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Gomaa I, Hosny NM, Elhaes H, Ezzat HA, Elmahgary MG, Ibrahim MA. Two-Dimensional MXene as a Promising Adsorbent for Trihalomethanes Removal: A Density-Functional Theory Study. NANOMATERIALS (BASEL, SWITZERLAND) 2024; 14:454. [PMID: 38470784 DOI: 10.3390/nano14050454] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/19/2023] [Revised: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 03/14/2024]
Abstract
This groundbreaking research delves into the intricate molecular interactions between MXene and trihalomethanes (THs) through a comprehensive theoretical study employing density-functional theory (DFT). Trihalomethanes are common carcinogenic chlorination byproducts found in water sanitation systems. This study focuses on a pristine MXene [Mn+1·Xn] monolayer and its various terminal [Tx] functional groups [Mn+1·XnTx], strategically placed on the surface for enhanced performance. Our investigation involves a detailed analysis of the adsorption energies of THs on different MXene types, with the MXene-Cl layer emerging as the most compatible variant. This specific MXene-Cl layer exhibits remarkable properties, including a total dipole moment (TDM) of 12.443 Debye and a bandgap of 0.570 eV, achieved through meticulous geometry optimization and computational techniques. Notably, THs such as trichloromethane (CHCl3), bromide-chloromethane (CHBrCl2), and dibromochloromethane (CHBr2Cl) demonstrate the highest TDM values, indicating substantial changes in electronic and optical parameters, with TDM values of 16.363, 15.998, and 16.017 Debye, respectively. These findings highlight the potential of the MXene-Cl layer as an effective adsorbent and detector for CHF3, CHClF2, CHCl3, CHBrCl2, and CHBr2Cl. Additionally, we observe a proportional increase in the TDM and bandgap energy, indicative of conductivity, for various termination atom combinations, such as Mxene-O-OH, Mxene-O-F, Mxene-O-Cl, Mxene-OH-F, Mxene-F-Cl, and Mxene-OH-Cl, with bandgap energies measured at 0.734, 0.940, 1.120, 0.835, and 0.927 eV, respectively. Utilizing DFT, we elucidate the adsorption energies of THs on different MXene surfaces. Our results conclusively demonstrate the significant influence of the termination atom nature and quantity on MXene's primitive TDM value. This research contributes to our understanding of MXene-THs interactions, offering promising avenues for the development of efficient adsorbents and detectors for THs. Ultimately, these advancements hold the potential to revolutionize water sanitation practices and enhance environmental safety.
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Affiliation(s)
- Islam Gomaa
- Nanotechnology Research Centre (NTRC), The British University in Egypt (BUE), Suez Desert Road, El-Sherouk 11837, Egypt
- Department of Chemistry, Faculty of Science, Port Said University, Port Said 42522, Egypt
| | - Nasser Mohammed Hosny
- Department of Chemistry, Faculty of Science, Port Said University, Port Said 42522, Egypt
| | - Hanan Elhaes
- Physics Department, Faculty of Women for Arts, Science and Education, Ain Shams University, Cairo 11757, Egypt
| | - Hend A Ezzat
- Nano Unit, Space Lab, Solar and Space Research Department, National Research Institute of Astronomy and Geophysics (NRIAG), Helwan 11421, Egypt
| | - Maryam G Elmahgary
- Chemical Engineering Department, The British University in Egypt (BUE), El Sherouk 11837, Egypt
- Department of Chemical Engineering, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, MA 02139, USA
| | - Medhat A Ibrahim
- Spectroscopy Department, National Research Centre, 33 El-Bohouth St., Dokki 12622, Egypt
- Molecular Spectroscopy and Modeling Laboratory, Centre of Excellence for Advanced Science, National Research Centre, 33 El-Bohouth St., Dokki 12622, Egypt
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2
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Determan JJ, Wilson AK. Correlation consistent basis sets designed for density functional theory: Third-row atoms (Ga-Br). J Chem Phys 2024; 160:084105. [PMID: 38385513 DOI: 10.1063/5.0176964] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 01/02/2024] [Indexed: 02/23/2024] Open
Abstract
The correlation consistent basis sets (cc-pVnZ with n = D, T, Q, 5) for the Ga-Br elements have been redesigned, tuning the sets for use for density functional approximations. Steps to redesign these basis sets for an improved correlation energy recovery and efficiency include truncation of higher angular momentum functions, recontraction of basis set coefficients, and reoptimization of basis set exponents. These redesigned basis sets are compared with conventional cc-pVnZ basis sets and other basis sets, which are, in principle, designed to achieve systematic improvement with respect to increasing basis set size. The convergence of atomic energies, bond lengths, bond dissociation energies, and enthalpies of formation to the Kohn-Sham limit is improved relative to other basis sets where convergence to the Kohn-Sham limit is typically not observed.
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Affiliation(s)
- John J Determan
- Department of Chemistry, Western Illinois University, Macomb, Illinois 61455, USA
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824, USA
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3
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Karuth A, Casanola-Martin GM, Lystrom L, Sun W, Kilin D, Kilina S, Rasulev B. Combined Machine Learning, Computational, and Experimental Analysis of the Iridium(III) Complexes with Red to Near-Infrared Emission. J Phys Chem Lett 2024; 15:471-480. [PMID: 38190332 DOI: 10.1021/acs.jpclett.3c02533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2024]
Abstract
Various coordination complexes have been the subject of experimental and theoretical studies in recent decades because of their fascinating photophysical properties. In this work, a combined experimental and computational approach was applied to investigate the optical properties of monocationic Ir(III) complexes. An interpretative machine learning-based quantitative structure-property relationship (ML/QSPR) model was successfully developed that could reliably predict the emission wavelength of the Ir(III) complexes and provide a foundation for the theoretical evaluation of the optical properties of Ir(III) complexes. A hypothesis was proposed to explain the differences in the emission wavelengths between structurally different individual Ir(III) complexes. The efficacy of the developed model was demonstrated by high R2 values of 0.84 and 0.87 for the training and test sets, respectively. It is worth noting that a relationship between the N-N distance in the diimine ligands of the Ir(III) complexes and emission wavelengths is detected. This effect is most probably associated with a degree of distortion in the octahedral geometry of the complexes, resulting in a perturbed ligand field. This combined experimental and computational approach shows great potential for the rational design of new Ir(III) complexes with the desired optical properties. Moreover, the developed methodology could be extended to other transition-metal complexes.
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Affiliation(s)
- Anas Karuth
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Gerardo M Casanola-Martin
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Levi Lystrom
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Wenfang Sun
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
- Department of Chemistry and Biochemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Dmitri Kilin
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Svetlana Kilina
- Department of Chemistry and Biochemistry, North Dakota State University, Fargo, North Dakota 58108, United States
| | - Bakhtiyor Rasulev
- Coatings and Polymeric Materials, North Dakota State University, Fargo, North Dakota 58108, United States
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4
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Rajabi A, Grotjahn R, Rappoport D, Furche F. A DFT perspective on organometallic lanthanide chemistry. Dalton Trans 2024; 53:410-417. [PMID: 38013481 DOI: 10.1039/d3dt03221c] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Computational studies of the coordination chemistry and bonding of lanthanides have grown in recent decades as the need for understanding the distinct physical, optical, and magnetic properties of these compounds increased. Density functional theory (DFT) methods offer a favorable balance of computational cost and accuracy in lanthanide chemistry and have helped to advance the discovery of novel oxidation states and electronic configurations. This Frontier article examines the scope and limitations of DFT in interpreting structural and spectroscopic data of low-valent lanthanide complexes, elucidating periodic trends, and predicting their properties and reactivity, presented through selected examples.
