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Density functional theory study of the CO adsorption on Ni4M (M = Mo, Sc, and Y) nanoclusters. COMPUT THEOR CHEM 2019. [DOI: 10.1016/j.comptc.2019.03.024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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2
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Shoji M, Isobe H, Shen JR, Yamaguchi K. Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex. Phys Chem Chem Phys 2017; 18:11330-40. [PMID: 27055567 DOI: 10.1039/c5cp07226c] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(Bu(t)COO)8(py)(Bu(t)COOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.
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Affiliation(s)
- Mitsuo Shoji
- Center for Computational Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8577, Japan and Graduate School of Pure and Applied Sciences, University of Tsukuba, Tennodai 1-1-1, Tsukuba 305-8571, Japan.
| | - Hiroshi Isobe
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Jian-Ren Shen
- Photosynthesis Research Center, Graduate School of Natural Science and Technology, Okayama University, Okayama 700-8530, Japan
| | - Kizashi Yamaguchi
- Institute for NanoScience Design, Osaka University, Toyonaka, Osaka 560-0043, Japan and Handairigaku Techno-Research (NPO), Toyonaka, Osaka 560-0043, Japan
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3
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Liu C, Han P, Liu Y, Tang M. Mechanism studies of the chemoselective ring opening of N-tosyl aziridines with aldehydes catalyzed by an N-heterocyclic carbene under aerobic conditions. Theor Chem Acc 2016. [DOI: 10.1007/s00214-016-1820-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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4
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Varga Z, Truhlar DG. B2N2O4: Prediction of a Magnetic Ground State for a Light Main-Group Molecule. Inorg Chem 2015; 54:8552-9. [PMID: 26273729 DOI: 10.1021/acs.inorgchem.5b01223] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Cyclobutanetetrone, (CO)4, has a triplet ground state. Here we predict, based on electronic structure calculations, that the B2N2O4 molecule also has a triplet ground state and is therefore paramagnetic; the structure is an analogue of (CO)4 in which the carbon ring is replaced by a (BN)2 ring. Similar to (CO)4, the triplet ground-state structure of B2N2O4 is also thermodynamically unstable. Besides analysis of the molecular orbitals, we found that the partial atomic charges are good indicators for predicting magnetic ground states.
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Affiliation(s)
- Zoltan Varga
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Donald G Truhlar
- Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota , Minneapolis, Minnesota 55455, United States
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5
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Singlet–triplet competition in the low-lying energy states of C4O4−n S n (n = 1–3) molecules. Struct Chem 2015. [DOI: 10.1007/s11224-015-0633-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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6
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Rohrmüller M, Hoffmann A, Thierfelder C, Herres-Pawlis S, Schmidt WG. The Cu2O2torture track for a real-life system: [Cu2(btmgp)2O2]2+oxo and peroxo species in density functional calculations†. J Comput Chem 2015; 36:1672-85. [DOI: 10.1002/jcc.23983] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2015] [Revised: 05/26/2015] [Accepted: 05/28/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Martin Rohrmüller
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
| | - Alexander Hoffmann
- RWTH Aachen University, Fachgruppe Chemie, Lehrstuhl für Bioanorganische Chemie; Landoltweg 1 52074 Aachen Germany
| | - Christian Thierfelder
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
| | - Sonja Herres-Pawlis
- RWTH Aachen University, Fachgruppe Chemie, Lehrstuhl für Bioanorganische Chemie; Landoltweg 1 52074 Aachen Germany
| | - Wolf Gero Schmidt
- Universität Paderborn, Department Physik, Lehrstuhl für Theoretische Physik; Pohlweg 55 33095 Paderborn Germany
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Saito T, Kawakami T, Yamanaka S, Okumura M. Computational Study of Catalytic Reaction of Quercetin 2,4-Dioxygenase. J Phys Chem B 2015; 119:6952-62. [PMID: 25990020 DOI: 10.1021/acs.jpcb.5b03564] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We present a quantum mechanics/molecular mechanics (QM/MM) and QM-only study on the oxidative ring-cleaving reaction of quercetin catalyzed by quercetin 2,4-dioxygenase (2,4-QD). 2,4-QD has a mononuclear type 2 copper center and incorporates two oxygen atoms at C2 and C4 positions of the substrate. It has not been clear whether dioxygen reacts with a copper ion or a substrate radical as the first step. We have found that dioxygen is more likely to bind to a Cu(2+) ion, involving the dissociation of the substrate from the copper ion. Then a Cu(2+)-alkylperoxo complex can be generated. Comparison of geometry and stability between QM-only and QM/MM results strongly indicates that steric effects of the protein environment contribute to maintain the orientation of the substrate dissociated from the copper center. The present QM/MM results also highlight that a prior rearrangement of the Cu(2+)-alkylperoxo complex and a subsequent hydrogen bond switching assisted by the movement of Glu73 can facilitate formation of an endoperoxide intermediate selectively.
