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Evangelista FA, Li C, Verma P, Hannon KP, Schriber JB, Zhang T, Cai C, Wang S, He N, Stair NH, Huang M, Huang R, Misiewicz JP, Li S, Marin K, Zhao Z, Burns LA. Forte: A suite of advanced multireference quantum chemistry methods. J Chem Phys 2024; 161:062502. [PMID: 39132791 DOI: 10.1063/5.0216512] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Accepted: 06/24/2024] [Indexed: 08/13/2024] Open
Abstract
Forte is an open-source library specialized in multireference electronic structure theories for molecular systems and the rapid prototyping of new methods. This paper gives an overview of the capabilities of Forte, its software architecture, and examples of applications enabled by the methods it implements.
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Affiliation(s)
- Francesco A Evangelista
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chenyang Li
- Key Laboratory of Theoretical and Computational Photochemistry, Ministry of Education, College of Chemistry, Beijing Normal University, Beijing 100875, China
| | - Prakash Verma
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Kevin P Hannon
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Jeffrey B Schriber
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
- Department of Chemistry and Biochemistry, Iona University, New Rochelle, New York 10801, USA
| | - Tianyuan Zhang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Chenxi Cai
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Shuhe Wang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Nan He
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Nicholas H Stair
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Meng Huang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Renke Huang
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Jonathon P Misiewicz
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Shuhang Li
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Kevin Marin
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Zijun Zhao
- Department of Chemistry and Cherry Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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2
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Calinsky R, Levy Y. Histidine in Proteins: pH-Dependent Interplay between π-π, Cation-π, and CH-π Interactions. J Chem Theory Comput 2024; 20:6930-6945. [PMID: 39037905 PMCID: PMC11325542 DOI: 10.1021/acs.jctc.4c00606] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/24/2024]
Abstract
Histidine (His) stands out as the most versatile natural amino acid due to its side chain's facile propensity to protonate at physiological pH, leading to a transition from aromatic to cationic characteristics and thereby enabling diverse biomolecular interactions. In this study, our objective was to quantify the energetics and geometries of pairwise interactions involving His at varying pH levels. Through quantum chemical calculations, we discovered that His exhibits robust participation in both π-π and cation-π interactions, underscoring its ability to adopt a π or cationic nature, akin to other common residues. Of particular note, we found that the affinity of protonated His for aromatic residues (via cation-π interactions) is greater than the affinity of neutral His for either cationic residues (also via cation-π interactions) or aromatic residues (via π-π interactions). Furthermore, His frequently engages in CH-π interactions, and notably, depending on its protonation state, we found that some instances of hydrogen bonding by His exhibit greater stability than is typical for interamino acid hydrogen bonds. The strength of the pH-dependent pairwise energies of His with aromatic residues is supported by the abundance of pairwise interactions with His of low and high predicted pKa values. Overall, our findings illustrate the contribution of His interactions to protein stability and its potential involvement in conformational changes despite its relatively low abundance in proteins.
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Affiliation(s)
- Rivka Calinsky
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
| | - Yaakov Levy
- Department of Chemical and Structural Biology, Weizmann Institute of Science, Rehovot 76100, Israel
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Egorov O, Rey M, Viglaska D, Nikitin AV. Rovibrational Line Lists of Triplet and Singlet Methylene. J Phys Chem A 2024. [PMID: 39119864 DOI: 10.1021/acs.jpca.4c04205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/10/2024]
Abstract
The methylene molecule (CH2) is a short-lived radical with lacking data on its spectral line intensities. Although the lifetime of CH2 is extremely short under Earth's conditions, it exists in a free form in interstellar media. CH2 is an important intermediate species in chemical reactions associated with the formation and destruction of complex hydrocarbons. We present the first rovibrational line lists of CH2 in its ground triplet and first excited singlet electronic state. To this end, our previously developed accurate ab initio potential energy surface (PES) was used for the ground electronic triplet state [Egorov et al. J. Comp. Chem. 2024. V. 45. (2). P. 83] while a new PES for the singlet state was constructed in this work using the single-reference coupled cluster approach [CCSD(T)] combined with the extrapolation to the complete basis set (CBS) limit based on the correlation-consistent orbital basis sets with the core-valence electron correlation effects [aug-cc-pCVXZ, X = T, Q, 5, and 6]. In addition, the contributions to the correlation energy from highly excited Slater determinants [CC(n), n = 3-5] were included as well as the scalar relativistic effects and DBOC. The most accurate description of the infrared band origins of singlet CH2 was thus achieved for the energy range where the impact of the nonadiabatic coupling due to the Renner-Teller effect can be neglected. To obtain the probabilities of the rovibrational transitions, new ab initio DMSs were constructed both for the triplet and singlet CH2 using the CCSD(T)/aug-cc-pCVQZ approach. Finally, the absorption spectra of triplet and singlet methylene were predicted from the variationally computed line lists.
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Affiliation(s)
- Oleg Egorov
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics SB RAS 1, Akademician Zuev Sq., Tomsk 634055, Russia
- Faculty of Physics, Tomsk State University 36, Lenin Ave., Tomsk 634050, Russia
| | - Michaël Rey
- Groupe de Spectrométrie Moléculaire et Atmosphérique UMR CNRS 7331, UFR Sciences BP 1039, Reims Cedex 2 51687, France
| | - Dominika Viglaska
- Groupe de Spectrométrie Moléculaire et Atmosphérique UMR CNRS 7331, UFR Sciences BP 1039, Reims Cedex 2 51687, France
| | - Andrei V Nikitin
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics SB RAS 1, Akademician Zuev Sq., Tomsk 634055, Russia
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Gray M, Herbert JM. Assessing the domain-based local pair natural orbital (DLPNO) approximation for non-covalent interactions in sizable supramolecular complexes. J Chem Phys 2024; 161:054114. [PMID: 39105555 PMCID: PMC11305816 DOI: 10.1063/5.0206533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2024] [Accepted: 07/18/2024] [Indexed: 08/07/2024] Open
Abstract
The titular domain-based local pair natural orbital (DLPNO) approximation is the most widely used method for extending correlated wave function models to large molecular systems, yet its fidelity for intermolecular interaction energies in large supramolecular complexes has not been thoroughly vetted. Non-covalent interactions are sensitive to tails of the electron density and involve nonlocal dispersion that is discarded or approximated if the screening of pair natural orbitals (PNOs) is too aggressive. Meanwhile, the accuracy of the DLPNO approximation is known to deteriorate as molecular size increases. Here, we test the DLPNO approximation at the level of second-order Møller-Plesset perturbation theory (MP2) and coupled-cluster theory with singles, doubles, and perturbative triples [CCSD(T)] for a variety of large supramolecular complexes. DLPNO-MP2 interaction energies are within 3% of canonical values for small dimers with ≲10 heavy atoms, but for larger systems, the DLPNO approximation is often quite poor unless the results are extrapolated to the canonical limit where the threshold for discarding PNOs is taken to zero. Counterpoise correction proves to be essential in reducing errors with respect to canonical results. For a sequence of nanoscale graphene dimers up to (C96H24)2, extrapolated DLPNO-MP2 interaction energies agree with canonical values to within 1%, independent of system size, provided that the basis set does not contain diffuse functions; these cause the DLPNO approximation to behave erratically, such that results cannot be extrapolated in a meaningful way. DLPNO-CCSD(T) calculations are typically performed using looser PNO thresholds as compared to DLPNO-MP2, but this significantly impacts accuracy for large supramolecular complexes. Standard DLPNO-CCSD(T) settings afford errors of 2-6 kcal/mol for dimers involving coronene (C24H12) and circumcoronene (C54H18), even at the DLPNO-CCSD(T1) level.
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Affiliation(s)
- Montgomery Gray
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry & Biochemistry, The Ohio State University, Columbus, Ohio 43210, USA
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Grèbol-Tomàs J, Matito E, Salvador P. Can Aromaticity Be Evaluated Using Atomic Partitions Based on the Hilbert-Space? Chemistry 2024; 30:e202401282. [PMID: 38773922 DOI: 10.1002/chem.202401282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/17/2024] [Accepted: 05/21/2024] [Indexed: 05/24/2024]
Abstract
Aromaticity is a fundamental concept in chemistry that explains the stability and reactivity of many compounds by identifying atoms within a molecule that form an aromatic ring. Reliable aromaticity indices focus on electron delocalization and depend on atomic partitions, which give rise to the concept of an atom-in-the-molecule (AIM). Real-space atomic partitions present two important drawbacks: a high computational cost and numerical errors, limiting some aromaticity measures to medium-sized molecules with rings up to 12 atoms. This restriction hinders the study of large conjugated systems like porphyrins and nanorings. On the other hand, traditional Hilbert-space schemes are free of the latter limitations but can be unreliable for the large basis sets required in modern computational chemistry. This paper explores AIMs based on three robust Hilbert-space partitions - meta-Löwdin, Natural Atomic Orbitals (NAO), and Intrinsic Atomic Orbitals (IAO) - which combine the advantages of real-space partitions without their disadvantages. These partitions can effectively replace real-space AIMs for evaluating the aromatic character. For the first time, we report multicenter index (MCI) and Iring values for large rings and introduce ESIpy, an open-source Python code for aromaticity analysis in large conjugated rings.
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Affiliation(s)
- Joan Grèbol-Tomàs
- Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
- Donostia International Physics Center (DIPC), Manuel de Lardizábal 4, 20018, Donostia, Euskadi, Spain
| | - Eduard Matito
- Donostia International Physics Center (DIPC), Manuel de Lardizábal 4, 20018, Donostia, Euskadi, Spain
- Ikerbasque Foundation for Science, Bilbao, Euskadi, Spain
| | - Pedro Salvador
- Departament de Química, Universitat de Girona, Campus de Montilivi, 17071, Girona, Spain
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6
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Loos PF, Jacquemin D. A mountaineering strategy to excited states: Accurate vertical transition energies and benchmarks for substituted benzenes. J Comput Chem 2024; 45:1791-1805. [PMID: 38661240 DOI: 10.1002/jcc.27358] [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: 01/24/2024] [Revised: 02/09/2024] [Accepted: 02/15/2024] [Indexed: 04/26/2024]
Abstract
In an effort to expand the existing QUEST database of accurate vertical transition energies [Véril et al. WIREs Comput. Mol. Sci. 2021, 11, e1517], we have modeled more than 100 electronic excited states of different natures (local, charge-transfer, Rydberg, singlet, and triplet) in a dozen of mono- and di-substituted benzenes, including aniline, benzonitrile, chlorobenzene, fluorobenzene, nitrobenzene, among others. To establish theoretical best estimates for these vertical excitation energies, we have employed advanced coupled-cluster methods including iterative triples (CC3 and CCSDT) and, when technically possible, iterative quadruples (CC4). These high-level computational approaches provide a robust foundation for benchmarking a series of popular wave function methods. The evaluated methods all include contributions from double excitations (ADC(2), CC2, CCSD, CIS(D), EOM-MP2, STEOM-CCSD), along with schemes that also incorporate perturbative or iterative triples (ADC(3), CCSDR(3), CCSD(T)(a) ⋆ , and CCSDT-3). This systematic exploration not only broadens the scope of the QUEST database but also facilitates a rigorous assessment of different theoretical approaches in the framework of a homologous chemical series, offering valuable insights into the accuracy and reliability of these methods in such cases. We found that both ADC(2.5) and CCSDT-3 can provide very consistent estimates, whereas among less expensive methods SCS-CC2 is likely the most effective approach. Importantly, we show that some lower order methods may offer reasonable trends in the homologous series while providing quite large average errors, and vice versa. Consequently, benchmarking the accuracy of a model based solely on absolute transition energies may not be meaningful for applications involving a series of similar compounds.
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Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, France
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, Nantes, France
- Institut Universitaire de France (IUF), Paris, France
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Kunze L, Froitzheim T, Hansen A, Grimme S, Mewes JM. ΔDFT Predicts Inverted Singlet-Triplet Gaps with Chemical Accuracy at a Fraction of the Cost of Wave Function-Based Approaches. J Phys Chem Lett 2024:8065-8077. [PMID: 39083761 DOI: 10.1021/acs.jpclett.4c01649] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/02/2024]
Abstract
Efficient OLEDs need to quickly convert singlet and triplet excitons into photons. Molecules with an inverted singlet-triplet energy gap (INVEST) are promising candidates for this task. However, typical INVEST molecules have drawbacks like too low oscillator strengths and excitation energies. High-throughput screening could identify suitable INVEST molecules, but existing methods are problematic: The workhorse method TD-DFT cannot reproduce gap inversion, while wave function-based methods are too slow. This study proposes a state-specific method based on unrestricted Kohn-Sham DFT with common hybrid functionals. Tuned on the new INVEST15 benchmark set, this method achieves an error of less than 1 kcal/mol, which is traced back to error cancellation between spin contamination and dynamic correlation. Applied to the larger and structurally diverse NAH159 set in a black-box fashion, the method maintains a small error (1.2 kcal/mol) and accurately predicts gap signs in 83% of cases, confirming its robustness and suitability for screening workflows.
