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Side-chain engineering on conjugated porous polymer photocatalyst with adenine groups enables high-performance hydrogen evolution from water. POLYMER 2022. [DOI: 10.1016/j.polymer.2021.124509] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Jezuita A, Wieczorkiewicz PA, Szatylowicz H, Krygowski TM. Effect of the Solvent and Substituent on Tautomeric Preferences of Amine-Adenine Tautomers. ACS OMEGA 2021; 6:18890-18903. [PMID: 34337229 PMCID: PMC8320138 DOI: 10.1021/acsomega.1c02118] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 06/23/2021] [Indexed: 06/13/2023]
Abstract
Adenine is one of the basic molecules of life; it is also an important building block in the synthesis of new pharmaceuticals, electrochemical (bio)sensors, or self-assembling molecular materials. Therefore, it is important to know the effects of the solvent and substituent on the electronic structure of adenine tautomers and their stability. The four most stable adenine amino tautomers (9H, 7H, 3H, and 1H), modified by substitution (C2- or C8-) of electron-withdrawing NO2 and electron-donating NH2 groups, are studied theoretically in the gas phase and in solvents of different polarities (1 ≤ ε < 109). Solvents have been modeled using the polarizable continuum model. Comparison of the stability of substituted adenine tautomers in various solvents shows that substitution can change tautomeric preferences with respect to the unsubstituted adenine. Moreover, C8 substitution results in slight energy differences between tautomers in polar solvents (<1 kcal/mol), which suggests that in aqueous solution, C8-X-substituted adenine systems may consist of a considerable amount of two tautomers-9H and 7H for X = NH2 and 3H and 9H for X = NO2. Furthermore, solvation enhances the effect of the nitro group; however, the enhancement strongly depends on the proximity effects. This enhancement for the NO2 group with two repulsive N···ON contacts can be threefold higher than that for the NO2 with one attractive NH···ON contact. The proximity effects are even more significant for the NH2 group, as the solvation may increase or decrease its electron-donating ability, depending on the type of proximity.
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Affiliation(s)
- Anna Jezuita
- Faculty of Science and Technology, Jan Dlugosz University in Czestochowa, Al. Armii Krajowej 113/15, 42-200 Czestochowa, Poland
| | | | - Halina Szatylowicz
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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3
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Padash R, Ramazani S. Investigation of stability of adenine and its tautomers in RNA and DNA, and their interaction with Na+, K+, Mg2+, Ca2+ and Zn2+. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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4
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Zhou Z, Wang X, Chen J, Xu J. Direct observation of an intramolecular charge transfer state in epigenetic nucleobase N6-methyladenine. Phys Chem Chem Phys 2019; 21:6878-6885. [PMID: 30887998 DOI: 10.1039/c9cp00325h] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
N6-Methyladenine (6MeAde), the most abundant internal modification in mRNA, has proved to be an important epigenetic biomarker for gene regulation just like 5-methylcytosine in DNA. Recently, a unique UV-induced response of 6MeAde was reported, which makes it instructive and intriguing to reveal the excited state relaxation mechanism in this methylated adenine and its derivatives. In this work, we investigated 6MeAde and its ribose species N6-methyladenosine (6MeAdo) by using femtosecond time-resolved fluorescence up-conversion (FUC) and broadband transient absorption (TA) spectroscopy. Both 6MeAde and 6MeAdo exhibit a hundreds of femtoseconds lifetime, which originates from the efficient depletion of the ππ* (La) state. A several picoseconds lifetime is also observed and it should be attributed to the ππ* (Lb) state. Surprisingly, dual peak fluorescence emission is observed in 6MeAde and the long wavelength emission is ascribed to an intramolecular charge transfer (ICT) state. The lifetime of this ICT state is determined to be 107 ps. The kinetic isotope effect shows that the ICT state is closely associated with the solute-solvent H-bonding in aqueous solution. In 6MeAdo, the ICT state is apparently quenched and adenine-like excited state dynamics suggests that DNA/RNA containing such modification could still possess excellent photostability under UV irradiation. Our results contain an important insight for understanding excited state properties in epigenetic modified DNA/RNA.
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Affiliation(s)
- Zhongneng Zhou
- State Key Laboratory of Precision Spectroscopy, East China Normal University, Shanghai 200062, China.
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5
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Thicoipe S, Carbonniere P, Pouchan C. DFT modelling of the infrared spectra for isolated and aqueous forms of adenine. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2076-0] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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6
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Hao MH. Theoretical Calculation of Hydrogen-Bonding Strength for Drug Molecules. J Chem Theory Comput 2015; 2:863-72. [PMID: 26626693 DOI: 10.1021/ct0600262] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Hydrogen bond is an important type of interaction between drug molecules and their receptors. We present here a computational method for accurately predicting the hydrogen-bonding strength for different acceptors with respect to a given donor or vice versa. The method is based on quantum chemistry DFT calculation of the interaction energy between hydrogen bond donors and acceptors. An excellent linear correlation is observed between the calculated hydrogen-bonding energies and the experimentally measured hydrogen-bonding constants log Kβ on a variety of known hydrogen bond acceptors and donors. These results not only indicate the predictive power of this method but also shed light on factors that determine the magnitude of experimentally measured hydrogen-bonding constants for different acceptors with respect to a given donor, suggesting a primarily enthalpic contribution from hydrogen-bonding energy. The method can be used for evaluating the effects of steric interference and inhibitor binding geometry on hydrogen-bonding strength in drug design.
