1
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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.
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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
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2
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Toldo JM, do Casal MT, Ventura E, do Monte SA, Barbatti M. Surface hopping modeling of charge and energy transfer in active environments. Phys Chem Chem Phys 2023; 25:8293-8316. [PMID: 36916738 PMCID: PMC10034598 DOI: 10.1039/d3cp00247k] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/05/2023]
Abstract
An active environment is any atomic or molecular system changing a chromophore's nonadiabatic dynamics compared to the isolated molecule. The action of the environment on the chromophore occurs by changing the potential energy landscape and triggering new energy and charge flows unavailable in the vacuum. Surface hopping is a mixed quantum-classical approach whose extreme flexibility has made it the primary platform for implementing novel methodologies to investigate the nonadiabatic dynamics of a chromophore in active environments. This Perspective paper surveys the latest developments in the field, focusing on charge and energy transfer processes.
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Affiliation(s)
| | | | - Elizete Ventura
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Silmar A do Monte
- Departamento de Química, CCEN, Universidade Federal da Paraíba, 58059-900, João Pessoa, Brazil.
| | - Mario Barbatti
- Aix-Marseille University, CNRS, ICR, Marseille, France.
- Institut Universitaire de France, 75231, Paris, France
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3
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Cárdenas G, Lucia‐Tamudo J, Mateo‐delaFuente H, Palmisano VF, Anguita‐Ortiz N, Ruano L, Pérez‐Barcia Á, Díaz‐Tendero S, Mandado M, Nogueira JJ. MoBioTools: A toolkit to setup quantum mechanics/molecular mechanics calculations. J Comput Chem 2023; 44:516-533. [PMID: 36507763 PMCID: PMC10107847 DOI: 10.1002/jcc.27018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 09/16/2022] [Accepted: 09/20/2022] [Indexed: 12/15/2022]
Abstract
We present a toolkit that allows for the preparation of QM/MM input files from a conformational ensemble of molecular geometries. The package is currently compatible with trajectory and topology files in Amber, CHARMM, GROMACS and NAMD formats, and has the possibility to generate QM/MM input files for Gaussian (09 and 16), Orca (≥4.0), NWChem and (Open)Molcas. The toolkit can be used in command line, so that no programming experience is required, although it presents some features that can also be employed as a python application programming interface. We apply the toolkit in four situations in which different electronic-structure properties of organic molecules in the presence of a solvent or a complex biological environment are computed: the reduction potential of the nucleobases in acetonitrile, an energy decomposition analysis of tyrosine interacting with water, the absorption spectrum of an azobenzene derivative integrated into a voltage-gated ion channel, and the absorption and emission spectra of the luciferine/luciferase complex. These examples show that the toolkit can be employed in a manifold of situations for both the electronic ground state and electronically excited states. It also allows for the automatic correction of the active space in the case of CASSCF calculations on an ensemble of geometries, as it is shown for the azobenzene derivative photoswitch case.
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Affiliation(s)
- Gustavo Cárdenas
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | | | | | | | - Lorena Ruano
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
| | | | - Sergio Díaz‐Tendero
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
- Condensed Matter Physics Center (IFIMAC)Universidad Autónoma de MadridMadridSpain
| | - Marcos Mandado
- Department of Physical ChemistryUniversity of VigoVigoSpain
| | - Juan J. Nogueira
- Department of ChemistryUniversidad Autónoma de MadridMadridSpain
- Institute for Advanced Research in Chemistry (IAdChem)Universidad Autónoma de MadridMadridSpain
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4
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Xie BB, Jia PK, Wang KX, Chen WK, Liu XY, Cui G. Generalized Ab Initio Nonadiabatic Dynamics Simulation Methods from Molecular to Extended Systems. J Phys Chem A 2022; 126:1789-1804. [PMID: 35266391 DOI: 10.1021/acs.jpca.1c10195] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Nonadiabatic dynamics simulation has become a powerful tool to describe nonadiabatic effects involved in photophysical processes and photochemical reactions. In the past decade, our group has developed generalized trajectory-based ab initio surface-hopping (GTSH) dynamics simulation methods, which can be used to describe a series of nonadiabatic processes, such as internal conversion, intersystem crossing, excitation energy transfer and charge transfer of molecular systems, and photoinduced nonadiabatic carrier dynamics of extended systems with and without spin-orbit couplings. In this contribution, we will first give a brief introduction to our recently developed methods and related numerical implementations at different computational levels. Later, we will present some of our latest applications in realistic systems, which cover organic molecules, biological proteins, organometallic compounds, periodic organic and inorganic materials, etc. Final discussion is given to challenges and outlooks of ab initio nonadiabatic dynamics simulations.
