1
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Nenadis N, Pyrka I, Tsimidou MZ. The Contribution of Theoretical Prediction Studies to the Antioxidant Activity Assessment of the Bioactive Secoiridoids Encountered in Olive Tree Products and By-Products. Molecules 2023; 28:2267. [PMID: 36903511 PMCID: PMC10005156 DOI: 10.3390/molecules28052267] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/04/2023] [Accepted: 02/21/2023] [Indexed: 03/05/2023] Open
Abstract
Assessment of the antioxidant activity of different types of natural compounds is a complex research area that encompasses various in vitro tests and in vivo studies. Sophisticated modern analytical tools permit the unambiguous characterization of the compounds present in a matrix. The contemporary researcher, knowing the chemical structure of the compounds present, can carry out quantum chemical calculations that provide important physicochemical information assisting the prediction of antioxidant potential and the mechanism behind the activity of target compounds before further experimentation. The efficiency of calculations is steadily improved due to the rapid evolution of both hardware and software. It is possible, consequently, to study compounds of medium or even larger size, incorporating also models that simulate the liquid phase (solution). This review contributes to the establishment of theoretical calculations as an inherent part of the antioxidant activity assessment process, having as a case study the complex mixtures of olive bioactive secoiridoids (oleuropein, ligstroside, and related compounds). The literature indicates great variability in theoretical approaches and models used so far for only a limited number of this group of phenolic compounds. Proposals are made for standardization of methodology (reference compounds, DFT functional, basis set size, and solvation model) to facilitate comparisons and communication of findings.
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Affiliation(s)
| | | | - Maria Z. Tsimidou
- Laboratory of Food Chemistry and Technology, School of Chemistry, Aristotle University of Thessaloniki, 54124 Thessaloniki, Greece
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2
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Bell M, Kumar A, Sevilla MD. Electron-Induced Repair of 2'-Deoxyribose Sugar Radicals in DNA: A Density Functional Theory (DFT) Study. Int J Mol Sci 2021; 22:ijms22041736. [PMID: 33572317 PMCID: PMC7916153 DOI: 10.3390/ijms22041736] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 02/01/2021] [Accepted: 02/05/2021] [Indexed: 12/19/2022] Open
Abstract
In this work, we used ωB97XD density functional and 6-31++G** basis set to study the structure, electron affinity, populations via Boltzmann distribution, and one-electron reduction potentials (E°) of 2′-deoxyribose sugar radicals in aqueous phase by considering 2′-deoxyguanosine and 2′-deoxythymidine as a model of DNA. The calculation predicted the relative stability of sugar radicals in the order C4′• > C1′• > C5′• > C3′• > C2′•. The Boltzmann distribution populations based on the relative stability of the sugar radicals were not those found for ionizing radiation or OH-radical attack and are good evidence the kinetic mechanisms of the processes drive the products formed. The adiabatic electron affinities of these sugar radicals were in the range 2.6–3.3 eV which is higher than the canonical DNA bases. The sugar radicals reduction potentials (E°) without protonation (−1.8 to −1.2 V) were also significantly higher than the bases. Thus the sugar radicals will be far more readily reduced by solvated electrons than the DNA bases. In the aqueous phase, these one-electron reduced sugar radicals (anions) are protonated from solvent and thus are efficiently repaired via the “electron-induced proton transfer mechanism”. The calculation shows that, in comparison to efficient repair of sugar radicals by the electron-induced proton transfer mechanism, the repair of the cyclopurine lesion, 5′,8-cyclo-2′-dG, would involve a substantial barrier.
