1
|
Huang H, Peng J, Zhang Y, Gu FL, Lan Z, Xu C. The development of the QM/MM interface and its application for the on-the-fly QM/MM nonadiabatic dynamics in JADE package: Theory, implementation, and applications. J Chem Phys 2024; 160:234101. [PMID: 38884395 DOI: 10.1063/5.0215036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/15/2024] [Indexed: 06/18/2024] Open
Abstract
Understanding the nonadiabatic dynamics of complex systems is a challenging task in computational photochemistry. Herein, we present an efficient and user-friendly quantum mechanics/molecular mechanics (QM/MM) interface to run on-the-fly nonadiabatic dynamics. Currently, this interface consists of an independent set of codes designed for general-purpose use. Herein, we demonstrate the ability and feasibility of the QM/MM interface by integrating it with our long-term developed JADE package. Tailored to handle nonadiabatic processes in various complex systems, especially condensed phases and protein environments, we delve into the theories, implementations, and applications of on-the-fly QM/MM nonadiabatic dynamics. The QM/MM approach is established within the framework of the additive QM/MM scheme, employing electrostatic embedding, link-atom inclusion, and charge-redistribution schemes to treat the QM/MM boundary. Trajectory surface-hopping dynamics are facilitated using the fewest switches algorithm, encompassing classical and quantum treatments for nuclear and electronic motions, respectively. Finally, we report simulations of nonadiabatic dynamics for two typical systems: azomethane in water and the retinal chromophore PSB3 in a protein environment. Our results not only illustrate the power of the QM/MM program but also reveal the important roles of environmental factors in nonadiabatic processes.
Collapse
Affiliation(s)
- Haiyi Huang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
- Center for Advanced Materials Research, Beijing Normal University, Zhuhai 519087, China
- MOE Key Laboratory of Theoretical and Computational Photochemistry, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Jiawei Peng
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Yulin Zhang
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Feng Long Gu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Zhenggang Lan
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| | - Chao Xu
- MOE Key Laboratory of Environmental Theoretical Chemistry and Guangdong Provincial Key Laboratory of Chemical Pollution and Environmental Safety, SCNU Environmental Research Institute, School of Environment, South China Normal University, Guangzhou 510006, China
| |
Collapse
|
2
|
Santoro F, Green JA, Martinez-Fernandez L, Cerezo J, Improta R. Quantum and semiclassical dynamical studies of nonadiabatic processes in solution: achievements and perspectives. Phys Chem Chem Phys 2021; 23:8181-8199. [PMID: 33875988 DOI: 10.1039/d0cp05907b] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
We concisely review the main methodological approaches to model nonadiabatic dynamics in isotropic solutions and their applications. Three general classes of models are identified as the most used to include solvent effects in the simulations. The first model describes the solvent as a set of harmonic collective modes coupled to the solute degrees of freedom, and the second as a continuum, while the third explicitly includes solvent molecules in the calculations. The issues related to the use of these models in semiclassical and quantum dynamical simulations are discussed, as well as the main limitations and perspectives of each approach.
Collapse
Affiliation(s)
- Fabrizio Santoro
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), SS di Pisa, Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy.
| | - James A Green
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| | - Lara Martinez-Fernandez
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Javier Cerezo
- Departamento de Química, Facultad de Ciencias and Institute for Advanced Research in Chemistry (IADCHEM), Universidad Autónoma de Madrid, Campus de Excelencia UAM-CSIC, 28049 Madrid, Spain
| | - Roberto Improta
- CNR-Consiglio Nazionale delle Ricerche, Istituto di Biostrutture e Bioimmagini (IBB-CNR), via Mezzocannone 16, I-80136 Napoli, Italy.
| |
Collapse
|
3
|
Martínez-Fernández L, Arslancan S, Ivashchenko D, Crespo-Hernández CE, Corral I. Tracking the origin of photostability in purine nucleobases: the photophysics of 2-oxopurine. Phys Chem Chem Phys 2019; 21:13467-13473. [DOI: 10.1039/c9cp00879a] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
Molding purine PES through functionalization: whilst purine C2-substitution maintains the features of the spectroscopic PES of the heterocycle, C6-functionalization reshapes its topography leading to photostable systems.
Collapse
Affiliation(s)
| | - Serra Arslancan
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
| | - Dmytro Ivashchenko
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- Departamento de Química e Bioquímica
| | | | - Inés Corral
- Departamento de Química
- Universidad Autónoma de Madrid
- 28049 Madrid
- Spain
- IADCHEM
| |
Collapse
|
4
|
Biagini T, Chillemi G, Mazzoccoli G, Grottesi A, Fusilli C, Capocefalo D, Castellana S, Vescovi AL, Mazza T. Molecular dynamics recipes for genome research. Brief Bioinform 2017; 19:853-862. [DOI: 10.1093/bib/bbx006] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2016] [Indexed: 01/17/2023] Open
Affiliation(s)
| | | | | | | | | | | | | | | | - Tommaso Mazza
- IRCCS Casa Sollievo della Sofferenza, Bioinformatics unit, viale Regina Margherita, Rome, Italy
| |
Collapse
|