1
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Seo S, Lee HS, Yoon TJ. Kirkwood-Buff Analysis of Binary and Ternary Systems Consisting of Alcohols (Methanol, Ethanol, 1-Propanol, and 2-Propanol), Water, and n-Hexane to Understand the Formation of Surfactant-Free Microemulsions. J Phys Chem B 2024; 128:5092-5108. [PMID: 38743587 DOI: 10.1021/acs.jpcb.4c01563] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Surfactant-free microemulsion (SFME) represents a class of fluid mixtures that can form microheterogeneous structures without detergents, offering an environmentally benign alternative to traditional microemulsions. However, the formation mechanism is still elusive. This work applies the Kirkwood-Buff theory to mixtures of alcohols, water, and n-hexane to elucidate the SFME formation mechanism. To ensure robust calculation of the Kirkwood-Buff integrals (KBIs), we construct a data set of densities and excess free energies of binary and ternary systems. Multiple excess Gibbs free energy models are assessed against this data set to select the most suitable model reproducing the experimental results. In addition, we introduce statistical methods to determine the optimal polynomial order of the Redlich-Kister correlation for the excess volume data. We first validate our methodology in binary systems. Then, we extend the calculation method to ternary mixtures. The KBI calculation results reveal that the alcohol-hexane and water-hexane interactions do not significantly affect SFME formation. In contrast, the interplay among water-water, water-alcohol, and alcohol-alcohol interactions critically influences the ability of a liquid mixture to form SFME structures. SFME systems exhibit the facile formation of water aggregates enveloped by alcohols, whereas non-SFME systems demonstrate homogeneous alcohol/water droplets dispersed in an oil continuous medium.
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Affiliation(s)
- Seungmin Seo
- Department of Chemical Engineering and Applied Chemistry, Chungnam National University, Daejeon 34134, Republic of Korea
| | - Hong-Shik Lee
- Low-Carbon Transition R&D Department, Korea Institute of Industrial Technology, Cheonan 31056, Republic of Korea
| | - Tae Jun Yoon
- School of Transdisciplinary Innovations, Seoul National University, Seoul 08826, Republic of Korea
- School of Chemical and Biological Engineering, Institute of Chemical Processes, Seoul National University, Seoul 08826, Republic of Korea
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2
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Paligaspe P, Weerasinghe S, Dissanayake DP, Senthilnithy R. Impact of Cd(II) on the stability of human uracil DNA glycosylase enzyme; an implication of molecular dynamics trajectories on stability analysis. J Biomol Struct Dyn 2022; 40:14027-14034. [PMID: 34738875 DOI: 10.1080/07391102.2021.1999329] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Uracil DNA glycosylase is a key enzyme that identifies and removes damaged bases from DNA in the base excision repair pathway. Experimentalists have identified the possibility of Cd(II) reducing the activity of human uracil DNA glycosylase (hUNG) by binding with the enzyme replacing the catalytic water molecule. The present study focus on the stability variation of the enzyme in the presence and absence of Cd(II) and confirms the reported results with the stability analysis done using molecular dynamic (MD) simulation trajectories. The CavityPlus web server identified seven cavities for the free enzyme as possible binding sites and a cavity containing the active site of the enzyme as the best binding cavity for a ligand. Based on the CavityPlus results and the previously reported work, a free hUNG system and two systems of the enzyme with Cd(II); one with Cd(II) replacing the catalytic water molecule in the active site of the enzyme and the other replacing a non-catalytic water molecule in the active site were generated for the simulation. The simulation trajectories were used for the structural stability analysis of the enzyme in all three systems. The binding free energy of the Cd(II) with the enzyme was calculated using molecular mechanics Poisson Boltzmann surface area method. The results showed that the enzyme achieves comparatively high stability with the removal of catalytic water of the enzyme by Cd(II). Therefore, this supports the previously reported idea that Cd(II) replaces catalytic water molecules and affects enzyme activity.
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Affiliation(s)
- Priyani Paligaspe
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
| | - Samantha Weerasinghe
- Department of Chemistry, Faculty of Science, University of Colombo, Colombo, Sri Lanka
| | | | - Rajendram Senthilnithy
- Department of Chemistry, Faculty of Natural Sciences, The Open University of Sri Lanka, Nugegoda, Sri Lanka
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3
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McIvor JAP, Larsen DS, Mercadante D. Simulating Polyproline II-Helix-Rich Peptides with the Latest Kirkwood-Buff Force Field: A Direct Comparison with AMBER and CHARMM. J Phys Chem B 2022; 126:7833-7846. [PMID: 36125334 DOI: 10.1021/acs.jpcb.2c03837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We simulated the dynamics of a set of peptides characterized by ensembles rich in PPII-helical content, to assess the ability of the most recent Kirkwood-Buff force field (KBFF20) to sample this conformational peculiarity. KBFF has been previously shown to capably reproduce experimental dimensions of disordered proteins, while being limited in confidently sampling structured proteins. Further development of the force field bridged this gap. It is however still unknown what are the main differences between KBFF and AMBER/CHARMM force fields. A direct comparison is now possible as both AMBER/CHARMM force fields have been used to sample peptides rich in PPII-helical content. We found that KBFF20 samples' PPII-helical content qualitatively matches both AMBER and CHARMM force fields, with the main difference being the KBFF ability to populate the αR region of the Ramachandran plot in the set of simulated peptides. Overall, KBFF20 is a well-balanced force field, able to sample the dynamics of both structured and unstructured proteins.
