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Burra VLSP, Sahoo PS, Dhankhar A, Jhajj J, Kasamuthu PS, K SSVK, Macha SKR. Understanding the structural basis of the binding specificity of c-di-AMP to M. smegmatis RecA using computational biology approach. J Biomol Struct Dyn 2024; 42:2043-2057. [PMID: 38093709 DOI: 10.1080/07391102.2023.2227709] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 04/09/2023] [Indexed: 02/21/2024]
Abstract
Mycobacterium tuberculosis RecA (MtRecA), a protein involved in DNA repair, homologous recombination and SOS pathway, contributes to the development of multidrug resistance. ATP binding-site in RecA has been a drug target to disable RecA dependent DNA repair. For the first time, experiments have shown the existence and binding of c-di-AMP to a novel allosteric site in the C-terminal-Domain (CTD) of Mycobacterium smegmatis RecA (MsRecA), a close homolog of MtRecA. In addition, it was observed that the c-di-AMP was not binding to Escherichia coli RecA (EcRecA). This article analyses the possible interactions of the three RecA homologs with the various c-di-AMP conformations to gain insights into the structural basis of the natural preference of c-di-AMP to MsRecA and not to EcRecA, using the structural biology tools. The comparative analysis, based on amino acid composition, homology, motifs, residue types, docking, molecular dynamics simulations and binding free energy calculations, indeed, conclusively indicates strong binding of c-di-AMP to MsRecA. Having very similar results as MsRecA, it is highly plausible for c-di-AMP to strongly bind MtRecA as well. These insights from the in-silico studies adds a new therapeutic approach against TB through design and development of novel allosteric inhibitors for the first time against MtRecA.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- V L S Prasad Burra
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Partha Sarathi Sahoo
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Amit Dhankhar
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Jatinder Jhajj
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Prasanna Sudharson Kasamuthu
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - S S V Kiran K
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
| | - Samuel Krupa Rakshan Macha
- Centre for Advanced Research and Innovation in Structural Biology of Diseases, K L E F (Deemed to be) University, Vaddeswaram, Andhra Pradesh, India
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2
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Henry B, Samokhvalov A. Characterization of tautomeric forms of anti-cancer drug gemcitabine and their interconversion upon mechano-chemical treatment, using ATR-FTIR spectroscopy and complementary methods. J Pharm Biomed Anal 2023; 226:115243. [PMID: 36657351 PMCID: PMC9977068 DOI: 10.1016/j.jpba.2023.115243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 12/30/2022] [Accepted: 01/09/2023] [Indexed: 01/12/2023]
Abstract
Gemcitabine is a widely used anti-cancer drug of pyrimidine structure, which can exist as a free base molecular form in crystals. Tautomers are structural isomers of molecules, which interconvert via proton transfer. Mechano-chemistry studies reactions of solids under mechanical impact. We investigated gemcitabine free base for the presence of specific molecular tautomers, using ATR-FTIR spectroscopic analysis, powder XRD, optical microscopy and HPLC. The amino-keto tautomer has the characteristic infrared (IR) peak of the amino group at 3390 cm-1. For the first time, the imino-keto tautomer of gemcitabine free base was detected. The imino-keto tautomer has the characteristic IR peak of the =N-H group, and its peak due to the CO group in pyrimidine ring is shifted vs. that of the amino-keto tautomer. This serves as the unique spectroscopic "fingerprints" of these tautomers. The ATR-FTIR spectroscopic analysis shows that gemcitabine free base can be enriched with the amino-keto or the imino-keto tautomer. Further, we studied the transformation of gemcitabine free base in crystals between its tautomers under conditions of liquid-assisted grinding (LAG). The imino-keto tautomer undergoes tautomerization to the amino-keto tautomer, while the amino-keto tautomer remains stable. No destruction of molecules of gemcitabine free base, when present as either tautomer, occurs during LAG as was verified by the HPLC-UV analysis. LAG is a new, straightforward, facile and fast method to interconvert tautomers in crystals, and ATR-FTIR spectroscopy is a method of choice to study tautomerization reactions of pharmaceuticals. The presented approach is promising for analysis of crystals of drugs containing one or more than one tautomer, and the knowledge-driven design of composite materials, which contain specific tautomeric molecular forms of pyrimidines, purines and other biologically active heterocyclic compounds.
