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Bakowies D. ATOMIC-2 Protocol for Thermochemistry. J Chem Theory Comput 2022; 18:4142-4163. [PMID: 35658473 DOI: 10.1021/acs.jctc.1c01272] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
ATOMIC is a midlevel thermochemistry protocol that uses Pople's concept of bond separation reactions (BSRs) as a theoretical framework to reduce computational demands in the evaluation of atomization energies and enthalpies of formation. Various composite models are available that approximate bond separation energies at the complete-basis-set limit of all-electron CCSD(T), each balancing computational cost with achievable accuracy. Evaluated energies are then combined with very high-level, precomputed atomization energies of all auxiliary molecules appearing in the BSR to obtain the atomization energy of the molecule under study. ATOMIC-2 is a new version of the protocol that retains the overall concept and all previously defined composite models but improves on ATOMIC-1 in various other ways: Geometry optimization and zero-point-energy evaluation are performed at the density functional level (PBE0-D3/6-311G(d)), which shows significant computational savings and better accuracy than the previously employed RI-MP2/cc-pVTZ. The BSR framework is improved, using more accurate complete-basis-set (CBS) extrapolations toward the Full CI limit for the atomization energies of all auxiliary molecules. Finally, and most importantly, an error and uncertainty model termed ATOMIC-2um is added that estimates average bias and uncertainty for each of the atomization energy contributions that arise from the simplified treatment of some contributions to bond separation energies (CCSD(T)) and the neglect of others (such as higher order, scalar relativistic, or diagonal Born-Oppenheimer corrections) or from residual error in the energies of auxiliary molecules. Large and diverse benchmarks including up to 1179 molecules are used to evaluate necessary reference data and to correlate the observed error for each of the contributions with appropriate proxies that are available without additional quantum-chemical calculations for a particular molecule and represent its size and type. The implementation of ATOMIC-2 considers neutral, closed-shell molecules containing H, C, N, O, and F atoms; compared to ATOMIC-1, the framework has been extended to cover a few challenging but rare bond topologies. In comparison to highly accurate reference data for 184 molecules taken from the ATcT database (V. 1.122r), regular ATOMIC-2 shows noticeable underbinding, but the bias-corrected protocol ATOMIC-2um is found to be more accurate than either ATOMIC-1 or standard Gaussian-4 theory, and the uncertainty model is consistent with statistics of actually observed errors. Problems arising from ambiguous or challenging Lewis-valence structures defining BSRs are discussed, and computational efficiency is demonstrated. Computer code is made available to perform ATOMIC-2um analyses.
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Affiliation(s)
- Dirk Bakowies
- Institute of Physical Chemistry, Department of Chemistry, University of Basel, Klingelbergstraße 80, CH 4056 Basel, Switzerland
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Loukhovitski BI, Pelevkin AV, Sharipov AS. Toward size-dependent thermodynamics of nanoparticles from quantum chemical calculations of small atomic clusters: a case study of (B 2O 3) n. Phys Chem Chem Phys 2022; 24:13130-13148. [PMID: 35587125 DOI: 10.1039/d2cp01672a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a method for obtaining canonical partition functions and, accordingly, temperature-dependent thermodynamics of arbitrary-sized (nano) particles from electronic structure calculations of the corresponding small size atomic clusters. The guiding idea here is to extrapolate the basic properties underlying the thermochemistry of clusters (electronic energies, rotational constants, and vibrational frequencies) rather than the thermodynamic functions themselves. The thus obtained scaling dependences for these basic properties expressed in a simple analytical form provide an efficient tool for fast evaluation of the size-selected thermochemical data for particles of any nuclearity. To exemplify the performance of the methodology, neutral stoichiometric boron oxide clusters are considered. To this end, the geometry and various physical properties of the energetically lowest-lying (B2O3)n (n = 1,…,8) structures are found using density functional theory and the authors' multistage hierarchical procedure customized for global optimization of quite large cluster structures. With these data and based on the physically consistent scaling regularities for the principal cluster properties, the size-selected thermodynamic functions of boron oxide particles in the gas phase, such as enthalpy, entropy, and specific heat capacity, are derived. The variation of these characteristics with increasing cluster size is discussed in detail as well. To facilitate handling of the temperature and size dependences we have found here in further chemical kinetic and equilibrium modeling, the tabulated thermodynamic functions of interest are fitted for n = 1,…,1000 to the standard seven-parameter Chemkin polynomials.