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Affiliation(s)
- Jordan A P McIvor
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Danaé S Larsen
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
| | - Davide Mercadante
- School of Chemical Sciences, The University of Auckland, 23 Symonds Street, Auckland 1010, New Zealand
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4
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Venetsanos F, Anogiannakis SD, Theodorou DN. Mixing Thermodynamics and Flory–Huggins Interaction Parameter of Polyethylene Oxide/Polyethylene Oligomeric Blends from Kirkwood–Buff Theory and Molecular Simulations. Macromolecules 2022. [DOI: 10.1021/acs.macromol.2c00642] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Fotis Venetsanos
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Athens 15780, Greece
| | - Stefanos D. Anogiannakis
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Athens 15780, Greece
| | - Doros N. Theodorou
- School of Chemical Engineering, National Technical University of Athens, 9 Heroon Polytechniou Street, Athens 15780, Greece
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5
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Boothroyd S, Madin OC, Mobley DL, Wang LP, Chodera JD, Shirts MR. Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties. J Chem Theory Comput 2022; 18:3577-3592. [PMID: 35533269 DOI: 10.1021/acs.jctc.1c01268] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Developing a sufficiently accurate classical force field representation of molecules is key to realizing the full potential of molecular simulations as a route to gaining a fundamental insight into a broad spectrum of chemical and biological phenomena. This is only possible, however, if the many complex interactions between molecules of different species in the system are accurately captured by the model. Historically, the intermolecular van der Waals (vdW) interactions have primarily been trained against densities and enthalpies of vaporization of pure (single-component) systems, with occasional usage of hydration free energies. In this study, we demonstrate how including physical property data of binary mixtures can better inform these parameters, encoding more information about the underlying physics of the system in complex chemical mixtures. To demonstrate this, we retrain a select number of Lennard-Jones parameters describing the vdW interactions of the OpenFF 1.0.0 (Parsley) fixed charge force field against training sets composed of densities and enthalpies of mixing for binary liquid mixtures as well as densities and enthalpies of vaporization of pure liquid systems and assess the performance of each of these combinations. We show that retraining against the mixture data improves the force field's ability to reproduce mixture properties, including solvation free energies, correcting some systematic errors that exist when training vdW interactions against properties of pure systems only.
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Affiliation(s)
- Simon Boothroyd
- Boothroyd Scientific Consulting Ltd., 71-75 Shelton Street, London WC2H 9JQ, Greater London, U.K
| | - Owen C Madin
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - David L Mobley
- Department of Chemistry, University of California, Irvine, California 92617, United States.,Department of Pharmaceutical Sciences, University of California, Irvine, California 92617, United States
| | - Lee-Ping Wang
- Department of Chemistry, University of California, Davis, California 95616, United States
| | - John D Chodera
- Computational & Systems Biology Program, Sloan Kettering Institute, Memorial Sloan Kettering Cancer Center, New York, New York 10065, United States
| | - Michael R Shirts
- Department of Chemical and Biological Engineering, University of Colorado Boulder, Boulder, Colorado 80309, United States
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6
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Paligaspe P, Weerasinghe S, Dissanayake D, Senthilnithy R. Identify the effect of As(III) on the structural stability of monomeric PKM2 and its carcinogenicity: A molecular dynamics and QM/MM based approach. J Mol Struct 2021. [DOI: 10.1016/j.molstruc.2021.130257] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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7
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Biomolecular Simulations with the Three-Dimensional Reference Interaction Site Model with the Kovalenko-Hirata Closure Molecular Solvation Theory. Int J Mol Sci 2021; 22:ijms22105061. [PMID: 34064655 PMCID: PMC8151972 DOI: 10.3390/ijms22105061] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2021] [Revised: 05/08/2021] [Accepted: 05/10/2021] [Indexed: 11/17/2022] Open
Abstract
The statistical mechanics-based 3-dimensional reference interaction site model with the Kovalenko-Hirata closure (3D-RISM-KH) molecular solvation theory has proven to be an essential part of a multiscale modeling framework, covering a vast region of molecular simulation techniques. The successful application ranges from the small molecule solvation energy to the bulk phase behavior of polymers, macromolecules, etc. The 3D-RISM-KH successfully predicts and explains the molecular mechanisms of self-assembly and aggregation of proteins and peptides related to neurodegeneration, protein-ligand binding, and structure-function related solvation properties. Upon coupling the 3D-RISM-KH theory with a novel multiple time-step molecular dynamic (MD) of the solute biomolecule stabilized by the optimized isokinetic Nosé-Hoover chain thermostat driven by effective solvation forces obtained from 3D-RISM-KH and extrapolated forward by generalized solvation force extrapolation (GSFE), gigantic outer time-steps up to picoseconds to accurately calculate equilibrium properties were obtained in this new quasidynamics protocol. The multiscale OIN/GSFE/3D-RISM-KH algorithm was implemented in the Amber package and well documented for fully flexible model of alanine dipeptide, miniprotein 1L2Y, and protein G in aqueous solution, with a solvent sampling rate ~150 times faster than a standard MD simulation in explicit water. Further acceleration in computation can be achieved by modifying the extent of solvation layers considered in the calculation, as well as by modifying existing closure relations. This enhanced simulation technique has proven applications in protein-ligand binding energy calculations, ligand/solvent binding site prediction, molecular solvation energy calculations, etc. Applications of the RISM-KH theory in molecular simulation are discussed in this work.