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Affiliation(s)
- Barrington Henry
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA
| | - Alexander Samokhvalov
- Department of Chemistry, Morgan State University, 1700 East Cold Spring Lane, Baltimore, MD 21251, USA.
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Singh M, Baruah JB. Combinations of Tautomeric Forms and Neutral-Cationic Forms in the Cocrystals of Sulfamethazine with Carboxylic Acids. ACS OMEGA 2019; 4:11609-11620. [PMID: 31460268 PMCID: PMC6682086 DOI: 10.1021/acsomega.9b01437] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Accepted: 06/24/2019] [Indexed: 05/15/2023]
Abstract
The cocrystals of sulfamethazine with different acids, namely, 2-mercaptophenylcarboxylic acid, 2,6-pyridinedicarboxylic acid, 4-(4-hydroxyphenylazo)phenylcarboxylic acid, 3-(4-hydroxyphenyl)propanoic acid, and 4-(phenyl)phenylcarboxylic acid, are studied here. Each has distinct notable supramolecular features. The pyrimidin-2-amine unit of the sulfamethazine provided unique examples of cocrystals in which amidine and imidine forms or neutral and protonated forms of sulfamethazine are observed in 2:2 ratios. Hence, this study provides avenues to explore cocrystals with tautomeric forms together in a cocrystal and also neutral and protonated cocrystal partners as apparent multicomponents in cocrystals. Among the cocrystals, three of them have the amidine form of the sulfamethazine in respective self-assembly. The cocrystal of 2-mercapto-phenylcarboxylic acid with sulfamethazine has the amidine form and it has the distinction of having S-H···π interactions. The cocrystal of sulfamethazine with 2,6-pyridinecarboxylic acid is a rare example of a 1:1 cocrystal of sulfmethazine with dicarboxylic acid. It has methanol molecules as a solvent of crystallization. Sulfamethazine forms a hydrated cocrystal with 4-(4-hydroxyphenylazo)-phenylcarboxylic acid that has conventional R 2 2(8) synthons of amidine hydrogen-bonding with carboxylic acid. The phenolic part of the acid component is anchored to the water molecule and provides a robust self-assembly. The hydrated cocrystal of sulfamethazine with 3-(4-hydroxyphenyl)propanoic acid (2:2 cocrystal) has two independent molecules of sulfamethazine, one in amidine form and the other in imidine form. It has two neutral carboxylic acids anchored through complementary hydrogen bonds and also has two water molecules of crystallization. The cocrystal of sulfamethazine with 4-(phenyl)phenylcarboxylic acid is also a 2:2 cocrystal. It is a di-hydrate, which has a neutral and protonated form of sulfamethazine. The neutral form is hydrogen-bonded to a neutral carboxylic acid, whereas the protonated form is charge-assisted hydrogen-bonded to the corresponding carboxylate anion.
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Affiliation(s)
- Munendra
Pal Singh
- Department of Chemistry, Indian
Institute of Technology Guwahati, Guwahati 781 039 Assam, India
| | - Jubaraj B. Baruah
- Department of Chemistry, Indian
Institute of Technology Guwahati, Guwahati 781 039 Assam, India
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Jawiczuk M. A theoretical study on the hydrogen bond and stability of cytosine and thymine dimers. COMPUT THEOR CHEM 2018. [DOI: 10.1016/j.comptc.2017.11.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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Basumatary J, Bezbaruah B, Kalita R, Barman TK, Medhi C. Quantum mechanical studies on the existence of AC mismatches through prototopic tautomerization pathway in adenine and cytosine recognition. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2017. [DOI: 10.1142/s0219633617500274] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The gas phase studies on the electronic stabilities and thermochemical properties of metastable AC mismatches have been performed and the results are analyzed to explain the features of experimentally available AC mismatches. The hydrogen bonding patterns observed in these mismatches are relevant to the formation of stable AC mismatches. In these AC pairs, the H migration mechanism to generate other tautomeric forms is not observed, which shows the compatibility of H bonding capacity of the sites involved in H bonds. The presence of hydrogen bond type –N[Formula: see text]H–N– may contribute to better AC pairing, hence cisA1-1cisC2, transA2-cisC1 and transA1-1cisC2 are found to be more favorable pairs compared to other AC pairs.
