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Oliveira MP, Gonçalves YMH, Ol Gheta SK, Rieder SR, Horta BAC, Hünenberger PH. Comparison of the United- and All-Atom Representations of (Halo)alkanes Based on Two Condensed-Phase Force Fields Optimized against the Same Experimental Data Set. J Chem Theory Comput 2022; 18:6757-6778. [PMID: 36190354 DOI: 10.1021/acs.jctc.2c00524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The level of accuracy that can be achieved by a force field is influenced by choices made in the interaction-function representation and in the relevant simulation parameters. These choices, referred to here as functional-form variants (FFVs), include for example the model resolution, the charge-derivation procedure, the van der Waals combination rules, the cutoff distance, and the treatment of the long-range interactions. Ideally, assessing the effect of a given FFV on the intrinsic accuracy of the force-field representation requires that only the specific FFV is changed and that this change is performed at an optimal level of parametrization, a requirement that may prove extremely challenging to achieve in practice. Here, we present a first attempt at such a comparison for one specific FFV, namely the choice of a united-atom (UA) versus an all-atom (AA) resolution in a force field for saturated acyclic (halo)alkanes. Two force-field versions (UA vs AA) are optimized in an automated way using the CombiFF approach against 961 experimental values for the pure-liquid densities ρliq and vaporization enthalpies ΔHvap of 591 compounds. For the AA force field, the torsional and third-neighbor Lennard-Jones parameters are also refined based on quantum-mechanical rotational-energy profiles. The comparison between the UA and AA resolutions is also extended to properties that have not been included as parameterization targets, namely the surface-tension coefficient γ, the isothermal compressibility κT, the isobaric thermal-expansion coefficient αP, the isobaric heat capacity cP, the static relative dielectric permittivity ϵ, the self-diffusion coefficient D, the shear viscosity η, the hydration free energy ΔGwat, and the free energy of solvation ΔGche in cyclohexane. For the target properties ρliq and ΔHvap, the UA and AA resolutions reach very similar levels of accuracy after optimization. For the nine other properties, the AA representation leads to more accurate results in terms of η; comparably accurate results in terms of γ, κT, αP, ϵ, D, and ΔGche; and less accurate results in terms of cP and ΔGwat. This work also represents a first step toward the calibration of a GROMOS-compatible force field at the AA resolution.
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Affiliation(s)
- Marina P Oliveira
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Yan M H Gonçalves
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - S Kashef Ol Gheta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Salomé R Rieder
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Bruno A C Horta
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie, ETH Zürich, ETH-Hönggerberg, HCI, CH-8093 Zürich, Switzerland
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Biomolecular force fields: where have we been, where are we now, where do we need to go and how do we get there? J Comput Aided Mol Des 2018; 33:133-203. [DOI: 10.1007/s10822-018-0111-4] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Accepted: 03/09/2018] [Indexed: 10/27/2022]
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3
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Wei L, Li P, Tang K. Iterative combining rules for the van der Waals potentials of mixed rare gas systems. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.02.066] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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5
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Li J, Wang F. The effects of replacing the water model while decoupling water-water and water-solute interactions on computed properties of simple salts. J Chem Phys 2016; 145:044501. [PMID: 27475375 DOI: 10.1063/1.4958955] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The effects of decoupling the water-water and water-solute interactions are studied with selected mono-valent ions as the solute. Using the ion-water cross terms developed for the BLYPSP-4F water model, we replaced the water potential with WAIL, TIP4P, and TIP3P without changing the ion-water parameters. When the adaptive force matching (AFM) derived BLYPSP-4F model is replaced by the other AFM derived WAIL model, the difference in ion properties, such as hydration free energies, radial distribution functions, relative diffusion constants, is negligible, demonstrating the feasibility for combining AFM parameters from different sources. Interestingly, when the AFM-derived ion-water cross-terms are used with a non-AFM based water model, only small changes in the ion properties are observed. The final combined models with TIP3P or TIP4P water reproduce the salt hydration free energies within 6% of experiments. The feasibility of combining AFM models with other non-AFM models is of significance since such combinations allow more complex systems to be studied without specific parameterization. In addition, the study suggests an interesting prospect of reusing the cross-terms when a part of a general force field is replaced with a different model. The prevailing practice, which is to re-derive all cross-terms with combining rules, may not have been optimal.
