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Puerta-Oteo R, Munarriz J, Polo V, Jiménez MV, Pérez-Torrente JJ. Carboxylate-Assisted β-(Z) Stereoselective Hydrosilylation of Terminal Alkynes Catalyzed by a Zwitterionic Bis-NHC Rhodium(III) Complex. ACS Catal 2020. [DOI: 10.1021/acscatal.0c01582] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Raquel Puerta-Oteo
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Julen Munarriz
- Departamento de Química Física, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Facultad de Ciencias, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
- Department of Chemistry & Biochemistry, University of California Los Angeles (UCLA), Los Angeles, California 90095, United States
| | - Víctor Polo
- Departamento de Química Física, Instituto de Biocomputación y Física de Sistemas Complejos (BIFI), Facultad de Ciencias, Universidad de Zaragoza, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - M. Victoria Jiménez
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
| | - Jesús J. Pérez-Torrente
- Departamento de Química Inorgánica, Instituto de Síntesis Química y Catálisis Homogénea (ISQCH), Facultad de Ciencias, Universidad de Zaragoza−CSIC, C/Pedro Cerbuna 12, 50009 Zaragoza, Spain
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202
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Kronberg R, Lappalainen H, Laasonen K. Revisiting the Volmer-Heyrovský mechanism of hydrogen evolution on a nitrogen doped carbon nanotube: constrained molecular dynamics versus the nudged elastic band method. Phys Chem Chem Phys 2020; 22:10536-10549. [PMID: 31998914 DOI: 10.1039/c9cp06474e] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Density functional theory (DFT) based computational electrochemistry has the potential to serve as a tool with predictive power in the rational development and screening of electrocatalysts for renewable energy technologies. It is, however, of paramount importance that simulations are conducted rigorously at a level of theory that is sufficiently accurate in order to obtain physicochemically sensible results. Herein, we present a comparative study of the performance of the static climbing image nudged elastic band method (CI-NEB) vs. DFT based constrained molecular dynamics simulations with thermodynamic integration in estimating activation and reaction (free) energies of the Volmer-Heyrovský mechanism on a nitrogen doped carbon nanotube. Due to cancellation of errors within the CI-NEB calculations, static and dynamic activation barriers are observed to be surprisingly similar, while a substantial decrease in reaction energies is seen upon incorporation of solvent dynamics. This finding is attributed to two competing effects; (1) solvent reorganization that stabilizes the transition and, in particular, the product states with respect to the reactant state and (2) destabilizing entropic contributions due to solvent fluctuations. Our results highlight the importance of explicitly sampling the interfacial solvent dynamics when studying hydrogen evolution at solid-liquid interfaces.
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Affiliation(s)
- Rasmus Kronberg
- Research Group of Computational Chemistry, Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, FI-00076 Aalto, Finland.
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203
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Frizon TEA, Vieira AA, da Silva FN, Saba S, Farias G, de Souza B, Zapp E, Lôpo MN, Braga HDC, Grillo F, Curcio SF, Cazati T, Rafique J. Synthesis of 2,1,3-Benzoxadiazole Derivatives as New Fluorophores-Combined Experimental, Optical, Electro, and Theoretical Study. Front Chem 2020; 8:360. [PMID: 32478032 PMCID: PMC7235381 DOI: 10.3389/fchem.2020.00360] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 04/07/2020] [Indexed: 01/04/2023] Open
Abstract
Herein, we report the synthesis and characterization of fluorophores containing a 2,1,3-benzoxadiazole unit associated with a π-conjugated system (D-π-A-π-D). These new fluorophores in solution exhibited an absorption maximum at around ~419 nm (visible region), as expected for electronic transitions of the π-π* type (ε ~2.7 × 107 L mol-1 cm-1), and strong solvent-dependent fluorescence emission (ΦFL ~0.5) located in the bluish-green region. The Stokes' shift of these compounds is ca. 3,779 cm-1, which was attributed to an intramolecular charge transfer (ICT) state. In CHCl3 solution, the compounds exhibited longer and shorter lifetimes, which was attributed to the emission of monomeric and aggregated molecules, respectively. Density functional theory was used to model the electronic structure of the compounds 9a-d in their excited and ground electronic states. The simulated emission spectra are consistent with the experimental results, with different solvents leading to a shift in the emission peak and the attribution of a π-π* state with the characteristics of a charge transfer excitation. The thermal properties were analyzed by thermogravimetric analysis, and a high maximum degradation rate occurred at around 300°C. Electrochemical studies were also performed in order to determine the band gaps of the molecules. The electrochemical band gaps (2.48-2.70 eV) showed strong correlations with the optical band gaps (2.64-2.67 eV).
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Affiliation(s)
- Tiago E. A. Frizon
- Department of Energy and Sustainability, Federal University of Santa Catarina, Araranguá, Brazil
| | - André A. Vieira
- Institute of Chemistry, Federal University of Bahia, Salvador, Brazil
| | | | - Sumbal Saba
- Center for Natural and Human Sciences-CCNH, Federal University of ABC, Santo André, Brazil
| | - Giliandro Farias
- Chemistry Department, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Bernardo de Souza
- Chemistry Department, Federal University of Santa Catarina, Florianópolis, Brazil
| | - Eduardo Zapp
- Department of Exact Sciences and Education, Federal University of Santa Catarina, Blumenau, Brazil
| | - Michell N. Lôpo
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
| | - Hugo de C. Braga
- Institute of Science and Technology, Federal University of São Paulo, São José dos Campos, Brazil
| | - Felipe Grillo
- Department of Materials and Metallurgy, Federal Institute of Espírito Santo, Vitória, Brazil
| | - Sergio F. Curcio
- Physics Department, Federal University of Ouro Preto, Ouro Preto, Brazil
| | - Thiago Cazati
- Physics Department, Federal University of Ouro Preto, Ouro Preto, Brazil
| | - Jamal Rafique
- Institute of Chemistry, Federal University of Mato Grosso do Sul, Campo Grande, Brazil
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204
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Zhou M, Springborg M. Theoretical study of the mechanism behind the site- and enantio-selectivity of C-H functionalization catalysed by chiral dirhodium catalyst. Phys Chem Chem Phys 2020; 22:9561-9572. [PMID: 32319983 DOI: 10.1039/d0cp00249f] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The C-H functionalization is very important for the synthesis of pharmaceuticals and complex natural products. Rhodium carbenoids, obtained when a dirhodium(ii) catalyst containing a crown formed by chiral ligands reacts with diazo compounds with both an electron donating group and an electron withdrawing group, play an important part in controlling site- and enantio-selectivity for functionalization of non-activated C-H bonds. It has earlier been demonstrated that the tertiary C-H bond is more favored to be functionalized inside the crown of the dirhodium catalyst with S-configuration ligands compared with the secondary and primary C-H bonds although the latter possess weaker steric effects. We argue that the higher site- and enantio-selectivity for some types of C-H bond functionalization can be related to intermolecular hydrogen bonding, steric hindrance, and weak interactions when the dirhodium catalyst is interacting with the chiral ligands.
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Affiliation(s)
- Meijuan Zhou
- Physical and Theoretical Chemistry Department, University of Saarland, 66123 Saarbrücken, Germany.
