1
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Villablanca D, Gazzari S, Herrera B. The study of the PES and the reaction mechanism between ketene and Lithium Carbenoids and the formation of cyclopropanone. Theor Chem Acc 2023. [DOI: 10.1007/s00214-023-02965-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/19/2023]
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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: Interaction chemical potential, hardness, and reactivity principles. Front Chem 2022; 10:929464. [PMID: 35936089 PMCID: PMC9352952 DOI: 10.3389/fchem.2022.929464] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2022] [Accepted: 06/27/2022] [Indexed: 11/13/2022] Open
Abstract
In the first paper of this series, the authors derived an expression for the interaction energy between two reagents in terms of the chemical reactivity indicators that can be derived from density functional perturbation theory. While negative interaction energies can explain reactivity, reactivity is often more simply explained using the “|dμ| big is good” rule or the maximum hardness principle. Expressions for the change in chemical potential (μ) and hardness when two reagents interact are derived. A partial justification for the maximum hardness principle is that the terms that appear in the interaction energy expression often reappear in the expression for the interaction hardness, but with opposite sign.
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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, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | | | - 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, Universit́e Claude Bernard Lyon 1, Institut des Sciences Analytiques, UMR CNRS 5280, Villeurbanne Cedex, 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, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | - 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, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, ON, Canada
- *Correspondence: Ramón Alain Miranda-Quintana, ; Tatiana Gómez, Carlos Cárdenas, ; Paul W. Ayers,
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3
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Liu Q, Tan J, Liu Z, Hu X, Yu J, Wang X, Wu J, Cai B, Wang Q, Fu Y, Liu H, Li B. Transference Number Reinforced-Based Gel Copolymer Electrolyte for Dendrite-Free Lithium Metal Batteries. ACS Appl Mater Interfaces 2022; 14:26612-26621. [PMID: 35638839 DOI: 10.1021/acsami.2c01513] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
The progress of electric vehicles is highly inhibited by the limited energy density and growth of dendrite Li in current power batteries. Breakthroughs and improvements in electrolyte chemistry are highlighted to directly address the above issues, namely, the development of electrolytes with a high lithium-ion transference number (tLi+), enabling one to effectively restrict the concentration polarization during repetitious cycling. Herein, we propose a novel ether-based copolymer-based gel polymer electrolyte (ECP-based GPE) by in situ copolymerization as an intriguing strategy to achieve a high tLi+ of ∼0.64. Molecular dynamics simulations and finite element method analyses illustrate the enhanced Li+ diffusion process (DLi+, ∼1.76 × 10-10 m2 s-1) in ECP-based GPE with a homogeneous electric potential accommodated around the lithium metal anode. Therefore, such a high-tLi+-based electrolyte renders a high reversibility of dendrite-free lithium plating/stripping at a high areal capacity (5 mA cm-2/5 mA h cm-2) in an Li||Li symmetric cell and facilitates superior cycling performances (over 1000 cycles) at a high rate (5 C) with a capacity retention of ∼91.1% in Li||LiFePO4 batteries, promoting the practical application of solid-state lithium metal batteries.
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Affiliation(s)
- Qi Liu
- College of Materials Science and Engineering, Hunan University, Changsha 410082, Hunan, China
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jin Tan
- College of Materials Science and Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Zhenfang Liu
- College of Materials Science and Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Xia Hu
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Jiahao Yu
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Xianshu Wang
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Junru Wu
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
| | - Biya Cai
- Guangdong TeamGiant New Energy Technology Co. Ltd., Shenzhen 518110, China
| | - Qiang Wang
- Guangdong TeamGiant New Energy Technology Co. Ltd., Shenzhen 518110, China
| | - Yongzhu Fu
- College of Chemistry, Zhengzhou University, Zhengzhou 450001, P.R. China
| | - Hongbo Liu
- College of Materials Science and Engineering, Hunan University, Changsha 410082, Hunan, China
| | - Baohua Li
- Shenzhen Key Laboratory of Power Battery Safety and Shenzhen Geim Graphene Center Tsinghua Shenzhen International Graduate School, Tsinghua University, Shenzhen 518055, China
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4
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Wang Y, Coppel Y, Lepetit C, Marty JD, Mingotaud C, Kahn ML. Anisotropic growth of ZnO nanoparticles driven by the structure of amine surfactants: the role of surface dynamics in nanocrystal growth. Nanoscale Adv 2021; 3:6088-6099. [PMID: 36133935 PMCID: PMC9418458 DOI: 10.1039/d1na00566a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 08/11/2021] [Indexed: 05/15/2023]
Abstract
Herein, we elucidate the key role of amine surfactants in the controlled anisotropic growth of ZnO nanoparticles that is achieved under mild conditions by organometallic hydrolysis. The structuring influence of alkyl substituents on the nitrogen atom of amines is jointly analyzed theoretically by DFT modeling, and experimentally by multinuclear NMR (1H, 13C and 17O) spectroscopy. We demonstrate that in initial steps leading to the growth of colloidal ZnO particles, the nature of molecular species that are involved in the solution strongly depends on the structure of the amine surfactant. By using tertiary, secondary or primary amines, no or weak adducts between the amine and zinc, or stable adducts, or adduct oligomers were identified, respectively. Afterwards, following the course of the reaction, the dynamic behavior of the amines on the grown ZnO nanocrystal surfaces is also strongly correlated with their structure. We identified that in the presence of tertiary, secondary or primary amines, no significant [Zn⋯N] adsorption, or surface adsorption with notable surface mobility, or a very strong adsorption is achieved, respectively. The last case, primary amines, significantly involves the structuring of a hydrogen bonding network. Therefore, such surface dynamic behavior has a predominant role in driving the nanocrystal growth, and orienting the ZnO material final morphology. By forming hydrogen bonds at the nanoparticle surface during the growth process, primary amines specifically lead to the formation of nanorods. Conversely, isotropic nanoparticles and aggregates are obtained when secondary and tertiary amines are used, respectively. These findings shed light on the role of weak surface interactions, herein H-bonding, that rule the growth of nano-objects and are as such crucial to identify, study, and control for achieving progress in nanoscience.
