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Rapacioli M, Buey MY, Spiegelman F. Addressing electronic and dynamical evolution of molecules and molecular clusters: DFTB simulations of energy relaxation in polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2024; 26:1499-1515. [PMID: 37933901 PMCID: PMC10793726 DOI: 10.1039/d3cp02852f] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023]
Abstract
We present a review of the capabilities of the density functional based Tight Binding (DFTB) scheme to address the electronic relaxation and dynamical evolution of molecules and molecular clusters following energy deposition via either collision or photoabsorption. The basics and extensions of DFTB for addressing these systems and in particular their electronic states and their dynamical evolution are reviewed. Applications to PAH molecules and clusters, carbonaceous systems of major interest in astrochemical/astrophysical context, are reported. A variety of processes are examined and discussed such as collisional hydrogenation, fast collisional processes and induced electronic and charge dynamics, collision-induced fragmentation, photo-induced fragmentation, relaxation in high electronic states, electronic-to-vibrational energy conversion and statistical versus non-statistical fragmentation. This review illustrates how simulations may help to unravel different relaxation mechanisms depending on various factors such as the system size, specific electronic structure or excitation conditions, in close connection with experiments.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Maysa Yusef Buey
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
| | - Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantique (LCPQ/FERMI), UMR5626, Université de Toulouse (UPS) and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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2
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Inakollu VSS, Yu H. Comparative studies of IR spectra of deprotonated serine with classical and thermostated ring polymer molecular dynamics simulations. STRUCTURAL DYNAMICS (MELVILLE, N.Y.) 2021; 8:054101. [PMID: 34549074 PMCID: PMC8443303 DOI: 10.1063/4.0000124] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 08/30/2021] [Indexed: 06/13/2023]
Abstract
Here we report the vibrational spectra of deprotonated serine calculated from the classical molecular dynamics (MD) simulations and thermostated ring-polymer molecular dynamics (TRPMD) simulation with third-order density-functional tight-binding. In our earlier study [Inakollu and Yu, "A systematic benchmarking of computational vibrational spectroscopy with DFTB3: Normal mode analysis and fast Fourier transform dipole autocorrelation function," J. Comput. Chem. 39, 2067 (2018)] of deprotonated serine, we observed a significant difference in the vibrational spectra with the classical MD simulations compared to the infrared multiple photon dissociation spectra. It was postulated that this is due to neglecting the nuclear quantum effects (NQEs). In this work, NQEs are considered in spectral calculation using the TRPMD simulations. With the help of potential of mean force calculations, the conformational space of deprotonated serine is analyzed and used to understand the difference in the spectra of classical MD and TRPMD simulations at 298.15 and 100 K. The high-frequency vibrational bands in the spectra are characterized using Fourier transform localized vibrational mode (FT-νN AC) and interatomic distance histograms. At room temperature, the quantum effects are less significant, and the free energy profiles in the classical MD and the TRPMD simulations are very similar. However, the hydrogen bond between the hydroxyl-carboxyl bond is slightly stronger in TRPMD simulations. At 100 K, the quantum effects are more prominent, especially in the 2600-3600 cm-1, and the free energy profile slightly differs between the classical MD and TRPMD simulations. Using the FT-νN AC and the interatomic distance histograms, the high-frequency vibrational bands are discussed in detail.
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Affiliation(s)
| | - Haibo Yu
- Author to whom correspondence should be addressed:
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3
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Oshiki J, Nakano H, Sato H. Controlling potential difference between electrodes based on self-consistent-charge density functional tight binding. J Chem Phys 2021; 154:144107. [PMID: 33858148 DOI: 10.1063/5.0047992] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
A proper understanding and description of the electronic response of the electrode surfaces in electrochemical systems are quite important because the interactions between the electrode surface and electrolyte give rise to unique and useful interfacial properties. Atomistic modeling of the electrodes requires not only an accurate description of the electronic response under a constant-potential condition but also computational efficiency in order to deal with systems large enough to investigate the interfacial electrolyte structures. We thus develop a self-consistent-charge density functional tight binding based method to model a pair of electrodes in electrochemical cells under the constant-potential condition. The method is more efficient than the (ab initio) density functional theory calculations so that it can treat systems as large as those studied in classical atomistic simulations. It can also describe the electronic response of electrodes quantum mechanically and more accurately than the classical counterparts. The constant-potential condition is introduced through a Legendre transformation of the electronic energy with respect to the difference in the number of electrons in the two electrodes and their electrochemical potential difference, through which the Kohn-Sham equations for each electrode are variationally derived. The method is applied to platinum electrodes faced parallel to each other under an applied voltage. The electronic response to the voltage and a charged particle is compared with the result of a classical constant-potential method based on the chemical potential equalization principle.
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Affiliation(s)
- Jun Oshiki
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hiroshi Nakano
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
| | - Hirofumi Sato
- Department of Molecular Engineering, Graduate School of Engineering, Kyoto University, Kyoto 615-8510, Japan
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4
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Cuny J, Cerda Calatayud J, Ansari N, Hassanali AA, Rapacioli M, Simon A. Simulation of Liquids with the Tight-Binding Density-Functional Approach and Improved Atomic Charges. J Phys Chem B 2020; 124:7421-7432. [PMID: 32696649 DOI: 10.1021/acs.jpcb.0c04167] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Theoretical description of liquids, especially liquid water, is an ongoing subject with important implications in various domains such as homogeneous catalysis; solvation of molecular, ionic, and biomolecular species; and reactivity. Various formalisms exist to describe liquids, each one displaying its own balance between accuracy and computational cost that defines its range of applications. The present article revisits the ability of the density-functional-based tight-binding (SCC-DFTB) approach to model liquids by focusing on liquid water and liquid benzene under ambient conditions. To do so, we benchmark a recent correction for the SCC-DFTB atomic charges that allows for a drastic improvement of the pair radial distribution functions of liquid water as compared to both experimental data and density-functional theory results performed in the generalized-gradient approximation. We also report the coupling of the deMonNano and i-PI codes to perform path-integral molecular dynamics. This allows us to rationalize the impact of nuclear quantum effects on the SCC-DFTB description of liquid water. This study evidences the rather good ability of SCC-DFTB to describe liquid water and liquid benzene. As the first example of application, we also present results for a benzene molecule solvated in water with the perspectives of further studies devoted to solvent/water interfaces.
