1
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Wittmann L, Gordiy I, Friede M, Helmich-Paris B, Grimme S, Hansen A, Bursch M. Extension of the D3 and D4 London dispersion corrections to the full actinides series. Phys Chem Chem Phys 2024. [PMID: 39092890 DOI: 10.1039/d4cp01514b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
Efficient dispersion corrections are an indispensable component of modern density functional theory, semi-empirical quantum mechanical, and even force field methods. In this work, we extend the well established D3 and D4 London dispersion corrections to the full actinides series, francium, and radium. To keep consistency with the existing versions, the original parameterization strategy of the D4 model was only slightly modified. This includes improved reference Hirshfeld atomic partial charges at the ωB97M-V/ma-def-TZVP level to fit the required electronegativity equilibration charge (EEQ) model. In this context, we developed a new actinide data set called AcQM, which covers the most common molecular actinide compound space. Furthermore, the efficient calculation of dynamic polarizabilities that are needed to construct CAB6 dispersion coefficients was implemented into the ORCA program package. The extended models are assessed for the computation of dissociation curves of actinide atoms and ions, geometry optimizations of crystal structure cutouts, gas-phase structures of small uranium compounds, and an example extracted from a small actinide complex protein assembly. We found that the novel parameterizations perform on par with the computationally more demanding density-dependent VV10 dispersion correction. With the presented extension, the excellent cost-accuracy ratio of the D3 and D4 models can now be utilized in various fields of computational actinide chemistry and, e.g., in efficient composite DFT methods such as r2SCAN-3c. They are implemented in our freely available standalone codes (dftd4, s-dftd3) and the D4 version will be also available in the upcoming ORCA 6.0 program package.
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Affiliation(s)
- Lukas Wittmann
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Igor Gordiy
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Marvin Friede
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Universität Bonn, Beringstr. 4, 53115 Bonn, Germany.
| | - Markus Bursch
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany.
- FACCTs GmbH, 50677, Köln, Germany
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2
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Franzke Y, Holzer C, Andersen JH, Begušić T, Bruder F, Coriani S, Della Sala F, Fabiano E, Fedotov DA, Fürst S, Gillhuber S, Grotjahn R, Kaupp M, Kehry M, Krstić M, Mack F, Majumdar S, Nguyen BD, Parker SM, Pauly F, Pausch A, Perlt E, Phun GS, Rajabi A, Rappoport D, Samal B, Schrader T, Sharma M, Tapavicza E, Treß RS, Voora V, Wodyński A, Yu JM, Zerulla B, Furche F, Hättig C, Sierka M, Tew DP, Weigend F. TURBOMOLE: Today and Tomorrow. J Chem Theory Comput 2023; 19:6859-6890. [PMID: 37382508 PMCID: PMC10601488 DOI: 10.1021/acs.jctc.3c00347] [Citation(s) in RCA: 37] [Impact Index Per Article: 37.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2023] [Indexed: 06/30/2023]
Abstract
TURBOMOLE is a highly optimized software suite for large-scale quantum-chemical and materials science simulations of molecules, clusters, extended systems, and periodic solids. TURBOMOLE uses Gaussian basis sets and has been designed with robust and fast quantum-chemical applications in mind, ranging from homogeneous and heterogeneous catalysis to inorganic and organic chemistry and various types of spectroscopy, light-matter interactions, and biochemistry. This Perspective briefly surveys TURBOMOLE's functionality and highlights recent developments that have taken place between 2020 and 2023, comprising new electronic structure methods for molecules and solids, previously unavailable molecular properties, embedding, and molecular dynamics approaches. Select features under development are reviewed to illustrate the continuous growth of the program suite, including nuclear electronic orbital methods, Hartree-Fock-based adiabatic connection models, simplified time-dependent density functional theory, relativistic effects and magnetic properties, and multiscale modeling of optical properties.
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Affiliation(s)
- Yannick
J. Franzke
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Christof Holzer
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Josefine H. Andersen
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Tomislav Begušić
- Division
of Chemistry and Chemical Engineering, California
Institute of Technology, Pasadena, California 91125, United States
| | - Florian Bruder
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Sonia Coriani
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabio Della Sala
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Eduardo Fabiano
- Institute
for Microelectronics and Microsystems (CNR-IMM), Via Monteroni, Campus Unisalento, 73100 Lecce, Italy
- Center for
Biomolecular Nanotechnologies @UNILE, Istituto
Italiano di Tecnologia, Via Barsanti, 73010 Arnesano, Italy
| | - Daniil A. Fedotov
- DTU
Chemistry, Department of Chemistry, Technical
University of Denmark, Kemitorvet Building 207, DK-2800 Kongens Lyngby, Denmark
- Institute
of Chemistry, The Hebrew University of Jerusalem, Jerusalem 91904, Israel
| | - Susanne Fürst
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Sebastian Gillhuber
- Institute
of Inorganic Chemistry, Karlsruhe Institute
of Technology (KIT), Engesserstr. 15, 76131 Karlsruhe, Germany
| | - Robin Grotjahn
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Martin Kaupp
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Max Kehry
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Marjan Krstić
- Institute
of Theoretical Solid State Physics, Karlsruhe
Institute of Technology (KIT), Wolfgang-Gaede-Str. 1, 76131 Karlsruhe, Germany
| | - Fabian Mack
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Sourav Majumdar
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Brian D. Nguyen
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Shane M. Parker
- Department
of Chemistry, Case Western Reserve University, 10900 Euclid Ave, Cleveland, Ohio 44106 United States
| | - Fabian Pauly
- Institute
of Physics, University of Augsburg, Universitätsstr. 1, 86159 Augsburg, Germany
| | - Ansgar Pausch
- Institute
of Physical Chemistry, Karlsruhe Institute
of Technology (KIT), Fritz-Haber-Weg 2, 76131 Karlsruhe, Germany
| | - Eva Perlt
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Gabriel S. Phun
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Ahmadreza Rajabi
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Dmitrij Rappoport
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Bibek Samal
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Tim Schrader
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Manas Sharma
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - Enrico Tapavicza
- Department
of Chemistry and Biochemistry, California
State University, Long Beach, 1250 Bellflower Boulevard, Long
Beach, California 90840-9507, United States
| | - Robert S. Treß
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Vamsee Voora
- Department
of Chemical Sciences, Tata Institute of
Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Artur Wodyński
- Institut
für Chemie, Theoretische Chemie/Quantenchemie, Sekr. C7, Technische Universität Berlin, Straße des 17 Juni 135, 10623, Berlin, Germany
| | - Jason M. Yu
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Benedikt Zerulla
- Institute
of Nanotechnology, Karlsruhe Institute of
Technology (KIT), Hermann-von-Helmholtz-Platz
