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Zhao Y, Cui X, Song Y, Zhang C, Meng Q. Photophysical properties of fluorescent nucleobase P-analogues expected to monitor DNA replication. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2021; 260:119926. [PMID: 34022693 DOI: 10.1016/j.saa.2021.119926] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/22/2021] [Accepted: 05/04/2021] [Indexed: 06/12/2023]
Abstract
In this work, we computationally design a series of fluorescent purine analogues based on the 2-amino-8-(1'-β-D-2'-deoxyribofuranosyl)-imidazo[1,2-a]-1,3,5-triazin-4(8H)-one (P) to monitor the DNA replication process with merely a minimal perturbation to the natural structure of nucleic acid. The P-modified fluorescent probes present red-shifted absorption spectra and enhanced photoluminescence due to the additional π-conjugation resulting from the fluorophore modification and the ring-expansion. Efficient fluorescence quenching of P-analogues occurs upon pairing with the complementary 6-amino-5-nitro-3-(1'-β-D-2'-deoxyribofuranosyl)-2(1H)-pyridone (Z) due to the nonradiative relaxation from the low-lying dark excited state to the ground state of Z moiety. Especially, the P3 and the P7, which have high fluorescence intensity in both gas and liquid phases, are proposed as the sensors for studying conformational switching in the presence and absence of a complementary sequence. Also examined are the influences of hydration and the linking to deoxyribose on absorption and emission processes. Besides, the potential phosphorescence emission of these modified base pairs is taken into account by constructing the relaxed potential energy curves of S0, T1 and S1 states.
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Affiliation(s)
- Yu Zhao
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Xixi Cui
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Yuzhi Song
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China
| | - Changzhe Zhang
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
| | - Qingtian Meng
- School of Physics and Electronics, Shandong Normal University, Jinan 250358, China.
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2
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Chattopadhyay S. Single-Root Multireference Brillouin-Wigner Perturbative Approach to Excitation Energies. ACS OMEGA 2021; 6:1668-1686. [PMID: 33490826 PMCID: PMC7818614 DOI: 10.1021/acsomega.0c05714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2020] [Accepted: 12/28/2020] [Indexed: 06/12/2023]
Abstract
The state-specific Brillouin-Wigner multireference perturbation theory [which employs Jeziorski-Monkhorst parametrization of the wave function] using improved virtual orbitals, denoted as IVO-BWMRPT, is applied to calculate excitation energies (EEs) for methylene, ethylene, trimethylenemethane, and benzyne systems exhibiting various degrees of diradical character. In IVO-BWMRPT, all of the parameters appearing in the wave function ansatz are optimized for a specific electronic state. For these systems, the IVO-BWMRPT method provides EEs that are in close agreement with the benchmark results and experiments, where available, indicating that the method does not introduce imbalance in the target-specific treatment of closed- and open-shell states involved. The good performance of the present methodology is primarily related to structural compactness of the formalism. Overall, present findings are encouraging for both further development of the approach and chemical applications on the energy differences of strongly correlated systems.
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Affiliation(s)
- Sudip Chattopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology,
Shibpur, Howrah 711103, India
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3
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Devillard M, Regnier V, Tripathi M, Martin D. A computational study of the interplay of steric and electronic effects in the stabilization of 1,3-(diamino)oxyallyls. J Mol Struct 2018. [DOI: 10.1016/j.molstruc.2018.02.029] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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4
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Chattopadhyay S. The effect of substituents on energy splitting in organic radicals: Quantitative cognizance from ab initio studies. Chem Phys 2018. [DOI: 10.1016/j.chemphys.2018.08.008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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5
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Evangelista FA. Perspective: Multireference coupled cluster theories of dynamical electron correlation. J Chem Phys 2018; 149:030901. [DOI: 10.1063/1.5039496] [Citation(s) in RCA: 69] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
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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Moreira RA. Energy Gaps of Polyradicals from an Effective and Transferable Hamiltonian with through-Bond Interactions. J Chem Theory Comput 2018; 14:1-8. [PMID: 29202223 DOI: 10.1021/acs.jctc.7b00930] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Current model Hamiltonians and ab initio many-body quantum treatments of π-conjugated polyradicals formed from hydrocarbons produce divergent results because of numerical complexity and large size of the basis-function set used. We propose an alternative, three-term Hamiltonian, to describe these various polyradicals that simplifies considerably the computational cost while providing a physical interpretation for all three terms and a high degree of model universality. The essential feature of this Hamiltonian is a term, not present in previous models, describing the three-sited through-bond interaction that governs the noninteracting spin-up and spin-down sectors. A computation of the lowest energy gaps and spin configurations for the smaller polyradicals demonstrates the efficacy of the model and its potential in applications in revealing electrical conductivity and ferromagnetism of the more complicated substituted polyradicals.