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Affiliation(s)
- Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Jesus Cerda Calatayud
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Narjes Ansari
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy.,Department of Chemistry and Applied Biosciences, ETH Zurich, 3 c/o USI Campus, Via Giuseppe Buffi13, 6900 Lugano, Switzerland.,Facoltà di informatica, Istituto di Scienze Computazionali, Università della Svizzera Italiana, CH-6900 Lugano, Switzerland
| | - Ali A Hassanali
- The Abdus Salam International Center for Theoretical Physics, Condensed Matter and Statistical Physics Section, Strada Costiera 11, 34151 Trieste, Italy
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse III [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France
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5
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Acocella A, Marforio TD, Calvaresi M, Bottoni A, Zerbetto F. Electron Dynamics with Explicit-Time Density Functional Theory of the [4+2] Diels–Alder Reaction. J Chem Theory Comput 2020; 16:2172-2180. [PMID: 32091885 PMCID: PMC7997368 DOI: 10.1021/acs.jctc.9b00690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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The prototype Diels–Alder
(DA) reaction between butadiene
and ethene (system 1) and the DA reaction involving 1-methoxy-butadiene
and cyano-ethylene (system 2) are investigated with an
explicit-time-dependent Density Functional Theory approach. Bond orders
and atomic net charges obtained in the dynamics at the transition
state geometry and along the reaction coordinate toward reactants
are used to provide a picture of the process in terms of VB/Lewis
resonance structures that contribute to a resonance hybrid. The entire
dynamics can be divided into different domains (reactant-like, product-like,
and transition state domains) where different Lewis resonance structures
contribute with different weights. The relative importance of these
three domains varies along the reaction coordinate. In addition to
the usual reactant-like and product-like covalent Lewis structures,
ionic Lewis structures have non-negligible weights. In system 2, the electron-donor OCH3 on the diene and the
electron-acceptor CN on the dienophile make more important the contributions
of ionic Lewis structures that stabilize the transition state and
determine the decrease of the reaction barrier with respect to system 1.
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Affiliation(s)
- Angela Acocella
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Tainah D. Marforio
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Matteo Calvaresi
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Andrea Bottoni
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
| | - Francesco Zerbetto
- Department of Chemistry “G. Ciamician”, Alma Mater Studiorum − University of Bologna, via Selmi 2, Bologna 40126, Italy
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6
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Spiegelman F, Tarrat N, Cuny J, Dontot L, Posenitskiy E, Martí C, Simon A, Rapacioli M. Density-functional tight-binding: basic concepts and applications to molecules and clusters. ADVANCES IN PHYSICS: X 2020; 5:1710252. [PMID: 33154977 PMCID: PMC7116320 DOI: 10.1080/23746149.2019.1710252] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2019] [Accepted: 12/19/2019] [Indexed: 06/10/2023] Open
Abstract
The scope of this article is to present an overview of the Density Functional based Tight Binding (DFTB) method and its applications. The paper introduces the basics of DFTB and its standard formulation up to second order. It also addresses methodological developments such as third order expansion, inclusion of non-covalent interactions, schemes to solve the self-interaction error, implementation of long-range short-range separation, treatment of excited states via the time-dependent DFTB scheme, inclusion of DFTB in hybrid high-level/low level schemes (DFT/DFTB or DFTB/MM), fragment decomposition of large systems, large scale potential energy landscape exploration with molecular dynamics in ground or excited states, non-adiabatic dynamics. A number of applications are reviewed, focusing on -(i)- the variety of systems that have been studied such as small molecules, large molecules and biomolecules, bare orfunctionalized clusters, supported or embedded systems, and -(ii)- properties and processes, such as vibrational spectroscopy, collisions, fragmentation, thermodynamics or non-adiabatic dynamics. Finally outlines and perspectives are given.