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Affiliation(s)
| | | | - Rinki Kalita
- Department of Chemistry, Gauhati University, P.O Gauhati University, Guwahati 781014, India
| | - Tapash Kumar Barman
- Department of Chemistry, Gauhati University, P.O Gauhati University, Guwahati 781014, India
| | - Chitrani Medhi
- Department of Chemistry, Gauhati University, P.O Gauhati University, Guwahati 781014, India
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TAUTOMERISM OF ADSORBED THYMINE ON GOLD ELECTRODES: AN IN SITU SURFACE-ENHANCED INFRARED SPECTROSCOPY STUDY. Electrochim Acta 2016. [DOI: 10.1016/j.electacta.2015.11.109] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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7
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Cui Y, Li Y, Dai Y, Verpoort F, Song P, Xia L. Detailed theoretical investigation of excited-state intramolecular proton transfer mechanism of a new chromophore II. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2016; 154:130-134. [PMID: 26523683 DOI: 10.1016/j.saa.2015.10.038] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/09/2015] [Revised: 10/20/2015] [Accepted: 10/22/2015] [Indexed: 06/05/2023]
Abstract
In the present work, TDDFT has been used to investigate the excited state intramolecular proton transfer (ESIPT) mechanism of a new chromophore II [Sensors and Actuators B: Chemical. 202 (2014) 1190]. The calculated absorption and fluorescence spectra agree well with experimental results. In addition, two types of II configurations are found in the first excited state (S1), which can be ascribed to the ESIPT reaction. Based on analysis of the calculated infrared (IR) spectra of O-H stretching vibration as well as the hydrogen bonding energies, the strengthening of the hydrogen bond in the S1 state has been confirmed. The frontier molecular orbitals (MOs), Hirshfeld charge distribution and the Natural bond orbital (NBO) have also been analyzed, which displays the tendency of the ESIPT process. Finally, potential energy curves of the S0 and S1 states were constructed, demonstrating that the ESIPT reaction can be facilitated based on the photo-excitation.
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Affiliation(s)
- Yanling Cui
- College of Physics and Chemistry, Liaoning University, Shenyang 110036, PR China
| | - Yafei Li
- College of Physics and Chemistry, Liaoning University, Shenyang 110036, PR China
| | - Yumei Dai
- Normal College, Shenyang University, Shenyang 110044, PR China
| | - Francis Verpoort
- Laboratory of Organometallics, Catalysis and Ordered Materials, State Key Laboratory of Advanced Technology for Materials Synthesis and Processing, Center for Chemical and Material Engineering, Wuhan University of Technology, Wuhan 430070, PR China
| | - Peng Song
- College of Physics and Chemistry, Liaoning University, Shenyang 110036, PR China; Liaoning Key Laboratory of Semiconductor Light Emitting and Photocatalytic Materials, Liaoning University, Shenyang 110036, PR China.
| | - Lixin Xia
- College of Physics and Chemistry, Liaoning University, Shenyang 110036, PR China.
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8
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Valadbeigi Y, Soleiman-Beigi M, Sahraei R. Catalysis effect of micro-hydration on the intramolecular proton transfer in cytosine. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.03.007] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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9
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Structure, stability, energy barrier and ionization energies of chemically modified DNA-bases: Quantum chemical calculations on 37 favored and rare tautomeric forms of tetraphosphoadenine. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.11.010] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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10
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Chai S, Cong SL. Excited state intramolecular proton transfer and substituent effect of 10-hydroxybenzo[h]quinoline: A time-dependent density functional theory study. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.02.019] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Babu Nanubolu J, Sridhar B, Ravikumar K. Understanding the amino ↔ imino tautomeric preference in (imidazole)imidazolidine-N-aryl(alkyl) systems: a case study of moxonidine drug and insights from the Cambridge structural database (CSD). CrystEngComm 2014. [DOI: 10.1039/c4ce01541j] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Moxonidine drug crystallizes exclusively as its imino tautomer. Conjugation plays a key role in the tautomer stability.