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Affiliation(s)
- Ming-Hong Hao
- Department of Medicinal Chemistry, Boehringer Ingelheim Pharmaceuticals, Inc., Ridgefield, Connecticut 06877
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7
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Raczyńska ED, Makowski M, Hallmann M, Kamińska B. Geometric and energetic consequences of prototropy for adenine and its structural models – a review. RSC Adv 2015. [DOI: 10.1039/c4ra17280a] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Prototropy for adenine and its convenient models causes parallel changes of geometric (HOMED) and energetic (ΔE) parameters for neutral tautomers.
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Affiliation(s)
- Ewa D. Raczyńska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | | | - Małgorzata Hallmann
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
| | - Beata Kamińska
- Department of Chemistry
- Warsaw University of Life Sciences (SGGW)
- 02-776 Warszawa
- Poland
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8
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Raczyńska ED, Makowski M. Geometric consequences of electron delocalization for adenine tautomers in aqueous solution. J Mol Model 2014; 20:2234. [PMID: 24842324 PMCID: PMC4072068 DOI: 10.1007/s00894-014-2234-4] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2014] [Accepted: 04/03/2014] [Indexed: 11/26/2022]
Abstract
Geometric consequences of electron delocalization were studied for all possible adenine tautomers in aqueous solution by means of ab initio methods {PCM(water)//DFT(B3LYP)/6-311+G(d,p)} and compared to those in the gas phase {DFT(B3LYP)/6-311+G(d,p)}. To measure the consequences of any type of resonance conjugation (π-π, n-π, and σ-π), the geometry-based harmonic oscillator model of electron delocalization (HOMED) index, recently extended to the isolated (DFT) and hydrated (PCM//DFT) molecules, was applied to the molecular fragments (imidazole, pyrimidine, 4-aminopyrimidine, and purine) and also to the whole tautomeric system. For individual tautomers, the resonance conjugations and consequently the bond lengths strongly depend on the position of the labile protons. The HOMED indices are larger for tautomers (or their fragments) possessing the labile proton(s) at the N rather than C atom. Solvent interactions with adenine tautomers slightly increase the resonance conjugations. Consequently, they slightly shorten the single bonds and lengthen the double bonds. When going from the gas phase to water solution, the HOMED indices increase (by less than 0.15 units). There is a good relation between the HOMED indices estimated in water solution and those in the gas phase for the neutral and ionized forms of adenine. Subtle effects, being a consequence of intramolecular interactions between the neighboring groups, are so strongly reduced by solvent that the relation between the HOMED indices and the relative energies for the neutral adenine tautomers seems to be better in water solution than in the gas phase.
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Affiliation(s)
- Ewa D Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 159c, 02-776, Warszawa, Poland,
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9
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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: 35] [Impact Index Per Article: 3.5] [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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10
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Muñoz Freán S, Alcolea Palafox M, Rastogi V. Effect of the microhydration on the tautomerism in the anticarcinogenic drug 5-fluorouracil and relationships with other 5-haloderivatives. J Mol Struct 2013. [DOI: 10.1016/j.molstruc.2013.09.008] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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11
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Metal–carboxylato–nucleobase systems: From supramolecular assemblies to 3D porous materials. Coord Chem Rev 2013. [DOI: 10.1016/j.ccr.2013.03.011] [Citation(s) in RCA: 75] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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12
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Raczyńska ED, Makowski M, Zientara-Rytter K, Kolczyńska K, Stępniewski TM, Hallmann M. Quantum-Chemical Studies on the Favored and Rare Tautomers of Neutral and Redox Adenine. J Phys Chem A 2013; 117:1548-59. [DOI: 10.1021/jp3081029] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Ewa D. Raczyńska
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska
159 c, 02-776 Warszawa, Poland
| | - Mariusz Makowski
- Faculty of Chemistry, Univeristy of Gdańsk, ul. Sobieskiego 18, 80-952
Gdańsk, Poland
| | - Katarzyna Zientara-Rytter
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Katarzyna Kolczyńska
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Tomasz M. Stępniewski
- Interdisciplinary
Department of
Biotechnology, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska 166, 02-776 Warszawa, Poland
| | - Małgorzata Hallmann
- Department of Chemistry, Warsaw University of Life Sciences (SGGW), ul. Nowoursynowska
159 c, 02-776 Warszawa, Poland
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13
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Ai H, Chen J, Zhang C. Amino–Imino Adenine Tautomerism Induced by the Cooperative Effect between Metal Ion and H2O/NH3. J Phys Chem B 2012; 116:13624-36. [DOI: 10.1021/jp308937k] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- Hongqi Ai
- Shandong Provincial Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan City, 250022, P. R. China
| | - Jinpeng Chen
- Shandong Provincial Key Laboratory
of Fluorine Chemistry and Chemical Materials, School of Chemistry
and Chemical Engineering, University of Jinan, Jinan City, 250022, P. R. China
| | - Chong Zhang
- Department of Chemistry and
Technology, Liaocheng University, Liaocheng
252059, P. R. China
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14
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15
