1
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Petrusevich EF, Reis H, Ośmiałowski B, Jacquemin D, Luis JM, Zaleśny R. One- and two-photon absorption spectra of organoboron complexes: vibronic and environmental effects. Phys Chem Chem Phys 2024; 26:13239-13250. [PMID: 38634828 DOI: 10.1039/d4cp01089b] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/19/2024]
Abstract
We synthesized a series of four parent aza-β-ketoiminate organoboron complexes and performed spectroscopic studies using both experimental and computational techniques. We studied how benzannulation influences the vibronic structure of the UV/Vis absorption bands with a focus on the bright lowest-energy π → π* electronic excitation. Theoretical simulations, accounting for inhomogeneous broadening effects using different embedding schemes, allowed gaining in-depth insights into the observed differences in band shapes induced by structural modifications. We observed huge variations in the distributions of vibronic transitions depending on the position of benzannulation. By and large, the harmonic approximation combined with the adiabatic hessian model delivers qualitatively correct band shapes for the one-photon absorption spectra, except in one case. We also assessed the importance of non-Condon effects (accounted for by the linear term in Herzberg-Teller expansion of the dipole moment) for S0 → S1 band shapes. It turned out that non-Condon contributions have no effect on the band shape in one-photon absorption spectra. In contrast, these effects significantly change the Franck-Condon band shapes of the two-photon absorption spectra. For one of the studied organoboron complexes we also performed a preliminary exploration of mechanical anharmonicity, resulting in an increase of the intensity of the 0-0 transition, which improves the agreement with the experimental data compared to the harmonic model.
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Affiliation(s)
- Elizaveta F Petrusevich
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Heribert Reis
- Institute of Chemical Biology, National Hellenic Research Foundation (NHRF), Vassileos Constantinou Ave 48th, 116 35 Athens, Greece
| | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina 7, 87-100 Toruń, Poland
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Josep M Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003, Girona, Catalonia, Spain.
| | - Robert Zaleśny
- Faculty of Chemistry, Wroclaw University of Science and Technology, Wybrzeże Wyspiańskiego 27, 50-370 Wrocław, Poland.
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2
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Sülzner N, Hättig C. Role of Singles Amplitudes in ADC(2) and CC2 for Low-Lying Electronically Excited States. J Chem Theory Comput 2024; 20:2462-2474. [PMID: 38449383 DOI: 10.1021/acs.jctc.3c01355] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
The closely related second-order methods CC2 and ADC(2) usually perform very similarly for single excitations of organic molecules. However, as rationalized in this work, significant deviations between these two methods can arise if the ground state and a low-lying singly excited state arise from a strong coupling between their leading configurations. Such a configuration mixing is partially accounted for in CC2 through the ground-state singles amplitudes but is omitted in ADC(2). This can cause unusual deviations between the results obtained with these methods. In this work, we study how severe this effect can become at the example of two solvatochromic dyes: the negatively solvatochromic betaine dye N1-tBu and the positively solvatochromic bithiophene P1. These two dyes allow one to study the limits of both small and somewhat larger excitation energies and configuration mixing by tuning the S0 → S1 transition energy through the polarity of the environment. Higher-level calculations at the CC3 level provide information on the accuracy of ADC(2) and CC2 in these cases. The most extreme deviation between ADC(2) and CC2 is found for N1-tBu in vacuum, where the ADC(2) result is 0.45 eV below that of CC2. In this case, the methodical error of CC2 with respect to CC3 is only 0.05 eV. With increasing excitation energy in polar solvents, the CC2-ADC(2) deviation decreases and reaches a value of only 0.15 eV. For P1, which has larger excitation energies, these effects are reversed due to the opposite solvatochromism but also smaller in magnitude: the deviation increases from 0.08 eV in vacuum to 0.16 eV in the so-called conductor limit of the continuum solvation model. Although for these two dyes larger deviations are observed for smaller excitation energies, the extent of configuration mixing does not generally correlate with only the size of excitation energy. For example, s-triazine (0.15 eV), formamide (0.19 eV), and formaldehyde (0.23 eV) also show large deviations between CC2 and ADC(2) despite their much higher excitation energies compared to those of N1-tBu and P1.
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Affiliation(s)
- Niklas Sülzner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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3
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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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4
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Petrusevich EF, Bousquet MHE, Ośmiałowski B, Jacquemin D, Luis JM, Zaleśny R. Cost-Effective Simulations of Vibrationally-Resolved Absorption Spectra of Fluorophores with Machine-Learning-Based Inhomogeneous Broadening. J Chem Theory Comput 2023; 19:2304-2315. [PMID: 37096370 PMCID: PMC10134414 DOI: 10.1021/acs.jctc.2c01285] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/08/2023]
Abstract
The results of electronic and vibrational structure simulations are an invaluable support for interpreting experimental absorption/emission spectra, which stimulates the development of reliable and cost-effective computational protocols. In this work, we contribute to these efforts and propose an efficient first-principle protocol for simulating vibrationally-resolved absorption spectra, including nonempirical estimations of the inhomogeneous broadening. To this end, we analyze three key aspects: (i) a metric-based selection of density functional approximation (DFA) so to benefit from the computational efficiency of time-dependent density function theory (TD-DFT) while safeguarding the accuracy of the vibrationally-resolved spectra, (ii) an assessment of two vibrational structure schemes (vertical gradient and adiabatic Hessian) to compute the Franck-Condon factors, and (iii) the use of machine learning to speed up nonempirical estimations of the inhomogeneous broadening. In more detail, we predict the absorption band shapes for a set of 20 medium-sized fluorescent dyes, focusing on the bright ππ★ S0 → S1 transition and using experimental results as references. We demonstrate that, for the studied 20-dye set which includes structures with large structural variability, the preselection of DFAs based on an easily accessible metric ensures accurate band shapes with respect to the reference approach and that range-separated functionals show the best performance when combined with the vertical gradient model. As far as band widths are concerned, we propose a new machine-learning-based approach for determining the inhomogeneous broadening induced by the solvent microenvironment. This approach is shown to be very robust offering inhomogeneous broadenings with errors as small as 2 cm-1 with respect to genuine electronic-structure calculations, with a total CPU time reduced by 98%.
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Affiliation(s)
- Elizaveta F. Petrusevich
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | | | - Borys Ośmiałowski
- Faculty of Chemistry, Nicolaus Copernicus University, Gagarina Street 7, PL-87-100 Toruń, Poland
| | - Denis Jacquemin
- Nantes Université, CNRS, CEISAM UMR 6230, F-44000 Nantes, France
- Institut Universitaire de France (IUF), F-75005 Paris, France
| | - Josep M. Luis
- Institute of Computational Chemistry and Catalysis and Department of Chemistry, University of Girona, Campus de Montilivi, 17003 Girona, Catalonia, Spain
| | - Robert Zaleśny
- Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland
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5
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Tsuru S, Sharma B, Marx D, Hättig C. Structural Sampling and Solvation Models for the Simulation of Electronic Spectra: Pyrazine as a Case Study. J Chem Theory Comput 2023; 19:2291-2303. [PMID: 36971352 DOI: 10.1021/acs.jctc.2c01129] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/29/2023]
Abstract
The impact of sampling methods on spectral broadening in the gas phase and on the convergence of spectra in aqueous solution when using microsolvation, continuum solvation, and hybrid models is studied using pyrazine as a test case. For the sake of comparing classical Maxwell-Boltzmann and Wigner samplings in the gas phase, static and time-resolved X-ray absorption spectra after photoexcitation to the lowest 1B2u(ππ*) state, as well as the static UV-vis absorption spectrum, are considered. In addition, the UV-vis absorption spectrum of pyrazine in aqueous solution is also computed in order to systematically investigate its convergence with the number of explicitly included solvent shells with and without taking bulk solvation effects into account with the conductor-like screening model to represent implicit water beyond such explicit solute complexes. Concerning the static and time-resolved X-ray absorption spectra of pyrazine at the carbon K-edge as well as its UV-vis absorption spectrum in the gas phase, we find that these spectra obtained with Wigner and Maxwell-Boltzmann samplings substantially agree. For the UV-vis absorption spectrum in the aqueous solution, only the first two energetically low-lying bands converge quickly with the size of the explicitly included solvation shells, either with or without an additional continuum solvation taken into account. In stark contrast, calculations of the higher-lying excitations relying on finite microsolvated clusters without additional continuum solvation severely suffer from unphysical charge-transfer excitations into Rydberg-like orbitals at the cluster/vacuum interface. This finding indicates that computational UV-vis absorption spectra covering sufficiently high-lying states converge only if continuum solvation of the explicitly microsolvated solutes is included in the models.