1, 76344 Eggenstein-Leopoldshafen Germany
| | - Filipp Furche
- Department
of Chemistry, University of California,
Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, United States
| | - Christof Hättig
- Lehrstuhl
für Theoretische Chemie, Ruhr-Universität
Bochum, 44801 Bochum, Germany
| | - Marek Sierka
- Otto-Schott-Institut
für Materialforschung, Friedrich-Schiller-Universität
Jena, Löbdergraben
32, 07743 Jena, Germany
| | - David P. Tew
- Physical
and Theoretical Chemistry Laboratory, University
of Oxford, South Parks
Road, Oxford OX1 3QZ, United Kingdom
| | - Florian Weigend
- Fachbereich
Chemie, Philipps-Universität Marburg, Hans-Meerwein-Str. 4, 35032 Marburg, Germany
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3
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Warthegau SS, Hillers-Bendtsen AE, Pedersen SK, Rindom C, Braestrup C, Jensen JS, Hammerich O, Thomsen MS, Kamounah FS, Norman P, Mikkelsen KV, Brock-Nannestad T, Pittelkow M. Heterocyclic [9]Helicenes Exhibiting Bright Circularly Polarized Luminescence. Chemistry 2023; 29:e202301815. [PMID: 37458527 DOI: 10.1002/chem.202301815] [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: 06/06/2023] [Accepted: 07/17/2023] [Indexed: 09/14/2023]
Abstract
We describe a concise synthetic strategy for the preparation of heterocyclic [9]helicenes and a simple preparative-scale protocol for the optical resolution of the resulting M- and P-enantiomers. The helicenes were characterized by single-crystal X-ray diffraction along with a range of spectroscopic and computational techniques. A fluorescence quantum yield of up to 65 % was observed, and the chiroptical properties of both M- and P-helicenes revealed large dissymmetry factors. The circularly polarized luminescence brightness reaches up to 17 M-1 cm-1 , as measured experimentally and verified computationally, which makes this the highest circularly polarized luminescence brightness among heterocyclic helicenes. We describe how chiroptical properties (both circular dichroism and circularly polarized luminescence) can be described and predicted using quantum chemical calculations. The synthetic approach also reveals by-products that originate from internal oxidation reactions, presumably mediated by the close proximity of the π-surfaces in the helicene structure.
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Affiliation(s)
- Stefan S Warthegau
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | | | - Stephan K Pedersen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Cecilie Rindom
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Christoffer Braestrup
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Jeppe S Jensen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Ole Hammerich
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Maria S Thomsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Fadhil S Kamounah
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Patrick Norman
- Division of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, 100 44, Stockholm, Sweden
| | - Kurt V Mikkelsen
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Theis Brock-Nannestad
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
| | - Michael Pittelkow
- Department of Chemistry, University of Copenhagen, Universitetsparken 5, 2100, Copenhagen Ø, Denmark
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4
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Scott M, Delcey MG. Complex Linear Response Functions for a Multiconfigurational Self-Consistent Field Wave Function in a High Performance Computing Environment. J Chem Theory Comput 2023; 19:5924-5937. [PMID: 37596971 PMCID: PMC10500980 DOI: 10.1021/acs.jctc.3c00317] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2023] [Indexed: 08/21/2023]
Abstract
We present novel developments for the highly efficient evaluation of complex linear response functions of a multiconfigurational self-consistent field (MCSCF) wave function as implemented in MultiPsi. Specifically, expressions for the direct evaluation of linear response properties at given frequencies using the complex polarization propagator (CPP) approach have been implemented, within both the Tamm-Dancoff approximation (TDA) and the random phase approximation (RPA). Purely real algebra with symmetric and antisymmetric trial vectors in a shared subspace is used wherein the linear response equations are solved. Two bottlenecks of large scale MC-CPP calculations, namely, the memory footprint and computational time, are addressed. The former is addressed by limiting the size of the subspace of trial vectors by using singular value decomposition (SVD) on either orbital or CI subspaces. The latter is addressed using an efficient parallel implementation as well as the strategy of dynamically adding linear response equations at near-convergence to neighboring roots. Furthermore, a novel methodology for decomposing MC-CPP spectra in terms of intuitive orbital excitations in an approximate fashion is presented. The performance of the code is illustrated with several numerical examples, including the X-ray spectrum of a molecule with nearly one hundred atoms. Additionally, for X-ray spectroscopy, the effect of including or excluding the core orbital in the active space on small covalent metal complexes is discussed.
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Affiliation(s)
- Mikael Scott
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mickael G. Delcey
- Division
of Theoretical Chemistry and Biology, School of Engineering Sciences
in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
- Division
of Theoretical Chemistry, Department of Chemistry, Lund University, SE-221 00 Lund, Sweden
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5
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Creutzberg J, Hedegård ED. A method to capture the large relativistic and solvent effects on the UV-vis spectra of photo-activated metal complexes. Phys Chem Chem Phys 2023; 25:6153-6163. [PMID: 36752122 DOI: 10.1039/d2cp04937f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
We have recently developed a method based on relativistic time-dependent density functional theory (TD-DFT) that allows the calculation of electronic spectra in solution (Creutzberg, Hedegård, J. Chem. Theory Comput.18, 2022, 3671). This method treats the solvent explicitly with a classical, polarizable embedding (PE) description. Furthermore, it employs the complex polarization propagator (CPP) formalism which allows calculations on complexes with a dense population of electronic states (such complexes are known to be problematic for conventional TD-DFT). Here, we employ this method to investigate both the dynamic and electronic effects of the solvent for the excited electronic states of trans-trans-trans-[Pt(N3)2(OH)2(NH3)2] in aqueous solution. This complex decomposes into species harmful to cancer cells under light irradiation. Thus, understanding its photo-physical properties may lead to a more efficient method to battle cancer. We quantify the effect of the underlying structure and dynamics by classical molecular mechanics simulations, refined with a subsequent DFT or semi-empirical optimization on a cluster. Moreover, we quantify the effect of employing different methods to set up the solvated system, e.g., how sensitive the results are to the method used for the refinement, and how large a solvent shell that is required. The electronic solvent effect is always included through a PE potential.
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Affiliation(s)
- Joel Creutzberg
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.
| | - Erik Donovan Hedegård
- Division of Theoretical Chemistry, Lund University, Lund, Sweden. .,Department of Physics, Chemistry and Pharmacy, Campusvej 55, 5230 Odense, Denmark.
