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Datar A, Paithankar H, Deb P, Chugh J, Bagchi S, Mukherjee A, Hazra A. Water-Controlled Keto-Enol Tautomerization of a Prebiotic Nucleobase. J Phys Chem B 2022; 126:5735-5743. [PMID: 35895006 DOI: 10.1021/acs.jpcb.2c02507] [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
Barbituric acid is believed to be a proto-RNA nucleobase that was used for biological information transfer on prebiotic earth before DNA and RNA in their present forms evolved. Nucleobases have various tautomeric forms and the relative stability of these forms is critical to their biological function. It has been shown that barbituric acid has a tri-keto form in the gas phase and an enol form in the solid state. However, its dominant tautomeric form in aqueous medium that is most relevant for biology has been investigated only to a limited extent and the findings are inconclusive. We have used multiple approaches, namely, molecular dynamics, quantum chemistry, NMR, and IR spectroscopy to determine the most stable tautomer of barbituric acid in solution. We find a delicate balance in the stability of the two tautomers, tri-keto and enol, which is tipped toward the enol as the extent of solvation by water increases.
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Affiliation(s)
- Avdhoot Datar
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | | | - Pranab Deb
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
| | | | - Sayan Bagchi
- Physical and Materials Chemistry Division, CSIR-National Chemical Laboratory, Dr. Homi Bhabha Road, Pune 411008, India.,Academy of Scientific and Innovative Research (AcSIR), Ghaziabad 201002, India
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Bassler MC, Rammler T, Wackenhut F, Zur Oven-Krockhaus S, Secic I, Ritz R, Meixner AJ, Brecht M. Accumulation and penetration behavior of hypericin in glioma tumor spheroids studied by fluorescence microscopy and confocal fluorescence lifetime imaging microscopy. Anal Bioanal Chem 2022; 414:4849-4860. [PMID: 35538227 PMCID: PMC9234035 DOI: 10.1007/s00216-022-04107-2] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2022] [Revised: 04/14/2022] [Accepted: 04/28/2022] [Indexed: 12/17/2022]
Abstract
Glioblastoma WHO IV belongs to a group of brain tumors that are still incurable. A promising treatment approach applies photodynamic therapy (PDT) with hypericin as a photosensitizer. To generate a comprehensive understanding of the photosensitizer-tumor interactions, the first part of our study is focused on investigating the distribution and penetration behavior of hypericin in glioma cell spheroids by fluorescence microscopy. In the second part, fluorescence lifetime imaging microscopy (FLIM) was used to correlate fluorescence lifetime (FLT) changes of hypericin to environmental effects inside the spheroids. In this context, 3D tumor spheroids are an excellent model system since they consider 3D cell-cell interactions and the extracellular matrix is similar to tumors in vivo. Our analytical approach considers hypericin as probe molecule for FLIM and as photosensitizer for PDT at the same time, making it possible to directly draw conclusions of the state and location of the drug in a biological system. The knowledge of both state and location of hypericin makes a fundamental understanding of the impact of hypericin PDT in brain tumors possible. Following different incubation conditions, the hypericin distribution in peripheral and central cryosections of the spheroids were analyzed. Both fluorescence microscopy and FLIM revealed a hypericin gradient towards the spheroid core for short incubation periods or small concentrations. On the other hand, a homogeneous hypericin distribution is observed for long incubation times and high concentrations. Especially, the observed FLT change is crucial for the PDT efficiency, since the triplet yield, and hence the O2 activation, is directly proportional to the FLT. Based on the FLT increase inside spheroids, an incubation time > 30 min is required to achieve most suitable conditions for an effective PDT.
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Affiliation(s)
- Miriam C Bassler
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany.,Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Tim Rammler
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Frank Wackenhut
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany.
| | - Sven Zur Oven-Krockhaus
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Ivona Secic
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany
| | - Rainer Ritz
- Department of Neurosurgery, Schwarzwald-Baar Clinic, Klinikstr. 11, 78052, Villingen-Schwenningen, Germany
| | - Alfred J Meixner
- Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany
| | - Marc Brecht
- Process Analysis and Technology (PA&T), Reutlingen University, Alteburgstr. 150, 72762, Reutlingen, Germany. .,Institute of Physical and Theoretical Chemistry, University of Tübingen, Auf der Morgenstelle 18, 72076, Tübingen, Germany.
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Thymine dissociation and dimer formation: A Raman and synchronous fluorescence spectroscopic study. Proc Natl Acad Sci U S A 2021; 118:2025263118. [PMID: 33526704 PMCID: PMC8017689 DOI: 10.1073/pnas.2025263118] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Abstract
In this study, absorption, fluorescence, synchronous fluorescence, and Raman spectra of nonirradiated and ultraviolet (UV)-irradiated thymine solutions were recorded in order to detect thymine dimer formation. The thymine dimer formation, as a function of irradiation dose, was determined by Raman spectroscopy. In addition, the formation of a mutagenic (6-4) photoproduct was identified by its synchronous fluorescence spectrum. Our spectroscopic data suggest that the rate of conversion of thymine to thymine dimer decreases after 20 min of UV irradiation, owing to the formation of an equilibrium between the thymine dimers and monomers. However, the formation of the (6-4) photoproduct continued to increase with UV irradiation. In addition, the Raman spectra of nonirradiated and irradiated calf thymus DNA were recorded, and the formation of thymine dimers was detected. The spectroscopic data presented make it possible to determine the mechanism of thymine dimer formation, which is known to be responsible for the inhibition of DNA replication that causes bacteria inactivation.
