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Pushkaran AC, Arabi AA. A review on point mutations via proton transfer in DNA base pairs in the absence and presence of electric fields. Int J Biol Macromol 2024; 277:134051. [PMID: 39069038 DOI: 10.1016/j.ijbiomac.2024.134051] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2024] [Revised: 07/12/2024] [Accepted: 07/18/2024] [Indexed: 07/30/2024]
Abstract
This comprehensive review focuses on spontaneous mutations that may occur during DNA replication, the fundamental process responsible for transferring genetic information. In 1963, Löwdin postulated that these mutations are primarily a result of proton transfer reactions within the hydrogen-bonded DNA base pairs. The single and double proton transfer reactions within the base pairs in DNA result in zwitterions and rare tautomers, respectively. For persistent mutations, these products must be generated at high rates and should be thermodynamically stable. This review covers the proton transfer reactions studied experimentally and computationally. The review also examines the influence of externally applied electric fields on the thermodynamics and kinetics of proton transfer reactions within DNA base pairs, and their biological implications.
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Affiliation(s)
- Anju Choorakottayil Pushkaran
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box: 15551, United Arab Emirates
| | - Alya A Arabi
- Department of Biochemistry and Molecular Biology, College of Medicine and Health Sciences, United Arab Emirates University, Al Ain, P.O. Box: 15551, United Arab Emirates.
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2
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Baweja S, Kalal B, Maity S. Spectroscopic Characterization of Hydrogen-Bonded 2,7-Diazaindole Water Complex Isolated in the Gas Phase. J Phys Chem A 2024; 128:3329-3338. [PMID: 38652167 DOI: 10.1021/acs.jpca.4c01113] [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
We present a systematic experimental analysis of the 1:1 complex of 2,7-diazaindole (27DAI) with water in the gas phase. The complex was characterized by using two-color-resonant two-photon ionization (R2PI), laser-induced fluorescence (LIF), single vibronic level fluorescence (SVLF), and photoionization efficiency (PIE) spectroscopic methods. The 000 band of the S1←S0 electronic transition of the 27DAI-H2O complex was observed at 33,074 cm-1, largely red-shifted by 836 cm-1 compared to that of the bare 27DAI. From the R2PI spectrum, the detected modes at 141 (ν'Tx), 169 (ν'Ty), and 194 (ν'Ry) cm-1 were identified as the internal motions of the H2O molecule in the complex. However, these modes were detected at 115 (ν″Tx), 152 (ν″Ty), and 190 (ν″Ry) cm-1 in the ground state, which suggested a stronger hydrogen bonding interaction in the photo-excited state. The structural determination was aided by the detection of νNH and νOH values in the ground and excited state complexes using the FDIR and IDIR spectroscopies. The detection of νNH at 3414 and νOH at 3447 cm-1 in 27DAI-H2O has shown an excellent correlation with the most stable structure consisting of N(1)-H···O and OH···N(7) hydrogen-bonded bridging water molecule in the ground state. The structure of the complex in the electronic excited state (S1) was confirmed by the corresponding bands at 3210 (νNH) and 3265 cm-1 (νOH). The IR-UV hole-burning spectroscopy confirmed the presence of only one isomer in the molecular beam. The ionization energy (IE) of the 27DAI-H2O complex was obtained as 8.789 ± 0.002 eV, which was significantly higher than the 7AI-H2O complex. The higher IE values of N-rich molecules suggest a higher resistivity of such molecules against photodamage. The obtained structure of the 27DAI-H2O complex has explicitly shown the formation of a cyclic one-solvent bridge incorporating N(1)-H···O and O-H···N(7) hydrogen bonds upon microsolvation. The lower excitation and higher ionization energies of the 27DAI-H2O complex compared to 7AI-H2O established higher stabilization of N-rich molecules. The solvent clusters forming a linear bridge between the hydrogen/proton acceptor and donor sites in the complex can be considered as a stepping stone to investigate the photoinduced deactivation mechanisms in nitrogen containing biologically relevant molecules.
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Affiliation(s)
- Simran Baweja
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Bhavika Kalal
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
| | - Surajit Maity
- Department of Chemistry, IIT Hyderabad, Kandi, Sangareddy, Telangana 502284, India
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3
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Tang X, Zhang Y, Sun C. Effect of external electric fields on the ESDPT process and photophysical properties of 1,8-dihydroxy-2-naphthaldehyde. Phys Chem Chem Phys 2024; 26:10439-10448. [PMID: 38502564 DOI: 10.1039/d3cp06175b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/21/2024]
Abstract
In this work, by capitalizing on the density functional theory (DFT) and the time-dependent density functional theory (TD-DFT) methods, it has been systematically studied that the excited state double intramolecular proton transfer (ESDPT) process and the photophysical properties of 1,8-dihydroxy-2-naphthaldehyde (DHNA) are affected by the distinct external electric fields (EEFs). The obtained intramolecular hydrogen bond (IHB) parameters containing bond lengths and angles, as well as infrared (IR) vibrational spectra demonstrate that IHB strength changes in the distinct EEFs. Moreover, not only do the potential energy surfaces (PESs) indicate that the ESDPT process of DHNA is stepwise, but also increasing the positive EEF results in a decrease in the energy barrier accordingly, while vice versa. The absorption and fluorescence spectra also undergo a corresponding red or blue shift in the EEF; for instance, when the EEF changes from +10 × 10-4 a.u. to +20 × 10-4 a.u., the fluorescence peak undergoes a blue shift from 602 nm to 513 nm in the keto2 form. In a nutshell, the ESDPT process of DHNA can be influenced by the EEF, which will serve as a reference in regulating and controlling proton transfer that causes luminescence.
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Affiliation(s)
- Xingzhu Tang
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
| | - Yajie Zhang
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
| | - Chaofan Sun
- College of Science, Northeast Forestry University, Harbin 150040, Heilongjiang, China.