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3
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Cao CT, Chen M, Fang Z, Au C, Cao C. Relationship Investigation between C(sp 2)-X and C(sp 3)-X Bond Energies Based on Substituted Benzene and Methane. ACS OMEGA 2020; 5:19304-19311. [PMID: 32775934 PMCID: PMC7409257 DOI: 10.1021/acsomega.0c02964] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2020] [Accepted: 07/09/2020] [Indexed: 06/11/2023]
Abstract
The C-X bonds of organic compounds between group X and a saturated or unsaturated carbon atom differ in bond energy. To identify the causes of variation is of great significance in terms of bond nature understanding and bond energy estimation. In this paper, the electronegativity χ[X] of group X was calculated by the "valence electron equalized electronegativity" method. Then, χ[X] and the electronic effect constant of the substituent were taken as variables to establish equations for quantitative correlation between C(sp3)-X and C(sp2)-X for the calculation of C-X bond energies. The aim is make comparison between substituted methane, Me-X, and substituted benzene, Ph-X, as well as that between Me-X and substituted ethylene, C2H3-X. We conducted calculation over 40 compounds that contain different X groups, and the results reveal that the C(sp3)-X and C(sp2)-X bond energies are under the influence of a number of factors. In addition to the covalent properties of C and X atoms and χ[X], the bond energies of C(sp2)-X (i.e., D[C(sp2)-X]) are under the influence of the field/inductive effect (σF[X]) and conjugated effect (σR[X]) of group X, with the former causing a decrease while the latter an increase of D[C(sp2)-X]. Using the acquired quantitative correlation equations and on the basis of a relatively rich set of measured D[Me-X] data, we estimated D[Ph-X] of Ph-X and D[C2H3-X] of C2H3-X, and the estimation accuracy is within experimental uncertainty. Employing the above method, the D[C(sp2)-X] of 33 substituted benzenes, 53 substituted ethenes, and 82 α-substituted naphthalenes was estimated with satisfactory outcomes.
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Affiliation(s)
- Chao-Tun Cao
- Key
Laboratory of Theoretical Organic Chemistry and Function Molecule,
Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan Province, P. R. China
| | - Miaomiao Chen
- Key
Laboratory of Theoretical Organic Chemistry and Function Molecule,
Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan Province, P. R. China
| | - Zhengjun Fang
- Hunan
Provincial Key Laboratory of Environmental Catalysis & Waste Recycling,
College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Chaktong Au
- Hunan
Provincial Key Laboratory of Environmental Catalysis & Waste Recycling,
College of Materials and Chemical Engineering, Hunan Institute of Engineering, Xiangtan 411104, China
| | - Chenzhong Cao
- Key
Laboratory of Theoretical Organic Chemistry and Function Molecule,
Ministry of Education, School of Chemistry and Chemical Engineering, Hunan University of Science and Technology, Xiangtan 411201, Hunan Province, P. R. China
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4
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Wang SD, Zhang RB, Cadet J. Enhanced reactivity of the pyrimidine peroxyl radical towards the C–H bond in duplex DNA – a theoretical study. Org Biomol Chem 2020; 18:3536-3543. [DOI: 10.1039/d0ob00302f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The peroxyl radical exhibits a much stronger reactivity towards C1′–H1′ in duplex DNA with respect to single-stranded DNA.
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Affiliation(s)
- Shu-dong Wang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry and Chemical Engineering
- Beijing Institute of Technology
- Beijing
- China
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie
- Faculté de Médecine
- Université de Sherbrooke
- Sherbrooke
- Canada JIH 5N4
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5
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Yu X, Hou H, Wang B. Double-Layered Composite Methods Extrapolating to Complete Basis-Set Limit for the Systems Involving More than Ten Heavy Atoms: Application to the Reaction of Heptafluoroisobutyronitrile with Hydroxyl Radical. J Phys Chem A 2017; 121:9020-9032. [DOI: 10.1021/acs.jpca.7b08844] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Xiaojuan Yu
- College of Chemistry and
Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Hua Hou
- College of Chemistry and
Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
| | - Baoshan Wang
- College of Chemistry and
Molecular Sciences, Wuhan University, Wuhan 430072, People’s Republic of China
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6
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Zhao S, Zhang RB, Li ZS. A new understanding towards the reactivity of DNA peroxy radicals. Phys Chem Chem Phys 2016; 18:23763-8. [DOI: 10.1039/c6cp04720c] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
New radical reaction paths for the formation of DNA oxidation products are suggested, which are strongly different from the previously suggested paths with the tetraoxide intermediate.