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Affiliation(s)
- Jagadeesh Babu Nanubolu
- Centre for X-ray Crystallography
- CSIR - Indian Institute of Chemical Technology
- Hyderabad, India
| | - Balasubramanian Sridhar
- Centre for X-ray Crystallography
- CSIR - Indian Institute of Chemical Technology
- Hyderabad, India
| | - Krishnan Ravikumar
- Centre for X-ray Crystallography
- CSIR - Indian Institute of Chemical Technology
- Hyderabad, India
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12
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Selvaraju M, Shiu WS, Kulkarni MV, Sun CM. Ionic liquid supported synthesis of tricyclic pyrimido[1,2-a]benzimidazoles by a telescoped Michael/hetero annulation strategy. RSC Adv 2013. [DOI: 10.1039/c3ra42658k] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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Kereselidze JA, Pachulia ZV, Zarqua TS. Quantum-chemical description of the prototropic tautomerism of pyrimidine bases. Chem Heterocycl Compd (N Y) 2009. [DOI: 10.1007/s10593-009-0331-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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14
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Chai S, Zhao GJ, Song P, Yang SQ, Liu JY, Han KL. Reconsideration of the excited-state double proton transfer (ESDPT) in 2-aminopyridine/acid systems: role of the intermolecular hydrogen bonding in excited states. Phys Chem Chem Phys 2009; 11:4385-90. [PMID: 19458842 DOI: 10.1039/b816589k] [Citation(s) in RCA: 170] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Shuo Chai
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Dalian, 116023, China
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15
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Sponer J, Riley KE, Hobza P. Nature and magnitude of aromatic stacking of nucleic acid bases. Phys Chem Chem Phys 2008; 10:2595-610. [PMID: 18464974 DOI: 10.1039/b719370j] [Citation(s) in RCA: 270] [Impact Index Per Article: 16.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
This review summarises recent advances in quantum chemical calculations of base-stacking forces in nucleic acids. We explain in detail the very complex relationship between the gas-phase base-stacking energies, as revealed by quantum chemical (QM) calculations, and the highly variable roles of these interactions in nucleic acids. This issue is rarely discussed in quantum chemical and physical chemistry literature. We further extensively discuss methods that are available for base-stacking studies, complexity of comparison of stacking calculations with gas phase experiments, balance of forces in stacked complexes of nucleic acid bases, and the relation between QM and force field descriptions. We also review all recent calculations on base-stacking systems, including details analysis of the B-DNA stacking. Specific attention is paid to the highest accuracy QM calculations, to the decomposition of the interactions, and development of dispersion-balanced DFT methods. Future prospects of computational studies of base stacking are discussed.
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Affiliation(s)
- Jirí Sponer
- Institute of Organic Chemistry and Biochemistry, vvi, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague 6, Czech Republic
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Salpin JY, Guillaumont S, Tortajada J, MacAleese L, Lemaire J, Maitre P. Infrared spectra of protonated uracil, thymine and cytosine. Chemphyschem 2007; 8:2235-44. [PMID: 17910021 DOI: 10.1002/cphc.200700284] [Citation(s) in RCA: 96] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Abstract
The gas-phase structures of protonated uracil, thymine, and cytosine are probed by using mid-infrared multiple-photon dissociation (IRMPD) spectroscopy performed at the Free Electron Laser facility of the Centre Laser Infrarouge d'Orsay (CLIO), France. Experimental infrared (IR) spectra are recorded for ions that were generated by electrospray ionization, isolated, and then irradiated in a quadrupole ion trap; the results are compared to the calculated infrared absorption spectra of the different low-lying isomers (computed at the B3LYP/6-31++G(d,p) level). For each protonated base, the global energy minimum corresponds to an enolic tautomer, whose infrared absorption spectrum matched very well with the experimental IRMPD spectrum, with the exception of a very weak IRMPD signal observed at about 1800 cm(-1) in the case of the three protonated bases. This signal is likely to be the signature of the second-energy-lying oxo tautomer. We thus conclude that within our experimental conditions, two tautomeric ions are formed which coexist in the quadrupole ion trap.
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Affiliation(s)
- Jean-Yves Salpin
- Laboratoire d'Analyse et de Modélisation pour la Biologie et l'Environnement (LAMBE), Université d'Evry Val d'Esonne-CNRS, Bâtiment Maupertuis, Boulevard François Mitterrand, 91025 Evry, France.
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Forde GK, Forde AE, Hill G, Ford A, Nazario A, Leszczynski J. Comprehensive study of the effects of methylation on tautomeric equilibria of nucleic acid bases. J Phys Chem B 2007; 110:15564-71. [PMID: 16884280 DOI: 10.1021/jp056574d] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Minor tautomers of nucleic acid bases can result by intramolecular proton transfer. These rare tautomers could be stabilized through the addition of methyl groups to DNA bases. A comprehensive theoretical study of tautomers of methylated derivatives of guanine, adenine, cytosine, thymine, and uracil was performed. Molecular geometries of all tautomers were obtained at the density functional theory and MP2 levels with the 6-31G(d,p) basis set, and single-point calculations were performed at the CCSD(T)/6-311G(d,p) level. Tautomers obtained by protonation at the preferred protonation site for methylated isolated bases were compared to their nonmethylated counterparts. The effects of methylation on the relative stabilities of nucleic acid base tautomers are also studied and discussed in this work. The results suggest that some sites on the bases may not be mutagenic and may even stabilize the canonical Watson-Crick form. The results also indicate that a number of methylation sites can stabilize the tautomers, suggesting possible mechanisms for mutagenic changes.