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Affiliation(s)
- Lukas Kunze
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Thomas Froitzheim
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan-Michael Mewes
- Mulliken Center for Theoretical Chemistry, Clausius Institute for Physical and Theoretical Chemistry, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
- beeOLED GmbH, Niedersedlitzer Str. 75c, 01257 Dresden, Germany
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Olive LN, Heide AD, Turney JM, Schaefer HF. Ethynyl Radical Hydrogen Abstraction Energetics and Kinetics Utilizing High-Level Theory. ACS EARTH & SPACE CHEMISTRY 2024; 8:1349-1358. [PMID: 39045226 PMCID: PMC11261607 DOI: 10.1021/acsearthspacechem.4c00040] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2024] [Revised: 06/12/2024] [Accepted: 06/25/2024] [Indexed: 07/25/2024]
Abstract
The ethynyl radical, C2H, is found in a variety of different environments ranging from interstellar space and planetary atmospheres to playing an important role in the combustion of various alkynes under fuel-rich conditions. Hydrogen-atom abstraction reactions are common for the ethynyl radical in these contrasting environments. In this study, the C2H + HX → C2H2 + X, where HX = HNCO, trans-HONO, cis-HONO, C2H4, and CH3OH, reactions have been investigated at rigorously high levels of theory, including CCSD(T)-F12a/cc-pVTZ-F12. For the stationary points thus located, much higher levels of theory have been used, with basis sets as large as aug-cc-pV5Z and methods up to CCSDT(Q), and core correlation was also included. These molecules were chosen because they can be found in either interstellar or combustion environments. Various additive energy corrections have been included to converge the relative enthalpies of the stationary points to subchemical accuracy (≤0.5 kcal mol-1). Barriers predicted here (2.19 kcal mol-1 for the HNCO reaction and 0.47 kcal mol-1 for C2H4) are significantly lower than previous predictions. Reliable kinetics were acquired over a wide range of temperatures (50-5000 K), which may be useful for future experimental studies of these reactions.
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Affiliation(s)
- Laura N Olive
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Alexandra D Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, United States
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9
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Romeu JGF, Hunt ARE, de Melo GF, Peterson KA, Dixon DA. Energetic and Electronic Properties of UO 0/± and UF 0/±. J Phys Chem A 2024; 128:5586-5604. [PMID: 38954748 DOI: 10.1021/acs.jpca.4c02845] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/04/2024]
Abstract
High-level electronic structure calculations were conducted to examine the bonding and spectroscopic properties of the UO0/± and UF0/± diatomic molecules. The low-lying Ω states were described by using multireference SO-CASPT2 calculations. The adiabatic electronic affinity (AEA), adiabatic ionization energy (IE), and bond dissociation energy (BDE) were calculated at the Feller-Peterson-Dixon (FPD) level. The ground state of UO is predicted to be 5I4, and that of UF is 4I9/2. The calculated AEAs of UO and UF are 1.123 and 0.453 eV, respectively, and the corresponding IEs are 5.976 and 6.278 eV. The BDE of UO (749.5 kJ/mol) is predicted to be considerably higher than that of UF (627.2 kJ/mol), and both are higher than those predicted for UB, UC, and UN. NBO calculations show strong ionic character for the ground states of UO and UF and bond orders that range from 2 to 3 and from 1 to 2, respectively. Comparisons of the calculated properties to those of the series comprising UB, UC, and UN diatomic molecules are given.
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Affiliation(s)
- João G F Romeu
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - Ashley R E Hunt
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - Gabriel F de Melo
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
| | - Kirk A Peterson
- Department of Chemistry, Washington State University, Pullman, Washington 99164-4630, United States
| | - David A Dixon
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487-0336, United States
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Mebel AM, Li W, Pratali Maffei L, Cavallotti C, Morozov AN, Wang CY, Yang JZ, Zhao L, Kaiser RI. Fulvenallenyl Radical (C 7H 5·)-Mediated Gas-Phase Synthesis of Bicyclic Aromatic C 10H 8 Isomers: Can Fulvenallenyl Efficiently React with Closed-Shell Hydrocarbons? J Phys Chem A 2024; 128:5707-5720. [PMID: 38967960 DOI: 10.1021/acs.jpca.4c02386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/06/2024]
Abstract
To understand the reactivity of resonantly stabilized radicals, often found in relevant concentrations in gaseous environments, it is important to determine their main reaction pathways. Here, it is investigated whether the fulvenallenyl radical (C7H5·) reacts preferentially with closed-shell molecules or radicals. Electronic structure calculations on the C10H9 potential energy surface accessed by the reactions of C7H5· with methylacetylene (CH3CCH) and allene (H2CCCH2) were combined with RRKM-ME calculations of temperature- and pressure-dependent rate constants using the automated EStokTP software suite and kinetic modeling to assess the reactivity of C7H5· with closed-shell unsaturated hydrocarbons. Experimentally, the reactions were attempted in a chemical microreactor heated to 998 ± 10 K by preparing fulvenallenyl radicals via pyrolysis of trichloromethylbenzene (C7H5Cl3) and seeding the radicals in methylacetylene or allene carrier gas, with product identification by means of photoionization mass spectrometry. The measured photoionization efficiency curve of m/z = 128 was assigned to a linear combination of the reference curves of two C10H8 isomers, azulene (minor) and naphthalene (major), presumably resulting from the C7H5· plus C3H4 reactions. However, the calculations demonstrated that these reactions are too slow, and kinetic modeling of processes in the reactor allowed us to conclude that the observation of naphthalene and azulene is due to the C7H5· plus C3H3· reaction, where propargyl is produced by direct hydrogen atom abstraction by chlorine (Cl) atoms from allene or methylacetylene and Cl stem from the pyrolysis of C7H5Cl3. Modeling results under the copyrolysis conditions of toluene and methylacetylene in high-temperature shock tube experiments confirmed the prevalence of the fulvenallenyl reaction with propargyl over its reactions with C3H4 even when the concentrations of allene and methylacetylene largely exceed that of propargyl. Overall, the reactions of fulvenallenyl with both allene and methylacetylene were found to be noncompetitive in the formation of naphthalene and azulene thus attesting the inefficiency of the fulvenallenyl radical reactions with the prototype closed-shell hydrocarbon species. In the meantime, the new reaction pathways revealed, including H-assisted isomerizations between C10H8 isomers and decomposition reactions of various C10H9 isomers, emerge as relevant and are recommended for inclusion in combustion kinetic models for naphthalene formation.
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Affiliation(s)
- Alexander M Mebel
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Wang Li
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, China
| | - Luna Pratali Maffei
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Carlo Cavallotti
- Department of Chemistry, Materials and Chemical Engineering "G. Natta", Politecnico di Milano, P.zza Leonardo da Vinci 32, 20133 Milano, Italy
| | - Alexander N Morozov
- Department of Chemistry and Biochemistry, Florida International University, Miami, Florida 33199, United States
| | - Chang-Yang Wang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, China
| | - Jiu-Zhong Yang
- National Synchrotron Radiation Laboratory, University of Science and Technology of China, Hefei, Anhui 230029, China
| | - Long Zhao
- School of Nuclear Science and Technology, University of Science and Technology of China, Hefei, Anhui 230027, China
- Deep Space Exploration Laboratory, University of Science and Technology of China, Hefei, Anhui 230026, China
| | - Ralf I Kaiser
- Department of Chemistry, University of Hawaii at Manoa, Honolulu, Hawaii 96888, United States
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11
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Goodlett SM, Kitzmiller NL, Turney JM, Schaefer HF. MolSym: A Python package for handling symmetry in molecular quantum chemistry. J Chem Phys 2024; 161:024107. [PMID: 38984965 DOI: 10.1063/5.0216738] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Accepted: 06/20/2024] [Indexed: 07/11/2024] Open
Abstract
A consideration of the point group symmetry of molecules is often advantageous from a computational efficiency standpoint and sometimes necessary for the correct treatment of chemical physics problems. Many modern electronic structure software packages include a treatment of symmetry, but these are sometimes incomplete or unusable outside of that program's environment. Therefore, we have developed the MolSym package for handling molecular symmetry and its associated functionalities to provide a platform for including symmetry in the implementation and development of other methods. Features include point group detection, molecule symmetrization, arbitrary generation of symmetry element sets and character tables, and symmetry adapted linear combinations of real spherical harmonic basis functions, Cartesian displacement coordinates, and internal coordinates. We present some of the advantages of using molecular symmetry as achieved by MolSym, particularly with respect to Hartree-Fock theory, and the reduction of finite difference displacements in gradient/Hessian computations. This package is designed to be easily integrated into other software development efforts and may be extended to further symmetry applications.
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Affiliation(s)
- Stephen M Goodlett
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Nathaniel L Kitzmiller
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
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12
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Kossoski F, Boggio-Pasqua M, Loos PF, Jacquemin D. Reference Energies for Double Excitations: Improvement and Extension. J Chem Theory Comput 2024; 20:5655-5678. [PMID: 38885174 DOI: 10.1021/acs.jctc.4c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
In the realm of photochemistry, the significance of double excitations (also known as doubly excited states), where two electrons are concurrently elevated to higher energy levels, lies in their involvement in key electronic transitions essential in light-induced chemical reactions as well as their challenging nature from the computational theoretical chemistry point of view. Based on state-of-the-art electronic structure methods (such as high-order coupled-cluster, selected configuration interaction, and multiconfigurational methods), we improve and expand our prior set of accurate reference excitation energies for electronic states exhibiting a substantial amount of double excitations [Loos et al. J. Chem. Theory Comput. 2019, 15, 1939]. This extended collection encompasses 47 electronic transitions across 26 molecular systems that we separate into two distinct subsets: (i) 28 "genuine" doubly excited states where the transitions almost exclusively involve doubly excited configurations and (ii) 19 "partial" doubly excited states which exhibit a more balanced character between singly and doubly excited configurations. For each subset, we assess the performance of high-order coupled-cluster (CC3, CCSDT, CC4, and CCSDTQ) and multiconfigurational methods (CASPT2, CASPT3, PC-NEVPT2, and SC-NEVPT2). Using as a probe the percentage of single excitations involved in a given transition (%T1) computed at the CC3 level, we also propose a simple correction that reduces the errors of CC3 by a factor of 3, for both sets of excitations. We hope that this more complete and diverse compilation of double excitations will help future developments of electronic excited-state methodologies.
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Affiliation(s)
- Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
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13
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Robertson NK, Onel L, Blitz MA, Shannon R, Stone D, Seakins PW, Robertson SH, Kühn C, Pazdera TM, Olzmann M. Temperature-Dependent, Site-Specific Rate Coefficients for the Reaction of OH (OD) with Methyl Formate Isotopologues via Experimental and Theoretical Studies. J Phys Chem A 2024; 128:5028-5040. [PMID: 38885649 PMCID: PMC11215782 DOI: 10.1021/acs.jpca.4c02524] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2024] [Revised: 05/30/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Methyl esters are an important component of combustion and atmospheric systems. Reaction with the OH radical plays an important role in the removal of the simplest methyl ester, methyl formate (MF, CH3OCHO). In this paper, the overall rate coefficients for the reactions of OH and OD with MF isotopologues, studied under pseudo-first-order conditions, are reported using two different laser flash photolysis systems with the decay of OH monitored by laser-induced fluorescence. The room-temperature rate coefficient for OH + MF, (1.95 ± 0.34) × 10-13 cm3 molecule-1 s-1, is in good agreement with the literature. The rate coefficient exhibits curved Arrhenius behavior, and our results bridge the gap between previous low-temperature and shock tube studies. In combination with the literature, the rate coefficient for the reaction of OH with MF between 230 and 1400 K can be parametrized as kOH+MF = (3.2 × 10-13) × (T/300 K)2.3 × exp(-141.4 K/T) cm3 molecule-1 s-1 with an overall estimated uncertainty of ∼30%. The reactions of OD with MF isotopologues show a small enhancement (inverse secondary isotope effect) compared to the respective OH reactions. The reaction of OH/OD with MF shows a normal primary isotope effect, a decrease in the rate coefficient when MF is partially or fully deuterated. Experimental studies have been supported by ab initio calculations at the CCSD(T)-F12/aug-cc-pVTZ//M06-2X/6-31+G** level of theory. The calculated, zero-point-corrected, barrier heights for abstraction at the methyl and formate sites are 1.3 and 6.0 kJ mol-1, respectively, and the ab initio predictions of kinetic isotope effects are in agreement with experiment. Fitting the experimental isotopologue data refines these barriers to 0.9 ± 0.6 and 4.1 ± 0.9 kJ mol-1. The branching ratio is approximately 50:50 at 300 K. Between 300 and 500 K, abstraction via the higher-energy, higher-entropy formate transition state becomes more favored (60:40). However, experiment and calculations suggest that as the temperature increases further, with higher energy, less constrained conformers of the methyl transition state become more significant. The implications of the experimental and theoretical results for the mechanisms of MF atmospheric oxidation and low-temperature combustion are discussed.