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8
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Ploetz EA, Karunaweera S, Bentenitis N, Chen F, Dai S, Gee MB, Jiao Y, Kang M, Kariyawasam NL, Naleem N, Weerasinghe S, Smith PE. Kirkwood-Buff-Derived Force Field for Peptides and Proteins: Philosophy and Development of KBFF20. J Chem Theory Comput 2021; 17:2964-2990. [PMID: 33878263 DOI: 10.1021/acs.jctc.1c00075] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
A new classical nonpolarizable force field, KBFF20, for the simulation of peptides and proteins is presented. The force field relies heavily on the use of Kirkwood-Buff theory to provide a comparison of simulated and experimental Kirkwood-Buff integrals for solutes containing the functional groups common in proteins, thus ensuring intermolecular interactions that provide a good balance between the peptide-peptide, peptide-solvent, and solvent-solvent distributions observed in solution mixtures. In this way, it differs significantly from other biomolecular force fields. Further development and testing of the intermolecular potentials are presented here. Subsequently, rotational potentials for the ϕ/ψ and χ dihedral degrees of freedom are obtained by analysis of the Protein Data Bank, followed by small modifications to provide a reasonable balance between simulated and observed α and β percentages for small peptides. This, the first of two articles, describes in detail the philosophy and development behind KBFF20.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Sadish Karunaweera
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nikolaos Bentenitis
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Feng Chen
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Shu Dai
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Moon B Gee
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Yuanfang Jiao
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Myungshim Kang
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nilusha L Kariyawasam
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | - Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
| | | | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid-Campus Drive North, Manhattan, Kansas 66506, United States
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9
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Primorac T, Požar M, Sokolić F, Zoranić L. The influence of binary mixtures' structuring on the calculation of Kirkwood-Buff integrals: A molecular dynamics study. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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10
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Požar M, Jukić I, Lovrinčević B. Thermodynamic, structural and dynamic properties of selected non-associative neat liquids. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:405101. [PMID: 32412441 DOI: 10.1088/1361-648x/ab935d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 05/14/2020] [Indexed: 06/11/2023]
Abstract
Non-associative neat liquids benzene, acetone and carbon tetrachloride have been examined via molecular dynamics simulations. Several models of each neat liquid have been simulated, and selected thermodynamic and structural results are presented. However, the models have been compared mainly in terms of their dynamic quantities. Since models are rarely parametrized with the dynamic properties in mind, the principal goal of this work is to present quantities such as the power spectra, rotational correlation functions and relaxation times, diffusion coefficients and self and distinct parts of the van Hove functions in relation to available experimental data. The general trends of the calculated data provide a benchmark for the behavior of neat simple liquids which will be built upon in the cases of mixtures with associative liquids.
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Affiliation(s)
- Martina Požar
- University of Split, Faculty of Science, Rud-era Boškovića 33, 21000 Split, Croatia
| | - Ivo Jukić
- University of Split, Faculty of Science, Rud-era Boškovića 33, 21000 Split, Croatia
| | - Bernarda Lovrinčević
- University of Split, Faculty of Science, Rud-era Boškovića 33, 21000 Split, Croatia
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11
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Banerjee P, Lipowsky R, Santer M. Coarse-Grained Molecular Model for the Glycosylphosphatidylinositol Anchor with and without Protein. J Chem Theory Comput 2020; 16:3889-3903. [PMID: 32392421 PMCID: PMC7303967 DOI: 10.1021/acs.jctc.0c00056] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2020] [Indexed: 01/17/2023]
Abstract
Glycosylphosphatidylinositol (GPI) anchors are a unique class of complex glycolipids that anchor a great variety of proteins to the extracellular leaflet of plasma membranes of eukaryotic cells. These anchors can exist either with or without an attached protein called GPI-anchored protein (GPI-AP) both in vitro and in vivo. Although GPIs are known to participate in a broad range of cellular functions, it is to a large extent unknown how these are related to GPI structure and composition. Their conformational flexibility and microheterogeneity make it difficult to study them experimentally. Simplified atomistic models are amenable to all-atom computer simulations in small lipid bilayer patches but not suitable for studying their partitioning and trafficking in complex and heterogeneous membranes. Here, we present a coarse-grained model of the GPI anchor constructed with a modified version of the MARTINI force field that is suited for modeling carbohydrates, proteins, and lipids in an aqueous environment using MARTINI's polarizable water. The nonbonded interactions for sugars were reparametrized by calculating their partitioning free energies between polar and apolar phases. In addition, sugar-sugar interactions were optimized by adjusting the second virial coefficients of osmotic pressures for solutions of glucose, sucrose, and trehalose to match with experimental data. With respect to the conformational dynamics of GPI-anchored green fluorescent protein, the accessible time scales are now at least an order of magnitude larger than for the all-atom system. This is particularly important for fine-tuning the mutual interactions of lipids, carbohydrates, and amino acids when comparing to experimental results. We discuss the prospective use of the coarse-grained GPI model for studying protein-sorting and trafficking in membrane models.