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Affiliation(s)
- Yinping Wang
- Laboratoire de Chimie de Coordination, CNRS, UPR-8241 205 route de Narbonne 31077 Toulouse Cedex 04 France
- Laboratoire des IMRCP, CNRS UMR 5623, University of Toulouse 118 route de Narbonne 31062 Toulouse Cedex 9 France
| | - Yannick Coppel
- Laboratoire de Chimie de Coordination, CNRS, UPR-8241 205 route de Narbonne 31077 Toulouse Cedex 04 France
| | - Christine Lepetit
- Laboratoire de Chimie de Coordination, CNRS, UPR-8241 205 route de Narbonne 31077 Toulouse Cedex 04 France
| | - Jean-Daniel Marty
- Laboratoire des IMRCP, CNRS UMR 5623, University of Toulouse 118 route de Narbonne 31062 Toulouse Cedex 9 France
| | - Christophe Mingotaud
- Laboratoire des IMRCP, CNRS UMR 5623, University of Toulouse 118 route de Narbonne 31062 Toulouse Cedex 9 France
| | - Myrtil L Kahn
- Laboratoire de Chimie de Coordination, CNRS, UPR-8241 205 route de Narbonne 31077 Toulouse Cedex 04 France
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5
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Yañez O, Báez-Grez R, Inostroza D, Pino-Rios R, Rabanal-León WA, Contreras-García J, Cardenas C, Tiznado W. Kick-Fukui: A Fukui Function-Guided Method for Molecular Structure Prediction. J Chem Inf Model 2021; 61:3955-3963. [PMID: 34378935 DOI: 10.1021/acs.jcim.1c00605] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Here, we introduce a hybrid method, named Kick-Fukui, to explore the potential energy surface (PES) of clusters and molecules using the Coulombic integral between the Fukui functions in the first screening of the best individuals. In the process, small stable molecules or clusters whose combination has the stoichiometry of the explored species are used as assembly units. First, a small set of candidates has been selected from a large and stochastically generated (Kick) population according to the maximum value of the Coulombic integral between the Fukui functions of both fragments. Subsequently, these few candidates are optimized using a gradient method and density functional theory (DFT) calculations. The performance of the program has been evaluated to explore the PES of various systems, including atomic and molecular clusters. In most cases studied, the global minimum (GM) has been identified with a low computational cost. The strategy does not allow to identify the GM of some silicon clusters; however, it predicts local minima very close in energy to the GM that could be used as the initial population of evolutionary algorithms.
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Affiliation(s)
- Osvaldo Yañez
- Center of New Drugs for Hypertension (CENDHY), 8380494 Santiago, Chile.,Department of Pharmaceutical Science and Technology, School of Chemical and Pharmaceutical Sciences, Universidad de Chile, 8380494 Santiago, Chile.,Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
| | - Rodrigo Báez-Grez
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
| | - Diego Inostroza
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile.,Universidad Andres Bello, Programa de Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, 8370035 Santiago, Chile
| | - Ricardo Pino-Rios
- Laboratorio de Química Teórica, Facultad de Química y Biología, Universidad de Santiago de Chile (USACH), 8320000 Santiago, Chile
| | - Walter A Rabanal-León
- Departamento de Química Analítica e Inorgánica, Facultad de Ciencias Químicas, Universidad de Concepción, Edmundo Larenas 129, Casilla 160-C, 4070371 Concepción, Chile
| | - Julia Contreras-García
- Sorbonne Universités and CNRS, Laboratoire de Chimie Théorique (LCT), 75005 Paris, France
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 635, Santiago 7790681, Chile.,Centro para el Desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Avenida Ecuador 3493, 9170124 Santiago, Chile
| | - William Tiznado
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, República 498, 8370035 Santiago, Chile
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6
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Klein J, Fleurat-Lessard P, Pilmé J. New insights in chemical reactivity from quantum chemical topology. J Comput Chem 2021; 42:840-854. [PMID: 33660292 DOI: 10.1002/jcc.26504] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2020] [Revised: 02/07/2021] [Accepted: 02/12/2021] [Indexed: 01/13/2023]
Abstract
Based on the quantum chemical topology of the modified electron localization function ELFx , an efficient and robust mechanistic methodology designed to identify the favorable reaction pathway between two reactants is proposed. We first recall and reshape how the supermolecular interaction energy can be evaluated from only three distinct terms, namely the intermolecular coulomb energy, the intermolecular exchange-correlation energy and the intramolecular energies of reactants. Thereafter, we show that the reactivity between the reactants is driven by the first-order variation in the coulomb intermolecular energy defined in terms of the response to changes in the number of electrons. Illustrative examples with the formation of the dative bond B-N involved in the BH3 NH3 molecule and the typical formation of the hydrogen bond in the canonical water dimer are presented. For these selected systems, our approach unveils a noticeable mimicking of Edual onto the DFT intermolecular interaction energy surface calculated between the both reactants. An automated reaction-path algorithm aimed to determine the most favorable relative orientations when the two molecules approach each other is also outlined.