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Affiliation(s)
| | - Lavinia Onel
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
| | - Mark A. Blitz
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
- National
Centre for Atmospheric Science, University
of Leeds, Leeds LS2 9JT, U.K.
| | - Robin Shannon
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
| | - Daniel Stone
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
| | - Paul W. Seakins
- School
of Chemistry, University of Leeds, Leeds LS2 9JT, U.K.
| | | | - Christian Kühn
- Institut
für Physikalische Chemie, Karlsruher
Institut für Technologie (KIT), 76131 Karlsruhe, Germany
| | - Tobias M. Pazdera
- Institut
für Physikalische Chemie, Karlsruher
Institut für Technologie (KIT), 76131 Karlsruhe, Germany
| | - Matthias Olzmann
- Institut
für Physikalische Chemie, Karlsruher
Institut für Technologie (KIT), 76131 Karlsruhe, Germany
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14
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Gál DR, Papp D, Czakó G. Benchmark ab initio characterization of the multi-channel Cl + CH 3X [X = F, Cl, Br, I] reactive potential energy surfaces. Phys Chem Chem Phys 2024; 26:17695-17706. [PMID: 38869051 DOI: 10.1039/d4cp01578a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
We determine benchmark geometries and relative energies for the stationary points of the Cl + CH3X [X = F, Cl, Br, I] reactions. We consider four possible reaction pathways: hydrogen abstraction, hydrogen substitution, halogen abstraction, and halogen substitution, where the substitution processes can proceed via either Walden inversion or front-side attack. We perform geometry optimizations and obtain harmonic vibrational frequencies at the explicitly-correlated UCCSD(T)-F12b/aug-cc-pVTZ level of theory, followed by UCCSD(T)-F12b/aug-cc-pVQZ single-point computations to make finite-basis-set error negligible. To reach chemical (<1 kcal mol-1), or even subchemical (<0.5 kcal mol-1) accuracy, we include core-correlation, scalar relativistic, post-(T), spin-orbit-splitting and zero-point-energy contributions, as well, in the relative energies of all the stationary points. Our benchmark 0 K reaction enthalpies are compared to available experimental results and show good agreement. The stationary-point structures and energetics are interpreted in terms of Hammond's postulate and used to make predictions related to the dynamical behavior of these reactive systems.
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Affiliation(s)
- Dorina R Gál
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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15
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Owens A. A highly accurate potential energy surface for carbonyl sulphide (OCS): how important are the ab initio calculations? Phys Chem Chem Phys 2024; 26:17684-17694. [PMID: 38869020 DOI: 10.1039/d4cp01205d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/14/2024]
Abstract
Ab initio quantum chemical methods can produce accurate molecular potential energy surfaces (PESs) capable of predicting the fundamental vibrational wavenumbers to within 1 cm-1. However, for high-resolution applications this is simply not good enough and empirical refinement is necessary, i.e. adjusting the PES to better match laboratory spectroscopic data. Here, the impact of the underlying ab initio calculations is rigorously investigated within the context of empirical refinement. For carbonyl sulphide (OCS), state-of-the-art electronic structure calculations are employed to construct higher- and lower-level ab initio PESs, which are then empirically refined in near-identical procedures. The initial ab initio calculations are shown to considerably affect the accuracy of the final refined PES, with an order-of-magnitude improvement in computed rotation-vibration energy levels achieved for OCS. In demonstrating this, the most accurate PES of the electronic ground state of OCS is produced, reproducing the fundamentals with a root-mean-square error (RMSE) of 0.004 cm-1, and 884 rovibrational energy levels below 14 000 cm-1 with an RMSE of 0.060 cm-1.
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Affiliation(s)
- Alec Owens
- Department of Physics and Astronomy, University College London, Gower Street, WC1E 6BT, London, UK.
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16
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Shi BX, Wales DJ, Michaelides A, Myung CW. Going for Gold(-Standard): Attaining Coupled Cluster Accuracy in Oxide-Supported Nanoclusters. J Chem Theory Comput 2024; 20:5306-5316. [PMID: 38856017 DOI: 10.1021/acs.jctc.4c00379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/11/2024]
Abstract
The structure of oxide-supported metal nanoclusters plays an essential role in their sharply enhanced catalytic activity over that of bulk metals. Simulations provide the atomic-scale resolution needed to understand these systems. However, the sensitive mix of metal-metal and metal-support interactions, which govern their structure, puts stringent requirements on the method used, requiring calculations beyond standard density functional theory (DFT). The method of choice is coupled cluster theory [specifically CCSD(T)], but its computational cost has so far prevented its application to these systems. In this work, we showcase two approaches to make CCSD(T) accuracy readily achievable in oxide-supported nanoclusters. First, we leverage the SKZCAM protocol to provide the first benchmarks of oxide-supported nanoclusters, revealing that it is specifically metal-metal interactions that are challenging to capture with DFT. Second, we propose a CCSD(T) correction (ΔCC) to the metal-metal interaction errors in DFT, reaching accuracy comparable to that of the SKZCAM protocol at significantly lower cost. This approach forges a path toward studying larger systems at reliable accuracy, which we highlight by identifying a ground-state structure in agreement with experiments for Au20 on MgO, a challenging system where DFT models have yielded conflicting predictions.
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Affiliation(s)
- Benjamin X Shi
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - David J Wales
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Angelos Michaelides
- Yusuf Hamied Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, U.K
| | - Chang Woo Myung
- Department of Energy Science, Sungkyunkwan University, Seobu-ro 2066, Suwon 16419, Korea
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17
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Di Grande S, Barone V. Toward Accurate Quantum Chemical Methods for Molecules of Increasing Dimension: The New Family of Pisa Composite Schemes. J Phys Chem A 2024; 128:4886-4900. [PMID: 38847454 DOI: 10.1021/acs.jpca.4c01673] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/21/2024]
Abstract
The new versions of the Pisa composite scheme introduced in the present paper are based on the careful selection of different quantum chemical models for energies, geometries, and vibrational frequencies, with the aim of maximizing the accuracy of the overall description while retaining a reasonable cost for all the steps. In particular, the computation of accurate electronic energies has been further improved introducing more reliable complete basis set extrapolations and estimation of core-valence correlation, together with improved basis sets for third-row atoms. Furthermore, the reduced-cost frozen natural orbital (FNO) model has been introduced and validated for large molecules. Accurate molecular structures can be obtained avoiding complete basis set extrapolation and evaluating core-valence correlation at the MP2 level. Unfortunately, analytical gradients are not available for the FNO version of the model. Therefore, for large molecules, an accurate reduced-cost alternative is offered by evaluation of valence contributions with a double-hybrid functional in conjunction with the same MP2 contribution for core-valence correlation or by means of a one-parameter approximation. The same double-hybrid functional and basis set are employed to evaluate zero-point energies and partition functions. After the validation of the new models for small systems, a panel of molecular bricks of life has been used to analyze their performances for problems of current fundamental or technological interest. The fully black-box implementation of the computational workflow paves the way toward the accurate yet not prohibitively expensive study of medium- to large-sized molecules also by experimentally oriented researchers.
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Affiliation(s)
- Silvia Di Grande
- Scuola Normale Superiore di Pisa, Piazza dei Cavalieri 7, 56126 Pisa, Italy
- Scuola Superiore Meridionale, Largo San Marcellino 10, 80138 Napoli, Italy
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18
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Costain TS, Ogden V, Neville SP, Schuurman MS. A DFT/MRCI Hamiltonian parameterized using only ab initio data: I. valence excited states. J Chem Phys 2024; 160:224106. [PMID: 38856682 DOI: 10.1063/5.0210897] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2024] [Accepted: 05/22/2024] [Indexed: 06/11/2024] Open
Abstract
A new combined density functional theory and multi-reference configuration interaction (DFT/MRCI) Hamiltonian parameterized solely using the benchmark ab initio vertical excitation energies obtained from the QUEST databases is presented. This new formulation differs from all previous versions of the method in that the choice of the underlying exchange-correlation (XC) functional employed to construct the one-particle (orbital) basis is considered, and a new XC functional, QTP17, is chosen for its ability to generate a balanced description of core and valence vertical excitation energies. The ability of the new DFT/MRCI Hamiltonian, termed QE8, to furnish accurate excitation energies is confirmed using benchmark quantum chemistry computations, and a mean absolute error of 0.16 eV is determined for the wide range of electronic excitations included in the validation dataset. In particular, the QE8 Hamiltonian dramatically improves the performance of DFT/MRCI for doubly excited states. The performance of fast approximate DFT/MRCI methods, p-DFT/MRCI and DFT/MRCI(2), is also evaluated using the QE8 Hamiltonian, and they are found to yield excitation energies in quantitative agreement with the parent DFT/MRCI method, with the two methods exhibiting a mean difference of 0.01 eV with respect to DFT/MRCI over the entire benchmark set.
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Affiliation(s)
- Teagan Shane Costain
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Victoria Ogden
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
| | - Simon P Neville
- National Research Council Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
| | - Michael S Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, Ottawa, Ontario K1N 6N5, Canada
- National Research Council Canada, 100 Sussex Dr., Ottawa, Ontario K1A 0R6, Canada
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19
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Weymuth T, Unsleber JP, Türtscher PL, Steiner M, Sobez JG, Müller CH, Mörchen M, Klasovita V, Grimmel SA, Eckhoff M, Csizi KS, Bosia F, Bensberg M, Reiher M. SCINE-Software for chemical interaction networks. J Chem Phys 2024; 160:222501. [PMID: 38857173 DOI: 10.1063/5.0206974] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2024] [Accepted: 05/09/2024] [Indexed: 06/12/2024] Open
Abstract
The software for chemical interaction networks (SCINE) project aims at pushing the frontier of quantum chemical calculations on molecular structures to a new level. While calculations on individual structures as well as on simple relations between them have become routine in chemistry, new developments have pushed the frontier in the field to high-throughput calculations. Chemical relations may be created by a search for specific molecular properties in a molecular design attempt, or they can be defined by a set of elementary reaction steps that form a chemical reaction network. The software modules of SCINE have been designed to facilitate such studies. The features of the modules are (i) general applicability of the applied methodologies ranging from electronic structure (no restriction to specific elements of the periodic table) to microkinetic modeling (with little restrictions on molecularity), full modularity so that SCINE modules can also be applied as stand-alone programs or be exchanged for external software packages that fulfill a similar purpose (to increase options for computational campaigns and to provide alternatives in case of tasks that are hard or impossible to accomplish with certain programs), (ii) high stability and autonomous operations so that control and steering by an operator are as easy as possible, and (iii) easy embedding into complex heterogeneous environments for molecular structures taken individually or in the context of a reaction network. A graphical user interface unites all modules and ensures interoperability. All components of the software have been made available as open source and free of charge.
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Affiliation(s)
- Thomas Weymuth
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jan P Unsleber
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Paul L Türtscher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Miguel Steiner
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Jan-Grimo Sobez
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Charlotte H Müller
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Maximilian Mörchen
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Veronika Klasovita
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Stephanie A Grimmel
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Marco Eckhoff
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Katja-Sophia Csizi
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Francesco Bosia
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Moritz Bensberg
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
| | - Markus Reiher
- ETH Zurich, Department of Chemistry and Applied Biosciences, Vladimir-Prelog-Weg 2, 8093 Zurich, Switzerland
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20
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Horváth K, Tajti V, Papp D, Czakó G. Dynamics of the HCl + C 2H 5 Multichannel Reaction on a Full-Dimensional Ab Initio Potential Energy Surface. J Phys Chem A 2024; 128:4474-4482. [PMID: 38807530 PMCID: PMC11163425 DOI: 10.1021/acs.jpca.4c02042] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/28/2024] [Revised: 05/13/2024] [Accepted: 05/15/2024] [Indexed: 05/30/2024]
Abstract
We report a full-dimensional ab initio analytical potential energy surface (PES), which accurately describes the HCl + C2H5 multichannel reaction. The new PES is developed by iteratively adding selected configurations along HCl + C2H5 quasi-classical trajectories (QCTs), thereby improving our previous Cl(2P3/2) + C2H6 PES using the Robosurfer program package. QCT simulations for the H'Cl + C2H5 reaction reveal hydrogen-abstraction, chlorine-abstraction, and hydrogen-exchange channels leading to Cl + C2H5H', H' + C2H5Cl, and HCl + C2H4H', respectively. Hydrogen abstraction dominates in the collision energy (Ecoll) range of 1-80 kcal/mol and proceeds with indirect isotropic scattering at low Ecoll and forward-scattered direct stripping at high Ecoll. Chlorine abstraction opens around 40 kcal/mol collision energy and becomes competitive with hydrogen abstraction at Ecoll = 80 kcal/mol. A restricted opening of the cone of acceptance in the Cl-abstraction reaction is found to result in the preference for a backward-scattering direct-rebound mechanism at all energies studied. Initial attack-angle distributions show mainly side-on collision preference of C2H5 for both abstraction reactions, and in the case of the HCl reactant, H/Cl-side preference for the H/Cl abstraction. For hydrogen abstraction, the collision energy transfer into the product translational and internal energy is almost equally significant, whereas in the case of chlorine abstraction, most of the available energy goes into the internal degrees of freedom. Hydrogen exchange is a minor channel with nearly constant reactivity in the Ecoll range of 10-80 kcal/mol.
