101
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Hofmann F, Schelter I, Kümmel S. Linear response time-dependent density functional theory without unoccupied states: The Kohn-Sham-Sternheimer scheme revisited. J Chem Phys 2018; 149:024105. [DOI: 10.1063/1.5030652] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Affiliation(s)
- Fabian Hofmann
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Ingo Schelter
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
| | - Stephan Kümmel
- Theoretical Physics IV, University of Bayreuth, D-95440 Bayreuth, Germany
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102
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Lian C, Guan M, Hu S, Zhang J, Meng S. Photoexcitation in Solids: First-Principles Quantum Simulations by Real-Time TDDFT. ADVANCED THEORY AND SIMULATIONS 2018. [DOI: 10.1002/adts.201800055] [Citation(s) in RCA: 40] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Chao Lian
- Beijing National Laboratory for Condensed Matter Physics; and Institute of Physics; Chinese Academy of Sciences; Beijing 100190 P. R. China
| | - Mengxue Guan
- Beijing National Laboratory for Condensed Matter Physics; and Institute of Physics; Chinese Academy of Sciences; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Shiqi Hu
- Beijing National Laboratory for Condensed Matter Physics; and Institute of Physics; Chinese Academy of Sciences; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Jin Zhang
- Beijing National Laboratory for Condensed Matter Physics; and Institute of Physics; Chinese Academy of Sciences; Beijing 100190 P. R. China
- University of Chinese Academy of Sciences; Beijing 100049 P. R. China
| | - Sheng Meng
- Beijing National Laboratory for Condensed Matter Physics; and Institute of Physics; Chinese Academy of Sciences; Beijing 100190 P. R. China
- Collaborative Innovation Center of Quantum Matter; Beijing 100871 P. R. China
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103
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Sarap CS, Partovi-Azar P, Fyta M. Optoelectronic Properties of Diamondoid-DNA Complexes. ACS APPLIED BIO MATERIALS 2018. [DOI: 10.1021/acsabm.8b00011] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Affiliation(s)
- Chandra Shekar Sarap
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
| | - Pouya Partovi-Azar
- Institute of Chemistry, Martin Luther University Halle-Wittenberg, Von-Danckelmann-Platz 4, 06120 Halle (Saale), Germany
| | - Maria Fyta
- Institute for Computational Physics, Universität Stuttgart, Allmandring 3, 70569 Stuttgart, Germany
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104
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Crespo-Otero R, Barbatti M. Recent Advances and Perspectives on Nonadiabatic Mixed Quantum–Classical Dynamics. Chem Rev 2018; 118:7026-7068. [DOI: 10.1021/acs.chemrev.7b00577] [Citation(s) in RCA: 301] [Impact Index Per Article: 50.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Rachel Crespo-Otero
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
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105
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Chalabala J, Uhlig F, Slavíček P. Assessment of Real-Time Time-Dependent Density Functional Theory (RT-TDDFT) in Radiation Chemistry: Ionized Water Dimer. J Phys Chem A 2018. [PMID: 29513531 DOI: 10.1021/acs.jpca.8b01259] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Ionization in the condensed phase and molecular clusters leads to a complicated chain of processes with coupled electron-nuclear dynamics. It is difficult to describe such dynamics with conventional nonadiabatic molecular dynamics schemes since the number of states swiftly increases as the molecular system grows. It is therefore attractive to use a direct electron and nuclear propagation such as the real-time time-dependent density functional theory (RT-TDDFT). Here we report a RT-TDDFT benchmark study on simulations of singly and doubly ionized states of a water monomer and dimer as a prototype for more complex processes in a condensed phase. We employed the RT-TDDFT based Ehrenfest molecular dynamics with a generalized gradient approximate (GGA) functional and compared it with wave-function-based surface hopping (SH) simulations. We found that the initial dynamics of a singly HOMO ionized water dimer is similar for both the RT-TDDFT/GGA and the SH simulations but leads to completely different reaction channels on a longer time scale. This failure is attributed to the self-interaction error in the GGA functionals and it can be avoided by using hybrid functionals with large fraction of exact exchange (represented here by the BHandHLYP functional). The simulations of doubly ionized states are reasonably described already at the GGA level. This suggests that the RT-TDDFT/GGA method could describe processes following the autoionization processes such as Auger emission, while its applicability to more complex processes such as intermolecular Coulombic decay remains limited.
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Affiliation(s)
- Jan Chalabala
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic
| | - Frank Uhlig
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic.,Institute for Computational Physics , University of Stuttgart , Allmandring 3 , 70569 Stuttgart , Germany
| | - Petr Slavíček
- Department of Physical Chemistry , University of Chemistry and Technology , Technická 5 , 16628 Prague , Czech Republic.,Jaroslav Heyrovský Institute of Physical Chemistry, Academy of Sciences of the Czech Republic , Dolejškova 3 , 18200 Prague , Czech Republic
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106
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Marcolongo JP, Zeida A, Semelak JA, Foglia NO, Morzan UN, Estrin DA, González Lebrero MC, Scherlis DA. Chemical Reactivity and Spectroscopy Explored From QM/MM Molecular Dynamics Simulations Using the LIO Code. Front Chem 2018; 6:70. [PMID: 29619365 PMCID: PMC5871697 DOI: 10.3389/fchem.2018.00070] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2018] [Accepted: 03/05/2018] [Indexed: 12/13/2022] Open
Abstract
In this work we present the current advances in the development and the applications of LIO, a lab-made code designed for density functional theory calculations in graphical processing units (GPU), that can be coupled with different classical molecular dynamics engines. This code has been thoroughly optimized to perform efficient molecular dynamics simulations at the QM/MM DFT level, allowing for an exhaustive sampling of the configurational space. Selected examples are presented for the description of chemical reactivity in terms of free energy profiles, and also for the computation of optical properties, such as vibrational and electronic spectra in solvent and protein environments.
