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For: Koner D, Salehi SM, Mondal P, Meuwly M. Non-conventional force fields for applications in spectroscopy and chemical reaction dynamics. J Chem Phys 2020;153:010901. [DOI: 10.1063/5.0009628] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]  Open
Number Cited by Other Article(s)
1
Töpfer K, Boittier E, Devereux M, Pasti A, Hamm P, Meuwly M. Force Fields for Deep Eutectic Mixtures: Application to Structure, Thermodynamics and 2D-Infrared Spectroscopy. J Phys Chem B 2024;128:10937-10949. [PMID: 39446046 DOI: 10.1021/acs.jpcb.4c05480] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2024]
2
Aydin S, Salehi SM, Töpfer K, Meuwly M. SCN as a local probe of protein structural dynamics. J Chem Phys 2024;161:055101. [PMID: 39092954 DOI: 10.1063/5.0216657] [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: 04/30/2024] [Accepted: 07/03/2024] [Indexed: 08/04/2024]  Open
3
Bowles J, Jähnigen S, Agostini F, Vuilleumier R, Zehnacker A, Calvo F, Clavaguéra C. Vibrational Circular Dichroism Spectroscopy with a Classical Polarizable Force Field: Alanine in the Gas and Condensed Phases. Chemphyschem 2024;25:e202300982. [PMID: 38318765 DOI: 10.1002/cphc.202300982] [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: 12/21/2023] [Revised: 02/05/2024] [Accepted: 02/06/2024] [Indexed: 02/07/2024]
4
Fan ZX, Chao SD. A Machine Learning Force Field for Bio-Macromolecular Modeling Based on Quantum Chemistry-Calculated Interaction Energy Datasets. Bioengineering (Basel) 2024;11:51. [PMID: 38247928 PMCID: PMC11154266 DOI: 10.3390/bioengineering11010051] [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: 12/07/2023] [Revised: 12/23/2023] [Accepted: 12/25/2023] [Indexed: 01/23/2024]  Open
5
Chen JA, Chao SD. Intermolecular Non-Bonded Interactions from Machine Learning Datasets. Molecules 2023;28:7900. [PMID: 38067629 PMCID: PMC10707888 DOI: 10.3390/molecules28237900] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2023] [Revised: 11/22/2023] [Accepted: 11/29/2023] [Indexed: 04/04/2024]  Open
6
Houston PL, Qu C, Yu Q, Conte R, Nandi A, Li JK, Bowman JM. PESPIP: Software to fit complex molecular and many-body potential energy surfaces with permutationally invariant polynomials. J Chem Phys 2023;158:044109. [PMID: 36725524 DOI: 10.1063/5.0134442] [Citation(s) in RCA: 12] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]  Open
7
Salehi SM, Käser S, Töpfer K, Diamantis P, Pfister R, Hamm P, Rothlisberger U, Meuwly M. Hydration dynamics and IR spectroscopy of 4-fluorophenol. Phys Chem Chem Phys 2022;24:26046-26060. [PMID: 36268728 PMCID: PMC9627945 DOI: 10.1039/d2cp02857c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2022] [Accepted: 10/05/2022] [Indexed: 11/06/2022]
8
Bowman JM, Qu C, Conte R, Nandi A, Houston PL, Yu Q. The MD17 datasets from the perspective of datasets for gas-phase “small” molecule potentials. J Chem Phys 2022;156:240901. [DOI: 10.1063/5.0089200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
9
Töpfer K, Upadhyay M, Meuwly M. Quantitative molecular simulations. Phys Chem Chem Phys 2022;24:12767-12786. [PMID: 35593769 PMCID: PMC9158373 DOI: 10.1039/d2cp01211a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2022] [Accepted: 04/30/2022] [Indexed: 11/21/2022]
10
Töpfer K, Käser S, Meuwly M. Double proton transfer in hydrated formic acid dimer: Interplay of spatial symmetry and solvent-generated force on reactivity. Phys Chem Chem Phys 2022;24:13869-13882. [PMID: 35620978 PMCID: PMC9176184 DOI: 10.1039/d2cp01583h] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
11
