151
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Benny J, Saito T, Moe MM, Liu J. Singlet O 2 Reactions with Radical Cations of 8-Bromoguanine and 8-Bromoguanosine: Guided-Ion Beam Mass Spectrometric Measurements and Theoretical Treatments. J Phys Chem A 2021; 126:68-79. [PMID: 34941276 DOI: 10.1021/acs.jpca.1c09552] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
8-Bromoguanosine is generated in vivo as a biomarker for early inflammation. Its formation and secondary reactions lead to a variety of biological sequelae at inflammation sites, most of which are mutagenic and linked to cancer. Herein, we report the formation of radical cations of 8-bromoguanine (8BrG•+) and 8-bromoguanosine (8BrGuo•+) and their reactions toward the lowest excited singlet molecular oxygen (1O2)─a common reactive oxygen species generated in biological systems. This work aims to investigate synergistic, oxidatively generated damage of 8-brominated guanine and guanosine that may occur upon ionizing radiation, one-electron oxidation, and 1O2 oxidation. Capitalizing on measurements of reaction product ions and cross sections of 8BrG•+ and 8BrGuo•+ with 1O2 using guided-ion beam tandem mass spectrometry and augmented by computational modeling of the prototype reaction system, 8BrG•+ + 1O2, using the approximately spin-projected ωB97XD/6-31+G(d,p) density functional theory, the coupled cluster DLPNO-CCSD(T)/aug-cc-pVTZ and the multireference CASPT2(21,15)/6-31G**, probable reaction products, and potential energy surfaces (PESs) were mapped out. 8BrG•+ and 8BrGuo•+ present similar exothermic oxidation products, and their reaction efficiencies with 1O2 increase with decreasing collision energy. Both single- and multireference theories predicted that the two most energetically favorable reaction pathways correspond to 1O2-addition to the C8 and C5-positions of 8BrG•+, respectively. The CASPT2-calculated PES represents the best quantitative agreement with the experimental benchmark, in that the oxidation exothermicity is close to the water hydration energy of product ions and, thus, is able to eliminate a water ligand in the product ions.
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Affiliation(s)
- Jonathan Benny
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Toru Saito
- Department of Biomedical Information Science, Graduate School of Information Science, Hiroshima City University, 3-4-1 Ozuka-Higashi, Asa-Minami-Ku, 731-3194 Hiroshima, Japan
| | - May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, New York 11367, United States.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Avenue, New York, New York 10016, United States
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152
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Prasad VK, Pei Z, Edelmann S, Otero-de-la-Roza A, DiLabio GA. BH9, a New Comprehensive Benchmark Data Set for Barrier Heights and Reaction Energies: Assessment of Density Functional Approximations and Basis Set Incompleteness Potentials. J Chem Theory Comput 2021; 18:151-166. [PMID: 34911294 DOI: 10.1021/acs.jctc.1c00694] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
The calculation of accurate reaction energies and barrier heights is essential in computational studies of reaction mechanisms and thermochemistry. To assess methods regarding their ability to predict these two properties, high-quality benchmark sets are required that comprise a reasonably large and diverse set of organic reactions. Due to the time-consuming nature of both locating transition states and computing accurate reference energies for reactions involving large molecules, previous benchmark sets have been limited in scope, the number of reactions considered, and the size of the reactant and product molecules. Recent advances in coupled-cluster theory, in particular local correlation methods like DLPNO-CCSD(T), now allow the calculation of reaction energies and barrier heights for relatively large systems. In this work, we present a comprehensive and diverse benchmark set of barrier heights and reaction energies based on DLPNO-CCSD(T)/CBS called BH9. BH9 comprises 449 chemical reactions belonging to nine types common in organic chemistry and biochemistry. We examine the accuracy of DLPNO-CCSD(T) vis-a-vis canonical CCSD(T) for a subset of BH9 and conclude that, although there is a penalty in using the DLPNO approximation, the reference data are accurate enough to serve as a benchmark for density functional theory (DFT) methods. We then present two applications of the BH9 set. First, we examine the performance of several density functional approximations commonly used in thermochemical and mechanistic studies. Second, we assess our basis set incompleteness potentials regarding their ability to mitigate basis set incompleteness errors. The number of data points, the diversity of the reactions considered, and the relatively large size of the reactant molecules make BH9 the most comprehensive thermochemical benchmark set to date and a useful tool for the development and assessment of computational methods.
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Affiliation(s)
- Viki Kumar Prasad
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Zhipeng Pei
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Simon Edelmann
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
| | - Alberto Otero-de-la-Roza
- Departamento de Química Física y Analítica and MALTA Consolider Team, Facultad de Química, Universidad de Oviedo, 33006 Oviedo, Spain
| | - Gino A DiLabio
- Department of Chemistry, University of British Columbia, 3247 University Way, Kelowna, British Columbia, Canada V1V 1V7
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153
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Lesiuk M. Near-Exact CCSDT Energetics from Rank-Reduced Formalism Supplemented by Non-iterative Corrections. J Chem Theory Comput 2021; 17:7632-7647. [PMID: 34860018 DOI: 10.1021/acs.jctc.1c00933] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We introduce a non-iterative energy correction, added on top of the rank-reduced coupled-cluster method with single, double, and triple substitutions, that accounts for excitations excluded from the parent triple excitation subspace. The formula for the correction is derived by employing the coupled-cluster Lagrangian formalism, with an additional assumption that the parent excitation subspace is closed under the action of the Fock operator. Owing to the rank-reduced form of the triple excitation amplitudes tensor, the computational cost of evaluating the correction scales as N7, where N is the system size. The accuracy and computational efficiency of the proposed method is assessed for both total and relative correlation energies. We show that the non-iterative correction can fulfill two separate roles. If the accuracy level of a fraction of kJ/mol is sufficient for a given system, the correction significantly reduces the dimension of the parent triple excitation subspace needed in the iterative part of the calculations. Simultaneously, it enables reproducing the exact CCSDT results to an accuracy level below 0.1 kJ/mol, with a larger, yet still reasonable, dimension of the parent excitation subspace. This typically can be achieved at a computational cost only several times larger than required for the CCSD(T) method. The proposed method retains the black-box features of the single-reference coupled-cluster theory; the dimension of the parent excitation subspace remains the only additional parameter that has to be specified.
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Affiliation(s)
- Michał Lesiuk
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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154
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Bensberg M, Neugebauer J. Direct orbital selection within the domain-based local pair natural orbital coupled-cluster method. J Chem Phys 2021; 155:224102. [PMID: 34911318 DOI: 10.1063/5.0071347] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Domain-based local pair natural orbital coupled cluster (DLPNO-CC) has become increasingly popular to calculate relative energies (e.g., reaction energies and reaction barriers). It can be applied within a multi-level DLPNO-CC-in-DLPNO-CC ansatz to reduce the computational cost and focus the available computational resources on a specific subset of the occupied orbitals. We demonstrate how this multi-level DLPNO-CC ansatz can be combined with our direct orbital selection (DOS) approach [M. Bensberg and J. Neugebauer, J. Chem. Phys. 150, 214106 (2019)] to automatically select orbital sets for any multi-level calculation. We find that the parameters for the DOS procedure can be chosen conservatively such that they are transferable between reactions. The resulting automatic multi-level DLPNO-CC method requires no user input and is extremely robust and accurate. The computational cost is easily reduced by a factor of 3 without sacrificing accuracy. We demonstrate the accuracy of the method for a total of 61 reactions containing up to 174 atoms and use it to predict the relative stability of conformers of a Ru-based catalyst.
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Affiliation(s)
- Moritz Bensberg
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster, Corrensstraße 36, 48149 Münster, Germany
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155
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David J, Gómez S, Guerra D, Guerra D, Restrepo A. A Comprehensive Picture of the Structures, Energies, and Bonding in the Alanine Dimers. Chemphyschem 2021; 22:2401-2412. [PMID: 34554628 DOI: 10.1002/cphc.202100585] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Revised: 09/22/2021] [Indexed: 12/14/2022]
Abstract
High level quantum mechanical computations and extensive stochastic searches of the potential energy surfaces of the Alanine dimers uncover rich and complex structural and interaction landscapes. A total of 416 strongly bound (up 13.4 kcal mol-1 binding energies at the DLPNO-CCSD(T)/6-311++G(d,p) level corrected by the basis set superposition error and by the zero point vibrational energies over B3LYP-D3 geometries), close energy equilibrium structures were located, bonded via 32 specific types of intermolecular contacts including Y⋅⋅⋅H-X primary and Y⋅⋅⋅H-C secondary hydrogen bonds, H⋅⋅⋅H dihydrogen contacts, and non conventional anti-electrostatic Y δ - ⋯ X δ - interactions. The putative global minimum is triply degenerate, corresponding to the structure of the common dimer of a carboxylic acid. All quantum descriptors of chemical bonding point to a multitude of weak individual interactions within each dimer, whose cumulative effect results in large binding energies and in an attractive fluxional wall of non-covalent interactions in the interstitial region between the monomers.
