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Sarac K, Orek C, Koparir P. Experimental and Theoretical Investigations Regarding the Thione–Thiol Tautomerism in 4-Benzyl-5-(thiophene-2-yl)-2,4-dihydro-3H-1,2,4-triazole-3-thione. RUSSIAN JOURNAL OF ORGANIC CHEMISTRY 2021. [DOI: 10.1134/s1070428021010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Hamdi I, Bkhairia I, Roodt A, Roisnel T, Nasri M, Naïli H. Synthesis, intermolecular interactions and biological activities of two new organic-inorganic hybrids C 6H 10N 2,2Br and C 6H 10N 2,2Cl·H 2O. RSC Adv 2020; 10:5864-5873. [PMID: 35497437 PMCID: PMC9049630 DOI: 10.1039/c9ra09294c] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2019] [Accepted: 01/10/2020] [Indexed: 11/23/2022] Open
Abstract
A slow evaporation method has permitted the crystallization of two novel crystals of (2-aminomethyl)pyridindiumdihalide C6H10N2,2Br (1) and C6H10N2,2Cl·H2O (2). The structures of the prepared compounds (1) and (2) were elucidated by single-crystal X-ray diffraction which revealed that they crystallize, respectively, with triclinic and monoclinic symmetries. Their crystal packing was stabilized by non-covalent interactions, including N–H⋯Br, C–H⋯Br, N–H⋯Cl, O–H⋯Cl and N–H⋯O hydrogen bonds. 3-D Hirshfeld surface analysis followed by 2-D fingerprint schemes gives insights into the intermolecular interactions in the crystalline structure. Furthermore, the FT-IR spectroscopy of these two compounds was carried out. The synthesized products were also screened for in vitro antioxidant and antimicrobial activities, which reveals their favourable antioxidant activities against 1,1-diphenyl-2-picrylhydrazyl (DPPH) as well as the discolouration of β-carotene. A slow evaporation method has permitted the crystallization of two novel crystals of (2-aminomethyl)pyridindiumdihalide C6H10N2,2Br (1) and C6H10N2,2Cl·H2O (2).![]()
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Affiliation(s)
- Intissar Hamdi
- Laboratory of Physico-chemical of the Solid State, Department of Chemistry, Faculty of Sciences of Sfax, Université de Sfax BP 1171 3000 Sfax Tunisia +216 74 274 437 +216 98 660 026
| | - Intidhar Bkhairia
- Laboratory of Enzyme Engineering and Microbiology, University of Sfax, National School of Engineering of Sfax (ENIS) B.P. 1173-3038 Sfax Tunisia
| | - Andreas Roodt
- Department of Chemistry, University of the Free State P.O. Box 339 Bloemfontein 9300 South Africa
| | - Thierry Roisnel
- University of Rennes, CNRS, ISCR (Institute of Chemical Sciences of Rennes) - UMR 6226 F-35000 Rennes France
| | - Moncef Nasri
- Laboratory of Enzyme Engineering and Microbiology, University of Sfax, National School of Engineering of Sfax (ENIS) B.P. 1173-3038 Sfax Tunisia
| | - Houcine Naïli
- Laboratory of Physico-chemical of the Solid State, Department of Chemistry, Faculty of Sciences of Sfax, Université de Sfax BP 1171 3000 Sfax Tunisia +216 74 274 437 +216 98 660 026
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Cukurovali A, Karakurt T. Synthesis, spectroscopic, X-ray diffraction and tautomeric properties of 5-(diethylamino)-2-((2-(5-(3-methyl-3-phenylcyclobutyl)-6H-1,3,4-thiadiazin-2yl)hydrazono)methyl)phenol: A combined experimental and theoretical study. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.04.052] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Wei SC, Ho JW, Yen HC, Shi HQ, Cheng LH, Weng CN, Chou WK, Chiu CC, Cheng PY. Ultrafast Excited-State Dynamics of Hydrogen-Bonded Cytosine Microsolvated Clusters with Protic and Aprotic Polar Solvents. J Phys Chem A 2018; 122:9412-9425. [PMID: 30452255 DOI: 10.1021/acs.jpca.8b09526] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Microsolvation effects on the ultrafast excited-state deactivation dynamics of cytosine (Cy) were studied in hydrogen-bonded Cy clusters with protic and aprotic solvents using mass-resolved femtosecond pump-probe ionization spectroscopy. Two protic solvents, water (H2O) and methanol (MeOH), and one aprotic solvent, tetrahydrofuran (THF), were investigated, and transients of Cy·(H2O)1-6, Cy·(MeOH)1-3, and Cy·THF microsolvated clusters produced in supersonic expansions were measured. With the aid of electronic structure calculations, we assigned the observed dynamics to the low-energy isomers of various Cy clusters and discussed the microsolvation effect on the excited-state deactivation dynamics. With the protic solvents only the microsolvated clusters of Cy keto tautomer were observed. The observed decay time constants of Cy·(H2O) n are 0.5 ps for n = 1 and ∼0.2-0.25 ps for n = 2-6. For Cy·(MeOH) n clusters, the decay time constant for n = 1 cluster is similar to that of the Cy monohydrate, but for n = 2 and 3 the decays are about a factor of 2 slower than the corresponding microhydrates. With the aprotic solvent, THF, hydrogen-bonded complexes of both keto and enol tautomers are present in the beam. The keto-Cy·THF shows a decay similar to that of the keto-Cy monomer, whereas the enol-Cy·THF exhibits a 2-fold slower decay than the enol-Cy monomer, suggesting an increase in the barrier to excited-state deactivation upon binding of one THF molecule to the enol form of Cy.