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6
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Weng G, Pang A, Vlček V. Spatial Decay and Limits of Quantum Solute-Solvent Interactions. J Phys Chem Lett 2023; 14:2473-2480. [PMID: 36867592 DOI: 10.1021/acs.jpclett.3c00208] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Molecular excitations in the liquid-phase environment are renormalized by the surrounding solvent molecules. Herein, we employ the GW approximation to investigate the solvation effects on the ionization energy of phenol in various solvent environments. The electronic effects differ by up to 0.4 eV among the five investigated solvents. This difference depends on both the macroscopic solvent polarizability and the spatial decay of the solvation effects. The latter is probed by separating the electronic subspace and the GW correlation self-energy into fragments. The fragment correlation energy decays with increasing intermolecular distance and vanishes at ∼9 Å, and this pattern is independent of the type of solvent environment. The 9 Å cutoff defines an effective interacting volume within which the ionization energy shift per solvent molecule is proportional to the macroscopic solvent polarizability. Finally, we propose a simple model for computing the ionization energies of molecules in an arbitrary solvent environment.
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Affiliation(s)
- Guorong Weng
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Amanda Pang
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
| | - Vojtěch Vlček
- Department of Chemistry and Biochemistry, University of California, Santa Barbara, California 93106-9510, United States
- Materials Department, University of California, Santa Barbara, California 93106-5050, United States
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7
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Jørgensen FK, Reinholdt P, Hedegård ED, Kongsted J. Nuclear Magnetic Shielding Constants with the Polarizable Density Embedding Model. J Chem Theory Comput 2022; 18:7384-7393. [PMID: 36332108 DOI: 10.1021/acs.jctc.2c00829] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
Abstract
We extend the polarizable density embedding (PDE) model to support the calculation of nuclear magnetic resonance (NMR) shielding constants using gauge-including atomic orbitals (GIAOs) within a density functional theory (DFT) framework. The PDE model divides the total system into fragments, describing some by quantum mechanics (QM) and the others through an embedding model. The PDE model uses anisotropic polarizabilities, inter-fragment two-electron Coulomb integrals, and a non-local repulsion operator to emulate the QM effects. The terms involving Coulomb integrals are straightforwardly extended with GIAOs. In contrast, we consider two approaches to handle the gauge dependency of the non-local operator, employing either simple symmetrization or a gauge transformation. We find the latter approach to be most stable with respect to increasing the basis set size of the QM region. We examine the accuracy of the PDE model for calculating NMR shielding constants on several solutes in a water solution. The performance is compared with the classical polarizable embedding (PE) model in addition to supermolecular reference calculations. Based on these systems, we address the basis set convergence characteristics and the QM region size requirements. Furthermore, we investigate the performance of the PDE model for a system with significant electron spill-out. In many cases, we find that the PDE model outperforms the PE model, especially regarding the accuracy of nuclear shielding constants when using small QM region sizes and in systems with significant electron spill-out.
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Affiliation(s)
- Frederik Kamper Jørgensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Erik Donovan Hedegård
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230Odense M, Denmark
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8
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Treß RS, Liu J, Hättig C, Höfener S. Pushing the limits: Efficient wavefunction methods for excited states in complex systems using frozen-density embedding. J Chem Phys 2022; 157:204101. [DOI: 10.1063/5.0100393] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022] Open
Abstract
Frozen density embedding (FDE) is an embedding method for complex environments that is simple for users to set up. It reduces the computation time by dividing the total system into small subsystems and approximating the interaction by a functional of their densities. Its combination with wavefunction methods is, however, limited to small- or medium-sized molecules because of the steep scaling in computation time of these methods. To mitigate this limitation, we present a combination of the FDE approach with pair natural orbitals (PNOs) in the TURBOMOLE software package. It combines the uncoupled FDE (FDEu) approach for excitation energy calculations with efficient implementations of second-order correlation methods in the ricc2 and pnoccsd programs. The performance of this combination is tested for tetraazaperopyrene (TAPP) molecular crystals. It is shown that the PNO truncation error on environment-induced shifts is significantly smaller than the shifts themselves and, thus, that the local approximations of PNO-based wavefunction methods can without the loss of relevant digits be combined with the FDE method. Computational wall times are presented for two TAPP systems. The scaling of the wall times is compared to conventional supermolecular calculations and demonstrates large computational savings for the combination of FDE- and PNO-based methods. Additionally, the behavior of excitation energies with the system size is investigated. It is found that the excitation energies converge quickly with the size of the embedding environment for the TAPPs investigated in the current study.
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Affiliation(s)
- Robert S. Treß
- Department of Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Jing Liu
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Christof Hättig
- Department of Theoretical Chemistry, Ruhr University Bochum, 44801 Bochum, Germany
| | - Sebastian Höfener
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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9
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Sülzner N, Hättig C. Theoretical Study on the Photoacidity of Hydroxypyrene Derivatives in DMSO Using ADC(2) and CC2. J Phys Chem A 2022; 126:5911-5923. [PMID: 36037028 DOI: 10.1021/acs.jpca.2c04436] [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
This work applies the thermodynamic Förster cycle to theoretically investigate the pKa*, i.e., excited-state pKa values of pyranine-derived superphotoacids developed by Jung and co-workers. The latter photoacids are strong enough to transfer a proton to the aprotic solvent dimethyl sulfoxide (DMSO). The Förster cycle provides access to pKa* via the ground-state pKa and the electronic excitation energies. We use the conductor-like screening model for real solvents (COSMO-RS) to compute the ground-state pKa and the correlated wavefunction-based methods ADC(2) and CC2 with the continuum solvation model COSMO to calculate the pKa change upon excitation. A comparison of the calculated UV/Vis absorption and fluorescence emission energies to the experimental results leads us to infer that this approach allows for a proper description of the electronic excitations. In particular, implicit solvation by means of the COSMO model appears to be sufficient for the treatment of these photoacids in DMSO. The calculations confirm the presumption that a charge redistribution from the hydroxy group to the aromatic ring and the electron-withdrawing substituents is the origin of photoacidity for these photoacids. Moreover, the calculations with the continuum solvation model predict that the pKa jump upon excitation decreases with increasing solvent polarity, as rationalized based on the Förster cycle.