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Affiliation(s)
- Juan P Marcolongo
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Ari Zeida
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina.,Departamento de Bioquímica and Center for Free Radical and Biomedical Research, Facultad de Medicina, Universidad de la República, Montevideo, Uruguay
| | - Jonathan A Semelak
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Nicolás O Foglia
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Uriel N Morzan
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Dario A Estrin
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Mariano C González Lebrero
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| | - Damián A Scherlis
- DQIAyQF, INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
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107
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Morzan UN, Alonso de Armiño DJ, Foglia NO, Ramírez F, González Lebrero MC, Scherlis DA, Estrin DA. Spectroscopy in Complex Environments from QM–MM Simulations. Chem Rev 2018; 118:4071-4113. [DOI: 10.1021/acs.chemrev.8b00026] [Citation(s) in RCA: 97] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Affiliation(s)
- Uriel N. Morzan
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Diego J. Alonso de Armiño
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Nicolás O. Foglia
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Francisco Ramírez
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Mariano C. González Lebrero
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Damián A. Scherlis
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
| | - Darío A. Estrin
- Departamento de Química Inorgánica, Analítica y Química Física/INQUIMAE-CONICET, Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, C1428EHA Buenos Aires, Argentina
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108
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Cho D, Rouxel JR, Kowalewski M, Saurabh P, Lee JY, Mukamel S. Phase Cycling RT-TDDFT Simulation Protocol for Nonlinear XUV and X-ray Molecular Spectroscopy. J Phys Chem Lett 2018; 9:1072-1078. [PMID: 29431442 DOI: 10.1021/acs.jpclett.8b00061] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
Real-time time-dependent density functional theory (RT-TDDFT) provides a practical algorithm for propagating a many-electron system driven by external laser fields. The fields are included nonperturbatively in the propagation, and the molecular reduced single-electron density operator and various spectroscopic and diffraction signals can be computed directly, avoiding the expensive calculation of many-body states. Nonlinear optical signals contain contributions of multiple pathways. A phase cycling protocol is implemented in order to separate these pathways. Simulations of XUV four-wave mixing signals in the CO molecule are compared with ab initio sum-over-states calculations.
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Affiliation(s)
- Daeheum Cho
- Department of Chemistry, University of California , Irvine, California 92697, United States
- Department of Chemistry, Sungkyunkwan University , Suwon 16419, Korea
- Department of Physics and Astronomy, University of California , Irvine, California 92697, United States
| | - Jérémy R Rouxel
- Department of Chemistry, University of California , Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California , Irvine, California 92697, United States
| | - Markus Kowalewski
- Department of Chemistry, University of California , Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California , Irvine, California 92697, United States
| | - Prasoon Saurabh
- Department of Chemistry, University of California , Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California , Irvine, California 92697, United States
| | - Jin Yong Lee
- Department of Chemistry, Sungkyunkwan University , Suwon 16419, Korea
| | - Shaul Mukamel
- Department of Chemistry, University of California , Irvine, California 92697, United States
- Department of Physics and Astronomy, University of California , Irvine, California 92697, United States
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109
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Schelter I, Kümmel S. Accurate Evaluation of Real-Time Density Functional Theory Providing Access to Challenging Electron Dynamics. J Chem Theory Comput 2018; 14:1910-1927. [DOI: 10.1021/acs.jctc.7b01013] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ingo Schelter
- Department of Physics, University of Bayreuth, 95440 Bayreuth, Germany
| | - Stephan Kümmel
- Department of Physics, University of Bayreuth, 95440 Bayreuth, Germany
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110
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Bowman DN, Asher JC, Fischer SA, Cramer CJ, Govind N. Excited-state absorption in tetrapyridyl porphyrins: comparing real-time and quadratic-response time-dependent density functional theory. Phys Chem Chem Phys 2018; 19:27452-27462. [PMID: 28975162 DOI: 10.1039/c7cp04567k] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Three meso-substituted tetrapyridyl porphyrins (free base, Ni(ii), and Cu(ii)) were investigated for their optical limiting (OL) capabilities using real-time (RT-), linear-response (LR-), and quadratic-response (QR-) time-dependent density functional theory (TDDFT) methods. These species are experimentally known to display a prominent reverse saturable absorption feature between the Q and B bands of the ground-state absorption (GSA), which has been attributed to increased excited-state absorption (ESA) relative to GSA. A recently developed RT-TDDFT based method for calculating ESA from a LR-TDDFT density was utilized with eight exchange-correlation functionals (BLYP, PBE, B3LYP, CAM-B3LYP, PBE0, M06, BHLYP, and BHandH) and contrasted with calculations of ESA using QR-TDDFT with five exchange-correlation functionals (BLYP, B3LYP, CAM-B3LYP, BHLYP, and BHandH). This allowed for comparison between functionals with varying amounts of exact exchange as well as between the ability of RT-TDDFT and QR-TDDFT to reproduce OL behavior in porphyrin systems. The absorption peak positions and intensities for GSA and ESA are significantly impacted by the choice of DFT functional, with the most critical factor identified as the amount of exact exchange in the functional form. Calculating ESA with QR-TDDFT is found to be significantly more sensitive to the amount of exact exchange than GSA and ESA with RT-TDDFT, as well as GSA with LR-TDDFT. An analogous behavior is also demonstrated for the polycyclic aromatic hydrocarbon coronene. This is problematic when using the same approximate functional for calculation of both GSA and ESA, as the LR- and QR-TDDFT excitation energies will not have similar errors. Overall, the RT-TDDFT method with hybrid functionals reproduces the OL features for the porphyrin systems studied here and is a viable computational approach for efficient screening of molecular complexes for OL properties.
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Affiliation(s)
- David N Bowman
- Department of Chemistry, Supercomputing Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, USA.