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Sychrovský V, Sochorová Vokáčová Z, Trantírek L. Guanine bases in DNA G-quadruplex adopt nonplanar geometries owing to solvation and base pairing. J Phys Chem A 2012; 116:4144-51. [PMID: 22471881 DOI: 10.1021/jp2110049] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The effect of base pairing and solvation on pyramidalization of the glycosidic nitrogen found in the residues of parallel G-quadruplex with NDB ID UDF062 is analyzed and explained with theoretical calculations. The extent of the pyramidalization depends on the local geometry of the 2'-deoxyguanosine residues, namely on their glycosidic torsion and sugar pucker, which are predetermined by the 3D-architecture of G-quadruplex. Pyramidal inversion of the glycosidic nitrogen found in 2'-deoxyguanosines of G-quadruplex is induced owing to site-specifically coordinated solvent. Different adiabatic structural constraints used for fixing the base-to-sugar orientation of 2'-deoxyguanosine in geometry optimizations result in different extents of pyramidalization and induce pyramidal inversion of the glycosidic nitrogen. These model geometry constraints helped us analyze the effect of real constraints represented by explicit molecular environment of selected residues of the G-quadruplex. The maximal extent of the glycosidic nitrogen pyramidalization found in the high-resolution crystal structure corresponds to the calculation to deformation energy of only 1 kcal mol(-1). The out-of-plane deformations of nucleobases thus provide a way for compensating the site-specific external environmental stress on the G-quadruplex.
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Affiliation(s)
- Vladimír Sychrovský
- Institute of Organic Chemistry and Biochemistry, v.v.i., Academy of Sciences of the Czech Republic, Flemingovo square 2, 166 10 Prague 6, Czech Republic.
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WANG FENG, DOWNTON MATTHEWT, KIDWANI NADER. ADENINE TAUTOMER ELECTRONIC STRUCTURAL SIGNATURES STUDIED USING DUAL SPACE ANALYSIS. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s021963360500143x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Electronic structural signatures of the adenine-7H tautomer in its ground state ( X 1 A′) have been identified using dual space analysis. The RHF/TZVP and B3LYP/TZVP calculations employed in the present work have shown that proton transfer from N (9) to N (7) makes the purine rings of adenine-7H geometrically closer to purine rather than adenine-9H, at the cost distortion of the amino group local symmetry. The shifts in ring lengths in [Formula: see text] and [Formula: see text], which are proposed in this work as the summation of the bond lengths in the hex- and pentagon-rings, respectively, are [Formula: see text] and [Formula: see text] for adenine-9H and [Formula: see text] and [Formula: see text] for adenine-7H, respectively, from the corresponding rings in purine. We also demonstrate that energetic properties such as the orbital energies are insensitive to tautomerism. However, the N (9) to N (7) proton transfer significantly changes the dipole moments: a large increase from 2.44D (adenine-9H) to 7.49D (adenine-7H) is observed. Finally, four molecular orbitals, 27a′, 25a′, 24a′ and 23a′ are identified in momentum space as bearing the most important structural signatures of the adenine-7H tautomer.
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Affiliation(s)
- FENG WANG
- Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Melbourne, Victoria 3122, Australia
| | - MATTHEW T. DOWNTON
- Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Melbourne, Victoria 3122, Australia
| | - NADER KIDWANI
- Centre for Molecular Simulation, Swinburne University of Technology, Hawthorn, Melbourne, Victoria 3122, Australia
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17
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Pérez-Yáñez S, Castillo O, Cepeda J, García-Terán JP, Luque A, Román P. Supramolecular architectures of metal–oxalato complexes containing purine nucleobases. Inorganica Chim Acta 2011. [DOI: 10.1016/j.ica.2010.09.012] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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18
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Furmanchuk A, Isayev O, Gorb L, Shishkin OV, Hovorun DM, Leszczynski J. Novel view on the mechanism of water-assisted proton transfer in the DNA bases: bulk water hydration. Phys Chem Chem Phys 2011; 13:4311-7. [DOI: 10.1039/c0cp02177f] [Citation(s) in RCA: 55] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
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19
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20
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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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21
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Furmanchuk A, Shishkin OV, Isayev O, Gorb L, Leszczynski J. New insight on structural properties of hydrated nucleic acid bases from ab initio molecular dynamics. Phys Chem Chem Phys 2010; 12:9945-54. [DOI: 10.1039/c002934c] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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22
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Furmanchuk A, Isayev O, Shishkin OV, Gorb L, Leszczynski J. Hydration of nucleic acid bases: a Car–Parrinello molecular dynamics approach. Phys Chem Chem Phys 2010; 12:3363-75. [DOI: 10.1039/b923930h] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Pérez-Yáñez S, Castillo O, Cepeda J, García-Terán JP, Luque A, Román P. Analysis of the Interaction between Adenine Nucleobase and Metal-Malonato Complexes. Eur J Inorg Chem 2009. [DOI: 10.1002/ejic.200900124] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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24
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Shukla M, Leszczynski J. Hydration of guanine: Electronic singlet excited states for complexes with 19 and 27 water molecules. Chem Phys Lett 2009. [DOI: 10.1016/j.cplett.2009.07.081] [Citation(s) in RCA: 13] [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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Rajabi K, Theel K, Gillis EAL, Beran G, Fridgen TD. The Structure of the Protonated Adenine Dimer by Infrared Multiple Photon Dissociation Spectroscopy and Electronic Structure Calculations. J Phys Chem A 2009; 113:8099-107. [DOI: 10.1021/jp9033062] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Khadijeh Rajabi
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Kelly Theel
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Elizabeth A. L. Gillis
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Gregory Beran
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
