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Hudson PS, Aviat F, Meana-Pañeda R, Warrensford L, Pollard BC, Prasad S, Jones MR, Woodcock HL, Brooks BR. Obtaining QM/MM binding free energies in the SAMPL8 drugs of abuse challenge: indirect approaches. J Comput Aided Mol Des 2022; 36:263-277. [PMID: 35597880 PMCID: PMC9148874 DOI: 10.1007/s10822-022-00443-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 02/17/2022] [Indexed: 11/28/2022]
Abstract
Accurately predicting free energy differences is essential in realizing the full potential of rational drug design. Unfortunately, high levels of accuracy often require computationally expensive QM/MM Hamiltonians. Fortuitously, the cost of employing QM/MM approaches in rigorous free energy simulation can be reduced through the use of the so-called “indirect” approach to QM/MM free energies, in which the need for QM/MM simulations is avoided via a QM/MM “correction” at the classical endpoints of interest. Herein, we focus on the computation of QM/MM binding free energies in the context of the SAMPL8 Drugs of Abuse host–guest challenge. Of the 5 QM/MM correction coupled with force-matching submissions, PM6-D3H4/MM ranked submission proved the best overall QM/MM entry, with an RMSE from experimental results of 2.43 kcal/mol (best in ranked submissions), a Pearson’s correlation of 0.78 (second-best in ranked submissions), and a Kendall \documentclass[12pt]{minimal}
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Affiliation(s)
- Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA.
| | - Félix Aviat
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Rubén Meana-Pañeda
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Luke Warrensford
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Benjamin C Pollard
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Samarjeet Prasad
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - Michael R Jones
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, FL, 33620, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
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2
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Sun Z, He Q. Seeding the multi-dimensional nonequilibrium pulling for Hamiltonian variation: indirect nonequilibrium free energy simulations at QM levels. Phys Chem Chem Phys 2022; 24:8800-8819. [PMID: 35352744 DOI: 10.1039/d2cp00355d] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The combination of free energy simulations in the alchemical and configurational spaces provides a feasible route to access the thermodynamic profiles under a computationally demanding target Hamiltonian. Normally, due to the significant differences between the computational cost of ab initio quantum mechanics (QM) calculations and those of semi-empirical quantum mechanics (SQM) and molecular mechanics (MM), this indirect method could be used to obtain the QM thermodynamics by combining the SQM or MM results and the SQM-to-QM or MM-to-QM corrections. In our previous work, a multi-dimensional nonequilibrium pulling framework for Hamiltonian variations was introduced based on bidirectional pulling and bidirectional reweighting. The method performs nonequilibrium free energy simulations in the configurational space to obtain the thermodynamic profile along the conformational change pathway under a selected computationally efficient Hamiltonian, and uses the nonequilibrium alchemical method to correct or perturb the thermodynamic profile to that under the target Hamiltonian. The BAR-based method is designed to achieve the best generality and transferability and thus leads to modest (∼20 fold) speedup. In this work, we explore the possibility of further accelerating the nonequilibrium free energy simulation by employing unidirectional pulling and using the selection criterion to obtain the initial configurations used to initiate nonequilibrium trajectories following the idea of adaptive steered molecular dynamics (ASMD). A single initial condition is used to seed the whole multi-dimensional nonequilibrium free energy simulation and the sampling is performed fully in the nonequilibrium ensemble. Introducing very short ps-length equilibrium sampling to grab more initial seeds could also be helpful. The ASMD scheme estimates the free energy difference with the unidirectional exponential average (EXP), but it does not follow exactly the requirements of the EXP estimator. Another deficiency of the seeding simulation is the inherently sequential or serial pulling due to the inter-segment dependency, which triggers some problems in the parallelizability of the simulation. Numerical tests are performed to grasp some insights and guidelines for using this selection-criterion-based ASMD scheme. The presented selection-criterion-based multi-dimensional ASMD scheme follows the same perturbation network of the BAR-based method, and thus could be used in various Hamiltonian-variation cases.
