Self-Diffusion in Molecular Fluids and Noble Gases: Available Data

Suárez-Iglesias, Octavio; Medina, Ignacio; Sanz, María de los Ángeles; Pizarro, Consuelo; Bueno, Julio L.

doi:10.1021/acs.jced.5b00323

Cited by 67 publications

(54 citation statements)

References 539 publications

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“…The first considers studies of water in the bulk phase [27]- [197], while the second explores studies of water under confinement [198]- [286]. (ii) To present comparisons of the most reliable calculations with available experimental data [287]- [298]. (iii) To discuss issues that could affect the accuracy of the self-diffusion coefficient calculated using molecular 7 undertaken for the self-diffusivities obtained from ab initio models.…”

Section: Introductionmentioning

confidence: 99%

Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies

Tsimpanogiannis

Moultos

Franco

et al. 2018

Molecular Simulation

165

115

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Section: Introductionmentioning

confidence: 99%

Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies

Tsimpanogiannis

Moultos

Franco

et al. 2018

Molecular Simulation

165

115

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“…All the calculated quantities are reported along with an estimate of the statistical error, calculated as the standard deviation over five independent simulation repeats (for D and ε, see Sections II.4.5 and II.4.7), or using block-averaging 1 over a single simulation (for all other quantities).For each property, experimental data was usually only available for a subset of the 57 molecules. The corresponding experimental values are listed inTable B.3 based onRefs [126][127][128][129][130][131][132][133][134][135][136][137][138][139][140][141][142][143][144][174][175][176][177][178][179][180][181][182][183][184][185][186]. .The classical[187][188][189][190] (i.e.…”

mentioning

confidence: 99%

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Horta

Merz

Fuchs

et al. 2016

J. Chem. Theory Comput.

147

287

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This article reports on the calibration and validation of a new GROMOS-compatible parameter set 2016H66 for small organic molecules in the condensed phase. The calibration is based on 62 organic molecules spanning the chemical functions alcohol, ether, aldehyde, ketone, carboxylic acid, ester, amine, amide, thiol, sulfide, and disulfide, as well as aromatic compounds and nucleic-acid bases. For 57 organic compounds, the calibration targets are the experimental pure-liquid density ρliq and the vaporization enthalpy ΔHvap, as well as the hydration free energy ΔGwat and the solvation free energy ΔGche in cyclohexane, at atmospheric pressure and at (or close to) room temperature. The final root-mean-square deviations (RMSD) for these four quantities over the set of compounds are 32.4 kg m(-3), 3.5 kJ mol(-1), 4.1 kJ mol(-1), and 2.1 kJ mol(-1), respectively, and the corresponding average deviations (AVED) are 1.0 kg m(-3), 0.2 kJ mol(-1), 2.6 kJ mol(-1), and 1.0 kJ mol(-1), respectively. For the five nucleic-acid bases, the parametrization is performed by transferring the final 2016H66 parameters from analogous organic compounds followed by a slight readjustment of the charges to reproduce the experimental water-to-chloroform transfer free energies ΔGtrn. The final RMSD for this quantity over the five bases is 1.7 kJ mol(-1), and the corresponding AVED is 0.8 kJ mol(-1). As an initial validation of the 2016H66 set, seven additional thermodynamic, transport, and dielectric properties are calculated for the 57 organic compounds in the liquid phase. The agreement with experiment in terms of these additional properties is found to be reasonable, with significant deviations typically affecting either a specific chemical function or a specific molecule. This suggests that in most cases, a classical force-field description along with a careful parametrization against ρliq, ΔHvap, ΔGwat, and ΔGche results in a model that appropriately describes the liquid in terms of a wide spectrum of its physical properties.

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“…It should also be noted that in the force fields FF-2, FF-3, and FF-5, the molecule was rigid, and in the FF-1, FF-4, only bonding lengths were fixed (the potentials of valence and torsion angles are given). A comparison of the calculated self-diffusion coefficients of alcohols with experimental data from research work [42] was conducted in the first stage. The comparison at atmospheric pressure is shown in Figures 1-3.…”

Section: Force Fields For Alcoholsmentioning

confidence: 99%

“…Temperature dependence of the isopropanol self-diffusion coefficient; open symbols represent experimental data[42], full symbols represent molecular dynamics simulation.…”

mentioning

confidence: 99%

Diffusion in Binary Aqueous Solutions of Alcohols by Molecular Simulation

Klinov

Анашкин

2019

Processes

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Based on the molecular dynamics method, the calculations for diffusion coefficients were carried out in binary aqueous solutions of three alcohols: ethanol, isopropanol, and tert-butanol. The intermolecular potential TIP4P/2005 was used for water; and five force fields were analyzed for the alcohols. The force fields providing the best accuracy of calculation were identified based on a comparison of the calculated self-diffusion coefficients of pure alcohols with the experimental data for internal (Einstein) diffusion coefficients of alcohols in solutions. The temperature and concentration dependences of the interdiffusion coefficients were determined using Darken’s Equation. Transport (Fickian) diffusion coefficients were calculated using a thermodynamic factor determined by the non-random two-liquid (NRTL) and Willson models. It was demonstrated that for adequate reproduction of the experimental data when calculating the transport diffusion coefficients, the thermodynamic factor has to be 0.64. Simple approximations were obtained, providing satisfactory accuracy in calculating the concentration and temperature dependences of the transport diffusion coefficients in the studied mixtures.

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Self-Diffusion in Molecular Fluids and Noble Gases: Available Data

Cited by 67 publications

References 539 publications

Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies

Self-diffusion coefficient of bulk and confined water: a critical review of classical molecular simulation studies

A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set

Diffusion in Binary Aqueous Solutions of Alcohols by Molecular Simulation

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