| | - Michael Springborg
- Physical and Theoretical Chemistry Department, University of Saarland, 66123 Saarbrücken, Germany. and Materials Science, Tianjin University, Tianjin 300072, China
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205
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Chantelle L, Menezes de Oliveira AL, Kennedy BJ, Maul J, da Silva MRS, Duarte TM, Albuquerque AR, Sambrano JR, Landers R, Siu-Li M, Longo E, dos Santos IMG. Probing the Site-Selective Doping in SrSnO3:Eu Oxides and Its Impact on the Crystal and Electronic Structures Using Synchrotron Radiation and DFT Simulations. Inorg Chem 2020; 59:7666-7680. [PMID: 32338503 DOI: 10.1021/acs.inorgchem.0c00664] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Laís Chantelle
- NPE-LACOM, Dept de Quı́mica, Universidade Federal da Paraı́ba, João Pessoa - Paraı́ba 58051−085, Brazil
| | - André L. Menezes de Oliveira
- NPE-LACOM, Dept de Quı́mica, Universidade Federal da Paraı́ba, João Pessoa - Paraı́ba 58051−085, Brazil
- School of Chemistry, The University of Sydney, Sydney - New South Wales 2006, Australia
| | - Brendan J. Kennedy
- School of Chemistry, The University of Sydney, Sydney - New South Wales 2006, Australia
| | - Jefferson Maul
- Dipartimento di Chimica, Universita di Torino, via Giuria 5, 10125, Torino, Italy
| | - Márcia R. S. da Silva
- NPE-LACOM, Dept de Quı́mica, Universidade Federal da Paraı́ba, João Pessoa - Paraı́ba 58051−085, Brazil
| | - Thiago M. Duarte
- NPE-LACOM, Dept de Quı́mica, Universidade Federal da Paraı́ba, João Pessoa - Paraı́ba 58051−085, Brazil
| | - Anderson R. Albuquerque
- Instituto de Química, Universidade Federal do Rio Grande do Norte, Natal - Rio Grande do Norte 59078-970, Brazil
| | - Julio R. Sambrano
- Grupo de Simulação e Modelagem Molecular, Universidade Estadual Paulista, Bauru − São Paulo 17033-360, Brazil
| | - Richard Landers
- Instituto de Fı́sica Gleb Wataghin, Universidade Estadual de Campinas, Campinas − São Paulo 13083-859, Brazil
| | - Máximo Siu-Li
- Instituto de Física, Universidade de São Paulo, São Carlos - São Paulo 13563-120, Brazil
| | - Elson Longo
- LIEC/INCTMN, Universidade Estadual Paulista, Araraquara - São Paulo 14800-060, Brazil
| | - Iêda M. G. dos Santos
- NPE-LACOM, Dept de Quı́mica, Universidade Federal da Paraı́ba, João Pessoa - Paraı́ba 58051−085, Brazil
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206
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Schaub TA, Prantl EA, Kohn J, Bursch M, Marshall CR, Leonhardt EJ, Lovell TC, Zakharov LN, Brozek CK, Waldvogel SR, Grimme S, Jasti R. Exploration of the Solid-State Sorption Properties of Shape-Persistent Macrocyclic Nanocarbons as Bulk Materials and Small Aggregates. J Am Chem Soc 2020; 142:8763-8775. [DOI: 10.1021/jacs.0c01117] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Tobias A. Schaub
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
- Institute of Organic Chemistry, Ruprecht-Karls University of Heidelberg, Heidelberg 69120, Germany
| | - Ephraim A. Prantl
- Department of Organic Chemistry, Johannes Gutenberg-University Mainz, Mainz 55128, Germany
| | - Julia Kohn
- Mulliken Center for Theoretical Chemistry, University Bonn, Bonn 53115, Germany
| | - Markus Bursch
- Mulliken Center for Theoretical Chemistry, University Bonn, Bonn 53115, Germany
| | - Checkers R. Marshall
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Erik J. Leonhardt
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Terri C. Lovell
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
| | - Lev N. Zakharov
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | - Carl K. Brozek
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
| | - Siegfried R. Waldvogel
- Department of Organic Chemistry, Johannes Gutenberg-University Mainz, Mainz 55128, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, University Bonn, Bonn 53115, Germany
| | - Ramesh Jasti
- Department of Chemistry & Biochemistry and Material Science Institute, University of Oregon, Eugene, Oregon 97403, United States
- Knight Campus for Accelerating Scientific Impact, University of Oregon, Eugene, Oregon 97403, United States
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207
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Berger RJ, Håkansson P, Mera-Adasme R. A consistent model for the key complex in chronic beryllium disease. ACTA ACUST UNITED AC 2020. [DOI: 10.1515/znb-2020-0010] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Abstract
A hypothesis on the structure of the key complex in chronic beryllium disease (CBD) is discussed with respect to the current knowledge on CBD, and with respect to the constraints implied by the coordination chemistry of beryllium and experimental data on the engaged protein complexes. The structure hypothesis is based on the [Be4O]6+ moiety as a coordination center, which is also found in the so called “basic beryllium carboxylates”. The structure of a small molecular model, optimized at the DFT level of theory, is used to compare the structural demands of this coordination center with a structure of the in vitro model of a beryllium immunoprotein complex determined previously by protein crystallography (Clayton & al., Cell
2014, 158, 132). 9Be NMR chemical shielding values, quadrupole coupling constants and asymmetry parameters (η) have been calculated.
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Affiliation(s)
- Raphael J.F. Berger
- Department for Chemistry and Physics of Materials , Universität Salzburg , Jakob-Haringer-Str.2 a , A-5020 Salzburg , Austria
| | - Pär Håkansson
- NMR Research Unit , University of Oulu , P. O. Box 3000 , 90014 Oulu , Finland
| | - Raúl Mera-Adasme
- Departamento de Ciencias del Ambiente, Facultad de Química y Biología , Universidad de Santiago de Chile (USACH) , Santiago de Chile , Chile , E-mail:
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208
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Stein CJ, Reiher M. Semiclassical Dispersion Corrections Efficiently Improve Multiconfigurational Theory with Short-Range Density-Functional Dynamic Correlation. J Phys Chem A 2020; 124:2834-2841. [PMID: 32186877 DOI: 10.1021/acs.jpca.0c02130] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Multiconfigurational wave functions are known to describe the electronic structure across a Born-Oppenheimer surface qualitatively correct. However, for quantitative reaction energies, dynamic correlation originating from the many configurations involving excitations out of the restricted orbital space, the active space, must be considered. Standard procedures involve approximations that eventually limit the ultimate accuracy achievable (most prominently, multireference perturbation theory). At the same time, the computational cost increases dramatically due to the necessity to obtain higher-order reduced density matrices. It is this disproportion that leads us here to propose an MC-srDFT-D hybrid approach of semiclassical dispersion (D) corrections to cover long-range dynamic correlation in a multiconfigurational (MC) wave function theory, which includes short-range (sr) dynamic correlation by density functional theory (DFT) without double counting. We demonstrate that the reliability of this approach is very good (at negligible cost), especially when considering that standard second-order multireference perturbation theory usually overestimates dispersion interactions.
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Affiliation(s)
- Christopher J Stein
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
| | - Markus Reiher
- ETH Zürich, Laboratorium für Physikalische Chemie, Vladimir-Prelog-Weg 2, 8093 Zürich, Switzerland
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209
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Egan CK, Bizzarro BB, Riera M, Paesani F. Nature of Alkali Ion–Water Interactions: Insights from Many-Body Representations and Density Functional Theory. II. J Chem Theory Comput 2020; 16:3055-3072. [DOI: 10.1021/acs.jctc.0c00082] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- Colin K. Egan
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Brandon B. Bizzarro
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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210
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Riera M, Yeh EP, Paesani F. Data-Driven Many-Body Models for Molecular Fluids: CO2/H2O Mixtures as a Case Study. J Chem Theory Comput 2020; 16:2246-2257. [DOI: 10.1021/acs.jctc.9b01175] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- Marc Riera
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Eric P. Yeh
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
| | - Francesco Paesani
- Department of Chemistry and Biochemistry, University of California San Diego, La Jolla, California 92093, United States
- Materials Science and Engineering, University of California San Diego, La Jolla, California 92093, United States
- San Diego Supercomputer Center, University of California San Diego, La Jolla, California 92093, United States
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211
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Herbers S, Fritz SM, Mishra P, Nguyen HVL, Zwier TS. Local and global approaches to treat the torsional barriers of 4-methylacetophenone using microwave spectroscopy. J Chem Phys 2020; 152:074301. [PMID: 32087663 DOI: 10.1063/1.5142401] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Sven Herbers
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Sean M. Fritz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Piyush Mishra
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Ha Vinh Lam Nguyen
- Laboratoire Interuniversitaire des Systèmes Atmosphériques (LISA), CNRS UMR 7583, Université Paris-Est Créteil, Université de Paris, Institute Pierre Simon Laplace, 61 avenue du Général de Gaulle, Créteil, France
| | - Timothy S. Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
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212
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Fedorov IA. Elastic properties of the molecular crystals of hydrocarbons from first principles calculations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2020; 32:085704. [PMID: 31698348 DOI: 10.1088/1361-648x/ab554e] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
I studied the elastic properties of oligoacenes and polycyclic aromatic hydrocarbons crystals within the framework of density functional theory with van der Waals interactions. The full sets of elastic constants were computed. The computed parameters have good agreement with experimental data. The study of four forms (α, β, γ and dimeric) demonstrate that the stacking of molecules leads to different character of interaction between molecules. Crystals with dimeric form have lower anisotropy. If symmetry of crystals is the same, the increase in number of aromatic rings results in anisotropy increase.
