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Examination of the performance of semiempirical methods in QM/MM studies of the SN2-like reaction of an adenylyl group transfer catalysed by ANT4′. Theor Chem Acc 2019. [DOI: 10.1007/s00214-019-2507-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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2
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Gütlein P, Lang L, Reuter K, Blumberger J, Oberhofer H. Toward First-Principles-Level Polarization Energies in Force Fields: A Gaussian Basis for the Atom-Condensed Kohn-Sham Method. J Chem Theory Comput 2019; 15:4516-4525. [PMID: 31276382 DOI: 10.1021/acs.jctc.9b00415] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
The last 20 years of force field development have shown that even well parametrized classical models need to at least approximate the dielectric response of molecular systems-based, e.g., on atomic polarizabilities-in order to correctly render their structural and dynamic properties. Yet, despite great advances most approaches tend to be based on ad hoc assumptions and often insufficiently capture the dielectric response of the system to external perturbations, such as, e.g., charge carriers in semiconducting materials. A possible remedy was recently introduced with the atom-condensed Kohn-Sham density-functional theory approximated to second order (ACKS2), which is fully derived from first principles. Unfortunately, specifically its reliance on first-principles derived parameters so far precluded the widespread adoption of ACKS2. Opening up ACKS2 for general use, we here present a reformulation of the method in terms of Gaussian basis functions, which allows us to determine many of the ACKS2 parameters analytically. Two sets of parameters depending on exchange-correlation interactions are still calculated numerically, but we show that they could be straightforwardly parametrized owing to the smoothness of the new basis. Our approach exhibits three crucial benefits for future applications in force fields: i) efficiency, ii) accuracy, and iii) transferability. We numerically validate our Gaussian augmented ACKS2 model for a set of small hydrocarbons which shows a very good agreement with density-functional theory reference calculations. To further demonstrate the method's accuracy and transferability for realistic systems, we calculate polarization responses and energies of anthracene and tetracene, two major building blocks in organic semiconductors.
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Affiliation(s)
- Patrick Gütlein
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstrasse 4 , D-85747 Garching , Germany
| | - Lucas Lang
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstrasse 4 , D-85747 Garching , Germany
| | - Karsten Reuter
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstrasse 4 , D-85747 Garching , Germany
| | - Jochen Blumberger
- Department of Physics and Astronomy , University College London , London WC1E 6BT , U.K.,Institute for Advanced Study , Technische Universität München , Lichtenbergstrasse 2 a , D-85748 Garching , Germany
| | - Harald Oberhofer
- Chair for Theoretical Chemistry and Catalysis Research Center , Technische Universität München , Lichtenbergstrasse 4 , D-85747 Garching , Germany
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3
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Nishimura Y, Nakai H. D
cdftbmd
: Divide‐and‐Conquer Density Functional Tight‐Binding Program for Huge‐System Quantum Mechanical Molecular Dynamics Simulations. J Comput Chem 2019; 40:1538-1549. [DOI: 10.1002/jcc.25804] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/31/2019] [Accepted: 02/05/2019] [Indexed: 12/17/2022]
Affiliation(s)
- Yoshifumi Nishimura
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
| | - Hiromi Nakai
- Waseda Research Institute for Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- Department of Chemistry and BiochemistrySchool of Advanced Science and Engineering, Waseda University 3‐4‐1 Okubo, Shinjuku‐ku, Tokyo 169‐8555 Japan
- ESICB, Kyoto University Kyotodaigaku‐Katsura, Kyoto 615‐8520 Japan
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4
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Giese TJ, York DM. Quantum mechanical force fields for condensed phase molecular simulations. JOURNAL OF PHYSICS. CONDENSED MATTER : AN INSTITUTE OF PHYSICS JOURNAL 2017; 29:383002. [PMID: 28817382 PMCID: PMC5821073 DOI: 10.1088/1361-648x/aa7c5c] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Molecular simulations are powerful tools for providing atomic-level details into complex chemical and physical processes that occur in the condensed phase. For strongly interacting systems where quantum many-body effects are known to play an important role, density-functional methods are often used to provide the model with the potential energy used to drive dynamics. These methods, however, suffer from two major drawbacks. First, they are often too computationally intensive to practically apply to large systems over long time scales, limiting their scope of application. Second, there remain challenges for these models to obtain the necessary level of accuracy for weak non-bonded interactions to obtain quantitative accuracy for a wide range of condensed phase properties. Quantum mechanical force fields (QMFFs) provide a potential solution to both of these limitations. In this review, we address recent advances in the development of QMFFs for condensed phase simulations. In particular, we examine the development of QMFF models using both approximate and ab initio density-functional models, the treatment of short-ranged non-bonded and long-ranged electrostatic interactions, and stability issues in molecular dynamics calculations. Example calculations are provided for crystalline systems, liquid water, and ionic liquids. We conclude with a perspective for emerging challenges and future research directions.