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Affiliation(s)
- Kitti Horváth
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Viktor Tajti
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Dóra Papp
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
| | - Gábor Czakó
- MTA-SZTE Lendület
Computational Reaction Dynamics Research Group, Interdisciplinary
Excellence Centre and Department of Physical Chemistry and Materials
Science, Institute of Chemistry, University
of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary
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21
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Horváth Á, Benkő Z. Phthalazine as a Diene in Diels-Alder Reactions With P- and As-Containing Anionic Dienophiles: Comparison of Possible Reaction Channels. Chempluschem 2024:e202400140. [PMID: 38819996 DOI: 10.1002/cplu.202400140] [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: 02/18/2024] [Revised: 05/30/2024] [Accepted: 05/31/2024] [Indexed: 06/02/2024]
Abstract
Phthalazine can behave as a diene in Diels-Alder (DA) cycloadditions, typically at the pyridazine ring, however, its application is somewhat limited because these reactions usually require harsh conditions or sophisticated catalysts. As an unconventional example, phthalazine was reported to undergo cycloaddition with the [PCO]- anion without any catalyst. In this computational study, we scrutinise the mechanism of the DA reactions between phthalazine and the so far known [ECX]- (E: P, As; X: O, S, Se) anions as dienophiles. In principle, the attack of an [ECX]- anion may occur at two different sites of phthalazine, either at the benzene or the pyridazine ring, and both of these possible reaction channels were juxtaposed on the basis of energetic aspects. In all of the investigated cases, the analysis of the energy profiles reveals a clear regioselectivity that favours the attack at the pyridazine ring. As a result, so far unprecedented 2-pnictanaphth-3-olate analogues seem achievable as final products. Comparing the characteristics of these pathways allowed us to clarify the source of this regioselectivity: The pyridazine ring of phthalazine exhibits lower aromaticity than the benzene subring; therefore, in the DA step, the former ring shows a higher affinity toward a dienophile than the latter, leading to lower activation barriers. To further map the electronic and structural features of the cycloaddition steps, the local interactions evolving in the transition states were analysed and compared using global and local descriptors. In most aspects, the characteristics of both pathways were found to be rather similar, in contrast to the markedly differing activation barriers on the two routes.
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Affiliation(s)
- Ádám Horváth
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp 3., H-1111, Budapest, Hungary
| | - Zoltán Benkő
- Department of Inorganic and Analytical Chemistry, Budapest University of Technology and Economics, Műegyetem rkp 3., H-1111, Budapest, Hungary
- HUN-REN-BME Computation Driven Chemistry Research Group, Műegyetem rkp 3., H-1111, Budapest, Hungary
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22
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Tang CL, Heide AG, Heide AD, Douberly GE, Turney JM, Schaefer HF. Exploring the Tl 2 H 2 potential energy surface: A comparative analysis with group 13 systems and experiment. J Comput Chem 2024; 45:985-994. [PMID: 38197269 DOI: 10.1002/jcc.27293] [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: 10/05/2023] [Revised: 12/04/2023] [Accepted: 12/10/2023] [Indexed: 01/11/2024]
Abstract
Thallium chemistry is experiencing unprecedented importance. Therefore, it is valuable to characterize some of the simplest thallium compounds. Stationary points along the singlet and triplet Tl 2 H 2 potential energy surface have been characterized. Stationary point geometries were optimized with the CCSD(T)/aug-cc-pwCVQZ-PP method. Harmonic vibrational frequencies were computed at the same level of theory while anharmonic vibrational frequencies were computed at the CCSD(T)/aug-cc-pwCVTZ-PP level of theory. Final energetics were obtained with the CCSDT(Q) method. Basis sets up to augmented quintuple-zeta cardinality (aug-cc-pwCV5Z-PP) were employed to obtain energetics in order to extrapolate to the complete basis set limits using the focal point approach. Zero-point vibrational energy corrections were appended to the extrapolated energies in order to determine relative energies at 0 K. It was found that the planar dibridged isomer lies lowest in energy while the linear structure lies highest in energy. The results were compared to other group 13 M 2 H 2 (M = B, Al, Ga, In, and Tl) theoretical studies and some interesting variations are found. With respect to experiment, incompatibilities exist.
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Affiliation(s)
- Carson L Tang
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Alexander G Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Alexandra D Heide
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Gary E Douberly
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Justin M Turney
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, USA
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23
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Szirmai ÁB, Hégely B, Tajti A, Kállay M, Szalay PG. Projected Atomic Orbitals As Optimal Virtual Space for Excited State Projection-Based Embedding Calculations. J Chem Theory Comput 2024; 20:3420-3425. [PMID: 38626416 DOI: 10.1021/acs.jctc.4c00104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/18/2024]
Abstract
The projected atomic orbital (PAO) technique is presented for the construction of virtual orbital spaces in projection-based embedding (PbE) applications. The proposed straightforward procedure produces a set of virtual orbitals that are used in the final, high-level calculation of the embedded active subsystem. The PAO scheme is demonstrated on intermolecular potentials of bimolecular complexes in ground and excited states, including Rydberg excitations. The results show the outstanding performance of the PbE method when used with PAO virtual orbitals compared with those produced using common orbital localization techniques. The good agreement of the resulting PbE potential curves with those from high-level ab initio dimer calculations, also in diffuse basis sets, confirms that the PAO technique can be suggested for future applications using top-down embedding methods.
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Affiliation(s)
- Ádám B Szirmai
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest, Hungary
- György Hevesy Doctoral School, ELTE Eötvös Loŕnd University, Institute of Chemistry, H-1117 Budapest, Hungary
| | - Bence Hégely
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Attila Tajti
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Péter G Szalay
- Laboratory of Theoretical Chemistry, Institute of Chemistry, ELTE Eötvös Loránd University, P.O. Box 32, H-1518 Budapest, Hungary
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24
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Irikura KK. Ab initio spectroscopy and thermochemistry of the platinum hydride ions, PtH+ and PtH. J Chem Phys 2024; 160:184309. [PMID: 38738614 DOI: 10.1063/5.0207505] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Accepted: 04/26/2024] [Indexed: 05/14/2024] Open
Abstract
Rovibrational levels of low-lying electronic states of the gas-phase, diatomic molecules, PtH+ and PtH-, are computed on potential-energy functions obtained by using a hybrid spin-orbit configuration-interaction procedure. PtH- has a well-separated Σ0++1 ground state, while the first two electronic states of PtH+ (Σ0++1 and 3Δ3) are nearly degenerate. Combining the experimental photoelectron (PE) spectra of PtH- with theoretical photodetachment spectroscopy leads to an improved value for the electron affinity of PtH, EA(PtH) = (1.617 ± 0.015) eV. When PtH- is a product of photodissociation of PtHCO2-, its PE spectrum is broad because of rotational excitation. Temperature-dependent thermodynamic functions and thermochemistry of dissociation are computed from the theoretical energy levels. Previously published energetic quantities for PtH+ and PtH- are revised. The ground 1Σ+ term of PtH+ is not well described using single-reference theory.
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Affiliation(s)
- Karl K Irikura
- Chemical Sciences Division, National Institute of Standards and Technology, Gaithersburg, Maryland, 20899 , USA
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25
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Bakó I, Jicsinszky L, Pothoczki S. Systematic Study of Different Types of Interactions in α-, β- and γ-Cyclodextrin: Quantum Chemical Investigation. Molecules 2024; 29:2205. [PMID: 38792067 PMCID: PMC11124371 DOI: 10.3390/molecules29102205] [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: 04/17/2024] [Revised: 05/03/2024] [Accepted: 05/06/2024] [Indexed: 05/26/2024] Open
Abstract
In this work, comprehensive ab initio quantum chemical calculations using the DFT level of theory were performed to characterize the stabilization interactions (H-bonding and hyperconjugation effects) of two stable symmetrical conformations of α-, β-, and γ-cyclodextrins (CDs). For this purpose, we analyzed the electron density using "Atom in molecules" (AIM), "Natural Bond Orbital" (NBO), and energy decomposition method (CECA) in 3D and in Hilbert space. We also calculated the H-bond lengths and OH vibrational frequencies. In every investigated CD, the quantum chemical descriptors characterizing the strength of the interactions between the H-bonds of the primary OH (or hydroxymethyl) and secondary OH groups are examined by comparing the same quantity calculated for ethylene glycol, α-d-glucose (α-d-Glcp) and a water cluster as reference systems. By using these external standards, we can characterize more quantitatively the properties of these bonds (e.g., strength). We have demonstrated that bond critical points (BCP) of intra-unit H-bonds are absent in cyclodextrins, similar to α-d-Glcp and ethylene glycol. In contrast, the CECA analysis showed the existence of an exchange (bond-like) interaction between the interacting O…H atoms. Consequently, the exchange interaction refers to a chemical bond, namely the H-bond between two atoms, unlike BCP, which is not suitable for its detection.
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Affiliation(s)
- Imre Bakó
- HUN-REN Research Centre for Natural Sciences, Magyar Tudósok Körútja 2, H-1117 Budapest, Hungary
| | - László Jicsinszky
- Dipartimento di Scienza e Tecnologia del Farmaco, University of Turin, Via P. Giuria, 9, 10125 Turin, Italy;
| | - Szilvia Pothoczki
- HUN-REN Wigner Research Centre for Physics, Konkoly Thege M. út 29-33, H-1121 Budapest, Hungary
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26
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Deng G, Reimann M, Müller C, Lu Y, Kaupp M, Riedel S. Spectroscopic Identification of Trifluorosilylphosphinidene and Isomeric Phosphasilene and Silicon Trifluorophosphine Complex. Inorg Chem 2024; 63:7286-7292. [PMID: 38592208 DOI: 10.1021/acs.inorgchem.4c00135] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/10/2024]
Abstract
The perfluorinated silylphosphinidene, F3SiP, in the triplet ground state is generated by the reaction of laser-ablated silicon atoms with PF3 in solid neon and argon matrices. The reactions proceed with the initial formation of a silicon trifluorophosphine complex, F3PSi, in the triplet ground state, and a more stable inserted phosphasilene, FPSiF2, in the singlet ground state upon deposition. The trifluorosilylphosphinidene was formed through F-migration reactions of FPSiF2 and F3PSi following a two-state mechanism under irradiation with visible light (λ = 470 nm) and full arc light (λ > 220 nm), respectively. High-level quantum-chemical methods support the identification of F3PSi, FPSiF2, and F3SiP by matrix-isolation IR spectroscopy.
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Affiliation(s)
- Guohai Deng
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Marc Reimann
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, Berlin 10623, Germany
| | - Carsten Müller
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Yan Lu
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Strasse des 17. Juni 135, Berlin 10623, Germany
| | - Sebastian Riedel
- Institut für Chemie und Biochemie-Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34/36, Berlin 14195, Germany
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27
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Csóka J, Hégely B, Nagy PR, Kállay M. Development of analytic gradients for the Huzinaga quantum embedding method and its applications to large-scale hybrid and double hybrid DFT forces. J Chem Phys 2024; 160:124113. [PMID: 38530010 DOI: 10.1063/5.0194463] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Accepted: 03/06/2024] [Indexed: 03/27/2024] Open
Abstract
The theory of analytic gradients is presented for the projector-based density functional theory (DFT) embedding approach utilizing the Huzinaga-equation. The advantages of the Huzinaga-equation-based formulation are demonstrated. In particular, it is shown that the projector employed does not appear in the Lagrangian, and the potential risk of numerical problems is avoided at the evaluation of the gradients. The efficient implementation of the analytic gradient theory is presented for approaches where hybrid DFT, second-order Møller-Plesset perturbation theory, or double hybrid DFT are embedded in lower-level DFT environments. To demonstrate the applicability of the method and to gain insight into its accuracy, it is applied to equilibrium geometry optimizations, transition state searches, and potential energy surface scans. Our results show that bond lengths and angles converge rapidly with the size of the embedded system. While providing structural parameters close to high-level quality for the embedded atoms, the embedding approach has the potential to relax the coordinates of the environment as well. Our demonstrations on a 171-atom zeolite and a 570-atom protein system show that the Huzinaga-equation-based embedding can accelerate (double) hybrid gradient computations by an order of magnitude with sufficient active regions and enables affordable force evaluations or geometry optimizations for molecules of hundreds of atoms.
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Affiliation(s)
- József Csóka
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Bence Hégely
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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28
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Beck IT, Lahm ME, Douberly GE, Schaefer HF. Convergent ab initio analysis of the multi-channel HOBr + H reaction. J Chem Phys 2024; 160:124304. [PMID: 38516979 DOI: 10.1063/5.0200276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Accepted: 03/06/2024] [Indexed: 03/23/2024] Open
Abstract
High-level potential energy surfaces for three reactions of hypobromous acid with atomic hydrogen were computed at the CCSDTQ/CBS//CCSDT(Q)/complete basis set level of theory. Focal point analysis was utilized to extrapolate energies and gradients for energetics and optimizations, respectively. The H attack at Br and subsequent Br-O cleavage were found to proceed barrierlessly. The slightly submerged transition state lies -0.2 kcal mol-1 lower in energy than the reactants and produces OH and HBr. The two other studied reaction paths are the radical substitution to produce H2O and Br with a 4.0 kcal mol-1 barrier and the abstraction at hydrogen to produce BrO and H2 with an 11.2 kcal mol-1 barrier. The final product energies lie -37.2, -67.9, and -7.3 kcal mol-1 lower in energy than reactants, HOBr + H, for the sets of products OH + HBr, H2O + Br, and H2 + BrO, respectively. Additive corrections computed for the final energetics, particularly the zero-point vibrational energies and spin-orbit corrections, significantly impacted the final stationary point energies, with corrections up to 6.2 kcal mol-1.