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213
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Humphrey JJL, Kronberg R, Cai R, Laasonen K, Palmer RE, Wain AJ. Active site manipulation in MoS 2 cluster electrocatalysts by transition metal doping. NANOSCALE 2020; 12:4459-4472. [PMID: 32030382 DOI: 10.1039/c9nr10702a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
The development of non-platinum group metal catalysts for the hydrogen evolution reaction (HER) in water electrolyser devices is essential for their widespread and sustainable deployment. In recent years, molybdenum disulfide (MoS2) catalysts have received significant attention as they not only exhibit good electrocatalytic HER activity but also, crucially, acid-stability. However, further performance enhancement is required for these materials to be competitive with Pt and to that end transition metal doping of MoS2 has been explored as a route to further increasing its catalytic activity. In this work, cluster beam deposition was employed to produce controlled cobalt-doped MoS2 clusters (MoS2-Co). We demonstrate that, in contrast to previous observations of performance enhancement in MoS2 resulting from nickel doping (MoS2-Ni), the introduction of Co has a detrimental effect on HER activity. The contrasting behaviours of Ni and Co doping are rationalized by density functional theory (DFT) calculations, which suggest that HER-active surface vacancies are deactivated by combination with Co dopant atoms, whilst their activity is retained, or even partially enhanced, by combination with Ni dopant atoms. Furthermore, the adatom dopant-vacancy combination kinetics appear to be more than three orders of magnitude faster in MoS2-Co than for MoS2-Ni. These findings highlight a fundamental difference in the influence of transition metal dopants on the HER performance of MoS2 electrocatalysts and stress the importance of considering surface atomic defects when predicting their behaviour.
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Affiliation(s)
- Jo J L Humphrey
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
| | - Rasmus Kronberg
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Rongsheng Cai
- College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea, SA1 8EN, UK
| | - Kari Laasonen
- Department of Chemistry and Materials Science, Aalto University, P.O. Box 16100, 00076 Aalto, Finland
| | - Richard E Palmer
- College of Engineering, Swansea University, Bay Campus, Fabian Way, Swansea, SA1 8EN, UK
| | - Andrew J Wain
- National Physical Laboratory, Hampton Road, Teddington, TW11 0LW, UK.
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214
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Rebrov O, Poline M, Ryding MJ, Thomas RD, Uggerud E, Larsson M. Non-covalently bonded diastereomeric adducts of amino acids and (S)-1-phenylethanol in low-energy dissociative collisions. Mol Phys 2020. [DOI: 10.1080/00268976.2019.1615145] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- O. Rebrov
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm, Sweden
| | - M. Poline
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm, Sweden
| | - M. J. Ryding
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - R. D. Thomas
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm, Sweden
| | - E. Uggerud
- Department of Chemistry and Hylleraas Centre for Quantum Molecular Sciences, University of Oslo, Oslo, Norway
| | - M. Larsson
- Department of Physics, AlbaNova University Center, Stockholm University, Stockholm, Sweden
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215
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Herbers S, Fritz SM, Mishra P, Kim Y, Slipchenko L, Zwier TS. The unusual symmetry of hexafluoro-o-xylene-A microwave spectroscopy and computational study. J Chem Phys 2020; 152:064302. [PMID: 32061218 DOI: 10.1063/1.5142169] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The rotational constants and quartic centrifugal distortion coefficients of hexafluoro-o-xylene were precisely derived from the 8 GHz to 18 GHz gas phase microwave spectrum. In addition, the rotational constants of all singly substituted 13C isotopologues were determined. Instead of the intuitively expected symmetry of C2v, as in o-xylene, calculations with a variety of methods (B3LYP, CAM-B3LYP, ωB97XD, MP2, and coupled-cluster singles, doubles, and perturbative triples) predict a C2 symmetry structure in which the two CF3 groups rotate in opposite directions by about 16°. While the experimental results in this study are not capable of proving this unusual symmetry, they can support future microwave, gas phase electron diffraction or nuclear magnetic resonance studies. From the presented data, a preliminary r0 structure was determined, reproducing the experimental rotational constants with deviations of no more than 15 kHz. Analysis of the interactions between the two CF3 groups using an effective fragment potential approach identifies two major contributions to their interaction, due to exchange-repulsion and electrostatic repulsion, with electrostatic repulsion responsible for the barrier at the C2v geometry.
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Affiliation(s)
- Sven Herbers
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Sean M Fritz
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Piyush Mishra
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Yongbin Kim
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Lyudmila Slipchenko
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
| | - Timothy S Zwier
- Department of Chemistry, Purdue University, 560 Oval Drive, West Lafayette, Indiana 47907, USA
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216
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Fedorov I, Korabel'nikov D, Nguyen C, Prosekov A. Physicochemical properties of L- and DL-valine: first-principles calculations. Amino Acids 2020; 52:425-433. [PMID: 32008092 DOI: 10.1007/s00726-020-02818-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2019] [Accepted: 01/14/2020] [Indexed: 11/25/2022]
Abstract
At present, physicochemical properties of amino acid molecular crystals are of the utmost interest. The compounds where molecules have different chirality are the focus of particular interest. This paper, presents a study on the structural and electronic properties of crystalline L- and DL-valine within the framework of density functional theory including van der Waals interactions. The results of this study showed that electronic properties of the two forms of valine are similar at zero pressure. Pressure leads to different responses in these crystals which is manifested as various deformations of molecules. The pressure effect on the infrared spectra and distribution of electron density of L- and DL-valine has been studied.
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Affiliation(s)
- Igor Fedorov
- Department of Theoretical Physics, Institute of Fundamental Sciences, Kemerovo State University, Krasnaya 6, Kemerovo, 650000, Russia.
| | - Dmitry Korabel'nikov
- Department of Theoretical Physics, Institute of Fundamental Sciences, Kemerovo State University, Krasnaya 6, Kemerovo, 650000, Russia
| | - Chuong Nguyen
- Institute of Research and Development, Duy Tan University, Da Nang, 550000, Vietnam.
| | - Alexander Prosekov
- Department of Bionanotechnology, Kemerovo State University, Krasnaya 6, Kemerovo, 650000, Russia
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217
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Wang J, Herbers S, Buschmann P, Lengsfeld K, Grabow JU, Feng G, Gou Q. Rotational spectra and molecular structures of ethylanilines. CHINESE J CHEM PHYS 2020. [DOI: 10.1063/1674-0068/cjcp1912215] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Affiliation(s)
- Juan Wang
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany
| | - Sven Herbers
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany
| | - Philipp Buschmann
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany
| | - Kevin Lengsfeld
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie, Leibniz Universität Hannover, Callinstraße 3A, 30167 Hannover, Germany
| | - Gang Feng
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
| | - Qian Gou
- School of Chemistry and Chemical Engineering, Chongqing University, Chongqing 401331, China
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218
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Poline M, Rebrov O, Larsson M, Zhaunerchyk V. Theoretical studies of infrared signatures of proton-bound amino acid dimers with homochiral and heterochiral moieties. Chirality 2020; 32:359-369. [PMID: 31943359 DOI: 10.1002/chir.23165] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Revised: 11/14/2019] [Accepted: 12/16/2019] [Indexed: 01/23/2023]
Abstract
Proton-bound homochiral and heterochiral dimers, X-H+ -X, of five amino acids (X = Ser, Ala, Thr, Phe, and Arg) are investigated theoretically using quantum chemical density functional theory (DFT) calculations and molecular dynamics simulations with the aim to unveil diastereomer-specific mid-infrared (mid-IR) absorption bands in the spectral range of 1000 to 1800 cm-1 . The theoretical calculations performed in this work imply that all systems, except Ala2 H+ , have distinct mid-IR absorption bands in homochiral and heterochiral configurations, which make them appropriate systems to be studied experimentally with mid-IR spectroscopy. We show that intermolecular interaction with the side chain, in the form of hydrogen bonding or cation-π interaction, is necessary for chiral effects to be present in the mid-IR spectra of proton-bound dimers of amino acids. We also report new conformers for Ala2 H+ , Thr2 H+ , Phe2 H+ , and Arg2 H+ , which were not found in earlier studies of these dimers.
