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Lew-Yee JFH, Del Campo JM, Piris M. Electron Correlation in the Iron(II) Porphyrin by Natural Orbital Functional Approximations. J Chem Theory Comput 2023; 19:211-220. [PMID: 36579972 PMCID: PMC9996833 DOI: 10.1021/acs.jctc.2c01093] [Citation(s) in RCA: 7] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The relative stability of the singlet, triplet, and quintet spin states of iron(II) porphyrin (FeP) represents a challenging problem for electronic structure methods. While it is currently accepted that the ground state is a triplet, multiconfigurational wave function-based methods predict a quintet, and density functional approximations vary between triplet and quintet states, leading to a prediction that highly depends on the features of the method employed. The recently proposed Global Natural Orbital Functional (GNOF) aims to provide a balanced treatment between static and dynamic correlation, and together with the previous Piris Natural Orbital Functionals (PNOFs), allowed us to explore the importance of each type of correlation in the stability order of the states of FeP with a method that conserves the spin of the system. It is noteworthy that GNOF correlates all electrons in all available orbitals for a given basis set; in the case of the FeP with a double-ζ basis set as used in this work, this means that GNOF can properly correlate 186 electrons in 465 orbitals, significantly increasing the sizes of systems amenable to multiconfigurational treatment. Results show that PNOF5, PNOF7s, and PNOF7 predict the quintet to have a lower energy than the triplet state; however, the addition of dynamic correlation via second-order Møller-Plesset corrections (NOF-MP2) turns the triplet state to be lower than the quintet state, a prediction also reproduced by GNOF that incorporates much more dynamic correlation than its predecessors.
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Affiliation(s)
- Juan Felipe Huan Lew-Yee
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México CityC.P. 04510, México
| | - Jorge M Del Campo
- Departamento de Física y Química Teórica, Facultad de Química, Universidad Nacional Autónoma de México, México CityC.P. 04510, México
| | - Mario Piris
- Kimika Fakultatea, Euskal Herriko Unibertsitatea (UPV/EHU), P.K. 1072, 20080Donostia, Euskadi, Spain.,Donostia International Physics Center (DIPC), 20018Donostia, Euskadi, Spain.,IKERBASQUE, Basque Foundation for Science, 48013Bilbao, Euskadi, Spain
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2
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Reliably assessing the electronic structure of cytochrome P450 on today's classical computers and tomorrow's quantum computers. Proc Natl Acad Sci U S A 2022; 119:e2203533119. [PMID: 36095200 PMCID: PMC9499570 DOI: 10.1073/pnas.2203533119] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Chemical simulation is one of the most promising applications for future quantum computers. It is thought that quantum computers may enable accurate simulation for complex molecules that are otherwise impossible to simulate classically; that is, it displays quantum advantage. To better understand quantum advantage in chemical simulation, we explore what quantum and classical resources are required to simulate a series of pharmaceutically relevant molecules. Using classical methods, we show that reliable classical simulation of these molecules requires significant resources and therefore is a promising candidate for quantum simulation. We estimate the quantum resources, both in overall simulation time and the size. The insights from this study pave the way for future quantum simulation of complex molecules. An accurate assessment of how quantum computers can be used for chemical simulation, especially their potential computational advantages, provides important context on how to deploy these future devices. To perform this assessment reliably, quantum resource estimates must be coupled with classical computations attempting to answer relevant chemical questions and to define the classical algorithms simulation frontier. Herein, we explore the quantum computation and classical computation resources required to assess the electronic structure of cytochrome P450 enzymes (CYPs) and thus define a classical–quantum advantage boundary. This is accomplished by analyzing the convergence of density matrix renormalization group plus n-electron valence state perturbation theory (DMRG+NEVPT2) and coupled-cluster singles doubles with noniterative triples [CCSD(T)] calculations for spin gaps in models of the CYP catalytic cycle that indicate multireference character. The quantum resources required to perform phase estimation using qubitized quantum walks are calculated for the same systems. Compilation into the surface code provides runtime estimates to compare directly to DMRG runtimes and to evaluate potential quantum advantage. Both classical and quantum resource estimates suggest that simulation of CYP models at scales large enough to balance dynamic and multiconfigurational electron correlation has the potential to be a quantum advantage problem and emphasizes the important interplay between classical computations and quantum algorithms development for chemical simulation.
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3
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Rettig A, Shee J, Lee J, Head-Gordon M. Revisiting the Orbital Energy-Dependent Regularization of Orbital-Optimized Second-Order Møller-Plesset Theory. J Chem Theory Comput 2022; 18:5382-5392. [PMID: 36050889 DOI: 10.1021/acs.jctc.2c00641] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Optimizing orbitals in the presence of electron correlation, as in orbital-optimized second-order Møller-Plesset perturbation theory (OOMP2), can remove artifacts associated with mean-field orbitals such as spin contamination and artificial symmetry-breaking. However, OOMP2 is known to suffer from divergent correlation energies in regimes of small orbital energy gaps. To address this issue, several approaches to amplitude regularization have been explored, with those featuring energy-gap-dependent regularizers appearing to be most transferable and physically justifiable. For instance, κ-OOMP2 was shown to address the energy divergence issue in, for example, bond-breaking processes while offering a significant improvement in accuracy for the W4-11 thermochemistry data set, and a parameter of κ = 1.45 was recommended. A more recent investigation of regularized MP2 with Hartree-Fock orbitals revealed that stronger regularization (i.e., smaller values of κ) than what had previously been recommended for κ-OOMP2 may offer huge improvements in certain cases such as noncovalent interactions while retaining a high level of accuracy for main-group thermochemistry data sets. In this study, we investigate the transferability of those findings to κ-OOMP2 and assess the implications of stronger regularization on the ability of κ-OOMP2 to diagnose strong static correlation. We found similar results using κ-OOMP2 for several main-group thermochemistry, barrier height, and noncovalent interaction data sets including both closed shell and open shell species. However, stronger regularization yielded substantially higher accuracy for open-shell transition-metal (TM) thermochemistry and is necessary to provide qualitatively correct spin symmetry breaking behavior for several large and electrochemically relevant TM systems. We therefore find a single κ value insufficient to treat all systems using κ-OOMP2.