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Affiliation(s)
- Shih-Chun Wei
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Jr-Wei Ho
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hung-Chien Yen
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Hui-Qi Shi
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Li-Hao Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Nan Weng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Wei-Kuang Chou
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Chih-Chung Chiu
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
| | - Po-Yuan Cheng
- Department of Chemistry , National Tsing Hua University , Hsinchu , Taiwan 30043 , Republic of China
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Ding Y, Wang X, Xie L, Yao X, Xu W. Two-dimensional self-assembled nanostructures of nucleobases and their related derivatives on Au(111). Chem Commun (Camb) 2018; 54:9259-9269. [PMID: 30027963 DOI: 10.1039/c8cc03585g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The construction of two-dimensional (2D) self-assembled nanostructures has been one of the considerably interesting areas of on-surface chemistry in the past few decades, and has benefited from the rapid development and improvement of scanning probe microscopy techniques. In this research field, many attempts have been made in the controllable fabrication of well-ordered and multifunctional surface nanostructures, which attracted interest because of the prospect for artificial design of functional molecular nanodevices. DNA and RNA are considered to be programmable self-assembly systems and it is possible to use their base sequences to encode instructions for assembly in a predetermined fashion at the nanometer scale. As important constituents of nucleic acids, nucleobases, with intrinsic functional groups for hydrogen bonding, coordination bonding, and electrostatic interactions, can be employed as a potential system for the versatile construction of various biomolecular nanostructures, which may be used to structure the self-assembly of DNA-based artificial molecular constructions and play an important role in novel biosensors based on surface functionalization. In this article, we will review the recent progress of on-surface self-assembly of nucleobases and their derivatives together with different reactants (e.g., metals, halogens, salts and water), and as a result, various 2D surface nanostructures are summarized.
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Affiliation(s)
- Yuanqi Ding
- Interdisciplinary Materials Research Center, Tongji-Aarhus Joint Research Center for Nanostructures and Functional Nanomaterials, College of Materials Science and Engineering, Tongji University, Shanghai 201804, P. R. China.
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Aouad MR, Messali M, Rezki N, Al-Zaqri N, Warad I. Single proton intramigration in novel 4-phenyl-3-((4-phenyl-1H-1,2,3-triazol-1-yl)methyl)-1H-1,2,4-triazole-5(4H)-thione: XRD-crystal interactions, physicochemical, thermal, Hirshfeld surface, DFT realization of thiol/thione tautomerism. J Mol Liq 2018. [DOI: 10.1016/j.molliq.2018.05.085] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/16/2022]
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7
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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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Saikia N, Johnson F, Waters K, Pandey R. Dynamics of self-assembled cytosine nucleobases on graphene. NANOTECHNOLOGY 2018; 29:195601. [PMID: 29461252 DOI: 10.1088/1361-6528/aab0ea] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Molecular self-assembly of cytosine (C n ) bases on graphene was investigated using molecular dynamics methods. For free-standing C n bases, simulation conditions (gas versus aqueous) determine the nature of self-assembly; the bases prefer to aggregate in the gas phase and are stabilized by intermolecular H-bonds, while in the aqueous phase, the water molecules disrupt base-base interactions, which facilitate the formation of π-stacked domains. The substrate-induced effects, on the other hand, find the polarity and donor-acceptor sites of the bases to govern the assembly process. For example, in the gas phase, the assembly of C n bases on graphene displays short-range ordered linear arrays stabilized by the intermolecular H-bonds. In the aqueous phase, however, there are two distinct configurations for the C n bases assembly on graphene. For the first case corresponding to low surface coverage, the bases are dispersed on graphene and are isolated. The second configuration archetype is disordered linear arrays assembled with medium and high surface coverage. The simulation results establish the role of H-bonding, vdW π-stacking, and the influence of graphene surface towards the self-assembly. The ability to regulate the assembly into well-defined patterns can aid in the design of self-assembled nanostructures for the next-generation DNA based biosensors and nanoelectronic devices.
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Mroczek T, Plech T, Wujec M. Novel Concept of Discrimination of 1,2,4-Triazole-3-thione and 3-Thiol Tautomers. J Chromatogr Sci 2016; 55:117-129. [PMID: 27777224 DOI: 10.1093/chromsci/bmw151] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Revised: 04/19/2016] [Accepted: 09/08/2016] [Indexed: 11/14/2022]
Abstract
Till now, three major spectroscopic techniques, fourier transform infrared (FT-IR), nuclear magnetic resonance (NMR) spectroscopy and X-ray crystallography, have been used for determination of thiol-thione tautomeric forms. Therefore, a novel analytical concept of discrimination of 1,2,4-triazole-3-thione and 3-thiol tautomers using two high-resolution mass spectrometers has been proposed. It comprises the high-performance liquid chromatography (HPLC) hyphenated with electrospray ionization (ESI)-time-of-flight mass spectrometry (ESI-TOF-MS, positive ion mode) followed by in-source collision-induced dissociation (CID) and low-energy CID-tandem mass spectrometry (MS/MS) analysis measured with a Quadruple-TOF-MS instrument. The HPLC column was a Zorbax Stable Bond RP-18 and a rapid isocratic elution. Selected 3-thione and 3-thiol tautomers were rapidly separated, within 6 min and detected both by in-source CID ESI(+)-TOF-MS and CID ESI(+)-QTOF-MS with a high mass accuracy and high sensitivity. The method limits of detection were of 2.8-5.6 pg/μl (at S/N 3:1) for ESI-TOF-MS and 0.25-0.55 pg/μl for ESI-QTOF-MS. The tautomeric form could be easily discriminated by both methods and by the different gas-phase fragmentation patterns. Differences and similarities between in-source CID MS and CID MS/MS spectra have also been presented. These findings were also supported by recorded FT-IR spectra in solid state. The developed methodology using both the high-resolution MS systems is considerably the most sensitive among the others.