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Affiliation(s)
- Rodrigo A Moreira
- Departamento de Física, Universidade Federal de Pernambuco , 50670-901 Recife, Pernambuco, Brasil
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A comparative study on seniority-based MO and VB calculations of the singlet and triplet energy gaps of open-shell molecules. COMPUT THEOR CHEM 2017. [DOI: 10.1016/j.comptc.2017.03.031] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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8
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Fang W, Wei Y, Tang XY, Shi M. Gold(I)-Catalyzed Cycloisomerization of ortho
-(Propargyloxy)arenemethylenecyclopropanes Controlled by Adjacent Substituents at Aromatic Rings. Chemistry 2017; 23:6845-6852. [DOI: 10.1002/chem.201700600] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Wei Fang
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Meilong Road No. 130 Shanghai 200237 P.R. China
| | - Yin Wei
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 P.R. China
| | - Xiang-Ying Tang
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 P.R. China
| | - Min Shi
- Key Laboratory for Advanced Materials and Institute of Fine Chemicals, School of Chemistry and Molecular Engineering; East China University of Science and Technology; Meilong Road No. 130 Shanghai 200237 P.R. China
- State Key Laboratory of Organometallic Chemistry, Shanghai Institute of Organic Chemistry; Chinese Academy of Sciences; 345 Lingling Road Shanghai 200032 P.R. China
- State Key Laboratory and Institute of Elemento-organic Chemistry; Nankai University; Tianjin 300071 P.R. China)
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Lang J, Švaňa M, Demel O, Brabec J, Kedžuch S, Noga J, Kowalski K, Pittner J. A MRCC study of the isomerisation of cyclopropane. Mol Phys 2017. [DOI: 10.1080/00268976.2017.1317112] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Jakub Lang
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
- Faculty of Science, Charles University in Prague, Prague 2, Czech Republic
| | - Matej Švaňa
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Ondřej Demel
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Jiri Brabec
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
| | - Stanislav Kedžuch
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
| | - Jozef Noga
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
- Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Karol Kowalski
- William R. Wiley Environmental Molecular Sciences Laboratory, Battelle, Pacific Northwest National Laboratory, Richland, WA 99352, USA
| | - Jiří Pittner
- J. Heyrovsky Institute of Physical Chemistry, Academy of Sciences of the Czech Republic, Prague 8, Czech Republic
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Perera A, Molt RW, Lotrich VF, Bartlett RJ. Singlet–triplet separations of di-radicals treated by the DEA/DIP-EOM-CCSD methods. Theor Chem Acc 2014. [DOI: 10.1007/s00214-014-1514-5] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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11
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Qiao Y, Han KL. Theoretical investigations toward the tandem reactions of N-aziridinyl imine compounds forming triquinanes via trimethylenemethane diyls: mechanisms and stereoselectivity. Org Biomol Chem 2014; 12:1220-31. [PMID: 24336836 DOI: 10.1039/c3ob42115e] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this paper, we have investigated the tandem reaction mechanism for the N-aziridinyl imine compounds forming triquinanes via trimethylenemethane (TMM) diyls in detail. Based on the calculated results, the reaction is initiated by the cleavage of the N-aziridinyl in the substrate, followed by an intramolecular 1,3-dipolar (3 + 2) cycloaddition preferentially leading to a linearly-fused tetrahydrocyclopentapyrazole intermediate. Next, the intermediate loses N2 to form the singlet TMM diyl M3S, which can then undergo another concerted (3 + 2) cycloaddition to generate the linearly-fused cis–trans or cis–syn triquinane products. In addition, M3S can also undergo intersystem crossing to the triplet TMM diyl M3T, and the six possible reaction pathways associated with M3T have also been identified. The calculated results reveal that the cis–trans fused pathway associated with M3S is energetically preferred with the highest free energy barrier of 25.0 kcal mol(−1). In comparison, the cyclization of M3T requires much higher activation free energies (ΔG(≠) = 34.4–57.8 kcal mol(−1)). At the experimental temperature 110 °C, only the linearly-fused cis–trans and cis–syn pathways associated with M3T (ΔG(≠) = 34.4 and 35.5 kcal mol(−1) respectively) are possible. The calculated results also indicate that for both M3S and M3T, the linearly-fused cis–trans triquinane should be the main product, which is consistent with the experimental observation. At last, conformational and NBO analyses on key transition states identified the cis–trans stereocontrol factors. Further calculations indicate that the methyl substituent on the allene group of the reactant substrate improves the stereoselectivity of the reaction but does not affect the rate-determining step.
