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For: Reif MM, Hünenberger PH. Computation of methodology-independent single-ion solvation properties from molecular simulations. III. Correction terms for the solvation free energies, enthalpies, entropies, heat capacities, volumes, compressibilities, and expansivities of solvated ions. J Chem Phys 2011;134:144103. [PMID: 21495738 DOI: 10.1063/1.3567020] [Citation(s) in RCA: 60] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
Number Cited by Other Article(s)
1
Sun Z, Procacci P. Methodological and force field effects in the molecular dynamics-based prediction of binding free energies of host-guest systems. Phys Chem Chem Phys 2024. [PMID: 38990073 DOI: 10.1039/d4cp01804d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2024]
2
Baumann H, Dybeck E, McClendon CL, Pickard FC, Gapsys V, Pérez-Benito L, Hahn DF, Tresadern G, Mathiowetz AM, Mobley DL. Broadening the Scope of Binding Free Energy Calculations Using a Separated Topologies Approach. J Chem Theory Comput 2023;19:5058-5076. [PMID: 37487138 PMCID: PMC10413862 DOI: 10.1021/acs.jctc.3c00282] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Indexed: 07/26/2023]
3
Caceres-Delpiano J, Wang LP, Essex JW. The automated optimisation of a coarse-grained force field using free energy data. Phys Chem Chem Phys 2021;23:24842-24851. [PMID: 34723311 PMCID: PMC8579472 DOI: 10.1039/d0cp05041e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 10/18/2021] [Indexed: 11/21/2022]
4
Künzel N, Helms V. How phosphorylation of peptides affects their interaction with 14-3-3η domains. Proteins 2021;90:351-362. [PMID: 34462973 DOI: 10.1002/prot.26224] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2020] [Revised: 05/22/2021] [Accepted: 08/18/2021] [Indexed: 01/04/2023]
5
Solvation free energy of the proton in acetonitrile. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116032] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
6
Lopez-Redondo M, Fan S, Koide A, Koide S, Beckstein O, Stokes DL. Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP. J Gen Physiol 2021;153:212464. [PMID: 34254979 PMCID: PMC8282283 DOI: 10.1085/jgp.202112873] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 06/14/2021] [Indexed: 11/20/2022]  Open
7
Peng J, Zhang Y, Jiang Y, Zhang H. Developing and Assessing Nonbonded Dummy Models of Magnesium Ion with Different Hydration Free Energy References. J Chem Inf Model 2021;61:2981-2997. [PMID: 34080414 DOI: 10.1021/acs.jcim.1c00281] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
8
Amezcua M, El Khoury L, Mobley DL. SAMPL7 Host-Guest Challenge Overview: assessing the reliability of polarizable and non-polarizable methods for binding free energy calculations. J Comput Aided Mol Des 2021;35:1-35. [PMID: 33392951 PMCID: PMC8121194 DOI: 10.1007/s10822-020-00363-5] [Citation(s) in RCA: 38] [Impact Index Per Article: 12.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 11/24/2020] [Indexed: 12/15/2022]
9
Malloum A, Fifen JJ, Conradie J. Determination of the absolute solvation free energy and enthalpy of the proton in solutions. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2020.114919] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
10
Öhlknecht C, Perthold JW, Lier B, Oostenbrink C. Charge-Changing Perturbations and Path Sampling via Classical Molecular Dynamic Simulations of Simple Guest-Host Systems. J Chem Theory Comput 2020;16:7721-7734. [PMID: 33136389 PMCID: PMC7726903 DOI: 10.1021/acs.jctc.0c00719] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/10/2020] [Indexed: 01/24/2023]
11
Öhlknecht C, Petrov D, Engele P, Kröß C, Sprenger B, Fischer A, Lingg N, Schneider R, Oostenbrink C. Enhancing the promiscuity of a member of the Caspase protease family by rational design. Proteins 2020;88:1303-1318. [PMID: 32432825 PMCID: PMC7497161 DOI: 10.1002/prot.25950] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Revised: 03/19/2020] [Accepted: 04/29/2020] [Indexed: 12/12/2022]
12
Saric D, Kohns M, Vrabec J. Dielectric constant and density of aqueous alkali halide solutions by molecular dynamics: A force field assessment. J Chem Phys 2020;152:164502. [PMID: 32357782 DOI: 10.1063/1.5144991] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
13
Prasetyo N, Hofer TS. Carbon dioxide in liquid ammonia: An ab initio Quantum Mechanical/Molecular Mechanical Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) simulation study on structure, dynamics and thermodynamics of solvation. J Mol Liq 2020. [DOI: 10.1016/j.molliq.2020.112667] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
14
Öhlknecht C, Lier B, Petrov D, Fuchs J, Oostenbrink C. Correcting electrostatic artifacts due to net-charge changes in the calculation of ligand binding free energies. J Comput Chem 2020;41:986-999. [PMID: 31930547 DOI: 10.1002/jcc.26143] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 12/16/2019] [Accepted: 12/22/2019] [Indexed: 01/06/2023]
15