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Affiliation(s)
- Adam Rettig
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
| | - James Shee
- Department of Chemistry, University of California, Berkeley, California 94720, United States
| | - Joonho Lee
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Martin Head-Gordon
- Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, United States
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4
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Gu H, Dong Y, Lv R, Huang X, Chen Q. Rapid quantification of acid value in frying oil using iron tetraphenylporphyrin fluorescent sensor coupled with density functional theory and multivariate analysis. FOOD QUALITY AND SAFETY 2022. [DOI: 10.1093/fqsafe/fyac046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/14/2022]
Abstract
Abstract
Metalloporphyrin-based fluorescent sensor was developed for the acid value in frying oil. The electronic and structural performances of iron tetraphenylporphyrin (FeTPP) were theoretically investigated using time-dependent density functional theory (TD-DFT) and DFT at the B3LYP/LANL2DZ level. The quantified FeTPP-based fluorescent sensor results revealed its excellent performance in discriminating different analytes. In the present work, the acid value of palm olein was determined after every single frying cycle. A total of 10 frying cycles were conducted each day for 10 consecutive days. The FeTPP-based fluorescent sensor was used to quantify the acid value and the results were compared with the chemical data obtained by conventional titration method. The synchronous fluorescence spectrum for each sample was recorded. Parallel factor analysis (PARAFAC) was used to decompose the three-dimensional spectrum data. Then, the support vector regression (SVR), partial least squares (PLS), and back-propagation artificial neural network (BP-ANN) methods were applied to build the regression models. After the comparison of the constructed models, the SVR models exhibited the highest correlation coefficients among all models, with 0.9748 and 0.9276 for the training and test set, respectively. The findings suggested the potential of FeTPP-based fluorescent sensor in rapid monitoring of the used frying oil quality and perhaps also in other foods with higher oil content.
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5
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Lemke Y, Kussmann J, Ochsenfeld C. Efficient Integral-Direct Methods for Self-Consistent Reduced Density Matrix Functional Theory Calculations on Central and Graphics Processing Units. J Chem Theory Comput 2022; 18:4229-4244. [DOI: 10.1021/acs.jctc.2c00231] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Y. Lemke
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - J. Kussmann
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
| | - C. Ochsenfeld
- Chair of Theoretical Chemistry, Department of Chemistry, University of Munich (LMU), Butenandtstr. 5−13, D-81377 Munich, Germany
- Max Planck Institute for Solid State Research, Heisenbergstr. 1, D-70569 Stuttgart, Germany
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6
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Gu H, Dong Y, Zhu S, Huang X, Sun Y, Chen Q. Development of a sensor-based fluorescent method for quality evaluation of used frying oils. J Food Compost Anal 2022. [DOI: 10.1016/j.jfca.2022.104640] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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7
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Guo Y, Zhang N, Lei Y, Liu W. iCISCF: An Iterative Configuration Interaction-Based Multiconfigurational Self-Consistent Field Theory for Large Active Spaces. J Chem Theory Comput 2021; 17:7545-7561. [PMID: 34757746 DOI: 10.1021/acs.jctc.1c00781] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
An iterative configuration interaction (iCI)-based multiconfigurational self-consistent field (SCF) theory, iCISCF, is proposed to handle systems that require large active spaces. The success of iCISCF stems from three ingredients: (1) efficient selection of individual configuration state functions spanning the active space while maintaining full spin symmetry; (2) the use of Jacobi rotation for optimization of the active orbitals in conjunction with a quasi-Newton algorithm for the core/active-virtual and core-active orbital rotations; (3) a second-order perturbative treatment of the residual space left over by the selection procedure (i.e., iCISCF(2)). Several examples that go beyond the capability of CASSCF are taken as showcases to reveal the efficacy of iCISCF and iCISCF(2), facilitated by iCAS for imposed automatic selection and localization of active orbitals.
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Affiliation(s)
- Yang Guo
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
| | - Ning Zhang
- Beijing National Laboratory for Molecular Sciences, Institute of Theoretical and Computational Chemistry, College of Chemistry and Molecular Engineering, Peking University, Beijing 100871, China
| | - Yibo Lei
- Key Laboratory of Synthetic and Natural Functional Molecule Chemistry of Ministry of Education, College of Chemistry and Materials Science, Shaanxi Key Laboratory of Physico-Inorganic Chemistry, Northwest University, Xi'an, Shaanxi 710127, China
| | - Wenjian Liu
- Qingdao Institute for Theoretical and Computational Sciences, Institute of Frontier and Interdisciplinary Science, Shandong University, Qingdao, Shandong 266237, China
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8
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Weser O, Guther K, Ghanem K, Li Manni G. Stochastic Generalized Active Space Self-Consistent Field: Theory and Application. J Chem Theory Comput 2021; 18:251-272. [PMID: 34898215 PMCID: PMC8757470 DOI: 10.1021/acs.jctc.1c00936] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
An algorithm to perform stochastic generalized active space calculations, Stochastic-GAS, is presented, that uses the Slater determinant based FCIQMC algorithm as configuration interaction eigensolver. Stochastic-GAS allows the construction and stochastic optimization of preselected truncated configuration interaction wave functions, either to reduce the computational costs of large active space wave function optimizations, or to probe the role of specific electron correlation pathways. As for the conventional GAS procedure, the preselection of the truncated wave function is based on the selection of multiple active subspaces while imposing restrictions on the interspace excitations. Both local and cumulative minimum and maximum occupation number constraints are supported by Stochastic-GAS. The occupation number constraints are efficiently encoded in precomputed probability distributions, using the precomputed heat bath algorithm, which removes nearly all runtime overhead of GAS. This strategy effectively allows the FCIQMC dynamics to a priori exclude electronic configurations that are not allowed by GAS restrictions. Stochastic-GAS reduced density matrices are stochastically sampled, allowing orbital relaxations via Stochastic-GASSCF, and direct evaluation of properties that can be extracted from density matrices, such as the spin expectation value. Three test case applications have been chosen to demonstrate the flexibility of Stochastic-GAS: (a) the Stochastic-GASSCF [5·(6, 6)] optimization of a stack of five benzene molecules, that shows the applicability of Stochastic-GAS toward fragment-based chemical systems; (b) an uncontracted stochastic MRCISD calculation that correlates 96 electrons and 159 molecular orbitals, and uses a large (32, 34) active space reference wave function for an Fe(II)-porphyrin model system, showing how GAS can be applied to systematically recover dynamic electron correlation, and how in the specific case of the Fe(II)-porphyrin dynamic correlation further differentially stabilizes the 3Eg over the 5A1g spin state; (c) the study of an Fe4S4 cluster's spin-ladder energetics via highly truncated stochastic-GAS [4·(5, 5)] wave functions, where we show how GAS can be applied to understand the competing spin-exchange and charge-transfer correlating mechanisms in stabilizing different spin-states.