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Affiliation(s)
- Pallavi Banerjee
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Reinhard Lipowsky
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
- Institute
of Biochemistry and Biology, University
of Potsdam, Potsdam 14469, Germany
| | - Mark Santer
- Max
Planck Institute of Colloids and Interfaces, Potsdam 14476, Germany
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12
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Piana S, Robustelli P, Tan D, Chen S, Shaw DE. Development of a Force Field for the Simulation of Single-Chain Proteins and Protein-Protein Complexes. J Chem Theory Comput 2020; 16:2494-2507. [PMID: 31914313 DOI: 10.1021/acs.jctc.9b00251] [Citation(s) in RCA: 83] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The accuracy of atomistic physics-based force fields for the simulation of biological macromolecules has typically been benchmarked experimentally using biophysical data from simple, often single-chain systems. In the case of proteins, the careful refinement of force field parameters associated with torsion-angle potentials and the use of improved water models have enabled a great deal of progress toward the highly accurate simulation of such monomeric systems in both folded and, more recently, disordered states. In living organisms, however, proteins constantly interact with other macromolecules, such as proteins and nucleic acids, and these interactions are often essential for proper biological function. Here, we show that state-of-the-art force fields tuned to provide an accurate description of both ordered and disordered proteins can be limited in their ability to accurately describe protein-protein complexes. This observation prompted us to perform an extensive reparameterization of one variant of the Amber protein force field. Our objective involved refitting not only the parameters associated with torsion-angle potentials but also the parameters used to model nonbonded interactions, the specification of which is expected to be central to the accurate description of multicomponent systems. The resulting force field, which we call DES-Amber, allows for more accurate simulations of protein-protein complexes, while still providing a state-of-the-art description of both ordered and disordered single-chain proteins. Despite the improvements, calculated protein-protein association free energies still appear to deviate substantially from experiment, a result suggesting that more fundamental changes to the force field, such as the explicit treatment of polarization effects, may simultaneously further improve the modeling of single-chain proteins and protein-protein complexes.
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Affiliation(s)
- Stefano Piana
- D. E. Shaw Research, New York, New York 10036, United States
| | - Paul Robustelli
- D. E. Shaw Research, New York, New York 10036, United States
| | - Dazhi Tan
- D. E. Shaw Research, New York, New York 10036, United States
| | - Songela Chen
- D. E. Shaw Research, New York, New York 10036, United States
| | - David E Shaw
- D. E. Shaw Research, New York, New York 10036, United States.,Department of Biochemistry and Molecular Biophysics, Columbia University, New York, New York 10032, United States
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13
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Petris PC, Anogiannakis SD, Tzounis PN, Theodorou DN. Thermodynamic Analysis of n-Hexane-Ethanol Binary Mixtures Using the Kirkwood-Buff Theory. J Phys Chem B 2019; 123:247-257. [PMID: 30516991 DOI: 10.1021/acs.jpcb.8b10425] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A complete thermodynamic analysis of mixtures consisting of molecules with complex chemical constitution can be rather demanding. The Kirkwood-Buff theory of solutions allows the estimation of thermodynamic properties, which cannot be directly extracted from atomistic simulations, such as the Gibbs energy of mixing (Δmix G). In this work, we perform molecular dynamics simulations of n-hexane-ethanol binary mixtures in the liquid state under two temperature-pressure conditions and at various mole fractions. On the basis of the recently published methodology of Galata [ Fluid Phase Equilib. 2018 , 470 , 25 - 37 ] , we first calculate the Kirkwood-Buff integrals in the isothermal-isobaric ( NpT) ensemble, identifying how system size affects their estimation. We then extract the activity coefficients, excess Gibbs energy, excess enthalpy, and excess entropy for the n-hexane-ethanol binary mixtures we simulate. We employ two approaches for quantifying composition fluctuations: one based on counting molecular centers of mass and a second one based on counting molecular segments. Results from the two approaches are practically indistinguishable. We compare our results against predictions of vapor-liquid equilibria obtained in a previous simulation work using the same force field, as well as with experimental data, and find very good agreement. In addition, we develop a simple methodology to identify the hydrogen bonds between ethanol molecules and analyze their effects on mixing properties.