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Affiliation(s)
- Fernand Spiegelman
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Nathalie Tarrat
- CEMES, Université de Toulouse (UPS), CNRS, UPR8011, Toulouse, Toulouse, France
| | - Jérôme Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Leo Dontot
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Evgeny Posenitskiy
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, UMR5589, Université de Toulouse (UPS) and CNRS, Toulouse, France
| | - Carles Martí
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
- Laboratoire de Chimie, UMR5182, Ecole Normale Supérieure de Lyon, Université de Lyon and CNRS, Lyon, France
| | - Aude Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
| | - Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, UMR5626, Université de Toulouse (UPS)and CNRS, Toulouse, France
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7
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Podeszwa R, Jankiewicz W, Krzuś M, Witek HA. Correcting long-range electrostatics in DFTB. J Chem Phys 2019; 150:234110. [DOI: 10.1063/1.5099694] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Rafał Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Wojciech Jankiewicz
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
| | - Magdalena Krzuś
- Institute of Chemistry, University of Silesia, Szkolna 9, 41-006 Katowice, Poland
- Faculty of Chemistry, Jagiellonian University, Gronostajowa 2, 30-387 Kraków, Poland
| | - Henryk A. Witek
- Department of Applied Chemistry and Institute of Molecular Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
- Center for Emergent Functional Matter Science, National Chiao Tung University, 1001 University Rd., Hsinchu 30010, Taiwan
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8
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Rossano-Tapia M, Brown A. Determination of Two-Photon-Absorption Cross Sections Using Time-Dependent Density Functional Theory Tight Binding: Application to Fluorescent Protein Chromophores. J Chem Theory Comput 2019; 15:3153-3161. [DOI: 10.1021/acs.jctc.9b00082] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Affiliation(s)
- Maria Rossano-Tapia
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
| | - Alex Brown
- Department of Chemistry, University of Alberta, Edmonton, Alberta, T6G 2G2, Canada
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9
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Simon A, Rapacioli M, Michoulier E, Zheng L, Korchagina K, Cuny J. Contribution of the density-functional-based tight-binding scheme to the description of water clusters: methods, applications and extension to bulk systems. MOLECULAR SIMULATION 2018. [DOI: 10.1080/08927022.2018.1554903] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- A. Simon
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - M. Rapacioli
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - E. Michoulier
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
- Laboratoire Collisions Agrégats et Réactivité LCAR/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - L. Zheng
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - K. Korchagina
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
| | - J. Cuny
- Laboratoire de Chimie et Physique Quantiques LCPQ/IRSAMC, Université de Toulouse and CNRS, Toulouse, France
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10
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Affiliation(s)
- Yoshifumi NISHIMURA
- Waseda Research Institute for Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo169-8555, JAPAN
| | - Takeshi YOSHIKAWA
- Department of Chemistry and Biochemistry, School of Advanced 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, Tokyo169-8555, JAPAN
- Department of Chemistry and Biochemistry, School of Advanced Science and Engineering, Waseda University, 3-4-1 Okubo, Shinjuku-ku, Tokyo 169-8555, JAPAN
- ESICB Kyoto University, Kyotodaigaku-Katsura, Nishigyo-ku, Kyoto, Kyoto 615-8520, JAPAN
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11
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Vuong VQ, Akkarapattiakal Kuriappan J, Kubillus M, Kranz JJ, Mast T, Niehaus TA, Irle S, Elstner M. Parametrization and Benchmark of Long-Range Corrected DFTB2 for Organic Molecules. J Chem Theory Comput 2017; 14:115-125. [PMID: 29232515 DOI: 10.1021/acs.jctc.7b00947] [Citation(s) in RCA: 48] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present the parametrization and benchmark of long-range corrected second-order density functional tight binding (DFTB), LC-DFTB2, for organic and biological molecules. The LC-DFTB2 model not only improves fundamental orbital energy gaps but also ameliorates the DFT self-interaction error and overpolarization problem, and further improves charge-transfer excited states significantly. Electronic parameters for the construction of the DFTB2 Hamiltonian as well as repulsive potentials were optimized for molecules containing C, H, N, and O chemical elements. We use a semiautomatic parametrization scheme based on a genetic algorithm. With the new parameters, LC-DFTB2 describes geometries and vibrational frequencies of organic molecules similarly well as third-order DFTB3/3OB, the de facto standard parametrization based on a GGA functional. LC-DFTB2 performs well also for atomization and reaction energies, however, slightly less satisfactorily than DFTB3/3OB.
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Affiliation(s)
- Van Quan Vuong
- Bredesen Center for Interdisciplinary Research and Graduate Education, University of Tennessee , Knoxville, Tennessee 37996, United States
| | - Jissy Akkarapattiakal Kuriappan
- Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , D-76131 Karlsruhe, Germany
| | - Maximilian Kubillus
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , D-76131 Karlsruhe, Germany
| | - Julian J Kranz
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , D-76131 Karlsruhe, Germany
| | - Thilo Mast
- Institute of Physical Chemistry, Karlsruhe Institute of Technology , D-76131 Karlsruhe, Germany
| | - Thomas A Niehaus
- Institut Lumière Matière, CNRS, Univ Lyon, Université Claude Bernard Lyon 1 , 69622 Villeurbanne, France
| | - Stephan Irle
- Computational Sciences and Engineering Division & Chemical Sciences Division, Oak Ridge National Laboratory , Oak Ridge, Tennessee 37831, United States
| | - Marcus Elstner
- Institute of Physical Chemistry and Institute of Biological Interfaces (IBG-2), Karlsruhe Institute of Technology , D-76131 Karlsruhe, Germany
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12
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Heck A, Kranz JJ, Elstner M. Simulation of Temperature-Dependent Charge Transport in Organic Semiconductors with Various Degrees of Disorder. J Chem Theory Comput 2016; 12:3087-96. [DOI: 10.1021/acs.jctc.6b00215] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Alexander Heck
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
- HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
| | - Julian J. Kranz
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe, Germany
- HEiKA - Heidelberg Karlsruhe Research Partnership, Heidelberg University, Karlsruhe Institute of Technology (KIT), Germany
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13
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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: 243] [Impact Index Per Article: 30.4] [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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14
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Dontot L, Suaud N, Rapacioli M, Spiegelman F. An extended DFTB-CI model for charge-transfer excited states in cationic molecular clusters: model studies versus ab initio calculations in small PAH clusters. Phys Chem Chem Phys 2016; 18:3545-57. [PMID: 26750534 DOI: 10.1039/c5cp06344b] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present an extension of the constrained density functional tight binding scheme combined with configuration interaction (DFTB-CI) to efficiently compute excited states of molecular cluster cations.
