1
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Richer M, Heidar-Zadeh F, Ríos-Gutiérrez M, Yang XD, Ayers PW. Spin-Polarized Conceptual Density Functional Theory from the Convex Hull. J Chem Theory Comput 2024; 20:4616-4628. [PMID: 38819213 DOI: 10.1021/acs.jctc.4c00213] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2024]
Abstract
We present a new, nonarbitrary, internally consistent, and unambiguous framework for spin-polarized conceptual density-functional theory (SP-DFT). We explicitly characterize the convex hull of energy, as a function of the number of electrons and their spin, as the only accessible ground states in spin-polarized density functional theory. Then, we construct continuous linear and quadratic models for the energy. The nondifferentiable linear model exactly captures the simplicial geometry of the complex hull about the point of interest and gives exact representations for the conceptual DFT reactivity indicators. The continuous quadratic energy model is the paraboloid of maximum curvature, which most tightly encloses the point of interest and neighboring vertices. The quadratic model is invariant to the choice of coordinate system (i.e., {N, S} vs {Nα, Nβ}) and reduces to a sensible formulation of spin-free conceptual DFT in the appropriate limit. Using the quadratic model, we generalize the Parr functions {P+(r), P-(r)} (and their derivatives with respect to number of electrons) to this new spin-polarized framework, integrating the Parr function concept into the context of (spin-polarized) conceptual DFT, and extending it to include higher-order effects.
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Affiliation(s)
- Michelle Richer
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7L 3N6, Canada
| | - Mar Ríos-Gutiérrez
- Department of Organic Chemistry, University of Valencia, Dr. Moliner 50, 46100 Burjassot, Valencia, Spain
| | - Xiaotian Derrick Yang
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W Ayers
- Department of Chemistry, McMaster University, 1280 Main St. West, Hamilton, Ontario L8S 4M1, Canada
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2
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Oller J, Jaque P. Connection between nuclear and electronic Fukui functions beyond frontier molecular orbitals. J Chem Phys 2023; 159:124112. [PMID: 38127388 DOI: 10.1063/5.0169403] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 09/07/2023] [Indexed: 12/23/2023] Open
Abstract
Based on the relationship between average local ionization energy Ī(r) and average local electron affinity Ā(r) with the electronic Fukui functions, i.e., f-(r) and f+(r), respectively, in this paper, we establish a connection between nuclear and electronic Fukui functions beyond frontier molecular orbitals. As a consequence of this connection, we obtain expressions of average nuclear Fukui functions interpreted as a variation of average nucleophilicity or electrophilicity (weighted by the electronic orbital Fukui functions) with respect to nuclear displacements, which goes beyond the highest occupied molecular orbital/or lowest unoccupied molecular orbital consideration. Furthermore, from this connection and considering the frontier molecular orbital approximation, we derive expressions of nuclear Fukui functions in terms of the atom-condensed electronic Fukui functions, which imply a locality in the chemical reactivity and could be used to study the variation of local nucleophilicity or electrophilicity with respect to nuclear displacements. Finally, this new way to interpret the nuclear Fukui function could be useful in the future to study the chemical reactivity related to molecular vibrations, internal rotations, bond dissociation, chemical reaction along the model of reaction coordinate, and so on.
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Affiliation(s)
- Javier Oller
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, CM2B2, Universidad de Chile, Sergio Livingstone, 1007, Independencia, Santiago, Chile
| | - Pablo Jaque
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Sergio Livingstone 1007, Independencia, Santiago, Chile
- Centro de Modelamiento Molecular, Biofísica y Bioinformática, CM2B2, Universidad de Chile, Sergio Livingstone, 1007, Independencia, Santiago, Chile
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3
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Zhang Y, Zhao J. A density fitting scheme for the fast evaluation of molecular electrostatic potential. J Comput Chem 2023; 44:806-813. [PMID: 36411980 DOI: 10.1002/jcc.27042] [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: 09/22/2022] [Revised: 11/01/2022] [Accepted: 11/03/2022] [Indexed: 11/23/2022]
Abstract
Molecular electrostatic potential (MEP) is a significant and crucial physical quantity that can be applied to a large number of scenarios, such as the prediction of nucleophilic or electrophilic attacks, fitting atomic charges, σ-hole, and so forth. The computational cost for the MEP has an O(N2 ) scaling with the increase of atoms, which is intractable and laborious for macromolecules. Herein, a density fitting molecular electrostatic potential (DF-MEP) is used to reduce the computational costs for the macromolecular MEP. It is found that the accuracy of DF-MEP is almost identical to the conventional molecular electrostatic potential (Conv-MEP), while the computational costs can be reduced to an O(N) scaling, for example, the computational time of 699,200 grids for the Trp-cage molecule (304 atoms) only takes 16.6 s at the B3LYP-D3(BJ)/def2-SVP level of theory with 16 CPU cores compared with 3060.2 s for the Conv-MEP method.