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Affiliation(s)
- Zhaoxi Sun
- Beijing National Laboratory for Molecular Sciences, College of Chemistry and Molecular Engineering, Institute of Theoretical and Computational Chemistry, Peking University, Beijing 100871, China.
| | - Qiaole He
- AI Department of Enzymaster (Ningbo) Bio-Engineering Co., Ltd, North Century Avenue 333, 315100 Ningbo, China
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3
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Demapan D, Kussmann J, Ochsenfeld C, Cui Q. Factors That Determine the Variation of Equilibrium and Kinetic Properties of QM/MM Enzyme Simulations: QM Region, Conformation, and Boundary Condition. J Chem Theory Comput 2022; 18:2530-2542. [PMID: 35226489 PMCID: PMC9652774 DOI: 10.1021/acs.jctc.1c00714] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
To analyze the impact of various technical details on the results of quantum mechanical (QM)/molecular mechanical (MM) enzyme simulations, including the QM region size, catechol-O-methyltransferase (COMT) is studied as a model system using an approximate QM/MM method (DFTB3/CHARMM). The results show that key equilibrium and kinetic properties for methyl transfer in COMT exhibit limited variations with respect to the size of the QM region, which ranges from ∼100 to ∼500 atoms in this study. With extensive sampling, local and global structural characteristics of the enzyme are largely conserved across the studied QM regions, while the nature of the transition state (e.g., secondary kinetic isotope effect) and reaction exergonicity are largely maintained. Deviations in the free energy profile with different QM region sizes are similar in magnitude to those observed with changes in other simulation protocols, such as different initial enzyme conformations and boundary conditions. Electronic structural properties, such as the covariance matrix of residual charge fluctuations, appear to exhibit rather long-range correlations, especially when the peptide backbone is included in the QM region; this observation holds when a range-separated DFT approach is used as the QM region, suggesting that delocalization error is unlikely the origin. Overall, the analyses suggest that multiple simulation details determine the results of QM/MM enzyme simulations with comparable contributions.
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Affiliation(s)
- Darren Demapan
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany.,Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Jörg Kussmann
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Christian Ochsenfeld
- Department of Chemistry, University of Munich (LMU), Butenandtstr. 7 (C), D-81377 Munich, Germany
| | - Qiang Cui
- Departments of Chemistry, Physics and Biomedical Engineering, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, United States
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4
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Pan X, Yang J, Van R, Epifanovsky E, Ho J, Huang J, Pu J, Mei Y, Nam K, Shao Y. Machine-Learning-Assisted Free Energy Simulation of Solution-Phase and Enzyme Reactions. J Chem Theory Comput 2021; 17:5745-5758. [PMID: 34468138 DOI: 10.1021/acs.jctc.1c00565] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Despite recent advances in the development of machine learning potentials (MLPs) for biomolecular simulations, there has been limited effort on developing stable and accurate MLPs for enzymatic reactions. Here we report a protocol for performing machine-learning-assisted free energy simulation of solution-phase and enzyme reactions at the ab initio quantum-mechanical/molecular-mechanical (ai-QM/MM) level of accuracy. Within our protocol, the MLP is built to reproduce the ai-QM/MM energy and forces on both QM (reactive) and MM (solvent/enzyme) atoms. As an alternative strategy, a delta machine learning potential (ΔMLP) is trained to reproduce the differences between the ai-QM/MM and semiempirical (se) QM/MM energies and forces. To account for the effect of the condensed-phase environment in both MLP and ΔMLP, the DeePMD representation of a molecular system is extended to incorporate the external electrostatic potential and field on each QM atom. Using the Menshutkin and chorismate mutase reactions as examples, we show that the developed MLP and ΔMLP reproduce the ai-QM/MM energy and forces with errors that on average are less than 1.0 kcal/mol and 1.0 kcal mol-1 Å-1, respectively, for representative configurations along the reaction pathway. For both reactions, MLP/ΔMLP-based simulations yielded free energy profiles that differed by less than 1.0 kcal/mol from the reference ai-QM/MM results at only a fraction of the computational cost.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Junjie Yang
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Richard Van
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
| | - Evgeny Epifanovsky
- Q-Chem, Inc., 6601 Owens Drive, Suite 105, Pleasanton, California 94588, United States
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jing Huang
- Key Laboratory of Structural Biology of Zhejiang Province, School of Life Sciences, Westlake University, 18 Shilongshan Road, Hangzhou, Zhejiang 310024, China
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 North Blackford Street, LD326, Indianapolis, Indiana 46202, United States
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Electronic Science, East China Normal University, Shanghai 200062, China.,NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China.,Collaborative Innovation Center of Extreme Optics, Shanxi University, Taiyuan, Shanxi 030006, China
| | - Kwangho Nam
- Department of Chemistry and Biochemistry, University of Texas at Arlington, Arlington, Texas 76019, United States
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Parkway, Norman, Oklahoma 73019, United States
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5
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Zheng D, Yuan Y, Wang F. Determining the hydration free energies of selected small molecules with MP2 and local MP2 through adaptive force matching. J Chem Phys 2021; 154:104113. [PMID: 33722038 DOI: 10.1063/5.0044712] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Force fields for seven small solute molecules, ethanol, 2-methyl-1-propanol, 2-butanol, cyclohexene, tetrahydropyran, 1,4-dioxane, and 1,4-butanediol, in dilute aqueous solutions were created with the adaptive force matching (AFM) method using MP2 or local MP2 as reference. The force fields provide a way to predict the hydration free energies (HFEs) of these molecules with only electronic structure calculations as reference. For six of the seven molecules, the predicted HFEs are in very good agreement with experiments. For 1,4-butanediol, the model created by force matching LMP2 provides a HFE that is too positive. Further investigation suggests that LMP2 may not be sufficiently accurate for computing HFEs for alcohols with AFM. Other properties, such as enthalpy of hydration, diffusion constants, and vibrational spectra, are also computed with the force field developed. The force fields developed by AFM provide a bridge for computing ensemble properties of the reference electronic structure method. With MP2 and LMP2 as reference methods, the computed properties of the small molecular solutes are found to be in good agreement with experiments.