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Affiliation(s)
- Ahmadreza Rajabi
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA.
| | - Robin Grotjahn
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA.
| | - Dmitrij Rappoport
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA.
| | - Filipp Furche
- Department of Chemistry, University of California Irvine, 1102 Natural Sciences II, Irvine, CA 92697-2025, USA.
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5
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Almeida NMS, Bali SK, James D, Wang C, Wilson AK. Binding of Per- and Polyfluoroalkyl Substances (PFAS) to the PPARγ/RXRα-DNA Complex. J Chem Inf Model 2023; 63:7423-7443. [PMID: 37990410 DOI: 10.1021/acs.jcim.3c01384] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2023]
Abstract
Nuclear receptors are the fundamental building blocks of gene expression regulation and the focus of many drug targets. While binding to DNA, nuclear receptors act as transcription factors, governing a multitude of functions in the human body. Peroxisome proliferator-activator receptor γ (PPARγ) and the retinoid X receptor α (RXRα) form heterodimers with unique properties and have a primordial role in insulin sensitization. This PPARγ/RXRα heterodimer has been shown to be impacted by per- and polyfluoroalkyl substances (PFAS) and linked to a variety of significant health conditions in humans. Herein, a selection of the most common PFAS (legacy and emerging) was studied utilizing molecular dynamics simulations for PPARγ/RXRα. The local and global structural effects of PFAS binding on the known ligand binding pockets of PPARγ and RXRα as well as the DNA binding domain (DBD) of RXRα were inspected. The binding free energies were predicted computationally and were compared between the different binding pockets. In addition, two electronic structure approaches were utilized to model the interaction of PFAS within the DNA binding domain, density functional theory (DFT) and domain-based pair natural orbital coupled cluster with perturbative triples (DLPNO-CCSD(T)) approaches, with implicit solvation. Residue decomposition and hydrogen-bonding analysis were also performed, detailing the role of prominent residues in molecular recognition. The role of l-carnitine is explored as a potential in vivo remediation strategy for PFAS interaction with the PPARγ/RXRα heterodimer. In this work, it was found that PFAS can bind and act as agonists for all of the investigated pockets. For the first time in the literature, PFAS are postulated to bind to the DNA binding domain in a nonspecific manner. In addition, for the PPARγ ligand binding domain, l-carnitine shows promise in replacing smaller PFAS from the pocket.
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Affiliation(s)
- Nuno M S Almeida
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Semiha Kevser Bali
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Deepak James
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Cong Wang
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48864, United States
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6
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Hostaš J, Pérez-Becerra KO, Calaminici P, Barrios-Herrera L, Lourenço MP, Tchagang A, Salahub DR, Köster AM. How important is the amount of exact exchange for spin-state energy ordering in DFT? Case study of molybdenum carbide cluster, Mo4C2. J Chem Phys 2023; 159:184301. [PMID: 37947508 DOI: 10.1063/5.0169409] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2023] [Accepted: 10/23/2023] [Indexed: 11/12/2023] Open
Abstract
Since the form of the exact functional in density functional theory is unknown, we must rely on density functional approximations (DFAs). In the past, very promising results have been reported by combining semi-local DFAs with exact, i.e. Hartree-Fock, exchange. However, the spin-state energy ordering and the predictions of global minima structures are particularly sensitive to the choice of the hybrid functional and to the amount of exact exchange. This has been already qualitatively described for single conformations, reactions, and a limited number of conformations. Here, we have analyzed the mixing of exact exchange in exchange functionals for a set of several hundred isomers of the transition metal carbide, Mo4C2. The analysis of the calculated energies and charges using PBE0-type functional with varying amounts of exact exchange yields the following insights: (1) The sensitivity of spin-energy splitting is strongly correlated with the amount of exact exchange mixing. (2) Spin contamination is exacerbated when correlation is omitted from the exchange-correlation functional. (3) There is not one ideal value for the exact exchange mixing which can be used to parametrize or choose among the functionals. Calculated energies and electronic structures are influenced by exact exchange at a different magnitude within a given distribution; therefore, to extend the application range of hybrid functionals to the full periodic table the spin-energy splitting energies should be investigated.
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Affiliation(s)
- Jiří Hostaš
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Kevin O Pérez-Becerra
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Patrizia Calaminici
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
| | - Lizandra Barrios-Herrera
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Maicon Pierre Lourenço
- Departamento de Química e Física - Centro de Ciências Exatas, Naturais e da Saúde - CCENS - Universidade Federal do Espírito Santo, 29500-000 Alegre, Espírito Santo, Brazil
| | - Alain Tchagang
- Digital Technologies Research Centre, National Research Council of Canada, 1200 Montréal Road, Ottawa, Ontario K1A 0R6, Canada
| | - Dennis R Salahub
- Department of Chemistry, CMS - Centre for Molecular Simulation, IQST - Institute for Quantum Science and Technology, Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta T2N 1N4, Canada
| | - Andreas M Köster
- Departamento de Química, Cinvestav, Avenida Instituto Politécnico Nacional 2508, A.P. 14-740, CDMX C.P. 07360, Mexico
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7
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Reyna-Luna J, Soriano-Agueda L, Vera CJ, Franco-Pérez M. Insights into the coordination chemistry of antineoplastic doxorubicin with 3d-transition metal ions Zn 2+, Cu 2+, and VO 2+: a study using well-calibrated thermodynamic cycles and chemical interaction quantum chemistry models. J Comput Aided Mol Des 2023:10.1007/s10822-023-00506-4. [PMID: 37245168 DOI: 10.1007/s10822-023-00506-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2023] [Accepted: 05/19/2023] [Indexed: 05/29/2023]
Abstract
We present a computational strategy based on thermodynamic cycles to predict and describe the chemical equilibrium between the 3d-transition metal ions Zn2+, Cu2+, and VO2+ and the widely used antineoplastic drug doxorubicin. Our method involves benchmarking a theoretical protocol to compute gas-phase quantities using DLPNO Coupled-Cluster calculations as reference, followed by estimating solvation contributions to the reaction Gibbs free energies using both explicit partial (micro)solvation steps for charged solutes and neutral coordination complexes, as well as a continuum solvation procedure for all solutes involved in the complexation process. We rationalized the stability of these doxorubicin-metal complexes by inspecting quantities obtained from the topology of their electron densities, particularly the bond critical points and non-covalent interaction index. Our approach allowed us to identify representative species in solution phase, infer the most likely complexation process for each case, and identify key intramolecular interactions involved in the stability of these compounds. To the best of our knowledge, this is the first study reporting thermodynamic constants for the complexation of doxorubicin with transition metal ions. Unlike other methods, our procedure is computationally affordable for medium-sized systems and provides valuable insights even with limited experimental data. Furthermore, it can be extended to describe the complexation process between 3d-transition metal ions and other bioactive ligands.