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Affiliation(s)
- Niklas Sülzner
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44780 Bochum, Germany
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10
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Tsuru S, Sharma B, Nagasaka M, Hättig C. Solvent Effects in the Ultraviolet and X-ray Absorption Spectra of Pyridazine in Aqueous Solution. J Phys Chem A 2021; 125:7198-7206. [PMID: 34379425 DOI: 10.1021/acs.jpca.1c05183] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Electrostatic interaction of the solvent with the solute and fluctuations of the solvent configurations may make excitation energies of the solute different from those in the gas phase. These effects may dominate photoinduced or chemical reaction dynamics in solution systems and can be observed as shifts or broadening of peaks in absorption spectra. In this work, the nitrogen K-edge X-ray absorption spectra were measured for pyridazine in the gas phase and in aqueous solution. The ultraviolet and X-ray absorption spectra of pyridazine in aqueous solution, as well as those in the gas phase, were then calculated with models based on the algebraic-diagrammatic construction through second order [ADC(2)] with the resolution-of-identity (RI) approximation and compared with the spectra obtained in experiments. For aqueous solution, explicit local solvation structures were extracted from an ab initio molecular dynamics (AIMD) trajectory of pyridazine in bulk water, and RI-ADC(2) was combined with the conductor-like screening model (COSMO). The experimental absorption spectra of pyridazine in aqueous solution were reproduced with good accuracy by theoretical treatment of an ensemble containing the explicit local solvation structures of pyridazine with relevant water molecules combined with the COSMO solvation model of water for long-range solvation.
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Affiliation(s)
- Shota Tsuru
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Bikramjit Sharma
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
| | - Masanari Nagasaka
- Institute for Molecular Science and SOKENDAI (The Graduate University for Advanced Studies), Myodaiji, Okazaki 444-8585, Japan
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, D-44780 Bochum, Germany
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11
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Karbalaei Khani S, Marefat Khah A, Hättig C. Comparison of Reaction Field Schemes for Coupling Continuum Solvation Models with Wave Function Methods for Excitation Energies. J Chem Theory Comput 2020; 16:4554-4564. [DOI: 10.1021/acs.jctc.0c00316] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität, Bochum 44780, Germany
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12
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Balasubramani SG, Chen GP, Coriani S, Diedenhofen M, Frank MS, Franzke YJ, Furche F, Grotjahn R, Harding ME, Hättig C, Hellweg A, Helmich-Paris B, Holzer C, Huniar U, Kaupp M, Marefat Khah A, Karbalaei Khani S, Müller T, Mack F, Nguyen BD, Parker SM, Perlt E, Rappoport D, Reiter K, Roy S, Rückert M, Schmitz G, Sierka M, Tapavicza E, Tew DP, van Wüllen C, Voora VK, Weigend F, Wodyński A, Yu JM. TURBOMOLE: Modular program suite for ab initio quantum-chemical and condensed-matter simulations. J Chem Phys 2020; 152:184107. [PMID: 32414256 PMCID: PMC7228783 DOI: 10.1063/5.0004635] [Citation(s) in RCA: 523] [Impact Index Per Article: 130.8] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2020] [Accepted: 04/07/2020] [Indexed: 01/30/2023] Open
Abstract
TURBOMOLE is a collaborative, multi-national software development project aiming to provide highly efficient and stable computational tools for quantum chemical simulations of molecules, clusters, periodic systems, and solutions. The TURBOMOLE software suite is optimized for widely available, inexpensive, and resource-efficient hardware such as multi-core workstations and small computer clusters. TURBOMOLE specializes in electronic structure methods with outstanding accuracy-cost ratio, such as density functional theory including local hybrids and the random phase approximation (RPA), GW-Bethe-Salpeter methods, second-order Møller-Plesset theory, and explicitly correlated coupled-cluster methods. TURBOMOLE is based on Gaussian basis sets and has been pivotal for the development of many fast and low-scaling algorithms in the past three decades, such as integral-direct methods, fast multipole methods, the resolution-of-the-identity approximation, imaginary frequency integration, Laplace transform, and pair natural orbital methods. This review focuses on recent additions to TURBOMOLE's functionality, including excited-state methods, RPA and Green's function methods, relativistic approaches, high-order molecular properties, solvation effects, and periodic systems. A variety of illustrative applications along with accuracy and timing data are discussed. Moreover, available interfaces to users as well as other software are summarized. TURBOMOLE's current licensing, distribution, and support model are discussed, and an overview of TURBOMOLE's development workflow is provided. Challenges such as communication and outreach, software infrastructure, and funding are highlighted.
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Affiliation(s)
- Sree Ganesh Balasubramani
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Guo P Chen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Michael Diedenhofen
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Marius S Frank
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Yannick J Franzke
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Filipp Furche
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Robin Grotjahn
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | | | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Arnim Hellweg
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Benjamin Helmich-Paris
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Christof Holzer
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Uwe Huniar
- Dassault Systèmes Deutschland GmbH, Imbacher Weg 46, 51379 Leverkusen, Germany
| | - Martin Kaupp
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, Straße des 17. Juni 135, 10623 Berlin, Germany
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | | | - Thomas Müller
- Forschungszentrum Jülich, Jülich Supercomputer Centre, Wilhelm-Jonen Straße, 52425 Jülich, Germany
| | - Fabian Mack
- Institute of Physical Chemistry, Karlsruhe Institute of Technology (KIT), KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Brian D Nguyen
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Shane M Parker
- Department of Chemistry, Case Western Reserve University, 10900 Euclid Avenue, Cleveland, Ohio 44106, USA
| | - Eva Perlt
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Dmitrij Rappoport
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA
| | - Kevin Reiter
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Saswata Roy
- Department of Chemistry, University of California, Irvine, 1102 Natural Sciences II, Irvine, California 92697-2025, USA
| | - Matthias Rückert
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum, 44801 Bochum, Germany
| | - Gunnar Schmitz
- Department of Chemistry, Aarhus Universitet, Langelandsgade 140, DK-8000 Aarhus, Denmark
| | - Marek Sierka
- TURBOMOLE GmbH, Litzenhardtstraße 19, 76135 Karlsruhe, Germany
| | - Enrico Tapavicza
- Department of Chemistry and Biochemistry, California State University, Long Beach, 1250 Bellflower Boulevard, Long Beach, California 90840, USA
| | - David P Tew
- Max Planck Institute for Solid State Research, Heisenbergstaße 1, 70569 Stuttgart, Germany
| | - Christoph van Wüllen
- Fachbereich Chemie and Forschungszentrum OPTIMAS, Technische Universität Kaiserslautern, Erwin-Schrödinger-Staße 52, 67663 Kaiserslautern, Germany
| | - Vamsee K Voora
- Department of Chemical Sciences, Tata Institute of Fundamental Research, Homi Bhabha Road, Colaba, Mumbai 400005, India
| | - Florian Weigend
- Institute of Nanotechnology, Karlsruhe Institute of Technology (KIT), KIT Campus North, P.O. Box 3640, 76021 Karlsruhe, Germany
| | - Artur Wodyński
- Institut für Chemie, Theoretische Chemie/Quantenchemie, Technische Universität Berlin, Sekr. C7, 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, USA
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13
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Marefat Khah A, Reinholdt P, Olsen JMH, Kongsted J, Hättig C. Avoiding Electron Spill-Out in QM/MM Calculations on Excited States with Simple Pseudopotentials. J Chem Theory Comput 2020; 16:1373-1381. [PMID: 32031806 DOI: 10.1021/acs.jctc.9b01162] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
QM/MM calculations of electronic excitations with diffuse basis sets often have large errors due to spill-out of electrons from the quantum subsystem. The Pauli repulsion of the electrons by the environment has to be included to avoid this. We propose transferable atomic all-electron pseudopotentials that can readily be combined with most MM force fields to avoid electron spill-out. QM/MM excitation energies computed with time-dependent Hartree-Fock and the algebraic diagrammatic construction through second-order are benchmarked against supermolecular calculations to validate these new pseudopotentials. The QM/MM calculations with pseudopotentials give accurate results that are stable with augmentation of the basis set with diffuse functions. We show that the largest contribution to residual deviations from full QM calculations is caused by the missing London dispersion interaction.
