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Jin L, Lv M, Zhao M, Wang R, Zhao C, Lu J, Wang L, Wang W, Wei Y. Formic acid catalyzed isomerization of protonated cytosine: a lower barrier reaction for tautomer production of potential biological importance. Phys Chem Chem Phys 2018; 19:13515-13523. [PMID: 28497833 DOI: 10.1039/c7cp01008g] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
Tautomerism in nucleotide bases is one of the possible mechanisms of DNA mutation. In spite of numerous studies on the structure and energy of protonated cytosine tautomers, little information is available on the process of their intra- and intermolecular tautomerizations. The catalytic ability of H2O, HCOOH, and the HCOOHH2O group to facilitate the tautomerism of the Cyt2t+ to CytN3+ isomer has been studied. It is shown that the activation free energies of tautomerism in the gas phase are 161.17, 58.96, 26.06, and 15.69 kJ mol-1, respectively, when the reaction is carried out in the absence and presence of H2O, HCOOH, or the HCOOHH2O group. The formation of a doubly hydrogen bonded transition state is central to lowering the activation free energy and facilitating the intramolecular hydrogen atom transfer that is required for isomerization. In the aqueous phase, although the solvent effects of water significantly decrease the activation free energy of intramolecular tautomerization, the isomerization of the Cyt2t+ to CytN3+ isomer remains unfavorable, and the HCOOH and HCOOHH2O group mediated mechanisms are still more favorable. Meanwhile, conventional transition state theory (CTST) followed by Wigner tunneling correction is then applied to estimate the rate constants. The rate constant with Wigner tunneling correction for direct tautomerization is obviously smaller than that of HCOOH-mediated tautomerization, which is the most plausible mechanism. Finally, another important finding is that the product complex (CytN3+HCOOH) is in the rapid tautomeric equilibrium with the reaction complex (Cyt2t+HCOOH) (τ99.9% = 3.84 × 10-12 s), which is implemented by the mechanism of the concerted synchronous double proton transfer. Its lifetime of the formed CytN3+HCOOH complex (τ = 8.33 × 10-9 s) is almost one order of magnitude larger than the time required for the replication machinery to forcibly dissociate a base pair into the monomers during DNA replication (several ns), which is further dissociated into the CytN3+ and HCOOH monomers. The results of the present study demonstrate the feasibility of acid catalysis for DNA base isomerization reactions that would otherwise be forbidden.
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Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Mengdan Lv
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Mengting Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Rui Wang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Ling Wang
- Shaanxi Key Laboratory of Catalysis, School of Chemical & Environment Science, Shaanxi Sci-Tech University, Hanzhong 723001, China.
| | - Wenliang Wang
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
| | - Yawen Wei
- Institute of publication Science, Chang'an University, Xi'an 710064, China
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Jin L, Shi S, Zhao Y, Luo L, Zhao C, Lu J, Jiang M. Effects of C5-substituent group on the hydrogen peroxide-mediated tautomerisation of protonated cytosine: a theoretical perspective. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1406159] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- Lingxia Jin
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Shengnan Shi
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Yang Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Liyang Luo
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Caibin Zhao
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Jiufu Lu
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
| | - Min Jiang
- Shaanxi Key Laboratory of Catalysis, School of Chemical and Environment Science, Shaanxi University of Technology, Hanzhong, China
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Alabugin IV, Bresch S, dos Passos Gomes G. Orbital hybridization: a key electronic factor in control of structure and reactivity. J PHYS ORG CHEM 2014. [DOI: 10.1002/poc.3382] [Citation(s) in RCA: 92] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Igor V. Alabugin
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Stefan Bresch
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
| | - Gabriel dos Passos Gomes
- Department of Chemistry and Biochemistry; Florida State University; Tallahassee FL 32306-4390 USA
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Ab initio and DFT studies on 1-(thionitrosomethylene) hydrazine: conformers, energies, and intramolecular hydrogen-bond strength. Struct Chem 2012. [DOI: 10.1007/s11224-012-0144-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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Chandra AK, Zeegers-Huyskens T. A theoretical investigation of the interaction between substituted carbonyl derivatives and water: Open or cyclic complexes? J Comput Chem 2012; 33:1131-41. [PMID: 22344933 DOI: 10.1002/jcc.22943] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2011] [Revised: 12/17/2011] [Accepted: 01/08/2012] [Indexed: 02/06/2023]
Affiliation(s)
- Asit K Chandra
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India.
