1
|
Imamura K, Yokogawa D, Sato H. Recent developments and applications of reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED): A hybrid model of quantum chemistry and integral equation theory of molecular liquids. J Chem Phys 2024; 160:050901. [PMID: 38341702 DOI: 10.1063/5.0190116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2023] [Accepted: 01/04/2024] [Indexed: 02/13/2024] Open
Abstract
The significance of solvent effects in electronic structure calculations has long been noted, and various methods have been developed to consider this effect. The reference interaction site model self-consistent field with constrained spatial electron density (RISM-SCF-cSED) is a hybrid model that combines the integral equation theory of molecular liquids with quantum chemistry. This method can consider the statistically convergent solvent distribution at a significantly lower cost than molecular dynamics simulations. Because the RISM theory explicitly considers the solvent structure, it performs well for systems where hydrogen bonds are formed between the solute and solvent molecules, which is a challenge for continuum solvent models. Taking advantage of being founded on the variational principle, theoretical developments have been made in calculating various properties and incorporating electron correlation effects. In this review, we organize the theoretical aspects of RISM-SCF-cSED and its distinctions from other hybrid methods involving integral equation theories. Furthermore, we carefully present its progress in terms of theoretical developments and recent applications.
Collapse
Affiliation(s)
- Kosuke Imamura
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Daisuke Yokogawa
- Graduate School of Arts and Science, The University of Tokyo, Komaba, Meguro-ku, Tokyo 153-8902, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
- Fukui Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| |
Collapse
|
2
|
Ortín-Fernández J, González-Vázquez J, Martínez-Fernández L, Corral I. Molecular Identification of the Transient Species Mediating the Deactivation Dynamics of Solvated Guanosine and Deazaguanosine. Molecules 2022; 27:989. [PMID: 35164254 PMCID: PMC8839017 DOI: 10.3390/molecules27030989] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 01/24/2022] [Accepted: 01/27/2022] [Indexed: 11/16/2022] Open
Abstract
Small structural alterations of the purine/pyrimidine core have been related to important photophysical changes, such as the loss of photostability. Similarly to canonical nucleobases, solute-solvent interactions can lead to a change in the excited state lifetimes and/or to the interplay of different states in the photophysics of these modified nucleobases. To shed light on both effects, we here report a complete picture of the absorption spectra and excited state deactivation of deoxyguanosine and its closely related derivative, deoxydeazaguanosine, in water and methanol through the mapping of the excited state potential energy surfaces and molecular dynamics simulations at the TD-DFT level of theory. We show that the N by CH exchange in the imidazole ring of deoxyguanosine translates into a small red-shift of the bright states and slightly faster dynamics. In contrast, changing solvent from water to methanol implies the opposite, i.e., that the deactivation of both systems to the ground state is significantly hindered.
Collapse
Affiliation(s)
- Javier Ortín-Fernández
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
| | - Jesús González-Vázquez
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Lara Martínez-Fernández
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Inés Corral
- Departamento de Química, Módulo 13, Universidad Autónoma de Madrid, 28049 Madrid, Spain; (J.O.-F.); (J.G.-V.)
- Institute for Advanced Research in Chemistry (IAdChem), Universidad Autónoma de Madrid, 28049 Madrid, Spain
| |
Collapse
|
3
|
Zhang X, Herbert JM. Nonadiabatic dynamics with spin-flip vs linear-response time-dependent density functional theory: A case study for the protonated Schiff base C 5H 6NH 2. J Chem Phys 2021; 155:124111. [PMID: 34598550 DOI: 10.1063/5.0062757] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Abstract
Nonadiabatic trajectory surface hopping simulations are reported for trans-C5H6NH2 +, a model of the rhodopsin chromophore, using the augmented fewest-switches algorithm. Electronic structure calculations were performed using time-dependent density functional theory (TDDFT) in both its conventional linear-response (LR) and its spin-flip (SF) formulations. In the SF-TDDFT case, spin contamination in the low-lying singlet states is removed by projecting out the lowest triplet component during iterative solution of the TDDFT eigenvalue problem. The results show that SF-TDDFT qualitatively describes the photoisomerization of trans-C5H6NH2 +, with favorable comparison to previous studies using multireference electronic structure methods. In contrast, conventional LR-TDDFT affords qualitatively different photodynamics due to an incorrect excited-state potential surface near the Franck-Condon region. In addition, the photochemistry (involving pre-twisting of the central double bond) appears to be different for SF- and LR-TDDFT, which may be a consequence of different conical intersection topographies afforded by these two methods. The present results contrast with previous surface-hopping studies suggesting that the LR-TDDFT method's incorrect topology around S1/S0 conical intersections is immaterial to the photodynamics.