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Affiliation(s)
- Shuang Zhao
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ru-bo Zhang
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
| | - Ze-sheng Li
- School of Chemistry
- Beijing Institute of Technology
- 100081 Beijing
- China
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7
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Peterson C, Penchoff D, Wilson A. Prediction of Thermochemical Properties Across the Periodic Table. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1016/bs.arcc.2016.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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8
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Rationalization of regioselectivity of electrophilic substitution reaction for cyclic compounds in terms of Dpb values. CHINESE CHEM LETT 2015. [DOI: 10.1016/j.cclet.2014.12.013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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9
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 738] [Impact Index Per Article: 82.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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10
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Li M, Diao L, Liao X, Kou L, Lu W. DFT study on addition reaction mechanism of guanine-cytosine base pair with OH radical. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3434] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Minjie Li
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Ling Diao
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Xiaofei Liao
- School of Information Science and Technology; Donghua University; Shanghai 201620 China
| | - Li Kou
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
| | - Wencong Lu
- Department of Chemistry, Innovative Drug Research Center, College of Sciences; Shanghai University; Shanghai 200444 China
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11
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Li MD, Dang L, Liu M, Du L, Zheng X, Phillips DL. Ultrafast Time Resolved Spectroscopic Studies on the Generation of the Ketyl-Sugar Biradical by Intramolecular Hydrogen Abstraction among Ketoprofen and Purine Nucleoside Dyads. J Org Chem 2015; 80:3462-70. [DOI: 10.1021/acs.joc.5b00047] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ming-De Li
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Li Dang
- Department
of Chemistry, South University of Science and Technology of China, Shenzhen, Guangdong 518055, China
| | - Mingyue Liu
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Lili Du
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
| | - Xuming Zheng
- Department
of Chemistry, Zhejiang Sci-Tech University, Hangzhou 310018, China
| | - David Lee Phillips
- Department
of Chemistry, The University of Hong Kong, Pokfulam Road, Hong Kong S.A.R., P.R. China
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12
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Zubatiuk TA, Shishkin OV, Gorb L, Hovorun DM, Leszczynski J. B-DNA characteristics are preserved in double stranded d(A)3·d(T)3 and d(G)3·d(C)3 mini-helixes: conclusions from DFT/M06-2X study. Phys Chem Chem Phys 2014; 15:18155-66. [PMID: 24065071 DOI: 10.1039/c3cp51584b] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
We report the results of the first comprehensive DFT study on the d(A)3·d(T)3 and d(G)3·d(C)3 nucleic acid duplexes. The ability of mini-helixes to preserve the conformation of B-DNA in the gas phase and under the influence of such factors as: solvent, uncompensated charge, and counter-ions was evaluated using M06-2X functional with 6-31G(d,p) basis set. The accuracy of the models was ascertained based on their ability to reproduce key structural features of natural B-DNA. Analysis of the helicity suggests that the helical conformations adopt geometrical parameters which are close to those of the B-DNA form. The torsion angles fall somewhere between the values observed for BI/BII conformational classes. The comparative analysis of parameters of isolated Watson-Crick base pairs versus B-DNA-like conformations indicates the same tendency of base-pair polarization and hydration. Specifically, effects of polarization of nucleobases in continuum type dielectric medium mimicking water are stronger than those caused by the presence of backbone. Polar environment as well as the presence of counterions stabilizes duplexes, facilitating helix formation. Substantial conformational changes of nucleotides upon duplex formation decrease the binding energy. In spite of structural and energetic changes, the placement of a mini-helix into the gas phase does not lead to significant disruption of the structure. On the contrary, the duplex preserves its helicity and the strands remain bound.
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Affiliation(s)
- Tetiana A Zubatiuk
- Division of Functional Materials Chemistry, SSI "Institute for Single Crystals" National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv, 61001, Ukraine
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13
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Abstract
Computational prediction of condensed phase acidity is a topic of much interest in the field today. We introduce the methods available for predicting gas phase acidity and pKas in aqueous and non-aqueous solvents including high-level electronic structure methods, empirical linear free energy relationships (LFERs), implicit solvent methods, explicit solvent statistical free energy methods, and hybrid implicit–explicit approaches. The focus of this paper is on implicit solvent methods, and we review recent developments including new electronic structure methods, cluster-continuum schemes for calculating ionic solvation free energies, as well as address issues relating to the choice of proton solvation free energy to use with implicit solvation models, and whether thermodynamic cycles are necessary for the computation of pKas. A comparison of the scope and accuracy of implicit solvent methods with ab initio molecular dynamics free energy methods is also presented. The present status of the theory and future directions are outlined.
