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For: Tolmachev DA, Boyko OS, Lukasheva NV, Martinez-Seara H, Karttunen M. Overbinding and Qualitative and Quantitative Changes Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Force Fields with and without NBFIX and ECC Corrections. J Chem Theory Comput 2019;16:677-687. [DOI: 10.1021/acs.jctc.9b00813] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Number Cited by Other Article(s)
1
Marien J, Prévost C, Sacquin-Mora S. nP-Collabs: Investigating Counterion-Mediated Bridges in the Multiply Phosphorylated Tau-R2 Repeat. J Chem Inf Model 2024;64:6570-6582. [PMID: 39092904 DOI: 10.1021/acs.jcim.4c00742] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
2
Nencini R, Tempra C, Biriukov D, Riopedre-Fernandez M, Cruces Chamorro V, Polák J, Mason PE, Ondo D, Heyda J, Ollila OHS, Jungwirth P, Javanainen M, Martinez-Seara H. Effective Inclusion of Electronic Polarization Improves the Description of Electrostatic Interactions: The prosECCo75 Biomolecular Force Field. J Chem Theory Comput 2024. [PMID: 39186899 DOI: 10.1021/acs.jctc.4c00743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/28/2024]
3
Kastinen T, Batys P, Tolmachev D, Laasonen K, Sammalkorpi M. Ion-Specific Effects on Ion and Polyelectrolyte Solvation. Chemphyschem 2024;25:e202400244. [PMID: 38712639 DOI: 10.1002/cphc.202400244] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Revised: 05/02/2024] [Accepted: 05/02/2024] [Indexed: 05/08/2024]
4
Wilson C, Karttunen M, de Groot BL, Gapsys V. Accurately Predicting Protein pKa Values Using Nonequilibrium Alchemy. J Chem Theory Comput 2023;19:7833-7845. [PMID: 37820376 PMCID: PMC10653114 DOI: 10.1021/acs.jctc.3c00721] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2023] [Indexed: 10/13/2023]
5
Huang C, Pettitt BM. Parameter Dependence of the Solubility Limit for Disodium Phosphate. J Phys Chem B 2023;127:8690-8696. [PMID: 37788371 PMCID: PMC10913426 DOI: 10.1021/acs.jpcb.3c05343] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/05/2023]
6
Mohammadi E, Joshi SY, Deshmukh SA. Development, Validation, and Applications of Nonbonded Interaction Parameters between Coarse-Grained Amino Acid and Water Models. Biomacromolecules 2023;24:4078-4092. [PMID: 37603467 DOI: 10.1021/acs.biomac.3c00441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/23/2023]
7
Yesylevskyy S, Martinez-Seara H, Jungwirth P. Curvature Matters: Modeling Calcium Binding to Neutral and Anionic Phospholipid Bilayers. J Phys Chem B 2023;127:4523-4531. [PMID: 37191140 DOI: 10.1021/acs.jpcb.3c01962] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
8
Shen K, Nguyen M, Sherck N, Yoo B, Köhler S, Speros J, Delaney KT, Shell MS, Fredrickson GH. Predicting surfactant phase behavior with a molecularly informed field theory. J Colloid Interface Sci 2023;638:84-98. [PMID: 36736121 DOI: 10.1016/j.jcis.2023.01.015] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Revised: 12/24/2022] [Accepted: 01/03/2023] [Indexed: 01/09/2023]
9
Fedotova VS, Sokolova MP, Vorobiov VK, Sivtsov EV, Lukasheva NV, Smirnov MA. Water Influence on the Physico-Chemical Properties and 3D Printability of Choline Acrylate-Bacterial Cellulose Inks. Polymers (Basel) 2023;15:polym15092156. [PMID: 37177302 PMCID: PMC10181127 DOI: 10.3390/polym15092156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 04/25/2023] [Accepted: 04/28/2023] [Indexed: 05/15/2023]  Open
10
Phan LX, Chamorro VC, Martinez-Seara H, Crain J, Sansom MSP, Tucker SJ. Influence of electronic polarization on the binding of anions to a chloride-pumping rhodopsin. Biophys J 2023;122:1548-1556. [PMID: 36945777 PMCID: PMC10147828 DOI: 10.1016/j.bpj.2023.03.026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2023] [Revised: 03/07/2023] [Accepted: 03/16/2023] [Indexed: 03/23/2023]  Open
