1
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Cernatic F, Fromager E. Extended N-centered ensemble density functional theory of double electronic excitations. J Comput Chem 2024; 45:1945-1962. [PMID: 38700389 DOI: 10.1002/jcc.27387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2024] [Revised: 04/12/2024] [Accepted: 04/19/2024] [Indexed: 05/05/2024]
Abstract
A recent work (arXiv:2401.04685) has merged N-centered ensembles of neutral and charged electronic ground states with ensembles of neutral ground and excited states, thus providing a general and in-principle exact (so-called extended N-centered) ensemble density functional theory of neutral and charged electronic excitations. This formalism made it possible to revisit the concept of density-functional derivative discontinuity, in the particular case of single excitations from the highest occupied Kohn-Sham (KS) molecular orbital, without invoking the usual "asymptotic behavior of the density" argument. In this work, we address a broader class of excitations, with a particular focus on double excitations. An exact implementation of the theory is presented for the two-electron Hubbard dimer model. A thorough comparison of the true physical ground- and excited-state electronic structures with that of the fictitious ensemble density-functional KS system is also presented. Depending on the choice of the density-functional ensemble as well as the asymmetry of the dimer and the correlation strength, an inversion of states can be observed. In some other cases, the strong mixture of KS states within the true physical system makes the assignment "single excitation" or "double excitation" irrelevant.
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Affiliation(s)
- Filip Cernatic
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, Strasbourg, France
| | - Emmanuel Fromager
- Laboratoire de Chimie Quantique, Institut de Chimie, CNRS/Université de Strasbourg, Strasbourg, France
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2
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Kossoski F, Boggio-Pasqua M, Loos PF, Jacquemin D. Reference Energies for Double Excitations: Improvement and Extension. J Chem Theory Comput 2024; 20:5655-5678. [PMID: 38885174 DOI: 10.1021/acs.jctc.4c00410] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/20/2024]
Abstract
In the realm of photochemistry, the significance of double excitations (also known as doubly excited states), where two electrons are concurrently elevated to higher energy levels, lies in their involvement in key electronic transitions essential in light-induced chemical reactions as well as their challenging nature from the computational theoretical chemistry point of view. Based on state-of-the-art electronic structure methods (such as high-order coupled-cluster, selected configuration interaction, and multiconfigurational methods), we improve and expand our prior set of accurate reference excitation energies for electronic states exhibiting a substantial amount of double excitations [Loos et al. J. Chem. Theory Comput. 2019, 15, 1939]. This extended collection encompasses 47 electronic transitions across 26 molecular systems that we separate into two distinct subsets: (i) 28 "genuine" doubly excited states where the transitions almost exclusively involve doubly excited configurations and (ii) 19 "partial" doubly excited states which exhibit a more balanced character between singly and doubly excited configurations. For each subset, we assess the performance of high-order coupled-cluster (CC3, CCSDT, CC4, and CCSDTQ) and multiconfigurational methods (CASPT2, CASPT3, PC-NEVPT2, and SC-NEVPT2). Using as a probe the percentage of single excitations involved in a given transition (%T1) computed at the CC3 level, we also propose a simple correction that reduces the errors of CC3 by a factor of 3, for both sets of excitations. We hope that this more complete and diverse compilation of double excitations will help future developments of electronic excited-state methodologies.
