acetonitrile with an accuracy of 0.1% for the saturated liquid density, 4.9% for the vapour pressure and 3.7% for the enthalpy of vaporisation. These accuracies are superior to data obtained with previously published force fields for acetonitrile. [ABSTRACT FROM AUTHOR]

We have previously proposed a force-field refinement method. This method consists of minimising the sum of the square of the force acting on each atom in the proteins with the structures from the Protein Data Bank. In addition, we also proposed a new backbone-torsion-energy term, which is represented by a double Fourier series in two variables, the backbone dihedral anglesand. In this paper, we apply our optimisation method and backbone-torsion-energy term to AMBER ff94 (ff96) force field for molecular simulation of protein systems. The results imply that the new force-field parameters give structures of two peptides more consistent with the experimental implications for secondary-structure-forming tendencies than the original force field. [ABSTRACT FROM AUTHOR]

Computer simulation of biomolecular systems has become a standard research instrument for the investigation of biomolecular processes at the atomic level of modelling and interpretation. A bird's eye view of the development of simulation methodology, of biomolecular interaction functions and simulation software is presented, together with the challenges in regard to these three aspects of biomolecular simulation. [ABSTRACT FROM AUTHOR]

The L-cysteine zwitterions in the orthorhombic crystal structure and in aqueous solution, including the deuterated isotopologues HSCD2CH(NH3 +)COO−, DSCH2CH(ND3 +)COO−, and DSCD2CH(ND3 +)COO−, have been studied by mid-infrared, far-infrared, and Raman spectroscopy. Density functional theory (DFT) calculations were performed for an equilibrium molecular geometry of the cysteine zwitterion to obtain vibrational frequencies of fundamental modes, infrared (IR) and Raman intensities, and the depolarization ratio of the Raman bands and combined with normal coordinate force field analyses. The force field obtained for dissolved (in H2O and D2O) cysteine, based on the 4 × 36 experimental fundamental modes of the four isotopologues, was successfully transferred to the two conformers in the solid state. The experimentally observed multiple bands (generally doublets) of L-cysteine and its deuterated isotopologues in the solid state were interpreted based on the coexistence of two conformers in the unit cell. The calculated frequencies were used for full assignments of the fundamental IR and Raman vibrational transitions, including an attempt to interpret all low-frequency vibrations (below 400 cm−1) of the zwitterion also in the solid state. In particular, the hydrogen bonding effects on conformation, bond lengths, and force constants were studied, including those of the distorted NH3 + amino group. The –S-H and -S-D stretching vibrations were found to be local modes, not sensitive to deuterium substitution of the -CH2 and -NH3 + groups in the molecule or to the H(D)-S-C-C torsional angle. The two major -S-H or -S-D stretching bands observed in the solid state correspond to different S-H/D bond lengths and resulted in the force constants K SH = 3.618 N·cm−1 and 3.657 N·cm−1 for the SH… S and SH… O hydrogen-bonded interactions. A remarkable result was that the S(H)… O interaction was weaker than the S(H)… S interaction in the solid state and even weaker in aqueous solution, K SH = 3.715 N·cm−1, possibly due to intramolecular interactions between the thiol and amino groups. A general correlation between the S-H/D bond length and vibrational frequency was developed, allowing the bond length to be estimated for sulfhydryl groups in, for example, proteins. The C-S stretching modes were fitted with different C-S stretching force constants, K CS = 3.213 and 2.713 N·cm−1, consistent with the different CS bond lengths for the two solid-state conformers. [ABSTRACT FROM AUTHOR]