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Affiliation(s)
- Johanna Klein
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
| | - Paul Fleurat-Lessard
- Université de Bourgogne, UMR CNRS 6302, Université, Bourgogne Franche-Comté (UBFC), Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB), 9 avenue Alain Savary, Dijon Cedex, 21078, France
| | - Julien Pilmé
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, Paris Cedex, France
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7
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8
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Taakili R, Barthes C, Goëffon A, Lepetit C, Duhayon C, Valyaev DA, Canac Y. NHC Core Phosphonium Ylide-based Palladium(II) Pincer Complexes: The Second Ylide Extremity Makes the Difference. Inorg Chem 2020; 59:7082-7096. [DOI: 10.1021/acs.inorgchem.0c00561] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Rachid Taakili
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Cécile Barthes
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Amel Goëffon
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Christine Lepetit
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Carine Duhayon
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Dmitry A. Valyaev
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
| | - Yves Canac
- LCC−CNRS, Université de Toulouse, CNRS, 205 route de Narbonne, 31077 Toulouse cedex 4, France
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9
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Zanocco RP, Bresoli-Obach R, Nonell S, Lemp E, Zanocco AL. Structure-activity study of furyl aryloxazole fluorescent probes for the detection of singlet oxygen. PLoS One 2018; 13:e0200006. [PMID: 29965981 PMCID: PMC6028117 DOI: 10.1371/journal.pone.0200006] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Accepted: 06/18/2018] [Indexed: 12/29/2022] Open
Abstract
In this study, we report the synthesis and the photochemical behavior of a series of new "click-on" fluorescent probes designed to detect singlet oxygen. They include a highly fluorescent chemical structure, an aryloxazole ring, linked to a furan moiety operating as singlet oxygen trap. Their activity depends on both the structure of the aryloxazole fluorophore and the electron-donating and electron-accepting properties of the substituents attached to the C-5 of the furan ring. All probes are selectively oxidized by singlet oxygen to give a single fluorescent product in methanol and produce negligible amounts of singlet oxygen themselves by self-sensitization. The most promising dyad, (E)-2-(2-(5-methylfuran-2-yl)vinyl)naphtho[1,2-d]oxazole, FN-6, shows outstanding reactivity and sensitivity: it traps singlet oxygen with a rate constant (5,8 ± 0.1) x 1(07) M-1 s-1 and its fluorescence increases by a factor of 500 upon reaction. Analysis of the dyads reactivity in terms of linear free energy relationships using the modified Swain and Lupton parameter F and the Fukui condensed function for the electrophilic attack, suggests that cycloaddition of singlet oxygen to the furan ring is partially concerted and possibly involves an exciplex with a "more open" structure than could be expected for a concerted cycloaddition.
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Affiliation(s)
- Renzo P. Zanocco
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | | | - Santi Nonell
- Institut Químic de Sarrià, Universitat Ramon Llull, Barcelona, Spain
| | - Else Lemp
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
| | - Antonio L. Zanocco
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago, Chile
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10
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Avdović EH, Milenković D, Dimitrić Marković JM, Đorović J, Vuković N, Vukić MD, Jevtić VV, Trifunović SR, Potočňák I, Marković Z. Synthesis, spectroscopic characterization (FT-IR, FT-Raman, and NMR), quantum chemical studies and molecular docking of 3-(1-(phenylamino)ethylidene)-chroman-2,4-dione. Spectrochim Acta A Mol Biomol Spectrosc 2018; 195:31-40. [PMID: 29367024 DOI: 10.1016/j.saa.2018.01.023] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/21/2017] [Revised: 01/06/2018] [Accepted: 01/09/2018] [Indexed: 06/07/2023]
Abstract
The experimental and theoretical investigations of structure of the 3-(1-(phenylamino)ethylidene)-chroman-2,4-dione were performed. X-ray structure analysis and spectroscopic methods (FTIR and FT-Raman, 1H and 13C NMR), along with the density functional theory calculations (B3LYP functional with empirical dispersion corrections D3BJ in combination with the 6-311 + G(d,p) basis set), were used in order to characterize the molecular structure and spectroscopic behavior of the investigated coumarin derivative. Molecular docking analysis was carried out to identify the potency of inhibition of the title molecule against human's Ubiquinol-Cytochrome C Reductase Binding Protein (UQCRB) and Methylenetetrahydrofolate reductase (MTHFR). The inhibition activity was obtained for ten conformations of ligand inside the proteins.
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Affiliation(s)
- Edina H Avdović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Dejan Milenković
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
| | | | - Jelena Đorović
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia
| | - Nenad Vuković
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Milena D Vukić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Verica V Jevtić
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Srećko R Trifunović
- University of Kragujevac, Faculty of Science, Department of Chemistry, Radoja Domanovića 12, 34000 Kragujevac, Serbia
| | - Ivan Potočňák
- Institute of Chemistry, P. J. Šafárik University in Košice, Moyzesova 11, 04154 Košice, Slovak Republic
| | - Zoran Marković
- Bioengineering Research and Development Center, Prvoslava Stojanovića 6, 34000 Kragujevac, Serbia; Department of Chemical-Technological Sciences, State University of Novi Pazar, Vuka Karadžića bb, 36300 Novi Pazar, Serbia.