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Affiliation(s)
- Fábris Kossoski
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
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3
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Manna S, Chaudhuri RK, Chattopadhyay S. Taming the excited states of butadiene, hexatriene, and octatetraene using state specific multireference perturbation theory with density functional theory orbitals. J Chem Phys 2020; 152:244105. [DOI: 10.1063/5.0007198] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Shovan Manna
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, India
| | | | - Sudip Chattopadhyay
- Department of Chemistry, Indian Institute of Engineering Science and Technology, Shibpur, Howrah 711103, India
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4
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Coffman AJ, Dou W, Hammes-Schiffer S, Subotnik JE. Modeling voltammetry curves for proton coupled electron transfer: The importance of nuclear quantum effects. J Chem Phys 2020; 152:234108. [PMID: 32571072 DOI: 10.1063/5.0010412] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We investigate rates of proton-coupled electron transfer (PCET) in potential sweep experiments for a generalized Anderson-Holstein model with the inclusion of a quantized proton coordinate. To model this system, we utilize a quantum classical Liouville equation embedded inside of a classical master equation, which can be solved approximately with a recently developed algorithm combining diffusional effects and surface hopping between electronic states. We find that the addition of nuclear quantum effects through the proton coordinate can yield quantitatively (but not qualitatively) different IV curves under a potential sweep compared to electron transfer (ET). Additionally, we find that kinetic isotope effects give rise to a shift in the peak potential, but not the peak current, which would allow for quantification of whether an electrochemical ET event is proton-coupled or not. These findings suggest that it will be very difficult to completely understand coupled nuclear-electronic effects in electrochemical voltammetry experiments using only IV curves, and new experimental techniques will be needed to draw inferences about the nature of electrochemical PCET.
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Affiliation(s)
- Alec J Coffman
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
| | - Wenjie Dou
- Department of Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | | | - Joseph E Subotnik
- Department of Chemistry, University of Pennsylvania, Philadelphia, Pennsylvania 19104, USA
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5
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Zimmerman PM, Rask AE. Evaluation of full valence correlation energies and gradients. J Chem Phys 2019; 150:244117. [PMID: 31255060 DOI: 10.1063/1.5100934] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Complete-active-space self-consistent field (CASSCF) wave functions are central to understanding strongly correlated molecules as they capture the entirety of electronic interactions within a subset of the orbital space. The most interesting case for CASSCF is the full valence limit, where all bonding and an equal number of virtual orbitals are included in the active space, and no approximation is made in selecting the important valence orbitals or electrons. While conventional algorithms require exponential computational time to evaluate full valence CASSCF, this article shows that the method of increments can do the same with polynomial effort, in a new method denoted iCASSCF. The method of increments can also provide density matrices and other necessary ingredients for the construction of the nuclear gradient. These goals are met through a many-body expansion that breaks the problem into smaller pieces that are subsequently reassembled to form close approximations of conventional CAS results. Practical demonstrations on a number of medium-sized molecules, with up to 116 valence electrons correlated in 116 orbitals, show the power of this methodology.
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Affiliation(s)
- Paul M Zimmerman
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
| | - Alan E Rask
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA
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6
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Rabidoux SM, Cave RJ, Stanton JF. Nonadiabatic Investigation of the Electronic Spectroscopy of trans-1,3-Butadiene. J Phys Chem A 2019; 123:3255-3271. [DOI: 10.1021/acs.jpca.9b01021] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Affiliation(s)
- Scott M. Rabidoux
- Institute for Computational Engineering and Sciences, The University of Texas at Austin, Austin, Texas 78712, United States
| | - Robert J. Cave
- Department of Chemistry, Harvey Mudd College, 241 Platt Boulevard, Claremont, California 91711, United States
| | - John F. Stanton
- Department of Chemistry and Biochemistry, The University of Texas at Austin, 1 University Avenue, Austin, Texas 78712, United States
- The Department of Chemistry, The University of Florida, Gainesville, Florida 32611, United States
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7
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Loos PF, Boggio-Pasqua M, Scemama A, Caffarel M, Jacquemin D. Reference Energies for Double Excitations. J Chem Theory Comput 2019; 15:1939-1956. [DOI: 10.1021/acs.jctc.8b01205] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Pierre-François Loos
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Martial Boggio-Pasqua
