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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Small-Basis Set Density-Functional Theory Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2913-2930. [PMID: 35412817 DOI: 10.1021/acs.jctc.2c00036] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Density functional theory (DFT) is currently the most popular method for modeling noncovalent interactions and thermochemistry. The accurate calculation of noncovalent interaction energies, reaction energies, and barrier heights requires choosing an appropriate functional and, typically, a relatively large basis set. Deficiencies of the density-functional approximation and the use of a limited basis set are the leading sources of error in the calculation of noncovalent and thermochemical properties in molecular systems. In this article, we present three new DFT methods based on the BLYP, M06-2X, and CAM-B3LYP functionals in combination with the 6-31G* basis set and corrected with atom-centered potentials (ACPs). ACPs are one-electron potentials that have the same form as effective-core potentials, except they do not replace any electrons. The ACPs developed in this work are used to generate energy corrections to the underlying DFT/basis-set method such that the errors in predicted chemical properties are minimized while maintaining the low computational cost of the parent methods. ACPs were developed for the elements H, B, C, N, O, F, Si, P, S, and Cl. The ACP parameters were determined using an extensive training set of 118655 data points, mostly of complete basis set coupled-cluster level quality. The target molecular properties for the ACP-corrected methods include noncovalent interaction energies, molecular conformational energies, reaction energies, barrier heights, and bond separation energies. The ACPs were tested first on the training set and then on a validation set of 42567 additional data points. We show that the ACP-corrected methods can predict the target molecular properties with accuracy close to complete basis set wavefunction theory methods, but at a computational cost of double-ζ DFT methods. This makes the new BLYP/6-31G*-ACP, M06-2X/6-31G*-ACP, and CAM-B3LYP/6-31G*-ACP methods uniquely suited to the calculation of noncovalent, thermochemical, and kinetic properties in large molecular systems.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, MALTA Consolider Team, Oviedo E-33006, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia V1V 1V7, Canada
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Prasad VK, Otero-de-la-Roza A, DiLabio GA. Fast and Accurate Quantum Mechanical Modeling of Large Molecular Systems Using Small Basis Set Hartree-Fock Methods Corrected with Atom-Centered Potentials. J Chem Theory Comput 2022; 18:2208-2232. [PMID: 35313106 DOI: 10.1021/acs.jctc.1c01128] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
There has been significant interest in developing fast and accurate quantum mechanical methods for modeling large molecular systems. In this work, by utilizing a machine learning regression technique, we have developed new low-cost quantum mechanical approaches to model large molecular systems. The developed approaches rely on using one-electron Gaussian-type functions called atom-centered potentials (ACPs) to correct for the basis set incompleteness and the lack of correlation effects in the underlying minimal or small basis set Hartree-Fock (HF) methods. In particular, ACPs are proposed for ten elements common in organic and bioorganic chemistry (H, B, C, N, O, F, Si, P, S, and Cl) and four different base methods: two minimal basis sets (MINIs and MINIX) plus a double-ζ basis set (6-31G*) in combination with dispersion-corrected HF (HF-D3/MINIs, HF-D3/MINIX, HF-D3/6-31G*) and the HF-3c method. The new ACPs are trained on a very large set (73 832 data points) of noncovalent properties (interaction and conformational energies) and validated additionally on a set of 32 048 data points. All reference data are of complete basis set coupled-cluster quality, mostly CCSD(T)/CBS. The proposed ACP-corrected methods are shown to give errors in the tenths of a kcal/mol range for noncovalent interaction energies and up to 2 kcal/mol for molecular conformational energies. More importantly, the average errors are similar in the training and validation sets, confirming the robustness and applicability of these methods outside the boundaries of the training set. In addition, the performance of the new ACP-corrected methods is similar to complete basis set density functional theory (DFT) but at a cost that is orders of magnitude lower, and the proposed ACPs can be