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Affiliation(s)
- Julieta Reyna-Luna
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México
| | - Luis Soriano-Agueda
- Donostia International Physics Center (DIPC), 20018, Donostia, Euskadi, Spain
| | - Christiaan Jardinez Vera
- Laboratorio de Modelado y Simulación Computacional en Nanomedicina, Escuela Superior de Apan, Universidad Autónoma del Estado de Hidalgo, Carretera Apan-Calpulalpan S/N, Colonia, 43920, Chimalpa Tlalayote, Hgo, México
| | - Marco Franco-Pérez
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, Cd. Universitaria, 04510, Ciudad de Mexico, México.
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8
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Pangh A, Esrafili MD, Nejad MR. A DFT investigation of CO and NO adsorption on Cu5Sc and Cu6Sc+ metallic clusters. COMPUT THEOR CHEM 2022. [DOI: 10.1016/j.comptc.2022.113657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Zhang NX, Wang C, Wu Q, Lan J, Chai Z, Shi W. Highly stable actinide(III) complexes supported by doubly aromatic ligands. Phys Chem Chem Phys 2022; 24:5921-5928. [DOI: 10.1039/d1cp05058c] [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
Owing to the electron-deficient nature of boron atom, the structures and properties of boron clusters can be enriched by doping various metal atoms, including lanthanide metal atoms. Nevertheless, the viability...
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10
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Zhong X, Zhou S, Ao J, Guo A, Xiao Q, Huang Y, Zhu W, Cai H, Ishiwata A, Ito Y, Liu XW, Ding F. Zinc(II) Iodide-Directed β-Mannosylation: Reaction Selectivity, Mode, and Application. J Org Chem 2021; 86:16901-16915. [PMID: 34797079 DOI: 10.1021/acs.joc.1c02091] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A direct, efficient, and versatile glycosylation methodology promises the systematic synthesis of oligosaccharides and glycoconjugates in a streamlined fashion like the synthesis of medium to long-chain nucleotides and peptides. The development of a generally applicable approach for the construction of 1,2-cis-glycosidic bond with controlled stereoselectivity remains a major challenge, especially for the synthesis of β-mannosides. Here, we report a direct mannosylation strategy mediated by ZnI2, a mild Lewis acid, for the highly stereoselective construction of 1,2-cis-β linkages employing easily accessible 4,6-O-tethered mannosyl trichloroacetimidate donors. The versatility and effectiveness of this strategy were demonstrated with successful β-mannosylation of a wide variety of alcohol acceptors, including complex natural products, amino acids, and glycosides. Through iteratively performing ZnI2-mediated mannosylation with the chitobiosyl azide acceptor followed by site-selective deprotection of the mannosylation product, the novel methodology enables the modular synthesis of the key intermediate trisaccharide with Man-β-(1 → 4)-GlcNAc-β-(1 → 4)-GlcNAc linkage for N-glycan synthesis. Theoretical investigations with density functional theory calculations delved into the mechanistic details of this β-selective mannosylation and elucidated two zinc cations' essential roles as the activating agent of the donor and the principal mediator of the cis-directing intermolecular interaction.
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Affiliation(s)
- Xuemei Zhong
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Siai Zhou
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Jiaming Ao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Aoxin Guo
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore 637371, Singapore
| | - Qian Xiao
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Yan Huang
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Wanmeng Zhu
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Hui Cai
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
| | - Akihiro Ishiwata
- RIKEN Cluster for Pioneering Research, Wako, Saitama 3510198, Japan
| | - Yukishige Ito
- RIKEN Cluster for Pioneering Research, Wako, Saitama 3510198, Japan.,Graduate School of Science, Osaka University, Toyonaka, Osaka 5600043, Japan
| | - Xue-Wei Liu
- Division of Chemistry and Biological Chemistry, Nanyang Technological University, Singapore 637371, Singapore
| | - Feiqing Ding
- School of Pharmaceutical Sciences (Shenzhen), Sun Yat-sen University, Shenzhen 518107, China
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11
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Golub P, Antalik A, Veis L, Brabec J. Machine Learning-Assisted Selection of Active Spaces for Strongly Correlated Transition Metal Systems. J Chem Theory Comput 2021; 17:6053-6072. [PMID: 34570505 DOI: 10.1021/acs.jctc.1c00235] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Active space quantum chemical methods could provide very accurate description of strongly correlated electronic systems, which is of tremendous value for natural sciences. The proper choice of the active space is crucial but a nontrivial task. In this article, we present a neural network-based approach for automatic selection of active spaces, focused on transition metal systems. The training set has been formed from artificial systems composed of one transition metal and various ligands, on which we have performed the density matrix renormalization group and calculated the single-site entropy. On the selected set of systems, ranging from small benchmark molecules up to larger challenging systems involving two metallic centers, we demonstrate that our machine learning models could predict the active space orbitals with reasonable accuracy. We also tested the transferability on out-of-the-model systems, including bimetallic complexes and complexes with ligands, which were not involved in the training set. Also, we tested the correctness of the automatically selected active spaces on a Fe(II)-porphyrin model, where we studied the lowest states at the DMRG level and compared the energy difference between spin states or the energy difference between conformations of ferrocene with recent studies.
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Affiliation(s)
- Pavlo Golub
- J. Heyrovsky Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Andrej Antalik
- J. Heyrovsky Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Libor Veis
- J. Heyrovsky Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Prague 8, Czech Republic
| | - Jiri Brabec
- J. Heyrovsky Institute of Physical Chemistry, v.v.i., Academy of Sciences of the Czech Republic, Dolejskova 3, 18223 Prague 8, Czech Republic
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12
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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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13
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Brakestad A, Wind P, Jensen SR, Frediani L, Hopmann KH. Multiwavelets applied to metal-ligand interactions: Energies free from basis set errors. J Chem Phys 2021; 154:214302. [PMID: 34240981 DOI: 10.1063/5.0046023] [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
Transition metal-catalyzed reactions invariably include steps where ligands associate or dissociate. In order to obtain reliable energies for such reactions, sufficiently large basis sets need to be employed. In this paper, we have used high-precision multiwavelet calculations to compute the metal-ligand association energies for 27 transition metal complexes with common ligands, such as H2, CO, olefins, and solvent molecules. By comparing our multiwavelet results to a variety of frequently used Gaussian-type basis sets, we show that counterpoise corrections, which are widely employed to correct for basis set superposition errors, often lead to underbinding. Additionally, counterpoise corrections are difficult to employ when the association step also involves a chemical transformation. Multiwavelets, which can be conveniently applied to all types of reactions, provide a promising alternative for computing electronic interaction energies free from any basis set errors.
