1
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The antioxidant capacity of myricetin. A molecular electrostatic potential analysis based on DFT calculations. Chem Phys Lett 2022. [DOI: 10.1016/j.cplett.2022.139708] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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2
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Miranda-Quintana RA, Heidar-Zadeh F, Fias S, Chapman AEA, Liu S, Morell C, Gómez T, Cárdenas C, Ayers PW. Molecular Interactions From the Density Functional Theory for Chemical Reactivity: The Interaction Energy Between Two-Reagents. Front Chem 2022; 10:906674. [PMID: 35769444 PMCID: PMC9234655 DOI: 10.3389/fchem.2022.906674] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Reactivity descriptors indicate where a reagent is most reactive and how it is most likely to react. However, a reaction will only occur when the reagent encounters a suitable reaction partner. Determining whether a pair of reagents is well-matched requires developing reactivity rules that depend on both reagents. This can be achieved using the expression for the minimum-interaction-energy obtained from the density functional reactivity theory. Different terms in this expression will be dominant in different circumstances; depending on which terms control the reactivity, different reactivity indicators will be preferred.
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Affiliation(s)
- Ramón Alain Miranda-Quintana
- Department of Chemistry and Quantum Theory Project, University of Florida, Gainesville, FL, United States
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | | | - Stijn Fias
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Allison E. A. Chapman
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
| | - Shubin Liu
- Research Computing Center, University of North Carolina, Chapel Hill, NC, United States
| | - Christophe Morell
- Université de Lyon, Université Claude Bernard Lyon 1, Institut des Sciences Analytiques-UMR CNRS 5280, Villeurbanne, France
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | - Carlos Cárdenas
- Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Santiago, Chile
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- *Correspondence: Ramón Alain Miranda-Quintana, ; Carlos Cárdenas, ; Paul W. Ayers, ; Tatiana Gómez,
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3
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Martínez-Araya JI, Islas R. Analysis in silico of chemical reactivity employing the local hyper-softness in some classic aromatic compounds, boron aromatic clusters and all-metal aromatic clusters. J Comput Chem 2022; 43:29-42. [PMID: 34664736 DOI: 10.1002/jcc.26769] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2021] [Revised: 08/19/2021] [Accepted: 10/04/2021] [Indexed: 11/07/2022]
Abstract
In the current work, the authors analyzed and compared the chemical behavior of some (anti)aromatic compounds. The species selected are benzene and cyclobutadiene as the aromatic and antiaromatic classical examples, respectively. Next, the anion Al 4 2 - , which is the first all-metal molecule catalogued as aromatic and its non-metallic isoelectronic analog, B 4 2 - were also analyzed. The antiaromatic clusters Al 4 4 - and B 4 4 - were studied in form of lithium salts. And the end, the non-planar B 12 boron cluster and its isoelectronic analogs ( B 11 Be - and B 11 C + ) were considered for being analyzed under the same criterium. The analysis was realized employing the following descriptors: molecular electrostatic potential and local hyper-softness to get insights concerning local reactivity when facing reagents leading to ionic or covalent interactions. The results show that all the molecules analyzed presented some specific variations in their respective local reactivity despite being labeled as aromatic compounds. This analysis provides a notion that the local reactivity is more based on the nature of the atoms and the molecular geometry than the aromatic character by itself.
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Affiliation(s)
- Jorge I Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Santiago, Chile
| | - Rafael Islas
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello (UNAB), Santiago, Chile
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4
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Modelling the Anti-Methicillin-Resistant Staphylococcus Aureus (MRSA) Activity of Cannabinoids: A QSAR and Docking Study. CRYSTALS 2020. [DOI: 10.3390/cryst10080692] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Twenty-four cannabinoids active against MRSA SA1199B and XU212 were optimized at WB97XD/6-31G(d,p), and several molecular descriptors were obtained. Using a multiple linear regression method, several mathematical models with statistical significance were obtained. The robustness of the models was validated, employing the leave-one-out cross-validation and Y-scrambling methods. The entire data set was docked against penicillin-binding protein, iso-tyrosyl tRNA synthetase, and DNA gyrase. The most active cannabinoids had high affinity to penicillin-binding protein (PBP), whereas the least active compounds had low affinities for all of the targets. Among the cannabinoid compounds, Cannabinoid 2 was highlighted due to its suitable combination of both antimicrobial activity and higher scoring values against the selected target; therefore, its docking performance was compared to that of oxacillin, a commercial PBP inhibitor. The 2D figures reveal that both compounds hit the protein in the active site with a similar type of molecular interaction, where the hydroxyl groups in the aromatic ring of cannabinoids play a pivotal role in the biological activity. These results provide some evidence that the anti-Staphylococcus aureus activity of these cannabinoids may be related to the inhibition of the PBP protein; besides, the robustness of the models along with the docking and Quantitative Structure–Activity Relationship (QSAR) results allow the proposal of three new compounds; the predicted activity combined with the scoring values against PBP should encourage future synthesis and experimental testing.