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111
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Zhu Y, Herbert JM. Self-consistent predictor/corrector algorithms for stable and efficient integration of the time-dependent Kohn-Sham equation. J Chem Phys 2018; 148:044117. [PMID: 29390834 DOI: 10.1063/1.5004675] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Ying Zhu
- Department of Chemistry and Biochemistry, and Chemical Physics Program, The Ohio State University, Columbus, Ohio 43210, USA
| | - John M. Herbert
- Department of Chemistry and Biochemistry, and Chemical Physics Program, The Ohio State University, Columbus, Ohio 43210, USA
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112
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Lestrange PJ, Hoffmann MR, Li X. Time-Dependent Configuration Interaction Using the Graphical Unitary Group Approach: Nonlinear Electric Properties. NOVEL ELECTRONIC STRUCTURE THEORY: GENERAL INNOVATIONS AND STRONGLY CORRELATED SYSTEMS 2018. [DOI: 10.1016/bs.aiq.2017.06.003] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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113
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Benussi L, Bianco S, Saviano G, Muhammad S, Piccolo D, Ferrini M, Parvis M, Grassini S, Colafranceschi S, Kjølbro J, Sharma A, Yang D, Chen G, Ban Y, Li Q. Candidate eco-friendly gas mixtures for MPGDs. EPJ WEB OF CONFERENCES 2018. [DOI: 10.1051/epjconf/201817405004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Modern gas detectors for detection of particles require F-based gases for optimal performance. Recent regulations demand the use of environmentally unfriendly F-based gases to be limited or banned. This review studies properties of potential eco-friendly gas candidate replacements.
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114
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Cho D, Rouxel JR, Kowalewski M, Lee JY, Mukamel S. Attosecond X-ray Diffraction Triggered by Core or Valence Ionization of a Dipeptide. J Chem Theory Comput 2017; 14:329-338. [DOI: 10.1021/acs.jctc.7b00920] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Affiliation(s)
- Daeheum Cho
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
- School
of Advanced Materials Science and Engineering, SKKU Advanced Institute
of Nanotechnology (SAINT), Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Jérémy R. Rouxel
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Markus Kowalewski
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
| | - Jin Yong Lee
- Department
of Chemistry, Sungkyunkwan University, Suwon 16419, Republic of Korea
| | - Shaul Mukamel
- Department
of Chemistry, University of California, Irvine, California 92697-2025, United States
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115
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Maitra NT. Charge transfer in time-dependent density functional theory. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:423001. [PMID: 28766507 DOI: 10.1088/1361-648x/aa836e] [Citation(s) in RCA: 58] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Charge transfer plays a crucial role in many processes of interest in physics, chemistry, and bio-chemistry. In many applications the size of the systems involved calls for time-dependent density functional theory (TDDFT) to be used in their computational modeling, due to its unprecedented balance between accuracy and efficiency. However, although exact in principle, in practise approximations must be made for the exchange-correlation functional in this theory, and the standard functional approximations perform poorly for excitations which have a long-range charge-transfer component. Intense progress has been made in developing more sophisticated functionals for this problem, which we review. We point out an essential difference between the properties of the exchange-correlation kernel needed for an accurate description of charge-transfer between open-shell fragments and between closed-shell fragments. We then turn to charge-transfer dynamics, which, in contrast to the excitation problem, is a highly non-equilibrium, non-perturbative, process involving a transfer of one full electron in space. This turns out to be a much more challenging problem for TDDFT functionals. We describe dynamical step and peak features in the exact functional evolving over time, that are missing in the functionals currently used. The latter underestimate the amount of charge transferred and manifest a spurious shift in the charge transfer resonance position. We discuss some explicit examples.
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Affiliation(s)
- Neepa T Maitra
- Department of Physics and Astronomy, Hunter College and the Physics Program at the Graduate Center of the City University of New York, 695 Park Avenue, NY 10065, United States of America
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116
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117
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Goings JJ, Lestrange PJ, Li X. Real‐time time‐dependent electronic structure theory. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2017. [DOI: 10.1002/wcms.1341] [Citation(s) in RCA: 84] [Impact Index Per Article: 12.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
Affiliation(s)
| | | | - Xiaosong Li
- Department of ChemistryUniversity of Washington Seattle WA USA
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118
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Bruner A, Hernandez S, Mauger F, Abanador PM, LaMaster DJ, Gaarde MB, Schafer KJ, Lopata K. Attosecond Charge Migration with TDDFT: Accurate Dynamics from a Well-Defined Initial State. J Phys Chem Lett 2017; 8:3991-3996. [PMID: 28792225 DOI: 10.1021/acs.jpclett.7b01652] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/23/2023]
Abstract
We investigate the ability of time-dependent density functional theory (TDDFT) to capture attosecond valence electron dynamics resulting from sudden X-ray ionization of a core electron. In this special case the initial state can be constructed unambiguously, allowing for a simple test of the accuracy of the dynamics. The response following nitrogen K-edge ionization in nitrosobenzene shows excellent agreement with fourth-order algebraic diagrammatic construction (ADC(4)) results, suggesting that a properly chosen initial state allows TDDFT to adequately capture attosecond charge migration. Visualizing hole motion using an electron localization picture (ELF), we provide an intuitive chemical interpretation of the charge migration as a superposition of Lewis dot resonance structures.