In the first paper of this series [C. Avendaño, T. Lafitte, A. Galindo, C.S. Adjiman, G. Jackson, and E.A. Müller, J. Phys. Chem. B 115, 11154 (2011)] our methodology for the development of accurate coarse-grained (CG) SAFT-γ force fields for the computer simulation of molecular fluids was introduced with carbon dioxide as a particular case study. The procedure involves the use of a molecular-based equation of state to obtain effective intermolecular parameters (from experimental fluid phase equilibrium data) appropriate for molecular simulation over a wide range of fluid conditions. We now extend the methodology to develop coarse-grained models for benzene (C6H6) that can be used in fluid phase simulations. Our SAFT-γ CG force fields for benzene consist of a simple single-segment spherical model, and a rigid three-segment ring structure of tangent spherical groups interacting via Mie (generalized Lennard-Jones) segment–segment interactions. The description of the fluid phase behaviour of benzene with our simplified CG force fields is found to be comparable to that obtained with the more sophisticated models commonly used in the field; a marked improvement is seen with our SAFT-γ models for the vapour pressure, particularly at lower temperatures. These models of benzene together with the previously developed SAFT-γ three-segment chain model of n-decane are used to develop hetero-group force fields for n-decylbenzene, in the spirit of a group contribution methodology. In our approach, the parameters of the phenyl and n-decyl groups are obtained transferably from the individual models of benzene and n-decane, respectively, and the unlike energetic parameters between the phenyl and decyl segments can be obtained from vapour–liquid equilibria data for n-decylbenzene using the SAFT-γ equation of state. The resulting CG hetero-group models are found to describe the fluid properties of n-decylbenzene over a wide range of conditions, exemplifying how our approach can be used as a group contribution methodology. This is the first example of the development of hetero-group SAFT-γ force fields for molecules formed from Mie segments of different size, energy, softness/hardness, and range. [ABSTRACT FROM PUBLISHER]

We have carried out a structural and vibrational study for 5-phenyl-1,3,4-oxadiazole-2-thiol by using the infrared (IR) spectrum and theoretical calculations. For a complete assignment of the compound IR spectrum, density functional theory calculations were combined with Pulay's scaled quantum mechanical force field methodology in order to fit the theoretical wavenumber values to the experimental ones. An agreement between theoretical and available experimental results was found. The theoretical vibrational calculations allowed us to obtain a set of scaled force constants fitting the observed wavenumbers. The results were then used to predict the Raman spectra, for which there are no experimental data. The nature of the benzyl and oxadiazole rings was studied by means of natural bond order and atoms in molecules theory calculations. In addition, the frontier molecular (highest occupied molecular orbital (HOMO) and lowest unoccupied molecular orbital (LUMO)) orbitals were analysed and compared with those calculated for the oxadiazole molecule. [ABSTRACT FROM PUBLISHER]

An improved torsional force field for cis-enol malonaldehyde is presented. First, the conformational potential energy has been calculated by ab initio method at MP2/6-31G** level as a function of two torsional angles around C–C and C–O single bonds. Then, the calculated 2D potential energy surface has been fitted to a potential function, where cross terms of the two dihedrals are added to the ordinary single cosine terms of the optimised potentials for liquid simulations all atom (OPLS-aa) type. The optimised function excellently reproduces the energies with the standard deviation as small as 1.9 kJ/mol. The function may be used easily in the molecular dynamics calculation. [ABSTRACT FROM PUBLISHER]

This review focuses on force-field-based approaches to investigate – through computer simulations – reactive processes in chemical and biological systems. Both, reactions in the gas-phase and in condensed-phase environments are discussed and opportunities and the potential for further developments are pointed out. Where available, results are compared with alternative methods and the advantages and drawbacks of the methods are compared. Particular applications include vibrationally and electronically induced (photo)dissociation of small molecules, proton transfer in the gas- and condensed phase and ligand un- and re-binding in proteins. [ABSTRACT FROM AUTHOR]

A united-atom potential model for naproxen suitable for molecular dynamics (MD) simulation has been developed. The charge distribution is approximated by point charges obtained from ab initio calculations using the CHELPG method. Also the intramolecular interactions such as bond and angle vibration, and the torsion potential are obtained from ab initio calculations. The dispersive interaction contribution is taken from the literature. By MD simulation using a naproxen film in slap geometry, the temperature dependence of the density, surface tension and self-diffusion coefficient as well as the melting temperature for the developed potential model are obtained. [ABSTRACT FROM PUBLISHER]

A rigid five-site united atom model for dimethyl sulfone (DMSO2) compatible with the GROMOS force field is parametrized and tested. The parameters were optimized with respect to experimental quantities such as liquid density, heat of vaporization, shear viscosity and excess free energy. Good agreement with pure component properties is achieved except for the static dielectric permittivity which is calculated too low. Together with the SPC model for water the new DMSO2 model was used to study aqueous mixtures at low concentrations and compared to aqueous mixtures of DMSO. It is concluded that interaction parameters for sulfoxide oxygen are not directly transferable to sulfonyl oxygen. [ABSTRACT FROM PUBLISHER]