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Anthony Scemama
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Michel Caffarel
- Laboratoire de Chimie et Physique Quantiques (UMR 5626), Université de Toulouse, CNRS, UPS, 31062 Toulouse, France
| | - Denis Jacquemin
- Laboratoire CEISAM (UMR 6230), CNRS, Université de Nantes, 44399 Cedex 3 Nantes, France
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8
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Influence of pseudopotentials on excitation energies from selected configuration interaction and diffusion Monte Carlo. RESULTS IN CHEMISTRY 2019. [DOI: 10.1016/j.rechem.2019.100002] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
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9
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Lischka H, Nachtigallová D, Aquino AJA, Szalay PG, Plasser F, Machado FBC, Barbatti M. Multireference Approaches for Excited States of Molecules. Chem Rev 2018; 118:7293-7361. [DOI: 10.1021/acs.chemrev.8b00244] [Citation(s) in RCA: 197] [Impact Index Per Article: 32.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Affiliation(s)
- Hans Lischka
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
| | - Dana Nachtigallová
- Institute of Organic Chemistry and Biochemistry v.v.i., The Czech Academy of Sciences, Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Palacký University, 78371 Olomouc, Czech Republic
| | - Adélia J. A. Aquino
- School of Pharmaceutical Sciences and Technology, Tianjin University, Tianjin 300072, P.R. China
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409, United States
- Institute for Soil Research, University of Natural Resources and Life Sciences Vienna, Peter-Jordan-Strasse 82, A-1190 Vienna, Austria
| | - Péter G. Szalay
- ELTE Eötvös Loránd University, Laboratory of Theoretical Chemistry, Pázmány Péter sétány 1/A, 1117 Budapest, Hungary
| | - Felix Plasser
- Institute of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Währinger Straße 17, 1090 Vienna, Austria
- Department of Chemistry, Loughborough University, Leicestershire LE11 3TU, United Kingdom
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica, São José dos Campos 12228-900, São Paulo, Brazil
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10
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Sutton C, Yang Y, Zhang D, Yang W. Single, Double Electronic Excitations and Exciton Effective Conjugation Lengths in π-Conjugated Systems. J Phys Chem Lett 2018; 9:4029-4036. [PMID: 29939751 PMCID: PMC6205815 DOI: 10.1021/acs.jpclett.8b01366] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The 21Ag and 11Bu excited states of two prototypical π-conjugated compounds, polyacetylene and polydiacetylene, are investigated with the recently developed particle-particle random phase approximation (pp-RPA) method combined with the B3LYP functional. The polymer-limit transition energies are estimated as 1.38 and 1.72 eV for the 21Ag and 11Bu states, respectively, from an extrapolation of the computed excitation energies of model oligomers. These values increase to 1.95 and 2.24 eV for the same transitions when ground-state structures with ∼33% larger bond length alternation are adopted. Applying the pp-RPA to the vertical excitation energies in oligodiacetylene, the polymer-limit transition energies of the 21Ag and 11Bu states are computed to be 2.06 and 2.28 eV, respectively. These results are in good agreement with experimental values or theoretical best estimates, indicating that the pp-RPA method shows great promise for understanding many photophysical phenomena involving both single and double excitations.
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Affiliation(s)
- Christopher Sutton
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Yang Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Du Zhang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
| | - Weitao Yang
- Department of Chemistry, Duke University, Durham, North Carolina 27708, United States
- Department of Physics, Duke University, Durham, North Carolina 27708, United States
- Key Laboratory of Theoretical Chemistry of Environment School of Chemistry and Environment, South China Normal University, Guangzhou 510631, China
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11
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Schalk O, Boguslavskiy AE, Stolow A. Two-Photon Excited State Dynamics of Dark Valence, Rydberg, and Superexcited States in 1,3-Butadiene. J Phys Chem Lett 2014; 5:560-565. [PMID: 26276609 DOI: 10.1021/jz402725u] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Two-photon absorption in systems with parity permits access to states that cannot be prepared by one-photon absorption. Here we present the first time-resolved photoelectron spectroscopy study using this technique, applied to 1,3-butadiene, in which we investigated the dynamics of its dark valence, Rydberg, and superexcited states. The dark valence state dynamics are accessed via the Rydberg manifold, excited by two photons of 400 nm. We find that the 'dark' 2(1)Ag state populated in this manner has a much longer lifetime than when accesses via the 1(1)Bu 'bright' valence state when populated by one photon of 200 nm. In addition, we compared the dynamics of the 3sπ- and 3dπ-Rydberg states. These Rydberg states relax to the valence manifold on a subpicosecond time scale, with the 3sπ-Rydberg state decay rate being larger due to a stronger valence-Rydberg mixing. Finally, we investigated superexcited valence states that fragment or autoionize within 200 fs, likely without involving Rydberg states.
