101
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Chval Z, Šíp M. Transition States of Cisplatin Binding to Guanine and Adenine: ab initio Reactivity Study. ACTA ACUST UNITED AC 2003. [DOI: 10.1135/cccc20031105] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Fully optimised HF and DFT transition states of cisplatin binding to adenine and guanine are presented for the first time. They have similar structure as the recently published transition states for cisplatin hydrolysis with the angle of about 70° between entering and leaving ligands and corresponding bonds prolonged up to 0.5 Å. Calculated activation energies are in the range of 10.5-18 kcal/mol. The lowest activation energies were found for the binding of cis-Pt[(NH3)2(H2O)(OH)]+ to guanine. The role of hydrogen bonds in recognition of binding sites, stabilisation of reactants and final yields of individual cisplatin-DNA adducts is discussed.
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102
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Šponer J, Hobza P. Molecular Interactions of Nucleic Acid Bases. A Review of Quantum-Chemical Studies. ACTA ACUST UNITED AC 2003. [DOI: 10.1135/cccc20032231] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Ab initio quantum-chemical calculations with inclusion of electron correlation significantly contributed to our understanding of molecular interactions of DNA and RNA bases. Some of the most important findings are introduced in the present overview: structures and energies of hydrogen bonded base pairs, nature of base stacking, interactions between metal cations and nucleobases, nonplanarity of isolated nucleobases and other monomer properties, tautomeric equilibria of nucleobases, out-of-plane hydrogen bonds and amino acceptor interactions. The role of selected molecular interactions in nucleic acids is discussed and representative examples where these interactions occur are given. Also, accuracy of density functional theory, semiempirical methods, distributed multipole analysis and empirical potentials is commented on. Special attention is given to our very recent reference calculations on base stacking and H-bonding. Finally, we briefly comment on the relationship between advanced ab initio quantum-chemical methods and large-scale explicit solvent molecular dynamics simulations of nucleic acids.
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103
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Muñoz J, Gelpí JL, Soler-López M, Subirana JA, Orozco M, Luque FJ. Can Divalent Metal Cations Stabilize the Triplex Motif? Theoretical Study of the Interaction of the Hydrated Mg2+ Cation with the G−G·C Triplet. J Phys Chem B 2002. [DOI: 10.1021/jp026096w] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jordi Muñoz
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - J. L. Gelpí
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Montserrat Soler-López
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Juan A. Subirana
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - Modesto Orozco
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Av. Diagonal s/n, 08028 Barcelona, Spain, Departament d'Enginyeria Química, Universitat Politécnica de Catalunya, Av. Diagonal 647, 08028 Barcelona, Spain, and Molecular Modeling and Bioinformatics Unit, Parc Científic de Barcelona, Baldiri i Reixach 1-5, 08028 Barcelona, Spain
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104
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Rulíšek L, Havlas Z. Theoretical Studies of Metal Ion Selectivity.† 2. DFT Calculations of Complexation Energies of Selected Transition Metal Ions (Co2+, Ni2+, Cu2+, Zn2+, Cd2+, and Hg2+) in Metal-Binding Sites of Metalloproteins. J Phys Chem A 2002. [DOI: 10.1021/jp013951n] [Citation(s) in RCA: 54] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lubomír Rulíšek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
| | - Zdeněk Havlas
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, and Center for Complex Molecular Systems and Biomolecules, Flemigovo náměstí. 2, 166 10 Prague 6, Czech Republic
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105
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Affiliation(s)
- Anton S. Petrov
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - Gene Lamm
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
| | - George R. Pack
- Department of Chemistry, University of Louisville, Louisville, Kentucky 40292
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106
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Šponer JE, Glahé F, Leszczynski J, Lippert B, Šponer J. How Nucleobases Rotate When Bonded to a Metal Ion: Detailed View from an Ab Initio Quantum Chemical Study of a Cytosine Complex of trans-a2PtII. J Phys Chem B 2001. [DOI: 10.1021/jp012795h] [Citation(s) in RCA: 19] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Judit E. Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Frank Glahé
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jerzy Leszczynski
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Bernhard Lippert
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
| | - Jiří Šponer
- J. Heyrovský Institute of Physical Chemistry, Center for Complex Molecular Clusters and Biomolecules, Academy of Sciences of the Czech Republic, Dolejškova 3, 182 23 Prague, Czech Republic, Fachbereich Chemie, Universität Dortmund, 44221 Dortmund, Germany, Department of Chemistry and Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 61265 Brno,
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107
