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Wu H, Payne AM, Pang HW, Menon A, Grambow CA, Ranasinghe DS, Dong X, Grinberg Dana A, Green WH. Toward Accurate Quantum Mechanical Thermochemistry: (1) Extensible Implementation and Comparison of Bond Additivity Corrections and Isodesmic Reactions. J Phys Chem A 2024; 128:4335-4352. [PMID: 38752854 DOI: 10.1021/acs.jpca.4c00949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/31/2024]
Abstract
Obtaining accurate enthalpies of formation of chemical species, ΔHf, often requires empirical corrections that connect the results of quantum mechanical (QM) calculations with the experimental enthalpies of elements in their standard state. One approach is to use atomization energy corrections followed by bond additivity corrections (BACs), such as those defined by Petersson et al. or Anantharaman and Melius. Another approach is to utilize isodesmic reactions (IDRs) as shown by Buerger et al. We implement both approaches in Arkane, an open-source software that can calculate species thermochemistry using results from various QM software packages. In this work, we collect 421 reference species from the literature to derive ΔHf corrections and fit atomization energy corrections and BACs for 15 commonly used model chemistries. We find that both types of BACs yield similar accuracy, although Anantharaman- and Melius-type BACs appear to generalize better. Furthermore, BACs tend to achieve better accuracy than IDRs for commonly used model chemistries, and IDRs can be less robust because of the sensitivity to the chosen reference species and reactions. Overall, Anantharaman- and Melius-type BACs are our recommended approach for achieving accurate QM corrections for enthalpies.
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Affiliation(s)
- Haoyang Wu
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - A Mark Payne
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Hao-Wei Pang
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Angiras Menon
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Colin A Grambow
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Duminda S Ranasinghe
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Xiaorui Dong
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Alon Grinberg Dana
- Wolfson Department of Chemical Engineering and Grand Technion Energy Program, Technion─Israel Institute of Technology, Haifa 3200003, Israel
| | - William H Green
- Department of Chemical Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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2
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Zhao SS, He ZH, Liu X, Shen Y, Tan XC, Wang Q, Yan J, Zhu WW. Dialdehyde starch-enclosed silver nanoparticles substrate with controlled-release "hotspots" for ultrasensitive SERS detection of thiabendazole. Food Chem 2024; 436:137706. [PMID: 37844511 DOI: 10.1016/j.foodchem.2023.137706] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2023] [Revised: 08/28/2023] [Accepted: 10/07/2023] [Indexed: 10/18/2023]
Abstract
Pesticide residues have long been a major concern for food safety. In this study, a dialdehyde starch-encapsulated silver nanoparticles composite with controlled-release "hotspots" was developed as a surface-enhanced Raman scattering (SERS) substrate. At room temperature, most of the Ag NPs were encapsulated in dialdehyde starch, which is beneficial for improving stability, and when heated to the gelatinization point, Ag NPs are completely released and abundant hot spots are formed. We demonstrated sensitive detection of thiabendazole (TBZ) in or on the surface of an apple by means of two ways, i.e., detecting the analyte in solution after pretreatment and in-situ detecting the analyte by using a flexible paper-based substrate. The results showed that the detection limits of TBZ by the two ways were 0.052 ppm and 0.051 ppm respectively, and the recoveries of TBZ range from 96.80 % to 105.46 %. Overall, this SERS substrate shows great potential for pesticide residue detection in food.
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Affiliation(s)
- Song-Song Zhao
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China
| | - Zhi-Hao He
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China
| | - Xin Liu
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China
| | - Yu Shen
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China
| | - Xue-Cai Tan
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China
| | - Qi Wang
- College of Material Science and Engineering, Kunming University of Science and Technology, Kunming 615000, China
| | - Jun Yan
- College of Chemistry and Chemical Engineering, Guangxi Minzu University, Key Laboratory of Applied Analytical Chemistry (Guangxi Minzu University), Education Department of Guangxi Zhuang Autonomous Region, Key Laboratory of Chemistry and Engineering of Forest Products of State Ethnic Affairs Commission, Guangxi Collaborative Innovation Center for Chemistry and Engineering of Forest Products, Nanning 530006, China.
| | - Wei-Wei Zhu
- School of Materials and Environment, Guangxi Minzu University, Nanning 530006, China.
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3
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Paulechka E, Kazakov A. Formation Enthalpies of C 3 and C 4 Brominated Hydrocarbons: Bringing Together Classical Thermodynamics, Modern Mass Spectrometry, and High-Level Ab Initio Calculations. J Phys Chem A 2024; 128:1339-1357. [PMID: 38324611 DOI: 10.1021/acs.jpca.3c04937] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2024]
Abstract
The enthalpies of formation of brominated C3-C4 hydrocarbons were critically evaluated using experimental data sources ranging from classical thermodynamics methods to modern high-precision mass spectrometry and reported in a time span of a century. The experimental data were used in conjunction with the results of modern high-level ab initio calculations. To facilitate quantitative analysis, a recently developed local coupled cluster-based computational protocol was extended to organic compounds containing univalent Br. Several erroneous data sources were identified in a course of the study. Possible reasons for the inconsistency between the ΔfHm° values recommended by the Committee on Data of the International Science Council (CODATA) and Active Thermochemical Tables for HBr in the gas and aqueous solution were discussed. The most up-to-date recommendations based on the comprehensive analysis of collected information are provided for 23 brominated hydrocarbons. For several compounds under consideration, the recommended values were previously lacking, while improved values and uncertainties were obtained for those with existing recommendations.
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Affiliation(s)
- Eugene Paulechka
- Thermodynamics Research Center, National Institute of Standards and Technology, Boulder, Colorado 80305-3337, United States
| | - Andrei Kazakov
- Thermodynamics Research Center, National Institute of Standards and Technology, Boulder, Colorado 80305-3337, United States
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4
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Eisele NF, Rahrt R, Giachanou L, Shikho F, Koszinowski K. Gas-Phase Alkali-Metal Cation Affinities of Stabilized Enolates. Chemistry 2023; 29:e202302540. [PMID: 37752885 DOI: 10.1002/chem.202302540] [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: 08/04/2023] [Revised: 09/23/2023] [Accepted: 09/25/2023] [Indexed: 09/28/2023]
Abstract
The chemistry of alkali-metal enolates is dominated by ion pairing. To improve our understanding of the intrinsic interactions between the alkali-metal cations and the enolate anions, we have applied Cooks' kinetic method to determine relative M+ (M=Li, Na, K) affinities of the stabilized enolates derived from acetylacetone, ethyl acetoacetate, diethyl malonate, ethyl cyanoacetate, 2-cyanoacetamide, and methyl malonate monoamide in the gas phase. Quantum chemical calculations support the experimental results and moreover afford insight into the structures of the alkali-metal enolate complexes. The affinities decrease with increasing size of the alkali-metal cations, reflecting weaker electrostatic interactions and lower charge densities of the free M+ ions. For the different enolates, a comparison of their coordinating abilities is complicated by the fact that some of the free anions undergo conformational changes resulting in stabilizing intramolecular interactions. If these complicating effects are disregarded, the M+ affinities correlate with the electron density of the chelating functionalities, that is, the carbonyl and/or the nitrile groups of the enolates. A comparison with the known association constants of the corresponding alkali-metal enolates in solution points to the importance of solvation effects for these systems.
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Affiliation(s)
- Niklas F Eisele
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Rene Rahrt
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Lamprini Giachanou
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Fadi Shikho
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Georg-August-Universität Göttingen, Tammannstraße 2, 37077, Göttingen, Germany
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Lukyanova VA, Kuznetsov VV, Konstantinova NM, Dmitrenok AS, Kosaya MP, Dorofeeva OV, Druzhinina AI. Enthalpy of formation of 6-phenyl-1,5-diazabicyclo[3.1.0]hexane by combustion calorimetry and theoretical approach for efficient prediction of thermochemistry of diaziridines. Phys Chem Chem Phys 2023; 25:25289-25298. [PMID: 37701931 DOI: 10.1039/d3cp03290f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/14/2023]
Abstract
The combustion energy and standard molar enthalpy of formation of crystalline 6-phenyl-1,5-diazabicyclo[3.1.0]hexane (PDABH) were determined using an isoperibolic calorimeter with a static bomb. PDABH is the first diaziridine for which the experimental value of the enthalpy of formation was obtained. This value was validated by the theoretical values of gas phase enthalpy of formation and enthalpy of sublimation. The gas phase enthalpy of formation was calculated using the DLPNO-CCSD(T1)/CBS method in conjunction with isodesmic-type reactions. This method was chosen in comparison to another high quality evaluative method (G4), which has been shown to provide unreliable results for cyclic nitrogen containing compounds. The descriptors of the molecular electrostatic potential (MEP) were used to estimate the enthalpy of sublimation of PDABH. The proposed MEP model is based on experimental enthalpies of sublimation for 75 compounds structurally similar to PDABH. The high-level ab initio calculations of gas phase enthalpies of formation combined with enthalpies of sublimations estimated using descriptors of MEP allow predicting the enthalpies of formation of diaziridines in the solid phase.