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Affiliation(s)
- Dong Zheng
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, USA
| | - Ying Yuan
- 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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6
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Functionalized boron nitride nanosheet as a membrane for removal of Pb2+ and Cd2+ ions from aqueous solution. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114920] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
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7
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Lee TS, Allen BK, Giese TJ, Guo Z, Li P, Lin C, McGee TD, Pearlman DA, Radak BK, Tao Y, Tsai HC, Xu H, Sherman W, York DM. Alchemical Binding Free Energy Calculations in AMBER20: Advances and Best Practices for Drug Discovery. J Chem Inf Model 2020; 60:5595-5623. [PMID: 32936637 PMCID: PMC7686026 DOI: 10.1021/acs.jcim.0c00613] [Citation(s) in RCA: 148] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Predicting protein-ligand binding affinities and the associated thermodynamics of biomolecular recognition is a primary objective of structure-based drug design. Alchemical free energy simulations offer a highly accurate and computationally efficient route to achieving this goal. While the AMBER molecular dynamics package has successfully been used for alchemical free energy simulations in academic research groups for decades, widespread impact in industrial drug discovery settings has been minimal because of the previous limitations within the AMBER alchemical code, coupled with challenges in system setup and postprocessing workflows. Through a close academia-industry collaboration we have addressed many of the previous limitations with an aim to improve accuracy, efficiency, and robustness of alchemical binding free energy simulations in industrial drug discovery applications. Here, we highlight some of the recent advances in AMBER20 with a focus on alchemical binding free energy (BFE) calculations, which are less computationally intensive than alternative binding free energy methods where full binding/unbinding paths are explored. In addition to scientific and technical advances in AMBER20, we also describe the essential practical aspects associated with running relative alchemical BFE calculations, along with recommendations for best practices, highlighting the importance not only of the alchemical simulation code but also the auxiliary functionalities and expertise required to obtain accurate and reliable results. This work is intended to provide a contemporary overview of the scientific, technical, and practical issues associated with running relative BFE simulations in AMBER20, with a focus on real-world drug discovery applications.
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Affiliation(s)
- Tai-Sung Lee
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Bryce K. Allen
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Timothy J. Giese
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Zhenyu Guo
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Pengfei Li
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Charles Lin
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - T. Dwight McGee
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - David A. Pearlman
- QSimulate Incorporated, Cambridge, Massachusetts 02139, United States
| | - Brian K. Radak
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Yujun Tao
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Hsu-Chun Tsai
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
| | - Huafeng Xu
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Woody Sherman
- Silicon Therapeutics, Boston, Massachusetts 02210, United States
| | - Darrin M. York
- Rutgers, the State University of New Jersey, Laboratory for Biomolecular Simulation Research, and Department of Chemistry and Chemical Biology, United States
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8
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Pan X, Li P, Ho J, Pu J, Mei Y, Shao Y. Accelerated computation of free energy profile at ab initio quantum mechanical/molecular mechanical accuracy via a semi-empirical reference potential. II. Recalibrating semi-empirical parameters with force matching. Phys Chem Chem Phys 2019; 21:20595-20605. [PMID: 31508625 PMCID: PMC6761017 DOI: 10.1039/c9cp02593f] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
An efficient and accurate reference potential simulation protocol is proposed for producing ab initio quantum mechanical/molecular mechanical (AI-QM/MM) quality free energy profiles for chemical reactions in a solvent or macromolecular environment. This protocol involves three stages: (a) using force matching to recalibrate a semi-empirical quantum mechanical (SE-QM) Hamiltonian for the specific reaction under study; (b) employing the recalibrated SE-QM Hamiltonian (in combination with molecular mechanical force fields) as the reference potential to drive umbrella samplings along the reaction pathway; and (c) computing AI-QM/MM energy values for collected configurations from the sampling and performing weighted thermodynamic perturbation to acquire an AI-QM/MM corrected reaction free energy profile. For three model reactions (identity SN2 reaction, Menshutkin reaction, and glycine proton transfer reaction) in aqueous solution and one enzyme reaction (Claisen arrangement in chorismate mutase), our simulations using recalibrated PM3 SE-QM Hamiltonians well reproduced QM/MM free energy profiles at the B3LYP/6-31G* level of theory all within 1 kcal mol-1 with a 20 to 45 fold reduction in the computer time.