Wade AD, Huggins DJ. Optimization of Protein-Ligand Electrostatic Interactions Using an Alchemical Free-Energy Method. J Chem Theory Comput 2019;15:6504-6512. [PMID: 31584802 PMCID: PMC7007198 DOI: 10.1021/acs.jctc.9b00976] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
16
Doyle CC, Shi Y, Beck TL. The Importance of the Water Molecular Quadrupole for Estimating Interfacial Potential Shifts Acting on Ions Near the Liquid–Vapor Interface. J Phys Chem B 2019;123:3348-3358. [DOI: 10.1021/acs.jpcb.9b01289] [Citation(s) in RCA: 25] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
17
Prasetyo N, Hofer TS. Structure, Dynamics, and Hydration Free Energy of Carbon Dioxide in Aqueous Solution: A Quantum Mechanical/Molecular Mechanics Molecular Dynamics Thermodynamic Integration (QM/MM MD TI) Simulation Study. J Chem Theory Comput 2018;14:6472-6483. [PMID: 30336013 DOI: 10.1021/acs.jctc.8b00557] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
18
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]
19
Ekimoto T, Yamane T, Ikeguchi M. Elimination of Finite-Size Effects on Binding Free Energies via the Warp-Drive Method. J Chem Theory Comput 2018;14:6544-6559. [DOI: 10.1021/acs.jctc.8b00280] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
20
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
21
Olsson MA, García-Sosa AT, Ryde U. Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking. J Comput Aided Mol Des 2018;32:211-224. [PMID: 28879536 PMCID: PMC5767205 DOI: 10.1007/s10822-017-0056-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2017] [Accepted: 08/29/2017] [Indexed: 01/07/2023]
22
Liao Q, Pabis A, Strodel B, Kamerlin SCL. Extending the Nonbonded Cationic Dummy Model to Account for Ion-Induced Dipole Interactions. J Phys Chem Lett 2017;8:5408-5414. [PMID: 29022713 PMCID: PMC5672556 DOI: 10.1021/acs.jpclett.7b02358] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 10/12/2017] [Indexed: 05/28/2023]
23
Duignan TT, Baer MD, Schenter GK, Mundy CJ. Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions. J Chem Phys 2017;147:161716. [DOI: 10.1063/1.4994912] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
24
Atkovska K, Hub JS. Energetics and mechanism of anion permeation across formate-nitrite transporters. Sci Rep 2017;7:12027. [PMID: 28931899 PMCID: PMC5607303 DOI: 10.1038/s41598-017-11437-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/24/2017] [Indexed: 01/13/2023]  Open
25
Frenzel J, Meyer B, Marx D. Bicanonical ab Initio Molecular Dynamics for Open Systems. J Chem Theory Comput 2017. [DOI: 10.1021/acs.jctc.7b00263] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
26
Xia M, Chai Z, Wang D. Polarizable and Non-Polarizable Force Field Representations of Ferric Cation and Validations. J Phys Chem B 2017;121:5718-5729. [PMID: 28508639 DOI: 10.1021/acs.jpcb.7b02010] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
27
Satarifard V, Kashefolgheta S, Vila Verde A, Grafmüller A. Is the Solution Activity Derivative Sufficient to Parametrize Ion-Ion Interactions? Ions for TIP5P Water. J Chem Theory Comput 2017;13:2112-2122. [PMID: 28394606 DOI: 10.1021/acs.jctc.6b01229] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
28
Ekimoto T, Matubayasi N, Ikeguchi M. Finite-size effect on the charging free energy of protein in explicit solvent. J Chem Theory Comput 2016;11:215-23. [PMID: 26574219 DOI: 10.1021/ct5008394] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
29
Réal F, Gomes ASP, Guerrero Martínez YO, Ayed T, Galland N, Masella M, Vallet V. Structural, dynamical, and transport properties of the hydrated halides: How do At(-) bulk properties compare with those of the other halides, from F(-) to I(-)? J Chem Phys 2016;144:124513. [PMID: 27036467 DOI: 10.1063/1.4944613] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]  Open
30
Jiang Y, Zhang H, Tan T. Rational Design of Methodology-Independent Metal Parameters Using a Nonbonded Dummy Model. J Chem Theory Comput 2016;12:3250-60. [DOI: 10.1021/acs.jctc.6b00223] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
31
Reif MM, Hünenberger PH. Origin of Asymmetric Solvation Effects for Ions in Water and Organic Solvents Investigated Using Molecular Dynamics Simulations: The Swain Acity-Basity Scale Revisited. J Phys Chem B 2016;120:8485-517. [PMID: 27173101 DOI: 10.1021/acs.jpcb.6b02156] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
32
Williams CD, Carbone P. A classical force field for tetrahedral oxyanions developed using hydration properties: The examples of pertechnetate (TcO4(-)) and sulfate (SO4(2-)). J Chem Phys 2016;143:174502. [PMID: 26547171 DOI: 10.1063/1.4934964] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
33
Ions and solvation at biointerfaces. Biointerphases 2016;11:018801. [PMID: 26968212 DOI: 10.1116/1.4942207] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]  Open
34
Wilkins DM, Manolopoulos DE, Dang LX. Nuclear quantum effects in water exchange around lithium and fluoride ions. J Chem Phys 2016;142:064509. [PMID: 25681925 DOI: 10.1063/1.4907554] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