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Affiliation(s)
- Ian T Beck
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Mitchell E Lahm
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Gary E Douberly
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
| | - Henry F Schaefer
- Department of Chemistry and Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia 30602, USA
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29
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Semidalas E, Karton A, Martin JML. W4Λ: Leveraging Λ Coupled-Cluster for Accurate Computational Thermochemistry Approaches. J Phys Chem A 2024; 128:1715-1724. [PMID: 38400740 PMCID: PMC10926103 DOI: 10.1021/acs.jpca.3c08158] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Revised: 01/28/2024] [Accepted: 01/31/2024] [Indexed: 02/26/2024]
Abstract
High-accuracy composite wave function methods like Weizmann-4 (W4) theory, high-accuracy extrapolated ab initio thermochemistry (HEAT), and the Feller-Peterson-Dixon (FPD) approach enable sub-kJ/mol accuracy in gas-phase thermochemical properties. Their biggest computational bottleneck is the evaluation of the valence post-CCSD(T) correction term. We demonstrate here, for the W4-17 thermochemistry benchmark and subsets thereof, that the Λ coupled-cluster expansion converges more rapidly and smoothly than the regular coupled-cluster series. By means of CCSDT(Q)Λ and CCSDTQ(5)Λ, we can considerably (up to an order of magnitude) accelerate W4- and W4.3-type calculations without loss in accuracy, leading to the W4Λ and W4.3Λ computational thermochemistry protocols.
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Affiliation(s)
- Emmanouil Semidalas
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
| | - Amir Karton
- School
of Science and Technology, University of
New England, Armidale, New South Wales 2351, Australia
| | - Jan M. L. Martin
- Department
of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Reḥovot, Israel
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30
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Salo VT, Chen J, Runeberg N, Kjaergaard HG, Kurtén T. Multireference and Coupled-Cluster Study of Dimethyltetroxide (MeO 4Me) Formation and Decomposition. J Phys Chem A 2024. [PMID: 38417845 DOI: 10.1021/acs.jpca.3c08043] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/01/2024]
Abstract
Peroxyl radicals (RO2) are important intermediates in the atmospheric oxidation processes. The RO2 can react with other RO2 to form reactive intermediates known as tetroxides, RO4R. The reaction mechanisms of RO4R formation and its various decomposition channels have been investigated in multiple computational studies, but previous approaches have not been able to provide a unified methodology that is able to connect all relevant reactions together. An apparent difficulty in modeling the RO4R formation and its decomposition is the involvement of open-shell singlet electronic states along the reaction pathway. Modeling such electronic states requires multireference (MR) methods, which we use in the present study to investigate in detail a model reaction of MeO2 + MeO2 → MeO4Me, and its decomposition, MeO4Me → MeO + O2 + MeO, as well as the two-body product complexes MeO···O2 + MeO and MeO···MeO + O2. The used MR methods are benchmarked against relative energies of MeO2 + MeO2, MeO4Me, and MeO + MeO + O2, calculated with CCSD(T)/CBS, W2X, and W3X-L methods. We found that the calculated relative energies of the overall MeO2 + MeO2 → MeO4Me → MeO + O2 + MeO reaction are very sensitive to the chosen MR method and that the CASPT2(22e,14o)-IPEA method is able to reproduce the relative energies obtained by the various coupled-cluster methods. Furthermore, CASPT2(22e,14o)-IPEA and W3X-L results show that the MeO···O2 product complex + MeO is lower in energy than the MeO···MeO complex + O2. The formation of MeO4Me is exothermic, and its decomposition is endothermic, relative to the tetroxide. Both the formation and decomposition reactions appear to follow pathways with no saddle points. According to potential energy surface scans of the decomposition pathway, the concerted cleavage of both MeO···O bonds in MeO4Me is energetically preferred over the corresponding sequential decomposition.
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Affiliation(s)
- Vili-Taneli Salo
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki FI-00014, Finland
| | - Jing Chen
- Department of Chemistry, University of Copenhagen, Copenhagen 2100, Denmark
| | - Nino Runeberg
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki FI-00014, Finland
| | | | - Theo Kurtén
- Department of Chemistry, Faculty of Science, University of Helsinki, Helsinki FI-00014, Finland
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31
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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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32
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Yang X, Wang H, Lu K, Ma X, Tan Z, Long B, Chen X, Li C, Zhai T, Li Y, Qu K, Xia Y, Zhang Y, Li X, Chen S, Dong H, Zeng L, Zhang Y. Reactive aldehyde chemistry explains the missing source of hydroxyl radicals. Nat Commun 2024; 15:1648. [PMID: 38388476 PMCID: PMC10883920 DOI: 10.1038/s41467-024-45885-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Accepted: 02/06/2024] [Indexed: 02/24/2024] Open
Abstract
Hydroxyl radicals (OH) determine the tropospheric self-cleansing capacity, thus regulating air quality and climate. However, the state-of-the-art mechanisms still underestimate OH at low nitrogen oxide and high volatile organic compound regimes even considering the latest isoprene chemistry. Here we propose that the reactive aldehyde chemistry, especially the autoxidation of carbonyl organic peroxy radicals (R(CO)O2) derived from higher aldehydes, is a noteworthy OH regeneration mechanism that overwhelms the contribution of the isoprene autoxidation, the latter has been proved to largely contribute to the missing OH source under high isoprene condition. As diagnosed by the quantum chemical calculations, the R(CO)O2 radicals undergo fast H-migration to produce unsaturated hydroperoxyl-carbonyls that generate OH through rapid photolysis. This chemistry could explain almost all unknown OH sources in areas rich in both natural and anthropogenic emissions in the warm seasons, and may increasingly impact the global self-cleansing capacity in a future low nitrogen oxide society under carbon neutrality scenarios.
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Affiliation(s)
- Xinping Yang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
- State Environmental Protection Key Laboratory of Vehicle Emission Control and Simulation, Vehicle Emission Control Center, Chinese Research Academy of Environmental Sciences, Beijing, 100012, China
| | - Haichao Wang
- School of Atmospheric Sciences, Sun Yat-sen University and Southern Marine Science and Engineering Guangdong Laboratory (Zhuhai), Zhuhai, 519082, China
- Guangdong Provincial Observation and Research Station for Climate Environment and Air Quality Change in the Pearl River Estuary, Key Laboratory of Tropical Atmosphere-Ocean System, Ministry of Education, Zhuhai, 519082, China
| | - Keding Lu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
| | - Xuefei Ma
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Zhaofeng Tan
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Bo Long
- College of Material Science and Engineering, Guizhou Minzu University, Guizhou, China
| | - Xiaorui Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Chunmeng Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Tianyu Zhai
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yang Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Kun Qu
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yu Xia
- College of Material Science and Engineering, Guizhou Minzu University, Guizhou, China
| | - Yuqiong Zhang
- College of Material Science and Engineering, Guizhou Minzu University, Guizhou, China
| | - Xin Li
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Shiyi Chen
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Huabin Dong
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Limin Zeng
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China
| | - Yuanhang Zhang
- State Key Joint Laboratory of Environmental Simulation and Pollution Control, State Environmental Protection Key Laboratory of Atmospheric Ozone Pollution Control, College of Environmental Sciences and Engineering, Peking University, Beijing, 100871, China.
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33
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Nigam A, Pollice R, Friederich P, Aspuru-Guzik A. Artificial design of organic emitters via a genetic algorithm enhanced by a deep neural network. Chem Sci 2024; 15:2618-2639. [PMID: 38362419 PMCID: PMC10866360 DOI: 10.1039/d3sc05306g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 01/10/2024] [Indexed: 02/17/2024] Open
Abstract
The design of molecules requires multi-objective optimizations in high-dimensional chemical space with often conflicting target properties. To navigate this space, classical workflows rely on the domain knowledge and creativity of human experts, which can be the bottleneck in high-throughput approaches. Herein, we present an artificial molecular design workflow relying on a genetic algorithm and a deep neural network to find a new family of organic emitters with inverted singlet-triplet gaps and appreciable fluorescence rates. We combine high-throughput virtual screening and inverse design infused with domain knowledge and artificial intelligence to accelerate molecular generation significantly. This enabled us to explore more than 800 000 potential emitter molecules and find more than 10 000 candidates estimated to have inverted singlet-triplet gaps (INVEST) and appreciable fluorescence rates, many of which likely emit blue light. This class of molecules has the potential to realize a new generation of organic light-emitting diodes.
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Affiliation(s)
- AkshatKumar Nigam
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto 80 St. George St Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George St Toronto Ontario M5S 2E4 Canada
| | - Robert Pollice
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto 80 St. George St Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George St Toronto Ontario M5S 2E4 Canada
| | - Pascal Friederich
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto 80 St. George St Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George St Toronto Ontario M5S 2E4 Canada
- Institute of Nanotechnology, Karlsruhe Institute of Technology Hermann-von-Helmholtz-Platz 1 76344 Eggenstein-Leopoldshafen Germany
- Institute of Theoretical Informatics, Karlsruhe Institute of Technology Am Fasanengarten 5 76131 Karlsruhe Germany
| | - Alán Aspuru-Guzik
- Chemical Physics Theory Group, Department of Chemistry, University of Toronto 80 St. George St Toronto Ontario M5S 3H6 Canada
- Department of Computer Science, University of Toronto 40 St. George St Toronto Ontario M5S 2E4 Canada
- Vector Institute for Artificial Intelligence 661 University Ave Suite 710 Toronto Ontario M5G 1M1 Canada
- Department of Chemical Engineering & Applied Chemistry, University of Toronto 200 College St. Ontario M5S 3E5 Canada
- Department of Materials Science & Engineering, University of Toronto, 184 College St. Ontario M5S 3E4 Canada
- Lebovic Fellow, Canadian Institute for Advanced Research (CIFAR) 661 University Ave Toronto Ontario M5G Canada
- Acceleration Consortium Toronto Ontario M5G 3H6 Canada
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34
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Zhang YQ, Francisco JS, Long B. Rapid Atmospheric Reactions between Criegee Intermediates and Hypochlorous Acid. J Phys Chem A 2024; 128:909-917. [PMID: 38271208 DOI: 10.1021/acs.jpca.3c06144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2024]
Abstract
Hypochlorous acid (HOCl) is a paramount compound in the atmosphere due to its significant contribution to both tropospheric oxidation capacity and ozone depletion. The main removal routes for HOCl are photolysis and the reaction with OH during the daytime, while these processes are unimportant during the nighttime. Here, we report the rapid reactions of Criegee intermediates (CH2OO and anti/syn-CH3CHOO) with HOCl by using high-level quantum chemical methods as the benchmark; their accuracy is close to coupled cluster theory with single, double, and triple excitations and quasiperturbative connected quadruple excitations with a complete basis limit by extrapolation [CCSDT(Q)/CBS]. Their rate constants have been calculated by using a dual-level strategy; this combines conventional transition state theory calculated at the benchmark level with variational transition state theory with small-curvature tunneling by a validated density functional method. We find that the introduction of the methyl group into Criegee intermediates not only affects their reactivities but also exerts a remarkable influence on anharmonicity. The calculated results uncover that anharmonicity increases the rate constants of CH2OO + HOCl by a factor of 18-5, while it is of minor importance in the anti/syn-CH3CHOO + HOCl reaction at 190-350 K. The present findings reveal that the loose transition state for anti-CH3CHOO and HOCl is a rate-determining step at 190-350 K. We also find that the reaction of Criegee intermediates with HOCl contributes significantly to the sink of HOCl during the nighttime in the atmosphere.