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He Y, Buch A, Morisson M, Szopa C, Freissinet C, Williams A, Millan M, Guzman M, Navarro-Gonzalez R, Bonnet J, Coscia D, Eigenbrode J, Malespin C, Mahaffy P, Glavin D, Dworkin J, Lu P, Johnson S. Application of TMAH thermochemolysis to the detection of nucleobases: Application to the MOMA and SAM space experiment. Talanta 2019; 204:802-811. [DOI: 10.1016/j.talanta.2019.06.076] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2019] [Revised: 06/16/2019] [Accepted: 06/19/2019] [Indexed: 10/26/2022]
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Ostakhov SS, Ovchinnikov MY, Masyagutova GA, Khursan SL. Luminescent and DFT Study of Keto-Enol Tautomers of 5-Fluorouracil and Its Derivatives in Aqueous Solutions. J Phys Chem A 2019; 123:7956-7964. [PMID: 31442039 DOI: 10.1021/acs.jpca.9b04701] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Fluorescence (FL) spectra were recorded and identified for the following 5-fluorouracil (FU) tautomers: 5-fluoropyrimidine-2,4(1H,3H)-dione (A), 5-fluoro-2-hydroxypyrimidine-4(3H)-one (B), and 5-fluoro-4-hydroxypyrimidine-2(1H)-one (D), as well as the corresponding tautomers A and D of 1-(tetrahydrofuranyl-2)-5-fluorouracil and 1-methyl-5-fluorouracil, tautomers A and B of 3-methyl-5-fluorouracil, and the diketo tautomer of 1,3-dimethyl-5-fluorouracil. It was shown that the FL of rare tautomers of FU derivatives occurs by the excitation of uracil homoassociates followed by intramolecular proton transfer (IPT), formation of a pair of rare tautomers, and radiative deactivation of one of them. The FL quantum yields φi were estimated. In the case of rare tautomers, the φi value includes the probability of IPT in the homoassociate, and density functional theory calculations in the TPSSTPSS/6-311+G(d,p) approximation were used to determine the relative energies of tautomers, associated FU forms, and their spectral properties that agree with the observed luminescence pattern.
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Affiliation(s)
- S S Ostakhov
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - M Yu Ovchinnikov
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - G A Masyagutova
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
| | - S L Khursan
- Ufa Institute of Chemistry , Ufa Federal Research Centre of the Russian Academy of Sciences , 71 Prospect Oktyabrya , 450054 Ufa , Russian Federation
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Li D, Han Y, Li H, Zhang P, Kang Q, Li Z, Shen D. The influence of isolated and penta-hydrated Zn 2+ on some of the intramolecular proton-transfer processes of thymine: a quantum chemical study. RSC Adv 2018; 8:11021-11026. [PMID: 35541537 PMCID: PMC9078977 DOI: 10.1039/c7ra13750h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2017] [Accepted: 02/27/2018] [Indexed: 02/02/2023] Open
Abstract
Zinc cation (Zn2+) plays an important role in the chemistry of DNA base pairs. In this work, the influence of isolated and penta-hydrated Zn2+ on some of the intramolecular proton-transfer processes of thymine (T) is investigated by the density functional theory method. It is shown that the calculated binding energies between Zn2+ and T are exothermic in vacuum. Compared to T, Zn2+ increases the stability of tautomer T' by 28.7 kcal mol-1, promoting the intramolecular proton transfer of T. But in a micro-water environment, the attachment processes of Zn2+ to T hydrates, penta-hydrated Zn2+ to T, and penta-hydrated Zn2+ to T hydrates lead to the rearrangement of molecules and the redistribution of charges. The conventional T is still the most stable form and the influence of Zn2+ is much reduced and the proton transfer is thermodynamically unfavored. The detailed characterization is helpful to understand the genotoxicity of zinc ions.
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Affiliation(s)
- Dejie Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Ying Han
- National Engineering Research Center for Colloidal Materials, School of Chemistry and Chemical Engineering, Shandong University Jinan 250100 P. R. China
| | - Huijuan Li
- College of Chemical and Environmental Engineering, Shandong University of Science and Technology Qingdao 266590 P. R. China
| | - Ping Zhang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Qi Kang
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Zhihua Li
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
| | - Dazhong Shen
- College of Chemistry, Chemical Engineering and Materials Science, Collaborative Innovation Center of Functionalized Probes for Chemical Imaging in Universities of Shandong, Key Laboratory of Molecular and Nano Probes, Ministry of Education, Shandong Provincial Key Laboratory of Clean Production of Fine Chemicals, Shandong Normal University Jinan 250014 P. R. China
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7
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Bilkan MT, Şahin O, Yurdakul Ş. Experimental and DFT studies of solvent effects on molecular structure and physical properties of Dipyridylamine pyridine based ligand. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.11.078] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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8
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Ostakhov SS, Sultanbaev MV, Ovchinnikov MY, Kayumov RR, Khursan SL. Spectral-luminescence and quantum-chemical study of the anionic forms of 5-fluorouracil. HIGH ENERGY CHEMISTRY 2017. [DOI: 10.1134/s0018143917010076] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ten GN, Glukhova OE, Slepchenkov MM, Shcherbakova NE, Baranov VI. A theoretical and optical spectroscopic study of the mechanism of a tautomeric transformation in the 7-azaindole dimer and the 7-azaindole complex with a water molecule. J STRUCT CHEM+ 2017. [DOI: 10.1134/s0022476617020020] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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10
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Pandey M, Muthu S, Nanje Gowda N. Quantum mechanical and spectroscopic (FT-IR, FT-Raman,1H,13C NMR, UV-Vis) studies, NBO, NLO, HOMO, LUMO and Fukui function analysis of 5-Methoxy-1H-benzo[d]imidazole-2(3H)-thione by DFT studies. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.10.064] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Mohammadi M, Ramazani S. Theoretical kinetics study of thymine tautomerism and interaction of Na+ with its tautomers. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1232845] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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12
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Ribot JC, Chatterjee A, Nagpal P. Measurements of single nucleotide electronic states as nanoelectronic fingerprints for identification of DNA nucleobases, their protonated and unprotonated states, isomers, and tautomers. J Phys Chem B 2015; 119:4968-74. [PMID: 25793310 DOI: 10.1021/acs.jpcb.5b01403] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Several nanoelectronic techniques have been explored to distinguish the sequence of nucleic acids in DNA macromolecules. Identification of unique electronic signatures using nanopore conductance, tunneling spectroscopy, or other nanoelectronic techniques depends on electronic states of the DNA nucleotides. While several experimental and computational studies have focused on interaction of nucleobases with different substrates, the effect of nucleic acid biochemistry on its electronic properties has been largely unexplored. Here, we present correlated measurements of frontier molecular orbitals and higher-order electronic states for four DNA nucleobases (adenine, cytosine, thymine, and guanine), and first-principle quantum chemical density functional theoretical (DFT) computations. Using different pH conditions in our experiments, we show that small changes in the biochemical state of these nucleic acids strongly affect the intrinsic electronic structure, measured using scanning tunneling spectroscopy (STS). In our experimental measurements and computations, significant differences were observed between the position of frontier orbitals and higher-energy states between protonated and unprotonated nucleic acids, isomers, and different keto-enol tautomer's formed in these nucleotides, leading to their facile identification. Furthermore, we show unique "electronic fingerprints" for all nucleotides (A, G, T, C) using STS, with most distinct states identified at acidic pH. These results can have important implications for identification of nucleic acid sequences in DNA molecules using a high-throughput nanoelectronic identification technique.