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14
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Du X, Zhao DX, Yang ZZ. Quick estimation of the Dpb for predicting the strength of chemical bond in situ. CHINESE CHEM LETT 2013. [DOI: 10.1016/j.cclet.2013.06.008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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15
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Insight into reaction mechanism and product formation a C8-purine radical in RNA: a theoretical perspective. Theor Chem Acc 2013. [DOI: 10.1007/s00214-013-1355-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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16
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Du X, Zhao DX, Yang ZZ. Development of a method to accurately calculate the Dpb and quickly predict the strength of a chemical bond. Chem Phys 2013. [DOI: 10.1016/j.chemphys.2012.12.016] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
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17
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Riojas AG, John JR, Williams TG, Wilson AK. Proton affinities of deoxyribonucleosides via the ONIOM-ccCA methodology. J Comput Chem 2012; 33:2590-601. [DOI: 10.1002/jcc.23102] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2012] [Accepted: 08/04/2012] [Indexed: 11/11/2022]
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18
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Kumar A, Pottiboyina V, Sevilla MD. One-electron oxidation of neutral sugar radicals of 2'-deoxyguanosine and 2'-deoxythymidine: a density functional theory (DFT) study. J Phys Chem B 2012; 116:9409-16. [PMID: 22793263 DOI: 10.1021/jp3059068] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
One electron oxidation of neutral sugar radicals has recently been suggested to lead to important intermediates in the DNA damage process culminating in DNA strand breaks. In this work, we investigate sugar radicals in a DNA model system to understand the energetics of sugar radical formation and oxidation. The geometries of neutral sugar radicals C(1')(•), C(2')(•), C(3')(•), C(4')(•), and C(5')(•) of 2'-deoxyguanosine (dG) and 2'-deoxythymidine (dT) were optimized in the gas phase and in solution using the B3LYP and ωB97x functionals and 6-31++G(d) basis set. Their corresponding cations (C(1')(+), C(2')(+), C(3')(+), C(4')(+), and C(5')(+)) were generated by removing an electron (one-electron oxidation) from the neutral sugar radicals, and their geometries were also optimized using the same methods and basis set. The calculation predicts the relative stabilities of the neutral sugar radicals in the order C(1')(•) > C(4')(•) > C(5')(•) > C(3')(•) > C(2')(•), respectively. Of the neutral sugar radicals, C(1')(•) has the lowest vertical ionization potential (IP(vert)), ca. 6.33 eV in the gas phase and 4.71 eV in solution. C(2')(•) has the highest IP(vert), ca. 8.02 eV, in the gas phase, and the resultant C(2') cation is predicted to undergo a barrierless hydride transfer from the C(1') site to produce the C(1') cation. One electron oxidation of C(2')(•) in dG is predicted to result in a low lying triplet state consisting of G(+•) and C(2')(•). The 5',8-cyclo-2'-deoxyguanosin-7-yl radical formed by intramolecular bonding between C(5')(•) and C(8) of guanine transfers spin density from C(5') site to guanine, and this structure has IP(vert) 6.25 and 5.48 eV in the gas phase and in solution.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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19
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Shi J, Huang XY, Wang HJ, Fu Y. Hydride Dissociation Energies of Six-Membered Heterocyclic Organic Hydrides Predicted by ONIOM-G4Method. J Chem Inf Model 2011; 52:63-75. [DOI: 10.1021/ci2001567] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jing Shi
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Xiong-Yi Huang
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Hua-Jing Wang
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
| | - Yao Fu
- Department of
Chemistry, University of Science and
Technology of China, Hefei 230026, China
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20
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ZOU CHUNSEN, LIU JING. THEORETICAL STUDY ON OXYGEN–OXYGEN HOMOLYTIC BOND DISSOCIATION ENTHALPIES OF PEROXIDES. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633610005839] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Seven theoretical methods (B3LYP, B3P86, X3LYP, BMK, MP2, CBS-QB3, G3B3) were employed to calculate oxygen–oxygen homolytic bond dissociation enthalpies of 13 peroxides. Comparison of the performances of these methods with the available experimental data showed that ROBMK method is suitable and economical for calculating O–O homolytic bond dissociation enthalpies of peroxides. Then ROBMK method was used to calculate O–O homolytic bond dissociation enthalpies of a series of peroxides. Meanwhile, the α-substituent effect and Hammett relationship were also discussed.
