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Hoffmann G, Guégan F, Labet V, Joubert L, Chermette H, Morell C, Tognetti V. Expanding horizons in conceptual density functional theory: Novel ensembles and descriptors to decipher reactivity patterns. J Comput Chem 2024; 45:1716-1726. [PMID: 38580454 DOI: 10.1002/jcc.27363] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 02/16/2024] [Accepted: 02/22/2024] [Indexed: 04/07/2024]
Abstract
Conceptual density functional theory (CDFT) and the quantum reactivity descriptors stemming from it have proven to be valuable tools for understanding the chemical behavior of molecules. This article is presented as being intrinsically of dual character. In a first part, it briefly reviews, in a deliberately didactical way, the main ensembles in CDFT, while the second half presents two additional ensembles, where the chemical hardness acts as a natural variable, and their respective reactivity descriptors. The evaluation of these reactivity descriptors on common organic chemical reagents are presented and discussed.
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Affiliation(s)
- Guillaume Hoffmann
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Frédéric Guégan
- IC2MP UMR 7285, Université de Poitiers - CNRS, Poitiers, France
| | - Vanessa Labet
- Sorbonne Université CNRS, MONARIS, UMR8233, Paris, France
| | - Laurent Joubert
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, Rouen, France
| | - Henry Chermette
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Christophe Morell
- Université de Lyon, Institut des Sciences Analytiques, UMR 5280, CNRS, Villeurbanne, France
| | - Vincent Tognetti
- Univ Rouen Normandie, INSA Rouen Normandie, CNRS, Normandie Univ, COBRA UMR 6014, INC3M FR 3038, Rouen, France
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2
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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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3
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Chan M, Verstraelen T, Tehrani A, Richer M, Yang XD, Kim TD, Vöhringer-Martinez E, Heidar-Zadeh F, Ayers PW. The tale of HORTON: Lessons learned in a decade of scientific software development. J Chem Phys 2024; 160:162501. [PMID: 38651814 DOI: 10.1063/5.0196638] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 02/28/2024] [Indexed: 04/25/2024] Open
Abstract
HORTON is a free and open-source electronic-structure package written primarily in Python 3 with some underlying C++ components. While HORTON's development has been mainly directed by the research interests of its leading contributing groups, it is designed to be easily modified, extended, and used by other developers of quantum chemistry methods or post-processing techniques. Most importantly, HORTON adheres to modern principles of software development, including modularity, readability, flexibility, comprehensive documentation, automatic testing, version control, and quality-assurance protocols. This article explains how the principles and structure of HORTON have evolved since we started developing it more than a decade ago. We review the features and functionality of the latest HORTON release (version 2.3) and discuss how HORTON is evolving to support electronic structure theory research for the next decade.
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Affiliation(s)
- Matthew Chan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Ghent, Belgium
| | - Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Michelle Richer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Xiaotian Derrick Yang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Taewon David Kim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, 4070371 Concepción, Chile
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, Kingston, Ontario K7L-3N6, Canada
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S-4L8, Canada
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4
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Tehrani A, Anderson JSM, Chakraborty D, Rodriguez-Hernandez JI, Thompson DC, Verstraelen T, Ayers PW, Heidar-Zadeh F. An information-theoretic approach to basis-set fitting of electron densities and other non-negative functions. J Comput Chem 2023; 44:1998-2015. [PMID: 37526138 DOI: 10.1002/jcc.27170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2023] [Revised: 05/03/2023] [Accepted: 05/08/2023] [Indexed: 08/02/2023]
Abstract
The numerical ill-conditioning associated with approximating an electron density with a convex sum of Gaussian or Slater-type functions is overcome by using the (extended) Kullback-Leibler divergence to measure the deviation between the target and approximate density. The optimized densities are non-negative and normalized, and they are accurate enough to be used in applications related to molecular similarity, the topology of the electron density, and numerical molecular integration. This robust, efficient, and general approach can be used to fit any non-negative normalized functions (e.g., the kinetic energy density and molecular electron density) to a convex sum of non-negative basis functions. We present a fixed-point iteration method for optimizing the Kullback-Leibler divergence and compare it to conventional gradient-based optimization methods. These algorithms are released through the free and open-source BFit package, which also includes a L2-norm squared optimization routine applicable to any square-integrable scalar function.