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Affiliation(s)
- Adam Bruner
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Samuel Hernandez
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - François Mauger
- Department of Physics and Astronomy, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Paul M Abanador
- Department of Physics and Astronomy, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Daniel J LaMaster
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Mette B Gaarde
- Department of Physics and Astronomy, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Kenneth J Schafer
- Department of Physics and Astronomy, Louisiana State University , Baton Rouge, Louisiana 70803, United States
| | - Kenneth Lopata
- Department of Chemistry, Louisiana State University , Baton Rouge, Louisiana 70803, United States
- Center for Computation & Technology, Louisiana State University , Baton Rouge, Louisiana 70803, United States
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119
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Tassi M, Morphis A, Lambropoulos K, Simserides C. RT-TDDFT study of hole oscillations in B-DNA monomers and dimers. ACTA ACUST UNITED AC 2017. [DOI: 10.1080/23311940.2017.1361077] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Affiliation(s)
- M. Tassi
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - A. Morphis
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - K. Lambropoulos
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
| | - C. Simserides
- Department of Physics, National and Kapodistrian University of Athens, Panepistimiopolis, Zografos GR-15784, Athens, Greece
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120
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Ghosh S, Andersen A, Gagliardi L, Cramer CJ, Govind N. Modeling Optical Spectra of Large Organic Systems Using Real-Time Propagation of Semiempirical Effective Hamiltonians. J Chem Theory Comput 2017; 13:4410-4420. [DOI: 10.1021/acs.jctc.7b00618] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Soumen Ghosh
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Amity Andersen
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
| | - Laura Gagliardi
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Christopher J. Cramer
- Department
of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, 207 Pleasant Street SE, Minneapolis, Minnesota 55455-0431, United States
| | - Niranjan Govind
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, Washington 99338, United States
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121
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Zhang Y, Rouxel JR, Autschbach J, Govind N, Mukamel S. X-ray circular dichroism signals: a unique probe of local molecular chirality. Chem Sci 2017; 8:5969-5978. [PMID: 28989627 PMCID: PMC5620991 DOI: 10.1039/c7sc01347g] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2017] [Accepted: 06/23/2017] [Indexed: 11/21/2022] Open
Abstract
Core-resonant circular dichroism (CD) signals are induced by molecular chirality and vanish for achiral molecules and racemic mixtures. The highly localized nature of core excitations makes them ideal probes of local chirality within molecules. Simulations of the circular dichroism spectra of several molecular families illustrate how these signals vary with the electronic coupling to substitution groups, the distance between the X-ray chromophore and the chiral center, geometry, and chemical structure. Clear insight into the molecular structure is obtained through analysis of the X-ray CD spectra.
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Affiliation(s)
- Yu Zhang
- Department of Chemistry , University of California , Irvine , CA 92697 , USA . ; ;
| | - Jérémy R Rouxel
- Department of Chemistry , University of California , Irvine , CA 92697 , USA . ; ;
| | - Jochen Autschbach
- Department of Chemistry , University at Buffalo , State University of New York , Buffalo , NY 14260 , USA .
| | - Niranjan Govind
- Environmental Molecular Sciences Laboratory , Pacific Northwest National Laboratory , Richland , WA 99352 , USA .
| | - Shaul Mukamel
- Department of Chemistry , University of California , Irvine , CA 92697 , USA . ; ;
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122
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Wu X, Teuler JM, Cailliez F, Clavaguéra C, Salahub DR, de la Lande A. Simulating Electron Dynamics in Polarizable Environments. J Chem Theory Comput 2017; 13:3985-4002. [DOI: 10.1021/acs.jctc.7b00251] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Xiaojing Wu
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Jean-Marie Teuler
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Fabien Cailliez
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Carine Clavaguéra
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
| | - Dennis R. Salahub
- Department
of Chemistry, Centre for Molecular Simulation, Institute for Quantum
Science and Technology and Quantum Alberta, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4
- College
of Chemistry and Chemical Engineering, Henan University of Technology, No. 100, Lian Hua Street, High-Tech Development Zone, Zhengzhou 450001, P. R. China
| | - Aurélien de la Lande
- Laboratoire
de Chimie Physique, CNRS - Université Paris Sud, Université Paris-Saclay, 15 avenue Jean Perrin, 91405 Orsay CEDEX, France
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123
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Koh KJ, Nguyen-Beck TS, Parkhill J. Accelerating Realtime TDDFT with Block-Orthogonalized Manby–Miller Embedding Theory. J Chem Theory Comput 2017; 13:4173-4178. [DOI: 10.1021/acs.jctc.7b00494] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin J. Koh
- Department of Chemistry and
Biochemistry, The University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Triet S. Nguyen-Beck
- Department of Chemistry and
Biochemistry, The University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - John Parkhill
- Department of Chemistry and
Biochemistry, The University of Notre Dame, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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124
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Hendriks FC, Schmidt JE, Rombouts JA, Lammertsma K, Bruijnincx PCA, Weckhuysen BM. Probing Zeolite Crystal Architecture and Structural Imperfections using Differently Sized Fluorescent Organic Probe Molecules. Chemistry 2017; 23:6305-6314. [PMID: 28217845 PMCID: PMC5434937 DOI: 10.1002/chem.201700078] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/06/2017] [Indexed: 01/27/2023]
Abstract
A micro‐spectroscopic method has been developed to probe the accessibility of zeolite crystals using a series of fluorescent 4‐(4‐diethylaminostyryl)‐1‐methylpyridinium iodide (DAMPI) probes of increasing molecular size. Staining large zeolite crystals with MFI (ZSM‐5) topology and subsequent mapping of the resulting fluorescence using confocal fluorescence microscopy reveal differences in structural integrity: the 90° intergrowth sections of MFI crystals are prone to develop structural imperfections, which act as entrance routes for the probes into the zeolite crystal. Polarization‐dependent measurements provide evidence for the probe molecule's alignment within the MFI zeolite pore system. The developed method was extended to BEA (Beta) crystals, showing that the previously observed hourglass pattern is a general feature of BEA crystals with this morphology. Furthermore, the probes can accurately identify at which crystal faces of BEA straight or sinusoidal pores open to the surface. The results show this method can spatially resolve the architecture‐dependent internal pore structure of microporous materials, which is difficult to assess using other characterization techniques such as X‐ray diffraction.