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Affiliation(s)
- Tomasz Mroczek
- Department of Pharmacognosy with Medicinal Plants Laboratory, Medical University, 1 Chodzki St., 20-093 Lublin, Poland
| | - Tomasz Plech
- Department of Organic Chemistry, Medical University, 4a Chodzki St., 20-093 Lublin, Poland
| | - Monika Wujec
- Department of Organic Chemistry, Medical University, 4a Chodzki St., 20-093 Lublin, Poland
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Wincel H. Microhydration of Deprotonated Nucleobases. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2016; 27:1383-92. [PMID: 27178262 PMCID: PMC4942500 DOI: 10.1007/s13361-016-1411-3] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2016] [Revised: 04/17/2016] [Accepted: 04/19/2016] [Indexed: 06/05/2023]
Abstract
Hydration reactions of deprotonated nucleobases (uracil, thymine, 5-fluorouracil,2-thiouracil, cytosine, adenine, and hypoxanthine) produced by electrospray have been experimentally studied in the gas phase at 10 mbar using a pulsed ion-beam high-pressure mass spectrometer. The thermochemical data, ΔH (o) , ΔS (o) , and ΔG (o) , for the monohydrated systems were determined. The hydration enthalpies were found to be similar for all studied systems and varied between 39.4 and 44.8 kJ/mol. A linear correlation was found between water binding energies in the hydrated complexes and the corresponding acidities of the most acidic site of nucleobases. The structural and energetic aspects of the precursors for the hydrated complexes are discussed in conjunction with available literature data. Graphical Abstract ᅟ.
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Affiliation(s)
- Henryk Wincel
- Institute of Physical Chemistry, Polish Academy of Sciences, 01-224, Warsaw, Poland.
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11
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Li T, Li F, Li Z, Sun C, Tong J, Fang W, Men Z. Influence of strong and weak hydrogen bonds in ices on stimulated Raman scattering. OPTICS LETTERS 2016; 41:1297-1300. [PMID: 26977693 DOI: 10.1364/ol.41.001297] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/05/2023]
Abstract
Stimulated Raman scattering (SRS) in liquid water and ice Ih using Nd:YAG laser is investigated. The spectrum of backward SRS (BSRS) in water is acquired. The spectrum shows an unexpected SRS peak at around 3453 cm(-1) besides the normal peak, which is similar to the spontaneous Raman spectrum of ice VII. The ice VII phase will be formed by laser-induced shock compression in liquid water. Simultaneously, unlike the spontaneous Raman spectrum, the pre-resonance SRS of ice Ih at around 3110 and 3210 cm(-1) is observed. The Raman peaks appeared in liquid water and ice Ih are attributed to the effect of strong and weak hydrogen bonds (H bonds), which should be ubiquitous in other ice phases.
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Shao P, Ding LP, Cai JT, Lu C, Liu B, Sun CB. Microhydration effects on the structures and electrophilic properties of cytidine. RSC Adv 2016. [DOI: 10.1039/c6ra11720a] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Adiabatic electron affinities (AEAs) for cytidine hydrates with up to four water molecules.
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Affiliation(s)
- Peng Shao
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Li-Ping Ding
- Department of Optoelectronic Science & Technology
- College of Electrical & Information Engineering
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Jiang-Tao Cai
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Cheng Lu
- Beijing Computational Science Research Center
- Beijing 100084
- China
| | - Bo Liu
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
| | - Chang-Bo Sun
- Department of Physics
- Shaanxi University of Science & Technology
- Xi'an 710021
- China
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Ho J, Yen H, Shi H, Cheng L, Weng C, Chou W, Chiu C, Cheng P. Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence. Angew Chem Int Ed Engl 2015. [DOI: 10.1002/ange.201507524] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hung‐Chien Yen
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hui‐Qi Shi
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Li‐Hao Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Nan Weng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Wei‐Kuang Chou
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Chung Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Po‐Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
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Ho J, Yen H, Shi H, Cheng L, Weng C, Chou W, Chiu C, Cheng P. Microhydration Effects on the Ultrafast Photodynamics of Cytosine: Evidences for a Possible Hydration‐Site Dependence. Angew Chem Int Ed Engl 2015; 54:14772-6. [DOI: 10.1002/anie.201507524] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Revised: 09/18/2015] [Indexed: 11/10/2022]
Affiliation(s)
- Jr‐Wei Ho
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hung‐Chien Yen
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Hui‐Qi Shi
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Li‐Hao Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Nan Weng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Wei‐Kuang Chou
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Chih‐Chung Chiu
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
| | - Po‐Yuan Cheng
- Department of Chemistry, National Tsing Hua University, Hsinchu, Taiwan 30043 (R.O.C.)