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5
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A screening DFT study of the para-substituent effect on local hyper-softness in bis(phenoxy-imine) titanium complexes to get insights about their catalytic activity in ethylene polymerization. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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6
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Structural and thermodynamic studies of cytosine to thymine conversion in gas and solution phases using steered molecular dynamic simulations. J Mol Liq 2019. [DOI: 10.1016/j.molliq.2018.12.152] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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7
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Ai Y, Xing J, Zhang A, Zhao C, Liu Y, Xie B, Chen W, Cui G, Lu Z, Wang X. Computational Study on the Excited-State Decay of 5-Methylcytosine and 5-Hydroxymethylcytosine: The Common Form of DNA Methylation and Its Oxidation Product. J Phys Chem B 2018; 122:10424-10434. [DOI: 10.1021/acs.jpcb.8b07830] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | | | | | | | - Binbin Xie
- Hangzhou Institute of Advanced Studies, Zhejiang Normal University, 1108 Gengwen Road, Hangzhou 311231, Zhejiang, P. R. China
| | | | - Ganglong Cui
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, P. R. China
| | | | - Xiangke Wang
- NAAM Research Group, Faculty of Science, King Abdulaziz University, Jeddah 21589, Saudi Arabia
- Collaborative Innovation Centre of Radiation Medicine of Jiangsu Higher Education Institutions, School for Radiological and Interdisciplinary Sciences, Soochow University, Suzhou 215123, P. R. China
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8
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Su X, Liang R, Stolee JA. A facile one-step fluorescence method for the quantitation of low-content single base deamination impurity in synthetic oligonucleotides. J Pharm Biomed Anal 2018; 155:50-55. [PMID: 29614399 DOI: 10.1016/j.jpba.2018.03.051] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 03/20/2018] [Accepted: 03/25/2018] [Indexed: 11/27/2022]
Abstract
Oligonucleotides are being researched and developed as potential drug candidates for the treatment of a broad spectrum of diseases. The characterization of antisense oligonucleotide (ASO) impurities caused by base mutations (e.g. deamination) which are closely related to the target ASO is a significant analytical challenge. Herein, we describe a novel one-step method, utilizing a strategy that combines fluorescence-ON detection with competitive hybridization, to achieve single base mutation quantitation in extensively modified synthetic ASOs. Given that this method is highly specific and sensitive (LoQ = 4 nM), we envision that it will find utility for screening other impurities as well as sequencing modified oligonucleotides.
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Affiliation(s)
- Xiaoye Su
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
| | - Ruiting Liang
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
| | - Jessica A Stolee
- Analytical Development, Biogen Inc., Cambridge, MA 02142, United States.
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9
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Assessment of ten density functionals through the use of local hyper–softness to get insights about the catalytic activity. J Mol Model 2018; 24:42. [DOI: 10.1007/s00894-017-3576-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2017] [Accepted: 12/25/2017] [Indexed: 10/18/2022]
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10
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Ignacio Martínez-Araya J, Grand A, Glossman-Mitnik D. Towards the rationalization of catalytic activity values by means of local hyper-softness on the catalytic site: a criticism about the use of net electric charges. Phys Chem Chem Phys 2015; 17:29764-75. [PMID: 26480020 DOI: 10.1039/c5cp03822g] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
By means of the Spin-Polarized Conceptual Density Functional Theory (SP-CDFT), three 2,6-bis(imino)pyridine catalysts based on iron(II), used for polymerization of ethylene, were studied. The catalysts differed by the substituent group, bearing either -H, -NO2 or -OCH3. To date, catalytic activity, a purely experimental parameter measuring the mass of polyethylene produced per millimole of iron per time and pressure unit at a fixed temperature, has not been explained in terms of local hyper-softness. The latter is a purely theoretical parameter designed for quantifying electronic effects; it is measured using the metal atom responsible for the coordination process with the monomer (ethylene). Because steric effects are not relevant in these kinds of catalysts and only electronic effects drive the catalytic process, an interesting link is found between catalytic activity and the local hyper-softness condensed on the iron atom by means of four functionals (B3LYP, BP86, B97D, and VSXC). This work demonstrates that the use of local hyper-softness, predicted by the SP-CDFT, is a suitable parameter for explaining order relationships among catalytic activity values, thus quantifying the electronic influence of the substituent group inducing this difference; the use of only net electric charges does not lead to clear conclusions. This finding can aid in estimating catalytic activities leading to a more rational design of new catalysts via computational chemistry.
