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Nagami S, Kaguchi R, Akahane T, Harabuchi Y, Taniguchi T, Monde K, Maeda S, Ichikawa S, Katsuyama A. Photoinduced dual bond rotation of a nitrogen-containing system realized by chalcogen substitution. Nat Chem 2024; 16:959-969. [PMID: 38418536 DOI: 10.1038/s41557-024-01461-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2022] [Accepted: 01/26/2024] [Indexed: 03/01/2024]
Abstract
Photoinduced concerted multiple-bond rotation has been proposed in some biological systems. However, the observation of such phenomena in synthetic systems, in other words, the synthesis of molecules that undergo photoinduced multiple-bond rotation upon photoirradiation, has been a challenge in the photochemistry field. Here we describe a chalcogen-substituted benzamide system that exhibits photoinduced dual bond rotation in heteroatom-containing bonds. Introduction of the chalcogen substituent into a sterically hindered benzamide system provides sufficient kinetic stability and photosensitivity to enable the photoinduced concerted rotation. The presence of two different substituents on the phenyl ring in the thioamide derivative enables the generation of a pair of enantiomers and E/Z isomers. Using these four stereoisomers as indicators of which bonds are rotated, we monitor the photoinduced C-N/C-C concerted bond rotation in the thioamide derivative depending on external stimuli such as temperature and photoirradiation. Theoretical calculations provide insight on the mechanism of this selective photoinduced C-N/C-C concerted rotation.
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Affiliation(s)
- Shotaro Nagami
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Rintaro Kaguchi
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Taichi Akahane
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan
| | - Yu Harabuchi
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- JST, ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Sapporo, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Tohru Taniguchi
- Frontier Research Center of Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Kenji Monde
- Frontier Research Center of Advanced Material and Life Science, Faculty of Advanced Life Science, Hokkaido University, Sapporo, Japan
| | - Satoshi Maeda
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo, Japan
- JST, ERATO, Maeda Artificial Intelligence in Chemical Reaction Design and Discovery Project, Sapporo, Japan
- Department of Chemistry, Faculty of Science, Hokkaido University, Sapporo, Japan
| | - Satoshi Ichikawa
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
| | - Akira Katsuyama
- Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
- Global Institution for Collaborative Research and Education, Hokkaido University, Sapporo, Japan.
- Center for Research and Education on Drug Discovery, Faculty of Pharmaceutical Sciences, Hokkaido University, Sapporo, Japan.
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Xu J, Hao J, Bu C, Meng Y, Xiao H, Zhang M, Li C. XMECP: Reaching State-of-the-Art MECP Optimization in Multiscale Complex Systems. J Chem Theory Comput 2024; 20:3590-3600. [PMID: 38651739 DOI: 10.1021/acs.jctc.4c00033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2024]
Abstract
The Python-based program, XMECP, is developed for realizing robust, efficient, and state-of-the-art minimum energy crossing point (MECP) optimization in multiscale complex systems. This article introduces the basic capabilities of the XMECP program by theoretically investigating the MECP mechanism of several example systems including (1) the photosensitization mechanism of benzophenone, (2) photoinduced proton-coupled electron transfer in the cytosine-guanine base pair in DNA, (3) the spin-flip process in oxygen activation catalyzed by an iron-containing 2-oxoglutarate-dependent oxygenase (Fe/2OGX), and (4) the photochemical pathway of flavoprotein adjusted by the intensity of an external electric field. MECPs related to multistate reaction and multistate reactivity in large-scale complex biochemical systems can be well-treated by workflows suggested by the XMECP program. The branching plane updating the MECP optimization algorithm is strongly recommended as it provides derivative coupling vector (DCV) with explicit calculation and can equivalently evaluate contributions from non-QM residues to DCV, which can be nonadiabatic coupling or spin-orbit coupling in different cases. In the discussed QM/MM examples, we also found that the influence on the QM region by DCV can occur through noncovalent interactions and decay with distance. In the example of DNA base pairs, the nonadiabatic coupling occurs across the π-π stacking structure formed in the double-helix system. In contrast to general intuition, in the example of Fe/2OGX, the central ferrous and oxygen part contribute little to the spin-orbit coupling; however, a nearby arginine residue, which is treated by molecular mechanics in the QM/MM method, contributes significantly via two hydrogen bonds formed with α-ketoglutarate (α-KG). This indicates that the arginine residue plays a significant role in oxygen activation, driving the initial triplet state toward the productive quintet state, which is more than the previous knowledge that the arginine residue can bind α-KG at the reaction site by hydrogen bonds.