Recently, the majority of the investigation into computational chemistry has been focused on the examination of molecules submerged in various solvents and the interaction of anticancer drug with carbon nanotubes (CNTs). The most likely tendency is toward the interaction between anticancer drug and single-walled carbon nanotubes (SWCNTs). In this investigation, the interaction of Temozolomide, a common form of anticancer drug with open-end of SWCNT, are examined, with MM+, Amber and OPLS force field in molecular mechanic (MM) method. We investigate effects of water, methanol and a mixture of them on interaction of Temozolomide with SWCNT, utilizing these force fields. The interaction of Temozolomide with open-end of SWCNT in gas phase, water and methanol have been processed applying the abinitio calculations. The calculations have been done with the GAUSSIAN 98 program according to Hartree-Fock (HF) theory at the HF/STO-3G level. Gibbs free energy, enthalpy, entropy and dipole moment values are compared in gas phase, water and methanol in this research. Thus, by utilizing a Hartree-Fock method, we studied the effects of different solvents on interaction of Temozolomide with open-end SWCNT within the onsager self-consistent reaction field (SCRF) model, as well as the temperature effects on the stability of the interaction between Temozolomide and single-walled carbon in various solvents. [ABSTRACT FROM AUTHOR]

In this research, we studied solvent effects on the relative energies, dipole moment values, and structural properties of water, methanol, ethanol, and mixtures of them surrounding single-walled carbon nanotubes (SWCNT), by using molecular dynamics simulation. Calculations were carried out with the Hyper Chem program. We used different force fields to determine energy and other types of geometrical parameters on the particular SWCNT. Because of the differences among force fields, the energy of a molecule calculated using two different force fields will not be the same. In this study, differences in force fields was illustrated by comparing the energy calculated by using force fields MM+, Amber and OPLS. The quantum Mechanics (QM) calculations were carried out with the GAUSSIAN 98 program based on density functional theory (DFT) at the B1LYP/3-21G level. In this study, we have compared gas phase and solvent calculations that considered solvents such as water, methanol and ethanol and a mixture of them. Therefore, we investigate polar solvents effects on SWCNT within the Onsager self-consistent reaction field (SCRF) model using a Hartree-Fock method and the temperature effect on the stability of SWCNT in various solvents. [ABSTRACT FROM AUTHOR]

This paper is part of our pursuit to develop an efficient procedure for optimising parameters that provide a reliable foundation for highly predictive molecular simulations. We tested whether DesParO, a mathematical tool originally used in automotive design, is suitable for creating Lennard-Jones (LJ) parameters that accurately reproduce the experimental phase behaviour for our test compound ethylene oxide (EO). So, we created a multitude of diverse random parameter sets, performed Gibbs ensemble Monte Carlo simulations and collected the resulting physical properties. On that data basis, DesParO derived a meta-model through a multidimensional interpolation. We then explored, in an interactive fashion unique to DesParO, the LJ parameter space and selected some suitable parameter sets, which were then tested by simulations. For EO, the selected parameter sets were indeed superior to the initial parameters. Furthermore, the new parameters can be reliably used as input for further optimisation by other methods, resulting in extremely robust LJ parameters. Beyond the prediction of parameter sets, DesParO enabled us to examine the underlying parameter-property relationships that help us solve future optimisation problems by creating subordinate parameter optimisation tasks in a systematic manner; this ability makes DesParO a valuable tool in the overall optimisation process. [ABSTRACT FROM AUTHOR]

We have previously proposed a method for refining force-field parameters of protein systems, which consists of minimising the summation of the square of the force acting on each atom in the proteins with the structures from the protein data bank (PDB). The results showed that the modified force-field parameters for all-atom model gave structures more consistent with the experimental implications than the original force fields. In this work, we applied this method and a new method to the OPLS-UA force field. In the new method, we perform a minimisation of the average of the root-mean-square deviation of various protein structures from the native structure. We selected some torsion-energy parameters for this optimisation, and 100 molecules from the PDB were used. The results imply that the new force-field parameters gave structures of two peptides more consistent with the experimental implications for the secondary structure-forming tendencies than the original OPLS-UA force field. [ABSTRACT FROM AUTHOR]