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Affiliation(s)
- Jorge Ignacio Martínez-Araya
- Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Av. República 230, Código Postal 8370134, Santiago, Chile.
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11
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Martínez-Araya JI, Glossman-Mitnik D. The substituent effect from the perspective of local hyper-softness. An example applied on normeloxicam, meloxicam and 4-meloxicam: Non-steroidal anti-inflammatory drugs. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.11.004] [Citation(s) in RCA: 4] [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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12
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Dostál L, Růžička A, Jambor R. Deamination of N→Sn‐Coordinated Organotin(II) Hydroxide: Formation of a New C–O Covalent Bond. Eur J Inorg Chem 2014. [DOI: 10.1002/ejic.201402836] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Affiliation(s)
- Libor Dostál
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 95, 53210 Pardubice, Czech Republic, http://www.upce.cz
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 95, 53210 Pardubice, Czech Republic, http://www.upce.cz
| | - Roman Jambor
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice, Studentská 95, 53210 Pardubice, Czech Republic, http://www.upce.cz
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13
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Jin L, Wang W, Hu D, Lü J. A new insight into the 5-carboxycytosine and 5-formylcytosine under typical bisulfite conditions: a deamination mechanism study. Phys Chem Chem Phys 2014; 16:3573-85. [PMID: 24413472 DOI: 10.1039/c3cp54266a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
5-Methylcytosine (5-MeCyt) can be converted to 5-hydroxymethylcytosine (5-hmCyt) in mammalian DNA by the ten-eleven translocation enzymes. The conventional bisulfite sequencing cannot discriminate 5-hmCyt from 5-MeCyt, whereas the oxidation products of 5-hmCyt, 5-carboxycytosine (5-caCyt) and 5-formylcytosine (5-fCyt) enable them to be identified in bisulfite sequencing. This mechanism likely involves the decarboxylation of 5-caCyt and deformylation of 5-fCyt to cytosine (Cyt) before deamination. Another possibility could be a direct bisulfite-induced deamination reaction followed by decarboxylation and deformylation. Here the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) (paths A and B) and 5-O(+)fCytN3(+)-SO3(-) (paths C and D) has been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energy (ΔG(s≠) = 54.16 kJ mol(-1)) of the direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A is much lower than the ΔG(s≠) of CytN3(+)-SO3(-) (100.91 kJ mol(-1)) under bisulfite conditions, implying that 5-caCyt may firstly involve a process of deamination. Meanwhile, the ΔG(s≠) (103.84 kJ mol(-1)) of the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C is in close proximity to our previous theoretical data for CytN3(+)-SO3(-), indicating that the deamination of 5-fCyt is also likely to occur in the presence of bisulfite. Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A and 5-O(+)fCytN3(+)-SO3(-) path C is represented and has been further explored in the presence of one and two water molecules. The results show that both in the gas and aqueous phases, the participation of one and two water molecules makes the HSO3(-)-induced direct hydrolytic deamination of 5-caCytN3(+)-SO3(-) path A unfavorable, whereas the contribution of one and two water molecules facilitates the HSO3(-)-induced direct hydrolytic deamination of 5-O(+)fCytN3(+)-SO3(-) path C.
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Affiliation(s)
- Lingxia Jin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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14
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Jin L, Wang L, Zhang C, Wang W, Min S, Hu D. Is the contribution of cis and trans protonated 5-methylcytosine-SO3(-) isomers equal in the conversion to thymine-SO3(-) under bisulfite conditions? A theoretical perspective. Phys Chem Chem Phys 2014; 16:16264-77. [PMID: 24974803 DOI: 10.1039/c4cp00387j] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cytosine (Cyt) can be converted to 5-methylcytosine (5-MeCyt) in CpG sequences of DNA. Conventional bisulfite sequencing can discriminate Cyt from 5-MeCyt, however inappropriate conversion of 5-MeCyt to thymine and a failure to convert Cyt to uracil always occur when Cyt and 5-MeCyt are treated with bisulfite, which would lead to erroneous estimates of DNA methylation densities. Here, the direct hydrolytic deamination of cis (paths A-C) and trans (paths A'-C') 5-MeCytN3(+)-SO3(-) isomers with bisulfite have been explored at the MP2/6-311++G(3df,3pd)//B3LYP/6-311++G(d,p) level. The activation free energies (ΔG(s-a≠)) of the cis and trans 5-MeCytN3(+)-SO3(-) isomers' paths exhibit no obvious differences, implying both isomers may make an equal contribution to the hydrolytic deamination of 5-MeCyt under bisulfite conditions. It is greatly expected that these results could aid experimental scientists to explore new methods to avoid the formation of the deaminated reactants (5-MeCytN3(+)-SO3(-)). Meanwhile, the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers is represented by paths A and A', respectively, and has been further explored in the presence of two water molecules. It was found that the contribution of two water molecules renders the HSO3(-)-induced direct hydrolytic deamination of cis and trans 5-MeCytN3(+)-SO3(-) isomers by paths A and A' favourable. In addition, the ΔG(s-a≠) values (85.74-85.34 kJ mol(-1)) of the rate-limiting steps of the two water-mediated paths A and A' are very close to that of the theoretical value for CytN3(+)-SO3(-) (88.18 kJ mol(-1)), implying that the free barrier gap between Cyt and 5-MeCyt is very small under bisulfite conditions. This further suggests that bisulfite sequencing technology may be easily influenced by the external environment.