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Affiliation(s)
- Oskar Weser
- Max-Planck-Institute for Solid State Research, Stuttgart, 70569, Germany
| | - Kai Guther
- Max-Planck-Institute for Solid State Research, Stuttgart, 70569, Germany.,RIKEN Center for Computational Science, 7-1-26 minatojima-minami, Chuo Kobe 650-0047, Japan
| | - Khaldoon Ghanem
- Max-Planck-Institute for Solid State Research, Stuttgart, 70569, Germany
| | - Giovanni Li Manni
- Max-Planck-Institute for Solid State Research, Stuttgart, 70569, Germany
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9
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Nottoli T, Gauss J, Lipparini F. A black-box, general purpose quadratic self-consistent field code with and without Cholesky decomposition of the two-electron integrals. Mol Phys 2021. [DOI: 10.1080/00268976.2021.1974590] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Tommaso Nottoli
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
| | - Jürgen Gauss
- Department Chemie, Johannes Gutenberg-Universität Mainz, Mainz, Germany
| | - Filippo Lipparini
- Dipartimento di Chimica e Chimica Industriale, Università di Pisa, Pisa, Italy
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10
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Shafizadeh N, Crestoni ME, de la Lande A, Soep B. Heme ligation in the gas phase. INT REV PHYS CHEM 2021. [DOI: 10.1080/0144235x.2021.1952006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
| | - Maria Elisa Crestoni
- Dipartimento di Chimica e Tecnologie del Farmaco, Università di Roma “La Sapienza”, Roma, Italy
| | | | - Benoît Soep
- ISMO-CNRS, Université Paris Saclay, Orsay Cedex, France
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11
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Karnaukh EA, Bravaya KB. The redox potential of a heme cofactor in Nitrosomonas europaea cytochrome c peroxidase: a polarizable QM/MM study. Phys Chem Chem Phys 2021; 23:16506-16515. [PMID: 34017969 PMCID: PMC11178132 DOI: 10.1039/d0cp06632j] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2024]
Abstract
Redox reactions are crucial to biological processes that protect organisms against oxidative stress. Metalloenzymes, such as peroxidases which reduce excess reactive oxygen species into water, play a key role in detoxification mechanisms. Here we present the results of a polarizable QM/MM study of the reduction potential of the electron transfer heme in the cytochrome c peroxidase of Nitrosomonas europaea. We have found that environment polarization does not substantially affect the computed value of the redox potential. Particular attention has been given to analyzing the role of electrostatic interactions within the protein environment and the solvent on tuning the redox potential of the heme co-factor. We have found that the electrostatic interactions predominantly explain the fluctuations of the vertical ionization/attachment energies of the heme for the sampled configurations, and that the long range electrostatic interactions (up to 40 Å) contribute substantially to the absolute values of the vertical energy gaps.
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12
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Blunt NS, Mahajan A, Sharma S. Efficient multireference perturbation theory without high-order reduced density matrices. J Chem Phys 2020; 153:164120. [DOI: 10.1063/5.0023353] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Affiliation(s)
- Nick S. Blunt
- Department of Chemistry, Lensfield Road, Cambridge CB2 1EW, United Kingdom
| | - Ankit Mahajan
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
| | - Sandeep Sharma
- Department of Chemistry, University of Colorado, Boulder, Colorado 80302, USA
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13
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Dixit VA, Warwicker J, Visser SP. How Do Metal Ions Modulate the Rate‐Determining Electron‐Transfer Step in Cytochrome P450 Reactions? Chemistry 2020; 26:15270-15281. [DOI: 10.1002/chem.202003024] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Indexed: 12/16/2022]
Affiliation(s)
- Vaibhav A. Dixit
- Department of Pharmacy Birla Institute of Technology and Sciences Pilani (BITS-Pilani) Vidya Vihar Campus 41 Pilani 333031 Rajasthan India
| | - Jim Warwicker
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemistry The University of Manchester Oxford Road Manchester M139PL United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology The University of Manchester 131 Princess Street Manchester M17DN United Kingdom
- Department of Chemical Engineering and Analytical Science The University of Manchester Oxford Road Manchester M13 9PL United Kingdom
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14
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Melchakova I, Kuklin A, Avramov P. Towards spin quantum materials: Structure and potential energy profiles of weakly interacting arrays of iron porphyrin complexes at graphene armchair nanoribbon. Chem Phys Lett 2020. [DOI: 10.1016/j.cplett.2020.137807] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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15
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Linscott EB, Cole DJ, Hine NDM, Payne MC, Weber C. ONETEP + TOSCAM: Uniting Dynamical Mean Field Theory and Linear-Scaling Density Functional Theory. J Chem Theory Comput 2020; 16:4899-4911. [PMID: 32433876 DOI: 10.1021/acs.jctc.0c00162] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We introduce the unification of dynamical mean field theory (DMFT) and linear-scaling density functional theory (DFT), as recently implemented in ONETEP, a linear-scaling DFT package, and TOSCAM, a DMFT toolbox. This code can account for strongly correlated electronic behavior while simultaneously including the effects of the environment, making it ideally suited for studying complex and heterogeneous systems that contain transition metals and lanthanides, such as metalloproteins. We systematically introduce the necessary formalism, which must account for the nonorthogonal basis set used by ONETEP. In order to demonstrate the capabilities of this code, we apply it to carbon monoxide ligated iron porphyrin and explore the distinctly quantum-mechanical character of the iron 3d electrons during the process of photodissociation.
