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Nakanishi T, Hori Y, Shigeta Y, Sato H, Kiyanagi R, Munakata K, Ohhara T, Okazawa A, Shimada R, Sakamoto A, Sato O. Development of an Iron(II) Complex Exhibiting Thermal- and Photoinduced Double Proton-Transfer-Coupled Spin Transition in a Short Hydrogen Bond. J Am Chem Soc 2023; 145:19177-19181. [PMID: 37623927 DOI: 10.1021/jacs.3c06323] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/26/2023]
Abstract
Multiple proton transfer (PT) controllable by external stimuli plays a crucial role in fundamental chemistry, biological activity, and material science. However, in crystalline systems, controlling multiple PT, which results in a distinct protonation state, remains challenging. In this study, we developed a novel tridentate ligand and iron(II) complex with a short hydrogen bond (HB) that exhibits a PT-coupled spin transition (PCST). Single-crystal X-ray and neutron diffraction measurements revealed that the positions of the two protons in the complex can be controlled by temperature and photoirradiation based on the thermal- and photoinduced PCST. The obtained results suggest that designing molecules that form short HBs is a promising approach for developing multiple PT systems in crystals.
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Affiliation(s)
- Takumi Nakanishi
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
| | - Yuta Hori
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Yasuteru Shigeta
- Center for Computational Sciences, University of Tsukuba, Tsukuba 305-8577, Japan
| | - Hiroyasu Sato
- Rigaku Corporation, 3-9-12 Matsubaracho, Akishima, Tokyo 196-8666, Japan
| | - Ryoji Kiyanagi
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Koji Munakata
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Takashi Ohhara
- J-PARC center, Japan Atomic Energy Agency, Tokai, Ibaraki 319-1195, Japan
| | - Atsushi Okazawa
- Department of Electrical Engineering and Bioscience, Waseda University, Okubo 3-4-1, Shinjuku-ku, Tokyo, 169-8555, Japan
| | - Rintaro Shimada
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Akira Sakamoto
- Graduate School of Science and Engineering, Aoyama Gakuin University, 5-10-1 Fuchinobe, Chuo-ku, Sagamihara, Kanagawa 252-5258, Japan
| | - Osamu Sato
- Institute for Materials Chemistry and Engineering & IRCCS, Kyushu University, 744 Motooka, Nishi-ku, Fukuoka 819-0395, Japan
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Too HL, Guo N, Zhang C, Wang Z. Importance of Sugar-Phosphate Backbone and Counterions to First-Principles Modeling of Nucleobases. J Phys Chem B 2022; 126:5744-5751. [PMID: 35903034 DOI: 10.1021/acs.jpcb.2c02621] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
DFT-based first-principles calculations were carried out to understand the electronic structure difference among a backbone-free nucleobase, a backbone-containing Na counterion nucleotide, and a backbone-containing H counterion nucleotide and their difference in the adsorption on graphene and on graphitic-carbon nitride. The study discovered that the inclusion of a sugar-phosphate backbone changes the electron affinity of most nucleobases from electron acceptors to electron donors. The methyl-terminated backbone-free model cannot replicate the steric effect induced by the sugar-phosphate backbone during the adsorption of nucleobases on 2D materials. Overall, we established that the sugar phosphate backbone should be included in the study of DNA nucleobase adsorption on 2D material. We also showed that when it comes to the adsorption on 2D materials, the backbone-containing H counterion model is superior to the Na counterion model because the Na counterion produces a LUMO near the Fermi energy, which may significantly affect the interaction with the 2D material.
