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Sahre MJ, von Rudorff GF, Marquetand P, von Lilienfeld OA. Transferability of atomic energies from alchemical decomposition. J Chem Phys 2024; 160:054106. [PMID: 38341696 DOI: 10.1063/5.0187298] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2023] [Accepted: 01/09/2024] [Indexed: 02/13/2024] Open
Abstract
We study alchemical atomic energy partitioning as a method to estimate atomization energies from atomic contributions, which are defined in physically rigorous and general ways through the use of the uniform electron gas as a joint reference. We analyze quantitatively the relation between atomic energies and their local environment using a dataset of 1325 organic molecules. The atomic energies are transferable across various molecules, enabling the prediction of atomization energies with a mean absolute error of 23 kcal/mol, comparable to simple statistical estimates but potentially more robust given their grounding in the physics-based decomposition scheme. A comparative analysis with other decomposition methods highlights its sensitivity to electrostatic variations, underlining its potential as a representation of the environment as well as in studying processes like diffusion in solids characterized by significant electrostatic shifts.
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Affiliation(s)
- Michael J Sahre
- Vienna Doctoral School in Chemistry (DoSChem) and Institute of Theoretical Chemistry and Faculty of Physics, University of Vienna, 1090 Vienna, Austria
| | - Guido Falk von Rudorff
- Department of Chemistry, University Kassel, Heinrich-Plett-Str.40, 34132 Kassel, Germany
- Center for Interdisciplinary Nanostructure Science and Technology (CINSaT), Heinrich-Plett-Straße 40, 34132 Kassel, Germany
| | - Philipp Marquetand
- Faculty of Chemistry, Institute of Theoretical Chemistry, University of Vienna, Währinger Str. 17, 1090 Vienna, Austria
| | - O Anatole von Lilienfeld
- Vienna Doctoral School in Chemistry (DoSChem) and Institute of Theoretical Chemistry and Faculty of Physics, University of Vienna, 1090 Vienna, Austria
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto, St. George Campus, Toronto, M5S 3H6 Ontario, Canada
- Department of Materials Science and Engineering, University of Toronto, St. George Campus, Toronto, M5S 3E4 Ontario, Canada
- Vector Institute for Artificial Intelligence, Toronto, M5S 1M1 Ontario, Canada
- ML Group, Technische Universität Berlin and Institute for the Foundations of Learning and Data, 10587 Berlin, Germany
- Berlin Institute for the Foundations of Learning and Data, 10587 Berlin, Germany
- Department of Physics, University of Toronto, St. George Campus, Toronto, M5S 1A7 Ontario, Canada
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Kjeldal FØ, Eriksen JJ. Properties of Local Electronic Structures. J Chem Theory Comput 2023; 19:9228-9238. [PMID: 38051663 DOI: 10.1021/acs.jctc.3c00963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
The simulation of intrinsic contributions to molecular properties holds the potential to allow for chemistry to be directly inferred from changes to electronic structures at the atomic level. In the present study, we demonstrate how such local properties can be readily derived from suitable molecular orbitals to yield effective fingerprints of various types of atoms in organic molecules. In contrast, corresponding inferences from schemes that instead make use of individual atomic orbitals for this purpose are generally found to fail in expressing much uniqueness in atomic environments. By further studying the extent to which entire chemical reactions may be decomposed into meaningful and continuously evolving atomic contributions, schemes based on molecular rather than atomic orbitals are once again found to be the more consistent, even allowing for intricate differences between seemingly uniform nucleophilic substitutions to be probed.