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Affiliation(s)
- Vera A Lukyanova
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Vladimir V Kuznetsov
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | | | - Andrey S Dmitrenok
- N. D. Zelinsky Institute of Organic Chemistry, Russian Academy of Sciences, 119991 Moscow, Russia
| | - Maria P Kosaya
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Olga V Dorofeeva
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
| | - Anna I Druzhinina
- Department of Chemistry, M. V. Lomonosov Moscow State University, 119991 Moscow, Russia.
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6
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Ariai J, Gellrich U. The entropic penalty for associative reactions and their physical treatment during routine computations. Phys Chem Chem Phys 2023; 25:14005-14015. [PMID: 37161492 DOI: 10.1039/d3cp00970j] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
A systematic study of the entropic penalty for associative reactions is presented. It is shown that computed solution-phase Gibbs free energies typically overestimate entropic contributions. This entropic penalty for associative reactions in solution, i.e., if the number of particles decreases along the reaction coordinate (sum of stoichiometric numbers ), originates from the insufficient treatment of entropic effects by implicit solvent models. We propose an additive correction scheme to Gibbs free energies that is suitable for routine applications by non-expert users. This correction is based on Garza's formalism for the solution-phase entropy [A. J. Garza, J. Chem. Theory Comput., 2019, 15, 3204.] that is physically sound and embedded into an efficient black-box type algorithm. To critically evaluate the entropic penalty and its proposed treatment, we compiled an experimental benchmark set of 31 ΔrG and 22 in 15 different solvents. Using a representative best-practice computational protocol (at wave function theory (WFT) based DLPNO-CCSD(T) and density functional theory (DFT) based revDSD-PBEP86-D4 level with an implicit solvent model), we determined a sizeable entropic penalty ranging from 2-11 kcal mol-1. Using the correction scheme presented herein, the entropic penalty is corrected to the chemical accuracy of ≤1 kcal mol-1 (WFT and DFT). The same applies to at the WFT level. Barriers at the DFT level are overestimated by 2 kcal mol-1 (classic) and underestimated by 2 kcal mol-1 (corrected). This effect is attributed to the finding that barriers computed at the DFT level are systematically 2-3 kcal mol-1 lower than barriers obtained with WFT.
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Affiliation(s)
- Jama Ariai
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
| | - Urs Gellrich
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392 Giessen, Germany.
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7
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Altun A, Riplinger C, Neese F, Bistoni G. Exploring the Accuracy Limits of PNO-Based Local Coupled-Cluster Calculations for Transition-Metal Complexes. J Chem Theory Comput 2023; 19:2039-2047. [PMID: 36917767 PMCID: PMC10100528 DOI: 10.1021/acs.jctc.3c00087] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/15/2023]
Abstract
While the domain-based local pair natural orbital coupled-cluster method with singles, doubles, and perturbative triples (DLPNO-CCSD(T)) has proven instrumental for computing energies and properties of large and complex systems accurately, calculations on first-row transition metals with a complex electronic structure remain challenging. In this work, we identify and address the two main error sources that influence the DLPNO-CCSD(T) accuracy in this context, namely, (i) correlation effects from the 3s and 3p semicore orbitals and (ii) dynamic correlation-induced orbital relaxation (DCIOR) effects that are not described by the local MP2 guess. We present a computational strategy that allows us to completely eliminate the DLPNO error associated with semicore correlation effects, while increasing, at the same time, the efficiency of the method. As regards the DCIOR effects, we introduce a diagnostic for estimating the deviation between DLPNO-CCSD(T) and canonical CCSD(T) for systems with significant orbital relaxation.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Department of Chemistry, Biology, and Biotechnology, University of Perugia, 06123 Perugia, Italy
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8
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Melin TRL, Harell P, Ali B, Loganathan N, Wilson AK. Thermochemistry of per- and polyfluoroalkyl substances. J Comput Chem 2023; 44:570-580. [PMID: 36334029 PMCID: PMC10098614 DOI: 10.1002/jcc.27023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2022] [Revised: 09/08/2022] [Accepted: 09/30/2022] [Indexed: 11/06/2022]
Abstract
The determination of gas phase thermochemical properties of per- and polyfluoroalkyl substances (PFAS) is central to understanding the long-range transport behavior of PFAS in the atmosphere. Prior gas-phase studies have reported the properties of perfluorinated sulfonic acid (PFOS) and perfluorinated octanoic acid (PFOA). Here, this study reports the gas phase enthalpies of formation of short- and long-chain PFAS and their precursor molecules determined using density functional theory (DFT) and ab initio approaches. Two density functionals, two ab initio methods and an empirical method were used to compute enthalpies of formation with the total atomization approach and an isogyric reaction. The performance of the computational methods employed in this work were validated against the experimental enthalpies of linear alkanoic acids and perfluoroalkanes. The gas-phase determinations will be useful for future studies of PFAS in the atmosphere, and the methodological choices will be helpful in the study of other PFAS.
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Affiliation(s)
- Timothé R L Melin
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Preston Harell
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | - Betoul Ali
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
| | | | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan, USA
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9
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Fang X, Li Y, Kua YL, Chew ZL, Gan S, Tan KW, Lee TZE, Cheng WK, Lau HLN. Insights on the potential of natural deep eutectic solvents (NADES) to fine-tune durian seed gum for use as edible food coating. Food Hydrocoll 2022. [DOI: 10.1016/j.foodhyd.2022.107861] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
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10
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Döntgen M, Wildenberg A, Heufer KA. Theoretical Investigation of Key Properties of the Pyrolysis of Methyl, Ethyl, and Dimethyl Dioxolane Isomers. J Phys Chem A 2022; 126:8326-8336. [DOI: 10.1021/acs.jpca.2c06564] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Malte Döntgen
- Chair of High Pressure Gas Dynamics, Shock Wave Laboratory, RWTH Aachen University, 52056Aachen, Germany
| | - Alina Wildenberg
- Chair of High Pressure Gas Dynamics, Shock Wave Laboratory, RWTH Aachen University, 52056Aachen, Germany
| | - K. Alexander Heufer
- Chair of High Pressure Gas Dynamics, Shock Wave Laboratory, RWTH Aachen University, 52056Aachen, Germany
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11
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Development, structural, spectroscopic and in silico investigation of new complexes relevant as anti-toxoplasma metallopharmacs. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133380] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
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12
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Xu Z, Xu H, Liu L, Jiang R, Ren H, Li X. High-precision standard enthalpy of formation for polycyclic aromatic hydrocarbons predicting from general connectivity based hierarchy with discrete correction of atomization energy. Front Chem Sci Eng 2022. [DOI: 10.1007/s11705-022-2184-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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13
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Koszinowski K, Rahrt R. Anionic Dimers of Fluorinated Alcohols. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2022; 33:1411-1418. [PMID: 35609237 DOI: 10.1021/jasms.2c00070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Negative-ion mode electrospray ionization of solutions of ethanol (RF0OH), 2-fluoroethanol (RF1OH), 2,2-difluoroethanol (RF2OH), and/or 2,2,2-trifluoroethanol (RF3OH) produces anionic dimers of the types (RFnO)2H- and (RFnO)(RFn+1O)H-. The exchange reactions of these anionic dimers with the neutral alcohols are examined in a quadrupole-ion trap to extract kinetic data, from which the reaction Gibbs energies are obtained. In all cases, the formation of anionic dimers containing the more highly fluorinated alcohols is favored. Quantum chemical calculations confirm this trend and, besides affording structural data, also determine the dissociation energies of the anionic dimers. These dissociation energies are much higher than those of the corresponding neutral dimers and increase further for the more highly fluorinated alcohols due to the stronger hydrogen-bond donor ability of the latter. The present results on the interaction of individual alkoxide anions and neutral alcohol molecules contribute to a better understanding of the association of the fluorinated alcohols in solution.