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Affiliation(s)
- Xiaoliang Pan
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
| | - Pengfei Li
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China.
| | - Junming Ho
- School of Chemistry, University of New South Wales, Sydney, NSW 2052, Australia
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis, 402 N Blackford St, LD326, Indianapolis, IN 46202, USA.
| | - Ye Mei
- State Key Laboratory of Precision Spectroscopy, School of Physics and Materials Science, East China Normal University, Shanghai 200062, China. and NYU-ECNU Center for Computational Chemistry at NYU Shanghai, Shanghai 200062, China
| | - Yihan Shao
- Department of Chemistry and Biochemistry, University of Oklahoma, 101 Stephenson Pkwy, Norman, OK 73019, USA.
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9
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Giese TJ, York DM. Development of a Robust Indirect Approach for MM → QM Free Energy Calculations That Combines Force-Matched Reference Potential and Bennett's Acceptance Ratio Methods. J Chem Theory Comput 2019; 15:5543-5562. [PMID: 31507179 DOI: 10.1021/acs.jctc.9b00401] [Citation(s) in RCA: 33] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
We use the PBE0/6-31G* density functional method to perform ab initio quantum mechanical/molecular mechanical (QM/MM) molecular dynamics (MD) simulations under periodic boundary conditions with rigorous electrostatics using the ambient potential composite Ewald method in order to test the convergence of MM → QM/MM free energy corrections for the prediction of 17 small-molecule solvation free energies and eight ligand binding free energies to T4 lysozyme. The "indirect" thermodynamic cycle for calculating free energies is used to explore whether a series of reference potentials improve the statistical quality of the predictions. Specifically, we construct a series of reference potentials that optimize a molecular mechanical (MM) force field's parameters to reproduce the ab initio QM/MM forces from a QM/MM simulation. The optimizations form a systematic progression of successively expanded parameters that include bond, angle, dihedral, and charge parameters. For each reference potential, we calculate benchmark quality reference values for the MM → QM/MM correction by performing the mixed MM and QM/MM Hamiltonians at 11 intermediate states, each for 200 ps. We then compare forward and reverse application of Zwanzig's relation, thermodynamic integration (TI), and Bennett's acceptance ratio (BAR) methods as a function of reference potential, simulation time, and the number of simulated intermediate states. We find that Zwanzig's equation is inadequate unless a large number of intermediate states are explicitly simulated. The TI and BAR mean signed errors are very small even when only the end-state simulations are considered, and the standard deviations of the TI and BAR errors are decreased by choosing a reference potential that optimizes the bond and angle parameters. We find a robust approach for the data sets of fairly rigid molecules considered here is to use bond + angle reference potential together with the end-state-only BAR analysis. This requires QM/MM simulations to be performed in order to generate reference data to parametrize the bond + angle reference potential, and then this same simulation serves a dual purpose as the full QM/MM end state. The convergence of the results with respect to time suggests that computational resources may be used more efficiently by running multiple simulations for no more than 50 ps, rather than running one long simulation.
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Affiliation(s)
- Timothy J Giese
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
| | - Darrin M York
- Laboratory for Biomolecular Simulation Research, Center for Integrative Proteomics Research and Department of Chemistry and Chemical Biology , Rutgers University , Piscataway , New Jersey 08854-8087 , United States
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10
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Li J, Wang F. Surface Penetration without Enrichment: Simulations Show Ion Surface Propensities Consistent with Both Elevated Surface Tension and Surface Sensitive Spectroscopy. J Phys Chem B 2019; 123:7197-7203. [PMID: 31361137 DOI: 10.1021/acs.jpcb.9b04424] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Molecular dynamics was used to investigate ion surface propensities in NaCl, KBr, and CsI solutions with an MP2-based force field. Although NaCl is found to be strongly repelled from the liquid-vapor interface, softer ions, such as I-, penetrate closely to the interface. Despite the surface penetration, the concentration of CsI near the interface is still lower than that in the bulk, thus leading to no surface enrichment. The salt concentration is found to affect relative surface propensities of the ions. More significant surface penetration is observed at higher salt concentrations. Softer ions at higher concentrations form a complex multilayer arrangement that can not be characterized as a simple surface bilayer. The simulated ion distributions explain the spectroscopic evidence of surface perturbation by soft ions with a negative surface excess consistent with an increased surface tension of salt solutions.