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Affiliation(s)
- Josep Casamada Ribot
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
| | - Anushree Chatterjee
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
| | - Prashant Nagpal
- †Department of Chemical and Biological Engineering, ‡Renewable and Sustainable Energy Institute, §BioFrontiers Institute, and ∥Materials Science and Engineering, University of Colorado, Boulder, Colorado, 80309, United States
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Stasyuk OA, Szatylowicz H, Krygowski TM. Tautomerisation of thymine acts against the Hückel 4N + 2 rule. The effect of metal ions and H-bond complexations on the electronic structure of thymine. Org Biomol Chem 2014; 12:6476-83. [DOI: 10.1039/c4ob00964a] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Not necessarily the π-electron delocalization is responsible for the stability of thymine tautomers.
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Affiliation(s)
- Olga A. Stasyuk
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
| | - Halina Szatylowicz
- Faculty of Chemistry
- Warsaw University of Technology
- 00-664 Warsaw, Poland
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14
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ZHAO YUAN, CAO ZEXING. ABSORPTION SPECTRA OF NUCLEIC ACID BASES IN WATER ENVIRONMENT: INSIGHTS INTO FROM COMBINED QM/MM AND CLUSTER-CONTINUUM MODEL CALCULATIONS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2013. [DOI: 10.1142/s0219633613410137] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electronic spectra of uracil, thymine, adenine, guanine, and cytosine in the gas phase and aqueous solution have been studied by extensive time-dependent density functional calculations. Calculations show that the Quantum mechanics/molecular mechanics (QM/MM) geometry optimization based on the molecular dynamics (MD) equilibrated configuration can locate an optimal solvated cluster for the base solvation, and the combined QM/MM and cluster-continuum computational protocol is capable of handling the solvent effect on the excited states of nucleic acid bases and providing realistic absorption spectra in water environment with relatively low computational costs. Generally, the vertical excitation energies in aqueous solution by PCM/TD-X3LYP calculations show excellent agreement with the experimental observations and the maximum deviation is less than 0.2 eV. The present results reveal that the hydrogen bond network around the excited-state base and its dipole moment change may remarkably modify the absorption spectra of nucleic acid bases in aqueous solution.
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Affiliation(s)
- YUAN ZHAO
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
| | - ZEXING CAO
- State Key Laboratory of Physical Chemistry of Solid Surfaces and Fujian Provincial Key Laboratory of Theoretical and Computational Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen 360015, P. R. China
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Comparison of gas phase intrinsic properties of cytosine and thymine nucleobases with their O-alkyl adducts: different hydrogen bonding preferences for thymine versus O-alkyl thymine. J Mol Model 2013; 19:2993-3005. [DOI: 10.1007/s00894-013-1813-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2012] [Accepted: 03/03/2013] [Indexed: 12/11/2022]
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Shukla MK, Leszczynski J. Tautomerism in nucleic acid bases and base pairs: a brief overview. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1145] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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17
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Optimization of Environmentally Benign Polymers Based on Thymine and Polyvinyl Sulfonate Using Plackett-Burman Design and Surface Response. J CHEM-NY 2013. [DOI: 10.1155/2013/947137] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Traditional approaches to the development of integrated circuits involve the use and/or manufacture of toxic materials that have a potential environmental impact. An extensive research has been done to design environmentally benign synthetic polymers containing nucleic acid bases, which can be used to enhance the photoresistor technologies. Water soluble, environmentally benign photopolymers of 1-(4-vinylbenzyl) thymine (VBT) and vinylphenyl sufonate (VPS) undergo a photodimerization reaction when exposed to low levels of ultraviolet irradiation leading to an immobilization of the copolymer on a variety of substrates. Plackett-Burman design (PBD) and central composite design (CCD) were applied to identify the significant factors influencing the polymer crosslinking and dye adsorption processes, which are relevant in the fabrication of copolymer films for potential photoresist use. The PBD results assigned a maximum absorption signal of 0.67, while optimal conditions obtained in this experiment following the CCD method predictions provided a response of 0.83 ± 0.03, being a solid foundation for further use of this methodology in the production of potential photoresistors. The pH effect was relevant for low concentrations but not significant for higher concentrations. To the best of our knowledge, this was the first report applying statistical experimental designs to optimize the crosslinking of thymine-based polymers.