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4
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Lamas I, Montero R, Martínez-Martínez V, Longarte A. Photodynamics of azaindoles in polar media: the influence of the environment. Phys Chem Chem Phys 2024; 26:3240-3252. [PMID: 38193884 DOI: 10.1039/d3cp03412g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
We have studied the relaxation dynamics of a family of azaindole (AI) structural isomers, 4-, 5-, 6- and 7-AI, by steady-state and time-resolved methods (fs-transient absorption and fluorescence up-conversion), in solvents of different polarity. The measurements in aprotic solvents show distinctive fluorescence yields and excited state lifetimes among the isomers, which are tuned by the polarity of the medium. Guided by simple TD-DFT calculations and based on the behavior observed in the isolated species, it has been possible to address the influence of the environment polarity on the relaxation route. According to the obtained picture, the energy of the nπ* state, which is strongly dependent on the position of the pyridinic nitrogen, controls the rate of the internal conversion channel that accounts for the distinctive photophysical behavior of the isomers. On the other hand, preliminary measurements in protic media (methanol) show a very different photodynamical behavior, in which the anomalous measured fluorescent patterns are very likely the result of reactive channels (proton transfer) triggered by the electronic excitation.
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Affiliation(s)
- Iker Lamas
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
| | - Raúl Montero
- SGIKER Laser Facility Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) 48940, Leioa, Spain.
| | - Virginia Martínez-Martínez
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
| | - Asier Longarte
- Departamento de Química-Física Facultad de Ciencia y Tecnología. Universidad del País Vasco (UPV/EHU) Apart. 644, 48080 Bilbao, Spain.
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5
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Demchenko AP. Proton transfer reactions: from photochemistry to biochemistry and bioenergetics. BBA ADVANCES 2023. [DOI: 10.1016/j.bbadva.2023.100085] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/12/2023] Open
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Mehata MS, Aneesha. Selectively probing ferric ions in aqueous environments using protonated and neutral forms of 7-azaindole as a multiparametric chemosensor. Photochem Photobiol Sci 2023:10.1007/s43630-023-00393-6. [PMID: 36805446 DOI: 10.1007/s43630-023-00393-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2022] [Accepted: 02/05/2023] [Indexed: 02/21/2023]
Abstract
7-azaindole (7AI) dimer is a model molecule for DNA study and understanding the mutagenic behavior based on the excited-state proton transfer process in hydrogen-bonded networks. The neutral and protonated forms of 7AI monomer with significant fluorescence (FL) intensity fit the fluorescent sensor strategy to recognize selective metal ions. Out of several metal ions (Fe3+, Al3+, Fe2+, Pb2+, Ba2+, Ni2+, Zn2+, Mg2+, Ca2+, Cu2+, Hg2+ and Cd2+), the absorption, fluorescence and fluorescence lifetime of 7AI in the aqueous medium are selectively sensitive to the ferric (Fe3+) ions. The absolute value of absorption intensity increases linearly with concentration of a particular metal ions. FL intensity of both the forms of 7AI decreases gradually with Fe3+ ions and trails the linear Stern-Volmer relation. The formation of non-fluorescent complexes was confirmed with Benesi-Hildebrand and Job plots, along with FL and FL decays. The FL lifetime of the protonated form of 7AI, which is 0.83 ± 0.01 ns, is nearly constant with Fe3+ ions concentrations, confirming the static quenching mechanism. The limit of detection (LoD) of Fe3+ ions over the long range of 16-363 µM for the neutral and protonated forms of 7AI is 0.46 ± 0.02 and 0.49 ± 0.02 µM, respectively, estimated using FL spectra. Additionally, the linear plot of absorbance with Fe3+ ions of both the forms of 7AI can also act as a calibration curve with very close LoDs, as obtained by FL spectra. Thus, the multi-parameters-based probe for detecting the Fe3+ ions over long-range in real aqueous environments with operational, high sensitivity, fast response (< 5 s), and good selectivity (over 12 metal ions) is undoubtedly a superior approach over other methods.
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Affiliation(s)
- Mohan Singh Mehata
- Laser Spectroscopy Laboratory, Department of Applied Physics, Delhi Technological University, Bawana Road, Delhi, 110042, India.
| | - Aneesha
- Laser Spectroscopy Laboratory, Department of Applied Physics, Delhi Technological University, Bawana Road, Delhi, 110042, India
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7
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Li C, Hu B, Cao Y, Li Y. Elaborating the excited-state double proton transfer mechanism and multiple fluorescent characteristics of 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 258:119854. [PMID: 33933943 DOI: 10.1016/j.saa.2021.119854] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2020] [Revised: 02/28/2021] [Accepted: 04/15/2021] [Indexed: 06/12/2023]
Abstract
Recently, Krishnamoorthy and coworkers reported a new type of proton transfer, which was labeled as 'proton transfer triggered proton transfer', in 3,5-bis(2-hydroxypheny)-1H-1,2,4-triazole (bis-HPTA). In this work, the excited-state double proton transfer (ESDPT) mechanism and multiple fluorescent characteristics of bis-HPTA were investigated. Upon photo-excitation, the intramolecular hydrogen bonding strength changed and the electron density of bis-HPTA redistributed. These changes will affect the proton transfer process. In S0 state, the proton transfer processes of bis-HPTA were prohibited on the stepwise and concerted pathways. After vertical excitation to the S1 state, the ESIPT-II process was more likely to occur than the ESIPT-I process, which was contrary to the conclusion that the ESIPT-II process is blocked and the ESIPT-II process takes place after the ESIPT-I process proposed by Krishnamoorthy and coworkers. When the K2 tautomer was formed through the ESIPT-II process, the second proton transfer process on the stepwise pathway was prohibited. On another stepwise pathway, after the ESIPT-I process (form the K1 tautomer), the second proton transfer process should overcome a higher potential barrier than the ESIPT-I process to form ESDPT tautomer. On the concerted pathway, the bis-HPTA can synchronous transfer double protons to form the ESDPT tautomer. The ESDPT tautomer was unstable and immediately converted to the K2 tautomer via a barrierless reverse proton transfer process. Thus, the fluorescent maximum at 465 nm from the ESDPT tautomer reported by Krishnamoorthy and coworkers was ascribed to the K2 tautomer. Most of the fluorophores show dual fluorescent properties, while the bis-HPTA undergoing ESDPT process exhibited three well-separated fluorescent peaks, corresponding to its normal form (438 nm), K1 tautomer (462 nm) and K2 tautomer (450 nm), respectively.