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Affiliation(s)
- Oliver Schalk
- †Stockholm University, AlbaNova University Center, Roslagstullsbacken 21, SE-106 91 Stockholm, Sweden
- ‡National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Andrey E Boguslavskiy
- ‡National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
| | - Albert Stolow
- ‡National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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12
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Gieseking RL, Mukhopadhyay S, Risko C, Marder SR, Brédas JL. 25th anniversary article: Design of polymethine dyes for all-optical switching applications: guidance from theoretical and computational studies. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2014; 26:68-83. [PMID: 24302357 DOI: 10.1002/adma.201302676] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/11/2013] [Revised: 07/29/2013] [Indexed: 06/02/2023]
Abstract
All-optical switching--controlling light with light--has the potential to meet the ever-increasing demand for data transmission bandwidth. The development of organic π-conjugated molecular materials with the requisite properties for all-optical switching applications has long proven to be a significant challenge. However, recent advances demonstrate that polymethine dyes have the potential to meet the necessary requirements. In this review, we explore the theoretical underpinnings that guide the design of π-conjugated materials for all-optical switching applications. We underline, from a computational chemistry standpoint, the relationships among chemical structure, electronic structure, and optical properties that make polymethines such promising materials.
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Affiliation(s)
- Rebecca L Gieseking
- School of Chemistry and Biochemistry Center for Organic Photonics and Electronics and Center for Organic Materials for All-Optical Switching, Georgia Institute of Technology, Atlanta, Georgia, 30332-0400, USA
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13
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Tassi M, Theophilou I, Thanos S. Double excitations from modified Hartree Fock subsequent minimization scheme. J Chem Phys 2013; 138:124107. [PMID: 23556709 DOI: 10.1063/1.4797466] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Doubly excited states have nowadays become important in technological applications, e.g., in increasing the efficiency of solar cells and therefore, their description using ab initio methods is a great theoretical challenge as double excitations cannot be described by linear response theories based on a single Slater determinant. In the present work we extend our recently developed Hartree-Fock (HF) approximation for calculating singly excited states [M. Tassi, I. Theophilou, and S. Thanos, Int. J. Quantum Chem. 113, 690 (2013)] in order to allow for the calculation of doubly excited states. We describe the double excitation as two holes in the subspace spanned from the occupied HF orbitals and two particles in the subspace of virtual HF orbitals. A subsequent minimization of the energy results to the determination of the spin orbitals of both the holes and the particles in the occupied and virtual subspaces, respectively. We test our method, for various atoms, H2 and polyene molecules which are known to have excitations presenting a significant double excitation character. Importantly, our approach is computationally inexpensive.
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Affiliation(s)
- M Tassi
- Institute of Material Science, Demokritos National Center for Scientific Research, 15310 Athens, Greece.