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Affiliation(s)
- Yingfeng Zhang
- Key Laboratory of Magnetic Resonance in Biological Systems, State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics, Wuhan Institute of Physics and Mathematics, Innovation Academy of Precision Measurement Science and Technology, Chinese Academy of Sciences, Wuhan, China.,University of Chinese Academy of Sciences, Beijing, China
| | - Jian Zhao
- State Key Laboratory of Catalysis, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, China
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4
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Fias S, Ayers PW, De Proft F, Geerlings P. Properties of the density functional response kernels and its implications on chemistry. J Chem Phys 2022; 157:114102. [PMID: 36137804 DOI: 10.1063/5.0094653] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
An overview of mathematical properties of the non-local second order derivatives of the canonical, grand canonical, isomorphic, and grand isomorphic ensembles is given. The significance of their positive or negative semidefiniteness and the implications of these properties for atoms and molecules are discussed. Based on this property, many other interesting properties can be derived, such as the expansion in eigenfunctions, bounds on the diagonal and off-diagonal elements, and the eigenvalues of these kernels. We also prove Kato's theorem for the softness kernel and linear response and the dissociation limit of the linear responses as the sum of the linear responses of the individual fragments when dissociating a system into two non-interacting molecular fragments. Finally, strategies for the practical calculation of these kernels, their eigenfunctions, and their eigenvalues are discussed.
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Affiliation(s)
- Stijn Fias
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Paul W Ayers
- McMaster University, 1280 Main St. W, Hamilton, Ontario L8S 4L8, Canada
| | - Frank De Proft
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
| | - Paul Geerlings
- Research Group of General Chemistry (ALGC), Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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5
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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: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [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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6
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Kaya S, Robles-Navarro A, Mejía E, Gómez T, Cardenas C. On the Prediction of Lattice Energy with the Fukui Potential: Some Supports on Hardness Maximization in Inorganic Solids. J Phys Chem A 2022; 126:4507-4516. [PMID: 35766899 PMCID: PMC9289887 DOI: 10.1021/acs.jpca.1c09898] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Using perturbation theory within the framework of conceptual density functional theory, we derive a lower bound for the lattice energy of the ionic solids. The main element of the lower bound is the Fukui potential in the nuclei of the molecule corresponding to the unit formula of the solid. Thus, we propose a model to calculate the lattice energy in terms of the Fukui potential. Our method, which is extremely simple, performs well as other methods using the crystal structure information of alkali halide solids. The method proposed here correlates surprisingly well with the experimental data on the lattice energy of a diverse series of solids having even a non-negligible covalent characteristic. Finally, the validity of the maximum hardness principle (MHP) is assessed, showing that in this case, the MHP is limited.
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Affiliation(s)
- Savaş Kaya
- Health Services Vocational School, Department of Pharmacy, Sivas Cumhuriyet University, Sivas58140, Turkey
| | - Andrés Robles-Navarro
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla653, Chile
| | - Erica Mejía
- Facultad de Ingeniería-(Medellin-Colombia), Institución Universitaria Pascual Bravo, Medellín050025, Colombia
| | - Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago9170124, Chile
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla653, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Santiago9170124, Chile
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7
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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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8
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Robles-Navarro A, Cárdenas C, Fuentealba P. Electronegativity under Confinement. Molecules 2021; 26:molecules26226924. [PMID: 34834015 PMCID: PMC8620044 DOI: 10.3390/molecules26226924] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 09/29/2021] [Accepted: 11/10/2021] [Indexed: 11/16/2022] Open
Abstract
The electronegativity concept was first formulated by Pauling in the first half of the 20th century to explain quantitatively the properties of chemical bonds between different types of atoms. Today, it is widely known that, in high-pressure regimes, the reactivity properties of atoms can change, and, thus, the bond patterns in molecules and solids are affected. In this work, we studied the effects of high pressure modeled by a confining potential on different definitions of electronegativity and, additionally, tested the accuracy of first-order perturbation theory in the context of density functional theory for confined atoms of the second row at the Hartree–Fock level. As expected, the electronegativity of atoms at high confinement is very different than that of their free counterparts since it depends on the electronic configuration of the atom, and, thus, its periodicity is modified at higher pressures.
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Affiliation(s)
- Andrés Robles-Navarro
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
| | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Estación Central, Santiago 9170124, Chile
- Correspondence: (C.C.); (P.F.)
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Santiago 7800003, Chile;
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Estación Central, Santiago 9170124, Chile
- Correspondence: (C.C.); (P.F.)
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9
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Moulandou-Koumba RD, Doggui MY, N'Sikabaka S, Ouamba JM, Arfaoui Y, Frapper G, Guégan F. Proposal of a Fermi-Dirac-Derived Reactivity Descriptor: Beyond the Frontier MO Model. J Phys Chem A 2021; 125:8090-8097. [PMID: 34473520 DOI: 10.1021/acs.jpca.1c04415] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
In this paper, we derive a reactivity descriptor stemming from the Fermi-Dirac population scheme, applied to density functional calculations on molecular systems. Assuming that molecular orbitals only marginally change when temperature is slightly increased from 0 K, we study the response of electron density to a change in temperature. Connection with usual conceptual density functional theory descriptors is made, and the T-variation of electron density for some representative examples is given and discussed.