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Affiliation(s)
- Konrad Koszinowski
- Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077 Göttingen, Germany
| | - Rene Rahrt
- Universität Göttingen, Institut für Organische und Biomolekulare Chemie, Tammannstr. 2, 37077 Göttingen, Germany
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14
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Zhang X, Adelman SL, Arko BT, De Silva CR, Su J, Kozimor SA, Mocko V, Shafer JC, Stein BW, Schreckenbach G, Batista ER, Yang P. Advancing the Am Extractant Design through the Interplay among Planarity, Preorganization, and Substitution Effects. Inorg Chem 2022; 61:11556-11570. [PMID: 35866884 DOI: 10.1021/acs.inorgchem.2c00534] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Advancing the field of chemical separations is important for nearly every area of science and technology. Some of the most challenging separations are associated with the americium ion Am(III) for its extraction in the nuclear fuel cycle, 241Am production for industrial usage, and environmental cleanup efforts. Herein, we study a series of extractants, using first-principle calculations, to identify the electronic properties that preferentially influence Am(III) binding in separations. As the most used extractant family and because it affords a high degree of functionalization, the polypyridyl family of extractants is chosen to study the effects of the planarity of the structure, preorganization of coordinating atoms, and substitution of various functional groups. The actinyl ions are used as a structurally simplified surrogate model to quickly screen the most promising candidates that can separate these metal ions. The down-selected extractants are then tested for the Am(III)/Eu(III) system. Our results show that π interactions, especially those between the central terpyridine ring and Am(III), play a crucial role in separation. Adding an electron-donating group onto the terpyridine backbone increases the binding energies to Am(III) and stabilizes Am-terpyridine coordination. Increasing the planarity of the extractant increases the binding strength as well, although this effect is found to be rather weak. Preorganizing the coordinating atoms of an extractant to their binding configuration as in the bound metal complex speeds up the binding process and significantly improves the kinetics of the separation process. This conclusion is validated by the synthesized 1,2-dihydrodipyrido[4,3-b;5,6-b]acridine (13) extractant, a preorganized derivative of the terpyridine extractant, which we experimentally showed was four times more effective than terpyridine at separating Am3+ from Eu3+ (SFAm/Eu ∼ 23 ± 1).
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Affiliation(s)
- Xiaobin Zhang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Sara L Adelman
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Brian T Arko
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States.,Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Channa R De Silva
- Department of Chemistry & Physics, Western Carolina University, Cullowhee, North Carolina 28723, United States
| | - Jing Su
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Stosh A Kozimor
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Veronika Mocko
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Jenifer C Shafer
- Department of Chemistry, Colorado School of Mines, Golden, Colorado 80401, United States
| | - Benjamin W Stein
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, Manitoba, Canada R3T 2N2
| | - Enrique R Batista
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Ping Yang
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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15
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Inverse molecular design of alkoxides and phenoxides for aqueous direct air capture of CO 2. Proc Natl Acad Sci U S A 2022; 119:e2123496119. [PMID: 35709322 DOI: 10.1073/pnas.2123496119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Aqueous direct air capture (DAC) is a key technology toward a carbon negative infrastructure. Developing sorbent molecules with water and oxygen tolerance and high CO2 binding capacity is therefore highly desired. We analyze the CO2 absorption chemistries on amines, alkoxides, and phenoxides with density functional theory calculations, and perform inverse molecular design of the optimal sorbent. The alkoxides and phenoxides are found to be more suitable for aqueous DAC than amines thanks to their water tolerance (lower pKa prevents protonation by water) and capture stoichiometry of 1:1 (2:1 for amines). All three molecular systems are found to generally obey the same linear scaling relationship (LSR) between [Formula: see text] and [Formula: see text], since both CO2 and proton are bonded to the nucleophilic (alkoxy or amine) binding site through a majorly [Formula: see text] bonding orbital. Several high-performance alkoxides are proposed from the computational screening. Phenoxides have comparatively poorer correlation between [Formula: see text] and [Formula: see text], showing promise for optimization. We apply a genetic algorithm to search the chemical space of substituted phenoxides for the optimal sorbent. Several promising off-LSR candidates are discovered. The most promising one features bulky ortho substituents forcing the CO2 adduct into a perpendicular configuration with respect to the aromatic ring. In this configuration, the phenoxide binds CO2 and a proton using different molecular orbitals, thereby decoupling the [Formula: see text] and [Formula: see text]. The [Formula: see text] trend and off-LSR behaviors are then confirmed by experiments, validating the inverse molecular design framework. This work not only extensively studies the chemistry of the aqueous DAC, but also presents a transferrable computational workflow for understanding and optimization of other functional molecules.
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16
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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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17
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Altun A, Neese F, Bistoni G. Open-Shell Variant of the London Dispersion-Corrected Hartree-Fock Method (HFLD) for the Quantification and Analysis of Noncovalent Interaction Energies. J Chem Theory Comput 2022; 18:2292-2307. [PMID: 35167304 PMCID: PMC9009084 DOI: 10.1021/acs.jctc.1c01295] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The London dispersion
(LD)-corrected Hartree–Fock (HF) method
(HFLD) is an ab initio approach for the quantification
and analysis of noncovalent interactions (NCIs) in large systems that
is based on the domain-based local pair natural orbital coupled-cluster
(DLPNO-CC) theory. In the original HFLD paper, we discussed the implementation,
accuracy, and efficiency of its closed-shell variant. Herein, an extension
of this method to open-shell molecular systems is presented. Its accuracy
is tested on challenging benchmark sets for NCIs, using CCSD(T) energies
at the estimated complete basis set limit as reference. The HFLD scheme
was found to be as accurate as the best-performing dispersion-corrected
exchange-correlation functionals, while being nonempirical and equally
efficient. In addition, it can be combined with the well-established
local energy decomposition (LED) for the analysis of NCIs, thus yielding
additional physical insights.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany.,Department of Chemistry, Biology and Biotechnology, University of Perugia, 06123 Perugia, Italy
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18
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Minenkova I, Otlyotov AA, Cavallo L, Minenkov Y. Gas-phase thermochemistry of polycyclic aromatic hydrocarbons: an approach integrating the quantum chemistry composite scheme and reaction generator. Phys Chem Chem Phys 2022; 24:3163-3181. [PMID: 35040851 DOI: 10.1039/d1cp03702a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We introduce a protocol aimed at predicting the accurate gas-phase enthalpies of formation of polycyclic aromatic hydrocarbons (PAHs). Automatic generation of a dataset of equilibrated chemical reactions preserving the number of carbon atoms in each hybridization state on each side of equations is at the core of our scheme. The performed tests suggest the recommended enthalpy of formation to be derived via a two-step scheme. First, we consider the reactions with a minimal sum of the total number of particles involved, N, and the absolute difference between the total number of products and reactants, |ΔN|. Second, among these reactions, we identify the one with the smallest absolute reaction enthalpy change, . This approach has been applied to predict the gas-phase enthalpies of formation of 113 PAHs via the Feller-Peterson-Dixon approach. Our calculated values provide the mean absolute deviations of 1.7, 1.9, 4.2, 8.1, and 18.5 kJ mol-1 with respect to the literature group-based error corrected (GBEC) G3MP2B3, ATOMIC (HC), group equivalent M06-2X, GBEC B3LYP, and G4MP2 values. Our predicted values give the mean signed and mean absolute errors of -7.5 and 12.9 kJ mol-1 with respect to the experimental enthalpies of formation. The combination of our predicted and the experimental values provide the solid-state enthalpies of formation, , which are not available for a few species. Approaching these values as well as , producing large discrepancies from the experimental side, would be indispensable for testing and further tuning of computational chemistry approaches.
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Affiliation(s)
- Irina Minenkova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119071, Russian Federation
| | - Arseniy A Otlyotov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation.
| | - Luigi Cavallo
- KAUST Catalysis Center (KCC), King Abdullah University of Science and Technology, Thuwal-23955-6900, Saudi Arabia.
| | - Yury Minenkov
- N. N. Semenov Federal Research Center for Chemical Physics RAS, Kosygina Street 4, 119991 Moscow, Russian Federation. .,Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russian Federation
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19
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Seeger ZL, Izgorodina EI. A DLPNO-CCSD(T) benchmarking study of intermolecular interactions of ionic liquids. J Comput Chem 2022; 43:106-120. [PMID: 34687062 DOI: 10.1002/jcc.26776] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/11/2022]
Abstract
The accuracy of correlation energy recovered by coupled cluster single-, double-, and perturbative triple-excitations, CCSD(T), has led to the method being considered the gold standard of computational chemistry. The application of CCSD(T) has been limited to medium-sized molecular systems due to its steep scaling with molecular size. The recent development of alternative domain-based local pair natural orbital coupled-cluster method, DLPNO-CCSD(T), has significantly broadened the range of chemical systems to which CCSD(T) level calculations can be applied. Condensed systems such as ionic liquids (ILs) have a large contribution from London dispersion forces of up to 150 kJ mol-1 in large-scale clusters. Ionic liquids show appreciable charge transfer effects that result in the increased valence orbital delocalization over the entire ionic network, raising the question whether the application of methods based on localized orbitals is reliable for these semi-Coulombic materials. Here the performance of DLPNO-CCSD(T) is validated for the prediction of correlation interaction energies of two data sets incorporating single-ion pairs of protic and aprotic ILs. DLPNO-CCSD(T) produced results within chemical accuracy with tight parameter settings and a non-iterative treatment of triple excitations. To achieve spectroscopic accuracy of 1 kJ mol-1 , especially for hydrogen-bonded ILs and those containing halides, the DLPNO settings had to be increased by two orders of magnitude and include the iterative treatment of triple excitations, resulting in a 2.5-fold increase in computational cost. Two new sets of parameters are put forward to produce the performance of DLPNO-CCSD(T) within chemical and spectroscopic accuracy.