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Affiliation(s)
- Panagiotis C Petris
- School of Chemical Engineering , National Technical University of Athens , GR 15780 Athens , Greece
| | - Stefanos D Anogiannakis
- School of Chemical Engineering , National Technical University of Athens , GR 15780 Athens , Greece
| | | | - Doros N Theodorou
- School of Chemical Engineering , National Technical University of Athens , GR 15780 Athens , Greece
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14
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Cloutier T, Sudrik C, Sathish HA, Trout BL. Kirkwood–Buff-Derived Alcohol Parameters for Aqueous Carbohydrates and Their Application to Preferential Interaction Coefficient Calculations of Proteins. J Phys Chem B 2018; 122:9350-9360. [DOI: 10.1021/acs.jpcb.8b07623] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Theresa Cloutier
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Chaitanya Sudrik
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hasige A. Sathish
- Formulation Sciences, MedImmune LLC, Gaithersburg, Maryland 20878, United States
| | - Bernhardt L. Trout
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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15
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Toward Expanded Diversity of Host–Guest Interactions via Synthesis and Characterization of Cyclodextrin Derivatives. J SOLUTION CHEM 2018. [DOI: 10.1007/s10953-018-0769-1] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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16
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Schmalhorst PS, Deluweit F, Scherrers R, Heisenberg CP, Sikora M. Overcoming the Limitations of the MARTINI Force Field in Simulations of Polysaccharides. J Chem Theory Comput 2017; 13:5039-5053. [DOI: 10.1021/acs.jctc.7b00374] [Citation(s) in RCA: 60] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
| | - Felix Deluweit
- Wyatt Technology Europe, Hochstraße
18, 56307 Dernbach, Germany
| | - Roger Scherrers
- Wyatt Technology Europe, Hochstraße
18, 56307 Dernbach, Germany
| | | | - Mateusz Sikora
- Institute of Science and Technology Austria, Am Campus 1, 3400 Klosterneuburg, Austria
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17
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Mercadante D, Wagner JA, Aramburu IV, Lemke EA, Gräter F. Sampling Long- versus Short-Range Interactions Defines the Ability of Force Fields To Reproduce the Dynamics of Intrinsically Disordered Proteins. J Chem Theory Comput 2017; 13:3964-3974. [DOI: 10.1021/acs.jctc.7b00143] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Davide Mercadante
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Johannes A. Wagner
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
| | - Iker V. Aramburu
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Edward A. Lemke
- Structural
and Computational Biology Unit, Cell Biology and Biophysics Unit, European Molecular Biology Laboratory (EMBL), Meyerhofstraße 1, 69117 Heidelberg, Germany
| | - Frauke Gräter
- HITS—Heidelberg Institute for Theoretical Studies, 35 Schloß Wolfsbrunnenweg, 69118 Heidelberg, Germany
- IWR—Interdisciplinary
Center for Scientific Computing, Heidelberg University, Mathematikon,
Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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18
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Henriksen NM, Gilson MK. Evaluating Force Field Performance in Thermodynamic Calculations of Cyclodextrin Host-Guest Binding: Water Models, Partial Charges, and Host Force Field Parameters. J Chem Theory Comput 2017; 13:4253-4269. [PMID: 28696692 PMCID: PMC5606194 DOI: 10.1021/acs.jctc.7b00359] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/05/2022]
Abstract
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Computational
prediction of noncovalent binding free energies with
methods based on molecular mechanical force fields has become increasingly
routine in drug discovery projects, where they promise to speed the
discovery of small molecule ligands to bind targeted proteins with
high affinity. Because the reliability of free energy methods still
has significant room for improvement, new force fields, or modifications
of existing ones, are regularly introduced with the aim of improving
the accuracy of molecular simulations. However, comparatively little
work has been done to systematically assess how well force fields
perform, particularly in relation to the calculation of binding affinities.
Hardware advances have made these calculations feasible, but comprehensive
force field assessments for protein–ligand sized systems still
remain costly. Here, we turn to cyclodextrin host–guest systems,
which feature many hallmarks of protein–ligand binding interactions
but are generally much more tractable due to their small size. We
present absolute binding free energy and enthalpy calculations, using
the attach-pull-release (APR) approach, on a set of 43 cyclodextrin-guest
pairs for which experimental ITC data are available. The test set
comprises both α- and β-cyclodextrin hosts binding a series
of small organic guests, each with one of three functional groups:
ammonium, alcohol, or carboxylate. Four water models are considered
(TIP3P, TIP4Pew, SPC/E, and OPC), along with two partial charge assignment
procedures (RESP and AM1-BCC) and two cyclodextrin host force fields.
The results suggest a complex set of considerations when choosing
a force field for biomolecular simulations. For example, some force
field combinations clearly outperform others at the binding enthalpy
calculations but not for the binding free energy. Additionally, a
force field combination which we expected to be the worst performer
gave the most accurate binding free energies – but the least
accurate binding enthalpies. The results have implications for the
development of improved force fields, and we propose this test set,
and potential future elaborations of it, as a powerful validation
suite to evaluate new force fields and help guide future force field
development.
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Affiliation(s)
- Niel M Henriksen
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California 92093-0736, United States
| | - Michael K Gilson
- Skaggs School of Pharmacy and Pharmaceutical Sciences, University of California San Diego , La Jolla, California 92093-0736, United States
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19
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Naleem N, Ploetz EA, Smith PE. Gaussian and non-Gaussian fluctuations in pure classical fluids. J Chem Phys 2017. [DOI: 10.1063/1.4977455] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Nawavi Naleem
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
| | - Elizabeth A. Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
| | - Paul E. Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, 1212 Mid Campus Dr. North, Manhattan, Kansas 66506-0401, USA
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20
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Požar M, Perera A. Lifshitz phase: the microscopic structure of aqueous and ethanol mixtures of 1,n-diols. Phys Chem Chem Phys 2017; 19:14992-15004. [DOI: 10.1039/c7cp01949a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
We study binary mixtures of ethylene glycol and 1,3-propandiol with water or ethanol using computer simulations.