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Affiliation(s)
- CHUN-SEN ZOU
- School of Life Science, University of Science and Technology of China, Hefei 230027, P. R. China
| | - JING LIU
- School of Life Science, University of Science and Technology of China, Hefei 230027, P. R. China
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21
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Gilbert TM. Testing the ONIOM G2R3 model against donor-acceptor dissociation energies of group 13-15 complexes: Accuracy comparable to CCSD(T)/aug-CC-pVTZ at a fraction of the resource cost. J Comput Chem 2011; 32:1493-9. [DOI: 10.1002/jcc.21725] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2010] [Revised: 09/12/2010] [Accepted: 11/06/2010] [Indexed: 12/23/2022]
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22
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Shi J, He J, Wang HJ. A computational study of CX (X = H, C, F, Cl) bond dissociation enthalpies (BDEs) in polyhalogenated methanes and ethanes. J PHYS ORG CHEM 2010. [DOI: 10.1002/poc.1704] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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23
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24
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Das SR, Williams TG, Drummond ML, Wilson AK. A QM/QM Multilayer Composite Methodology: The ONIOM Correlation Consistent Composite Approach (ONIOM-ccCA). J Phys Chem A 2010; 114:9394-7. [DOI: 10.1021/jp1060396] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Somak R. Das
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle No. 305070, Denton, Texas 76203-5070
| | - T. Gavin Williams
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle No. 305070, Denton, Texas 76203-5070
| | - Michael L. Drummond
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle No. 305070, Denton, Texas 76203-5070
| | - Angela K. Wilson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, 1155 Union Circle No. 305070, Denton, Texas 76203-5070
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Condic-Jurkic K, Zipse H, Smith DM. A compound QM/MM procedure: Comparative performance on a pyruvate formate-lyase model system. J Comput Chem 2009; 31:1024-35. [DOI: 10.1002/jcc.21389] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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26
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Wang HJ, Fu Y. Designing new free-radical reducing reagents: Theoretical study on Si–H bond dissociation energies of organic silanes. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.09.017] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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Fu Y, Wang HJ, Chong SS, Guo QX, Liu L. An Extensive Ylide Thermodynamic Stability Scale Predicted by First-Principle Calculations. J Org Chem 2008; 74:810-9. [DOI: 10.1021/jo802128w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Hua-Jing Wang
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Sha-Sha Chong
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Qing-Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Tsinghua University, Beijing 100084, China
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28
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ZHU C, RUI L, FU Y. Homolytic Bond Dissociation Enthalpies of C-C and C-H Bonds in Highly Crowded Alkanes. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890270] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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29
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Vall-llosera G, Huels MA, Coreno M, Kivimäki A, Jakubowska K, Stankiewicz M, Rachlew E. Photofragmentation of 2-Deoxy-D-Ribose Molecules in the Gas Phase. Chemphyschem 2008; 9:1020-9. [DOI: 10.1002/cphc.200700635] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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30
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MENG XM, ZOU LF, XIE M, FU Y. Strength of C–H Bonds at Nitrogenα-Position:Implication for Metabolic Stability of Nitrogen-containing Drug Molecules. CHINESE J CHEM 2008. [DOI: 10.1002/cjoc.200890147] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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31
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Chong SS, Fu Y, Liu L, Guo QX. O−H Bond Dissociation Enthalpies of Oximes: A Theoretical Assessment and Experimental Implications. J Phys Chem A 2007; 111:13112-25. [DOI: 10.1021/jp075699a] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Sha-Sha Chong
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Lei Liu
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
| | - Qing-Xiang Guo
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China, and Department of Chemistry, Key Laboratory of Bioorganic Phosphorus Chemistry and Chemical Biology, Tsinghua University, Beijing 100084, China
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32