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Affiliation(s)
- Mathias Poline
- Department of Physics, Stockholm University, Stockholm, Sweden
| | - Oleksii Rebrov
- Department of Physics, Stockholm University, Stockholm, Sweden
| | - Mats Larsson
- Department of Physics, Stockholm University, Stockholm, Sweden
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219
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Understanding chemical reactivity using the activation strain model. Nat Protoc 2020; 15:649-667. [PMID: 31925400 DOI: 10.1038/s41596-019-0265-0] [Citation(s) in RCA: 168] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/29/2019] [Indexed: 12/20/2022]
Abstract
Understanding chemical reactivity through the use of state-of-the-art computational techniques enables chemists to both predict reactivity and rationally design novel reactions. This protocol aims to provide chemists with the tools to implement a powerful and robust method for analyzing and understanding any chemical reaction using PyFrag 2019. The approach is based on the so-called activation strain model (ASM) of reactivity, which relates the relative energy of a molecular system to the sum of the energies required to distort the reactants into the geometries required to react plus the strength of their mutual interactions. Other available methods analyze only a stationary point on the potential energy surface, but our methodology analyzes the change in energy along a reaction coordinate. The use of this methodology has been proven to be critical to the understanding of reactions, spanning the realms of the inorganic and organic, as well as the supramolecular and biochemical, fields. This protocol provides step-by-step instructions-starting from the optimization of the stationary points and extending through calculation of the potential energy surface and analysis of the trend-decisive energy terms-that can serve as a guide for carrying out the analysis of any given reaction of interest within hours to days, depending on the size of the molecular system.
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220
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Zimmermann C, Gottschalk HC, Suhm MA. Three-dimensional docking of alcohols to ketones: an experimental benchmark based on acetophenone solvation energy balances. Phys Chem Chem Phys 2020; 22:2870-2877. [PMID: 31913366 DOI: 10.1039/c9cp06128b] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
The two hydrogen bond solvation sites exhibited by the carbonyl group in acetophenone are influenced by alkylation of the methyl group in both the acetophenone and in the prototype solvent methanol, largely due to London dispersion forces. Phenyl docking and alkyl docking preferences can be realized at will by appropriate substitution. In particular, cyclopropylation helps to stabilize the opposite phenyl docking site. In all cases, the energy gap is small enough to allow for a simultaneous detection even under low temperature conditions. This density functional prediction is checked experimentally by jet FTIR spectroscopy and largely confirmed. A spurious out-of-plane solvation preference predicted for cyclopropylphenylketone with tert-butyl alcohol by B3LYP-D3 calculations is not confirmed experimentally. It is unlikely that this discrepancy is due to zero-point energy effects. Instead, the second most stable alkyl-side solvation motif predicted with a more in-plane coordination is found in the jet expansion. Overall, the ability of carbonyl solvation balances to benchmark subtle electronic structure effects for non-covalent interactions without major nuclear motion corrections is supported.
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Affiliation(s)
- C Zimmermann
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | - H C Gottschalk
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
| | - M A Suhm
- Georg-August-Universität Göttingen, Tammannstraße 6, 37077 Göttingen, Germany.
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221
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Grubova IY, Surmeneva MA, Surmenev RA, Neyts EC. Effect of van der Waals interactions on the adhesion strength at the interface of the hydroxyapatite–titanium biocomposite: a first-principles study. RSC Adv 2020; 10:37800-37805. [PMID: 35515192 PMCID: PMC9057198 DOI: 10.1039/d0ra06006b] [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: 07/09/2020] [Accepted: 09/28/2020] [Indexed: 01/10/2023] Open
Abstract
Hydroxyapatite (HAP) is frequently used as biocompatible coating on Ti-based implants. In this context, the HAP-Ti adhesion is of crucial importance. Here, we report ab initio calculations to investigate the influence of Si incorporation into the amorphous calcium-phosphate (a-HAP) structure on the interfacial bonding mechanism between the a-HAP coating and an amorphous titanium dioxide (a-TiO2) substrate, contrasting two different density functionals: PBE-GGA, and DFT-D3, which are capable of describing the influence of the van der Waals (vdW) interactions. In particular, we discuss the effect of dispersion on the work of adhesion (Wad), equilibrium geometries, and charge density difference (CDD). We find that replacement of P by Si in a-HAP (a-Si-HAP) with the creation of OH vacancies as charge compensation results in a significant increase in the bond strength between the coating and substrate in the case of using the PBE-GGA functional. However, including the vdW interactions shows that these forces considerably contribute to the Wad. We show that the difference (Wad − Wad(vdW)) is on average more than 1.1 J m−2 and 0.5 J m−2 for a-HAP/a-TiO2 and a-Si-HAP/a-TiO2, respectively. These results reveal that including vdW interactions is essential for accurately describing the chemical bonding at the a-HAP/a-TiO2 interface. Dispersion interactions play a significant role in altering the bonding strength of the hydroxyapatite coating to the substrate, and such interactions is critical in molecular simulations.![]()
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Affiliation(s)
- Irina Yu. Grubova
- Research Center for Physical Materials Science and Composite Materials
- Research School of Chemistry & Applied Biomedical Sciences
- National Research Tomsk Polytechnic University
- 634050 Tomsk
- Russia
| | - Maria A. Surmeneva
- Research Center for Physical Materials Science and Composite Materials
- Research School of Chemistry & Applied Biomedical Sciences
- National Research Tomsk Polytechnic University
- 634050 Tomsk
- Russia
| | - Roman A. Surmenev
- Research Center for Physical Materials Science and Composite Materials
- Research School of Chemistry & Applied Biomedical Sciences
- National Research Tomsk Polytechnic University
- 634050 Tomsk
- Russia
| | - Erik C. Neyts
- Department of Chemistry
- PLASMANT Research Group
- NANOlab Center of Excellence
- University of Antwerp
- B-2610 Wilrijk
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222
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Orenha RP, Nagurniak GR, Colaço MC, Caramori GF, Piotrowski MJ, de Araújo Batista KE, Muñoz-Castro A, de Almeida Silva B, Esteves BJ, Parreira RLT. The simultaneous recognition mechanism of cations and anions using macrocyclic–iodine structures: insights from dispersion-corrected DFT calculations. Phys Chem Chem Phys 2020; 22:23795-23803. [DOI: 10.1039/d0cp04291a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The design of structures to recognize ions is growing in recent years. Here, the simultaneous recognition of cations and anions by a macrocycle comprising a simple crown ether and an iodine-triazole unit has been investigated using DFT calculations.
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Affiliation(s)
- Renato Pereira Orenha
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
| | - Glaucio Régis Nagurniak
- Universidade Federal de Santa Catarina
- Departamento de Ciências Exatas e da Educação
- Blumenau
- Brazil
| | - Matheus Cachoeira Colaço
- Departamento de Química
- Universidade Federal de Santa Catarina, Campus Universitário Trindade
- Florianópolis
- Brazil
| | - Giovanni Finoto Caramori
- Departamento de Química
- Universidade Federal de Santa Catarina, Campus Universitário Trindade
- Florianópolis
- Brazil
| | | | | | - Alvaro Muñoz-Castro
- Laboratorio de Química Inorgánica y Materiales Moleculares
- Facultad de Ingenieria
- Universidad Autonoma de Chile
- Llano Subercaceaux
- San Miguel
| | | | - Benjamim José Esteves
- Núcleo de Pesquisas em Ciências Exatas e Tecnológicas
- Universidade de Franca
- Franca
- Brazil
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223
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Chrayteh M, Savoia A, Huet TR, Dréan P. Microhydration of verbenone: how the chain of water molecules adapts its structure to the host molecule. Phys Chem Chem Phys 2020; 22:5855-5864. [DOI: 10.1039/c9cp06678k] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The microsolvation of verbenone (C10H14O)·(H2O)n (n = 1, 2, 3) was investigated in a supersonic expansion using a cavity-based Fourier transform microwave spectrometer, in the 2.8–14 GHz frequency range and by computational chemistry.