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Affiliation(s)
- Frederik Ø Kjeldal
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs. Lyngby, Denmark
| | - Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs. Lyngby, Denmark
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Kjeldal FØ, Eriksen JJ. Decomposing Chemical Space: Applications to the Machine Learning of Atomic Energies. J Chem Theory Comput 2023; 19:2029-2038. [PMID: 36926874 DOI: 10.1021/acs.jctc.2c01290] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/18/2023]
Abstract
We apply a number of atomic decomposition schemes across the standard QM7 data set─a small model set of organic molecules at equilibrium geometry─to inspect the possible emergence of trends among contributions to atomization energies from distinct elements embedded within molecules. Specifically, a recent decomposition scheme of ours based on spatially localized molecular orbitals is compared to alternatives that instead partition molecular energies on account of which nuclei individual atomic orbitals are centered on. We find these partitioning schemes to expose the composition of chemical compound space in very dissimilar ways in terms of the grouping, binning, and heterogeneity of discrete atomic contributions, e.g., those associated with hydrogens bonded to different heavy atoms. Furthermore, unphysical dependencies on the one-electron basis set are found for some, but not all of these schemes. The relevance and importance of these compositional factors for training tailored neural network models based on atomic energies are next assessed. We identify both limitations and possible advantages with respect to contemporary machine learning models and discuss the design of potential counterparts based on atoms and the intrinsic energies of these as the principal decomposition units.
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Affiliation(s)
- Frederik Ø Kjeldal
- DTU Chemistry, Technical University of Denmark Kemitorvet Building 206, 2800 Kongens Lyngby, Denmark
| | - Janus J Eriksen
- DTU Chemistry, Technical University of Denmark Kemitorvet Building 206, 2800 Kongens Lyngby, Denmark
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Sahre MJ, von Rudorff GF, von Lilienfeld OA. Quantum Alchemy Based Bonding Trends and Their Link to Hammett's Equation and Pauling's Electronegativity Model. J Am Chem Soc 2023; 145:5899-5908. [PMID: 36862462 DOI: 10.1021/jacs.2c13393] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/03/2023]
Abstract
We present an intuitive and general analytical approximation estimating the energy of covalent single and double bonds between participating atoms in terms of their respective nuclear charges with just three parameters, [EAB ≈ a - bZAZB + c(ZA7/3 + ZB7/3) ]. The functional form of our expression models an alchemical atomic energy decomposition between participating atoms A and B. After calibration, reasonably accurate bond dissociation energy estimates are obtained for hydrogen-saturated diatomics composed of p-block elements coming from the same row 2 ≤ n ≤ 4 in the periodic table. Corresponding changes in bond dissociation energies due to substitution of atom B by C can be obtained via simple formulas. While being of different functional form and origin, our model is as simple and accurate as Pauling's well-known electronegativity model. Analysis indicates that the model's response in covalent bonding to variation in nuclear charge is near-linear, which is consistent with Hammett's equation.
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Affiliation(s)
- Michael J Sahre
- Faculty of Physics, University of Vienna, Vienna, 1090, Austria.,Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Vienna, 1090, Austria
| | | | - O Anatole von Lilienfeld
- Vector Institute for Artificial Intelligence, Toronto, M5S 1M1, Canada.,Departments of Chemistry, Materials Science and Engineering, and Physics, University of Toronto, St. George Campus, Toronto, M5R 0A3, Canada.,Machine Learning Group, Technische Universität Berlin and Institute for the Foundations of Learning and Data, Berlin, 10587, Germany
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Eriksen JJ. Erratum: "Mean-field density matrix decompositions" [J. Chem. Phys. 153, 214109 (2020)]. J Chem Phys 2023; 158:029902. [PMID: 36641410 DOI: 10.1063/5.0138751] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Affiliation(s)
- Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, 2800 Kgs. Lyngby, Denmark
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Eriksen JJ. Electronic excitations through the prism of mean-field decomposition techniques. J Chem Phys 2022; 156:061101. [PMID: 35168332 DOI: 10.1063/5.0082938] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
The potential of mean-field decomposition techniques in interpreting electronic transitions in molecules is explored, in particular, the usefulness of these for offering computational signatures of different classes of such excitations. When viewed as a conceptual lens for this purpose, decomposed results are presented for ground- and excited-state energies and dipole moments of selected prototypical organic dyes, and the discrete nature of these properties as well as how they change upon transitioning from one state to another is analyzed without recourse to a discussion based on the involved molecular orbitals. On the basis of results obtained both with and without an account of continuum solvation, our work is further intended to shed new light on practical and pathological differences in between various functional approximations in orbital-optimized Kohn-Sham density functional theory for excited states, equipping practitioners and developers in the field with new probes and possible validation tools.
