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Suryana S, Mutakin, Rosandi Y, Hasanah AN. An Update on Molecularly Imprinted Polymer Design through a Computational Approach to Produce Molecular Recognition Material with Enhanced Analytical Performance. Molecules 2021; 26:1891. [PMID: 33810542 PMCID: PMC8036856 DOI: 10.3390/molecules26071891] [Citation(s) in RCA: 24] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2021] [Revised: 03/23/2021] [Accepted: 03/23/2021] [Indexed: 12/23/2022] Open
Abstract
Molecularly imprinted polymer (MIP) computational design is expected to become a routine technique prior to synthesis to produce polymers with high affinity and selectivity towards target molecules. Furthermore, using these simulations reduces the cost of optimizing polymerization composition. There are several computational methods used in MIP fabrication and each requires a comprehensive study in order to select a process with results that are most similar to properties exhibited by polymers synthesized through laboratory experiments. Until now, no review has linked computational strategies with experimental results, which are needed to determine the method that is most appropriate for use in designing MIP with high molecular recognition. This review will present an update of the computational approaches started from 2016 until now on quantum mechanics, molecular mechanics and molecular dynamics that have been widely used. It will also discuss the linear correlation between computational results and the polymer performance tests through laboratory experiments to examine to what extent these methods can be relied upon to obtain polymers with high molecular recognition. Based on the literature search, density functional theory (DFT) with various hybrid functions and basis sets is most often used as a theoretical method to provide a shorter MIP manufacturing process as well as good analytical performance as recognition material.
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Affiliation(s)
- Shendi Suryana
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia; (S.S.); (M.)
- Pharmacy Department, Faculty of Mathematics and Natural Sciences, Garut University, Jl. Jati No.42B, Tarogong, Garut 44151, Indonesia
| | - Mutakin
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia; (S.S.); (M.)
| | - Yudi Rosandi
- Geophysic Department, Faculty of Mathematics and Natural Sciences, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia;
| | - Aliya Nur Hasanah
- Department of Pharmaceutical Analysis and Medicinal Chemistry, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia; (S.S.); (M.)
- Drug Development Study Center, Faculty of Pharmacy, Padjadjaran University, Jl. Raya Bandung Sumedang KM 21, Sumedang 45363, Indonesia
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2
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Kumar A, Sevilla MD. Excited States of One-Electron Oxidized Guanine-Cytosine Base Pair Radicals: A Time Dependent Density Functional Theory Study. J Phys Chem A 2019; 123:3098-3108. [PMID: 30896952 DOI: 10.1021/acs.jpca.9b00906] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
One-electron oxidized guanine (G•+) in DNA generates several short-lived intermediate radicals via proton transfer reactions resulting in the formation of neutral guanine radicals. The identification of these radicals in DNA is of fundamental interest to understand the early stages of DNA damage. Herein, we used time-dependent density functional theory (TD-ωB97XD-PCM/6-31G(3df,p)) to calculate the vertical excitation energies of one-electron oxidized G and G-cytosine (C) base pair in various protonation states: G•+, G(N1-H)•, and G(N2-H)•, as well as G•+-C, G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C), G(N1-H)•-C, and G(N2-H)•-C in aqueous phase. The calculated UV-vis spectra of these radicals are in good agreement with the experiment for the G radical species when the calculated values are red-shifted by 40-70 nm. The present calculations show that the lowest energy transitions of proton transfer species (G(N1-H)•-(H+)C, G(N1-H)•-(N4-H+)C, and G(N1-H)•-C) are substantially red-shifted in comparison to the spectrum of G•+-C. The calculated spectrum of G(N2-H)•-C shows intense absorption (high oscillator strength), which matches the strong absorption in the experimental spectra of G(N2-H)• at 600 nm. The present calculations predict the lowest charge transfer transition of C → G•+ is π → π* in nature and lies in the UV region (3.4-4.3 eV) with small oscillator strength.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry , Oakland University , Rochester , Michigan 48309 , United States
| | - Michael D Sevilla
- Department of Chemistry , Oakland University , Rochester , Michigan 48309 , United States
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Arabi AA, Matta CF. Effects of Intense Electric Fields on the Double Proton Transfer in the Watson–Crick Guanine–Cytosine Base Pair. J Phys Chem B 2018; 122:8631-8641. [DOI: 10.1021/acs.jpcb.8b05053] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Affiliation(s)