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Affiliation(s)
- Frank C Hendriks
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Joel E Schmidt
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Jeroen A Rombouts
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV A, msterdam, The Netherlands
| | - Koop Lammertsma
- Department of Chemistry and Pharmaceutical Sciences, VU University Amsterdam, De Boelelaan 1083, 1081 HV A, msterdam, The Netherlands
| | - Pieter C A Bruijnincx
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
| | - Bert M Weckhuysen
- Inorganic Chemistry and Catalysis, Debye Institute for Nanomaterials Science, Utrecht University, Universiteitsweg 99, 3584CG, Utrecht, The Netherlands
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125
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Grånäs O, Kolesov G, Kaxiras E. Impact of Vibrations and Electronic Coherence on Electron Transfer in Flat Molecular Wires. ACTA ACUST UNITED AC 2017. [DOI: 10.1557/adv.2017.157] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
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126
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Partovi-Azar P, Kaghazchi P. Time-dependent density functional theory study on direction-dependent electron and hole transfer processes in molecular systems. J Comput Chem 2017; 38:698-703. [DOI: 10.1002/jcc.24730] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Revised: 12/10/2016] [Accepted: 12/19/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Pouya Partovi-Azar
- Institute of Chemistry and Biochemistry, Physical and Theoretical Chemistry, Freie Universität Berlin; Takustr. 3 Berlin 14195 Germany
| | - Payam Kaghazchi
- Institute of Chemistry and Biochemistry, Physical and Theoretical Chemistry, Freie Universität Berlin; Takustr. 3 Berlin 14195 Germany
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127
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Wang F, Schmidhammer U, de La Lande A, Mostafavi M. Ultra-fast charge migration competes with proton transfer in the early chemistry of H2O˙+. Phys Chem Chem Phys 2017; 19:2894-2899. [DOI: 10.1039/c6cp07013b] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxidation by the ultra-short lived radical cation of water, H2O˙+, can potentially take place at the interface of water and numerous heterogeneous systems involved in radiation therapy, energy and environmental industries.
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Affiliation(s)
- Furong Wang
- Laboratoire de Chimie Physique
- CNRS-Université Pari-Sud
- Orsay
- France
| | - Uli Schmidhammer
- Laboratoire de Chimie Physique
- CNRS-Université Pari-Sud
- Orsay
- France
| | | | - Mehran Mostafavi
- Laboratoire de Chimie Physique
- CNRS-Université Pari-Sud
- Orsay
- France
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128
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Goings JJ, Lingerfelt DB, Li X. Can Quantized Vibrational Effects Be Obtained from Ehrenfest Mixed Quantum-Classical Dynamics? J Phys Chem Lett 2016; 7:5193-5197. [PMID: 27973884 DOI: 10.1021/acs.jpclett.6b02424] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We explore the question of whether mean-field or "Ehrenfest" mixed quantum-classical dynamics is capable of capturing the quantized vibrational features in photoabsorption spectra that result from infrared and Raman-active vibrational transitions. We show that vibrational and electronic absorption spectra can indeed be obtained together within a single Ehrenfest simulation. Furthermore, the electronic transitions show new sidebands that are absent in electronic dynamics simulations with fixed nuclei. Inspection of the electronic sidebands reveals that the spacing corresponds to vibrational frequencies of totally symmetric vibrational modes of the ground electronic state. A simple derivation of the time-evolving dipole in the presence of external fields and vibrational motion shows the origin of these features, demonstrating that mixed quantum-classical Ehrenfest dynamics is capable of producing infrared, Raman, and electronic absorption spectra from a single simulation.
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Affiliation(s)
- Joshua J Goings
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - David B Lingerfelt
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
| | - Xiaosong Li
- Department of Chemistry, University of Washington , Seattle, Washington 98195, United States
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129
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Lambropoulos K, Kaklamanis K, Morphis A, Tassi M, Lopp R, Georgiadis G, Theodorakou M, Chatzieleftheriou M, Simserides C. Wire and extended ladder model predict THz oscillations in DNA monomers, dimers and trimers. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2016; 28:495101. [PMID: 27731310 DOI: 10.1088/0953-8984/28/49/495101] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
We call monomer a B-DNA base pair and study, analytically and numerically, electron or hole oscillations in monomers, dimers and trimers. We employ two tight binding (TB) approaches: (I) at the base-pair level, using the on-site energies of the base pairs and the hopping parameters between successive base pairs i.e. a wire model, and (II) at the single-base level, using the on-site energies of the bases and the hopping parameters between neighbouring bases, specifically between (a) two successive bases in the same strand, (b) complementary bases that define a base pair, and (c) diagonally located bases of successive base pairs, i.e. an extended ladder model since it also includes the diagonal hoppings (c). For monomers, with TB II, we predict periodic carrier oscillations with frequency [Formula: see text]-550 THz. For dimers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-100 THz. For trimers made of identical monomers, with TB I, we predict periodic carrier oscillations with [Formula: see text]-33 THz. In other cases, either with TB I or TB II, the oscillations may be not strictly periodic, but Fourier analysis shows similar frequency content. For dimers and trimers, TB I and TB II are successfully compared giving complementary aspects of the oscillations.