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Yurdakul S, Badoğlu S. FT-IR and FT-Raman spectroscopic and DFT theoretical studies on 4-azabenzimidazole. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2012; 89:252-258. [PMID: 22265951 DOI: 10.1016/j.saa.2011.12.073] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2011] [Revised: 12/09/2011] [Accepted: 12/28/2011] [Indexed: 05/31/2023]
Abstract
The Becke, three-parameter, Lee-Yang-Parr exchange-correlation functional have been used to study the geometry, relative energy, frequency and intensity of the vibrational bands of the 4-azabenzimidazole (4AB) tautomers and the most stable tautomer's homodimers. FT-IR and Raman spectra of the 4AB have been measured in the regions 4000-100 cm(-1) and 3500-100 cm(-1), respectively for the first time. The stability of 4AB tautomers were reported. All vibrational frequencies assigned in detail with the help of total energy distribution (TED) and isotopic shifts. The energy and atomic charges were discussed. NH⋯N type intermolecular hydrogen bonding interactions were suggested for 4AB dimeric forms. 1H and 13C NMR properties have been calculated for the most stable two tautomeric forms using the gauge independent atomic orbital (GIAO) method.
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Affiliation(s)
- Senay Yurdakul
- Department of Physics, Faculty of Science, Gazi University, Teknikokullar, 06500 Ankara, Turkey.
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Burova TG, Ermolenkov VV, Ten GN, Shcherbakov RS, Baranov VI, Lednev IK. Raman Spectroscopic Study of the Tautomeric Composition of Adenine in Water. J Phys Chem A 2011; 115:10600-9. [DOI: 10.1021/jp2033033] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tatiana G. Burova
- Saratov State University, 83 Astrakhanskaya Street, Saratov, 410026, Russia
| | - Vladimir V. Ermolenkov
- University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
| | - Galina N. Ten
- Saratov State University, 83 Astrakhanskaya Street, Saratov, 410026, Russia
| | | | - Victor I. Baranov
- Vernadsky Institute of Geochemistry and Analytical Chemistry, Russian Academy of Sciences, 19 Kosygin Street, Moscow, 119991, Russia
| | - Igor K. Lednev
- University at Albany, State University of New York, 1400 Washington Avenue, Albany, New York 12222, United States
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Chen J, Ai H, Zhao Y, Liu J. A theoretical prediction on the ground-state complexes bound by metal ions to thymine base isomers. J PHYS ORG CHEM 2011. [DOI: 10.1002/poc.1881] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Affiliation(s)
- Jinpeng Chen
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Hongqi Ai
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Yongping Zhao
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
| | - Jingjing Liu
- Shandong Provincial Key Laboratory of Fluorine Chemistry and Chemical Materials, School of Chemistry and Chemical Engineering; University of Jinan; Jinan City 250022 China
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Ostakhov SS, Gantsev SK, Kazakov VP, Sultanbaev MV, Khamitova GV, Ishmuratova RS. Fluorescence of 5-fluorouracil upon the transition from the second singlet excited state S 2 to the ground state. HIGH ENERGY CHEMISTRY 2011. [DOI: 10.1134/s0018143911020111] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Sultanbaev MV, Ostakhov SS, Gantsev SK, Khalilullin FA, Kazakov VP. Fluorescent study of the keto-enol equilibrium of 5-fluorouracil tautomers in aqueous solutions. HIGH ENERGY CHEMISTRY 2010. [DOI: 10.1134/s001814391005005x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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23
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Ko YJ, Wang H, Radisic D, Stokes ST, Eustis SN, Bowen KH, Mazurkiewicz K, Storoniak P, Kowalczyk A, Haranczyk M, Gutowski M, Rak J. Barrier-free proton transfer induced by electron attachment to the complexes between 1‐methylcytosine and formic acid. Mol Phys 2010. [DOI: 10.1080/00268976.2010.515623] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Yeon Jae Ko
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Haopeng Wang
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Dunja Radisic
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Sarah T. Stokes
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Soren N. Eustis
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Kit H. Bowen
- a Department of Chemistry , Johns Hopkins University , Baltimore , MD 21218 , USA
| | - Kamil Mazurkiewicz
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Piotr Storoniak
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Arkadiusz Kowalczyk
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
| | - Maciej Haranczyk
- c Computational Research Division, Lawrence Berkeley National Laboratory , Berkeley , CA 94720 , USA
| | - Maciej Gutowski
- d Chemistry-School of Engineering and Physical Sciencs, Heriot-Watt University , Edinburgh EH14 4AS , UK
| | - Janusz Rak
- b Department of Chemistry , University of Gdańsk , Sobieskiego 18 , 80-952 Gdańsk , Poland
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24
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Systematic theoretical investigations on the tautomers of thymine in gas phase and solution. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.047] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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25
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Alcolea Palafox M, Iza N. Tautomerism of the natural thymidine nucleoside and the antiviral analogue D4T. Structure and influence of an aqueous environment using MP2 and DFT methods. Phys Chem Chem Phys 2010; 12:881-93. [DOI: 10.1039/b915566j] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
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26
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FT-IR spectra, vibrational assignments, and density functional calculations of imidazo[1,2-a]pyridine molecule and its Zn(II) halide complexes. Struct Chem 2009. [DOI: 10.1007/s11224-009-9433-0] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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27
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Palafox MA, Iza N, Fuente MDL, Navarro R. Simulation of the First Hydration Shell of Nucleosides D4T and Thymidine: Structures Obtained Using MP2 and DFT Methods. J Phys Chem B 2009; 113:2458-76. [DOI: 10.1021/jp806684v] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- M. Alcolea Palafox
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - N. Iza
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - M. de la Fuente
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
| | - R. Navarro
- Departamento de Química-Física I, Facultad de Ciencias Químicas, Universidad Complutense, Ciudad Universitaria, Madrid-28040, Spain, and Departamento de Ciencias y Técnicas Fisicoquímicas, Universidad Nacional de Educación a Distancia (UNED), c/ Senda del Rey s/n, Madrid-28040, Spain
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28
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Abstract
The structures and the relative energies of six possible tautomers of the thymine base have been studied by density functional theory (DFT) using the B3LYP and BP86 functionals. The keto-thymine (T1) is predicted to be the most stable thymine tautomer, which is consistent with the other theoretical results and experimental data. The corresponding thymine cations and anions are studied using the same level of theory with double-ζ plus polarization and diffuse functions (DZP++) basis sets. The ionization potentials (IPs), the electron affinities (EAs), and proton affinities (PAs) for different protonation sites in thymine base are obtained. T1 has the largest ionization potential and the lowest proton affinity among all the considered thymine tautomers.