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6
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Brand M, Norman P. Nontrivial spectral band progressions in electronic circular dichroism spectra of carbohelicenes revealed by linear response calculations. Phys Chem Chem Phys 2022; 24:19321-19332. [PMID: 35929836 DOI: 10.1039/d2cp02371g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We demonstrate that contemporary computational resources allow for accurate theoretical studies of systems matching recent advances in experimental helicene chemistry. Concerned with first-principles calculations of carbohelicenes, our work surpasses CH[12] as the largest system investigated to date and unravels trends in the electronic structure of the low-lying states of the homologous series. Utilizing a highly efficient implementation of linear response algorithms, we present electronic circular dichroism (CD) spectra of carbohelicenes ranging from CH[5] to CH[30] at the level of Kohn-Sham density-functional theory. Our results for a systematic increase in system size show the emergence of new CD bands that subsequently rise to intensities dominating the spectrum. The spectral band progressions exhibit a periodicity directly linked to the number of overlapping layers of conjugation. While our findings rectify the current understanding of the electronic structure of carbohelicenes, they also serve as a general call for caution regarding the extrapolation of trends from small system ranges.
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Affiliation(s)
- Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden.
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7
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Hait D, Oosterbaan KJ, Carter-Fenk K, Head-Gordon M. Computing x-ray absorption spectra from linear-response particles atop optimized holes. J Chem Phys 2022; 156:201104. [PMID: 35649868 DOI: 10.1063/5.0092987] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
State specific orbital optimized density functional theory (OO-DFT) methods, such as restricted open-shell Kohn-Sham (ROKS), can attain semiquantitative accuracy for predicting x-ray absorption spectra of closed-shell molecules. OO-DFT methods, however, require that each state be individually optimized. In this Communication, we present an approach to generate an approximate core-excited state density for use with the ROKS energy ansatz, which is capable of giving reasonable accuracy without requiring state-specific optimization. This is achieved by fully optimizing the core-hole through the core-ionized state, followed by the use of electron-addition configuration interaction singles to obtain the particle level. This hybrid approach can be viewed as a DFT generalization of the static-exchange (STEX) method and can attain ∼0.6 eV rms error for the K-edges of C-F through the use of local functionals, such as PBE and OLYP. This ROKS(STEX) approach can also be used to identify important transitions for full OO ROKS treatment and can thus help reduce the computational cost of obtaining OO-DFT quality spectra. ROKS(STEX), therefore, appears to be a useful technique for the efficient prediction of x-ray absorption spectra.
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Affiliation(s)
- Diptarka Hait
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Katherine J Oosterbaan
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Kevin Carter-Fenk
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Kenneth S. Pitzer Center for Theoretical Chemistry, Department of Chemistry, University of California, Berkeley, California 94720, USA
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8
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Creutzberg J, Hedegård ED. Polarizable Embedding Complex Polarization Propagator in Four- and Two-Component Frameworks. J Chem Theory Comput 2022; 18:3671-3686. [PMID: 35549262 DOI: 10.1021/acs.jctc.1c01249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Explicit embedding methods combined with the complex polarization propagator (CPP) enable the modeling of spectroscopy for increasingly complex systems with a high density of states. We present the first derivation and implementation of the CPP in four- and exact-two-component (X2C) polarizable embedding (PE) frameworks. We denote the developed methods PE-4c-CPP and PE-X2C-CPP, respectively. We illustrate the methods by estimating the solvent effect on ultraviolet-visible (UV-vis) and X-ray atomic absorption (XAS) spectra of [Rh(H2O)6]3+ and [Ir(H2O)6]3+ immersed in aqueous solution. We moreover estimate solvent effects on UV-vis spectra of a platinum complex that can be photochemically activated (in water) to kill cancer cells. Our results clearly show that the inclusion of the environment is required: UV-vis and (to a lesser degree) XAS spectra can become qualitatively different from vacuum calculations. Comparison of PE-4c-CPP and PE-X2C-CPP methods shows that X2C essentially reproduces the solvent effect obtained with the 4c methods.
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Affiliation(s)
- Joel Creutzberg
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden
| | - Erik D Hedegård
- Division of Theoretical Chemistry, Lund University, SE-223 62 Lund, Sweden.,Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense, Denmark
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9
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Fedotov DA, Coriani S, Hättig C. Damped (linear) response theory within the resolution-of-identity coupled cluster singles and approximate doubles (RI-CC2) method. J Chem Phys 2021; 154:124110. [PMID: 33810703 DOI: 10.1063/5.0042759] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
An implementation of a complex solver for the solution of the linear equations required to compute the complex response functions of damped response theory is presented for the resolution-of-identity (RI) coupled cluster singles and approximate doubles (CC2) method. The implementation uses a partitioned formulation that avoids the storage of double excitation amplitudes to make it applicable to large molecules. The solver is the keystone element for the development of the damped coupled cluster response formalism for linear and nonlinear effects in resonant frequency regions at the RI-CC2 level of theory. Illustrative results are reported for the one-photon absorption cross section of C60, the electronic circular dichroism of n-helicenes (n = 5, 6, 7), and the C6 dispersion coefficients of a set of selected organic molecules and fullerenes.
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Affiliation(s)
- Daniil A Fedotov
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
| | - Christof Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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10
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Brand M, Ahmadzadeh K, Li X, Rinkevicius Z, Saidi WA, Norman P. Size-dependent polarizabilities and van der Waals dispersion coefficients of fullerenes from large-scale complex polarization propagator calculations. J Chem Phys 2021; 154:074304. [PMID: 33607910 DOI: 10.1063/5.0040009] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
While the anomalous non-additive size-dependencies of static dipole polarizabilities and van der Waals C6 dispersion coefficients of carbon fullerenes are well established, the widespread reported scalings for the latter (ranging from N2.2 to N2.8) call for a comprehensive first-principles investigation. With a highly efficient implementation of the linear complex polarization propagator, we have performed Hartree-Fock and Kohn-Sham density functional theory calculations of the frequency-dependent polarizabilities for fullerenes consisting of up to 540 carbon atoms. Our results for the static polarizabilities and C6 coefficients show scalings of N1.2 and N2.2, respectively, thereby deviating significantly from the previously reported values obtained with the use of semi-classical/empirical methods. Arguably, our reported values are the most accurate to date as they represent the first ab initio or first-principles treatment of fullerenes up to a convincing system size.