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Affiliation(s)
- Anders Brakestad
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Peter Wind
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stig Rune Jensen
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Luca Frediani
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
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14
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Kaviani S, Shahab S, Sheikhi M, Khaleghian M, Al Saud S. Characterization of the binding affinity between some anti-Parkinson agents and Mn2+, Fe3+ and Zn2+ metal ions: A DFT insight. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.108582] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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15
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Dub PA, Tkachenko NV, Vyas VK, Wills M, Smith JS, Tretiak S. Enantioselectivity in the Noyori–Ikariya Asymmetric Transfer Hydrogenation of Ketones. Organometallics 2021. [DOI: 10.1021/acs.organomet.1c00201] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Pavel A. Dub
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Nikolay V. Tkachenko
- Chemistry Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322, United States
| | - Vijyesh K. Vyas
- Department of Chemistry, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Martin Wills
- Department of Chemistry, The University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Justin S. Smith
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
| | - Sergei Tretiak
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, United States
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16
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Patel P, Wilson AK. Computational chemistry considerations in catalysis: Regioselectivity and metal-ligand dissociation. Catal Today 2020. [DOI: 10.1016/j.cattod.2020.07.057] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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17
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Bao JL, Welch BK, Ulusoy IS, Zhang X, Xu X, Wilson AK, Truhlar DG. Predicting Bond Dissociation Energies and Bond Lengths of Coordinatively Unsaturated Vanadium-Ligand Bonds. J Phys Chem A 2020; 124:9757-9770. [PMID: 33180508 DOI: 10.1021/acs.jpca.0c06519] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Understanding the electronic structure of coordinatively unsaturated transition-metal compounds and predicting their physical properties are of great importance for catalyst design. Bond dissociation energy De and bond length re are two of the fundamental quantities for which good predictions are important for a successful design strategy. In the present work, recent experimentally measured bond energies and bond lengths of VX diatomic molecules (X = C, N, S) are used as a gauge to consider the utility of a number of electronic structure methods. Single-reference methods are one focus because of their efficiency and utility in practical calculations, and multireference configuration interaction (MRCISD) methods and a composite coupled cluster (CCC) method are a second focus because of their potential high accuracy. The comparison is especially challenging because of the large multireference M diagnostics of these molecules, in the range 0.15-0.19. For the single-reference methods, Kohn-Sham density functional theory (KS-DFT) has been tested with a variety of approximate exchange-correlation functionals. Of these, MOHLYP provides the bond dissociation energies in best agreement with experiments, and BLYP provides the bond lengths that are in best agreement with experiments; but by requiring good performance for both the De and re of the vanadium compounds, MOHLYP, MN12-L, MGGA_MS1, MGGA_MS0, O3LYP, and M06-L are the most highly recommended functionals. The CCC calculations include up to connected pentuple excitations for the valence electrons and up to connected quadruple excitations for the core-valence terms; this results in highly accurate dissociation energies and good bond lengths. Averaged over the three molecules, the mean unsigned deviation of CCC bond energies from experimental ones is only 0.4 kcal/mol, demonstrating excellent convergence of theory and experiments.
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Affiliation(s)
- Junwei Lucas Bao
- Department of Chemistry, Boston College, Chestnut Hill, Massachusetts 02467, United States
| | - Bradley K Welch
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Inga S Ulusoy
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States.,Theoretical Chemistry, Institute of Physical Chemistry, Heidelberg University, Im Neuenheimer Feld 229, Heidelberg 69120, Germany
| | - Xin Zhang
- State Key Laboratory of Chemical Resource Engineering, Beijing Advanced Innovation Center for Soft Matter Science and Engineering, Beijing University of Chemical Technology, Beijing 100029, People's Republic of China.,Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Xuefei Xu
- Center for Combustion Energy, Department of Energy and Power Engineering, and Key Laboratory for Thermal Science and Power Engineering of Ministry of Education, Tsinghua University, Beijing 100084, China
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, 578 S Shaw Lane, East Lansing, Michigan 48824-1322, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, Inorganometallic Catalyst Design Center, and Minnesota Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
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18
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Patel P, Wang J, Wilson AK. Prediction of pK a s of Late Transition-Metal Hydrides via a QM/QM Approach. J Comput Chem 2020; 41:171-183. [PMID: 31495951 DOI: 10.1002/jcc.26057] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2019] [Accepted: 08/04/2019] [Indexed: 11/09/2022]
Abstract
Three implicit solvation models, the conductor-like polarizable continuum model (C-PCM), the conductor-like screening model (COSMO), and universal implicit solvent model (SMD), combined with a hybrid two layer QM/QM approach (ONIOM), were utilized to calculate the pKa values, using a direct thermodynamic scheme, of a set of Group 10 transition metal (TM) hydrides in acetonitrile. To obtain the optimal combination of quantum methods for ONIOM calculations with implicit solvation models, the influence of factors, such as the choice of density functional and basis set, the atomic radii used to build a cavity in the solvent, and the size of the model system in an ONIOM scheme, was examined. Additionally, the impact of Grimme's empirical dispersion correction and exact exchange was also investigated. The results were calibrated by experimental data. This investigation provides insight about effective models for the prediction of thermodynamic properties of TM-containing complexes with bulky ligands. © 2019 Wiley Periodicals, Inc.
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Affiliation(s)
- Prajay Patel
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824-1322
| | - Jiaqi Wang
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Beijing Forestry University, Beijing, China, 100083
| | - Angela K Wilson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas, 76203-5017.,Department of Chemistry, Michigan State University, East Lansing, Michigan, 48824-1322
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19
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Khan SN, Miliordos E. Methane to Methanol Conversion Facilitated by Transition-Metal Methyl and Methoxy Units: The Cases of FeCH3+ and FeOCH3+. J Phys Chem A 2019; 123:5590-5599. [DOI: 10.1021/acs.jpca.9b04005] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Shahriar N. Khan
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
| | - Evangelos Miliordos
- Department of Chemistry and Biochemistry, Auburn University, Auburn, Alabama 36849-5312, United States
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20
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Francés‐Monerris A, Gros PC, Assfeld X, Monari A, Pastore M. Toward Luminescent Iron Complexes: Unravelling the Photophysics by Computing Potential Energy Surfaces. CHEMPHOTOCHEM 2019. [DOI: 10.1002/cptc.201900100] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
- Antonio Francés‐Monerris
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Philippe C. Gros
- Laboratoire Lorrain de Chimie Moléculaire (L2CM)Université de Lorraine, CNRS 54000 Nancy France
| | - Xavier Assfeld
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Antonio Monari
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
| | - Mariachiara Pastore
- Laboratoire de Physique et Chimie Théoriques (LPCT)Université de Lorraine, CNRS 54000 Nancy France
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21
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Sampathkumar S, Paranthaman S. Performance of density functionals for the structure and energetics of (M–O)0,± (M=Al, Si, Sc–Zn). MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1557331] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Suresh Sampathkumar
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil, India
| | - Selvarengan Paranthaman
- Department of Physics and International Research Centre, Kalasalingam Academy of Research and Education (Deemed to be University), Krishnankoil, India
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22
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Saranya V, Shankar R, Vijayakumar S. Structural exploration of viral matrix protein 40 interaction with the transition metal ions (Ag+ and Cu2+). J Biomol Struct Dyn 2018; 37:2875-2896. [DOI: 10.1080/07391102.2018.1498803] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Affiliation(s)
- V. Saranya
- Department of Physics, Bharathiar University, Coimbatore, India
| | - R. Shankar
- Department of Physics, Bharathiar University, Coimbatore, India
| | - S. Vijayakumar
- Department of Medical Physics, Bharathiar University, Coimbatore, India
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23
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Jara-Cortés J, Landeros-Rivera B, Hernández-Trujillo J. Unveiling the role of intra and interatomic interactions in the energetics of reaction schemes: a quantum chemical topology analysis. Phys Chem Chem Phys 2018; 20:27558-27570. [PMID: 30371704 DOI: 10.1039/c8cp03775b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
In this work we present a detailed analysis of selected reaction schemes in terms of the atomic components of the electronic energy defined by the quantum theory of atoms in molecules and the interacting quantum atoms method. The aim is to provide an interpretation tool for the energy change involved in a chemical reaction by means of the atomic and interaction contributions to the energies of the molecules involved. Ring strain in cyclic alkanes, the resonance energy of aromatic and antiaromatic molecules, local aromaticity in polycyclic aromatic hydrocarbons, intermolecular bonding in hydrogen fluoride clusters, and hydration of d-block metal dications were selected for the study. It was found that in addition to the changes in the strong C-C interactions in the carbon skeleton of the organic molecular rings, other contributions not usually considered to be important such as those between C and H atoms (either bonded or not) need to be considered in order to account for the net energy changes. The analysis unveils the role of the ionic and covalent contributions to the hydrogen bonding in HF clusters and the energetic origin and extent of cooperative effects involved. Moreover, the "double-hump" behavior observed for the hydration energy trend of [M(H2O)6]2+ complexes is explained in terms of the deformation energy of the metal cation and the increasingly covalent metal-water interactions. In addition, proper comparisons with the description provided by other methodologies are briefly discussed. The topological approach proposed in this contribution proves to be useful for the description of energy changes of apposite reaction schemes in chemically meaningful terms.