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Affiliation(s)
- Bin-Bin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Pei-Ke Jia
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Ke-Xin Wang
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | - Wen-Kai Chen
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | - Xiang-Yang Liu
- College of Chemistry and Material Science, Sichuan Normal University, Chengdu 610068, Sichuan, P. R. China
| | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
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5
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Mališ M, Luber S. Trajectory Surface Hopping Nonadiabatic Molecular Dynamics with Kohn–Sham ΔSCF for Condensed-Phase Systems. J Chem Theory Comput 2020; 16:4071-4086. [DOI: 10.1021/acs.jctc.0c00372] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Momir Mališ
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Sandra Luber
- University of Zurich, Department of Chemistry, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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6
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Gahlaut A, Paranjothy M. Unimolecular decomposition of formamide via direct chemical dynamics simulations. Phys Chem Chem Phys 2018. [DOI: 10.1039/c8cp00541a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Classical chemical dynamics simulations show that formamide (NH2CHO) can dissociate via multiple pathways, either by direct dissociations or via intramolecular rearrangements to different isomers followed by dissociation.
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Affiliation(s)
- Anchal Gahlaut
- Department of Chemistry, Indian Institute of Technology Jodhpur
- Jodhpur
- India
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7
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Du L, Lan Z. An On-the-Fly Surface-Hopping Program JADE for Nonadiabatic Molecular Dynamics of Polyatomic Systems: Implementation and Applications. J Chem Theory Comput 2016; 11:1360-74. [PMID: 26574348 DOI: 10.1021/ct501106d] [Citation(s) in RCA: 89] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nonadiabatic dynamics simulations have rapidly become an indispensable tool for understanding ultrafast photochemical processes in complex systems. Here, we present our recently developed on-the-fly nonadiabatic dynamics package, JADE, which allows researchers to perform nonadiabatic excited-state dynamics simulations of polyatomic systems at an all-atomic level. The nonadiabatic dynamics is based on Tully's surface-hopping approach. Currently, several electronic structure methods (CIS, TDHF, TDDFT(RPA/TDA), and ADC(2)) are supported, especially TDDFT, aiming at performing nonadiabatic dynamics on medium- to large-sized molecules. The JADE package has been interfaced with several quantum chemistry codes, including Turbomole, Gaussian, and Gamess (US). To consider environmental effects, the Langevin dynamics was introduced as an easy-to-use scheme into the standard surface-hopping dynamics. The JADE package is mainly written in Fortran for greater numerical performance and Python for flexible interface construction, with the intent of providing open-source, easy-to-use, well-modularized, and intuitive software in the field of simulations of photochemical and photophysical processes. To illustrate the possible applications of the JADE package, we present a few applications of excited-state dynamics for various polyatomic systems, such as the methaniminium cation, fullerene (C20), p-dimethylaminobenzonitrile (DMABN) and its primary amino derivative aminobenzonitrile (ABN), and 10-hydroxybenzo[h]quinoline (10-HBQ).