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Affiliation(s)
- Jicun Li
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
| | - Feng Wang
- Department of Chemistry and Biochemistry , University of Arkansas , Fayetteville , Arkansas 72701 , United States
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11
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Kearns FL, Warrensford L, Boresch S, Woodcock HL. The Good, the Bad, and the Ugly: "HiPen", a New Dataset for Validating (S)QM/MM Free Energy Simulations. Molecules 2019; 24:E681. [PMID: 30769826 PMCID: PMC6413162 DOI: 10.3390/molecules24040681] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 11/25/2022] Open
Abstract
Indirect (S)QM/MM free energy simulations (FES) are vital to efficiently incorporating sufficient sampling and accurate (QM) energetic evaluations when estimating free energies of practical/experimental interest. Connecting between levels of theory, i.e., calculating Δ A l o w → h i g h , remains to be the most challenging step within an indirect FES protocol. To improve calculations of Δ A l o w → h i g h , we must: (1) compare the performance of all FES methods currently available; and (2) compile and maintain datasets of Δ A l o w → h i g h calculated for a wide-variety of molecules so that future practitioners may replicate or improve upon the current state-of-the-art. Towards these two aims, we introduce a new dataset, "HiPen", which tabulates Δ A g a s M M → 3 o b (the free energy associated with switching from an M M to an S C C - D F T B molecular description using the 3ob parameter set in gas phase), calculated for 22 drug-like small molecules. We compare the calculation of this value using free energy perturbation, Bennett's acceptance ratio, Jarzynski's equation, and Crooks' equation. We also predict the reliability of each calculated Δ A g a s M M → 3 o b by evaluating several convergence criteria including sample size hysteresis, overlap statistics, and bias metric ( Π ). Within the total dataset, three distinct categories of molecules emerge: the "good" molecules, for which we can obtain converged Δ A g a s M M → 3 o b using Jarzynski's equation; "bad" molecules which require Crooks' equation to obtain a converged Δ A g a s M M → 3 o b ; and "ugly" molecules for which we cannot obtain reliably converged Δ A g a s M M → 3 o b with either Jarzynski's or Crooks' equations. We discuss, in depth, results from several example molecules in each of these categories and describe how dihedral discrepancies between levels of theory cause convergence failures even for these gas phase free energy simulations.
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Affiliation(s)
- Fiona L Kearns
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA.
| | - Luke Warrensford
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA.
| | - Stefan Boresch
- Department of Computational Biological Chemistry, Faculty of Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria.
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, 4202 E. Fowler Avenue, Tampa, FL 33620, USA.
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12
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Hudson PS, Boresch S, Rogers DM, Woodcock HL. Accelerating QM/MM Free Energy Computations via Intramolecular Force Matching. J Chem Theory Comput 2018; 14:6327-6335. [PMID: 30300543 PMCID: PMC6314469 DOI: 10.1021/acs.jctc.8b00517] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The calculation of free energy differences between levels of theory has numerous potential pitfalls. Chief among them is the lack of overlap, i.e., ensembles generated at one level of theory (e.g., "low") not being good approximations of ensembles at the other (e.g., "high"). Numerous strategies have been devised to mitigate this issue. However, the most straightforward approach is to ensure that the "low" level ensemble more closely resembles that of the "high". Ideally, this is done without increasing computational cost. Herein, we demonstrate that by reparametrizing classical intramolecular potentials to reproduce high level forces (i.e., force matching) configurational overlap between a "low" (i.e., classical) and "high" (i.e., quantum) level can be significantly improved. This procedure is validated on two test cases and results in vastly improved convergence of free energy simulations.