| | - Travis D. Fridgen
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada, A1B 3X7, and Department of Chemistry, University of California, Riverside, California 92521
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26
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Shishkin OV, Gorb L, Leszczynski J. Conformational flexibility of pyrimidine rings of nucleic acid bases in polar environment: PCM study. Struct Chem 2009. [DOI: 10.1007/s11224-009-9477-1] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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27
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Shishkin OV, Konovalova IS, Gorb L, Leszczynski J. Novel type of mixed O–H···N/O–H···π hydrogen bonds: monohydrate of pyridine. Struct Chem 2009. [DOI: 10.1007/s11224-009-9412-5] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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28
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Su CF, Li YM, Zhou ZY, Wang XX, Ma KS. The density functional theory study on the ionization potentials and electron affinities of cytosine-formamide complexes. RUSSIAN JOURNAL OF PHYSICAL CHEMISTRY A 2009. [DOI: 10.1134/s0036024409030200] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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29
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Park HS, Nam SH, Song JK, Park SM, Ryu S. Density Functional Study of Intradimer Proton Transfers in Hydrated Adenine Dimer Ions, A2+(H2O)n (n = 0−2). J Phys Chem A 2008; 112:9023-30. [DOI: 10.1021/jp801238b] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hye Sun Park
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Sang Hwan Nam
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Jae Kyu Song
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Seung Min Park
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
| | - Seol Ryu
- Department of Chemistry, Kyunghee University, Seoul 130-701, Republic of Korea
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30
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Shukla MK, Leszczynski J. Hydration-Dependent Structural Deformation of Guanine in the Electronic Singlet Excited State. J Phys Chem B 2008; 112:5139-52. [DOI: 10.1021/jp7100557] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- M. K. Shukla
- Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
| | - Jerzy Leszczynski
- Computational Centre for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217
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31
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Kumar A, Sevilla MD, Suhai S. Microhydration of the guanine-cytosine (GC) base pair in the neutral and anionic radical states: a density functional study. J Phys Chem B 2008; 112:5189-98. [PMID: 18380501 DOI: 10.1021/jp710957p] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional study of the effects of microhydration on the guanine-cytosine (GC) base pair and its anion radical is presented. Geometries of the GC base pair in the presence of 6 and 11 water molecules were fully optimized in the neutral (GC-nH2O) and anion radical [(GC-nH2O)*-] (n = 6 and 11) states using the B3LYP method and the 6-31+G** basis set. Further, vibrational frequency analysis at the same level of theory (B3LYP/6-31+G**) was also performed to ensure the existence of local minima in these hydrated structures. It was found that water molecules surrounding the GC base pair have significant effects on the geometry of the GC base pair and promote nonplanarity in the GC base pair. The calculated structures were found to be in good agreement with those observed experimentally and obtained in molecular dynamics (MD) simulation studies. The water molecules in neutral GC-nH2O complexes lie near the ring plane of the GC base pair where they undergo hydrogen bonding with both GC and each other. However, in the GC anion radical complexes (GC-nH2O, n = 6, 11), the water molecules are displaced substantially from the GC ring plane. For GC-11H2O*-, a water molecule is hydrogen-bonded with the C6 atom of the cytosine base. We found that the hydration shell initially destabilizes the GC base pair toward electron capture as a transient anion. Energetically unstable diffuse states in the hydration shell are suggested to provide an intermediate state for the excess electron before molecular reorganization of the water molecules and the base pair results in a stable anion formation. The singly occupied molecular orbital (SOMO) in the anion radical complexes clearly shows that an excess electron localizes into a pi orbital of cytosine. The zero-point-energy (ZPE-) corrected adiabatic electron affinities (AEAs) of the GC-6H2O and GC-11H2O complexes, at the B3LYP/6-31+G** level of theory, were found to be 0.74 and 0.95 eV, respectively. However, the incorporation of bulk water as a solvent using the polarized continuum model (PCM) increases the EAs of these complexes to 1.77 eV.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University, Rochester, Michigan 48309, USA
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van Mourik T, Danilov VI, Gonzalez E, Deriabina A, Poltev VI. Indication of water droplet formation in hydrated clusters of cytosine and adenine: An electronic structure study using B3LYP, LMP2 and PM6. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.07.081] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kim HS, Ahn DS, Chung SY, Kim SK, Lee S. Tautomerization of Adenine Facilitated by Water: Computational Study of Microsolvation. J Phys Chem A 2007; 111:8007-12. [PMID: 17637049 DOI: 10.1021/jp074229d] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present calculations for the mechanism and the barrier heights of tautomerization of adenine. We find various pathways for the 9(H) <--> 7(H) and 9(H) <--> 3(H) tautomerization. One mechanism for the 9(H) --> 7(H) tautomerization involves an sp(3)- or carbene-type intermediate, whereas the other proceeds via imine intermediates. Tautomerization from the 9(H) tautomer to 7(H) or 3(H) is predicted to occur with a very large activation barrier (60-70 kcal/mol), indicating that the processes may not occur readily in the gas phase. Interactions with the water molecule(s) are found to lower the barrier tremendously. We suggest that dramatic lowering of the 9(H) --> 3(H) and 9(H) --> 7(H) barriers by microsolvating water molecules may facilitate the formation and observation of the 7(H) and 3(H) tautomers in the solution phase.
