Molecular Simulation (MOL SIMULAT )

Publisher: Taylor & Francis

Description

Molecular Simulation covers all aspects of research related to, or of importance to, molecular modelling and simulation (including informatics, theoretical and experimental work). Molecular Simulation exists to bring together the most significant papers concerned with applications of simulation methods, and original contributions to the development of simulation methodology from biology and biochemistry, chemistry, chemical engineering, materials and nanomaterials, medicine, physics and information science. The aim is to provide a forum in which cross fertilization between application areas, methodologies, disciplines, as well as academic and industrial researchers can take place and new developments can be encouraged. Molecular Simulation is of interest to all researchers using or developing simulation methods (for example those based on statistical mechanics) and to those experimentalists, theorists and information scientists who wish to use simulation data or address a simulation audience. This journal is abstracted and indexed within the ISI science citation index. Current impact factor is 0.946.

  • Impact factor
    1.06
    Hide impact factor history
     
    Impact factor
  • 5-year impact
    1.08
  • Cited half-life
    6.60
  • Immediacy index
    0.18
  • Eigenfactor
    0.00
  • Article influence
    0.32
  • Website
    Molecular Simulation website
  • Other titles
    Molecular simulation (Online)
  • ISSN
    0892-7022
  • OCLC
    50166441
  • Material type
    Document, Periodical, Internet resource
  • Document type
    Internet Resource, Computer File, Journal / Magazine / Newspaper

Publisher details

Taylor & Francis

  • Pre-print
    • Author can archive a pre-print version
  • Post-print
    • Author can archive a post-print version
  • Conditions
    • Some individual journals may have policies prohibiting pre-print archiving
    • On author's personal website or departmental website immediately
    • On institutional repository or subject-based repository after either 12 months embargo for STM, Behavioural Science and Public Health Journals or 18 months embargo for SSH journals
    • Publisher's version/PDF cannot be used
    • On a non-profit server
    • Published source must be acknowledged
    • Must link to publisher version
    • Set statements to accompany deposits (see policy)
    • The publisher will deposit in on behalf of authors to a designated institutional repository including PubMed Central, where a deposit agreement exists with the repository
    • STM: Science, Technology and Medicine
    • SSH: Social Science and Humanities
    • Publisher last contacted on 25/03/2014
    • 'Taylor & Francis (Psychology Press)' is an imprint of 'Taylor & Francis'
  • Classification
    ​ green