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Affiliation(s)
- Léo Dontot
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Nicolas Suaud
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Mathias Rapacioli
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
| | - Fernand Spiegelman
- Laboratoire de Chimie et de Physique Quantiques (LCPQ)
- IRSAMC
- Université de Toulouse (UPS) and CNRS
- F-31062 Toulouse
- France
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15
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Marenich AV, Olson RM, Kelly CP, Cramer CJ, Truhlar DG. Self-Consistent Reaction Field Model for Aqueous and Nonaqueous Solutions Based on Accurate Polarized Partial Charges. J Chem Theory Comput 2015; 3:2011-33. [PMID: 26636198 DOI: 10.1021/ct7001418] [Citation(s) in RCA: 360] [Impact Index Per Article: 40.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
A new universal continuum solvation model (where "universal" denotes applicable to all solvents), called SM8, is presented. It is an implicit solvation model, also called a continuum solvation model, and it improves on earlier SMx universal solvation models by including free energies of solvation of ions in nonaqueous media in the parametrization. SM8 is applicable to any charged or uncharged solute composed of H, C, N, O, F, Si, P, S, Cl, and/or Br in any solvent or liquid medium for which a few key descriptors are known, in particular dielectric constant, refractive index, bulk surface tension, and acidity and basicity parameters. It does not require the user to assign molecular-mechanics types to an atom or group; all parameters are unique and continuous functions of geometry. It may be used with any level of electronic structure theory as long as accurate partial charges can be computed for that level of theory; we recommend using it with self-consistently polarized Charge Model 4 or other self-consistently polarized class IV charges, in which case analytic gradients are available. The model separates the observable solvation free energy into two components: the long-range bulk electrostatic contribution arising from a self-consistent reaction field treatment using the generalized Born approximation for electrostatics is augmented by the non-bulk-electrostatic contribution arising from short-range interactions between the solute and solvent molecules in the first solvation shell. The cavities for the bulk electrostatics calculation are defined by superpositions of nuclear-centered spheres whose sizes are determined by intrinsic atomic Coulomb radii. The radii used for aqueous solution are the same as parametrized previously for the SM6 aqueous solvation model, and the radii for nonaqueous solution are parametrized by a training set of 220 bare ions and 21 clustered ions in acetonitrile, methanol, and dimethyl sulfoxide. The non-bulk-electrostatic terms are proportional to the solvent-accessible surface areas of the atoms of the solute and have been parametrized using solvation free energies for a training set of 2346 solvation free energies for 318 neutral solutes in 90 nonaqueous solvents and water and 143 transfer free energies for 93 neutral solutes between water and 15 organic solvents. The model is tested with three density functionals and with four basis sets: 6-31+G(d,p), 6-31+G(d), 6-31G(d), and MIDI!6D. The SM8 model achieves mean unsigned errors of 0.5-0.8 kcal/mol in the solvation free energies of tested neutrals and mean unsigned errors of 2.2-7.0 kcal/mol for ions. The model outperforms the earlier SM5.43R and SM7 universal solvation models as well as the default Polarizable Continuum Model (PCM) implemented in Gaussian 98/03, the Conductor-like PCM as implemented in GAMESS, Jaguar's continuum model based on numerical solution of the Poisson equation, and the GCOSMO model implemented in NWChem.
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Affiliation(s)
- Aleksandr V Marenich
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Ryan M Olson
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Casey P Kelly
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, 207 Pleasant Street S.E., Minneapolis, Minnesota 55455-0431
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16
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Kelly CP, Cramer CJ, Truhlar DG. SM6: A Density Functional Theory Continuum Solvation Model for Calculating Aqueous Solvation Free Energies of Neutrals, Ions, and Solute-Water Clusters. J Chem Theory Comput 2015; 1:1133-52. [PMID: 26631657 DOI: 10.1021/ct050164b] [Citation(s) in RCA: 356] [Impact Index Per Article: 39.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A new charge model, called Charge Model 4 (CM4), and a new continuum solvent model, called Solvation Model 6 (SM6), are presented. Using a database of aqueous solvation free energies for 273 neutrals, 112 ions, and 31 ion-water clusters, parameter sets for the mPW0 hybrid density functional of Adamo and Barone (Adamo, C.; Barone, V. J. Chem. Phys. 1998, 108, 664-675) were optimized for use with the following four basis sets: MIDI!6D, 6-31G(d), 6-31+G(d), and 6-31+G(d,p). SM6 separates the observable aqueous solvation free energy into two different components: one arising from long-range bulk electrostatic effects and a second from short-range interactions between the solute and solvent molecules in the first solvation shell. This partition of the observable solvation free energy allows SM6 to effectively model a wide range of solutes. For the 273 neutral solutes in the test set, SM6 achieves an average error of ∼0.50 kcal/mol in the aqueous solvation free energies. For solutes, especially ions, that have highly concentrated regions of charge density, adding an explicit water molecule to the calculation significantly improves the performance of SM6 for predicting solvation free energies. The performance of SM6 was tested against several other continuum models, including SM5.43R and several different implementations of the Polarizable Continuum Model (PCM). For both neutral and ionic solutes, SM6 outperforms all of the models against which it was tested. Also, SM6 is the only model (except for one with an average error 3.4 times larger) that improves when an explicit solvent molecule is added to solutes with concentrated charge densities. Thus, in SM6, unlike the other continuum models tested here, adding one or more explicit solvent molecules to the calculation is an effective strategy for improving the prediction of the aqueous solvation free energies of solutes with strong local solute-solvent interactions. This is important, because local solute-solvent interactions are not specifically accounted for by bulk electrostatics, but modeling these interactions correctly is important for predicting the aqueous solvation free energies of certain solutes. Finally, SM6 retains its accuracy when used in conjunction with the B3LYP and B3PW91 functionals, and in fact the solvation parameters obtained with a given basis set may be used with any good density functional or fraction of Hartree-Fock exchange.
