1
|
Dasari S, Mallik BS. Association of Nucleobases in Hydrated Ionic Liquid from Biased Molecular Dynamics Simulations. J Phys Chem B 2018; 122:9635-9645. [PMID: 30260229 DOI: 10.1021/acs.jpcb.8b05778] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
We employed metadynamics-based classical molecular dynamics simulations to methylated adenine-thymine (mA-mT) and guanine-cytosine (mG-mC) base pairs to see favorable conformations in various concentrations of hydrated 1-ethyl, 3-methyl imidazolium acetate. We investigated various stacked and hydrogen-bonded conformations of association of base pairs through appropriately chosen collective variables. Stacked conformations more favored in water for both base pairs, whereas Watson-Crick (WC) hydrogen-bonding conformations are favored in pure and hydrated ionic liquids (ILs) except for 0.75 mol fraction IL. We observe that EMIm cations surround the base pairs in WC conformations creating a kind of hydrophobic cavity and protect the hydrogen bonds between base pairs. However, the five-membered heteroaromatic rings of cations stack with the nucleobases in the cation-base-cation (π-π-π) model, which resembles the base-base-base stacking in a DNA duplex. Interestingly, from additional simulations of 0.5 mol fraction hydrated choline dihydrogen phosphate IL, we observe that the stacked conformations become more favored than the WC conformation due to the absence of π-bonds in cations. The calculated values of relative solubility of base pairs in pure and hydrated ionic liquids compared to those in pure water correlate well with the free energy values of WC and stacked conformations.
Collapse
Affiliation(s)
- Sathish Dasari
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi , Sangareddy 502285 , Telangana , India
| | - Bhabani S Mallik
- Department of Chemistry , Indian Institute of Technology Hyderabad , Kandi , Sangareddy 502285 , Telangana , India
| |
Collapse
|
2
|
Monajjemi M, Chahkandi B, Zare K, Amiri A. Study of the hydrogen bond in different orientations of adenine-thymine base pairs: An ab initio study. BIOCHEMISTRY (MOSCOW) 2005; 70:366-76. [PMID: 15823092 DOI: 10.1007/s10541-005-0123-2] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
Abstract
In order to gain deeper insight into structure, charge distribution, and energies of A-T base pairs, we have performed quantum chemical ab initio and density functional calculations at the HF (Hartree-Fock) and B3LYP levels with 3-21G*, 6-31G*, 6-31G**, and 6-31++G** basis sets. The calculated donor-acceptor atom distances in the Watson-Crick A-T base pair are in good agreement with the experimental mean values obtained from an analysis of 21 high resolution DNA structures. In addition, for further correction of interaction energies between adenine and thymine, the basis set superposition error (BSSE) associated with the hydrogen bond energy has been computed via the counterpoise method using the individual bases as fragments. In the Watson-Crick A-T base pair there is a good agreement between theory and experimental results. The distances for (N2...H23-N19), (N8-H13...O24), and (C1...O18) are 2.84, 2.94, and 3.63 A, respectively, at B3LYP/6-31G** level, which is in good agreement with experimental results (2.82, 2.98, and 3.52 A). Interaction energy of the Watson-Crick A-T base pair is -13.90 and -10.24 kcal/mol at B3LYP/6-31G** and HF/6-31G** levels, respectively. The interaction energy of model (9) A-T base pair is larger than others, -18.28 and -17.26 kcal/mol, and for model (2) is the smallest value, -13.53 and -13.03 kcal/mol, at B3LYP/6-31G** and B3LYP/6-31++G** levels, respectively. The computed B3LYP/6-31G** bond enthalpies for Watson-Crick A-T pairs of -14.4 kcal/mol agree well with the experimental results of -12.1 kcal/mol deviating by as little as -2.3 kcal/mol. The BSSE of some cases is large (9.85 kcal/mol) and some is quite small (0.6 kcal/mol).