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Affiliation(s)
- Yu-Qiong Zhang
- College of Physics and Mechatronic Engineering, Guizhou Minzu University, Guiyang 550025, China
| | - Joseph S Francisco
- Department of Earth and Environmental Sciences and Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, United States
| | - Bo Long
- College of Physics and Mechatronic Engineering, Guizhou Minzu University, Guiyang 550025, China
- College of Materials Science and Engineering, Guizhou Minzu University, Guiyang 550025, China
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35
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McCarver GA, Hinde RJ. High Accuracy Ab Initio Potential Energy Curves and Dipole Moment Functions for the X1Σ + and a3Π Spin States of the CF + Diatomic Molecule. J Phys Chem A 2024; 128:539-547. [PMID: 38227217 DOI: 10.1021/acs.jpca.3c04517] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2024]
Abstract
Potential energy curves and dipole moment functions constructed using high-accuracy ab initio methods allow for an in-depth examination of the electronic structure of diatomic molecules. Ab initio computations serve as a valuable complement to experimental data, offering insights into the nature of short-lived molecules such as those encountered within the interstellar medium (ISM). While laboratory experiments provide critical groundwork, the ISM's conditions often permit longer lifetimes for lower stability molecules, enabling unique observations. The CF+ diatomic molecule is one such molecule that has been observed spectroscopically in the ISM. Previous experimental and theoretical work have examined different spectroscopic aspects of the CF+ molecule, but the development of newer, more complete potential energy curves and dipole moment functions allows for even greater insight. We constructed both potential energy curves and dipole moment functions for the ground X1Σ+ and first excited a3Π states of CF+ for both the 12C and 13C isotopologues. The potential energy curves were constructed using coupled cluster with single, double, and perturbative triple excitations (CCSD(T)) at the complete basis set limit with corrections from full triple, quadruple, quintuple, and hextuple excitations within a finite-basis coupled cluster wave function as well as corrections from full configuration interaction and relativistic effects. Rovibrational wave functions were calculated using a vibrational Hamiltonian matrix, which moves beyond the harmonic oscillator approximation. The equilibrium bond length, vibrational constant, and rotational constant were reproduced to within 0.00013 Å, 0.28 cm-1, and 0.00045 cm-1, respectively, of experimental values. Experimental transition energies from rovibrational spectra were reproduced with an error of no larger than 0.63 cm-1. The triplet excited state (a3Π) was found to have a longer equilibrium bond length at 1.21069 Å, a vibrational constant of 1611.29 cm-1, and a rotational constant of 1.56376 cm-1. Rovibrational line lists for the 12C and 13C isotopologues for both the X1Σ+ and the excited a3Π states were generated.
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Affiliation(s)
- Gavin A McCarver
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996-1320, United States
| | - Robert J Hinde
- Department of Chemistry, University of Tennessee, Knoxville, Tennessee 37996-1320, United States
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36
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Monge-Palacios M, Wang Q, Alshaarawi A, Sepulveda ACC, Sarathy SM. Quantum chemistry and kinetics of hydrogen sulphide oxidation. Phys Chem Chem Phys 2024; 26:3219-3228. [PMID: 38193631 DOI: 10.1039/d3cp04535h] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
A fundamental understanding of the acid gas (H2S and CO2) chemistry is key to efficiently implement the desulphurisation process and even the production of clean fuels such as hydrogen or syngas. In this work, we developed a new kinetic model for the pyrolysis and oxidation of hydrogen sulphide by merging two previously reported models with the goal of covering a wider range of conditions and including the effect of carbon dioxide. The resulting model, which consists of 75 species and 514 reactions, was used to conduct rate of production and sensitivity analysis in plug flow reactor simulations, and the results were used to determine the most prominent reactions in which hydrogen sulphide, molecular hydrogen, and sulphur monoxide are involved. The resulting list of important reactions was screened and the kinetics of three of them, i.e., SO2 + S2 → S2O + SO, S2O + S2 → S3 + SO, and SO + SH → S2 + OH, was found to warrant further investigation. With the goal of improving the accurancy of our new kinetic model, we carried out a robust quantum chemistry and Rice-Ramsperger-Kassel-Marcus master equation study to obtain, for the first time, the forward and reverse rate constants for those three reactions at temperatures and pressures of interest for combustion and atmospheric chemistry. This work is the first step of a kinetic study that is aimed at improving the understanding of the chemistry of the pyrolysis and oxidation of H2S, highlighting the importance of sulphur-sulphur interactions and providing a fundamental basis for future kinetic models of H2S not only in the field of combustion, but also in atmospheric chemistry.
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Affiliation(s)
- M Monge-Palacios
- King Abdullah University of Science and Technology, Thuwal (Makkah) 23955, Saudi Arabia.
| | - Q Wang
- King Abdullah University of Science and Technology, Thuwal (Makkah) 23955, Saudi Arabia.
| | - A Alshaarawi
- Exploration and Petroleum Engineering Center-Advanced Research Center (EXPEC ARC), Saudi Aramco, Dhahran 34465, Saudi Arabia
| | - A C Cavazos Sepulveda
- Exploration and Petroleum Engineering Center-Advanced Research Center (EXPEC ARC), Saudi Aramco, Dhahran 34465, Saudi Arabia
| | - S M Sarathy
- King Abdullah University of Science and Technology, Thuwal (Makkah) 23955, Saudi Arabia.
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37
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Delgado JM, Nagy PR, Varma S. Polarizable AMOEBA Model for Simulating Mg 2+·Protein·Nucleotide Complexes. J Chem Inf Model 2024; 64:378-392. [PMID: 38051630 DOI: 10.1021/acs.jcim.3c01513] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/07/2023]
Abstract
Molecular mechanics (MM) simulations have the potential to provide detailed insights into the mechanisms of enzymes that utilize nucleotides as cofactors. In most cases, the activities of these enzymes also require the binding of divalent cations to catalytic sites. However, modeling divalent cations in MM simulations has been challenging. The inclusion of explicit polarization was considered promising, but despite improvements over nonpolarizable force fields and despite the inclusion of "Nonbonded-fix (NB-fix)" corrections, errors in interaction energies of divalent cations with proteins remain large. Importantly, the application of these models fails to reproduce the experimental structural data on Mg2+·Protein·ATP complexes. Focusing on these complexes, here we provide a systematic assessment of the polarizable AMOEBA model and recommend critical changes that substantially improve its predictive performance. Our key results are as follows. We first show that our recent revision of the AMOEBA protein model (AMOEBABIO18-HFC), which contains high field corrections (HFCs) to induced dipoles, dramatically improves Mg2+-protein interaction energies, reducing the mean absolute error (MAE) from 17 to 10 kcal/mol. This further supports the general applicability of AMOEBABIO18-HFC. The inclusion of many-body NB-fix corrections further reduces MAE to 6 kcal/mol, which amounts to less than 2% error. The errors are estimated with respect to vdW-inclusive density functional theory that we benchmark against CCSD(T) calculations and experiments. We also present a new model of ATP with revised polarization parameters to better capture its high field response, as well as new vdW and dihedral parameters. The ATP model accurately predicts experimental Mg2+-ATP binding free energy in the aqueous phase and provides new insights into how Mg2+ associates with ATP. Finally, we show that molecular dynamics (MD) simulations of Mg2+·Kinase·ATP complexes carried out with these improvements lead to a better agreement in global and local catalytic site structures between MD and X-ray crystallography.
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Affiliation(s)
- Julian M Delgado
- Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
| | - Péter R Nagy
- Department of Physical Chemistry and Materials Science, Faculty of Chemical Technology and Biotechnology, Budapest University of Technology and Economics, Műegyetem rkp. 3., Budapest H-1111, Hungary
- HUN-REN-BME Quantum Chemistry Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
- MTA-BME Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., Budapest H-1111, Hungary
| | - Sameer Varma
- Department of Molecular Biosciences, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
- Department of Physics, University of South Florida, 4202 E. Fowler Avenue, Tampa, Florida 33620, United States
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38
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Egorov O, Rey M, Viglaska D, Nikitin AV. Accurate ab initio potential energy surface, rovibrational energy levels and resonance interactions of triplet ( X ~ 3 B 1 ) methylene. J Comput Chem 2024; 45:83-100. [PMID: 37681560 DOI: 10.1002/jcc.27220] [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: 07/14/2023] [Revised: 08/15/2023] [Accepted: 08/17/2023] [Indexed: 09/09/2023]
Abstract
In this work, we report rovibrational energy levels for four isotopologues of methylene (CH2 , CHD, CD2 , and 13 CH2 ) in their ground triplet electronic state (X ~ 3 B1 ) from variational calculation up to ~10,000 cm-1 and using a new accurate ab initio potential energy surface (PES). Triplet methylene exhibits a large-amplitude bending vibration and can reach a quasilinear configuration due to its low barrier (~2000 cm-1 ). To construct the ab initio PES, the Dunning's augmented correlation-consistent core-valence orbital basis sets were employed up to the sextuple-ζ quality [aug-cc-pCVXZ, X = T, Q, 5, and 6] combined with the single- and double-excitation unrestricted coupled cluster approach with a perturbative treatment of triple excitations [RHF-UCCSD(T)]. We have shown that the accuracy of the ab initio energies is further improved by including the corrections due to the scalar relativistic effects, DBOC and high-order electronic correlations. For the first time, all the available experimental rovibrational transitions were reproduced with errors less than 0.12 cm-1 , without any empirical corrections. Unlike more "traditional" nonlinear triatomic molecules, we have shown that even the energies of the ground vibrational state (000) with rather small rotational quantum numbers are strongly affected by the very pronounced rovibrational resonance interactions. Accordingly, the polyad structure of the vibrational levels of CH2 and CD2 was analyzed and discussed. The comparison between the energy levels obtained from the effective Watson A-reduced Hamiltonian, from the generating-function approach and from a variational calculation was given.
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Affiliation(s)
- Oleg Egorov
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics SB RAS, Tomsk, Russia
- Faculty of Physics, Tomsk State University, Tomsk, Russia
| | - Michaël Rey
- Groupe de Spectrométrie Moléculaire et Atmosphérique, UMR CNRS 7331, UFR Sciences, Reims, France
| | - Dominika Viglaska
- Groupe de Spectrométrie Moléculaire et Atmosphérique, UMR CNRS 7331, UFR Sciences, Reims, France
| | - Andrei V Nikitin
- Laboratory of Theoretical Spectroscopy, V.E. Zuev Institute of Atmospheric Optics SB RAS, Tomsk, Russia
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39
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Chan B. DAPD Set of Pd-Containing Diatomic Molecules: Accurate Molecular Properties and the Great Lengths to Obtain Them. J Chem Theory Comput 2023; 19:9260-9268. [PMID: 38096563 DOI: 10.1021/acs.jctc.3c01060] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2023]
Abstract
In the present study, we obtained reliable bond energy, bond length, and zero-point vibrational frequency for a set of diatomic Pd species (the DAPD set). It includes PdH, Pd2, and PdX (X = B, C, N, O, F, Al, Si, P, S, and Cl). Our highest-level protocol (W4X-L) represents scalar and spin-orbit relativistic, valence- and inner-valence correlated, extrapolated CCSDTQ(5) energy. The DAPD set of molecules is challenging for computational chemistry methods in different manners; for Pd2, the spin-orbit contribution to the bond energy is fairly large, whereas for PdC and PdSi, the post-CCSD(T) correlation components are considerable. The diverse range of requirements represents a significant challenge for lower-level methods. While density functional theory (DFT) methods generally yield good agreements for bond lengths and vibrational frequencies, large deviations are found for bond energies. In general, hybrid DFT methods are more accurate than nonhybrid functionals, but the agreement in individual cases varies. This illustrates the critical role that new high-quality reference data would play in the continual development of lower-cost methods.
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Affiliation(s)
- Bun Chan
- Graduate School of Engineering, Nagasaki University, Bunkyo 1-14, Nagasaki 852-8521, Japan
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40
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Cai W, Zhong C, Ma ZW, Cai ZY, Qiu Y, Sajid Z, Wu DY. Machine-learning-assisted performance improvements for multi-resonance thermally activated delayed fluorescence molecules. Phys Chem Chem Phys 2023; 26:144-152. [PMID: 38063043 DOI: 10.1039/d3cp04441f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2023]
Abstract
With favorable colour purity, multi-resonance thermally activated delayed fluorescence (MR-TADF) molecules exhibit enormous potential in high-definition displays. Due to the relatively small chemical space of MR-TADF molecules, it is challenging to improve molecular performance through domain-specific expertise alone. To address this problem, we focused on optimizing the classic molecule, DABNA-1, using machine learning (ML). Molecular morphing operations were initially employed to generate the adjacent chemical space of DABNA-1. Subsequently, a machine learning model was trained with a limited database and used to predict the properties throughout the generated chemical space. It was confirmed that the top 100 molecules suggested by machine learning present excellent electronic structures, characterized by small reorganization energy and singlet-triplet energy gaps. Our results indicate that the improvement in electronic structures can be elucidated through the view of the molecular orbital (MO). The results also reveal that the top 5 molecules present weaker vibronic peaks of the emission spectrum, demonstrating higher colour purity when compared to DABNA-1. Notably, the M2 molecule presents a high RISC rate, indicating its promising future as a high-efficiency MR-TADF molecule. Our machine-learning-assisted approach facilitates the rapid optimization of classical molecules, addressing a crucial requirement within the organic optoelectronic materials community.
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Affiliation(s)
- Wanlin Cai
- State Key Laboratory of Physical Chemistry of Solid Surface, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
| | - Cheng Zhong
- Hubei Key Lab on Organic and Polymeric Optoelectronic Materials, Department of Chemistry, Wuhan University, Wuhan, Hubei, 430072, P. R. China
| | - Zi-Wei Ma
- State Key Laboratory of Physical Chemistry of Solid Surface, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
| | - Zhuan-Yun Cai
- State Key Laboratory of Physical Chemistry of Solid Surface, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
| | - Yue Qiu
- Grimwade Centre for Cultural Materials Conservation, School of Historical and Philosophical Studies, Faculty of Arts, University of Melbourne, Parkville, VIC 3052, Australia
| | - Zubia Sajid
- State Key Laboratory of Physical Chemistry of Solid Surface, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
| | - De-Yin Wu
- State Key Laboratory of Physical Chemistry of Solid Surface, Collaborative Innovation Center of Chemistry for Energy Materials, and Department of Chemistry, College of Chemistry and Chemical Engineering, Xiamen University, Xiamen, 361005, P. R. China.
