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Rasmussen AM, Lind MC, Kim S, Schaefer HF. Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines. J Chem Theory Comput 2010; 6:930-9. [DOI: 10.1021/ct900478c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Rasmussen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Sunghwan Kim
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
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2
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Jaeger HM, Schaefer HF. Characterizing radiation-induced oxidation of DNA by way of the monohydrated guanine-cytosine radical cation. J Phys Chem B 2009; 113:8142-8. [PMID: 19445496 DOI: 10.1021/jp900444k] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The interaction of one water molecule with the guanine-cytosine radical cation has been studied with ab initio and density functional methods in order to help elucidate the nature of oxidized aqueous DNA. The theoretical spin density of [GC]*(+) reveals that the radical center is localized on guanine. The adiabatic ionization potential lowers from 7.63 to 6.71 eV in concurrence with the formation of the Watson-Crick base pair and hydration by one water molecule. A natural bond orbital analysis of partial charges shows that approximately 80% of the positive charge persists on guanine upon hydration and formation of the Watson-Crick base pair with cytosine. Hydration energies were computed with second-order Z-averaged perturbation theory (ZAPT2) using the aug-cc-pVDZ basis set at 11 stationary points on the B3LYP/DZP++ potential energy surface. The hydration energy at the global minimum is 14.2 kcal mol(-1). The lowest energy structures correspond to hydration near the glycosidic bond sites. Structural changes in the Watson-Crick base pair are predominantly seen for monohydration in the groove regions of double-helix DNA.
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Affiliation(s)
- Heather M Jaeger
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602-2556, USA.
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3
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Takenaka N, Koyano Y, Nakagawa Y, Nagaoka M. An optimum strategy for solution chemistry using semiempirical molecular orbital method: Importance of description of charge distribution. J Comput Chem 2009; 31:1287-96. [DOI: 10.1002/jcc.21416] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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4
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Buckin VA. Hydration of nucleic bases in dilute aqueous solutions. Apparent molar adiabatic and isothermal compressibilities, apparent molar volumes and their temperature slopes at 25 degrees C. Biophys Chem 2008; 29:283-92. [PMID: 17010915 DOI: 10.1016/0301-4622(88)85050-6] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/1987] [Revised: 11/10/1987] [Accepted: 11/16/1987] [Indexed: 10/18/2022]
Abstract
The concentration increment of the ultrasound velocity has been measured with an accuracy of +/- 0.03 cm/s in dilute aqueous solutions of a variety of nucleic bases and their derivatives in the concentration range 0.5-1.5 mg/g H2O at temperatures of 15-35 degrees C. A new method for the precise measurement of ultrasound velocity in small volumes of liquids has been used. The values of the apparent molar adiabatic compressibilities plus the corresponding temperature slopes, apparent molar volumes with their temperature slopes, and apparent molar isothermal compressibilities at infinite dilution have been obtained. The regularities describing the signs of these values and their dependence on the chemical structure of the solute have been revealed. It is shown that these regularities can be described as a consequence of partial 'normalization' of some of the properties of water around the bases, namely, weaker structural contribution to compressibility, less negative temperature slope of compressibility and less negative structural contribution to the coefficient of thermal expansion of water.
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Affiliation(s)
- V A Buckin
- Institute of Biological Physics, U.S.S.R Academy of Sciences, Pushchino 142292, U.S.S.R
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5
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Abstract
Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.