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Substituent effects on the intramolecular hydrogen bond in 1-hydroxyanthraquinone: AIM and NBO analyses. Struct Chem 2012. [DOI: 10.1007/s11224-012-9949-6] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022]
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PARVEEN SALMA, DAS SUBOJIT, CHANDRA ASITK, ZEEGERS-HUYSKENS THERESE. THEORETICAL STUDIES OF HYDROGEN BONDING INTERACTION BETWEEN TRIMETHYLAMINE AND SUBSTITUTED PHENOLS, INFLUENCE OF THE SUBSTITUENTS ON THE HYDROGEN BOND PROPERTIES AND THE VIBRATIONAL SPECTRUM. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2011. [DOI: 10.1142/s0219633608004507] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Hydrogen bonding interactions between trimethylamine (TMA) and a series of para substituted phenols (X– C 6 H 4 OH , X = H , CH 3, NH 2, Cl , CN , and NO 2) are studied by using density functional theory with the hybrid B3LYP functional and the 6-31++G(d,p) basis set. Both electron donor and acceptor substituents (X) are chosen to study systematically the relation between the proton donor ability of the phenols and the strength of the OH … N hydrogen bond. The effect of hydrogen bonding on spectral and structural parameters and their inter relation are discussed. The natural bond orbital (NBO) analysis (occupation of σ* orbitals, hyperconjugative energies and atomic charges) is also carried out to elucidate the reason behind the spectral and structural changes due to hydrogen bond formation. Several correlations between hydrogen bond strength and bond properties are discussed.
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Affiliation(s)
- SALMA PARVEEN
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India
| | - SUBOJIT DAS
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India
| | - ASIT K. CHANDRA
- Department of Chemistry, North Eastern Hill University, Shillong 793022, India
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Theoretical study of hydrogen peroxide interacting with DNA base and DNA base pair in terms of ab initio method and ABEEMσπ/MM fluctuating charge potential model. COMPUT THEOR CHEM 2011. [DOI: 10.1016/j.comptc.2011.03.025] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Diep PN, Nguyen HMT, Hue TT, Zeegers-Huyskens T. Theoretical investigation of the interaction between monohalogenated ethenes and hydrogen peroxide. J Mol Struct 2010. [DOI: 10.1016/j.molstruc.2010.01.062] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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F–H···N hydrogen bonds: Influence of substituent and hybridization of nitrogen on H-bond properties and two-bond 19F–15N spin–spin coupling constants (2hJF–N). Chem Phys Lett 2010. [DOI: 10.1016/j.cplett.2010.03.051] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Zervos N, Kolocouris A. Improper hydrogen-bonded cyclohexane C–Hax⋯Yax contacts: experimental evidence from 1H NMR spectroscopy of suitable axial cyclohexane models. Tetrahedron Lett 2010. [DOI: 10.1016/j.tetlet.2010.02.170] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Kolocouris A. C-Hax···Yax Contacts in Cyclohexane Derivatives Revisited−Identification of Improper Hydrogen-Bonded Contacts. J Org Chem 2009; 74:1842-9. [DOI: 10.1021/jo801835a] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Antonios Kolocouris
- Faculty of Pharmacy, Department of Pharmaceutical Chemistry, University of Athens, Panepistimioupolis-Zografou, 15771 Athens, Greece
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Relationship between calculated NMR data and intermolecular hydrogen bond properties in X-pyridine⋯HF. Chem Phys 2009. [DOI: 10.1016/j.chemphys.2008.11.004] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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Ghiasi R, Monajjemi M. Theoretical study of the dihydrogen bonded HMH…HB≡NH and HMH…HN≡BH complexes (M[dbnd]Be, Mg and Ca): properties and structures. MAIN GROUP CHEMISTRY 2008. [DOI: 10.1080/10241220802230666] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/07/2022]
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ETO I, FUJIWARA H, AKIYOSHI M, MATSUNAGA T. Theoretical Study of Hydrogen Peroxide–Metal Ion Complexes by DFT Method. JOURNAL OF COMPUTER CHEMISTRY-JAPAN 2008. [DOI: 10.2477/jccj.h1919] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
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Ebrahimi A, Habibi M, Masoodi HR. Theoretical study of the influence of para- and meta-substituents on X-pyridine⋯HF hydrogen bonding. Chem Phys 2007. [DOI: 10.1016/j.chemphys.2007.08.012] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Theoretical study of the acidity and basicity of uric acid and its interaction with water. ACTA ACUST UNITED AC 2007. [DOI: 10.1016/j.theochem.2007.02.021] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rutkowski K, Rodziewicz P, Melikova S, Koll A. Theoretical study of Hal3CH/F2CD2 (Hal=F,Cl) and F3CH/FH heterodimers with blue shifted hydrogen bonds. Chem Phys 2006. [DOI: 10.1016/j.chemphys.2006.04.