Publications in this journal

  • Molecular Simulation 02/2015; 41.
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    ABSTRACT: The complex chemistry of coal pyrolysis is difficult to be captured by experimental techniques or simulated with the quantum mechanics computational methods. The emerging of both the large-scale coal models and the promising capability of reactive molecular dynamics (ReaxFF MD) motivated us to develop a new methodology by combining graphics processing unit (GPU)-enabled high performance computing with cheminformatics analysis in order to explore the coal pyrolysis mechanisms using ReaxFF MD. The methodology is rooted in two new software tools, GMD-Reax, the first GPU-enabled ReaxFF MD codes that make it practical to simulate large-scale models (∼10,000 atoms) on desktop workstations, and visualisation and analysis of reactive molecular dynamics (VARMD), the first software dedicated to analysis of detailed chemical reactions from the trajectories of ReaxFF MD simulation. With this methodology, reasonable product profiles and gas generation sequences of pyrolysis for bituminous coal models ranging from ∼1000 to ∼10,000 atoms (including the system with 28,351 atoms, one of the largest systems used in ReaxFF MD) have been obtained. The complex and detailed chemical reactions directly revealed by VARMD can provide further information on radical behaviours and their connection with pyrolysates. The methodology presented here offers a new and promising approach to systematically understand the complex chemical reactions in thermolysis of very complicated molecular systems.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: Mechanism is a core chemical concept that has vital implications for reaction rate, efficiency and selectivity. The discovery of mechanism is not easy due to the great diversity of possible chemical rearrangements in even relatively simple systems. For this reason, mechanisms involving bond breaking and forming are usually proposed via chemical intuition – which limits the scope of considered possibilities – and these hypotheses are then tested using simulation or experiment. This article discusses an automated simulation strategy for investigating multiple elementary step reaction mechanisms in chemical systems. The method starts from a single input structure and seeks out nearby intermediates, optimises the proposed structures and then determines the kinetic viability of each elementary step. The kinetically accessible intermediates are catalogued and new searches are performed on each unique structure. This process is repeated for an arbitrary number of steps without human intervention, and massively parallel computation enables fast searches in chemical space. Importantly, this strategy can be empirically shown to lead to a finite number of accessible structures, not a combinatorial explosion of intermediates. Therefore, the method should be able to predict multi-step reaction pathways in many interesting chemical systems. Demonstrations on organic reactions and a hydrogen storage material, ammonia borane, show that the herein proposed strategy can uncover complex reactivity without relying on existing chemical intuition.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: We review recent advances in the understanding of ejection mechanisms of solvated ions and charged macromolecules from highly charged nanodroplets. While the physical basis for the instability leading to droplet fragmentation is relatively well understood, a description of molecular mechanism of the fragmentation in complex systems is still missing. Development of a comprehensive model for the droplet fragmentation is further complicated by chemical modifications of the charged macromolecules (macroions) in a changing droplet environment. We highlight several different molecular simulation techniques used to study fragmentation of charged droplets with different solutes. Ejection of simple ions is analysed using theory of activated processes and transfer reaction coordinate (TRC). The TRC was shown to adequately represent complex rearrangement of solvent molecules in the course of evaporation. The critical value of the square of the charge to volume ratio for spontaneous ejection of simple solvated ions from aqueous droplets is found to be very close to that predicted by Rayleigh's model. On the contrary, the presence of macromolecules adds a level of complexity into the system where the charge-induced instabilities cannot be described by a conventional theory such as Rayleigh or ion-evaporation mechanism. Additional charge–charge interactions between charged sites on a macromolecule dramatically change the macroion ejection mechanism. Molecular dynamics simulations reveal a number of distinct scenarios: contiguous extrusion, drying-out, star-like formation of solvent surrounding a macroion and pearl formation along the macromolecular chain.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: We review a minimalist's reactive force field, reactive state summation (RSS) potential. The essence of RSS potential scheme is to model each reactive state by individual non-reactive force fields, then modulate each term by a reaction-coordinate-dependent weight function, finally sum together to obtain the reactive potential. Compared with existing reactive potentials, RSS potential is easier to formulate and parameterise and is computationally efficient, at the expense of lesser accuracy. Thus, RSS potential can be regarded as a ‘reactive Lennard-Jones’ potential. Three exemplary RSS potentials are described in the context of their respective chemical systems: RSS-nitrogen for modelling detonation, RSS-carbon for modelling pyrolysis of activated carbon and RSS-fuel-catalyst for modelling catalytic chemical reaction.