- Alya A. Arabi
- College of Natural and Health Sciences, Zayed University, Abu Dhabi, P.O. Box 144534, United Arab Emirates
| | - Chérif F. Matta
- Department of Chemistry and Physics, Mount Saint Vincent University, Halifax, Nova Scotia B3M 2J6, Canada
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia B3H 4J3, Canada
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4
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Wu X, Karsili TNV, Domcke W. Role of Electron-Driven Proton-Transfer Processes in the Ultrafast Deactivation of Photoexcited Anionic 8-oxoGuanine-Adenine and 8-oxoGuanine-Cytosine Base Pairs. Molecules 2017; 22:molecules22010135. [PMID: 28098833 PMCID: PMC6155867 DOI: 10.3390/molecules22010135] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2016] [Revised: 12/28/2016] [Accepted: 01/10/2017] [Indexed: 11/16/2022] Open
Abstract
It has been reported that 8-oxo-7,8-dihydro-guanosine (8-oxo-G), which is the main product of oxidative damage of DNA, can repair cyclobutane pyrimidine dimer (CPD) lesions when incorporated into DNA or RNA strands in proximity to such lesions. It has therefore been suggested that the 8-oxo-G nucleoside may have been a primordial precursor of present-day flavins in DNA or RNA repair. Because the electron transfer leading to the splitting of a thymine-thymine pair in a CPD lesion occurs in the photoexcited state, a reasonably long excited-state lifetime of 8-oxo-G is required. The neutral (protonated) form of 8-oxo-G exhibits a very short (sub-picosecond) intrinsic excited-state lifetime which is unfavorable for repair. It has therefore been argued that the anionic (deprotonated) form of 8-oxo-G, which exhibits a much longer excited-state lifetime, is more likely to be a suitable cofactor for DNA repair. Herein, we have investigated the exited-state quenching mechanisms in the hydrogen-bonded complexes of deprotonated 8-oxo-G- with adenine (A) and cytosine (C) using ab initio wave-function-based electronic-structure calculations. The calculated reaction paths and potential-energy profiles reveal the existence of barrierless electron-driven inter-base proton-transfer reactions which lead to low-lying S₁/S₀ conical intersections. The latter can promote ultrafast excited-state deactivation of the anionic base pairs. While the isolated deprotonated 8-oxo-G- nucleoside may have been an efficient primordial repair cofactor, the excited states of the 8-oxo-G--A and 8-oxo-G--C base pairs are likely too short-lived to be efficient electron-transfer repair agents.
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Affiliation(s)
- Xiuxiu Wu
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
| | - Tolga N V Karsili
- Department of Chemistry, Temple University, 130 Beury Hall, 1901 N. 13th St., Philadelphia, PA 19122, USA.
| | - Wolfgang Domcke
- Department of Chemistry, Technische Universitat Munchen, Lichtenbergstr. 4, Garching D-85747, Germany.
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Zhang Y, Li XB, Fleming AM, Dood J, Beckstead AA, Orendt AM, Burrows CJ, Kohler B. UV-Induced Proton-Coupled Electron Transfer in Cyclic DNA Miniduplexes. J Am Chem Soc 2016; 138:7395-401. [DOI: 10.1021/jacs.6b03216] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Yuyuan Zhang
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Xi-Bo Li
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Aaron M. Fleming
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Jordan Dood
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Ashley A. Beckstead
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
| | - Anita M. Orendt
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
- Center
for High Performance Computing, University of Utah, Salt Lake City, Utah 84112-0190, United States
| | - Cynthia J. Burrows
- Department
of Chemistry, University of Utah, 315 S. 1400 East, Salt Lake City, Utah 84112, United States
| | - Bern Kohler
- Department
of Chemistry and Biochemistry, Montana State University, Bozeman, Montana 59717, United States
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Kumar A, Adhikary A, Shamoun L, Sevilla MD. Do Solvated Electrons (e(aq)⁻) Reduce DNA Bases? A Gaussian 4 and Density Functional Theory-Molecular Dynamics Study. J Phys Chem B 2016; 120:2115-23. [PMID: 26878197 PMCID: PMC4863935 DOI: 10.1021/acs.jpcb.5b11269] [Citation(s) in RCA: 40] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