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Affiliation(s)
- Edward B Linscott
- Theory and Simulation of Materials (THEOS), École Polytechnique Fédérale de Lausanne, 1015 Lausanne, Switzerland
| | - Daniel J Cole
- School of Natural and Environmental Sciences, Newcastle University, Newcastle upon Tyne NE1 7RU, United Kingdom
| | - Nicholas D M Hine
- Department of Physics, University of Warwick, Coventry CV4 7AL, United Kingdom
| | - Michael C Payne
- Theory of Condensed Matter, Cavendish Laboratory, University of Cambridge, 19 JJ Thomson Avenue, Cambridge CB3 0HE, United Kingdom
| | - Cédric Weber
- Theory and Simulation of Condensed Matter, King's College London, The Strand, London WC2R 2LS, United Kingdom
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16
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Lee J, Malone FD, Morales MA. Utilizing Essential Symmetry Breaking in Auxiliary-Field Quantum Monte Carlo: Application to the Spin Gaps of the C36 Fullerene and an Iron Porphyrin Model Complex. J Chem Theory Comput 2020; 16:3019-3027. [DOI: 10.1021/acs.jctc.0c00055] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Joonho Lee
- Department of Chemistry, Columbia University, New York, New York 10027, United States
| | - Fionn D. Malone
- Quantum Simulations Group, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551, United States
| | - Miguel A. Morales
- Quantum Simulations Group, Lawrence Livermore National Laboratory, 7000 East Avenue, Livermore, California 94551, United States
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17
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Levine DS, Hait D, Tubman NM, Lehtola S, Whaley KB, Head-Gordon M. CASSCF with Extremely Large Active Spaces Using the Adaptive Sampling Configuration Interaction Method. J Chem Theory Comput 2020; 16:2340-2354. [PMID: 32109055 DOI: 10.1021/acs.jctc.9b01255] [Citation(s) in RCA: 65] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The complete active space self-consistent field (CASSCF) method is the principal approach employed for studying strongly correlated systems. However, exact CASSCF can only be performed on small active spaces of ∼20 electrons in ∼20 orbitals due to exponential growth in the computational cost. We show that employing the Adaptive Sampling Configuration Interaction (ASCI) method as an approximate Full CI solver in the active space allows CASSCF-like calculations within chemical accuracy (<1 kcal/mol for relative energies) in active spaces with more than ∼50 active electrons in ∼50 active orbitals, significantly increasing the sizes of systems amenable to accurate multiconfigurational treatment. The main challenge with using any selected CI-based approximate CASSCF is the orbital optimization problem; they tend to exhibit large numbers of local minima in orbital space due to their lack of invariance to active-active rotations (in addition to the local minima that exist in exact CASSCF). We highlight methods that can avoid spurious local extrema as a practical solution to the orbital optimization problem. We employ ASCI-SCF to demonstrate a lack of polyradical character in moderately sized periacenes with up to 52 correlated electrons and compare against heat-bath CI on an iron porphyrin system with more than 40 correlated electrons.
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Affiliation(s)
- Daniel S Levine
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Norm M Tubman
- Quantum Artificial Intelligence Lab (QuAIL), Exploration Technology Directorate, NASA Ames Research Center, Moffett Field, California 94035, United States
| | - Susi Lehtola
- Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - K Birgitta Whaley
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, United States.,Chemical Sciences Division, Lawrence Berkeley National Laboratory Berkeley, Berkeley, California 94720, United States
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18
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Theoretical Study on Electronic Structural Properties of Catalytically Reactive Metalloporphyrin Intermediates. Catalysts 2020. [DOI: 10.3390/catal10020224] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Metalloporphyrins have attracted great attention in the potential application of biomimetic catalysis. Especially, they were widely investigated as green catalysts in the chemical oxidation of various hydrocarbons through the catalytic activation of molecular oxygen. The structural properties of active central metal ions were reported to play a decisive role in catalytic activity. However, those delicate structural changes are difficult to be experimentally captured or elucidated in detail. Herein, we explored the electronic structural properties of metalloporphyrins (metal porphyrin (PMII, PMIIICl)) and their corresponding catalytically active intermediates (metal(III)-peroxo(PMIII-O2), metal(III)-hydroperoxo(PMIII-OH), and metal(IV)-oxo(PMIV=O), (M=Fe, Mn, and Co)) through the density functional theory method. The ground states of these intermediates were determined based on the assessment of relative energy and the corresponding geometric structures of ground states also further confirmed the stability of energy. Furthermore, our analyses of Mulliken charges and frontier molecular orbitals revealed the potential catalytic behavior of reactive metalloporphyrin intermediates.
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19
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Stoneburner SJ, Truhlar DG, Gagliardi L. Transition Metal Spin-State Energetics by MC-PDFT with High Local Exchange. J Phys Chem A 2020; 124:1187-1195. [PMID: 31962045 DOI: 10.1021/acs.jpca.9b10772] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The energetics of the spin states of transition metal complexes have been explored with a variety of electronic structure methods, but the calculations require a compromise between accuracy and affordability. In this work, the spin splittings of several iron complexes are studied with multiconfiguration pair-density functional theory (MC-PDFT). The results are compared to previously published results obtained by complete active space second-order perturbation theory (CASPT2) and CASPT2 with coupled-cluster semicore correlation (CASPT2/CC). In contrast to CASPT2's systematic overstabilization of high-spin states with respect to the CASPT2/CC reference, MC-PDFT with the tPBE on-top functional understabilizes high-spin states. This systematic understabilization is largely corrected by revising the exchange and correlation contributions to the on-top functional using the high local-exchange approximation (tPBE-HLE). Moreover, tPBE-HLE correctly predicts the spin of the ground state in most cases, while CASPT2 incorrectly predicts high-spin ground states in all cases. This is encouraging for practical work because tPBE and tPBE-HLE are faster than CASPT2 by a factor of 50 even in a moderately sized example.
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Affiliation(s)
- Samuel J Stoneburner
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455-0431 , United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455-0431 , United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Minnesota Supercomputing Institute , University of Minnesota , 207 Pleasant Street SE , Minneapolis , Minnesota 55455-0431 , United States
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20
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Li X, Dong L, Liu Y. Theoretical Study of Iron Porphyrin Nitrene: Formation Mechanism, Electronic Nature, and Intermolecular C–H Amination. Inorg Chem 2020; 59:1622-1632. [DOI: 10.1021/acs.inorgchem.9b02216] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xinyi Li
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
| | - Lihua Dong
- School of Chemistry and Chemical Engineering, Qilu Normal University, Jinan, Shandong 250013, China
| | - Yongjun Liu
- School of Chemistry and Chemical Engineering, Shandong University, Jinan, Shandong 250100, China
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21
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Antalík A, Nachtigallová D, Lo R, Matoušek M, Lang J, Legeza Ö, Pittner J, Hobza P, Veis L. Ground state of the Fe(ii)-porphyrin model system corresponds to quintet: a DFT and DMRG-based tailored CC study. Phys Chem Chem Phys 2020; 22:17033-17037. [DOI: 10.1039/d0cp03086d] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Fe(ii)-porphyrins play an important role in many reactions, due to their closely lying spin states. We present a thorough study of a Fe(ii)-porphyrin model system, in which we examine how the geometrical parameters influence its spin state ordering.