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Affiliation(s)
- Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Karan Ahmadzadeh
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Wissam A Saidi
- Department of Mechanical Engineering and Materials Science, University of Pittsburgh, Pittsburgh, Pennsylvania 15261, USA
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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11
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Ahmadzadeh K, Scott M, Brand M, Vahtras O, Li X, Rinkevicius Z, Norman P. Efficient implementation of isotropic cubic response functions for two-photon absorption cross sections within the self-consistent field approximation. J Chem Phys 2021; 154:024111. [PMID: 33445884 DOI: 10.1063/5.0031851] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Within the self-consistent field approximation, computationally tractable expressions for the isotropic second-order hyperpolarizability have been derived and implemented for the calculation of two-photon absorption cross sections. The novel tensor average formulation presented in this work allows for the evaluation of isotropic damped cubic response functions using only ∼3.3% (one-photon off-resonance regions) and ∼10% (one-photon resonance regions) of the number of auxiliary Fock matrices required when explicitly calculating all the needed individual tensor components. Numerical examples of the two-photon absorption cross section in the one-photon off-resonance and resonance regions are provided for alanine-tryptophan and 2,5-dibromo-1,4-bis(2-(4-diphenylaminophenyl)vinyl)-benzene. Furthermore, a benchmark set of 22 additional small- and medium-sized organic molecules is considered. In all these calculations, a quantitative assessment is made of the reduced and approximate forms of the cubic response function in the one-photon off-resonance regions and results demonstrate a relative error of less than ∼5% when using the reduced expression as compared to the full form of the isotropic cubic response function.
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Affiliation(s)
- Karan Ahmadzadeh
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Mikael Scott
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
| | - Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
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12
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Nanda KD, Krylov AI. Cherry-picking resolvents: A general strategy for convergent coupled-cluster damped response calculations of core-level spectra. J Chem Phys 2020; 153:141104. [DOI: 10.1063/5.0020843] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Affiliation(s)
- Kaushik D. Nanda
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
| | - Anna I. Krylov
- Department of Chemistry, University of Southern California, Los Angeles, California 90089-0482, USA
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13
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Faber R, Ghidinelli S, Hättig C, Coriani S. Magnetic circular dichroism spectra from resonant and damped coupled cluster response theory. J Chem Phys 2020; 153:114105. [PMID: 32962374 DOI: 10.1063/5.0013398] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
A computational expression for the Faraday A term of magnetic circular dichroism (MCD) is derived within coupled cluster response theory and alternative computational expressions for the B term are discussed. Moreover, an approach to compute the (temperature-independent) MCD ellipticity in the context of coupled cluster damped response is presented, and its equivalence with the stick-spectrum approach in the limit of infinite lifetimes is demonstrated. The damped response approach has advantages for molecular systems or spectral ranges with a high density of states. Illustrative results are reported at the coupled cluster singles and doubles level and compared to time-dependent density functional theory results.
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Affiliation(s)
- R Faber
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
| | - S Ghidinelli
- Department of Molecular and Translational Medicine, Università degli Studi di Brescia, Viale Europa 11, I-25123 Brescia, Italy
| | - C Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität Bochum, Bochum D-44780, Germany
| | - S Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Bldg. 207, DK-2800 Kongens Lyngby, Denmark
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14
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Niemeyer N, Tölle J, Neugebauer J. Approximate versus Exact Embedding for Chiroptical Properties: Reconsidering Failures in Potential and Response. J Chem Theory Comput 2020; 16:3104-3120. [PMID: 32301613 DOI: 10.1021/acs.jctc.0c00125] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
We investigate the suitability of subsystem time-dependent density-functional theory (sTDDFT) for describing chiroptical properties with a focus on optical rotation parameters. Our starting point is a new implementation of the recently proposed projection-based, coupled frozen-density embedding (FDEc) framework. We adapt the generalized, non-Hermitian formulation of TDDFT and derive corresponding expressions for regular and damped response properties from subsystem TDDFT. We verify that our implementation of this "exact" formulation allows to reproduce supermolecular results of electronic circular dichroism (ECD) spectra, of optical rotatory dispersion, and of polarizabilities. We present a systematic test of the main approximations typically introduced in practical frozen-density embedding (FDE) calculations of response properties: (i) the use of approximate nonadditive kinetic-energy (NAKE) functionals, which can be avoided through projection techniques, (ii) the use of monomer (subsystem) basis sets rather than supersystem basis sets, and (iii) the neglect of intersubsystem response coupling within the so-called uncoupled FDE (or FDEu) approximation. While approximation (i) is known to generally lead to large errors for covalently bound subsystems, we present cases in which either the basis set or the coupling step are similarly or even (much) more important. In particular, we explicitly demonstrate by comparison to a fully coupled calculation that missing intersubsystem response couplings are responsible for the failure of FDE reported in a previous study [ J. Chem. Theory Comput. 2015, 11, 5305-5315]. We show that good agreement with reference results can be obtained in this case even with standard NAKE approximations for the FDE potentials and efficient monomer basis sets, making calculations for larger systems well accessible.
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Affiliation(s)
- Niklas Niemeyer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Tölle
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster Corrensstraße 40, 48149 Münster, Germany
| | - Johannes Neugebauer
- Theoretische Organische Chemie, Organisch-Chemisches Institut and Center for Multiscale Theory and Computation, Westfälische Wilhelms-Universität Münster Corrensstraße 40, 48149 Münster, Germany
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15
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Faber R, Coriani S. Core–valence-separated coupled-cluster-singles-and-doubles complex-polarization-propagator approach to X-ray spectroscopies. Phys Chem Chem Phys 2020; 22:2642-2647. [DOI: 10.1039/c9cp03696b] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
The iterative subspace algorithm to solve the CCSD complex linear response equations has been modified to include a core–valence separation projection step to overcome convergence problems. Illustrative results are reported for XAS, XCD, XES and RIXS.
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Affiliation(s)
- Rasmus Faber
- DTU Chemistry - Department of Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
| | - Sonia Coriani
- DTU Chemistry - Department of Chemistry
- Technical University of Denmark
- DK-2800 Kongens Lyngby
- Denmark
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16
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Nanda KD, Vidal ML, Faber R, Coriani S, Krylov AI. How to stay out of trouble in RIXS calculations within equation-of-motion coupled-cluster damped response theory? Safe hitchhiking in the excitation manifold by means of core–valence separation. Phys Chem Chem Phys 2020; 22:2629-2641. [DOI: 10.1039/c9cp03688a] [Citation(s) in RCA: 34] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
We present a novel approach with robust convergence of the response equations for computing resonant inelastic X-ray scattering (RIXS) cross sections within the equation-of-motion coupled-cluster (EOM-CC) framework.