35
Huggins DJ. Estimating Translational and Orientational Entropies Using the k-Nearest Neighbors Algorithm. J Chem Theory Comput 2015;10:3617-25. [PMID: 26588506 DOI: 10.1021/ct500415g] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
36
Cendagorta JR, Ichiye T. The Surface Potential of the Water–Vapor Interface from Classical Simulations. J Phys Chem B 2015;119:9114-22. [DOI: 10.1021/jp508878v] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
37
Reif MM, Oostenbrink C. Toward the correction of effective electrostatic forces in explicit-solvent molecular dynamics simulations: restraints on solvent-generated electrostatic potential and solvent polarization. Theor Chem Acc 2015;134:2. [PMID: 26097404 PMCID: PMC4470580 DOI: 10.1007/s00214-014-1600-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2014] [Accepted: 11/19/2014] [Indexed: 11/26/2022]
38
Carvalho NF, Pliego JR. Cluster-continuum quasichemical theory calculation of the lithium ion solvation in water, acetonitrile and dimethyl sulfoxide: an absolute single-ion solvation free energy scale. Phys Chem Chem Phys 2015;17:26745-55. [DOI: 10.1039/c5cp03798k] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
39
Steele-MacInnis M, Reimer J, Bachmann S. Hydrothermal properties of the COS/D2 water model: a polarizable charge-on-spring water model, at elevated temperatures and pressures. RSC Adv 2015. [DOI: 10.1039/c5ra13495a] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]  Open
40
de Ruiter A, Zagrovic B. Absolute binding-free energies between standard RNA/DNA nucleobases and amino-acid sidechain analogs in different environments. Nucleic Acids Res 2014;43:708-18. [PMID: 25550435 PMCID: PMC4333394 DOI: 10.1093/nar/gku1344] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]  Open
41
Kann ZR, Skinner JL. A scaled-ionic-charge simulation model that reproduces enhanced and suppressed water diffusion in aqueous salt solutions. J Chem Phys 2014;141:104507. [DOI: 10.1063/1.4894500] [Citation(s) in RCA: 85] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]  Open
42
Hansen N, van Gunsteren WF. Practical Aspects of Free-Energy Calculations: A Review. J Chem Theory Comput 2014;10:2632-47. [PMID: 26586503 DOI: 10.1021/ct500161f] [Citation(s) in RCA: 289] [Impact Index Per Article: 28.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
43
Miguel ELM, Silva PL, Pliego JR. Theoretical Prediction of pKa in Methanol: Testing SM8 and SMD Models for Carboxylic Acids, Phenols, and Amines. J Phys Chem B 2014;118:5730-9. [DOI: 10.1021/jp501379p] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
44
Reif MM, Oostenbrink C. Net charge changes in the calculation of relative ligand-binding free energies via classical atomistic molecular dynamics simulation. J Comput Chem 2014;35:227-43. [PMID: 24249099 PMCID: PMC4237198 DOI: 10.1002/jcc.23490] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Accepted: 10/13/2013] [Indexed: 12/11/2022]
45
Christ CD, Fox T. Accuracy Assessment and Automation of Free Energy Calculations for Drug Design. J Chem Inf Model 2013;54:108-20. [DOI: 10.1021/ci4004199] [Citation(s) in RCA: 102] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
46
Rocklin GJ, Mobley DL, Dill KA, Hünenberger PH. Calculating the binding free energies of charged species based on explicit-solvent simulations employing lattice-sum methods: an accurate correction scheme for electrostatic finite-size effects. J Chem Phys 2013;139:184103. [PMID: 24320250 PMCID: PMC3838431 DOI: 10.1063/1.4826261] [Citation(s) in RCA: 169] [Impact Index Per Article: 15.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Accepted: 09/30/2013] [Indexed: 01/12/2023]  Open
47
Vlcek L, Chialvo AA, Simonson JM. Correspondence between Cluster-Ion and Bulk Solution Thermodynamic Properties: On the Validity of the Cluster-Pair-Based Approximation. J Phys Chem A 2013;117:11328-38. [DOI: 10.1021/jp408632e] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
48
Schnell SK, Englebienne P, Simon JM, Krüger P, Balaji SP, Kjelstrup S, Bedeaux D, Bardow A, Vlugt TJ. How to apply the Kirkwood–Buff theory to individual species in salt solutions. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.07.043] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
49
Liu Y, Fan X, Jin Y, Hu X, Hu H. Computing pKa Values with a Mixing Hamiltonian Quantum Mechanical/Molecular Mechanical Approach. J Chem Theory Comput 2013;9:4257-65. [DOI: 10.1021/ct400406v] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
50
Odinokov AV, Titov SV, Tikhomirov VA, Basilevsky MV, Alfimov MV. Inclusion complexes of β-cyclodextrine with organic ligands: molecular dynamics simulation of the thermodynamic stability in gas phase and in water solution. MOLECULAR SIMULATION 2013. [DOI: 10.1080/08927022.2012.740636] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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