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For: Vasilevskaya T, Thiel W. Periodic Boundary Conditions in QM/MM Calculations: Implementation and Tests. J Chem Theory Comput 2016;12:3561-70. [DOI: 10.1021/acs.jctc.6b00269] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Number Cited by Other Article(s)
1
Bonfrate S, Park W, Trejo‐Zamora D, Ferré N, Ho Choi C, Huix‐Rotllant M. Assessment of Free Energies From Electrostatic Embedding Density Functional Tight Binding-Based/Molecular Mechanics in Periodic Boundary Conditions. J Comput Chem 2025;46:e70107. [PMID: 40260846 PMCID: PMC12012883 DOI: 10.1002/jcc.70107] [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: 01/21/2025] [Revised: 03/26/2025] [Accepted: 04/02/2025] [Indexed: 04/24/2025]
2
Yagi K, Gunst K, Shiozaki T, Sugita Y. High-performance QM/MM Enhanced Sampling Molecular Dynamics Simulations with GENESIS SPDYN and QSimulate-QM. J Chem Theory Comput 2025;21:4016-4029. [PMID: 40174884 PMCID: PMC12020374 DOI: 10.1021/acs.jctc.5c00163] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2025] [Revised: 03/10/2025] [Accepted: 03/12/2025] [Indexed: 04/04/2025]
3
Tesi M, Cammi R, Granucci G, Persico M. An algorithm for very high pressure molecular dynamics simulations. J Comput Chem 2024;45:2848-2861. [PMID: 39207220 DOI: 10.1002/jcc.27461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 05/28/2024] [Accepted: 06/17/2024] [Indexed: 09/04/2024]
4
Zhu L, Xu G, Zhang Q, Wang G, Wang W, Wang Q. Semirational Design Strategy To Enhance the Thermostability and Catalytic Activity of Cytochrome P450 105D7 for the Degradation of the Pharmaceutically Active Compounds: Diclofenac. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2024;58:15681-15690. [PMID: 38668375 DOI: 10.1021/acs.est.3c10482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/22/2024]
5
Pederson JP, McDaniel JG. PyDFT-QMMM: A modular, extensible software framework for DFT-based QM/MM molecular dynamics. J Chem Phys 2024;161:034103. [PMID: 39007371 DOI: 10.1063/5.0219851] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2024] [Accepted: 06/24/2024] [Indexed: 07/16/2024]  Open
6
Bonfrate S, Ferré N, Huix-Rotllant M. Analytic Gradients for the Electrostatic Embedding QM/MM Model in Periodic Boundary Conditions Using Particle-Mesh Ewald Sums and Electrostatic Potential Fitted Charge Operators. J Chem Theory Comput 2024;20:4338-4349. [PMID: 38712506 DOI: 10.1021/acs.jctc.4c00201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/08/2024]
7
Deng WH, Liao RZ. Cysteine Radical and Glutamate Collaboratively Enable C-H Bond Activation and C-N Bond Cleavage in a Glycyl Radical Enzyme HplG. J Chem Inf Model 2024;64:4168-4179. [PMID: 38745447 DOI: 10.1021/acs.jcim.4c00122] [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: 05/16/2024]
8
Kvedaravičiūtė S, Carrasco-Busturia D, Møller KB, Olsen JMH. Polarizable Embedding without Artificial Boundary Polarization. J Chem Theory Comput 2023;19:5122-5141. [PMID: 37458793 DOI: 10.1021/acs.jctc.3c00434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/09/2023]
9
Csizi K, Reiher M. Universal QM / MM approaches for general nanoscale applications. WIRES COMPUTATIONAL MOLECULAR SCIENCE 2023. [DOI: 10.1002/wcms.1656] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
10
Bonfrate S, Ferré N, Huix-Rotllant M. An efficient electrostatic embedding QM/MM method using periodic boundary conditions based on particle-mesh Ewald sums and electrostatic potential fitted charge operators. J Chem Phys 2023;158:021101. [PMID: 36641406 DOI: 10.1063/5.0133646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
11
Avagliano D, Bonfanti M, Nenov A, Garavelli M. Automatized protocol and interface to simulate QM/MM time-resolved transient absorption at TD-DFT level with COBRAMM. J Comput Chem 2022;43:1641-1655. [PMID: 35815854 PMCID: PMC9544370 DOI: 10.1002/jcc.26966] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2022] [Revised: 06/07/2022] [Accepted: 06/10/2022] [Indexed: 12/24/2022]
12
Pederson JP, McDaniel J. DFT-based QM/MM with Particle-Mesh Ewald for Direct, Long-Range Electrostatic Embedding. J Chem Phys 2022;156:174105. [DOI: 10.1063/5.0087386] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
13
Le Breton G, Bonhomme O, Benichou E, Loison C. First Hyperpolarizability of Water in Bulk Liquid Phase: Long-Range Electrostatic Effects Included via the Second Hyperpolarizability. Phys Chem Chem Phys 2022;24:19463-19472. [DOI: 10.1039/d2cp00803c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
14
Nottoli M, Nifosì R, Mennucci B, Lipparini F. Energy, Structures, and Response Properties with a Fully Coupled QM/AMOEBA/ddCOSMO Implementation. J Chem Theory Comput 2021;17:5661-5672. [PMID: 34476941 PMCID: PMC8444335 DOI: 10.1021/acs.jctc.1c00555] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
15
Nottoli M, Bondanza M, Lipparini F, Mennucci B. An enhanced sampling QM/AMOEBA approach: The case of the excited state intramolecular proton transfer in solvated 3-hydroxyflavone. J Chem Phys 2021;154:184107. [PMID: 34241028 DOI: 10.1063/5.0046844] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
16