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Affiliation(s)
- K Lambropoulos
- National and Kapodistrian University of Athens, Department of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
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130
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Foglia NO, Morzan UN, Estrin DA, Scherlis DA, Gonzalez Lebrero MC. Role of Core Electrons in Quantum Dynamics Using TDDFT. J Chem Theory Comput 2016; 13:77-85. [DOI: 10.1021/acs.jctc.6b00771] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nicolás O. Foglia
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Uriel N. Morzan
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Dario A. Estrin
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Damian A. Scherlis
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
| | - Mariano C. Gonzalez Lebrero
- Departamento de Química
Inorgánica, Analítica y Química Física/INQUIMAE-CONICET,
Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Ciudad Universitaria, Pab. II, Buenos Aires C1428EHA, Argentina
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131
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Konecny L, Kadek M, Komorovsky S, Malkina OL, Ruud K, Repisky M. Acceleration of Relativistic Electron Dynamics by Means of X2C Transformation: Application to the Calculation of Nonlinear Optical Properties. J Chem Theory Comput 2016; 12:5823-5833. [DOI: 10.1021/acs.jctc.6b00740] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Lukas Konecny
- Department
of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, 811
02 Bratislava, Slovak Republic
| | - Marius Kadek
- The Centre
for
Theoretical and Computational Chemistry, Department of
Chemistry, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Stanislav Komorovsky
- The Centre
for
Theoretical and Computational Chemistry, Department of
Chemistry, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Olga L. Malkina
- Department
of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, 811
02 Bratislava, Slovak Republic
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava 814 38, Slovak Republic
| | - Kenneth Ruud
- The Centre
for
Theoretical and Computational Chemistry, Department of
Chemistry, UiT The Arctic University of Norway, 9019 Tromsø, Norway
| | - Michal Repisky
- The Centre
for
Theoretical and Computational Chemistry, Department of
Chemistry, UiT The Arctic University of Norway, 9019 Tromsø, Norway
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132
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Nascimento DR, DePrince AE. Linear Absorption Spectra from Explicitly Time-Dependent Equation-of-Motion Coupled-Cluster Theory. J Chem Theory Comput 2016; 12:5834-5840. [DOI: 10.1021/acs.jctc.6b00796] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Daniel R. Nascimento
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
| | - A. Eugene DePrince
- Department of Chemistry and
Biochemistry, Florida State University, Tallahassee, Florida 32306-4390, United States
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133
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Goings JJ, Kasper JM, Egidi F, Sun S, Li X. Real time propagation of the exact two component time-dependent density functional theory. J Chem Phys 2016; 145:104107. [DOI: 10.1063/1.4962422] [Citation(s) in RCA: 53] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Joshua J. Goings
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Joseph M. Kasper
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Franco Egidi
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Shichao Sun
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
| | - Xiaosong Li
- Department of Chemistry, University of Washington, Seattle, Washington 98195, USA
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134
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Sissay A, Abanador P, Mauger F, Gaarde M, Schafer KJ, Lopata K. Angle-dependent strong-field molecular ionization rates with tuned range-separated time-dependent density functional theory. J Chem Phys 2016; 145:094105. [DOI: 10.1063/1.4961731] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Affiliation(s)
- Adonay Sissay
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Paul Abanador
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - François Mauger
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Mette Gaarde
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Kenneth J. Schafer
- Department of Physics and Astronomy, Louisiana State University, Baton Rouge, Louisiana 70803, USA
| | - Kenneth Lopata
- Department of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, USA
- Center for Computation and Technology, Louisiana State University, Baton Rouge, Louisiana 70803, USA
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135
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Nguyen TS, Parkhill J. Nonradiative Relaxation in Real-Time Electronic Dynamics OSCF2: Organolead Triiodide Perovskite. J Phys Chem A 2016; 120:6880-7. [DOI: 10.1021/acs.jpca.6b06937] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Triet S. Nguyen
- Department
of Chemistry and Biochemistry, The University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - John Parkhill
- Department
of Chemistry and Biochemistry, The University of Notre Dame du Lac, 251 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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136
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Modrzejewski M, Hapka M, Chalasinski G, Szczesniak MM. Employing Range Separation on the meta-GGA Rung: New Functional Suitable for Both Covalent and Noncovalent Interactions. J Chem Theory Comput 2016; 12:3662-73. [PMID: 27428668 DOI: 10.1021/acs.jctc.6b00406] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We devise a scheme for converting an existing exchange functional into its range-separated hybrid variant. The underlying exchange hole of the Becke-Roussel type has the exact second-order expansion in the interelectron distance. The short-range part of the resulting range-separated exchange energy depends on the kinetic energy density and the Laplacian even if the base functional lacks the dependence on these variables. The most successful practical realization of the scheme, named LC-PBETPSS, combines the range-separated Perdew-Burke-Ernzerhof (PBE) exchange lifted to the hybrid meta-generalized gradient approximation rung and the Tao-Perdew-Staroverov-Scuseria (TPSS) correlation. The value of the range-separation parameter is estimated theoretically and confirmed by empirical optimization. The D3 dispersion correction is recommended for all energy computations employing the presented functional. Numerical tests show remarkably robust performance of the method for noncovalent interaction energies, barrier heights, main-group thermochemistry, and excitation energies.
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Affiliation(s)
- Marcin Modrzejewski
- Faculty of Chemistry, University of Warsaw , 02-093 Warsaw, Pasteura 1, Poland
| | - Michal Hapka
- Faculty of Chemistry, University of Warsaw , 02-093 Warsaw, Pasteura 1, Poland
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137
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Bruner A, LaMaster D, Lopata K. Accelerated Broadband Spectra Using Transition Dipole Decomposition and Padé Approximants. J Chem Theory Comput 2016; 12:3741-50. [DOI: 10.1021/acs.jctc.6b00511] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Adam Bruner
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Daniel LaMaster
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Kenneth Lopata
- Department
of Chemistry, Louisiana State University, Baton Rouge, Louisiana 70803, United States
- Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
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138
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Furche F, Krull BT, Nguyen BD, Kwon J. Accelerating molecular property calculations with nonorthonormal Krylov space methods. J Chem Phys 2016; 144:174105. [DOI: 10.1063/1.4947245] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023] Open
Affiliation(s)
- Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Brandon T. Krull
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Brian D. Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Jake Kwon
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
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139
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Fischer SA, Cramer CJ, Govind N. Excited-State Absorption from Real-Time Time-Dependent Density Functional Theory: Optical Limiting in Zinc Phthalocyanine. J Phys Chem Lett 2016; 7:1387-91. [PMID: 27007445 DOI: 10.1021/acs.jpclett.6b00282] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Optical-limiting materials are capable of attenuating light to protect delicate equipment from high-intensity light sources. Phthalocyanines have attracted a lot of attention for optical-limiting applications due to their versatility and large nonlinear absorption. With excited-state absorption (ESA) being the primary mechanism for optical limiting behavior in phthalocyanines, the ability to tune the optical absorption of ground and excited states in phthalocyanines would allow for the development of advanced optical limiters. We recently developed a method for the calculation of ESA based on real-time time-dependent density functional theory propagation of an excited-state density. In this work, we apply the approach to zinc phthalocyanine, demonstrating the ability of our method to efficiently identify the optical limiting potential of a molecular complex.