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Affiliation(s)
- Ho-Sung Kim
- College of Environmental Science and Applied Chemistry (BK21), Kyunghee University, Kyungki-do 449-701, Korea
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Delchev VB, Shterev IG, Mikosch H, Kochev NT. Investigation of the intermolecular proton transfer in the supersystems adenine-methanol/ethanol/i-propanol: MP2 and DFT levels study. J Mol Model 2007; 13:1001-8. [PMID: 17629753 DOI: 10.1007/s00894-007-0226-3] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2007] [Accepted: 06/13/2007] [Indexed: 11/24/2022]
Abstract
Twelve H-bonded supersystems constructed between the adenine tautomers and methanol, ethanol, and i-propanol were studied at the B3LYP and MP2 levels of theory using 6-311G(d,p) and 6-311++G(d,p) basis functions. The thermodynamic parameters of the complex formations were calculated in order to estimate the exact stability of the supersystems. It was proven that the calculated energy barriers of the alcohol-assisted proton transfers are about 60% lower than those of the intramolecular proton transfers in adenine found earlier (Gu and Leszczynski in J Phys Chem A 103:2744-2750, 1999).
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Affiliation(s)
- Vassil B Delchev
- Computer Chemistry group, University of Plovdiv, Plovdiv, Bulgaria.
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Rejnek J, Hobza P. Hydrogen-bonded nucleic acid base pairs containing unusual base tautomers: complete basis set calculations at the MP2 and CCSD(T) levels. J Phys Chem B 2007; 111:641-5. [PMID: 17228922 DOI: 10.1021/jp0661692] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The total interaction energies of altogether 15 hydrogen-bonded nucleic acid base pairs containing unusual base tautomers were calculated. The geometry properties of all selected adenine-thymine and guanine-cytosine hydrogen-bonded base pairs enable their incorporation into DNA. Unusual base pairing patterns were compared with Watson-Crick H-bonded structures of the adenine-thymine and guanine-cytosine pairs. The complete basis set (CBS) limit of the MP2 interaction energy and the CCSD(T) correction term, determined as the difference between the CCSD(T) and MP2 interaction energies, was evaluated. Extrapolation to the MP2 CBS limit was done using the aug-cc-pVDZ and aug-cc-pVTZ results, and the CCSD(T) correction term was determined with the 6-31G*(0.25) basis set. Final interaction energies were corrected while taking into account both tautomeric penalization determined at the CBS level and solvation/desolvation free energies. The situation for the adenine-thymine pairs is straightforward, and tautomeric pairs are significantly less stable than the Watson-Crick pair consisting of the canonical forms. In the case of the guanine-cytosine pair, the Watson-Crick structure made by canonical forms is again the most stable. The other two structures are, however, energetically rather similar (by 5 and 6 kcal/mol), which provides a very small but non-negligible chance of detecting these structures in the DNA double helix (1:5000). Due to the fact that DNA bases and base pairs incorporated into DNA are solvated less favorably than in isolated systems, this probability represents the very upper limit. The results clearly show how precisely the canonical building blocks of DNA molecules were chosen and how well their stability is maintained.
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Affiliation(s)
- Jaroslav Rejnek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo nAm. 2, 166 10 Prague 6, Czech Republic
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García-Teran JP, Castillo O, Luque A, García-Couceiro U, Beobide G, Roman P. Molecular recognition of adeninium cations on anionic metal-oxalato frameworks: an experimental and theoretical analysis. Inorg Chem 2007; 46:3593-602. [PMID: 17375914 DOI: 10.1021/ic062448s] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Reactions of adenine with water-soluble oxalato complexes at acidic pH give the compounds (1H,9H-ade)2[Cu(ox)2(H2O)] (1) [H2ade=adeninium cation (1+), ox=oxalato ligand (2-)] and (3H,7H-ade)2[M(ox)2(H2O)2].2H2O [M(II)=Co (2), Zn (3)]. The X-ray single crystal analyses show that the supramolecular architecture of all compounds is built up of anionic sheets of metal-oxalato-water complexes and ribbons of cationic nucleobases among them to afford lamellar inorganic-organic hybrid materials. The molecular recognition process between the organic and the inorganic frameworks determines the isolated tautomeric form of the adeninium cation found in the crystal structures: the canonical 1H,9H for compound 1, and the first solid-state characterized 3H,7H-adeninium tautomer for compounds 2 and 3. Density functional theory calculations have been performed to study the stability of the protonated nucleobase forms and their hydrogen-bonded associations by comparing experimental and theoretical results.