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Affiliation(s)
- R D Moulandou-Koumba
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - M Y Doggui
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France.,Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - S N'Sikabaka
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - J-M Ouamba
- Université Marien NGOUABI, Faculté des Sciences et Techniques, Unité de Chimie du Végétal et de la Vie, BP 69 Brazzaville, Congo
| | - Y Arfaoui
- Laboratory of Characterizations, Applications & Modeling of Materials (LR18ES08), Department of Chemistry, Faculty of Sciences, University of Tunis El Manar, 2092 Tunis, Tunisia
| | - G Frapper
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
| | - F Guégan
- IC2MP UMR 7285, Université de Poitiers-CNRS, 4, rue Michel Brunet, TSA 51106, 86073 Cedex 9 Poitiers, France
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10
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Gómez T, Fuentealba P, Robles-Navarro A, Cárdenas C. Links among the Fukui potential, the alchemical hardness and the local hardness of an atom in a molecule. J Comput Chem 2021; 42:1681-1688. [PMID: 34121207 DOI: 10.1002/jcc.26705] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Revised: 05/24/2021] [Accepted: 05/31/2021] [Indexed: 02/01/2023]
Abstract
This paper presents a brief summary of the difficulty that resides in the definition of the elusive concept of local chemical hardness. We argue that a definition of local hardness should be useful to a reactivity principle and not just as a mere definition. We then continue with a formal discussion about the benefits and difficulties of using the Fukui potential, which is interpreted as an alchemical derivative (alchemical hardness), as descriptor of local hardness of molecules. Computational evidence shows that the alchemical hardness is at least as good a descriptor as the combination of other two well-stabilized descriptors of local hardness, such as the Fukui function and grand canonical local hardness. Although our results are auspicious for the alchemical hardness as descriptor of local hardness, we finish by calling the attention of the community on the importance of discussing the raison d'être of a local hardness function and its main characteristics. We suggest that an axiomatic construction of local hardness could be they way of constructing a local hardness which is both useful and free of arbitrariness.
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Affiliation(s)
- Tatiana Gómez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, Santiago, Chile
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago, Chile
| | | | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Santiago, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Santiago, Chile
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11
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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] [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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12
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Kenouche S, Belkadi A, Djebaili R, Melkemi N. High regioselectivity in the amination reaction of isoquinolinequinone derivatives using conceptual DFT and NCI analysis. J Mol Graph Model 2021; 104:107828. [PMID: 33444977 DOI: 10.1016/j.jmgm.2020.107828] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Revised: 12/17/2020] [Accepted: 12/21/2020] [Indexed: 11/27/2022]
Abstract
DFT-derived reactivity descriptors and Non-Covalent interaction (NCI) analysis were performed to rationalize the regioselectivity in the amination reaction of some isoquinolinequinone derivatives. Statistical analysis was performed to assess robustness of atomic charges to the basis set. Various electronic population schemes including Mulliken population analysis (MPA), electrostatic method (ChelpG), Hirshfeld population analysis (HPA) and Natural population analysis (NPA) have been considered. The results revealed that NPA was the most efficient for this purpose. NCI study using the reduced density gradient (RDG) was performed for revealing weak interactions. Domains defined by isosurfaces of RDG have been integrated to quantitatively study the strength of weak interactions and their stabilities have also been examined. Steric hindrance caused by coordination of ethanol with the neighboring carbonyl prevents the nucleophilic attack on C-6 and therefore leads to preferential C-7 substitution. The quantitative study of NCI clearly demonstrates that the hydrogen bond of carbonyl (2) is more stabilizing. Consequently, the high polarity of hydrogen bond on this carbonyl may explain the high electrophilicity of C-5 compared to C-8. Our work proved that the difference in local reactivity, as well as the steric hindrance are the key elements explaining the high regioselectivity exhibited by the amination reaction.
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Affiliation(s)
- S Kenouche
- Research Team: Modeling of Chemical Systems Using Quantum Calculations, LCA Laboratory, University Mohamed Khider of Biskra, 07000, Biskra, Algeria.
| | - A Belkadi
- Research Team: Computational and Pharmaceutical Chemistry, LMCE Laboratory, University Mohamed Khider of Biskra, 07000, Biskra, Algeria
| | - R Djebaili
- Research Team: Computational and Pharmaceutical Chemistry, LMCE Laboratory, University Mohamed Khider of Biskra, 07000, Biskra, Algeria
| | - N Melkemi
- Research Team: Computational and Pharmaceutical Chemistry, LMCE Laboratory, University Mohamed Khider of Biskra, 07000, Biskra, Algeria
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13
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Stuyver T, Shaik S. Unifying Conceptual Density Functional and Valence Bond Theory: The Hardness-Softness Conundrum Associated with Protonation Reactions and Uncovering Complementary Reactivity Modes. J Am Chem Soc 2020; 142:20002-20013. [PMID: 33180491 PMCID: PMC7735708 DOI: 10.1021/jacs.0c09041] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
In this study, we address the long-standing issue-arising prominently from conceptual density functional theory (CDFT)-of the relative importance of electrostatic, i.e., "hard-hard", versus spin-pairing, i.e., "soft-soft", interactions in determining regiochemical preferences. We do so from a valence bond (VB) perspective and demonstrate that VB theory readily enables a clear-cut resolution of both of these contributions to the bond formation/breaking process. Our calculations indicate that appropriate local reactivity descriptors can be used to gauge the magnitude of both interactions individually, e.g., Fukui functions or HOMO/LUMO orbitals for the spin-pairing/(frontier) orbital interactions and molecular electrostatic potentials (and/or partial charges) for the electrostatic interactions. In contrast to previous reports, we find that protonation reactions cannot generally be classified as either charge- or frontier orbital-controlled; instead, our results indicate that these two bonding contributions generally interplay in more subtle patterns, only giving the impression of a clear-cut dichotomy. Finally, we demonstrate that important covalent, i.e., spin pairing, reactivity modes can be missed when only a single spin-pairing/orbital interaction descriptor is considered. This study constitutes an important step in the unification of CDFT and VB theory.
