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Oliwia M. Szklarczyk Eirini Arvaniti Wilfred F. van Gunsteren 《Journal of computational chemistry》2015,36(17):1311-1321
Force field parameters for polarizable coarse‐grained (CG) supra‐atomic models of liquid cyclohexane are proposed. Two different bead sizes were investigated, one representing two fine‐grained (FG) CH2r united atoms of the cyclohexane ring, and one representing three FG CH2r united atoms. Electronic polarizability is represented by a massless charge‐on‐spring particle connected to each CG bead. The model parameters were calibrated against the experimental density and heat of vaporization of liquid cyclohexane, and the free energy of cyclohexane hydration. Both models show good agreement with thermodynamic properties of cyclohexane, yet overestimate the self‐diffusion. The dielectric properties of the polarizable models agree very well with experiment. © 2015 Wiley Periodicals, Inc. 相似文献
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Cecilia Devi Wilfred 《合成通讯》2013,43(22):2859-2867
A tandem oxidation reaction has been utilized to prepare ethyl (E)‐4,5‐dioxo‐2‐hexadecenoate, the immediate precusor to the antiviral fungal metabolite podoscyphic acid. 相似文献
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Prof. Dr. Wilfred F. van Gunsteren Prof. Xavier Daura Dr. Patrick F. J. Fuchs Prof. Niels Hansen Prof. Dr. Bruno A. C. Horta Prof. Dr. Philippe H. Hünenberger Prof. Dr. Alan E. Mark Dr. Maria Pechlaner Prof. Dr. Sereina Riniker Prof. Dr. Chris Oostenbrink 《Chemphyschem》2021,22(3):264-282
Computer simulations of molecular systems enable structure-energy-function relationships of molecular processes to be described at the sub-atomic, atomic, supra-atomic or supra-molecular level and plays an increasingly important role in chemistry, biology and physics. To interpret the results of such simulations appropriately, the degree of uncertainty and potential errors affecting the calculated properties must be considered. Uncertainty and errors arise from (1) assumptions underlying the molecular model, force field and simulation algorithms, (2) approximations implicit in the interatomic interaction function (force field), or when integrating the equations of motion, (3) the chosen values of the parameters that determine the accuracy of the approximations used, and (4) the nature of the system and the property of interest. In this overview, advantages and shortcomings of assumptions and approximations commonly used when simulating bio-molecular systems are considered. What the developers of bio-molecular force fields and simulation software can do to facilitate and broaden research involving bio-molecular simulations is also discussed. 相似文献
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A polarizable empirical force field for molecular dynamics simulation of liquid hydrocarbons 下载免费PDF全文
Oliwia M. Szklarczyk Stephan J. Bachmann Wilfred F. van Gunsteren 《Journal of computational chemistry》2014,35(10):789-801
Electronic polarizability is usually treated implicitly in molecular simulations, which may lead to imprecise or even erroneous molecular behavior in spatially electronically inhomogeneous regions of systems such as proteins, membranes, interfaces between compounds, or mixtures of solvents. The majority of available molecular force fields and molecular dynamics simulation software packages does not account explicitly for electronic polarization. Even the simplest charge‐on‐spring (COS) models have only been developed for few types of molecules. In this work, we report a polarizable COS model for cyclohexane, as this molecule is a widely used solvent, and for linear alkanes, which are also used as solvents, and are the precursors of lipids, amino acid side chains, carbohydrates, or nucleic acid backbones. The model is an extension of a nonpolarizable united‐atom model for alkanes that had been calibrated against experimental values of the density, the heat of vaporization and the Gibbs free energy of hydration for each alkane. The latter quantity was used to calibrate the parameters governing the interaction of the polarizable alkanes with water. Subsequently, the model was tested for other structural, thermodynamic, dielectric, and dynamic properties such as trans/gauche ratios, excess free energy, static dielectric permittivity, and self‐diffusion. A good agreement with the experimental data for a large set of properties for each considered system was obtained, resulting in a transferable set of polarizable force‐field parameters for CH2, CH3, and CH4 moieties. © 2014 Wiley Periodicals, Inc. 相似文献
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Andreas P. Eichenberger Zrinka Gattin Garif Yalak Wilfred F. vanGunsteren 《Helvetica chimica acta》2010,93(10):1857-1869
The three‐dimensional structure of a protein is stabilized by a number of different atomic interactions. One of these is hydrogen bonding. Its influence on the spatial structure of the hen egg white lysozyme is investigated by replacing peptide bonds (except those of the two proline residues) by ester bonds. Molecular dynamics simulations of native and ester‐linked lysozyme are compared with the native crystal structure and with NOE distance bounds derived from solution NMR experiments. The ester‐linked protein shows a slight compaction while losing its native structure. However, it does not unfold completely. The structure remains compact due to its hydrophobic core and a changed network of hydrogen bonds involving side chains. 相似文献
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David Poger Wilfred F. Van Gunsteren Alan E. Mark 《Journal of computational chemistry》2010,31(6):1117-1125
A new force field for the simulation of dipalmitoylphosphatidylcholine (DPPC) in the liquid‐crystalline, fluid phase at zero surface tension is presented. The structure of the bilayer with the area per lipid (0.629 nm2; experiment 0.629–0.64 nm2), the volume per lipid (1.226 nm3; experiment 1.229–1.232 nm3), and the ordering of the palmitoyl chains (order parameters) are all in very good agreement with experiment. Experimental electron density profiles are well reproduced in particular with regard to the penetration of water into the bilayer. The force field was further validated by simulating the spontaneous assembly of DPPC into a bilayer in water. Notably, the timescale on which membrane sealing was observed using this model appears closer to the timescales for membrane resealing suggested by electroporation experiments than previous simulations using existing models. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 相似文献