1
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Garrison A, Heras-Domingo J, Kitchin JR, dos Passos Gomes G, Ulissi ZW, Blau SM. Applying Large Graph Neural Networks to Predict Transition Metal Complex Energies Using the tmQM_wB97MV Data Set. J Chem Inf Model 2023; 63:7642-7654. [PMID: 38049389 PMCID: PMC10751796 DOI: 10.1021/acs.jcim.3c01226] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 11/08/2023] [Accepted: 11/20/2023] [Indexed: 12/06/2023]
Abstract
Machine learning (ML) methods have shown promise for discovering novel catalysts but are often restricted to specific chemical domains. Generalizable ML models require large and diverse training data sets, which exist for heterogeneous catalysis but not for homogeneous catalysis. The tmQM data set, which contains properties of 86,665 transition metal complexes calculated at the TPSSh/def2-SVP level of density functional theory (DFT), provided a promising training data set for homogeneous catalyst systems. However, we find that ML models trained on tmQM consistently underpredict the energies of a chemically distinct subset of the data. To address this, we present the tmQM_wB97MV data set, which filters out several structures in tmQM found to be missing hydrogens and recomputes the energies of all other structures at the ωB97M-V/def2-SVPD level of DFT. ML models trained on tmQM_wB97MV show no pattern of consistently incorrect predictions and much lower errors than those trained on tmQM. The ML models tested on tmQM_wB97MV were, from best to worst, GemNet-T > PaiNN ≈ SpinConv > SchNet. Performance consistently improves when using only neutral structures instead of the entire data set. However, while models saturate with only neutral structures, more data continue to improve the models when including charged species, indicating the importance of accurately capturing a range of oxidation states in future data generation and model development. Furthermore, a fine-tuning approach in which weights were initialized from models trained on OC20 led to drastic improvements in model performance, indicating transferability between ML strategies of heterogeneous and homogeneous systems.
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Affiliation(s)
- Aaron
G. Garrison
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
| | - Javier Heras-Domingo
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
| | - John R. Kitchin
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
| | - Gabriel dos Passos Gomes
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
- Department
of Chemistry, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
- Wilton
E. Scott Institute for Energy Innovation, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Zachary W. Ulissi
- Department
of Chemical Engineering, Carnegie Mellon
University, Pittsburgh, Pennsylvania 15213, United States
- Wilton
E. Scott Institute for Energy Innovation, Carnegie Mellon University, Pittsburgh, Pennsylvania 15213, United States
| | - Samuel M. Blau
- Lawrence
Berkeley National Laboratory, Berkeley, California 94720, United States
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2
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Malcomson T, Repiščák P, Erhardt S, Paterson MJ. Protocols for Understanding the Redox Behavior of Copper-Containing Systems. ACS OMEGA 2022; 7:45057-45066. [PMID: 36530299 PMCID: PMC9753522 DOI: 10.1021/acsomega.2c05484] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/25/2022] [Accepted: 11/09/2022] [Indexed: 06/17/2023]
Abstract
Suitability of single-reference density functional theory (DFT) methods for the calculation of redox potentials of copper-containing macrocycle complexes was confirmed by the use of T 1 diagnostics along with a verification of negligible spin contamination or wave function instability. When examining the effect of improvement in the cc-pVnZ basis set series on calculated redox potentials, the results readily converged at the cc-pVTZ level. The all-electron Def2-TZVPP basis set is shown to be a suitable choice of a basis set for the calculation of redox potentials when utilizing a cc-pVTZ geometry. The best-performing model chemistries are determined to be the M06/polarizable continuum model (PCM); therefore, a scheme for redox potential calculations of copper macrocycles using either M06/cc-pVTZ with PCM solvation is proposed to reliably reproduce experimental trends.
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Affiliation(s)
- Thomas Malcomson
- Department
of Chemistry, School of Natural Sciences, The University of Manchester, ManchesterM13 9PL, U.K.
| | - Peter Repiščák
- Beatson
Institute for Cancer Research, University
of Glasgow, Garscube Estate Switchback Road, BearsdenG61 1QH, U.K.
| | - Stefan Erhardt
- School
of Applied Sciences, Edinburgh Napier University, EdinburghEH11 4BN, Scotland, U.K.
| | - Martin J. Paterson
- Institute
of Chemical Sciences, School of Engineering and Physical Sciences, Heriot-Watt University, EdinburghEH14 4AS, U.K.