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11
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Milenković D, Avdović EH, Dimić D, Bajin Z, Ristić B, Vuković N, Trifunović SR, Marković ZS. Reactivity of the coumarine derivative towards cartilage proteins: combined NBO, QTAIM, and molecular docking study. Monatsh Chem 2017. [DOI: 10.1007/s00706-017-2051-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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12
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Morgenstern A, Wilson TR, Eberhart ME. Predicting Chemical Reactivity from the Charge Density through Gradient Bundle Analysis: Moving beyond Fukui Functions. J Phys Chem A 2017; 121:4341-4351. [DOI: 10.1021/acs.jpca.7b00630] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Amanda Morgenstern
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Timothy R. Wilson
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
| | - M. E. Eberhart
- Molecular Theory Group, Colorado School of Mines, Golden, Colorado 80401, United States
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13
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Yañez O, Vásquez-Espinal A, Inostroza D, Ruiz L, Pino-Rios R, Tiznado W. A Fukui function-guided genetic algorithm. Assessment on structural prediction of Sin(n = 12-20) clusters. J Comput Chem 2017; 38:1668-1677. [DOI: 10.1002/jcc.24810] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2017] [Revised: 03/29/2017] [Accepted: 03/30/2017] [Indexed: 11/10/2022]
Affiliation(s)
- Osvaldo Yañez
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Alejandro Vásquez-Espinal
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Diego Inostroza
- Centro de Bioinformatica y Simulación Molecular; Facultad de Ingeniería, Universidad de Talca; 2 Norte 685, Casilla 721 Talca Chile
| | - Lina Ruiz
- Centro de Investigación Biomédica, Universidad Autónoma de Chile; Santiago Chile
| | - Ricardo Pino-Rios
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - William Tiznado
- Doctorado en Fisicoquímica Molecular; Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
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14
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Pino-Rios R, Yañez O, Inostroza D, Ruiz L, Cardenas C, Fuentealba P, Tiznado W. Proposal of a simple and effective local reactivity descriptor through a topological analysis of an orbital-weighted fukui function. J Comput Chem 2017; 38:481-488. [DOI: 10.1002/jcc.24699] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2016] [Revised: 10/28/2016] [Accepted: 11/18/2016] [Indexed: 11/06/2022]
Affiliation(s)
- Ricardo Pino-Rios
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Osvaldo Yañez
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
| | - Diego Inostroza
- Centro de Bioinformática y Simulación Molecular, Facultad de Ingeniería, Universidad de Talca; 2 Norte 685, Casilla 721 Talca Chile
| | - Lina Ruiz
- Centro de Investigación Biomédica, Universidad Autónoma de Chile; Santiago Chile
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias; Universidad de Chile; 653-Santiago Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA; Av. Ecuador 3493 Santiago Chile
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias; Universidad de Chile; 653-Santiago Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA; Av. Ecuador 3493 Santiago Chile
| | - William Tiznado
- Doctorado en Fisicoquímica Molecular, Facultad de Ciencias Exactas, Universidad Andres Bello; República 275 Santiago Chile
- Departamento de Ciencias Químicas; Facultad de Ciencias Exactas Universidad Andres Bello; República 275 Santiago Chile
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15
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Fu CW, Lin TH. Predicting the Metabolic Sites by Flavin-Containing Monooxygenase on Drug Molecules Using SVM Classification on Computed Quantum Mechanics and Circular Fingerprints Molecular Descriptors. PLoS One 2017; 12:e0169910. [PMID: 28072829 PMCID: PMC5224990 DOI: 10.1371/journal.pone.0169910] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2016] [Accepted: 12/22/2016] [Indexed: 01/02/2023] Open
Abstract
As an important enzyme in Phase I drug metabolism, the flavin-containing monooxygenase (FMO) also metabolizes some xenobiotics with soft nucleophiles. The site of metabolism (SOM) on a molecule is the site where the metabolic reaction is exerted by an enzyme. Accurate prediction of SOMs on drug molecules will assist the search for drug leads during the optimization process. Here, some quantum mechanics features such as the condensed Fukui function and attributes from circular fingerprints (called Molprint2D) are computed and classified using the support vector machine (SVM) for predicting some potential SOMs on a series of drugs that can be metabolized by FMO enzymes. The condensed Fukui function fA- representing the nucleophilicity of central atom A and the attributes from circular fingerprints accounting the influence of neighbors on the central atom. The total number of FMO substrates and non-substrates collected in the study is 85 and they are equally divided into the training and test sets with each carrying roughly the same number of potential SOMs. However, only N-oxidation and S-oxidation features were considered in the prediction since the available C-oxidation data was scarce. In the training process, the LibSVM package of WEKA package and the option of 10-fold cross validation are employed. The prediction performance on the test set evaluated by accuracy, Matthews correlation coefficient and area under ROC curve computed are 0.829, 0.659, and 0.877 respectively. This work reveals that the SVM model built can accurately predict the potential SOMs for drug molecules that are metabolizable by the FMO enzymes.