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14
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Szalay PG, Müller T, Gidofalvi G, Lischka H, Shepard R. Multiconfiguration Self-Consistent Field and Multireference Configuration Interaction Methods and Applications. Chem Rev 2011; 112:108-81. [DOI: 10.1021/cr200137a] [Citation(s) in RCA: 470] [Impact Index Per Article: 36.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Péter G. Szalay
- Laboratory for Theoretical Chemistry, Institute of Chemistry, Eötvös Loránd University, P. O. Box 32, H-1518 Budapest, Hungary
| | - Thomas Müller
- Jülich Supercomputer Centre, Institute of Advanced Simulation, Forschungszentrum Jülich, D-52425 Jülich, Germany
| | - Gergely Gidofalvi
- Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Hans Lischka
- Department of Chemistry and Biochemistry, Texas Tech University, Lubbock, Texas 79409-1061, United States
- Institute for Theoretical Chemistry, University of Vienna, Waehringerstrasse 17, A-1090 Vienna, Austria
| | - Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States
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15
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Assessment of dressed time-dependent density-functional theory for the low-lying valence states of 28 organic chromophores. Chem Phys 2011. [DOI: 10.1016/j.chemphys.2011.03.019] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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16
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Lehtonen O, Sundholm D, Send R, Johansson MP. Coupled-cluster and density functional theory studies of the electronic excitation spectra of trans-1,3-butadiene and trans-2-propeniminium. J Chem Phys 2009; 131:024301. [DOI: 10.1063/1.3158990] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
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17
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Mazur G, Włodarczyk R. Application of the dressed time-dependent density functional theory for the excited states of linear polyenes. J Comput Chem 2009; 30:811-7. [PMID: 18727156 DOI: 10.1002/jcc.21102] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Dressed Time-Dependent Density Functional Theory (Maitra et al., J Chem Phys 2004, 120, 5932) is applied to selected linear polyenes. Limits of validity of the approximation are briefly discussed. The implementation strategy is described. Results for the 2(1)B(u) and 2(1)A(g) states of selected linear polyenes are presented and compared with accessible experimental and theoretical results.
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Affiliation(s)
- Grzegorz Mazur
- Department of Computational Methods in Chemistry, Jagiellonian University, Ingardena 3, 30-060 Kraków, Poland.
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18
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Ghosh D, Hachmann J, Yanai T, Chan GKL. Orbital optimization in the density matrix renormalization group, with applications to polyenes and β-carotene. J Chem Phys 2008; 128:144117. [DOI: 10.1063/1.2883976] [Citation(s) in RCA: 268] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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19
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Schreiber M, Silva-Junior MR, Sauer SPA, Thiel W. Benchmarks for electronically excited states: CASPT2, CC2, CCSD, and CC3. J Chem Phys 2008; 128:134110. [DOI: 10.1063/1.2889385] [Citation(s) in RCA: 749] [Impact Index Per Article: 46.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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20
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Timerghazin QK, Carlson HJ, Liang C, Campbell RE, Brown A. Computational prediction of absorbance maxima for a structurally diverse series of engineered green fluorescent protein chromophores. J Phys Chem B 2008; 112:2533-41. [PMID: 18247600 DOI: 10.1021/jp709900k] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
By virtue of its self-sufficiency to form a visible wavelength chromophore within the confines of its tertiary structure, the Aequorea victoria green fluorescent protein (GFP) is single-handedly responsible for the ever-growing popularity of fluorescence imaging of recombinant fusion proteins in biological research. Engineered variants of GFP with altered excitation or emission wavelength maxima have helped to expand the range of applications of GFP. The engineering of the GFP variants is usually done empirically by genetic modifications of the chromophore structure and/or its environment in order to find variants with new photophysical properties. The process of identifying improved variants could be greatly facilitated if augmented or guided by computational studies of the chromophore ground and excited-state properties and dynamics. In pursuit of this goal, we now report a thorough investigation of computational methods for prediction of the absorbance maxima for an experimentally validated series of engineered GFP chromophore analogues. The experimental dataset is composed of absorption maxima for 10 chemically distinct GFP chromophore analogues, including a previously unreported Y66D variant, measured under identical denaturing conditions. For each chromophore analogue, excitation energies and oscillator strengths were calculated using configuration interaction with single excitations (CIS), CIS with perturbative correction for double substitutions [CIS(D)], and time-dependent density functional theory (TD DFT) using several density functionals with solvent effects included using a polarizable continuum model. Comparison of the experimental and computational results show generally poor quantitative agreement with all methods attempted. However, good linear correlations between the calculated and experimental excitation energies (R2>0.9) could be obtained. Oscillator strengths obtained with TD DFT using pure density functionals also correlate well with the experimental values. Interestingly, most of the computational methods used in this work fail in the case of nonaromatic Y66S and Y66L protein chromophores, which may be related to a significant contribution of double excitations to their excited-state wavefunctions. These results provide an important benchmark of the reliability of the computational methods as applied to GFP chromophore analogues and lays a foundation for the computational design of GFP variants with improved properties for use in biological imaging.