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Affiliation(s)
- Kaushik D. Nanda
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
| | - Marta L. Vidal
- DTU Chemistry – Department of Chemistry
- Technical University of Denmark
- DK-2800
- Denmark
| | - Rasmus Faber
- DTU Chemistry – Department of Chemistry
- Technical University of Denmark
- DK-2800
- Denmark
| | - Sonia Coriani
- DTU Chemistry – Department of Chemistry
- Technical University of Denmark
- DK-2800
- Denmark
| | - Anna I. Krylov
- Department of Chemistry
- University of Southern California
- Los Angeles
- USA
- The Hamburg Centre for Ultrafast Imaging
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17
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Rinkevicius Z, Li X, Vahtras O, Ahmadzadeh K, Brand M, Ringholm M, List NH, Scheurer M, Scott M, Dreuw A, Norman P. VeloxChem: A Python‐driven density‐functional theory program for spectroscopy simulations in high‐performance computing environments. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1457] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Affiliation(s)
- Zilvinas Rinkevicius
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
- Department of Physics Kaunas University of Technology Kaunas Lithuania
| | - Xin Li
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Olav Vahtras
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Karan Ahmadzadeh
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Manuel Brand
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Magnus Ringholm
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
| | - Nanna Holmgaard List
- Department of Chemistry and the PULSE Institute Stanford University Stanford California
- SLAC National Accelerator Laboratory Menlo Park California
| | - Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Mikael Scott
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing Ruprecht‐Karls University Heidelberg Germany
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health KTH Royal Institute of Technology Stockholm Sweden
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18
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Konecny L, Repisky M, Ruud K, Komorovsky S. Relativistic four-component linear damped response TDDFT for electronic absorption and circular dichroism calculations. J Chem Phys 2019; 151:194112. [DOI: 10.1063/1.5128564] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Affiliation(s)
- Lukas Konecny
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
- Department of Inorganic Chemistry, Faculty of Natural Sciences, Comenius University, Bratislava, Slovakia
| | - Michal Repisky
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Kenneth Ruud
- Hylleraas Centre for Quantum Molecular Sciences, UiT The Arctic University of Norway, 9037 Tromsø, Norway
| | - Stanislav Komorovsky
- Institute of Inorganic Chemistry, Slovak Academy of Sciences, Bratislava, Slovakia
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19
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Skrzyński G, Radula-Janik K, Kupka T, Pluta T. Dynamic Polarizability and Higher-Order Electric Properties of Fluorene, Carbazole, and Dibenzofuran. J Phys Chem A 2019; 123:9753-9762. [DOI: 10.1021/acs.jpca.9b06889] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Affiliation(s)
- Grzegorz Skrzyński
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
| | | | - Teobald Kupka
- Faculty of Chemistry, University of Opole, Oleska 48, 45-052 Opole, Poland
| | - Tadeusz Pluta
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006 Katowice, Poland
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20
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Štěpánek P, Coriani S. Spatial localization in nuclear spin-induced circular dichroism - a quadratic response function analysis. Phys Chem Chem Phys 2019; 21:18082-18091. [PMID: 31145406 DOI: 10.1039/c9cp01716j] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
Nuclear magneto-optic (NMO) effects are recently described phenomena originating from the interaction of light with local magnetic fields produced by nuclear spins. The phenomena border nuclear magnetic resonance and optical spectroscopy and are expected to provide rather unique spectroscopic features, borrowing from both localized response of the atomic nuclei as well as more global excitation properties of the whole molecule or its chromophore moieties. A number of quantum-chemical computational studies have been carried out, offering a reasonable agreement with nuclear magneto-optics experiments performed so far. However, the detailed structure-spectra relation is still poorly understood. In this report we address the question of locality of one of the NMO effects, namely nuclear spin-induced circular dichroism (NSCD). We implement an alternative computational approach for calculation of the NSCD intensities, based on residues of quadratic response functions, and use it to investigate the NSCD response of different nuclei in a model molecular system with well-defined separate chromophores. The results show that significant NSCD at a given energy only occurs at the nuclei which are located in the chromophore that is excited. We rationalize these findings using analysis via difference densities, and approximate sum-over-states calculations. This behaviour of NSCD opens a way to experimental studies of localization of excited states in molecules, potentially with resolution down to the order of bond-length.
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Affiliation(s)
- Petr Štěpánek
- NMR Research Unit, Faculty of Science, University of Oulu, PO Box 3000, FI-90014 Oulu, Finland.
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21
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Neville SP, Schuurman MS. Efficient calculation of X-ray absorption spectra using Chebyshev-Slepian filter diagonalisation. J Chem Phys 2019; 150:184115. [DOI: 10.1063/1.5092975] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023] Open
Affiliation(s)
- Simon P. Neville
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
| | - Michael S. Schuurman
- Department of Chemistry and Biomolecular Sciences, University of Ottawa, 10 Marie Curie, Ottawa, Ontario K1N 6N5, Canada
- National Research Council of Canada, 100 Sussex Drive, Ottawa, Ontario K1A 0R6, Canada
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22
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Liu J, Matthews D, Coriani S, Cheng L. Benchmark Calculations of K-Edge Ionization Energies for First-Row Elements Using Scalar-Relativistic Core–Valence-Separated Equation-of-Motion Coupled-Cluster Methods. J Chem Theory Comput 2019; 15:1642-1651. [DOI: 10.1021/acs.jctc.8b01160] [Citation(s) in RCA: 42] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Affiliation(s)
- Junzi Liu
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
| | - Devin Matthews
- Department of Chemistry, Southern Methodist University, Dallas, Texas 75275, United States
| | - Sonia Coriani
- Department of Chemistry, Technical University of Denmark, DK-2800 Kongens Lyngby, Denmark
| | - Lan Cheng
- Department of Chemistry, The Johns Hopkins University, Baltimore, Maryland 21218, United States
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23
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Zhovtobriukh I, Norman P, Pettersson LGM. X-ray absorption spectrum simulations of hexagonal ice. J Chem Phys 2019; 150:034501. [DOI: 10.1063/1.5078385] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Affiliation(s)
- Iurii Zhovtobriukh
- FYSIKUM, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
| | - Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Lars G. M. Pettersson
- FYSIKUM, Stockholm University, AlbaNova University Center, SE-106 91 Stockholm, Sweden
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24
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Reinholdt P, Nørby MS, Kongsted J. Modeling of Magnetic Circular Dichroism and UV/Vis Absorption Spectra Using Fluctuating Charges or Polarizable Embedding within a Resonant-Convergent Response Theory Formalism. J Chem Theory Comput 2018; 14:6391-6404. [DOI: 10.1021/acs.jctc.8b00660] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Morten S. Nørby
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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25
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Nielsen C, Nørby MS, Kongsted J, Solov'yov IA. Absorption Spectra of FAD Embedded in Cryptochromes. J Phys Chem Lett 2018; 9:3618-3623. [PMID: 29905481 DOI: 10.1021/acs.jpclett.8b01528] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The magnetic compass sense utilized by migratory birds for long-distance navigation functions only once light of a certain wavelength is present. This piece of evidence fits partially with the popular hypothesis of chemical magnetoreception in cryptochrome proteins, located in the bird retina. According to this hypothesis a magnetosensitive radical pair is produced after photoexcitation of an FAD cofactor inside cryptochrome, and as such the absorption properties of FAD are of crucial importance for cryptochrome activation. However, we reveal that absorption spectra of FAD show very little variation between six different cryptochromes, suggesting that the electronic transitions are barely affected by the chemical differences in the proteins. This conclusion hints on the presence of a secondary photoreceptor or cofactor that could be necessary to explain green-light-activated magnetoreception in birds.