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Yang J, Li S, Zhao H, Song B, Zhang G, Zhang J, Zhu Y, Han J. Molecular recognition and interaction between uracil and urea in solid-state studied by terahertz time-domain spectroscopy. J Phys Chem A 2014; 118:10927-33. [PMID: 25386785 DOI: 10.1021/jp506045q] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Using terahertz time-domain spectroscopy characterization, we observe that urea is able to recognize and interact with uracil efficiently even in the solid phase without involving water or solvents. A cocrystal configuration linked by a pair of hydrogen bonds between uracil and urea was formed. The terahertz absorption spectrum of the cocrystal shows a distinct new absorption at 0.8 THz (26.7 cm(-1)), which originates from the intermolecular hydrogen bonding. Both mechanical milling and heating can accelerate the reaction efficiently. Density functional theory was adopted to simulate the vibrational modes of the cocrystal, and the results agree well with the experimental observation. Multiple techniques, including powder X-ray diffraction, scanning electron microscopy, and Fourier transform infrared spectroscopy, were performed to investigate the reaction process, and they presented supportive evidence. This work enables in-depth understanding of recognition and interaction of urea with nucleobases and comprehension of the denaturation related to RNA. We also demonstrate that terahertz spectroscopy is an effective and alternative tool for online measurement and quality control in pharmaceutical and chemical industries.
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Affiliation(s)
- Jingqi Yang
- Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences , Shanghai 201800, People's Republic of China
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González E, Lino J, Deriabina A, Herrera JNF, Poltev VI. Interactions of DNA bases with individual water molecules. Molecular mechanics and quantum mechanics computation results vs. experimental data. Biophysics (Nagoya-shi) 2014. [DOI: 10.1134/s0006350913050047] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
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Theoretical investigation of thione-thiol tautomerism, intermolecular double proton transfer reaction and hydrogen bonding interactions in 4-ethyl-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.10.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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Shao P, Kuang XY, Ding LP, Zhao YR. Structures, electrophilic properties, and hydrogen bonds of cytidine, uridine, and their radical anions: Microhydration effects. J Chem Phys 2013; 139:024305. [PMID: 23862941 DOI: 10.1063/1.4812500] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
Structures, electrophilic properties, and hydrogen bonds of the neutral and anionic monohydrated nucleoside, (cytidine)H2O, and (uridine)H2O have been systematically investigated using density functional theory. Various water-binding sites were predicted by explicitly considering the optimized monohydrated structures. Meanwhile, predictions of electron affinities and vertical detachment energies were also carried out to investigate their electrophilic properties. By examining the singly occupied molecular orbital and natural population analysis, we found the excess negative charge is localized on the cytidine and uridine moiety in anionic monohydrates. This may be the reason why the strength of hydrogen bonding undergoes an obvious change upon the extra electron attachment. Based on the electron density (ρ) and reduced density gradient (RDG), we present an approach to map and analyze the weak interaction (especially hydrogen bond) in monohydrated cytidine and uridine. The scatter plots of RDG versus ρ allow us to identify the different type interactions. Meanwhile, the maps of the gradient isosurfaces show a rich visualization of hydrogen bond, van der Waals interaction, and steric effect.
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Affiliation(s)
- Peng Shao
- Institute of Atomic and Molecular Physics, Sichuan University, Chengdu 610065, China
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19
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Özdemir N, Dayan S, Dayan O, Dinçer M, Kalaycıoğlu NÖ. Experimental and molecular modeling investigation of (E)-N-{2-[(2-hydroxybenzylidene)amino]phenyl}benzenesulfonamide. Mol Phys 2012. [DOI: 10.1080/00268976.2012.742209] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Namık Özdemir
- a Department of Physics , Faculty of Arts and Sciences, Ondokuz Mayıs University , 55139, Samsun , Turkey
| | - Serkan Dayan
- b Department of Chemistry , Faculty of Science, Erciyes University , 38039, Kayseri , Turkey
| | - Osman Dayan
- c Laboratory of Inorganic Synthesis and Molecular Catalysis , Çanakkale Onsekiz Mart University , 17020, Çanakkale , Turkey
| | - Muharrem Dinçer
- a Department of Physics , Faculty of Arts and Sciences, Ondokuz Mayıs University , 55139, Samsun , Turkey
| | - Nilgün Ö. Kalaycıoğlu
- b Department of Chemistry , Faculty of Science, Erciyes University , 38039, Kayseri , Turkey
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Quantum chemical investigation of the intra- and intermolecular proton transfer reactions and hydrogen bonding interactions in 4-amino-5-(2-hydroxyphenyl)-2H-1,2,4-triazole-3(4H)-thione. J Mol Model 2012; 19:397-406. [DOI: 10.1007/s00894-012-1567-0] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/09/2012] [Indexed: 10/27/2022]
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21
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Stasyuk OA, Szatyłowicz H, Krygowski TM. Effect of the H-bonding on aromaticity of purine tautomers. J Org Chem 2012; 77:4035-45. [PMID: 22448684 DOI: 10.1021/jo300406r] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four tautomers of purine (1-H, 3-H, 7-H, and 9-H) and their equilibrium H-bonded complexes with F(-) and HF for acidic and basic centers, respectively, were optimized by means of the B3LYP/6-311++G(d,p) level of theory. Purine tautomer stability increases in the following series: 1-H < 3-H < 7-H < 9-H, consistent with increasing aromaticity. Furthermore, the presence of a hydrogen bond with HF does not change this order. For neutral H-bonded complexes, the strongest and the weakest intermolecular interactions occur (-14.12 and -10.49 kcal/mol) for less stable purine tautomers when the proton acceptor is located in the five- and six-membered rings, respectively. For 9-H and 7-H tautomers the order is reversed. The H-bond energy for the imidazole complex with HF amounts to -14.03 kcal/mol; hence, in the latter case, the fusion of imidazole to pyrimidine decreases its basicity. The ionic H-bonds of N(-)···HF type are stronger by ~10 kcal/mol than the neutral N···HF intermolecular interactions. The hydrogen bond N(-)···HF energies in pyrrole and imidazole are -32.28 and -30.03 kcal/mol, respectively, and are substantially stronger than those observed in purine complexes. The aromaticity of each individual ring and of the whole molecule for all tautomers in ionic complexes is very similar to that observed for the anion of purine. This is not the case for neutral complexes and purine as a reference. The N···HF bonds perturb much more the π-electron structure of five-membered rings than that of the six-membered ones. The H-bonding complexes for 7-H and 9-H tautomers are characterized by higher aromaticity and a much lower range of HOMA variability.