11
Tolmachev D, Nazarychev V, Fedotova V, Vorobiov V, Lukasheva N, Smirnov M, Karttunen M. Investigation of structure and properties of polymerizable deep eutectic solvent based on choline chloride and acrylic acid. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2022.121030] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
12
Liu H, Fu H, Chipot C, Shao X, Cai W. Accurate Description of Solvent-Exposed Salt Bridges with a Non-polarizable Force Field Incorporating Solvent Effects. J Chem Inf Model 2022;62:3863-3873. [PMID: 35920605 DOI: 10.1021/acs.jcim.2c00678] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
13
Phan LX, Lynch CI, Crain J, Sansom MS, Tucker SJ. Influence of effective polarization on ion and water interactions within a biomimetic nanopore. Biophys J 2022;121:2014-2026. [DOI: 10.1016/j.bpj.2022.05.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 03/25/2022] [Accepted: 05/04/2022] [Indexed: 11/16/2022]  Open
14
Bernhardt MP, Nagata Y, van der Vegt NFA. Where Lennard-Jones Potentials Fail: Iterative Optimization of Ion-Water Pair Potentials Based on Ab Initio Molecular Dynamics Data. J Phys Chem Lett 2022;13:3712-3717. [PMID: 35439420 DOI: 10.1021/acs.jpclett.2c00121] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
15
Chávez-García C, Hénin J, Karttunen M. Multiscale Computational Study of the Conformation of the Full-Length Intrinsically Disordered Protein MeCP2. J Chem Inf Model 2022;62:958-970. [PMID: 35130441 DOI: 10.1021/acs.jcim.1c01354] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
16
Lukasheva N, Tolmachev D, Martinez-Seara H, Karttunen M. Changes in the Local Conformational States Caused by Simple Na+ and K+ Ions in Polyelectrolyte Simulations: Comparison of Seven Force Fields with and without NBFIX and ECC Corrections. Polymers (Basel) 2022;14:252. [PMID: 35054659 PMCID: PMC8779100 DOI: 10.3390/polym14020252] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Revised: 12/29/2021] [Accepted: 01/04/2022] [Indexed: 11/23/2022]  Open
17
Tolmachev D, Lukasheva N, Ramazanov R, Nazarychev V, Borzdun N, Volgin I, Andreeva M, Glova A, Melnikova S, Dobrovskiy A, Silber SA, Larin S, de Souza RM, Ribeiro MCC, Lyulin S, Karttunen M. Computer Simulations of Deep Eutectic Solvents: Challenges, Solutions, and Perspectives. Int J Mol Sci 2022;23:645. [PMID: 35054840 PMCID: PMC8775846 DOI: 10.3390/ijms23020645] [Citation(s) in RCA: 30] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 01/02/2022] [Accepted: 01/04/2022] [Indexed: 12/13/2022]  Open
18
González-Fernández C, Bringas E, Oostenbrink C, Ortiz I. In silico investigation and surmounting of Lipopolysaccharide barrier in Gram-Negative Bacteria: How far has molecular dynamics Come? Comput Struct Biotechnol J 2022;20:5886-5901. [PMID: 36382192 PMCID: PMC9636410 DOI: 10.1016/j.csbj.2022.10.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2022] [Revised: 10/24/2022] [Accepted: 10/24/2022] [Indexed: 11/29/2022]  Open
19
Maglia de Souza R, Karttunen M, Ribeiro MCC. Fine-Tuning the Polarizable CL&Pol Force Field for the Deep Eutectic Solvent Ethaline. J Chem Inf Model 2021;61:5938-5947. [PMID: 34797679 DOI: 10.1021/acs.jcim.1c01181] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
20
Bakulin I, Kondratyuk N, Lankin A, Norman G. Properties of aqueous 1,4-dioxane solution via molecular dynamics. J Chem Phys 2021;155:154501. [PMID: 34686058 DOI: 10.1063/5.0059337] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
