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Gorb L, Shishkin OV, Zubatiuk T. The Structure of DNA Fragments: Quantum-Chemical Modelling. BBA ADVANCES 2023; 3:100082. [PMID: 37082263 PMCID: PMC10074966 DOI: 10.1016/j.bbadva.2023.100082] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/24/2022] [Revised: 02/07/2023] [Accepted: 02/08/2023] [Indexed: 02/13/2023] Open
Abstract
In this review, we analyze and systematize our computational studies of the nucleic acid duplex formations and thermodynamic stability under the different factors of investigation. The proposed structural models of mini-helix contains N nucleobase pairs (N = 3-5); QM structural data suggest that the helical conformations of mini-helix adopt geometrical parameters comparable to those of natural A- and B-DNA forms under specific conditions as micro hydration and charge compensation. The gas-phase models adopt non regular conformations between the helical form and a ladder form.. The natural helical shape of DNA mini-helix is stabilized by the presence of counterions or by explicit micro-hydration of the major and minor groves. The presence of aqueous solution is shown as a minor factor for the helical shape formation. The studies are performed at the level of density functional theory.
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Affiliation(s)
- Leonid Gorb
- Institute of Molecular Biology and Genetics, National Academy of Sciences of Ukraine, 150 Zabolotnogo str., 03680 Kyiv, Ukraine
- QSAR Lab Ltd., Trzy Lipy 3, B, 80-172 Gdańsk, Poland
- Corresponding author
| | - Oleg V. Shishkin
- State Scientific Institution “Institute for Single Crystals” of National Academy of Sciences of Ukraine, Nauky Av. 60, 61072 Kharkiv, Ukraine
| | - Tetiana Zubatiuk
- Department of Chemistry, Mellon College of Science, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
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Karpel RL, Kustin K, Wolff MA. Relaxation and NMR Spectra of Nickel (II) - Purine Complexes. Isr J Chem 2013. [DOI: 10.1002/ijch.197300073] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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4
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Danilov V, Tolokh I, Poltev V, Malenkov G. Nature of the stacking interaction of nucleotide bases in water: a Monte Carlo study of the hydration of uracil molecule associates. FEBS Lett 2001. [DOI: 10.1016/0014-5793(84)80135-0] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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Colson AO, Sevilla MD. Elucidation of primary radiation damage in DNA through application of ab initio molecular orbital theory. Int J Radiat Biol 1995; 67:627-45. [PMID: 7608626 DOI: 10.1080/09553009514550751] [Citation(s) in RCA: 145] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
This review summarizes the results of recent ab initio molecular orbital calculations performed on DNA constituents that attempt to further our understanding of the radiation-induced damage to DNA. The results reviewed include calculations performed on the four individual DNA bases, the base pairs in gas phase and modelled aqueous phase, the deoxyribose moiety, and a portion of the sugar-phosphate backbone. The emphasis is on the electron affinities and ionization potentials of the radical species calculated under various conditions (i.e. gas phase, aqueous phase, proton transfer, base stacking), as it has been shown that the initial ion radical distribution is largely a function of these two properties. Theoretical studies of the electronic excited states of the individual bases and radioprotection of the biomolecule by various thiol compounds are also reviewed. Finally, a summary is provided to allow for further elaboration of the current model for radiation damage to DNA and to show the present advantages and limitations of ab initio theory in the investigation of such processes.