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Affiliation(s)
- Thijs Stuyver
- Institute of Chemistry, Edmond J. Safara Campus at Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
| | - Sason Shaik
- Institute of Chemistry, Edmond J. Safara Campus at Givat Ram, The Hebrew University, Jerusalem 9190401, Israel
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14
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Muñoz M, Robles-Navarro A, Fuentealba P, Cárdenas C. Predicting Deprotonation Sites Using Alchemical Derivatives. J Phys Chem A 2020; 124:3754-3760. [PMID: 32286831 DOI: 10.1021/acs.jpca.9b09472] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
An alchemical transformation is any process, physical or fictitious, that connects two points in the chemical space. A particularly important transformation is the vanishing of a proton, whose energy can be linked to the proton dissociation enthalpy of acids. In this work we assess the reliability of alchemical derivatives in predicting the proton dissociation enthalpy of a diverse series of mono- and polyprotic molecules. Alchemical derivatives perform remarkably well in ranking the proton affinity of all molecules. Additionally, alchemical derivatives could be use also as a predictive tool because their predictions correlate quite well with calculations based on energy differences and experimental values. Although second-order alchemical derivatives underestimate the dissociation enthalpy, the deviation seems to be almost constant. This makes alchemical derivatives extremely accurate to evaluate the difference in proton affinity between two acid sites of polyprotic molecule. Finally, we show that the reason for the underestimation of the dissociation enthalpy is most likely the contribution of higher-order derivatives.
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Affiliation(s)
- Macarena Muñoz
- Facultad de Ingenierı́a y Ciencias, Universidad Adolfo Ibañez, Diagonal Las Torres 2640, Santiago 7941169, Chile
| | - Andrés Robles-Navarro
- Departamento de Fı́sica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnologı́a (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
| | - Patricio Fuentealba
- Departamento de Fı́sica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnologı́a (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
| | - Carlos Cárdenas
- Departamento de Fı́sica, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Santiago Casilla 653, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnologı́a (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
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15
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Cerón ML, Gomez T, Calatayud M, Cárdenas C. Computing the Fukui Function in Solid-State Chemistry: Application to Alkaline Earth Oxides Bulk and Surfaces. J Phys Chem A 2020; 124:2826-2833. [DOI: 10.1021/acs.jpca.0c00950] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- M. L. Cerón
- Facultad de Ingenierı́a, Universidad Finis Terrae, Av. Pedro de Valdivia 1509, Providencia, Santiago, Chile
| | - T. Gomez
- Theoretical and Computational Chemistry Center, Institute of Applied Chemical Sciences, Faculty of Engineering, Universidad Autonoma de Chile, El Llano Subercaseaux 2801, Santiago, Chile
| | - M. Calatayud
- Sorbonne Université, CNRS, Laboratoire de Chimie Théorique, LCT, F. 75005 Paris, France
| | - C. Cárdenas
- Departamento de Fı́sica, Facultad de Ciencias, Universidad de Chile, Casilla 635, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnologı́a (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
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16
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Geerlings P, Chamorro E, Chattaraj PK, De Proft F, Gázquez JL, Liu S, Morell C, Toro-Labbé A, Vela A, Ayers P. Conceptual density functional theory: status, prospects, issues. Theor Chem Acc 2020. [DOI: 10.1007/s00214-020-2546-7] [Citation(s) in RCA: 77] [Impact Index Per Article: 19.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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17
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Abstract
The interaction between a Lewis base and a proton produces large changes in the electron distribution of the proton-accepting species. The quantum description of the change in the electronic properties can be predicted by perturbative models. Density functional theory-based reactivity indices are useful quantities to predict the changes in the energy and the electron density of electronic systems. However, the perturbation produced by the proton, namely, the electric field of a bare nucleus, usually leads to the use of perturbative terms beyond the first order. In this work, we analyze the effect of the protonation on the electronic structure of different Lewis bases. We also identify the leading term in the perturbative expansion that determines the protonation site and try to relate it with the chemical nature of the Lewis base. Even when the interaction is initially dominated by the electrostatic forces, we found that the electron redistribution effects can play a more relevant role for highly polarizable species.
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Affiliation(s)
- Andrés Cedillo
- Departamento de Química , Universidad Autónoma Metropolitana-Iztapalapa , San Rafael Atlixco 186 , Ciudad de México , DF 09340 , México
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18
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Pino-Rios R, Inostroza D, Cárdenas-Jirón G, Tiznado W. Orbital-Weighted Dual Descriptor for the Study of Local Reactivity of Systems with (Quasi-) Degenerate States. J Phys Chem A 2019; 123:10556-10562. [PMID: 31710492 DOI: 10.1021/acs.jpca.9b07516] [Citation(s) in RCA: 56] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
An alternative response function, based on the dual descriptor in terms of Koopmans' approximation, is hereby proposed for the description of chemical reactivity in systems with (quasi-) degenerate frontier molecular orbitals. This descriptor is constructed from Fukui functions that include contributions from different orbitals, i.e., orbital-weighted Fukui functions. The methodology is applied to three case studies: the first case consists of a series of benchmark organic and inorganic molecules from which the dual descriptor, based only on frontier orbitals, is not appropriate to describe their reactivity. The second case deals with the proper description of chemical reactivity in Diels-Alder reactions between fullerene C60 and cyclopentadiene (CP), revealing the importance of considering secondary orbital interactions for an adequate regioselectivity description. The third, and last case, consists of a series of polycyclic aromatic hydrocarbons (PAHs) possessing molecular orbital degeneracy. By means of analyzing of this descriptor, an alternative approach to the description of aromaticity is proposed. In all cases, the proposed index called "orbital-weighted dual descriptor" has proven to accurately describe the chemical reactivity and aromaticity of the studied systems.