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Affiliation(s)
- Hon Lin Too
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117542.,Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542
| | - Na Guo
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.,National University of Singapore Chongqing Research Institute, Chongqing 401123, China
| | - Chun Zhang
- Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542.,National University of Singapore Chongqing Research Institute, Chongqing 401123, China.,Centre for Advanced 2D Materials (CA2DM), National University of Singapore, 6 Science Drive 2, Singapore 117546.,Department of Chemistry, National University of Singapore, 3 Science Drive 3, Singapore 117543
| | - Zhisong Wang
- NUS Graduate School for Integrative Science and Engineering, National University of Singapore, Singapore 117542.,Department of Physics, National University of Singapore, 2 Science Drive 3, Singapore 117542
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Stochastic dynamic quantitative and 3D structural matrix assisted laser desorption/ionization mass spectrometric analyses of mixture of nucleosides. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.132701] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Noble BB, Todorova N, Yarovsky I. Electromagnetic bioeffects: a multiscale molecular simulation perspective. Phys Chem Chem Phys 2022; 24:6327-6348. [PMID: 35245928 DOI: 10.1039/d1cp05510k] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Electromagnetic bioeffects remain an enigma from both the experimental and theoretical perspectives despite the ubiquitous presence of related technologies in contemporary life. Multiscale computational modelling can provide valuable insights into biochemical systems and predict how they will be perturbed by external stimuli. At a microscopic level, it can be used to determine what (sub)molecular scale reactions various stimuli might induce; at a macroscopic level, it can be used to examine how these changes affect dynamic behaviour of essential molecules within the crowded biomolecular milieu in living tissues. In this review, we summarise and evaluate recent computational studies that examined the impact of externally applied electric and electromagnetic fields on biologically relevant molecular systems. First, we briefly outline the various methodological approaches that have been employed to study static and oscillating field effects across different time and length scales. The practical value of such modelling is then illustrated through representative case-studies that showcase the diverse effects of electric and electromagnetic field on the main physiological solvent - water, and the essential biomolecules - DNA, proteins, lipids, as well as some novel biomedically relevant nanomaterials. The implications and relevance of the theoretical multiscale modelling to practical applications in therapeutic medicine are also discussed. Finally, we summarise ongoing challenges and potential opportunities for theoretical modelling to advance the current understanding of electromagnetic bioeffects for their modulation and/or beneficial exploitation in biomedicine and industry.
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Affiliation(s)
- Benjamin B Noble
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Nevena Todorova
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, GPO Box 2476, Melbourne, Australia. .,Australian Centre for Electromagnetic Bioeffects Research, Australia
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Gheorghiu A, Coveney PV, Arabi AA. The influence of external electric fields on proton transfer tautomerism in the guanine-cytosine base pair. Phys Chem Chem Phys 2021; 23:6252-6265. [PMID: 33735350 PMCID: PMC8330266 DOI: 10.1039/d0cp06218a] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2020] [Accepted: 02/23/2021] [Indexed: 12/28/2022]
Abstract
The Watson-Crick base pair proton transfer tautomers would be widely considered as a source of spontaneous mutations in DNA replication if not for their short lifetimes and thermodynamic instability. This work investigates the effects external electric fields have on the stability of the guanine-cytosine proton transfer tautomers within a realistic strand of aqueous DNA using a combination of ensemble-based classical molecular dynamics (MD) coupled to quantum mechanics/molecular mechanics (QM/MM). Performing an ensemble of calculations accounts for the stochastic aspects of the simulations while allowing for easier identification of systematic errors. The methodology applied in this work has previously been shown to estimate base pair proton transfer rate coefficients that are in good agreement with recent experimental data. A range of electric fields in the order of 104 to 109 V m-1 is investigated based on their real-life medicinal applications which include gene therapy and cancer treatments. The MD trajectories confirm that electric fields up to 1.00 × 109 V m-1 have a negligible influence on the structure of the base pairs within DNA. The QM/MM results show that the application of large external electric fields (1.00 × 109 V m-1) parallel to the hydrogen bonds increases the thermodynamic population of the tautomers by up to one order of magnitude; moreover, the lifetimes of the tautomers remain insignificant when compared to the timescale of DNA replication.
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Affiliation(s)
- Alexander Gheorghiu
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK.
| | - Peter V Coveney
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and Informatics Institute, University of Amsterdam, P.O. Box 94323 1090 GH, Amsterdam, The Netherlands
| | - Alya A Arabi
- Centre for Computational Science, University College London, 20 Gordon St, London, WC1H 0AJ, UK. and College of Medicine and Health Sciences, Biochemistry Department, United Arab Emirates University, AlAin, P. O. Box: 17666, United Arab Emirates.
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