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Affiliation(s)
- Claus Nielsen
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Morten S Nørby
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
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26
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Norman P, Dreuw A. Simulating X-ray Spectroscopies and Calculating Core-Excited States of Molecules. Chem Rev 2018; 118:7208-7248. [DOI: 10.1021/acs.chemrev.8b00156] [Citation(s) in RCA: 164] [Impact Index Per Article: 27.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Patrick Norman
- Department of Theoretical Chemistry and Biology, School of Engineering Sciences in Chemistry, Biotechnology and Health, KTH Royal Institute of Technology, SE-106 91 Stockholm, Sweden
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Ruprecht-Karls University, Im Neuenheimer Feld 205, 69120 Heidelberg, Germany
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27
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Zhovtobriukh I, Besley NA, Fransson T, Nilsson A, Pettersson LGM. Relationship between x-ray emission and absorption spectroscopy and the local H-bond environment in water. J Chem Phys 2018; 148:144507. [DOI: 10.1063/1.5009457] [Citation(s) in RCA: 29] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Affiliation(s)
- Iurii Zhovtobriukh
- FYSIKUM, Stockholm University, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Nicholas A. Besley
- School of Chemistry, The University of Nottingham, University Park, Nottingham NG72RD, United Kingdom
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California 94025,
USA
| | - Anders Nilsson
- FYSIKUM, Stockholm University, Albanova University Center, SE-106 91 Stockholm, Sweden
| | - Lars G. M. Pettersson
- FYSIKUM, Stockholm University, Albanova University Center, SE-106 91 Stockholm, Sweden
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28
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29
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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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30
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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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31
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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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32
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Relation between molecular electronic structure and nuclear spin-induced circular dichroism. Sci Rep 2017; 7:46617. [PMID: 28436463 PMCID: PMC5402291 DOI: 10.1038/srep46617] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2016] [Accepted: 03/21/2017] [Indexed: 11/16/2022] Open
Abstract
The recently theoretically described nuclear spin-induced circular dichroism (NSCD) is a promising method for the optical detection of nuclear magnetization. NSCD involves both optical excitations of the molecule and hyperfine interactions and, thus, it offers a means to realize a spectroscopy with spatially localized, high-resolution information. To survey the factors relating the molecular and electronic structure to the NSCD signal, we theoretically investigate NSCD of twenty structures of the four most common nucleic acid bases (adenine, guanine, thymine, cytosine). The NSCD signal correlates with the spatial distribution of the excited states and couplings between them, reflecting changes in molecular structure and conformation. This constitutes a marked difference to the nuclear magnetic resonance (NMR) chemical shift, which only reflects the local molecular structure in the ground electronic state. The calculated NSCD spectra are rationalized by means of changes in the electronic density and by a sum-over-states approach, which allows to identify the contributions of the individual excited states. Two separate contributions to NSCD are identified and their physical origins and relative magnitudes are discussed. The results underline NSCD spectroscopy as a plausible tool with a power for the identification of not only different molecules, but their specific structures as well.
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33
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Fossard F, Hug G, Gilmore K, Kas J, Rehr J, Vila F, Shirley E. Quantitative first-principles calculations of valence and core excitation spectra of solid C 60. PHYSICAL REVIEW. B 2017; 95:115112. [PMID: 28819652 PMCID: PMC5557304 DOI: 10.1103/physrevb.95.115112] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
We present calculated valence and C 1s near-edge excitation spectra of solid C60 and experimental results measured with high-resolution electron energy-loss spectroscopy. The near-edge calculations are carried out using three different methods: solution of the Bethe-Salpeter equation (BSE) as implemented in the OCEAN suite (Obtaining Core Excitations with ab initio methods and the NIST BSE solver), the excited-electron core-hole approach (XCH), and the constrained-occupancy method using the Stockholm-Berlin core-excitation code, StoBe. The three methods give similar results and are in good agreement with experiment, though the BSE results are the most accurate. The BSE formalism is also used to carry out valence level calculations using the NIST Bethe-Salpeter Equation solver (NBSE). Theoretical results include self-energy corrections to the band gap and band widths, lifetime-damping effects, and Debye-Waller effects in the core-excitation case. A comparison of spectral features to those observed experimentally illustrates the sensitivity of certain features to computational details, such as self-energy corrections to the band structure and core-hole screening.
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Affiliation(s)
- F. Fossard
- ONERA-CNRS, Laboratoire d’Etude des Microstructures, BP 72, 92322, Châtillon Cedex, FRANCE
| | - G. Hug
- ONERA-CNRS, Laboratoire d’Etude des Microstructures, BP 72, 92322, Châtillon Cedex, FRANCE
| | - K. Gilmore
- European Synchrotron Radiation Facility (ESRF), BP 220, F-38043 Grenoble, FRANCE
| | - J.J. Kas
- Dept. of Physics, University of Washington, Seattle, WA 98195, USA
| | - J.J. Rehr
- Dept. of Physics, University of Washington, Seattle, WA 98195, USA
| | - F.D. Vila
- Dept. of Physics, University of Washington, Seattle, WA 98195, USA
| | - E.L. Shirley
- Sensor Science Division, National Institute of Standards and Technology, 100 Bureau Dr. MS 8441, Gaithersburg MD 20899-8441, USA
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34
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Kumar C, Kjærgaard T, Helgaker T, Fliegl H. Nuclei-selected atomic-orbital response-theory formulation for the calculation of NMR shielding tensors using density-fitting. J Chem Phys 2016; 145:234108. [DOI: 10.1063/1.4972212] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Affiliation(s)
- Chandan Kumar
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Thomas Kjærgaard
- Department of Chemistry, Aarhus University, Langelandsgade 140, 8000 Aarhus C, Denmark
| | - Trygve Helgaker
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
| | - Heike Fliegl
- Centre for Theoretical and Computational Chemistry (CTCC), Department of Chemistry, University of Oslo, P.O. Box 1033, Blindern, 0315 Oslo, Norway
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35
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List NH, Saue T, Norman P. Rotationally averaged linear absorption spectra beyond the electric-dipole approximation. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1187773] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques, UMR 5626 — CNRS/Université Toulouse III (Paul Sabatier), 31062 Toulouse Cedex 09, France
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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36
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Abstract
A complex polarization propagator approach has been developed to third order and implemented in density functional theory (DFT), allowing for the direct calculation of nonlinear molecular properties in the X-ray wavelength regime without explicitly addressing the excited-state manifold. We demonstrate the utility of this propagator method for the modeling of coherent near-edge X-ray two-photon absorption using, as an example, DFT as the underlying electronic structure model. Results are compared with the corresponding near-edge X-ray absorption fine structure spectra, illuminating the differences in the role of symmetry, localization, and correlation between the two spectroscopies. The ramifications of this new technique for nonlinear X-ray research are briefly discussed.