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Affiliation(s)
- Phillip S Hudson
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue, CHE205 , Tampa , Florida 33620-5250 , United States
- Laboratory of Computational Biology , National Institutes of Health, National Heart, Lung and Blood Institute , 12 South Drive Rm 3053 , Bethesda , Maryland 20892-5690 , United States
| | - Stefan Boresch
- Faculty of Chemistry, Department of Computational Biological Chemistry , University of Vienna , Währingerstraße 17 , A-1090 Vienna , Austria
| | - David M Rogers
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue, CHE205 , Tampa , Florida 33620-5250 , United States
| | - H Lee Woodcock
- Department of Chemistry , University of South Florida , 4202 East Fowler Avenue, CHE205 , Tampa , Florida 33620-5250 , United States
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13
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Prasetyo N, Hünenberger PH, Hofer TS. Single-Ion Thermodynamics from First Principles: Calculation of the Absolute Hydration Free Energy and Single-Electrode Potential of Aqueous Li + Using ab Initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Simulations. J Chem Theory Comput 2018; 14:6443-6459. [PMID: 30284829 DOI: 10.1021/acs.jctc.8b00729] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A recently proposed thermodynamic integration (TI) approach formulated in the framework of quantum mechanical/molecular mechanical molecular dynamics (QM/MM MD) simulations is applied to study the structure, dynamics, and absolute intrinsic hydration free energy Δs GM+,wat◦ of the Li+ ion at a correlated ab initio level of theory. Based on the results, standard values (298.15 K, ideal gas at 1 bar, ideal solute at 1 molal) for the absolute intrinsic hydration free energy [Formula: see text] of the proton, the surface electric potential jump χwat◦ upon entering bulk water, and the absolute single-electrode potential [Formula: see text] of the reference hydrogen electrode are calculated to be -1099.9 ± 4.2 kJ·mol-1, 0.13 ± 0.08 V, and 4.28 ± 0.04 V, respectively, in excellent agreement with the standard values recommended by Hünenberger and Reif on the basis of an extensive evaluation of the available experimental data (-1100 ± 5 kJ·mol-1, 0.13 ± 0.10 V, and 4.28 ± 0.13 V). The simulation results for Li+ are also compared to those for Na+ and K+ from a previous study in terms of relative hydration free energies ΔΔs GM+,wat◦ and relative electrode potentials [Formula: see text]. The calculated values are found to agree extremely well with the experimental differences in standard conventional hydration free energies ΔΔs GM+,wat• and redox potentials [Formula: see text]. The level of agreement between simulation and experiment, which is quantitative within error bars, underlines the substantial accuracy improvement achieved by applying a highly demanding QM/MM approach at the resolution-of-identity second-order Møller-Plesset perturbation (RIMP2) level over calculations relying on purely molecular mechanical or density functional theory (DFT) descriptions. A detailed analysis of the structural and dynamical properties of the Li+ hydrate indicates that a correct description of the solvation structure and dynamics is achieved as well at this level of theory. Consideration of the QM/MM potential-energy components also shows that the partitioning into QM and MM zones does not induce any significant energetic artifact for the system considered.
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Affiliation(s)
- Niko Prasetyo
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria.,Austria-Indonesia Centre (AIC) for Computational Chemistry , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia.,Department of Chemistry, Faculty of Mathematics and Natural Sciences , Universitas Gadjah Mada , Sekip Utara , Yogyakarta 55281 , Indonesia
| | - Philippe H Hünenberger
- Laboratorium für Physikalische Chemie , ETH Zürich, ETH-Hönggerberg , HCI Building , CH-8093 Zürich , Switzerland
| | - Thomas S Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry , University of Innsbruck , Innrain 80-82 , A-6020 Innsbruck , Austria
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14
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Hudson PS, Han K, Woodcock HL, Brooks BR. Force matching as a stepping stone to QM/MM CB[8] host/guest binding free energies: a SAMPL6 cautionary tale. J Comput Aided Mol Des 2018; 32:983-999. [PMID: 30276502 PMCID: PMC6867086 DOI: 10.1007/s10822-018-0165-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 09/14/2018] [Indexed: 10/28/2022]
Abstract
Use of quantum mechanical/molecular mechanical (QM/MM) methods in binding free energy calculations, particularly in the SAMPL challenge, often fail to achieve improvement over standard additive (MM) force fields. Frequently, the implementation is through use of reference potentials, or the so-called "indirect approach", and inherently relies on sufficient overlap existing between MM and QM/MM configurational spaces. This overlap is generally poor, particularly for the use of free energy perturbation to perform the MM to QM/MM free energy correction at the end states of interest (e.g., bound and unbound states). However, by utilizing MM parameters that best reproduce forces obtained at the desired QM level of theory, it is possible to lessen the configurational disparity between MM and QM/MM. To this end, we sought to use force matching to generate MM parameters for the SAMPL6 CB[8] host-guest binding challenge, classically compute binding free energies, and apply energetic end state corrections to obtain QM/MM binding free energy differences. For the standard set of 11 molecules and the bonus set (including three additional challenge molecules), error statistics, such as the root mean square deviation (RMSE) were moderately poor (5.5 and 5.4 kcal/mol). Correlation statistics, however, were in the top two for both standard and bonus set submissions ([Formula: see text] of 0.42 and 0.26, [Formula: see text] of 0.64 and 0.47 respectively). High RMSE and moderate correlation strongly indicated the presence of systematic error. Identifiable issues were ameliorated for two of the guest molecules, resulting in a reduction of error and pointing to strong prospects for the future use of this methodology.