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Affiliation(s)
- Mhamad Chrayteh
- University of Lille
- CNRS
- UMR 8523 – PhLAM – Physique des Lasers
- Atomes et Molécules
- F-59000 Lille
| | - Annunziata Savoia
- University of Lille
- CNRS
- UMR 8523 – PhLAM – Physique des Lasers
- Atomes et Molécules
- F-59000 Lille
| | - Thérèse R. Huet
- University of Lille
- CNRS
- UMR 8523 – PhLAM – Physique des Lasers
- Atomes et Molécules
- F-59000 Lille
| | - Pascal Dréan
- University of Lille
- CNRS
- UMR 8523 – PhLAM – Physique des Lasers
- Atomes et Molécules
- F-59000 Lille
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224
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Souza JKD, Duarte TM, dos Santos IMG, Sambrano JR, Maia ADS, dos Reis Albuquerque A. Intra-octahedral distortion on lamellar potassium niobate K 4Nb 6O 17: a periodic DFT study of structural, electronic and vibrational properties. Phys Chem Chem Phys 2020; 22:16562-16570. [DOI: 10.1039/d0cp01581d] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
DFT calculation applied to K4Nb6O17 allowed to identify and correlate its electronic and vibrational properties with [NbO6] intraoctahedral distortion.
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Affiliation(s)
| | - Thiago M. Duarte
- NPE-Lacom
- INCTMN-UFPB
- Universidade Federal da Paraíba
- João Pessoa
- Brazil
| | | | - Júlio Ricardo Sambrano
- Grupo de Modelagem e Simulação Molecular
- INCTMN-UNESP
- São Paulo State University
- Bauru
- Brazil
| | - Ary da Silva Maia
- NPE-Lacom
- INCTMN-UFPB
- Universidade Federal da Paraíba
- João Pessoa
- Brazil
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225
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Berryman VEJ, Shephard JJ, Ochiai T, Price AN, Arnold PL, Parsons S, Kaltsoyannis N. Quantum chemical topology and natural bond orbital analysis of M–O covalency in M(OC6H5)4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np). Phys Chem Chem Phys 2020; 22:16804-16812. [DOI: 10.1039/d0cp02947e] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
VXC(M,O): the exchange–correlation metric quantifies covalency between M and O atomic basins in M(OC6H5)4 (M = Ti, Zr, Hf, Ce, Th, Pa, U, Np).
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Affiliation(s)
| | - Jacob J. Shephard
- EaStCHEM School of Chemistry and The Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - Tatsumi Ochiai
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
- Department of Chemistry
| | - Amy N. Price
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
| | - Polly L. Arnold
- EaStCHEM School of Chemistry
- The University of Edinburgh
- Edinburgh
- UK
- Department of Chemistry
| | - Simon Parsons
- EaStCHEM School of Chemistry and The Centre for Science at Extreme Conditions
- The University of Edinburgh
- Edinburgh
- UK
| | - Nikolas Kaltsoyannis
- Department of Chemistry
- School of Natural Sciences
- The University of Manchester
- Manchester
- UK
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226
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Alipour M, Izadkhast T. Appraising spin-state energetics in transition metal complexes using double-hybrid models: accountability of SOS0-PBESCAN0-2(a) as a promising paradigm. Phys Chem Chem Phys 2020; 22:9388-9404. [DOI: 10.1039/d0cp00807a] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Through a comprehensive survey, reliable double-hybrid models have been validated and proposed for spin-state energetics in transition metal complexes.
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Affiliation(s)
- Mojtaba Alipour
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz 71946-84795
- Iran
| | - Tahereh Izadkhast
- Department of Chemistry
- College of Sciences
- Shiraz University
- Shiraz 71946-84795
- Iran
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227
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Vela S, Fumanal M, Cirera J, Ribas-Arino J. Thermal spin crossover in Fe(ii) and Fe(iii). Accurate spin state energetics at the solid state. Phys Chem Chem Phys 2020; 22:4938-4945. [DOI: 10.1039/d0cp00162g] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Parametrization of PBE+U under the D3 and D3-BJ dispersion corrections to study FeII and FeIII-based Spin Crossover complexes.
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Affiliation(s)
- Sergi Vela
- Laboratory for Computational Molecular Design
- Institute of Chemical Sciences and Engineering
- EPFL
- CH-1015 Lausanne
- Switzerland
| | - Maria Fumanal
- Laboratoire de Chimie Quantique
- UMR 7111
- CNRS-Université de Strasbourg
- F-67000 Strasbourg
- France
| | - Jordi Cirera
- Departament de Química Inorganica i Orgànica and IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
| | - Jordi Ribas-Arino
- Departament de Ciència de Materials i Química Física and IQTCUB
- Universitat de Barcelona
- Barcelona
- Spain
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228
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Kraus P, Obenchain DA, Herbers S, Wachsmuth D, Frank I, Grabow JU. Xe⋯OCS: relatively straightforward? Phys Chem Chem Phys 2020; 22:5615-5624. [DOI: 10.1039/d0cp00334d] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Spectroscopy meets theory in a study of Xe⋯OCS complex: accurate near-equilibrium structures, experimental interaction energies, and CCSD(T)/CBS results presented.
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Affiliation(s)
- Peter Kraus
- Theoretical Chemistry
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Daniel A. Obenchain
- Institut für Physikalische Chemie und Elektrochemie
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Sven Herbers
- Institut für Physikalische Chemie und Elektrochemie
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Dennis Wachsmuth
- Institut für Physikalische Chemie und Elektrochemie
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Irmgard Frank
- Theoretical Chemistry
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
| | - Jens-Uwe Grabow
- Institut für Physikalische Chemie und Elektrochemie
- Leibniz Universität Hannover
- 30167 Hannover
- Germany
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229
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Affiliation(s)
- Steven M. Bachrach
- School of Science, Monmouth University, 400 Cedar Avenue, West Long Branch, New Jersey 07764, United States
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230
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Teixeira MH, Curtolo F, Camilo SRG, Field MJ, Zheng P, Li H, Arantes GM. Modeling the Hydrolysis of Iron-Sulfur Clusters. J Chem Inf Model 2019; 60:653-660. [PMID: 31790241 DOI: 10.1021/acs.jcim.9b00881] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Iron-sulfur (FeS) clusters are essential metal cofactors involved in a wide variety of biological functions. Their catalytic efficiency, biosynthesis, and regulation depend on FeS stability in aqueous solution. Here, molecular modeling is used to investigate the hydrolysis of an oxidized (ferric) mononuclear FeS cluster by bare dissociation and water substitution mechanisms in neutral and acidic solution. First, approximate electronic structure descriptions of FeS reactions by density functional theory are validated against high-level wave function CCSD(T) calculations. Solvation contributions are included by an all-atom model with hybrid quantum chemical/molecular mechanical (QM/MM) potentials and enhanced sampling molecular dynamics simulations. The free energy profile obtained for FeS cluster hydrolysis indicates that the hybrid functional M06 together with an implicit solvent correction capture the most important aspects of FeS cluster reactivity in aqueous solution. Then, 20 reaction channels leading to two consecutive Fe-S bond ruptures were explored with this calibrated model. For all protonation states, nucleophilic substitution with concerted bond breaking and forming to iron is the preferred mechanism, both kinetic and thermodynamically. In neutral solution, proton transfer from water to the sulfur leaving group is also concerted. Dissociative reactions show higher barriers and will not be relevant for FeS reactivity when exposed to solvent. These hydrolysis mechanisms may help to explain the stability and catalytic mechanisms of FeS clusters of multiple sizes and proteins.