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Affiliation(s)
- Zoe L Seeger
- School of Chemistry, Monash University, Clayton, Victoria, Australia
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20
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Klippenstein SJ. Spiers Memorial Lecture: theory of unimolecular reactions. Faraday Discuss 2022; 238:11-67. [DOI: 10.1039/d2fd00125j] [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
One hundred years ago, at an earlier Faraday Discussion meeting, Lindemann presented a mechanism that provides the foundation for contemplating the pressure dependence of unimolecular reactions. Since that time, our...
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21
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Abstract
We have applied a combination of tandem-mass spectrometry, quantum-chemical calculations, and statistical rate theory computations to examine the gas phase reactions between the trisarylzincate anions ArXZnPh2- (ArX = p-X-C6H4, X = NMe2, OMe, Me, H, F, and Cl) and 2,2,2-trifluoroethanol at T = 310 ± 20 K. The observed reactions bring about the protonation of one of the aryl anions, which is then released as the corresponding arene, while the formed alkoxide binds to the zinc center. The protonation is faster for the more electron-rich aryl groups and shows a linear Hammett plot if the rate constant for X = NMe2 is discarded from the analysis. Although the reactions are highly exothermic, they proceed only with relatively low efficiencies (0.1% ≤ φ ≤ 1.3%). According to the quantum-chemical calculations, this behavior can be ascribed to the reactions proceeding through a double-well potential with a tight transition structure located at the central barrier. Based on these potential energy surfaces, the statistical rate theory computations can reproduce the measured rate constants within factors of 2 to 8. A comparison of the protolysis of the trisarylzincates with that of the corresponding free aryl anions demonstrates how the coordination to the metal center not only stabilizes the carbanions energetically but also moderates their reactivity. Thus, our gas phase study contributes to a better understanding of the fundamentals of organometallic reactivity.
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Affiliation(s)
- Rene Rahrt
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
| | - Konrad Koszinowski
- Institut für Organische und Biomolekulare Chemie, Universität Göttingen, Tammannstr. 2, Göttingen 37077, Germany
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22
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Dale HJA, Leach AG, Lloyd-Jones GC. Heavy-Atom Kinetic Isotope Effects: Primary Interest or Zero Point? J Am Chem Soc 2021; 143:21079-21099. [PMID: 34870970 DOI: 10.1021/jacs.1c07351] [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
Chemists have many options for elucidating reaction mechanisms. Global kinetic analysis and classic transition-state probes (e.g., LFERs, Eyring) inevitably form the cornerstone of any strategy, yet their application to increasingly sophisticated synthetic methodologies often leads to a wide range of indistinguishable mechanistic proposals. Computational chemistry provides powerful tools for narrowing the field in such cases, yet wholly simulated mechanisms must be interpreted with great caution. Heavy-atom kinetic isotope effects (KIEs) offer an exquisite but underutilized method for reconciling the two approaches, anchoring the theoretician in the world of calculable observables and providing the experimentalist with atomistic insights. This Perspective provides a personal outlook on this synergy. It surveys the computation of heavy-atom KIEs and their measurement by NMR spectroscopy, discusses recent case studies, highlights the intellectual reward that lies in alignment of experiment and theory, and reflects on the changes required in chemical education in the area.
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Affiliation(s)
- Harvey J A Dale
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
| | - Andrew G Leach
- School of Health Sciences, The University of Manchester, Stopford Building, Oxford Road, Manchester M13 9PT, U.K
| | - Guy C Lloyd-Jones
- EaStChem, University of Edinburgh, Joseph Black Building, David Brewster Road, Edinburgh EH9 3FJ, U.K
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23
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Altun A, Ghosh S, Riplinger C, Neese F, Bistoni G. Addressing the System-Size Dependence of the Local Approximation Error in Coupled-Cluster Calculations. J Phys Chem A 2021; 125:9932-9939. [PMID: 34730360 PMCID: PMC8607505 DOI: 10.1021/acs.jpca.1c09106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last two decades, the local approximation has been successfully used to extend the range of applicability of the "gold standard" singles and doubles coupled-cluster method with perturbative triples CCSD(T) to systems with hundreds of atoms. The local approximation error grows in absolute value with the increasing system size, i.e., by increasing the number of electron pairs in the system. In this study, we demonstrate that the recently introduced two-point extrapolation scheme for approaching the complete pair natural orbital (PNOs) space limit in domain-based pair natural orbital CCSD(T) calculations drastically reduces the dependence of the error on the system size, thus opening up unprecedented opportunities for the calculation of benchmark quality relative energies for large systems.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Soumen Ghosh
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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24
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Villegas-Escobar N, Toro-Labbé A, Schaefer HF. Contrasting the Mechanism of H 2 Activation by Monomeric and Potassium-Stabilized Dimeric Al I Complexes: Do Potassium Atoms Exert any Cooperative Effect? Chemistry 2021; 27:17369-17378. [PMID: 34613646 DOI: 10.1002/chem.202103082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/06/2022]
Abstract
Aluminyl anions are low-valent, anionic, and carbenoid aluminum species commonly found stabilized with potassium cations from the reaction of Al-halogen precursors and alkali compounds. These systems are very reactive toward the activation of σ-bonds and in reactions with electrophiles. Various research groups have detected that the potassium atoms play a stabilization role via electrostatic and cation ⋯ π interactions with nearby (aromatic)-carbocyclic rings from both the ligand and from the reaction with unsaturated substrates. Since stabilizing K⋯H bonds are witnessed in the activation of this class of molecules, we aim to unveil the role of these metals in the activation of the smaller and less polarizable H2 molecule, together with a comprehensive characterization of the reaction mechanism. In this work, the activation of H2 utilizing a NON-xanthene-Al dimer, [K{Al(NON)}]2 (D) and monomeric, [Al(NON)]- (M) complexes are studied using density functional theory and high-level coupled-cluster theory to reveal the potential role of K+ atoms during the activation of this gas. Furthermore, we aim to reveal whether D is more reactive than M (or vice versa), or if complicity between the two monomer units exits within the D complex toward the activation of H2 . The results suggest that activation energies using the dimeric and monomeric complexes were found to be very close (around 33 kcal mol-1 ). However, a partition of activation energies unveiled that the nature of the energy barriers for the monomeric and dimeric complexes are inherently different. The former is dominated by a more substantial distortion of the reactants (and increased interaction energies between them). Interestingly, during the oxidative addition, the distortion of the Al complex is minimal, while H2 distorts the most, usually over 0.77 Δ E d i s t ≠ . Overall, it is found here that electrostatic and induction energies between the complexes and H2 are the main stabilizing components up to the respective transition states. The results suggest that the K+ atoms act as stabilizers of the dimeric structure, and their cooperative role on the reaction mechanism may be negligible, acting as mere spectators in the activation of H2 . Cooperation between the two monomers in D is lacking, and therefore the subsequent activation of H2 is wholly disengaged.
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Affiliation(s)
- Nery Villegas-Escobar
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O'Higgins, General Gana 1702, Santiago, 8370854, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602, USA
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25
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Gertig C, Fleitmann L, Hemprich C, Hense J, Bardow A, Leonhard K. CAT-COSMO-CAMPD: Integrated in silico design of catalysts and processes based on quantum chemistry. Comput Chem Eng 2021. [DOI: 10.1016/j.compchemeng.2021.107438] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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26
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Paulechka E, Kazakov A. Efficient Ab Initio Estimation of Formation Enthalpies for Organic Compounds: Extension to Sulfur and Critical Evaluation of Experimental Data. J Phys Chem A 2021; 125:8116-8131. [PMID: 34469173 PMCID: PMC9809154 DOI: 10.1021/acs.jpca.1c05882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The efficient protocol for the estimation of gas-phase enthalpies of formation developed previously for C, H, O, N, and F elements was extended to sulfur. The protocol is based on a local coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] approximation and allows rapid evaluation of compounds with sizes computationally prohibitive to canonical CCSD(T) using quadruple zeta basis sets. As a part of model development, a comprehensive review and critical evaluation of experimental data were performed for 87 sulfur-containing organic and inorganic compounds. A compact model with only three empirical parameters for sulfur introduced to address the effects beyond frozen core CCSD(T) was developed. The model exhibits approximately 2 kJ·mol-1 standard deviation over a set of experimental values for a diverse collection of sulfur-containing compounds. The complete basis set version of the model demonstrates a similar performance and requires only one empirical parameter. Multiple problems with the existing experimental data were identified and discussed. In addition, a lack of reliable data for certain important classes of sulfur compounds was found to impede the model generalization and confident performance assessment.