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Affiliation(s)
- Jorge David
- Escuela de Ciencias, Departamento de Ciencias Físicas, Universidad Eafit, AA 3300, Medellín, Colombia
| | - Sara Gómez
- Scuola Normale Superiore, Classe di Scienze, Piazza dei Cavalieri 7, 56126, Pisa, Italy
| | - Doris Guerra
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
| | - Dario Guerra
- Departamento de Educación y Ciencias Básicas, Instituto Tecnológico Metropolitano, Calle 73 No. 76 A-354, Medellín, Colombia
| | - Albeiro Restrepo
- Instituto de Química, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín, Colombia
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156
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Altun A, Ghosh S, Riplinger C, Neese F, Bistoni G. Addressing the System-Size Dependence of the Local Approximation Error in Coupled-Cluster Calculations. J Phys Chem A 2021; 125:9932-9939. [PMID: 34730360 PMCID: PMC8607505 DOI: 10.1021/acs.jpca.1c09106] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Over the last two decades, the local approximation has been successfully used to extend the range of applicability of the "gold standard" singles and doubles coupled-cluster method with perturbative triples CCSD(T) to systems with hundreds of atoms. The local approximation error grows in absolute value with the increasing system size, i.e., by increasing the number of electron pairs in the system. In this study, we demonstrate that the recently introduced two-point extrapolation scheme for approaching the complete pair natural orbital (PNOs) space limit in domain-based pair natural orbital CCSD(T) calculations drastically reduces the dependence of the error on the system size, thus opening up unprecedented opportunities for the calculation of benchmark quality relative energies for large systems.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Soumen Ghosh
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | | | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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157
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Affiliation(s)
- Marvin H. Lechner
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung, Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Department of Chemistry and Biochemistry, Middlebury College, Middlebury, VT, USA
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158
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Nhat PV, Si NT, Kiselev VG, Nguyen MT. Another look at energetically quasi-degenerate structures of the gold cluster Au 27 q with q = 1, 0, -1. J Comput Chem 2021; 42:2145-2153. [PMID: 34435682 DOI: 10.1002/jcc.26744] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2021] [Revised: 08/09/2021] [Accepted: 08/11/2021] [Indexed: 11/06/2022]
Abstract
Quantum chemical computations were used to reinvestigate the geometries, spectroscopic, and energetic properties of the gold clusters Au27 q in three charge states (q = 1, 0, -1). Density functional theory (DFT) and the domain-based local pair natural orbital modification of the coupled-cluster theory DLPNO-CCSD(T) calculations revealed that, at variance with earlier reports in the literature, while the anion Au27 - tends to exist in a tube-like form, both the lowest-energy Au27 and Au27 + isomers exhibit a pyramidal shape. However, several isomers were found to lie very close in energy, thus rendering a structural transition and their coexistence easy to occur. More specifically, the equilibrium geometry of the neutral Au27 is a core-shell pyramid-like structure with one gold atom located inside. We also identified a novel ground state for the anion Au27 - and located for the first time the global minimum of the cation Au27 + . The vertical detachment energies of the neutral and anionic states were also computed and used to assign the available experimental photoelectron spectra. Although many Au27 isomers were predicted to be energetically quasi-degenerate, the corresponding distinctive vibrational signatures can be used as fingerprints for the identification of cluster geometrical features.
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Affiliation(s)
- Pham Vu Nhat
- Department of Chemistry, Can Tho University, Can Tho, Vietnam
| | - Nguyen Thanh Si
- Department of Chemistry, Can Tho University, Can Tho, Vietnam
| | - Vitaly G Kiselev
- Novosibirsk State University, Novosibirsk, Russia.,Institute of Chemical Kinetics and Combustion SB RAS, Novosibirsk, Russia
| | - Minh Tho Nguyen
- Institute for Computational Science and Technology (ICST), Ho Chi Minh City, Vietnam
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159
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Dolgonos GA. Exploring the Properties of H
2
O@C
60
with the Local Second‐Order Møller‐Plesset Perturbation Theory: Blue or Red Shift in C
60
and H
2
O Fundamentals to Expect? ChemistrySelect 2021. [DOI: 10.1002/slct.202103004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Affiliation(s)
- Grygoriy A. Dolgonos
- Institute of Chemistry University of Graz Heinrichstrasse 28/IV A-8010 Graz Austria
- Life Chemicals Inc. Murmanska Str. 5 02660 Kyiv Ukraine
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160
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Pina AF, Sousa SF, Cerqueira NMFSA. The Catalytic Mechanism of Pdx2 Glutaminase Driven by a Cys-His-Glu Triad: A Computational Study. Chembiochem 2021; 23:e202100555. [PMID: 34762772 DOI: 10.1002/cbic.202100555] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Revised: 11/10/2021] [Indexed: 11/08/2022]
Abstract
The catalytic mechanism of Pdx2 was studied with atomic detail employing the computational ONIOM hybrid QM/MM methodology. Pdx2 employs a Cys-His-Glu catalytic triad to deaminate glutamine to glutamate and ammonia - the source of the nitrogen of pyridoxal 5'-phosphate (PLP). This enzyme is, therefore, a rate-limiting step in the PLP biosynthetic pathway of Malaria and Tuberculosis pathogens that rely on this mechanism to obtain PLP. For this reason, Pdx2 is considered a novel and promising drug target to treat these diseases. The results obtained show that the catalytic mechanism of Pdx2 occurs in six steps that can be divided into four stages: (i) activation of Cys87 , (ii) deamination of glutamine with the formation of the glutamyl-thioester intermediate, (iii) hydrolysis of the formed intermediate, and (iv) enzymatic turnover. The kinetic data available in the literature (19.1-19.5 kcal mol-1 ) agree very well with the calculated free energy barrier of the hydrolytic step (18.2 kcal.mol-11 ), which is the rate-limiting step of the catalytic process when substrate is readily available in the active site. This catalytic mechanism differs from other known amidases in three main points: i) it requires the activation of the nucleophile Cys87 to a thiolate; ii) the hydrolysis occurs in a single step and therefore does not require the formation of a second tetrahedral reaction intermediate, as it is proposed, and iii) Glu198 does not have a direct role in the catalytic process. Together, these results can be used for the synthesis of new transition state analogue inhibitors capable of inhibiting Pdx2 and impair diseases like Malaria and Tuberculosis.
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Affiliation(s)
- André F Pina
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Sérgio F Sousa
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
| | - Nuno M F S A Cerqueira
- Associate Laboratory i4HB - Institute for Health and Bioeconomy, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal.,UCIBIO - Applied Molecular Biosciences Unit, BioSIM - Department of Biomedicine, Faculty of Medicine, University of Porto, 4200-319, Porto, Portugal
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161
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Eickhoff L, Ohms L, Bresien J, Villinger A, Michalik D, Schulz A. A Phosphorus-Based Pacman Dication Generated by Cooperative Self-Activation of a Pacman Phosphane. Chemistry 2021; 28:e202103983. [PMID: 34761445 PMCID: PMC9298836 DOI: 10.1002/chem.202103983] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Indexed: 11/08/2022]
Abstract
Formal coordination of phosphorus(III) by a calix[4]pyrrole Schiff base ligand was achieved through the reaction of this ligand with PCl3 under basic conditions. The reaction product adopts a Pacman conformation with two P-Cl moieties, one in exo and one in endo position. It represents the first non-metal compound of calix[4]pyrrole Schiff base ligands and of Pacman ligands in general. The spatial neighborhood of the two phosphorus atoms enables cooperative reactions. As a first example, the chloride abstraction with AgOTf is presented, yielding a macrocyclic dication with two embedded phosphorus(III) monocations, which both undergo a cooperative, internal activation reaction with an adjacent C=N double bond. This intramolecular redox process affords two pentacoordinated phosphorus(V) centers within the Pacman dication. All reaction products were fully characterized and all results are supported by computations.
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Affiliation(s)
- Liesa Eickhoff
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Leon Ohms
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Jonas Bresien
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Alexander Villinger
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany
| | - Dirk Michalik
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany.,Leibniz-Institut für Katalyse e. V., Albert-Einstein-Str. 29a, 18059, Rostock, Germany
| | - Axel Schulz
- Institut für Chemie, Universität Rostock, Albert-Einstein-Str. 3a, 18059, Rostock, Germany.,Leibniz-Institut für Katalyse e. V., Albert-Einstein-Str. 29a, 18059, Rostock, Germany
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162
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Piotrowski MJ, Orenha RP, Parreira RLT, Guedes-Sobrinho D. Assessment of the van der Waals, Hubbard U parameter and spin-orbit coupling corrections on the 2D/3D structures from metal gold congeners clusters. J Comput Chem 2021; 43:230-243. [PMID: 34751955 DOI: 10.1002/jcc.26784] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2021] [Revised: 10/17/2021] [Accepted: 10/25/2021] [Indexed: 11/07/2022]
Abstract
The coinage-metal clusters possess a natural complexity in their theoretical treatment that may be accompanied by inherent shortcomings in the methodological approach. Herein, we performed a scalar-relativistic density functional theory study, considering Perdew, Burke, and Ernzerhof (PBE) with (empirical and semi empirical) van der Waals (vdW), spin-orbit coupling (SOC), +U (Hubbard term), and their combinations, to treat the Cu 13 , Ag 13 , and Au 13 clusters in different structural motifs. The energetic scenario is given by the confirmation of the 3D lowest energy configurations for Cu 13 and Ag 13 within all approaches, while for Au 13 there is a 2D/3D competition, depending on the applied correction. The 2D geometry is 0.43 eV more stable with plain PBE than the 3D one, the SOC, +U, and/or vdW inclusion decreases the overestimated stability of the planar configurations, where the most surprising result is found by the D3 and D3BJ vdW corrections, for which the 3D configuration is 0.29 and 0.11 eV, respectively, more stable than the 2D geometry (with even higher values when SOC and/or +U are added). The D3 dispersion correction represents 7.9% (4.4%) of the total binding energy for the 3D (2D) configuration, (not) being enough to change the sd hybridization and the position of the occupied d -states. Our predictions are in agreement with experimental results and in line with the best results obtained for bulk systems, as well as with hybrid functionals within D3 corrections. The properties description undergoes small corrections with the different approaches, where general trends are maintained, that is, the average bond length is smaller (larger) for lower (higher)-coordinated structures, since a same number of electrons are shared by a smaller (larger) number of bonds, consequently, the bonds are stronger (weaker) and shorter (longer) and the sd hybridization index is larger (smaller). Thus, Au has a distinct behavior in relation to its lighter congeners, with a complex potential energy surface, where in addition to the relevant relativistic effects, correlation and dispersion effects must also be considered.