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Affiliation(s)
- Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - James S M Anderson
- Instituto de Química, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Debajit Chakraborty
- Department of Physics, Wake Forest University, Winston-Salem, North Carolina, USA
- Center for Functional Materials, Wake Forest University, Winston-Salem, North Carolina, USA
| | | | | | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
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5
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Rong C, Heidar-Zadeh F, Miranda-Quintana RA, Liu S, Ayers PW. Ranking the energy minima of the 20 natural amino acids using conceptual tools. Theor Chem Acc 2022. [DOI: 10.1007/s00214-022-02929-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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6
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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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7
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Geerlings P. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems. Pharmaceuticals (Basel) 2022; 15:ph15091112. [PMID: 36145333 PMCID: PMC9505550 DOI: 10.3390/ph15091112] [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] [Received: 08/02/2022] [Revised: 08/26/2022] [Accepted: 08/27/2022] [Indexed: 12/03/2022] Open
Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
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Affiliation(s)
- Paul Geerlings
- Research Group of General Chemistry (ALGC), Faculty of Science and Bio-Engineering Science, Vrije Universiteit Brussel (VUB), Pleinlaan 2, B-1050 Brussels, Belgium
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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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9
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Douglas-Gallardo OA, Murillo-López JA, Oller J, Mulholland AJ, Vöhringer-Martinez E. Carbon Dioxide Fixation in RuBisCO Is Protonation-State-Dependent and Irreversible. ACS Catal 2022. [DOI: 10.1021/acscatal.2c01677] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Oscar A. Douglas-Gallardo
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry, CV4 7AL, United Kingdom
| | - Juliana A. Murillo-López
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
| | - Javier Oller
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
- Departamento de Química Orgánica y Fisicoquímica, Facultad de Ciencias Químicas y Farmacéuticas, Universidad de Chile, Santiago 8380000, Chile
| | - Adrian J. Mulholland
- Centre for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción 4030000, Chile
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10
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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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11
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González-Quintela M, Viltres-Portales M, Díaz-García AM, Bustamante-Sánchez M, Sánchez-Díaz G, Lazo-Fraga AR, Estévez-Hernández O. On the analytical response of lead(II) selective electrodes using 1-aroyl-3,3-dimethylthioureas as ionophores: membrane analysis and quantum chemical calculations. PHOSPHORUS SULFUR 2022. [DOI: 10.1080/10426507.2022.2085270] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Affiliation(s)
- M. González-Quintela
- Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, La Habana, Cuba
| | - M. Viltres-Portales
- Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, La Habana, Cuba
| | | | - M. Bustamante-Sánchez
- Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, La Habana, Cuba
| | - G. Sánchez-Díaz
- Faculty of Science, Department of Chemistry & Chemical Biology, MacMaster University, Hamilton, Canada
| | - A. R. Lazo-Fraga
- Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, La Habana, Cuba
| | - O. Estévez-Hernández
- Instituto de Ciencia y Tecnología de Materiales (IMRE), Universidad de La Habana, La Habana, Cuba
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12
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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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13
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Pujal L, van Zyl M, Vöhringer-Martinez E, Verstraelen T, Bultinck P, Ayers PW, Heidar-Zadeh F. Constrained iterative Hirshfeld charges: A variational approach. J Chem Phys 2022; 156:194109. [PMID: 35597660 DOI: 10.1063/5.0089466] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We develop a variational procedure for the iterative Hirshfeld (HI) partitioning scheme. The main practical advantage of having a variational framework is that it provides a formal and straightforward approach for imposing constraints (e.g., fixed charges on certain atoms or molecular fragments) when computing HI atoms and their properties. Unlike many other variants of the Hirshfeld partitioning scheme, HI charges do not arise naturally from the information-theoretic framework, but only as a reverse-engineered construction of the objective function. However, the procedure we use is quite general and could be applied to other problems as well. We also prove that there is always at least one solution to the HI equations, but we could not prove that its self-consistent equations would always converge for any given initial pro-atom charges. Our numerical assessment of the constrained iterative Hirshfeld method shows that it satisfies many desirable traits of atoms in molecules and has the potential to surpass existing approaches for adding constraints when computing atomic properties.