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Affiliation(s)
- Lingxia Jin
- Key Laboratory for Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an 710062, China.
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15
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Genomic methylation patterns in archaeological barley show de-methylation as a time-dependent diagenetic process. Sci Rep 2014; 4:5559. [PMID: 24993353 PMCID: PMC4081896 DOI: 10.1038/srep05559] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2014] [Accepted: 06/16/2014] [Indexed: 11/08/2022] Open
Abstract
Genomic methylation is variable under biotic and abiotic stresses in plants. In particular, viral infection is thought to significantly increase genomic methylation with particularly high activity around transposable elements. Here we present the genomic methylation profiles of grains of archaeological barley (Hordeum vulgare) from several strata from a site in southern Egypt, from the Napatan to the Islamic periods (800 BCE - 1812 CE). One sample tested positive for viral infection and exhibits an unusually high degree of genomic methylation compared to the rest. A decreasing trend in global methylation levels according to deposition date shows in-situ de-methylation of 5-methylcytosine, which can be described as a diagenetic process. This is most likely a deamination mediated de-methylation process and is expected to lead to 5 mC > T base modifications in addition to the C > U modifications due to cytosine deamination, so represents a time-dependent process of DNA diagenesis in ancient DNA.
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16
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Grand A, Jorge N, Morell C, Cadet J, Eriksson LA. Deamination features of 5-hydroxymethylcytosine, a radical and enzymatic DNA oxidation product. J Mol Model 2014; 20:2290. [PMID: 24863534 DOI: 10.1007/s00894-014-2290-9] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2014] [Accepted: 05/05/2014] [Indexed: 02/03/2023]
Abstract
The 5-methylcytosine derivative 5-hydroxymethylcytosine (5hmCyt), which is generated via enzymatic oxidation, is sometimes referred to as the sixth nucleobase due to its widespread presence in the DNA of brain and embryonic stem cells. In this study, we used density functional based methods and reactivity indices from conceptual DFT to explore the mechanism and key features of the hydrolytic deamination of 5hmCyt. The data obtained are used to compare and contrast this deamination reaction with those of other cytosine derivatives. The deamination process for 5hmCyt is similar to the corresponding processes for other unsaturated derivatives in that the amino form is the reactive one and water addition is the rate-limiting step. However, several differences due to the rotameric asymmetry of the current system are also noted.
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Affiliation(s)
- André Grand
- Laboratoire "Lésions des Acides Nucléiques", INAC/SCIB - UMR-E n°3 CEA-UJF, CEA Grenoble, 17 avenue des Martyrs, 38054, Grenoble cedex 9, France
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17
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Madugundu GS, Cadet J, Wagner JR. Hydroxyl-radical-induced oxidation of 5-methylcytosine in isolated and cellular DNA. Nucleic Acids Res 2014; 42:7450-60. [PMID: 24852253 PMCID: PMC4066766 DOI: 10.1093/nar/gku334] [Citation(s) in RCA: 96] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
The methylation and oxidative demethylation of cytosine in CpG dinucleotides plays a critical role in the regulation of genes during cell differentiation, embryogenesis and carcinogenesis. Despite its low abundance, 5-methylcytosine (5mC) is a hotspot for mutations in mammalian cells. Here, we measured five oxidation products of 5mC together with the analogous products of cytosine and thymine in DNA exposed to ionizing radiation in oxygenated aqueous solution. The products can be divided into those that arise from hydroxyl radical (•OH) addition at the 5,6-double bond of 5mC (glycol, hydantoin and imidazolidine products) and those that arise from H-atom abstraction from the methyl group of 5mC including 5-hydroxymethylcytosine (5hmC) and 5-formylcytosine (5fC). Based on the analysis of these products, we show that the total damage at 5mC is about 2-fold greater than that at C in identical sequences. The formation of hydantoin products of 5mC is favored, compared to analogous reactions of thymine and cytosine, which favor the formation of glycol products. The distribution of oxidation products is sequence dependent in specific ODN duplexes. In the case of 5mC, the formation of 5hmC and 5fC represents about half of the total of •OH-induced oxidation products of 5mC. Several products of thymine, cytosine, 5mC, as well as 8-oxo-7,8-dihydroguanine (8oxoG), were also estimated in irradiated cells.