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Affiliation(s)
- Martina Požar
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
- Department of Physics
| | - Aurélien Perera
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
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21
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Požar M, Kerasidou A, Lovrinčević B, Zoranić L, Mijaković M, Primorac T, Sokolić F, Teboul V, Perera A. The microscopic structure of cold aqueous methanol mixtures. J Chem Phys 2016; 145:144502. [DOI: 10.1063/1.4964487] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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22
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Chiba S, Furuta T, Shimizu S. Kirkwood–Buff Integrals for Aqueous Urea Solutions Based upon the Quantum Chemical Electrostatic Potential and Interaction Energies. J Phys Chem B 2016; 120:7714-23. [DOI: 10.1021/acs.jpcb.6b05611] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Shuntaro Chiba
- Education
Academy of Computational Life Sciences, Tokyo Institute of Technology, J3-141 4259 Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Tadaomi Furuta
- School
of Life Science and Technology, Tokyo Institute of Technology, B-62 4259
Nagatsuta-cho, Midori-ku, Yokohama 226-8501, Japan
| | - Seishi Shimizu
- York
Structural Biology Laboratory, Department of Chemistry, University of York, Heslington, York YO10 5DD, United Kingdom
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23
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Ley RT, Fuerst GB, Redeker BN, Paluch AS. Developing a Predictive Form of MOSCED for Nonelectrolyte Solids Using Molecular Simulation: Application to Acetanilide, Acetaminophen, and Phenacetin. Ind Eng Chem Res 2016. [DOI: 10.1021/acs.iecr.5b04807] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ryan T. Ley
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Georgia B. Fuerst
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Bryce N. Redeker
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
| | - Andrew S. Paluch
- Department
of Chemical, Paper
and Biomedical Engineering, Miami University, Oxford, Ohio 45056, United States
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24
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Miller MS, Lay WK, Elcock AH. Osmotic Pressure Simulations of Amino Acids and Peptides Highlight Potential Routes to Protein Force Field Parameterization. J Phys Chem B 2016; 120:8217-29. [PMID: 27052117 DOI: 10.1021/acs.jpcb.6b01902] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Recent molecular dynamics (MD) simulations of proteins have suggested that common force fields overestimate the strength of amino acid interactions in aqueous solution. In an attempt to determine the causes of these effects, we have measured the osmotic coefficients of a number of amino acids using the AMBER ff99SB-ILDN force field with two popular water models, and compared the results with available experimental data. With TIP4P-Ew water, interactions between aliphatic residues agree well with experiment, but interactions of the polar residues serine and threonine are found to be excessively attractive. For all tested amino acids, the osmotic coefficients are lower when the TIP3P water model is used. Additional simulations performed on charged amino acids indicate that the osmotic coefficients are strongly dependent on the parameters assigned to the salt ions, with a reparameterization of the sodium/carboxylate interaction reported by the Aksimentiev group significantly improving description of the osmotic coefficient for glutamate. For five neutral amino acids, we also demonstrate a decrease in solute-solute attractions using the recently reported TIP4P-D water model and using the KBFF force field. Finally, we show that for four two-residue peptides improved agreement with experiment can be achieved by rederiving the partial charges for each peptide.
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Affiliation(s)
- Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Wesley K Lay
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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25
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Ploetz EA, Rustenburg AS, Geerke DP, Smith PE. To Polarize or Not to Polarize? Charge-on-Spring versus KBFF Models for Water and Methanol Bulk and Vapor–Liquid Interfacial Mixtures. J Chem Theory Comput 2016; 12:2373-87. [DOI: 10.1021/acs.jctc.5b01115] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Elizabeth A. Ploetz
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
| | - Ariën S. Rustenburg
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Daan P. Geerke
- AIMMS
Division of Molecular Toxicology, Department of Chemistry and Pharmaceutical
Sciences, Faculty of Sciences, VU University Amsterdam, 1081 HV Amsterdam, The Netherlands
| | - Paul E. Smith
- Department
of Chemistry, Kansas State University, Manhattan, Kansas 66506, United States
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26
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Lay WK, Miller MS, Elcock AH. Optimizing Solute-Solute Interactions in the GLYCAM06 and CHARMM36 Carbohydrate Force Fields Using Osmotic Pressure Measurements. J Chem Theory Comput 2016; 12:1401-7. [PMID: 26967542 DOI: 10.1021/acs.jctc.5b01136] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
GLYCAM06 and CHARMM36 are successful force fields for modeling carbohydrates. To correct recently identified deficiencies with both force fields, we adjusted intersolute nonbonded parameters to reproduce the experimental osmotic coefficient of glucose at 1 M. The modified parameters improve behavior of glucose and sucrose up to 4 M and improve modeling of a dextran 55-mer. While the modified parameters may not be applicable to all carbohydrates, they highlight the use of osmotic simulations to optimize force fields.
