A simple, efficient polarizable molecular model for liquid carbon tetrachloride

Kunz, Anna-Pitschna E.; Eichenberger, Andreas P.; Gunsteren, Wilfred F. van

doi:10.1080/00268976.2010.533208

Cited by 16 publications

(16 citation statements)

References 56 publications

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“…5,6,8–15 We take a different approach here. Here, we develop classical fixed-charge molecular solvent models for water, CCl 4 , CHCl 3 , and CH 2 Cl 2 , but we parameterize them based on experimental dielectric constants, in addition to the solvent density and enthalpy of vaporization.…”

Section: Introductionmentioning

confidence: 99%

Simple Liquid Models with Corrected Dielectric Constants

2012

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Molecular simulations often use explicit-solvent models. Sometimes explicit-solvent models can give inaccurate values for basic liquid properties, such as the density, heat capacity, and permittivity, as well as inaccurate values for molecular transfer free energies. Such errors have motivated the development of more complex solvents, such as polarizable models. We describe an alternative here. We give new fixed-charge models of solvents for molecular simulations – water, carbon tetrachloride, chloroform and dichloromethane. Normally, such solvent models are parameterized to agree with experimental values of the neat liquid density and enthalpy of vaporization. Here, in addition to those properties, our parameters are chosen to give the correct dielectric constant. We find that these new parameterizations also happen to give better values for other properties, such as the self-diffusion coefficient. We believe that parameterizing fixed-charge solvent models to fit experimental dielectric constants may provide better and more efficient ways to treat solvents in computer simulations.

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Section: Introductionmentioning

confidence: 99%

Simple Liquid Models with Corrected Dielectric Constants

2012

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“…Schematic representation of a thermodynamic cycle in which H nonpol and H pol denote a deca-alanine solute in a nonpolarizable and a polarizable solvent, respectively; H nonpol+rest and H pol+rest denote a decaalanine solute with α-helical or β-hairpin hydrogen-bond restraining in a nonpolarizable and a polarizable solvent, respectively; C α and C β denote the α-helical and the β-hairpin conformation, respectively. polarizability in the latter, 13 whereas for the other solvents, other nonbonded force-field parameters are also different.…”

Section: Resultsmentioning

confidence: 96%

Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide

Lin¹,

Gunsteren²

2015

J. Chem. Theory Comput.

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The free enthalpy of changing a nonpolarizable solvent into a polarizable solvent is calculated for an alanine decapeptide solvated in water, methanol, chloroform, or carbon tetrachloride. Introducing polarizability into a water solvent does not change the relative stability between the α-helix and the β-hairpin, while for methanol and chloroform the α-helix is stabilized by about 1 kJ mol(-1) per residue and for carbon tetrachloride by about 2 kJ mol(-1) per residue. These results suggest that the less polar the solvent is, the more the α-helical structure is stabilized with respect to the β-hairpin structure by the use of a polarizable solvent model instead of a nonpolarizable one. This highlights that inclusion of polarizability in models for less polar and nonpolar solvents or protein environments is as important as, if not more important than, including polarizability in models for liquid water.

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“…The scattering lengths of b C = 6.646 fm and b Cl = 9.58 fm were used (Lide 2007). The root-meansquare displacements r CCl and r ClCl were estimated from those of water, see (Kunz et al 2011). The neutron scattering intensities determined in that way and those measured (Misawa 1989;Pusztai and McGreevy 1997) are displayed in Fig.…”

Section: Neutron Scatteringmentioning

confidence: 98%

“…For the validation of a new charge-on-spring (COS) polarisable model of CCl 4 (Kunz et al 2011), the methodology described above was used to determine the neutron scattering intensities. A 1 ns production simulation was carried out.…”

Section: Neutron Scatteringmentioning

confidence: 99%

Biomolecular structure refinement using the GROMOS simulation software

et al. 2011

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For the understanding of cellular processes the molecular structure of biomolecules has to be accurately determined. Initial models can be significantly improved by structure refinement techniques. Here, we present the refinement methods and analysis techniques implemented in the GROMOS software for biomolecular simulation. The methodology and some implementation details of the computation of NMR NOE data, (3)J-couplings and residual dipolar couplings, X-ray scattering intensities from crystals and solutions and neutron scattering intensities used in GROMOS is described and refinement strategies and concepts are discussed using example applications. The GROMOS software allows structure refinement combining different types of experimental data with different types of restraining functions, while using a variety of methods to enhance conformational searching and sampling and the thermodynamically calibrated GROMOS force field for biomolecular simulation.

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A simple, efficient polarizable molecular model for liquid carbon tetrachloride

Cited by 16 publications

References 56 publications

Simple Liquid Models with Corrected Dielectric Constants

Simple Liquid Models with Corrected Dielectric Constants

Effects of Polarizable Solvent Models upon the Relative Stability of an α-Helical and a β-Hairpin Structure of an Alanine Decapeptide

Biomolecular structure refinement using the GROMOS simulation software

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