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Affiliation(s)
- Yan Qiao
- State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Science, Zhongshan Road 457, Dalian 116023, P. R. China.
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12
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Malrieu JP, Caballol R, Calzado CJ, de Graaf C, Guihéry N. Magnetic interactions in molecules and highly correlated materials: physical content, analytical derivation, and rigorous extraction of magnetic Hamiltonians. Chem Rev 2013; 114:429-92. [PMID: 24102410 DOI: 10.1021/cr300500z] [Citation(s) in RCA: 282] [Impact Index Per Article: 25.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Jean Paul Malrieu
- Laboratoire de Chimie et Physique Quantiques, Université de Toulouse 3 , 118 route de Narbonne, 31062 Toulouse, France
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Shen J, Piecuch P. Doubly electron-attached and doubly ionized equation-of-motion coupled-cluster methods with 4-particle–2-hole and 4-hole–2-particle excitations and their active-space extensions. J Chem Phys 2013; 138:194102. [DOI: 10.1063/1.4803883] [Citation(s) in RCA: 62] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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14
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Shen J, Piecuch P. Merging Active-Space and Renormalized Coupled-Cluster Methods via the CC(P;Q) Formalism, with Benchmark Calculations for Singlet–Triplet Gaps in Biradical Systems. J Chem Theory Comput 2012; 8:4968-88. [DOI: 10.1021/ct300762m] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jun Shen
- Department of Chemistry, Michigan State University,
East Lansing, Michigan 48824, United States
| | - Piotr Piecuch
- Department of Chemistry, Michigan State University,
East Lansing, Michigan 48824, United States
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15
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State specific multireference Møller–Plesset perturbation theory: A few applications to ground, excited and ionized states. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.04.011] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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16
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Šimsa D, Demel O, Bhaskaran-Nair K, Hubač I, Mach P, Pittner J. Multireference coupled cluster study of the oxyallyl diradical. Chem Phys 2012. [DOI: 10.1016/j.chemphys.2011.08.018] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Bozkaya U, Özkan İ. Potential Energy Surfaces for Rearrangements of Berson Trimethylenemethanes. J Phys Chem A 2012; 116:2309-21. [DOI: 10.1021/jp211518f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Uǧur Bozkaya
- Department of Chemistry, Atatürk University, Erzurum 25240, Turkey
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
| | - İlker Özkan
- Department of Chemistry, Middle East Technical University, Ankara 06800, Turkey
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Bozkaya U, Özkan I. Thermal denitrogenation of 7-isopropylidene-2,3-diaza-norbornene: formation of substituted 3-methylene-(1,4)-pentadienes. Phys Chem Chem Phys 2012; 14:14282-92. [DOI: 10.1039/c2cp42349a] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Brabec J, Krishnamoorthy S, van Dam HJ, Kowalski K, Pittner J. Massively parallel implementation of the multireference Brillouin–Wigner CCSD method. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.08.016] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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20
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Saito T, Yasuda N, Kataoka Y, Nakanishi Y, Kitagawa Y, Kawakami T, Yamanaka S, Okumura M, Yamaguchi K. Potential Energy Curve for Ring-Opening Reactions: Comparison Between Broken-Symmetry and Multireference Coupled Cluster Methods. J Phys Chem A 2011; 115:5625-31. [DOI: 10.1021/jp201463h] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Toru Saito
- Department of Chemistry, Graduate School of Science, Osaka University, 1-1 Machikaneyama, Toyonaka, Osaka 560-0043, Japan
| | - Natsumi Yasuda
- 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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Bhaskaran-Nair K, Demel O, Šmydke J, Pittner J. Multireference state-specific Mukherjee's coupled cluster method with noniterative triexcitations using uncoupled approximation. J Chem Phys 2011; 134:154106. [DOI: 10.1063/1.3573373] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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22
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Lopez X, Ruipérez F, Piris M, Matxain JM, Ugalde JM. Diradicals and Diradicaloids in Natural Orbital Functional Theory. Chemphyschem 2011; 12:1061-5. [DOI: 10.1002/cphc.201100136] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2011] [Indexed: 11/06/2022]