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Affiliation(s)
- Sean A Fischer
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
| | - Christopher J Cramer
- Department of Chemistry, Supercomputing Institute and Chemical Theory Center, University of Minnesota , Minneapolis, Minnesota 55455, United States
| | - Niranjan Govind
- William R. Wiley Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory , P.O. Box 999, Richland, Washington 99352, United States
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140
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Cao Y, Hughes T, Giesen D, Halls MD, Goldberg A, Vadicherla TR, Sastry M, Patel B, Sherman W, Weisman AL, Friesner RA. Highly efficient implementation of pseudospectral time-dependent density-functional theory for the calculation of excitation energies of large molecules. J Comput Chem 2016; 37:1425-41. [DOI: 10.1002/jcc.24350] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2015] [Revised: 02/02/2016] [Accepted: 02/03/2016] [Indexed: 12/25/2022]
Affiliation(s)
- Yixiang Cao
- Schrödinger Inc; 120 West 45th Street, Tower 45, 17th Floor New York New York 10036
| | - Thomas Hughes
- Schrödinger Inc; 120 West 45th Street, Tower 45, 17th Floor New York New York 10036
| | - Dave Giesen
- Schrödinger Inc; 120 West 45th Street, Tower 45, 17th Floor New York New York 10036
| | - Mathew D. Halls
- Schrödinger Inc; 120 West 45th Street, Tower 45, 17th Floor New York New York 10036
| | - Alexander Goldberg
- Schrödinger Inc; 8910 University Lane, Suite 270 San Diego California 92122
| | - Tati Reddy Vadicherla
- Schrödinger; Plot No. 573, B & C, Road No. 1 Jubilee Hills, Hyderabad Telangana 5000096 India
| | - Madhavi Sastry
- Schrödinger; Sanali Infopark, 8-2-120/113 Banjara Hills, Hyderabad Andhra Pradesh 500034 India
| | - Bhargav Patel
- Schrödinger; Sanali Infopark, 8-2-120/113 Banjara Hills, Hyderabad Andhra Pradesh 500034 India
| | - Woody Sherman
- Schrödinger Inc; 245 First St. Riverview II, 18th Floor Cambridge Massachusetts 02142
| | - Andrew L. Weisman
- Department of Applied Physics and Applied Mathematics; Columbia University; New York New York 10027
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141
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Brabec J, Lin L, Shao M, Govind N, Yang C, Saad Y, Ng EG. Efficient Algorithms for Estimating the Absorption Spectrum within Linear Response TDDFT. J Chem Theory Comput 2016; 11:5197-208. [PMID: 26894238 DOI: 10.1021/acs.jctc.5b00887] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Abstract
We present a special symmetric Lanczos algorithm and a kernel polynomial method (KPM) for approximating the absorption spectrum of molecules within the linear response time-dependent density functional theory (TDDFT) framework in the product form. In contrast to existing algorithms, the new algorithms are based on reformulating the original non-Hermitian eigenvalue problem as a product eigenvalue problem and the observation that the product eigenvalue problem is self-adjoint with respect to an appropriately chosen inner product. This allows a simple symmetric Lanczos algorithm to be used to compute the desired absorption spectrum. The use of a symmetric Lanczos algorithm only requires half of the memory compared with the nonsymmetric variant of the Lanczos algorithm. The symmetric Lanczos algorithm is also numerically more stable than the nonsymmetric version. The KPM algorithm is also presented as a low-memory alternative to the Lanczos approach, but the algorithm may require more matrix-vector multiplications in practice. We discuss the pros and cons of these methods in terms of their accuracy as well as their computational and storage cost. Applications to a set of small and medium-sized molecules are also presented.
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142
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Kolesov G, Grånäs O, Hoyt R, Vinichenko D, Kaxiras E. Real-Time TD-DFT with Classical Ion Dynamics: Methodology and Applications. J Chem Theory Comput 2015; 12:466-76. [DOI: 10.1021/acs.jctc.5b00969] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Grigory Kolesov
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Oscar Grånäs
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics and Astronomy, Division of Materials Theory, Uppsala University, Box
516, SE-75120 Uppsala, Sweden
| | - Robert Hoyt
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Dmitry Vinichenko
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Efthimios Kaxiras
- John
A. Paulson School of Engineering and Applied Sciences, Harvard University, Cambridge, Massachusetts 02138, United States
- Department
of Physics, Harvard University, Cambridge, Massachusetts 02138, United States
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143
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Ma J, Wang Z, Wang LW. Interplay between plasmon and single-particle excitations in a metal nanocluster. Nat Commun 2015; 6:10107. [PMID: 26673449 PMCID: PMC4703846 DOI: 10.1038/ncomms10107] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2015] [Accepted: 11/02/2015] [Indexed: 12/03/2022] Open
Abstract
Plasmon-generated hot carriers are used in photovoltaic or photochemical applications. However, the interplays between the plasmon and single-particle excitations in nanosystems have not been theoretically addressed using ab initio methods. Here we show such interplays in a Ag55 nanocluster using real-time time-dependent density functional theory simulations. We find that the disappearance of the zero-frequency peak in the Fourier transform of the band-to-band transition coefficient is a hallmark of the plasmon. We show the importance of the d-states for hot-carrier generations. If the single-particle d-to-s excitations are resonant to the plasmon frequency, the majority of the plasmon energy will be converted into hot carriers, and the overall hot-carrier generation is enhanced by the plasmon; if such resonance does not exist, we observe an intriguing Rabi oscillation between the plasmon and hot carriers. Phonons play a minor role in plasmonic dynamics in such small systems. This study provides guidance on improving plasmonic applications. Plasmons can enhance hot-carrier generation for efficient photochemical reactions, but the interplay between plasmons and single-particle excitations are difficult to capture in models. Here, the authors use real-time time-dependent density functional theory to study these interactions in silver nanocrystals.