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Affiliation(s)
- Gareth K Forde
- Computational Center for Molecular Structure and Interactions, Jackson State University, Jackson, Mississippi 39217, USA
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Fonseca Guerra C, Bickelhaupt FM, Saha S, Wang F. Adenine tautomers: relative stabilities, ionization energies, and mismatch with cytosine. J Phys Chem A 2007; 110:4012-20. [PMID: 16539424 DOI: 10.1021/jp057275r] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this study, we have investigated 12 tautomers of the DNA base adenine at the BP86/TZ2P and BP86/QZ4P levels of density functional theory. The vertical and adiabatic ionization energies of all tautomers were determined as the difference in energy between the radical cation and the corresponding neutral system. Furthermore, an evaluation is made for the eigenvalue spectra calculated with the SAOP functional, which is shown to lead to substantial improvements for orbital energies compared to BP86. We have also explored the correlations between the Kohn-Sham orbitals of the different tautomers at the BP86/QZ4P and SAOP/QZ4P levels. Finally, we discuss implications of the existence of the tautomeric forms of adenine for the DNA replication.
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Affiliation(s)
- C Fonseca Guerra
- Theoretische Chemie, Scheikundig Laboratorium der Vrije Universiteit, De Boelelaan 1083, NL-1081 HV Amsterdam, The Netherlands
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Malone RJ, Miller AM, Kohler B. Singlet Excited-state Lifetimes of Cytosine Derivatives Measured by Femtosecond Transient Absorption¶. Photochem Photobiol 2007. [DOI: 10.1562/0031-8655(2003)0770158sesloc2.0.co2] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Hasanein AAEG, Senior SAEA. Ab Initio and DFT Calculations on 2-Aminopyrimidine, 2-Amino-4,6-dichloropyrimidine, and Their Dimers. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2007; 80:307-315. [DOI: 10.1246/bcsj.80.307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
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21
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Quantum-chemical study of the effects of noncovalent interactions on the nuclear magnetic screening constants of pyrimidine base associates. J STRUCT CHEM+ 2007. [DOI: 10.1007/s10947-007-0150-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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22
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Freeman F, Po HN. Dimers of and Tautomerism between 2-Pyrimidinethiol and 2(1H)-Pyrimidinethione: A Density Functional Theory (DFT) Study. J Phys Chem A 2006; 110:7904-12. [PMID: 16789779 DOI: 10.1021/jp058312h] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Density functional theory (BLYP, B3LYP, B3P86, B3PW91) with the 6-31+G(d,p), 6-311+G(d,p), and cc-pVTZ basis sets has been used to calculate structural parameters, relative energies, and vibrational spectra of 2-pyrimidinethiol (1) and 2(1H)-pyrimidinethione (2) and their hydrogen-bonded homodimers (C(2) 3, C(2h) [4](double dagger), C(2h) 5), monohydrates, and dihydrates and a heterodimer (6). Several transition state structures proposed for the tautomerization process have also been examined. At the B3PW91/6-311+G(d,p)//B3PW91/6-31+G(d,p) level of theory 2-pyrimidinethiol (1) is predicted to be 3.41 kcal/mol more stable (E(rel)) than 2(1H)-pyrimidinethione (2) in the gas phase and 2 is predicted to be 6.47 kcal/mol more stable than 1 in aqueous medium. An unfavorable planar intramolecular strained four center transition state (TS1) for the tautomerization of 1 and 2 in the gas-phase lies 29.07 kcal/mol higher in energy than 2-pyrimidinethiol (1). The C(2) 2-pyrimidinethiol dimer (3) is 6.84 kcal/mol lower in energy than the C(2) homodimer transition state structure ([11](double dagger)) that connects dimers 3 and 4. Transition state [11](double dagger) provides a facile pathway for tautomerization between 1 and 2 in the gas phase (monomer-dimer promoted tautomerization). The hydrogen bonded 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O structures are predicted to be 1.27 and 1.55 kcal/mol, respectively, higher in energy than 2(1H)-pyrimidinethione- - -H(2)O and 2(1H)-pyrimidinethione- - -2H(2)O. Water promoted tautomerization via cyclic transition states involving one water molecule (TS- - -H(2)O, [12](double dagger)) and two water molecules (TS- - -2H(2)O, [13](double dagger)) lie 11.42 and 11.44 kcal/mol, respectively, higher in energy than 2-pyrimidinethiol- - -H(2)O and 2-pyrimidinethiol- - -2H(2)O. Thus, the hydrated transition states [12](double dagger) and [13](double dagger) are involved in the tautomerism between 1 and 2 in aqueous medium.