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Affiliation(s)
- Leila Pujal
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
| | - Maximilian van Zyl
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
| | - Esteban Vöhringer-Martinez
- Departamento de Físico-Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Technologiepark-Zwijnaarde 46, B-9052 Zwijnaarde, Belgium
| | - Patrick Bultinck
- Ghent Quantum Chemistry Group, Department of Chemistry, Ghent University, Krijgslaan 281 S3, B-9000 Ghent, Belgium
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
| | - Farnaz Heidar-Zadeh
- Department of Chemistry, Queen's University, 90 Bader Lane, Kingston, Ontario K7N 3N6, Canada
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14
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Guan X, Leven I, Heidar-Zadeh F, Head-Gordon T. Protein C-GeM: A Coarse-Grained Electron Model for Fast and Accurate Protein Electrostatics Prediction. J Chem Inf Model 2021; 61:4357-4369. [PMID: 34490776 DOI: 10.1021/acs.jcim.1c00388] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The electrostatic potential (ESP) is a powerful property for understanding and predicting electrostatic charge distributions that drive interactions between molecules. In this study, we compare various charge partitioning schemes including fitted charges, density-based quantum mechanical (QM) partitioning schemes, charge equilibration methods, and our recently introduced coarse-grained electron model, C-GeM, to describe the ESP for protein systems. When benchmarked against high quality density functional theory calculations of the ESP for tripeptides and the crambin protein, we find that the C-GeM model is of comparable accuracy to ab initio charge partitioning methods, but with orders of magnitude improvement in computational efficiency since it does not require either the electron density or the electrostatic potential as input.
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Affiliation(s)
- Xingyi Guan
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Itai Leven
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Farnaz Heidar-Zadeh
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Department of Chemistry, Queen's University, Kingston, Ontario K7L 3N6, Canada
| | - Teresa Head-Gordon
- Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States.,Departments of Bioengineering and Chemical and Biomolecular Engineering, University of California, Berkeley, California 94720, United States
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15
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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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16
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Verstraelen T, Adams W, Pujal L, Tehrani A, Kelly BD, Macaya L, Meng F, Richer M, Hernández-Esparza R, Yang XD, Chan M, Kim TD, Cools-Ceuppens M, Chuiko V, Vöhringer-Martinez E, Ayers PW, Heidar-Zadeh F. IOData: A python library for reading, writing, and converting computational chemistry file formats and generating input files. J Comput Chem 2021; 42:458-464. [PMID: 33368350 DOI: 10.1002/jcc.26468] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2020] [Accepted: 10/06/2020] [Indexed: 11/07/2022]
Abstract
IOData is a free and open-source Python library for parsing, storing, and converting various file formats commonly used by quantum chemistry, molecular dynamics, and plane-wave density-functional-theory software programs. In addition, IOData supports a flexible framework for generating input files for various software packages. While designed and released for stand-alone use, its original purpose was to facilitate the interoperability of various modules in the HORTON and ChemTools software packages with external (third-party) molecular quantum chemistry and solid-state density-functional-theory packages. IOData is designed to be easy to use, maintain, and extend; this is why we wrote IOData in Python and adopted many principles of modern software development, including comprehensive documentation, extensive testing, continuous integration/delivery protocols, and package management. This article is the official release note of the IOData library.