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Affiliation(s)
- A O Colson
- Chemistry Department, Oakland University, Rochester, MI 48309, USA
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6
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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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Párkányi C, Boniface C, Aaron JJ, Gaye MD, Ghosh R, von Szentpály L, RaghuVeer KS. Electronic absorption and fluorescence spectra and excited singlet-state dipole moments of biologically important pyrimidines. Struct Chem 1992. [DOI: 10.1007/bf00672795] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Smith PE, al-Obeidi F, Pettitt BM. Aspects of the design of conformationally constrained peptides. Methods Enzymol 1991; 202:411-36. [PMID: 1664477 DOI: 10.1016/0076-6879(91)02021-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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Techera M, Daemen LL, Prohofsky EW. Analysis of a nonlinear model for the DNA double helix: Energy transfer in an inhomogeneous chain. PHYSICAL REVIEW. A, ATOMIC, MOLECULAR, AND OPTICAL PHYSICS 1990; 42:1008-1011. [PMID: 9904120 DOI: 10.1103/physreva.42.1008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/22/2023]
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Aida M. Characteristics of the Watson-Crick type hydrogen-bonded DNA base pairs: Anab initio molecular orbital study. J Comput Chem 1988. [DOI: 10.1002/jcc.540090411] [Citation(s) in RCA: 47] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Hobza P, Mehlhorn A, Čársky P, Zahradník R. Stacking interactions: Ab initio SCF and MP2 study on (H2O)2, (H2S)2, (HCN)2, (CH2O)2 and (C2H4)2. ACTA ACUST UNITED AC 1986. [DOI: 10.1016/0166-1280(86)80030-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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13
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Danilov VI, Tolokh IS. Nature of the stacking of nucleic acid bases in water: A Monte Carlo study. ACTA ACUST UNITED AC 1985. [DOI: 10.1016/0166-1280(85)80195-0] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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14
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Danilov VI, Tolokh IS. Nature of the stacking of nucleic acid bases in water: a Monte Carlo simulation. J Biomol Struct Dyn 1984; 2:119-30. [PMID: 6400926 DOI: 10.1080/07391102.1984.10507551] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
The results of a Monte Carlo simulation of the hydration of uracil and thymine molecules, their stacked dimers and hydrogen-bonded base pairs are presented. Simulations have been performed in a cluster approximation. The semiempirical atom-atom potential functions have been used (cluster consisting of 200 water molecules). It has been shown that the stacking interactions of uracil and thymine molecules in water arise mainly due to the increase in the water-water interaction during the transition from monomers to dimer. It has been found out that stacked base associates are more preferable than base pairs in water. This preference is mainly due to the energetically more favourable structure of water around the stack.
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Affiliation(s)
- V I Danilov
- Department of Quantum Biophysics, Academy of Sciences of the Ukrainian SSR, Kiev, USSR
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Abstract
Enthalpies and entropies of helix stabilization due to addition of 3' terminal unpaired nucleotides to a CCGG or GGCC core double helix are derived from UV melting studies. The results suggest stacking provides a significant fraction of the free energy of a terminal base pair. The effects of temperature, aggregation, and ionic strength on the determination of thermodynamic parameters are considered. Helix propagation parameters are revised and extended based on recent additions to the data set.
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Affiliation(s)
- S M Freier
- Department of Chemistry, University of Rochester, New York 14627
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Förner W, Otto P, Ladik J. Energies of interactions between purine and pyrimidine bases in B- and Z-DNA. Chem Phys 1984. [DOI: 10.1016/0301-0104(84)85155-1] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Bubienko E, Cruz P, Thomason JF, Borer PN. Nearest-neighbor effects in the structure and function of nucleic acids. PROGRESS IN NUCLEIC ACID RESEARCH AND MOLECULAR BIOLOGY 1983; 30:41-90. [PMID: 6198694 DOI: 10.1016/s0079-6603(08)60683-2] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Albergo DD, Turner DH. Solvent effects on thermodynamics of double-helix formation in (dG-dC)3. Biochemistry 1981; 20:1413-8. [PMID: 7225339 DOI: 10.1021/bi00509a002] [Citation(s) in RCA: 40] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The thermodynamics of double-helix formation by (dG-dC)3 have been measured in aqueous solvent mixtures containing 10 mol % methanol, ethanol, 1-propanol, formamide, N,N-dimethylformamide, or urea and 20 mol % ethanol. Optical activity measurements indicate the conformation of the double helix at 3 degree C is the same in all the solvent mixtures except 20 mol % ethanol. All the cosolvents destabilize the helix relative to water. With 10 mol % alcohol cosolvents, this destabilization is associated with a more unfavorable entropy change averaging approximately 8% and a more favorable enthalpy change averaging approximately 5%. This is consistent with a small contribution of hydrophobic bonding to stability. In contrast, the destabilization by formamide, N,N-dimethylformamide, and urea is associated with a more unfavorable enthalpy change averaging approximately 23% and a more favorable entropy change averaging approximately 21%. Since all three of these cosolvents have dipole moments larger than water, this is consistent with increased competition for dipolar interactions between the nucleic acid bases. None of the results correlate with any one bulk solvent parameter such as surface tension, viscosity, or dielectric constant. With 20 mol % ethanol, optical activity measurements are consistent with a partial B to C form transition. This is associated with a 27% less favorable enthalpy and 25% more favorable entropy for helix formation relative to water. Since the B to C transition is associated with helix dehydration, this may imply a significant contribution of bound water to stability.