The solvated electron (e(aq)⁻) is a primary intermediate after an ionization event that produces reductive DNA damage. Accurate standard redox potentials (E(o)) of nucleobases and of e(aq)⁻ determine the extent of reaction of e(aq)⁻ with nucleobases. In this work, E(o) values of e(aq)⁻ and of nucleobases have been calculated employing the accurate ab initio Gaussian 4 theory including the polarizable continuum model (PCM). The Gaussian 4-calculated E(o) of e(aq)⁻ (-2.86 V) is in excellent agreement with the experimental one (-2.87 V). The Gaussian 4-calculated E(o) of nucleobases in dimethylformamide (DMF) lie in the range (-2.36 V to -2.86 V); they are in reasonable agreement with the experimental E(o) in DMF and have a mean unsigned error (MUE) = 0.22 V. However, inclusion of specific water molecules reduces this error significantly (MUE = 0.07). With the use of a model of e(aq)⁻ nucleobase complex with six water molecules, the reaction of e(aq)⁻ with the adjacent nucleobase is investigated using approximate ab initio molecular dynamics (MD) simulations including PCM. Our MD simulations show that e(aq)⁻ transfers to uracil, thymine, cytosine, and adenine, within 10 to 120 fs and e(aq)⁻ reacts with guanine only when a water molecule forms a hydrogen bond to O6 of guanine which stabilizes the anion radical.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Amitava Adhikary
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Lance Shamoun
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
| | - Michael D Sevilla
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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7
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Huix-Rotllant M, Nikiforov A, Thiel W, Filatov M. Description of Conical Intersections with Density Functional Methods. Top Curr Chem (Cham) 2015; 368:445-76. [PMID: 25896441 DOI: 10.1007/128_2015_631] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Conical intersections are perhaps the most significant mechanistic features of chemical reactions occurring through excited states. By providing funnels for efficient non-adiabatic population transfer, conical intersections govern the branching ratio of products of such reactions, similar to what the transition states do for ground-state reactivity. In this regard, intersections between the ground and the lowest excited states play a special role, and the correct description of the potential energy surfaces in their vicinity is crucial for understanding the mechanism and dynamics of excited-state reactions. The methods of density functional theory, such as time-dependent density functional theory, are widely used to describe the excited states of large molecules. However, are these methods suitable for describing the conical intersections or do they lead to artifacts and, consequently, to erroneous description of reaction dynamics? Here we address the first part of this question and analyze the ability of several density functional approaches, including the linear-response time-dependent approach as well as the spin-flip and ensemble formalisms, to provide the correct description of conical intersections and the potential energy surfaces in their vicinity. It is demonstrated that the commonly used linear-response time-dependent theory does not yield a proper description of these features and that one should instead use alternative computational approaches.
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Affiliation(s)
- Miquel Huix-Rotllant
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, 60438, Frankfurt am Main, Germany
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Migliore A, Polizzi NF, Therien M, Beratan DN. Biochemistry and theory of proton-coupled electron transfer. Chem Rev 2014; 114:3381-465. [PMID: 24684625 PMCID: PMC4317057 DOI: 10.1021/cr4006654] [Citation(s) in RCA: 340] [Impact Index Per Article: 34.0] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2013] [Indexed: 02/01/2023]
Affiliation(s)
- Agostino Migliore
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Nicholas F. Polizzi
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - Michael
J. Therien
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
| | - David N. Beratan
- Department
of Chemistry, Department of Biochemistry, and Department of Physics, Duke University, Durham, North Carolina 27708, United States
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Chen S, Navizet I, Lindh R, Liu Y, Ferré N. Hybrid QM/MM Simulations of the Obelin Bioluminescence and Fluorescence Reveal an Unexpected Light Emitter. J Phys Chem B 2014; 118:2896-903. [DOI: 10.1021/jp412198w] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shufeng Chen
- Key
Laboratory of Theoretical and Computational Photochemistry, Ministry
of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P.R. China
- Aix-Marseille
Université, CNRS, Institut de Chimie Radicalaire (UMR-7273), Marseille 13397, France
| | - Isabelle Navizet
- Laboratoire
de Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS. 5 bd Descartes, 77454 Marne-la-Vallé, France
- Molecular
Sciences Institute, School of Chemistry, University of the Witwatersrand, PO
Wits, Johannesburg 2050, South Africa
| | - Roland Lindh
- Department
of Chemistry − Ångström, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
- Uppsala
Center
of Computational Chemistry - UC3, Uppsala University, P.O. Box 518, SE-751 20 Uppsala, Sweden
| | - Yajun Liu
- Key