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Affiliation(s)
- Likai Du
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China
| | - Zhenggang Lan
- Key Laboratory of Biobased Materials, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China.,University of Chinese Academy of Sciences , Beijing 100049, People's Republic of China.,The Qingdao Key Lab of Solar Energy Utilization and Energy Storage Technology, Qingdao Institute of Bioenergy and Bioprocess Technology, Chinese Academy of Sciences , Qingdao, 266101 Shandong, People's Republic of China
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8
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Xia SH, Liu XY, Fang Q, Cui G. Photodissociation dynamics of CH3C(O)SH in argon matrix: A QM/MM nonadiabatic dynamics simulation. J Chem Phys 2015; 143:194303. [DOI: 10.1063/1.4935598] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
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9
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Cui G, Thiel W. Generalized trajectory surface-hopping method for internal conversion and intersystem crossing. J Chem Phys 2015; 141:124101. [PMID: 25273406 DOI: 10.1063/1.4894849] [Citation(s) in RCA: 117] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Trajectory-based fewest-switches surface-hopping (FSSH) dynamics simulations have become a popular and reliable theoretical tool to simulate nonadiabatic photophysical and photochemical processes. Most available FSSH methods model internal conversion. We present a generalized trajectory surface-hopping (GTSH) method for simulating both internal conversion and intersystem crossing processes on an equal footing. We consider hops between adiabatic eigenstates of the non-relativistic electronic Hamiltonian (pure spin states), which is appropriate for sufficiently small spin-orbit coupling. This choice allows us to make maximum use of existing electronic structure programs and to minimize the changes to available implementations of the traditional FSSH method. The GTSH method is formulated within the quantum mechanics (QM)/molecular mechanics framework, but can of course also be applied at the pure QM level. The algorithm implemented in the GTSH code is specified step by step. As an initial GTSH application, we report simulations of the nonadiabatic processes in the lowest four electronic states (S0, S1, T1, and T2) of acrolein both in vacuo and in acetonitrile solution, in which the acrolein molecule is treated at the ab initio complete-active-space self-consistent-field level. These dynamics simulations provide detailed mechanistic insight by identifying and characterizing two nonadiabatic routes to the lowest triplet state, namely, direct S1 → T1 hopping as major pathway and sequential S1 → T2 → T1 hopping as minor pathway, with the T2 state acting as a relay state. They illustrate the potential of the GTSH approach to explore photoinduced processes in complex systems, in which intersystem crossing plays an important role.
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Affiliation(s)
- Ganglong Cui
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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10
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Xia SH, Liu XY, Fang Q, Cui G. Excited-State Ring-Opening Mechanism of Cyclic Ketones: A MS-CASPT2//CASSCF Study. J Phys Chem A 2015; 119:3569-76. [DOI: 10.1021/acs.jpca.5b00302] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shu-Hua Xia
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Xiang-Yang Liu
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Qiu Fang
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Ganglong Cui
- Key Laboratory of
Theoretical and Computational Photochemistry, Ministry of Education,
College of Chemistry, Beijing Normal University, Beijing 100875, China
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11
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Maeda S, Taketsugu T, Ohno K, Morokuma K. From Roaming Atoms to Hopping Surfaces: Mapping Out Global Reaction Routes in Photochemistry. J Am Chem Soc 2015; 137:3433-45. [DOI: 10.1021/ja512394y] [Citation(s) in RCA: 82] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023]
Affiliation(s)
- Satoshi Maeda
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Tetsuya Taketsugu
- Department
of Chemistry, Faculty of Science, Hokkaido University, Sapporo 060-0810, Japan
| | - Koichi Ohno
- Graduate
School of Science, Tohoku University, Sendai 980-8578, Japan
- Institute for Quantum Chemical Exploration, Tokyo 108-0022, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
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12
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Chen X, Zhao Y, Zhang H, Xue J, Zheng X. Excited state proton transfer dynamics of thioacetamide in S2(ππ*) state: resonance Raman spectroscopic and quantum mechanical calculations study. J Phys Chem A 2015; 119:832-42. [PMID: 25559740 DOI: 10.1021/jp510396y] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The photophysics and photochemistry of thioacetamide (CH3CSNH2) after excitation to the S2 electronic state were investigated by using resonance Raman spectroscopy in conjunction with the complete active space self-consistent field (CASSCF) method and density functional theory (DFT) calculations. The A-band resonance Raman spectra in acetonitrile, methanol, and water were obtained at 299.1, 282.4, 266.0, 252.7, and 245.9 nm excitation wavelengths to probe the structural dynamics of thioacetamide in the S2 state. CASSCF calculations were done to determine the transition energies and structures of the lower-lying excited states, the conical intersection points CI(S2/S1) and CI(S1/S0), and intersystem crossing points. The structural dynamics of thioacetamide in the S2 state was revealed to be along eight Franck-Condon active vibrational modes ν15, ν11, ν14, ν10, ν8, ν12, ν18, and ν19, mostly in the CC/CS/CN stretches and the CNH8,9/CCH5,6,7/CCN/CCS in-plane bends as indicated by the corresponding normal mode descriptions. The S2 → S1 decay process via the S2/S1 conical intersection point as the major channel were excluded. The thione-thiol photoisomerization reaction mechanism of thioacetamide via the S2,FC → S'1,min excited state proton transfer (ESPT) reaction channel was proposed.