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Affiliation(s)
- Casey P Kelly
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Christopher J Cramer
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
| | - Donald G Truhlar
- Department of Chemistry and Supercomputing Institute, 207 Pleasant St. SE, University of Minnesota, Minneapolis, Minnesota 55455-0431
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17
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Heck A, Kranz JJ, Kubař T, Elstner M. Multi-Scale Approach to Non-Adiabatic Charge Transport in High-Mobility Organic Semiconductors. J Chem Theory Comput 2015; 11:5068-82. [DOI: 10.1021/acs.jctc.5b00719] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alexander Heck
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
- Heidelberg
Karlsruhe Research Partnership (HEiKA), Heidelberg University, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
| | - Julian J. Kranz
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Tomáš Kubař
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
| | - Marcus Elstner
- Department
of Chemistry, Karlsruhe Institute of Technology, Kaiserstraße 12, 76131 Karlsruhe, Germany
- Heidelberg
Karlsruhe Research Partnership (HEiKA), Heidelberg University, Karlsruhe Institute of Technology (KIT), 76131 Karlsruhe, Germany
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18
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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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20
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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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21
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Isegawa M, Fiedler L, Leverentz HR, Wang Y, Nachimuthu S, Gao J, Truhlar DG. Polarized Molecular Orbital Model Chemistry 3. The PMO Method Extended to Organic Chemistry. J Chem Theory Comput 2013; 9:33-45. [PMID: 23704835 PMCID: PMC3658842 DOI: 10.1021/ct300509d] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The polarized molecular orbital (PMO) method, a neglect-of-diatomic-differential-overlap (NDDO) semiempirical molecular orbital method previously parameterized for systems composed of O and H, is here extended to carbon. We modified the formalism and optimized all the parameters in the PMO Hamiltonian by using a genetic algorithm and a database containing both electrostatic and energetic properties; the new parameter set is called PMO2. The quality of the resulting predictions is compared to results obtained by previous NDDO semiempirical molecular orbital methods, both including and excluding dispersion terms. We also compare the PMO2 properties to SCC-DFTB calculations. Within the class of semiempirical molecular orbital methods, the PMO2 method is found to be especially accurate for polarizabilities, atomization energies, proton transfer energies, noncovalent complexation energies, and chemical reaction barrier heights and to have good across-the-board accuracy for a range of other properties, including dipole moments, partial atomic charges, and molecular geometries.
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Affiliation(s)
- Miho Isegawa
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Luke Fiedler
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Hannah R. Leverentz
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Yingjie Wang
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Santhanamoorthi Nachimuthu
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Jiali Gao
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455, USA
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22
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Miró P, Cramer CJ. Water clusters to nanodrops: a tight-binding density functional study. Phys Chem Chem Phys 2013; 15:1837-43. [DOI: 10.1039/c2cp43305b] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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23
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Gaus M, Goez A, Elstner M. Parametrization and Benchmark of DFTB3 for Organic Molecules. J Chem Theory Comput 2012; 9:338-54. [DOI: 10.1021/ct300849w] [Citation(s) in RCA: 583] [Impact Index Per Article: 48.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Michael Gaus
- Institute of Physical Chemistry,
Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe,
Germany
- Department of Chemistry
and
Theoretical Chemistry Institute, University of Wisconsin—Madison,
1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Albrecht Goez
- Institute for Physical and Theoretical
Chemistry, Braunschweig Institute of Technology, Hans-Sommer-Str.
10, 38106 Braunschweig, Germany
| | - Marcus Elstner
- Institute of Physical Chemistry,
Karlsruhe Institute of Technology, Kaiserstr. 12, 76131 Karlsruhe,
Germany
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24
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Kaminski S, Gaus M, Elstner M. Improved electronic properties from third-order SCC-DFTB with cost efficient post-SCF extensions. J Phys Chem A 2012; 116:11927-37. [PMID: 23167841 DOI: 10.1021/jp307264f] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The present work outlines the implementation and performance of two cost efficient post-SCF extensions into the third-order SCC-DFTB code. The first one, the charge model 3 (CM3), corrects for errors in bond dipoles for an improved description of molecular charge distribution as compared to the standard Mulliken partitioning scheme. The second one focuses on the response of the charge density, that is, the electronic molecular polarizability, described inaccurately from SCC-DFTB due to the usage of a minimal atomic orbital basis. Here, a variational approach, based on scaled dipole integrals, was implemented, which clearly outperforms standard finite electric field approaches for polarizability calculations by approximately 1 order of magnitude. Both extensions in the present work rely on a set of empirical parameters, which were fitted against 112 organic molecules to match a reference data set from full density functional calculations with a large basis. As an achievement, notably improved electronic properties, that is, molecular dipole moments and polarizabilities, result from SCC-DFTB calculations at negligible additional computational cost. Furthermore, the accuracy of infrared and Raman intensities was tested as first-order derivatives of the new dipoles and polarizabilities as a function of normal mode vibrations. As a result, the current implementations cannot contribute to an improved prediction of relative intensity pattern from SCC-DFTB as compared to ab initio reference data.
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Affiliation(s)
- Steve Kaminski
- Karlsruher Institut für Technologie, Institut für Physikalische Chemie, Karlsruhe, Germany
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25
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Hou G, Zhu X, Elstner M, Cui Q. A modified QM/MM Hamiltonian with the Self-Consistent-Charge Density-Functional-Tight-Binding Theory for highly charged QM regions. J Chem Theory Comput 2012; 8:4293-4304. [PMID: 23275762 PMCID: PMC3529911 DOI: 10.1021/ct300649f] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
To improve the description of electrostatic interaction between QM and MM atoms when the QM is SCC-DFTB, we adopt a Klopman-Ohno (KO) functional form which considers the finite size of the QM and MM charge distributions. Compared to the original implementation that used a simple Coulombic interaction between QM Mulliken and MM point charges, the KO based QM/MM scheme takes charge penetration effect into consideration and therefore significantly improves the description of QM/MM interaction at short range, especially when the QM region is highly charged. To be consistent with the third-order formulation of SCC-DFTB, the Hubbard parameter in the KO functional is dependent on the QM charge. As a result, the effective size of the QM charge distribution naturally adjusts as the QM region undergoes chemical transformations, making the KO based QM/MM scheme particularly attractive for describing chemical reactions in the condensed phase. Together with the van der Waals parameters for the QM atom, the KO based QM/MM model introduces four parameters for each element type. They are fitted here based on microsolvation models of small solutes, focusing on negatively charged molecular ions, for elements O, C, H and P with a specific version of SCC-DFTB (SCC-DFTBPR). Test calculations confirm that the KO based QM/MM scheme significantly improves the interactions between QM and MM atoms over the original point charge based model and it is transferable due to the small number of parameters. The new form of QM/MM Hamiltonian will greatly improve the applicability of SCC-DFTB based QM/MM methods to problems that involve highly charged QM regions, such as enzyme catalyzed phosphoryl transfers.