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Affiliation(s)
- Jesús Jara-Cortés
- Departamento de Física y Química Teórica, Facultad de Química, UNAM, México City, 04510, Mexico.
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24
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Liang G, Hollis TK, Webster CE. Computational Analysis of the Intramolecular Oxidative Amination of an Alkene Catalyzed by the Extreme π-Loading N-Heterocyclic Carbene Pincer Tantalum(V) Bis(imido) Complex. Organometallics 2018. [DOI: 10.1021/acs.organomet.8b00097] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Guangchao Liang
- Department of Chemistry and Center for Computational Sciences, Mississippi State University, Mississippi State, Mississippi 39762-9573, United States
| | - T. Keith Hollis
- Department of Chemistry and Center for Computational Sciences, Mississippi State University, Mississippi State, Mississippi 39762-9573, United States
| | - Charles Edwin Webster
- Department of Chemistry and Center for Computational Sciences, Mississippi State University, Mississippi State, Mississippi 39762-9573, United States
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25
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Husch T, Freitag L, Reiher M. Calculation of Ligand Dissociation Energies in Large Transition-Metal Complexes. J Chem Theory Comput 2018; 14:2456-2468. [PMID: 29595973 DOI: 10.1021/acs.jctc.8b00061] [Citation(s) in RCA: 52] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
The accurate calculation of ligand dissociation (or equivalently, ligand binding) energies is crucial for computational coordination chemistry. Despite its importance, obtaining accurate ab initio reference data is difficult, and density-functional methods of uncertain reliability are chosen for feasibility reasons. Here, we consider advanced coupled-cluster and multiconfigurational approaches to reinvestigate our WCCR10 set of 10 gas-phase ligand dissociation energies [ J. Chem. Theory Comput. 2014, 10, 3092]. We assess the potential multiconfigurational character of all molecules involved in these reactions with a multireference diagnostic [ Mol. Phys. 2017, 115, 2110] in order to determine where single-reference coupled-cluster approaches can be applied. For some reactions of the WCCR10 set, large deviations of density-functional results including semiclassical dispersion corrections from experimental reference data had been observed. This puzzling observation deserves special attention here, and we tackle the issue (i) by comparing to ab initio data that comprise dispersion effects on a rigorous first-principles footing and (ii) by a comparison of density-functional approaches that model dispersion interactions in various ways. For two reactions, species exhibiting nonnegligible static electron correlation were identified. These two reactions represent hard problems for electronic structure methods and also for multireference perturbation theories. However, most of the ligand dissociation reactions in WCCR10 do not exhibit static electron correlation effects, and hence, we may choose standard single-reference coupled-cluster approaches to compare with density-functional methods. For WCCR10, the Minnesota M06-L functional yielded the smallest mean absolute deviation of 13.2 kJ mol-1 out of all density functionals considered (PBE, BP86, BLYP, TPSS, M06-L, PBE0, B3LYP, TPSSh, and M06-2X) without additional dispersion corrections in comparison to the coupled-cluster results, and the PBE0-D3 functional produced the overall smallest mean absolute deviation of 4.3 kJ mol-1. The agreement of density-functional results with coupled-cluster data increases significantly upon inclusion of any type of dispersion correction. It is important to emphasize that different density-functional schemes available for this purpose perform equally well. The coupled-cluster dissociation energies, however, deviate from experimental results on average by 30.3 kJ mol-1. Possible reasons for these deviations are discussed.
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Affiliation(s)
- Tamara Husch
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Leon Freitag
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
| | - Markus Reiher
- Laboratorium für Physikalische Chemie , ETH Zürich , Vladimir-Prelog-Weg 2 , 8093 Zürich , Switzerland
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26
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Hu L, Chen K, Chen H. Modeling σ-Bond Activations by Nickel(0) Beyond Common Approximations: How Accurately Can We Describe Closed-Shell Oxidative Addition Reactions Mediated by Low-Valent Late 3d Transition Metal? J Chem Theory Comput 2017; 13:4841-4853. [PMID: 28881134 DOI: 10.1021/acs.jctc.7b00708] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Accurate modelings of reactions involving 3d transition metals (TMs) are very challenging to both ab initio and DFT approaches. To gain more knowledge in this field, we herein explored typical σ-bond activations of H-H, C-H, C-Cl, and C-C bonds promoted by nickel(0), a low-valent late 3d TM. For the key parameters of activation energy (ΔE‡) and reaction energy (ΔER) for these reactions, various issues related to the computational accuracy were systematically investigated. From the scrutiny of convergence issue with one-electron basis set, augmented (A) basis functions are found to be important, and the CCSD(T)/CBS level with complete basis set (CBS) limit extrapolation based on augmented double-ζ and triple-ζ basis pair (ADZ and ATZ), which produces deviations below 1 kcal/mol from the reference, is recommended for larger systems. As an alternative, the explicitly correlated F12 method can accelerate the basis set convergence further, especially after its CBS extrapolations. Thus, the CCSD(T)-F12/CBS(ADZ-ATZ) level with computational cost comparable to the conventional CCSD(T)/CBS(ADZ-ATZ) level, is found to reach the accuracy of the conventional CCSD(T)/A5Z level, which produces deviations below 0.5 kcal/mol from the reference, and is also highly recommendable. Scalar relativistic effects and 3s3p core-valence correlation are non-negligible for achieving chemical accuracy of around 1 kcal/mol. From the scrutiny of convergence issue with the N-electron basis set, in comparison with the reference CCSDTQ result, CCSD(T) is found to be able to calculate ΔE‡ quite accurately, which is not true for the ΔER calculations. Using highest-level CCSD(T) results of ΔE‡ in this work as references, we tested 18 DFT methods and found that PBE0 and CAM-B3LYP are among the three best performing functionals, irrespective of DFT empirical dispersion correction. With empirical dispersion correction included, ωB97XD is also recommendable due to its improved performance.