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: Biopolymer fluorescence in biology and biochemistry is increasingly used for characterising equilibrium, dynamics and imaging. This is typically done by monitoring wavelength and intensity changes without necessarily knowing what causes such changes in detail. Simulations have been at the core of the considerable recent progress in improving the microscopic understanding of wavelength and quenching of fluorescence intensity in biopolymers. This review focuses on one of the most used intrinsic probes for protein behaviour, tryptophan (Trp), which is arguably now one of the best understood probes of internal structure and dynamics for proteins – despite its reputation to the contrary. In this review, we highlight selected classical molecular dynamics in combination with quantum mechanics simulations from our group and others during the past 20 years that support this view. The work includes simulations of time-dependent wavelength shifts in solvents and proteins, fluorescence-quenching rates, dielectric compensation by water, heterogeneity of quenching rates and applications to protein folding.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: The quantum–classical Liouville equation (QCLE) provides a rigorous approach for modelling the dynamics of systems that can be effectively partitioned into a quantum subsystem and a classical environment. Several surface-hopping algorithms have been developed for solving the QCLE and successfully applied to simple model systems, but simulating the long-time dynamics of complex, realistic systems using these schemes has proven to be computationally demanding. Motivated by the need for computationally efficient algorithms, two approximate solutions of the QCLE, the Poisson bracket mapping equation (PBME) solution and the forward–backward trajectory solution (FBTS), were developed. These solutions involve simple algorithms in which both the quantum and classical degrees of freedom are described in terms of continuous variables and evolve according to classical-like equations of motion. However, since these schemes are approximate, they must be benchmarked against the exact quantum and QCLE surface-hopping solutions for a variety of simple and complex systems to determine the conditions under which they are valid. To illustrate the validity of the PBME and FBTS approaches, we review the results of a simple model for a condensed-phase photo-induced electron transfer and present new results for a realistic model for a proton transfer in a hydrogen-bonded complex dissolved in a polar nanocluster. Overall, the results demonstrate that caution must be taken when applying these approximate methods, since they can manifest non-physical behaviour for systems where a mean-field-like description is not valid.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: Metadynamics (MetaD) is a method that augments molecular dynamics (MD) calculations of all types (classical and quantum) to help systems overcome energy barriers and explore regions of phase space that would otherwise not be seen during a simulation. The method has seen wide ranging uses, and it has proven especially useful for the study of reactions in which bonds break and form. In such cases, the timescale challenges of MD are profoundly limiting, and the advent of this new paradigm for biasing simulations has proven to be incredibly useful. In this review, we set out to summarise the large body of work that uses MetaD for studying reactions so that others can more easily implement this method in their own work. After a brief introduction of the method, we provide detailed summaries of the method applied in various contexts including condensed phase and biological reactions.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: Charge-transfer-to-solvent excited iodide–polar solvent molecule clusters, [I− (Solv)n ]*, have attracted substantial interest over the past 20 years as they can undergo intriguing relaxation processes leading ultimately to the formation of gas-phase molecular analogues of the solvated electron. In this review article, we present a comprehensive overview of the development and application of state-of-the-art first-principles molecular dynamics simulation approaches to understand and interpret the results of femtosecond photoelectron spectroscopy experiments on [I− (Solv)n ]* relaxation, which point to a high degree of solvent specificity in the electron solvation dynamics. The intricate molecular details of the [I− (Solv)n ]* relaxation process are presented, and by contrasting the relaxation mechanisms of clusters with several different solvents (water, methanol and acetonitrile), the molecular basis of the solvent specificity of electron solvation in [I− (Solv)n ]* is uncovered, leading to a more refined view of the manifestation of electron solvation in small gas-phase clusters.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: Although the force field (FF)-based molecular dynamics (MD) simulation has been widely applied to rationalise the experimental observations and measurements in chemistry, physics, materials and life science for years, traditional FF suffers from the incapability for describing chemical reactions, which are crucial in many important transformation processes. In order to simulate the collective switching process in azobenzene-based self-assemble monolayers on Au(111) surface, reactive MD simulations with alternative FF were implemented. The classic torsion function has been modified to depict the diabatic potential energy curves for cis and trans isomers, respectively. A switching function is further introduced to connect two N = N rotation functions, and the surface hopping between the cis and trans curves is allowed. By using the reactive rotation potential and switching function, the collective effect of numerous reaction centres and the influence of environment on the quantum yield in the complex system were explored at mesoscopic dimension and timescales. The reactive FF may be also applicable for other complicated systems containing stilbene derivatives. Limitation and perspective for further developments for the other complicated reactions are also addressed.
    Molecular Simulation 02/2015; 41.