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Affiliation(s)
- Juan P García-Teran
- Departamento de Química Inorgánica, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apartado 644, E-48080 Bilbao, Spain
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Saha S, Wang F, Brunger MJ. Intramolecular proton transfer in adenine imino tautomers. MOLECULAR SIMULATION 2006. [DOI: 10.1080/08927020601067557] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Danilov VI, van Mourik T, Poltev VI. Modeling of the ‘hydration shell’ of uracil and thymine in small water clusters by DFT and MP2 methods. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.08.035] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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Mirzaei M, Elmi F, Hadipour NL. A Systematic Investigation of Hydrogen-Bonding Effects on the 17O, 14N, and 2H Nuclear Quadrupole Resonance Parameters of Anhydrous and Monohydrated Cytosine Crystalline Structures: A Density Functional Theory Study. J Phys Chem B 2006; 110:10991-6. [PMID: 16771352 DOI: 10.1021/jp060301g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.
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Affiliation(s)
- Mahmoud Mirzaei
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Hydrogen-bonding between cytosine and water: Computational evidence for a ring-opened complex. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.02.092] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Bao X, Sun H, Wong NB, Gu J. Microsolvation Effect, Hydrogen-Bonding Pattern, and Electron Affinity of the Uracil−Water Complexes U−(H2O)n (n = 1, 2, 3). J Phys Chem B 2006; 110:5865-74. [PMID: 16553392 DOI: 10.1021/jp055329r] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To achieve a systematic understanding of the influence of microsolvation on the electron accepting behaviors of nucleobases, the reliable theoretical method (B3LYP/DZP++) has been applied to a comprehensive conformational investigation on the uracil-water complexes U-(H(2)O)(n) (n = 1, 2, 3) in both neutral and anionic forms. For the neutral complexes, the conformers of hydration on the O2 of uracil are energetically favored. However, hydration on the O4 atom of uracil is more stable for the radical anions. The electron structure analysis for the H-bonding patterns reveal that the CH...OH(2) type H-bond exists only for di- and trihydrated uracil complexes in which a water dimer or trimer is involved. The electron density structure analysis and the atoms-in-molecules (AIM) analysis for U-(H(2)O)(n) suggest a threshold value of the bond critical point (BCP) density to justify the CH...OH(2) type H-bond; that is, CH...OH(2) could be considered to be a H-bond only when its BCP density value is equal to or larger than 0.010 au. The positive adiabatic electron affinity (AEA) and vertical detachment energy (VDE) values for the uracil-water complexes suggest that these hydrated uracil anions are stable. Moreover, the average AEA and VDE of U-(H(2)O)(n) increase as the number of the hydration waters increases.
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Affiliation(s)
- Xiaoguang Bao
- Drug Design & Discovery Center, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203, P. R. China
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Ekanayake KS, Lebreton PR. Activation barriers for DNA alkylation by carcinogenic methane diazonium ions. J Comput Chem 2006; 27:277-86. [PMID: 16342081 DOI: 10.1002/jcc.20334] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
Methylation reactions of the DNA bases with the methane diazonium ion, which is the reactive intermediate formed from several carcinogenic methylating agents, were examined. The SN2 transition states of the methylation reactions at N7, N3, and O6 of guanine; N7, N3, and N1 of adenine; N3 and O2 of cytosine; and O2 and O4 of thymine were calculated using the B3LYP density functional method. Solvation effects were examined using the conductor-like polarizable continuum method and the combined discrete/SCRF method. The transition states for reactions at guanine N3, adenine N7, and adenine N1 are influenced by steric interactions between the methane diazonium ion and exocyclic amino groups. Both in the gas phase and in aqueous solution, the methylation reactions at N atoms have transition states that are looser, and generally occur earlier along the reaction pathways than reactions at O atoms. The forming bonds in the transition states in water are 0.03 to 0.13 A shorter than those observed in the gas phase, and the activation energies are 13 to 35 kcal/mol higher. The combined discrete/SCRF solvation energy calculations using base-water complexes with three water molecules yield base solvation energies that are larger than those obtained from the CPCM continuum method, especially for cytosine. Reactivities calculated using barriers obtained with the discrete/SCRF method are consistent with the experimentally observed high reactivity at N7 of guanine.