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Affiliation(s)
- Xiao Chen
- Department of Chemistry, Zhejiang Sci-Tech University , Hangzhou 310018, People's Republic of China
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13
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Zámečníková M, Nachtigallová D. Photodynamic behavior of electronic coupling in a N-methylformamide dimer. Phys Chem Chem Phys 2015; 17:12356-64. [DOI: 10.1039/c4cp04573d] [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]
Abstract
The role of the bridging water molecules has been studied during the excited state photodynamics of a N-methylformamide dimer in complex with water molecules employing the complete active space self-consistent field (CASSCF) and CAS perturbation theory (CASPT2) methods.
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14
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Tuna D, Došlić N, Mališ M, Sobolewski AL, Domcke W. Mechanisms of Photostability in Kynurenines: A Joint Electronic-Structure and Dynamics Study. J Phys Chem B 2014; 119:2112-24. [DOI: 10.1021/jp501782v] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Deniz Tuna
- Department
of Chemistry, Technische Universität München, 85747 Garching, Germany
| | - Nađa Došlić
- Division
of Physical Chemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | - Momir Mališ
- Division
of Physical Chemistry, Ruđer Bošković Institute, 10002 Zagreb, Croatia
| | | | - Wolfgang Domcke
- Department
of Chemistry, Technische Universität München, 85747 Garching, Germany
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15
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Eckert-Maksić M, Antol I, Vazdar M. Acetamide as the model of the peptide bond: Nonadiabatic photodynamical simulations in the gas phase and in the argon matrix. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.025] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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16
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Schmidt TC, Paasche A, Grebner C, Ansorg K, Becker J, Lee W, Engels B. QM/MM investigations of organic chemistry oriented questions. Top Curr Chem (Cham) 2014; 351:25-101. [PMID: 22392477 DOI: 10.1007/128_2011_309] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
About 35 years after its first suggestion, QM/MM became the standard theoretical approach to investigate enzymatic structures and processes. The success is due to the ability of QM/MM to provide an accurate atomistic picture of enzymes and related processes. This picture can even be turned into a movie if nuclei-dynamics is taken into account to describe enzymatic processes. In the field of organic chemistry, QM/MM methods are used to a much lesser extent although almost all relevant processes happen in condensed matter or are influenced by complicated interactions between substrate and catalyst. There is less importance for theoretical organic chemistry since the influence of nonpolar solvents is rather weak and the effect of polar solvents can often be accurately described by continuum approaches. Catalytic processes (homogeneous and heterogeneous) can often be reduced to truncated model systems, which are so small that pure quantum-mechanical approaches can be employed. However, since QM/MM becomes more and more efficient due to the success in software and hardware developments, it is more and more used in theoretical organic chemistry to study effects which result from the molecular nature of the environment. It is shown by many examples discussed in this review that the influence can be tremendous, even for nonpolar reactions. The importance of environmental effects in theoretical spectroscopy was already known. Due to its benefits, QM/MM can be expected to experience ongoing growth for the next decade.In the present chapter we give an overview of QM/MM developments and their importance in theoretical organic chemistry, and review applications which give impressions of the possibilities and the importance of the relevant effects. Since there is already a bunch of excellent reviews dealing with QM/MM, we will discuss fundamental ingredients and developments of QM/MM very briefly with a focus on very recent progress. For the applications we follow a similar strategy.