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Affiliation(s)
- Murilo H Teixeira
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Felipe Curtolo
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Sofia R G Camilo
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
| | - Martin J Field
- CNRS, CEA, IRIG, Laboratoire de Chimie et Biologie des Métaux , Université Grenoble Alpes , 17 rue des Martyrs , 38000 Grenoble , France.,Institut Laue-Langevin , BP 156, 41 Avenue des Martyrs , 38042 Grenoble , Cedex 9, France
| | - Peng Zheng
- State Key Laboratory of Coordination Chemistry, School of Chemistry and Chemical Engineering , Nanjing University , Nanjing , Jiangsu 210023 , China
| | - Hongbin Li
- Department of Chemistry , University of British Columbia , Vancouver , British Columbia V6T 1Z1 , Canada
| | - Guilherme M Arantes
- Department of Biochemistry, Instituto de Química , Universidade de São Paulo , Av. Prof. Lineu Prestes 748 , 05508-900 São Paulo , SP , Brazil
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231
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Barabás J, Vanbuel J, Ferrari P, Janssens E, Höltzl T. Non-covalent Interactions and Charge Transfer between Propene and Neutral Yttrium-Doped and Pure Gold Clusters. Chemistry 2019; 25:15795-15804. [PMID: 31696987 PMCID: PMC6916555 DOI: 10.1002/chem.201902794] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 09/08/2019] [Indexed: 12/03/2022]
Abstract
The dopant and size-dependent propene adsorption on neutral gold (Aun ) and yttrium-doped gold (Aun-1 Y) clusters in the n=5-15 size range are investigated, combining mass spectrometry and gas phase reactions in a low-pressure collision cell and density functional theory calculations. The adsorption energies, extracted from the experimental data using an RRKM analysis, show a similar size dependence as the quantum chemical results and are in the range of ≈0.6-1.2 eV. Yttrium doping significantly alters the propene adsorption energies for n=5, 12 and 13. Chemical bonding and energy decomposition analysis showed that there is no covalent bond between the cluster and propene, and that charge transfer and other non-covalent interactions are dominant. The natural charges, Wiberg bond indices, and the importance of charge transfer all support an electron donation/back-donation mechanism for the adsorption. Yttrium plays a significant role not only in the propene binding energy, but also in the chemical bonding in the cluster-propene adduct. Propene preferentially binds to yttrium in small clusters (n<10), and to a gold atom at larger sizes. Besides charge transfer, relaxation also plays an important role, illustrating the non-local effect of the yttrium dopant. It is shown that the frontier molecular orbitals of the clusters determine the chemical bonding, in line with the molecular-like electronic structure of metal clusters.
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Affiliation(s)
- Júlia Barabás
- Department of Inorganic and Analytical ChemistryBudapest University of Technology and EconomicsSzent Gellért tér 4Budapest1111Hungary
| | - Jan Vanbuel
- Quantum Solid State PhysicsKU LeuvenCelestijnenlaan 200d3001LeuvenBelgium
| | - Piero Ferrari
- Quantum Solid State PhysicsKU LeuvenCelestijnenlaan 200d3001LeuvenBelgium
| | - Ewald Janssens
- Quantum Solid State PhysicsKU LeuvenCelestijnenlaan 200d3001LeuvenBelgium
| | - Tibor Höltzl
- Furukawa Electric Institute of TechnologyKésmárk utca 28/ABudapest1158Hungary
- MTA-BME Computation Driven Chemistry Research GroupBudapest University of Technology and EconomicsSzent Gellért tér 4Budapest1111Hungary
- Department of Inorganic and Analytical ChemistryBudapest University of Technology and EconomicsSzent Gellért tér 4Budapest1111Hungary
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232
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Tay DWP, Nobbs JD, Romain C, White AJP, Aitipamula S, van Meurs M, Britovsek GJP. gem-Dialkyl Effect in Diphosphine Ligands: Synthesis, Coordination Behavior, and Application in Pd-Catalyzed Hydroformylation. ACS Catal 2019. [DOI: 10.1021/acscatal.9b03007] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Dillon W. P. Tay
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - James D. Nobbs
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology & Research, Jurong Island 627833, Singapore
| | - Charles Romain
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Andrew J. P. White
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
| | - Srinivasulu Aitipamula
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology & Research, Jurong Island 627833, Singapore
| | - Martin van Meurs
- Institute of Chemical and Engineering Sciences, Agency for Science, Technology & Research, Jurong Island 627833, Singapore
| | - George J. P. Britovsek
- Department of Chemistry, Imperial College London, Molecular Sciences Research Hub, White City Campus, 80 Wood Lane, London W12 0BZ, United Kingdom
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233
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Weber S, Veiros LF, Kirchner K. Old Concepts, New Application - Additive-Free Hydrogenation of Nitriles Catalyzed by an Air Stable Alkyl Mn(I) Complex. Adv Synth Catal 2019; 361:5412-5420. [PMID: 31875866 PMCID: PMC6916632 DOI: 10.1002/adsc.201901040] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2019] [Revised: 10/16/2019] [Indexed: 01/26/2023]
Abstract
An efficient additive-free manganese-catalyzed hydrogenation of nitriles to primary amines with molecular hydrogen is described. The pre-catalyst, a well-defined bench-stable alkyl bisphosphine Mn(I) complex fac-[Mn(dpre)(CO)3(CH3)] (dpre=1,2-bis(di-n-propylphosphino)ethane), undergoes CO migratory insertion into the manganese-alkyl bond to form acyl complexes which upon hydrogenolysis yields the active coordinatively unsaturated Mn(I) hydride catalyst [Mn(dpre)(CO)2(H)]. A range of aromatic and aliphatic nitriles were efficiently and selectively converted into primary amines in good to excellent yields. The hydrogenation of nitriles proceeds at 100 °C with a catalyst loading of 2 mol % and a hydrogen pressure of 50 bar. Mechanistic insights are provided by means of DFT calculations.
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Affiliation(s)
- Stefan Weber
- Institute of Applied Synthetic ChemistryVienna University of TechnologyGetreidemarkt 9/163-ACA-1060WienAustria
| | - Luis F. Veiros
- Centro de Química Estrutural, Instituto Superior TécnicoUniversidade de LisboaAv. Rovisco Pais No. 11049-001LisboaPortugal
| | - Karl Kirchner
- Institute of Applied Synthetic ChemistryVienna University of TechnologyGetreidemarkt 9/163-ACA-1060WienAustria
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234
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Patra A, Jana S, Samal P. Performance of Tao–Mo Semilocal Functional with rVV10 Dispersion-Correction: Influence of Different Correlation. J Phys Chem A 2019; 123:10582-10593. [DOI: 10.1021/acs.jpca.9b08644] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Abhilash Patra
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Subrata Jana
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
| | - Prasanjit Samal
- School of Physical Sciences, National Institute of Science Education and Research, HBNI, Bhubaneswar 752050, India
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235
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Bennett CK, Bhagat MN, Zhu Y, Yu Y, Raghuraman A, Belowich ME, Nguyen ST, Notestein JM, Broadbelt LJ. Strong Influence of the Nucleophile on the Rate and Selectivity of 1,2-Epoxyoctane Ring Opening Catalyzed by Tris(pentafluorophenyl)borane, B(C6F5)3. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02607] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
| | | | - Youlong Zhu
- Materials Science Institute, School of Chemistry, Sun Yat-Sen University, Guangzhou, Guangdong 510275, P. R. China
| | - Ying Yu
- The Dow Chemical Company, Lake Jackson, Texas 77566, United States
| | - Arjun Raghuraman
- The Dow Chemical Company, Lake Jackson, Texas 77566, United States
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236
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Wang H, Wang Y, Liu S, Mai Y, Zong X, Gao H, Hu R, Jiang X, Yeung Y. Enantioselective Fluorocyclizations Mediated by Amino‐Acid‐Derived Phthalazine. Adv Synth Catal 2019. [DOI: 10.1002/adsc.201900814] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Haitao Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Yongheng Wang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Shenghui Liu
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Yudong Mai
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Xiangxin Zong
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Hao Gao
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Rongbin Hu
- Department of ChemistryThe Chinese University of Hong Kong Shatin, NT, Hong Kong People's Republic of China
| | - Xiaojian Jiang
- International Cooperative Laboratory of Traditional Chinese Medicine Modernization and Innovative Drug Development of Chinese Ministry of Education (MOE), College of PharmacyJinan University Guangzhou 510632 People's Republic of China
| | - Ying‐Yeung Yeung
- Department of ChemistryThe Chinese University of Hong Kong Shatin, NT, Hong Kong People's Republic of China
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237
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Ojeda‐Amador AI, Munarriz J, Alamán‐Valtierra P, Polo V, Puerta‐Oteo R, Jiménez MV, Fernández‐Alvarez FJ, Pérez‐Torrente JJ. Mechanistic Insights on the Functionalization of CO
2
with Amines and Hydrosilanes Catalyzed by a Zwitterionic Iridium Carboxylate‐Functionalized Bis‐NHC Catalyst. ChemCatChem 2019. [DOI: 10.1002/cctc.201901687] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Affiliation(s)
- Ana I. Ojeda‐Amador
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Julen Munarriz
- Departamento de Química Física Instituto de Biocomputación y Física de Sistemas complejos (BIFI) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Pablo Alamán‐Valtierra
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Víctor Polo
- Departamento de Química Física Instituto de Biocomputación y Física de Sistemas complejos (BIFI) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Raquel Puerta‐Oteo