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Affiliation(s)
- Andrej Antalík
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
- Faculty of Mathematics and Physics
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Mikuláš Matoušek
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
- Faculty of Mathematics and Physics
| | - Jakub Lang
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
| | - Örs Legeza
- Strongly Correlated Systems “Lendület” Research group
- Wigner Research Centre for Physics
- Budapest
- Hungary
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 16610 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry
- Academy of Sciences of the Czech Republic
- 18223 Prague 8
- Czech Republic
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22
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Mubarak MQE, Visser SP. Computational Study on the Catalytic Reaction Mechanism of Heme Haloperoxidase Enzymes. Isr J Chem 2019. [DOI: 10.1002/ijch.201900099] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- M. Qadri E. Mubarak
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
| | - Sam P. Visser
- Manchester Institute of Biotechnology and Department of Chemical Engineering and Analytical Science The University of Manchester 131 Princess Street Manchester M1 7DN United Kingdom
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23
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Kreplin DA, Knowles PJ, Werner HJ. Second-order MCSCF optimization revisited. I. Improved algorithms for fast and robust second-order CASSCF convergence. J Chem Phys 2019; 150:194106. [PMID: 31117783 DOI: 10.1063/1.5094644] [Citation(s) in RCA: 54] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
A new improved implementation of the second-order multiconfiguration self-consistent field optimization method of Werner and Knowles [J. Chem. Phys. 82, 5053 (1985)] is presented. It differs from the original method by more stable and efficient algorithms for minimizing the second-order energy approximation in the so-called microiterations. Conventionally, this proceeds by alternating optimizations of the orbitals and configuration (CI) coefficients and is linearly convergent. The most difficult part is the orbital optimization, which requires solving a system of nonlinear equations that are often strongly coupled. We present a much improved algorithm for solving this problem, using an iterative subspace method that includes part of the orbital Hessian explicitly, and discuss different strategies for performing the uncoupled optimization in a most efficient manner. Second, we present a new solver in which the orbital-CI coupling is treated explicitly. This leads to quadratic convergence of the microiterations but requires many additional evaluations of reduced (transition) density matrices. In difficult optimization problems with a strong coupling of the orbitals and CI coefficients, it leads to much improved convergence of both the macroiterations and the microiterations. Third, the orbital-CI coupling is treated approximately using a quasi-Newton approach with Broyden-Fletcher-Goldfarb-Shanno updates of the orbital Hessian. It is demonstrated that this converges almost as well as the explicitly coupled method but avoids the additional effort for computing many transition density matrices. The performance of the three methods is compared for a set of 21 aromatic molecules, an Fe(ii)-porphine transition metal complex, as well as for the [Cu2O2(NH3) 6]2+, FeCl3, Co2(CO)6C2H2, and Al4O2 complexes. In all cases, faster and more stable convergence than with the original implementation is achieved.
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Affiliation(s)
- David A Kreplin
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
| | - Peter J Knowles
- School of Chemistry, Cardiff University, Main Building, Park Place, Cardiff CF10 3AT, United Kingdom
| | - Hans-Joachim Werner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, D-70569 Stuttgart, Germany
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24
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Kollmar C, Sivalingam K, Helmich‐Paris B, Angeli C, Neese F. A perturbation‐based super‐CI approach for the orbital optimization of a CASSCF wave function. J Comput Chem 2019; 40:1463-1470. [DOI: 10.1002/jcc.25801] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2018] [Revised: 01/28/2019] [Accepted: 01/29/2019] [Indexed: 11/11/2022]
Affiliation(s)
- Christian Kollmar
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, D‐45470 Mülheim an der Ruhr Germany
| | - Kantharuban Sivalingam
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, D‐45470 Mülheim an der Ruhr Germany
| | - Benjamin Helmich‐Paris
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, D‐45470 Mülheim an der Ruhr Germany
| | - Celestino Angeli
- Dipartimento di Scienze Chimiche e Farmaceutiche Università di Ferrara Via Borsari 46, I‐44100 Ferrara Italy
| | - Frank Neese
- Max‐Planck‐Institut für Kohlenforschung Kaiser‐Wilhelm‐Platz 1, D‐45470 Mülheim an der Ruhr Germany
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25
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Zhou C, Gagliardi L, Truhlar DG. Multiconfiguration Pair-Density Functional Theory for Iron Porphyrin with CAS, RAS, and DMRG Active Spaces. J Phys Chem A 2019; 123:3389-3394. [DOI: 10.1021/acs.jpca.8b12479] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Chen Zhou
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - Laura Gagliardi
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455-0431, United States
| | - 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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26
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Aarabi M, Omidyan R, Soorkia S, Grégoire G, Broquier M, Crestoni ME, de la Lande A, Soep B, Shafizadeh N. The dramatic effect of N-methylimidazole on trans axial ligand binding to ferric heme: experiment and theory. Phys Chem Chem Phys 2019; 21:1750-1760. [PMID: 30623949 DOI: 10.1039/c8cp06210b] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
The binding energy of CO, O2 and NO to isolated ferric heme, [FeIIIP]+, was studied in the presence and absence of a σ donor (N-methylimidazole and histidine) as the trans axial ligand. This study combines the experimental determination of binding enthalpies by equilibrium measurements in a low temperature ion trap using the van't Hoff equation and high level DFT calculations. It was found that the presence of N-methylimidazole as the axial ligand on the [FeIIIP]+ porphyrin dramatically weakens the [FeIIIP-ligand]+ bond with an up to sevenfold decrease in binding energy owing to the σ donation by N-methylimidazole to the FeIII(3d) orbitals. This trans σ donor effect is characteristic of ligation to iron in hemes in both ferrous and ferric redox forms; however, to date, this has not been observed for ferric heme.
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Affiliation(s)
- Mohammad Aarabi
- Department of Chemistry, University of Isfahan, 81746-73441 Isfahan, Iran.