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27
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Illés Á, Rózsa ZB, Thangaraj R, Décsiné Gombos E, Dóbé S, Giri BR, Szőri M. An experimental and theoretical kinetic study of the reactions of hydroxyl radicals with tetrahydrofuran and two deuterated tetrahydrofurans. Chem Phys Lett 2021. [DOI: 10.1016/j.cplett.2021.138698] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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28
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Lechner MH, Izsák R, Nooijen M, Neese F. A perturbative approach to multireference equation-of-motion coupled cluster. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1939185] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Affiliation(s)
- Marvin H. Lechner
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, USA
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, Waterloo, Canada
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
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29
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Wylie L, Hakatayama-Sato K, Go C, Oyaizu K, Izgorodina EI. Electrochemical characterization and thermodynamic analysis of TEMPO derivatives in ionic liquids. Phys Chem Chem Phys 2021; 23:10205-10217. [PMID: 33481976 DOI: 10.1039/d0cp05350c] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
In this study we investigate the reversibility of the reduction process of three TEMPO derivatives - TEMPOL, 4-cyano-TEMPO, and 4-oxo-TEMPO. The [C2mim][BF4] and [C4mpyr][OTf] ionic liquids (ILs) were used to perform cyclic voltammetry (CV) to analyse the redox potentials of the TEMPO derivatives. The former was previously shown to quench the aminoxy anion of TEMPO through a proton transfer reaction with the cation, whereas the latter supported the irreversibility of the TEMPO reduction process. In CV results on TEMPO derivatives, it was shown that [C4mpyr][OTf] could allow for a high degree of reversibility in the reduction of 4-cyano-TEMPO and a moderate degree of reversibility in the reduction of TEMPOL. In comparison, reduction of 4-cyano-TEMPO was predominantly irreversible in [C2mim][BF4], whilst TEMPOL showed complete irreversibility. 4-Oxo-TEMPO did not show any notable reduction reversibility in either IL tested. Reduction potentials showed little variation between the derivatives and 0.2 V variation between the ILs, with the most negative reduction potential being observed at -1.43 V vs. Fc/Fc+ for TEMPOL in [C4mpyr][OTf]. To explain the varying degrees of reversibility of the reduction process, four types of side reactions involving proton transfer to the aminoxy anion were studied using highly correlated quantum chemical methods. Proton transfer from the IL cation was shown to have the ability to quench all three aminoxy anions depending on the IL used. On average, TEMPOL was shown to be the most susceptible to proton transfer from the IL cation, having an average Gibbs free energy (GFE) of 10.5 kJ mol-1 more negative than that of 4-cyano-TEMPO, which was shown to have the highest GFE of proton transfer. Side reactions between water and aminoxy anions were also seen to have the potential to contribute to degradation of the aminoxy anions tested, with 4-oxo-TEMPO being shown to be the most reactive to degradation with water with a GFE of -12.6 kJ mol-1. 4-Oxo-TEMPO was found to be highly susceptible to self-quenching by its aminoxy anion and radical form with highly negative proton transfer GFEs of -47.9 kJ mol-1 and -57.7 kJ mol-1, respectively. Overall, 4-cyano-TEMPO is recommended as being the most stable of the aminoxy anions tested with TEMPOL, thus providing a viable alternative to improve solubility should the IL be tuned to maximize its stability.
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Affiliation(s)
- Luke Wylie
- School of Chemistry, Monash University, Wellington Rd, Clayton, VIC 3800, Australia.
| | - Kan Hakatayama-Sato
- Department of Applied Chemistry, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Choitsu Go
- Department of Applied Chemistry, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
| | - Kenichi Oyaizu
- Department of Applied Chemistry, Waseda University, 3-4-1 Okubo, Shinjuku, Tokyo 169-8555, Japan
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30
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Das SK, Chakraborty S, Ramakrishnan R. Critical benchmarking of popular composite thermochemistry models and density functional approximations on a probabilistically pruned benchmark dataset of formation enthalpies. J Chem Phys 2021; 154:044113. [PMID: 33514111 DOI: 10.1063/5.0032713] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
First-principles calculation of the standard formation enthalpy, ΔHf° (298 K), in such a large scale as required by chemical space explorations, is amenable only with density functional approximations (DFAs) and certain composite wave function theories (cWFTs). Unfortunately, the accuracies of popular range-separated hybrid, "rung-4" DFAs, and cWFTs that offer the best accuracy-vs-cost trade-off have until now been established only for datasets predominantly comprising small molecules; their transferability to larger systems remains vague. In this study, we present an extended benchmark dataset of ΔHf° for structurally and electronically diverse molecules. We apply quartile-ranking based on boundary-corrected kernel density estimation to filter outliers and arrive at probabilistically pruned enthalpies of 1694 compounds (PPE1694). For this dataset, we rank the prediction accuracies of G4, G4(MP2), ccCA, CBS-QB3, and 23 popular DFAs using conventional and probabilistic error metrics. We discuss systematic prediction errors and highlight the role an empirical higher-level correction plays in the G4(MP2) model. Furthermore, we comment on uncertainties associated with the reference empirical data for atoms and the systematic errors stemming from these that grow with the molecular size. We believe that these findings will aid in identifying meaningful application domains for quantum thermochemical methods.
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Affiliation(s)
- Sambit Kumar Das
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Sabyasachi Chakraborty
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500107, India
| | - Raghunathan Ramakrishnan
- Tata Institute of Fundamental Research, Centre for Interdisciplinary Sciences, Hyderabad 500107, India
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31
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Muravyev NV, Monogarov KA, Melnikov IN, Pivkina AN, Kiselev VG. Learning to fly: thermochemistry of energetic materials by modified thermogravimetric analysis and highly accurate quantum chemical calculations. Phys Chem Chem Phys 2021; 23:15522-15542. [PMID: 34286759 DOI: 10.1039/d1cp02201f] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The standard state enthalpy of formation and the enthalpy of sublimation are essential thermochemical parameters determining the performance and application prospects of energetic materials (EM). Direct experimental measurements of these properties are complicated by low volatility and high heat release in bomb calorimetry experiments. As a result, the uncertainties in the reported enthalpies of formation for a number of even well-known CHNO-containing compounds might amount up to tens kJ mol-1, while for some novel high-nitrogen molecules they reach even hundreds of kJ mol-1. The present study reports a facile approach to determining the solid-state formation enthalpies comprised of complementary high-level quantum chemical calculations of the gas-phase thermochemistry and advanced thermal analysis techniques yielding sublimation enthalpies. The thermogravimetric procedure for the measurement of sublimation enthalpy was modified by using low external pressures (down to 0.2 Pa). This allows for observing sublimation/vaporization instead of thermal decomposition of the compounds studied. Extensive benchmarking on nonenergetic and energetic compounds reveals the average and maximal absolute errors of the sublimation enthalpies of 3.3 and 11.0 kJ mol-1, respectively. The comparison of the results with those obtained from the widely used Trouton-Williams empirical equation shows that the latter underestimates the sublimation enthalpy up to 140 kJ mol-1. Therefore, we performed a reparametrization of the latter equation with simple chemical descriptors that reduces the mean error down to 30 kJ mol-1. Highly accurate multi-level procedures W2-F12 and/or W1-F12 in conjunction with the atomization energy approach were used to calculate theoretically the gas-phase formation enthalpies. In several cases, the DLPNO-CCSD(T) enthalpies of isodesmic reactions were also employed to obtain the gas-phase thermochemistry for medium-sized important EMs. Combining the obtained thermochemical properties, we determined the solid-state enthalpies of formation for nearly 60 species containing various important explosophoric groups, from common nitroaromatics, nitroethers, and nitramines to novel nitrogen-rich heterocyclic species (e.g., the derivatives of pyrazole, tetrazole, furoxan, etc.). The large-scale benchmarking against the available experimental solid-state enthalpies of formation yielded the maximal inaccuracy of the proposed method of 25 kJ mol-1.