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Affiliation(s)
- Phillip S Hudson
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA.
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA.
| | - Kyungreem Han
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health, Bethesda, MD, 20852, USA
| | - H Lee Woodcock
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA
| | - Bernard R Brooks
- Department of Chemistry, University of South Florida, Tampa, Florida, 33620, USA
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15
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Hofer TS, Hünenberger PH. Absolute proton hydration free energy, surface potential of water, and redox potential of the hydrogen electrode from first principles: QM/MM MD free-energy simulations of sodium and potassium hydration. J Chem Phys 2018; 148:222814. [DOI: 10.1063/1.5000799] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Thomas S. Hofer
- Theoretical Chemistry Division, Institute of General, Inorganic and Theoretical Chemistry, Centre for Chemistry and Biomedicine, University of Innsbruck, Innrain 80-82, A-6020 Innsbruck, Austria
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16
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Koziol L, Fried LE, Goldman N. Using Force Matching To Determine Reactive Force Fields for Water under Extreme Thermodynamic Conditions. J Chem Theory Comput 2016; 13:135-146. [DOI: 10.1021/acs.jctc.6b00707] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lucas Koziol
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Laurence E. Fried
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
| | - Nir Goldman
- Physical and Life Sciences
Directorate, Lawrence Livermore National Laboratory, Livermore, California 94550, United States
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17
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Li J, Wang F. The Effect of Core Correlation on the MP2 Hydration Free Energies of Li+, Na+, and K+. J Phys Chem B 2016; 120:9088-96. [DOI: 10.1021/acs.jpcb.6b06102] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jicun Li
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
| | - Feng Wang
- Department of Chemistry and
Biochemistry, University of Arkansas, Fayetteville, Arkansas 72701, United States
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18
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Dybeck EC, Schieber NP, Shirts MR. Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials. J Chem Theory Comput 2016; 12:3491-505. [DOI: 10.1021/acs.jctc.6b00397] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Eric C. Dybeck
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
| | - Natalie P. Schieber
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Michael R. Shirts
- Department
of Chemical Engineering, University of Virginia, Charlottesville, Virginia 22904, United States
- Department
of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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19
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Li J, Wang F. Pairwise-additive force fields for selected aqueous monovalent ions from adaptive force matching. J Chem Phys 2016; 143:194505. [PMID: 26590540 DOI: 10.1063/1.4935599] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Simple non-polarizable potentials were developed for Na(+), K(+), Cl(-), and Br(-) using the adaptive force matching (AFM) method with ab initio MP2 method as reference. Our MP2-AFM force field predicts the solvation free energies of the four salts formed by the ions with an error of no more than 5%. Other properties such as the ion-water radial distribution functions, first solvation shell water tilt angle distributions, ion diffusion constants, concentration dependent diffusion constant of water, and concentration dependent surface tension of the solutions were calculated with this potential. Very good agreement was achieved for these properties. In particular, the diffusion constants of the ions are within 6% of experimental measurements. The model predicts bromide to be enriched at the interface in the 1.6M KBr solution but predicts the ion to be repelled for the surface at lower concentration.
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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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20
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Dybeck EC, König G, Brooks BR, Shirts MR. Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials. J Chem Theory Comput 2016; 12:1466-80. [PMID: 26928941 PMCID: PMC6497519 DOI: 10.1021/acs.jctc.5b01188] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
We examine methods to reweight classical molecular mechanics solvation calculations to more expensive QM/MM energy functions. We first consider the solvation free energy difference between ethane and methanol in a QM/MM Hamiltonian from configurations generated in a cheaper MM potential. The solute molecules in the QM/MM Hamiltonian are treated with B3LYP/6-31G*, and the solvent water molecules are treated classically. The free energy difference in the QM/MM Hamiltonian is estimated using Boltzmann reweighting with both the non-Boltzmann Bennett method (NBB) and the multistate Bennett acceptance ratio (MBAR), and the variance of each method is directly compared for an identical data set. For this system, MBAR-derived methods are found to produce smaller overall uncertainties than NBB-based methods. Additionally, we show that to reduce the variance in the overall free energy difference estimate in this system for a fixed amount of QM/MM calculations, the energy re-evaluations in the Boltzmann reweighting step should be concentrated on the physical MM states with the highest overlap to the QM/MM states, rather than allocated equally over all sampled MM states. We also show that reallocating the QM/MM re-evaluations can be used to diagnose poor overlap between the sampled and target state. The solvation free energies for molecules in the SAMPL4 solvation data set are also calculated in the QM/MM Hamiltonian with NBB and MBAR, and the variances are marginally smaller for MBAR. Overall, NBB and MBAR produce similar variances for systems with poor sampling efficiency, and MBAR provides smaller variances than NBB in systems with high sampling efficiency. Both NBB and MBAR converge to identical solvation free energy estimates in the QM/MM Hamiltonian, and the RMSD to experimental values for molecules in the SAMPL4 solvation data set decreases by approximately 28% when switching from the MM Hamiltonian to the QM/MM Hamiltonian.