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Affiliation(s)
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense, Denmark
| | - Christof Hättig
- Quantum Chemistry Group, Ruhr University of Bochum, D-44801 Bochum, Germany
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14
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Scheurer M, Reinholdt P, Kjellgren ER, Haugaard Olsen JM, Dreuw A, Kongsted J. CPPE: An Open-Source C++ and Python Library for Polarizable Embedding. J Chem Theory Comput 2019; 15:6154-6163. [PMID: 31580670 DOI: 10.1021/acs.jctc.9b00758] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
We present a modular open-source library for polarizable embedding (PE) named CPPE. The library is implemented in C++, and it additionally provides a Python interface for rapid prototyping and experimentation in a high-level scripting language. Our library integrates seamlessly with existing quantum chemical program packages through an intuitive and minimal interface. Until now, CPPE has been interfaced to three packages, Q-Chem, Psi4, and PySCF. Furthermore, we show CPPE in action using all three program packages for a computational spectroscopy application. With CPPE, host program interfaces only require minor programming effort, paving the way for new combined methodologies and broader availability of the PE model.
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Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing , Heidelberg University , D-69120 Heidelberg , Germany.,Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Erik Rosendahl Kjellgren
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry , UiT the Arctic University of Norway , N-9037 Tromsø , Norway
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing , Heidelberg University , D-69120 Heidelberg , Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy , University of Southern Denmark , DK-5230 Odense M , Denmark
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15
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Izsák R. Single‐reference coupled cluster methods for computing excitation energies in large molecules: The efficiency and accuracy of approximations. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2019. [DOI: 10.1002/wcms.1445] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
Affiliation(s)
- Róbert Izsák
- Max‐Planck‐Institut für Kohlenforschung Mülheim an der Ruhr Germany
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16
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Haldar S, Riplinger C, Demoulin B, Neese F, Izsak R, Dutta AK. Multilayer Approach to the IP-EOM-DLPNO-CCSD Method: Theory, Implementation, and Application. J Chem Theory Comput 2019; 15:2265-2277. [DOI: 10.1021/acs.jctc.8b01263] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Soumi Haldar
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
| | | | - Baptiste Demoulin
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Frank Neese
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Robert Izsak
- Max-Planck-Institut
für Kohlenforschung, 1 Kaiser-Wilhelm Platz, Mülheim an der Ruhr 45470, Germany
| | - Achintya Kumar Dutta
- Department of Chemistry, Indian Institute of Technology Bombay, Powai, Mumbai 400 076, India
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17
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Khani SK, Faber R, Santoro F, Hättig C, Coriani S. UV Absorption and Magnetic Circular Dichroism Spectra of Purine, Adenine, and Guanine: A Coupled Cluster Study in Vacuo and in Aqueous Solution. J Chem Theory Comput 2018; 15:1242-1254. [DOI: 10.1021/acs.jctc.8b00930] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sarah Karbalaei Khani
- Arbeitsgruppe Quantenchemie, Ruhr-Universität, Bochum D-44780, Germany
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Rasmus Faber
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
| | - Fabrizio Santoro
- Istituto di Chimica dei Composti Organo-Metallici, Consiglio Nazionale delle Ricerche (ICCOM-CNR), Area della Ricerca, via G. Moruzzi 1, I-56124 Pisa, Italy
| | - Christof Hättig
- Arbeitsgruppe Quantenchemie, Ruhr-Universität, Bochum D-44780, Germany
| | - Sonia Coriani
- DTU Chemistry, Technical University of Denmark, Kemitorvet Build. 207, DK-2800 Kongens Lyngby, Denmark
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18
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Wehner J, Brombacher L, Brown J, Junghans C, Çaylak O, Khalak Y, Madhikar P, Tirimbò G, Baumeier B. Electronic Excitations in Complex Molecular Environments: Many-Body Green's Functions Theory in VOTCA-XTP. J Chem Theory Comput 2018; 14:6253-6268. [PMID: 30404449 PMCID: PMC6293448 DOI: 10.1021/acs.jctc.8b00617] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Many-body Green's functions theory within the GW approximation and the Bethe-Salpeter Equation (BSE) is implemented in the open-source VOTCA-XTP software, aiming at the calculation of electronically excited states in complex molecular environments. Based on Gaussian-type atomic orbitals and making use of resolution of identity techniques, the code is designed specifically for nonperiodic systems. Application to a small molecule reference set successfully validates the methodology and its implementation for a variety of excitation types covering an energy range from 2 to 8 eV in single molecules. Further, embedding each GW-BSE calculation into an atomistically resolved surrounding, typically obtained from Molecular Dynamics, accounts for effects originating from local fields and polarization. Using aqueous DNA as a prototypical system, different levels of electrostatic coupling between the regions in this GW-BSE/MM setup are demonstrated. Particular attention is paid to charge-transfer (CT) excitations in adenine base pairs. It is found that their energy is extremely sensitive to the specific environment and to polarization effects. The calculated redshift of the CT excitation energy compared to a nucelobase dimer treated in vacuum is of the order of 1 eV, which matches expectations from experimental data. Predicted lowest CT energies are below that of a single nucleobase excitation, indicating the possibility of an initial (fast) decay of such an UV excited state into a binucleobase CT exciton. The results show that VOTCA-XTP's GW-BSE/MM is a powerful tool to study a wide range of types of electronic excitations in complex molecular environments.
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Affiliation(s)
- Jens Wehner
- Max Planck Institute for Polymer Research , Ackermannweg 10 , D-55128 Mainz , Germany.,Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
| | - Lothar Brombacher
- Max Planck Institute for Polymer Research , Ackermannweg 10 , D-55128 Mainz , Germany
| | - Joshua Brown
- Department of Electrical Computer and Energy Engineering , University of Colorado Boulder , 425 UCB, Boulder , Colorado 80309 , United States.,Renewable and Sustainable Energy Institute , University of Colorado Boulder , 4001 Discovery Drive , Boulder , Colorado 80303 , United States
| | - Christoph Junghans
- Computer, Computational, and Statistical Sciences Division , Los Alamos National Laboratory , Los Alamos , New Mexico 87545 , United States
| | - Onur Çaylak
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
| | - Yuriy Khalak
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
| | - Pranav Madhikar
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
| | - Gianluca Tirimbò
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
| | - Björn Baumeier
- Department of Mathematics and Computer Science & Institute for Complex Molecular Systems , Eindhoven University of Technology , P.O. Box 513, 5600MB Eindhoven , The Netherlands
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19
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Marefat Khah A, Karbalaei Khani S, Hättig C. Analytic Excited State Gradients for the QM/MM Polarizable Embedded Second-Order Algebraic Diagrammatic Construction for the Polarization Propagator PE-ADC(2). J Chem Theory Comput 2018; 14:4640-4650. [PMID: 30040882 DOI: 10.1021/acs.jctc.8b00396] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
An implementation of a QM/MM embedding in a polarizable environment is presented for second-order Møller-Plesset perturbation theory, MP2, for ground state energies and molecular gradients and for the second-order Algebraic Diagrammatic Construction, ADC(2), for excitation energies and excited state molecular gradients. In this implementation of PE-MP2 and PE-ADC(2), the polarizable embedded Hartree-Fock wave function is used as uncorrelated reference state. The polarization-correlation cross terms for the ground and excited states are included in this model via an approximate coupling density. A Lagrangian formulation is used to derive the relaxed electron densities and molecular gradients. The resolution-of-the-identity approximation speeds up the calculation of four-index electron repulsion integrals in the molecular orbital basis. As a first application, the method is used to study the photophysical properties of host-guest complexes where the accuracy and weaknesses of the model are also critically examined. It is demonstrated that the ground state geometries of the full quantum mechanical calculation for the supermolecule can be well reproduced. For excited state geometries, the deviations from the supermolecular calculation are slightly larger, but still the environment effects are captured qualitatively correctly, and energy gaps between the ground and excited states are obtained with sufficient accuracy.