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Affiliation(s)
- Dongsheng Jiao
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Hongyan Wang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yanlan Zhang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
| | - Yu Tang
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, P.R. China
- College of Sciences, Southwest Jiaotong University, Chengdu 610031, P.R. China
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29
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Ten GN, Baranov VI. Calculation and analysis of lifetimes of thymine and 5-chlorouracil tautomers in aqueous solutions at different pH values. J STRUCT CHEM+ 2009. [DOI: 10.1007/s10947-009-0011-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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30
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González-Vázquez J, González L, Samoylova E, Schultz T. Thymine relaxation after UV irradiation: the role of tautomerization and πσ* states. Phys Chem Chem Phys 2009; 11:3927-34. [DOI: 10.1039/b815602f] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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31
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Cysewski P, Kozłowska K, Szefler B. Accurate micro- and macro- gas phase basicities of hydroxyl-radical-modified pyrimidines estimated by advanced quantum chemistry methods. J Mol Model 2008; 15:711-22. [PMID: 19089468 DOI: 10.1007/s00894-008-0423-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2008] [Accepted: 11/18/2008] [Indexed: 12/01/2022]
Abstract
The gas phase basicities (GPB) of 16 hydroxyl-radical-derived analogues of model pyrimidine nucleosides were analysed at B3LYP/aug-cc-pVDZ and G3MP2B3 levels of theory. All possible tautomeric equilibriums of neutral and protonated forms of pyrimidine analogues were taken into account. The oxidation of pyrimidines usually reduces the GPB values with respect to canonical values. The only exception was observed in the case of 5,6-dihydroxycytidine, which is more basic than model cytidine if both macro- and micro-scopic measures of basicities are used for comparison. In addition, 6-hydroxycytidine is characterised more by the basic character of the O2 atom compared to the more basic centre of cytidine, despite the fact that the GPB values of both these compounds are almost identical. Although the B3LYP/aug-cc-pVDZ approach seems to be an accurate and robust method for GPB estimation, the microscopic protonation properties are much more sensitive to this method since the difference in energy between some tautomers is often less than 1 kcal/mol with method-dependent succession. In such cases, G3MP2B3 is recommended.
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Affiliation(s)
- Piotr Cysewski
- Department of Physical Chemistry, Collegium Medicum, Nicolaus Copernicus University, Kurpińskiego 5, 85-950 Bydgoszcz, Poland.
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32
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Haug A, Schweizer S, Latteyer F, Casu MB, Peisert H, Ochsenfeld C, Chassé T. Thin-Film Properties of DNA and RNA Bases: A Combined Experimental and Theoretical Study. Chemphyschem 2008; 9:740-7. [DOI: 10.1002/cphc.200700667] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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33
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Kwok WM, Ma C, Phillips DL. A doorway state leads to photostability or triplet photodamage in thymine DNA. J Am Chem Soc 2008; 130:5131-9. [PMID: 18335986 DOI: 10.1021/ja077831q] [Citation(s) in RCA: 158] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ultraviolet irradiation of DNA produces electronic excited states that predominantly eliminate the excitation energy by returning to the ground state (photostability) or following minor pathways into mutagenic photoproducts (photodamage). The cyclobutane pyrimidine dimer (CPD) formed from photodimerization of thymines in DNA is the most common form of photodamage. The underlying molecular processes governing photostability and photodamage of thymine-constituted DNA remain unclear. Here, a combined femtosecond broadband time-resolved fluorescence and transient absorption spectroscopies were employed to study a monomer thymidine and a single-stranded thymine oligonucleotide. We show that the protecting deactivation of a thymine multimer is due to an ultrafast single-base localized stepwise mechanism where the initial excited state decays via a doorway state to the ground state or proceeds via the doorway state to a triplet state identified as a major precursor for CPD photodamage. These results provide new mechanistic characterization of and a dynamic link between the photoexcitation of DNA and DNA photostability and photodamage.
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Affiliation(s)
- Wai-Ming Kwok
- Department of Applied Biology and Chemical Technology, The Hong Kong Polytechnic University, Hung Hom, Kowloon, Hong Kong, China.
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34
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Shukla MK, Leszczynski J. Electronic Spectra, Excited State Structures and Interactions of Nucleic Acid Bases and Base Assemblies: A Review. J Biomol Struct Dyn 2007; 25:93-118. [PMID: 17676942 DOI: 10.1080/07391102.2007.10507159] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
A comprehensive review of recent theoretical and experimental advances in the singlet electronic transitions, excited state structures and dynamics of nucleic acid bases (NABs) and base assemblies are presented. It is well known that NABs absorb ultraviolet radiation, but the absorbed energy is efficiently dissipated in the form of ultrafast internal conversion processes believed to occur in the subpicosecond time scale and, therefore, enabling NABs highly photostable. It is not known how much evolutionary role was played in evolving these molecules and the ultimate selection by nature as genetic materials, but it is well accepted that survival-of-fittest prevails. Recently, significant efforts have been continuously paid to understand the mechanism of electronic excitation deactivation, but universally acceptable mechanism is still elusive. However, recent investigations reveal that electronic excited state geometries of DNA bases are usually nonplanar and this structural nonplanarity may facilitate nonradiative deactivation. Investigation of excited state structures is challenging and, therefore, it is not surprising that despite the impressive theoretical and computational advances, this research area is still hampered by the methodological and computational limitations. Further, stacking has significant influence on the emission properties of molecules. The 2-aminopurine, a fluorescent adenine derivative frequently used in studying DNA dynamics, shows significant attenuations in fluorescence quantum yield when incorporated in the DNA. Theoretical and computational bottlenecks limit a thorough theoretical understanding of effect of stacking interactions on the excited state dynamics of NABs. Despite these limitations the investigations of excited state properties are progressing in the right direction and our better understanding of excited state structure and dynamics of NABs and nucleic acids may help to design preventive strategy for radiation induced illness and photostable materials.