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Affiliation(s)
- Olga A Stasyuk
- Faculty of Chemistry, Warsaw University of Technology, Noakowskiego 3, 00-664 Warsaw, Poland
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22
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Can anion interaction accelerate transformation of cytosine tautomers? Detailed view form QTAIM analysis. Struct Chem 2012. [DOI: 10.1007/s11224-012-9993-2] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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23
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Cheng Q, Gu J, Compaan KR, Schaefer HF. Isoguanine formation from adenine. Chemistry 2012; 18:4877-86. [PMID: 22411110 DOI: 10.1002/chem.201102415] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2011] [Indexed: 11/06/2022]
Abstract
Several possible mechanisms underlying isoguanine formation when OH radical attacks the C(2) position of adenine (A C 2) are investigated theoretically for the first time. Two steps are involved in this process. In the first step, one of two low-lying A C 2⋅⋅⋅OH reactant complexes is formed, leading to C(2)-H(2) bond cleavage. Between the two reactant complexes there is a small isomerization barrier, which lies well below separated adenine plus OH radical. The complex dissociates to free molecular hydrogen and an isoguanine tautomer (isoG 1 or isoG 2). The local and activation barriers for the two pathways are very similar. This evidence suggests that the two pathways are competitive. After dehydrogenation, there are two possible routes for the second step of the reaction. One is direct hydrogen transfer, via enol-keto tautomerization, which has high local barriers for both tautomers and is not favored. The other option is indirect hydrogen transfer involving microsolvation by one water molecule. The water lowers the reaction barrier by over 20 kcal mol(-1) , indicating that water-mediated hydrogen transfer is much more favorable. Both A+OH(⋅) →isoG+H(⋅) reactions are exothermic and spontaneous. Among four isoguanine tautomers, isoG 1 has the lowest energy. Our findings explain why only the N(1)H and O(2)H tautomers of isolated isoguanine and isoguanosine have been observed experimentally.
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Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602, USA
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24
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Lu N, Meng L, Chen D, Zhang G. Retracted article: Enantioselectivity of aza-MBH-type reaction of nitroalkene to N-tosylimine catalyzed by thiourea-tertiary amine: a theoretical study. RSC Adv 2011. [DOI: 10.1039/c1ra00015b] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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Cheng Q, Gu J, Compaan KR, Schaefer HF. Hydroxyl Radical Reactions with Adenine: Reactant Complexes, Transition States, and Product Complexes. Chemistry 2010; 16:11848-58. [DOI: 10.1002/chem.201001236] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Qianyi Cheng
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Jiande Gu
- Discovery Center, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, CAS, Shanghai 201203 (P. R. China)
| | - Katherine R. Compaan
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, GA 30602 (USA), Fax: (+1) 706‐542‐0406
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Computational study of the intramolecular proton transfer reactions of 3-hydroxytropolone (2,7-dihydroxycyclohepta-2,4,6-trien-1-one) and its dimers. J Mol Model 2010; 16:1877-82. [PMID: 20232098 DOI: 10.1007/s00894-010-0674-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2009] [Accepted: 02/02/2010] [Indexed: 10/19/2022]
Abstract
The proton transfer reaction and dimerization processes of 3-hydroxytropolone (3-OHTRN) have been investigated using density functional theory (DFT) at the B3LYP/6-31+G** level. The influence of the solvent on the proton transfer reaction of 3-OHTRN was examined using the self-consistent isodensity polarized continuum model (SCI-PCM) with different dielectric constants (ε = 4.9, CHCI₃; ε = 32.63, CH₃OH; ε = 78.39, H₂O). The intramolecular proton transfer reaction occurs more readily in the gas phase than in solution. Results also show that the stability of 3-OHTRN dimers in the gas phase is directly affected by the hydrogen bond length in the dimer structure.
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Rasmussen AM, Lind MC, Kim S, Schaefer HF. Hydration of the Lowest Triplet States of the DNA/RNA Pyrimidines. J Chem Theory Comput 2010; 6:930-9. [DOI: 10.1021/ct900478c] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Andrew M. Rasmussen
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Maria C. Lind
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Sunghwan Kim
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
| | - Henry F. Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602
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28
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Theoretical study of the interaction pattern and the binding affinity between procaine and DNA bases. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2009.09.039] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
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29
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Millen AL, Wetmore SD. Glycosidic bond cleavage in deoxynucleotides — A density functional study. CAN J CHEM 2009. [DOI: 10.1139/v09-024] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Density functional theory was used to study the glycosidic bond cleavage in deoxynucleotides with the main goal to determine the effects of the nucleobase, hydrogen bonding with the nucleobase, and the (bulk) environment on the reaction energetics. Since direct glycosidic bond cleavage is a high-energy process, two nucleophile models were considered (HCOO–···H2O and HO–), which represent different stages of activation of a water nucleophile. The glycosidic bond cleavage barriers were found to decrease, while the reaction exothermicity increases, with an increase in the nucleobase acidity. The gas-phase barriers and reaction energies for bond cleavage in all deoxynucleotides were found to be significantly affected by hydrogen-bonding interactions with the nucleobase (by up to 30 kJ mol–1 depending on the nucleophile). Although the barriers increase and reaction energies become less exothermic in enzymatic and aqueous environments, the effects of the bulk environment are similar in the presence and absence of small molecules bound to the nucleobase. Therefore, the effects of hydrogen bonding with the bases are approximately the same in all environments. Our results suggest that hydrogen bonding with the nucleobase may play an important role in the glycosidic bond cleavage in both pyrimidine and purine nucleotides in a variety of environments.