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27
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Guo M, Källman E, Pinjari RV, Couto RC, Kragh Sørensen L, Lindh R, Pierloot K, Lundberg M. Fingerprinting Electronic Structure of Heme Iron by Ab Initio Modeling of Metal L-Edge X-ray Absorption Spectra. J Chem Theory Comput 2018; 15:477-489. [DOI: 10.1021/acs.jctc.8b00658] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Meiyuan Guo
- Department of Chemistry and Chemical Engineering, Southwest University, Chongqing 400715, China
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Erik Källman
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Rahul V. Pinjari
- School of Chemical Sciences, Swami Ramanand Teerth Marathwada University, Nanded 431606, Maharashtra, India
| | - Rafael C. Couto
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Lasse Kragh Sørensen
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Roland Lindh
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
| | - Kristine Pierloot
- Department of Chemistry, University of Leuven, Celestijnenlaan 200F, B-3001 Heverlee Leuven, Belgium
| | - Marcus Lundberg
- Department of Chemistry - Ångström Laboratory, Uppsala University, 751 20 Uppsala, Sweden
- Department of Biotechnology, Chemistry and Pharmacy, Università di Siena, Via A. Moro 2, 53100 Siena, Italy
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28
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Torrent-Sucarrat M, Arrastia I, Arrieta A, Cossío FP. Stereoselectivity, Different Oxidation States, and Multiple Spin States in the Cyclopropanation of Olefins Catalyzed by Fe–Porphyrin Complexes. ACS Catal 2018. [DOI: 10.1021/acscatal.8b01492] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Affiliation(s)
- Miquel Torrent-Sucarrat
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO−CINQA), Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
- Ikerbasque, Basque Foundation for Science, Alameda Urquijo, 36-5 Plaza Bizkaia, 48011 Bilbao, Spain
| | - Iosune Arrastia
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO−CINQA), Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
| | - Ana Arrieta
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO−CINQA), Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
| | - Fernando P. Cossío
- Department of Organic Chemistry I, Universidad del País Vasco/Euskal Herriko Unibertsitatea (UPV/EHU), Centro de Innovación en Química Avanzada (ORFEO−CINQA), Manuel Lardizabal Ibilbidea 3, 20018 San Sebastián/Donostia, Spain
- Donostia International Physics Center (DIPC), Manuel Lardizabal Ibilbidea 4, 20018 San Sebastián/Donostia, Spain
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29
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Gannouni A, Michel C, Delbecq F, Zina MS, Sautet P. DFT investigations for the catalytic reaction mechanism of methane combustion occurring on Pd(ii)/Al-MCM-41. Phys Chem Chem Phys 2018; 20:25377-25386. [PMID: 30264067 DOI: 10.1039/c8cp04178d] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this work, a theoretical analysis was carried out on the mechanism of methane combustion occurring on single site palladium oxide species [Pd]2+ supported on Al-MCM-41 silica. Single site Pd-oxo and PdO2-superoxo structures were used to represent the active centers. Activation energies for all the elementary steps involved in the oxidation of methane into formaldehyde are presented. The competition of methane/methanol substrates on active sites was examined. It was found that the formation of methanol via the reaction of methane with the superoxo species, formed via the adsorption of O2 on reduced Pd(ii) centers, facilitates the production of the very active Pd-oxo catalytic sites.
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Affiliation(s)
- Anis Gannouni
- Université de Tunis El Manar, Faculté des Sciences de Tunis, Laboratoire de Chimie des Matériaux et Catalyse, Campus Universitaire, Tunis 2092, Tunisia
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30
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Nachtigallová D, Antalík A, Lo R, Sedlák R, Manna D, Tuček J, Ugolotti J, Veis L, Legeza Ö, Pittner J, Zbořil R, Hobza P. An Isolated Molecule of Iron(II) Phthalocyanin Exhibits Quintet Ground-State: A Nexus between Theory and Experiment. Chemistry 2018; 24:13413-13417. [DOI: 10.1002/chem.201803380] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2018] [Revised: 07/31/2018] [Indexed: 01/07/2023]
Affiliation(s)
- Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Andrej Antalík
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
- Faculty of Mathematics and Physics; Charles University Prague; 11636 Prague Czech Republic Republic
| | - Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Robert Sedlák
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Debashree Manna
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Jiří Tuček
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Juri Ugolotti
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Libor Veis
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Örs Legeza
- Strongly Correlated Systems “ Lendület” Research group; Wigner Research Centre for Physics; 1525 Budapest Hungary
| | - Jiří Pittner
- J. Heyrovský Institute of Physical Chemistry; Academy of Sciences of the Czech Republic; v.v.i., Dolejškova 3 18223 Prague 8 Czech Republic
| | - Radek Zbořil
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry; Academy of Sciences of the Czech Republic; v.v.i., Flemingovo nám. 2 16610 Prague 6 Czech Republic
- Regional Centre of Advanced Technologies and Materials; Department of Physical Chemistry; Faculty of Science, Palacký University in Olomouc; Šlechtitelů 27 78371 Olomouc Czech Republic
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31
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Lábas A, Menyhárd DK, Harvey JN, Oláh J. First Principles Calculation of the Reaction Rates for Ligand Binding to Myoglobin: The Cases of NO and CO. Chemistry 2018; 24:5350-5358. [PMID: 29285802 DOI: 10.1002/chem.201704867] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2017] [Indexed: 12/12/2022]
Abstract
Ligand binding by proteins is among the most fundamental processes in nature. Among these processes the binding of small gas molecules, such as O2 , CO and NO to heme proteins has traditionally received vivid interest, which was further boosted by their recently recognized significant role in gas sensing in the body. At the heart of the binding of these ligands to the heme group is the spinforbidden reaction between high-spin iron(II) and the ligand yielding a low-spin adduct. We use computational means to address the complete mechanism of CO and NO binding by myoglobin. Considering that it involves several steps occurring on different time scales, molecular dynamics simulations were performed to address the diffusion of the ligand through the enzyme, and DFT calculations in combination with statistical rate calculation to investigate the spin-forbidden reaction. The calculations yielded rate constants in qualitative agreement with experiments and revealed that the bottleneck of NO and CO binding is different; for NO, diffusion was found to be rate-limiting, whereas for CO, the spin-forbidden step is the slowest.
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Affiliation(s)
- Anikó Lábas
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
| | - Dóra K Menyhárd
- MTA-ELTE Protein Modelling Research Group, H-1117, Budapest, Pázmány Péter st. 1/A, Hungary
| | - Jeremy N Harvey
- Department of Chemistry, KU Leuven, B-3001, Leuven Celestijnenlaan 200F- box 2404, Belgium
| | - Julianna Oláh
- Department of Inorganic Chemistry, Budapest University of Technology and Economics, H-1111, Budapest, Szent Gellért tér 4., Hungary
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32
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Samajdar RN, Manogaran D, Yashonath S, Bhattacharyya AJ. Using porphyrin–amino acid pairs to model the electrochemistry of heme proteins: experimental and theoretical investigations. Phys Chem Chem Phys 2018; 20:10018-10029. [DOI: 10.1039/c8cp00605a] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Deconstructing the complex electrochemistry of heme proteins into simpler heme–amino acid interactions.