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Affiliation(s)
- Lianrui Hu
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Kejuan Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
| | - Hui Chen
- Beijing National Laboratory for Molecular Sciences (BNLMS), CAS Key Laboratory of Photochemistry, CAS Research/Education Center for Excellence in Molecular Sciences, Institute of Chemistry, Chinese Academy of Sciences , Beijing 100190, China
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27
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Determan JJ, Poole K, Scalmani G, Frisch MJ, Janesko BG, Wilson AK. Comparative Study of Nonhybrid Density Functional Approximations for the Prediction of 3d Transition Metal Thermochemistry. J Chem Theory Comput 2017; 13:4907-4913. [PMID: 28877436 DOI: 10.1021/acs.jctc.7b00809] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The utility of several nonhybrid density functional approximations (DFAs) is considered for the prediction of gas phase enthalpies of formation for a large set of 3d transition metal-containing molecules. Nonhybrid DFAs can model thermochemical values for 3d transition metal-containing molecules with accuracy comparable to that of hybrid functionals. The GAM-generalized gradient approximation (GGA); the TPSS, M06-L, and MN15-L meta-GGAs; and the Rung 3.5 PBE+ΠLDA(s) DFAs all give root-mean-square deviations below that of the widely used B3LYP hybrid. Modern nonhybrid DFAs continue to show utility for transition metal thermochemistry.
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Affiliation(s)
- John J Determan
- Department of Chemistry, Texas Christian University , Fort Worth, Texas 76129, United States
| | - Katelyn Poole
- Department of Chemistry, Texas Christian University , Fort Worth, Texas 76129, United States.,Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas , Denton, Texas 76203-5017, United States
| | - Giovanni Scalmani
- Gaussian, Inc. , 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Michael J Frisch
- Gaussian, Inc. , 340 Quinnipiac Street, Building 40, Wallingford, Connecticut 06492, United States
| | - Benjamin G Janesko
- Department of Chemistry, Texas Christian University , Fort Worth, Texas 76129, United States
| | - Angela K Wilson
- Department of Chemistry, Michigan State University , East Lansing, Michigan 48824 United States
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28
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Reeta Felscia U, Rajkumar BJM, Sankar P, Philip R, Briget Mary M. Optical nonlinearity and charge transfer analysis of pyrene adsorbed on silver: Computational and experimental investigations. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2017; 184:286-293. [PMID: 28525863 DOI: 10.1016/j.saa.2017.05.021] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/17/2017] [Revised: 05/05/2017] [Accepted: 05/09/2017] [Indexed: 06/07/2023]
Abstract
The interaction of pyrene on silver has been investigated using both experimental and computational methods. Hyperpolarizabilities computed theoretically together with experimental nonlinear absorption from open aperture Z-scan measurements, point towards a possible use of pyrene adsorbed on silver in the rational design of NLO devices. Presence of a red shift in both simulated and experimental UV-Vis spectra confirms the adsorption on silver, which is due to the electrostatic interaction between silver and pyrene, inducing variations in the structural parameters of pyrene. Fukui calculations along with MEP plot predict the electrophilic nature of the silver cluster in the presence of pyrene, with NBO analysis revealing that the adsorption causes charge redistribution from the first three rings of pyrene towards the fourth ring, from where the 2p orbitals of carbon interact with the valence 5s orbitals of the cluster. This is further confirmed by the downshifting of ring breathing modes in both the experimental and theoretical Raman spectra.
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Affiliation(s)
- U Reeta Felscia
- PG & Research Department of Physics, Lady Doak College, Madurai 625002, India
| | - Beulah J M Rajkumar
- PG & Research Department of Physics, Lady Doak College, Madurai 625002, India.
| | - Pranitha Sankar
- Light and Matter Physics Group, Raman Research Institute, Bangalore 560080, India
| | - Reji Philip
- Light and Matter Physics Group, Raman Research Institute, Bangalore 560080, India
| | - M Briget Mary
- PG & Research Department of Physics, Lady Doak College, Madurai 625002, India
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29
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Mahler A, Janesko BG, Moncho S, Brothers EN. Why are GGAs so accurate for reaction kinetics on surfaces? Systematic comparison of hybrid vs. nonhybrid DFT for representative reactions. J Chem Phys 2017. [DOI: 10.1063/1.4986404] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Aebersold LE, Yuwono SH, Schoendorff G, Wilson AK. Efficacy of Density Functionals and Relativistic Effective Core Potentials for Lanthanide-Containing Species: The Ln54 Molecule Set. J Chem Theory Comput 2017; 13:2831-2839. [DOI: 10.1021/acs.jctc.6b01223] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lucas E. Aebersold
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Stephen H. Yuwono
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - George Schoendorff
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
| | - Angela K. Wilson
- Department of Chemistry, Michigan State University, East Lansing, Michigan 48824-1322, United States
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31
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Abstract
Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.
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Affiliation(s)
| | - Kenneth M. Merz
- Department of Chemistry, Department of Biochemistry and Molecular Biology, and Institute of Cyber-Enabled Research, Michigan State University, East Lansing, Michigan 48824, United States
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32
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Letterman RG, DeYonker NJ, Burkey TJ, Webster CE. Calibrating Reaction Enthalpies: Use of Density Functional Theory and the Correlation Consistent Composite Approach in the Design of Photochromic Materials. J Phys Chem A 2016; 120:9982-9997. [PMID: 27936738 DOI: 10.1021/acs.jpca.6b09278] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Acquisition of highly accurate energetic data for chromium-containing molecules and various chromium carbonyl complexes is a major step toward calibrating bond energies and thermal isomerization energies from mechanisms for Cr-centered photochromic materials being developed in our laboratories. The performance of six density functionals in conjunction with seven basis sets, utilizing Gaussian-type orbitals, has been evaluated for the calculation of gas-phase enthalpies of formation and enthalpies of reaction at 298.15 K on various chromium-containing systems. Nineteen molecules were examined: Cr(CO)6, Cr(CO)5, Cr(CO)5(C2H4), Cr(CO)5(C2ClH3), Cr(CO)5(cis-(C2Cl2H2)), Cr(CO)5(gem-(C2Cl2H2)), Cr(CO)5(trans-(C2Cl2H2)), Cr(CO)5(C2Cl3H), Cr(CO)5(C2Cl4), CrO2, CrF2, CrCl2, CrCl4, CrBr2, CrBr4, CrOCl2, CrO2Cl2, CrOF2, and CrO2F2. The performance of 69 density functionals in conjunction with a single basis set utilizing Slater-type orbitals (STO) and a zeroth-order relativistic approximation was also evaluated for the same test set. Values derived from density functional theory were compared to experimental values where available, or values derived from the correlation consistent composite approach (ccCA). When all reactions were considered, the functionals that exhibited the smallest mean absolute deviations (MADs, in kcal mol-1) from ccCA-derived values were B97-1 (6.9), VS98 (9.0), and KCIS (9.4) in conjunction with quadruple-ζ STO basis sets and B97-1 (9.3) in conjunction with cc-pVTZ basis sets. When considering only the set of gas-phase reaction enthalpies (ΔrH°gas), the functional that exhibited the smallest MADs from ccCA-derived values were B97-1 in conjunction with cc-pVTZ basis sets (9.1) and PBEPBE in conjunction with polarized valence triple-ζ basis set/effective core potential combination for Cr and augmented and multiple polarized triple-ζ Pople style basis sets (9.5). Also of interest, certainly because of known cancellation of errors, PBEPBE with the least-computationally expensive basis set combination considered in the present study (valence double-ζ basis set/effective core potential combination for Cr and singly-polarized double-ζ Pople style basis sets) also provided reasonable accuracy (11.1). An increase in basis set size was found to have an improvement in accuracy for the best performing functional (B97-1).