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5
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Boleininger M, Guilbert AAY, Horsfield AP. Gaussian polarizable-ion tight binding. J Chem Phys 2016; 145:144103. [DOI: 10.1063/1.4964391] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Affiliation(s)
- Max Boleininger
- Department of Physics and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Anne AY Guilbert
- Department of Physics and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
| | - Andrew P. Horsfield
- Department of Materials and Thomas Young Centre, Imperial College London, South Kensington Campus, London SW7 2AZ, United Kingdom
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6
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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7
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Lutsker V, Aradi B, Niehaus TA. Implementation and benchmark of a long-range corrected functional in the density functional based tight-binding method. J Chem Phys 2016; 143:184107. [PMID: 26567646 DOI: 10.1063/1.4935095] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Bridging the gap between first principles methods and empirical schemes, the density functional based tight-binding method (DFTB) has become a versatile tool in predictive atomistic simulations over the past years. One of the major restrictions of this method is the limitation to local or gradient corrected exchange-correlation functionals. This excludes the important class of hybrid or long-range corrected functionals, which are advantageous in thermochemistry, as well as in the computation of vibrational, photoelectron, and optical spectra. The present work provides a detailed account of the implementation of DFTB for a long-range corrected functional in generalized Kohn-Sham theory. We apply the method to a set of organic molecules and compare ionization potentials and electron affinities with the original DFTB method and higher level theory. The new scheme cures the significant overpolarization in electric fields found for local DFTB, which parallels the functional dependence in first principles density functional theory (DFT). At the same time, the computational savings with respect to full DFT calculations are not compromised as evidenced by numerical benchmark data.
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Affiliation(s)
- V Lutsker
- Department of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
| | - B Aradi
- BCCMS, University of Bremen, 28359 Bremen, Germany
| | - T A Niehaus
- Department of Theoretical Physics, University of Regensburg, 93040 Regensburg, Germany
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8
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Huang M, Giese TJ, York DM. Nucleic acid reactivity: challenges for next-generation semiempirical quantum models. J Comput Chem 2015; 36:1370-89. [PMID: 25943338 PMCID: PMC4760688 DOI: 10.1002/jcc.23933] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2014] [Revised: 03/02/2015] [Accepted: 03/28/2015] [Indexed: 01/09/2023]
Abstract
Semiempirical quantum models are routinely used to study mechanisms of RNA catalysis and phosphoryl transfer reactions using combined quantum mechanical (QM)/molecular mechanical methods. Herein, we provide a broad assessment of the performance of existing semiempirical quantum models to describe nucleic acid structure and reactivity to quantify their limitations and guide the development of next-generation quantum models with improved accuracy. Neglect of diatomic differential overlap and self-consistent density-functional tight-binding semiempirical models are evaluated against high-level QM benchmark calculations for seven biologically important datasets. The datasets include: proton affinities, polarizabilities, nucleobase dimer interactions, dimethyl phosphate anion, nucleoside sugar and glycosidic torsion conformations, and RNA phosphoryl transfer model reactions. As an additional baseline, comparisons are made with several commonly used density-functional models, including M062X and B3LYP (in some cases with dispersion corrections). The results show that, among the semiempirical models examined, the AM1/d-PhoT model is the most robust at predicting proton affinities. AM1/d-PhoT and DFTB3-3ob/OPhyd reproduce the MP2 potential energy surfaces of 6 associative RNA phosphoryl transfer model reactions reasonably well. Further, a recently developed linear-scaling "modified divide-and-conquer" model exhibits the most accurate results for binding energies of both hydrogen bonded and stacked nucleobase dimers. The semiempirical models considered here are shown to underestimate the isotropic polarizabilities of neutral molecules by approximately 30%. The semiempirical models also fail to adequately describe torsion profiles for the dimethyl phosphate anion, the nucleoside sugar ring puckers, and the rotations about the nucleoside glycosidic bond. The modeling of pentavalent phosphorus, particularly with thio substitutions often used experimentally as mechanistic probes, was problematic for all of the models considered. Analysis of the strengths and weakness of the models suggests that the creation of robust next-generation models should emphasize the improvement of relative conformational energies and barriers, and nonbonded interactions.