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Affiliation(s)
- Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
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Almatarneh MH, Flinn CG, Poirier RA. Mechanisms for the Deamination Reaction of Cytosine with H2O/OH− and 2H2O/OH−: A Computational Study. J Chem Inf Model 2008; 48:831-43. [DOI: 10.1021/ci7003219] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Mansour H. Almatarneh
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada A1B 3X7
| | - Christopher G. Flinn
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada A1B 3X7
| | - Raymond A. Poirier
- Department of Chemistry, Memorial University of Newfoundland, St. John’s, Newfoundland, Canada A1B 3X7
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31
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Zhang G, Ji A, Chen D. Origin of blue and red shifts of C–H and C–N stretching vibrations in formamide–HF/H2O/H2S/NH3 complexes. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2007.12.019] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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32
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Kim S, Schaefer HF. Effects of Microsolvation on the Adenine−Uracil Base Pair and Its Radical Anion: Adenine−Uracil Mono- and Dihydrates. J Phys Chem A 2007; 111:10381-9. [PMID: 17705454 DOI: 10.1021/jp072727g] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Microhydration effects upon the adenine-uracil (AU) base pair and its radical anion have been investigated by explicitly considering various structures of their mono- and dihydrates at the B3LYP/DZP++ level of theory. For the neutral AU base pair, 5 structures were found for the monohydrate and 14 structures for the dihydrate. In the lowest-energy structures of the neutral mono- and dihydrates, one and two water molecules bind to the AU base pair through a cyclic hydrogen bond via the N(9)-H and N(3) atoms of the adenine moiety, while the lowest-lying anionic mono- and dihydrates have a water molecule which is involved in noncyclic hydrogen bonding via the O4 atom of the uracil unit. Both the vertical detachment energy (VDE) and adiabatic electron affinity (AEA) of the AU base pair are predicted to increase upon hydration. While the VDE and AEA of the unhydrated AU pair are 0.96 and 0.40 eV, respectively, the corresponding predictions for the lowest-lying anionic dihydrates are 1.36 and 0.75 eV, respectively. Because uracil has a greater electron affinity than adenine, an excess electron attached to the AU base pair occupies the pi* orbital of the uracil moiety. When the uracil moiety participates in hydrogen bonding as a hydrogen bond acceptor (e.g., the N(6)-H(6a)...O(4) hydrogen bond between the adenine and uracil bases and the O(w)-H(w)...N and O(w)-H(w)...O hydrogen bonds between the AU pair and the water molecules), the transfer of the negative charge density from the uracil moiety to either the adenine or water molecules efficiently stabilizes the system. In addition, anionic structures which have C-H...O(w) contacts are energetically more favorable than those with N-H...O(w) hydrogen bonds, because the C-H...O(w) contacts do not allow the unfavorable electron density donation from the water to the uracil moiety. This delocalization effect makes the energetic ordering for the anionic hydrates very different from that for the corresponding neutrals.
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Affiliation(s)
- Sunghwan Kim
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
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33
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Gomes JRB, Ribeiro da Silva MDMC, Freitas VLS, Ribeiro da Silva MAV. Molecular Energetics of Cytosine Revisited: A Joint Computational and Experimental Study. J Phys Chem A 2007; 111:7237-42. [PMID: 17616179 DOI: 10.1021/jp0729009] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A static bomb calorimeter has been used to measure the standard molar energy of combustion, in oxygen, at T = 298.15 K, of a commercial sample of cytosine. From this energy, the standard (p degrees = 0.1 MPa) molar enthalpy of formation in the crystalline state was derived as -(221.9 +/- 1.7) kJ.mol(-1). This value confirms one experimental value already published in the literature but differs from another literature value by 13.5 kJ.mol(-1). Using the present standard molar enthalpy of formation in the condensed phase and the enthalpy of sublimation due to Burkinshaw and Mortimer [J. Chem. Soc., Dalton Trans. 1984, 75], (155.0 +/- 3.0) kJ.mol(-1), results in a value for the gas-phase standard molar enthalpy of formation for cytosine of -66.9 kJ.mol(-1). A similar value, -65.1 kJ.mol(-1), has been estimated after G3MP2B3 calculations combined with the reaction of atomization on three different tautomers of cytosine. In agreement with experimental evidence, the hydroxy-amino tautomer is the most stable form of cytosine in the gas phase. The enthalpies of formation of the other two tautomers were also estimated as -60.7 kJ.mol(-1) and -57.2 kJ.mol(-1) for the oxo-amino and oxo-imino tautomers, respectively. The same composite approach was also used to compute other thermochemical data, which is difficult to be measured experimentally, such as C-H, N-H, and O-H bond dissociation enthalpies, gas-phase acidities, and ionization enthalpies.
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Affiliation(s)
- José R B Gomes
- CIQUP/Centro de Investigação em Química da Universidade do Porto, Department of Chemistry, Faculty of Science, University of Porto, Rua do Campo Alegre 687, P-4169-007 Porto, Portugal
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Wu R, McMahon TB. Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations. J Am Chem Soc 2007; 129:569-80. [PMID: 17227020 DOI: 10.1021/ja065088g] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.