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Affiliation(s)
- Toon Verstraelen
- Center for Molecular Modeling (CMM), Ghent University, Zwijnaarde, Belgium
| | - William Adams
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Leila Pujal
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Alireza Tehrani
- Department of Chemistry, Queen's University, Kingston, Ontario, Canada
| | - Braden D Kelly
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Luis Macaya
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Fanwang Meng
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Michael Richer
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Xiaotian Derrick Yang
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada.,Laboratoire de Chimie Théorique, Sorbonne Université, Paris, France
| | - Matthew Chan
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | - Taewon David Kim
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
| | | | - Valerii Chuiko
- Faculty of Physics, Taras Shevchenko National University of Kyiv, 01601, Kyiv, Ukraine
| | - Esteban Vöhringer-Martinez
- Departamento de Físico Química, Facultad de Ciencias Químicas, Universidad de Concepción, Concepción, Chile
| | - Paul W Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario, Canada
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17
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Miranda‐Quintana RA, Ayers PW, Heidar‐Zadeh F. Reactivity and Charge Transfer Beyond the Parabolic Model: the “|Δμ| Big is Good” Principle. ChemistrySelect 2021. [DOI: 10.1002/slct.202004055] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
| | - Paul W. Ayers
- Department of Chemistry & Chemical Biology McMaster University Hamilton Ontario Canada
| | - Farnaz Heidar‐Zadeh
- Department of Chemistry Queen's University 90 Bader Lane Kingston Ontario Canada
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18
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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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19
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Kamencek T, Wieser S, Kojima H, Bedoya-Martínez N, Dürholt JP, Schmid R, Zojer E. Evaluating Computational Shortcuts in Supercell-Based Phonon Calculations of Molecular Crystals: The Instructive Case of Naphthalene. J Chem Theory Comput 2020; 16:2716-2735. [PMID: 32155063 PMCID: PMC7205391 DOI: 10.1021/acs.jctc.0c00119] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
![]()
Phonons crucially
impact a variety of properties of organic semiconductor
materials. For instance, charge- and heat transport depend on low-frequency
phonons, while for other properties, such as the free energy, especially
high-frequency phonons count. For all these quantities one needs to
know the entire phonon band structure, whose simulation becomes exceedingly
expensive for more complex systems when using methods like dispersion-corrected
density functional theory (DFT). Therefore, in the present contribution
we evaluate the performance of more approximate methodologies, including
density functional tight binding (DFTB) and a pool of force fields
(FF) of varying complexity and sophistication. Beyond merely comparing
phonon band structures, we also critically evaluate to what extent
derived quantities, like temperature-dependent heat capacities, mean
squared thermal displacements, and temperature-dependent free energies
are impacted by shortcomings in the description of the phonon bands.
As a benchmark system, we choose (deuterated) naphthalene, as the
only organic semiconductor material for which to date experimental
phonon band structures are available in the literature. Overall, the
best performance among the approximate methodologies is observed for
a system-specifically parametrized second-generation force field.
Interestingly, in the low-frequency regime also force fields with
a rather simplistic model for the bonding interactions (like the General
Amber Force Field) perform rather well. As far as the tested DFTB
parametrization is concerned, we obtain a significant underestimation
of the unit-cell volume resulting in a pronounced overestimation of
the phonon energies in the low-frequency region. This cannot be mended
by relying on the DFT-calculated unit cell, since with this unit cell
the DFTB phonon frequencies significantly underestimate the experiments.
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Affiliation(s)
- Tomas Kamencek
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz, Petersgasse 16, 8010 Graz, Austria.,Institute of Physical and Theoretical Chemistry, Graz University of Technology, NAWI Graz, Stremayrgasse 9, 8010 Graz, Austria
| | - Sandro Wieser
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz, Petersgasse 16, 8010 Graz, Austria
| | - Hirotaka Kojima
- Division of Materials Science, Nara Institute of Science and Technology, 8916-5 Takayama, Ikoma, Nara 630-0192, Japan
| | | | - Johannes P Dürholt
- Computational Materials Chemistry Group, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Rochus Schmid
- Computational Materials Chemistry Group, Faculty of Chemistry and Biochemistry, Ruhr-University Bochum, Universitätsstraße 150, 44801 Bochum, Germany
| | - Egbert Zojer
- Institute of Solid State Physics, Graz University of Technology, NAWI Graz, Petersgasse 16, 8010 Graz, Austria
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20
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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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21
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Oller J, Saez DA, Vöhringer-Martinez E. Atom-Condensed Fukui Function in Condensed Phases and Biological Systems and Its Application to Enzymatic Fixation of Carbon Dioxide. J Phys Chem A 2020; 124:849-857. [PMID: 31951411 DOI: 10.1021/acs.jpca.9b07012] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Local reactivity descriptors such as atom-condensed Fukui functions are promising computational tools to study chemical reactivity at specific sites within a molecule. Their applications have been mainly focused on isolated molecules in their most stable conformation without considering the effects of the surroundings. Here we propose to combine quantum mechanics/molecular mechanics Born-Oppenheimer molecular dynamics simulations to obtain the microstates (configurations) of a molecular system using different representations of the molecular environment and calculate Boltzmann-weighted atom-condensed local reactivity descriptors based on conceptual density functional theory. Our approach takes the conformational fluctuations of the molecular system and the polarization of its electron density by the environment into account, allowing us to analyze the effect of the molecular environment on reactivity. In this contribution, we apply the method mentioned above to the catalytic fixation of carbon dioxide by crotonyl-CoA carboxylase/reductase and study if the enzyme alters the reactivity of its substrate compared with an aqueous solution. Our main result is that the protein environment activates the substrate by the elimination of solute-solvent hydrogen bonds from aqueous solution in the two elementary steps of the reaction mechanism: the nucleophilic attack of a hydride anion from NADPH on the α,β-unsaturated thioester and the electrophilic attack of carbon dioxide on the formed enolate species.