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Affiliation(s)
- Maurício J Piotrowski
- Department of Physics, Federal University of Pelotas, Pelotas, Rio Grande do Sul, Brazil
| | - Renato P Orenha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
| | - Renato L T Parreira
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas, Universidade de Franca, Franca, São Paulo, Brazil
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163
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Zhou W, Liu J. Reaction mechanism and dynamics for C8-hydroxylation of 9-methylguanine radical cation by water molecules. Phys Chem Chem Phys 2021; 23:24464-24477. [PMID: 34698322 DOI: 10.1039/d1cp03884b] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In contrast to their spontaneous deprotonation in aqueous solution, reactions of guanine and guanosine radical cations with water in the gas phase are exclusively initiated by hydration of the radical cations as reported in recent work (Y. Sun et al., Phys. Chem. Chem. Phys., 2018, 20, 27510). As gas-phase hydration reactions closely mimic the actual scenario for guanine radical cations in double-stranded DNA, exploration of subsequent reactions within their water complexes can provide an insight into the resulting oxidative damage to nucleosides. Herein guided-ion beam mass spectrometry experiment and direct dynamics trajectory simulations were carried out to examine prototype complexes of the 9-methylguanine radical cation with one and two water ligands (i.e., 9MG˙+·(H2O)1-2) in the gas phase, wherein the complexes were activated by collisional activation in the experiment and by thermal excitation at high temperatures in the simulations. Guided by mass spectroscopic measurements, trajectory results and reaction potential energy surface, three reaction pathways were identified. The first two reaction pathways start with H-atom abstraction from water by the O6 and N7 atoms in 9MG˙+ and are referred to as HAO6 and HAN7, respectively. The primary products of HAO6 and HAN7 reactions, including [9MG + HO6]+/[9MG + HN7]+ and ˙OH, react further to either form [8OH-9MG + HO6]˙+ and [8OH-9MG + HN7]˙+via C8-hydroxylation or form radical cations of 6-enol-guanine (6-enol-G˙+) and 7H-guanine (7HG˙+) via SN2-type methanol elimination. The third reaction pathway corresponds to the formation of 8OH-9MG+ by H elimination from the complex, referred to as HE. Among these product channels, [8OH-9MG + HN7]˙+ has the most favorable formation probability, especially in the presence of additional water molecules. This product may serve as a preceding structure to the 8-oxo-7,8-dihydroguanine lesion in DNA and has implications for health effects of radiation exposure and radiation therapy.
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Affiliation(s)
- Wenjing Zhou
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA. .,PhD Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY 10016, USA
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164
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Drosou M, Mitsopoulou CA, Pantazis DA. Spin-state energetics of manganese spin crossover complexes: Comparison of single-reference and multi-reference ab initio approaches. Polyhedron 2021. [DOI: 10.1016/j.poly.2021.115399] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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165
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Understanding water mediated proton migration in conversion of π-bond in olefinic carbon atoms into C–N bond to form β-amino adducts. Tetrahedron 2021. [DOI: 10.1016/j.tet.2021.132482] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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166
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Efremenko I, Martin JML. Coupled Cluster Benchmark of New DFT and Local Correlation Methods: Mechanisms of Hydroarylation and Oxidative Coupling Catalyzed by Ru(II, III) Chloride Carbonyls. J Phys Chem A 2021. [PMID: 34586809 DOI: 10.1063/1.5137916] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
We have evaluated a set of accurate canonical CCSD(T) energies for stationary points on the potential energy surface for Ru(II, III) chloride carbonyl catalysis of two competing reactions between benzene and methyl acrylate (MA), namely, hydroarylation and oxidative coupling. We have then applied this set to evaluate the performance of localized orbital coupled-cluster methods and several new and common density functionals. We find that (a) DLPNO-CCSD(T) with TightPNO cutoffs is an acceptable substitute for full canonical CCSD(T) calculations on this system; (b) for the closed-shell systems where it could be applied, LNO-CCSD(T) with tight convergence criteria is very close to the canonical results; (c) the recent ωB97X-V and ωB97M-V functionals exhibit superior performance to commonly used DFT functionals in both closed- and open-shell calculations; (d) the revDSD-PBEP86 revision of the DSD-PBEP86 double hybrid represents an improvement over the original, even though transition metals were not involved in its parametrization; and (e) DSD-SCAN and DOD-SCAN show comparable efficiency. Most tested (meta)-GGA and hybrid density functionals perform better for open-shell than for closed-shell complexes; this is not the case for the double hybrids considered.
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Affiliation(s)
- Irena Efremenko
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
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167
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Efremenko I, Martin JML. Coupled Cluster Benchmark of New DFT and Local Correlation Methods: Mechanisms of Hydroarylation and Oxidative Coupling Catalyzed by Ru(II, III) Chloride Carbonyls. J Phys Chem A 2021; 125:8987-8999. [PMID: 34586809 DOI: 10.1021/acs.jpca.1c05124] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We have evaluated a set of accurate canonical CCSD(T) energies for stationary points on the potential energy surface for Ru(II, III) chloride carbonyl catalysis of two competing reactions between benzene and methyl acrylate (MA), namely, hydroarylation and oxidative coupling. We have then applied this set to evaluate the performance of localized orbital coupled-cluster methods and several new and common density functionals. We find that (a) DLPNO-CCSD(T) with TightPNO cutoffs is an acceptable substitute for full canonical CCSD(T) calculations on this system; (b) for the closed-shell systems where it could be applied, LNO-CCSD(T) with tight convergence criteria is very close to the canonical results; (c) the recent ωB97X-V and ωB97M-V functionals exhibit superior performance to commonly used DFT functionals in both closed- and open-shell calculations; (d) the revDSD-PBEP86 revision of the DSD-PBEP86 double hybrid represents an improvement over the original, even though transition metals were not involved in its parametrization; and (e) DSD-SCAN and DOD-SCAN show comparable efficiency. Most tested (meta)-GGA and hybrid density functionals perform better for open-shell than for closed-shell complexes; this is not the case for the double hybrids considered.
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Affiliation(s)
- Irena Efremenko
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
| | - Jan M L Martin
- Department of Molecular Chemistry and Materials Science, Weizmann Institute of Science, 7610001 Rehovot, Israel
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168
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Elangovan N, Thomas R, Sowrirajan S, Manoj KP, Irfan A. Synthesis, Spectral Characterization, Electronic Structure and Biological Activity Screening of the Schiff Base 4-((4-Hydroxy-3-Methoxy-5-Nitrobenzylidene)Amino)-N-(Pyrimidin-2-yl)Benzene Sulfonamide from 5-Nitrovaniline and Sulphadiazene. Polycycl Aromat Compd 2021. [DOI: 10.1080/10406638.2021.1991392] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- N. Elangovan
- Department of Chemistry, Arignar Anna Government Arts College, Tiruchirappalli, Tamilnadu, India
| | - Renjith Thomas
- Department of Chemistry, St Berchmans College (Autonomous), Changanassery, Kerala, India
| | - S. Sowrirajan
- Department of Chemistry, King Fahd University of Petroleum and Minerals, Dhahran, Saudi Arabia
| | - K. P. Manoj
- Department of Chemistry, Arignar Anna Government Arts College, Tiruchirappalli, Tamilnadu, India
| | - Ahmad Irfan
- Research Center for Advanced Materials Science (RCAMS), King Khalid University, Abha, Saudi Arabia
- Department of Chemistry, Faculty of Science, King Khalid University, Abha, Saudi Arabia
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169
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Maurer LR, Bursch M, Grimme S, Hansen A. Assessing Density Functional Theory for Chemically Relevant Open-Shell Transition Metal Reactions. J Chem Theory Comput 2021; 17:6134-6151. [PMID: 34546754 DOI: 10.1021/acs.jctc.1c00659] [Citation(s) in RCA: 55] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Due to the principle lack of systematic improvement possibilities of density functional theory, careful assessment of the performance of density functional approximations (DFAs) on well-designed benchmark sets, for example, for reaction energies and barrier heights, is crucial. While main-group chemistry is well covered by several available sets, benchmark data for transition metal chemistry is sparse. This is especially the case for larger, chemically relevant molecules. Addressing this issue, we recently introduced the MOR41 benchmark which covers chemically relevant reactions of closed-shell complexes. In this work, we extend these efforts to single-reference open-shell systems and introduce the "reactions of open-shell single-reference transition metal complexes" (ROST61) benchmark set. ROST61 includes accurate coupled-cluster reference values for 61 reaction energies with a mean reaction energy of -42.8 kcal mol-1. Complexes with 13-93 atoms covering 20 d-block elements are included, but due to the restriction to single-reference open-shell systems, important elements such as iron or platinum could not be taken into account, or only to a small extent. We assess the performance of 31 DFAs in combination with three London dispersion (LD) correction schemes. Further, DFT-based composite methods, MP2, and a few semiempirical quantum chemical methods are evaluated. Consistent with the results for the MOR41 closed-shell benchmark, we find that the ordering of DFAs according to Jacob's ladder is preserved and that adding an LD correction is crucial, clearly improving almost all tested methods. The recently introduced r2SCAN-3c composite method stands out with a remarkable mean absolute deviation (MAD) of only 2.9 kcal mol-1, which is surpassed only by hybrid DFAs with low amounts of Fock exchange (e.g., 2.3 kcal mol-1 for TPSS0-D4/def2-QZVPP) and double-hybrid (DH) DFAs but at a significantly higher computational cost. The lowest MAD of only 1.6 kcal mol-1 is obtained with the DH DFA PWPB95-D4 in the def2-QZVPP basis set approaching the estimated accuracy of the reference method. Overall, the ROST61 set adds important reference data to a sparsely sampled but practically relevant area of chemistry. At this point, it provides valuable orientation for the application and development of new DFAs and electronic structure methods in general.
