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Effects of ionization on stability of 1-methylcytosine - DFT and PCM studies. J Mol Model 2016; 22:146. [PMID: 27259531 PMCID: PMC4893064 DOI: 10.1007/s00894-016-3020-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2016] [Accepted: 05/26/2016] [Indexed: 01/01/2023]
Abstract
Consequences of ionization were studied by quantum-chemical methods (DFT and PCM) for 1-methylcytosine (MC)—a model of the nucleobase cytosine (C) connected with sugar in DNA. For calculations, three prototropic tautomers (one amino and two imino forms) and two imino zwitterions were considered, including conformational or configurational isomerism of exo heterogroups. Ionization and interactions between neighboring groups affect intramolecular proton-transfers, geometric and thermodynamic parameters, and electron delocalization for individual isomers. We discovered that an imino isomer is present in the isomeric mixture in the highest amount for positively ionized MC. Its contribution in neutral and negatively ionized MC is considerably smaller. Acid-base parameters for selected radical ions were estimated in the gas phase and compared to those of neutral MC. Gas-phase acidity of radical cations is close to that of the conjugate acid of MC, and gas-phase basicity of radical anions is close to that of the conjugate base of MC. Various routes of amino-imino conversion between neutral and ionized isomers were considered. Energetic-barrier for intramolecular proton-transfer in MC is close to that in the parent system—formamidine.
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Karwowski BT. The influence of phosphorothioate on charge migration in single and double stranded DNA: a theoretical approach. Phys Chem Chem Phys 2015. [PMID: 26219639 DOI: 10.1039/c5cp01382h] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
In this study the influence of the phosphorothioate internucleotide bond on the electronic properties of single and double-stranded short nucleotides has been investigated at the M06-2X/6-31+G** level of theory in the gaseous phase. Due to the chirality of the phosphorus atom in a phosphorothioate (PT) internucleotide diester bond, the adiabatic/vertical mode of electron affinity/ionization potential, spin density and molecular orbital distribution, as well as structural analysis were taken under consideration for the single stranded (ss) R(P) and S(P) diastereomers of d[G(PS)G] and for double stranded (ds) d[G(PS)G]*d[C(PO)C], in comparison with the corresponding parent phosphate compounds. Moreover, the excitation states, HOMO and LUMO energies were calculated using a TD-DFT methodology at the M06-2X/6-31+G**//M06-2X/6-31++G** level of theory in the aqueous phase. The obtained results show that the PT plays a significant role in the case of ss-oligonucleotides, and to a much smaller extent in ds-oligomers.
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Affiliation(s)
- Boleslaw T Karwowski
- Food Science Department, Medical University of Lodz, ul. Muszynskiego 1, 90-151 Lodz, Poland.
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Storoniak P, Rak J, Ko YJ, Wang H, Bowen KH. Photoelectron spectroscopic and density functional theoretical studies of the 2′-deoxycytidine homodimer radical anion. J Chem Phys 2013; 139:075101. [DOI: 10.1063/1.4817779] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Gu J, Leszczynski J, Schaefer HF. Interactions of electrons with bare and hydrated biomolecules: from nucleic acid bases to DNA segments. Chem Rev 2012; 112:5603-40. [PMID: 22694487 DOI: 10.1021/cr3000219] [Citation(s) in RCA: 158] [Impact Index Per Article: 13.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, CAS, PR China.