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41
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Alton MW, Johnson VL, Sharma S, Browne EC. Volatile Methyl Siloxane Atmospheric Oxidation Mechanism from a Theoretical Perspective─How is the Siloxanol Formed? J Phys Chem A 2023; 127:10233-10242. [PMID: 38011037 DOI: 10.1021/acs.jpca.3c06287] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Despite several investigations on the atmospheric fate of cyclic volatile methyl siloxanes (VMS), the oxidation chemistry of these purely anthropogenic, high production volume compounds is poorly understood. This led to uncertainties in the environmental impact and fate of the oxidation products. According to laboratory measurements, the main VMS oxidation product is the siloxanol (a -CH3 replaced with an -OH); however, none of the mechanisms proposed to date satisfactorily explain its formation. Motivated by our previous experimental observations of VMS oxidation products, we use theoretical quantum chemical calculations to (1) explore a previously unconsidered reaction pathway to form the siloxanol from a reaction of a siloxy radical with gas-phase water, (2) investigate differences in reaction rates of radical intermediates in hexamethylcyclotrisiloxane (D3) and octamethylcyclotetrasiloxane (D4) oxidation, and (3) attempt to explain the experimentally observed products. Our results suggest that while the proposed reaction of the siloxy radical with water to form the siloxanol can occur, it is too slow to compete with other unimolecular reactions and thus cannot explain the observed siloxanol formation. We also find that the reaction between the initial D3 peroxy radical (RO2•) with HO2• is slower than previously anticipated (calculated as 3 × 10-13 cm3 molecule-1 s-1 for D3 and 2 × 10-11 cm3 molecule-1 s-1 for D4 compared to the general rate of ∼1 × 10-11 cm3 molecule-1 s-1). Finally, we compare the anticipated fates of the RO2• under a variety of conditions and find that a reaction with NO (assuming a general RO2• + NO bimolecular rate constant of 9 × 10-12 cm3 molecule-1 s-1) will likely be the dominant fate in urban conditions, while isomerization can be important in cleaner environments.
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Affiliation(s)
- Mitchell W Alton
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
| | - Virginia L Johnson
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Sandeep Sharma
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
| | - Eleanor C Browne
- Department of Chemistry, University of Colorado, Boulder, Colorado 80309, United States
- Cooperative Institute for Research in Environmental Sciences, University of Colorado, Boulder, Colorado 80309, United States
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42
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Zhang C, Yu P, Conn CJ, Hutzler NR, Cheng L. Relativistic coupled-cluster calculations of RaOH pertinent to spectroscopic detection and laser cooling. Phys Chem Chem Phys 2023; 25:32613-32621. [PMID: 38009218 DOI: 10.1039/d3cp04040b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2023]
Abstract
A relativistic coupled-cluster study of the low-lying electronic states in the radium monohydroxide molecule (RaOH), a radioactive polyatomic molecule of interest to laser cooling and to the search of new physics beyond the Standard Model, is reported. The level positions of the A2Π1/2 and C2Σ states have been computed with an accuracy of around 200 cm-1 to facilitate spectroscopic observation of RaOH using laser induced fluorescence spectroscopy, thereby exploiting the systematic convergence of electron-correlation and basis-set effects in relativistic coupled-cluster calculations. The energy level for the B2Δ3/2 state has also been calculated accurately to conclude that the B2Δ3/2 state lies above the A2Π1/2 state. This confirms X2Σ ↔ A2Π1/2 as a promising optical cycling transition for laser cooling RaOH.
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Affiliation(s)
- Chaoqun Zhang
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA.
| | - Phelan Yu
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Chandler J Conn
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Nicholas R Hutzler
- Division of Physics, Mathematics, and Astronomy, California Institute of Technology, Pasadena, CA 91125, USA.
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, MD 21218, USA.
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43
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Mester D, Kállay M. Basis Set Limit of CCSD(T) Energies: Explicit Correlation Versus Density-Based Basis-Set Correction. J Chem Theory Comput 2023; 19:8210-8222. [PMID: 37950703 PMCID: PMC10688194 DOI: 10.1021/acs.jctc.3c00979] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Revised: 10/21/2023] [Accepted: 10/23/2023] [Indexed: 11/13/2023]
Abstract
A thorough comparison is carried out for explicitly correlated and density-based basis-set correction approaches, which were primarily developed to mitigate the basis-set incompleteness error of wave function methods. An efficient implementation of the density-based scheme is also presented, utilizing the density-fitting approximation. The performance of these approaches is comprehensively tested for the second-order Møller-Plesset (MP2), coupled-cluster singles and doubles (CCSD), and CCSD with perturbative triples [CCSD(T)] methods with respect to the corresponding complete basis set references. It is demonstrated that the density-based correction together with complementary auxiliary basis set (CABS)-corrected Hartree-Fock energies is highly robust and effectively reduces the error of the standard approaches; however, it does not outperform the corresponding explicitly correlated methods. Nevertheless, what still makes the density-corrected CCSD and CCSD(T) methods competitive is that their computational costs are roughly half of those of the corresponding explicitly correlated variants. Additionally, an incremental approach for standard CCSD and CCSD(T) is introduced. In this simple scheme, the total energies are corrected with the CABS correction and explicitly correlated MP2 contributions. As demonstrated, the resulting methods yield surprisingly good results, below 1 kcal/mol for thermochemical properties even with a double-ζ basis, while their computational expenses are practically identical to those of the density-based basis-set correction approaches.
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Affiliation(s)
- Dávid Mester
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3., H-1111 Budapest, Hungary
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44
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Szabó PB, Csóka J, Kállay M, Nagy PR. Linear-Scaling Local Natural Orbital CCSD(T) Approach for Open-Shell Systems: Algorithms, Benchmarks, and Large-Scale Applications. J Chem Theory Comput 2023; 19:8166-8188. [PMID: 37921429 PMCID: PMC10687875 DOI: 10.1021/acs.jctc.3c00881] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Revised: 10/05/2023] [Accepted: 10/16/2023] [Indexed: 11/04/2023]
Abstract
The extension of the highly optimized local natural orbital (LNO) coupled cluster (CC) with single-, double-, and perturbative triple excitations [LNO-CCSD(T)] method is presented for high-spin open-shell molecules based on restricted open-shell references. The techniques enabling the outstanding efficiency of the closed-shell LNO-CCSD(T) variant are adopted, including the iteration- and redundancy-free second-order Møller-Plesset and (T) formulations as well as the integral-direct, memory- and disk use-economic, and OpenMP-parallel algorithms. For large molecules, the efficiency of our open-shell LNO-CCSD(T) method approaches that of its closed-shell parent method due to the application of restricted orbital sets for demanding integral transformations and a novel approximation for higher-order long-range spin-polarization effects. The accuracy of open-shell LNO-CCSD(T) is extensively tested for radicals and reactions thereof, ionization processes, as well as spin-state splittings, and transition-metal compounds. At the size range where the canonical CCSD(T) reference is accessible (up to 20-30 atoms), the average open-shell LNO-CCSD(T) correlation energies are found to be 99.9 to 99.95% accurate, which translates into average absolute deviations of a few tenths of kcal/mol in the investigated energy differences already with the default settings. For more extensive molecules, the local errors may grow, but they can be estimated and decreased via affordable systematic convergence studies. This enables the accurate modeling of large systems with complex electronic structures, as illustrated on open-shell organic radicals and transition-metal complexes of up to 179 atoms as well as on challenging biochemical systems, including up to 601 atoms and 11,000 basis functions. While the protein models involve difficulties for local approximations, such as the spin states of a bounded iron ion or an extremely delocalized singly occupied orbital, the corresponding single-node LNO-CCSD(T) computations were feasible in a matter of days with 10s to 100 GB of memory use. Therefore, the new LNO-CCSD(T) implementation enables highly accurate computations for open-shell systems of unprecedented size and complexity with widely accessible hardware.
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Affiliation(s)
- P. Bernát Szabó
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - József Csóka
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Mihály Kállay
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Műegyetem rkp. 3, H-1111 Budapest, Hungary
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45
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Shi B, Zen A, Kapil V, Nagy PR, Grüneis A, Michaelides A. Many-Body Methods for Surface Chemistry Come of Age: Achieving Consensus with Experiments. J Am Chem Soc 2023; 145:25372-25381. [PMID: 37948071 PMCID: PMC10683001 DOI: 10.1021/jacs.3c09616] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/12/2023]
Abstract
The adsorption energy of a molecule onto the surface of a material underpins a wide array of applications, spanning heterogeneous catalysis, gas storage, and many more. It is the key quantity where experimental measurements and theoretical calculations meet, with agreement being necessary for reliable predictions of chemical reaction rates and mechanisms. The prototypical molecule-surface system is CO adsorbed on MgO, but despite intense scrutiny from theory and experiment, there is still no consensus on its adsorption energy. In particular, the large cost of accurate many-body methods makes reaching converged theoretical estimates difficult, generating a wide range of values. In this work, we address this challenge, leveraging the latest advances in diffusion Monte Carlo (DMC) and coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] to obtain accurate predictions for CO on MgO. These reliable theoretical estimates allow us to evaluate the inconsistencies in published temperature-programed desorption experiments, revealing that they arise from variations in employed pre-exponential factors. Utilizing this insight, we derive new experimental estimates of the (electronic) adsorption energy with a (more) precise pre-exponential factor. As a culmination of all of this effort, we are able to reach a consensus between multiple theoretical calculations and multiple experiments for the first time. In addition, we show that our recently developed cluster-based CCSD(T) approach provides a low-cost route toward achieving accurate adsorption energies. This sets the stage for affordable and reliable theoretical predictions of chemical reactions on surfaces to guide the realization of new catalysts and gas storage materials.
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Affiliation(s)
- Benjamin
X. Shi
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Andrea Zen
- Dipartimento
di Fisica Ettore Pancini, Università
di Napoli Federico II, Monte S. Angelo, I-80126 Napoli, Italy
- Department
of Earth Sciences, University College London, Gower Street, WC1E 6BT London, U.K.
| | - Venkat Kapil
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
| | - Péter R. Nagy
- Department
of Physical Chemistry and Materials Science, Faculty of Chemical Technology
and Biotechnology, Budapest University of
Technology and Economics, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- HUN-REN-BME
Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
- MTA-BME
Lendület Quantum Chemistry Research Group, Müegyetem rkp. 3, H-1111 Budapest, Hungary
| | - Andreas Grüneis
- Institute
for Theoretical Physics, TU Wien, Wiedner Hauptstraße 8-10/136, 1040 Vienna, Austria
| | - Angelos Michaelides
- Yusuf
Hamied Department of Chemistry, University
of Cambridge, Lensfield Road, CB2 1EW Cambridge, U.K.
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46
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Cubiss JG, Andreyev AN, Barzakh AE, Van Duppen P, Hilaire S, Péru S, Goriely S, Al Monthery M, Althubiti NA, Andel B, Antalic S, Atanasov D, Blaum K, Cocolios TE, Day Goodacre T, de Roubin A, Farooq-Smith GJ, Fedorov DV, Fedosseev VN, Fink DA, Gaffney LP, Ghys L, Harding RD, Huyse M, Imai N, Joss DT, Kreim S, Lunney D, Lynch KM, Manea V, Marsh BA, Martinez Palenzuela Y, Molkanov PL, Neidherr D, O'Neill GG, Page RD, Prosnyak SD, Rosenbusch M, Rossel RE, Rothe S, Schweikhard L, Seliverstov MD, Sels S, Skripnikov LV, Stott A, Van Beveren C, Verstraelen E, Welker A, Wienholtz F, Wolf RN, Zuber K. Deformation versus Sphericity in the Ground States of the Lightest Gold Isotopes. PHYSICAL REVIEW LETTERS 2023; 131:202501. [PMID: 38039485 DOI: 10.1103/physrevlett.131.202501] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Revised: 08/02/2023] [Accepted: 09/18/2023] [Indexed: 12/03/2023]
Abstract
The changes in mean-squared charge radii of neutron-deficient gold nuclei have been determined using the in-source, resonance-ionization laser spectroscopy technique, at the ISOLDE facility (CERN). From these new data, nuclear deformations are inferred, revealing a competition between deformed and spherical configurations. The isotopes ^{180,181,182}Au are observed to possess well-deformed ground states and, when moving to lighter masses, a sudden transition to near-spherical shapes is seen in the extremely neutron-deficient nuclides, ^{176,177,179}Au. A case of shape coexistence and shape staggering is identified in ^{178}Au which has a ground and isomeric state with different deformations. These new data reveal a pattern in ground-state deformation unique to the gold isotopes, whereby, when moving from the heavy to light masses, a plateau of well-deformed isotopes exists around the neutron midshell, flanked by near-spherical shapes in the heavier and lighter isotopes-a trend hitherto unseen elsewhere in the nuclear chart. The experimental charge radii are compared to those from Hartree-Fock-Bogoliubov calculations using the D1M Gogny interaction and configuration mixing between states of different deformation. The calculations are constrained by the known spins, parities, and magnetic moments of the ground states in gold nuclei and show a good agreement with the experimental results.