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Zou LF, Shen K, Fu Y, Guo QX. Initiation of petroleum formation and antioxidant function - a DFT study of sulfursulfur bond dissociation enthalpies. J PHYS ORG CHEM 2007. [DOI: 10.1002/poc.1236] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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33
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Fu Y, Liu L, Wang YM, Li JN, Yu TQ, Guo QX. Quantum-chemical predictions of redox potentials of organic anions in dimethyl sulfoxide and reevaluation of bond dissociation enthalpies measured by the electrochemical methods. J Phys Chem A 2007; 110:5874-86. [PMID: 16640384 DOI: 10.1021/jp055682x] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A first-principle theoretical protocol was developed that could predict the absolute pK(a) values of over 250 structurally unrelated compounds in DMSO with a precision of 1.4 pK(a) units. On this basis we developed the first theoretical protocol that could predict the standard redox potentials of over 250 structurally unrelated organic anions in DMSO with a precision of 0.11 V. Using the two new protocols we systematically reevaluated the bond dissociation enthalpies (BDEs) measured previously by the electrochemical methods. It was confirmed that for most compounds the empirical equation (BDE = 1.37 pK(HA) + 23.1E(o) + constant) was valid. The constant in this equation was determined to be 74.0 kcal/mol, compared to 73.3 kcal/mol previously reported. Nevertheless, for a few compounds the empirical equation could not be used because the solvation energy changed dramatically during the bond cleavage, which resulted from the extraordinary change of dipole moment during the reaction. In addition, we found 40 compounds (mostly oximes and amides) for which the experimental values were questionable by over 5 kcal/mol. Further analyses revealed that all these questionable BDEs could be explained by one of the three following reasons: (1) the experimental pK(a) value is questionable; (2) the experimental redox potential is questionable; (3) the solvent effect cannot be neglected. Thus, by developing practical theoretical methods and utilizing them to solve realistic problems, we hope to demonstrate that ab initio theoretical methods can now be developed to make not only reliable, but also useful, predictions for solution-phase organic chemistry.
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Affiliation(s)
- Yao Fu
- Department of Chemistry, University of Science and Technology of China, Hefei.
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34
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Accurate bond dissociation enthalpies of popular antioxidants predicted by the ONIOM-G3B3 method. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.03.012] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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35
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Li MJ, Liu L, Wei K, Fu Y, Guo QX. Significant effects of phosphorylation on relative stabilities of DNA and RNA sugar radicals: remarkably high susceptibility of h-2' abstraction in RNA. J Phys Chem B 2007; 110:13582-9. [PMID: 16821885 DOI: 10.1021/jp060331j] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The roles of nucleic acid radicals in DNA and RNA damage cannot be properly understood in the absence of knowledge of the C-H bond strengths depicting the energy cost to generate each of these radicals. However, previous theoretical studies on the relative energies of different nucleic acid radicals are not fully convincing mainly because of the use of oversimplified model compounds. In the present study we chose nucleoside 3',5'-bisphosphates as model compounds for DNA and RNA, in which the effects of both the nucleobase and phosphorylation were taken into consideration. Using the newly developed ONIOM-G3B3 methods, we calculated the gas-phase bond dissociation enthalpies and solution-phase bond dissociation free energies of all the carbohydrate C-H bonds in the model compounds. It was found that the monoanionic phosphate group (OPO3H-) was a better radical stabilization group than the OH group by 1.3 kcal/mol, whereas the neutral phosphate group (OPO3H2) was a significantly worse radical stabilization group than OH by 4.4 kcal/mol. Due to these reasons, the relative thermodynamic susceptibility of H-abstraction from deoxyribonucleotides and ribonucleotides varied considerably depending on the phosphorylation state and the charge carried by the phosphate groups. Strikingly, the bond dissociation free energy of C2'-H in ribonucleotides was dramatically lower than that of all the other C-H bonds by 5-6 kcal/mol regardless of the phosphorylation state and the charge carried by the phosphate group. This explained the previous experimental finding that radiation damage of RNA occurs mainly via H-abstraction at H-2'. A model study suggested that the strength of the hydrogen bonding interaction between the 2'-OH and 3-phosphate groups should dramatically increase from ribonucleoside 3',5'-bisphosphate to its C2' radical. The strengthened hydrogen bonding stabilized the C2' radical, rendering the C2'-H bond of RNA extraordinarily vulnerable to H-abstraction.