Collapse
Affiliation(s)
- Xing Zhang
- Department of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - John M Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
4
|
Sasaki S, Suzuki S, Sameera WMC, Igawa K, Morokuma K, Konishi GI. Highly Twisted N,N-Dialkylamines as a Design Strategy to Tune Simple Aromatic Hydrocarbons as Steric Environment-Sensitive Fluorophores. J Am Chem Soc 2016; 138:8194-206. [DOI: 10.1021/jacs.6b03749] [Citation(s) in RCA: 112] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Shunsuke Sasaki
- Department
of Organic and Polymeric Materials, Tokyo Institute of Technology, Tokyo 152-8552, Japan
| | - Satoshi Suzuki
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - W. M. C. Sameera
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Kazunobu Igawa
- Institute
for Materials Chemistry and Engineering, Kyushu University, Fukuoka 816-8580, Japan
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Gen-ichi Konishi
- Department
of Organic and Polymeric Materials, Tokyo Institute of Technology, Tokyo 152-8552, Japan
- PRESTO, Japan Science and Technology Agency (JST), Tokyo 102-0076, Japan
| |
Collapse
|
5
|
Dobryakov A, Quick M, Lenoir D, Detert H, Ernsting N, Kovalenko S. Time-resolved photoisomerization of 1,1′-di-tert-butylstilbene and 1,1′-dicyanostilbene. Chem Phys Lett 2016. [DOI: 10.1016/j.cplett.2016.04.060] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
|
6
|
Improta R, Santoro F, Blancafort L. Quantum Mechanical Studies on the Photophysics and the Photochemistry of Nucleic Acids and Nucleobases. Chem Rev 2016; 116:3540-93. [PMID: 26928320 DOI: 10.1021/acs.chemrev.5b00444] [Citation(s) in RCA: 341] [Impact Index Per Article: 42.6] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
The photophysics and photochemistry of DNA is of great importance due to the potential damage of the genetic code by UV light. Quantum mechanical studies have played a key role in interpretating the results of modern time-resolved pump-probe spectroscopy, and in elucidating the main photoactivated reactive paths. This review provides a concise, complete picture of the computational studies carried out, approximately, in the past decade. We start with an overview of the photophysics of the nucleobases in the gas phase and in solution. We discuss the proposed mechanisms for ultrafast decay to the ground state, that involve conical intersections, consider the role of triplet states, and analyze how the solvent modulates the photophysics. Then we move to larger systems, from dinucleotides to single- and double-stranded oligonucleotides. We focus on the possible role of charge transfer and delocalized or excitonic states in the photophysics of these systems and discuss the main photochemical paths. We finish with an outlook on the current challenges in the field and future directions of research.
Collapse
Affiliation(s)
- Roberto Improta
- Istituto di Biostrutture Biommagini (IBB-CNR), CNR-Consiglio Nazionale delle Ricerche , Via Mezzocannone 16, I-80134, Napoli, Italy
| | - Fabrizio Santoro
- Area della Ricerca di Pisa, Istituto di Chimica dei Composti Organo Metallici (ICCOM-CNR), CNR-Consiglio Nazionale delle Ricerche , Via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Lluís Blancafort
- Institut de Química Computacional i Catàlisi and Departament de Química, Universitat de Girona, Campus de Montilivi , 17071 Girona, Spain
| |
Collapse
|
7
|
Hua X, Hua L, Liu X. The methyl- and aza-substituent effects on nonradiative decay mechanisms of uracil in water: a transient absorption study in the UV region. Phys Chem Chem Phys 2016; 18:13904-11. [DOI: 10.1039/c6cp00732e] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The C5, C6 methyl- and aza-substituent effects on the decay mechanism of uracil and vibrational cooling dynamics are investigated using a continuous UV probe.
Collapse
Affiliation(s)
- XinZhong Hua
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- P. R. China
| | - LinQiang Hua
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- P. R. China
| | - XiaoJun Liu
- State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics
- Wuhan Institute of Physics and Mathematics
- Chinese Academy of Sciences
- Wuhan 430071
- P. R. China
| |
Collapse
|
8
|
Zhang X, Herbert JM. Spin-flip, tensor equation-of-motion configuration interaction with a density-functional correction: A spin-complete method for exploring excited-state potential energy surfaces. J Chem Phys 2015; 143:234107. [DOI: 10.1063/1.4937571] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Xing Zhang
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| |
Collapse
|
9
|
Ruiz-Barragan S, Morokuma K, Blancafort L. Conical Intersection Optimization Using Composed Steps Inside the ONIOM(QM:MM) Scheme: CASSCF:UFF Implementation with Microiterations. J Chem Theory Comput 2015; 11:1585-94. [DOI: 10.1021/acs.jctc.5b00004] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sergi Ruiz-Barragan
- Institut
de Química Computacional i Catàlisis and Departament
de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| | - Keiji Morokuma
- Fukui
Institute for Fundamental Chemistry, Kyoto University, Kyoto 606-8103, Japan
| | - Lluís Blancafort
- Institut
de Química Computacional i Catàlisis and Departament
de Química, Universitat de Girona, Campus de Montilivi, 17071 Girona, Spain
| |
Collapse
|
10
|
Buchner F, Nakayama A, Yamazaki S, Ritze HH, Lübcke A. Excited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation. J Am Chem Soc 2015; 137:2931-8. [PMID: 25671554 DOI: 10.1021/ja511108u] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
Time-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys. 2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.
Collapse
Affiliation(s)
- Franziska Buchner
- Max-Born-Institut für nichtlineare Optik und Kurzzeitspektroskopie , Max-Born-Straße 2A, 12489 Berlin, Germany
| | | | | | | | | |
Collapse
|
11
|
Casida ME, Huix-Rotllant M. Many-Body Perturbation Theory (MBPT) and Time-Dependent Density-Functional Theory (TD-DFT): MBPT Insights About What Is Missing In, and Corrections To, the TD-DFT Adiabatic Approximation. DENSITY-FUNCTIONAL METHODS FOR EXCITED STATES 2015; 368:1-60. [DOI: 10.1007/128_2015_632] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
|