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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, Flemingovo, Prague, Czech Republic
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6
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Riauba L, Niaura G, Eicher-Lorka O, Butkus E. A Study of Cysteamine Ionization in Solution by Raman Spectroscopy and Theoretical Modeling. J Phys Chem A 2006; 110:13394-404. [PMID: 17165864 DOI: 10.1021/jp063816g] [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: 11/28/2022]
Abstract
Different cysteamine (H2N-CH2-CH2-SH) ionization forms have been studied by polarized Raman spectroscopy in solutions prepared with H2O and D2O and by DFT calculations at the B3LYP/6-31++G(d,p) level. To account for solvation effects, we employed the integral equation formalism polarizable continuum model (IEFPCM) option and explicit water molecules. Calculated relative energies and Raman spectra revealed that gauche rotamers around the C-C bond are the most stable conformers in solution. The experimental pKa values and Raman spectra of various ionization forms were best predicted by using a model with three explicit water molecules and the IEFPCM option. In general, the use of IEFPCM tends to lower the calculated frequencies for a few bands, but in some cases (S-H stretching mode) this effect is expressed very strongly. Potential energy distribution (PED) analysis of gauche conformers of various cysteamine ionization forms provided the possibility of discriminating spectroscopically methylene groups adjacent to sulfur, (CH2)S, and nitrogen, (CH2)N, sites. In general, stretching and scissoring modes as well as wagging and twisting vibrations of the (CH2)N group were found to be at higher frequencies. The influence of ionization of SH and NH2 groups on the vibrational spectrum is discussed, and Raman markers for further amine group ionization studies are suggested.
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Affiliation(s)
- Laurynas Riauba
- Department of Organic Chemistry, Vilnius University, Naugarduko 24, LT-03225 Vilnius, Lithuania.
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7
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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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8
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Whittleton SR, Hunter KC, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Uracil Derivatives. J Phys Chem A 2004. [DOI: 10.1021/jp048318r] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sarah R. Whittleton
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
| | - Ken C. Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
| | - Stacey D. Wetmore
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8 Canada
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9
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Gaigeot MP, Sprik M. Ab Initio Molecular Dynamics Study of Uracil in Aqueous Solution. J Phys Chem B 2004. [DOI: 10.1021/jp049940m] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marie-Pierre Gaigeot
- Laboratoire de Modelisation des Systemes Moleculaires Complexes, Université d'Evry val d'Essonne, Rue Pere A Jarland, F-91025, France
| | - Michiel Sprik
- Department of Chemistry, University of Cambridge, Lensfield Road, CB2 1EW, United Kingdom
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10
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Di Laudo M, Whittleton SR, Wetmore SD. Effects of Hydrogen Bonding on the Acidity of Uracil. J Phys Chem A 2003. [DOI: 10.1021/jp035496w] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Mariana Di Laudo
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Sarah R. Whittleton
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
| | - Stacey D. Wetmore
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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11
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Tong J, Li XY. Ab initio study on electron excitation and electron transfer in tryptophan–tyrosine system. Chem Phys 2002. [DOI: 10.1016/s0301-0104(02)00789-9] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Li XY, Hu CX. Theoretical investigation of electron transfer transition in tetracyanoethylene-contained organic complexes. J Comput Chem 2002; 23:874-86. [PMID: 11984849 DOI: 10.1002/jcc.10079] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
In this work, the authors use complete active space self-consistent field method to investigate the photoinduced charge-separated states and the electron transfer transition in complexes ethylene-tetracyanoethylene and tetramethylethylene-tetracyanoethylene. Geometries of isolated tetracyanoethylene, ethylene, and tetramethylethylene have been optimized. The ground state and the low-lying excited states of ethylene and tetracyanoethylene have been optimized. The state energies in the gas phase have been obtained and compared with the experimentally observed values. The torsion barrier of tetracyanoethylene has been investigated through the state energy calculation at different conformations. Attention has been particularly paid to the charge-separated states and the electron transfer transition of complexes. The stacked conformations of the donor-acceptor complexes have been chosen for the optimization of the ground and low-lying excited states. Equilibrium solvation has been considered by means of conductor-like screening model both in water and in dichloromethane. It has been found that the donor and tetracyanoethylene remain neutral in complexes in ground state (1)A(1) and in lowest triplet state (3)B(1), but charge separation appears in excited singlet state (1)B(1). Through the correction of nonequilibrium solvation energy based on the spherical cavity approximation, pi-->pi* electron transfer transition energies have been obtained. Compared with the experimental measurements in dichloromethane, the theoretical results in the same solvent are found higher by about 0.5 eV.