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3
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Amuthakala S, Bharathi S, Kalilur Rahiman A. Semicarbazone and thiosemicarbazone appended 4-diethylamino-2-hydroxybenzyl compounds as highly selective bifunctional chemosensors: An experimental and computational approach. Inorganica Chim Acta 2022. [DOI: 10.1016/j.ica.2022.121302] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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4
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Buelna-García CE, Castillo-Quevedo C, Quiroz-Castillo JM, Paredes-Sotelo E, Cortez-Valadez M, Martin-del-Campo-Solis MF, López-Luke T, Utrilla-Vázquez M, Mendoza-Wilson AM, Rodríguez-Kessler PL, Vazquez-Espinal A, Pan S, de Leon-Flores A, Mis-May JR, Rodríguez-Domínguez AR, Martínez-Guajardo G, Cabellos JL. Relative Populations and IR Spectra of Cu38 Cluster at Finite Temperature Based on DFT and Statistical Thermodynamics Calculations. Front Chem 2022; 10:841964. [PMID: 35300385 PMCID: PMC8921525 DOI: 10.3389/fchem.2022.841964] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/24/2022] [Indexed: 11/13/2022] Open
Abstract
The relative populations of Cu38 isomers depend to a great extent on the temperature. Density functional theory and nanothermodynamics can be combined to compute the geometrical optimization of isomers and their spectroscopic properties in an approximate manner. In this article, we investigate entropy-driven isomer distributions of Cu38 clusters and the effect of temperature on their IR spectra. An extensive, systematic global search is performed on the potential and free energy surfaces of Cu38 using a two-stage strategy to identify the lowest-energy structure and its low-energy neighbors. The effects of temperature on the populations and IR spectra are considered via Boltzmann factors. The computed IR spectrum of each isomer is multiplied by its corresponding Boltzmann weight at finite temperature. Then, they are summed together to produce a final temperature-dependent, Boltzmann-weighted spectrum. Our results show that the disordered structure dominates at high temperatures and the overall Boltzmann-weighted spectrum is composed of a mixture of spectra from several individual isomers.
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Affiliation(s)
- Carlos Emiliano Buelna-García
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
- Organización Científica y Tecnológica del Desierto, Hermosillo, Mexico
| | - Cesar Castillo-Quevedo
- Departamento de Fundamentos del Conocimiento, Centro Universitario del Norte, Universidad de Guadalajara, Colotlán, Mexico
| | | | - Edgar Paredes-Sotelo
- Departamento de Investigación en Polímeros y Materiales, Universidad de Sonora, Hermosillo, Mexico
| | - Manuel Cortez-Valadez
- CONACYT-Departamento de Investigación en Física, Universidad de Sonora, Hermosillo, Mexico
| | | | - Tzarara López-Luke
- Instituto de Investigación en Metalurgia y Materiales, Universidad Michoacana de San Nicolás de Hidalgo, Ciudad Universitaria, Morelia, Mexico
| | | | | | - Peter L. Rodríguez-Kessler
- Laboratorio de Química Inorgánica y Materiales Moleculares, Facultad de Ingeniería, Universidad Autonoma de Chile, Santiago, Chile
| | - Alejandro Vazquez-Espinal
- Comput. Theor. Chem. Group Departamento de Ciencias Químicas, Facultad de Ciencias Exactas, Universidad Andres Bello, Santiago, Chile
| | - Sudip Pan
- Fachbereich Chemie, Philipps-Universität Marburg, Marburg, Germany
| | - Aned de Leon-Flores
- Departamento de Ciencias Químico Biologicas, Universidad de Sonora, Hermosillo, Mexico
| | | | | | - Gerardo Martínez-Guajardo
- Unidad Académica de Ciencias Químicas, Área de Ciencias de la Salud, Universidad Autónoma de Zacatecas, Zacatecas, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
| | - Jose Luis Cabellos
- Universidad Politécnica de Tapachula, Tapachula, Mexico
- *Correspondence: Gerardo Martinez-Guajardo, ; Jose Luis Cabellos,
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5
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Shaji LK, Ashok Kumar S. Antipyrine derived Schiff's base as a colorimetric probe for the rapid and selective detection of Cu2+ions. INORG CHEM COMMUN 2021. [DOI: 10.1016/j.inoche.2021.109037] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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6
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Hoque MM, Bari MA, Khan MW. Rh(II)‐mediated one‐pot synthesis of dihydrobenzofuran and spiro[2.5]oct‐1‐ene: Experimental and DFT studies. J PHYS ORG CHEM 2021. [DOI: 10.1002/poc.4300] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Abdul Bari
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
| | - Md. Wahab Khan
- Department of Chemistry Bangladesh University of Engineering and Technology Dhaka Bangladesh
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7
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Synthesis and structural elucidation for new pyrano thiazole complexes: Biological screening and effects on DNA through in-vitro and in-silico approaches. J Mol Liq 2021. [DOI: 10.1016/j.molliq.2021.115844] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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8