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    ABSTRACT: The fact that chemical reactions at environmental interfaces are becoming accessible to quantum mechanical computational studies provides geochemical researchers with a new means to predict properties that cannot readily be measured and to develop molecular-level understanding of geochemical model systems. Recent computational studies of Cu2+ and adsorption onto the Keggin-based aqueous aluminium nanoparticle (), or Al30, revealed opposing trends in adsorption site preference as a function of molecule surface topology. Specifically, the adsorption site favourable for the inner-sphere adsorption of Cu2+ is on the caps of Al30 while outer-sphere prefers adsorption in the so-called beltway region of the molecule. When co-adsorbed, it is predicted that both species adsorb in the beltway, consistent with an experimental crystal structure. Here, we discuss results for individual cation and anion adsorption to Al30. Our goals are to better understand how the adsorbate properties govern interactions with Al30 and to assess whether generalisations can be formed. We test the reactivity of cations (Cu2+, Pb2+, Zn2+) and anions (, Cl− ) to aqueous Al30 by using density functional theory modelling. It is determined that all the cations favour the adsorption sites on the caps of Al30 and both anions favour outer-sphere adsorption in the beltway region. The results are discussed in terms of the electrostatic potential of Al30 and three-dimensional induced charge density mapping.
    Molecular Simulation 02/2015; 41.
  • Praveenkumar Sappidi, Upendra Natarajan
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    ABSTRACT: The conformational structure of dilute atactic-poly(methacrylic acid) (PMA) solution in binary water–ethanol mixture was investigated by molecular dynamics simulations, over 0–0.9 ethanol (co-solvent) fraction. The radius of gyration 〈Rg〉, torsion angle distribution, intra-chain hydrogen bonds (H-bonds), and H-bonds for PMA–water, PMA–ethanol and water–ethanol, atom–atom and atom–group pair radial distribution functions were analysed. An increase in the ethanol fraction leads to chain expansion. The non-monotonic variation of 〈Rg〉, commensurate with the experimentally observed behaviour of intrinsic viscosity [η], takes place by H-bonding effects between PMA, water and ethanol, as driven by the differences in the chemical structure of water and ethanol. The PMA repeat units are closer to the CH2 groups as compared with CH3 groups of ethanol, in the nearest coordination shell. Water as compared with ethanol is able to coordinate closer to the PMA repeat unit centre of mass. Intra-chain H-bonding depreciates with an increase in the ethanol content in solution. The changes, across the ethanol fraction range, in chain dimensions and of predicted intrinsic viscosity by the simulations, compare well with experimental results in the literature.
    Molecular Simulation 01/2015;
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    ABSTRACT: A data set comprising of 27 myo-inositol derivatives based on tetrakisphosphates and bispyrophosphates were used in the development of quantitative structure-activity relationship (QSAR) model for investigating its allosteric effector property against human hemoglobin. Three-dimensional structures of the investigated compounds were subjected to geometry optimizations at the density functional theory level. Physicochemical features of low-energy conformers were represented by quantum chemical and molecular descriptors. Feature selection by means of unsupervised forward selection and stepwise linear regression resulted in a set of 4 important descriptors. Multivariate analysis was performed using multiple linear regression (MLR), artificial neural network (ANN) and support vector machine (SVM). Robustness of the predictive performance of all methods was deduced from internal and external validation, which afforded Q2CV values of 0.6306, 0.7484 and 0.8722 using MLR, ANN and SVM, respectively, for the former and Q2Ext values of 0.8332, 0.8847 and 0.9694, respectively, for the latter. The predictive model is anticipated to be useful for further guiding the rational design of robust allosteric effectors of human hemoglobin.
    Molecular Simulation 12/2014;
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    ABSTRACT: Human serotonin N-acetyltransferase (hAANAT), included in the melatonin biosynthesis, plays a pivotal role in the regulation of the biological clock and the daily rhythm. In this research, a reliable model of hAANAT was first constructed by the homology modelling method. Then the inhibition mode of two representative rhodanine-based inhibitors was explored by molecular dynamics simulations and energy analyses. The results show that the inhibitor class could share a similar inhibition mechanism in which the carboxyl moiety is positioned in the Ac-CoA binding region while the other end spans the serotonin binding pocket. The interaction between the inhibitor's carboxyl and the enzyme seems to be more important according to the decomposition of binding free energy. Based on the proposed inhibition mode, the inhibitor's improvement was carried out to obtain a more potent compound. The newly designed inhibitor, with the larger binding free energy, exhibits the stronger interaction with the related residues of the enzyme by the added chemical groups. This work will shed light on the inhibition mechanism of the rhodanine-based inhibitors and promote the development of a new drug targeting hAANAT.
    Molecular Simulation 12/2014; 40(15).