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Affiliation(s)
- Guanhua Hou
- Department of Chemistry and Theoretical Chemistry Institute, University of Wisconsin, Madison, 1101 University Ave., Madison, WI 53706
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26
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Simon A, Rapacioli M, Mascetti J, Spiegelman F. Vibrational spectroscopy and molecular dynamics of water monomers and dimers adsorbed on polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2012; 14:6771-86. [PMID: 22495405 DOI: 10.1039/c2cp40321h] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper reports structures, energetics, dynamics and spectroscopy of H2O and (H2O)2 systems adsorbed on coronene (C24H12), a compact polycyclic aromatic hydrocarbon (PAH). On-the-fly Born-Oppenheimer molecular dynamics simulations are performed for temperatures T varying from 10 to 300 K, on a potential energy surface obtained within the self-consistent-charge density-functional based tight-binding (SCC-DFTB) approach. Anharmonic infrared (IR) spectra are extracted from these simulations. We first benchmark the SCC-DFTB semi-empirical hamiltonian vs. DFT (Density Functional Theory) calculations that include dispersion, on (C6H6)(H2O)1,2 small complexes. We find that charge corrections and inclusion of dispersion contributions in DFTB are necessary to obtain consistent structures, energetics and IR spectra. Using this Hamiltonian, the structures, energetics and IR features of the low-energy isomers of (C24H12)(H2O)1,2 are found to be similar to the DFT ones, with evidence for a stabilizing edge-coordination. The temperature dependence of the motions of H2O and (H2O)2 on the surface of C24H12 is analysed, revealing ultra-fast periodic motion. The water dimer starts diffusing at a higher temperature than the water monomer (150 K vs. 10 K respectively), which appears to be consistent with the binding energies. Qualitative and quantitative analyses of the effects of T on the IR spectra are performed. Anharmonic factors in particular are derived and it is shown that they can be used as signatures for the presence of PAH-water complexes. Finally, this paper lays the foundations for the studies of larger (PAH)m(H2O)n clusters, that can be treated with the efficient computational approach benchmarked in this paper.
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Affiliation(s)
- Aude Simon
- Laboratoire de Chimie et Physique Quantiques (LCPQ), Université de Toulouse [UPS] and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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27
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LU TIAN, CHEN FEIWU. ATOMIC DIPOLE MOMENT CORRECTED HIRSHFELD POPULATION METHOD. JOURNAL OF THEORETICAL & COMPUTATIONAL CHEMISTRY 2012. [DOI: 10.1142/s0219633612500113] [Citation(s) in RCA: 250] [Impact Index Per Article: 20.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Charge preservation is a necessary condition in population analysis. However, one such constraint is not enough to solve the arbitrariness involved in the population analysis such as Hirshfeld population. This arbitrariness results in too small Hirshfeld charges and poor reproducibility of molecular dipolar moments. In this article, the preservation of the molecular dipole moment is imposed upon the Hirshfeld population analysis as another constraint to improve the original Hirshfeld charges. In the scheme each atomic dipolar moment defined by the deformation density is expanded as contributions from all atoms in the molecule. The corresponding correction charges are then accumulated for each atom together with the original Hirshfeld charge as the predicted charge. All computed charges are generally larger than Hirshfeld charges, independent of basis set, and have very good electrostatic potential reproducibility and high correlation with the charges derived from the electrostatic potential fitting.
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Affiliation(s)
- TIAN LU
- Department of Chemistry, University of Science and Technology Beijing Beijing, 100083, P. R. China
| | - FEIWU CHEN
- Department of Chemistry, University of Science and Technology Beijing Beijing, 100083, P. R. China
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28
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Abstract
We discuss the source of errors in semiempirical density functional expansion (VE) methods. In particular, we show that VE methods are capable of well-reproducing their standard Kohn-Sham density functional method counterparts, but suffer from large errors upon using one or more of these approximations: the limited size of the atomic orbital basis, the Slater monopole auxiliary basis description of the response density, and the one- and two-body treatment of the core-Hamiltonian matrix elements. In the process of discussing these approximations and highlighting their symptoms, we introduce a new model that supplements the second-order density-functional tight-binding model with a self-consistent charge-dependent chemical potential equalization correction; we review our recently reported method for generalizing the auxiliary basis description of the atomic orbital response density; and we decompose the first-order potential into a summation of additive atomic components and many-body corrections, and from this examination, we provide new insights and preliminary results that motivate and inspire new approximate treatments of the core-Hamiltonian.
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Affiliation(s)
- Timothy J. Giese
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854-8087
| | - Darrin M. York
- Department of Chemistry and Chemical Biology and BioMaPS Institute for Quantitative Biology, Rutgers University, Piscataway, NJ 08854-8087
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29
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Giese TJ, York DM. Density-functional expansion methods: generalization of the auxiliary basis. J Chem Phys 2011; 134:194103. [PMID: 21599040 DOI: 10.1063/1.3587052] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
The formulation of density-functional expansion methods is extended to treat the second and higher-order terms involving the response density and spin densities with an arbitrary single-center auxiliary basis. The two-center atomic orbital products are represented by the auxiliary functions centered about those two atoms, and the mapping coefficients are determined from a local constrained variational procedure. This two-center variational procedure allows the mapping coefficients to be pretabulated and splined as a function of internuclear separation for efficient look up. The splines of mapping coefficients have a range no longer than that of the overlap integrals, and the auxiliary density appears as a single point-multipole expansion to all nonoverlapping atoms, thus allowing for the trivial implementation of a linear-scaling algorithm. The method is tested using Gaussian multipole expansions, and the effect of angular and radial completeness is explored. Several auxiliary basis sets are parametrized and compared to an auxiliary basis analogous to that used in the self-consistent-charge density-functional tight-binding model, and the method is demonstrated to greatly improve the representation of the density response with respect to a reference expansion model that does not use an auxiliary basis.