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Affiliation(s)
- M K Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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35
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Ito T, Shinohara H, Nishimoto S. Conformational Effects on Photophysical Characteristics of C5-C5′-linked Dihydrothymine Dimers in Solution¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2000)0720719ceopco2.0.co2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Mazurkiewicz K, Bachorz RA, Gutowski M, Rak J. On the Unusual Stability of Valence Anions of Thymine Based on Very Rare Tautomers: A Computational Study. J Phys Chem B 2006; 110:24696-707. [PMID: 17134233 DOI: 10.1021/jp065666f] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
We characterized anionic states of thymine using various electronic structure methods, with the most accurate results obtained at the CCSD(T)/aug-cc-pVDZ level of theory followed by extrapolations to complete basis set limits. We found that the most stable anion in the gas phase is related to an imino-oxo tautomer, in which the N1H proton is transferred to the C5 atom. This valence anion, aT(c5)(nl), is characterized by an electron vertical detachment energy (VDE) of 1251 meV and it is adiabatically stable with respect to the canonical neutral nT(can) by 2.4 kcal/mol. It is also more stable than the dipole-bound (aT(dbs)(can)), and valence anion aT(val)(can) of the canonical tautomer. The VDE values for aT(dbs)(can)and T(val)(can) are 55 and 457 meV, respectively. Another, anionic, low-lying imino-oxo tautomer with a VDE of 2458 meV has a proton transferred from N3H to C5 aT(c5)(n3). It is less stable than aT(val)(can) by 3.3 kcal/mol. The mechanism of formation of anionic tautomers with the carbons C5 or C6 protonated may involve intermolecular proton transfer or dissociative electron attachment to the canonical neutral tautomer followed by a barrier-free attachment of a hydrogen atom to C5. The six-member ring structure of the anionic tautomers with carbon atoms protonated is unstable upon an excess electron detachment. Within the PCM hydration model, the low-lying valence anions become adiabatically bound with respect to the canonical neutral; becomes the most stable, being followed by aT(c5)(nl), aT(c5)(n3), aT(can), and aT(c5)(nl).
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Affiliation(s)
- Kamil Mazurkiewicz
- Faculty of Chemistry, University of Gdańsk, Sobieskiego 18, 80-952 Gdańsk, Poland
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37
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Hare PM, Crespo-Hernández CE, Kohler B. Solvent-Dependent Photophysics of 1-Cyclohexyluracil: Ultrafast Branching in the Initial Bright State Leads Nonradiatively to the Electronic Ground State and a Long-Lived1nπ* State. J Phys Chem B 2006; 110:18641-50. [PMID: 16970494 DOI: 10.1021/jp064714t] [Citation(s) in RCA: 101] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The modified nucleic acid base, 1-cyclohexyluracil, was studied by femtosecond transient absorption spectroscopy in protic and aprotic solvents of varying polarity. UV excitation at 267 nm populates the lowest-energy bright state, a (1)pipi* state, which has a lifetime of 120-270 fs, depending on the solvent. In all solvents, this initial bright state population bifurcates with approximately 60% undergoing subpicosecond nonradiative decay to the electronic ground state and the remaining population branching to a singlet dark state. The latter absorbs between 340 and 450 nm. The latter state is assigned to the lowest-energy (1)npi* state. It decays to the electronic ground state with a lifetime that varies from 26 ps in water to at least several nanoseconds in aprotic solvents. The results suggest that the two nonradiative decay pathways identified for photoexcited uracil in recent quantum chemical calculations (Matsika, S. J. Phys. Chem. A. 2004, 108, 7584) are simultaneously operative in a wide variety of solvent environments. The lowest-energy triplet state was also detected by transient absorption. The triplet population appears in a few picoseconds and is not formed from the thermalized (1)npi* state. It is suggested that high spin-orbit coupling is found only along initial segments of the nonradiative decay pathways. Efficient intersystem crossing prior to vibrational cooling offers a possible explanation for the wavelength-dependent triplet yields seen in single DNA bases.
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Affiliation(s)
- Patrick M Hare
- Department of Chemistry, The Ohio State University, 100 West 18th Avenue, Columbus, OH 43210, USA
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38
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Close DM, Crespo-Hernandez CE, Gorb L, Leszczynski J. Influence of Microhydration on the Ionization Energy Thresholds of Thymine: Comparisons of Theoretical Calculations with Experimental Values. J Phys Chem A 2006; 110:7485-90. [PMID: 16759139 DOI: 10.1021/jp061064k] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In the present study the ionization energy thresholds (IETs) of thymine, and thymine keto-enol tautomers, have been calculated (with the B3LYP, and P3 levels of theory using the standard 6-31++G(d,p) basis set) with 1-3 water molecules placed in the first hydration shell. Calculations show there is a distinct effect of microhydration on the IET of thymine. The first water molecule is seen to decrease the IET by about 0.1 eV, whereas the second and third water molecules cause a further decrease of less than 0.1 eV each. The changes in IET calculated here for thymine with 1-3 waters of hydration are smaller than the experimental values determined by Kim et al. (J. Phys. Chem. 1996, 100, 7933). Therefore calculations have been performed on the microhydrated keto-enol tautomers of thymine. The calculated results on the keto-enol tautomers are seen to be in better agreement with the experimental results. However, the keto-enol thymine tautomers are considerably higher in energy than the canonical form of thymine, and there is presently no good evidence that these thymine tautomers are actually present in a supersonic jet-cooled experiment.