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Affiliation(s)
- Xiang-Yuan Li
- College of Chemical Engineering, Sichuan University, Chengdu 610065, People's Republic of China.
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13
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The keto–amino/enol tautomerism of cytosine in aqueous solution. A theoretical study using combined discrete/self-consistent reaction field models. Chem Phys 2000. [DOI: 10.1016/s0301-0104(99)00371-7] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Cramer CJ, Truhlar DG. Implicit Solvation Models: Equilibria, Structure, Spectra, and Dynamics. Chem Rev 1999; 99:2161-2200. [PMID: 11849023 DOI: 10.1021/cr960149m] [Citation(s) in RCA: 1722] [Impact Index Per Article: 68.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christopher J. Cramer
- Department of Chemistry and Supercomputer Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431
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15
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Chahinian M, Seba H, Ancian B. Hydration structure of uracil as studied by 1D and 2D heteronuclear Overhauser spectroscopy: evidence for the formation of a trihydrate in the first solvation shell. Chem Phys Lett 1998. [DOI: 10.1016/s0009-2614(98)00109-2] [Citation(s) in RCA: 53] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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16
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Danilov VI, Zheltovsky NV, Slyusarchuk ON, Poltev VI, Alderfer JL. The study of the stability of Watson-Crick nucleic acid base pairs in water and dimethyl sulfoxide: computer simulation by the Monte Carlo method. J Biomol Struct Dyn 1997; 15:69-80. [PMID: 9283981 DOI: 10.1080/07391102.1997.10508947] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
An extensive computer simulation of nucleic acid bases and Watson-Crick base pairs in a water cluster and DMSO cluster is performed by the Monte Carlo method. It is demonstrated that the unfavorable energetics of pair formation in a water cluster is determined by the significant destabilizing contribution of solvent to the energy of complex formation. It is shown that the formation of coplanar base pairs in a DMSO cluster is favorable. The DMSO cluster stabilizes A-U and A-T base pairs and the insignificant destabilization of the G-C base pair by a DMSO cluster is much less than the stabilization which occurs due to the attraction between bases.
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Affiliation(s)
- V I Danilov
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, Kiev, Ukraine
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17
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Donnamaria MC, Marañon J, Howard EI, Fantoni A, Grigera JR. The Influence of Charge Calculation on Molecular Dynamics Simulation of Adenine in Water. MOLECULAR SIMULATION 1996. [DOI: 10.1080/08927029608022356] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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18
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Varnek AA, Wipff G, Glebov AS, Feil D. An application of the Miertus-Scrocco-Tomasi solvation model in molecular mechanics and dynamics simulations. J Comput Chem 1995. [DOI: 10.1002/jcc.540160102] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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19
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Orozco M, Luque FJ. Self-consistent reaction field computation of the reactive characteristics of DNA bases in water. Biopolymers 1993. [DOI: 10.1002/bip.360331211] [Citation(s) in RCA: 33] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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20
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21
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Sukhodub LF, Teplitsky AB. Associate hydrations and energies of nucleotide bases as revealed by low-temperature field ionization mass-spectrometric data. J Biomol Struct Dyn 1991; 8:889-907. [PMID: 2059345 DOI: 10.1080/07391102.1991.10507851] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The formation of water clusters, polyhydrates of nucleotide bases and their associates during simultaneous condensation of water and base molecules in vacuo onto a surface of a needle emitter cooled to 170 K was studied by field ionization mass spectrometry. It was found that different emitter temperatures are characterized by a specific distribution of intensities of cluster currents, depending on the number of water molecules in clusters. These distributions correlate with structural peculiarities and the relative energetics of formation of water clusters, polyhydrates of nucleotide bases and their associates at low temperature. The features observed in mass spectra for clusters m9Ade (H2O)5, m1Ura (H2O)4 and m9Ade m1Ura (H2O)2 are treated as a result of formation of energetically favorable structures stabilized by H-bonded bridges of water molecules. The relative association constants and formation enthalpies of the noncomplementary pairs Ade Cyt, Gua Ura and the associates which model the aminoacid-base complexes m1Ura Gln and m1.3(2)Thy Gln were determined from the temperature dependencies of the intensities of mass spectra peaks in the range 290-320 K.