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Affiliation(s)
- Chaozheng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China.
| | - Bo Hu
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yonghua Cao
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
| | - Yongfeng Li
- School of Mechanical and Electrical Engineering, Henan Institute of Science and Technology, Xinxiang 453003, China
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8
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Yu XF, Fu TH, Xiao B, Yu HY, Li Q. A theoretical study on the excited-state deactivation paths for the A-5FU dimer. Phys Chem Chem Phys 2021; 23:16089-16106. [PMID: 34291779 DOI: 10.1039/d1cp00030f] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The photostability of DNA plays a key role in the normal function of organisms. A-5FU is a base pair derivative of the A-T dimer where the methyl group is replaced by a F atom. Here, accurate static TDDFT calculations and non-adiabatic dynamic simulations are used to systematically investigate the excited-state decay paths of the A-5FU dimer related to the proton transfer and the out-of-plane twisting deformation motion of A and 5FU in the 1ππ* and 1nπ* states. CC2 is used to check the accuracy of the current TDDFT calculations. Our results show that the deformation of the C[double bond, length as m-dash]C or C[double bond, length as m-dash]N double bond in A and 5FU provides an efficient pathway for the depopulation of the lowest excited states, which can compete with the excited-state proton transfer paths in the dimer. This finding indicates that monomer-like decay paths could be important for the photostability of weakly hydrogen-bonded DNA base pairs and provide a new insight into the excited-state decay paths in base pairs and their analogues.
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Affiliation(s)
- Xue-Fang Yu
- The Laboratory of Theoretical and Computational Chemistry, School of Chemistry and Chemical Engineering, Yantai University, Yantai 264005, People's Republic of China.
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9
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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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10
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Li C, Tang Z, Zhou P, Guo W. A distinct excited-state proton transfer mechanism for 4-(N-Substituted-amino)-1H-pyrrolo[2,3-b]pyridines in aprotic and protic solvents. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2020; 231:117800. [PMID: 31836400 DOI: 10.1016/j.saa.2019.117800] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 11/14/2019] [Accepted: 11/14/2019] [Indexed: 06/10/2023]
Abstract
Time-dependent density functional theory (TDDFT) method was used to study the different excited states proton transfer mechanism of DPP in cyclohexane (CHE) and Methanol (MeOH). The results indicate that the concerted mechanism and the stepwise mechanism coexist in the double proton transfer process of DPP dimer in the aprotic solvent CHE, the stepwise mechanism predominates. The stepwise mechanism can only carry out single proton transfer (DPP-SPT), the second proton cannot be transferred because it is hindered by high energy barriers. The concerted mechanism produces a double proton transfer (DPP-DPT). The potential energy surface of the DPP dimer was calculated and the double fluorescence phenomenon of DPP dimer observed by Chou et al. (P.T. Chou, Y.I. Liu, H.W. Liu, W.S. Yu, Dual Excitation behavior of double proton transfer versus Charge Transfer in 4-(N-Substituted Amino)-1H-pyrrolo[2,3-b]pyridines tuned by dielectric and hydrogen-bonding perturbation, J. Am. Chem. Soc., 123 (2001) 12119-12120) was explained. In view of the protonic solvent effect of methanol, the potential energy curve of the DPP/MeOH cluster was constructed. The fluorescence quenching process of DPP/MeOH clusters was elucidated. The proton transfer pathways of DPP/MeOH clusters are revealed in two different concerted ways (Type A: protons transfer from DPP molecules to MeOH solvent molecules; Type B: protons transfer from MeOH solvent to DPP molecules). The ESPT process of DPP molecules in the protic solvent MeOH was found to be more prone to Type B. The results can help to better understand the intermolecular hydrogen bonding mechanism of DPP molecules.
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Affiliation(s)
- Changming Li
- School of Electrical Engineering, University of South China, Hengyang 421001, PR China; Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Zhe Tang
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China
| | - Panwang Zhou
- Institute of Molecular Sciences and Engineering, Shandong University, Qingdao 266235, PR China; State Key Lab of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, PR China
| | - Wei Guo
- School of Electrical Engineering, University of South China, Hengyang 421001, PR China.
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Yi J, Fang H. Effect of water on excited‐state double proton transfer in 7‐azaindole‐H
2
O complex: A theoretical study. J PHYS ORG CHEM 2020. [DOI: 10.1002/poc.4060] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Jiacheng Yi
- Department of Chemistry and Material Science, College of ScienceNanjing Forestry University Nanjing China
| | - Hua Fang
- Department of Chemistry and Material Science, College of ScienceNanjing Forestry University Nanjing China
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12
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Stokes ST, Vlk A, Wang Y, Martinez-Martinez C, Zhang X, Bowen KH. Electron-induced proton transfer (EIPT) in 2-hydroxypyridine/2-pyridone tautomeric dimer anions: A photoelectron spectroscopic and density functional theory study. Chem Phys Lett 2019. [DOI: 10.1016/j.cplett.2019.06.066] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Abstract
Hydrogen bonds play a critical role in nucleobase studies as they encode genes, map protein structures, provide stability to the base pairs, and are involved in spontaneous and induced mutations. Proton transfer mechanism is a critical phenomenon that is related to the acid-base characteristics of the nucleobases in Watson-Crick base pairs. The energetic and dynamical behavior of the proton can be depicted from these characteristics and their adjustment to the water molecules or the surrounding ions. Further, new pathways open up in which protonated nucleobases are generated by proton transfer from the ionized water molecules and elimination of a hydroxyl radical in this review, the analysis will be focused on understanding the mechanism of untargeted mutations in canonical, wobble, Hoogsteen pairs, and mutagenic tautomers through the non-covalent interactions. Further, rare tautomer formation through the single proton transfer (SPT) and the double proton transfer (DPT), quantum tunneling in nucleobases, radiation-induced bystander effects, role of water in proton transfer (PT) reactions, PT in anticancer drugs-DNA interaction, displacement and oriental polarization, possible models for mutations in DNA, genome instability, and role of proton transfer using kinetic parameters for RNA will be discussed.