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Affiliation(s)
- Tobias Fahleson
- Department of Physics, Chemistry and Biology, Linköping University , SE-581 83 Linköping, Sweden
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , SE-106 91, Stockholm, Sweden
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University , SE-581 83 Linköping, Sweden
- Division of Theoretical Chemistry and Biology, School of Biotechnology, KTH Royal Institute of Technology , SE-106 91, Stockholm, Sweden
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37
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Fransson T, Harada Y, Kosugi N, Besley NA, Winter B, Rehr JJ, Pettersson LGM, Nilsson A. X-ray and Electron Spectroscopy of Water. Chem Rev 2016; 116:7551-69. [PMID: 27244473 DOI: 10.1021/acs.chemrev.5b00672] [Citation(s) in RCA: 109] [Impact Index Per Article: 13.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Here we present an overview of recent developments of X-ray and electron spectroscopy to probe water at different temperatures. Photon-induced ionization followed by detection of electrons from either the O 1s level or the valence band is the basis of photoelectron spectroscopy. Excitation between the O 1s and the unoccupied states or occupied states is utilized in X-ray absorption and X-ray emission spectroscopies. These techniques probe the electronic structure of the liquid phase and show sensitivity to the local hydrogen-bonding structure. Both experimental aspects related to the measurements and theoretical simulations to assist in the interpretation are discussed in detail. Different model systems are presented such as the different bulk phases of ice and various adsorbed monolayer structures on metal surfaces.
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Affiliation(s)
- Thomas Fransson
- Department of Physics, Chemistry and Biology, Linköping University , S-581 83 Linköping, Sweden
| | - Yoshihisa Harada
- Institute for Solid State Physics (ISSP), The University of Tokyo , Kashiwanoha, Kashiwa, Chiba 277-8581, Japan
| | - Nobuhiro Kosugi
- Institute for Molecular Science , Myodaiji, Okazaki 444-8585, Japan
| | - Nicholas A Besley
- Department of Physical and Theoretical Chemistry, School of Chemistry, The University of Nottingham , University Park, Nottingham NG7 2RD, United Kingdom
| | - Bernd Winter
- Institute of Methods for Material Development, Helmholtz Center Berlin , Albert-Einstein-Strasse 15, D-12489 Berlin, Germany
| | - John J Rehr
- Department of Physics, University of Washington , Seattle, Washington 98195, United States
| | - Lars G M Pettersson
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
| | - Anders Nilsson
- Department of Physics, AlbaNova University Center, Stockholm University , S-106 91 Stockholm, Sweden
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38
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Fransson T, Burdakova D, Norman P. K- and L-edge X-ray absorption spectrum calculations of closed-shell carbon, silicon, germanium, and sulfur compounds using damped four-component density functional response theory. Phys Chem Chem Phys 2016; 18:13591-603. [PMID: 27136720 DOI: 10.1039/c6cp00561f] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
X-ray absorption spectra of carbon, silicon, germanium, and sulfur compounds have been investigated by means of damped four-component density functional response theory. It is demonstrated that a reliable description of relativistic effects is obtained at both K- and L-edges. Notably, an excellent agreement with experimental results is obtained for L2,3-spectra-with spin-orbit effects well accounted for-also in cases when the experimental intensity ratio deviates from the statistical one of 2 : 1. The theoretical results are consistent with calculations using standard response theory as well as recently reported real-time propagation methods in time-dependent density functional theory, and the virtues of different approaches are discussed. As compared to silane and silicon tetrachloride, an anomalous error in the absolute energy is reported for the L2,3-spectrum of silicon tetrafluoride, amounting to an additional spectral shift of ∼1 eV. This anomaly is also observed for other exchange-correlation functionals, but it is seen neither at other silicon edges nor at the carbon K-edge of fluorine derivatives of ethene. Considering the series of molecules SiH4-XFX with X = 1, 2, 3, 4, a gradual divergence from interpolated experimental ionization potentials is observed at the level of Kohn-Sham density functional theory (DFT), and to a smaller extent with the use of Hartree-Fock. This anomalous error is thus attributed partly to difficulties in correctly emulating the electronic structure effects imposed by the very electronegative fluorines, and partly due to inconsistencies in the spurious electron self-repulsion in DFT. Substitution with one, or possibly two, fluorine atoms is estimated to yield small enough errors to allow for reliable interpretations and predictions of L2,3-spectra of more complex and extended silicon-based systems.
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Affiliation(s)
- Thomas Fransson
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden.