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Affiliation(s)
- Eric C Dybeck
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
| | - Gerhard König
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health , 5635 Fishers Lane, T-900 Suite, Rockville, Maryland 20852, United States
| | - Michael R Shirts
- Department of Chemical Engineering, University of Virginia , Charlottesville, Virginia 22904, United States
- Department of Chemical and Biological Engineering, University of Colorado Boulder , Boulder, Colorado 80309, United States
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21
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Hu H, Wang F. The liquid-vapor equilibria of TIP4P/2005 and BLYPSP-4F water models determined through direct simulations of the liquid-vapor interface. J Chem Phys 2016; 142:214507. [PMID: 26049508 DOI: 10.1063/1.4922166] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022] Open
Abstract
In this paper, the surface tension and critical properties for the TIP4P/2005 and BLYPSP-4F models are reported. A clear dependence of surface tension on the van der Waals cutoff radius (rvdw) is shown when van der Waals interactions are modeled with a simple cutoff scheme. A linear extrapolation formula is proposed that can be used to determine the infinite rvdw surface tension through a few simulations with finite rvdw. A procedure for determining liquid and vapor densities is proposed that does not require fitting to a profile function. Although the critical temperature of water is also found to depend on the choice of rvdw, the dependence is weaker. We argue that a rvdw of 1.75 nm is a good compromise for water simulations when long-range van der Waals correction is not applied. Since the majority of computational programs do not support rigorous treatment of long-range dispersion, the establishment of a minimal acceptable rvdw is important for the simulation of a variety of inhomogeneous systems, such as water bubbles, and water in confined environments. The BLYPSP-4F model predicts room temperature surface tension marginally better than TIP4P/2005 but overestimates the critical temperature. This is expected since only liquid configurations were fit during the development of the BLYPSP-4F potential. The potential is expected to underestimate the stability of vapor and thus overestimate the region of stability for the liquid.
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Affiliation(s)
- Hongyi Hu
- 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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22
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Liu H, Dai S, Jiang DE. Molecular Dynamics Simulation of Anion Effect on Solubility, Diffusivity, and Permeability of Carbon Dioxide in Ionic Liquids. Ind Eng Chem Res 2014. [DOI: 10.1021/ie501501k] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Hongjun Liu
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
| | - Sheng Dai
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
- Department
of Chemistry, University of Tennessee, Knoxville, Tennessee 37966, United States
| | - De-en Jiang
- Chemical
Sciences Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, United States
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23
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On the Transferability of Three Water Models Developed by Adaptive Force Matching. ACTA ACUST UNITED AC 2014. [DOI: 10.1016/b978-0-444-63378-1.00002-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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24
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Rusnak AJ, Pinnick ER, Calderon CE, Wang F. Static dielectric constants and molecular dipole distributions of liquid water and ice-Ih investigated by the PAW-PBE exchange-correlation functional. J Chem Phys 2012; 137:034510. [PMID: 22830714 DOI: 10.1063/1.4734594] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The static dielectric constants, ε(s), of ice-Ih and liquid water were calculated using density functional theory with the Perdew-Burke-Ernzerhof (PBE) exchange-correlation functional and the projector-augmented-wave (PAW) approach. Proton disordered ice configurations and uncorrelated liquid configurations were sampled with the electrostatic switching method using force fields specially designed to facilitate the ab initio free energy perturbation calculations. Our results indicate that PAW-PBE underestimates the ε(s) of both ice-Ih and liquid water but predicts the ratio of ice and water ε(s) in good agreement with experimental measurements. PAW-PBE gives average water dipole moments of 2.50 D in ice-Ih and 2.48 D in the liquid. Our results show that the fixed-charge water models developed by adaptive force matching can reproduce the PAW-PBE dipole moments with an error of approximately 5%. The ice and liquid models created in this work have polarizabilities of 1.32 Å(3) and 1.30 Å(3), respectively, along the HOH bisector direction.
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Affiliation(s)
- Andrew J Rusnak
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
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