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Affiliation(s)
- Min-Jie Li
- Department of Chemistry, University of Science and Technology of China, Hefei 230026, China
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36
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37
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Zhu XQ, Wang CH, Liang H, Cheng JP. Theoretical Prediction of the Hydride Affinities of Various p- and o-Quinones in DMSO. J Org Chem 2007; 72:945-56. [PMID: 17253815 DOI: 10.1021/jo0621928] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The hydride affinities of 80 various p- and o-quinones in DMSO solution were predicted by using B3LYP/6-311++G (2df,p)//B3LYP/6-31+G* and MP2/6-311++G**//B3LYP/6-31+G* methods, combined with the PCM cluster continuum model for the first time. The results show that the hydride affinity scale of the 80 quinones in DMSO ranges from -47.4 kcal/mol for 9,10-anthraquinone to -124.5 kcal/mol for 3,4,5,6-tetracyano-1,2-quinone. Such a long scale of the hydride affinities (-47.4 to -124.5 kcal/mol) indicates that the 80 quinones can form a large and useful library of organic oxidants, which can provide various organic hydride acceptors that the hydride affinities are known for chemists to choose in organic syntheses. By examining the effect of substituent on the hydride affinities of quinones, it is found that the hydride affinities of quinones in DMSO are linearly dependent on the sum of the Hammett substituent parameters sigma: DeltaGH-(Q) approximately -16.0Sigmasigmai - 70.5 (kcal/mol) for p-quinones and DeltaGH-(Q) approximately -16.2Sigmasigmai - 81.5 (kcal/mol) for o-quinones only if the substituents have no large electrostatic inductive effect and large ortho-effect. Study of the effect of the aromatic properties of quinone on the hydride affinities showed that the larger the aromatic system of quinone is, the smaller the hydride affinity of the quinone is, and the decrease of the hydride affinities is linearly to take place with the increase of the number of benzene rings in the molecule of quinones, from which the hydride affinities of aromatic quinones with multiple benzene rings can be predicted. By comparing the hydride affinities of p-quinones and the corresponding o-quinones, it is found that the hydride affinities of o-quinones are generally larger than those of the corresponding p-quinones by ca. 11 kcal/mol. Analyzing the effect of solvent on the hydride affinities of quinones showed that the effects of solvent (DMSO) on the hydride affinities of quinones are mainly dependent on the electrostatic interaction of the charged hydroquinone anions (QH-) with solvent (DMSO). All the information disclosed in this work should provide some valuable clues to chemists to choose suitable quinones or hydroquinones as efficient hydride acceptors or donors in organic syntheses and to predict the thermodynamics of hydride exchange between quinones and hydroquinones in DMSO solution.
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Affiliation(s)
- Xiao-Qing Zhu
- Department of Chemistry, the State Key Laboratory of Elemento-Organic Chemistry, Nankai University, Tianjin 300071, China.
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38
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Adhikary A, Kumar A, Sevilla MD. Photo-induced hole transfer from base to sugar in DNA: relationship to primary radiation damage. Radiat Res 2006; 165:479-84. [PMID: 16579661 DOI: 10.1667/rr3563.1] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
This work presents the hypothesis that photo-excitation of G.+ in DNA and model systems results in the same electronic states expected from direct ionization of the sugar phosphate backbone and that these states lead to specific sugar radicals on the DNA sugar phosphate backbone. As evidence we show that visible photo-excitation of guanine cation radicals (G.+) in the dinucleoside phosphate TpdG results in high yields (about 85%) of deoxyribose sugar radicals at the C1' and C3' sites. Further, we have calculated transition energies of hole transfer from G.+ in TpdG using time-dependent density functional theory (TD-DFT) at the B3LYP/6-31G(d) level in gas phase as well as in a solvated environment. These calculations clearly predict that visible excitation of G.+ in TpdG causes transitions from only inner-shell filled molecular orbitals (MOs) to the singly occupied molecular orbital (SOMO) that effectively result in hole transfer from guanine either to the sugar phosphate backbone or to the adjacent base, thymine. The hole transfer is followed by rapid deprotonation from the sugar to form C1' and C3' radicals. These experimental and theoretical results are in agreement with our previously published experimental and theoretical results that photo-excitation of G.+ results in high yields of deoxyribose sugar radicals in DNA, guanine deoxyribonucleosides and deoxyribonucleotides. Photo-excitation of G.+ therefore provides a convenient method to produce and study sugar radicals that are expected to be formed in gamma-irradiated DNA systems unencumbered by the many other pathways involved in direct ionization.