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Affiliation(s)
- Jie Ma
- Joint Center for Artificial Photosynthesis and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Zhi Wang
- Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
| | - Lin-Wang Wang
- Joint Center for Artificial Photosynthesis and Materials Sciences Division, Lawrence Berkeley National Laboratory, Berkeley, California 94720, USA
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144
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Provorse MR, Habenicht BF, Isborn CM. Peak-Shifting in Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2015; 11:4791-802. [DOI: 10.1021/acs.jctc.5b00559] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Makenzie R. Provorse
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Bradley F. Habenicht
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
| | - Christine M. Isborn
- Chemistry and Chemical Biology, University of California Merced, Merced, California 95343, United States
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145
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Lambropoulos K, Chatzieleftheriou M, Morphis A, Kaklamanis K, Theodorakou M, Simserides C. Unbiased charge oscillations in B-DNA: monomer polymers and dimer polymers. PHYSICAL REVIEW. E, STATISTICAL, NONLINEAR, AND SOFT MATTER PHYSICS 2015; 92:032725. [PMID: 26465516 DOI: 10.1103/physreve.92.032725] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/10/2015] [Indexed: 06/05/2023]
Abstract
We call monomer a B-DNA base pair and examine, analytically and numerically, electron or hole oscillations in monomer and dimer polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a tight-binding (TB) approach at the base-pair level to readily determine the spatiotemporal evolution of a single extra carrier along a N base-pair B-DNA segment. We study highest occupied molecular orbital and lowest unoccupied molecular orbital eigenspectra as well as the mean over time probabilities to find the carrier at a particular monomer. We use the pure mean transfer rate k to evaluate the easiness of charge transfer. The inverse decay length β for exponential fits k(d), where d is the charge transfer distance, and the exponent η for power-law fits k(N) are computed; generally power-law fits are better. We illustrate that increasing the number of different parameters involved in the TB description, the fall of k(d) or k(N) becomes steeper and show the range covered by β and η. Finally, for both the time-independent and the time-dependent problems, we analyze the palindromicity and the degree of eigenspectrum dependence of the probabilities to find the carrier at a particular monomer.
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Affiliation(s)
- K Lambropoulos
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - M Chatzieleftheriou
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - A Morphis
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - K Kaklamanis
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - M Theodorakou
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
| | - C Simserides
- National and Kapodistrian University of Athens, Faculty of Physics, Panepistimiopolis, 15784 Zografos, Athens, Greece
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146
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Fischer SA, Cramer CJ, Govind N. Excited State Absorption from Real-Time Time-Dependent Density Functional Theory. J Chem Theory Comput 2015; 11:4294-303. [DOI: 10.1021/acs.jctc.5b00473] [Citation(s) in RCA: 56] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Affiliation(s)
- Sean A. Fischer
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
| | - Christopher J. Cramer
- Department
of Chemistry, Supercomputing Institute and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Niranjan Govind
- Environmental
Molecular Sciences Laboratory, Pacific Northwest National Laboratory, P.O. Box 999, Richland, Washington 99352, United States
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147
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Peralta JE, Hod O, Scuseria GE. Magnetization Dynamics from Time-Dependent Noncollinear Spin Density Functional Theory Calculations. J Chem Theory Comput 2015; 11:3661-8. [DOI: 10.1021/acs.jctc.5b00494] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Juan E. Peralta
- Department
of Physics, Central Michigan University, Mt. Pleasant, Michigan 48859, United States
| | - Oded Hod
- Department
of Chemical Physics, School of Chemistry, Raymond and Beverly Sackler
Faculty of Exact Sciences, Tel Aviv University, Tel Aviv 6997801, Israel
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148
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Nguyen TS, Parkhill J. Nonadiabatic Dynamics for Electrons at Second-Order: Real-Time TDDFT and OSCF2. J Chem Theory Comput 2015; 11:2918-24. [DOI: 10.1021/acs.jctc.5b00262] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Triet S. Nguyen
- 251 Nieuwland Science
Hall, Notre Dame, Indiana 46556, United States
| | - John Parkhill
- 251 Nieuwland Science
Hall, Notre Dame, Indiana 46556, United States
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149
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Akama T, Kobayashi O, Nanbu S. Development of efficient time-evolution method based on three-term recurrence relation. J Chem Phys 2015; 142:204104. [PMID: 26026431 DOI: 10.1063/1.4921465] [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
The advantage of the real-time (RT) propagation method is a direct solution of the time-dependent Schrödinger equation which describes frequency properties as well as all dynamics of a molecular system composed of electrons and nuclei in quantum physics and chemistry. Its applications have been limited by computational feasibility, as the evaluation of the time-evolution operator is computationally demanding. In this article, a new efficient time-evolution method based on the three-term recurrence relation (3TRR) was proposed to reduce the time-consuming numerical procedure. The basic formula of this approach was derived by introducing a transformation of the operator using the arcsine function. Since this operator transformation causes transformation of time, we derived the relation between original and transformed time. The formula was adapted to assess the performance of the RT time-dependent Hartree-Fock (RT-TDHF) method and the time-dependent density functional theory. Compared to the commonly used fourth-order Runge-Kutta method, our new approach decreased computational time of the RT-TDHF calculation by about factor of four, showing the 3TRR formula to be an efficient time-evolution method for reducing computational cost.
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Affiliation(s)
- Tomoko Akama
- Department of Materials and Life Science, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Osamu Kobayashi
- Department of Materials and Life Science, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
| | - Shinkoh Nanbu
- Department of Materials and Life Science, Faculty of Science and Technology, Sophia University, Tokyo 102-8554, Japan
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150
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Repisky M, Konecny L, Kadek M, Komorovsky S, Malkin OL, Malkin VG, Ruud K. Excitation Energies from Real-Time Propagation of the Four-Component Dirac–Kohn–Sham Equation. J Chem Theory Comput 2015; 11:980-91. [DOI: 10.1021/ct501078d] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023]
Affiliation(s)
- Michal Repisky
- The
Centre for Theoretical and Computational Chemistry, Department of
Chemistry, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Lukas Konecny
- Department
of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
| | - Marius Kadek
- The
Centre for Theoretical and Computational Chemistry, Department of
Chemistry, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Stanislav Komorovsky
- The
Centre for Theoretical and Computational Chemistry, Department of
Chemistry, UiT, The Arctic University of Norway, Tromsø, Norway
| | - Olga L. Malkin
- Department
of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovak Republic
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Vladimir G. Malkin
- Institute
of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovak Republic
| | - Kenneth Ruud
- The
Centre for Theoretical and Computational Chemistry, Department of
Chemistry, UiT, The Arctic University of Norway, Tromsø, Norway
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