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Affiliation(s)
- Nikita V Muravyev
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Konstantin A Monogarov
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Igor N Melnikov
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Alla N Pivkina
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia.
| | - Vitaly G Kiselev
- Semenov Federal Research Center for Chemical Physics, RAS, 4 Kosygina Str., 119991 Moscow, Russia. and Novosibirsk State University, 1 Pirogova Str., 630090 Novosibirsk, Russia and Institute of Chemical Kinetics and Combustion, SB RAS, 3 Institutskaya Str., 630090 Novosibirsk, Russia
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32
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Laner JN, Silva Junior HDC, Rodembusch FS, Moreira EC. New insights on the ESIPT process based on solid-state data and state-of-the-art computational methods. Phys Chem Chem Phys 2021; 23:1146-1155. [PMID: 33349817 DOI: 10.1039/d0cp05502f] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Benzothiazole derivatives were used as models to study the excited-state intramolecular proton transfer (ESIPT) from an experimental and theoretical point of view. The experimental electronic and vibrational results were compared with a comprehensive selection of state-of-the-art computational methods in a workflow approach. The latter were performed based on modern techniques, such as DLPNO-CCSD(T), which gives the reference energies and current methodologies for ESIPT analysis, such as molecular dynamics and charge density difference testing. The theoretical vibrational results were focused on the stretch vibrational-mode of the hydroxyl group, which indicated a large increase in the intramolecular hydrogen bond strength, which facilitates the ESIPT process. Theoretically, the optimization of a large number of molecules shows that π-stacking plays a fundamental role in benzothiazole stabilization, with a remarkably strong intramolecular hydrogen bond. The potential energy surface of the ESIPT reactive benzothiazole (4HBS) has a clear transition state where ESIPT is easily observed with a large difference in energy between the enol and keto tautomer. Additionally, molecular dynamics showed that the ESIPT process occurs very fast. The tautomer appears around 8.7 fs and the enolic form is regenerated in just 24 fs, closing the Förster cycle. The calculated Stokes shift could be related to the ESIPT process and the experimental solid-state emission spectrum matched almost perfectly with the theoretical one. In contrast, for the non-ESIPT benzothiazole (4HBSN), the agreement between theory and experiment was limited, probably due to intermolecular interaction effects that are not considered in these calculations.
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Affiliation(s)
- Jean Nunes Laner
- PPCEM - Fundação Universidade Federal do Pampa, Bagé - RS, Brazil.
| | | | - Fabiano Severo Rodembusch
- Universidade Federal do Rio Grande do Sul - Instituto de Química, 9500, CEP 91501-970., Av. Bento Gonçalves, Porto Alegre-RS, Brazil
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Han Y, Zhu L, Yao Y, Shi X, Zhang Y, Xiao H, Chen X. Strong bases behave as weak bases in nanoscale chemical environments: implication in humidity-swing CO 2 air capture. Phys Chem Chem Phys 2021; 23:14811-14817. [PMID: 34212971 DOI: 10.1039/d1cp01121a] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Hydration of ions/molecules in nanometer-sized clusters or nanoscopic pores is ubiquitous and plays a key role in many chemical and physical systems. In this work, guanidine-H2O reactions with n = 1-8 water molecules were systematically studied by ab initio methods. The result suggests that the reduced availability of water molecules greatly inhibits the strong base guanidine from producing OH-. That is, guanidine exhibits the behavior of a weak bases in low-humidity nanoscale environments. Intriguingly, this effect is not limited to guanidine but could be applied to other strong bases. Furthermore, we demonstrate that the direction of guanidine-CO2 reactions can be controlled by changing the number of water molecules present, which in turn responds to the humidity change in air. These findings not only shed some light on unconventional chemical reactions of strong bases in atmospheric clusters and on solid porous surfaces, but also provide insights into the development of guanidine-based CO2 air-capture sorbents.
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Affiliation(s)
- Yingying Han
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China.
| | - Liangliang Zhu
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China.
| | - Yutong Yao
- Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
| | - Xiaoyang Shi
- Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
| | - Yayun Zhang
- State Key Laboratory of Chemical Engineering, East China University of Science and Technology, Shanghai, 200237, China
| | - Hang Xiao
- Shaanxi Institute of Energy and Chemical Engineering, School of Chemical Engineering, Northwest University, Xi'an, 710069, China.
| | - Xi Chen
- Earth Engineering Center, Center for Advanced Materials for Energy and Environment, Department of Earth and Environmental Engineering, Columbia University, New York, NY10027, USA
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34
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Döntgen M, Fenard Y, Heufer KA. Atomic Partial Charges as Descriptors for Barrier Heights. J Chem Inf Model 2020; 60:5928-5931. [PMID: 33094609 DOI: 10.1021/acs.jcim.0c00787] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Atomic partial charges are found to be valuable descriptors for barrier heights of unimolecular reactions due to the considerable information about the electronic structure embedded in them. If the chemical changes of the reactions are somewhat centralized at a single atom, the respective partial charge is a potentially meaningful descriptor and might outperform bond dissociation energies as descriptors. We propose that atomic partial charges should be considered as barrier height descriptors in future research.
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Affiliation(s)
- Malte Döntgen
- Physico-Chemical Fundamentals of Combustion, RWTH Aachen University, 52062 Aachen, Germany
| | - Yann Fenard
- Physico-Chemical Fundamentals of Combustion, RWTH Aachen University, 52062 Aachen, Germany
| | - K Alexander Heufer
- Physico-Chemical Fundamentals of Combustion, RWTH Aachen University, 52062 Aachen, Germany
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Minenkova I, Osina EL, Cavallo L, Minenkov Y. Gas-Phase Thermochemistry of MX 3 and M 2X 6 (M = Sc, Y; X = F, Cl, Br, I) from a Composite Reaction-Based Approach: Homolytic versus Heterolytic Cleavage. Inorg Chem 2020; 59:17084-17095. [PMID: 33210914 DOI: 10.1021/acs.inorgchem.0c02292] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A domain-based local-pair natural-orbital coupled-cluster approach with single, double, and improved linear-scaling perturbative triple correction via an iterative algorithm, DLPNO-CCSD(T1), was applied within the framework of the Feller-Peterson-Dixon approach to derive gas-phase heats of formation of scandium and yttrium trihalides and their dimers via a set of homolytic and heterolytic dissociation reactions. All predicted heats of formation moderately depend on the reaction type with the most and least negative values obtained for homolytic and heterolytic dissociation, respectively. The basis set size dependence, as well as the influence of static correlation effects not covered by the standard (DLPNO-)CCSD(T) approach, suggests that exploitation of the heterolytic dissociation reactions with the formation of M3+ and X- ions leads to the most robust heats of formation. The gas-phase formation enthalpies ΔHf°(0 K)/ΔHf°(298.15 K) and absolute entropies S°(298.15 K) were obtained for the first time for the Sc2F6, Sc2Br6, and Sc2I6 species. For ScBr3, ScI3, Sc2Cl6, and Y2Cl6, we suggest a reexamination of the experimental heats of formation available in the literature. For other compounds, the predicted values were found to be in good agreement with the experimental estimates. Extracted MX3 (M = Sc, Y; X = F, Cl, Br, and I) 0 K atomization enthalpies indicate weaker bonding when moving from fluorine to iodine and from yttrium to scandium. Likewise, the stability of yttrium trihalide dimers degrades when going from fluorine to iodine. Respective scandium trihalide dimers are less stable, with 0 K dimer dissociation energy decreasing in the row fluorine - chlorine - bromine ≈ iodine. Correlation of the (n - 1)s2p6 electrons on bromine and iodine, inclusion of zero-point energy, relativistic effects, and the effective-core-potential correction as well as amelioration of the DLPNO localization inaccuracy are shown to be of similar magnitude, which is critical if accurate heats of formation are a goal.
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Affiliation(s)
- Irina Minenkova
- Frumkin Institute of Physical Chemistry and Electrochemistry, Russian Academy of Sciences, Leninskii pr. 31, Moscow 119071, Russia
| | - Evgeniya L Osina
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia
| | - Luigi Cavallo
- Catalysis Center, King Abdullah University of Science and Technology (KAUST), Thuwal 23955-6900, Saudi Arabia
| | - Yury Minenkov
- Joint Institute for High Temperatures, Russian Academy of Sciences, 13-2 Izhorskaya Street, Moscow 125412, Russia.,N.N. Semenov Federal Research Center for Chemical Physics, Russian Academy of Sciences, Kosygina Street 4, Moscow 119991, Russia
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36
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Tang Y, Shen C, Yao Q, Tian X, Wang B, Dong K. Efficient Synthesis of γ‐Lactones by Cobalt‐Catalyzed Carbonylative Ring Expansion of Oxetanes under Syngas Atmosphere. ChemCatChem 2020. [DOI: 10.1002/cctc.202001294] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Yitian Tang
- Chang-Kung Chuang Institute and Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 P. R. China
| | - Chaoren Shen
- Chang-Kung Chuang Institute and Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 P. R. China
| | - Qiyi Yao
- Chang-Kung Chuang Institute and Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 P. R. China
| | - Xinxin Tian
- Institute of Molecular Science Key Laboratory of Materials for Energy Conversion and Storage of Shanxi Province Shanxi University Taiyuan 030006 P. R. China
| | - Bo Wang
- Shanghai Puyi Chemical Co., Ltd. Shanghai 201612 P. R. China
| | - Kaiwu Dong
- Chang-Kung Chuang Institute and Shanghai Key Laboratory of Green Chemistry and Chemical Processes School of Chemistry and Molecular Engineering East China Normal University Shanghai 200062 P. R. China
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Chamkin AA, Serkova ES. DFT, DLPNO-CCSD(T), and NEVPT2 benchmark study of the reaction between ferrocenium and trimethylphosphine. J Comput Chem 2020; 41:2388-2397. [PMID: 32812657 DOI: 10.1002/jcc.26398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2020] [Accepted: 07/25/2020] [Indexed: 11/10/2022]
Abstract
The reaction between ferrocenium and trimethylphosphine was studied using density functional theory (DFT), domain-based local pair natural orbital coupled cluster theory with single-, double-, and perturbative triple excitations (DLPNO-CCSD(T)), and N-electron valence state perturbation theory (NEVPT2). The accuracy of the DFT functionals decreases compared to the DLPNO-CCSD(T) level in the following order: M06-L > TPSS > M06, BLYP > PBE, PBE0, B3LYP > > PWPB95 > > DSD-BLYP. The roles of thermochemical, continuum solvation (SMD), and counterpoise corrections were evaluated. Grimme's D3 empirical dispersion correction is essential for all functionals studied except M06 and M06-L. The reliability of the frequency calculations performed directly within the SMD was confirmed. The systems showed no significant multireference character according to T1 and T2 diagnostics and the fractional occupation number (FOD) weighted electron density analysis. The multireference NEVPT2 calculations gave qualitatively valid conclusions about the reaction mechanism. However, a multireference approach is generally not recommended because it requires arbitrary chosen active spaces.