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Affiliation(s)
- Ricardo Pino-Rios
- Laboratorio de Quı́mica Teórica, Facultad de Quı́mica y Biologı́a , Universidad de Santiago de Chile (USACH) Av. Libertador Bernardo O'Higgins 3363 , Santiago , Estación Central, Región Metropolitana 9170022 , Chile
| | - Diego Inostroza
- Doctorado en Fisicoquı́mica Molecular. Facultad de Ciencias Exactas , Universidad Andres Bello (UNAB) , Av. República 275 , Santiago , Región Metropolitana 8370146 , Chile
| | - Gloria Cárdenas-Jirón
- Laboratorio de Quı́mica Teórica, Facultad de Quı́mica y Biologı́a , Universidad de Santiago de Chile (USACH) Av. Libertador Bernardo O'Higgins 3363 , Santiago , Estación Central, Región Metropolitana 9170022 , Chile
| | - William Tiznado
- Computational and Theoretical Chemistry Group, Departamento de Ciencias Quı́micas, Facultad de Ciencias Exactas , Universidad Andres Bello , Av. República 498 , Santiago , Región Metropolitana 8370251 , Chile
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19
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Cedillo A, Cárdenas C. Reactivity of Carbon Molecular Clusters from a Hückel-Type Model. J Phys Chem A 2019; 123:8696-8701. [DOI: 10.1021/acs.jpca.9b07934] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Andrés Cedillo
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, San Rafael Atlixco 186, México City, Distrito Federal 09340, México
| | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Las Palmeras 3425, Ñuñoa, Casilla 653, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Santiago, 9170124, Chile
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20
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Sánchez-Márquez J. New advances in conceptual-DFT: an alternative way to calculate the Fukui function and dual descriptor. J Mol Model 2019; 25:123. [PMID: 31020412 DOI: 10.1007/s00894-019-4000-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2018] [Accepted: 03/21/2019] [Indexed: 10/26/2022]
Abstract
An alternative way of calculating the Fukui function and the partial derivative of second order of the electronic density with respect to the number of electrons N is presented, the new formulas agree with the usual ones but only in cases without degeneracy. The new operative formulas are more general than the previous ones and are the right ones for those problematic cases where one or both of the frontier molecular orbitals are degenerate. Finally, we present a new way of applying the finite difference approximation that leads to more realistic results than the usual formulas. Graphical abstract A new way of calculating the Fukui function is presented that results in a new operative formula of the function. It has also been obtained the partial derivative of second order of the electronic density with respect to the number of electrons N, and it agree with the usual formula of the dual descriptor function but only in cases without degeneration.
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Affiliation(s)
- Jesús Sánchez-Márquez
- Departamento de Química-Física, Facultad de Ciencias, Campus Universitario Río San Pedro, Universidad de Cádiz, 11510, Puerto Real, Cádiz, Spain.
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21
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Roos G, Miranda-Quintana RA, Martínez González M. How Biochemical Environments Fine-Tune a Redox Process: From Theoretical Models to Practical Applications. J Phys Chem B 2018; 122:8157-8165. [PMID: 30040409 DOI: 10.1021/acs.jpcb.8b04736] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
In this study, we give a new physical insight into how enzymatic environments influence a redox process. This is particularly important in a biochemical context, in which oxidoreductase enzymes and low-molecular-weight cofactors create a microenvironment, fine-tuning their specific redox potential. We present a new theoretical model, quantitatively backed up by quantum chemically calculated data obtained for key biological sulfur-based model reactions involved in preserving the cellular redox homeostasis during oxidative stress. We show that environmental effects can be quantitatively predicted from the thermodynamic cycle linking ΔΔ G(OX/RED)ref-ligand values to the differential interaction energy ΔΔ Gint of the reduced and oxidized species with the environment. Our obtained data can be linked to hydrogen-bond patterns found in protein active sites. The thermodynamic model is further understood in the framework of molecular orbital theory. The key insight of this work is that the intrinsic properties of neither a redox couple nor the interacting environment (e.g., ligand) are enough by themselves to uniquely predict reduction potentials. Instead, system-environment interactions need to be considered. This study is of general interest as redox processes are pivotal to empower, protect, or damage organisms. Our presented thermodynamic model allows a pragmatically evaluation on the expected influence of a particular environment on a redox process, necessary to fully understand how redox processes take place in living organisms.
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Affiliation(s)
- Goedele Roos
- CNRS UMR 8576, Unité de Glycobiologie Structurale et Fonctionnelle (UGSF) , Université de Lille , 1 Sciences et Technologies 50 Avenue de Halley BP 70478, 59658 Villeneuve d'Ascq Cedex, France
| | | | - Marco Martínez González
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry , University of Havana , 10400 Havana , Cuba.,Departamento de Química, y Centro de Química , Universidade de Coimbra , 3004-535 Coimbra , Portugal
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22
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Cárdenas C, Heidar-Zadeh F, Ayers PW. Benchmark values of chemical potential and chemical hardness for atoms and atomic ions (including unstable anions) from the energies of isoelectronic series. Phys Chem Chem Phys 2018; 18:25721-25734. [PMID: 27711480 DOI: 10.1039/c6cp04533b] [Citation(s) in RCA: 43] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present benchmark values for the electronic chemical potential and chemical hardness from reference data for ionization potentials and electron affinities. In cases where the energies needed to compute these quantities are not available, we estimate the ionization potential of the metastable (di)anions by extrapolation along the isoelectronic series, taking care to ensure that the extrapolated data satisfy reasonable intuitive rules to the maximum possible extent. We also propose suitable values for the chemical potential and chemical hardness of zero-electron species. Because the values we report are faithful to the trends in accurate data on atomic energies, we believe that our proposed values for the chemical potential and chemical hardness are ideally suited to conceptual studies of chemical trends across the periodic table. The critical nuclear charge (Z critical) of the isoelectronic series with 2 < N < 96 has also been reported for the first time.