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Affiliation(s)
- Rudra N. Samajdar
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - Dhivya Manogaran
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
| | - S. Yashonath
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore 560012
- India
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33
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Smith JET, Mussard B, Holmes AA, Sharma S. Cheap and Near Exact CASSCF with Large Active Spaces. J Chem Theory Comput 2017; 13:5468-5478. [DOI: 10.1021/acs.jctc.7b00900] [Citation(s) in RCA: 103] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- James E. T. Smith
- Department of Chemistry and
Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Bastien Mussard
- Department of Chemistry and
Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Adam A. Holmes
- Department of Chemistry and
Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
| | - Sandeep Sharma
- Department of Chemistry and
Biochemistry, University of Colorado Boulder, Boulder, Colorado 80309, United States
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34
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Sun Q, Yang J, Chan GKL. A general second order complete active space self-consistent-field solver for large-scale systems. Chem Phys Lett 2017. [DOI: 10.1016/j.cplett.2017.03.004] [Citation(s) in RCA: 56] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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35
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Gannouni A, Delbecq F, Saïd Zina M, Sautet P. Oxidation of Methane to Methanol over Single Site Palladium Oxide Species on Silica: A Mechanistic view from DFT. J Phys Chem A 2017; 121:5500-5508. [DOI: 10.1021/acs.jpca.7b01509] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Anis Gannouni
- Laboratoire
de Chimie des Matériaux et Catalyse, Faculté des Sciences
de Tunis, Université de Tunis El Manar, Campus Universitaire, Tunis 2092, Tunisie
| | - Françoise Delbecq
- Laboratoire
de Chimie, École Normale Supérieure de Lyon, CNRS UMR5182, Université de Lyon, 46 Allée d’Italie, F-69046 Lyon, France
| | - Mongia Saïd Zina
- Laboratoire
de Chimie des Matériaux et Catalyse, Faculté des Sciences
de Tunis, Université de Tunis El Manar, Campus Universitaire, Tunis 2092, Tunisie
| | - Philippe Sautet
- Laboratoire
de Chimie, École Normale Supérieure de Lyon, CNRS UMR5182, Université de Lyon, 46 Allée d’Italie, F-69046 Lyon, France
- Department
of Chemical and Biomolecular Engineering, University of California Los Angeles, Los Angeles, California 90095, United States
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36
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Marchand G, Siri O, Jacquemin D. On the structures, spin states, and optical properties of titanium, platinum, and iron azacalixphyrins: a DFT study. Phys Chem Chem Phys 2017; 19:15903-15913. [PMID: 28589971 DOI: 10.1039/c7cp02600e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Azacalixphyrins (ACP) constitute a new class of macrocycles isoelectronic and isostructural to porphyrins. Herein, we report the first theoretical investigation of the properties of the ACP macrocycles metallated at their centre by titanium, platinum, and iron ions. We considered both the original phenyl-type ACP and new pyridyl-type forms. Our results indicate that the metallation greatly impacts the global structure of the macrocycle through pseudo Jahn-Teller effects, giving rise to a possible conformational transition between D2d and S4 structures. Such an effect could not be found in the metal-free ACPs. In addition, we find that, in contrast to the purely singlet platinum ACPs, and the purely triplet iron ACPs, several spin states are energetically close in the titanium ACPs, especially when weak field ligands are bound in axial positions to the metallic centre. According to TD-DFT calculations, metallation also tunes the optical properties. In particular, the absorption band in the near infrared region undergoes a hypsochromic shift of ca. 100-200 nm when going from the D2d to the S4 structures. We quantify how the addition of electroactive ligands in the axial position can increase or tune down these spectral changes. This contribution therefore supports the development of ACP coordination complexes.
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Affiliation(s)
- Gabriel Marchand
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes, Cedex 3, France.
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37
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Suzuki H, Inabe K, Shirakawa Y, Umezawa N, Kato N, Higuchi T. Role of Thiolate Ligand in Spin State and Redox Switching in the Cytochrome P450 Catalytic Cycle. Inorg Chem 2017; 56:4245-4248. [DOI: 10.1021/acs.inorgchem.6b02499] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hiroshi Suzuki
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
| | - Kanako Inabe
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
| | - Yoshinori Shirakawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
| | - Naoki Umezawa
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
| | - Nobuki Kato
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
| | - Tsunehiko Higuchi
- Graduate School of Pharmaceutical Sciences, Nagoya City University, 3-1 Tanabe-dori, Mizuho-ku,
Nagoya 467-8603, Japan
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38
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Phung QM, Wouters S, Pierloot K. Cumulant Approximated Second-Order Perturbation Theory Based on the Density Matrix Renormalization Group for Transition Metal Complexes: A Benchmark Study. J Chem Theory Comput 2016; 12:4352-61. [DOI: 10.1021/acs.jctc.6b00714] [Citation(s) in RCA: 78] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Quan Manh Phung
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
| | - Sebastian Wouters
- Center
for Molecular Modelling, Ghent University, Technologiepark 903, 9052 Zwijnaarde, Belgium
| | - Kristine Pierloot
- Department
of Chemistry, KU Leuven, Celestijnenlaan 200F, 3001 Leuven, Belgium
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39
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Zhao H, Fang C, Gao J, Liu C. Spin-state energies of heme-related models from spin-flip TDDFT calculations. Phys Chem Chem Phys 2016; 18:29486-29494. [DOI: 10.1039/c6cp04826a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The spin-state energies of heme-related models were calculated by using the spin-flip TDDFT method avoiding spin contamination.
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Affiliation(s)
- Hui Zhao
- Institute of Theoretical Chemistry
- School of Chemistry & Chemical Engineering
- Shandong University
- Jinan
- People's Republic of China
| | - Changfeng Fang
- Department of Physics
- Jining University
- Qufu
- People's Republic of China
| | - Jun Gao
- Institute of Theoretical Chemistry
- School of Chemistry & Chemical Engineering
- Shandong University
- Jinan
- People's Republic of China
| | - Chengbu Liu
- Institute of Theoretical Chemistry
- School of Chemistry & Chemical Engineering
- Shandong University
- Jinan
- People's Republic of China
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40
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Aquilante F, Malmqvist PÅ, Pedersen TB, Ghosh A, Roos BO. Cholesky Decomposition-Based Multiconfiguration Second-Order Perturbation Theory (CD-CASPT2): Application to the Spin-State Energetics of Co(III)(diiminato)(NPh). J Chem Theory Comput 2015; 4:694-702. [PMID: 26621084 DOI: 10.1021/ct700263h] [Citation(s) in RCA: 292] [Impact Index Per Article: 32.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The electronic structure and low-lying electronic states of a Co(III)(diiminato)(NPh) complex have been studied using multiconfigurational wave function theory (CASSCF/CASPT2). The results have been compared to those obtained with density functional theory. The best agreement with ab initio results is obtained with a modified B3LYP functional containing a reduced amount (15%) of Hartree-Fock exchange. A relativistic basis set with 869 functions has been employed in the most extensive ab initio calculations, where a Cholesky decomposition technique was used to overcome problems arising from the large size of the two-electron integral matrix. It is shown that this approximation reproduces results obtained with the full integral set to a high accuracy, thus opening the possibility to use this approach to perform multiconfigurational wave-function-based quantum chemistry on much larger systems relative to what has been possible until now.