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Ghosh Dastidar D, Mukherjee P, Ghosh D, Banerjee D. Carbon quantum dots prepared from onion extract as fluorescence turn-on probes for selective estimation of Zn2+ in blood plasma. Colloids Surf A Physicochem Eng Asp 2021. [DOI: 10.1016/j.colsurfa.2020.125781] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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9
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Elsaady MM, Youssef AO, Attia MS, Abdel‐Mottaleb MSA. A stable and sensitive luminescent photoprobe based on tris(3‐acetylindole) terbium(III) complex: Molecular modeling, luminescence quenching, and Ab initio molecular dynamics. Appl Organomet Chem 2020. [DOI: 10.1002/aoc.6115] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Mostafa Mohamed Elsaady
- Analytical‐Nano‐Photochemistry, Solar Chemistry, and Computational Chemistry Labs, Department of Chemistry, Faculty of Science Ain Shams University Cairo Egypt
| | - Ahmed Osman Youssef
- Analytical‐Nano‐Photochemistry, Solar Chemistry, and Computational Chemistry Labs, Department of Chemistry, Faculty of Science Ain Shams University Cairo Egypt
| | - Mohamed Said Attia
- Analytical‐Nano‐Photochemistry, Solar Chemistry, and Computational Chemistry Labs, Department of Chemistry, Faculty of Science Ain Shams University Cairo Egypt
| | - Mohamed Sabry A. Abdel‐Mottaleb
- Analytical‐Nano‐Photochemistry, Solar Chemistry, and Computational Chemistry Labs, Department of Chemistry, Faculty of Science Ain Shams University Cairo Egypt
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10
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Amuthakala S, Bharathi S, Rahiman AK. Thiosemicarbazone-based bifunctional chemosensors for simultaneous detection of inorganic cations and fluoride anion. J Mol Struct 2020. [DOI: 10.1016/j.molstruc.2020.128640] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
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11
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Hoque MM, Hussen MS, Kumer A, Khan MW. Synthesis of 5, 6-diaroylisoindoline-1, 3-dione and computational approaches for investigation on structural and mechanistic insights by DFT. MOLECULAR SIMULATION 2020. [DOI: 10.1080/08927022.2020.1811866] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Affiliation(s)
- Mohammad Mazharol Hoque
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Sajib Hussen
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Ajoy Kumer
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
| | - Md. Wahab Khan
- Department of Chemistry, Bangladesh University of Engineering and Technology, Dhaka, Bangladesh
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12
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Abdel‐Mottaleb M, Abdullah L, Attia M. Terbium Crown‐Ether Complex as a Stable Photoprobe. Appl Organomet Chem 2019. [DOI: 10.1002/aoc.5420] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- M.S.A. Abdel‐Mottaleb
- Photochemistry, Solarchemistry and Computational Chemistry Labs, Department of Chemistry, Faculty of ScienceAin Shams University Abbassia 11566 , Cairo Egypt
| | - L.M. Abdullah
- Photochemistry, Solarchemistry and Computational Chemistry Labs, Department of Chemistry, Faculty of ScienceAin Shams University Abbassia 11566 , Cairo Egypt
| | - M.S. Attia
- Photochemistry, Solarchemistry and Computational Chemistry Labs, Department of Chemistry, Faculty of ScienceAin Shams University Abbassia 11566 , Cairo Egypt
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13
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Venkatesan V, Selva Kumar R, Ashok Kumar S, Sahoo SK. Dual optical properties of new schiff base based on bisthiophene for sensing of Cu2+ in protic media. J Mol Struct 2019. [DOI: 10.1016/j.molstruc.2019.126906] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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14
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Lei WL, Wang T, Feng KW, Wu LZ, Liu Q. Visible-Light-Driven Synthesis of 4-Alkyl/Aryl-2-Aminothiazoles Promoted by In Situ Generated Copper Photocatalyst. ACS Catal 2017. [DOI: 10.1021/acscatal.7b02818] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Wen-Long Lei
- State
Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Tao Wang
- State
Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Kai-Wen Feng
- State
Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
| | - Li-Zhu Wu
- Key Laboratory of Photochemical Conversion and Optoelectronic Materials, Technical Institute of Physics and Chemistry & University of Chinese Academy of Sciences, Chinese Academy of Sciences, Beijing 100190, P. R. China
| | - Qiang Liu
- State
Key Laboratory of Applied Organic Chemistry, Lanzhou University, Lanzhou 730000, P. R. China
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15
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Schaefer AW, Kieber-Emmons MT, Adam SM, Karlin KD, Solomon EI. Phenol-Induced O-O Bond Cleavage in a Low-Spin Heme-Peroxo-Copper Complex: Implications for O 2 Reduction in Heme-Copper Oxidases. J Am Chem Soc 2017; 139:7958-7973. [PMID: 28521498 PMCID: PMC5605297 DOI: 10.1021/jacs.7b03292] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