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Affiliation(s)
- Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, DK-2800 Kgs. Lyngby, Denmark
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Ceriotti M, Jensen L, Manolopoulos DE, Martinez TJ, Michaelides A, Ogilvie JP, Reichman DR, Shi Q, Straub JE, Vega C, Wang LS, Weiss E, Zhu X, Stein JL, Lian T. 2020 JCP Emerging Investigator Special Collection. J Chem Phys 2021; 155:230401. [PMID: 34937385 DOI: 10.1063/5.0078934] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michele Ceriotti
- Laboratory of Computational Science and Modeling, Institute of Materials, École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Lasse Jensen
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania 16802, USA
| | - David E Manolopoulos
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
| | - Todd J Martinez
- Department of Chemistry, Stanford University, Stanford, California 94305, USA
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Jennifer P Ogilvie
- Department of Physics and Biophysics, University of Michigan, 450 Church St., Ann Arbor, Michigan 48109, USA
| | - David R Reichman
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | - Qiang Shi
- Beijing National Laboratory for Molecular Sciences, State Key Laboratory for Structural Chemistry of Unstable and Stable Species, Institute of Chemistry, Chinese Academy of Sciences, Zhongguancun, Beijing 100190, China; University of Chinese Academy of Sciences, Beijing 100049, China; and Physical Science Laboratory, Huairou National Comprehensive Science Center, Beijing 101407, China
| | - John E Straub
- Department of Chemistry, Boston University, 590 Commonwealth Avenue, Boston, Massachusetts 02215, USA
| | - Carlos Vega
- Departamento de Química Física, Facultad de Ciencias Químicas, Universidad Complutense de Madrid, 28040 Madrid, Spain
| | - Lai-Sheng Wang
- Department of Chemistry, Brown University, Providence, Rhode Island 02912, USA
| | - Emily Weiss
- Departments of Chemistry, Materials Science and Engineering, Northwestern University, Evanston, Illinois 60208, USA
| | - Xiaoyang Zhu
- Department of Chemistry, Columbia University, New York, New York 10027, USA
| | | | - Tianquan Lian
- Department of Chemistry, Emory University, Atlanta, Georgia 30322, USA
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Eriksen JJ. Decomposed Mean-Field Simulations of Local Properties in Condensed Phases. J Phys Chem Lett 2021; 12:6048-6055. [PMID: 34165982 DOI: 10.1021/acs.jpclett.1c01375] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/13/2023]
Abstract
The present work demonstrates a robust protocol for probing localized electronic structure in condensed-phase systems, operating in terms of a recently proposed theory for decomposing the results of Kohn-Sham density functional theory in a basis of spatially localized molecular orbitals. In an initial application to liquid, ambient water and the assessment of the solvation energy and the embedded dipole moment of H2O in solution, we find that both properties are amplified on average-in accordance with expectation-and that correlations are indeed observed to exist between them. However, the simulated solvent-induced shift to the dipole moment of water is found to be significantly dampened with respect to typical literature values. The local nature of our methodology has further allowed us to evaluate the convergence of bulk properties with respect to the extent of the underlying one-electron basis set, ranging from single-ζ to full (augmented) quadruple-ζ quality. Albeit a pilot example, our work paves the way toward future studies of local effects and defects in more complex phases, e.g., liquid mixtures and even solid-state crystals.
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Affiliation(s)
- Janus J Eriksen
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 206, DK-2800 Kgs. Lyngby, Denmark
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