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Affiliation(s)
- Ronghu Wu
- Department of Chemistry, University of Waterloo, Waterloo, Ontario, Canada
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35
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Mirzaei M, Hadipour NL. Study of hydrogen bonds in 1-methyluracil by DFT calculations of oxygen, nitrogen, and hydrogen quadrupole coupling constants and isotropic chemical shifts. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.03.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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36
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Millen AL, Archibald LAB, Hunter KC, Wetmore SD. A kinetic and thermodynamic study of the glycosidic bond cleavage in deoxyuridine. J Phys Chem B 2007; 111:3800-12. [PMID: 17388517 DOI: 10.1021/jp063841m] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Density functional theory was used to study the thermodynamics and kinetics for the glycosidic bond cleavage in deoxyuridine. Two reaction pathways were characterized for the unimolecular decomposition in vacuo. However, these processes are associated with large reaction barriers and highly endothermic reaction energies, which is in agreement with experiments that suggest a (water) nucleophile is required for the nonenzymatic glycosidic bond cleavage. Two (S(N)1 and S(N)2) reaction pathways were characterized for direct hydrolysis of the glycosidic bond by a single water molecule; however, both pathways also involve very large barriers. Activation of the water nucleophile via partial proton abstraction steadily decreases the barrier and leads to a more exothermic reaction energy as the proton affinity of the molecule interacting with water increases. Indeed, our data suggests that the barrier heights and reaction energies range from that for hydrolysis by water to that for hydrolysis by the hydroxyl anion, which represents the extreme of (full) water activation (deprotonation). Hydrogen bonds between small molecules (hydrogen fluoride, water, or ammonia) and the nucleobase were found to further decrease the barrier and overall reaction energy but not to the extent that the same hydrogen-bonding interactions increase the acidity of the nucleobase. Our results suggest that the nature of the nucleophile plays a more important role in reducing the barrier to glycosidic bond cleavage than the nature of the small molecule bound, and models with more than one hydrogen fluoride molecule interacting with the nucleobase provide further support for this conclusion. Our results lead to a greater fundamental understanding of the effects of the nucleophile, activation of the nucleophile, and interactions with the nucleobase for this important biological reaction.
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Affiliation(s)
- Andrea L Millen
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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37
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Hunter KC, Wetmore SD. Environmental Effects on the Enhancement in Natural and Damaged DNA Nucleobase Acidity Because of Discrete Hydrogen-Bonding Interactions. J Phys Chem A 2007; 111:1933-42. [PMID: 17302396 DOI: 10.1021/jp066641j] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The present study uses density functional theory to carefully consider the effects of the environment on the enhancement in (natural and damaged) DNA nucleobase acidities because of multiple hydrogen-bonding interactions. Although interactions with one small molecule can increase the acidity of the nucleobases by up to 60 kJ mol-1 in the gas phase, the maximum increase in enzymatic-like environments is expected to be approximately 40 kJ mol-1, which reduces to approximately 30 kJ mol-1 in water. Furthermore, the calculated (simultaneous) effects of two, three, or four molecules are increasingly less than the sum of the individual (additive) effects with an increase in the number and acidity of the small molecules bound or the dielectric constant of the solvent. Regardless of these trends, our calculations reveal that additional hydrogen-bonding interactions will have a significant effect on nucleobase acidity in a variety of environments, where the exact magnitude of the effect depends on the properties of the small molecule bound, the nucleobase binding site, and the solvent. The maximum increase in nucleobase acidity because of interactions with up to four small molecules is approximately 80 kJ mol-1 in enzymatic-like environments (or 65 kJ mol-1 in water). These results suggest that hydrogen-bonding interactions likely play an important role in many biological processes by changing the physical and chemical properties of the nucleobases.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, E4L 1G8, Canada
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38
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Kim S, Schaefer HF. Microhydration of cytosine and its radical anion: Cytosine∙(H2O)n (n=1–5). J Chem Phys 2007; 126:064301. [PMID: 17313209 DOI: 10.1063/1.2432123] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Microhydration effects on cytosine and its radical anion have been investigated theoretically, by explicitly considering various structures of cytosine complexes with up to five water molecules. Each successive water molecule (through n=5) is bound by 7-10 kcal mol(-1) to the relevant cytosine complex. The hydration energies are uniformly higher for the analogous anion systems. While the predicted vertical detachment energy (VDE) of the isolated cytosine is only 0.48 eV, it is predicted to increase to 1.27 eV for the lowest-lying pentahydrate of cytosine. The adiabatic electron affinity (AEA) of cytosine was also found to increase from 0.03 to 0.61 eV for the pentahydrate, implying that the cytosine anion, while questionable in the gas phase, is bound in aqueous solution. Both the VDE and AEA values for cytosine are smaller than those of uracil and thymine for a given hydration number. These results are in qualitative agreement with available experimental results from photodetachment-photoelectron spectroscopy studies of Schiedt et al. [Chem. Phys. 239, 511 (1998)].