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39
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List NH, Kauczor J, Saue T, Jensen HJA, Norman P. Beyond the electric-dipole approximation: A formulation and implementation of molecular response theory for the description of absorption of electromagnetic field radiation. J Chem Phys 2016; 142:244111. [PMID: 26133414 DOI: 10.1063/1.4922697] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We present a formulation of molecular response theory for the description of a quantum mechanical molecular system in the presence of a weak, monochromatic, linearly polarized electromagnetic field without introducing truncated multipolar expansions. The presentation focuses on a description of linear absorption by adopting the energy-loss approach in combination with the complex polarization propagator formulation of response theory. Going beyond the electric-dipole approximation is essential whenever studying electric-dipole-forbidden transitions, and in general, non-dipolar effects become increasingly important when addressing spectroscopies involving higher-energy photons. These two aspects are examined by our study of the near K-edge X-ray absorption fine structure of the alkaline earth metals (Mg, Ca, Sr, Ba, and Ra) as well as the trans-polyenes. In following the series of alkaline earth metals, the sizes of non-dipolar effects are probed with respect to increasing photon energies and a detailed assessment of results is made in terms of studying the pertinent transition electron densities and in particular their spatial extension in comparison with the photon wavelength. Along the series of trans-polyenes, the sizes of non-dipolar effects are probed for X-ray spectroscopies on organic molecules with respect to the spatial extension of the chromophore.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Joanna Kauczor
- Department of Physics, Chemistry and Biology, Linköping University, Linköping SE 58183, Sweden
| | - Trond Saue
- Laboratoire de Chimie et Physique Quantiques, UMR 5626-CNRS/Université Toulouse III (Paul Sabatier), 118 route de Narbonne, F-31062 Toulouse Cedex, France
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense M, Denmark
| | - Patrick Norman
- Department of Physics, Chemistry and Biology, Linköping University, Linköping SE 58183, Sweden
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40
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Fransson T, Saue T, Norman P. Four-Component Damped Density Functional Response Theory Study of UV/Vis Absorption Spectra and Phosphorescence Parameters of Group 12 Metal-Substituted Porphyrins. J Chem Theory Comput 2016; 12:2324-34. [DOI: 10.1021/acs.jctc.6b00030] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Thomas Fransson
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Trond Saue
- Laboratoire
de Chimie et Physique Quantiques, UMR 5626, CNRS — Université Toulouse III-Paul Sabatier, 118 route de Narbonne, F-31062 Toulouse, France
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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41
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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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42
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Petrenko T, Rauhut G. Time-independent eigenstate-free calculation of vibronic spectra beyond the harmonic approximation. J Chem Phys 2015; 143:234106. [DOI: 10.1063/1.4937380] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Affiliation(s)
- Taras Petrenko
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
| | - Guntram Rauhut
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569 Stuttgart, Germany
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43
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Fransson T, Zhovtobriukh I, Coriani S, Wikfeldt KT, Norman P, Pettersson LGM. Requirements of first-principles calculations of X-ray absorption spectra of liquid water. Phys Chem Chem Phys 2015; 18:566-83. [PMID: 26619162 DOI: 10.1039/c5cp03919c] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
A computational benchmark study on X-ray absorption spectra of water has been performed by means of transition-potential density functional theory (TP-DFT), damped time-dependent density functional theory (TDDFT), and damped coupled cluster (CC) linear response theory. For liquid water, using TDDFT with a tailored CAM-B3LYP functional and a polarizable embedding, we find that an embedding with over 2000 water molecules is required to fully converge spectral features for individual molecules, but a substantially smaller embedding can be used within averaging schemes. TP-DFT and TDDFT calculations on 100 MD structures demonstrate that TDDFT produces a spectrum with spectral features in good agreement with experiment, while it is more difficult to fully resolve the spectral features in the TP-DFT spectrum. Similar trends were also observed for calculations of bulk ice. In order to further establish the performance of these methods, small water clusters have been considered also at the CC2 and CCSD levels of theory. Issues regarding the basis set requirements for spectrum simulations of liquid water and the determination of gas-phase ionization potentials are also discussed.
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Affiliation(s)
- Thomas Fransson
- Department of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
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44
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Godtliebsen IH, Christiansen O. Calculating vibrational spectra without determining excited eigenstates: Solving the complex linear equations of damped response theory for vibrational configuration interaction and vibrational coupled cluster states. J Chem Phys 2015; 143:134108. [DOI: 10.1063/1.4932010] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Affiliation(s)
| | - Ove Christiansen
- Department of Chemistry, Aarhus University, 8000 Aarhus C, Denmark
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45
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Baseggio O, Fronzoni G, Stener M. A new time dependent density functional algorithm for large systems and plasmons in metal clusters. J Chem Phys 2015; 143:024106. [DOI: 10.1063/1.4923368] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Affiliation(s)
- Oscar Baseggio
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Giovanna Fronzoni
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
| | - Mauro Stener
- Dipartimento di Scienze Chimiche e Farmaceutiche, Università di Trieste, Via Giorgieri 1, 34127 Trieste, Italy
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46
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Fahleson T, Kauczor J, Norman P, Santoro F, Improta R, Coriani S. TD-DFT Investigation of the Magnetic Circular Dichroism Spectra of Some Purine and Pyrimidine Bases of Nucleic Acids. J Phys Chem A 2015; 119:5476-89. [DOI: 10.1021/jp512468k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Tobias Fahleson
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Joanna Kauczor
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Patrick Norman
- Department
of Physics, Chemistry and Biology, Linköping University, SE-581 83 Linköping, Sweden
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organometallici (ICCOM−CNR), Area della Ricerca del CNR, Via
Moruzzi 1, I-56124 Pisa, Italy
| | - Roberto Improta
- Istituto di Biostrutture e Bioimmagini-CNR, Via Mezzocannone 6, I-80134 Napoli, Italy
| | - Sonia Coriani
- Dipartimento
di Scienze Chimiche e Farmaceutiche, Università degli Studi di Trieste, Via L. Giorgieri 1, I-34127 Trieste, Italy
- Aarhus Institute of Advanced Studies, Aarhus University, DK-8000 Aarhus C, Denmark
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47
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Tussupbayev S, Govind N, Lopata K, Cramer CJ. Comparison of Real-Time and Linear-Response Time-Dependent Density Functional Theories for Molecular Chromophores Ranging from Sparse to High Densities of States. J Chem Theory Comput 2015; 11:1102-9. [DOI: 10.1021/ct500763y] [Citation(s) in RCA: 83] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Affiliation(s)
- Samat Tussupbayev
- 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, Richland, Washington 99338, United States
| | - Kenneth Lopata
- Department of Chemistry and Center for Computation & Technology, Louisiana State University, Baton Rouge, Louisiana 70803, United States
| | - Christopher J. Cramer
- Department
of Chemistry, Supercomputing Institute, and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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48
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Straka M, Štěpánek P, Coriani S, Vaara J. Nuclear spin circular dichroism in fullerenes: a computational study. Chem Commun (Camb) 2014; 50:15228-31. [PMID: 25341745 DOI: 10.1039/c4cc07271e] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Chemically different carbons in C70 give distinct signals in nuclear spin circular dichroism spectroscopy, a novel candidate for high-resolution identification of chemical compounds.
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Affiliation(s)
- Michal Straka
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6, Czech Republic
| | - Petr Štěpánek
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- Praha 6, Czech Republic
| | - Sonia Coriani
- Dipartimento di Scienze Chimiche e Farmaceutiche
- Università degli Studi di Trieste
- I-34127 Trieste, Italy
| | - Juha Vaara
- NMR Research Group
- Department of Physics and Chemistry
- , Finland
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