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Affiliation(s)
- Qadir K Timerghazin
- University of Alberta, Department of Chemistry, Edmonton, Alberta T6G 2G2, Canada
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Hachmann J, Cardoen W, Chan GKL. Multireference correlation in long molecules with the quadratic scaling density matrix renormalization group. J Chem Phys 2006; 125:144101. [PMID: 17042573 DOI: 10.1063/1.2345196] [Citation(s) in RCA: 135] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023] Open
Abstract
We have devised a local ab initio density matrix renormalization group algorithm to describe multireference correlations in large systems. For long molecules that are extended in one of their spatial dimensions, we can obtain an exact characterization of correlation, in the given basis, with a cost that scales only quadratically with the size of the system. The reduced scaling is achieved solely through integral screening and without the construction of correlation domains. We demonstrate the scaling, convergence, and robustness of the algorithm in polyenes and hydrogen chains. We converge to exact correlation energies (in the sense of full configuration interaction, with 1-10 microE(h) precision) in all cases and correlate up to 100 electrons in 100 active orbitals. We further use our algorithm to obtain exact energies for the metal-insulator transition in hydrogen chains and compare and contrast our results with those from conventional quantum chemical methods.
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Affiliation(s)
- Johannes Hachmann
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853-1301, USA.
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22
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Saha B, Ehara M, Nakatsuji H. Singly and doubly excited states of butadiene, acrolein, and glyoxal: Geometries and electronic spectra. J Chem Phys 2006; 125:014316. [PMID: 16863307 DOI: 10.1063/1.2200344] [Citation(s) in RCA: 51] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Excited-state geometries and electronic spectra of butadiene, acrolein, and glyoxal have been investigated by the symmetry adapted cluster configuration interaction (SAC-CI) method in their s-trans conformation. Valence and Rydberg states below the ionization threshold have been precisely calculated with sufficiently flexible basis sets. Vertical and adiabatic excitation energies were well reproduced and the detailed assignments were given taking account of the second moments. The deviations of the vertical excitation energies from the experiment were less than 0.3 eV for all cases. The SAC-CI geometry optimization has been applied to some valence and Rydberg excited states of these molecules in the planar structure. The optimized ground- and excited-state geometries agree well with the available experimental values; deviations lie within 0.03 A and 0.7 degrees for the bond lengths and angles, respectively. The force acting on the nuclei caused by the excitations has been discussed in detail by calculating the SAC-CI electron density difference between the ground and excited states; the geometry relaxation was well interpreted with the electrostatic force theory. In Rydberg excitations, geometry changes were also noticed. Doubly excited states (so-called 2 (1)A(g) states) were investigated by the SAC-CI general-R method considering up to quadruple excitations. The characteristic geometrical changes and large energetic relaxations were predicted for these states.