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Affiliation(s)
- Javier Oller
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
| | - David Adrian Saez
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
| | - Esteban Vöhringer-Martinez
- Departamento de Fı́sico-Quı́mica, Facultad de Ciencias Quı́micas , Universidad de Concepción , Concepción 4070386 , Chile
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22
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Maulén B, Echeverri A, Gómez T, Fuentealba P, Cárdenas C. Electron Localization Function in Excited States: The Case of the Ultrafast Proton Transfer of the Salicylidene Methylamine. J Chem Theory Comput 2019; 15:5532-5542. [DOI: 10.1021/acs.jctc.9b00691] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Boris Maulén
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Andrea Echeverri
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
| | - Tatiana Gómez
- Instituto de Ciencias Químicas Aplicadas, Theoretical and Computational Chemistry Center, Facultad de Ingeniería, Universidad Autónoma de Chile, Av. El Llano Subercaseaux 2801, San Miguel, Santiago, Chile
| | - Patricio Fuentealba
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, Santiago, Chile
- Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Santiago 9170124, Chile
| | - Carlos Cárdenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, 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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23
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A screening DFT study of the para-substituent effect on local hyper-softness in bis(phenoxy-imine) titanium complexes to get insights about their catalytic activity in ethylene polymerization. MOLECULAR CATALYSIS 2019. [DOI: 10.1016/j.mcat.2019.02.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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24
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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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25
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Miranda-Quintana RA, Heidar-Zadeh F, Ayers PW. Elementary Derivation of the "|Δμ| Big Is Good" Rule. J Phys Chem Lett 2018; 9:4344-4348. [PMID: 29944379 DOI: 10.1021/acs.jpclett.8b01312] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
Thirty years ago, Parr and Yang postulated that favorable chemical processes are associated with large changes in the electronic chemical potential or, equivalently, the electronegativity. They called this the "|Δμ| big is good" rule and noted that if the rule could be justified, then it "would constitute a validation of frontier theory from first principles." We provide a simple and insightful justification for the "|Δμ| big is good" rule, with special emphasis on electron-transfer reactions. Furthermore, we show that it implies Pearson's hard/soft acid/base principle mathematically and confirm this result with numerical examples. This supports Parr's intuition that many other reactivity precepts arise as corollaries to the more fundamental "|Δμ| big is good" rule. In all of this, it is essential to consider the intensive nature of the chemical potential.
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Affiliation(s)
| | - Farnaz Heidar-Zadeh
- Department of Chemistry & Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
- Center for Molecular Modeling , Ghent University , Technologiepark 903 , 9052 Zwijnaarde , Belgium
- Physics and Materials Science Research Unit , University of Luxembourg , L-1511 Luxembourg , Luxembourg
| | - Paul W Ayers
- Department of Chemistry & Chemical Biology , McMaster University , Hamilton , Ontario L8S 4M1 , Canada
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26
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Miranda-Quintana RA, Ayers PW. Note: Maximum hardness and minimum electrophilicity principles. J Chem Phys 2018; 148:196101. [DOI: 10.1063/1.5033964] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | - Paul W. Ayers
- Department of Chemistry and Chemical Biology, McMaster University, Hamilton, Ontario L8S 4L8, Canada
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27
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Abstract
The chemical space contains all possible compounds that can be imagined. Its size easily equals the number of fundamental particles in the observable universe. Rational design of compounds aims to find those sectors of the chemical space where compounds optimize a set of desired properties. Then, rational design demands tools to efficiently navigate the chemical space. Ab initio alchemical derivatives offer the possibility to navigate, without empiricism, the energy landscape through alchemical transformations. An alchemical transformation is any process, physical or fictitious, that connects to points in the chemical space. In this work, those transformations are constructed as a perturbative expansion of the energy with respect to perturbations in the stoichiometry. The response functions of that expansion are what is called alchemical derivatives. In this work we assess how effective alchemical derivatives are in predicting energy changes associated to changes in the composition. We do this by including in the expansion, for the first time, electrostatic, polarization and electron-transfer effects. The system we chose is one that challenges alchemical derivatives because none of these effects dominates its behavior. The transmutations studied here correspond to substitutional doping of Al13 with up to four atoms of Si, Al13-nSin. Two types of transformations are considered, those in which the number of electrons remains constant and those in which the number of electrons also changes. It is found that contrary to what has been reported before, polarization cannot be neglected. If polarization is not included, alchemical derivatives fail to predict the change of energy and the relative energy between isomers. For isoelectronic substitution of four or more atoms, the perturbative approach collapses because the strength of the perturbation becomes too strong to guarantee convergence of the series. It is shown, however, that if only one atom is mutated at a time, alchemical derivatives rank pretty well the isomers of Al13-nSin according to their energy. In the case of non-isoelectronic transformations, it is observed that the series rapidly diverges with increasing number of electrons. In this situation, it becomes more important to keep the degree of transmutation of the parent system small.