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Affiliation(s)
- L F Sukhodub
- Applied Physics Division, Ukrainian Academy of Sciences, Sumy, USSR
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22
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Sorokin VA, Galkin VL, Valeev VA, Arkhipova ES, Gladchenko GO, Blagoi YP. Studies in hydration energetics of nucleic acid components by the differential UV-spectroscopic method. ACTA ACUST UNITED AC 1989. [DOI: 10.7124/bc.0000e4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- V. A. Sorokin
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
| | - V. L. Galkin
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
| | - V. A. Valeev
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
| | - E. S. Arkhipova
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
| | - G. O. Gladchenko
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
| | - Yu. P. Blagoi
- Institute for Low Temperature Physics and Engineering, Academy of Sciences of the Ukrainian SSR
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23
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Frecer V, Májeková M, Miertuš S. Approximate methods for solvent effects calculations on biomolecules. ACTA ACUST UNITED AC 1989. [DOI: 10.1016/0166-1280(89)80020-x] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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24
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25
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Neto MDO. Rapid Location of the Preferred Interaction Sites between Small Polar Molecules and Macromolecules. I. Binding of Water to the Component Units of Nucleic Acids. J Comput Chem 1986. [DOI: 10.1002/jcc.540070503] [Citation(s) in RCA: 21] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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26
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Zielenkiewicz A, Zielenkiewicz W, Sukhodub LF, Glukhova OT, Teplitsky AB, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases V. Enthalpies of hydration of N-methylated adenines. J SOLUTION CHEM 1984. [DOI: 10.1007/bf00647691] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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27
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Giessner-Prettre C, Langlet J, Caron F. Theoretical study of the geometrical arrangement of GT and GA wobble pairs in two short duplexes, Proton NMR chemical shifts and interaction energy calculations. J Theor Biol 1984; 107:211-28. [PMID: 6325825 DOI: 10.1016/s0022-5193(84)80023-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
NMR shielding constants are calculated for the base protons of duplexes formed by the dodecamer d(CGTGAATTCGCG) and the decamer d(CCAAGATTGG). A good agreement with experimental data is obtained for B-DNA helices in which the wobble GT and GA pairs are in the plane of the corresponding GC pairs of the parent duplexes formed by d(CGCGAATTCGCG) and d(CCAAGCTTGG), if the glycosyl bonds of T and G or A and G are symmetrical with respect to the dyad axis of the Watson-Crick GC pair. Interaction energy calculations show that this type of geometrical arrangement, which implies a distortion of the ribonphosphate backbone of both strands of the duplexes are more stable than those in which only one strand has its conformation modified by the presence of the wobble pair. For the duplex containing the GA pair, NMR chemical shifts as well as interaction energy computations favour the Watson-Crick hydrogen bonding scheme. The variation of the different contributions (intrastrand, interstrand, pair-pair) to the interaction energy between the bases of the duplexes, with the geometrical arrangement of the wobble pairs, is reported.