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Affiliation(s)
- Toru Saito
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Takashi Kawakami
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shusuke Yamanaka
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
| | - Mitsutaka Okumura
- †Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan.,‡Core Research for Evolutional Science and Technology (CREST), Japan Science and Technology (JST) Agency, Kawaguchi, Saitama 332-0012, Japan
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Abstract
A method is suggested to build simple multiconfigurational wave functions specified uniquely by an energy cutoff Λ. These are constructed from a model space containing determinants with energy relative to that of the most stable determinant no greater than Λ. The resulting Λ-CI wave function is adaptive, being able to represent both single-reference and multireference electronic states. We also consider a more compact wave function parameterization (Λ+SD-CI), which is based on a small Λ-CI reference and adds a selection of all the singly and doubly excited determinants generated from it. We report two heuristic algorithms to build Λ-CI wave functions. The first is based on an approximate prescreening of the full configuration interaction space, while the second performs a breadth-first search coupled with pruning. The Λ-CI and Λ+SD-CI approaches are used to compute the dissociation curve of N2 and the potential energy curves for the first three singlet states of C2. Special attention is paid to the issue of energy discontinuities caused by changes in the size of the Λ-CI wave function along the potential energy curve. This problem is shown to be solvable by smoothing the matrix elements of the Hamiltonian. Our last example, involving the Cu2O2(2+) core, illustrates an alternative use of the Λ-CI method: as a tool to both estimate the multireference character of a wave function and to create a compact model space to be used in subsequent high-level multireference coupled cluster computations.
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Affiliation(s)
- Francesco A Evangelista
- Department of Chemistry and Cherry L. Emerson Center for Scientific Computation, Emory University, Atlanta, Georgia 30322, USA
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Saito T, Thiel W. Quantum mechanics/molecular mechanics study of oxygen binding in hemocyanin. J Phys Chem B 2014; 118:5034-43. [PMID: 24762083 DOI: 10.1021/jp5003885] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We report a combined quantum mechanics/molecular mechanics (QM/MM) study on the mechanism of reversible dioxygen binding in the active site of hemocyanin (Hc). The QM region is treated by broken-symmetry density functional theory (DFT) with spin projection corrections. The X-ray structures of deoxygenated (deoxyHc) and oxygenated (oxyHc) hemocyanin are well reproduced by QM/MM geometry optimizations. The computed relative energies strongly depend on the chosen density functional. They are consistent with the available thermodynamic data for oxygen binding in hemocyanin and in synthetic model complexes when the BH&HLYP hybrid functional with 50% Hartree-Fock exchange is used. According to the QM(BH&HLYP)/MM results, the reaction proceeds stepwise with two sequential electron transfer (ET) processes in the triplet state followed by an intersystem crossing to the singlet product. The first ET step leads to a nonbridged superoxo CuB(II)-O2(•-) intermediate via a low-barrier transition state. The second ET step is even more facile and yields a side-on oxyHc complex with the characteristic Cu2O2 butterfly core, accompanied by triplet-singlet intersystem crossing. The computed barriers are very small so that the two ET processes are expected to very rapid and nearly simultaneous.
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Affiliation(s)
- Toru Saito
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
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Rohrmüller M, Herres-Pawlis S, Witte M, Schmidt WG. Bis-μ-oxo and μ-η2:η2-peroxo dicopper complexes studied within (time-dependent) density-functional and many-body perturbation theory. J Comput Chem 2013; 34:1035-45. [DOI: 10.1002/jcc.23230] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2012] [Revised: 12/13/2012] [Accepted: 12/14/2012] [Indexed: 02/03/2023]
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11
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Peng D, Hu X, Devarajan D, Ess DH, Johnson ER, Yang W. Variational fractional-spin density-functional theory for diradicals. J Chem Phys 2012; 137:114112. [DOI: 10.1063/1.4749242] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
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12
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Ess DH, Cook TC. Unrestricted prescriptions for open-shell singlet diradicals: using economical ab initio and density functional theory to calculate singlet-triplet gaps and bond dissociation curves. J Phys Chem A 2012; 116:4922-9. [PMID: 22578025 DOI: 10.1021/jp300633j] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
Here we present and test several computational prescriptions for calculating singlet-triplet (ST) gap energies and bond dissociation curves for open-shell singlet diradicals using economical unrestricted single reference type calculations. For ST gap energies from Slipchenko and Krylov's atom and molecule test set (C, O, Si, NH, NF, OH(+), O(2), CH(2), and NH(2)(+)) spin unrestricted Hartree-Fock and MP2 energies result in errors greater than 15 kcal/mol. However, spin-projected (SP) Hartree-Fock theory in combination with spin-component-scaled (SCS) or scaled-opposite-spin (SOS) second-order perturbation theory gives ST gap energies with a mean unsigned error (MUE) of less than 2 kcal/mol. Density functionals generally give poor results for unrestricted energies and only the ωB97X-D, the M06, and the M06-2X functionals provide reasonable accuracy after spin-projection with MUE values of 4.7, 4.3, and 3.0 kcal/mol, respectively, with the 6-311++G(2d,2p) basis set. We also present a new one parameter hybrid density functional, diradical-1 (DR-1), based on Adamo and Barone's modified PW exchange functional with the PW91 correlation functional. This DR-1 method gives a mean error (ME) of 0.0 kcal/mol and a MUE value of 1.3 kcal/mol for ST gap energies. As another test of unrestricted methods the bond dissociation curves for methane (CH(4)) and hydrofluoric acid (H-F) were calculated with the M06-2X, DR-1, and ωB97X-D density functionals. All three of these functionals give reasonable results for the methane C-H bond but result in errors greater than 50 kcal/mol for the H-F bond dissociation. Spin-projection is found to significantly degrade bond dissociation curves past ~2.2 Å. Although unrestricted Hartree-Fock theory provides a very poor description of H-F bond dissociation, unrestricted SCS-MP2 and SOS-MP2 methods give accurate results.
