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Abstract
Semiempirical quantum-mechanical (QM) computational methods are an increasingly popular tool for the study of biomolecular systems. They were, however, developed and tested mostly on small model molecules. In this work, we explore one topic fundamental to these applications: the ability of the methods to describe the structure of proteins. In a set of 19 proteins for which a crystal structure with very high resolution is available, we analyze the properties of the protein geometries optimized using several semiempirical QM methods including PM6-D3H4, PM7, and GFN2-xTB. Some of the methods provide a very good description of the general structural features of the protein, yielding results better than or comparable to the AMBER ff03 force field. However, PM7 and PM6-D3H4 optimizations introduce artificial close contacts in the structure, which is partially remediated by reparameterization.
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Affiliation(s)
- J Řezáč
- Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences, 16000 Prague, Czech Republic
| | - J J P Stewart
- Stewart Computational Chemistry, 15210 Paddington Circle, Colorado Springs, Colorado 80921, USA
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Hourahine B, Aradi B, Blum V, Bonafé F, Buccheri A, Camacho C, Cevallos C, Deshaye MY, Dumitrică T, Dominguez A, Ehlert S, Elstner M, van der Heide T, Hermann J, Irle S, Jakowski J, Kranz JJ, Köhler C, Kowalczyk T, Kubař T, Lee IS, Lutsker V, Maurer RJ, Min SK, Mitchell I, Negre C, Niehaus TA, Niklasson AMN, Page AJ, Pecchia A, Penazzi G, Persson MP, Řezáč J, Sánchez CG, Sternberg M, Stöhr M, Stuckenberg F, Tkatchenko A, Yu VWZ, Frauenheim T. Erratum: “DFTB+, a software package for efficient approximate density functional theory based atomistic simulations” [J. Chem. Phys. 152, 124101 (2020)]. J Chem Phys 2022; 157:039901. [DOI: 10.1063/5.0103026] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- B. Hourahine
- SUPA, Department of Physics, The University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - B. Aradi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - V. Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - F. Bonafé
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - A. Buccheri
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol BS8 1TS, United Kingdom
| | - C. Camacho
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - C. Cevallos
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - M. Y. Deshaye
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T. Dumitrică
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - A. Dominguez
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
- Computational Science Research Center (CSRC) Beijing and Computational Science Applied Research (CSAR) Institute Shenzhen, Shenzhen, China
| | | | - M. Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T. van der Heide
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - J. Hermann
- Freie Universität Berlin, Berlin, Germany
| | - S. Irle
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. Jakowski
- Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J. J. Kranz
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - C. Köhler
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - T. Kowalczyk
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T. Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - I. S. Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - V. Lutsker
- Institut I–Theoretische Physik, University of Regensburg, Regensburg, Germany
| | - R. J. Maurer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - S. K. Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - I. Mitchell
- Center for Multidimensional Carbon Materials, Institute of Basic Science, Ulsan, South Korea
| | - C. Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T. A. Niehaus
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - A. M. N. Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A. J. Page
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - A. Pecchia
- CNR-ISMN, Via Salaria km 29,600, 00014 Monterotondo, Rome
| | - G. Penazzi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | | | - J. Řezáč
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - C. G. Sánchez
- Instituto Interdisciplinario de Ciencias Básicas, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
| | - M. Sternberg
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M. Stöhr
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City, Luxembourg
| | - F. Stuckenberg
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - A. Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, Luxembourg City, Luxembourg
| | - V. W.-z. Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - T. Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
- Computational Science Research Center (CSRC) Beijing and Computational Science Applied Research (CSAR) Institute Shenzhen, Shenzhen, China
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Hourahine B, Aradi B, Blum V, Bonafé F, Buccheri A, Camacho C, Cevallos C, Deshaye MY, Dumitrică T, Dominguez A, Ehlert S, Elstner M, van der Heide T, Hermann J, Irle S, Kranz JJ, Köhler C, Kowalczyk T, Kubař T, Lee IS, Lutsker V, Maurer RJ, Min SK, Mitchell I, Negre C, Niehaus TA, Niklasson AMN, Page AJ, Pecchia A, Penazzi G, Persson MP, Řezáč J, Sánchez CG, Sternberg M, Stöhr M, Stuckenberg F, Tkatchenko A, Yu VWZ, Frauenheim T. DFTB+, a software package for efficient approximate density functional theory based atomistic simulations. J Chem Phys 2020; 152:124101. [PMID: 32241125 DOI: 10.1063/1.5143190] [Citation(s) in RCA: 350] [Impact Index Per Article: 87.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
DFTB+ is a versatile community developed open source software package offering fast and efficient methods for carrying out atomistic quantum mechanical simulations. By implementing various methods approximating density functional theory (DFT), such as the density functional based tight binding (DFTB) and the extended tight binding method, it enables simulations of large systems and long timescales with reasonable accuracy while being considerably faster for typical simulations than the respective ab initio methods. Based on the DFTB framework, it additionally offers approximated versions of various DFT extensions including hybrid functionals, time dependent formalism for treating excited systems, electron transport using non-equilibrium Green's functions, and many more. DFTB+ can be used as a user-friendly standalone application in addition to being embedded into other software packages as a library or acting as a calculation-server accessed by socket communication. We give an overview of the recently developed capabilities of the DFTB+ code, demonstrating with a few use case examples, discuss the strengths and weaknesses of the various features, and also discuss on-going developments and possible future perspectives.