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    ABSTRACT: We present a dissipative particle dynamics (DPD) study of scaling behaviour for three polymer models. The scaling behaviour is explored for the conformational and dynamic properties of unentangled polymer melts. DPD employs a bead–spring model together with an aggressive coarse-graining to represent polymers at the mesoscale. The first model studied utilises a simple soft repulsion potential for the bead–bead interactions together with a harmonic spring potential to connect beads into a polymer chain. The second model differs from the first model by replacing the harmonic spring with a finitely extensible nonlinear elastic spring. The third model uses realistic coarse-grain potentials for the bead–bead, spring and bending interactions based on the iterative Boltzmann inversion procedure and it corresponds to a mesoscopic model of polyethylene. We systematically vary the chain length and spring constant (in the case of the first and second models), and simulate the conformational properties such as the end-to-end distance or radius of gyration, and dynamic properties such as the centre-of-mass self-diffusion coefficient or viscosity. The scaling of the conformational and dynamic properties with chain length (scaling laws) is compared with the Rouse theory, which is considered as a standard theory for unentangled polymer melts. The comparison shows that simulated scaling laws typically agree with the Rouse scaling laws for the DPD polymer models with more than 10 DPD beads. For the shorter DPD polymers, deviations from the Rouse theory exist and become significant for the dynamic properties, especially for the viscosity of the polymer melts.
    Molecular Simulation 12/2014; 40(15).
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    ABSTRACT: PcrA DNA helicase uses the free energy of hydrolysis and binding of ATP to unwind double-stranded DNA (ds-DNA). There are two states of PcrA, termed the substrate and product complexes and, through the conformational changes between these two states, PcrA moves along ds-DNA and separates the two strands. In this study, two different methods, namely chain minimisation (CM, less reliable method) and auto targeted molecular dynamic (TMD) simulation (more reliable), were performed to generate two different initial reaction pathways between these two states, and then fixed root mean square distance (RMSD) TMD simulation was performed to optimise these two initial pathways. In general, the two optimised pathways share very similar major conformational changes, but are different in the minor motions. The potential energy profiles of the two improved pathways are generally similar, but the one generated by the improved TMD path is slightly lower. Considering the poor reliability of the initial path generated by CM and insignificant improvements of the auto-TMD path, our study suggests that fixed RMSD TMD simulation can generate reliable reaction pathways, but the different initial paths still have some influence on the detailed conformational analysis.
    Molecular Simulation 12/2014; 40(15).
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    ABSTRACT: The increase in number of cancer-affected patients worldwide has amplified the need for the development of new anticancer drug-like molecules. In this background, the quantitative structure–activity relationship (QSAR) has proved to be an efficient tool for the drug-designing process. In this work, the in silico technique is applied to study the anticancer activity of two different sets of triphenyl methyl (TPM) derivatives on SK-MEL 5 cell line. Chemometric tools such as genetic partial least squares (G/PLS) algorithm was used for phenethylamine and d-phenylalanine TPM derivatives, whereas genetic function approximation technique was utilised for phosphonate and phosphonochloridate TPM derivatives in development of QSAR models. The calculated descriptors represent the influence of geometry, topology, molecular shape and polarisability of the molecules on the anticancer activity of TPM derivatives. Internal and external validation tests of the models provide satisfactory results (R 2 = 0.823, 0.880, Q 2 = 0.732, 0.771, [Inline formula] = 0.644, 0.716) proving the fitness and predictivity of the model in compliance with Organization for Economic Co-operation and Development principles. The developed models can be effectively utilised further for the prediction of anticancer activity of new compounds that fall within the domain of applicability of the referred models.
    Molecular Simulation 12/2014; 40(15).
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    ABSTRACT: Owing to its unique function to release the progeny virus particles from the surface of an infected cell, neuraminidase has drawn special attention for developing new drugs to treat influenza viruses. The 150-cavity that is adjacent to the active pocket of the group-1 neuraminidase (N1) renders the conformational change from ‘open’ form to ‘closed’ form when enzyme is binding with a ligand. Consequently, it would be a better strategy to design multi-binding-site inhibitors including X and R groups with proper shapes, sizes and electronic charges fitting into the active site. The NCI and ZINC fragment databases were screened for finding the optimal fragments with de novo design technique. By doing so, 24 derivatives of oseltamivir were obtained by linking the fragments at two different sites of the scaffold of oseltamivir. Molecular docking and dynamics showed that these compounds not only adopt more favourable conformation but also have stronger binding interaction with receptor. Most importantly, all compounds skilfully pass through the cleft (formed by Glu119 and Arg156) and fit into 150-cavity. Therefore, the selected 24 derivatives may become promising candidates for treating influenza virus; in addition, the findings reported here may at least provide useful insights and stimulate new strategy in this area.
    Molecular Simulation 12/2014; 40(15).
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    ABSTRACT: A polyelectrolyte (PEL) chain having a smeared charge distribution is simulated by using Metropolis Monte Carlo simulation technique. The PEL chain is charged in such a way that the total charge is smeared along the chain. The system is studied in various solvent conditions; good solvents, [Inline formula], where a neutral chain behaves as if it did not interact with itself, and poor solvents. In each solvent regime, the strength of electrostatic interaction is varied. Equilibrium quantities are obtained, and the results are analysed. A continuous transition from a coiled structure to a stretched structure is observed in good and [Inline formula] solvents, while in poor solvent regime intermediate structures are observed.
    Molecular Simulation 12/2014; 40(15).