Collapse
Affiliation(s)
- M Monajjemi
- Science and Research Campus, Islamic Azad University, Hesarak, Poonak, PO Box 14515-775, Tehran, Iran.
| | | | | | | |
Collapse
|
3
|
Tautomerism of heterocycles: Condensed five-six, five-five, and six-six ring systems with heteroatoms in both rings. ADVANCES IN HETEROCYCLIC CHEMISTRY 2000. [DOI: 10.1016/s0065-2725(00)77004-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/21/2023]
|
4
|
Schmidt A, Kindermann MK, Vainiotalo P, Nieger M. Charge-Separated Modified Nucleobases. On π-Interactions and Hydrogen Bonding of Self-Complementary Cationic and Betainic Uracils. J Org Chem 1999. [DOI: 10.1021/jo991125t] [Citation(s) in RCA: 22] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Andreas Schmidt
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Chemie und Biochemie, Soldmannstrasse 16, D-17487 Greifswald, Germany, University of Joensuu, Department of Chemistry, P.O. Box 111, FIN-80101 Joensuu, Finland, and Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Markus Karl Kindermann
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Chemie und Biochemie, Soldmannstrasse 16, D-17487 Greifswald, Germany, University of Joensuu, Department of Chemistry, P.O. Box 111, FIN-80101 Joensuu, Finland, and Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Pirjo Vainiotalo
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Chemie und Biochemie, Soldmannstrasse 16, D-17487 Greifswald, Germany, University of Joensuu, Department of Chemistry, P.O. Box 111, FIN-80101 Joensuu, Finland, and Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| | - Martin Nieger
- Ernst-Moritz-Arndt-Universität Greifswald, Institut für Chemie und Biochemie, Soldmannstrasse 16, D-17487 Greifswald, Germany, University of Joensuu, Department of Chemistry, P.O. Box 111, FIN-80101 Joensuu, Finland, and Rheinische Friedrich-Wilhelms-Universität Bonn, Institut für Anorganische Chemie, Gerhard-Domagk-Strasse 1, D-53121 Bonn, Germany
| |
Collapse
|
5
|
Hobza P, Sponer J. Structure, energetics, and dynamics of the nucleic Acid base pairs: nonempirical ab initio calculations. Chem Rev 1999; 99:3247-76. [PMID: 11749516 DOI: 10.1021/cr9800255] [Citation(s) in RCA: 814] [Impact Index Per Article: 32.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Affiliation(s)
- P Hobza
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Dolejskova 3, 182 23 Prague 8, Czech Republic
| | | |
Collapse
|
6
|
Application of Molecular Orbital Theory to the Elucidation of Radical Processes Induced by Radiation Damage to DNA. ACTA ACUST UNITED AC 1999. [DOI: 10.1016/s1380-7323(99)80082-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/07/2023]
|
7
|
Zhanpeisov NU, Leszczynski J. Specific Solvation Effects on Structures and Properties of Isocytosine−Cytosine Complexes: A Theoretical ab Initio Study. J Phys Chem B 1998. [DOI: 10.1021/jp9817271] [Citation(s) in RCA: 24] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nurbosyn U. Zhanpeisov
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Boreskov Institute of Catalysis, Novosibirsk 630090, Russia
| | - Jerzy Leszczynski
- Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, and Boreskov Institute of Catalysis, Novosibirsk 630090, Russia
| |
Collapse
|
8
|
Gohda K, Kimura Y, Mori I, Ohta D, Kikuchi T. Theoretical evidence of the existence of a diazafulvene intermediate in the reaction pathway of imidazoleglycerol phosphate dehydratase: design of a novel and potent heterocycle structure for the inhibitor on the basis of the electronic structure-activity relationship study. BIOCHIMICA ET BIOPHYSICA ACTA 1998; 1385:107-14. [PMID: 9630553 DOI: 10.1016/s0167-4838(98)00049-1] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The reaction mechanism of imidazoleglycerol phosphate dehydratase has not yet been clearly revealed. Structural comparison between inhibitors and the substrate IGP implicates that the reaction involves a diazafulvene intermediate. Here, we present evidence to support this hypothesis by investigating the electronic structure-enzyme inhibitory activity relationship on inhibitors