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Affiliation(s)
- Macarena Muñoz
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, 653-Santiago, Chile.
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28
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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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29
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Heidar-Zadeh F, Ayers PW, Bultinck P. Fractional nuclear charge approach to isolated anion densities for Hirshfeld partitioning methods. J Mol Model 2017; 23:348. [DOI: 10.1007/s00894-017-3514-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2017] [Accepted: 10/26/2017] [Indexed: 11/30/2022]
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30
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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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31
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Miranda-Quintana RA, Kim TD, Cárdenas C, Ayers PW. The HSAB principle from a finite-temperature grand-canonical perspective. Theor Chem Acc 2017. [DOI: 10.1007/s00214-017-2167-y] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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32
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Contreras-García J, Cardenas C. On understanding the chemical origin of band gaps. J Mol Model 2017; 23:271. [PMID: 28842804 DOI: 10.1007/s00894-017-3434-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2016] [Accepted: 07/28/2017] [Indexed: 10/19/2022]
Abstract
Conceptual DFT and quantum chemical topology provide two different approaches based on the electron density to grasp chemical concepts. We present a model merging both approaches, in order to obtain physical properties from chemically meaningful fragments (bonds, lone pairs) in the solid. One way to do so is to use an energetic model that includes chemical quantities explicitly, so that the properties provided by conceptual DFT are directly related to the inherent organization of electrons within the regions provided by topological analysis. An example of such energy model is the bond charge model (BCM) by Parr and collaborators. Bonds within an ELF-BCM coupled approach present very stable chemical features, with a bond length of ca. 1 Å and 2[Formula: see text]. Whereas the 2[Formula: see text] corroborate classical views of chemical bonding, the fact that bonds always expand along 1 Å introduces the concept of geometrical transferability and enables estimating crystalline cell parameters. Moreover, combining these results with conceptual DFT enables deriving a model for the band gap where the chemical hardness of a solid is given by the bond properties, charge, length, and a Madelung factor, where the latter plays the major role. In short, the fundamental gap of zinc-blende solids can be understood as given by a 2[Formula: see text] bond particle asymmetrically located on a 1 Å length box and electrostatically interacting with other bonds and with a core matrix. This description is able to provide semi-quantitative insight into the band gap of zinc-blende semiconductors and insulators on equal footing, as well as a relationship between band gap and compressibility. In other words, merging these different approaches to bonding enables to connect measurable macroscopic behavior with microscopic electronic structure properties and to obtain microscopic insight into the chemical origin of band gaps, whose prediction is still nowadays a difficult task. Graphical Abstract Conceptual DFT couples to quatum chemcial topology to explain the band gap of zinc-blende solids.
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Affiliation(s)
- J Contreras-García
- Laboratoire de Chimie Théorique, UPMC, Sorbonne Universités and CNRS, 75005, Paris, France.
| | - Carlos Cardenas
- Departamento de Física, Facultad de Ciencias, Universidad de Chile, Casilla 653, 7800024, Santiago, Chile.,Centro para el Desarrollo de la Nanociencia y la Nanotecnología (CEDENNA), Avda. Ecuador 3493, Santiago, 9170124, Chile
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Miranda-Quintana RA. Note: The minimum electrophilicity and the hard/soft acid/base principles. J Chem Phys 2017; 146:046101. [DOI: 10.1063/1.4974987] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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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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