MD simulations of hydrogen diffusion in ZIF-11 with a force field fitted to experimental adsorption data

We present a hierarchical Bayesian framework for the selection of force fields in molecular dynamics (MD) simulations. The framework associates the variability of the optimal parameters of the MD potentials under different environmental conditions with the corresponding variability in experimental data. The high computational cost associated with the hierarchical Bayesian framework is reduced by orders of magnitude through a parallelized Transitional Markov Chain Monte Carlo method combined with the Laplace Asymptotic Approximation. The suitability of the hierarchical approach is demonstrated by performing MD simulations with prescribed parameters to obtain data for transport coefficients under different conditions, which are then used to infer and evaluate the parameters of the MD model. We demonstrate the selection of MD models based on experimental data and verify that the hierarchical model can accurately quantify the uncertainty across experiments; improve the posterior probability density function estimation of the parameters, thus, improve predictions on future experiments; identify the most plausible force field to describe the underlying structure of a given dataset. The framework and associated software are applicable to a wide range of nanoscale simulations associated with experimental data with a hierarchical structure.

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Analysis of carbon dioxide sequestration in shale gas reservoirs by using experimental adsorption data and adsorption models

Journal of Natural Gas Science and Engineering ◽

10.1016/j.jngse.2016.02.052 ◽

2016 ◽

Vol 36 ◽

pp. 1087-1105 ◽

Cited By ~ 36

Author(s):

Sukru Merey ◽

Caglar Sinayuc

Keyword(s):

Carbon Dioxide ◽

Shale Gas ◽

Carbon Dioxide Sequestration ◽

Gas Reservoirs ◽

Adsorption Models ◽

Experimental Adsorption ◽

Shale Gas Reservoirs ◽

Adsorption Data

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Development of a ReaxFF Force Field for Cu/S/C/H and Reactive MD Simulations of Methyl Thiolate Decomposition on Cu (100)

The Journal of Physical Chemistry B ◽

10.1021/acs.jpcb.7b06976 ◽

2017 ◽

Vol 122 (2) ◽

pp. 888-896 ◽

Cited By ~ 9

Author(s):

Jejoon Yeon ◽

Heather L. Adams ◽

Chad E. Junkermeier ◽

Adri C. T. van Duin ◽

Wilfred T. Tysoe ◽

...

Keyword(s):

Force Field ◽

Md Simulations ◽

Reaxff Force Field

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Simulating Absorption Spectra of Flavonoids in Aqueous Solution: A Polarizable QM/MM Study

Molecules ◽

10.3390/molecules25245853 ◽

2020 ◽

Vol 25 (24) ◽

pp. 5853

Author(s):

Sulejman Skoko ◽

Matteo Ambrosetti ◽

Tommaso Giovannini ◽

Chiara Cappelli

Keyword(s):

Molecular Dynamics ◽

Aqueous Solution ◽

Hydrogen Bonding ◽

Force Field ◽

Absorption Spectra ◽

Computational Study ◽

Md Simulations ◽

Quantum Mechanical ◽

Hydrogen Bonding Interactions

We present a detailed computational study of the UV/Vis spectra of four relevant flavonoids in aqueous solution, namely luteolin, kaempferol, quercetin, and myricetin. The absorption spectra are simulated by exploiting a fully polarizable quantum mechanical (QM)/molecular mechanics (MM) model, based on the fluctuating charge (FQ) force field. Such a model is coupled with configurational sampling obtained by performing classical molecular dynamics (MD) simulations. The calculated QM/FQ spectra are compared with the experiments. We show that an accurate reproduction of the UV/Vis spectra of the selected flavonoids can be obtained by appropriately taking into account the role of configurational sampling, polarization, and hydrogen bonding interactions.

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Adsorption of chromium (VI) from aqueous solutions on activated carbon

Water Science & Technology ◽

10.2166/wst.1994.0477 ◽

1994 ◽

Vol 30 (9) ◽

pp. 191-197 ◽

Cited By ~ 78

Author(s):

R. Leyva Ramos ◽

A. Juarez Martinez ◽

R. M. Guerrero Coronado

Keyword(s):

Activated Carbon ◽

Adsorption Isotherm ◽

Adsorption Capacity ◽

Ph Effect ◽

Freundlich Isotherm ◽

Maximum Adsorption Capacity ◽

Experimental Adsorption ◽

Ph Values ◽

Chromium Vi ◽

Adsorption Data

The adsorption isotherm of chromium (VI) on activated carbon was obtained in a batch adsorber. The experimental adsorption data were fitted reasonably well to the Freundlich isotherm. The effect of pH on the adsorption isotherm was investigated at pH values of 4, 6, 7, 8, 10 and 12. It was found that at pH < 6, Cr(VI) was adsorbed and reduced to Cr(III) by the catalytic action of the carbon and that at pH ≥ 12, Cr(VI) was not adsorbed on activated carbon. Maximum adsorption capacity was observed at pH 6 and the adsorption capacity was diminished about 17 times by increasing the pH from 6 to 10. The pH effect was attributed to the different complexes that Cr(VI) can form in aqueous solution. The adsorption isotherm was also affected by the temperature since the adsorption capacity was increased by raising the temperature from 25 to 40°C. It was concluded that Cr(VI) was adsorbed significantly on activated carbon at pH 6 and that the adsorption capacity was greatly dependent upon pH.

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A force field for MD simulations on rhenium organometallic compounds developed from enthalpy of sublimation and X-ray diffraction measurements

The Journal of Chemical Thermodynamics ◽

10.1016/j.jct.2019.01.016 ◽

2019 ◽

Vol 133 ◽

pp. 60-69 ◽

Cited By ~ 1

Author(s):

Carlos E.S. Bernardes ◽

Mariana T. Donato ◽

M. Fátima M. Piedade ◽

Hermínio P. Diogo ◽

José N. Canongia Lopes ◽

...

Keyword(s):

Force Field ◽

Organometallic Compounds ◽

Md Simulations ◽

Enthalpy Of Sublimation ◽

X Ray Diffraction ◽

X Ray

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Force field development and simulations of senior dialkyl sulfoxides

Physical Chemistry Chemical Physics ◽

10.1039/c5cp08006a ◽

2016 ◽

Vol 18 (15) ◽

pp. 10507-10515 ◽

Cited By ~ 8

Author(s):

Vitaly V. Chaban

Keyword(s):

Molecular Dynamics ◽

Force Field ◽

Ab Initio ◽

Md Simulations ◽

Field Development ◽

Force Field Development ◽

Structure And Dynamics ◽

Ethyl Methyl ◽

Methyl Sulfoxide ◽

Diethyl Sulfoxide

Thermodynamics, structure, and dynamics of diethyl sulfoxide (DESO) and ethyl methyl sulfoxide (EMSO) were investigated using ab initio calculations and non-polarizable potential based molecular dynamics (MD) simulations.

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