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Affiliation(s)
- Jicun Li
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Feng Wang
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
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Horta BAC, Merz PT, Fuchs PFJ, Dolenc J, Riniker S, Hünenberger PH. A GROMOS-Compatible Force Field for Small Organic Molecules in the Condensed Phase: The 2016H66 Parameter Set. J Chem Theory Comput 2016; 12:3825-50. [DOI: 10.1021/acs.jctc.6b00187] [Citation(s) in RCA: 88] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Bruno A. C. Horta
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Instituto de Química, Universidade Federal do Rio de Janeiro, Rio de Janeiro 21941-909, Brazil
| | - Pascal T. Merz
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Patrick F. J. Fuchs
- Institut Jacques Monod, UMR 7592 CNRS, Université Paris-Diderot, Sorbonne Paris Cité, F-75205 Paris, France
| | - Jozica Dolenc
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
- Chemistry,
Biology and Pharmacy Information Center, ETH Zürich, CH-8093 Zürich, Switzerland
| | - Sereina Riniker
- Laboratory
of Physical Chemistry, ETH Zürich, CH-8093 Zürich, Switzerland
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8
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Lorenzen K, Wichmann C, Tavan P. Including the Dispersion Attraction into Structure-Adapted Fast Multipole Expansions for MD Simulations. J Chem Theory Comput 2014; 10:3244-59. [DOI: 10.1021/ct500319a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Konstantin Lorenzen
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Christoph Wichmann
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
| | - Paul Tavan
- Lehrstuhl
für Biomolekulare
Optik, Ludwig-Maximilians-Universität, Oettingenstr. 67, 80538 München, Germany
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Angelikopoulos P, Papadimitriou C, Koumoutsakos P. Bayesian uncertainty quantification and propagation in molecular dynamics simulations: a high performance computing framework. J Chem Phys 2013; 137:144103. [PMID: 23061835 DOI: 10.1063/1.4757266] [Citation(s) in RCA: 51] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a Bayesian probabilistic framework for quantifying and propagating the uncertainties in the parameters of force fields employed in molecular dynamics (MD) simulations. We propose a highly parallel implementation of the transitional Markov chain Monte Carlo for populating the posterior probability distribution of the MD force-field parameters. Efficient scheduling algorithms are proposed to handle the MD model runs and to distribute the computations in clusters with heterogeneous architectures. Furthermore, adaptive surrogate models are proposed in order to reduce the computational cost associated with the large number of MD model runs. The effectiveness and computational efficiency of the proposed Bayesian framework is demonstrated in MD simulations of liquid and gaseous argon.
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Reif MM, Hünenberger PH. Computation of methodology-independent single-ion solvation properties from molecular simulations. IV. Optimized Lennard-Jones interaction parameter sets for the alkali and halide ions in water. J Chem Phys 2011; 134:144104. [DOI: 10.1063/1.3567022] [Citation(s) in RCA: 118] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Thermodynamic Properties for Applications in Chemical Industry via Classical Force Fields. MULTISCALE MOLECULAR METHODS IN APPLIED CHEMISTRY 2011; 307:201-49. [DOI: 10.1007/128_2011_164] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Fischer W, Brickmann J. Lennard-Jones (12,6) Parameters for the Non-Ionic Contributions to Interionic Pairpotentials of Alkali Cations and Halide Anions from Crystal Data. ACTA ACUST UNITED AC 2010. [DOI: 10.1002/bbpc.19820860715] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Mousis O, Lunine JI, Picaud S, Cordier D. Volatile inventories in clathrate hydrates formed in the primordial nebula. Faraday Discuss 2010; 147:509-25; discussion 527-52. [DOI: 10.1039/c003658g] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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van 't Hof A, Peters CJ, de Leeuw SW. An advanced Gibbs-Duhem integration method: Theory and applications. J Chem Phys 2006; 124:054906. [PMID: 16468917 DOI: 10.1063/1.2137706] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The conventional Gibbs-Duhem integration method is very convenient for the prediction of phase equilibria of both pure components and mixtures. However, it turns out to be inefficient. The method requires a number of lengthy simulations to predict the state conditions at which phase coexistence occurs. This number is not known from the outset of the numerical integration process. Furthermore, the molecular configurations generated during the simulations are merely used to predict the coexistence condition and not the liquid- and vapor-phase densities and mole fractions at coexistence. In this publication, an advanced Gibbs-Duhem integration method is presented that overcomes above-mentioned disadvantage and inefficiency. The advanced method is a combination of Gibbs-Duhem integration and multiple-histogram reweighting. Application of multiple-histogram reweighting enables the substitution of the unknown number of simulations by a fixed and predetermined number. The advanced method has a retroactive nature; a current simulation improves the predictions of previously computed coexistence points as well. The advanced Gibbs-Duhem integration method has been applied for the prediction of vapor-liquid equilibria of a number of binary mixtures. The method turned out to be very convenient, much faster than the conventional method, and provided smooth simulation results. As the employed force fields perfectly predict pure-component vapor-liquid equilibria, the binary simulations were very well suitable for testing the performance of different sets of combining rules. Employing Lorentz-Hudson-McCoubrey combining rules for interactions between unlike molecules, as opposed to Lorentz-Berthelot combining rules for all interactions, considerably improved the agreement between experimental and simulated data.