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Affiliation(s)
- Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago 7800024, Chile. and Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
| | - Farnaz Heidar-Zadeh
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada and Department of Inorganic & Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium and Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Paul W Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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23
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Fias S, Heidar-Zadeh F, Anderson JSM, Ayers PW, Parr RG. A reference-free stockholder partitioning method based on the force on electrons. J Comput Chem 2017; 39:1044-1050. [DOI: 10.1002/jcc.25114] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2017] [Revised: 09/14/2017] [Accepted: 10/06/2017] [Indexed: 11/08/2022]
Affiliation(s)
- Stijn Fias
- Department of Chemistry & Chemical Biology; McMaster University; Hamilton Ontario Canada L8S 4M1
| | - Farnaz Heidar-Zadeh
- Department of Chemistry & Chemical Biology; McMaster University; Hamilton Ontario Canada L8S 4M1
- Center for Molecular Modeling; Ghent University, Technologiepark 903; 9052 Zwijnaarde Belgium
- Department of Inorganic and Physical Chemistry; Ghent University, Krijgslaan 281 (S3); 9000 Gent Belgium
| | | | - Paul W. Ayers
- Department of Chemistry & Chemical Biology; McMaster University; Hamilton Ontario Canada L8S 4M1
| | - Robert G. Parr
- Department of Chemistry; University of North Carolina; Chapel Hill NC USA 27599
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24
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Heidar-Zadeh F, Ayers PW, Verstraelen T, Vinogradov I, Vöhringer-Martinez E, Bultinck P. Information-Theoretic Approaches to Atoms-in-Molecules: Hirshfeld Family of Partitioning Schemes. J Phys Chem A 2017; 122:4219-4245. [DOI: 10.1021/acs.jpca.7b08966] [Citation(s) in RCA: 68] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Farnaz Heidar-Zadeh
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
- Department of Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Toon Verstraelen
- Center for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Ivan Vinogradov
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Patrick Bultinck
- Department of Chemistry, Ghent University, Krijgslaan 281 (S3), 9000 Gent, Belgium
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25
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Franco-Pérez M, Ayers PW, Gázquez JL, Vela A. Thermodynamic responses of electronic systems. J Chem Phys 2017; 147:094105. [DOI: 10.1063/1.4999761] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marco Franco-Pérez
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Paul W. Ayers
- Department of Chemistry, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - José L. Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, Ciudad de México 09340, Mexico
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados, Av. Instituto Politécnico Nacional 2508, Ciudad de México 07360, Mexico
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26
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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] [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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27
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Analysis of molecular and (di)atomic dual-descriptor functions and matrices. J Mol Model 2017; 23:185. [PMID: 28493204 DOI: 10.1007/s00894-017-3334-8] [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: 11/16/2016] [Accepted: 03/27/2017] [Indexed: 10/19/2022]
Abstract
In this work, the dual-descriptor is studied in matrix form [Formula: see text] and both coordinates condensed to atoms, resulting in atomic and diatomic (or where applicable, bond) condensed single values. This double partitioning method of the dual-descriptor matrix is proposed within the Hirshfeld-I atoms-in-molecule framework although it is easily extended to other atoms-in-molecules methods. Diagonalizing the resulting atomic and bond dual-descriptor matrices gives eigenvalues and eigenvectors describing the reactivity of atoms and bonds. The dual-descriptor function is the diagonal element of the underlying matrix. The extra information contained in the atom and bond resolution is highlighted and the effect of choosing either the fragment of molecular response or response of molecular fragment approach is quantified. Graphical Abstract Atom and bond condensed dual descriptor matrices and functions are derived from molecular ones using Hirshfeld-I atoms in molecules weight functions.
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28
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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] [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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29
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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] [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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30
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Franco-Pérez M, Heidar-Zadeh F, Ayers PW, Gázquez JL, Vela A. Going beyond the three-state ensemble model: the electronic chemical potential and Fukui function for the general case. Phys Chem Chem Phys 2017; 19:11588-11602. [DOI: 10.1039/c7cp00224f] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The analytical working equations for the chemical potential and the Fukui function for the case of any number of ground and excited states is presented.