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Freier SM, Hill KO, Dewey TG, Marky LA, Breslauer KJ, Turner DH. Solvent effects on the kinetics and thermodynamics of stacking in poly(cytidylic acid). Biochemistry 1981; 20:1419-26. [PMID: 7225340 DOI: 10.1021/bi00509a003] [Citation(s) in RCA: 64] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The Raman laser temperature-jump technique has been used to measure the kinetics of the coil to helix reaction of poly(cytidylic acid) [poly(C)] in aqueous cosolvent mixtures. The rate of helix formation has a low activation energy and is proportional to reciprocal solvent viscosity. The observations suggest helix formation is rotationally diffusion controlled. The rate of coil formation in poly(C) has an activation energy of approximately 11 kcal/mol, presumably reflecting the electronic stacking interactions which stabilize the helix. Viscous cosolvents, glycerol or sucrose, slow down the rate of coil formation; acetonitrile and formamide at 5 mol % increase the rate relative to that in water. The polar cosolvents may specifically attack a cytosine stack. The absorbance vs. temperature profiles for poly(C) are analyzed with the one-dimensional Ising model. When only optical data are used, the cooperativity parameter, sigma, and the enthalpy, delta H, cannot be uniquely determined. A method is proposed that allows determination of sigma by combining spectroscopic and calorimetric data. The values of sigma derived for poly(C) are between 0.8 and 1.0, and delta H is about -9 kcal/mol of stack. An alternative method using integration of the excess heat capacity curve and extrapolation to fully stacked and random coil species yields a delta H of -7 kcal/mol of stack.
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Schwartz HM, MacCoss M, Danyluk SS. 17O NMR spectroscopy of nucleoside derivatives; bonding characteristics of pyrimidine carbonyls. Tetrahedron Lett 1980. [DOI: 10.1016/0040-4039(80)80194-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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22
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Otto P. Ab intio calculationns of the vertical interaction between two and three cytosine molecules. Chem Phys Lett 1979. [DOI: 10.1016/0009-2614(79)80758-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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23
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Hydration scheme of the purine and pyrimidine bases and base-pairs of the nucleic acids. ACTA ACUST UNITED AC 1979. [DOI: 10.1007/bf00551339] [Citation(s) in RCA: 61] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Zverev VV, Ermolaev LV, Kitaev YP. A theoretical study of the basicity of methylamines in the gaseous phase. Russ Chem Bull 1977. [DOI: 10.1007/bf01152688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Quantum-Mechanical Approach to the Conformational Basis of Molecular Pharmacology. ADVANCES IN QUANTUM CHEMISTRY 1977. [DOI: 10.1016/s0065-3276(08)60582-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Abstract
Expression for the long-range intermolecular interaction energy obtained by the perturbation theory method in atomic dipole approximation are used for the study of the nature of base interaction in stacked dimers formed of two neighbouring DNA base pairs. Base wave functions are computed by the CNDO-CI method. The inplane interactions are shown to give the dominant contribution into the DNA stabilization energy in vacuum. The estimations performed for the solvent effect on intermolecular interaction energy allowed us to draw conclusions about the decisive role of hydrophobic interactions in a base stacking.