While force-field development has been discussed extensively in the literature, the question of what analytical expressions make the best function choices, particularly in the context of matching quantum mechanic potential energy surfaces (PES), is less explored. Traditional forms based upon harmonic oscillators and Lennard-Jones types have dominated the field owing to the focus on fitting properties. However, with the advent of gradient-fitting approaches, it is now possible with the correct force-field expressions to achieve consistent high-accuracy results with molecular dynamics calculations. Using the general principle that power series can fit surfaces of any shape well, we have utilised harmonic series functions to fit a two-body PES represented by a Morse function. The harmonic functions are fast because they have only integer exponents, and they fit accurately with a limited number of terms. [ABSTRACT FROM AUTHOR]

We performed folding simulations of three proteins using four force fields, AMBER parm96, AMBER parm99, CHARMM 27 and OPLS-AA/L, in order to examine the features of these force fields. We studied three proteins, protein A (all α-helix), cold-shock protein (all β-strand) and protein G (α/β-structures), for the folding simulations. For the simulation, we used the simulated annealing molecular dynamics method, which was performed 50 times for each protein using the four force fields. The results showed that the secondary-structure-forming tendencies are largely different among the four force fields. AMBER parm96 favours β-bridge structures and extended β-strand structures, and AMBER parm99 favours α-helix structures and 310-helix structures. CHARMM 27 slightly favours α-helix structures, and there are also π-helix and β-bridge structures. OPLS-AA/L favours α-helix structures and 310-helix structures. [ABSTRACT FROM AUTHOR]

We examined a new backbone torsion-energy term proposed by us in the force field for protein systems. This torsion-energy term is represented by a double Fourier series in two variables, namely the backbone dihedral angles φ and ψ. It gives a natural representation of the torsion energy in the Ramachandran space in the sense that any two-dimensional energy surface periodic in both φ and ψ can be expanded by the double Fourier series. We can then easily control secondary-structure-forming tendencies by modifying the torsion-energy surface. For instance, we can increase or decrease the α-helix-forming-tendencies by lowering or raising the torsion-energy surface in the α-helix region and likewise increase or decrease the β-sheet-forming tendencies by lowering or raising the surface in the β-sheet region in the Ramachandran space. We applied this torsion-energy modification method to six force fields, AMBER parm94, AMBER parm96, AMBER parm99, CHARMM27, OPLS-AA and OPLS-AA/L, and demonstrated that our modifications of the torsion-energy terms resulted in the expected changes of secondary-structure-forming tendencies by performing folding simulations of α-helical and β-hairpin peptides. [ABSTRACT FROM AUTHOR]

We propose a new method of optimisation of backbone torsion-energy parameters in the force field for molecular simulations of protein systems. This method is based on the idea of balancing the secondary-structure-forming tendencies, namely, those of α-helix and β-sheet structures. We perform a minimisation of the backbone dihedral angle-based root-mean-square deviation of the helix and β structure regions in many protein structures. As an example, we optimised the backbone torsion-energy parameters of AMBER parm96 force field using 100 protein molecules from the Protein Data Bank. We then performed folding simulations of α-helical and β-hairpin peptides, using the optimised force field. The results imply that the new force-field parameters give structures more consistent with the experimental implications than the original AMBER parm96 force field. [ABSTRACT FROM AUTHOR]

Compared with imidazolium-based ionic liquids (ILs), phosphonium-based ILs have been proven to be more stable in thermodynamics and less expensive to manufacture. In this work, a kind of phosphonium-based IL, [PC6C6C6C14][Tf2N], was studied under several conditions using molecular dynamics simulations based on both the all-atom force field (AAFF) and the united-atom force field. Liquid density was calculated to validate the force field. Compared with experimental data, good agreement was obtained for the simulated density based on the AAFF. Heat capacities at constant pressure were calculated at several temperatures, and good linear relationships were observed. Self-diffusion coefficients, viscosities and conductivities were also calculated to study the dynamics properties of this IL. The viscosity of this IL at 293 K was also compared with experimental data, and the error was in a reasonable range. In order to depict the microstructures of the IL, centre-of-mass and site-to-site radial distribution functions were employed. In addition, spatial distribution functions were investigated to present the more intuitive features. [ABSTRACT FROM AUTHOR]