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Affiliation(s)
- Kaushalya S Ekanayake
- Department of Chemistry, The University of Illinois at Chicago, 845 W. Taylor Street, Chicago, Illinois 60607-7061, USA
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Canuel C, Elhanine M, Mons M, Piuzzi F, Tardivel B, Dimicoli I. Time-resolved photoelectron and photoion fragmentation spectroscopy study of 9-methyladenine and its hydrates: a contribution to the understanding of the ultrafast radiationless decay of excited DNA bases. Phys Chem Chem Phys 2006; 8:3978-87. [PMID: 17028688 DOI: 10.1039/b606437j] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The excited state dynamics of the purine base 9-methyladenine (9Me-Ade) has been investigated by time- and energy-resolved photoelectron imaging spectroscopy and mass-selected ion spectroscopy, in both vacuum and water-cluster environments. The specific probe processes used, namely a careful monitoring of time-resolved photoelectron energy distributions and of photoion fragmentation, together with the excellent temporal resolution achieved, enable us to derive additional information on the nature of the excited states (pipi*, npi*, pisigma*, triplet) involved in the electronic relaxation of adenine. The two-step pathway we propose to account for the double exponential decay observed agrees well with recent theoretical calculations. The near-UV photophysics of 9Me-Ade is dominated by the direct excitation of the pipi* ((1)L(b)) state (lifetime of 100 fs), followed by internal conversion to the npi* state (lifetime in the ps range) via conical intersection. No evidence for the involvement of a pisigma* or a triplet state was found. 9Me-Ade-(H(2)O)(n) clusters have been studied, focusing on the fragmentation of these species after the probe process. A careful analysis of the fragments allowed us to provide evidence for a double exponential decay profile for the hydrates. The very weak second component observed, however, led us to conclude that the photophysics were very different compared with the isolated base, assigned to a competition between (i) a direct one-step decay of the initially excited state (pipi* L(a) and/or L(b), stabilised by hydration) to the ground state and (ii) a modified two-step decay scheme, qualitatively comparable to that occurring in the isolated molecule.
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Affiliation(s)
- Clélia Canuel
- Laboratoire Francis Perrin URA 2453 CEA-CNRS, CEA Saclay, Bat. 522, 91191, Gif-sur-Yvette Cedex, France.
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Hunter KC, Rutledge LR, Wetmore SD. The Hydrogen Bonding Properties of Cytosine: A Computational Study of Cytosine Complexed with Hydrogen Fluoride, Water, and Ammonia. J Phys Chem A 2005; 109:9554-62. [PMID: 16866407 DOI: 10.1021/jp0527709] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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McConnell TL, Wheaton CA, Hunter KC, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Adenine, Guanine, and Their 8-Oxo Derivatives. J Phys Chem A 2005; 109:6351-62. [PMID: 16833978 DOI: 10.1021/jp0509919] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Complexes between ammonia, water, or hydrogen fluoride and adenine, guanine, or their 8-oxo derivatives are investigated using density-functional theory. The binding strengths of the neutral and (N9) anionic complexes are considered for a variety of purine binding sites. The effects of hydrogen-bonding interactions on the (N9) acidity of the purine derivatives are considered as a function of the molecule bound and the binding site. It is found that hydrogen-bonding interactions with one molecule can increase the acidity of purine derivatives by up to 60 kJ mol(-1). The (calculated) simultaneous effects of up to four molecules on the acidity of the purine derivatives are also considered. Our data suggest that the effects of more than one molecule on the acidity of the purines are generally less than the sum of the individual (additive) effects, where the magnitude of the deviation from additivity increases with the number, as well as the acidity, of molecules bound. Nevertheless, the increase in the acidity due to additional hydrogen-bonding interactions is significant, where the effect of two, three, or four hydrogen-bonding interactions can be as large as approximately 95, 115, and 130 kJ mol(-1), respectively. The present study provides a greater fundamental understanding of hydrogen-bonding interactions involving the natural purines, as well as those generated through oxidative DNA damage, which may aid the understanding of important biological processes.
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Affiliation(s)
- Tom L McConnell
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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Kabelác M, Zendlová L, Reha D, Hobza P. Potential Energy Surfaces of an Adenine−Thymine Base Pair and Its Methylated Analogue in the Presence of One and Two Water Molecules: Molecular Mechanics and Correlated Ab Initio Study. J Phys Chem B 2005; 109:12206-13. [PMID: 16852505 DOI: 10.1021/jp045970d] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Potential energy surfaces of monohydrated and dihydrated adenine-thymine and 9-methyladenine-1-methylthymine base pairs were examined by the molecular dynamics/quenching technique using the Cornell et al. force field (J. Am. Chem. Soc. 1995, 117, 5179). Long runs of molecular dynamics/quenching calculations allowed us to evaluate the free energy surface. The most stable and populated structures found were fully reoptimized at the correlated ab initio level employing the resolution of identity Møller-Plesset method. A systematic study of the base pairs' microhydration using both the empirical and the high-level correlated ab initio approaches is presented for the first time. We show that the occurrence of water molecules and their gradually increasing number as well as the methylation of the bases favor stacked structures over the planar hydrogen-bonded ones. These results based on the correlated ab initio calculations are in the excellent agreement with data obtained from our previous empirical potential molecular dynamics study (Kabelác et al. Chem.-Eur. J. 2001, 7, 2067).