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Mohapatra M, Mishra AK. Excited state proton transfer based fluorescent molecular probes and their application in studying lipid bilayer membranes. Photochem Photobiol Sci 2019; 18:2830-2848. [DOI: 10.1039/c9pp00294d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
The distribution and prototropic equilibria of 1-naphthol (NpOH) in lipid bilayer membrane.
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Affiliation(s)
| | - Ashok Kumar Mishra
- Department of Chemistry
- Indian Institute of Technology Madras
- Chennai 600036
- India
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Concerted-asynchronous reaction path of the excited-state double proton transfer in the 7-azaindole homodimer and 6H-indolo[2,3-b]quinoline/7-azaindole heterodimer. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2017.11.009] [Citation(s) in RCA: 3] [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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16
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Yi J, Fang H. Effect of different alkyl groups on excited-state tautomerization of 7AI-azaindole-H 2O: A theoretical study. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2018; 202:58-64. [PMID: 29777935 DOI: 10.1016/j.saa.2018.05.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2017] [Revised: 04/21/2018] [Accepted: 05/09/2018] [Indexed: 06/08/2023]
Abstract
The effect of substituted alkyl groups at different substituted position on the first excited-state proton transfer of nR7AI-H2O (n = 2-6; R = CH3, C2H5, CF3) complexes were theoretically investigated at the TD-M06-2X/6-31 + G(d, p) level. Here n value denoted the substituted position Cn of R group. The replacement of alkyl R group had no effect on the features of HOMO and LUMO, but influenced the S0 → S1 adiabatic transition energies of the nR7AI-H2O complex. Through computation, we found that the double proton transfer took place in a concerted but asynchronous protolysis pattern regardless of substituted group R and substituted position in the nR7AI-H2O complex. The vibrational-mode specific nature of ESPT was verified. The alkyl group R changed the geometrical parameters of TS, and resulted in enlarging/narrowing the asynchronousity of ESPT. The ESPT barrier height was also affected by the substituted group and position.
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Affiliation(s)
- Jiacheng Yi
- Department of Chemistry and Material Science, College of Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China
| | - Hua Fang
- Department of Chemistry and Material Science, College of Science, Nanjing Forestry University, Nanjing 210037, People's Republic of China.
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Abstract
As one of the most fundamental processes, excited-state proton transfer (ESPT) plays a major role in both chemical and biological systems. In the past several decades, experimental and theoretical studies on ESPT systems have attracted considerable attention because of their tremendous potential in fluorescent probes, biological imaging, white-light-emitting materials, and organic optoelectronic materials. ESPT is related to fluorescence properties and usually occurs on an ultrafast time scale at or below 100 fs. Consequently, steady-state and femtosecond time-resolved absorption, fluorescence, and vibrational spectra have been used to explore the mechanism of ESPT. However, based on previous experimental studies, direct information, such as transition state geometries, energy barrier, and potential energy surface (PES) of the ESPT reaction, is difficult to obtain. These data are important for unravelling the detailed mechanism of ESPT reaction and can be obtained from state-of-the-art ab initio excited-state calculations. In recent years, an increasing number of experimental and theoretical studies on the detailed mechanism of ESPT systems have led to tremendous progress. This Account presents the recent advances in theoretical studies, mainly those from our group. We focus on the cases where the theoretical studies are of great importance and indispensable, such as resolving the debate on the stepwise and concerted mechanism of excited-state double proton transfer (ESDPT), revealing the sensing mechanism of ESPT chemosensors, illustrating the effect of intermolecular hydrogen bonding on the excited-state intramolecular proton transfer (ESIPT) reaction, investigating the fluorescence quenching mechanism of ESPT systems by twisting process, and determining the size of the solute·(solvent) n cluster for the solvent-assisted ESPT reaction. Through calculation of vertical excitation energies, optimization of excited-state geometries, and construction of PES of the ESPT reactions, we provide modifications to experimentally proposed mechanisms or completely new mechanism. Our proposed new and inspirational mechanisms based on theoretical studies can successfully explain the previous experimental results; some of the mechanisms have been further confirmed by experimental studies and provided guidance for researchers to design new ESPT chemosensors. Determination of the energy barrier from an accurate PES is the key to explore the ESPT mechanism with theoretical methods. This approach becomes complicated when the charge transfer state is involved for time-dependent density functional theory (TDDFT) method and optimally tuned range-separated TDDFT provides an alternative way. To unveil the driving force of ESPT reaction, the excited-state molecular dynamics combined with the intrinsic reaction coordinate calculations can be employed. These advanced approaches should be used for further studies on ESPT systems.