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Affiliation(s)
- Ming Huang
- Scientific Computation, University of Minnesota, 207 Pleasant St. SE, Minneapolis, MN 55455–0431, USA
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854–8076, USA
| | - Timothy J. Giese
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854–8076, USA
| | - Darrin M. York
- Center for Integrative Proteomics Research, BioMaPS Institute for Quantitative Biology, and Department of Chemistry and Chemical Biology, Rutgers University, 174 Frelinghuysen Road, Piscataway, NJ 08854–8076, USA
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9
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Friederich P, Meded V, Symalla F, Elstner M, Wenzel W. QM/QM approach to model energy disorder in amorphous organic semiconductors. J Chem Theory Comput 2015; 11:560-7. [PMID: 26580913 DOI: 10.1021/ct501023n] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
It is an outstanding challenge to model the electronic properties of organic amorphous materials utilized in organic electronics. Computation of the charge carrier mobility is a challenging problem as it requires integration of morphological and electronic degrees of freedom in a coherent methodology and depends strongly on the distribution of polaron energies in the system. Here we represent a QM/QM model to compute the polaron energies combining density functional methods for molecules in the vicinity of the polaron with computationally efficient density functional based tight binding methods in the rest of the environment. For seven widely used amorphous organic semiconductor materials, we show that the calculations are accelerated up to 1 order of magnitude without any loss in accuracy. Considering that the quantum chemical step is the efficiency bottleneck of a workflow to model the carrier mobility, these results are an important step toward accurate and efficient disordered organic semiconductors simulations, a prerequisite for accelerated materials screening and consequent component optimization in the organic electronics industry.
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Affiliation(s)
- Pascal Friederich
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (INT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Velimir Meded
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (INT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Franz Symalla
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (INT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry (IPC), Karlsruhe Institute of Technology (KIT) , Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Wolfgang Wenzel
- Institute of Nanotechnology (INT), Karlsruhe Institute of Technology (INT) , Hermann-von-Helmholtz-Platz 1, 76344 Eggenstein-Leopoldshafen, Germany
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10
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Nishimoto Y, Fedorov DG, Irle S. Density-Functional Tight-Binding Combined with the Fragment Molecular Orbital Method. J Chem Theory Comput 2014; 10:4801-12. [DOI: 10.1021/ct500489d] [Citation(s) in RCA: 73] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
| | - Dmitri G. Fedorov
- Nanosystem
Research Institute (NRI), National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba 305-8565, Japan
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11
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Cui Q, Elstner M. Density functional tight binding: values of semi-empirical methods in an ab initio era. Phys Chem Chem Phys 2014; 16:14368-77. [PMID: 24850383 PMCID: PMC4836871 DOI: 10.1039/c4cp00908h] [Citation(s) in RCA: 102] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Semi-empirical (SE) methods are derived from Hartree-Fock (HF) or Density Functional Theory (DFT) by neglect and approximation of electronic integrals. Thereby, parameters are introduced which have to be determined from reference calculations and/or by fitting to available experimental data. This leads to computational methods that are about 2-3 orders of magnitude faster than the standard HF/DFT methods using medium sized basis sets while being about 3 orders of magnitude slower than empirical force field methods (Molecular Mechanics: MM). Therefore, SE methods are most appropriate for a specific range of applications. These include the study of systems that contain a large number of atoms and therefore being too large for ab initio or DFT methods and also problems where dynamic or entropic effects are particularly important. In the latter case, the errors made by considering a very limited number of molecular structures or neglecting entropic contributions can be much larger than the accuracy lost due to the use of SE methods. Another area where SE methods are attractive concerns the analysis of systems for which reliable MM models are not readily available. Therefore, even in an era when rapid progress is being made in ab initio methods, there is considerable interest in further developing SE methods. We illustrate this point by focusing on the discussion of recent development and application of the Density Functional Tight Binding method.