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Affiliation(s)
- Guru S Madugundu
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
| | - Jean Cadet
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada Institut Nanosciences & Cryogénie/DSM, CEA/Grenoble, 38054 Grenoble, France
| | - J Richard Wagner
- Département de Médecine Nucléaire et Radiobiologie, Faculté de Médecine et des Sciences de la Santé, Université de Sherbrooke, 3001 12e Avenue Nord, Québec J1H 5N4, Canada
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18
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Bacolla A, Cooper DN, Vasquez KM. Mechanisms of base substitution mutagenesis in cancer genomes. Genes (Basel) 2014; 5:108-46. [PMID: 24705290 PMCID: PMC3978516 DOI: 10.3390/genes5010108] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 02/07/2014] [Accepted: 02/11/2014] [Indexed: 01/24/2023] Open
Abstract
Cancer genome sequence data provide an invaluable resource for inferring the key mechanisms by which mutations arise in cancer cells, favoring their survival, proliferation and invasiveness. Here we examine recent advances in understanding the molecular mechanisms responsible for the predominant type of genetic alteration found in cancer cells, somatic single base substitutions (SBSs). Cytosine methylation, demethylation and deamination, charge transfer reactions in DNA, DNA replication timing, chromatin status and altered DNA proofreading activities are all now known to contribute to the mechanisms leading to base substitution mutagenesis. We review current hypotheses as to the major processes that give rise to SBSs and evaluate their relative relevance in the light of knowledge acquired from cancer genome sequencing projects and the study of base modifications, DNA repair and lesion bypass. Although gene expression data on APOBEC3B enzymes provide support for a role in cancer mutagenesis through U:G mismatch intermediates, the enzyme preference for single-stranded DNA may limit its activity genome-wide. For SBSs at both CG:CG and YC:GR sites, we outline evidence for a prominent role of damage by charge transfer reactions that follow interactions of the DNA with reactive oxygen species (ROS) and other endogenous or exogenous electron-abstracting molecules.
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Affiliation(s)
- Albino Bacolla
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
| | - David N Cooper
- Institute of Medical Genetics, School of Medicine, Cardiff University, Cardiff CF14 4XN, UK.
| | - Karen M Vasquez
- Dell Pediatric Research Institute, Division of Pharmacology and Toxicology, College of Pharmacy, The University of Texas at Austin, 1400 Barbara Jordan Blvd., Austin, TX 78723, USA.
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Cadet J, Wagner JR. TET enzymatic oxidation of 5-methylcytosine, 5-hydroxymethylcytosine and 5-formylcytosine. MUTATION RESEARCH-GENETIC TOXICOLOGY AND ENVIRONMENTAL MUTAGENESIS 2013; 764-765:18-35. [PMID: 24045206 DOI: 10.1016/j.mrgentox.2013.09.001] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2013] [Accepted: 09/04/2013] [Indexed: 12/14/2022]
Abstract
5-Methylcytosine and methylated histones have been considered for a long time as stable epigenetic marks of chromatin involved in gene regulation. This concept has been recently revisited with the detection of large amounts of 5-hydroxymethylcytosine, now considered as the sixth DNA base, in mouse embryonic stem cells, Purkinje neurons and brain tissues. The dioxygenases that belong to the ten eleven translocation (TET) oxygenase family have been shown to initiate the formation of this methyl oxidation product of 5-methylcytosine that is also generated although far less efficiently by radical reactions involving hydroxyl radical and one-electron oxidants. It was found as additional striking data that iterative TET-mediated oxidation of 5-hydroxymethylcytosine gives rise to 5-formylcytosine and 5-carboxylcytosine. This survey focuses on chemical and biochemical aspects of the enzymatic oxidation reactions of 5-methylcytosine that are likely to be involved in active demethylation pathways through the implication of enzymatic deamination of 5-methylcytosine oxidation products and/or several base excision repair enzymes. The high biological relevance of the latter modified bases explains why major efforts have been devoted to the design of a broad range of assays aimed at measuring globally or at the single base resolution, 5-hydroxymethylcytosine and the two other oxidation products in the DNA of cells and tissues. Another critical issue that is addressed in this review article deals with the assessment of the possible role of 5-methylcytosine oxidation products, when present in elevated amounts in cellular DNA, in terms of mutagenesis and interference with key cellular enzymes including DNA and RNA polymerases.