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Affiliation(s)
- Boris I Loukhovitski
- Central Institute of Aviation Motors, Aviamotornaya 2, Moscow 111116, Russia. .,Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya 13 Bldg. 2, Moscow 125412, Russia
| | - Alexey V Pelevkin
- Central Institute of Aviation Motors, Aviamotornaya 2, Moscow 111116, Russia. .,Prokhorov General Physics Institute of the Russian Academy of Sciences, Vavilova 38, Moscow 119991, Russia
| | - Alexander S Sharipov
- Central Institute of Aviation Motors, Aviamotornaya 2, Moscow 111116, Russia. .,Joint Institute for High Temperatures of the Russian Academy of Sciences, Izhorskaya 13 Bldg. 2, Moscow 125412, Russia
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How much aromatic are naphthalene and graphene? COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.112504] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Basis Set Effects in the Description of the Cl-O Bond in ClO and XClO/ClOX Isomers (X = H, O, and Cl) Using DFT and CCSD(T) Methods. J CHEM-NY 2019. [DOI: 10.1155/2019/4057848] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The performance of a group of density functional methods of progressive complexity for the description of the ClO bond in a series of chlorine oxides was investigated. The simplest ClO radical species and the two isomeric structures XClO/ClOX for each X = H, Cl, and O were studied using the PW91, TPSS, B3LYP, PBE0, M06, M06-2X, BMK, and B2PLYP functionals. Geometry optimizations and reaction enthalpies and enthalpies of formation for each species were calculated using Pople basis sets and the (aug)-cc-pVnZ Dunning sets, with n = D, T, Q, 5, and 6. For the calculation of enthalpies of formation, atomization and isodesmic reactions were employed. Both the precision of the methods with respect to the increase of the basis sets, as well as their accuracy, were gauged by comparing the results with the more accurate CCSD(T) calculations, performed using the same basis sets as for the DFT methods. The results obtained employing composite chemical methods (G4, CBS-QB3, and W1BD) were also used for the comparisons, as well as the experimental results when they are available. The results obtained show that error compensation is the key for successful description of molecular properties (geometries and energies) by carefully selecting the method and basis sets. In general, expansion of the one-electron basis set to the limit of completeness does not improve results at the DFT level, but just the opposite. The enthalpies of formation calculated at the CCSD(T)/aug-cc-pV6Z for the species considered are generally in agreement with experimental determinations and the most accurate theoretical values. Different sources of error in the calculations are discussed in detail.
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Zhang IY, Wu J, Xu X. Accurate heats of formation of polycyclic saturated hydrocarbons predicted by using the XYG3 type of doubly hybrid functionals. J Comput Chem 2018; 40:1113-1122. [PMID: 30379331 DOI: 10.1002/jcc.25726] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 09/26/2018] [Accepted: 09/27/2018] [Indexed: 11/06/2022]
Abstract
Polycyclic saturated hydrocarbons (PSHs) are attractive candidates as hydrocarbon propellants. To assess their potential values, one of the key factors is to determine their energy contents, such as to calculate their heats of formation (HOF). In this work, we have calculated HOFs for a set of 36 PSHs including exo-Tricyclo[5.2.1.0(2,6) ] decane, the principal component of the high-energy density hydrocarbon fuel commonly identified as JP-10. The results from B3LYP, B3LYP-D3BJ, M06-2X, B2PLYP, B2PLYP-D3BJ, and the XYG3 type of doubly hybrid (xDH) functionals are presented. It is demonstrated here that the xDH functionals yield accurate HOFs in good agreement with those from experiments or the G4 theory. In particular, XYGJ-OS, a low scaling xDH functional, is shown to hold the promise for accurate prediction of HOFs for PSHs of larger sizes. © 2018 Wiley Periodicals, Inc.