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12
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Elstner M, Seifert G. Density functional tight binding. PHILOSOPHICAL TRANSACTIONS. SERIES A, MATHEMATICAL, PHYSICAL, AND ENGINEERING SCIENCES 2014; 372:20120483. [PMID: 24516180 DOI: 10.1098/rsta.2012.0483] [Citation(s) in RCA: 188] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
This paper reviews the basic principles of the density-functional tight-binding (DFTB) method, which is based on density-functional theory as formulated by Hohenberg, Kohn and Sham (KS-DFT). DFTB consists of a series of models that are derived from a Taylor series expansion of the KS-DFT total energy. In the lowest order (DFTB1), densities and potentials are written as superpositions of atomic densities and potentials. The Kohn-Sham orbitals are then expanded to a set of localized atom-centred functions, which are obtained for spherical symmetric spin-unpolarized neutral atoms self-consistently. The whole Hamilton and overlap matrices contain one- and two-centre contributions only. Therefore, they can be calculated and tabulated in advance as functions of the distance between atomic pairs. The second contributions to DFTB1, the DFT double counting terms, are summarized together with nuclear repulsion energy terms and can be rewritten as the sum of pairwise repulsive terms. The second-order (DFTB2) and third-order (DFTB3) terms in the energy expansion correspond to a self-consistent representation, where the deviation of the ground-state density from the reference density is represented by charge monopoles only. This leads to a computationally efficient representation in terms of atomic charges (Mulliken), chemical hardness (Hubbard) parameters and scaled Coulomb laws. Therefore, no additional adjustable parameters enter the DFTB2 and DFTB3 formalism. The handling of parameters, the efficiency, the performance and extensions of DFTB are briefly discussed.
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Affiliation(s)
- Marcus Elstner
- Physical Chemistry, Karlsruhe Institute of Technology, , Kaiserstrasse 12, Karlsruhe 76131, Germany
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13
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Gaus M, Cui Q, Elstner M. Density functional tight binding: application to organic and biological molecules. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2013. [DOI: 10.1002/wcms.1156] [Citation(s) in RCA: 117] [Impact Index Per Article: 10.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Michael Gaus
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Qiang Cui
- Department of Chemistry and Theoretical Chemistry Institute University of Wisconsin Madison WI 53706 USA
| | - Marcus Elstner
- Karlsruhe Institute of Technology Physical Chemistry, Kaiserstrasse 12 D‐76131 Karlsruhe Germany
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14
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Barone V, Carnimeo I, Scalmani G. Computational Spectroscopy of Large Systems in Solution: The DFTB/PCM and TD-DFTB/PCM Approach. J Chem Theory Comput 2013; 9:2052-71. [DOI: 10.1021/ct301050x] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- Vincenzo Barone
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126, Pisa, Italy
- INFN Sezione di Pisa, Edificio
C - Polo Fibonacci Largo B. Pontecorvo, 3-56127 Pisa, Italy
| | - Ivan Carnimeo
- Scuola Normale Superiore, Piazza
dei Cavalieri 7, 56126, Pisa, Italy
- INFN Sezione di Pisa, Edificio
C - Polo Fibonacci Largo B. Pontecorvo, 3-56127 Pisa, Italy
| | - Giovanni Scalmani
- Gaussian, Inc., 340 Quinnipiac
Street Building 40, Wallingford, Connecticut 06492, United States
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