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Affiliation(s)
- Chien-wei Fu
- Department of Pharmacy, National Taiwan University Hospital Hsin-Chu Branch, Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, HsinChu, Taiwan, ROC
| | - Thy-Hou Lin
- Department of Pharmacy, National Taiwan University Hospital Hsin-Chu Branch, Institute of Molecular Medicine and Department of Life Science, National Tsing Hua University, HsinChu, Taiwan, ROC
- * E-mail:
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16
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Fakhar Z, Govender T, Lamichhane G, Maguire GE, Kruger HG, Honarparvar B. Computational model for the acylation step of the β-lactam ring: Potential application for l,d-transpeptidase 2 in mycobacterium tuberculosis. J Mol Struct 2017. [DOI: 10.1016/j.molstruc.2016.08.049] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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17
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18
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Fuentealba P, Cardenas C, Pino-rios R, Tiznado W. Topological Analysis of the Fukui Function. In: Chauvin R, Lepetit C, Silvi B, Alikhani E, editors. Applications of Topological Methods in Molecular Chemistry. Cham: Springer International Publishing; 2016. pp. 227-41. [DOI: 10.1007/978-3-319-29022-5_8] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register]
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19
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Anderson JSM, Melin J, Ayers PW. Using the general-purpose reactivity indicator: challenging examples. J Mol Model 2016; 22:57. [DOI: 10.1007/s00894-016-2910-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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20
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Valdés C, Alzate-Morales J, Osorio E, Villaseñor J, Navarro-Retamal C. A characterization of the two-step reaction mechanism of phenol decomposition by a Fenton reaction. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2015.10.005] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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21
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Chamorro E, Duque-Noreña M. Understanding the Highly Varying pKa of Arylamines. A Perspective from the Average Local Ionization Condensed-to-Atom Framework. J Phys Chem A 2015; 119:8156-62. [PMID: 26107310 DOI: 10.1021/acs.jpca.5b03252] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The highly varying experimental pKa values for 36 arylamines spanning 7 orders of magnitude is carefully examined. Within this framework, a valence condensed-to-atom model for the average ionization energy is introduced and tested. The theoretical approach is connected to orbital Fukui functions directly mapped into semilocal or regional site-specific responses. It is revealed that the average local ionization energies associated with the amino nitrogen atom is linearly correlated to the basicity of the substituted arylamines, properly reproducing the experimental ordering of basicity. The condensed-to-atom descriptor exhibits a high predictive power, providing a new direct reactivity evaluation of significant value.
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Affiliation(s)
- Eduardo Chamorro
- Departamento de Ciencias Quimicas. Facultad de Ciencias Exactas. Nucleus Millennium of Chemical Processes and Catalysis, Universidad Andres Bello, Avenida República 275, 8370146 Santiago, Chile
| | - Mario Duque-Noreña
- Departamento de Ciencias Quimicas. Facultad de Ciencias Exactas. Nucleus Millennium of Chemical Processes and Catalysis, Universidad Andres Bello, Avenida República 275, 8370146 Santiago, Chile
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22
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Anderson JS, Ayers PW. Resolving the nature of the reactive sites of phenylsulfinate (<mml:math altimg="si1.gif" overflow="scroll" xmlns:xocs="http://www.elsevier.com/xml/xocs/dtd" xmlns:xs="http://www.w3.org/2001/XMLSchema" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xmlns="http://www.elsevier.com/xml/ja/dtd" xmlns:ja="http://www.elsevier.com/xml/ja/dtd" xmlns:mml="http://www.w3.org/1998/Math/MathML" xmlns:tb="http://www.elsevier.com/xml/common/table/dtd" xmlns:sb="http://www.elsevier.com/xml/common/struct-bib/dtd" xmlns:ce="http://www.elsevier.com/xml/common/dtd" xmlns:xlink="http://www.w3.org/1999/xlink" xmlns:cals="http://www.elsevier.com/xml/common/cals/dtd" xmlns:sa="http://www.elsevier.com/xml/common/struct-aff/dtd"><mml:mrow><mml:msubsup><mml:mrow><mml:mtext>PhSO</mml:mtext></mml:mrow><mml:mrow><mml:mn>2</mml:mn></mml:mrow><mml:mrow><mml:mo>-</mml:mo></mml:mrow></mml:msubsup></mml:mrow></mml:math>) with a single general-purpose reactivity indicator. COMPUT THEOR CHEM 2014; 1043:1-4. [DOI: 10.1016/j.comptc.2014.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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23
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Echegaray E, Rabi S, Cárdenas C, Zadeh FH, Rabi N, Lee S, Anderson JSM, Toro-labbe A, Ayers PW. In pursuit of negative Fukui functions: molecules with very small band gaps. J Mol Model 2014; 20. [DOI: 10.1007/s00894-014-2162-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2014] [Accepted: 01/27/2014] [Indexed: 10/25/2022]
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24
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Ma Y, Liang J, Zhao D, Chen YL, Shen J, Xiong B. Condensed Fukui function predicts innate C–H radical functionalization sites on multi-nitrogen containing fused arenes. RSC Adv 2014. [DOI: 10.1039/c4ra01853b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The condensed Fukui function (values in blue and red) predicts innate radical C–H functionalization sites (dark green circles) observed in experiments.
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Affiliation(s)
- Yuchi Ma
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203, P. R. China
| | - Jin Liang
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203, P. R. China
- School of Pharmaceutical Engineering
- Shenyang Pharmaceutical University
| | - Dongmei Zhao
- School of Pharmaceutical Engineering
- Shenyang Pharmaceutical University
- Shenyang 100016, P. R. China
| | - Yue-Lei Chen
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203, P. R. China
| | - Jingkang Shen
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203, P. R. China
| | - Bing Xiong
- Shanghai Institute of Materia Medica
- Chinese Academy of Sciences
- Shanghai 201203, P. R. China
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25
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Heidar Zadeh F, Fuentealba P, Cárdenas C, Ayers PW. An information-theoretic resolution of the ambiguity in the local hardness. Phys Chem Chem Phys 2014; 16:6019-26. [PMID: 24553911 DOI: 10.1039/c3cp52906a] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A definition of the local hardness, suitable for application in the local hard/soft acid/base principle, is derived by applying information theory.