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Affiliation(s)
- Thomas C Schmidt
- Institut für Phys. und Theor. Chemie, Emil-Fischer-Strasse 42, Campus Hubland Nord, 97074, Würzburg, Germany
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17
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Curchod BFE, Rothlisberger U, Tavernelli I. Trajectory-Based Nonadiabatic Dynamics with Time-Dependent Density Functional Theory. Chemphyschem 2013; 14:1314-40. [DOI: 10.1002/cphc.201200941] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2012] [Indexed: 11/11/2022]
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18
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Ruckenbauer M, Barbatti M, Müller T, Lischka H. Nonadiabatic photodynamics of a retinal model in polar and nonpolar environment. J Phys Chem A 2013; 117:2790-9. [PMID: 23470211 PMCID: PMC3619535 DOI: 10.1021/jp400401f] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
The nonadiabatic photodynamics of
the all-trans-2,4-pentadiene-iminium cation (protonated
Schiff base 3, PSB3) and
the all-trans-3-methyl-2,4-pentadiene-iminium cation
(MePSB3) were investigated in the gas phase and in polar (aqueous)
and nonpolar (n-hexane) solutions by means of surface
hopping using a multireference configuration-interaction (MRCI) quantum
mechanical/molecular mechanics (QM/MM) level. Spectra, lifetimes for
radiationless deactivation to the ground state, and structural and
electronic parameters are compared. A strong influence of the polar
solvent on the location of the crossing seam, in particular in the
bond length alternation (BLA) coordinate, is found. Additionally,
inclusion of the polar solvent changes the orientation of the intersection
cone from sloped in the gas phase to peaked, thus enhancing considerably
its efficiency for deactivation of the molecular system to the ground
state. These factors cause, especially for MePSB3, a substantial decrease
in the lifetime of the excited state despite the steric inhibition
by the solvent.
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Affiliation(s)
- Matthias Ruckenbauer
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria
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19
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Ruzi M, Anderson DT. Photodissociation of N-methylformamide isolated in solid parahydrogen. J Chem Phys 2012. [DOI: 10.1063/1.4765372] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Crespo‐Otero R, Mardyukov A, Sanchez‐Garcia E, Barbatti M, Sander W. Photochemistry of
N
‐Methylformamide: Matrix Isolation and Nonadiabatic Dynamics. Chemphyschem 2012; 14:827-36. [DOI: 10.1002/cphc.201200573] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2012] [Indexed: 11/11/2022]
Affiliation(s)
- Rachel Crespo‐Otero
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Artur Mardyukov
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
| | - Elsa Sanchez‐Garcia
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Mario Barbatti
- Department of Theory, Max Planck Institute for Coal Research, Kaiser‐Wilhelm‐Platz 1, 45470 Mülheim an der Ruhr (Germany), Fax: (+49) (0)208/306‐2980
| | - Wolfram Sander
- Lehrstuhl für Organische Chemie II, Ruhr Universität Bochum, Universitätsstraße 150 44801 Bochum (Germany), Fax: (+49) (0)234‐3214353
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Antol I, Eckert-Maksić M, Vazdar M, Ruckenbauer M, Lischka H. QM/MM non-adiabatic decay dynamics of formamide in polar and non-polar solvents. Phys Chem Chem Phys 2012; 14:13262-72. [DOI: 10.1039/c2cp41830d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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Nonadiabatic dynamics with trajectory surface hopping method. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.64] [Citation(s) in RCA: 279] [Impact Index Per Article: 21.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Ruckenbauer M, Barbatti M, Sellner B, Muller T, Lischka H. Azomethane: Nonadiabatic Photodynamical Simulations in Solution. J Phys Chem A 2010; 114:12585-90. [DOI: 10.1021/jp108844g] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthias Ruckenbauer
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria, Max Plank Institute fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany, and Institute for Advanced Simulation, Research Center Jülich, 53425 Juelich, Germany
| | - Mario Barbatti
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria, Max Plank Institute fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany, and Institute for Advanced Simulation, Research Center Jülich, 53425 Juelich, Germany
| | - Bernhard Sellner
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria, Max Plank Institute fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany, and Institute for Advanced Simulation, Research Center Jülich, 53425 Juelich, Germany
| | - Thomas Muller
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria, Max Plank Institute fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany, and Institute for Advanced Simulation, Research Center Jülich, 53425 Juelich, Germany
| | - Hans Lischka
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, 1090 Vienna, Austria, Max Plank Institute fuer Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Muelheim, Germany, and Institute for Advanced Simulation, Research Center Jülich, 53425 Juelich, Germany
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