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Affiliation(s)
- Leonard R Maurer
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institute for Physical and Theoretical Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
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170
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Villegas-Escobar N, Toro-Labbé A, Schaefer HF. Contrasting the Mechanism of H 2 Activation by Monomeric and Potassium-Stabilized Dimeric Al I Complexes: Do Potassium Atoms Exert any Cooperative Effect? Chemistry 2021; 27:17369-17378. [PMID: 34613646 DOI: 10.1002/chem.202103082] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Indexed: 11/06/2022]
Abstract
Aluminyl anions are low-valent, anionic, and carbenoid aluminum species commonly found stabilized with potassium cations from the reaction of Al-halogen precursors and alkali compounds. These systems are very reactive toward the activation of σ-bonds and in reactions with electrophiles. Various research groups have detected that the potassium atoms play a stabilization role via electrostatic and cation ⋯ π interactions with nearby (aromatic)-carbocyclic rings from both the ligand and from the reaction with unsaturated substrates. Since stabilizing K⋯H bonds are witnessed in the activation of this class of molecules, we aim to unveil the role of these metals in the activation of the smaller and less polarizable H2 molecule, together with a comprehensive characterization of the reaction mechanism. In this work, the activation of H2 utilizing a NON-xanthene-Al dimer, [K{Al(NON)}]2 (D) and monomeric, [Al(NON)]- (M) complexes are studied using density functional theory and high-level coupled-cluster theory to reveal the potential role of K+ atoms during the activation of this gas. Furthermore, we aim to reveal whether D is more reactive than M (or vice versa), or if complicity between the two monomer units exits within the D complex toward the activation of H2 . The results suggest that activation energies using the dimeric and monomeric complexes were found to be very close (around 33 kcal mol-1 ). However, a partition of activation energies unveiled that the nature of the energy barriers for the monomeric and dimeric complexes are inherently different. The former is dominated by a more substantial distortion of the reactants (and increased interaction energies between them). Interestingly, during the oxidative addition, the distortion of the Al complex is minimal, while H2 distorts the most, usually over 0.77 Δ E d i s t ≠ . Overall, it is found here that electrostatic and induction energies between the complexes and H2 are the main stabilizing components up to the respective transition states. The results suggest that the K+ atoms act as stabilizers of the dimeric structure, and their cooperative role on the reaction mechanism may be negligible, acting as mere spectators in the activation of H2 . Cooperation between the two monomers in D is lacking, and therefore the subsequent activation of H2 is wholly disengaged.
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Affiliation(s)
- Nery Villegas-Escobar
- Centro Integrativo de Biología y Química Aplicada (CIBQA), Universidad Bernardo O'Higgins, General Gana 1702, Santiago, 8370854, Chile
| | - Alejandro Toro-Labbé
- Laboratorio de Química Teórica Computacional (QTC), Facultad de Química, Pontificia Universidad Católica de Chile, Avenida Vicuña Mackenna 4860, Santiago, Chile
| | - Henry F Schaefer
- Center for Computational Quantum Chemistry, University of Georgia, Athens, Georgia, 30602, USA
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171
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Jaworski A, Hedin N. Local energy decomposition analysis and molecular properties of encapsulated methane in fullerene (CH 4@C 60). Phys Chem Chem Phys 2021; 23:21554-21567. [PMID: 34550137 DOI: 10.1039/d1cp02333k] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Methane has been successfully encapsulated within cages of C60 fullerene, which is an appropriate model system to study confinement effects. Its chemistry and physics are also relevant for theoretical model descriptions. Here we provide insights into intermolecular interactions and predicted spectroscopic responses of the CH4@C60 complex and compared them with results from other methods and with data from the literature. Local energy decomposition analysis (LED) within the domain-based local pair natural orbital coupled cluster singles, doubles, and perturbative triples (DLPNO-CCSD(T)) framework was used, and an efficient protocol for studies of endohedral complexes of fullerenes is proposed. This approach allowed us to assess energies in relation to electronic and geometric preparation, electrostatics, exchange, and London dispersion for the CH4@C60 endohedral complex. The calculated stabilization energy of CH4 inside the C60 fullerene was -13.5 kcal mol-1 and its magnitude was significantly larger than the latent heat of evaporation of CH4. Evaluation of vibrational frequencies and polarizabilities of the CH4@C60 complex revealed that the infrared (IR) and Raman bands of the endohedral CH4 were essentially "silent" due to the dielectric screening effect of C60, which acted as a molecular Faraday cage. Absorption spectra in the UV-vis domain and ionization potentials of C60 and CH4@C60 were predicted. They were almost identical. The calculated 1H/13C NMR shifts and spin-spin coupling constants were in very good agreement with experimental data. In addition, reference DLPNO-CCSD(T) interaction energies for complexes with noble gases (Ng@C60; Ng = He, Ne, Ar, Kr) were calculated. The values were compared with those derived from supramolecular MP2/SCS-MP2 calculations and estimates with London-type formulas by Pyykkö and coworkers [Phys. Chem. Chem. Phys., 2010, 12, 6187-6203], and with values derived from DFT-based symmetry-adapted perturbation theory (DFT-SAPT) by Hesselmann & Korona [Phys. Chem. Chem. Phys., 2011, 13, 732-743]. Selected points at the potential energy surface of the endohedral He2@C60 trimer were considered. In contrast to previous theoretical attempts with the DFT/MP2/SCS-MP2/DFT-SAPT methods, our calculations at the DLPNO-CCSD(T) level of theory predicted the He2@C60 trimer to be thermodynamically stable, which is in agreement with experimental observations.
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Affiliation(s)
- Aleksander Jaworski
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
| | - Niklas Hedin
- Department of Materials and Environmental Chemistry, Stockholm University, SE-106 91 Stockholm, Sweden.
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172
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Altun A, Garcia-Ratés M, Neese F, Bistoni G. Unveiling the complex pattern of intermolecular interactions responsible for the stability of the DNA duplex. Chem Sci 2021; 12:12785-12793. [PMID: 34703565 PMCID: PMC8494058 DOI: 10.1039/d1sc03868k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 08/26/2021] [Indexed: 01/21/2023] Open
Abstract
Herein, we provide new insights into the intermolecular interactions responsible for the intrinsic stability of the duplex structure of a large portion of human B-DNA by using advanced quantum mechanical methods. Our results indicate that (i) the effect of non-neighboring bases on the inter-strand interaction is negligibly small, (ii) London dispersion effects are essential for the stability of the duplex structure, (iii) the largest contribution to the stability of the duplex structure is the Watson-Crick base pairing - consistent with previous computational investigations, (iv) the effect of stacking between adjacent bases is relatively small but still essential for the duplex structure stability and (v) there are no cooperativity effects between intra-strand stacking and inter-strand base pairing interactions. These results are consistent with atomic force microscope measurements and provide the first theoretical validation of nearest neighbor approaches for predicting thermodynamic data of arbitrary DNA sequences.
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Affiliation(s)
- Ahmet Altun
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Miquel Garcia-Ratés
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Frank Neese
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für Kohlenforschung Kaiser-Wilhelm-Platz 1 D-45470 Mülheim an der Ruhr Germany
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173
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Elangovan N, Thomas R, Sowrirajan S, Irfan A. Synthesis, spectral and quantum mechanical studies and molecular docking studies of Schiff base (E)2-hydroxy-5-(((4-(N-pyrimidin-2-yl)sulfamoyl)phenyl)imino)methyl benzoic acid from 5-formyl salicylic acid and sulfadiazine. J INDIAN CHEM SOC 2021. [DOI: 10.1016/j.jics.2021.100144] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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174
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Singh G, Gamboa S, Orio M, Pantazis DA, Roemelt M. Magnetic exchange coupling in Cu dimers studied with modern multireference methods and broken-symmetry coupled cluster theory. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02830-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
AbstractSpin-state energetics of exchange-coupled copper complexes pose a persistent challenge for applied quantum chemistry. Here, we provide a comprehensive comparison of all available theoretical approaches to the problem of exchange coupling in two antiferromagnetically coupled bis-μ-hydroxo Cu(II) dimers. The evaluated methods include multireference methods based on the density matrix renormalization group (DMRG), multireference methods that incorporate dynamic electron correlation either perturbatively, such as the N-electron valence state perturbation theory, or variationally, such as the difference-dedicated configuration interaction. In addition, we contrast the multireference results with those obtained using broken-symmetry approaches that utilize either density functional theory or, as demonstrated here for the first time in such systems, a local implementation of coupled cluster theory. The results show that the spin-state energetics of these copper dimers are dominated by dynamic electron correlation and represent an impossible challenge for multireference methods that rely on brute-force expansion of the active space to recover correlation energy. Therefore, DMRG-based methods even at the limit of their applicability cannot describe quantitatively the antiferromagnetic exchange coupling in these dimers, in contrast to dinuclear complexes of earlier transition metal ions. The convergence of the broken-symmetry coupled cluster approach is studied and shown to be a limiting factor for the practical application of the method. The advantages and disadvantages of all approaches are discussed, and recommendations are made for future developments.