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Affiliation(s)
| | - Patricio Fuentealba
- Departamento de Física
- Facultad de Ciencias
- Universidad de Chile
- 653-Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia
| | - Carlos Cárdenas
- Departamento de Física
- Facultad de Ciencias
- Universidad de Chile
- 653-Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia
| | - Paul W. Ayers
- Dept. of Chemistry & Chemical Biology
- McMaster University
- Hamilton, Canada
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26
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Aliaga ME, Tiznado W, Cassels BK, Nuñez MT, Millán D, Pérez EG, García-Beltrán O, Pavez P. Substituent effects on reactivity of 3-cinnamoylcoumarins with thiols of biological interest. RSC Adv 2014. [DOI: 10.1039/c3ra44695f] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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27
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Reyes A, Cuervo PA, Orozco F, Abonia R, Duque-noreña M, Pérez P, Chamorro E. Theoretical investigation of the selectivity in intramolecular cyclizations of some 2’–aminochalcones to dihydroquinolin–8–ones and indolin–3–ones. J Mol Model 2013; 19:3611-8. [DOI: 10.1007/s00894-013-1893-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2013] [Accepted: 05/15/2013] [Indexed: 11/26/2022]
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28
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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29
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Rincon E, Zuloaga F, Chamorro E. Global and local chemical reactivities of mutagen X and simple derivatives. J Mol Model 2013; 19:2573-82. [PMID: 23463265 DOI: 10.1007/s00894-013-1799-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2012] [Accepted: 02/06/2013] [Indexed: 11/30/2022]
Abstract
Registered by the World Health Organization (WHO), 3-chloro-4-(dichloromethyl)-5-hydroxy-2(5H)-furanone (MX) is one of the strongest bacterial mutagens ever tested, as highlighted by the Ames Salmonella typhimurium TA100 assay. We provide new insights concerning this mutagenic activity on the basis of global and local theoretically defined electrophilicity indices. Our results further support the idea that mutagenicity of MX and its analogues is related more closely to one-electron transfer processes from the electron-rich biological environment than to adduct formation processes. We also stress that, although the Z-open tautomers are intrinsically more electrophilic than furanone ring analogues, the observed mutagenic activity is significantly correlated only to the electrophilicity response of the ring forms. In that context, we also emphasize that it is electrophilicity at the C α in the α-β unsaturated carbonyl moiety that exhibits a strong correlation with the observed mutagenic activity.
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Affiliation(s)
- Elizabeth Rincon
- Instituto de Ciencias Quimicas, Facultad de Ciencias, Universidad Austral de Chile, Las encinas 220, Valdivia, Chile.
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30
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Acelas NY, Mejia SM, Mondragón F, Flórez E. Density functional theory characterization of phosphate and sulfate adsorption on Fe-(hydr)oxide: Reactivity, pH effect, estimation of Gibbs free energies, and topological analysis of hydrogen bonds. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2012.11.002] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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31
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Osorio E, Pérez EG, Areche C, Ruiz LM, Cassels BK, Flórez E, Tiznado W. Why is quercetin a better antioxidant than taxifolin? Theoretical study of mechanisms involving activated forms. J Mol Model 2013; 19:2165-72. [PMID: 23283546 DOI: 10.1007/s00894-012-1732-5] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2012] [Accepted: 12/12/2012] [Indexed: 10/27/2022]
Abstract
The stronger antioxidant capacity of the flavonoid quercetin (Q) compared with taxifolin (dihydroquercetin, T) has been the subject of previous experimental and theoretical studies. Theoretical work has focused on the analysis of hydrogen bond dissociation energies (BDE) of the OH phenolic groups, but consider mechanisms that only involve the transfer of one hydrogen atom. In the present work we consider other mechanisms involving a second hydrogen transfer in reactions with free radicals. The relative stability of the radicals formed after the first hydrogen transfer reaction is considered in discussing the antioxidant activity of Q and T. In terms of global and local theoretical reactivity descriptors, we propose that the radical arising from Q should be more persistent in the environment and with the capability to react with a second radical by hydrogen transfer, proton transfer and electron transfer mechanisms. These mechanisms could be responsible of the stronger antioxidant capacity of Q.
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32
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Echegaray E, Cárdenas C, Rabi S, Rabi N, Lee S, Zadeh FH, Toro-Labbe A, Anderson JSM, Ayers PW. In pursuit of negative Fukui functions: examples where the highest occupied molecular orbital fails to dominate the chemical reactivity. J Mol Model 2012; 19:2779-83. [PMID: 23090502 DOI: 10.1007/s00894-012-1637-3] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2012] [Accepted: 10/07/2012] [Indexed: 10/27/2022]
Abstract
In our quest to explore molecules with chemically significant regions where the Fukui function is negative, we explored reactions where the frontier orbital that indicates the sites for electrophilic attack is not the highest occupied molecular orbital. The highest occupied molecular orbital (HOMO) controls the location of the regions where the Fukui function is negative, supporting the postulate that negative values of the Fukui function are associated with orbital relaxation effects and nodal surfaces of the frontier orbitals. Significant negative values for the condensed Fukui function, however, were not observed.
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Affiliation(s)
- Eleonora Echegaray
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
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33
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Acelas NY, López D, Mondragón F, Tiznado W, Flórez E. Topological analysis of tetraphosphorus oxides (P4O6+n (n = 0–4)). J Mol Model 2012; 19:2057-67. [DOI: 10.1007/s00894-012-1633-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2012] [Accepted: 10/05/2012] [Indexed: 10/27/2022]
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34
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Abstract
Detection of singlet oxygen emission, λ(max) = 1270 nm, following laser excitation and steady-state methods were employed to measure the total reaction rate constant, k(T), and the reactive reaction rate constant, k(r), for the reaction between singlet oxygen and several flavonoids. Values of k(T) determined in deuterated water, ranging from 2.4×10(7) M(-1) s(-1) to 13.4×10(7) M(-1) s(-1), for rutin and morin, respectively, and the values measured for k(r), ranging from 2.8×10(5) M(-1) s(-1) to 65.7×10(5) M(-1) s(-1) for kaempferol and morin, respectively, being epicatechin and catechin chemically unreactive. These results indicate that all the studied flavonoids are good quenchers of singlet oxygen and could be valuable antioxidants in systems under oxidative stress, in particular if a flavonoid-rich diet was previously consumed. Analysis of the dependence of rate constant values with molecular structure in terms of global descriptors and condensed Fukui functions, resulting from electronic structure calculations, supports the formation of a charge transfer exciplex in all studied reactions. The fraction of exciplex giving reaction products evolves through a hydroperoxide and/or an endoperoxide intermediate produced by singlet oxygen attack on the double bond of the ring C of the flavonoid.