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Affiliation(s)
- Wesley K Lay
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Mark S Miller
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
| | - Adrian H Elcock
- Department of Biochemistry, University of Iowa , Iowa City, Iowa 52242, United States
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27
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Abstract
AbstractConcentration fluctuations play an important role in the statistical description of the stability of liquids, particularly in the neighborhood of phase transitions. Classical thermodynamics is blind to fluctuations, and statistical thermodynamics is required to fully understand quantities such as the isothermal compressibility or heat capacity, by linking them to fluctuations of appropriate statistical microscopic quantities and showing that they are response functions. This is illustrated by the seminal Kirkwood–Buff theory of solutions. However, the existence of micro-heterogeneous structures, particularly in aqueous mixtures, which leads to large Kirkwood–Buff integrals, suggest that micro-heterogeneity is a form of concentration fluctuation. This interpretation becomes difficult to accept when extrapolated to larger micro-heterogeneous structures such as micellar aggregates in micro-emulsions. By analyzing how different methods, experimental, computer experiments and theoretical approaches deal with the underlying duality behind these two physical manifestations, we put in evidence the need to reconsider the description of liquids by incorporating the description of emergent “objects”, such as the micro-heterogeneous structures from a molecular point of view. On this path, the concept of “molecular emulsion” allows to describe in a unified way all type of disordered liquids, from solutions to the organized liquids of soft matter.
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Affiliation(s)
- Aurélien Perera
- 1Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600), Université Pierre et Marie Curie, 4 Place Jussieu, F75252, Paris cedex 05, France
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28
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Mercadante D, Milles S, Fuertes G, Svergun DI, Lemke EA, Gräter F. Kirkwood-Buff Approach Rescues Overcollapse of a Disordered Protein in Canonical Protein Force Fields. J Phys Chem B 2015; 119:7975-84. [PMID: 26030189 DOI: 10.1021/acs.jpcb.5b03440] [Citation(s) in RCA: 68] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Understanding the function of intrinsically disordered proteins is intimately related to our capacity to correctly sample their conformational dynamics. So far, a gap between experimentally and computationally derived ensembles exists, as simulations show overcompacted conformers. Increasing evidence suggests that the solvent plays a crucial role in shaping the ensembles of intrinsically disordered proteins and has led to several attempts to modify water parameters and thereby favor protein-water over protein-protein interactions. This study tackles the problem from a different perspective, which is the use of the Kirkwood-Buff theory of solutions to reproduce the correct conformational ensemble of intrinsically disordered proteins (IDPs). A protein force field recently developed on such a basis was found to be highly effective in reproducing ensembles for a fragment from the FG-rich nucleoporin 153, with dimensions matching experimental values obtained from small-angle X-ray scattering and single molecule FRET experiments. Kirkwood-Buff theory presents a complementary and fundamentally different approach to the recently developed four-site TIP4P-D water model, both of which can rescue the overcollapse observed in IDPs with canonical protein force fields. As such, our study provides a new route for tackling the deficiencies of current protein force fields in describing protein solvation.
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Affiliation(s)
- Davide Mercadante
- †HITS-Heidelberg Institut for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,‡IWR-Interdisciplinary Center for Scientific Computing, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
| | - Sigrid Milles
- ∥EMBL-European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Gustavo Fuertes
- §EMBL-European Molecular Biology Laboratory, Notkestraße 85, 22607, Hamburg, Germany.,∥EMBL-European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Dmitri I Svergun
- §EMBL-European Molecular Biology Laboratory, Notkestraße 85, 22607, Hamburg, Germany
| | - Edward A Lemke
- ∥EMBL-European Molecular Biology Laboratory, Meyerhofstraße 1, 69117, Heidelberg, Germany
| | - Frauke Gräter
- †HITS-Heidelberg Institut for Theoretical Studies, Schloß-Wolfsbrunnenweg 35, 69118, Heidelberg, Germany.,‡IWR-Interdisciplinary Center for Scientific Computing, Im Neuenheimer Feld 368, 69120, Heidelberg, Germany
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29
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Goh GB, Eike DM, Murch BP, Brooks CL. Accurate Modeling of Ionic Surfactants at High Concentration. J Phys Chem B 2015; 119:6217-24. [DOI: 10.1021/acs.jpcb.5b01765] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Garrett B. Goh
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
| | - David M. Eike
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Bruce P. Murch
- Computational Chemistry, Modeling and Simulation, The Procter & Gamble Company, 8611 Beckett Road, West Chester, Ohio 45069, United States
| | - Charles L. Brooks
- Department
of Chemistry, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
- Biophysics
Program, University of Michigan, 930 N. University, Ann Arbor, Michigan 48109, United States
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30
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Ploetz EA, Smith PE. Experimental triplet and quadruplet fluctuation densities and spatial distribution function integrals for liquid mixtures. J Chem Phys 2015; 142:094504. [PMID: 25747091 PMCID: PMC4352168 DOI: 10.1063/1.4913514] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2014] [Accepted: 02/12/2015] [Indexed: 11/15/2022] Open
Abstract
Kirkwood-Buff or Fluctuation Solution Theory can be used to provide experimental pair fluctuations, and/or integrals over the pair distribution functions, from experimental thermodynamic data on liquid mixtures. Here, this type of approach is used to provide triplet and quadruplet fluctuations, and the corresponding integrals over the triplet and quadruplet distribution functions, in a purely thermodynamic manner that avoids the use of structure factors. The approach is then applied to binary mixtures of water + methanol and benzene + methanol over the full composition range under ambient conditions. The observed correlations between the different species vary significantly with composition. The magnitude of the fluctuations and integrals appears to increase as the number of the most polar molecule involved in the fluctuation or integral also increases. A simple physical picture of the fluctuations is provided to help rationalize some of these variations.