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Affiliation(s)
- Fillmore Freeman
- Department of Chemistry, University of California, Irvine, 92697-2025, USA
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Akai N, Harada T, Shin-Ya K, Ohno K, Aida M. Photoinduced Amino−Imino Tautomerism: An Infrared Study of 2-Amino-5-methylpyridine in a Low-Temperature Argon Matrix. J Phys Chem A 2006; 110:6016-22. [PMID: 16671670 DOI: 10.1021/jp056290t] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The photoreaction of 2-amino-5-methylpyridine was investigated by matrix-isolation infrared spectroscopy and DFT calculation. Photoinduced reversible amino (N=C-NH(2))-imino (NH-C=NH) tautomerism was found between 2-amino-5-methylpyridine and 5-methyl-2(1H)-pyridinimine; the amino tautomer changes to the imino tautomer by UV irradiation (340>lambda>or= 300 nm) and the reverse change occurs by longer-wavelength light irradiation (420>lambda>or= 340 nm). The results of the CASSCF calculation revealed that the amino-imino tautomerism proceeds in vibrational relaxation process from electronic excited state to the ground state. The IR spectra of 2-amino-5-methylpyridine in the T(1) state and 5-methyl-2-pyridinamino radical were also obtained by UV irradiation (lambda>or= 300 nm).
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Affiliation(s)
- Nobuyuki Akai
- Center for Quantum Life Sciences, Hiroshima University, 1-3-1, Kagamiyama, Higashi-Hiroshima, Hiroshima 739-8530, Japan.
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Stanovnik B, Tišler M, Katritzky AR, Denisko OV. The Tautomerism of Heterocycles: Substituent Tautomerism of Six-Membered Ring Heterocycles. ADVANCES IN HETEROCYCLIC CHEMISTRY 2006. [DOI: 10.1016/s0065-2725(06)91001-0] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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Huertas O, Blas JR, Soteras I, Orozco M, Luque FJ. Benzoderivatives of Nucleic Acid Bases as Modified DNA Building Blocks. J Phys Chem A 2005; 110:510-8. [PMID: 16405323 DOI: 10.1021/jp052126u] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The tautomeric properties of benzoderivatives of the canonical nucleic acid bases have been studied by using different computational approaches. Attention has been paid to the impact of the benzene group in altering the tautomeric preferences of the canonical bases both in the gas phase and in aqueous solution. To this end, relative solvation free energies of the tautomers determined from Self-Consistent Reaction Field continuum calculations and Monte Carlo-Free Energy Perturbation are combined with gas-phase tautomerization free energies determined from quantum mechanical calculations. The results provide a detailed picture of the tautomeric preferences of the benzoderivatives of nucleic acid bases. This information is used to examine the recognition properties of the preferred tautomers of the benzo-fused derivatives, paying particular attention to the ability to form Watson-Crick hydrogen-bonding and stacking interactions as well as to the hydrophobic nature of the modified bases. The implications of present results on the potential use of benzo-fused bases as potential building blocks in modified DNA duplexes are examined.