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Singlet–triplet energy gap for trimethylenemethane, oxyallyl diradical, and related species: single- and multireference computational results. Theor Chem Acc 2011. [DOI: 10.1007/s00214-011-0914-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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24
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Mahapatra US, Chattopadhyay S. Evaluation of the performance of single root multireference coupled cluster method for ground and excited states, and its application to geometry optimization. J Chem Phys 2011; 134:044113. [DOI: 10.1063/1.3523573] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Shen J, Kou Z, Xu E, Li S. A coupled cluster approach with a hybrid treatment of connected triple excitations: Implementation and applications for open-shell systems. J Chem Phys 2010; 133:234106. [DOI: 10.1063/1.3518100] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
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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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Pittner J, Piecuch† P. Method of moments for the continuous transition between the Brillouin–Wigner-type and Rayleigh–Schrödinger-type multireference coupled cluster theories. Mol Phys 2010. [DOI: 10.1080/00268970902824235] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
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29
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Demel O, Bhaskaran-Nair K, Pittner J. Uncoupled multireference state-specific Mukherjee’s coupled cluster method with triexcitations. J Chem Phys 2010; 133:134106. [DOI: 10.1063/1.3495679] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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30
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Chattopadhyay S, Chaudhuri RK, Freed KF. Geometry Optimization of Radicaloid Systems Using Improved Virtual Orbital-Complete Active Space Configuration Interaction (IVO-CASCI) Analytical Gradient Method. J Phys Chem A 2010; 115:3665-78. [DOI: 10.1021/jp103536w] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Sudip Chattopadhyay
- Department of Chemistry, Bengal Engineering and Science University, Shibpur, Howrah 711103, India
| | | | - Karl F. Freed
- The James Franck Institute and Department of Chemistry, University of Chicago, Chicago, Illinois 60637, United States
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31
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Yu A, Xue X, Wang J, Wang Y. The rearrangement of 2-(1,6-methano[10]annulenyl)-3,3-dimethylmethylenecyclopropane: A computational study. ACTA ACUST UNITED AC 2010. [DOI: 10.1016/j.theochem.2010.03.011] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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32
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Bhaskaran-Nair K, Demel O, Pittner J. Multireference Mukherjee’s coupled cluster method with triexcitations in the linked formulation: Efficient implementation and applications. J Chem Phys 2010; 132:154105. [DOI: 10.1063/1.3376053] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
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Paldus J, Pittner J, Čársky P. Multireference Coupled-Cluster Methods: Recent Developments. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-2885-3_17] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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Multireference R12 Coupled Cluster Theory. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2010. [DOI: 10.1007/978-90-481-2885-3_10] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
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Ichino T, Villano S, Gianola A, Goebbert D, Velarde L, Sanov A, Blanksby S, Zhou X, Hrovat D, Borden W, Lineberger W. The Lowest Singlet and Triplet States of the Oxyallyl Diradical. Angew Chem Int Ed Engl 2009. [DOI: 10.1002/ange.200904417] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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37
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Li X, Paldus J. Accounting for the exact degeneracy and quasidegeneracy in the automerization of cyclobutadiene via multireference coupled-cluster methods. J Chem Phys 2009; 131:114103. [DOI: 10.1063/1.3225203] [Citation(s) in RCA: 44] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022] Open
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Dong H, Hrovat DA, Quast H, Borden WT. Calculations of the Relative Energies of the Low-Lying Electronic States of 2-Methylenedihydrophenalene-1,3-diyl: Effects of a 1,8-Naphtho Bridging Group on Trimethylenemethane and of a Vinylidene Bridging Group on 1,8-Naphthoquinodimethane. J Phys Chem A 2009; 113:895-901. [DOI: 10.1021/jp809715v] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Hao Dong
- Department of Chemistry and the Center for Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle, 305070, Denton, Texas 76203-5070, and Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - David A. Hrovat