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Affiliation(s)
- Panwang Zhou
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning, China
| | - Keli Han
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, Liaoning, China
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18
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Xiao B, Yu XF, Li Q, Cheng J. Photophysical properties and excited state proton transfer in 1,8-Dihydroxydibenzo[a,h]phenazine: A theoretical study. J Photochem Photobiol A Chem 2018. [DOI: 10.1016/j.jphotochem.2017.11.036] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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19
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Yi J, Fang H. Theoretical Study on the Substituent Effect on the Excited-State Proton Transfer in the 7-Azaindole-Water Derivatives. Photochem Photobiol 2017; 94:27-35. [DOI: 10.1111/php.12839] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2017] [Accepted: 08/21/2017] [Indexed: 11/27/2022]
Affiliation(s)
- Jiacheng Yi
- Department of Chemistry and Material Science; College of Science; Nanjing Forestry University; Nanjing Jiangsu China
| | - Hua Fang
- Department of Chemistry and Material Science; College of Science; Nanjing Forestry University; Nanjing Jiangsu China
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20
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Tang Z, Wang Y, Bao D, Lv M, Yang Y, Tian J, Dong L. Theoretical Investigation of an Excited-State Intramolecular Proton-Transfer Mechanism for an Asymmetric Structure of 3,7-Dihydroxy-4-oxo-2-phenyl-4H-chromene-8-carbaldehyde: Single or Double? J Phys Chem A 2017; 121:8807-8814. [DOI: 10.1021/acs.jpca.7b08266] [Citation(s) in RCA: 53] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Zhe Tang
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yi Wang
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Dongshuai Bao
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Meiheng Lv
- State
Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian 116023, China
| | - Yi Yang
- School of Light Industry & Chemical Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Jing Tian
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
| | - Liang Dong
- School
of Biological Engineering, Dalian Polytechnic University, Dalian 116034, China
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21
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Yi J, Fang H. Theoretical investigation on the water-assisted excited-state proton transfer of 7-azaindole derivatives: substituent effect. J Mol Model 2017; 23:312. [DOI: 10.1007/s00894-017-3487-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 09/25/2017] [Indexed: 11/28/2022]
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22
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Insight into the excited-state intramolecular double-proton transfer of the 2,5-bis(benzoxazol-2-yl)thiophene-3,4-diol: one-step or stepwise mechanism? Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2088-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Zilberg S, Dick B. Less stable tautomers form stronger hydrogen bonds: the case of water complexes. Phys Chem Chem Phys 2017; 19:25086-25094. [PMID: 28880041 DOI: 10.1039/c7cp04105e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Hydrogen bonding in cyclic complexes of water with tautomeric pairs of molecules M0 and M1 is calculated to be stronger by more than 25% for the less stable tautomer M1 in all cases where the energy gap between the two tautomers is large (ΔE(M0 − M1) > 10 kcal mol−1).
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Affiliation(s)
- Shmuel Zilberg
- Chemical Sciences Department
- Ariel University
- Ariel 40700
- Israel
| | - Bernhard Dick
- Institute of Physical and Theoretical Chemistry
- University of Regensburg
- 93040 Regensburg
- Germany
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24
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Nowak MJ, Reva I, Rostkowska H, Lapinski L. UV-induced hydrogen-atom transfer and hydrogen-atom detachment in monomeric 7-azaindole isolated in Ar and n-H2 matrices. Phys Chem Chem Phys 2017; 19:11447-11454. [DOI: 10.1039/c7cp01363a] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Upon UV excitation, the N1H form of 7-azaindole isolated in an Ar matrix transforms into N7H, C3H tautomers and the 7-azaindolyl radical; whereas only C3H and 7-azaindolyl radical products are photogenerated in solid H2 environment.
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Affiliation(s)
- Maciej J. Nowak
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Igor Reva
- CQC
- Department of Chemistry
- University of Coimbra
- 3004-535 Coimbra
- Portugal
| | - Hanna Rostkowska
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
| | - Leszek Lapinski
- Institute of Physics
- Polish Academy of Sciences
- 02-668 Warsaw
- Poland
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25
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Li C, Yang Y, Li D, Liu Y. A theoretical study of the potential energy surfaces for the double proton transfer reaction of model DNA base pairs. Phys Chem Chem Phys 2017; 19:4802-4808. [DOI: 10.1039/c6cp07716a] [Citation(s) in RCA: 42] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited-state double proton transfer (ESDPT) mechanism in a model DNA base pair, 7-azaindole (7AI) dimer, has been debated over the years.
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Affiliation(s)
- Chaozheng Li
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yonggang Yang
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Donglin Li
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
| | - Yufang Liu
- College of Physics and Materials Science
- Henan Normal University
- Xinxiang 453007
- China
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26
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Yu XF, Yamazaki S, Taketsugu T. Solvent effects on the excited-state double proton transfer mechanism in the 7-azaindole dimer: a TDDFT study with the polarizable continuum model. Phys Chem Chem Phys 2017; 19:23289-23301. [DOI: 10.1039/c7cp04942k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Solvent effects on the excited-state double proton transfer (ESDPT) mechanism in the 7-azaindole (7AI) dimer were investigated using the time-dependent density functional theory (TDDFT) method.
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Affiliation(s)
- Xue-fang Yu
- The Laboratory of Theoretical and Computational Chemistry
- School of Chemistry and Chemical Engineering
- Yantai University
- Yantai 264005
- China
| | - Shohei Yamazaki
- Department of Frontier Materials Chemistry
- Graduate School of Science and Technology
- Hirosaki University
- Hirosaki 036-8561
- Japan
| | - Tetsuya Taketsugu
- Department of Chemistry
- Faculty of Science
- Hokkaido University
- Sapporo 060-0810
- Japan
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27
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Zilberg S, Dick B. Finding structural principles for strong hydrogen-bonds: Less stable tautomers form dimers with stronger hydrogen bonds. ChemistrySelect 2016. [DOI: 10.1002/slct.201600063] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Shmuel Zilberg
- Chemical Sciences Department; Ariel University; Ariel 40700 Israel
| | - Bernhard Dick
- Institute of Physical and Theoretical Chemistry; University of Regensburg; 93040 Regensburg Germany
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28
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Nagaoka SI, Nitta A, Suemitsu A, Mukai K. Tunneling effect in vitamin E recycling by green tea. RSC Adv 2016. [DOI: 10.1039/c6ra05986d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
A tunneling effect was found to play an important role in vitamin E recycling reactions by catechins contained in green tea.