This study evaluates the reaction of a biomimetic heme-peroxo-copper complex, {[(DCHIm)(F8)FeIII]-(O22-)-[CuII(AN)]}+ (1), with a phenolic substrate, involving a net H-atom abstraction to cleave the bridging peroxo O-O bond that produces FeIV═O, CuII-OH, and phenoxyl radical moieties, analogous to the chemistry carried out in heme-copper oxidases (HCOs). A 3D potential energy surface generated for this reaction reveals two possible reaction pathways: one involves nearly complete proton transfer (PT) from the phenol to the peroxo ligand before the barrier; the other involves O-O homolysis, where the phenol remains H-bonding to the peroxo OCu in the transition state (TS) and transfers the H+ after the barrier. In both mechanisms, electron transfer (ET) from phenol occurs after the PT (and after the barrier); therefore, only the interaction with the H+ is involved in lowering the O-O cleavage barrier. The relative barriers depend on covalency (which governs ET from Fe), and therefore vary with DFT functional. However, as these mechanisms differ by the amount of PT at the TS, kinetic isotope experiments were conducted to determine which mechanism is active. It is found that the phenolic proton exhibits a secondary kinetic isotope effect, consistent with the calculations for the H-bonded O-O homolysis mechanism. The consequences of these findings are discussed in relation to O-O cleavage in HCOs, supporting a model in which a peroxo intermediate serves as the active H+ acceptor, and both the H+ and e- required for O-O cleavage derive from the cross-linked Tyr residue present at the active site.
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Affiliation(s)
- Andrew W Schaefer
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
| | - Matthew T Kieber-Emmons
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
- Department of Chemistry, The University of Utah , Salt Lake City, Utah 84112, United States
| | - Suzanne M Adam
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Kenneth D Karlin
- Department of Chemistry, The Johns Hopkins University , Baltimore, Maryland 21218, United States
| | - Edward I Solomon
- Department of Chemistry, Stanford University , Stanford, California 94305, United States
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16
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Sadhu B, Sundararajan M. Asn47 and Phe114 modulate the inner sphere reorganization energies of type zero copper proteins. Phys Chem Chem Phys 2016; 18:16748-56. [PMID: 27271560 DOI: 10.1039/c6cp00747c] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The geometric structures and electron transfer properties of type 1 Cu proteins are reasonably understood at the molecular level (E. I. Solomon and R. G. Hadt, Coord. Chem. Rev., 2011, 255, 774-789, J. J. Warren, K. M. Lancaster, J. H. Richards and H. B. Gray, J. Inorg. Biochem., 2012, 115, 119-126). Much understanding of type 1 copper electron transfer reactivity has come from site directed mutagenesis studies. For example, artificial "type zero" Cu-centres constructed in cupredoxin-azurin have showcased the capacity of outer-sphere hydrogen bonding networks to enhance Cu II/I electron transfer reactivity. In this paper, we have elaborated on earlier kinetics and electronic structural studies of type zero Cu by calculating the inner sphere reorganization energies of type 1, type 2, and type zero Cu proteins using density functional theory (DFT). Although the choice of density functionals for copper systems is not straightforward, we have benchmarked the density functionals against the recently reported ESI-PES data for two synthetic copper models (S. Niu, D.-L. Huang, P. D. Dau, H.-T. Liu, L.-S. Wang and T. J. Ichiye, Chem. Theory Comput., 2014, 10, 1283). For the Cu proteins, our calculations predict that changes in the coordination number upon metal reduction lead to large inner sphere reorganization energies for type 2 Cu sites, whereas retention in the coordination number is observed for type zero Cu sites. These variations in the coordination number are modulated by the outer-sphere coordinating residues Asn47 and Phe114, which are involved in hydrogen bonding with the Asp112 side chain.
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Affiliation(s)
- Biswajit Sadhu
- Radiation Safety Systems Division, Bhabha Atomic Research Centre, Mumbai - 400 085, India
| | - Mahesh Sundararajan
- Theoretical Chemistry Section, Bhabha Atomic Research Centre, Mumbai - 400 094, India.
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17
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Pruitt CJM, Goebbert DJ. Experimental and Theoretical Study of the Decomposition of Copper Nitrate Cluster Anions. J Phys Chem A 2015; 119:4755-62. [DOI: 10.1021/acs.jpca.5b02467] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Carrie Jo M. Pruitt
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
| | - Daniel J. Goebbert
- Department of Chemistry, The University of Alabama, Tuscaloosa, Alabama 35487, United States
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