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28
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Pohorille A, Pratt LR, Burt SK, MacElroy RD. Solution influence on biomolecular equilibria: nucleic acid base associations. J Biomol Struct Dyn 1984; 1:1257-80. [PMID: 6401105 DOI: 10.1080/07391102.1984.10507516] [Citation(s) in RCA: 31] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
This paper consists of two parts. In the first part, the general problem of biomolecular equilibria in solution is considered, stressing that molecular interactions ultimately determine the answer to this problem. It is discussed how computer simulation techniques can reliably treat the problem and several pitfalls of computer simulation to be avoided are pointed out. Other approaches based on modeling and conceptual simplifications such as perturbative methods, long-range interaction approximations, surface thermodynamic approaches, and hydration shell models are discussed. In the second part, the results of Monte Carlo calculations on the associations of nucleic acid bases in water and carbon tetrachloride are presented. Stacked self-associations are found to be preferred in water and hydrogen-bonded complexes are favored in nonpolar solutions, in agreement with experimental data. The influence of the solvent on base associations is explained in terms of solute-solvent and solvent-solvent contributions to the total energy. No enthalpic stabilization of the complexes by the solvent was found. The results are used to examine the validity of various approximations discussed in the first part of the paper.
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Affiliation(s)
- A Pohorille
- Department of Chemistry, University of California, Berkeley 94720
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29
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Ray NK, Bolis G, Shibata M, Rein R. Potential derived point charge model study of electrostatic interaction energies in some complexes of water with uracil, thymine, and cytosine. INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY. QUANTUM BIOLOGY SYMPOSIUM : PROCEEDINGS OF THE INTERNATIONAL SYMPOSIUM ON QUANTUM BIOLOGY AND QUANTUM PHARMACOLOGY. INTERNATIONAL SYMPOSIUM ON QUANTUM BIOLOGY AND QUANTUM PHARMACOLOGY 1984; 11:257-66. [PMID: 11540815 DOI: 10.1002/qua.560260727] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/16/2023]
Abstract
Potential derived (PD) point charges and segmental multipole moments are calculated for water, uracil, thymine, and cytosine using STO-3G quality wave functions. The PD point charges are used to estimate the electrostatic interaction energies for a series of complexes of water with these nucleic acid bases. It is shown here that the results obtained using simple PD charge model is very similar to those obtained from more elaborate segmental multipole moment analysis.
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Affiliation(s)
- N K Ray
- Department of Experimental Pathology and Biophysics, Roswell Park Memorial Institute, Buffalo, New York 14263, USA
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30
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Abstract
The molecular electrostatic potential (MEP) and the molecular electrostatic field (MEF) are associated with significantly different patterns of distribution in the nucleic acids and their constituents. In particular, a) while the values of the minimal potentials at the reactive sites of the bases or at the phosphates increase manyfold when going from the subunits to the double helix, the values of the field undergo only very small changes under the same circumstances and b) while the deepest potentials are located in the grooves of the double helix, the greatest fields are concentrated on the phosphates of the backbone. They are also influenced differently by such environmental factors as counterion screening: while the absolute values of the potentials are profoundly reduced, the fields are increased with respect to those of the unscreened acids. MEP and MEF also govern the electrostatics of interaction of DNA with different types of species. The MEP being of particular significance in this respect for interaction with cations and the MEF for the association with neutral dipolar molecules. A number of examples are given to illustrate the significance of this situation for different conformers of DNA.