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Biomolecules and Complex Molecular Systems, 166 10 Prague 6, Czech Republic
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Kumar A, Mishra PC, Suhai S. Adiabatic Electron Affinities of the Polyhydrated Adenine−Thymine Base Pair: A Density Functional Study. J Phys Chem A 2005; 109:3971-9. [PMID: 16833718 DOI: 10.1021/jp0456178] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Adiabatic electron affinities (AEAs) of the adenine-thymine (AT) base pair surrounded by 5 and 13 water molecules have been studied by density functional theory (DFT). Geometries of neutral AT x nH2O and anionic (AT x nH2O)- complexes (n = 5 and 13) were fully optimized, and vibrational frequency analysis was performed at the B3LYP/6-31+G** level of theory. The optimized structures of the neutral (AT x nH2O) and (AT x nH2O)- complexes were found to be somewhat nonplanar. Some of the water molecules are displaced away from the AT ring plane and linked with one another by hydrogen bonds. The optimized structures of the complexes are found to be in a satisfactory agreement with the observed experimental and molecular dynamics simulation results. In the optimized anionic complexes, the thymine (T) moiety was found to be puckered, whereas the adenine (A) moiety remained almost planar. Natural population analysis (NPA) performed using the B3LYP/6-31+G** method shows that the thymine moiety in the anionic (AT x nH2O)- complexes (n = 5 and 13) has most of the excess electronic charge, i.e., approximately -0.87 and approximately -0.81 (in the unit of magnitude of the electronic charge), respectively. The zero-point energy corrected adiabatic electron affinities of the hydrated AT base pair were found to be positive both for n = 5 and 13 and have the values of 0.97 and 0.92 eV, respectively, which are almost three times the AEA of the AT base pair. The results show that the presence of water molecules appreciably enhances the EA of the base pair.
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Affiliation(s)
- Anil Kumar
- Department of Physics, Banaras Hindu University, Varanasi-221 005, India
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49
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Shishkin OV, Gorb L, Zhikol OA, Leszczynski J. Conformational analysis of canonical 2-deoxyribonucleotides. 2. Purine nucleotides. J Biomol Struct Dyn 2005; 22:227-44. [PMID: 15317483 DOI: 10.1080/07391102.2004.10506998] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
Abstract
The molecular structure of different conformers of isolated canonical purine 2'-deoxyribonucleotides 2-deoxyadenosine-5'-phosphate (pdA) and 2'-deoxyguanosine-5'-phosphate (pdG) was optimized using the B3LYP/6-31G(d) method. The results of the calculations reveal that the geometrical parameters and relative stability of the conformers significantly depend on the nature of the nucleobase, its orientation, the conformation of the furanose ring, the charge of the phosphate group and the character of the intramolecular hydrogen bonds. Analysis of the electron density distribution in purine nucleotides reveals the existence of a number of intramolecular hydrogen bonds. In general, the south conformer has a lower energy at the anti orientation of the base, and both conformers occur as the most stable for the syn orientation of the nucleobases. The results of the calculations reveal that the geometry and relative energy of the conformers of purine DNTs may be easily tuned by the charge of the phosphate group.
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Affiliation(s)
- Oleg V Shishkin
- Institute for Scintillation Materials, National Academy of Science of Ukraine, 60 Lenina Ave., Kharkiv 61001, Ukraine.
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50
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García-Terán JP, Castillo O, Luque A, García-Couceiro U, Román P, Lloret F. One-Dimensional Oxalato-Bridged Cu(II), Co(II), and Zn(II) Complexes with Purine and Adenine as Terminal Ligands. Inorg Chem 2004; 43:5761-70. [PMID: 15332829 DOI: 10.1021/ic049569h] [Citation(s) in RCA: 105] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
The reaction of nucleobases (adenine or purine) with a metallic salt in the presence of potassium oxalate in an aqueous solution yields one-dimensional complexes of formulas [M(mu-ox)(H(2)O)(pur)](n) (pur = purine, ox = oxalato ligand (2-); M = Cu(II) [1], Co(II) [2], and Zn(II) [3]), [Co(mu-ox)(H(2)O)(pur)(0.76)(ade)(0.24)](n)(4) and ([M(mu-ox)(H(2)O)(ade)].2(ade).(H(2)O))(n) (ade = adenine; M = Co(II) [5] and Zn(II) [6]). Their X-ray single-crystal structures, variable-temperature magnetic measurements, thermal behavior, and FT-IR spectroscopy are reported. The complexes 1-4 crystallize in the monoclinic space group P2(1)/a (No. 14) with similar crystallographic parameters. The compounds 5 and 6 are also isomorphous but crystallize in the triclinic space group P (No. 2). All compounds contain one-dimensional chains in which cis-[M(H(2)O)(L)](2+) units are bridged by bis-bidentate oxalato ligands with M(.)M intrachain distances in the range 5.23-5.57 A. In all cases, the metal atoms are six-coordinated by four oxalato oxygen atoms, one water molecule, and one nitrogen atom from a terminal nucleobase, building distorted octahedral MO(4)O(w)N surroundings. The purine ligand is bound to the metal atom through the most basic imidazole N9 atom in 1-4, whereas in 5 and 6 the minor groove site N3 of the adenine nucleobase is the donor atom. The crystal packing of compounds 5 and 6 shows the presence of uncoordinated adenine and water crystallization molecules. The cohesiveness of the supramolecular 3D structure of the compounds is achieved by means of an extensive network of noncovalent interactions (hydrogen bonds and pi-pi stacking interactions). Variable-temperature magnetic susceptibility measurements of the Cu(II) and Co(II) complexes in the range 2-300 K show the occurrence of antiferromagnetic intrachain interactions.
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Affiliation(s)
- Juan P García-Terán
- Departamento de Química Inorgánica, Universidad del País Vasco, Apartado 644, E-48080 Bilbao, Spain
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