QM/MM Nonadiabatic Dynamics: the SHARC/COBRAMM Approach

Click to copy article linkArticle link copied!

This article is cited by 24 publications.

1. Guijie Li, Zhecun Shi, Lei Huang, Linjun Wang. Multiconfigurational Surface Hopping: a Time-Dependent Variational Approach with Momentum-Jump Trajectories. Journal of Chemical Theory and Computation 2024, 20 (18) , 7755-7765. https://doi.org/10.1021/acs.jctc.4c00842
2. Severin Polonius, David Lehrner, Leticia González, Sebastian Mai. Resolving Photoinduced Femtosecond Three-Dimensional Solute–Solvent Dynamics through Surface Hopping Simulations. Journal of Chemical Theory and Computation 2024, 20 (11) , 4738-4750. https://doi.org/10.1021/acs.jctc.4c00169
3. Severin Polonius, Oleksandra Zhuravel, Brigitta Bachmair, Sebastian Mai. LVC/MM: A Hybrid Linear Vibronic Coupling/Molecular Mechanics Model with Distributed Multipole-Based Electrostatic Embedding for Highly Efficient Surface Hopping Dynamics in Solution. Journal of Chemical Theory and Computation 2023, 19 (20) , 7171-7186. https://doi.org/10.1021/acs.jctc.3c00805
4. Giovanni Li Manni, Ignacio Fdez. Galván, Ali Alavi, Flavia Aleotti, Francesco Aquilante, Jochen Autschbach, Davide Avagliano, Alberto Baiardi, Jie J. Bao, Stefano Battaglia, Letitia Birnoschi, Alejandro Blanco-González, Sergey I. Bokarev, Ria Broer, Roberto Cacciari, Paul B. Calio, Rebecca K. Carlson, Rafael Carvalho Couto, Luis Cerdán, Liviu F. Chibotaru, Nicholas F. Chilton, Jonathan Richard Church, Irene Conti, Sonia Coriani, Juliana Cuéllar-Zuquin, Razan E. Daoud, Nike Dattani, Piero Decleva, Coen de Graaf, Mickaël G. Delcey, Luca De Vico, Werner Dobrautz, Sijia S. Dong, Rulin Feng, Nicolas Ferré, Michael Filatov(Gulak), Laura Gagliardi, Marco Garavelli, Leticia González, Yafu Guan, Meiyuan Guo, Matthew R. Hennefarth, Matthew R. Hermes, Chad E. Hoyer, Miquel Huix-Rotllant, Vishal Kumar Jaiswal, Andy Kaiser, Danil S. Kaliakin, Marjan Khamesian, Daniel S. King, Vladislav Kochetov, Marek Krośnicki, Arpit Arun Kumaar, Ernst D. Larsson, Susi Lehtola, Marie-Bernadette Lepetit, Hans Lischka, Pablo López Ríos, Marcus Lundberg, Dongxia Ma, Sebastian Mai, Philipp Marquetand, Isabella C. D. Merritt, Francesco Montorsi, Maximilian Mörchen, Artur Nenov, Vu Ha Anh Nguyen, Yoshio Nishimoto, Meagan S. Oakley, Massimo Olivucci, Markus Oppel, Daniele Padula, Riddhish Pandharkar, Quan Manh Phung, Felix Plasser, Gerardo Raggi, Elisa Rebolini, Markus Reiher, Ivan Rivalta, Daniel Roca-Sanjuán, Thies Romig, Arta Anushirwan Safari, Aitor Sánchez-Mansilla, Andrew M. Sand, Igor Schapiro, Thais R. Scott, Javier Segarra-Martí, Francesco Segatta, Dumitru-Claudiu Sergentu, Prachi Sharma, Ron Shepard, Yinan Shu, Jakob K. Staab, Tjerk P. Straatsma, Lasse Kragh Sørensen, Bruno Nunes Cabral Tenorio, Donald G. Truhlar, Liviu Ungur, Morgane Vacher, Valera Veryazov, Torben Arne Voß, Oskar Weser, Dihua Wu, Xuchun Yang, David Yarkony, Chen Zhou, J. Patrick Zobel, Roland Lindh. The OpenMolcas Web: A Community-Driven Approach to Advancing Computational Chemistry. Journal of Chemical Theory and Computation 2023, 19 (20) , 6933-6991. https://doi.org/10.1021/acs.jctc.3c00182