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Affiliation(s)
- Shin-ichi Nagaoka
- Department of Chemistry
- Faculty of Science and Graduate School of Science and Engineering
- Ehime University
- Matsuyama 790-8577
- Japan
| | - Akiko Nitta
- Department of Chemistry
- Faculty of Science and Graduate School of Science and Engineering
- Ehime University
- Matsuyama 790-8577
- Japan
| | - Ai Suemitsu
- Department of Chemistry
- Faculty of Science and Graduate School of Science and Engineering
- Ehime University
- Matsuyama 790-8577
- Japan
| | - Kazuo Mukai
- Department of Chemistry
- Faculty of Science and Graduate School of Science and Engineering
- Ehime University
- Matsuyama 790-8577
- Japan
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29
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Arulmozhiraja S, Coote ML, Hasegawa JY. Electronic spectra of azaindole and its excited state mixing: A symmetry-adapted cluster configuration interaction study. J Chem Phys 2015; 143:204304. [PMID: 26627956 DOI: 10.1063/1.4935578] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
Abstract
Electronic structures of azaindole were studied using symmetry-adapted cluster configuration interaction theory utilizing Dunning's cc-pVTZ basis set augmented with appropriate Rydberg spd functions on carbon and nitrogen atoms. The results obtained in the present study show good agreement with the available experimental values. Importantly, and contrary to previous theoretical studies, the excitation energy calculated for the important n-π(∗) state agrees well with the experimental value. A recent study by Pratt and co-workers concluded that significant mixing of π-π(∗) and n-π(∗) states leads to major change in the magnitude and direction of the dipole moment of the upper state vibrational level in the 0,0 + 280 cm(-1) band in the S1←S0 transition when compared to that of the zero-point level of the S1 state. The present study, however, shows that all the four lowest lying excited states, (1)Lb π-π(∗), (1)La π-π(∗), n-π(∗), and π-σ(∗), cross each other in one way or another, and hence, significant state mixing between them is likely. The upper state vibrational level in the 0,0 + 280 cm(-1) band in the S1←S0 transition benefits from this four-state mixing and this can explain the change in magnitude and direction of the dipole moment of the S1 excited vibrational level. This multistate mixing, and especially the involvement of π-σ(∗) state in mixing, could also provide a route for hydrogen atom detachment reactions. The electronic spectra of benzimidazole, a closely related system, were also investigated in the present study.
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Affiliation(s)
- Sundaram Arulmozhiraja
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, The Australian National University, Canberra, 2601 ACT, Australia
| | - Michelle L Coote
- ARC Centre of Excellence for Electromaterials Science, Research School of Chemistry, The Australian National University, Canberra, 2601 ACT, Australia
| | - Jun-ya Hasegawa
- Institute for Catalysis, Hokkaido University, Kita 21, Nishi 10, Kita-Ku, Sapporo 001-0021, Japan
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30
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Double-proton transfer mechanism in 1,8-dihydroxydibenzo[a,c]phenazine: a TDDFT and ab initio study. Theor Chem Acc 2015. [DOI: 10.1007/s00214-015-1714-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Crespo-Otero R, Kungwan N, Barbatti M. Stepwise double excited-state proton transfer is not possible in 7-azaindole dimer. Chem Sci 2015; 6:5762-5767. [PMID: 29861905 PMCID: PMC5947511 DOI: 10.1039/c5sc01902h] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2015] [Accepted: 07/06/2015] [Indexed: 11/29/2022] Open
Abstract
Topographical analysis of the dimer's excited state shows that internal conversion after first proton transfer blocks the stepwise process.
The nature of the excited-state double proton transfer in 7-azaindole (7AI) dimer—whether it is stepwise or concerted—has been under a fierce debate for two decades. Based on high-level computational simulations of static and dynamic properties, we show that much of the earlier discussions was induced by inappropriate theoretical modelling, which led to biased conclusions towards one or other mechanism. A proper topographical description of the excited-state potential energy surface of 7AI dimer in the gas phase clearly reveals that the stepwise mechanism is not accessible due to kinetic and thermodynamic reasons. Single proton transfer can occur, but when it does, an energy barrier blocks the transfer of the second proton and the dimer relaxes through internal conversion. Double proton transfer takes place exclusively by an asynchronous concerted mechanism. This case-study illustrates how computational simulations may lead to unphysical interpretation of experimental results.
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Affiliation(s)
- Rachel Crespo-Otero
- School of Biological and Chemical Sciences , Queen Mary University of London , Mile End Road , London E1 4NS , UK .
| | - Nawee Kungwan
- Department of Chemistry , Faculty of Science , Chiang Mai University , Chiang Mai 50200 , Thailand .
| | - Mario Barbatti
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1 , D-45470 , Mülheim an der Ruhr , Germany .
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32
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Wierzchowski J. Excited-state proton transfer and phototautomerism in nucleobase and nucleoside analogs: a mini-review. NUCLEOSIDES NUCLEOTIDES & NUCLEIC ACIDS 2015; 33:626-44. [PMID: 25105453 DOI: 10.1080/15257770.2014.913065] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Abstract
Intermolecular excited-state proton transfer (ESPT) has been observed in several fluorescent nucleobase and/or nucleoside analogs. In the present work, some new examples of ESPT in this class of compounds are presented together with a brief recapitulation of the previously published data. The nucleobases, nucleosides, and their analogs contain many basic and acidic centers and therefore their ESPT behavior may be complex. To interpret the complex data, it is usually necessary to determine the microscopic pK* values for each (or most) of the possible ESPT centers. Typical approach to solve this problem is by analysis of the alkyl derivatives, in which the possibility of the ESPT is reduced. Of particular interest are examples of "phototautomerization via the cation," observed in several systems, which in the neutral media do not undergo ESPT. Protonation of the molecule in the ground state facilitates the two-step phototautomerism in several systems, including formycin A and 2-amino-8-azadenine. Fluorescence of the nucleobase and nucleoside analogs undergoing ESPT is usually solvent-, isotope-, and buffer-ion sensitive, and in some systems the ESPT can be promoted by environmental factors, e.g., the presence of buffer ions. This sensitivity to the microenvironment parameters makes the ESPT systems potentially useful for biological applications.