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Affiliation(s)
- Aleksandr A Chamkin
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Moscow, Russia
| | - Elena S Serkova
- A.N. Nesmeyanov Institute of Organoelement Compounds of Russian Academy of Sciences, Moscow, Russia
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38
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Dorofeeva OV. Accurate prediction of norbornadiene cycle enthalpies by DLPNO-CCSD(T 1 )/CBS method. J Comput Chem 2020; 41:2352-2364. [PMID: 32798279 DOI: 10.1002/jcc.26394] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 07/04/2020] [Accepted: 07/15/2020] [Indexed: 11/06/2022]
Abstract
The DLPNO-CCSD(T1 )/CBS method combined with simple reactions containing small reference species leads to an improvement in the accuracy of theoretically evaluated enthalpies of formation of medium-sized polyalicyclic hydrocarbons when compared with the widely used composite approach. The efficiency of the DLPNO-CCSD(T1 )/CBS method is most vividly demonstrated by comparing with the results of G4 calculations for adamantane. The most important factor in choosing appropriate working reaction is the same number of species on both sides of the equation. Among these reactions, the reactions with small enthalpy change usually provide a better cancellation of errors. The DLPNO-CCSD(T1 )/CBS method was used to calculate the enthalpies of formation of compounds belonging to the norbornadiene cycle (norbornadiene, quadricyclane, norbornene, nortricyclane, and norbornane). The most reliable experimental enthalpies of formation are recommended for these compounds by comparing calculated values with conflicting experimental data.
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Affiliation(s)
- Olga V Dorofeeva
- Faculty of Chemistry, Lomonosov Moscow State University, Moscow, Russia
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39
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Döntgen M, Kopp WA, vom Lehn F, Kröger LC, Pitsch H, Leonhard K, Heufer KA. Updated thermochemistry for renewable transportation fuels: New groups and group values for acetals and ethers, their radicals, and peroxy species. INT J CHEM KINET 2020. [DOI: 10.1002/kin.21443] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Affiliation(s)
- Malte Döntgen
- Physico‐Chemical Fundamentals of Combustion RWTH Aachen University Aachen Germany
| | - Wassja A. Kopp
- Chair of Technical Thermodynamics RWTH Aachen University Aachen Germany
| | - Florian vom Lehn
- Institute for Combustion Technology RWTH Aachen University Aachen Germany
| | - Leif C. Kröger
- Chair of Technical Thermodynamics RWTH Aachen University Aachen Germany
| | - Heinz Pitsch
- Institute for Combustion Technology RWTH Aachen University Aachen Germany
| | - Kai Leonhard
- Chair of Technical Thermodynamics RWTH Aachen University Aachen Germany
| | - K. Alexander Heufer
- Physico‐Chemical Fundamentals of Combustion RWTH Aachen University Aachen Germany
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40
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Fasano V, McFord AW, Butts CP, Collins BSL, Fey N, Alder RW, Aggarwal VK. How Big is the Pinacol Boronic Ester as a Substituent? Angew Chem Int Ed Engl 2020; 59:22403-22407. [DOI: 10.1002/anie.202007776] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2020] [Revised: 08/20/2020] [Indexed: 11/10/2022]
Affiliation(s)
- Valerio Fasano
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Aidan W. McFord
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Craig P. Butts
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Natalie Fey
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Roger W. Alder
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
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41
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Fasano V, McFord AW, Butts CP, Collins BSL, Fey N, Alder RW, Aggarwal VK. How Big is the Pinacol Boronic Ester as a Substituent? Angew Chem Int Ed Engl 2020. [DOI: 10.1002/ange.202007776] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Valerio Fasano
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Aidan W. McFord
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Craig P. Butts
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | | | - Natalie Fey
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
| | - Roger W. Alder
- School of Chemistry University of Bristol Cantock's Close Bristol BS8 1TS UK
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42
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Mallick S, Roy B, Kumar P. A comparison of DLPNO-CCSD(T) and CCSD(T) method for the determination of the energetics of hydrogen atom transfer reactions. COMPUT THEOR CHEM 2020. [DOI: 10.1016/j.comptc.2020.112934] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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Altun A, Neese F, Bistoni G. Extrapolation to the Limit of a Complete Pair Natural Orbital Space in Local Coupled-Cluster Calculations. J Chem Theory Comput 2020; 16:6142-6149. [PMID: 32897712 PMCID: PMC7586325 DOI: 10.1021/acs.jctc.0c00344] [Citation(s) in RCA: 38] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022]
Abstract
![]()
The domain-based
local pair natural orbital (PNO) coupled-cluster
DLPNO-CCSD(T) method allows one to perform single point energy calculations
for systems with hundreds of atoms while retaining essentially the
accuracy of its canonical counterpart, with errors that are typically
smaller than 1 kcal/mol for relative energies. Crucial to the accuracy
and efficiency of the method is a proper definition of the virtual
space in which the coupled-cluster equations are solved, which is
spanned by a highly compact set of pair natural orbitals (PNOs) that
are specific for each electron pair. The dimension of the PNO space
is controlled by the TCutPNO threshold:
only PNOs with an occupation number greater than TCutPNO are included in the correlation space of a given
electron pair, whilst the remaining PNOs are discarded. To keep the
error of the method small, a conservative TCutPNO value is used in standard DLPNO-CCSD(T) calculations. This often
leads to unnecessarily large PNO spaces, which limits the efficiency
of the method. Herein, we introduce a new computational strategy to
approach the complete PNO space limit (for a given basis set) that
consists in extrapolating the results obtained with different TCutPNO values. The method is validated on the
GMTKN55 set using canonical CCSD(T) data as the reference. Our results
demonstrate that a simple two-point extrapolation scheme can be used
to significantly increase the efficiency and accuracy of DLPNO-CCSD(T)
calculations, thus extending the range of applicability of the technique.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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44
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Affiliation(s)
- Karl K. Irikura
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899-8320, United States
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45
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Ye HZ, Tran HK, Van Voorhis T. Bootstrap Embedding For Large Molecular Systems. J Chem Theory Comput 2020; 16:5035-5046. [PMID: 32589842 DOI: 10.1021/acs.jctc.0c00438] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Recent developments in quantum embedding theories have provided attractive approaches to correlated calculations for large systems. In this work, we extend our previous work [J. Chem. Theory Comput. 2019, 15, 4497-4506; J. Phys. Chem. Lett. 2019, 10, 6368-6374] on bootstrap embedding (BE) to enable correlated ab initio calculations at the coupled cluster with singles and doubles (CCSD) level for large molecules. We introduce several new algorithmic developments that significantly reduce the computational cost of BE, while maintaining its accuracy. The resulting implementation scales as O(N3) for the integral transform and O(N) for the CCSD calculation. Numerical results on a series of conjugated molecules suggest that BE with reasonably sized fragments can recover more than 99.5% of the total correlation energy of a full CCSD calculation, while the required computational resources (time and storage) compare favorably to one popular local correlation scheme: domain localized pair natural orbital (DLPNO). The largest BE calculation in this work involves ∼2900 basis functions and can be performed on a single node with 16 CPU cores and 64 GB of memory in a few days. We anticipate that these developments represent an important step toward the application of BE to solve practical problems.