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Affiliation(s)
- Alireza Marefat Khah
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie , Ruhr-Universität Bochum , Bochum D-44801 , Germany
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20
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Scheurer M, Herbst MF, Reinholdt P, Olsen JMH, Dreuw A, Kongsted J. Polarizable Embedding Combined with the Algebraic Diagrammatic Construction: Tackling Excited States in Biomolecular Systems. J Chem Theory Comput 2018; 14:4870-4883. [DOI: 10.1021/acs.jctc.8b00576] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Maximilian Scheurer
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Michael F. Herbst
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Hylleraas Centre for Quantum Molecular Sciences, Department of Chemistry, UiT The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, Heidelberg University, D-69120 Heidelberg, Germany
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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21
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Lu SI, Gao LT. Calculations of Electronic Excitation Energies and Excess Electric Dipole Moments of Solvated p-Nitroaniline with the EOM-CCSD-PCM Method. J Phys Chem A 2018; 122:6062-6070. [DOI: 10.1021/acs.jpca.8b02321] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Shih-I Lu
- Department of Chemistry, Soochow University, No. 70 Lin-Shih Road, Taipei City 111, Taiwan
| | - Li-Ting Gao
- Department of Chemistry, Soochow University, No. 70 Lin-Shih Road, Taipei City 111, Taiwan
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22
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Caricato M. Linear response coupled cluster theory with the polarizable continuum model within the singles approximation for the solvent response. J Chem Phys 2018; 148:134113. [DOI: 10.1063/1.5021781] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Affiliation(s)
- Marco Caricato
- Department of Chemistry, University of Kansas, 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, USA
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23
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Hršak D, Olsen JMH, Kongsted J. Polarizable Density Embedding Coupled Cluster Method. J Chem Theory Comput 2018; 14:1351-1360. [DOI: 10.1021/acs.jctc.7b01153] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Dalibor Hršak
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, 5230 Odense M, Denmark
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24
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Schröder H, Schwabe T. Corrected Polarizable Embedding: Improving the Induction Contribution to Perichromism for Linear Response Theory. J Chem Theory Comput 2018; 14:833-842. [DOI: 10.1021/acs.jctc.7b01033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Heiner Schröder
- ZBH−Center for Bioinformatics
and Institute of Physical Chemistry, University of Hamburg, Bundesstraße
43, 20146 Hamburg, Germany
| | - Tobias Schwabe
- ZBH−Center for Bioinformatics
and Institute of Physical Chemistry, University of Hamburg, Bundesstraße
43, 20146 Hamburg, Germany
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25
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Karbalaei Khani S, Marefat Khah A, Hättig C. COSMO-RI-ADC(2) excitation energies and excited state gradients. Phys Chem Chem Phys 2018; 20:16354-16363. [DOI: 10.1039/c8cp00643a] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Evaluating vertical excitation energies and excited state analytic gradients in solution at COSMO-ADC(2).
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Affiliation(s)
| | | | - Christof Hättig
- Arbeitsgruppe Quantenchemie
- Ruhr-Universität
- Bochum 44780
- Germany
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26
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Azarias C, Ponce-Vargas M, Navizet I, Fleurat-Lessard P, Romieu A, Le Guennic B, Richard JA, Jacquemin D. Rationalisation of the optical signatures of nor-dihydroxanthene-hemicyanine fused near-infrared fluorophores by first-principle tools. Phys Chem Chem Phys 2018; 20:12120-12128. [DOI: 10.1039/c8cp01587b] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The perfect pair towards more effective nor-DXH-hemicyanine fused NIR fluoroohores.
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Affiliation(s)
- Cloé Azarias
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM)
- UMR CNRS no. 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3
| | - Miguel Ponce-Vargas
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR-CNRS 6302)
- Université de Bourgogne Franche-Comté
- 21078 Dijon
- France
- Université Paris-Est
| | - Isabelle Navizet
- Université Paris-Est
- Laboratoire Modélisation et Simulation Multi Echelle
- MSME
- UMR 8208 CNRS
- UPEM
| | - Paul Fleurat-Lessard
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR-CNRS 6302)
- Université de Bourgogne Franche-Comté
- 21078 Dijon
- France
| | - Anthony Romieu
- Institut de Chimie Moléculaire de l'Université de Bourgogne (ICMUB, UMR-CNRS 6302)
- Université de Bourgogne Franche-Comté
- 21078 Dijon
- France
- Institut Universitaire de France
| | - Boris Le Guennic
- Univ Rennes
- CNRS
- ISCR (Institut des Sciences Chimiques de Rennes) – UMR 6226
- 35000 Rennes
- France
| | - Jean-Alexandre Richard
- Organic Chemistry
- Institute of Chemical and Engineering Sciences
- (ICES)
- Agency for Science, Technology and Research (A_STAR)
- Singapore
| | - Denis Jacquemin
- Chimie Et Interdisciplinarité, Synthèse, Analyse, Modélisation (CEISAM)
- UMR CNRS no. 6230
- BP 92208
- Université de Nantes
- 44322 Nantes Cedex 3
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27
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Bednarska J, Zaleśny R, Tian G, Murugan NA, Ågren H, Bartkowiak W. Nonempirical Simulations of Inhomogeneous Broadening of Electronic Transitions in Solution: Predicting Band Shapes in One- and Two-Photon Absorption Spectra of Chalcones. Molecules 2017; 22:E1643. [PMID: 28973973 PMCID: PMC6151831 DOI: 10.3390/molecules22101643] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2017] [Revised: 09/20/2017] [Accepted: 09/21/2017] [Indexed: 11/23/2022] Open
Abstract
We have examined several approaches relying on the Polarizable Embedding (PE) scheme to predict optical band shapes for two chalcone molecules in methanol solution. The PE-TDDFT and PERI-CC2 methods were combined with molecular dynamics simulations, where the solute geometry was kept either as rigid, flexible or partly-flexible (restrained) body. The first approach, termed RBMD-PE-TDDFT, was employed to estimate the inhomogeneous broadening for subsequent convolution with the vibrationally-resolved spectra of the molecule in solution determined quantum-mechanically (QM). As demonstrated, the RBMD-PE-TDDFT/QM-PCM approach delivers accurate band widths, also reproducing their correct asymmetric shapes. Further refinement can be obtained by the estimation of the inhomogeneous broadening using the RBMD-PERI-CC2 method. On the other hand, the remaining two approaches (FBMD-PE-TDDFT and ResBMD-PE-TDDFT), which lack quantum-mechanical treatment of molecular vibrations, lead to underestimated band widths. In this study, we also proposed a simple strategy regarding the rapid selection of the exchange-correlation functional for the simulations of vibrationally-resolved one- and two-photon absorption spectra based on two easy-to-compute metrics.