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Affiliation(s)
- A van 't Hof
- Physical Chemistry and Molecular Thermodynamics, Faculty of Applied Sciences, Delft University of Technology, Julianalaan 136, 2628 BL Delft, The Netherlands
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Galliéro G, Boned C, Baylaucq A. Molecular Dynamics Study of the Lennard−Jones Fluid Viscosity: Application to Real Fluids. Ind Eng Chem Res 2005. [DOI: 10.1021/ie050154t] [Citation(s) in RCA: 108] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Guillaume Galliéro
- Laboratoire des Fluides Complexes (UMR-5150), Université de Pau et des Pays de l'Adour, Centre Universitaire de Recherche Scientifique, BP 1155, F-64013 Pau Cedex, France
| | - Christian Boned
- Laboratoire des Fluides Complexes (UMR-5150), Université de Pau et des Pays de l'Adour, Centre Universitaire de Recherche Scientifique, BP 1155, F-64013 Pau Cedex, France
| | - Antoine Baylaucq
- Laboratoire des Fluides Complexes (UMR-5150), Université de Pau et des Pays de l'Adour, Centre Universitaire de Recherche Scientifique, BP 1155, F-64013 Pau Cedex, France
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18
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Gamache RR, Hartmann JM. An intercomparison of measured pressure-broadening and pressure-shifting parameters of water vapor. CAN J CHEM 2004. [DOI: 10.1139/v04-069] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The present work is an intercomparison of experimental results on the pressure broadening and pressure shifting of water vapor absorption lines. The work focuses on application to the Earth's atmosphere; hence measurements of nitrogen, oxygen, air, and H2O as the buffer, or perturbing gas, were considered. The literature was searched and over 100 papers found. The data, measured half-widths, their temperature dependence, and the line shifts, were taken and databases created for each perturbing gas. The databases were reordered, grouping data for rovibrational transitions, and intercomparisons of the measurements made. Trends in the data, relationships between the data sets, and dependences on temperature and quantum numbers were investigated. The data were averaged and an estimated uncertainty determined. The averaged data sets are evaluated with respect to the need of the spectroscopic and remote sensing communities. Based on these studies, recommendations for new measurements are made.Key words: water vapor, half-widths, line shifts, temperature dependence of half-width.
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Al-Matar AK, Rockstraw DA. A generating equation for mixing rules and two new mixing rules for interatomic potential energy parameters. J Comput Chem 2004; 25:660-8. [PMID: 14978709 DOI: 10.1002/jcc.10418] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
A generating equation for the mixing rules of interatomic potential energy parameters is proposed. It is demonstrated that this equation can, indeed, reproduce many popular mixing rules. A weighting matrix is used with the generating equation. This weighting matrix approach is superior to the present status of mixing rule development. A systematic framework is given for devising new mixing rules and/or comparing them. Two new mixing rules, which are more accurate than the available rules in the literature, are proposed. These rules are capable of reproducing the collision diameter and well-depth parameters for the binary values of noble gases to within their experimental uncertainties.
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El‐Sheikh SM, Tabisz GC, Pack RT. Search for a multiproperty empirical intermolecular potential for XeSF6. J Chem Phys 1990. [DOI: 10.1063/1.457781] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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New combining rules for well parameters and shapes of the van der Waals potential of mixed rare gas systems. ACTA ACUST UNITED AC 1986. [DOI: 10.1007/bf01384663] [Citation(s) in RCA: 138] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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23
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Fischer J, Lago S. Thermodynamic perturbation theory for molecular liquid mixtures. J Chem Phys 1983. [DOI: 10.1063/1.445458] [Citation(s) in RCA: 94] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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Diaz Peña M, Pando C, Renuncio JAR. Combination rules for intermolecular potential parameters. II. Rules based on approximations for the long‐range dispersion energy and an atomic distortion model for the repulsive interactions. J Chem Phys 1982. [DOI: 10.1063/1.442727] [Citation(s) in RCA: 39] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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