5. Maximilian F. S. J. Menger, Qi Ou, Yihan Shao, Shirin Faraji, Joseph E. Subotnik, D. Vale Cofer-Shabica. Nature of Hops, Coordinates, and Detailed Balance for Nonadiabatic Simulations in the Condensed Phase. The Journal of Physical Chemistry A 2023, 127 (40) , 8427-8436. https://doi.org/10.1021/acs.jpca.3c03546
6. Victor M. Freixas, Walter Malone, Xinyang Li, Huajing Song, Hassiel Negrin-Yuvero, Royle Pérez-Castillo, Alexander White, Tammie R. Gibson, Dmitry V. Makhov, Dmitrii V. Shalashilin, Yu Zhang, Nikita Fedik, Maksim Kulichenko, Richard Messerly, Luke Nambi Mohanam, Sahar Sharifzadeh, Adolfo Bastida, Shaul Mukamel, Sebastian Fernandez-Alberti, Sergei Tretiak. NEXMD v2.0 Software Package for Nonadiabatic Excited State Molecular Dynamics Simulations. Journal of Chemical Theory and Computation 2023, 19 (16) , 5356-5368. https://doi.org/10.1021/acs.jctc.3c00583
7. Pratip Chakraborty, Rafael C. Couto, Nanna H. List. Deciphering Methylation Effects on S2(ππ*) Internal Conversion in the Simplest Linear α,β-Unsaturated Carbonyl. The Journal of Physical Chemistry A 2023, 127 (25) , 5360-5373. https://doi.org/10.1021/acs.jpca.3c02582
8. Abed Mohamadzade, Artur Nenov, Marco Garavelli, Irene Conti, Susanne Ullrich. Double Thionated Pyrimidine Nucleobases: Molecular Tools with Tunable Photoproperties. Journal of the American Chemical Society 2023, 145 (22) , 11945-11958. https://doi.org/10.1021/jacs.2c12061
9. Shota Tsuru, Bikramjit Sharma, Dominik Marx, Christof Hättig. Structural Sampling and Solvation Models for the Simulation of Electronic Spectra: Pyrazine as a Case Study. Journal of Chemical Theory and Computation 2023, 19 (8) , 2291-2303. https://doi.org/10.1021/acs.jctc.2c01129
10. Marco Reidelbach, Mei Bai, Michaela Schneeberger, Martin Sebastian Zöllner, Katharina Kubicek, Henning Kirchberg, Christian Bressler, Michael Thorwart, Carmen Herrmann. Solvent Dynamics of Aqueous Halides before and after Photoionization. The Journal of Physical Chemistry B 2023, 127 (6) , 1399-1413. https://doi.org/10.1021/acs.jpcb.2c07992
11. Victor Manuel Freixas, Sergei Tretiak, Sebastian Fernandez-Alberti. Infinitene: Computational Insights from Nonadiabatic Excited State Dynamics. The Journal of Physical Chemistry Letters 2022, 13 (36) , 8495-8501. https://doi.org/10.1021/acs.jpclett.2c02296
12. Dustin A. Tracy, Sebastian Fernandez-Alberti, Sergei Tretiak, Adrian E. Roitberg. Adiabatic Excited-State Molecular Dynamics with an Explicit Solvent: NEXMD-SANDER Implementation. Journal of Chemical Theory and Computation 2022, 18 (9) , 5213-5220. https://doi.org/10.1021/acs.jctc.2c00561
13. D. Vale Cofer-Shabica, Maximilian F. S. J. Menger, Qi Ou, Yihan Shao, Joseph E. Subotnik, Shirin Faraji. INAQS, a Generic Interface for Nonadiabatic QM/MM Dynamics: Design, Implementation, and Validation for GROMACS/Q-CHEM simulations. Journal of Chemical Theory and Computation 2022, 18 (8) , 4601-4614. https://doi.org/10.1021/acs.jctc.2c00204