Laboratory of Theoretical and Computational Photochemistry, Ministry
of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P.R. China
| | - Nicolas Ferré
- Aix-Marseille
Université, CNRS, Institut de Chimie Radicalaire (UMR-7273), Marseille 13397, France
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Chen J, Zhang Y, Kohler B. Excited States in DNA Strands Investigated by Ultrafast Laser Spectroscopy. PHOTOINDUCED PHENOMENA IN NUCLEIC ACIDS II 2014; 356:39-87. [DOI: 10.1007/128_2014_570] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
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Lin Y, Wang H, Wu Y, Gao S, Schaefer III HF. Proton-transfer in hydrogenated guanine–cytosine trimer neutral species, cations, and anions embedded in B-form DNA. Phys Chem Chem Phys 2014; 16:6717-25. [DOI: 10.1039/c3cp54904f] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Zhang Y, Dood J, Beckstead A, Chen J, Li XB, Burrows CJ, Lu Z, Matsika S, Kohler B. Ultrafast excited-state dynamics and vibrational cooling of 8-oxo-7,8-dihydro-2'-deoxyguanosine in D2O. J Phys Chem A 2013; 117:12851-7. [PMID: 24215180 DOI: 10.1021/jp4095529] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Nguyen and Burrows recently demonstrated that UV-B irradiation of 8-oxo-7,8-dihydro-2'-deoxyguanosine (8-oxodG), a signature product of oxidatively damaged DNA, can repair cyclobutane pyrimidine dimers in double-stranded DNA (J. Am. Chem. Soc. 2011, 133, 14586 - 14589). In order to test the hypothesis that repair occurs by photoinduced electron transfer, it is critical to determine basic photophysical parameters of 8-oxodG including the excited-state lifetime. Here, femtosecond transient absorption spectroscopy was used to study the ultrafast excited-state dynamics of 8-oxodG with excitation in the UV and probing at visible and mid-IR wavelengths. The excited-state lifetimes of both neutral and basic forms of 8-oxodG in D2O are reported for the first time by monitoring the disappearance of excited-state absorption at 570 nm. The lifetime of the first excited state of the neutral form is 0.9 ± 0.1 ps, or nearly twice as long as that of 2'-deoxyguanosine. The basic form of 8-oxodG exhibits a much longer excited-state lifetime of 43 ± 3 ps. Following ultrafast internal conversion by neutral 8-oxodG, a vibrationally hot ground state is created that dissipates its excess vibrational energy to the solvent on a time scale of 2.4 ± 0.4 ps. Femtosecond time-resolved IR experiments provide additional insights into excited-state dynamics and the vibrational relaxation of several modes in the fingerprint region.
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Affiliation(s)
- Yuyuan Zhang
- Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717, United States
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Kumar A, Sevilla MD. π- vs σ-radical states of one-electron-oxidized DNA/RNA bases: a density functional theory study. J Phys Chem B 2013; 117:11623-32. [PMID: 24000793 DOI: 10.1021/jp407897n] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
As a result of their inherent planarity, DNA base radicals generated by one-electron oxidation/reduction or bond cleavage form π- or σ-radicals. While most DNA base systems form π-radicals, there are a number of nucleobase analogues such as one-electron-oxidized 6-azauraci1, 6-azacytosine, and 2-thiothymine or one-electron reduced 5-bromouracil that form more reactive σ-radicals. Elucidating the availability of these states within DNA, base radical electronic structure is important to the understanding of the reactivity of DNA base radicals in different environments. In this work, we address this question by the calculation of the relative energies of π- and σ-radical states in DNA/RNA bases and their analogues. We used density functional theory B3LYP/6-31++G** method to optimize the geometries of π- and σ-radicals in Cs symmetry (i.e., planar) in the gas phase and in solution using the polarized continuum model (PCM). The calculations predict that σ- and π-radical states in one-electron-oxidized bases of thymine, T(N3-H)(•), and uracil, U(N3-H)(•), are very close in energy; i.e., the π-radical is only ca. 4 kcal/mol more stable than the σ-radical. For the one-electron-oxidized radicals of cytosine, C(•+), C(N4-H)(•), adenine, A(•+), A(N6-H)(•), and guanine, G(•+), G(N2-H)(•), G(N1-H)(•), the π-radicals are ca. 16-41 kcal/mol more stable than their corresponding σ-radicals. Inclusion of solvent (PCM) is found to stabilize the π- over σ-radical of each of the systems. U(N3-H)(•) with three discrete water molecules in the gas phase is found to form a three-electron σ bond between the N3 atom of uracil and the O atom of a water molecule, but on inclusion of full solvation and discrete hydration, the π-radical remains most stable.
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Affiliation(s)
- Anil Kumar
- Department of Chemistry, Oakland University , Rochester, Michigan 48309, United States
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