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Affiliation(s)
- David M Close
- Department of Physics, Box 70652, East Tennessee State University, Johnson City, Tennessee 37614, USA.
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39
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DFT Study of Water-Assisted Intramolecular Proton Transfer in the Tautomers of Thymine Radical Cation. B KOREAN CHEM SOC 2006. [DOI: 10.5012/bkcs.2006.27.7.1009] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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40
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Gustavsson T, Bányász A, Lazzarotto E, Markovitsi D, Scalmani G, Frisch MJ, Barone V, Improta R. Singlet Excited-State Behavior of Uracil and Thymine in Aqueous Solution: A Combined Experimental and Computational Study of 11 Uracil Derivatives. J Am Chem Soc 2006; 128:607-19. [PMID: 16402849 DOI: 10.1021/ja056181s] [Citation(s) in RCA: 306] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The excited-state properties of uracil, thymine, and nine other derivatives of uracil have been studied by steady-state and time-resolved spectroscopy. The excited-state lifetimes were measured using femtosecond fluorescence upconversion in the UV. The absorption and emission spectra of five representative compounds have been computed at the TD-DFT level, using the PBE0 exchange-correlation functional for ground- and excited-state geometry optimization and the Polarizable Continuum Model (PCM) to simulate the aqueous solution. The calculated spectra are in good agreement with the experimental ones. Experiments show that the excited-state lifetimes of all the compounds examined are dominated by an ultrafast (<100 fs) component. Only 5-substituted compounds show more complex behavior than uracil, exhibiting longer excited-state lifetimes and biexponential fluorescence decays. The S(0)/S(1) conical intersection, located at CASSCF (8/8) level, is indeed characterized by pyramidalization and out of plane motion of the substituents on the C5 atom. A thorough analysis of the excited-state Potential Energy Surfaces, performed at the PCM/TD-DFT(PBE0) level in aqueous solution, shows that the energy barrier separating the local S(1) minimum from the conical intersection increases going from uracil through thymine to 5-fluorouracil, in agreement with the ordering of the experimental excited-state lifetime.
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Affiliation(s)
- Thomas Gustavsson
- Laboratoire Francis Perrin, CEA/DSM/DRECAM/SPAM - CNRS URA 2453, CEA Saclay, Gif-sur-Yvette, France.
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41
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Stanovnik B, Tišler M, Katritzky AR, Denisko OV. The Tautomerism of Heterocycles: Substituent Tautomerism of Six-Membered Ring Heterocycles. ADVANCES IN HETEROCYCLIC CHEMISTRY 2006. [DOI: 10.1016/s0065-2725(06)91001-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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42
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Markova N, Enchev V, Timtcheva I. Oxo−Hydroxy Tautomerism of 5-Fluorouracil: Water-Assisted Proton Transfer. J Phys Chem A 2005; 109:1981-8. [PMID: 16833532 DOI: 10.1021/jp046132m] [Citation(s) in RCA: 76] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Post-Hartree-Fock ab initio quantum chemical calculations were performed for 5-fluorouracil in the gas phase and in a three-water cluster. Full geometry optimizations of the 5-fluorouracil-water complexes were carried out at the MP2/6-31+G(d,p) level of theory. MP4/6-31+G(d,p)//MP2/6-31+G(d,p) and MP4/6-31++G(d,p)//MP2/6-31+G(d,p) single-point calculations were performed to obtain more accurate energies. In water solution, 5-fluorouracil exists mainly in the 2,4-dioxo form (A). We propose that the populations of the 2-hydroxy-4-oxo (B) and 4-hydroxy-2-oxo (D) tautomers are 1 x 10(-4)% and 3.9 x 10(-8)%, respectively, on the basis of the relative stabilities of the tautomers calculated at the MP4/6-31++G(d,p)//MP2/6-31+G(d,p) level of theory. A profound difference between isolated and hydrated 5-fluorouracil is noted for the height of the tautomerization barrier. In the absence of water, the process of proton transfer is very slow. The addition of water molecules decreases the barrier by 2.3 times, making the process much faster. The minimum energy path (MP2/6-31+G(d,p)) for water-assisted proton transfer in trihydrated 5-fluorouracil was followed. CNDO/S-CI calculations predict singlet pi-pi(*) electron transitions at 312 nm for B and at 318 nm for D. The fluorescence spectrum of 5-fluorouracil in water confirms the presence of the hydroxy tautomer.
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Affiliation(s)
- Nadezhda Markova
- Institute of Organic Chemistry, Bulgarian Academy of Sciences, 1113 Sofia, Bulgaria
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43
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Rejnek J, Hanus M, Kabeláč M, Ryjáček F, Hobza P. Correlated ab initio study of nucleic acid bases and their tautomers in the gas phase, in a microhydrated environment and in aqueous solution. Part 4. Uracil and thymine. Phys Chem Chem Phys 2005; 7:2006-17. [DOI: 10.1039/b501499a] [Citation(s) in RCA: 145] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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44
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Shukla MK, Leszczynski J. TDDFT investigation on nucleic acid bases: comparison with experiments and standard approach. J Comput Chem 2004; 25:768-78. [PMID: 14978720 DOI: 10.1002/jcc.20007] [Citation(s) in RCA: 96] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
A comprehensive theoretical study of electronic transitions of canonical nucleic acid bases, namely guanine, adenine, cytosine, uracil, and thymine, was performed. Ground state geometries were optimized at the MP2/6-311G(d,p) level. The nature of respective potential energy surfaces was determined using the harmonic vibrational frequency analysis. The MP2 optimized geometries were used to compute electronic vertical singlet transition energies at the time-dependent density functional theory (TDDFT) level using the B3LYP functional. The 6-311++G(d,p), 6-311(2+,2+)G(d,p), 6-311(3+,3+)G(df,pd), and 6-311(5+,5+)G(df,pd) basis sets were used for the transition energy calculations. Computed transition energies were found in good agreement with the corresponding experimental data. However, in higher transitions, the Rydberg contaminations were also obtained. The existence of pisigma* type Rydberg transition was found near the lowest singlet pipi* state of all bases, which may be responsible for the ultrafast deactivation process in nucleic acid bases.