Zaverkin V, Holzmüller D, Schuldt R, Kästner J. Predicting properties of periodic systems from cluster data: A case study of liquid water. J Chem Phys 2022;156:114103. [DOI: 10.1063/5.0078983] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]  Open
12
Houston PL, Qu C, Nandi A, Conte R, Yu Q, Bowman JM. Permutationally invariant polynomial regression for energies and gradients, using reverse differentiation, achieves orders of magnitude speed-up with high precision compared to other machine learning methods. J Chem Phys 2022;156:044120. [DOI: 10.1063/5.0080506] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]  Open
13
Penaloza-Amion M, C Rêgo CR, Wenzel W. Local Electronic Charge Transfer in the Helical Induction of Cis-Transoid Poly(4-carboxyphenyl)acetylene by Chiral Amines. J Chem Inf Model 2022;62:544-552. [PMID: 35080886 DOI: 10.1021/acs.jcim.1c01347] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
14
Kirchner B, Blasius J, Alizadeh V, Gansäuer A, Hollóczki O. Chemistry Dissolved in Ionic Liquids. A Theoretical Perspective. J Phys Chem B 2022;126:766-777. [PMID: 35034453 DOI: 10.1021/acs.jpcb.1c09092] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
15
Xu J, Zhang Y, Han J, Su A, Qiao H, Zhang C, Tang J, Shen X, Sun B, Yu W, Zhai S, Wang X, Wu Y, Su W, Duan H. Providing direction for mechanistic inferences in radical cascade cyclization using Transformer model. Org Chem Front 2022. [DOI: 10.1039/d2qo00188h] [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]
16
Mondal P, Cazade PA, Das AK, Bereau T, Meuwly M. Multipolar Force Fields for Amide-I Spectroscopy from Conformational Dynamics of the Alanine Trimer. J Phys Chem B 2021;125:10928-10938. [PMID: 34559531 DOI: 10.1021/acs.jpcb.1c05423] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
17
Meuwly M. Machine Learning for Chemical Reactions. Chem Rev 2021;121:10218-10239. [PMID: 34097378 DOI: 10.1021/acs.chemrev.1c00033] [Citation(s) in RCA: 136] [Impact Index Per Article: 45.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
18
Schriber JB, Nascimento DR, Koutsoukas A, Spronk SA, Cheney DL, Sherrill CD. CLIFF: A component-based, machine-learned, intermolecular force field. J Chem Phys 2021;154:184110. [PMID: 34241025 DOI: 10.1063/5.0042989] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]  Open
19
Salehi SM, Meuwly M. Site-selective dynamics of azidolysozyme. J Chem Phys 2021;154:165101. [PMID: 33940854 DOI: 10.1063/5.0047330] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]  Open
20
Salehi SM, Koner D, Meuwly M. Dynamics and Infrared Spectrocopy of Monomeric and Dimeric Wild Type and Mutant Insulin. J Phys Chem B 2020;124:11882-11894. [PMID: 33245663 DOI: 10.1021/acs.jpcb.0c08048] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
21
Complex reaction processes in combustion unraveled by neural network-based molecular dynamics simulation. Nat Commun 2020;11:5713. [PMID: 33177517 PMCID: PMC7658983 DOI: 10.1038/s41467-020-19497-z] [Citation(s) in RCA: 78] [Impact Index Per Article: 19.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2020] [Accepted: 10/06/2020] [Indexed: 12/21/2022]  Open
22
Westermayr J, Marquetand P. Deep learning for UV absorption spectra with SchNarc: First steps toward transferability in chemical compound space. J Chem Phys 2020;153:154112. [DOI: 10.1063/5.0021915] [Citation(s) in RCA: 33] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]  Open
23
Käser S, Koner D, Christensen AS, von Lilienfeld OA, Meuwly M. Machine Learning Models of Vibrating H2CO: Comparing Reproducing Kernels, FCHL, and PhysNet. J Phys Chem A 2020;124:8853-8865. [DOI: 10.1021/acs.jpca.0c05979] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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