used in any computational chemistry program that supports effective-core potentials without modification. It is also shown that ACPs improve the description of covalent and noncovalent bond geometries of the underlying methods and that the improvement brought about by the application of the ACPs is directly related to the number of atoms to which they are applied, allowing the treatment of systems containing some atoms for which ACPs are not available. Overall, the ACP-corrected methods proposed in this work constitute an alternative accurate, economical, and reliable quantum mechanical approach to describe the geometries, interaction energies, and conformational energies of systems with hundreds to thousands of atoms.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- MALTA Consolider Team, Departamento de Química Física y Analítica, Facultad de Química, Universidad de Oviedo, E-33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, Okanagan, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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Theoretical Description of Water from Single-Molecule to Condensed Phase: a Review of Recent Progress on Potential Energy Surfaces and Molecular Dynamics. CHINESE J CHEM PHYS 2022. [DOI: 10.1063/1674-0068/cjcp2201005] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
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Ball BT, Vanovac S, Odbadrakh TT, Shields GC. Monomers of Glycine and Serine Have a Limited Ability to Hydrate in the Atmosphere. J Phys Chem A 2021; 125:8454-8467. [PMID: 34529444 DOI: 10.1021/acs.jpca.1c05466] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The role of atmospheric aerosols on climate change is one of the biggest uncertainties in most global climate models. Organic aerosols have been identified as potential cloud condensation nuclei (CCN), and amino acids are organic molecules that could serve as CCN. Amino acids make up a significant portion of the total organic material in the atmosphere, and herein we present a systematic study of hydration for two of the most common atmospheric amino acids, glycine and serine. We compute DLPNO/CCSD(T)//M08-HX/MG3S thermodynamic properties and atmospheric concentrations of Gly(H2O)n and Ser(H2O)n, where n = 1-5. We predict that serine-water clusters have higher concentrations at n = 1 and 5, while glycine-water clusters have higher concentrations at n = 2-4. However, both glycine and serine are inferred to exist primarily in their nonhydrated monomer forms in the absence of other species such as sulfuric acid.
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Affiliation(s)
- Benjamin T Ball
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Sara Vanovac
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, United States
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Malloum A, Conradie J. Hydrogen bond networks of ammonia clusters: What we know and what we don’t know. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.116199] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
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Malloum A, Conradie J. Accurate binding energies of ammonia clusters and benchmarking of hybrid DFT functionals. COMPUT THEOR CHEM 2021. [DOI: 10.1016/j.comptc.2021.113236] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Rasmussen FR, Kubečka J, Besel V, Vehkamäki H, Mikkelsen KV, Bilde M, Elm J. Hydration of Atmospheric Molecular Clusters III: Procedure for Efficient Free Energy Surface Exploration of Large Hydrated Clusters. J Phys Chem A 2020; 124:5253-5261. [DOI: 10.1021/acs.jpca.0c02932] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Jakub Kubečka
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Vitus Besel
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Hanna Vehkamäki
- Institute for Atmospheric and Earth System Research, University of Helsinki, Helsinki FI-00014, Finland
| | - Kurt V. Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetesparken 5, 2100 Copenhagen, Denmark
| | - Merete Bilde
- Department of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
| | - Jonas Elm
- Department of Chemistry and iClimate, Aarhus University, Langelandsgade 140, 8000 Aarhus, Denmark
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Malloum A, Fifen JJ, Dhaouadi Z, Nana Engo SG, Conradie J. Structures, relative stability and binding energies of neutral water clusters, (H2O)2–30. NEW J CHEM 2019. [DOI: 10.1039/c9nj01659g] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
We have revised the structures of neutral water clusters, (H2O)n=2–30, with the affordable M06-2X functional, presenting up to 25 isomers for each cluster size.