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Affiliation(s)
- Javier Morales
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Ciencias y Tecnología Farmacéuticas, Santiago, Chile
| | - Germán Günther
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Química Orgánica y Fisicoquímica, Santiago, Chile
| | - Antonio L. Zanocco
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Química Orgánica y Fisicoquímica, Santiago, Chile
| | - Else Lemp
- Universidad de Chile, Facultad de Ciencias Químicas y Farmacéuticas, Departamento de Química Orgánica y Fisicoquímica, Santiago, Chile
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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37
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Abdellah I, Bernoud E, Lohier JF, Alayrac C, Toupet L, Lepetit C, Gaumont AC. Neutral copper–phosphido-borane complexes: synthesis, characterization, and use as precatalysts in Csp–P bond formation. Chem Commun (Camb) 2012; 48:4088-90. [PMID: 22430669 DOI: 10.1039/c2cc30723e] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Affiliation(s)
- Ibrahim Abdellah
- Laboratoire de Chimie Moléculaire et Thio-organique, UMR CNRS 6507, INC3M, FR 3038, ENSICAEN & Université de Caen, 6 boulevard du Maréchal Juin, F-14050 Caen, France
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38
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Chaudret R, Piquemal JP, Cisneros GA. Correlation between electron localization and metal ion mutagenicity in DNA synthesis from QM/MM calculations. Phys Chem Chem Phys 2011; 13:11239-47. [PMID: 21566841 DOI: 10.1039/c0cp02550j] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DNA polymerases require two divalent metal ions in the active site for catalysis. Mg(2+) has been confirmed to be the most probable cation utilized by most polymerases in vivo. Other metal ions are either potent mutagens or inhibitors. We used structural and topological analyses based on ab initio QM/MM calculations to study human DNA polymerase λ (Polλ) with different metals in the active site. Our results indicate a slightly longer O3'-Pα distance (∼3.6 Å) for most inhibitor cations compared to the natural and mutagenic metals (∼3.3-3.4 Å). Optimization with a larger basis set for the previously reported transition state (TS) structures (Cisneros et al., DNA Repair, 2008, 7, 1824.) gives barriers of 17.4 kcal mol(-1) and 15.1 kcal mol(-1) for the Mg(2+) and Mn(2+) catalyzed reactions respectively. Relying on the key relation between the topological signature of a metal cation and its selectivity within biological systems (de Courcy et al., J. Chem. Theor. Comput., 2010, 6, 1048.) we have performed electron localization function (ELF) topological analyses. These analyses show that all inhibitor and mutagenic metals considered, except Na(+), present a "split" of the outer-shell density of the metal. This "splitting" is not observed for the non-mutagenic Mg(2+) metal. Population and multipole analyses on the ELF basins reveal that the electronic dipolar and quadrupolar polarization is significantly different with Mg(2+) compared to all other cations. Our results shed light at the atomic level on the subtle differences between Mg(2+), mutagenic, and inhibitor metals in DNA polymerases. These results provide a correlation between the electronic distribution of the cations in the active site and the possible consequences on DNA synthesis.
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Affiliation(s)
- Robin Chaudret
- UPMC Université Paris 06, UMR 7616 Laboratoire de Chimie Théorique, Paris, France
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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Abdellah I, Lepetit C, Canac Y, Duhayon C, Chauvin R. Imidazoliophosphines are True N-Heterocyclic Carbene (NHC)-Phosphenium Adducts. Chemistry 2010; 16:13095-108. [DOI: 10.1002/chem.201001721] [Citation(s) in RCA: 86] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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Affiliation(s)
- Jorge David
- Escuela de Ciencias y Humanidades, Departamento de Ciencias básicas, Universidad Eafit AA 3300, Medellín, Colombia, and Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - Doris Guerra
- Escuela de Ciencias y Humanidades, Departamento de Ciencias básicas, Universidad Eafit AA 3300, Medellín, Colombia, and Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - C. Z. Hadad
- Escuela de Ciencias y Humanidades, Departamento de Ciencias básicas, Universidad Eafit AA 3300, Medellín, Colombia, and Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - Albeiro Restrepo
- Escuela de Ciencias y Humanidades, Departamento de Ciencias básicas, Universidad Eafit AA 3300, Medellín, Colombia, and Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
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Affiliation(s)
- Patricio Fuentealba
- Departamento de Física, Universidad de Chile, Las Palmeras 3425, Santiago-Chile, Instituto de Química, Universidad de Antioquia, A.A. 1226, Medellín, Colombia, and Departamento de Ciencias Químicas, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Av. República 275, Santiago-Chile
| | - Elizabeth Florez
- Departamento de Física, Universidad de Chile, Las Palmeras 3425, Santiago-Chile, Instituto de Química, Universidad de Antioquia, A.A. 1226, Medellín, Colombia, and Departamento de Ciencias Químicas, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Av. República 275, Santiago-Chile
| | - William Tiznado
- Departamento de Física, Universidad de Chile, Las Palmeras 3425, Santiago-Chile, Instituto de Química, Universidad de Antioquia, A.A. 1226, Medellín, Colombia, and Departamento de Ciencias Químicas, Facultad de Ecología y Recursos Naturales, Universidad Andres Bello, Av. República 275, Santiago-Chile
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Affiliation(s)
- Cinthia Jaramillo
- Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - Doris Guerra
- Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - Luis Fernando Moreno
- Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
| | - Albeiro Restrepo
- Grupo de Química-Física Teórica, Instituto de Química, Universidad de Antioquia, AA 1226 Medellín, Colombia