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Affiliation(s)
- Joanna Bednarska
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland.
| | - Robert Zaleśny
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland.
| | - Guangjun Tian
- Hebei Key Laboratory of Microstructural Material Physics, School of Science, Yanshan University, Qinhuangdao 066004, China.
| | - Natarajan Arul Murugan
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden.
| | - Hans Ågren
- Division of Theoretical Chemistry and Biology, School of Biotechnology, Royal Institute of Technology, SE-10691 Stockholm, Sweden.
| | - Wojciech Bartkowiak
- Department of Physical and Quantum Chemistry, Faculty of Chemistry, Wrocław University of Science and Technology, Wyb. Wyspiańskiego 27, PL-50370 Wrocław, Poland.
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28
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Nørby MS, Olsen JMH, Steinmann C, Kongsted J. Modeling Electronic Circular Dichroism within the Polarizable Embedding Approach. J Chem Theory Comput 2017; 13:4442-4451. [DOI: 10.1021/acs.jctc.7b00712] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Morten S. Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Casper Steinmann
- Department
of Theoretical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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29
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Hedegård ED, Bast R, Kongsted J, Olsen JMH, Jensen HJA. Relativistic Polarizable Embedding. J Chem Theory Comput 2017; 13:2870-2880. [DOI: 10.1021/acs.jctc.7b00162] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
| | - Radovan Bast
- High
Performance Computing Group, UiT The Arctic University of Norway, Tromsø 9037, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | | | - Hans Jørgen Aagaard Jensen
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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30
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Azarias C, Duchemin I, Blase X, Jacquemin D. Bethe-Salpeter study of cationic dyes: Comparisons with ADC(2) and TD-DFT. J Chem Phys 2017; 146:034301. [PMID: 28109224 DOI: 10.1063/1.4974097] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
We present a theoretical investigation of the excited-state properties of a large series of structurally diverse arylcarbonium derivatives that are known to be challenging for theoretical models. More specifically, we compare the pros and cons of TD-DFT (TD-M06-2X), ADC(2), and BSE/GW approaches for a large panel of compounds, using two different solvent models. Both 0-0 and vertical transition energies are considered and compared to the experimental values. All approaches reasonably reproduce the auxochromic and acidochromic shifts, although in most cases both TD-DFT and BSE/GW return larger correlation with experimental values than ADC(2) for these shifts. In contrast, the absolute transition energies obtained with ADC(2) tend to be closer to the measurements, TD-DFT using the M06-2X functional largely overestimating the experimental references (by ca. 0.5 eV), and BSE/GW providing intermediate values. In addition, we show that the selected solvent model has a significant impact on the results, the corrected linear-response approach providing larger transition energies than its linear-response counterpart.
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Affiliation(s)
- Cloé Azarias
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes Cedex 3, France
| | - Ivan Duchemin
- INAC, SP2M/L_Sim, CEA/UJF Cedex 09, 38054 Grenoble, France
| | - Xavier Blase
- Univ. Grenoble Alpes, Inst NEEL, F-38042 Grenoble, France
| | - Denis Jacquemin
- CEISAM, UMR CNRS 6230, BP 92208, Université de Nantes, 2, Rue de la Houssinière, 44322 Nantes Cedex 3, France
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31
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Ren S, Harms J, Caricato M. An EOM-CCSD-PCM Benchmark for Electronic Excitation Energies of Solvated Molecules. J Chem Theory Comput 2016; 13:117-124. [PMID: 27973775 DOI: 10.1021/acs.jctc.6b01053] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
In this work, we benchmark the equation of motion coupled cluster with single and double excitations (EOM-CCSD) method combined with the polarizable continuum model (PCM) for the calculation of electronic excitation energies of solvated molecules. EOM-CCSD is one of the most accurate methods for computing one-electron excitation energies, and accounting for the solvent effect on this property is a key challenge. PCM is one of the most widely employed solvation models due to its adaptability to virtually any solute and its efficient implementation with density functional theory methods (DFT). Our goal in this work is to evaluate the reliability of EOM-CCSD-PCM, especially compared to time-dependent DFT-PCM (TDDFT-PCM). Comparisons between calculated and experimental excitation energies show that EOM-CCSD-PCM consistently overestimates experimental results by 0.4-0.5 eV, which is larger than the expected EOM-CCSD error in vacuo. We attribute this decrease in accuracy to the approximated solvation model. Thus, we investigate a particularly important source of error: the lack of H-bonding interactions in PCM. We show that this issue can be addressed by computing an energy shift, ΔHB, from bare-PCM to microsolvation + PCM at DFT level. Our results show that such a shift is independent of the functional used, contrary to the absolute value of the excitation energy. Hence, we suggest an efficient protocol where the EOM-CCSD-PCM transition energy is corrected by ΔHB(DFT), which consistently improves the agreement with the experimental measurements.
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Affiliation(s)
- Sijin Ren
- Department of Chemistry, University of Kansas , 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, United States
| | - Joseph Harms
- Lawrence High School , 1901 Louisiana St., Lawrence, Kansas 66046, United States
| | - Marco Caricato
- Department of Chemistry, University of Kansas , 1251 Wescoe Hall Dr., Lawrence, Kansas 66045, United States
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32
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Li W, Li Y, Lin R, Li S. Generalized Energy-Based Fragmentation Approach for Localized Excited States of Large Systems. J Phys Chem A 2016; 120:9667-9677. [DOI: 10.1021/acs.jpca.6b11193] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Wei Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
| | - Yunzhi Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
| | - Ruochen Lin
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
| | - Shuhua Li
- Institute of Theoretical
and Computational Chemistry, Key Laboratory of Mesoscopic Chemistry
of MOE, School of Chemistry and Chemical Engineering, Nanjing University, Nanjing 210023, People’s Repubic of China
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33
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Nørby MS, Steinmann C, Olsen JMH, Li H, Kongsted J. Computational Approach for Studying Optical Properties of DNA Systems in Solution. J Chem Theory Comput 2016; 12:5050-5057. [DOI: 10.1021/acs.jctc.6b00706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Morten Steen Nørby
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Casper Steinmann
- Centre
for Computational Chemistry, School of Chemistry, University of Bristol, Bristol BS8 1TS, United Kingdom
| | | | - Hui Li
- Department
of Chemistry and Nebraska Center for Materials and Nanoscience, University of Nebraska—Lincoln, Lincoln, Nebraska 68588-0304, United States
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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34
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Schröder H, Schwabe T. Efficient determination of accurate atomic polarizabilities for polarizeable embedding calculations. J Comput Chem 2016; 37:2052-9. [PMID: 27317509 PMCID: PMC5094558 DOI: 10.1002/jcc.24425] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2016] [Revised: 05/03/2016] [Accepted: 05/23/2016] [Indexed: 12/16/2022]
Abstract
We evaluate embedding potentials, obtained via various methods, used for polarizable embedding computations of excitation energies of para-nitroaniline in water and organic solvents as well as of the green fluorescent protein. We found that isotropic polarizabilities derived from DFTD3 dispersion coefficients correlate well with those obtained via the LoProp method. We show that these polarizabilities in conjunction with appropriately derived point charges are in good agreement with calculations employing static multipole moments up to quadrupoles and anisotropic polarizabilities for both computed systems. The (partial) use of these easily-accessible parameters drastically reduces the computational effort to obtain accurate embedding potentials especially for proteins. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.