21
Orabi EA, Öztürk TN, Bernhardt N, Faraldo-Gómez JD. Corrections in the CHARMM36 Parametrization of Chloride Interactions with Proteins, Lipids, and Alkali Cations, and Extension to Other Halide Anions. J Chem Theory Comput 2021;17:6240-6261. [PMID: 34516741 DOI: 10.1021/acs.jctc.1c00550] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
22
Smirnov MA, Tolmachev DA, Glova AD, Sokolova MP, Geydt PV, Lukasheva NV, Lyulin SV. Combined Use of Atomic Force Microscopy and Molecular Dynamics in the Study of Biopolymer Systems. POLYMER SCIENCE SERIES C 2021. [DOI: 10.1134/s1811238221020089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
23
Development of coarse-grained force field to investigate sodium-ion transport mechanisms in cyanoborate-based ionic liquid. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116648] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
24
Tolmachev D, Mamistvalov G, Lukasheva N, Larin S, Karttunen M. Effects of Amino Acid Side-Chain Length and Chemical Structure on Anionic Polyglutamic and Polyaspartic Acid Cellulose-Based Polyelectrolyte Brushes. Polymers (Basel) 2021;13:polym13111789. [PMID: 34071693 PMCID: PMC8199235 DOI: 10.3390/polym13111789] [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: 05/09/2021] [Revised: 05/25/2021] [Accepted: 05/25/2021] [Indexed: 11/25/2022]  Open
25
Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021;17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
26
Espasa-Valdepeñas A, Vega JF, Cruz V, Ramos J, Müller AJ, Martinez-Salazar J. Revisiting Polymer-Particle Interaction in PEO Solutions. LANGMUIR : THE ACS JOURNAL OF SURFACES AND COLLOIDS 2021;37:3808-3816. [PMID: 33764765 PMCID: PMC9132384 DOI: 10.1021/acs.langmuir.0c02715] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/16/2020] [Revised: 03/17/2021] [Indexed: 06/12/2023]
27
Sterling JD, Jiang W, Botello-Smith WM, Luo YL. Ion Pairing and Dielectric Decrement in Glycosaminoglycan Brushes. J Phys Chem B 2021;125:2771-2780. [PMID: 33662212 DOI: 10.1021/acs.jpcb.0c11571] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
28
Oh KI, Baiz CR. Molecular heterogeneity in aqueous cosolvent systems. J Chem Phys 2021;152:190901. [PMID: 33687253 DOI: 10.1063/5.0007647] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]  Open
29
Duboué-Dijon E, Javanainen M, Delcroix P, Jungwirth P, Martinez-Seara H. A practical guide to biologically relevant molecular simulations with charge scaling for electronic polarization. J Chem Phys 2021;153:050901. [PMID: 32770904 DOI: 10.1063/5.0017775] [Citation(s) in RCA: 53] [Impact Index Per Article: 17.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]  Open
30
Kolafa J. Pressure in Molecular Simulations with Scaled Charges. 1. Ionic Systems. J Phys Chem B 2020;124:7379-7390. [PMID: 32790401 DOI: 10.1021/acs.jpcb.0c02641] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
31
Tolmachev D, Lukasheva N, Mamistvalov G, Karttunen M. Influence of Calcium Binding on Conformations and Motions of Anionic Polyamino Acids. Effect of Side Chain Length. Polymers (Basel) 2020;12:E1279. [PMID: 32503199 PMCID: PMC7362111 DOI: 10.3390/polym12061279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 05/29/2020] [Accepted: 05/31/2020] [Indexed: 11/21/2022]  Open
32
Machado MR, Pantano S. Split the Charge Difference in Two! A Rule of Thumb for Adding Proper Amounts of Ions in MD Simulations. J Chem Theory Comput 2020;16:1367-1372. [PMID: 31999456 DOI: 10.1021/acs.jctc.9b00953] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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