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108
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Brüning W, Sigel RKO, Freisinger E, Lippert B. Pt(II) Binding to N1 of Cytosine: Strengthening the Watson-Crick Pair with Guanine and yet Confining Its pH Existence Range This work was supported by the Deutsche Forschungsgemeinschaft and the Fonds der Chemischen Industrie. Angew Chem Int Ed Engl 2001; 40:3397-3399. [PMID: 11592150 DOI: 10.1002/1521-3773(20010917)40:18<3397::aid-anie3397>3.0.co;2-4] [Citation(s) in RCA: 34] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Wolfgang Brüning
- Fachbereich Chemie, Universität Dortmund 44221 Dortmund (Germany)
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109
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Brüning W, Sigel RKO, Freisinger E, Lippert B. PtII-Koordination an N1 von Cytosin: Verstärkung des Watson-Crick-Basenpaars mit Guanin bei gleichzeitiger Einschränkung seines pH-Existenzbereichs. Angew Chem Int Ed Engl 2001. [DOI: 10.1002/1521-3757(20010917)113:18<3497::aid-ange3497>3.0.co;2-v] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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110
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Sponer JE, Leszczynski J, Glahé F, Lippert B, Sponer J. Protonation of platinated adenine nucleobases. Gas phase vs condensed phase picture. Inorg Chem 2001; 40:3269-78. [PMID: 11421670 DOI: 10.1021/ic001276a] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Protonation of adenine carrying a Pt(II) moiety either at N7, N3, or N1 is possible in solution, but the site of protonation is influenced by the location of the Pt(II) electrophile and to some extent also by the overall charge of the metal entity (+2, +1, 0, -1), hence the other ligands (NH(3), Cl(-), OH(-)) bound to Pt(II). Quantum chemical calculations based on density functional theory (DFT) have been carried out for intrinsic protonation energies of adenine complexes carrying the following Pt(II) species at either of the three ring N atoms: [Pt(NH(3))(3)](2+) (1), trans- [Pt(NH(3))(2)Cl](+) (2a), cis-[Pt(NH(3))(2)Cl](+) (2b), trans-[Pt(NH(3))(2)Cl(2)] (3a), cis-[Pt(NH(3))Cl(2)] (3b), [PtCl(3)](-) (4), trans-[Pt(NH(3))(2)OH](+) (5a), cis-[Pt(NH(3))(2)(OH)](+) (5b), trans-[Pt(NH(3))(OH)(2)] (6a), cis-[Pt(NH(3))(OH)(2)] (6b), and [Pt(OH)(3)](-) (7). The data have been compared with results derived from solution studies (water) and X-ray crystallography, whenever available. The electrostatic effects associated with the charge of the metal entity have the major influence on the calculated intrinsic (gas phase) proton affinities, unlike the condensed phase data. Nevertheless, the relative gas phase trends correlate surprisingly well with condensed phase data; i.e., variation of the pK(a) values measured in solution is consistent with the calculated gas phase protonation energies. In addition to a systematic study of the ring proton affinities, proton transfer processes within the platinated adenine species were often observed when investigating Pt adducts with OH(-) ligands, and they are discussed in more detail. To the best of our knowledge, this is the first study attempting to find a systematic correlation between gas phase and condensed phase data on protonation of metalated nucleobases. The gas phase data provide a very useful complement to the condensed phase and X-ray experiments, showing that the gas phase studies are capable of valuable predictions and contribute to our understanding of the solvent and counterion effects on metal-assisted proton shift processes.
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Affiliation(s)
- J E Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic.
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111
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Sivanesan D, Subramanian V, Unni Nair B. Quantification of reactive sites in DNA bases using condensed Fukui functions. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(01)00386-4] [Citation(s) in RCA: 6] [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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112
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Muñoz J, Sponer J, Hobza P, Orozco M, Luque FJ. Interactions of Hydrated Mg2+ Cation with Bases, Base Pairs, and Nucleotides. Electron Topology, Natural Bond Orbital, Electrostatic, and Vibrational Study. J Phys Chem B 2001. [DOI: 10.1021/jp010486l] [Citation(s) in RCA: 86] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jordi Muñoz
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Jirí Sponer
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Pavel Hobza
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - Modesto Orozco
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
| | - F. Javier Luque
- Departament de Fisicoquímica, Facultat de Farmàcia, and Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Avgda Diagonal s/n, 08028 Barcelona, Spain, J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejökova 3, 182 23 Prague, Czech Republic, and Institute of Biophysics, Academy of Sciences of the Czech Republic, Královopolská 135, 612 65 Brno, Czech Republic
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113
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Rauhut G. Recent Advances in Computing Heteroatom-Rich Five- and Six-Membered Ring Systems. ADVANCES IN HETEROCYCLIC CHEMISTRY 2001. [DOI: 10.1016/s0065-2725(01)81010-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/04/2023]
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