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Affiliation(s)
- Amitava Adhikary
- Department of Chemistry, Oakland University, Rochester, Michigan 38309, USA.
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39
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Adhikary A, Becker D, Collins S, Koppen J, Sevilla MD. C5'- and C3'-sugar radicals produced via photo-excitation of one-electron oxidized adenine in 2'-deoxyadenosine and its derivatives. Nucleic Acids Res 2006; 34:1501-11. [PMID: 16537838 PMCID: PMC1401510 DOI: 10.1093/nar/gkl026] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report that photo-excitation of one-electron-oxidized adenine [A(-H)•] in dAdo and its 2′-deoxyribonucleotides leads to formation of deoxyribose sugar radicals in remarkably high yields. Illumination of A(-H)• in dAdo, 3′-dAMP and 5′-dAMP in aqueous glasses at 143 K leads to 80-100% conversion to sugar radicals at C5′ and C3′. The position of the phosphate in 5′- and 3′-dAMP is observed to deactivate radical formation at the site of substitution. In addition, the pH has a crucial influence on the site of sugar radical formation; e.g. at pH ∼5, photo-excitation of A(-H)• in dAdo at 143 K produces mainly C5′• whereas only C3′• is observed at high pH ∼12. 13C substitution at C5′ in dAdo yields 13C anisotropic couplings of (28, 28, 84) G whose isotropic component 46.7 G identifies formation of the near planar C5′•. A β-13C 16 G isotropic coupling from C3′• is also found. These results are found to be in accord with theoretically calculated 13C couplings at C5′ [DFT, B3LYP, 6-31(G) level] for C5′• and C3′•. Calculations using time-dependent density functional theory [TD-DFT B3LYP, 6-31G(d)] confirm that transitions in the near UV and visible induce hole transfer from the base radical to the sugar group leading to sugar radical formation.
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Affiliation(s)
| | | | | | | | - Michael D. Sevilla
- To whom correspondence should be addressed. Tel: +1 248 370 2328; Fax: +1 248 370 2321;
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40
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Dinescu A, Whiteley C, Combs RR, Cundari TR. Oxygen Atom Transfer Energetics: Assessment of the Effect of Method and Solvent. J Phys Chem A 2006; 110:4053-6. [PMID: 16539428 DOI: 10.1021/jp055060b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Several density functional methods, the semiempirical methods AM1 and PM3, Hartree-Fock, and Gaussian3 theories were applied to compute the oxygen atom transfer enthalpies for 14 X/XO couples (inorganic and organic systems, charged and neutral species, light and heavy main group element containing molecules). The calculated reaction enthalpies were compared to available experimental data. The G3 method alone was found to perform within the experimental error, while the popular B3LYP and BLYP functionals provided inadequate results. Solvent effects were estimated for 19 neutral and anionic X/XO couples by using the conductor-like polarizable continuum model and several cavity models coupled with the B3LYP/6-31++G(2d,2p) level of theory. Surprisingly, the magnitude of the aqueous solvent correction was found to vary significantly for different solute cavity models, occasionally giving larger errors than the gas-phase calculation.
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Affiliation(s)
- Adriana Dinescu
- Center for Advanced Scientific Computing and Modeling, Department of Chemistry, University of North Texas, Denton, Texas 76203, USA
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41
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Li H, Oshima Y. Kinetics and Mechanisms of Supercritical Water Oxidation of Methylamines. JOURNAL OF CHEMICAL ENGINEERING OF JAPAN 2006. [DOI: 10.1252/jcej.39.971] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Hong Li
- Department of Chemical System Engineering, School of Engineering, The University of Tokyo
| | - Yoshito Oshima
- Department of Environment Systems, Graduate School of Frontier Sciences, The University of Tokyo
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