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Melicherčík M, Pašteka LF, Neogrády P, Urban M. Electron Affinities of Uracil: Microsolvation Effects and Polarizable Continuum Model. J Phys Chem A 2012; 116:2343-51. [DOI: 10.1021/jp211994k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Miroslav Melicherčík
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
| | - Lukáš F. Pašteka
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
| | - Pavel Neogrády
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
| | - Miroslav Urban
- Department of Physical and Theoretical
Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
- Slovak University of Technology
in Bratislava, Faculty of Materials Science and Technology in Trnava, Institute of Materials Science, Bottova 25, SK-917
24 Trnava, Slovakia
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Gu J, Wang J, Leszczynski J. Electron Attachment to the Cytosine-Centered DNA Single Strands: Does Base Stacking Matter? J Phys Chem B 2012; 116:1458-66. [DOI: 10.1021/jp211386x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China
| | - Jing Wang
- Interdisciplinary Nanotoxicity
Center, Department of Chemistry, Jackson State University, Jackson,
Mississippi 39217, United States
| | - Jerzy Leszczynski
- Interdisciplinary Nanotoxicity
Center, Department of Chemistry, Jackson State University, Jackson,
Mississippi 39217, United States
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Li Z, Cloutier P, Sanche L, Wagner JR. Low-energy electron-induced damage in a trinucleotide containing 5-bromouracil. J Phys Chem B 2011; 115:13668-73. [PMID: 21902215 PMCID: PMC3818159 DOI: 10.1021/jp205194g] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The reaction of low-energy electrons (LEEs; 10 eV) with 5'-TpXpT-3' (TXT), where X is uracil (U), thymine (T), and 5-bromouracil (5BrU), was examined by HPLC-UV analysis. The presence of 5BrU increased total damage by >50%. The radiation products of T5BrUT included TUT (40%), free U, T, 5BrU (23%), and fragments (13%). These products may be explained by initial capture of LEEs by the nucleobase to form a transient anion, followed by transfer of the electron within the molecule and cleavage of susceptible bonds by dissociative electron attachment (C-Br, C-N, or C-O bonds). In addition, these products may arise from the uracilyl-5-yl (U-5-yl) radicals that undergo H-atom abstraction from the sugar moiety. Interestingly, several products contained two sites of cleavage (U, pUT, and TUp). The formation of these products was linear with dose, and thus, they arise from the single-electron reactions. To explain these products, we propose that the reaction of LEEs (10 eV) involves the coupling of two dissociative processes in the same molecule (for example, dissociative excitation and dissociative electron attachment). The latter reactions may contribute to the formation of clustered damage, which is the most deleterious damage induced by ionizing radiation.
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Affiliation(s)
- Zejun Li
- Center for Radiobiology and Radiotherapy, Department of Nuclear Medicine and Radiobiology, Faculty of Medicine, Université de Sherbrooke, Sherbrooke, Québec, Canada J1H 5N4
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Siefermann KR, Abel B. The Hydrated Electron: A Seemingly Familiar Chemical and Biological Transient. Angew Chem Int Ed Engl 2011; 50:5264-72. [DOI: 10.1002/anie.201006521] [Citation(s) in RCA: 78] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2010] [Revised: 02/15/2011] [Indexed: 11/05/2022]
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Siefermann KR, Abel B. Das hydratisierte Elektron - eine scheinbar vertraute transiente Spezies in chemischen und biologischen Systemen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201006521] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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Dedíková P, Neogrády P, Urban M. Electron Affinities of Small Uracil−Water Complexes: A Comparison of Benchmark CCSD(T) Calculations with DFT. J Phys Chem A 2011; 115:2350-8. [DOI: 10.1021/jp111104j] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Pavlína Dedíková
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
| | - Pavel Neogrády
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
| | - Miroslav Urban
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynská dolina, SK-842 15 Bratislava, Slovakia
- Faculty of Materials Science and Technology in Trnava, Institute of Materials Science, Slovak University of Technology in Bratislava, Bottova 25, SK-917 24 Trnava, Slovakia
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Gu J, Wong NB, Xie Y, Schaefer FH. Electron attachment to a hydrated DNA duplex: the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine. Chemistry 2011; 16:13155-62. [PMID: 20922718 DOI: 10.1002/chem.201001306] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