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Affiliation(s)
- B Hourahine
- SUPA, Department of Physics, The University of Strathclyde, Glasgow G4 0NG, United Kingdom
| | - B Aradi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - V Blum
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - F Bonafé
- Max Planck Institute for the Structure and Dynamics of Matter, Hamburg, Germany
| | - A Buccheri
- School of Chemistry, University of Bristol, Cantock's Close, Bristol BS8 1TS, United Kingdom
| | - C Camacho
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - C Cevallos
- School of Chemistry, University of Costa Rica, San José 11501-2060, Costa Rica
| | - M Y Deshaye
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T Dumitrică
- Department of Mechanical Engineering, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - A Dominguez
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - S Ehlert
- University of Bonn, Bonn, Germany
| | - M Elstner
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - T van der Heide
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - J Hermann
- Freie Universität Berlin, Berlin, Germany
| | - S Irle
- Computational Sciences and Engineering Division, Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831, USA
| | - J J Kranz
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - C Köhler
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - T Kowalczyk
- Department of Chemistry and Advanced Materials Science and Engineering Center, Western Washington University, Bellingham, Washington 98225, USA
| | - T Kubař
- Institute of Physical Chemistry, Karlsruhe Institute of Technology, Karlsruhe, Germany
| | - I S Lee
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - V Lutsker
- Institut I - Theoretische Physik, University of Regensburg, Regensburg, Germany
| | - R J Maurer
- Department of Chemistry, University of Warwick, Gibbet Hill Road, Coventry CV4 7AL, United Kingdom
| | - S K Min
- Department of Chemistry, Ulsan National Institute of Science and Technology, Ulsan, South Korea
| | - I Mitchell
- Center for Multidimensional Carbon Materials, Institute for Basic Science (IBS), Ulsan 44919, South Korea
| | - C Negre
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - T A Niehaus
- Université de Lyon, Université Claude Bernard Lyon 1, CNRS, Institut Lumière Matière, F-69622 Villeurbanne, France
| | - A M N Niklasson
- Theoretical Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87545, USA
| | - A J Page
- School of Environmental and Life Sciences, University of Newcastle, Callaghan, Australia
| | - A Pecchia
- CNR-ISMN, Via Salaria km 29.300, 00015 Monterotondo Stazione, Rome, Italy
| | - G Penazzi
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - M P Persson
- Dassault Systemes, Cambridge, United Kingdom
| | - J Řezáč
- Institute of Organic Chemistry and Biochemistry AS CR, Prague, Czech Republic
| | - C G Sánchez
- Instituto Interdisciplinario de Ciencias Básicas, Universidad Nacional de Cuyo, CONICET, Facultad de Ciencias Exactas y Naturales, Mendoza, Argentina
| | - M Sternberg
- Argonne National Laboratory, Lemont, Illinois 60439, USA
| | - M Stöhr
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - F Stuckenberg
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
| | - A Tkatchenko
- Department of Physics and Materials Science, University of Luxembourg, L-1511 Luxembourg City, Luxembourg
| | - V W-Z Yu
- Department of Mechanical Engineering and Materials Science, Duke University, Durham, North Carolina 27708, USA
| | - T Frauenheim
- Bremen Center for Computational Materials Science, University of Bremen, Bremen, Germany
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Miriyala VM, Řezáč J. Testing Semiempirical Quantum Mechanical Methods on a Data Set of Interaction Energies Mapping Repulsive Contacts in Organic Molecules. J Phys Chem A 2018; 122:2801-2808. [PMID: 29473742 DOI: 10.1021/acs.jpca.8b00260] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Semiempirical quantum mechanical (QM) methods with corrections for noncovalent interactions provide a favorable combination of accuracy and computational efficiency that makes them a useful tool for a study of large molecular systems. It was, however, noted that the accuracy of these methods deteriorates at intermolecular distances shorter than equilibrium. In this work, we explore this issue systematically using a newly developed data set of benchmark interaction energies named R160×6. This data set maps repulsive contacts in organic molecules, and it consists of 160 model complexes for which six points along the dissociation curve are provided. Testing a wide range of semiempirical QM methods against the CCSD(T)/CBS benchmark revealed that most methods, and all the dispersion-corrected ones, underestimate the repulsion systematically. The worst cases are usually hydrogen-hydrogen contacts. The best results were obtained with PM6-D3H4 and DFTB3-D3H4, as these methods already contain a correction for the H-H repulsion, but the errors are still about twice as large as in equilibrium geometries.
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Affiliation(s)
- V M Miriyala
- Department of Computational Chemistry , Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo Náměstí 542/2 , 16610 Prague , Czech Republic
| | - J Řezáč
- Department of Computational Chemistry , Institute of Organic Chemistry and Biochemistry, Czech Academy of Sciences , Flemingovo Náměstí 542/2 , 16610 Prague , Czech Republic
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