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Affiliation(s)
- B Pullman
- Institut de Biologie Physico-Chimique Laboratoire de Biochimie Theorique, associé au C.N.R.S., Paris, France
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31
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32
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Palmer MH, Wheeler J, Kwiatkowski JS, Lesyng B. AB initio and semiempirical molecular orbital studies on cytosine and N(4)-hydroxycytosine. ACTA ACUST UNITED AC 1983. [DOI: 10.1016/0166-1280(83)87008-0] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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33
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34
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Del Bene JE. Molecular orbital theory of the hydrogen bond. XXX. Water-cytosine complexes. J Comput Chem 1983. [DOI: 10.1002/jcc.540040213] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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35
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36
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Alkylated Uracils I, Sukhodu LF, Yanson IK, Shelkovski VS, Wierzchowski KL. Mass-spectrometric investigations on hydration of nucleic acid components in vacuum. Biophys Chem 1982; 15:149-55. [PMID: 17000425 DOI: 10.1016/0301-4622(82)80027-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/1981] [Revised: 12/02/1981] [Indexed: 11/16/2022]
Abstract
Association reactions between water and alkylated uracils. occurring under field-ionization conditions in a mass spectrometer at the tungsten point emitter surface, were studied at several temperatures. The origin of peaks observed in the mass spectra at m/e ratios corresponding to M+H and M+H-H2O were attributed to M-H2O and M-(H2O)2 hydrates, respectively, hydrogen-bonded via carbonyl groups of the diketopyrimidines (M) investigated. The appearance of these ions is explained in terms of the field-ionization mechanism of the neutral hydrates involving intramolecular H+ transfer and concomitant release of the OH+ radical. Measurements of the relative peak intensities allowed the calculation of apparent equilibrium constants. K(ass). for the association reactions, and hence the respective van't Hoff enthalpies of hydrat'on. The latter are discussed in connection with the available quantum-mechanical hydration energies for specific groups of respective canonical nucleic acid bases and experimental enthalpies of hydration of alkylated uracils with water. Specific hydration is estimated to contribute about 15-20% to the total enthalpy of interaction of the solutes with their hydration shells.
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Affiliation(s)
- I Alkylated Uracils
- Physico-Technical Institute of Low Temperatures, Ukrainian Academy of Sciences, 310164 Kharkov, U.S.S.R
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Teplitsky AB, Glukhova OT, Sukhodub LF, Yanson IK, Zielenkiewicz A, Zielenkiewicz W, Kosinski J, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases. Biophys Chem 1982; 15:139-47. [PMID: 17000424 DOI: 10.1016/0301-4622(82)80026-4] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/1981] [Revised: 12/02/1981] [Indexed: 10/17/2022]
Abstract
Enthalpies of sublimation, DeltaH degrees (subl) and of solution in water, DeltaH degrees (sol) were determined for a series of crystalline 1,3-dimethyl-uracil derivatives substituted at the C5-ring carbon atom with alkyl groups (-C(n)H(2n+1), n = 2-4) and some of their C(5.6)-cyclooligomethylene analogues (-(CH2)(n)-, n = 3-5). From these data. enthalpies of hydration DeltaH degrees (hydr)= DeltaH degrees (sol) - DeltaH degrees (subl) were calculated and corrected for energies of cavity formation in pure liquid water in order to obtain enthalpies of interaction, DeltaH degrees (int) of the solutes with their hydration shells. The latter are discussed together with the recalculated DeltaH degrees (int) for variously methylated uracils, obtained previously according to a simplified correction procedure, in terms of perturbations in the energy and scheme of hydration of the diketopyrimidine ring brought about by alkyl substitution. It was found that each -CH2-group added with an alkyl substitution contributes favorably about -20 kJ mol(-1) toDeltaH degrees (int). This contribution is partially cancelled by the unfavorable contribution to DeltaH degrees (int) connected with removal of some water molecules bound in the first and subsequent hydration layers by an alkyl substituent. This is particularly evident on substitution at the polar side of the diketopyrimidine ring on which water molecules are expected to be bound specifically.