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Affiliation(s)
- Marco Franco-Pérez
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
- Departamento de Química
| | - Farnaz Heidar-Zadeh
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
- Department of Inorganic and Physical Chemistry
| | - Paul W. Ayers
- Department of Chemistry
- McMaster University
- Hamilton
- Canada
| | - José L. Gázquez
- Departamento de Química
- División de Ciencias Básicas e Ingeniería
- Universidad Autónoma
- Metropolitana-Iztapalapa
- México
| | - Alberto Vela
- Centro de Investigación y de Estudios Avanzados
- Mexico
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31
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Heidar-Zadeh F, Miranda-Quintana RA, Verstraelen T, Bultinck P, Ayers PW. When is the Fukui Function Not Normalized? The Danger of Inconsistent Energy Interpolation Models in Density Functional Theory. J Chem Theory Comput 2016; 12:5777-5787. [DOI: 10.1021/acs.jctc.6b00494] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Farnaz Heidar-Zadeh
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, L8S 4M1 Ontario, Canada
- Department
of Inorganic and Physical Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Gent, Belgium
- Center
for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Ramón Alain Miranda-Quintana
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, L8S 4M1 Ontario, Canada
- Laboratory
of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Havana, Cuba
| | - Toon Verstraelen
- Center
for Molecular Modeling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Patrick Bultinck
- Department
of Inorganic and Physical Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Gent, Belgium
| | - Paul W. Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, L8S 4M1 Ontario, Canada
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32
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Kudur Jayaprakash G, Casillas N, Astudillo-Sánchez PD, Flores-Moreno R. Role of Defects on Regioselectivity of Nano Pristine Graphene. J Phys Chem A 2016; 120:9101-9108. [PMID: 27797503 DOI: 10.1021/acs.jpca.6b08810] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Gururaj Kudur Jayaprakash
- Departamento
de Ingeniería de Proyectos, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad de Guadalajara, Boulevard Marcelino García
Barragán 1421, Guadalajara, Jalisco, C.P. 44430, Mexico
| | - Norberto Casillas
- Departamento
de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad Guadalajara, Boulevard Marcelino García
Barragán 1421, Guadalajara, Jalisco, C.P. 44430, Mexico
| | - Pablo D. Astudillo-Sánchez
- Departamento
de Ingenierías, Centro Universitario de Tonalá, Universidad Guadalajara, Av. Nuevo Periférico No. 555, Ejido San
José Tatepozco, Tonalá, Jalisco, C.P. 48525, Mexico
| | - Roberto Flores-Moreno
- Departamento
de Química, Centro Universitario de Ciencias Exactas e Ingenierías, Universidad Guadalajara, Boulevard Marcelino García
Barragán 1421, Guadalajara, Jalisco, C.P. 44430, Mexico
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33
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Oña OB, De Clercq O, Alcoba DR, Torre A, Lain L, Van Neck D, Bultinck P. Atom and Bond Fukui Functions and Matrices: A Hirshfeld-I Atoms-in-Molecule Approach. Chemphyschem 2016; 17:2881-9. [PMID: 27381271 DOI: 10.1002/cphc.201600433] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Indexed: 11/09/2022]
Abstract
The Fukui function is often used in its atom-condensed form by isolating it from the molecular Fukui function using a chosen weight function for the atom in the molecule. Recently, Fukui functions and matrices for both atoms and bonds separately were introduced for semiempirical and ab initio levels of theory using Hückel and Mulliken atoms-in-molecule models. In this work, a double partitioning method of the Fukui matrix is proposed within the Hirshfeld-I atoms-in-molecule framework. Diagonalizing the resulting atomic and bond matrices gives eigenvalues and eigenvectors (Fukui orbitals) describing the reactivity of atoms and bonds. The Fukui function is the diagonal element of the Fukui matrix and may be resolved in atom and bond contributions. The extra information contained in the atom and bond resolution of the Fukui matrices and functions is highlighted. The effect of the choice of weight function arising from the Hirshfeld-I approach to obtain atom- and bond-condensed Fukui functions is studied. A comparison of the results with those generated by using the Mulliken atoms-in-molecule approach shows low correlation between the two partitioning schemes.
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Affiliation(s)
- Ofelia B Oña
- Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas, Universidad Nacional de la Plata, CCT La Plata, Consejo Nacional de Investigaciones Científicas y Técnicas, Diag. 113 y 64 (s/n), Sucursal 4, CC 16, 1900, La Plata, Argentina
| | - Olivier De Clercq
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000, Gent, Belgium
| | - Diego R Alcoba
- Departamento de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, 1428 Buenos Aires (Argentina), Instituto de Física de Buenos Aires, Consejo Nacional de Investigaciones Científicas y Técnicas, Ciudad Universitaria, 1428 Buenos, Aires, Argentina
| | - Alicia Torre
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080, Bilbao, Spain
| | - Luis Lain
- Departamento de Química Física, Facultad de Ciencia y Tecnología, Universidad del País Vasco, Apdo. 644, E-48080, Bilbao, Spain
| | - Dimitri Van Neck
- Center for Molecular Modeling, Ghent University, Technologiepark 903, B-9052, Zwijnaarde, Belgium
| | - Patrick Bultinck
- Department of Inorganic and Physical Chemistry, Ghent University, Krijgslaan 281 (S3), 9000, Gent, Belgium.
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34
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35
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A generalized operational formula based on total electronic densities to obtain 3D pictures of the dual descriptor to reveal nucleophilic and electrophilic sites accurately on closed-shell molecules. J Comput Chem 2016; 37:2279-303. [DOI: 10.1002/jcc.24453] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2016] [Revised: 06/20/2016] [Accepted: 06/27/2016] [Indexed: 11/07/2022]
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36
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Miranda-Quintana RA, Ayers PW. Interpolation of property-values between electron numbers is inconsistent with ensemble averaging. J Chem Phys 2016; 144:244112. [DOI: 10.1063/1.4953557] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ramón Alain Miranda-Quintana
- Laboratory of Computational and Theoretical Chemistry, Faculty of Chemistry, University of Havana, Havana, Cuba
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
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37
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38
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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] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2015] [Accepted: 01/07/2016] [Indexed: 11/29/2022]
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39
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Franco-Pérez M, Ayers PW, Gázquez JL, Vela A. Local and linear chemical reactivity response functions at finite temperature in density functional theory. J Chem Phys 2015; 143:244117. [DOI: 10.1063/1.4938422] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Marco Franco-Pérez
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340, Mexico
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4M1, Canada
| | - José L. Gázquez
- Departamento de Química, Universidad Autónoma Metropolitana-Iztapalapa, Av. San Rafael Atlixco 186, México, D.F. 09340, Mexico
| | - Alberto Vela
- Departamento de Química, Centro de Investigación y de Estudios Avanzados (Cinvestav), Av. Instituto Politécnico Nacional 2508, México, D.F. 07360, Mexico
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40
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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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41
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Verstraelen T, Vandenbrande S, Ayers PW. Direct computation of parameters for accurate polarizable force fields. J Chem Phys 2015; 141:194114. [PMID: 25416881 DOI: 10.1063/1.4901513] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
We present an improved electronic linear response model to incorporate polarization and charge-transfer effects in polarizable force fields. This model is a generalization of the Atom-Condensed Kohn-Sham Density Functional Theory (DFT), approximated to second order (ACKS2): it can now be defined with any underlying variational theory (next to KS-DFT) and it can include atomic multipoles and off-center basis functions. Parameters in this model are computed efficiently as expectation values of an electronic wavefunction, obviating the need for their calibration, regularization, and manual tuning. In the limit of a complete density and potential basis set in the ACKS2 model, the linear response properties of the underlying theory for a given molecular geometry are reproduced exactly. A numerical validation with a test set of 110 molecules shows that very accurate models can already be obtained with fluctuating charges and dipoles. These features greatly facilitate the development of polarizable force fields.