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Affiliation(s)
- Roger G Letterman
- Department of Chemistry and Computational Research on Materials Institute, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Nathan J DeYonker
- Department of Chemistry and Computational Research on Materials Institute, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Theodore J Burkey
- Department of Chemistry and Computational Research on Materials Institute, The University of Memphis , Memphis, Tennessee 38152, United States
| | - Charles Edwin Webster
- Department of Chemistry and Computational Research on Materials Institute, The University of Memphis , Memphis, Tennessee 38152, United States.,Department of Chemistry and Center for Computational Sciences, Mississippi State University , Mississippi State, Mississippi 39762-9573, United States
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33
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Jones MR, Brooks BR, Wilson AK. Partition coefficients for the SAMPL5 challenge using transfer free energies. J Comput Aided Mol Des 2016; 30:1129-1138. [PMID: 27646287 DOI: 10.1007/s10822-016-9964-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2016] [Accepted: 09/02/2016] [Indexed: 10/21/2022]
Abstract
SAMPL challenges (Mobley et al. in J Comput Aided Mol Des 28:135-150, 2014; Skillman in J Comput Aided Mol Des 26:473-474, 2012; Geballe in J Comput Aided Mol Des 24:259-279, 2010; Guthrie in J Phys Chem B 113:4501-4507, 2009) provide excellent opportunities to assess theoretical approaches on new data sets with a goal of gaining greater insight towards protein and ligand modeling. In the SAMPL5 experiment, cyclohexane-water partition coefficients were determined using a vertical solvation scheme in conjunction with the SMD continuum solvent model. Several DFT functionals partnered with correlation consistent basis sets were evaluated for the prediction of the partition coefficients. The approach chosen for the competition, a B3PW91 vertical solvation scheme, yields a mean absolute deviation of 1.9 logP units and performs well at estimating the correct hydrophilicity and hydrophobicity for the full SAMPL5 molecule set.
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Affiliation(s)
- Michael R Jones
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA.,Laboratory of Computational Biology, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Bernard R Brooks
- Laboratory of Computational Biology, National Heart, Lung and Blood Institute, 5635 Fishers Lane, T-900 Suite, Rockville, MD, 20852, USA
| | - Angela K Wilson
- Department of Chemistry, Michigan State University, 578 S. Shaw Ln, East Lansing, MI, 48824, USA.
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34
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Johnson EL, Davis QC, Morse MD. Predissociation measurements of bond dissociation energies: VC, VN, and VS. J Chem Phys 2016; 144:234306. [DOI: 10.1063/1.4953782] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Eric L. Johnson
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Quincy C. Davis
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
| | - Michael D. Morse
- Department of Chemistry, University of Utah, Salt Lake City, Utah 84112, USA
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35
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Wang J, Liu L, Wilson AK. Oxidative Cleavage of the β-O-4 Linkage of Lignin by Transition Metals: Catalytic Properties and the Performance of Density Functionals. J Phys Chem A 2016; 120:737-46. [DOI: 10.1021/acs.jpca.5b08854] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jiaqi Wang
- Department of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
| | - Lily Liu
- Department of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
| | - Angela K. Wilson
- Department of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
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36
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Ge X, Chen X, Qian C, Zhou S. Combined experimental/theoretical study of d-glucosamine promoted Ullmann-type C–N coupling catalyzed by copper(i): does amino really count? RSC Adv 2016. [DOI: 10.1039/c6ra03015g] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Ullmann type C–N coupling reaction catalyzed by copper(i) with d-glucosamine derivatives as promoters was studied by means of combined experimental/theoretical investigation.
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Affiliation(s)
- Xin Ge
- School of Chemical and Material Engineering
- Jiangnan University
- Wuxi
- P. R. China
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
| | - Xinzhi Chen
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- P. R. China
| | - Chao Qian
- Key Laboratory of Biomass Chemical Engineering of Ministry of Education
- College of Chemical and Biological Engineering
- Zhejiang University
- Hangzhou
- P. R. China
| | - Shaodong Zhou
- Institut für Chemie
- Technische Universität Berlin
- 10623 Berlin
- Germany
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37
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Peterson C, Penchoff D, Wilson A. Prediction of Thermochemical Properties Across the Periodic Table. ANNUAL REPORTS IN COMPUTATIONAL CHEMISTRY 2016. [DOI: 10.1016/bs.arcc.2016.04.001] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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38
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Peterson C, Penchoff DA, Wilson AK. Ab initio approaches for the determination of heavy element energetics: Ionization energies of trivalent lanthanides (Ln = La-Eu). J Chem Phys 2015; 143:194109. [DOI: 10.1063/1.4935809] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Charles Peterson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017, USA
| | - Deborah A. Penchoff
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017, USA
| | - Angela K. Wilson
- Department of Chemistry and Center for Advanced Scientific Computing and Modeling (CASCaM), University of North Texas, Denton, Texas 76203-5017, USA
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39
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T.N. R, M. U, Rajkumar BJ. Structural and spectroscopic study of adsorption of anthracene on silver. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1053544] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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40
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Manivasagam S, Laury ML, Wilson AK. Pseudopotential-Based Correlation Consistent Composite Approach (rp-ccCA) for First- and Second-Row Transition Metal Thermochemistry. J Phys Chem A 2015; 119:6867-74. [DOI: 10.1021/acs.jpca.5b02433] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Sivabalan Manivasagam
- Department
of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
| | - Marie L. Laury
- Department
of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
| | - Angela K. Wilson
- Department
of Chemistry and
Center for Advanced Scientific Computing and Modeling, University of North Texas, Denton, Texas 76203-5017, United States
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41
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Xu X, Zhang W, Tang M, Truhlar DG. Do Practical Standard Coupled Cluster Calculations Agree Better than Kohn–Sham Calculations with Currently Available Functionals When Compared to the Best Available Experimental Data for Dissociation Energies of Bonds to 3d Transition Metals? J Chem Theory Comput 2015; 11:2036-52. [DOI: 10.1021/acs.jctc.5b00081] [Citation(s) in RCA: 94] [Impact Index Per Article: 10.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Xuefei Xu
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Wenjing Zhang
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, People’s Republic of China
| | - Mingsheng Tang
- College
of Chemistry and Molecular Engineering, Zhengzhou University, Zhengzhou, Henan Province 450001, People’s Republic of China
| | - Donald G. Truhlar
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
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43
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Bondarchuk SV, Minaev BF. Thermally accessible triplet state of π-nucleophiles does exist. Evidence from first principles study of ethylene interaction with copper species. RSC Adv 2015. [DOI: 10.1039/c4ra12422g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Three different models of ethylene interaction with copper species, namely, the Cu(100) surface, odd-numbered copper clusters C2H4/Cun (where n = 3, 7, 11, 15, 17, 19, 21, 25 and 27) and atomic copper C2H4/Cu were studied theoretically.
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Affiliation(s)
- Sergey V. Bondarchuk
- Department of Organic Chemistry
- Bogdan Khmelnitsky Cherkasy National University
- 18031 Cherkasy
- Ukraine
| | - Boris F. Minaev
- Department of Organic Chemistry
- Bogdan Khmelnitsky Cherkasy National University
- 18031 Cherkasy
- Ukraine
- Department of Theoretical Chemistry and Biochemistry
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44
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Boussouf K, Boulmene R, Prakash M, Komiha N, Taleb M, Mogren Al-Mogren M, Hochlaf M. Characterization of Znq+–imidazole (q = 0, 1, 2) organometallic complexes: DFT methods vs. standard and explicitly correlated post-Hartree–Fock methods. Phys Chem Chem Phys 2015; 17:14417-26. [DOI: 10.1039/c4cp06108j] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
Benchmarking DFts for the characterization of the Znq+–imidazole (q= 0, 1, 2) complexes.