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Affiliation(s)
- Biswajit Saha
- Department of Synthetic Chemistry and Biological Chemistry, Graduate School of Engineering, Kyoto University, Katsura, Kyoto 615-8510, Japan
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Boggio-Pasqua M, Bearpark MJ, Klene M, Robb MA. A computational strategy for geometry optimization of ionic and covalent excited states, applied to butadiene and hexatriene. J Chem Phys 2004; 120:7849-60. [PMID: 15267700 DOI: 10.1063/1.1690756] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We propose a computational strategy that enables ionic and covalent pipi* excited states to be described in a balanced way. This strategy depends upon (1) the restricted active space self-consistent field method, in which the dynamic correlation between core sigma and valence pi electrons can be described by adding single sigma excitations to all pi configurations and (2) the use of a new conventional one-electron basis set specifically designed for the description of valence ionic states. Together, these provide excitation energies comparable with more accurate and expensive ab initio methods--e.g., multiconfigurational second-order perturbation theory and multireference configuration interaction. Moreover, our strategy also allows full optimization of excited-state geometries--including conical intersections between ionic and covalent excited states--to be routinely carried out, thanks to the availability of analytical energy gradients. The prototype systems studied are the cis and trans isomers of butadiene and hexatriene, for which the ground 1A(1/g), lower-lying dark (i.e., symmetry forbidden covalent) 2A(1/g) and spectroscopic 1B(2/u) (valence ionic) states were investigated.
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Affiliation(s)
- Martial Boggio-Pasqua
- Department of Chemistry, Imperial College London, South Kensington campus, London SW7 2AZ, United Kingdom
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Maitra NT, Zhang F, Cave RJ, Burke K. Double excitations within time-dependent density functional theory linear response. J Chem Phys 2004; 120:5932-7. [PMID: 15267474 DOI: 10.1063/1.1651060] [Citation(s) in RCA: 317] [Impact Index Per Article: 15.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Within the adiabatic approximation, time-dependent density functional theory yields only single excitations. Near states of double excitation character, the exact exchange-correlation kernel has a strong dependence on frequency. We derive the exact frequency-dependent kernel when a double excitation mixes with a single excitation, well separated from the other excitations, in the limit that the electron--electron interaction is weak. Building on this, we construct a nonempirical approximation for the general case, and illustrate our results on a simple model.
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Affiliation(s)
- Neepa T Maitra
- Department of Physics and Astronomy, City University of New York and Hunter College, New York, New York 10021, USA.
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Wanko M, Garavelli M, Bernardi F, Niehaus TA, Frauenheim T, Elstner M. A global investigation of excited state surfaces within time-dependent density-functional response theory. J Chem Phys 2004; 120:1674-92. [PMID: 15268299 DOI: 10.1063/1.1635798] [Citation(s) in RCA: 125] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
This work investigates the capability of time-dependent density functional response theory to describe excited state potential energy surfaces of conjugated organic molecules. Applications to linear polyenes, aromatic systems, and the protonated Schiff base of retinal demonstrate the scope of currently used exchange-correlation functionals as local, adiabatic approximations to time-dependent Kohn-Sham theory. The results are compared to experimental and ab initio data of various kinds to attain a critical analysis of common problems concerning charge transfer and long range (nondynamic) correlation effects. This analysis goes beyond a local investigation of electronic properties and incorporates a global view of the excited state potential energy surfaces.
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Affiliation(s)
- M Wanko
- Department of Theoretical Physics, University of Paderborn, D-33098 Paderborn, Germany
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Strodel P, Tavan P. A revised MRCI-algorithm coupled to an effective valence-shell Hamiltonian. II. Application to the valence excitations of butadiene. J Chem Phys 2002. [DOI: 10.1063/1.1497678] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Ostojić B, Domcke W. Ab initio investigation of the potential energy surfaces involved in the photophysics of s-trans-1,3-butadiene. Chem Phys 2001. [DOI: 10.1016/s0301-0104(01)00373-1] [Citation(s) in RCA: 41] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Liu J, Anderson SL. Multiphoton ionization and photoelectron spectroscopy of 1,3-trans-butadiene via its 3dπ Rydberg state. J Chem Phys 2001. [DOI: 10.1063/1.1356736] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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