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Affiliation(s)
- Alhadji Malloum
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jean Jules Fifen
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Zoubeida Dhaouadi
- Laboratoire de Spectroscopie Atomique Moléculaire et Applications
- Faculté des Sciences de Tunis
- Université de Tunis El Manar
- Tunis
- Tunisia
| | - Serge Guy Nana Engo
- Department of Physics
- Faculty of Science
- University of Ngaoundere
- Ngaoundere
- Cameroon
| | - Jeanet Conradie
- Department of Chemistry
- University of the Free State
- Bloemfontein
- South Africa
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Barclay AJ, Pietropolli Charmet A, Michaelian KH, McKellar ARW, Moazzen-Ahmadi N. Micro-solvation of CO in water: infrared spectra and structural calculations for (D2O)2–CO and (D2O)3–CO. Phys Chem Chem Phys 2019; 21:26564-26568. [DOI: 10.1039/c9cp05480d] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The weakly-bound molecular clusters (D2O)2–CO and (D2O)3–CO are observed in the C–O stretch fundamental region (≈2150 cm−1), and their rotationally-resolved infrared spectra yield precise rotational parameters.
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Affiliation(s)
- A. J. Barclay
- Department of Physics and Astronomy
- University of Calgary
- Calgary
- Canada
| | - A. Pietropolli Charmet
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- Mestre
- Italy
| | | | | | - N. Moazzen-Ahmadi
- Department of Physics and Astronomy
- University of Calgary
- Calgary
- Canada
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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Pérez C, León I, Lesarri A, Pate BH, Martínez R, Millán J, Fernández JA. Isomerism of the Aniline Trimer. Angew Chem Int Ed Engl 2018; 57:15112-15116. [DOI: 10.1002/anie.201808602] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2018] [Revised: 09/17/2018] [Indexed: 01/09/2023]
Affiliation(s)
- Cristóbal Pérez
- Deutsches Elektronen-Synchrotron DESY Notkestrasse 85 22607 Hamburg Germany
- Departamento de Química FísicaUniversidad del País Vasco 48940 Leioa Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Iker León
- Departamento de Química Física y QuímicaInorgánica, Universidad de Valladolid 47011 Valladolid Spain
| | - Alberto Lesarri
- Departamento de Química Física y QuímicaInorgánica, Universidad de Valladolid 47011 Valladolid Spain
| | - Brooks H. Pate
- Department of ChemistryUniversity of Virginia McCormick Rd. Charlottesville VA 22904 USA
| | - Rodrigo Martínez
- Departamento de QuímicaUniversidad de La Rioja 26006 Logroño Spain
| | - Judith Millán
- Departamento de QuímicaUniversidad de La Rioja 26006 Logroño Spain
| | - José A. Fernández
- Departamento de Química FísicaUniversidad del País Vasco 48080 Bilbao Spain
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12
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Pérez C, León I, Lesarri A, Pate BH, Martínez R, Millán J, Fernández JA. Isomerism of the Aniline Trimer. Angew Chem Int Ed Engl 2018. [DOI: 10.1002/ange.201808602] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Cristóbal Pérez
- Deutsches Elektronen-Synchrotron DESY Notkestrasse 85 22607 Hamburg Germany
- Departamento de Química FísicaUniversidad del País Vasco 48940 Leioa Spain
- Ikerbasque, Basque Foundation for Science 48013 Bilbao Spain
| | - Iker León
- Departamento de Química Física y QuímicaInorgánica, Universidad de Valladolid 47011 Valladolid Spain
| | - Alberto Lesarri
- Departamento de Química Física y QuímicaInorgánica, Universidad de Valladolid 47011 Valladolid Spain
| | - Brooks H. Pate
- Department of ChemistryUniversity of Virginia McCormick Rd. Charlottesville VA 22904 USA
| | - Rodrigo Martínez
- Departamento de QuímicaUniversidad de La Rioja 26006 Logroño Spain
| | - Judith Millán
- Departamento de QuímicaUniversidad de La Rioja 26006 Logroño Spain
| | - José A. Fernández
- Departamento de Química FísicaUniversidad del País Vasco 48080 Bilbao Spain
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