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - M. Victoria Jiménez
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Francisco J. Fernández‐Alvarez
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
| | - Jesús J. Pérez‐Torrente
- Departamento de Química Inorgánica Instituto de Síntesis Química y Catálisis Homogénea (ISQCH) Facultad de CienciasUniversidad de Zaragoza Zaragoza 50009 Spain
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238
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Proppe J, Gugler S, Reiher M. Gaussian Process-Based Refinement of Dispersion Corrections. J Chem Theory Comput 2019; 15:6046-6060. [PMID: 31603673 DOI: 10.1021/acs.jctc.9b00627] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
We employ Gaussian process (GP) regression to adjust for systematic errors in D3-type dispersion corrections. We refer to the associated, statistically improved model as D3-GP. It is trained on differences between interaction energies obtained from PBE-D3(BJ)/ma-def2-QZVPP and DLPNO-CCSD(T)/CBS calculations. We generated a data set containing interaction energies for 1248 molecular dimers, which resemble the dispersion-dominated systems contained in the S66 data set. Our systems represent not only equilibrium structures but also dimers with various relative orientations and conformations at both shorter and longer distances. A reparametrization of the D3(BJ) model based on 66 of these dimers suggests that two of its three empirical parameters, a1 and s8, are zero, whereas a2 = 5.6841 bohr. For the remaining 1182 dimers, we find that this new set of parameters is superior to all previously published D3(BJ) parameter sets. To train our D3-GP model, we engineered two different vectorial representations of (supra-)molecular systems, both derived from the matrix of atom-pairwise D3(BJ) interaction terms: (a) a distance-resolved interaction energy histogram, histD3(BJ), and (b) eigenvalues of the interaction matrix ordered according to their decreasing absolute value, eigD3(BJ). Hence, the GP learns a mapping from D3(BJ) information only, which renders D3-GP-type dispersion corrections comparable to those obtained with the original D3 approach. They improve systematically if the underlying training set is selected carefully. Here, we harness the prediction variance obtained from GP regression to select optimal training sets in an automated fashion. The larger the variance, the more information the corresponding data point may add to the training set. For a given set of molecular systems, variance-based sampling can approximately determine the smallest subset being subjected to reference calculations such that all dispersion corrections for the remaining systems fall below a predefined accuracy threshold. To render the entire D3-GP workflow as efficient as possible, we present an improvement over our variance-based, sequential active-learning scheme [ J. Chem. Theory Comput. 2018 , 14 , 5238 ]. Our refined learning algorithm selects multiple (instead of single) systems that can be subjected to reference calculations simultaneously. We refer to the underlying selection strategy as batchwise variance-based sampling (BVS). BVS-guided active learning is an essential component of our D3-GP workflow, which is implemented in a black-box fashion. Once provided with reference data for new molecular systems, the underlying GP model automatically learns to adapt to these and similar systems. This approach leads overall to a self-improving model (D3-GP) that predicts system-focused and GP-refined D3-type dispersion corrections for any given system of reference data.
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Affiliation(s)
- Jonny Proppe
- Department of Chemistry , and Department of Computer Science , University of Toronto , Toronto , Ontario M5S , Canada.,Laboratory of Physical Chemistry , ETH Zurich , Vladimir-Prelog-Weg 2 , 8093 Zurich , Switzerland
| | - Stefan Gugler
- Laboratory of Physical Chemistry , ETH Zurich , Vladimir-Prelog-Weg 2 , 8093 Zurich , Switzerland
| | - Markus Reiher
- Laboratory of Physical Chemistry , ETH Zurich , Vladimir-Prelog-Weg 2 , 8093 Zurich , Switzerland
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239
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Klein M, Xie X, Burghaus O, Sundermeyer J. Synthesis and Characterization of a N,C,N-Carbodiphosphorane Pincer Ligand and Its Complexes. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00489] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Marius Klein
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Xiulan Xie
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Olaf Burghaus
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
| | - Jörg Sundermeyer
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW), Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35043 Marburg, Germany
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240
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Iron MA, Gropp J. Cost-effective density functional theory (DFT) calculations of equilibrium isotopic fractionation in large organic molecules. Phys Chem Chem Phys 2019; 21:17555-17570. [PMID: 31342034 DOI: 10.1039/c9cp02975c] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The application of stable isotopes to address a wide range of biochemical, microbiological and environmental problems is hindered by the experimental difficulty and the computational cost of determining equilibrium isotopic fractionations (EIF) of large organic molecules. Here, we evaluate the factors that impact the accuracy of computed EIFs and develop a framework for cost-effective and accurate computation of EIFs by density functional theory (DFT). We generated two benchmark databases of experimentally determined EIFs, one for H isotopes and another for the isotopes of the heavy atoms C, N and O. The accuracy of several DFT exchange-correlation functionals in calculating EIFs was then evaluated by comparing the computational results to these experimental datasets. We find that with the def2-TZVP basis set, O3LYP had the lowest mean absolute deviation (21‰ and 3.9‰ for the isotopic fractionation of H and the heavier atoms, respectively), but the GGA/meta-GGA functionals τHCTHD3BJ, τHCTH and HCTH have similar performances (22‰ and 4.1‰, respectively, for τHCTHD3BJ). Leveraging the good performance of computationally efficient functionals, we provide a robust, practical, experimentally validated framework for using DFT to accurately predict EIFs of large organic molecules, including uncertainty estimates.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support, Weizmann Institute of Science, Rehovot, 7610001, Israel.
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241
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Nandy A, Zhu J, Janet JP, Duan C, Getman RB, Kulik HJ. Machine Learning Accelerates the Discovery of Design Rules and Exceptions in Stable Metal–Oxo Intermediate Formation. ACS Catal 2019. [DOI: 10.1021/acscatal.9b02165] [Citation(s) in RCA: 52] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
| | - Jiazhou Zhu
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
| | | | | | - Rachel B. Getman
- Department of Chemical & Biomolecular Engineering, Clemson University, Clemson, South Carolina 29634, United States
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242
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Pollice R, Chen P. A Universal Quantitative Descriptor of the Dispersion Interaction Potential. Angew Chem Int Ed Engl 2019; 58:9758-9769. [DOI: 10.1002/anie.201905439] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2019] [Indexed: 12/21/2022]
Affiliation(s)
- Robert Pollice
- ETH ZürichLaboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich 8093 Zürich Switzerland
| | - Peter Chen
- ETH ZürichLaboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich 8093 Zürich Switzerland
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243
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Torres Ò, Fernàndez M, Díaz-Jiménez À, Pla-Quintana A, Roglans A, Solà M. Examining the Factors That Govern the Regioselectivity in Rhodium-Catalyzed Alkyne Cyclotrimerization. Organometallics 2019. [DOI: 10.1021/acs.organomet.9b00347] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Òscar Torres
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Martí Fernàndez
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Àlex Díaz-Jiménez
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Anna Pla-Quintana
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Anna Roglans
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
| | - Miquel Solà
- Institut de Química Computacional i Catàlisi (IQCC) and Departament de Química, Universitat de Girona, C/Maria Aurèlia Capmany, 69, E-17003 Girona, Catalonia, Spain
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244
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Burganov TI, Monari A, Katsyuba SA, Mamedov VA, Zhukova NA, Assfeld X. 2,3-(Dibenzimidazol-2-yl)quinoxalines: Unexpected Dynamical Effect on Steady-State Electronic Absorption Spectra. J Phys Chem B 2019; 123:5514-5523. [PMID: 31192599 DOI: 10.1021/acs.jpcb.9b00974] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We report on the electronic absorption spectra, conformational behavior, and intra- and intermolecular hydrogen bonds of 2,3-(dibenzimidazol-2-yl)-quinoxaline (DBIQ). The experimentally found strong solvent dependence of the absorption spectra of DBIQ solutions cannot be assigned to electronic excitations of the equilibrium ground-state DBIQ structure. Extended consideration including the nonequilibrium structures within the framework of ab initio molecular dynamics (MD) revealed the importance of torsion molecular motions not covered by the static case. The strong impact of solute-solvent hydrogen bonding on stabilization of these nonequilibrium structures and on conformational composition of DBIQ was demonstrated. A presence of twisted nonplanar geometries along the whole MD trajectory was shown to drastically influence not only energies but also characters of electronic excitations, resulting in a change of local π-π* character in a solution of 1,2-dichloroethane to charge-transfer character in polar dimethylsulfoxide.