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175
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Paulechka E, Kazakov A. Efficient Ab Initio Estimation of Formation Enthalpies for Organic Compounds: Extension to Sulfur and Critical Evaluation of Experimental Data. J Phys Chem A 2021; 125:8116-8131. [PMID: 34469173 PMCID: PMC9809154 DOI: 10.1021/acs.jpca.1c05882] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
The efficient protocol for the estimation of gas-phase enthalpies of formation developed previously for C, H, O, N, and F elements was extended to sulfur. The protocol is based on a local coupled cluster with single, double, and perturbative triple excitation [CCSD(T)] approximation and allows rapid evaluation of compounds with sizes computationally prohibitive to canonical CCSD(T) using quadruple zeta basis sets. As a part of model development, a comprehensive review and critical evaluation of experimental data were performed for 87 sulfur-containing organic and inorganic compounds. A compact model with only three empirical parameters for sulfur introduced to address the effects beyond frozen core CCSD(T) was developed. The model exhibits approximately 2 kJ·mol-1 standard deviation over a set of experimental values for a diverse collection of sulfur-containing compounds. The complete basis set version of the model demonstrates a similar performance and requires only one empirical parameter. Multiple problems with the existing experimental data were identified and discussed. In addition, a lack of reliable data for certain important classes of sulfur compounds was found to impede the model generalization and confident performance assessment.
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176
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Drosou M, Pantazis DA. Redox Isomerism in the S 3 State of the Oxygen-Evolving Complex Resolved by Coupled Cluster Theory. Chemistry 2021; 27:12815-12825. [PMID: 34288176 PMCID: PMC8518824 DOI: 10.1002/chem.202101567] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2021] [Indexed: 01/19/2023]
Abstract
The electronic and geometric structures of the water-oxidizing complex of photosystem II in the steps of the catalytic cycle that precede dioxygen evolution remain hotly debated. Recent structural and spectroscopic investigations support contradictory redox formulations for the active-site Mn4 CaOx cofactor in the final metastable S3 state. These range from the widely accepted MnIV 4 oxo-hydroxo model, which presumes that O-O bond formation occurs in the ultimate transient intermediate (S4 ) of the catalytic cycle, to a MnIII 2 MnIV 2 peroxo model representative of the contrasting "early-onset" O-O bond formation hypothesis. Density functional theory energetics of suggested S3 redox isomers are inconclusive because of extreme functional dependence. Here, we use the power of the domain-based local pair natural orbital approach to coupled cluster theory, DLPNO-CCSD(T), to present the first correlated wave function theory calculations of relative stabilities for distinct redox-isomeric forms of the S3 state. Our results enabled us to evaluate conflicting models for the S3 state of the oxygen-evolving complex (OEC) and to quantify the accuracy of lower-level theoretical approaches. Our assessment of the relevance of distinct redox-isomeric forms for the mechanism of biological water oxidation strongly disfavors the scenario of early-onset O-O formation advanced by literal interpretations of certain crystallographic models. This work serves as a case study in the application of modern coupled cluster implementations to redox isomerism problems in oligonuclear transition metal systems.
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Affiliation(s)
- Maria Drosou
- Inorganic Chemistry LaboratoryNational and Kapodistrian University of AthensPanepistimiopolisZografou15771Greece
| | - Dimitrios A. Pantazis
- Max-Planck-Institut für KohlenforschungKaiser-Wilhelm-Platz 145470Mülheim an derRuhrGermany
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177
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Blaško M, Pašteka LF, Urban M. DFT Functionals for Modeling of Polyethylene Chains Cross-Linked by Metal Atoms. DLPNO-CCSD(T) Benchmark Calculations. J Phys Chem A 2021; 125:7382-7395. [PMID: 34428051 DOI: 10.1021/acs.jpca.1c04793] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Density functional theory (DFT) functionals for calculations of binding energies (BEs) of the polyethylene (PE) chains cross-linked by selected metal atoms (M) are benchmarked against DLPNO-CCSD(T) and DLPNO-CCSD(T1) data. PEX-M-PEX complexes as compared with plain parallel PEX···PEX chains with X = 3-9 carbon atoms are model species characterized by a cooperative effect of covalent C-M-C bonds and interchain dispersion interactions. The accuracy of DLPNO-CC methods was assessed by a comparison of BEs with the canonical CCSD(T) results for small PE3-M-PE3 complexes. Functionals for PEX···PEX and closed-shell PEX-M-PEX complexes (M = Be, Mg, Zn) were benchmarked against DLPNO-CCSD(T) BEs; open-shell complexes (M = Li, Ag, Au) were benchmarked against the DLPNO-CCSD(T1) method with iterative triples. Three dispersion corrections were combined with 25 DFT functionals for calculations of BEs with respect to PEX-M and PEX fragments employing def2-TZVPP and def2-QZVPP basis sets. Accuracy to within 5% for the closed-shell PEX-M-PEX complexes was achieved with five functionals. Less accurate are functionals for the open-shell PEX-M-PEX complexes; only two functionals deviate by less than 15% from DLPNO-CCSD(T1). Particularly problematic were PEX-Li-PEX complexes. A reasonable overall performance across all complexes in terms of the mean absolute percentage error is found for the range-separated hybrid functionals ωB97X-D3 and CAM-B3LYP/D3(BJ)-ABC.
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Affiliation(s)
- Martin Blaško
- FunGlass, A. Dubček University of Trenčín, Študentská 2, 911 50 Trenčín, Slovakia
| | - Lukáš F Pašteka
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
| | - Miroslav Urban
- Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University in Bratislava, Ilkovičova 6, 84215 Bratislava, Slovakia
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178
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McFord AW, Butts CP, Fey N, Alder RW. 3× Axial vs 3× Equatorial: The Δ GGA Value Is a Robust Computational Measure of Substituent Steric Effects. J Am Chem Soc 2021; 143:13573-13578. [PMID: 34465097 DOI: 10.1021/jacs.1c04247] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
We define ΔGGA as the free energy change for the formal equilibrium: [13]G-H + 1-X-adamantane → [13]G-X + adamantane, where [13]G-H is the C13H22 fragment of all-trans graphane with 3-fold symmetry. This compares with a situation where the group X is equatorial to three cyclohexane rings with one where it is axial to three rings. ΔGGA values vary from 2.9 (CN) to 145.7 kJ mol-1 (CCl3), and this wide range means that ΔG can be calculated with confidence. ΔGGA values for Me, Et, i-Pr, and t-Bu form a regular series, 34.9, 63.3, 101.6, and 142.0, and clearly reflect the steric size of the groups. We propose a model where the six axial hydrogens surrounding X on [13]G-X provide a nearly circular constriction on the substituent close to its point of attachment but which does not extend far above this. We compare these results with A values and with calculations on 2- and 7-substituted [1(2,3)4]pentamantanes. We show that electronic effects on ΔGGA values are negligible but that they correlate well with computed cone and solid angles subtended by the substituent.
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Affiliation(s)
- Aidan W McFord
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Craig P Butts
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Natalie Fey
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
| | - Roger W Alder
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, U.K
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179
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Garay-Ruiz D, Bo C. Rationalizing the Mechanism of Peroxyformate Decomposition: Computational Insights To Understand Solvent Influence. Chemistry 2021; 27:11618-11626. [PMID: 34076322 PMCID: PMC8457178 DOI: 10.1002/chem.202100755] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Indexed: 11/29/2022]
Abstract
The heterolytic decomposition of tert‐butyl peroxyformate to tert‐butanol and carbon dioxide, catalyzed by pyridine, is a long‐known example of a reaction whose kinetics are strongly affected by solvent polarity. From DFT and ab initio methods together with the SMD implicit solvation model, an extension on the formerly accepted mechanism is proposed. This novel proposal involves the formation of a carbonic acid ester intermediate and its further decomposition, through an unreported pyridine‐mediated stepwise route. Computed barriers for this mechanism at DLPNO/CCSD(T)‐def2‐TZVP are in excellent agreement with experimental kinetic data across different solvents. Furthermore, the strong relationships between activation energies, geometric parameters in the transition state and the characteristics of the different solvents are also analyzed in depth.
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Affiliation(s)
- Diego Garay-Ruiz
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Av. Països Catalans, 16, 43007, Tarragona, Spain
| | - Carles Bo
- Institute of Chemical Research of Catalonia (ICIQ), Barcelona Institute of Science & Technology (BIST), Av. Països Catalans, 16, 43007, Tarragona, Spain.,Departament de Química Física i Inorgànica, Universitat Rovira i Virgili (URV) C/ Marcel⋅lí Domingo s/n, 43007, Tarragona, Spain
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180
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Ballesteros F, Dunivan S, Lao KU. Coupled cluster benchmarks of large noncovalent complexes: The L7 dataset as well as DNA-ellipticine and buckycatcher-fullerene. J Chem Phys 2021; 154:154104. [PMID: 33887937 DOI: 10.1063/5.0042906] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
Abstract
In this work, benchmark binding energies for dispersion-bound complexes in the L7 dataset, the DNA-ellipticine intercalation complex, and the buckycatcher-C60 complex with 120 heavy atoms using a focal-point method based on the canonical form of second-order Møller-Plesset theory (MP2) and the domain based local pair natural orbital scheme for the coupled cluster with single, double, and perturbative triple excitations [CCSD(T)] extrapolated to the complete basis set (CBS) limit are reported. This work allows for increased confidence given the agreement with respect to values recently obtained using the local natural orbital CCSD(T) for L7 and the canonical CCSD(T)/CBS result for the coronene dimer (C2C2PD). Therefore, these results can be considered pushing the CCSD(T)/CBS binding benchmark to the hundred-atom scale. The disagreements between the two state-of-the-art methods, CCSD(T) and fixed-node diffusion Monte Carlo, are substantial with at least 2.0 (∼10%), 1.9 (∼5%), and 10.3 kcal/mol (∼25%) differences for C2C2PD in L7, DNA-ellipticine, and buckycatcher-C60, respectively. Such sizable discrepancy above "chemical accuracy" for large noncovalent complexes indicates how challenging it is to obtain benchmark binding interactions for systems beyond small molecules, although the three up-to-date density functionals, PBE0+D4, ωB97M-V, and B97M-V, agree better with CCSD(T) for these large systems. In addition to reporting these values, different basis sets and various CBS extrapolation parameters for Hartree-Fock and MP2 correlation energies were tested for the first time in large noncovalent complexes with the goal of providing some indications toward optimal cost effective routes to approach the CBS limit without substantial loss in quality.