with different heterocycles using 6-31G** level theory of the ab initio molecular orbital method. The calculation results showed that potent inhibitors can be distinguished from weak ones by the atomic charge density and by the energy levels of the highest occupied lone-pair orbital on the nitrogen atoms in the heterocycles. Furthermore, very good correlations (r2=0.8-0.9) were found between the charge density on the nitrogen atom and the inhibitory activity. It was also revealed that the diazafulvene is electronically similar to the potent inhibitors. Thus, these results strongly suggest the existence of the diazafulvene as an intermediate possessing tight-binding affinity to the enzyme. Based on the electronic structural similarity between the potent inhibitors and the proposed intermediate, a novel heterocycle was designed and predicted its inhibitory activity prior to the synthesis. Then, activity of synthesized inhibitors showed excellent agreement with this prediction. Hence, from the theoretical studies and experimental results, we conclude to obtain evidence of the hypothesis that the enzyme reaction proceeds via the diazafulvene intermediate.
Collapse
Affiliation(s)
- K Gohda
- Computer Chemistry Unit, International Research Laboratories, CIBA-GEIGY Japan, P.O. Box 1, Takarazuka, Hyogo 665, Japan.
| | | | | | | | | |
Collapse
|
9
|
A new method for predicting conduction anesthesia. Russ Chem Bull 1997. [DOI: 10.1007/bf02495116] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
|
10
|
Alhambra C, Luque FJ, Gago F, Orozco M. Ab Initio Study of Stacking Interactions in A- and B-DNA. J Phys Chem B 1997. [DOI: 10.1021/jp962626a] [Citation(s) in RCA: 75] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cristóbal Alhambra
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Francisco J. Luque
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Federico Gago
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| | - Modesto Orozco
- Departament de Bioquímica i Biologia Molecular, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain, Departament de Farmàcia, Unitat Fisicoquímica, Facultat de Farmàcia, Universitat de Barcelona, Avgda Diagonal s/n, Barcelona 08028, Spain, Departamento de Fisiología y Farmacología, Universidad de Alcalá de Henares, 28871 Madrid, Spain
| |
Collapse
|
11
|
On the role of the basis set and electron correlation in the description of stacking interactions. ACTA ACUST UNITED AC 1997. [DOI: 10.1016/s0097-8485(96)00035-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
12
|
Hobza P. Chapter 7. Accurate ab initio calculations on large van der Waals clusters. ACTA ACUST UNITED AC 1997. [DOI: 10.1039/pc093257] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
13
|
|
14
|
Hutter J, Carloni P, Parrinello M. Nonempirical Calculations of a Hydrated RNA Duplex. J Am Chem Soc 1996. [DOI: 10.1021/ja9612209] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jürg Hutter
- Contribution from the Max-Planck-Institut für Festkörperforschung, D-70569 Stuttgart, Germany, IBM Research Division, Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland, and Department of Chemistry, University of Florence, Via G. Capponi, 7, I-50121 Florence, Italy
| | - Paolo Carloni
- Contribution from the Max-Planck-Institut für Festkörperforschung, D-70569 Stuttgart, Germany, IBM Research Division, Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland, and Department of Chemistry, University of Florence, Via G. Capponi, 7, I-50121 Florence, Italy
| | - Michele Parrinello
- Contribution from the Max-Planck-Institut für Festkörperforschung, D-70569 Stuttgart, Germany, IBM Research Division, Zurich Research Laboratory, Säumerstrasse 4, CH-8803 Rüschlikon, Switzerland, and Department of Chemistry, University of Florence, Via G. Capponi, 7, I-50121 Florence, Italy
| |
Collapse
|
15
|