The minimal essential section of DNA helices, the dinucleoside phosphate deoxyguanylyl-3',5'-deoxycytidine dimer octahydrate, [dGpdC](2), has been constructed, fully optimized, and analyzed by using quantum chemical methods at the B3LYP/6-31+G(d,p) level of theory. Study of the electrons attached to [dGpdC](2) reveals that DNA double strands are capable of capturing low-energy electrons and forming electronically stable radical anions. The relatively large vertical electron affinity (VEA) predicted for [dGpdC](2) (0.38 eV) indicates that the cytosine bases are good electron captors in DNA double strands. The structure, charge distribution, and molecular orbital analysis for the fully optimized radical anion [dGpdC](2)(·-) suggest that the extra electron tends to be redistributed to one of the cytosine base moieties, in an electronically stable structure (with adiabatic electron affinity (AEA) 1.14 eV and vertical detachment energy (VDE) 2.20 eV). The structural features of the optimized radical anion [dGpdC](2)(·-) also suggest the probability of interstrand proton transfer. The interstrand proton transfer leads to a distonic radical anion [d(G-H)pdC:d(C+H)pdG](·-), which contains one deprotonated guanine anion and one protonated cytosine radical. This distonic radical anion is predicted to be more stable than [dGpdC](2)(·-). Therefore, experimental evidence for electron attachment to the DNA double helices should be related to [d(G-H)pdC:d(C+H)pdG](·-) complexes, for which the VDE might be as high as 2.7 eV (in dry conditions) to 3.3 eV (in fully hydrated conditions). Effects of the polarizable medium have been found to be important for increasing the electron capture ability of the dGpdC dimer. The ultimate AEA value for cytosine in DNA duplexes is predicted to be 2.03 eV in aqueous solution.
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Affiliation(s)
- Jiande Gu
- Drug Design & Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China.
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Yuan XX, Wang YF, Wang X, Chen W, Fossey JS, Wong NB. An ab initio and AIM investigation into the hydration of 2-thioxanthine. Chem Cent J 2010; 4:6. [PMID: 20331849 PMCID: PMC2853538 DOI: 10.1186/1752-153x-4-6] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2009] [Accepted: 03/23/2010] [Indexed: 01/14/2023] Open
Abstract
BACKGROUND Hydration is a universal phenomenon in nature. The interactions between biomolecules and water of hydration play a pivotal role in molecular biology. 2-Thioxanthine (2TX), a thio-modified nucleic acid base, is of significant interest as a DNA inhibitor yet its interactions with hydration water have not been investigated either computationally or experimentally. Here in, we reported an ab initio study of the hydration of 2TX, revealing water can form seven hydrated complexes. RESULTS Hydrogen-bond (H-bond) interactions in 1:1 complexes of 2TX with water are studied at the MP2/6-311G(d, p) and B3LYP/6-311G(d, p) levels. Seven 2TX...H2O hydrogen bonded complexes have been theoretically identified and reported for the first time. The proton affinities (PAs) of the O, S, and N atoms and deprotonantion enthalpies (DPEs) of different N-H bonds in 2TX are calculated, factors surrounding why the seven complexes have different hydrogen bond energies are discussed. The theoretical infrared and NMR spectra of hydrated 2TX complexes are reported to probe the characteristics of the proposed H-bonds. An improper blue-shifting H-bond with a shortened C-H bond was found in one case. NBO and AIM analysis were carried out to explain the formation of improper blue-shifting H-bonds, and the H-bonding characteristics are discussed. CONCLUSION 2TX can interact with water by five different H-bonding regimes, N-H...O, O-H...N, O-H...O, O-H...S and C-H...O, all of which are medium strength hydrogen bonds. The most stable H-bond complex has a closed structure with two hydrogen bonds (N(7)-H...O and O-H...O), whereas the least stable one has an open structure with one H-bond. The interaction energies of the studied complexes are correlated to the PA and DPE involved in H-bond formation. After formation of H-bonds, the calculated IR and NMR spectra of the 2TX-water complexes change greatly, which serves to identify the hydration of 2TX.
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Affiliation(s)
- Xiu-Xiang Yuan
- Faculty of Chemistry, Sichuan University, Chengdu, PR China
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How does microhydration impact on structure, spectroscopy and formation of disulfide radical anions? An ab initio investigation on dimethyldisulfide. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.09.079] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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