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Affiliation(s)
- Jean Cadet
- Direction des Sciences de la Matière, Institut Nanosciences et Cryogénie, CEA/Grenoble, 38054 Grenoble, France; Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
| | - J Richard Wagner
- Département de médecine nucléaire et radiobiologie, Faculté de médecine et des sciences de la santé, Université de Sherbrooke, Québec JIH 5N4, Canada.
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Martínez-Araya JI, Salgado-Morán G, Glossman-Mitnik D. Computational nanochemistry report on the oxicams--conceptual DFT indices and chemical reactivity. J Phys Chem B 2013; 117:6339-51. [PMID: 23656309 DOI: 10.1021/jp400241q] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A density functional theory study of eight oxicams was carried out in order to determine their global and local reactivities. These types of reactivities were measured by means of global and local reactivity descriptors coming from the conceptual density functional theory. Net electrophilicity as a global reactivity descriptor and local hypersoftness as a local reactivity descriptor were the used tools to distinguish reactivity and selectivity among these oxicams. Globally, isoxicam presents the highest electron donating capacity; meanwhile, the highest electron accepting capacity is exhibited by droxicam. Locally, two oxicams present neither nucleophilic nor electrophilic relevant reactivity in their peripheral pyridine ring, droxicam and tenoxicam, so that their more reactive zones are found on the respective fused rings. Oxicams have been divided into two subgroups in order to facilitate the local analysis of reactivity. One group is characterized because their most important condensed values for local hypersoftnes are well-separated: 4-meloxicam, lornoxicam, meloxicam, and normeloxicam. Meanwhile, the opposite situation is found in droxicam, isoxicam, piroxicam, and tenoxicam. As a whole, the nucleophilic characteristic noticeably predominates in these eight oxicams instead of an electrophilic behavior, thus meaning a greater tendency to donate electrons rather than withdrawing them; a consequence of this behavior implies a favorable interaction with a hypothetical receptor bearing one or more electron acceptor functional groups rather than electron donor functional groups; this would imply a maximization of this interaction from the covalent point of view.
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Affiliation(s)
- Jorge Ignacio Martínez-Araya
- Dirección de Investigación y Desarrollo, Universidad Pedro de Valdivia, Sede Santiago, Campus Tobalaba, Santiago, Chile
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Jin L, Wang W, Hu D, Lü J. The conversion of protonated cytosine-SO3− to uracil-SO3−: Insights into the novel induced hydrolytic deamination through bisulfite catalysis. Phys Chem Chem Phys 2013; 15:9034-42. [DOI: 10.1039/c3cp51275d] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Jin L, Wang W, Hu D, Min S. Effects of Protonation and C5 Methylation on the Electrophilic Addition Reaction of Cytosine: A Computational Study. J Phys Chem B 2012; 117:3-12. [DOI: 10.1021/jp304282z] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- Lingxia Jin
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, 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
| | - Daodao Hu
- Key Laboratory for
Macromolecular Science of Shaanxi Province, School of
Chemistry and Chemical Engineering, Shaanxi Normal University, Xi′an 710062, China
| | - Suotian Min
- School of Chemical
and Environmental Sciences, Shaanxi University of Technology, Hanzhong 723001, China
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Zhang N, Meng F. Theoretical study of the deamination of 1-(2-hydroxy-1-phenylethyl)adenine. COMPUT THEOR CHEM 2012. [DOI: 10.1016/j.comptc.2012.05.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Martínez-Araya JI. Revisiting caffeate's capabilities as a complexation agent to silver cation in mining processes by means of the dual descriptor--a conceptual DFT approach. J Mol Model 2012; 18:4299-307. [PMID: 22570079 DOI: 10.1007/s00894-012-1405-4] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/08/2012] [Indexed: 10/28/2022]
Abstract
Caffeic acid (C(9)H(8)O(4)) and its conjugate base C(9)H(7)O(4) (-) (anionic form-known as caffeate) were analyzed computationally through the use of quantum chemistry to assess their intrinsic global and local reactivity using the tools of conceptual density functional theory. The anionic form was found to be better at coordinating the silver cation than caffeic acid thus suggesting the use of caffeate as a complexation agent. The complexation capability of caffeate was compared with that of some of the most common ligand agents used to coordinate silver cations. Local reactivity descriptors allowed identification of the preferred sites on caffeate for silver cation coordination thus generating a plausible silver complex. All silver complexes were analyzed thermodynamically considering interaction energies in both gas and aqueous phases; the complexation free energy in aqueous phase was also determined. These results suggest that more attention be paid to the caffeate anion and its derivatives because this work has shed new light on the behavior of this anion in the recovery of silver cations that could be exploited in silver mining processes in a environmentally friendly way.