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Affiliation(s)
- Francisco Ballesteros
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Shelbie Dunivan
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
| | - Ka Un Lao
- Department of Chemistry, Virginia Commonwealth University, Richmond, Virginia 23284, USA
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181
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Kaczorowska MA, Kaczmarek-Kędziera A, Ośmiałowski B. Tautomeric equilibrium, proton affinity and mass spectrometry fragmentation of flexible hydrogen-bonded precursors and rigid [Formula: see text] fluorescent dyes. Sci Rep 2021; 11:15995. [PMID: 34362952 PMCID: PMC8346630 DOI: 10.1038/s41598-021-94978-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Accepted: 07/12/2021] [Indexed: 11/09/2022] Open
Abstract
The stability of two groups of conformationally locked molecules, similar in topology, but differing only by the type of the bridge rigidifying their structure, is studied. The series of the less-rigid 2-phenacylheterocyclic compounds and their stiff difluoroboranyl derivatives are investigated for the determination of the effect of [Formula: see text]/S/O replacement in a five-membered heterocyclic ring and the presence of a strong electron-donating group on the tautomeric equilibrium, protonation affinity, and fragmentation pattern observed in the structural elucidation by means of mass spectrometry technique. The results of the [Formula: see text]B97X-D/6-311++G(d,p) calculations, the topological analysis of electron density as well as the experimental MS measurements show the importance of the number of heteroatoms, their properties, and location in the molecule for the rational design of the systems of desired stable tautomers or the favorable protonation sites. The obtained data allow for the understanding of the fundamentals of the novel highly fluorescent difluoroborates fragmentation behavior, vital for their structural elucidation with the application of high-resolution tandem mass spectrometry methods.
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Affiliation(s)
- Małgorzata A. Kaczorowska
- Faculty of Chemical Technology and Engineering, UTP University of Science and Technology, Seminaryjna 3, 85-326 Bydgoszcz, Poland
| | - Anna Kaczmarek-Kędziera
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University in Torun, Gagarina 7, 87–100 Toruń, Poland
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182
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Naghani FF, Emamian S, Zare K. Exploring influence of fluorine substitution on the strength and nature of halogen bond between iodobenzene and hydrogen cyanide. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4213] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Affiliation(s)
| | - Saeedreza Emamian
- Chemistry Department, Shahrood Branch Islamic Azad University Shahrood Iran
| | - Karim Zare
- Department of Chemistry, Science and Research Branch Islamic Azad University Tehran Iran
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183
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Abstract
We present a case study to demonstrate how complex molecule synthesis can benefit from quantum mechanics (QM) calculations. Theory is applied in two contexts: testing the chemical intuition used in retrosynthetic planning, along with expediting the resolution of unexpected challenges encountered during the course of the synthesis. From a computational lens, we examine retrospectively the strategies employed and the decisions made during our synthetic efforts toward the diterpenoid natural product ineleganolide. Seemingly logical and robust hypotheses are found to be ill-fated after theoretical investigation. Prior knowledge of these issues may have potentially saved valuable time and resources during our synthetic efforts. This cautionary tale suggests that synthetic campaigns can benefit from computational evaluation of synthetic plans.
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Affiliation(s)
- Alexander Q Cusumano
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
| | - K N Houk
- Department of Chemistry and Biochemistry, University of California, Los Angeles, California 90095, USA
| | - Brian M Stoltz
- Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, California 91125, USA
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184
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Lewińska A, Kulbacka J, Domżał-Kędzia M, Witwicki M. Antiradical Properties of N-Oxide Surfactants-Two in One. Int J Mol Sci 2021; 22:ijms22158040. [PMID: 34360806 PMCID: PMC8346996 DOI: 10.3390/ijms22158040] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2021] [Revised: 07/14/2021] [Accepted: 07/22/2021] [Indexed: 12/26/2022] Open
Abstract
Surfactants are molecules that lower surface or interfacial tension, and thus they are broadly used as detergents, wetting agents, emulsifiers, foaming agents, or dispersants. However, for modern applications, substances that can perform more than one function are desired. In this study we evaluated antioxidant properties of two homological series of N-oxide surfactants: monocephalic 3-(alkanoylamino)propyldimethylamine-N-oxides and dicephalic N,N-bis[3,3′-(dimethylamino)propyl]alkylamide di-N-oxides. Their antiradical properties were tested against stable radicals using electron paramagnetic resonance (EPR) and UV-vis spectroscopy. The experimental investigation was supported by theoretical density functional theory (DFT) and ab initio modeling of the X–H bonds dissociation enthalpies, ionization potentials, and Gibbs free energies for radical scavenging reactions. The evaluation was supplemented with a study of biological activity. We found that the mono- and di-N-oxides are capable of scavenging reactive radicals; however, the dicephalic surfactants are more efficient than their linear analogues.
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Affiliation(s)
- Agnieszka Lewińska
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wroclaw, Poland
- Correspondence: (A.L.); (M.W.)
| | - Julita Kulbacka
- Department of Molecular and Cellular Biology, Faculty of Pharmacy, Wroclaw Medical University, Borowska 211A, 50-367 Wroclaw, Poland;
| | - Marta Domżał-Kędzia
- Department of Biotransformation, Faculty of Biotechnology, University of Wroclaw, Joliot-Curie 14a, 50-383 Wroclaw, Poland;
| | - Maciej Witwicki
- Faculty of Chemistry, University of Wrocław, Joliot-Curie 14, 50-383 Wroclaw, Poland
- Correspondence: (A.L.); (M.W.)
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185
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Li H, Brémond E, Sancho-García JC, Adamo C. Pairing double hybrid functionals with a tailored basis set for an accurate thermochemistry of hydrocarbons. RSC Adv 2021; 11:26073-26082. [PMID: 35479441 PMCID: PMC9037073 DOI: 10.1039/d1ra04108h] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Accepted: 07/19/2021] [Indexed: 11/21/2022] Open
Abstract
A collection of five challenging datasets, including noncovalent interactions, reaction barriers and electronic rearrangements of medium-sized hydrocarbons, has been selected to verify the robustness of double-hybrid functionals used in conjunction with the small DH-SVPD basis set, especially developed for noncovalent interactions. The analysis is completed by other, more standard functionals, for a total of 17 models, including also empirical corrections for dispersion. The obtained results show that the chemical accuracy threshold, that is an error lower than 1.0 kcal mol−1, can be obtained by pairing the nonempirical PBE-QIDH functional with the DH-SVPD basis set, as well as by other semi-empirical functionals, such as DSD-PBEP86, using larger basis sets and empirical corrections. More in general, a significant improvement can be obtained using the DH-SVPD basis set with DHs, without resorting to any empirical corrections. This choice leads to a fast computational protocol that, avoiding any empirical potential, remains on a fully quantum ground. The pairing of the PBE-QIDH double-hybrid functional with a tailored split-valence basis set leads to a fast computational protocol for the accurate evaluation of hydrocarbon thermochemistry, without resorting to any empirical correction.![]()
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Affiliation(s)
- Hanwei Li
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences F-75005 Paris France
| | - Eric Brémond
- Université de Paris, ITODYS, CNRS F-75006 Paris France
| | | | - Carlo Adamo
- Chimie ParisTech, PSL Research University, CNRS, Institute of Chemistry for Health and Life Sciences F-75005 Paris France .,Institut Universitaire de France 103 Boulevard Saint Michel F-75005 Paris France
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186
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Moe MM, Tsai M, Liu J. Singlet Oxygen Oxidation of the Radical Cations of 8-Oxo-2'-deoxyguanosine and Its 9-Methyl Analogue: Dynamics, Potential Energy Surface, and Products Mediated by C5-O 2 -Addition. Chempluschem 2021; 86:1243-1254. [PMID: 34268890 DOI: 10.1002/cplu.202100238] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2021] [Revised: 07/02/2021] [Indexed: 01/24/2023]
Abstract
8-Oxo-2'-deoxyguanosine (OG) is the most common DNA lesion. Notably, OG becomes more susceptible to oxidative damage than the undamaged nucleoside, forming mutagenic products in vivo. Herein the reactions of singlet O2 with the radical cations of 8-oxo-2'-deoxyguanosine (OG.+ ) and 9-methyl-8-oxoguanine (9MOG.+ ) were investigated using ion-molecule scattering mass spectrometry, from which barrierless, exothermic O2 -addition products were detected for both reaction systems. Corroborated by static reaction potential energy surface constructed using multi-reference CASPT2 theory and molecular dynamics simulated in the presence of the reactants' kinetic and internal energies, the C5-terminal O2 -addition was pinpointed as the most probable reaction pathway. By elucidating the reaction mechanism, kinetics and dynamics, and reaction products and energetics, this work constitutes the first report unraveling the synergetic damage of OG by ionizing radiation and singlet O2 .