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de Courcy B, Pedersen LG, Parisel O, Gresh N, Silvi B, Pilmé J, Piquemal JP. Understanding selectivity of hard and soft metal cations within biological systems using the subvalence concept. I. Application to blood coagulation: direct cation-protein electronic effects vs. indirect interactions through water networks. J Chem Theory Comput 2010; 6:1048-1063. [PMID: 20419068 PMCID: PMC2856951 DOI: 10.1021/ct100089s] [Citation(s) in RCA: 52] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Following a previous study by de Courcy et al. ((2009) Interdiscip. Sci. Comput. Life Sci. 1, 55-60), we demonstrate in this contribution, using quantum chemistry, that metal cations exhibit a specific topological signature in the electron localization of their density interacting with ligands according to its "soft" or "hard" character. Introducing the concept of metal cation subvalence, we show that a metal cation can split its outer-shell density (the so-called subvalent domains or basins) according to it capability to form a partly covalent bond involving charge transfer. Such behaviour is investigated by means of several quantum chemical interpretative methods encompasing the topological analysis of the Electron Localization Function (ELF) and Bader's Quantum Theory of Atoms in Molecules (QTAIM) and two energy decomposition analyses (EDA), namely the Restricted Variational Space (RVS) and Constrained Space Orbital Variations (CSOV) approaches. Further rationalization is performed by computing ELF and QTAIM local properties such as electrostatic distributed moments and local chemical descriptors such as condensed Fukui Functions and dual descriptors. These reactivity indexes are computed within the ELF topological analysis in addition to QTAIM offering access to non atomic reactivity local index, for example on lone pairs. We apply this "subvalence" concept to study the cation selectivity in enzymes involved in blood coagulation (GLA domains of three coagulation factors). We show that the calcium ions are clearly able to form partially covalent charge transfer networks between the subdomain of the metal ion and the carboxylate oxygen lone pairs whereas magnesium does not have such ability. Our analysis also explains the different role of two groups (high affinity and low affinity cation binding sites) present in GLA domains. If the presence of Ca(II) is mandatory in the central "high affinity" region to conserve a proper folding and a charge transfer network, external sites are better stabilised by Mg(II), rather than Ca(II), in agreement with experiment. The central role of discrete water molecules is also discussed in order to understand the stabilities of the observed X-rays structures of the Gla domain. Indeed, the presence of explicit water molecules generating indirect cation-protein interactions through water networks is shown to be able to reverse the observed electronic selectivity occuring when cations directly interact with the Gla domain without the need of water.
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Affiliation(s)
- B. de Courcy
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - L. G. Pedersen
- Laboratory of Structural Biology, National Institute of Environmental Health Sciences, Research Triangle Park, North Carolina 27709 (USA)
| | - O. Parisel
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - N. Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45, rue des Saints-Pères, 75006 Paris
| | - B. Silvi
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
| | - J. Pilmé
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- Université de Lyon, Université Lyon 1, Faculté de pharmacie, F-69373Lyon, Cedex 08, France
| | - J.-P. Piquemal
- UPMC Univ Paris 06, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
- CNRS, UMR 7616, Laboratoire de Chimie Théorique, case courrier 137, 4 place Jussieu, F-75005, Paris, France
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Martínez JI, Moncada JL, Larenas JM. The dual descriptor to measure local reactivity on Buckminster fullerenes: an analysis within the framework of conceptual DFT. J Mol Model 2010; 16:1825-32. [PMID: 20217163 DOI: 10.1007/s00894-009-0638-3] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2009] [Accepted: 12/08/2009] [Indexed: 11/27/2022]
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Chamorro E, Pérez P, Duque M, De Proft F, Geerlings P. Dual descriptors within the framework of spin-polarized density functional theory. J Chem Phys 2008; 129:064117. [DOI: 10.1063/1.2965594] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Cárdenas C, De Proft F, Chamorro E, Fuentealba P, Geerlings P. Theoretical study of the surface reactivity of alkaline earth oxides: Local density of states evaluation of the local softness. J Chem Phys 2008; 128:034708. [DOI: 10.1063/1.2819239] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Abstract
Cyanocuprates derived from propargylic amines or ethers react with aldehydes to give regioselectively the corresponding anti-homopropargylic alcohols with a high level of diastereoselectivity. Such selectivity could be obtained independently of the nature of the heteroatom (amine or ethers) or the acetylenic substituents. Excellent selectivities can be reached regardless of the aldehydes used, remarkably also with vinylic or acetylenic ones. A reactivity scale for the cuprates bearing different acetylenic substituents was established to be: SiMe3 >Ph> Et. The rate of the addition reaction to aldehydes was also found to be slowed down in the presence of HMPA underlining the crucial role of the Li counterion. DFT calculations have shown that the relationship between the rate and the acetylenic substituent is not connected to a possible metallotropic equilibrium but to the stability of the reactive allenic species compared to the less-stable propargylic isomer.
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Affiliation(s)
- Emmanuel Vrancken
- Institut Fédératif de Recherche FR 2769, UMR 7611, Université Pierre et Marie Curie, 4 Place Jussieu, F-75252 Paris Cedex, France.
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