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Affiliation(s)
- Jacek Wierzchowski
- a Department of Biophysics , University of Varmia & Masuria in Olsztyn , Olsztyn , Poland
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33
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McKenzie RH. A diabatic state model for double proton transfer in hydrogen bonded complexes. J Chem Phys 2014; 141:104314. [DOI: 10.1063/1.4895007] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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34
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Nuclear quantum effect and temperature dependency on the hydrogen-bonded structure of 7-azaindole dimer. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1553-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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35
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Ohyama K, Goto K, Shinmyozu T, Yamamoto N, Iizumi S, Miyagawa M, Nakata M, Sekiya H. Infrared spectroscopic studies on 4-amino-6-oxopyrimidine in a low-temperature Xe matrix and crystalline polymorphs composed of double hydrogen-bonded ribbons. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.01.059] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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36
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Sakota K, Schütz M, Schmies M, Moritz R, Bouchet A, Ikeda T, Kouno Y, Sekiya H, Dopfer O. Weak hydrogen bonding motifs of ethylamino neurotransmitter radical cations in a hydrophobic environment: infrared spectra of tryptamine+–(N2)n clusters (n ≤ 6). Phys Chem Chem Phys 2014; 16:3798-806. [DOI: 10.1039/c3cp54127d] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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37
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Carmona C, García-Fernández E, Hidalgo J, Sánchez-Coronilla A, Balón M. New Insights on the 7-azaindole Photophysics: The Overlooked Role of Its Non Phototautomerizable Hydrogen Bonded Complexes. J Fluoresc 2014; 24:45-55. [DOI: 10.1007/s10895-013-1267-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2013] [Accepted: 07/08/2013] [Indexed: 11/24/2022]
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38
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Shirota H, Fukuda T, Kato T. Solvent Dependence of 7-Azaindole Dimerization. J Phys Chem B 2013; 117:16196-205. [DOI: 10.1021/jp408040s] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Hideaki Shirota
- Department of Nanomaterial Science,
Graduate School of Advanced Integration
Science, ‡Department of Chemistry, Faculty of Science, and §Center for Frontier Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Takao Fukuda
- Department of Nanomaterial Science,
Graduate School of Advanced Integration
Science, ‡Department of Chemistry, Faculty of Science, and §Center for Frontier Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
| | - Tatsuya Kato
- Department of Nanomaterial Science,
Graduate School of Advanced Integration
Science, ‡Department of Chemistry, Faculty of Science, and §Center for Frontier Science, Chiba University, 1-33 Yayoi, Inage-ku, Chiba 263-8522, Japan
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39
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Vetokhina V, Nowacki J, Pietrzak M, Rode MF, Sobolewski AL, Waluk J, Herbich J. 7-Hydroxyquinoline-8-carbaldehydes. 1. Ground- and Excited-State Long-Range Prototropic Tautomerization. J Phys Chem A 2013; 117:9127-46. [DOI: 10.1021/jp403621p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Volha Vetokhina
- Institute of Physical
Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Jacek Nowacki
- Department
of Chemistry, Warsaw University, Pasteura 1, 03-093 Warsaw, Poland
| | - Mariusz Pietrzak
- Institute of Physical
Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Michał F. Rode
- Institute
of Physics, Polish Academy of Sciences, al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Andrzej L. Sobolewski
- Institute
of Physics, Polish Academy of Sciences, al. Lotników 32/46, 02-668 Warsaw, Poland
| | - Jacek Waluk
- Institute of Physical
Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty
of Mathematics
and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
| | - Jerzy Herbich
- Institute of Physical
Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
- Faculty
of Mathematics
and Science, Cardinal Stefan Wyszyński University, Dewajtis 5, 01-815 Warsaw, Poland
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40
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Ishikawa H, Nakano T, Takashima T, Yabuguchi H, Fuke K. Deuteration effect on the NH/ND stretch band of the jet-cooled 7-azaindole and its tautomeric dimers: Relation between the vibrational relaxation and the ground-state double proton-transfer reaction. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2013.02.031] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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41
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Karmakar S, Mukherjee M, Chakraborty T. Excited state tautomerization of 7-azaindole catalyzed by pyrazole. Chem Phys Lett 2013. [DOI: 10.1016/j.cplett.2013.01.037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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42
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Capello MC, Broquier M, Dedonder-Lardeux C, Jouvet C, Pino GA. Fast excited state dynamics in the isolated 7-azaindole-phenol H-bonded complex. J Chem Phys 2013; 138:054304. [DOI: 10.1063/1.4789426] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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43
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Brenlla A, Veiga M, Pérez Lustres JL, Ríos Rodríguez MC, Rodríguez-Prieto F, Mosquera M. Photoinduced Proton and Charge Transfer in 2-(2′-Hydroxyphenyl)imidazo[4,5-b]pyridine. J Phys Chem B 2013; 117:884-96. [DOI: 10.1021/jp311709c] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Alfonso Brenlla
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Manoel Veiga
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - J. Luis Pérez Lustres
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - M. Carmen Ríos Rodríguez
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Flor Rodríguez-Prieto
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
| | - Manuel Mosquera
- Departamento
de Química Física and Centro
Singular de Investigación en Química Biolóxica
e Materiais Moleculares (CIQUS), Universidade de Santiago de Compostela, E-15782 Santiago de Compostela, Spain
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44
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Jana S, Dalapati S, Guchhait N. Functional group induced excited state intramolecular proton transfer process in 4-amino-2-methylsulfanyl-pyrimidine-5-carboxylic acid ethyl ester: a combined spectroscopic and density functional theory study. Photochem Photobiol Sci 2013; 12:1636-48. [DOI: 10.1039/c3pp50010a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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45
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Sakota K, Kouno Y, Harada S, Miyazaki M, Fujii M, Sekiya H. IR spectroscopy of monohydrated tryptamine cation: Rearrangement of the intermolecular hydrogen bond induced by photoionization. J Chem Phys 2012; 137:224311. [DOI: 10.1063/1.4769878] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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46
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Gorski A, Gawinkowski S, Herbich J, Krauss O, Brutschy B, Thummel RP, Waluk J. 1H-pyrrolo[3,2-h]quinoline: a benchmark molecule for reliable calculations of vibrational frequencies, IR intensities, and Raman activities. J Phys Chem A 2012; 116:11973-86. [PMID: 23134592 DOI: 10.1021/jp309618b] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
Reliable assignment of 55 out of 57 vibrational modes has been achieved for 1H-pyrrolo[3,2-h]quinoline using IR, Raman, and fluorescence spectroscopy combined with quantum chemical calculations. The experiments provided a data set for assessing the performance of different models/basis sets for predicting the vibrational frequencies, as well as IR and Raman intensities for a molecule with 13 heavy atoms. Among six different tested DFT functionals, the hybrid B3LYP used with Pople's split-valence basis sets is suggested as the best choice for accurate and cost-effective IR/Raman spectral simulations. Neither HF nor MP2 methods can satisfactorily describe the vibrational structure. Increasing the basis set size from double to triple-ζ and by adding polarization and diffuse functions does not necessarily improve the results, especially regarding the predictions of vibrational frequencies. With respect to the intensities, extending the basis set helps, with the accuracy increasing systematically for the Raman spectra, and in a less regular fashion for the IR. A large difference in accuracy is observed while comparing the spectral parameters predicted for in-plane and out-of-plane normal modes. The former are reliably computed with modest basis sets, whereas for the out-of-plane vibrations, larger basis sets are necessary, but even in this case, the out-of-plane vibrations are reproduced with much less accuracy than in-plane modes. This effect is general, as it has been observed using different functionals and basis sets.