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
| | - Midas Tsai
- Department of Natural Sciences, LaGuardia Community College, 31-10 Thomson Ave., Long Island City, NY, 11101, USA
| | - Jianbo Liu
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY, 11367, USA.,Ph.D. Program in Chemistry, The Graduate Center of the City University of New York, 365 5th Ave., New York, NY, 10016, USA
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187
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Sorbelli D, Belanzoni P, Belpassi L. Tuning the Gold(I)‐Carbon σ Bond in Gold‐Alkynyl Complexes through Structural Modifications of the NHC Ancillary Ligand: Effect on Spectroscopic Observables and Reactivity. Eur J Inorg Chem 2021. [DOI: 10.1002/ejic.202100260] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Affiliation(s)
- Diego Sorbelli
- Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
| | - Paola Belanzoni
- Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
- CNR Institute of Chemical Science and Technologies “Giulio Natta” (CNR-SCITEC) c/o Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies “Giulio Natta” (CNR-SCITEC) c/o Department of Chemistry Biology and Biotechnology University of Perugia Via Elce di Sotto 8 I-06123 Perugia Italy
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188
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Affiliation(s)
- Agustí Lledós
- Departament de Química Universitat Autònoma de Barcelona Campus UAB 08193 Cerdanyola del Vallès Catalonia Spain
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189
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Myllys N, Myers D, Chee S, Smith JN. Molecular properties affecting the hydration of acid-base clusters. Phys Chem Chem Phys 2021; 23:13106-13114. [PMID: 34060578 DOI: 10.1039/d1cp01704g] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In the atmosphere, water in all phases is ubiquitous and plays important roles in catalyzing atmospheric chemical reactions, participating in cluster formation and affecting the composition of aerosol particles. Direct measurements of water-containing clusters are limited because water is likely to evaporate before detection, and therefore, theoretical tools are needed to study hydration in the atmosphere. We have studied thermodynamics and population dynamics of the hydration of different atmospherically relevant base monomers as well as sulfuric acid-base pairs. The hydration ability of a base seems to follow in the order of gas-phase base strength whereas hydration ability of acid-base pairs, and thus clusters, is related to the number of hydrogen binding sites. Proton transfer reactions at water-air interfaces are important in many environmental and biological systems, but a deeper understanding of their mechanisms remain elusive. By studying thermodynamics of proton transfer reactions in clusters containing up to 20 water molecules and a base molecule, we found that that the ability of a base to accept a proton in a water cluster is related to the aqueous-phase basicity. We also studied the second deprotonation reaction of a sulfuric acid in hydrated acid-base clusters and found that sulfate formation is most favorable in the presence of dimethylamine. Molecular properties related to the proton transfer ability in water clusters are discussed.
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Affiliation(s)
- Nanna Myllys
- Department of Chemistry, University of California, Irvine, California 92617, USA and Department of Chemistry, University of Jyväskylä, Jyväskylä 40014, Finland.
| | - Deanna Myers
- Department of Chemistry, University of California, Irvine, California 92617, USA
| | - Sabrina Chee
- Department of Chemistry, University of California, Irvine, California 92617, USA
| | - James N Smith
- Department of Chemistry, University of California, Irvine, California 92617, USA
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190
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Ghosh S, Neese F, Izsák R, Bistoni G. Fragment-Based Local Coupled Cluster Embedding Approach for the Quantification and Analysis of Noncovalent Interactions: Exploring the Many-Body Expansion of the Local Coupled Cluster Energy. J Chem Theory Comput 2021; 17:3348-3359. [PMID: 34037397 PMCID: PMC8190956 DOI: 10.1021/acs.jctc.1c00005] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Indexed: 11/30/2022]
Abstract
Herein, we introduce a fragment-based local coupled cluster embedding approach for the accurate quantification and analysis of noncovalent interactions in molecular aggregates. Our scheme combines two different expansions of the domain-based local pair natural orbital coupled cluster (DLPNO-CCSD(T)) energy: the many-body expansion (MBE) and the local energy decomposition (LED). The low-order terms in the MBE are initially computed in the presence of an environment that is treated at a low level of theory. Then, LED is used to decompose the energy of each term in the embedded MBE into additive fragment and fragment-pairwise contributions. This information is used to quantify the total energy of the system while providing at the same time in-depth insights into the nature and cooperativity of noncovalent interactions. Two different approaches are introduced and tested, in which the environment is treated at different levels of theory: the local coupled cluster in the Hartree-Fock (LCC-in-HF) method, in which the environment is treated at the HF level; and the electrostatically embedded local coupled cluster method (LCC-in-EE), in which the environment is replaced by point charges. Both schemes are designed to preserve as much as possible the accuracy of the parent local coupled cluster method for total energies, while being embarrassingly parallel and less memory intensive. These schemes appear to be particularly promising for the study of large and complex molecular aggregates at the coupled cluster level, such as condensed phase systems and protein-ligand interactions.
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Affiliation(s)
- Soumen Ghosh
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Frank Neese
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Róbert Izsák
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Giovanni Bistoni
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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191
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Rombach D, Birenheide B, Wagenknecht H. Photoredox Catalytic Pentafluorosulfanylative Domino Cyclization of α-Substituted Alkenes to Oxaheterocycles by Using SF 6. Chemistry 2021; 27:8088-8093. [PMID: 33831262 PMCID: PMC8252034 DOI: 10.1002/chem.202100767] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2021] [Indexed: 01/14/2023]
Abstract
Virtually inert sulfur hexafluoride becomes a precious pentafluorosulfanylation agent, if properly activated by photoredox catalysis, to access α-fluoro and α-alkoxy SF5 -compounds. This advanced protocol converts SF6 in the presence of alkynols as bifunctional C-C- and C-O-bond forming reagents directly into pentafluorosulfanylated oxygen-containing heterocycles in a single step from α-substituted alkenes. The proposed mechanism is supported by theoretical calculations and gives insights not only in the pentafluorosulfanylation step but also into formation of the carbon-carbon bond and is in full agreement with Baldwin's cyclization rules. The key step is a radical type 5-, 6- respectively 7-exo-dig-cyclization. The synthesized oxaheterocycles cannot be simply prepared by other synthetic methods, show a high level of structural complexity and significantly expand the scope of pentafluorosulfanylated building blocks valuable for medicinal and material chemistry.
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Affiliation(s)
- David Rombach
- Laboratory of Inorganic ChemistrySwiss Federal Institute of Technology (ETH)Vladimir-Prelog-Weg 1–5/108093ZürichSwitzerland
| | - Bernhard Birenheide
- Institute of Inorganic ChemistryKalsruhe Institute of Technology (KIT)Engesserstr. 1576131KarlsruheGermany
| | - Hans‐Achim Wagenknecht
- Institute of Organic ChemistryKarlsruhe Institute of Technology (KIT)Fritz-Haber-Weg 676131KarlsruheGermany
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192
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Leach IF, Belpassi L, Belanzoni P, Havenith RWA, Klein JEMN. Efficient Computation of Geometries for Gold Complexes. Chemphyschem 2021; 22:1262-1268. [PMID: 33729673 PMCID: PMC8252628 DOI: 10.1002/cphc.202001052] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2020] [Revised: 02/23/2021] [Indexed: 12/21/2022]
Abstract
Computationally obtaining structural parameters along a reaction coordinate is commonly performed with Kohn‐Sham density functional theory which generally provides a good balance between speed and accuracy. However, CPU times still range from inconvenient to prohibitive, depending on the size of the system under study. Herein, the tight binding GFN2‐xTB method [C. Bannwarth, S. Ehlert, S. Grimme, J. Chem. Theory Comput. 2019, 15, 1652] is investigated as an alternative to produce reasonable geometries along a reaction path, that is, reactant, product and transition state structures for a series of transformations involving gold complexes. A small mean error (1 kcal/mol) was found, with respect to an efficient composite hybrid‐GGA exchange‐correlation functional (PBEh‐3c) paired with a double‐ζ basis set, which is 2–3 orders of magnitude slower. The outlined protocol may serve as a rapid tool to probe the viability of proposed mechanistic pathways in the field of gold catalysis.
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Affiliation(s)
- Isaac F Leach
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen, 9747, AG Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, 9747, AG Groningen, The Netherlands
| | - Leonardo Belpassi
- CNR Institute of Chemical Science and Technologies, "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy
| | - Paola Belanzoni
- CNR Institute of Chemical Science and Technologies, "Giulio Natta" (CNR-SCITEC), via Elce di Sotto 8, 06123, Perugia, Italy.,Department of Chemistry, Biology and Biotechnology, University of Perugia, via Elce di Sotto 8, 06123, Perugia, Italy
| | - Remco W A Havenith
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen, 9747, AG Groningen, The Netherlands.,Zernike Institute for Advanced Materials, University of Groningen, 9747, AG Groningen, The Netherlands.,Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University, 9000, Gent, Belgium
| | - Johannes E M N Klein
- Molecular Inorganic Chemistry, Stratingh Institute for Chemistry, University of Groningen, 9747, AG Groningen, The Netherlands
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193
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Abstract
We present an EOM-CCSD-based quantum mechanical/molecular mechanical (QM/MM) study on the electron attachment process to solvated cytosine. The electron attachment in the bulk solvated cytosine occurs through a doorway mechanism, where the initial electron is localized on water. The electron is subsequently transferred to cytosine by the mixing of electronic and nuclear degrees of freedom, which occurs on an ultrafast time scale. The bulk water environment stabilizes the cytosine-bound anion by an extensive hydrogen-bond network and drastically enhances the electron transfer rate from that observed in the gas phase. Microhydration studies cannot reproduce the effect of the bulk water environment on the electron attachment process, and one needs to include a large number of water molecules in the calculation to obtain converged results. The predicted adiabatic electron affinity and electron transfer rate obtained from our QM/MM calculations are consistent with the available experimental results.