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Affiliation(s)
- Timothy J Giese
- BioMaPS Institute and Department of Chemistry and Chemical Biology, Rutgers University, Piscataway, New Jersey 08854-8087, USA
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30
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Zhang P, Bao P, Gao J. Dipole preserving and polarization consistent charges. J Comput Chem 2011; 32:2127-39. [PMID: 21541954 DOI: 10.1002/jcc.21795] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2011] [Accepted: 02/27/2011] [Indexed: 11/09/2022]
Abstract
A method for estimating dipole preserving and polarization consistent (DPPC) charges is described, which reproduces exactly the molecular dipole moment as well as the local, atomic hybridization dipoles determined from the corresponding wave function and can yield accurate molecular polarization. The method is based on a model described by Thole and van Duijnen and a new feature is introduced to treat molecular polarization. Thus, the DPPC method offers a convenient procedure to describe molecular polarization in applications using semiempirical models and ab initio molecular orbital theory with relatively small basis functions such as 6-31+G(d,p) or without inclusion of electron correlation; these methods tend to underestimate molecular polarizability. The trends of the DPPC partial atomic charges are found to be in good accord with those of the CM2 model, a class IV charge analysis method that has been used in a variety of applications. The DPPC method is illustrated to mimic the correct molecular polarizability in a water dimer test case and in water-halide ion complexes using the explicit polarization (X-Pol) potential with the Austin model 1 Hamiltonian.
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Affiliation(s)
- Peng Zhang
- Department of Chemistry, Digital Technology Center and Supercomputing Institute, University of Minnesota, Minneapolis, Minnesota 55455
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31
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Simon A, Rapacioli M, Lanza M, Joalland B, Spiegelman F. Molecular dynamics simulations on [FePAH]+ π-complexes of astrophysical interest: anharmonic infrared spectroscopy. Phys Chem Chem Phys 2011; 13:3359-74. [PMID: 21243160 DOI: 10.1039/c0cp00990c] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In this article, classical Born-Oppenheimer molecular dynamics (MD) simulations in the microcanonical ensemble are performed on neutral and cationic polycyclic aromatic hydrocarbon (PAH) species, focusing on [FePAH](+)π-complexes. Their anharmonic mid-infrared (mid-IR) spectra in the classical approximation are derived. This approach allows us to describe the influence of the energy of a system on its IR spectrum in terms of band-shifts and broadenings. The MD simulations are performed on a potential energy surface (PES) described at the self-consistent-charge density functional tight-binding level of theory. The PES is benchmarked on DFT calculations, showing the validity of the approach for complexes of Fe(+) with PAHs larger than coronene (C(24)H(12)) that are of astrophysical interest. MD simulations at high temperature show the occurrence of the diffusion of the Fe cation on the surface of the PAH. It proceeds through the edge of the carbon skeleton which is the lowest energy pathway presenting barriers smaller than 1 eV. Although only qualitative information on the band broadenings can be obtained, we show that the dependence of the computed positions of the main bands of [C(24)H(12)](0/+)and [FeC(24)H(12)](+)π-complexes on temperature can be fit by linear laws. The spectral trends determined for [FeC(24)H(12)](+) are compared to those of N-substituted [C(23)NH(12)](+)and [SiC(24)H(12)](+)π-complexes of astrophysical interest.
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Affiliation(s)
- Aude Simon
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université de Toulouse, UPS, LCPQ, 118 Route de Narbonne, F-31062 Toulouse, France.
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32
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Acocella A, Carbone F, Zerbetto F. Quantum Study of Laser-Induced Initial Activation of Graphite-to-Diamond Conversion. J Am Chem Soc 2010; 132:12166-7. [DOI: 10.1021/ja102497z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Angela Acocella
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126, Bologna, Italy, and DPMC, University of Geneva, 24 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Fabrizio Carbone
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126, Bologna, Italy, and DPMC, University of Geneva, 24 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
| | - Francesco Zerbetto
- Dipartimento di Chimica “G. Ciamician”, Università di Bologna, Via F. Selmi 2, 40126, Bologna, Italy, and DPMC, University of Geneva, 24 Quai Ernest-Ansermet, 1211 Geneva 4, Switzerland
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Rapacioli M, Spiegelman F, Talbi D, Mineva T, Goursot A, Heine T, Seifert G. Correction for dispersion and Coulombic interactions in molecular clusters with density functional derived methods: application to polycyclic aromatic hydrocarbon clusters. J Chem Phys 2009; 130:244304. [PMID: 19566150 DOI: 10.1063/1.3152882] [Citation(s) in RCA: 82] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
The density functional based tight binding (DFTB) is a semiempirical method derived from the density functional theory (DFT). It inherits therefore its problems in treating van der Waals clusters. A major error comes from dispersion forces, which are poorly described by commonly used DFT functionals, but which can be accounted for by an a posteriori treatment DFT-D. This correction is used for DFTB. The self-consistent charge (SCC) DFTB is built on Mulliken charges which are known to give a poor representation of Coulombic intermolecular potential. We propose to calculate this potential using the class IV/charge model 3 definition of atomic charges. The self-consistent calculation of these charges is introduced in the SCC procedure and corresponding nuclear forces are derived. Benzene dimer is then studied as a benchmark system with this corrected DFTB (c-DFTB-D) method, but also, for comparison, with the DFT-D. Both methods give similar results and are in agreement with references calculations (CCSD(T) and symmetry adapted perturbation theory) calculations. As a first application, pyrene dimer is studied with the c-DFTB-D and DFT-D methods. For coronene clusters, only the c-DFTB-D approach is used, which finds the sandwich configurations to be more stable than the T-shaped ones.
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Affiliation(s)
- Mathias Rapacioli
- Laboratoire de Chimie et Physique Quantiques, IRSAMC, Université de Toulouse, UPS and CNRS, 118 Route de Narbonne, F-31062 Toulouse, France.