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Affiliation(s)
- M K Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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45
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Crespo-Hernández CE, Cohen B, Hare PM, Kohler B. Ultrafast Excited-State Dynamics in Nucleic Acids. Chem Rev 2004; 104:1977-2019. [PMID: 15080719 DOI: 10.1021/cr0206770] [Citation(s) in RCA: 965] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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46
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Abstract
The relative energies of the energetically low-lying tautomers of pyridone, cytosine, uracil, thymine, guanine, and iso-cytosine are studied by a variety of different quantum chemical methods. In particular, we employ density functional theory (DFT) using the six functionals HCTH407, PBE, BP86, B-LYP, B3-LYP, and BH-LYP, and the ab initio methods Hartree-Fock (HF), standard second-order Møller-Plesset perturbation theory (MP2), an improved version of it (SCS-MP2), and quadratic configuration interaction including single and double excitations (QCISD) and perturbative triple corrections [QCISD(T)]. A detailed basis set study is performed for the formamide/formamidic acid tautomeric pair. In general, large AO basis sets of at least valence triple-zeta quality including f-functions (TZV) are employed, which are found to be necessary for an accurate energetic description of the various structures. The performance of the more approximate methods is evaluated with QCISD(T)/TZV(2df,2dp) data taken as reference. In general it is found that DFT is not an appropriate method for the problem. For the tautomers of pyridone and cytosine, most density functionals, including the popular B3-LYP hybrid, predict a wrong energetic order, and only for guanine, the correct sequence of tautomers is obtained with all functionals. Out of the density functionals tested, BH-LYP, which includes a rather large fraction of HF exchange, performs best. A consistent description of the nonaromatic versus aromatic tautomers seems to be a general problem especially for pure, nonhybrid functionals. Tentatively, this could be assigned to the exchange potentials used while the functional itself, including the correlation part, seems to be appropriate. Out of the ab initio methods tested, the new SCS-MP2 approach seems to perform best because it effectively reduces some outliers obtained with standard MP2. It outperforms the much more costly QCISD method and seems to be a very good compromise between computational effort and accuracy.
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Affiliation(s)
- M Piacenza
- Theoretische Organische Chemie, Organisch-Chemisches Institut der Universität Münster, Corrensstrasse 40, D-48149 Muenster, Germany
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47
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Morsy MA, Al-Khaldi MA, Suwaiyan A. Normal Vibrational Mode Analysis and Assignment of Benzimidazole by ab Initio and Density Functional Calculations and Polarized Infrared and Raman Spectroscopy. J Phys Chem A 2002. [DOI: 10.1021/jp0256948] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. A. Morsy
- Department of Chemistry, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia, and Department of Chemistry, Girls College, Dammam, Saudi Arabia
| | - M. A. Al-Khaldi
- Department of Chemistry, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia, and Department of Chemistry, Girls College, Dammam, Saudi Arabia
| | - A. Suwaiyan
- Department of Chemistry, King Fahd University of Petroleum & Minerals, Dhahran 31261, Saudi Arabia, and Department of Chemistry, Girls College, Dammam, Saudi Arabia
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48
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Shukla MK, Leszczynski J. Phototautomerism in Uracil: A Quantum Chemical Investigation. J Phys Chem A 2002. [DOI: 10.1021/jp0209650] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. K. Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
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49
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Shukla MK, Leszczynski J. A Theoretical Study of Excited State Properties of Adenine−Thymine and Guanine−Cytosine Base Pairs. J Phys Chem A 2002. [DOI: 10.1021/jp014516w] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- M. K. Shukla
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, 1400 J. R. Lynch Street, Jackson, Mississippi 39217
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50
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Li C, Huang J, Liang Y. Spectroscopic studies on molecular recognition capabilities of a nucleolipid bearing thymine headgroup to adenosine. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2001; 57:1587-1593. [PMID: 11471710 DOI: 10.1016/s1386-1425(01)00392-4] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
The Langmuir-Blodgett (LB) films of octadecanoyl ester of 1-(2-carboxyethyl) thymine deposited from pure water and aqueous adenosine subphases were investigated by ultraviolet-visible (UV-vis), Fourier transform infrared-attenuated total reflection (FTIR-ATR), and Fourier transform surface-enhanced Raman scattering (FT-SERS) spectroscopy. The obtained spectral results indicate that the adenosine molecules in the subphase can be transferred onto solid substrates by LB techniques as a result of the formation of base pairs at the air/water interface. UV-vis spectra alternations indicated that, with increasing adenosine concentration in subphase, more adenosine molecules were recognized by nucleolipid monolayer and were transferred onto the quartz substrates. The closed-packing of the constituent molecules facilitates the photodimerization of the thymine moieties in the headgroup under ultraviolet irradiation. FTIR-ATR results suggest that the hydrocarbon chains of nucleolipid in the LB films deposited from pure water and aqueous adenosine take on a close-packed all trans conformation. By analyzing the FT-SERS spectra results, it can be deduced that the orientation of nucleobase in the headgroup is different before and after the recognition effect occurred. For LB film deposited from pure water, the nucleobases are lying flat on the silver substrates; whereas for LB film deposited from aqueous adenosine, the base pairs take an end-on adsorption on silver substrate.
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Affiliation(s)
- C Li
- Lab of Mesoscopic Materials and Chemistry and State Key Laboratory of Coordination Chemistry, Nanjing University, People's Republic of China
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