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Affiliation(s)
- A B Teplitsky
- Physico-Technical Institute of Low Temperatures, Ukrainian Academy of Sciences, 310164 Kharkov, U.S.S.R
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38
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Del Bene JE. Molecular orbital theory of the hydrogen bond. XXIX. Water–thymine complexes. J Chem Phys 1982. [DOI: 10.1063/1.443097] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Rajalakshmi S, Rao PM, Sarma DS. Carcinogen-DNA interaction: complexing of distamycin-A with DNA is necessary for its inhibitory effect on the N-methyl-N-nitrosourea induced methylation of DNA. Chem Biol Interact 1981; 35:125-8. [PMID: 7471311 DOI: 10.1016/0009-2797(81)90068-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
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40
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Miertuš S, Scrocco E, Tomasi J. Electrostatic interaction of a solute with a continuum. A direct utilizaion of AB initio molecular potentials for the prevision of solvent effects. Chem Phys 1981. [DOI: 10.1016/0301-0104(81)85090-2] [Citation(s) in RCA: 5622] [Impact Index Per Article: 130.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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41
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Frechet D, Gabarro-Arpa J. Thermal perturbation differential spectra of ribonucleic acids. III. Chain length effect. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 609:1-13. [PMID: 6157416 DOI: 10.1016/0005-2787(80)90196-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
Thermal perturbation differential spectra of several adenylic acid oligomers, two single-strand polyribonucleotides, poly(A) and poly(C), and five trinucleoside diphosphates, U-A-A, U-A-G, U-G-A, C-U-C and C-U-A, were obtained and analysed. It is shown that these differential spectra cannot be entirely described by the nearest-neighbour approximation devised from the appropriate mononucleotides and dinucleoside monophosphates. In an attempt to determine the origin of this discrepancy, we have examined the possible optical changes arising from increased electronic interactions, changes in conformation, solvent accessibility or thermodynamic properties. This study indicates that dinucleoside monophosphates on one the hand and trinucleoside diphosphates on the other hand, are separate classes from the conformational point of view. The capacity to assume stacks, absent or negligible in higher oligomers or polymers, makes them poor models for the stacking interaction in longer nucleic acids. It is also shown that in trinucleoside diphosphates, interaction between the two terminal bases arising from bulging out of the middle base is very likely to occur. This type of interaction has to be taken into account in the description of the temperature perturbation differential spectra of trimers.
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Gresh N, Pullman B. A theoretical study of the interaction of guanine and cytosine with specific amino acid side chains. BIOCHIMICA ET BIOPHYSICA ACTA 1980; 608:47-53. [PMID: 6770903 DOI: 10.1016/0005-2787(80)90132-x] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Quantum-mechanical computations are performed on the in vacuo and in water interactions between the purine bases guanine and cytosine and the side chains of the amino acids arginine, lysine, glutamic acid and glutamine. The results predict that while guanine should be the more strongly interacting base both in vacuo and in water, lysine should be the most strongly interacting amino acid in vacuo and arginine the most strongly interacting amino acid in water solvent. The theoretical results on the interactions in water agree satisfactorily with experimentation.
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Teplitsky AB, Yanson IK, Glukhova OT, Zielenkiwicz A, Zielenkiewicz W, Wierzchowski KL. Thermochemistry of aqueous solutions of alkylated nucleic acid bases. Biophys Chem 1980; 11:17-21. [PMID: 16997235 DOI: 10.1016/0301-4622(80)85003-4] [Citation(s) in RCA: 44] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/1979] [Revised: 08/22/1979] [Indexed: 10/18/2022]
Abstract
Enthalpies of sublimation DeltaH(0)(subl) crystalline uracil, thymine and their methylated derivatives as well as of N,N-diethylthymine were determinated by the quartz-resonator method and mass spectrometry. Enthalpies of solution at infinite dilution DeltaH(0)(sol) in water of aBcylated compounds were obtained calorimetrically. Hence the calculated enthalpies of hydration: DeltaH(0)(hydrsubal) = DeltaH(0)(sol) - DeltaH(0)(subl), were corrected for energies of cavity formation in pure liquid water to yield enthalpies of interaction DeltaH(0)(sint) of the solutes with their hydration shells. For uracil DeltaH(0)(int) = -59.8 kJ mole(-1) was obtained in this way. This value decreased linearly on N-methyl substitution with a mean increment of about 6.5 kJ mole CH2(-1). After C(5) or C(6) ring substitution it increased by about 3 kJ. These results are discussed in connection with heat of dilution data and theoretical schemes of hydration.
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Affiliation(s)
- A B Teplitsky
- Physico-Technical Institute of Low Temperatures, Ukr. SSR, Academy of Sciences, 310164 Kharkov, USSR
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