A molecular dynamics (MD) study of α,ω-dimethoxypolyethylene glycol has been carried out under various conditions with respect to solvent composition, ionic strength, chain length, force field and temperature. A previous MD study on a 15-mer of polyethyleneglycol (PEG) suggested a helical equilibrium structure that was stabilised by hydrogen bonding and bridging water molecules. Experiments show that PEG is highly soluble in water, and indicate that clustering is not favoured. In the present study using different force fields, the GROMOS force fields 45A3 and 53A6, a variation on the latter 53A6_OE, and a force field by Smith et al. produced different results. For the GROMOS force fields 45A3 and 53A6 no helical structure was found, but formation of more or less compact random coils in aqueous solution due to hydrophobic interactions was observed. For the other two force fields used, α,ω-dimethoxypolyethylene glycol stayed flexible and more or less elongated in aqueous solution, more in agreement with experimental observations and the previous MD study. [ABSTRACT FROM AUTHOR]

This work presents the implementation and analysis of several damping functions for Coulomb, induction, and dispersion interactions within the framework of the general effective fragment potential (EFP) method. Damping is necessary to obtain the correct asymptotic short-range behavior of these interactions. Correctly chosen damping functions allow a balanced description of different parts of intermolecular potential energy surfaces and improve the accuracy of predicted intermolecular distances and binding energies. The performance of different damping functions is tested by comparing the EFP energy terms with the symmetry adapted perturbation theory (SAPT) energy terms in a range of intermolecular separations for ten molecular dimers. The total EFP binding energies in these dimers were compared with the binding energies obtained from SAPT and coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. A formula for electrostatic damping that was derived from first principles is recommended. This method employs the overlap of fragment localized molecular orbitals (LMO) within the spherical Gaussian approximation. The LMO overlap integrals are also used to determine the damping of dispersion. Gaussian polarization damping functions are recommended for use within the EFP framework. With this set of damping functions, the EFP binding energies are within 0.5 kcal/mol and intermolecular equilibrium separations are within 0.2 Å of the corresponding CCSD(T) and SAPT values. This consistent accuracy of EFP is encouraging for future studies of more complicated molecular complexes. [ABSTRACT FROM AUTHOR]

Controlling surface wettability, expressed in terms of contact angle, is a significant issue in nanotechnology. In this paper, through extensive molecular dynamics simulations, we show that the contact angle of water droplet on a TiO2 surface is considerably influenced by the temperature variations, i.e. as the temperature increases, the contact angle decreases and the surface becomes more hydrophilic. We address the issue of accurate force fields and determine the partial charges that can closely reproduce the experimental contact angle. Detailed understanding of the temperature-dependent variation of contact angle is developed by hydrogen bonding analysis. [ABSTRACT FROM AUTHOR]

With a view to protein hydration modelling, optimized geometries of pure water clusters, hydrated serine and hydrated tyrosine clusters are compared systematically. Geometries predicted by multipole models according to the theory of Quantum Chemical Topology and by point charge models are contrasted with ab initio geometries obtained at the B3LYP/aug-cc-pVDZ level of theory. The performance of popular point charge models such as AMBER, CHARMM, OPLS, MMFF, TAFF and TIP4P is scrutinized. [ABSTRACT FROM AUTHOR]

The effect of partial charge parameterization on the fluid phase behavior of dimethyl ether (DME) is investigated with grand canonical Monte Carlo simulations coupled with histogram reweighting techniques. A total of 16 optimized parameter sets are presented, covering a range of dipole moments from 0 to 2.4 D. Although all 16 parameter sets are able to reproduce experimental saturated liquid densities, only six of the parameter sets, corresponding to - 0.433 ≤ qO ≤ - 0.58 are able to simultaneously produce accurate predictions for the saturated liquid densities and vapor pressures over the temperature range 280 ≤ T ≤ 380. The heat of vaporization, acentric factor and radial distributions are also presented. [ABSTRACT FROM AUTHOR]