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Affiliation(s)
- Francesco Aquilante
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Per-Åke Malmqvist
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Thomas Bondo Pedersen
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Abhik Ghosh
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
| | - Björn Olof Roos
- Department of Theoretical Chemistry, Chemical Center, University of Lund, P.O. Box 124, S-221 00 Lund, Sweden, and Department of Chemistry, University of Tromsø, N-9037 Tromsø, Norway
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41
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De Petris A, Crestoni ME, Pirolli A, Rovira C, Iglesias-Fernández J, Chiavarino B, Ragno R, Fornarini S. Binding of azole drugs to heme: A combined MS/MS and computational approach. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.02.011] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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42
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de Sousa Sousa N, de Lima RB, Silva ALP, Tanaka AA, da Silva ABF, de Jesus Gomes Varela J. Theoretical study of dibenzotetraaza[14]annulene complexes with first row transition metals. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.12.005] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Olivares-Amaya R, Hu W, Nakatani N, Sharma S, Yang J, Chan GKL. Theab-initiodensity matrix renormalization group in practice. J Chem Phys 2015; 142:034102. [DOI: 10.1063/1.4905329] [Citation(s) in RCA: 231] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
| | - Weifeng Hu
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Naoki Nakatani
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
- Catalysis Research Center, Hokkaido University, Kita 21 Nishi 10, Sapporo, Hokkaido 001-0021, Japan
| | - Sandeep Sharma
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Jun Yang
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
| | - Garnet Kin-Lic Chan
- Department of Chemistry, Princeton University, Princeton, New Jersey 08544, USA
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44
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Dey G, Wrench JS, Hagen DJ, Keeney L, Elliott SD. Quantum chemical and solution phase evaluation of metallocenes as reducing agents for the prospective atomic layer deposition of copper. Dalton Trans 2015; 44:10188-99. [DOI: 10.1039/c5dt00922g] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We propose and evaluate the use of metallocene compounds as reducing agents for the chemical vapour deposition (and specifically atomic layer deposition, ALD) of the transition metal Cu from metalorganic precursors.
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Affiliation(s)
- Gangotri Dey
- Tyndall National Institute
- University College Cork
- Cork
- Ireland
| | | | - Dirk J. Hagen
- Tyndall National Institute
- University College Cork
- Cork
- Ireland
| | - Lynette Keeney
- Tyndall National Institute
- University College Cork
- Cork
- Ireland
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45
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Gheidi M, Safari N, Zahedi M. Chameleonic Nature of Hydroxyheme in Heme Oxygenase and Its Reactivity: A Density Functional Theory Study. Inorg Chem 2014; 53:2766-75. [DOI: 10.1021/ic402754y] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Mahin Gheidi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Nasser Safari
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
| | - Mansour Zahedi
- Department of Chemistry, Faculty
of Sciences, Shahid Beheshti University, G. C. Evin, 19839-63113 Tehran, Iran
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46
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Burggraf F, Koslowski T. Charge transfer through a cytochrome multiheme chain: Theory and simulation. BIOCHIMICA ET BIOPHYSICA ACTA-BIOENERGETICS 2014; 1837:186-92. [DOI: 10.1016/j.bbabio.2013.09.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Revised: 08/22/2013] [Accepted: 09/10/2013] [Indexed: 10/26/2022]
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47
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Myradalyyev S, Limpanuparb T, Wang X, Hirao H. Comparative computational analysis of binding energies between several divalent first-row transition metals (Cr2+, Mn2+, Fe2+, Co2+, Ni2+, and Cu2+) and ligands (porphine, corrin, and TMC). Polyhedron 2013. [DOI: 10.1016/j.poly.2012.11.018] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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48
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Zlatar M, Gruden-Pavlović M, Güell M, Swart M. Computational study of the spin-state energies and UV-Visspectra of bis(1,4,7-triazacyclononane) complexes of some first-row transition metal cations. Phys Chem Chem Phys 2013; 15:6631-9. [DOI: 10.1039/c2cp43735j] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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49
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Gheidi M, Safari N, Zahedi M. Structure and Redox Behavior of Iron Oxophlorin and Role of Electron Transfer in the Heme Degradation Process. Inorg Chem 2012; 51:12857-66. [DOI: 10.1021/ic3017497] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Mahin Gheidi
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
| | - Nasser Safari
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
| | - Mansour Zahedi
- Department
of Chemistry, Faculty of Sciences, Shahid
Beheshti University, G. C., Evin, 19839-63113, Tehran, Iran
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50
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Frühbeißer S, Gröhn F. Catalytic activity of macroion-porphyrin nanoassemblies. J Am Chem Soc 2012; 134:14267-70. [PMID: 22906213 DOI: 10.1021/ja307596q] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
A new type of catalytically active self-assembled nanostructures in aqueous solution is presented. Polyelectrolyte-porphyrin nanoscale assemblies consisting of anionic cylindrical poly(styrene sulfonate) brush molecules and cationic tetravalent meso-tetrakis(4-N-methyl-pyridinium)porphyrin (TMPyP) or meso-tetrakis(4-(trimethyl-ammonium)phenyl)-porphyrin (TAPP), respectively, exhibit up to 8-fold higher catalytic activity with regard to light induced iodide oxidation than the corresponding porphyrins without polymeric template. This is particularly interesting because a general concept rather than a specific binding motif is exploited. The approach introduced here hence is attractive due to its facility and versatility and bears potential, for example, in light harvesting and energy conversion.
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Affiliation(s)
- Sabine Frühbeißer
- Department of Chemistry and Pharmacy and Interdisciplinary Center for Molecular Materials, Friedrich-Alexander-Universität Erlangen-Nürnberg, Egerlandstrasse 3, D-91058 Erlangen, Germany
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