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Affiliation(s)
- Sunghwan Kim
- Center for Computational Chemistry, University of Georgia, Athens, Georgia 30602, USA
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39
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Hunter KC, Millen AL, Wetmore SD. Effects of Hydrogen-Bonding and Stacking Interactions with Amino Acids on the Acidity of Uracil. J Phys Chem B 2007; 111:1858-71. [PMID: 17256895 DOI: 10.1021/jp066902p] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The effects of hydrogen-bonding interactions with amino acids on the (N1) acidity of uracil are evaluated using (B3LYP) density functional theory. Many different binding arrangements of each amino acid to three uracil binding sites are considered. The effects on the uracil acidity are found to significantly depend upon the nature of the amino acid and the binding orientation, but weakly depend on the binding site. Our results reveal that in some instances small models for the amino acids can be used, while for other amino acids larger models are required to properly describe the binding to uracil. The gas-phase acidity of uracil is found to increase by up to approximately 60 kJ mol(-1) due to discrete hydrogen-bonding interactions. Although (MP2) stacking interactions with aromatic amino acids decrease the acidity of uracil, unexpected increases in the acidity are found when any of the aromatic amino acids, or the backbone, hydrogen bond to uracil. Consideration of enzymatic and aqueous environments leads to decreases in the effects of the amino acids on the acidity of uracil. However, we find that the magnitude of the decrease varies with the nature of the molecule bound, as well as the (gas-phase) binding orientations and strengths, and therefore solvation effects should be considered on a case-by-case basis in future work. Nevertheless, the effects of amino acid interactions within enzymatic environments are as much as approximately 35 kJ mol(-1). The present study has general implications for understanding the nature of active site amino acids in enzymes, such as DNA repair enzymes, that catalyze reactions involving anionic nucleobase intermediates.
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Affiliation(s)
- Ken C Hunter
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick E4L 1G8, Canada
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Tâme Parreira RL, Galembeck SE, Hobza P. On the Origin of Red and Blue Shifts of XH and CH Stretching Vibrations in Formic Acid (Formate Ion) and Proton Donor Complexes. Chemphyschem 2007; 8:87-92. [PMID: 17121408 DOI: 10.1002/cphc.200600435] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
Complexes between formic acid or formate anion and various proton donors (HF, H(2)O, NH(3), and CH(4)) are studied by the MP2 and B3LYP methods with the 6-311++G(3df,3pd) basis set. Formation of a complex is characterized by electron-density transfer from electron donor to ligands. This transfer is much larger with the formate anion, for which it exceeds 0.1 e. Electron-density transfer from electron lone pairs of the electron donor is directed into sigma* antibonding orbitals of X--H bonds of the electron acceptor and leads to elongation of the bond and a red shift of the X--H stretching frequency (standard H-bonding). However, pronounced electron-density transfer from electron lone pairs of the electron donor also leads to reorganization of the electron density in the electron donor, which results in changes in geometry and vibrational frequency. These changes are largest for the C--H bonds of formic acid and formate anion, which do not participate in H-bonding. The resulting blue shift of this stretching frequency is substantial and amounts to almost 35 and 170 cm(-1), respectively.
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Affiliation(s)
- Renato Luis Tâme Parreira
- Departamento de Química, Faculdade de Filosofia Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, Avenida dos Bandeirantes 3900, Ribeirão Preto, 14040-901 SP, Brazil
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Abstract
Empirical, quantum chemical calculations and molecular dynamics simulations of the role of a solvent on tautomerism of nucleic acid bases and structure and properties of nucleic acid base pairs are summarized. Attention was paid to microhydrated (by one and two water molecules) complexes, for which structures found by scanning of empirical potential surfaces were recalculated at a correlated ab initio level. Additionally, isolated as well as mono- and dihydrated H-bonded, T-shaped and stacked structures of all possible nucleic acid base pairs were studied at the same theoretical levels. We demonstrate the strong influence of a solvent on the tautomeric equilibrium between the tautomers of bases and on the spatial arrangement of the bases in a base pair. The results provide clear evidence that the prevalence of either the stacked or hydrogen-bonded structures of the base pairs in the solvent is not determined only by its bulk properties, but rather by specific hydrophilic interactions of the base pair with a small number of solvent molecules.
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Affiliation(s)
- Martin Kabelác
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Flemingovo, Prague, Czech Republic
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Mirzaei M, Elmi F, Hadipour NL. A Systematic Investigation of Hydrogen-Bonding Effects on the 17O, 14N, and 2H Nuclear Quadrupole Resonance Parameters of Anhydrous and Monohydrated Cytosine Crystalline Structures: A Density Functional Theory Study. J Phys Chem B 2006; 110:10991-6. [PMID: 16771352 DOI: 10.1021/jp060301g] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A systematic computational study was carried out to characterize the 17O, 14N, and 2H nuclear quadrupole resonance (NQR) parameters in the anhydrous and monohydrated cytosine crystalline structures. To include the hydrogen-bonding effects in the calculations, the most probable interacting molecules with the central molecule in the crystalline phase were considered in the pentameric clusters of both structures. To calculate the parameters, couples of the methods B3LYP and B3PW91 and the basis sets 6-311++G** and CC-pVTZ were employed. The mentioned methods calculated reliable values of 17O, 14N, and 2H NQR tensors in the pentameric clusters, which are in good agreements with the experiment. The different influences of various hydrogen-bonding interactions types, N-H...N, N-H...O, and O-H...O, were observed on the 17O, 14N, and 2H NQR tensors. Lower values of quadrupole coupling constants and higher values of asymmetry parameters in the crystalline monohydrated cytosine indicate the presence of stronger hydrogen-bonding interactions in the monohydrated form rather than that of crystalline anhydrous cytosine.
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Affiliation(s)
- Mahmoud Mirzaei
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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Hydrogen-bonding between cytosine and water: Computational evidence for a ring-opened complex. Chem Phys Lett 2006. [DOI: 10.1016/j.cplett.2006.02.092] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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