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“Multi-Scale” QM/MM Methods with Self-Consistent-Charge Density-Functional-Tight-Binding (SCC-DFTB). ACTA ACUST UNITED AC 2009. [DOI: 10.1007/978-1-4020-9956-4_7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023]
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Xiong Z, Liu Y, Sun H. Electrostatic and covalent contributions in the coordination bonds of transition metal complexes. J Phys Chem A 2008; 112:2469-76. [PMID: 18303868 DOI: 10.1021/jp710217p] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
To develop a molecular mechanics force field for modeling complexes of transition metals and organic ligands, the electrostatic and covalent contributions in the coordination bonds were investigated using quantum mechanical density functional theory and model complexes of glyoxal diimine and the 2+ cations of the first row transition metals. The VDD and Hirshfeld charges are found to be closely correlated with the extent of the electron transfer between the ligands and the cations. Assuming the electrostatic contribution can be represented by the atomic partial charges, the covalent contributions in the coordination bonds are estimated to be in a range of 54-92% for the systems calculated. A simple force field was parametrized to validate the partial charge representation.
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Affiliation(s)
- Zhenhai Xiong
- School of Chemistry and Chemical Technology, Shanghai Jiao Tong University, Shanghai 200240, China
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de M. Seabra G, Walker RC, Elstner M, Case DA, Roitberg AE. Implementation of the SCC-DFTB method for hybrid QM/MM simulations within the amber molecular dynamics package. J Phys Chem A 2007; 111:5655-64. [PMID: 17521173 PMCID: PMC3197852 DOI: 10.1021/jp070071l] [Citation(s) in RCA: 191] [Impact Index Per Article: 11.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Self-consistent charge density functional tight-binding (SCC-DFTB) is a semiempirical method based on density functional theory and has in many cases been shown to provide relative energies and geometries comparable in accuracy to full DFT or ab initio MP2 calculations using large basis sets. This article shows an implementation of the SCC-DFTB method as part of the new QM/MM support in the AMBER 9 molecular dynamics program suite. Details of the implementation and examples of applications are shown.
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Affiliation(s)
- Gustavo de M. Seabra
- Department of Chemistry and Quantum Theory Project, University of Florida; P.O. Box 118435; Gainesville, FL, 32611-8435. USA
| | - Ross C. Walker
- Dept. of Molecular Biology, TPC15, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037 USA
| | - Marcus Elstner
- Institut für Physikalische und Theoretische Chemie. Technische Universität Braunschweig. Hans-Sommer-Straße 10. D-38106 Braunschweig. Germany
| | - David A. Case
- Dept. of Molecular Biology, TPC15, The Scripps Research Institute, 10550 N. Torrey Pines Rd., La Jolla CA 92037 USA
| | - Adrian E. Roitberg
- Department of Chemistry and Quantum Theory Project, University of Florida; P.O. Box 118435; Gainesville, FL, 32611-8435. USA
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Sattelmeyer KW, Tirado-Rives J, Jorgensen WL. Comparison of SCC-DFTB and NDDO-Based Semiempirical Molecular Orbital Methods for Organic Molecules. J Phys Chem A 2006; 110:13551-9. [PMID: 17165882 DOI: 10.1021/jp064544k] [Citation(s) in RCA: 124] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Extensive testing of the SCC-DFTB method has been performed, permitting direct comparison to data available for NDDO-based semiempirical methods. For 34 diverse isomerizations of neutral molecules containing the elements C, H, N, and O, the mean absolute errors (MAE) for the enthalpy changes are 2.7, 3.2, 5.0, 5.1, and 7.2 kcal/mol from PDDG/PM3, B3LYP/6-31G(d), PM3, SCC-DFTB, and AM1, respectively. A more comprehensive test was then performed by computing heats of formation for 622 neutral, closed-shell H, C, N, and O-containing molecules; the MAE of 5.8 kcal/mol for SCC-DFTB is intermediate between AM1 (6.8 kcal/mol) and PM3 (4.4 kcal/mol) and significantly higher than for PDDG/PM3 (3.2 kcal/mol). Similarly, SCC-DFTB is found to be less accurate for heats of formation of ions and radicals; however, it is more accurate for conformational energetics and intermolecular interaction energies, though none of the methods perform well for hydrogen bonds with strengths under ca. 7 kcal/mol. SCC-DFTB and the NDDO methods all reproduce MP2/cc-pVTZ molecular geometries with average errors for bond lengths, bond angles, and dihedral angles of only ca. 0.01 A, 1.5 degrees , and 3 degrees . Testing was also carried out for sulfur containing molecules; SCC-DFTB currently yields much less accurate heats of formation in this case than the NDDO-based methods due to the over-stabilization of molecules containing an SO bond.
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Affiliation(s)
- Kurt W Sattelmeyer
- Department of Chemistry, Yale University, New Haven, Connecticut 06520-8107, USA
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Kelly CP, Cramer CJ, Truhlar DG. Accurate partial atomic charges for high-energy molecules using class IV charge models with the MIDI! basis set. Theor Chem Acc 2005. [DOI: 10.1007/s00214-004-0624-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Walewski Ł, Bała P, Elstner M, Frauenheim T, Lesyng B. Fast QM/MM method and its application to molecular systems. Chem Phys Lett 2004. [DOI: 10.1016/j.cplett.2004.09.012] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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Pu J, Gao J, Truhlar DG. Combining Self-Consistent-Charge Density-Functional Tight-Binding (SCC-DFTB) with Molecular Mechanics by the Generalized Hybrid Orbital (GHO) Method. J Phys Chem A 2004. [DOI: 10.1021/jp049529z] [Citation(s) in RCA: 83] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Jingzhi Pu
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - Jiali Gao
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
| | - Donald G. Truhlar
- Department of Chemistry and Supercomputer Institute, University of Minnesota, 207 Pleasant Street Southeast, Minneapolis, Minnesota 55455-0431
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