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Affiliation(s)
- Timur I Burganov
- FRC Kazan Scientific Center of RAS , Arbuzov Institute of Organic and Physical Chemistry , Arbuzov st. 8 , 420088 Kazan , Russia
| | - Antonio Monari
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
| | - Sergey A Katsyuba
- FRC Kazan Scientific Center of RAS , Arbuzov Institute of Organic and Physical Chemistry , Arbuzov st. 8 , 420088 Kazan , Russia
| | - Vakhid A Mamedov
- FRC Kazan Scientific Center of RAS , Arbuzov Institute of Organic and Physical Chemistry , Arbuzov st. 8 , 420088 Kazan , Russia
| | - Nataliya A Zhukova
- FRC Kazan Scientific Center of RAS , Arbuzov Institute of Organic and Physical Chemistry , Arbuzov st. 8 , 420088 Kazan , Russia
| | - Xavier Assfeld
- Université de Lorraine and CNRS, LPCT UMR 7019 , F-54000 Nancy , France
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245
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Rosales Martínez A, Castro Rodríguez M, Jaraíz M, Enríquez L, Díaz Ojeda E, Rodríguez Maecker RN, Cordobés Carmona F, Pozo Morales L. Reduction of furfural by Mn/2,4,6‐Coll
.
HCl/H
2
O: Mechanistic aspects of this reaction. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.4948] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Antonio Rosales Martínez
- Department of Chemical Engineering, Escuela Politécnica SuperiorUniversity of Sevilla 41011 Sevilla Spain
| | - María Castro Rodríguez
- Department of Chemical Engineering, Escuela Politécnica SuperiorUniversity of Sevilla 41011 Sevilla Spain
| | - Martín Jaraíz
- Department of Electricity and ElectronicsUniversity of Valladolid Valladolid Spain
| | - Lourdes Enríquez
- Department of Electricity and ElectronicsUniversity of Valladolid Valladolid Spain
| | - Emilio Díaz Ojeda
- Department of Chemical Engineering, Escuela Politécnica SuperiorUniversity of Sevilla 41011 Sevilla Spain
| | | | - Felipe Cordobés Carmona
- Department of Chemical Engineering, Escuela Politécnica SuperiorUniversity of Sevilla 41011 Sevilla Spain
| | - Laura Pozo Morales
- Department of Chemical Engineering, Escuela Politécnica SuperiorUniversity of Sevilla 41011 Sevilla Spain
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246
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Pollice R, Chen P. A Universal Quantitative Descriptor of the Dispersion Interaction Potential. Angew Chem Int Ed Engl 2019. [DOI: 10.1002/ange.201905439] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Robert Pollice
- ETH ZürichLaboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich 8093 Zürich Switzerland
| | - Peter Chen
- ETH ZürichLaboratorium für Organische Chemie Vladimir-Prelog-Weg 2, HCI G207/ETH Zürich 8093 Zürich Switzerland
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247
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Manz TA, Chen T, Cole DJ, Limas NG, Fiszbein B. New scaling relations to compute atom-in-material polarizabilities and dispersion coefficients: part 1. Theory and accuracy. RSC Adv 2019; 9:19297-19324. [PMID: 35519408 PMCID: PMC9064874 DOI: 10.1039/c9ra03003d] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2019] [Accepted: 06/03/2019] [Indexed: 11/21/2022] Open
Abstract
Polarizabilities and London dispersion forces are important to many chemical processes. Force fields for classical atomistic simulations can be constructed using atom-in-material polarizabilities and C n (n = 6, 8, 9, 10…) dispersion coefficients. This article addresses the key question of how to efficiently assign these parameters to constituent atoms in a material so that properties of the whole material are better reproduced. We develop a new set of scaling laws and computational algorithms (called MCLF) to do this in an accurate and computationally efficient manner across diverse material types. We introduce a conduction limit upper bound and m-scaling to describe the different behaviors of surface and buried atoms. We validate MCLF by comparing results to high-level benchmarks for isolated neutral and charged atoms, diverse diatomic molecules, various polyatomic molecules (e.g., polyacenes, fullerenes, and small organic and inorganic molecules), and dense solids (including metallic, covalent, and ionic). We also present results for the HIV reverse transcriptase enzyme complexed with an inhibitor molecule. MCLF provides the non-directionally screened polarizabilities required to construct force fields, the directionally-screened static polarizability tensor components and eigenvalues, and environmentally screened C6 coefficients. Overall, MCLF has improved accuracy compared to the TS-SCS method. For TS-SCS, we compared charge partitioning methods and show DDEC6 partitioning yields more accurate results than Hirshfeld partitioning. MCLF also gives approximations for C8, C9, and C10 dispersion coefficients and quantum Drude oscillator parameters. This method should find widespread applications to parameterize classical force fields and density functional theory (DFT) + dispersion methods.
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Affiliation(s)
- Thomas A Manz
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Taoyi Chen
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University Newcastle upon Tyne NE1 7RU UK
| | - Nidia Gabaldon Limas
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
| | - Benjamin Fiszbein
- Department of Chemical & Materials Engineering, New Mexico State University Las Cruces New Mexico 88003-8001 USA
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248
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Shahbaz M, Szalewicz K. Dispersion Energy from Local Polarizability Density. PHYSICAL REVIEW LETTERS 2019; 122:213001. [PMID: 31283348 DOI: 10.1103/physrevlett.122.213001] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2018] [Indexed: 06/09/2023]
Abstract
A simple nonlocal functional for calculation of dispersion energies is proposed. Compared to a similar formula used earlier, we introduced a regularization to remove its singularities and used a dynamic polarizability density similar to those in the so-called van der Waals density functionals. The performance of the new functional is tested on dispersion energies for a set of representative dimers, and it is found that it is significantly more accurate than published nonlocal functionals.
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Affiliation(s)
- Muhammad Shahbaz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, USA
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249
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Wu JI, Eikema Hommes NJ, Lenoir D, Bachrach SM. The quest for a triplet ground‐state alkene: Highly twisted C═C double bonds. J PHYS ORG CHEM 2019. [DOI: 10.1002/poc.3965] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Judy I. Wu
- Department of Chemistry University of Houston Houston TX USA
| | - Nico J.R. Eikema Hommes
- Computer Chemistry Center, Department of Chemistry and Pharmacy Friedrich‐Alexander University Erlangen‐Nürnberg Erlangen Germany
| | - Dieter Lenoir
- Helmholtz Center München, Molecular Exposomics Neuherberg Germany
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Iron MA, Janes T. Evaluating Transition Metal Barrier Heights with the Latest Density Functional Theory Exchange-Correlation Functionals: The MOBH35 Benchmark Database. J Phys Chem A 2019; 123:3761-3781. [PMID: 30973722 DOI: 10.1021/acs.jpca.9b01546] [Citation(s) in RCA: 88] [Impact Index Per Article: 17.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new database of transition metal reaction barrier heights (MOBH35) is presented. Benchmark energies (forward and reverse barriers and reaction energy) are calculated using DLPNO-CCSD(T) extrapolated to the complete basis set limit using a Weizmann-1-like scheme. Using these benchmark energies, the performance of a wide selection of density functional theory (DFT) exchange-correlation functionals, including the latest from the Martin, Truhlar, and Head-Gordon groups, is evaluated. It was found, using the def2-TZVPP basis set, that the ωB97M-V (MAD 1.7 kcal/mol), ωB97M-D3BJ (MAD 1.9 kcal/mol), ωB97X-V (MAD 2.0 kcal/mol), and revTPSS0-D4 (MAD 2.2 kcal/mol) hybrid functionals are recommended. The double-hybrid functionals B2K-PLYP (MAD 1.7 kcal/mol) and revDOD-PBEP86-D4 (MAD 1.8 kcal/mol) also performed well, but this has to be balanced by their increased computational cost.
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Affiliation(s)
- Mark A Iron
- Computational Chemistry Unit, Department of Chemical Research Support , Weizmann Institute of Science , Rehovot , Israel 7610001
| | - Trevor Janes
- Department of Organic Chemistry , Weizmann Institute of Science , Rehovot , Israel 7610001
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