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 1.12

  • 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

  • [Show abstract] [Hide abstract]
    ABSTRACT: The conformations of polydispersed polymer chains grafted on nanoparticles (NPs) are investigated by coarse-grained molecular dynamics simulations. Combined with the geometric and steric features, we find that most results can be understood by analysing the excluded volume interaction condition of the accommodated chains. By controlling suitable NP size and grafting density, as well as designing a suitable route for preparing the grafted chains with controllable polydispersity and length, it is possible to obtain polymer chains with various conformations, which may be greatly helpful for improving the dispersion of the grafted NPs in the polymer matrix. These results shed light on improved designs of grafted NPs and a better control of dispersion in polymer matrices for promoting the performance of polymer nanocomposite materials.
    Molecular Simulation 03/2015; 41(4).
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    ABSTRACT: The effects of morin and nordihydroguaiaretic acid (NDGA), two plant secondary metabolites, on porcine pancreatic phospholipase A2 (PLA2) were investigated by isothermal titration calorimetry (ITC) and in silico docking analyses. The binding energies obtained for NDGA and morin from the ITC studies are − 6.36 and − 5.91 kcal mol− 1, respectively. Similarly, the glide scores obtained for NDGA and morin towards PLA2 were − 7.32 and − 7.23 kcal mol− 1, respectively. Further the docked complexes were subjected to MD simulation in the presence of explicit water molecules to check the binding stability of the ligands in the active site of PLA2. The bound ligands make hydrogen bonds with the active site residues of the enzyme and coordinate bonds with catalytically important Ca2+ ion. The binding of ligands at the active site of PLA2 may also contribute to the reported anti-inflammatory properties of NDGA and morin.
    Molecular Simulation 03/2015; 41(4).
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    ABSTRACT: Benign prostatic hyperplasia (BPH) is caused by augmented levels of androgen dihydrotestosterone (DHT) which is involved in the growth of the prostate in humans. 5α-Reductase type II (5αR2) is an intracellular enzyme that catalyses the formation of DHT from testosterone; hence, the inhibition of 5αR2 has emerged as one of the most promising strategies for the treatment of BPH. In this study, a computational approach that integrates ligand-based pharmacophore modelling, virtual screening, molecular docking and molecular dynamics (MD) simulations was adopted to discover novel 5αR2 inhibitors with less side effects. After validating by Fischer's randomisation and Güner–Henry test, the best quantitative pharmacophore model (Hypo1), consisting of two hydrogen-bond acceptors and three hydrophobic features, was subsequently used as a three-dimensional-query in virtual screening to identify potential hits from Maybridge and National Cancer Institute databases. These hits were further filtered by ADMET (absorption, distribution, metabolism, elimination and toxicology) and molecular docking experiments, and their binding stabilities were validated by 10-ns MD simulations. Finally, only one hit was identified as a potential lead based on higher predicted inhibitory activity to 5αR2 compared with the most active inhibitor (finasteride). Our results further suggest that this potential lead could easily be synthesised and has structural novelty, making it a promising candidate for treating BPH.
    Molecular Simulation 03/2015; 41(4).
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    ABSTRACT: Benzodiazepines have been widely used therapeutically for their ability to act as tranquilizers, sedative-hypnotics, antiepileptics and frequently prescribed to women during pregnancy for managing preeclampsia or eclampsia. The present report deals with quantitative structure–toxicity relationship (QSTR) modelling of a series of benzodiazepines, in the context of the 3R concept, to provide an insight into the main structural fragments that impart toxicity to these molecules. Three different in silico techniques, namely descriptor-based QSTR, group-based QSTR and 3D-toxicophore mapping, were employed to obtain statistically significant models. Multiple in silico models made it possible to reach a unified conclusion regarding the structural fragments and features responsible for the toxicity and provide consensus predictions which can be effectively utilised to design and predict less toxic new benzodiazepines.
    Molecular Simulation 03/2015; 41(4).
  • 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.
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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 lens epithelium-derived growth factor/transcriptional co-activator p75 (LEDGF/p75) and hepatoma-derived growth factor related protein 2 (HRP2) are binding partners for human immunodeficiency virus type integrase protein in human cells. LEDGF/p75 and HRP2 share a similar domain organisation and have an apparent evolutionary and functional relationship. The integrase-binding domain (IBD) is located in the C-terminal region of both LEDGF/p75 and HRP2 protein. Unlike HRP2, the IBD of LEDGF/p75 is well explored and its NMR structure is available in Protein Data Bank (PDB) database. In this work, comparative sequence analysis and molecular modelling approaches were employed to characterise the IBD of human HRP2 protein. Sequence analysis of HRP2 IBD showed variability in C-terminal region while the other part remains conserved. The homologous sequence of the IBD in HRP2 was modelled by using NMR structure of LEDGF/p75 IBD as a template (PDB: 1Z9E). Secondary structure of variable region was initially predicted as an alpha helix using SAM-T06 server. The final model was subjected to molecular dynamics (MD) simulations up to 100 ns to find out the precise orientation of model structure. Root mean square deviation and B-factor analyses indicate stable IBD core region and loosely packed variable region during 100 ns MD simulation. The modelled IBD structure of HRP2 exhibits overall similar topology with LEDGF/p75 IBD and appears as a stable fold consisting of five compact alpha helices. However, the variable region (552–574 residues) shows unstable helix–loop–helix conformation. This comprehensive study of HRP2 IBD provides in-depth sequence and structural information that may be exploited in anti-retroviral drug design studies.
    Molecular Simulation 12/2014;
  • Feng Huo, Zhiping Liu
    Molecular Simulation 12/2014;