14. Danillo Valverde, Sebastian Mai, Sylvio Canuto, Antonio Carlos Borin, Leticia González. Ultrafast Intersystem Crossing Dynamics of 6-Selenoguanine in Water. JACS Au 2022, 2 (7) , 1699-1711. https://doi.org/10.1021/jacsau.2c00250
15. Yinan Shu, Linyao Zhang, Xiye Chen, Shaozeng Sun, Yudong Huang, Donald G. Truhlar. Nonadiabatic Dynamics Algorithms with Only Potential Energies and Gradients: Curvature-Driven Coherent Switching with Decay of Mixing and Curvature-Driven Trajectory Surface Hopping. Journal of Chemical Theory and Computation 2022, 18 (3) , 1320-1328. https://doi.org/10.1021/acs.jctc.1c01080
16. Hiroki Uratani, Hiromi Nakai. Scalable Ehrenfest Molecular Dynamics Exploiting the Locality of Density-Functional Tight-Binding Hamiltonian. Journal of Chemical Theory and Computation 2021, 17 (12) , 7384-7396. https://doi.org/10.1021/acs.jctc.1c00950
17. Gustavo Cárdenas, Jesús Lucia‐Tamudo, Henar Mateo‐delaFuente, Vito F. Palmisano, Nuria Anguita‐Ortiz, Lorena Ruano, Álvaro Pérez‐Barcia, Sergio Díaz‐Tendero, Marcos Mandado, Juan J. Nogueira. MoBioTools : A toolkit to setup quantum mechanics/molecular mechanics calculations. Journal of Computational Chemistry 2023, 44 (4) , 516-533. https://doi.org/10.1002/jcc.27018
18. Katja‐Sophia Csizi, Markus Reiher. Universal QM / MM approaches for general nanoscale applications. WIREs Computational Molecular Science 2023, 53 https://doi.org/10.1002/wcms.1656
19. Chenchen Song. State averaged CASSCF in AMOEBA polarizable water model for simulating nonadiabatic molecular dynamics with nonequilibrium solvation effects. The Journal of Chemical Physics 2023, 158 (1) , 014101. https://doi.org/10.1063/5.0131689
20. Davide Avagliano, Irene Conti, Mohsen M.T. El-Tahawy, Vishal K. Jaiswal, Artur Nenov, Marco Garavelli. Hybrid QM/MM Approach for the Calculation of Excited States in Complex Environments. 2023https://doi.org/10.1016/B978-0-12-821978-2.00059-3
21. Laura Alfonso Hernandez, Victor M. Freixas, Beatriz Rodriguez-Hernandez, Sergei Tretiak, Sebastian Fernandez-Alberti, Nicolas Oldani. Exciton-vibrational dynamics induces efficient self-trapping in a substituted nanoring. Physical Chemistry Chemical Physics 2022, 24 (39) , 24095-24104. https://doi.org/10.1039/D2CP03162K
22. Davide Avagliano, Matteo Bonfanti, Artur Nenov, Marco Garavelli. Automatized protocol and interface to simulate QM / MM time‐resolved transient absorption at TD‐DFT level with COBRAMM. Journal of Computational Chemistry 2022, 43 (24) , 1641-1655. https://doi.org/10.1002/jcc.26966
23. Davide Avagliano, Emilio Lorini, Leticia González. Sampling effects in quantum mechanical/molecular mechanics trajectory surface hopping non-adiabatic dynamics. Philosophical Transactions of the Royal Society A: Mathematical, Physical and Engineering Sciences 2022, 380 (2223) https://doi.org/10.1098/rsta.2020.0381
24. Xiang­-Yang Liu, Wei-Hai Fang, Ganglong Cui. Photochemistry of Biological Systems: Excited-State Electronic Structure Calculations and Nonadiabatic Dynamics Simulations with QM/MM Methods. 2022https://doi.org/10.1016/B978-0-12-821978-2.00047-7