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Affiliation(s)
- Heiner Schröder
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, Hamburg, 20146, Germany
| | - Tobias Schwabe
- Center for Bioinformatics and Institute of Physical Chemistry, University of Hamburg, Bundesstraße 43, Hamburg, 20146, Germany
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35
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Krause K, Klopper W. Communication: A simplified coupled-cluster Lagrangian for polarizable embedding. J Chem Phys 2016; 144:041101. [PMID: 26827193 DOI: 10.1063/1.4940895] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A simplified coupled-cluster Lagrangian, which is linear in the Lagrangian multipliers, is proposed for the coupled-cluster treatment of a quantum mechanical system in a polarizable environment. In the simplified approach, the amplitude equations are decoupled from the Lagrangian multipliers and the energy obtained from the projected coupled-cluster equation corresponds to a stationary point of the Lagrangian.
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Affiliation(s)
- Katharina Krause
- Karlsruhe Institute of Technology (KIT), Institute of Physical Chemistry, Theoretical Chemistry Group, KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Wim Klopper
- Karlsruhe Institute of Technology (KIT), Institute of Physical Chemistry, Theoretical Chemistry Group, KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
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36
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Baudin P, Kristensen K. LoFEx — A local framework for calculating excitation energies: Illustrations using RI-CC2 linear response theory. J Chem Phys 2016; 144:224106. [DOI: 10.1063/1.4953360] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023] Open
Affiliation(s)
- Pablo Baudin
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- qLEAP Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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37
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Krause K, Bauer M, Klopper W. Approaching Phosphorescence Lifetimes in Solution: The Two-Component Polarizable-Embedding Approximate Coupled-Cluster Method. J Chem Theory Comput 2016; 12:2853-60. [PMID: 27158835 DOI: 10.1021/acs.jctc.6b00239] [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
Theoretical description of phosphorescence lifetimes in the condensed phase requires a method that takes into account both spin-orbit coupling and solvent-solute interactions. To obtain such a method, we have coupled our recently developed two-component coupled-cluster method with singles and approximated doubles to a polarizable environment. With this new method, we investigate how different solvents effect the electronic phosphorescence energies and lifetimes of 4H-pyran-4-thione.
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Affiliation(s)
- Katharina Krause
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology , KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
| | - Mirko Bauer
- Mulliken Center for Theoretical Chemistry, Institute of Physical and Theoretical Chemistry, University of Bonn , Beringstraße 4, 53115 Bonn, Germany
| | - Wim Klopper
- Institute of Physical Chemistry, Theoretical Chemistry Group, Karlsruhe Institute of Technology , KIT Campus South, P.O. Box 6980, 76049 Karlsruhe, Germany
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38
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List NH, Olsen JMH, Kongsted J. Excited states in large molecular systems through polarizable embedding. Phys Chem Chem Phys 2016; 18:20234-50. [DOI: 10.1039/c6cp03834d] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Using the polarizable embedding model enables rational design of light-sensitive functional biological materials.
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Affiliation(s)
- Nanna Holmgaard List
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | | | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
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39
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Sjulstok E, Olsen JMH, Solov'yov IA. Quantifying electron transfer reactions in biological systems: what interactions play the major role? Sci Rep 2015; 5:18446. [PMID: 26689792 PMCID: PMC4686879 DOI: 10.1038/srep18446] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2015] [Accepted: 11/18/2015] [Indexed: 12/20/2022] Open
Abstract
Various biological processes involve the conversion of energy into forms that are usable for chemical transformations and are quantum mechanical in nature. Such processes involve light absorption, excited electronic states formation, excitation energy transfer, electrons and protons tunnelling which for example occur in photosynthesis, cellular respiration, DNA repair, and possibly magnetic field sensing. Quantum biology uses computation to model biological interactions in light of quantum mechanical effects and has primarily developed over the past decade as a result of convergence between quantum physics and biology. In this paper we consider electron transfer in biological processes, from a theoretical view-point; namely in terms of quantum mechanical and semi-classical models. We systematically characterize the interactions between the moving electron and its biological environment to deduce the driving force for the electron transfer reaction and to establish those interactions that play the major role in propelling the electron. The suggested approach is seen as a general recipe to treat electron transfer events in biological systems computationally, and we utilize it to describe specifically the electron transfer reactions in Arabidopsis thaliana cryptochrome-a signaling photoreceptor protein that became attractive recently due to its possible function as a biological magnetoreceptor.
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Affiliation(s)
- Emil Sjulstok
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark.,Laboratory of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
| | - Ilia A Solov'yov
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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40
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Jacquemin D, Duchemin I, Blase X. Assessment of the convergence of partially self-consistent BSE/GW calculations. Mol Phys 2015. [DOI: 10.1080/00268976.2015.1119901] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Affiliation(s)
- Denis Jacquemin
- Laboratoire CEISAM – UMR CNRS 6230, Université de Nantes, Nantes, France
- Institut Universitaire de France, Paris, France
| | | | - Xavier Blase
- Institut NEEL, Université Grenoble Alpes, Grenoble, France
- Institut NEEL, CNRS, Grenoble, France
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41
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Abstract
For the modeling of solvatochromism with an explicit representation of the solvent molecules, the quality of preceding molecular dynamics simulations is crucial. Therefore, the possibility to apply force fields which are derived with as little empiricism as possible seems desirable. Such an approach is tested here by exploiting the sensitive solvatochromism of p-nitroaniline, and the use of reliable excitation energies based on approximate second-order coupled cluster results within a polarizable embedding scheme. The quality of the various MD settings for four different solvents, water, methanol, ethanol, and dichloromethane, is assessed. In general, good agreement with the experiment is observed when polarizable force fields and special treatment of hydrogen bonding are applied.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute, University of Hamburg, Bundesstraße 43, D-20146 Hamburg, Germany
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42
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Hršak D, Marefat Khah A, Christiansen O, Hättig C. Polarizable Embedded RI-CC2 Method for Two-Photon Absorption Calculations. J Chem Theory Comput 2015; 11:3669-78. [PMID: 26574450 DOI: 10.1021/acs.jctc.5b00496] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
We present a novel polarizable embedded resolution-of-identity coupled cluster singles and approximate doubles (PERI-CC2) method for calculation of two-photon absorption (TPA) spectra of large molecular systems. The method was benchmarked for three types of systems: a water-solvated molecule of formamide, a uracil molecule in aqueous solution, and a set of mutants of the channelrhodopsin (ChR) protein. The first test case shows that the PERI-CC2 method is in excellent agreement with the PE-CC2 method and in good agreement with the PE-CCSD method. The uracil test case indicates that the effects of hydrogen bonding on the TPA of a chromophore with the nearest environment is well-described with the PERI-CC2 method. Finally, the ChR calculation shows that the PERI-CC2 method is well-suited and efficient for calculations on proteins with medium-sized chromophores.