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Affiliation(s)
- Daniel H Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, USA.
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13
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Saito T, Yasuda N, Nishihara S, Yamanaka S, Kitagawa Y, Kawakami T, Okumura M, Yamaguchi K. Broken-symmetry natural orbital (BSNO)–Mk-MRCC study on the exchange coupling in the binuclear copper(II) compounds. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.02.018] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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14
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Ess DH, Johnson ER, Hu X, Yang W. Singlet−Triplet Energy Gaps for Diradicals from Fractional-Spin Density-Functional Theory. J Phys Chem A 2010; 115:76-83. [DOI: 10.1021/jp109280y] [Citation(s) in RCA: 98] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Affiliation(s)
- Daniel H. Ess
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States, School of Natural Sciences, University of California—Merced, 5200 North Lake Road, Merced, California 95343, United States, and Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Erin R. Johnson
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States, School of Natural Sciences, University of California—Merced, 5200 North Lake Road, Merced, California 95343, United States, and Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Xiangqian Hu
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States, School of Natural Sciences, University of California—Merced, 5200 North Lake Road, Merced, California 95343, United States, and Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry and Biochemistry, Brigham Young University, Provo, Utah 84602, United States, School of Natural Sciences, University of California—Merced, 5200 North Lake Road, Merced, California 95343, United States, and Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
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15
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Saito T, Kataoka Y, Nakanishi Y, Kitagawa Y, Kawakami T, Yamanaka S, Okumura M, Yamaguchi K. Theoretical studies on the electronic structure of the synthetic complex of soluble methanemonooxygenase intermediate Q. Supramol Chem 2010. [DOI: 10.1080/10610278.2010.510560] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Toru Saito
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yusuke Kataoka
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasuyuki Nakanishi
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Yasutaka Kitagawa
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Takashi Kawakami
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Shusuke Yamanaka
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Mitsutaka Okumura
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
| | - Kizashi Yamaguchi
- a Department of Chemistry , Graduate School of Science, Osaka University , 1-1 Machikaneyama, Toyonaka, Osaka, 560-0043, Japan
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16
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Rezabal E, Ducháčková L, Milko P, Holthausen MC, Roithová J. Ligand Effects on the [Cu(PhO)(PhOH)]+ Redox Active Complex. Inorg Chem 2010; 49:8421-9. [DOI: 10.1021/ic100952q] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Elixabete Rezabal
- Institut für Anorganische und Analytische Chemie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Lucie Ducháčková
- Department of Organic and Nuclear Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Praha 2, Czech Republic
| | - Petr Milko
- Institute of Organic Chemistry and Biochemistry, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Max C. Holthausen
- Institut für Anorganische und Analytische Chemie, Johann Wolfgang Goethe-Universität Frankfurt, Max-von-Laue-Strasse 7, 60438 Frankfurt am Main, Germany
| | - Jana Roithová
- Department of Organic and Nuclear Chemistry, Faculty of Science, Charles University in Prague, Hlavova 8, 12840 Praha 2, Czech Republic
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17
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Saito T, Nishihara S, Kataoka Y, Nakanishi Y, Kitagawa Y, Kawakami T, Yamanaka S, Okumura M, Yamaguchi K. Reinvestigation of the Reaction of Ethylene and Singlet Oxygen by the Approximate Spin Projection Method. Comparison with Multireference Coupled-Cluster Calculations. J Phys Chem A 2010; 114:7967-74. [DOI: 10.1021/jp102635s] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Toru Saito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Satomichi Nishihara
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yusuke Kataoka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasuyuki Nakanishi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Yasutaka Kitagawa
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Takashi Kawakami
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Shusuke Yamanaka
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Mitsutaka Okumura
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Kizashi Yamaguchi
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
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