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Affiliation(s)
- Pooja Verma
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
| | - Debashree Ghosh
- School of Chemical Sciences, Indian Association for the Cultivation of Science, Kolkata 700032, India
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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194
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Wöhner K, Wulf T, Vankova N, Heine T. Strong Binding of Noble Gases to [B 12X 11] -: A Theoretical Study. J Phys Chem A 2021; 125:4760-4765. [PMID: 34036781 DOI: 10.1021/acs.jpca.1c01909] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
We systematically explore the stability and properties of [B12X11NG]- adducts resulting from the binding of noble gas atoms to anionic [B12X11]- clusters in the gas phase of mass spectrometers. [B12X11]- can be obtained by stripping one X- off the icosahedral closo-dodecaborate dianion [B12X12]2-. We study the binding of the noble gas atoms He, Ne, Ar, Kr, and Xe to [B12X11]- with substituents X = F, Cl, Br, I, and CN. While He cannot be captured by these clusters and Ne only binds at low temperatures, the complexes with the heavier noble gas atoms Ar, Kr, and Xe show appreciable complexation energies and exceed 1 eV at room temperature in the case of [B12(CN)11Xe]-. The predicted B-NG equilibrium distance in the complexes with Ar, Kr, and Xe is only 0.10-0.25 Å longer than the sum of the covalent radii of the two corresponding atoms, and a significant charge transfer from the noble gas atom to the icosahedral B12 cage is observed.
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Affiliation(s)
- Kevin Wöhner
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany.,Wilhelm Ostwald Institute of Physical and Theoretical Chemistry, Faculty for Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Toshiki Wulf
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Wilhelm Ostwald Institute of Physical and Theoretical Chemistry, Faculty for Chemistry and Mineralogy, Leipzig University, 04103 Leipzig, Germany
| | - Nina Vankova
- Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany
| | - Thomas Heine
- Institute of Resource Ecology, Research Site Leipzig, Helmholtz-Zentrum Dresden-Rossendorf, 04318 Leipzig, Germany.,Faculty of Chemistry and Food Chemistry, School of Science, TU Dresden, 01062 Dresden, Germany.,Department of Chemistry, Yonsei University, Seodaemun-gu, Seoul 120-749, Republic of Korea
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195
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Wappett DA, Goerigk L. A guide to benchmarking enzymatically catalysed reactions: the importance of accurate reference energies and the chemical environment. Theor Chem Acc 2021. [DOI: 10.1007/s00214-021-02770-9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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196
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Binuclear ethylenedithiolate iron carbonyls: A density functional theory study. Inorganica Chim Acta 2021. [DOI: 10.1016/j.ica.2021.120260] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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197
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Mounssef Jr B, de Alcântara Morais SF, de Lima Batista AP, de Lima LW, Braga AAC. DFT study of H 2 adsorption at a Cu-SSZ-13 zeolite: a cluster approach. Phys Chem Chem Phys 2021; 23:9980-9990. [PMID: 33870397 DOI: 10.1039/d1cp00422k] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work the H2 adsorption at a Cu(i)-SSZ-13 exchanged zeolite was theoretically investigated. A systematic cluster approach was used and different density functionals (B3LYP, B3LYP-D3(BJ), M06L, PBE, PBE-D3(BJ) and ωB97XD) and a def2-SVP basis set were benchmarked. In order to select the best approach to the H2 adsorption over a Cu(i)-SSZ-13 cluster with 78 atoms (16 T-sites), two main tasks were performed: (1) a comparison between theoretical and experimental structures and (2) a comparison between theoretical and experimental adsorption enthalpies. By employing the most suitable functional - the ωB97X-D - the H2 interaction with the zeolite structure was studied by means of NBO, NCI, AIM and DLPNO-CCSD(T)/LED analyses.
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Affiliation(s)
- Bassim Mounssef Jr
- GQCA - Grupo de Química Computacional Aplicada, Departamento de Química Fundamental, Instituto de Química, Universidade de São Paulo, Av. Prof. Lineu Prestes, 748, São Paulo, 05508-000, Brazil.
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198
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Moe MM, Benny J, Sun Y, Liu J. Experimental and theoretical assessment of protonated Hoogsteen 9-methylguanine-1-methylcytosine base-pair dissociation: kinetics within a statistical reaction framework. Phys Chem Chem Phys 2021; 23:9365-9380. [PMID: 33885080 DOI: 10.1039/d0cp06682f] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We investigated the collision-induced dissociation (CID) reactions of a protonated Hoogsteen 9-methylguanine-1-methylcytosine base pair (HG-[9MG·1MC + H]+), which aims to address the mystery of the literature reported "anomaly" in product ion distributions and compare the kinetics of a Hoogsteen base pair with its Watson-Crick isomer WC-[9MG·1MC + H]+ (reported recently by Sun et al.; Phys. Chem. Chem. Phys., 2020, 22, 24986). Product ion cross sections and branching ratios were measured as a function of center-of-mass collision energy using guided-ion beam tandem mass spectrometry, from which base-pair dissociation energies were determined. Product structures and energetics were assessed using various theories, of which the composite DLPNO-CCSD(T)/aug-cc-pVTZ//ωB97XD/6-311++G(d,p) was adopted as the best-performing method for constructing a reaction potential energy surface. The statistical Rice-Ramsperger-Kassel-Marcus theory was found to provide a useful framework for rationalizing the dominating abundance of [1MC + H]+ over [9MG + H]+ in the fragment ions of HG-[9MG·1MC + H]+. The kinetics analysis proved the necessity for incorporating into kinetics modeling not only the static properties of reaction minima and transition states but more importantly, the kinetics of individual base-pair conformers that have formed in collisional activation. The analysis also pinpointed the origin of the statistical kinetics of HG-[9MG·1MC + H]+vs. the non-statistical behavior of WC-[9MG·1MC + H]+ in terms of their distinctively different intra-base-pair hydrogen-bonds and consequently the absence of proton transfer between the N1 position of 9MG and the N3' of 1MC in the Hoogsteen base pair. Finally, the Hoogsteen base pair was examined in the presence of a water ligand, i.e., HG-[9MG·1MC + H]+·H2O. Besides the same type of base-pair dissociation as detected in dry HG-[9MG·1MC + H]+, secondary methanol elimination was observed via the SN2 reaction of water with nucleobase methyl groups.
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Affiliation(s)
- May Myat Moe
- Department of Chemistry and Biochemistry, Queens College of the City University of New York, 65-30 Kissena Blvd., Queens, NY 11367, USA.
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199
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Kurfman LA, Odbadrakh TT, Shields GC. Calculating Reliable Gibbs Free Energies for Formation of Gas-Phase Clusters that Are Critical for Atmospheric Chemistry: (H 2SO 4) 3. J Phys Chem A 2021; 125:3169-3176. [PMID: 33825467 DOI: 10.1021/acs.jpca.1c00872] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The effects of atmospheric aerosols on our climate are one of the biggest uncertainties in global climate models. Calculating the pathway for the formation of pre-nucleation clusters that become aerosols is challenging, requiring a comprehensive analysis of configurational space and highly accurate Gibbs free energy calculations. We identified a large set of minimum energy configurations of (H2SO4)3 using a sampling technique based on a genetic algorithm and a stepwise density functional theory (DFT) approach and computed the thermodynamics of formation of these configurations with more accurate wavefunction-based electronic energies computed on the DFT geometries. The DLPNO-CCSD(T) methods always return more positive energies compared to the DFT energies. Within the DLPNO-CCSD(T) methods, extrapolating to the complete basis set limit gives more positive free energies compared to explicitly correlated single-point energies. The CBS extrapolation was shown to be robust as both the 4-5 inverse polynomial and Riemann zeta function schemes were within chemical accuracy of one another.
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Affiliation(s)
- Luke A Kurfman
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
| | - Tuguldur T Odbadrakh
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
| | - George C Shields
- Department of Chemistry, Furman University, Greenville, South Carolina 29613-0002, United States
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200
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Mehta N, Fellowes T, White JM, Goerigk L. CHAL336 Benchmark Set: How Well Do Quantum-Chemical Methods Describe Chalcogen-Bonding Interactions? J Chem Theory Comput 2021; 17:2783-2806. [PMID: 33881869 DOI: 10.1021/acs.jctc.1c00006] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We present the CHAL336 benchmark set-the most comprehensive database for the assessment of chalcogen-bonding (CB) interactions. After careful selection of suitable systems and identification of three high-level reference methods, the set comprises 336 dimers each consisting of up to 49 atoms and covers both σ- and π-hole interactions across four categories: chalcogen-chalcogen, chalcogen-π, chalcogen-halogen, and chalcogen-nitrogen interactions. In a subsequent study of DFT methods, we re-emphasize the need for using proper London dispersion corrections when treating noncovalent interactions. We also point out that the deterioration of results and systematic overestimation of interaction energies for some dispersion-corrected DFT methods does not hint at problems with the chosen dispersion correction but is a consequence of large density-driven errors. We conclude this work by performing the most detailed DFT benchmark study for CB interactions to date. We assess 109 variations of dispersion-corrected and dispersion-uncorrected DFT methods and carry out a detailed analysis of 80 of them. Double-hybrid functionals are the most reliable approaches for CB interactions, and they should be used whenever computationally feasible. The best three double hybrids are SOS0-PBE0-2-D3(BJ), revDSD-PBEP86-D3(BJ), and B2NCPLYP-D3(BJ). The best hybrids in this study are ωB97M-V, PW6B95-D3(0), and PW6B95-D3(BJ). We do not recommend using the popular B3LYP functional nor the MP2 approach, which have both been frequently used to describe CB interactions in the past. We hope to inspire a change in computational protocols surrounding CB interactions that leads away from the commonly used, popular methods to the more robust and accurate ones recommended herein. We would also like to encourage method developers to use our set for the investigation and reduction of density-driven errors in new density functional approximations.
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Affiliation(s)
- Nisha Mehta
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
| | - Thomas Fellowes
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Jonathan M White
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia.,Bio21 Molecular Science and Biotechnology Institute, University of Melbourne, Victoria 3010, Australia
| | - Lars Goerigk
- School of Chemistry, The University of Melbourne, Victoria 3010, Australia
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