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Affiliation(s)
- Dalibor Hršak
- Center for Oxygen Microscopy and Imaging, Aarhus University , Langelandsgade 140, 8000 Aarhus, Denmark
| | - Alireza Marefat Khah
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
| | - Ove Christiansen
- Center for Oxygen Microscopy and Imaging, Aarhus University , Langelandsgade 140, 8000 Aarhus, Denmark
| | - Christof Hättig
- Lehrstuhl für Theoretische Chemie, Ruhr-Universität Bochum , Universitätsstraße 150, 44801 Bochum, Germany
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43
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Olsen JMH, List NH, Kristensen K, Kongsted J. Accuracy of Protein Embedding Potentials: An Analysis in Terms of Electrostatic Potentials. J Chem Theory Comput 2015; 11:1832-42. [DOI: 10.1021/acs.jctc.5b00078] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory
of Computational Chemistry and Biochemistry, École Polytechnique Fédérale de Lausanne (EPFL), CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Nanna Holmgaard List
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
| | - Kasper Kristensen
- qLEAP
Center for Theoretical Chemistry, Department of Chemistry, Aarhus University, DK-8000 Aarhus, Denmark
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense M, Denmark
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44
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Hedegård ED, Olsen JMH, Knecht S, Kongsted J, Jensen HJA. Polarizable embedding with a multiconfiguration short-range density functional theory linear response method. J Chem Phys 2015; 142:114113. [DOI: 10.1063/1.4914922] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Erik Donovan Hedegård
- Laboratorium fur Physikalische Chemie, ETH Zürich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Jógvan Magnus Haugaard Olsen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
- Laboratory of Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
| | - Stefan Knecht
- Laboratorium fur Physikalische Chemie, ETH Zürich, Vladimir Prelog Weg 2, CH-8093 Zürich, Switzerland
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
| | - Hans Jørgen Aagaard Jensen
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, Campusvej 55, DK-5230 Odense, Denmark
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45
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Mewes JM, You ZQ, Wormit M, Kriesche T, Herbert JM, Dreuw A. Experimental Benchmark Data and Systematic Evaluation of Two a Posteriori, Polarizable-Continuum Corrections for Vertical Excitation Energies in Solution. J Phys Chem A 2015; 119:5446-64. [DOI: 10.1021/jp511163y] [Citation(s) in RCA: 102] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Affiliation(s)
- Jan-Michael Mewes
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Zhi-Qiang You
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Michael Wormit
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
| | - Thomas Kriesche
- Institute
for Physical Chemistry, Ruprechts-Karls University, 69120 Heidelberg, Germany
| | - John M. Herbert
- Department
of Chemistry and Biochemistry, The Ohio State University, Columbus, Ohio 43210, United States
| | - Andreas Dreuw
- Interdisciplinary
Center for Scientific Computing, Ruprechts-Karls University, Im Neuenheimer
Feld 368, 69120 Heidelberg, Germany
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46
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Roncero O, Aguado A, Batista-Romero FA, Bernal-Uruchurtu MI, Hernández-Lamoneda R. Density-Difference-Driven Optimized Embedding Potential Method To Study the Spectroscopy of Br2 in Water Clusters. J Chem Theory Comput 2015; 11:1155-64. [DOI: 10.1021/ct501140p] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Octavio Roncero
- Instituto de Física Fundamental (IFF-CSIC), C.S.I.C., Serrano 123, 28006 Madrid, Madrid, Spain
| | - Alfredo Aguado
- Departamento
de Química Física Aplicada (UAM), Unidad Asociada a
IFF-CSIC, Facultad de Ciencias Módulo 14, Universidad Autónoma de Madrid, 28049 Madrid, Madrid, Spain
| | - Fidel A. Batista-Romero
- Centro
de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México 62209
| | | | - Ramón Hernández-Lamoneda
- Centro
de Investigaciones Químicas, Universidad Autónoma del Estado de Morelos, Cuernavaca, Morelos, México 62209
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47
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Olsen JMH, Steinmann C, Ruud K, Kongsted J. Polarizable Density Embedding: A New QM/QM/MM-Based Computational Strategy. J Phys Chem A 2015; 119:5344-55. [DOI: 10.1021/jp510138k] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jógvan Magnus Haugaard Olsen
- Laboratory of
Computational Chemistry and Biochemistry, Ecole Polytechnique Fédérale de Lausanne, CH-1015 Lausanne, Switzerland
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Casper Steinmann
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
| | - Kenneth Ruud
- Centre for Theoretical
and Computational Chemistry, Department of Chemistry, University of Tromsø—The Arctic University of Norway, N-9037 Tromsø, Norway
| | - Jacob Kongsted
- Department
of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK-5230 Odense
M, Denmark
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48
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Schwabe T, Beerepoot MTP, Olsen JMH, Kongsted J. Analysis of computational models for an accurate study of electronic excitations in GFP. Phys Chem Chem Phys 2015; 17:2582-8. [DOI: 10.1039/c4cp04524f] [Citation(s) in RCA: 39] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
The accuracy of PERI-CC2 is successfully assessed against RVS-CC2 for GFP model clusters and subsequently applied to a whole protein model.
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Affiliation(s)
- Tobias Schwabe
- Center for Bioinformatics and Physical Chemistry Institute
- D-22148 Hamburg
- Germany
| | - Maarten T. P. Beerepoot
- Centre for Theoretical and Computational Chemistry
- Department of Chemistry
- University of Tromsø – The Arctic University of Norway
- N-9037 Tromsø
- Norway
| | - Jógvan Magnus Haugaard Olsen
- Laboratory of Computational Chemistry and Biochemistry
- Ecole Polytechnique Fédérale de Lausanne
- CH-1015 Lausanne
- Switzerland
- Department of Physics
| | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- DK-5230 Odense
- Denmark
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49
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Harczuk I, Vahtras O, Ågren H. Frequency-dependent force fields for QMMM calculations. Phys Chem Chem Phys 2015; 17:7800-12. [DOI: 10.1039/c4cp05411c] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The frequency-dependent localized polarizabilities are calculated for the first time using analytical response theory and benchmarked for different water clusters and the tryptophan residue embedded in a protein.
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Affiliation(s)
- Ignat Harczuk
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Olav Vahtras
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
| | - Hans Ågren
- KTH Royal Institute of Technology
- School of Biotechnology
- Division of Theoretical Chemistry and Biology
- SE-106 91 Stockholm
- Sweden
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50
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Hršak D, Holmegaard L, Poulsen AS, List NH, Kongsted J, Denofrio MP, Erra-Balsells R, Cabrerizo FM, Christiansen O, Ogilby PR. Experimental and computational study of solvent effects on one- and two-photon absorption spectra of chlorinated harmines. Phys Chem Chem Phys 2015; 17:12090-9. [DOI: 10.1039/c5cp00773a] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present a combined experimental and computational study of one- and two-photon absorption spectra of protonated chloroharmines in aqueous and acetonitrile solutions.
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Affiliation(s)
- Dalibor Hršak
- Center for Oxygen Microscopy and Imaging, Aarhus University
- 8000 Aarhus C
- Denmark
| | - Lotte Holmegaard
- Center for Oxygen Microscopy and Imaging, Aarhus University
- 8000 Aarhus C
- Denmark
| | - Anton S. Poulsen
- Center for Oxygen Microscopy and Imaging, Aarhus University
- 8000 Aarhus C
- Denmark
| | - Nanna H. List
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | - Jacob Kongsted
- Department of Physics
- Chemistry and Pharmacy
- University of Southern Denmark
- 5230 Odense M
- Denmark
| | - M. Paula Denofrio
- Instituto de Investigaciones Biotecnológicas
- Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM)
- Consejo Nacional de Investigaciones
- Científicas y Técnicas (CONICET)
| | - Rosa Erra-Balsells
- CIHIDECAR–CONICET
- Departamento de Química Orgánica
- Facultad de Ciencias Exactas y Naturales
- Universidad de Buenos Aires
- Ciudad Universitaria
| | - Franco M. Cabrerizo
- Instituto de Investigaciones Biotecnológicas
- Instituto Tecnológico de Chascomús (IIB-INTECH)
- Universidad Nacional de San Martín (UNSAM)
- Consejo Nacional de Investigaciones
- Científicas y Técnicas (CONICET)
| | - Ove Christiansen
- Center for Oxygen Microscopy and Imaging, Aarhus University
- 8000 Aarhus C
- Denmark
| | - Peter R. Ogilby
- Center for Oxygen Microscopy and Imaging, Aarhus University
- 8000 Aarhus C
- Denmark
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