- Department of Chemistry and the Center for Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle, 305070, Denton, Texas 76203-5070, and Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Helmut Quast
- Department of Chemistry and the Center for Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle, 305070, Denton, Texas 76203-5070, and Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
| | - Weston Thatcher Borden
- Department of Chemistry and the Center for Advanced Scientific Computing and Modeling, University of North Texas, 1155 Union Circle, 305070, Denton, Texas 76203-5070, and Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany
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Bhaskaran-Nair K, Demel O, Pittner J. Multireference state-specific Mukherjee’s coupled cluster method with noniterative triexcitations. J Chem Phys 2008; 129:184105. [DOI: 10.1063/1.3006401] [Citation(s) in RCA: 98] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
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Li X, Paldus J. Electronic structure of organic diradicals: Evaluation of the performance of coupled-cluster methods. J Chem Phys 2008; 129:174101. [DOI: 10.1063/1.2999560] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
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Demel O, Shamasundar KR, Kong L, Nooijen M. Application of Double Ionization State-Specific Equation of Motion Coupled Cluster Method to Organic Diradicals. J Phys Chem A 2008; 112:11895-902. [PMID: 18956856 DOI: 10.1021/jp800577q] [Citation(s) in RCA: 66] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ondřej Demel
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - K. R. Shamasundar
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - Liguo Kong
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
| | - Marcel Nooijen
- Department of Chemistry, University of Waterloo, 200 University Avenue West, Waterloo, Ontario, N2L 3G1 Canada
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Quast H, Nüdling W, Klemm G, Kirschfeld A, Neuhaus P, Sander W, Hrovat DA, Borden WT. A Perimidine-Derived Non-Kekulé Triplet Diradical. J Org Chem 2008; 73:4956-61. [DOI: 10.1021/jo800589y] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Helmut Quast
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Wolfgang Nüdling
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Gerhard Klemm
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Andreas Kirschfeld
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Patrik Neuhaus
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Wolfram Sander
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - David A. Hrovat
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
| | - Weston Thatcher Borden
- Institut für Organische Chemie der Universität Würzburg, Am Hubland, D-97074 Würzburg, Germany, Lehrstuhl für Organische Chemie II der Ruhr-Universität Bochum, D-44780 Bochum, Germany, and Department of Chemistry, University of North Texas, P.O. Box 305070, Denton, Texas 76203-5070
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Demel O, Pittner J. Multireference Brillouin–Wigner coupled cluster method with singles, doubles, and triples: Efficient implementation and comparison with approximate approaches. J Chem Phys 2008; 128:104108. [DOI: 10.1063/1.2832865] [Citation(s) in RCA: 57] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Pittner J, Smydke J. Analytic gradient for the multireference Brillouin-Wigner coupled cluster method and for the state-universal multireference coupled cluster method. J Chem Phys 2007; 127:114103. [PMID: 17887824 DOI: 10.1063/1.2770705] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
We present the analytic gradient theory and its pilot implementation for the multireference Brillouin-Wigner coupled cluster (BWCC) method and for the state-universal multireference coupled cluster method. The analytic gradient has been derived for three cases: (i) BWCC method without a size-extensivity correction, (ii) BWCC method with the iterative size-extensivity correction, and (iii) for the rigorously size-extensive state-universal method. The pilot implementation is based on full-configuration interaction expansions and is presently limited to single and double excitation levels; however, the resulting equations are general. For BWCC methods, they also do not contain terms explicitly mixing amplitudes of different reference configurations and can thus be implemented in an efficient way. The analytic gradients have been verified with respect to numerically computed ones on the example of CH2 molecule, and geometry optimizations of CH2 and SiH2 have been carried out.
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Affiliation(s)
- Jirí Pittner
- J. Heyrovský Institute of Physical Chemistry of the Academy of Sciences of the Czech Republic, v. v. i. Dolejskova 3, 18223 Prague 8, Czech Republic.
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