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Chojnacki H, Sokalski WA. Interactions of 6-thioguanine in B-DNA: possible mechanism of its mutagenic action. J Theor Biol 1975; 54:167-74. [PMID: 1207132 DOI: 10.1016/s0022-5193(75)80121-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Taulomerism and Electronic Structure of Biological Pyrimidines. ADVANCES IN HETEROCYCLIC CHEMISTRY VOLUME 18 1975. [DOI: 10.1016/s0065-2725(08)60131-2] [Citation(s) in RCA: 152] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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Goddard JD, Mezey PG, Csizmadia IG. A note on a non-empirical molecular orbital study of some cytosine and thymine tautomers. ACTA ACUST UNITED AC 1975. [DOI: 10.1007/bf00547781] [Citation(s) in RCA: 34] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Simon Z. Spezifische Wechselwirkungen. Intermolekulare Kräfte, sterische Erfordernisse und Molekülgröße. Angew Chem Int Ed Engl 1974. [DOI: 10.1002/ange.19740862203] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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Simon Z. Specific Interactions. Intermolecular Forces, Steric Requirements, and Molecular Size. ACTA ACUST UNITED AC 1974. [DOI: 10.1002/anie.197407191] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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Kelly GR, Kurucsev T. Interactions between purine derivatives: Electronic spectral studies. II. Excition interactions in the dimer of 6-methylpurine in aqueous solution. Biopolymers 1974. [DOI: 10.1002/bip.1974.360130412] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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Glassman TA, Klopman G, Cooper C. Use of the generalized perturbation theory to predict the interaction of purine nucleotides with metal ions. Biochemistry 1973; 12:5013-9. [PMID: 4761979 DOI: 10.1021/bi00748a030] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Mantione MJ. [Interpretation of spectral modifications undertaken by aromatic hydrocarbons when they are stacked with nucleic acids]. Photochem Photobiol 1973; 17:169-77. [PMID: 4693284 DOI: 10.1111/j.1751-1097.1973.tb06346.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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Moore DS, Wagner TE. Origins of the differences between the circular dichroism of DNA and RNA: theoretical calculations. Biopolymers 1973; 12:201-21. [PMID: 4687148 DOI: 10.1002/bip.1973.360120119] [Citation(s) in RCA: 29] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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37
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Quantum Theory of DNA Summary of Results and Study Program. ADVANCES IN QUANTUM CHEMISTRY 1973. [DOI: 10.1016/s0065-3276(08)60569-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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Structures and reactivities of nitrogen-containing derivatives of carbonyl compounds. Chem Heterocycl Compd (N Y) 1971. [DOI: 10.1007/bf00471499] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Govil G, Saran A. Quantum chemical studies on the conformational structure of nucleic acids. I. Extended Hückel calculations on D-ribose phosphate. J Theor Biol 1971; 30:621-30. [PMID: 5575773 DOI: 10.1016/0022-5193(71)90014-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
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Pullman B, Pullman A. Electronic Aspects of Purine Tautomerism. ADVANCES IN HETEROCYCLIC CHEMISTRY 1971. [DOI: 10.1016/s0065-2725(08)60349-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/18/2023]
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43
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Weiler-Feilchenfeld H, Pullman A, Berthod H, Giessner-Prettre C. Experimental and quantum-chemical studies of the dipole moments of quinoline and indole. J Mol Struct 1970. [DOI: 10.1016/0022-2860(70)90013-x] [Citation(s) in RCA: 28] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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44
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Eaton WA, Lewis TP. Polarized single-crystal absorption spectrum of 1-methyluracil. J Chem Phys 1970; 53:2164-72. [PMID: 5449969 DOI: 10.1063/1.1674310] [Citation(s) in RCA: 71] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
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Julg A, Carles P. Recherches sur la structure �lectronique et les caract�ristiques des diff�rentes formes tautom�res de la purine. ACTA ACUST UNITED AC 1970. [DOI: 10.1007/bf00527456] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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47
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The Chemical Nature of the Receptor Site. INTERNATIONAL REVIEW OF NEUROBIOLOGY 1970. [DOI: 10.1016/s0074-7742(08)60170-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register]
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