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Theoretical study of the blue-shifting hydrogen bonds between CH2X2 and CHX3 (X=F, Cl, Br) and hydrogen peroxide. J Mol Struct 2006. [DOI: 10.1016/j.molstruc.2005.12.059] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Almatarneh MH, Flinn CG, Poirier RA, Sokalski WA. Computational Study of the Deamination Reaction of Cytosine with H2O and OH-. J Phys Chem A 2006; 110:8227-34. [PMID: 16805511 DOI: 10.1021/jp062300u] [Citation(s) in RCA: 52] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The mechanism for the deamination reaction of cytosine with H(2)O and OH(-) to produce uracil was investigated using ab initio calculations. Optimized geometries of reactants, transition states, intermediates, and products were determined at RHF/6-31G(d), MP2/6-31G(d), and B3LYP/6-31G(d) levels and for anions at the B3LYP/6-31+G(d) level. Single-point energies were also determined at B3LYP/6-31+G(d), MP2/GTMP2Large, and G3MP2 levels of theory. Thermodynamic properties (DeltaE, DeltaH, and DeltaG), activation energies, enthalpies, and free energies of activation were calculated for each reaction pathway that was investigated. Intrinsic reaction coordinate analysis was performed to characterize the transition states on the potential energy surface. Two pathways for deamination with H(2)O were found, a five-step mechanism (pathway A) and a two-step mechanism (pathway B). The activation energy for the rate-determining steps, the formation of the tetrahedral intermediate for pathway A and the formation of the uracil tautomer for pathway B, are 221.3 and 260.3 kJ/mol, respectively, at the G3MP2 level of theory. The deamination reaction by either pathway is therefore unlikely because of the high barriers that are involved. Two pathways for deamination with OH(-) were also found, and both of them are five-step mechanisms. Pathways C and D produce an initial tetrahedral intermediate by adding H(2)O to deprotonated cytosine which then undergoes three conformational changes. The final intermediate dissociates to product via a 1-3 proton shift. Deamination with OH(-), through pathway C, resulted in the lowest activation energy, 148.0 kJ/mol, at the G3MP2 level of theory.
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Affiliation(s)
- Mansour H Almatarneh
- Department of Chemistry, Memorial University of Newfoundland, St. John's, Newfoundland, Canada A1B 3X7
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Alabugin IV, Manoharan M. Rehybridization as a general mechanism for maximizing chemical and supramolecular bonding and a driving force for chemical reactions. J Comput Chem 2006; 28:373-90. [PMID: 17143865 DOI: 10.1002/jcc.20524] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Dynamic variations in hybridization patterns (rehybridization) were analyzed at B3LYP/6-31G** and MP2/6-31+G* levels. Computations clearly illustrate the generality of rehybridization in a variety of chemical phenomena, which involve structural reorganization in hydrogen-bonded complexes, nonhyperconjugative stereoelectronic effects in saturated heterocycles, Mills-Nixon effect, and contrasting substituent effects in cycloaromatization reactions.
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Affiliation(s)
- Igor V Alabugin
- Department of Chemistry and Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, USA.
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Chandra AK, Zeegers-Huyskens T. Theoretical Study of (CH···C)- Hydrogen Bonds in CH4-nXn(X = F, Cl; n = 0, 1, 2) Systems Complexed with Their Homoconjugate and Heteroconjugate Carbanions. J Phys Chem A 2005; 109:12006-13. [PMID: 16366655 DOI: 10.1021/jp054123n] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
This work deals with a theoretical study of the (CH...C)- hydrogen bonds in CH4, CH3X, and CH2X2 (X = F, Cl) complexed with their homoconjugate and heteroconjugate carbanions. The properties of the complexes are calculated with the B3LYP method using the 6-311++G(d,p) or 6-311++G(2df,2p) basis sets. The deprotonation enthalpies (DPE) of the CH bond or the proton affinities of the carbanions (PA(C-) are calculated as well. All the systems with the exception of the CH4...CHCl2(-) one are characterized by a double minimum potential. In some of the complexes, the (CH(b)...C)- hydrogen bond is linear. In other systems, such as CH3F...CH2F- and CH3F...CHF2(-), there is a large departure from linearity, the systems being stabilized by electrostatic interactions between the nonbonded H of the neutral molecule and the F atom of the carbanion. In the transition state, the (CH(b)...C)- bond is linear, and there is a large contraction of the intermolecular C...C distance. The binding energies vary within a large range, from -1.4 to -11.1 kcal mol(-1) for the stable complexes and -8.6 to -44.1 kcal mol(-1) for the metastable complexes. The energy barriers to proton transfer are between 5 and 20 kcal mol(-1) for the heteroconjugate systems and between 3.8 and 8.3 kcal mol(-1) for the homoconjugate systems. The binding energies of the linear complexes depend exponentially on 1.5DPE - PA(C-), showing that the proton donor is more important than the proton acceptor in determining hydrogen bond strength. The NBO analysis indicates an important electronic reorganization in the two partners. The elongations of the CH bond resulting from the interaction with the carbanion depend on the occupation of the sigma*(CH(b)) antibonding orbitals and on the hybridization of the C bonded to H(b). The frequency shifts of the nu(CH)(A1) stretching vibration range between 15 and 1150 cm(-1). They are linearly correlated to the elongation of the CH(b) bond.
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Affiliation(s)
- Asit K Chandra
- Department of Chemistry, North Eastern Hill University, Shillong, 793022 India
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