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Affiliation(s)
- Oscar Huertas
- Departament de Fisicoquímica, Facultat de Farmacia, Universitat de Barcelona, Avgda Diagonal 643, Barcelona 08028, Spain
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Malone RJ, Miller AM, Kohler B. Singlet excited-state lifetimes of cytosine derivatives measured by femtosecond transient absorption. Photochem Photobiol 2003; 77:158-64. [PMID: 12785054 DOI: 10.1562/0031-8655(2003)077<0158:sesloc>2.0.co;2] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Lifetimes of the lowest excited singlet (S1) electronic states of various derivatives of the pyrimidine nucleobase cytosine (Cyt) were measured by the femtosecond transient absorption technique. The bases were excited in room-temperature aqueous solution at 265 nm using approximately 200 fs pump pulses from a titanium-sapphire laser system. The decay of excited-state absorption (ESA) at visible probe wavelengths was used to determine the S1 lifetimes of a variety of modified Cyt compounds at different pH values by global fitting. Identical lifetimes were observed for Cyt and cytidine (Cyd) within experimental uncertainty, but ESA by the ribonucleoside was considerably stronger, suggesting that the ribose group increases the oscillator strength of the S1 --> SN transition. The S1 lifetime of the important minor base 5-methylcytosine (m5Cyt) is 7.2 +/- 0.4 ps at pH 6.8. The same lifetime was measured for the ribonucleoside 5-methylcytidine, but sugar substitution again increased the strength of the ESA signal. Protonation of Cyd and m5Cyt at low pH led to a modest decrease in their S1 lifetimes. On the other hand, deprotonation of Cyt and m5Cyt significantly increased the lifetime of their respective S1 states. These trends support the intermediacy of the n,pi* state localized on the carbonyl oxygen in the nonradiative decay mechanism of Cyt. Longer S1 lifetimes were observed for 5-fluorocytosine and N4-acetylcytosine. Collectively, these results illustrate the great potential of femtosecond laser spectroscopy for investigating excited-state dynamics in DNA and DNA components.
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Affiliation(s)
- Rosalie J Malone
- Department of Chemistry, The Ohio State University, Columbus, OH 43210, USA
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Moran D, Sukcharoenphon K, Puchta R, Schaefer HF, Schleyer PVR, Hoff CD. 2-Pyridinethiol/2-pyridinethione tautomeric equilibrium. A comparative experimental and computational study. J Org Chem 2002; 67:9061-9. [PMID: 12467429 DOI: 10.1021/jo0263768] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The gas phase and solvent dependent preference of the tautomerization between 2-pyridinethiol (2SH) and 2-pyridinethione (2S) has been assessed using variable temperature Fourier transform infrared (FTIR) experiments, as well as ab initio and density functional theory computations. No spectroscopic evidence (nu(S)(-)(H) stretch) for 2SH was observed in toluene, C(6)D(6), heptane, or methylene chloride solutions. Although, C(s)() 2SH is 2.61 kcal/mol more stable than C(s)() 2S (CCSD(T)/cc-pVTZ//B3LYP/6-311+G(3df,2p)+ZPE), cyclohexane solvent-field relative energies (IPCM-MP2/6-311+G(3df,2p)) favor 2S by 1.96 kcal/mol. This is in accord with the FTIR observations and in quantitative agreement with the -2.6 kcal/mol solution (toluene or C(6)D(6)) calorimetric enthalpy for the 2S/2SH tautomerization favoring the thione. As the intramolecular transition state for the 2S, 2SH tautomerization (2TS) lies 25 (CBS-Q) to 30 kcal/mol (CCSD/cc-pVTZ) higher in energy than either tautomer, tautomerization probably occurs in the hydrogen bonded dimer. The B3LYP/6-311+G(3df,2p) optimized C(2) 2SH dimer is 10.23 kcal/mol + ZPE higher in energy than the C(2)(h)() 2S dimer and is only 2.95 kcal/mol + ZPE lower in energy than the C(2) 2TS dimer transition state. Dimerization equilibrium measurements (FTIR, C(6)D(6)) over the temperature range 22-63 degrees C agree: K(eq)(298) = 165 +/- 40 M(-)(1), DeltaH = -7.0 +/- 0.7 kcal/mol, and DeltaS = -13.4 +/- 3.0 cal/(mol deg). The difference between experimental and B3LYP/6-311+G(3df,2p) [-34.62 cal/(mol deg)] entropy changes is due to solvent effects. The B3LYP/6-311+G(3df,2p) nucleus independent chemical shifts (NICS) are -8.8 and -3.5 ppm 1 A above the 2SH and 2S ring centers, respectively, and the thiol is aromatic. Although the thione is not aromatic, it is stabilized by the thioamide resonance. In solvent, the large 2S dipole, 2-3 times greater than 2SH, favors the thione tautomer and, in conclusion, 2S is thermodynamically more stable than 2SH in solution.
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Affiliation(s)
- Damian Moran
- Center for Computational Quantum Chemistry, University of Georgia, Athens 30602, USA
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