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Affiliation(s)
- Toon Verstraelen
- Center for Molecular Modeling (CMM), Member of the QCMM Ghent-Brussels Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Steven Vandenbrande
- Center for Molecular Modeling (CMM), Member of the QCMM Ghent-Brussels Alliance, Ghent University, Technologiepark 903, B9000 Ghent, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, 1280 Main Street West, Hamilton, Ontario L8S 4M1, Canada
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42
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A problematic issue for atoms in molecules: Impact of (quasi-)degenerate states on Quantum Theory Atoms in Molecules and Hirshfeld-I properties. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.06.017] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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43
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Resolving the nature of the reactive sites of phenylsulfinate ( PhSO2-) with a single general-purpose reactivity indicator. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.04.032] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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44
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Levy M, Anderson JSM, Zadeh FH, Ayers PW. Kinetic and electron-electron energies for convex sums of ground state densities with degeneracies and fractional electron number. J Chem Phys 2014; 140:18A538. [DOI: 10.1063/1.4871734] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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45
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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] [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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46
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Bultinck P, Cardenas C, Fuentealba P, Johnson PA, Ayers PW. How to Compute the Fukui Matrix and Function for Systems with (Quasi-)Degenerate States. J Chem Theory Comput 2013; 10:202-10. [DOI: 10.1021/ct400874d] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick Bultinck
- Ghent University, Department of Inorganic and Physical Chemistry, Krijgslaan 281 (S3), 9000 Gent, Belgium
| | - Carlos Cardenas
- Departamento
de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile and 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, Casilla 653, Santiago, Chile and Centro para el desarrollo de la
Nanociencias y Nanotecnologia, CEDENNA,
Av. Ecuador 3493, Santiago, Chile
| | - Paul A. Johnson
- Dept. of Chemistry and Chemical Biology, McMaster University, Hamilton ON Canada L8S 4M1
| | - Paul W. Ayers
- Dept. of Chemistry and Chemical Biology, McMaster University, Hamilton ON Canada L8S 4M1
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47
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Bultinck P, Cardenas C, Fuentealba P, Johnson PA, Ayers PW. Atomic Charges and the Electrostatic Potential Are Ill-Defined in Degenerate Ground States. J Chem Theory Comput 2013; 9:4779-88. [DOI: 10.1021/ct4005454] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Patrick Bultinck
- Department
of Inorganic and Physical Chemistry, Ghent University, Krijgslaan
281 (S3), 9000 Gent, Belgium
| | - Carlos Cardenas
- Departamento
de Física, Facultad de Ciencias, Universidad de Chile, Casilla 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, Casilla 653, Santiago, Chile
- Centro para el desarrollo de la Nanociencias y Nanotecnologia, CEDENNA, Av. Ecuador 3493, Santiago, Chile
| | - Paul A. Johnson
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, Canada L8S 4M1
| | - Paul W. Ayers
- Department of Chemistry & Chemical Biology, McMaster University, Hamilton, Ontario, Canada L8S 4M1
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48
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Bultinck P, Van Damme S, Cedillo A. Bond fukui indices: Comparison of frozen molecular orbital and finite differences through mulliken populations. J Comput Chem 2013; 34:2421-9. [PMID: 23939806 DOI: 10.1002/jcc.23405] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2013] [Revised: 07/19/2013] [Accepted: 07/22/2013] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick Bultinck
- Department of Inorganic and Physical Chemistry; Ghent University; Krijgslaan 281 (S3); 9000; Gent; Belgium
| | - Sofie Van Damme
- Department of Inorganic and Physical Chemistry; Ghent University; Krijgslaan 281 (S3); 9000; Gent; Belgium
| | - Andrés Cedillo
- Departamento de Química; Universidad Autónoma Metropolitana-Iztapalapa; San Rafael Atlixco 186; 09340; México; DF; México
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49
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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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50
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Computational Nutraceutics: Chemical Reactivity Properties of the Flavonoid Naringin by Means of Conceptual DFT. J CHEM-NY 2013. [DOI: 10.1155/2013/850297] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The M06 family of density functionals has been assessed for the calculation of the molecular structure and properties of the Naringin molecule. The chemical reactivity descriptors have been calculated through Conceptual DFT. The active sites for nucleophilic and electrophilic attacks have been chosen by relating them to the Fukui function indices and the dual descriptorf(2)(r). A comparison between the descriptors calculated through vertical energy values and those arising from the Koopmans' theorem approximation has been performed in order to check for the validity of the last procedure.
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