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Bende A, Farcaş AA, Toşa V. Theoretical Study of Light-Induced Crosslinking Reaction Between Pyrimidine DNA Bases and Aromatic Amino Acids. Front Bioeng Biotechnol 2022; 9:806415. [PMID: 35111737 PMCID: PMC8801568 DOI: 10.3389/fbioe.2021.806415] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2021] [Accepted: 12/16/2021] [Indexed: 11/13/2022] Open
Abstract
Low-lying electronic excited states and their relaxation pathways as well as energetics of the crosslinking reaction between uracil as a model system for pyrimidine-type building blocks of DNA and RNA and benzene as a model system for aromatic groups of tyrosine (Tyr) and phenylalanine (Phe) amino acids have been studied in the framework of density functional theory. The equilibrium geometries of the ground and electronic excited states as well as the crossing points between the potential energy surfaces of the uracil–benzene complex were computed. Based on these results, different relaxation pathways of the electronic excited states that lead to either back to the initial geometry configuration or the dimerization between the six-membered rings of the uracil–benzene complex have been identified, and the energetic conditions for their occurrence are discussed. It can be concluded that the DNA–protein crosslinking reaction can be induced by the external electromagnetic field via the dimerization reaction between the six-membered rings of the uracil–benzene pair at the electronic excited-state level of the complex. In the case of the uracil–phenol complex, the configuration of the cyclic adduct (dimerized) conformation is less likely to be formed.
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Affiliation(s)
- Attila Bende
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
- *Correspondence: Attila Bende,
| | - Alex-Adrian Farcaş
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
- Faculty of Physics, Babeş-Bolyai University, Cluj-Napoca, Romania
| | - Valer Toşa
- Molecular and Biomolecular Physics Department, National Institute for Research and Development of Isotopic and Molecular Technologies, Cluj-Napoca, Romania
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Hekele J, Yao Y, Kanai Y, Blum V, Kratzer P. All-electron real-time and imaginary-time time-dependent density functional theory within a numeric atom-centered basis function framework. J Chem Phys 2021; 155:154801. [PMID: 34686041 DOI: 10.1063/5.0066753] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Real-time time-dependent density functional theory (RT-TDDFT) is an attractive tool to model quantum dynamics by real-time propagation without the linear response approximation. Sharing the same technical framework of RT-TDDFT, imaginary-time time-dependent density functional theory (it-TDDFT) is a recently developed robust-convergence ground state method. Presented here are high-precision all-electron RT-TDDFT and it-TDDFT implementations within a numerical atom-centered orbital (NAO) basis function framework in the FHI-aims code. We discuss the theoretical background and technical choices in our implementation. First, RT-TDDFT results are validated against linear-response TDDFT results. Specifically, we analyze the NAO basis sets' convergence for Thiel's test set of small molecules and confirm the importance of the augmentation basis functions for adequate convergence. Adopting a velocity-gauge formalism, we next demonstrate applications for systems with periodic boundary conditions. Taking advantage of the all-electron full-potential implementation, we present applications for core level spectra. For it-TDDFT, we confirm that within the all-electron NAO formalism, it-TDDFT can successfully converge systems that are difficult to converge in the standard self-consistent field method. We finally benchmark our implementation for systems up to ∼500 atoms. The implementation exhibits almost linear weak and strong scaling behavior.
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Affiliation(s)
- Joscha Hekele
- Faculty of Physics, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
| | - Yi Yao
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Yosuke Kanai
- Department of Chemistry, University of North Carolina, Chapel Hill, North Carolina 27599, USA
| | - Volker Blum
- Thomas Lord Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - Peter Kratzer
- Faculty of Physics, University of Duisburg-Essen, Lotharstr. 1, 47057 Duisburg, Germany
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Zhao L, Zheng H, Zhan K, Guo Y, Liu B, Xu G. Position of the Benzene Ring Substituent Regulates the Excited-State Deactivation Process of the Benzyluracil Systems. J Phys Chem A 2021; 125:165-174. [PMID: 33373221 DOI: 10.1021/acs.jpca.0c08980] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
A systematic theoretical study of the regulating effect of the substituent position on the photoinduced deactivation process of the benzyluracil systems has been performed based on the high-level static electronic structure calculations and on-the-fly full-dimensional excited-state dynamics simulations. Similarities and differences coexist for the two systems by comparative studies on the photoinduced deactivation process of the 5-benzyluracil (5-BU) and 6-benzyluracil (6-BU) systems. They both obey an S2 → S1 → S0 two-step decay pattern, and the decay coordinates of the S2 → S1 and S1 → S0 processes are mainly driven by the elongation of the bridging bond and the out-of-plane ring deformation motion, respectively. However, the puckering motion occurring at the C2 atom in the uracil fragment dominates the decay pathway of the 5-BU system. On the contrary, the puckering motion at the C5 atom in the benzene fragment mainly drives the decay coordinate of the 6-BU system. Therefore, the substituent position could play significant roles in the deactivation process of the benzyluracil systems. Moreover, the S1 → S0 decay process of the 6-BU system consists of five pathways, possessing a more complex deactivation picture than the 5-BU system. The fitted time scale of the puckering motion is compatible with the experimentally observed lifetimes. This work provides a fundamental understanding of the photophysical and photochemical properties of the benzyluracil systems and can give rational suggestions to further design or regulate the bionic molecular systems.
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Affiliation(s)
- Li Zhao
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Haixia Zheng
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Kaiyun Zhan
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Yahui Guo
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Bing Liu
- School of Science, China University of Petroleum (East China), Qingdao 266580, Shandong, China
| | - Guiyin Xu
- Department of Nuclear Science and Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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Ghosh S, Asher JC, Gagliardi L, Cramer CJ, Govind N. A semiempirical effective Hamiltonian based approach for analyzing excited state wave functions and computing excited state absorption spectra using real-time dynamics. J Chem Phys 2019; 150:104103. [DOI: 10.1063/1.5061746] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Soumen Ghosh
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
| | - Jason C. Asher
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
| | - Christopher J. Cramer
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, USA
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, USA
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Rossi TP, Kuisma M, Puska MJ, Nieminen RM, Erhart P. Kohn–Sham Decomposition in Real-Time Time-Dependent Density-Functional Theory: An Efficient Tool for Analyzing Plasmonic Excitations. J Chem Theory Comput 2017; 13:4779-4790. [DOI: 10.1021/acs.jctc.7b00589] [Citation(s) in RCA: 72] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Tuomas P. Rossi
- COMP
Centre of Excellence, Department of Applied Physics, Aalto University, P.O.
Box 11100, FI-00076 Aalto, Finland
| | - Mikael Kuisma
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
- Department
of Chemistry, Nanoscience Center, University of Jyväskylä, FI-40014 Jyväskylä, Finland
| | - Martti J. Puska
- COMP
Centre of Excellence, Department of Applied Physics, Aalto University, P.O.
Box 11100, FI-00076 Aalto, Finland
| | - Risto M. Nieminen
- COMP
Centre of Excellence, Department of Applied Physics, Aalto University, P.O.
Box 11100, FI-00076 Aalto, Finland
| | - Paul Erhart
- Department
of Physics, Chalmers University of Technology, SE-412 96 Gothenburg, Sweden
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Provorse MR, Habenicht BF, Isborn CM. Peak-Shifting in Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2015; 11:4791-802. [DOI: 10.1021/acs.jctc.5b00559] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Bradley F. Habenicht
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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