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Affiliation(s)
- Hong-Zhou Ye
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Henry K Tran
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
| | - Troy Van Voorhis
- Department of Chemistry, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139, United States
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46
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Wu F, Deraedt C, Cornaton Y, Contreras-Garcia J, Boucher M, Karmazin L, Bailly C, Djukic JP. Making Base-Assisted C–H Bond Activation by Cp*Co(III) Effective: A Noncovalent Interaction-Inclusive Theoretical Insight and Experimental Validation. Organometallics 2020. [DOI: 10.1021/acs.organomet.0c00253] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Fule Wu
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Christophe Deraedt
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Yann Cornaton
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Julia Contreras-Garcia
- Laboratoire de Chimie Théorique UMR 7616 CNRS, Sorbonne Université, Site Jussieu, 4 place Jussieu, 75052 Paris cedex, France
| | - Mélanie Boucher
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
| | - Lydia Karmazin
- Service de Radiocristallographie, Fédération de Chimie Le Bel FR 2010, Université de Strasbourg, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Corinne Bailly
- Service de Radiocristallographie, Fédération de Chimie Le Bel FR 2010, Université de Strasbourg, 1 rue Blaise Pascal, 67000 Strasbourg, France
| | - Jean-Pierre Djukic
- Laboratoire de Chimie et Systémique Organométalliques, Institut de Chimie de Strasbourg UMR 7177 CNRS, Université de Strasbourg, 4 rue Blaise Pascal, 67000 Strasbourg, France
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47
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Neese F, Wennmohs F, Becker U, Riplinger C. The ORCA quantum chemistry program package. J Chem Phys 2020; 152:224108. [DOI: 10.1063/5.0004608] [Citation(s) in RCA: 697] [Impact Index Per Article: 174.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Frank Neese
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
- FAccTs GmbH, Rolandstr. 67, 50677 Köln, Germany
| | - Frank Wennmohs
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Ute Becker
- Max Planck Institut für Kohlenforschung, Kaiser-Wilhelm Platz 1, D-45470 Mülheim an der Ruhr, Germany
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48
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Semidalas E, Martin JML. Canonical and DLPNO-Based G4(MP2)XK-Inspired Composite Wave Function Methods Parametrized against Large and Chemically Diverse Training Sets: Are They More Accurate and/or Robust than Double-Hybrid DFT? J Chem Theory Comput 2020; 16:4238-4255. [PMID: 32456427 PMCID: PMC7366511 DOI: 10.1021/acs.jctc.0c00189] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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The
large and chemically diverse GMTKN55 benchmark was used as
a training set for parametrizing composite wave function thermochemistry
protocols akin to G4(MP2)XK theory (Chan, B.; Karton, A.; Raghavachari,
K. J. Chem. Theory Comput. 2019, 15, 4478–4484). On account of their availability
for elements H through Rn, Karlsruhe def2 basis sets were employed.
Even after reparametrization, the GMTKN55 WTMAD2 (weighted mean absolute
deviation, type 2) for G4(MP2)-XK is actually inferior to that of
the best rung-4 DFT functional, ωB97M-V. By increasing the basis
set for the MP2 part to def2-QZVPPD, we were able to substantially
improve performance at modest cost (if an RI-MP2 approximation is
made), with WTMAD2 for this G4(MP2)-XK-D method now comparable to
the better rung-5 functionals (albeit at greater cost). A three-tier
approach with a scaled MP3/def2-TZVPP intermediate step, however,
leads to a G4(MP3)-D method that is markedly superior to even the
best double hybrids ωB97M(2) and revDSD-PBEP86-D4. Evaluating
the CCSD(T) component with a triple-ζ, rather than split-valence,
basis set yields only a modest further improvement that is incommensurate
with the drastic increase in computational cost. G4(MP3)-D and G4(MP2)-XK-D
have about 40% better WTMAD2, at similar or lower computational cost,
than their counterparts G4 and G4(MP2), respectively: detailed comparison
reveals that the difference lies in larger molecules due to basis
set incompleteness error. An E2/{T,Q} extrapolation and a CCSD(T)/def2-TZVP
step provided the G4-T method of high accuracy and with just three
fitted parameters. Using KS orbitals in MP2 leads to the G4(MP3|KS)-D
method, which entirely eliminates the CCSD(T) step and has no steps
costlier than scaled MP3; this shows a path forward to further improvements
in double-hybrid density functional methods. None of our final selections
require an empirical HLC correction; this cuts the number of empirical
parameters in half and avoids discontinuities on potential energy
surfaces. G4-T-DLPNO, a variant in which post-MP2 corrections are
evaluated at the DLPNO-CCSD(T) level, achieves nearly the accuracy
of G4-T but is applicable to much larger systems.
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Affiliation(s)
- Emmanouil Semidalas
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḩovot, Israel
| | - Jan M L Martin
- Department of Organic Chemistry, Weizmann Institute of Science, 7610001 Reḩovot, Israel
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49
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Smith JS, Zubatyuk R, Nebgen B, Lubbers N, Barros K, Roitberg AE, Isayev O, Tretiak S. The ANI-1ccx and ANI-1x data sets, coupled-cluster and density functional theory properties for molecules. Sci Data 2020; 7:134. [PMID: 32358545 PMCID: PMC7195467 DOI: 10.1038/s41597-020-0473-z] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2019] [Accepted: 03/24/2020] [Indexed: 11/22/2022] Open
Abstract
Maximum diversification of data is a central theme in building generalized and accurate machine learning (ML) models. In chemistry, ML has been used to develop models for predicting molecular properties, for example quantum mechanics (QM) calculated potential energy surfaces and atomic charge models. The ANI-1x and ANI-1ccx ML-based general-purpose potentials for organic molecules were developed through active learning; an automated data diversification process. Here, we describe the ANI-1x and ANI-1ccx data sets. To demonstrate data diversity, we visualize it with a dimensionality reduction scheme, and contrast against existing data sets. The ANI-1x data set contains multiple QM properties from 5 M density functional theory calculations, while the ANI-1ccx data set contains 500 k data points obtained with an accurate CCSD(T)/CBS extrapolation. Approximately 14 million CPU core-hours were expended to generate this data. Multiple QM calculated properties for the chemical elements C, H, N, and O are provided: energies, atomic forces, multipole moments, atomic charges, etc. We provide this data to the community to aid research and development of ML models for chemistry.
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Affiliation(s)
- Justin S Smith
- Center for Nonlinear Studies, Los Alamos National Laboratory, Los Alamos, NM, USA
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Roman Zubatyuk
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA
| | - Benjamin Nebgen
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Nicholas Lubbers
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Kipton Barros
- Computer, Computational, and Statistical Sciences Division, Los Alamos National Laboratory, Los Alamos, NM, USA
| | - Adrian E Roitberg
- University of Florida, Department of Chemistry, PO Box 117200, 32611-7200, Gainesville, USA.
| | - Olexandr Isayev
- Department of Chemistry, Carnegie Mellon University, Pittsburgh, PA, USA.
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM, USA.
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50
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Flöser B, Guo Y, Riplinger C, Tuczek F, Neese F. Detailed Pair Natural Orbital-Based Coupled Cluster Studies of Spin Crossover Energetics. J Chem Theory Comput 2020; 16:2224-2235. [PMID: 32196337 PMCID: PMC7310951 DOI: 10.1021/acs.jctc.9b01109] [Citation(s) in RCA: 52] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2019] [Indexed: 11/28/2022]
Abstract
In this work, a detailed study of spin-state splittings in three spin crossover model compounds with DLPNO-CCSD(T) is presented. The performance in comparison to canonical CCSD(T) is assessed in detail. It was found that spin-state splittings with chemical accuracy, compared to the canonical results, are achieved when the full iterative triples (T1) scheme and TightPNO settings are applied and relativistic effects are taken into account. Having established the level of accuracy that can be reached relative to the canonical results, we have undertaken a detailed basis set study in the second part of the study. The slow convergence of the results of correlated calculations with respect to basis set extension is particularly acute for spin-state splittings for reasons discussed in detail in this Article. In fact, for some of the studied systems, 5Z basis sets are necessary in order to come close to the basis set limit that is estimated here by basis set extrapolation. Finally, the results of the present work are compared to available literature. In general, acceptable agreement with previous CCSD(T) results is found, although notable deviations stemming from differences in methodology and basis sets are noted. It is noted that the published CASPT2 numbers are far away from the extrapolated CCSD(T) numbers. In addition, dynamic quantum Monte Carlo results differ by several tens of kcal/mol from the CCSD(T) numbers. A comparison to DFT results produced with a range of popular density functionals shows the expected scattering of results and showcases the difficulty of applying DFT to spin-state energies.
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Affiliation(s)
- Benedikt
M. Flöser
- Institute
for Inorganic Chemistry, University of Kiel, Otto-Hahn-Platz 10, 24118 Kiel, Germany
| | - Yang Guo
- Max-Planck-Institute
for Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim a.d. Ruhr, Germany
| | | | - Felix Tuczek
- Institute
for Inorganic Chemistry, University of Kiel, Otto-Hahn-Platz 10, 24118 Kiel, Germany
| | - Frank Neese
- Max-Planck-Institute
for Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim a.d. Ruhr, Germany
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