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Affiliation(s)
- Elizabeth A Ploetz
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
| | - Paul E Smith
- Department of Chemistry, Kansas State University, 213 CBC Building, Manhattan, Kansas 66506, USA
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31
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Požar M, Seguier JB, Guerche J, Mazighi R, Zoranić L, Mijaković M, Kežić-Lovrinčević B, Sokolić F, Perera A. Simple and complex disorder in binary mixtures with benzene as a common solvent. Phys Chem Chem Phys 2015; 17:9885-98. [DOI: 10.1039/c4cp05970k] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Substituting benzene for water in computer simulations of binary mixtures, allows one to study the various forms of disorder, without the complications often encountered in aqueous mixtures.
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Affiliation(s)
- Martina Požar
- Department of Physics
- Faculty of Sciences
- University of Split
- Split
- Croatia
| | - Jean-Baptiste Seguier
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
| | - Jonas Guerche
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
| | - Redha Mazighi
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
| | - Larisa Zoranić
- Department of Physics
- Faculty of Sciences
- University of Split
- Split
- Croatia
| | | | | | - Franjo Sokolić
- Department of Physics
- Faculty of Sciences
- University of Split
- Split
- Croatia
| | - Aurélien Perera
- Laboratoire de Physique Théorique de la Matière Condensée (UMR CNRS 7600)
- Université Pierre et Marie Curie
- Paris cedex 05
- France
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32
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Lin B, He X, MacKerell AD. A comparative Kirkwood-Buff study of aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields. J Phys Chem B 2013; 117:10572-80. [PMID: 23947568 DOI: 10.1021/jp4061889] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A comparative study on aqueous methanol solutions modeled by the CHARMM additive and Drude polarizable force fields was carried out by employing Kirkwood-Buff analysis. It was shown that both models reproduced the experimental Kirkwood-Buff integrals and excess coordination numbers adequately well over the entire concentration range. The Drude model showed significant improvement over the additive model in solution densities, partial molar volumes, excess molar volumes, concentration-dependent diffusion constants, and dielectric constants. However, the additive model performed somewhat better than the Drude model in reproducing the activity derivative, excess molar Gibbs energy, and excess molar enthalpy of mixing. This is due to the additive achieving a better balance among solute-solute, solute-solvent, and solvent-solvent interactions, indicating the potential for improvements in the Drude polarizable alcohol model.
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Affiliation(s)
- Bin Lin
- Department of Pharmaceutical Sciences, School of Pharmacy, University of Maryland , 20 Penn Street HSFII, Baltimore, Maryland 21201, United States
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33
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Lin B, Lopes PEM, Roux B, MacKerell AD. Kirkwood-Buff analysis of aqueous N-methylacetamide and acetamide solutions modeled by the CHARMM additive and Drude polarizable force fields. J Chem Phys 2013; 139:084509. [PMID: 24007020 PMCID: PMC3772949 DOI: 10.1063/1.4818731] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2013] [Accepted: 08/04/2013] [Indexed: 11/14/2022] Open
Abstract
Kirkwood-Buff analysis was performed on aqueous solutions of N-methylacetamide and acetamide using the Chemistry at HARvard Molecular Mechanics additive and Drude polarizable all-atom force fields. Comparison of a range of properties with experimental results, including Kirkwood-Buff integrals, excess coordination numbers, solution densities, partial molar values, molar enthalpy of mixing, showed both models to be well behaved at higher solute concentrations with the Drude model showing systematic improvement at lower solution concentrations. However, both models showed difficulties reproducing experimental activity derivatives and the excess Gibbs energy, with the Drude model performing slightly better. At the molecular level, the improved agreement of the Drude model at low solute concentrations is due to increased structure in the solute-solute and solute-solvent interactions. The present results indicate that the explicit inclusion of electronic polarization leads to improved modeling of dilute solutions even when those properties are not included as target data during force field optimization.
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Affiliation(s)
- Bin Lin
- Department of Pharmaceutical Sciences, University of Maryland, School of Pharmacy, 20 Penn Street HSFII, Baltimore, Maryland 21201, USA
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34
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Ploetz EA, Smith PE. Local Fluctuations in Solution: Theory and Applications. ADVANCES IN CHEMICAL PHYSICS 2013; 153:311-372. [PMID: 24683278 DOI: 10.1002/9781118571767.ch4] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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