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Affiliation(s)
- Jiawei Xu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Jian Hao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Caijie Bu
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- College of Chemistry and Materials Science, Fujian Normal University, Fuzhou 350117, Fujian, P. R. China
| | - Yajie Meng
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
| | - Han Xiao
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Minyi Zhang
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
| | - Chunsen Li
- State Key Laboratory of Structural Chemistry, Fujian Institute of Research on the Structure of Matter, Chinese Academy of Sciences, Fuzhou 350002, Fujian, P. R. China
- School of Chemical Sciences, University of Chinese Academy of Sciences, Beijing 100049, P. R. China
- Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, Xiamen University, Xiamen 361005, Fujian, P. R. China
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Intermolecular-Type Conical Intersections in Benzene Dimer. Int J Mol Sci 2023; 24:ijms24032906. [PMID: 36769227 PMCID: PMC9917476 DOI: 10.3390/ijms24032906] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2023] [Revised: 01/27/2023] [Accepted: 01/30/2023] [Indexed: 02/05/2023] Open
Abstract
The equilibrium and conical intersection geometries of the benzene dimer were computed in the framework of the conventional, linear-response time-dependent and spin-flipped time-dependent density functional theories (known as DFT, TDDFT and SF-TDDFT) as well as using the multiconfigurational complete active space self-consistent field (CASSCF) method considering the minimally augmented def2-TZVPP and the 6-31G(d,p) basis sets. It was found that the stacking distance between the benzene monomers decreases by about 0.5 Å in the first electronic excited state, due to the stronger intermolecular interaction energy, bringing the two monomers closer together. Intermolecular-type conical intersection (CI) geometries can be formed between the two benzene molecules, when (i) both monomer rings show planar deformation and (ii) weaker (approximately 1.6-1.8 Å long) C-C bonds are formed between the two monomers, with parallel and antiparallel orientation with respect to the monomer. These intermolecular-type CIs look energetically more favorable than dimeric CIs containing only one deformed monomer. The validity of the dimer-type CI geometries obtained by SF-TDDFT was confirmed by the CASSCF method. The nudged elastic band method used for finding the optimal relaxation path has confirmed both the accessibility of these intermolecular-type CIs and the possibility of the radiationless deactivation of the electronic excited states through these CI geometries. Although not as energetically favorable as the previous two CI geometries, there are other CI geometries characterized by the relative rotation of monomers at different angles around a vertical C-C axis.
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Hernández-Segura LI, Köster AM. Efficient implementation of time-dependent auxiliary density functional theory. J Chem Phys 2023; 158:024108. [PMID: 36641386 DOI: 10.1063/5.0135263] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
The random phase approximation of time-dependent auxiliary density functional theory (TDADFT) is rederived from auxiliary density perturbation theory. Our exhaustive validation of TDADFT reveals an upshift of the excitation energies by ∼0.1 eV with respect to standard time-dependent density functional theory. For the computationally efficient implementation of TDADFT, floating point operation optimized three-center electron repulsion integral recurrence relations and their double asymptotic expansions are implemented into the Davidson solver. The computational efficiency of TDADFT is benchmarked with four sets of molecules comprising alkanes, fullerenes, DNA fragments, and zeolites. The results show that TDADFT has a computational scaling between 1.3 and 1.9 with respect to the number of basis functions, which is lower than the scaling of standard time-dependent density functional theory. Due to its computational simplifications, TDADFT is particularly well suited for Born-Oppenheimer molecular dynamics simulations. As illustrative examples, we present the temperature effects on the gas-phase absorption spectra of benzene, naphthalene, and anthracene.
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Affiliation(s)
- Luis I Hernández-Segura
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Andreas M Köster
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
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Niehaus TA. Ground-to-excited derivative couplings for the density functional-based tight-binding method: semi-local and long-range corrected formulations. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02735-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Ikemoto K, Tokuhira T, Uetani A, Harabuchi Y, Sato S, Maeda S, Isobe H. Fluorescence Enhancement of Aromatic Macrocycles by Lowering Excited Singlet State Energies. J Org Chem 2019; 85:150-157. [DOI: 10.1021/acs.joc.9b02379] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Koki Ikemoto
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Toshiki Tokuhira
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Akari Uetani
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
| | - Yu Harabuchi
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- JST, PRESTO, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
| | - Sota Sato
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Satoshi Maeda
- Department of Chemistry, Faculty of Science, Hokkaido University, Kita 10, Nishi 8, Kita-ku, Sapporo 060-0810, Japan
- Institute for Chemical Reaction Design and Discovery (WPI-ICReDD), Hokkaido University, Sapporo 001-0021, Japan
- Research and Services Division of Materials Data and Integrated System (MaDIS), National Institute for Materials Science (NIMS), Tsukuba 305-0044, Japan
| | - Hiroyuki Isobe
- Department of Chemistry, The University of Tokyo, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
- JST, ERATO Isobe Degenerate π-Integration Project, Hongo 7-3-1, Bunkyo-ku, Tokyo 113-0033, Japan
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