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Affiliation(s)
- Alexandr Gorski
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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Carnerero JM, González-Benjumea A, Carmona C, Balón M. Spectroscopic study of the ground and excited state prototropic equilibria of 4-azaindole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 97:1072-1078. [PMID: 22925984 DOI: 10.1016/j.saa.2012.07.099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2012] [Revised: 07/23/2012] [Accepted: 07/26/2012] [Indexed: 06/01/2023]
Abstract
The ground and singlet excited state prototropism of 4-azaindole, 4AI, in acid and basic aqueous solutions, inside and outside the pH range, has been systematically studied by using absorption and fluorescence spectroscopic techniques. These studies have thrown light on some interesting aspects on the nature and the photophysics of the 4-AI prototropic species. Thus, the changes of the 4AI absorption spectra reveal the existence of four ground state species; the pyridinic protonated cation, C (pK(a)(C)=7.5±0.1), the neutral molecule, N (pK(a)(N)=15.5±0.5), the pyrrolic deprotonated anion, A, and a previously unnoticed dication, DC (pK(a)(DC)=-4.6±0.4). Besides the emissions of these species, a new fluorescence profile appears in alkaline solutions at around 500nm. This extra band has been ascribed to the neutral phototautomer, NT. What is more relevant to this study is the fact that the position and the intensity of the emission band assigned to the monoprotonated cation are very different from those observed for the normal cation of the 7-azaindole, 7-AI. This together with the fact that for the formation of the DC species a cationic precursor with a quinoid structure must be invoked, have prompted us to assign this cationic emission to the isomeric CI cations. Finally, the excited-state pK(a)s of the prototropic species of 4AI have been theoretically estimated by using the Förster-Weller cycle.
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Affiliation(s)
- José M Carnerero
- Departamento de Química Física, Facultad de Farmacia, Universidad de Sevilla, 41012 Sevilla, Spain
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Yu XF, Yamazaki S, Taketsugu T. Theoretical Study on Water-Mediated Excited-State Multiple Proton Transfer in 7-Azaindole: Significance of Hydrogen Bond Rearrangement. J Phys Chem A 2012; 116:10566-73. [DOI: 10.1021/jp308535h] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xue-fang Yu
- Department of Chemistry, Faculty
of Science, Hokkaido University, Sapporo
060-0810, Japan
| | - Shohei Yamazaki
- 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
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Mukherjee M, Karmakar S, Chakraborty T. Excited State Tautomerization of 7-Azaindole in a 1:1 Complex with δ-Valerolactam: A Comparative Study with the Homodimer. J Phys Chem A 2012; 116:9888-96. [DOI: 10.1021/jp306959w] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Moitrayee Mukherjee
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India
| | - Shreetama Karmakar
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India
| | - Tapas Chakraborty
- Department of Physical
Chemistry, Indian Association for the Cultivation of Science, Jadavpur, Calcutta 700032, India
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Vetokhina V, Dobek K, Kijak M, Kamińska II, Muller K, Thiel WR, Waluk J, Herbich J. Three modes of proton transfer in one chromophore: photoinduced tautomerization in 2-(1H-pyrazol-5-yl)pyridines, their dimers and alcohol complexes. Chemphyschem 2012; 13:3661-71. [PMID: 22945637 DOI: 10.1002/cphc.201200602] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2012] [Indexed: 11/07/2022]
Abstract
Studies of 2-(1H-pyrazol-5-yl)pyridine (PPP) and its derivatives 2-(4-methyl-1H-pyrazol-5-yl)pyridine (MPP) and 2-(3-bromo-1H-pyrazol-5-yl)pyridine (BPP) by stationary and time-resolved UV/Vis spectroscopic methods, and quantum chemical computations show that this class of compounds provides a rare example of molecules that exhibit three types of photoreactions: 1) excited-state intramolecular proton transfer (ESIPT) in the syn form of MPP, 2) excited-state intermolecular double-proton transfer (ESDPT) in the dimers of PPP in nonpolar media, as well as 3) solvent-assisted double-proton transfer in hydrogen-bonded 1:1 complexes of PPP and MPP with alcoholic partners. The excited-state processes are manifested by the appearance of a dual luminescence and a bimodal irreversible kinetic coupling of the two fluorescence bands. Ground-state syn-anti equilibria are detected and discussed. The fraction of the higher-energy anti form varies for different derivatives and is strongly dependent on the solvent polarity and hydrogen-bond donor or acceptor abilities.
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Affiliation(s)
- Volha Vetokhina
- Institute of Physical Chemistry, Polish Academy of Sciences, Warsaw, Poland
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