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Affiliation(s)
- Igor Ying Zhang
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Jianming Wu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University, Shanghai 200433, China
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Jafari M, Ghani K, Keshavarz MH, Derikvandy F. Assessing the Detonation Performance of New Tetrazole Base High Energy Density materials. PROPELLANTS EXPLOSIVES PYROTECHNICS 2018. [DOI: 10.1002/prep.201800176] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Mohammad Jafari
- Department of Chemistry, Faculty of ScienceMalek-ashtar University of Technology Shahin-shahr Isfahan, I.R. Iran
| | - Kamal Ghani
- Department of Chemistry, Faculty of ScienceMalek-ashtar University of Technology Shahin-shahr Isfahan, I.R. Iran
| | - Mohammad Hossein Keshavarz
- Department of Chemistry, Faculty of ScienceMalek-ashtar University of Technology Shahin-shahr Isfahan, I.R. Iran
| | - Fatemeh Derikvandy
- Department of Chemistry, Faculty of ScienceMalek-ashtar University of Technology Shahin-shahr Isfahan, I.R. Iran
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Khan AM, Shawon J, Halim MA. Multiple receptor conformers based molecular docking study of fluorine enhanced ethionamide with mycobacterium enoyl ACP reductase (InhA). J Mol Graph Model 2017; 77:386-398. [DOI: 10.1016/j.jmgm.2017.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Revised: 09/07/2017] [Accepted: 09/09/2017] [Indexed: 01/11/2023]
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Jafari M, Keshavarz MH, Noorbala MR, Kamalvand M. A Reliable Method for Prediction of the Condensed Phase Enthalpy of Formation of High Nitrogen Content Materials through their Gas Phase Information. ChemistrySelect 2016. [DOI: 10.1002/slct.201601184] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
- Mohammad Jafari
- Department of Chemistry; Malek-ashtar University of Technology; Shahin-shahr, P.O. Box 83145/115 Islamic Republic of Iran
| | - Mohammad Hossein Keshavarz
- Department of Chemistry; Malek-ashtar University of Technology; Shahin-shahr, P.O. Box 83145/115 Islamic Republic of Iran
| | - Mohammad Reza Noorbala
- Department of Chemistry, Faculty of Science; Yazd University; Yazd, P.O. Box 89195/741 Islamic Republic of Iran
| | - Mohammad Kamalvand
- Department of Chemistry, Faculty of Science; Yazd University; Yazd, P.O. Box 89195/741 Islamic Republic of Iran
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Simmie JM, Sheahan JN. Validation of a Database of Formation Enthalpies and of Mid-Level Model Chemistries. J Phys Chem A 2016; 120:7370-84. [DOI: 10.1021/acs.jpca.6b07503] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- J. M. Simmie
- Combustion Chemistry Centre & School of Chemistry, National University of Ireland, Galway H91 TK33, Ireland
| | - J. N. Sheahan
- School of Mathematics & Statistics, National University of Ireland, Galway H91 TK33, Ireland
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Zhou Y, Wu J, Xu X. Improving B3LYP heats of formation with three-dimensional molecular descriptors. J Comput Chem 2016; 37:1175-90. [DOI: 10.1002/jcc.24308] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2015] [Revised: 12/27/2015] [Accepted: 12/29/2015] [Indexed: 11/09/2022]
Affiliation(s)
- Yuwei Zhou
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University; Shanghai 200433 China
| | - Jianming Wu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University; Shanghai 200433 China
| | - Xin Xu
- Collaborative Innovation Center of Chemistry for Energy Materials, Shanghai Key Laboratory of Molecular Catalysis and Innovative Materials, MOE Laboratory for Computational Physical Science, Department of Chemistry, Fudan University; Shanghai 200433 China
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12
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Leach S. Size effects on cation heats of formation. IV. Methyl and ethyl substitutions in methyl, methylene, acetylene and ethene. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1031838] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Lokhat D, Ramjugernath D, Starzak M. Gas-phase equilibrium constants for the thermally initiated oxidation of hexafluoropropene with molecular oxygen. J PHYS ORG CHEM 2015. [DOI: 10.1002/poc.3437] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- David Lokhat
- Reactor Technology Research Group, School of Engineering; University of KwaZulu-Natal; Durban 4041 South Africa
| | - Deresh Ramjugernath
- Reactor Technology Research Group, School of Engineering; University of KwaZulu-Natal; Durban 4041 South Africa
| | - Maciej Starzak
- Reactor Technology Research Group, School of Engineering; University of KwaZulu-Natal; Durban 4041 South Africa
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Kamalvand M, Keshavarz MH, Jafari M. Prediction of the Strength of Energetic Materials Using the Condensed and Gas Phase Heats of Formation. PROPELLANTS EXPLOSIVES PYROTECHNICS 2014. [DOI: 10.1002/prep.201400139] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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16
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Reliable approach for prediction of heats of formation of polycyclic saturated hydrocarbons using recently developed density functionals. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.01.015] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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