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Affiliation(s)
- K. Boussouf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - R. Boulmene
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - M. Prakash
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
| | - N. Komiha
- LS3ME-Equipe de Chimie Théorique et Modélisation
- Université Mohamed
- Faculté des Sciences
- Rabat
- Maroc
| | - M. Taleb
- Laboratoire LIMME
- Université Sidi Med Ben Abdellah
- Fac des Sciences Dhar El Mehrez
- Fès
- Maroc
| | - M. Mogren Al-Mogren
- Chemistry Department
- Faculty of Science
- King Saud University
- Riyadh 11451
- Kingdom of Saudi Arabia
| | - M. Hochlaf
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME UMR 8208 CNRS
- 77454 Marne-la-Vallée
- France
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45
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DeYonker NJ. What a Difference a Decade Has Not Made: The Murky Electronic Structure of Iron Monocyanide (FeCN) and Iron Monoisocyanide (FeNC). J Phys Chem A 2014; 119:215-23. [DOI: 10.1021/jp5110906] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Nathan J. DeYonker
- Department of Chemistry, The University of Memphis, Memphis, Tennessee 38152, United States
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46
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Otten BM, Figg TM, Cundari TR. The curious case of mesityl azide and its reactivity with bpyNiEt2. Inorg Chem 2014; 53:11633-9. [PMID: 25325403 DOI: 10.1021/ic501766k] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A DFT analysis of the reaction of bpyNiEt2 with ArN3 was performed for para-tolyl-azide (Ar = pTol), 3,5-dimethyl-phenyl-azide (Ar = mXy) and ortho-tolyl-azide (Ar = oTol), and mesityl-azide (MesN3). Of particular interest were the different products obtained for the latter (ethylene, butane, azomesitylene, mesityl-ethylamine, etc.) versus the other reagents, i.e., (bpyNi(N(Ar)Et)(Et)). Calculated thermodynamics and kinetics for metal-free reactions did not differentiate MesN3 from the other aryl azides. Once (2)bpyNiEt(•) was generated via bond homolysis, formation of ethylene by β-H elimination was facile, as was formation of nickel-imidyl (NR(-•)) intermediates by reaction of ArN3 with bpyNiEtx (x = 0-2). On the basis of computed energetics, three reactions of bpyNiEt2 were proposed to compete: Ni-C bond homolysis, reductive elimination of butane, and nucleophilic attack (NA) by ArN3. Inspection of their temperature dependence suggested that NA and Ni-Et bond homolysis dominated at lower and higher temperatures, respectively. Calculated Ni-N and Ni-C bond dissociation free energies (BDFEs) suggested the role of radical pathways in discriminating bpyNiEt2/ArN3 reactions, and implied that the concentration of radicals such as aminyl (ArN(•)(Et)), (2)bpyNiEt(•), and Et(•) will be greatest for MesN3.
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Affiliation(s)
- Brooke M Otten
- Department of Chemistry, Center for Advanced Scientific Computing and Modeling, University of North Texas , 1508 Mulberry, Denton, Texas 76203, United States
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47
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Lu X, Gaus M, Elstner M, Cui Q. Parametrization of DFTB3/3OB for magnesium and zinc for chemical and biological applications. J Phys Chem B 2014; 119:1062-82. [PMID: 25178644 PMCID: PMC4306495 DOI: 10.1021/jp506557r] [Citation(s) in RCA: 108] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
![]()
We report the parametrization of
the approximate density functional
theory, DFTB3, for magnesium and zinc for chemical and biological
applications. The parametrization strategy follows that established
in previous work that parametrized several key main group elements
(O, N, C, H, P, and S). This 3OB set of parameters can thus be used
to study many chemical and biochemical systems. The parameters are
benchmarked using both gas-phase and condensed-phase systems. The
gas-phase results are compared to DFT (mostly B3LYP), ab initio (MP2 and G3B3), and PM6, as well as to a previous DFTB parametrization
(MIO). The results indicate that DFTB3/3OB is particularly successful
at predicting structures, including rather complex dinuclear metalloenzyme
active sites, while being semiquantitative (with a typical mean absolute
deviation (MAD) of ∼3–5 kcal/mol) for energetics. Single-point
calculations with high-level quantum mechanics (QM) methods generally
lead to very satisfying (a typical MAD of ∼1 kcal/mol) energetic
properties. DFTB3/MM simulations for solution and two enzyme systems
also lead to encouraging structural and energetic properties in comparison
to available experimental data. The remaining limitations of DFTB3,
such as the treatment of interaction between metal ions and highly
charged/polarizable ligands, are also discussed.
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Affiliation(s)
- Xiya Lu
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin-Madison , 1101 University Avenue, Madison, Wisconsin 53706, United States
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48
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Fišer J. Ab initio study of zinc chloride dication ZnCl2+ in the gas phase. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.07.012] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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49
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Xu X, Yang KR, Truhlar DG. Testing Noncollinear Spin-Flip, Collinear Spin-Flip, and Conventional Time-Dependent Density Functional Theory for Predicting Electronic Excitation Energies of Closed-Shell Atoms. J Chem Theory Comput 2014; 10:2070-84. [DOI: 10.1021/ct500128s] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Xuefei Xu
- Department of Chemistry and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Ke R. Yang
- Department of Chemistry and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Donald G. Truhlar
- Department of Chemistry and
Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, United States
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50
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Weaver MN, Merz KM, Ma D, Kim HJ, Gagliardi L. Calculation of Heats of Formation for Zn Complexes: Comparison of Density Functional Theory, Second Order Perturbation Theory, Coupled-Cluster and Complete Active Space Methods. J Chem Theory Comput 2013; 9:10.1021/ct400856g. [PMID: 24409106 PMCID: PMC3881291 DOI: 10.1021/ct400856g] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Heats of formation were predicted for nine ZnX complexes (X= Zn, H, O, F2, S, Cl, Cl2, CH3, (CH3)2) using fourteen density functionals, MP2 calculations and the CCSD and CCSD(T) coupled-cluster methods. Calculations utilized the correlation consistent cc-pVTZ and aug-cc-pVTZ basis sets. Heats of formation were most accurately predicted by the TPSSTPSS and TPSSKCIS density functionals, and the BLYP, B3LYP, MP2, CCSD and CCSD(T) levels were among the poorest performing methods based on accuracy. A wide range of Zn2 equilibrium bond distances were predicted, indicating that many of the studied levels of theory may be unable to adequately describe this transition metal dimer. To further benchmark the accuracy of the density functional methods, high-level CASSCF and CASPT2 calculations were performed to estimate bond dissociation energies, equilibrium bond lengths and heats of formation for the diatomic Zn complexes and the latter two quantities were compared with the results of DFT, MP2 and coupled-cluster calculations as well as experimental values.
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Affiliation(s)
- Michael N. Weaver
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, University of Florida, Gainesville, FL 32611-8435
| | - Kenneth M. Merz
- Department of Chemistry, Quantum Theory Project, 2328 New Physics Building, University of Florida, Gainesville, FL 32611-8435
- Department of Chemistry, Department of Biochemistry and Molecular Biology, Michigan State University, 578 S. Shaw Lane, East Lansing, MI 48824-1322, 517-355-9715
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