Yagi K, Ito S, Sugita Y. Exploring the Minimum-Energy Pathways and Free-Energy Profiles of Enzymatic Reactions with QM/MM Calculations. J Phys Chem B 2021;125:4701-4713. [PMID: 33914537 PMCID: PMC10986901 DOI: 10.1021/acs.jpcb.1c01862] [Citation(s) in RCA: 29] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
17
Computational investigations of allostery in aromatic amino acid biosynthetic enzymes. Biochem Soc Trans 2021;49:415-429. [PMID: 33544132 DOI: 10.1042/bst20200741] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2020] [Revised: 01/14/2021] [Accepted: 01/15/2021] [Indexed: 12/22/2022]
18
Pan X, Nam K, Epifanovsky E, Simmonett AC, Rosta E, Shao Y. A simplified charge projection scheme for long-range electrostatics in ab initio QM/MM calculations. J Chem Phys 2021;154:024115. [PMID: 33445891 DOI: 10.1063/5.0038120] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]  Open
19
Bondanza M, Nottoli M, Cupellini L, Lipparini F, Mennucci B. Polarizable embedding QM/MM: the future gold standard for complex (bio)systems? Phys Chem Chem Phys 2020;22:14433-14448. [DOI: 10.1039/d0cp02119a] [Citation(s) in RCA: 59] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
20
A benchmark for the size of the QM system required for accurate hybrid QM/MM calculations on the metal site of the protein copper, zinc superoxide dismutase. J Mol Model 2019;25:176. [PMID: 31154525 DOI: 10.1007/s00894-019-4066-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Accepted: 05/14/2019] [Indexed: 12/12/2022]
21
Li P, Liu F, Shao Y, Mei Y. Computational Insights into Endo/Exo Selectivity of the Diels–Alder Reaction in Explicit Solvent at Ab Initio Quantum Mechanical/Molecular Mechanical Level. J Phys Chem B 2019;123:5131-5138. [DOI: 10.1021/acs.jpcb.9b01989] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
22
Holden ZC, Rana B, Herbert JM. Analytic gradient for the QM/MM-Ewald method using charges derived from the electrostatic potential: Theory, implementation, and application to ab initio molecular dynamics simulation of the aqueous electron. J Chem Phys 2019;150:144115. [DOI: 10.1063/1.5089673] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]  Open
23
Kawashima Y, Ishimura K, Shiga M. Ab initio quantum mechanics/molecular mechanics method with periodic boundaries employing Ewald summation technique to electron-charge interaction: Treatment of the surface-dipole term. J Chem Phys 2019;150:124103. [DOI: 10.1063/1.5048451] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
24
Sterling CM, Bjornsson R. Multistep Explicit Solvation Protocol for Calculation of Redox Potentials. J Chem Theory Comput 2018;15:52-67. [PMID: 30511855 DOI: 10.1021/acs.jctc.8b00982] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
25
Li P, Jia X, Pan X, Shao Y, Mei Y. Accelerated Computation of Free Energy Profile at ab Initio Quantum Mechanical/Molecular Mechanics Accuracy via a Semi-Empirical Reference Potential. I. Weighted Thermodynamics Perturbation. J Chem Theory Comput 2018;14:5583-5596. [DOI: 10.1021/acs.jctc.8b00571] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
26
Pan X, Rosta E, Shao Y. Representation of the QM Subsystem for Long-Range Electrostatic Interaction in Non-Periodic Ab Initio QM/MM Calculations. Molecules 2018;23:E2500. [PMID: 30274290 PMCID: PMC6222767 DOI: 10.3390/molecules23102500] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2018] [Revised: 09/21/2018] [Accepted: 09/25/2018] [Indexed: 11/16/2022]  Open
27
Efficient Computation of Free Energy Surfaces of Diels⁻Alder Reactions in Explicit Solvent at Ab Initio QM/MM Level. Molecules 2018;23:molecules23102487. [PMID: 30274188 PMCID: PMC6222833 DOI: 10.3390/molecules23102487] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Revised: 09/25/2018] [Accepted: 09/26/2018] [Indexed: 11/17/2022]  Open
28
Langan PS, Vandavasi VG, Cooper CJ, Weiss KL, Ginell SL, Parks JM, Coates L. Substrate Binding Induces Conformational Changes in a Class A β-lactamase That Prime It for Catalysis. ACS Catal 2018. [DOI: 10.1021/acscatal.7b04114] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
29
Benediktsson B, Bjornsson R. QM/MM Study of the Nitrogenase MoFe Protein Resting State: Broken-Symmetry States, Protonation States, and QM Region Convergence in the FeMoco Active Site. Inorg Chem 2017;56:13417-13429. [DOI: 10.1021/acs.inorgchem.7b02158] [Citation(s) in RCA: 57] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
30
Wang M, Li P, Jia X, Liu W, Shao Y, Hu W, Zheng J, Brooks BR, Mei Y. Efficient Strategy for the Calculation of Solvation Free Energies in Water and Chloroform at the Quantum Mechanical/Molecular Mechanical Level. J Chem Inf Model 2017;57:2476-2489. [DOI: 10.1021/acs.jcim.7b00001] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
31
Ohta A, Kobayashi O, Danielache SO, Nanbu S. Nonadiabatic ab initio molecular dynamics with PME-ONIOM scheme of photoisomerization reaction between 1,3-cyclohexadiene and 1,3,5-cis-hexatriene in solution phase. Chem Phys 2017. [DOI: 10.1016/j.chemphys.2017.01.006] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
32
Moeljadi AMP, Schmid R, Hirao H. Dioxygen binding to Fe-MOF-74: microscopic insights from periodic QM/MM calculations. CAN J CHEM 2016. [DOI: 10.1139/cjc-2016-0284] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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