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Affiliation(s)
- J G Cubiss
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - A N Andreyev
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
- Advanced Science Research Center (ASRC), Japan Atomic Energy Agency, Tokai-mura, Japan
| | - A E Barzakh
- Affiliated with an institute covered by a cooperation agreement with CERN
| | - P Van Duppen
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - S Hilaire
- Université Paris-Saclay, CEA, LMCE, 91680, Bruyères-le-Châtel, France
| | - S Péru
- Université Paris-Saclay, CEA, LMCE, 91680, Bruyères-le-Châtel, France
| | - S Goriely
- Institut d'Astronomie et d'Astrophysique, CP-226, Université Libre de Bruxelles, 1050 Brussels, Belgium
| | - M Al Monthery
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - N A Althubiti
- The University of Manchester, Department of Physics and Astronomy, Oxford Road, M13 9PL Manchester, United Kingdom
- Physics Department, College of Science, Jouf University, Sakakah, Kingdom of Saudi Arabia
| | - B Andel
- Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
| | - S Antalic
- Department of Nuclear Physics and Biophysics, Comenius University in Bratislava, 84248 Bratislava, Slovakia
| | - D Atanasov
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- CERN, 1211, Geneva 23, Switzerland
| | - K Blaum
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - T E Cocolios
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
- The University of Manchester, Department of Physics and Astronomy, Oxford Road, M13 9PL Manchester, United Kingdom
| | - T Day Goodacre
- The University of Manchester, Department of Physics and Astronomy, Oxford Road, M13 9PL Manchester, United Kingdom
- CERN, 1211, Geneva 23, Switzerland
| | - A de Roubin
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | - G J Farooq-Smith
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
- The University of Manchester, Department of Physics and Astronomy, Oxford Road, M13 9PL Manchester, United Kingdom
| | - D V Fedorov
- Affiliated with an institute covered by a cooperation agreement with CERN
| | | | - D A Fink
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- CERN, 1211, Geneva 23, Switzerland
| | - L P Gaffney
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
- CERN, 1211, Geneva 23, Switzerland
| | - L Ghys
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - R D Harding
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
- CERN, 1211, Geneva 23, Switzerland
| | - M Huyse
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - N Imai
- Center for Nuclear Study (CNS), Graduate School of Science The University of Tokyo, Japan
| | - D T Joss
- Department of Physics, University of Liverpool, Liverpool, L69 7ZE, United Kingdom
| | - S Kreim
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- CERN, 1211, Geneva 23, Switzerland
| | - D Lunney
- CSNSM-CNRS, Université de Paris Sud, 91400 Orsay, France
| | - K M Lynch
- The University of Manchester, Department of Physics and Astronomy, Oxford Road, M13 9PL Manchester, United Kingdom
- CERN, 1211, Geneva 23, Switzerland
| | - V Manea
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
| | | | - Y Martinez Palenzuela
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
- CERN, 1211, Geneva 23, Switzerland
| | - P L Molkanov
- Affiliated with an institute covered by a cooperation agreement with CERN
| | - D Neidherr
- GSI Helmholtzzentrum für Schwerionenforschung GmbH, Darmstadt 64291, Germany
| | - G G O'Neill
- Department of Physics, University of Liverpool, Liverpool, L69 7ZE, United Kingdom
| | - R D Page
- Department of Physics, University of Liverpool, Liverpool, L69 7ZE, United Kingdom
| | - S D Prosnyak
- Affiliated with an institute covered by a cooperation agreement with CERN
| | - M Rosenbusch
- Institut für Physik, Universität Greifswald, 17487 Greifswald, Germany
| | - R E Rossel
- CERN, 1211, Geneva 23, Switzerland
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Mainz, D-55128, Germany
| | - S Rothe
- CERN, 1211, Geneva 23, Switzerland
- Institut für Physik, Johannes Gutenberg-Universität Mainz, Mainz, D-55128, Germany
| | - L Schweikhard
- Institut für Physik, Universität Greifswald, 17487 Greifswald, Germany
| | - M D Seliverstov
- Affiliated with an institute covered by a cooperation agreement with CERN
| | - S Sels
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - L V Skripnikov
- Affiliated with an institute covered by a cooperation agreement with CERN
| | - A Stott
- School of Physics, Engineering and Technology, University of York, York, YO10 5DD, United Kingdom
| | - C Van Beveren
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - E Verstraelen
- KU Leuven, Instituut voor Kern- en Stralingsfysica, 3001 Leuven, Belgium
| | - A Welker
- CERN, 1211, Geneva 23, Switzerland
- Institut für Kern- und Teilchenphysik, Technische Universität Dresden, Dresden 01069, Germany
| | - F Wienholtz
- CERN, 1211, Geneva 23, Switzerland
- Institut für Physik, Universität Greifswald, 17487 Greifswald, Germany
| | - R N Wolf
- Max-Planck-Institut für Kernphysik, Saupfercheckweg 1, 69117 Heidelberg, Germany
- Institut für Physik, Universität Greifswald, 17487 Greifswald, Germany
| | - K Zuber
- Institut für Kern- und Teilchenphysik, Technische Universität Dresden, Dresden 01069, Germany
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47
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Jacquemin D, Kossoski F, Gam F, Boggio-Pasqua M, Loos PF. Reference Vertical Excitation Energies for Transition Metal Compounds. J Chem Theory Comput 2023. [PMID: 37965941 DOI: 10.1021/acs.jctc.3c01080] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
To enrich and enhance the diversity of the quest database of highly accurate excitation energies [Véril, M.; et al. Wiley Interdiscip. Rev.: Comput. Mol. Sci. 2021, 11, e1517], we report vertical transition energies in transition metal compounds. Eleven diatomic molecules with a singlet or doublet ground state containing a fourth-row transition metal (CuCl, CuF, CuH, ScF, ScH, ScO, ScS, TiN, ZnH, ZnO, and ZnS) are considered, and the corresponding excitation energies are computed using high-level coupled-cluster (CC) methods, namely, CC3, CCSDT, CC4, and CCSDTQ, as well as multiconfigurational methods such as CASPT2 and NEVPT2. In many cases, to provide more comprehensive benchmark data, we also provide full configuration interaction estimates computed with the configuration interaction using a perturbative selection made iteratively (CIPSI) method. Based on these calculations, theoretical best estimates of the transition energies are established in both the aug-cc-pVDZ and aug-cc-pVTZ basis sets. This allows us to accurately assess the performance of the CC and multiconfigurational methods for this specific set of challenging transitions. Furthermore, comparisons with experimental data and previous theoretical results are also reported.
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Affiliation(s)
- Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Franck Gam
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, F-31062 Toulouse, France
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48
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Hait D, Head-Gordon M. When Is a Bond Broken? The Polarizability Perspective. Angew Chem Int Ed Engl 2023; 62:e202312078. [PMID: 37713599 DOI: 10.1002/anie.202312078] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2023] [Revised: 09/15/2023] [Accepted: 09/15/2023] [Indexed: 09/17/2023]
Abstract
The question of when a chemical bond can be said to be broken is of fundamental chemical interest but has not been widely studied. Herein we propose that the maxima of static polarizability along bond dissociation coordinates naturally define cutoff points for bond rupture, as they represent the onset of localization of shared electron density into constituent fragments. Examples of computed polarizability maxima over the course of bond cleavage in main-group and transition metal compounds are provided, across covalent, dative and charge-shift bonds. The behavior along reaction paths is also considered. Overall, the static polarizability is found to be a sensitive reporter of electronic structure reorganization associated with bond stretching, and thus can serve as a metric for describing bond cleavage (or diagnose the absence of a chemical bond).
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Affiliation(s)
- Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
- Department of Chemistry and PULSE Institute, Stanford University, Stanford, CA 94305, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, Berkeley, CA 94720, USA
- Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA
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49
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Ballay B, Szűcs T, Papp D, Czakó G. Phosphorus-centered ion-molecule reactions: benchmark ab initio characterization of the potential energy surfaces of the X - + PH 2Y [X, Y = F, Cl, Br, I] systems. Phys Chem Chem Phys 2023; 25:28925-28940. [PMID: 37855143 DOI: 10.1039/d3cp03733a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2023]
Abstract
In the present work we determine the benchmark relative energies and geometries of all the relevant stationary points of the X- + PH2Y [X, Y = F, Cl, Br, I] identity and non-identity reactions using state-of-the-art electronic-structure methods. These phosphorus-centered ion-molecule reactions follow two main reaction routes: bimolecular nucleophilic substitution (SN2), leading to Y- + PH2X, and proton transfer, resulting in HX + PHY- products. The SN2 route can proceed through Walden-inversion, front-side-attack retention, and double-/multiple-inversion pathways. In addition, we also identify the following product channels: H--formation, PH2-- and PH2-formation, 1PH- and 3PH-formation, H2-formation and HY + PHX- formation. The benchmark classical relative energies are obtained by taking into account the core-correlation, scalar relativistic, and post-(T) corrections, which turn out to be necessary to reach subchemical (<1 kcal mol-1) accuracy of the results. Classical relative energies are augmented with zero-point-energy contributions to gain the benchmark adiabatic energies.
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Affiliation(s)
- Boldizsár Ballay
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Tímea Szűcs
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Dóra Papp
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
| | - Gábor Czakó
- MTA-SZTE Lendület Computational Reaction Dynamics Research Group, Interdisciplinary Excellence Centre and Department of Physical Chemistry and Materials Science, Institute of Chemistry, University of Szeged, Rerrich Béla tér 1, Szeged H-6720, Hungary.
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50
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Di Felice R, Mayes ML, Richard RM, Williams-Young DB, Chan GKL, de Jong WA, Govind N, Head-Gordon M, Hermes MR, Kowalski K, Li X, Lischka H, Mueller KT, Mutlu E, Niklasson AMN, Pederson MR, Peng B, Shepard R, Valeev EF, van Schilfgaarde M, Vlaisavljevich B, Windus TL, Xantheas SS, Zhang X, Zimmerman PM. A Perspective on Sustainable Computational Chemistry Software Development and Integration. J Chem Theory Comput 2023; 19:7056-7076. [PMID: 37769271 PMCID: PMC10601486 DOI: 10.1021/acs.jctc.3c00419] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2023] [Indexed: 09/30/2023]
Abstract
The power of quantum chemistry to predict the ground and excited state properties of complex chemical systems has driven the development of computational quantum chemistry software, integrating advances in theory, applied mathematics, and computer science. The emergence of new computational paradigms associated with exascale technologies also poses significant challenges that require a flexible forward strategy to take full advantage of existing and forthcoming computational resources. In this context, the sustainability and interoperability of computational chemistry software development are among the most pressing issues. In this perspective, we discuss software infrastructure needs and investments with an eye to fully utilize exascale resources and provide unique computational tools for next-generation science problems and scientific discoveries.
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Affiliation(s)
- Rosa Di Felice
- Departments
of Physics and Astronomy and Quantitative and Computational Biology, University of Southern California, Los Angeles, California 90089, United States
- CNR-NANO
Modena, Modena 41125, Italy
| | - Maricris L. Mayes
- Department
of Chemistry and Biochemistry, University
of Massachusetts Dartmouth, North Dartmouth, Massachusetts 02747, United States
| | | | | | - Garnet Kin-Lic Chan
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Wibe A. de Jong
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
| | - Niranjan Govind
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Martin Head-Gordon
- Pitzer Center
for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Matthew R. Hermes
- Department
of Chemistry, Chicago Center for Theoretical Chemistry, University of Chicago, Chicago, Illinois 60637, United States
| | - Karol Kowalski
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Xiaosong Li
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
| | - Hans Lischka
- Department
of Chemistry and Biochemistry, Texas Tech
University, Lubbock, Texas 79409, United States
| | - Karl T. Mueller
- Physical
and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Erdal Mutlu
- Advanced
Computing, Mathematics, and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Anders M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Mark R. Pederson
- Department
of Physics, The University of Texas at El
Paso, El Paso, Texas 79968, United States
| | - Bo Peng
- Physical
Sciences Division, Pacific Northwest National
Laboratory, Richland, Washington 99354, United States
| | - Ron Shepard
- Chemical
Sciences and Engineering Division, Argonne
National Laboratory, Lemont, Illinois 60439, United States
| | - Edward F. Valeev
- Department
of Chemistry, Virginia Tech, Blacksburg, Virginia 24061, United States
| | | | - Bess Vlaisavljevich
- Department
of Chemistry, University of South Dakota, Vermillion, South Dakota 57069, United States
| | - Theresa L. Windus
- Department
of Chemistry, Iowa State University and
Ames Laboratory, Ames, Iowa 50011, United States
| | - Sotiris S. Xantheas
- Department
of Chemistry, University of Washington, Seattle, Washington 98195, United States
- Advanced
Computing, Mathematics and Data Division, Pacific Northwest National Laboratory, Richland, Washington 99354, United States
| | - Xing Zhang
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Paul M. Zimmerman
- Department
of Chemistry, University of Michigan, Ann Arbor, Michigan 48109, United States
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