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Affiliation(s)
- Jorge Ignacio Martínez-Araya
- Vicerrectoría de Investigación y Desarrollo and Facultad de Ingeniería, Campus República, Sede Santiago, Universidad Pedro de Valdivia, Av. Libertador Bernardo O'Higgins 2222, Código Postal 8370962, Santiago, Chile.
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LIU XINLIN, ZENG HUI, MENG FANCUI, LIU JUNXIANG. THE HYDROLYTIC DEAMINATION MECHANISM OF PROTONATED ADENINE: A DFT STUDY. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633611006463] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The hydrolytic deamination mechanism of protonated adenine has been studied using density functional theory method. There are five pathways according to adenine protonated at N1, N3 and N7, respectively. As for the N1 protonated adenine only one pathway has been found, while for N3 and N7 protonated adenine two pathways have been found. Pathway c2 is preferred due to lowest activation free energy barrier of 53.02 kcal/mol. In this pathway, the hydroxyl group of water attacks C6 atom and hydrogen atom attacks N10 atom to produce enol form of protonated hypoxanthine and ammonia, then hydrogen transfer occurs to cause enol-keto tautomerization of protonated hypoxanthine with the assistance of ammonia. Adenine deamination is easier to take place under acidic condition than under neutral condition owing to lower activation energy barrier.
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Affiliation(s)
- XINLIN LIU
- Institute of Cardiovascular Disease, Pingjin Hospital, Medical College of Chinese People's, Armed Police Forces, Tianjin, 300162, P. R. China
| | - HUI ZENG
- Department of Pathology, Chinese People's Armed, Police Corps Hospital of Qinghai Province, Xining, 810000, P. R. China
| | - FANCUI MENG
- Tianjin Key Lab of Molecular Design and Drug Discovery, Tianjin Institute of Pharmaceutical Research, Tianjin, 300193, P. R. China
| | - JUNXIANG LIU
- Institute of Cardiovascular Disease, Pingjin Hospital, Medical College of Chinese People's, Armed Police Forces, Tianjin, 300162, P. R. China
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Comparison of the mechanism of deamination of 5,6-dihydro-5-methylcytosine with other cytosine derivatives. Theor Chem Acc 2012. [DOI: 10.1007/s00214-012-1187-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022]
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Wang T, Bowie JH. Can cytosine, thymine and uracil be formed in interstellar regions? A theoretical study. Org Biomol Chem 2012; 10:652-62. [DOI: 10.1039/c1ob06352a] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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Cárdenas C, Ayers PW, Cedillo A. Reactivity indicators for degenerate states in the density-functional theoretic chemical reactivity theory. J Chem Phys 2011; 134:174103. [PMID: 21548669 DOI: 10.1063/1.3585610] [Citation(s) in RCA: 56] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Carlos Cárdenas
- Departamento de Fisica, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
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Chen ZQ, Zhang CH, Kim CK, Xue Y. Quantum mechanics study and Monte Carlo simulation on the hydrolytic deamination of 5-methylcytosine glycol. Phys Chem Chem Phys 2011; 13:6471-83. [PMID: 21380473 DOI: 10.1039/c0cp02783a] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The efficient formation of 5-methylcytosine glycol (mCg) and its facile deamination to thymine glycol (Tg) may account for the prevalent C → T transition mutation found at methylated CpG site (mCpG) in human p53 gene, a hallmark for many types of human tumors. In this work, the hydrolytic deamination of mCg was investigated at the MP2 and B3LYP levels of theory using the 6-311G(d,p) basis set. In the gas phase, three pathways were explored, paths A-C, and it indicates that the direct deamination of mCg with H(2)O by either pathway is unlikely because of the high activation free energies involved in the rate-determining steps, the formation of the tetrahedral intermediate for paths A and B as well as the formation of the Tg tautomer for path C. In aqueous solution, the role of the water molecules in the deamination of mCg with H(2)O was analyzed in two separate parts: the direct participation of one water molecule in the reaction pathway, called the water-assisted mechanism; and the complementary participation of the aqueous solvation. The water-assisted mechanism was carried out for mCg and the cluster of two water molecules by quantum mechanical calculations in the gas phase. This indicates that the presence of the auxiliary water molecule significantly contributes to decreasing all the activation free energies. The bulk solution effect on the water-assisted mechanism was included by free energy perturbation implemented on Monte Carlo simulations, which is found to be substantial and decisive in the deamination mechanism of mCg. In this case, the water-assisted path A is the most plausible mechanism reported for the deamination of mCg, where the calculated activation free energy (22.6 kcal mol(-1) at B3LYP level of theory) agrees well with the experimentally determined activation free energy (24.8 kcal mol(-1)). The main striking results of the present DFT computational study which is in agreement with previous experimental data is the higher rate of deamination displayed by mCg residues with respect to 5-methylcytosine (mC) bases, which supports that the deamination of mCg contributes significantly to the C → T transition mutation at mCpG dinucleotide site.