Sponer J, Leszczynski J, Hobza P. Hydrogen bonding and stacking of DNA bases: a review of quantum-chemical ab initio studies. J Biomol Struct Dyn 1996; 14:117-35. [PMID: 8877568 DOI: 10.1080/07391102.1996.10508935] [Citation(s) in RCA: 178] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Ab initio quantum-chemical calulations with inclusion of electron correlation made since 1994 (such reliable calculations were not feasible before) significantly modified our view on interactions of nucleic acid bases. These calculations allowed to perform the first reliable comparison of the strength of stacked and hydrogen bonded pairs of nucleic acid bases, and to characterize the nature of the base-base interactions. Although hydrogen-bonded complexes of nucleobases are primarily stabilized by the electrostatic interaction, the dispersion attraction is also important. The stacked pairs are stabilized by dispersion attraction, however, the mutual orientation of stacked bases is determined rather by the electrostatic energy. Some popular theories of stacking were ruled out: The theory based on attractive interactions of polar exocyclic groups of bases with delocalized electrons of the aromatic rings (Bugg et al., Biopolymers 10, 175 (1971), and the pi-pi interactions model (C.A. Hunter, J. Mol. Biol. 230, 1025 (1993)). The calculations demonstrated that amino groups of nucleobases are very flexible and intrinsically nonplanar, allowing hydrogen-bond-like interactions which are oriented out of the plane of the nucleobase. Many H-bonded DNA base pairs are intrinsically nonplanar. Higher-level ab initio calculations provide a unique set of reliable and consistent data for parametrization and verification of empirical potentials. In this article, we present a short survey of the recent calculations, and discuss their significance and limitations. This summary is written for readers which are not experts in computational quantum chemistry.
Collapse
Affiliation(s)
- J Sponer
- J. Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague, Czech Republic. J.S.-
| | | | | |
Collapse
|
16
|
Sponer J, Leszczynski J, Vetterl V, Hobza P. Base stacking and hydrogen bonding in protonated cytosine dimer: the role of molecular ion-dipole and induction interactions. J Biomol Struct Dyn 1996; 13:695-706. [PMID: 8906890 DOI: 10.1080/07391102.1996.10508882] [Citation(s) in RCA: 105] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
An ab initio quantum-chemical study of stacked and hydrogen-bonded protonated cytosine dimer has been carried out. The calculations were made using the second-order Moller-Plesset perturbational method (MP2) with a medium-sized polarized set of atomic orbitals. H-bonded as well as stacked protonated base pairs are more stable than the neutral base pairs. Two energy contributions not present in the neutral base pairs stabilize the protonated base pairs: the molecular ion - dipole interaction, and the induction interaction. The molecular ion - dipole stabilization dominates in base pairs with highly polar neutral monomers, such as the C...CH+ base pair. The induction interaction is not included in the commonly used empirical potentials, which do not reproduce the changes in intermolecular stabilization due to protonation. We demonstrate that the base stacking of several consecutive C...CH + pairs, as proposed for polycytidylic acid and i-DNA, is strongly repulsive. We also show that the intermolecular interactions strongly prefer protonation of adenine in protonated adenine-cytosine pairs.
Collapse
Affiliation(s)
- J Sponer
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague.
| | | | | | | |
Collapse
|
17
|
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.
Collapse
Affiliation(s)
- A O Colson
- Chemistry Department, Oakland University, Rochester, MI 48309, USA
| | | |
Collapse
|
18
|
Molecular electric field mapping of some anions and cations of 2- aminopurine and 6- thioguanine. J CHEM SCI 1994. [DOI: 10.1007/bf02840750] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
|
19
|
Carrupt PA, el Tayar N, Karlén A, Testa B. Molecular electrostatic potentials for characterizing drug-biosystem interactions. Methods Enzymol 1991; 203:638-77. [PMID: 1662332 DOI: 10.1016/0076-6879(91)03033-d] [Citation(s) in RCA: 35] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
|