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Affiliation(s)
- Ze Qin Chen
- College of Chemistry, Key Laboratory of Green Chemistry and Technology in Ministry of Education, Sichuan University, Chengdu 610064, People's Republic of China
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Acosta-Silva C, Branchadell V, Bertran J, Oliva A. Mutual relationship between stacking and hydrogen bonding in DNA. Theoretical study of guanine-cytosine, guanine-5-methylcytosine, and their dimers. J Phys Chem B 2010; 114:10217-27. [PMID: 20684646 DOI: 10.1021/jp103850h] [Citation(s) in RCA: 67] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
The mutual relationship between stacking and hydrogen-bonding and the possible influence of stacking in the different behavior of cytosine (C) and 5-methylcytosine (C') in DNA have been studied through complete DFT optimization of different structures of G-C and G-C' dimers (i.e., G-C/C-G and G-C'/C'-G), using four different functionals. Our results show that stacking leads to an increase of the O(6)...H-N(4) hydrogen bond length and to a simultaneous decrease of the N(2)-H...O(2) one, in such a way that both lengths approach each other and, in some cases, an inversion occurs. These results suggest that stacking can be a factor to explain the disparity between theory and experiment on the relative strength of the two lateral hydrogen bonds. Regarding the difference between cytosine and 5-methylcytosine, we have shown that methylation enhances the stacking interactions, mainly due to the increase of polarizability. Methylation also favors the existence of slid structures which can produce local distortions of DNA.
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Affiliation(s)
- Carles Acosta-Silva
- Departament de Química, Universitat Autònoma de Barcelona, Bellaterra 08193 Spain
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Labet V, Morell C, Douki T, Cadet J, Eriksson LA, Grand A. Hydrolytic Deamination of 5,6-Dihydrocytosine in a Protic Medium: A Theoretical Study. J Phys Chem A 2010; 114:1826-34. [DOI: 10.1021/jp9049044] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Vanessa Labet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Christophe Morell
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Thierry Douki
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Jean Cadet
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - Leif A. Eriksson
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
| | - André Grand
- Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB—UMR-E no. 3 CEA-UJF, CEA Grenoble, 17 rue des Martyrs, F-38 054 Grenoble cedex 9, France, and School of Science and Technology and Örebro Life Science Center, Örebro University, 701 82 Örebro, Sweden
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Roy RK, Saha S. Studies of regioselectivity of large molecular systems using DFT based reactivity descriptors. ACTA ACUST UNITED AC 2010. [DOI: 10.1039/b811052m] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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Labet V, Morell C, Toro-Labbé A, Grand A. Is an elementary reaction step really elementary? Theoretical decomposition of asynchronous concerted mechanisms. Phys Chem Chem Phys 2010; 12:4142-51. [DOI: 10.1039/b924589h] [Citation(s) in RCA: 24] [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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Zheng H, Meng F. Theoretical study of water-assisted hydrolytic deamination mechanism of adenine. Struct Chem 2009. [DOI: 10.1007/s11224-009-9495-z] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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Cárdenas C, Rabi N, Ayers PW, Morell C, Jaramillo P, Fuentealba P. Chemical Reactivity Descriptors for Ambiphilic Reagents: Dual Descriptor, Local Hypersoftness, and Electrostatic Potential. J Phys Chem A 2009; 113:8660-7. [PMID: 19580251 DOI: 10.1021/jp902792n] [Citation(s) in RCA: 119] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Carlos Cárdenas
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
| | - Nataly Rabi
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
| | - Paul W. Ayers
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
| | - Christophe Morell
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
| | - Paula Jaramillo
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
| | - Patricio Fuentealba
- Department of Chemistry, McMaster University, Hamilton, ON, Canada L8S 4M1, Laboratoire “Lésions des Acides Nucléiques”, INAC/SCIB - UMR-E no. 3 CEA-UJF, CEA Grenoble, rue des Martyrs, F-38 054 Grenoble Cedex 9, France, Departamento de Fisica Geral, Instituto de Fisica, Universidade de Sao Paulo, Cidade Universitaria, S.P. Brazil, and Department of Physics, Faculty of Science, University of Chile, Santiago, Chile
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Cárdenas C, Echegaray E, Chakraborty D, Anderson JSM, Ayers PW. Relationships between the third-order reactivity indicators in chemical density-functional theory. J Chem Phys 2009; 130:244105. [DOI: 10.1063/1.3151599] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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