151
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Tuna D, Lu Y, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks of Electronically Excited States. J Chem Theory Comput 2016; 12:4400-22. [DOI: 10.1021/acs.jctc.6b00403] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - You Lu
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, 45470 Mülheim an der Ruhr, Germany
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152
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Margraf JT, Claudino D, Bartlett RJ. Determination of consistent semiempirical one-centre integrals based on coupled-cluster theory. Mol Phys 2016. [DOI: 10.1080/00268976.2016.1200755] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Affiliation(s)
| | - Daniel Claudino
- Quantum Theory Project, University Of Florida , Gainesville, FL, USA
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153
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Zhou Y, Ojeda-May P, Nagaraju M, Pu J. Toward Determining ATPase Mechanism in ABC Transporters: Development of the Reaction Path-Force Matching QM/MM Method. Methods Enzymol 2016; 577:185-212. [PMID: 27498639 PMCID: PMC4985252 DOI: 10.1016/bs.mie.2016.05.054] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Adenosine triphosphate (ATP)-binding cassette (ABC) transporters are ubiquitous ATP-dependent membrane proteins involved in translocations of a wide variety of substrates across cellular membranes. To understand the chemomechanical coupling mechanism as well as functional asymmetry in these systems, a quantitative description of how ABC transporters hydrolyze ATP is needed. Complementary to experimental approaches, computer simulations based on combined quantum mechanical and molecular mechanical (QM/MM) potentials have provided new insights into the catalytic mechanism in ABC transporters. Quantitatively reliable determination of the free energy requirement for enzymatic ATP hydrolysis, however, requires substantial statistical sampling on QM/MM potential. A case study shows that brute force sampling of ab initio QM/MM (AI/MM) potential energy surfaces is computationally impractical for enzyme simulations of ABC transporters. On the other hand, existing semiempirical QM/MM (SE/MM) methods, although affordable for free energy sampling, are unreliable for studying ATP hydrolysis. To close this gap, a multiscale QM/MM approach named reaction path-force matching (RP-FM) has been developed. In RP-FM, specific reaction parameters for a selected SE method are optimized against AI reference data along reaction paths by employing the force matching technique. The feasibility of the method is demonstrated for a proton transfer reaction in the gas phase and in solution. The RP-FM method may offer a general tool for simulating complex enzyme systems such as ABC transporters.
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Affiliation(s)
- Y Zhou
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - P Ojeda-May
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - M Nagaraju
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States
| | - J Pu
- Indiana University-Purdue University Indianapolis, Indianapolis, IN, United States.
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154
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Spörkel L, Thiel W. Adaptive time steps in trajectory surface hopping simulations. J Chem Phys 2016; 144:194108. [DOI: 10.1063/1.4948956] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Affiliation(s)
- Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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155
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Charchar P, Christofferson AJ, Todorova N, Yarovsky I. Understanding and Designing the Gold-Bio Interface: Insights from Simulations. SMALL (WEINHEIM AN DER BERGSTRASSE, GERMANY) 2016; 12:2395-418. [PMID: 27007031 DOI: 10.1002/smll.201503585] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2015] [Revised: 02/01/2016] [Indexed: 05/20/2023]
Abstract
Gold nanoparticles (AuNPs) are an integral part of many exciting and novel biomedical applications, sparking the urgent need for a thorough understanding of the physicochemical interactions occurring between these inorganic materials, their functional layers, and the biological species they interact with. Computational approaches are instrumental in providing the necessary molecular insight into the structural and dynamic behavior of the Au-bio interface with spatial and temporal resolutions not yet achievable in the laboratory, and are able to facilitate a rational approach to AuNP design for specific applications. A perspective of the current successes and challenges associated with the multiscale computational treatment of Au-bio interfacial systems, from electronic structure calculations to force field methods, is provided to illustrate the links between different approaches and their relationship to experiment and applications.
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Affiliation(s)
- Patrick Charchar
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | | | - Nevena Todorova
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
| | - Irene Yarovsky
- School of Engineering, RMIT University, Melbourne, Victoria, 3001, Australia
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156
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Affiliation(s)
- Matúš Dubecký
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
| | - Lubos Mitas
- Department
of Physics and CHiPS, North Carolina State University, Raleigh, North Carolina 27695, United States
| | - Petr Jurečka
- Regional
Centre of Advanced Technologies and Materials, Department of Physical
Chemistry, Faculty of Science, Palacký University Olomouc, tř.
17 listopadu 12, 771 46 Olomouc, Czech Republic
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157
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Ryde U, Söderhjelm P. Ligand-Binding Affinity Estimates Supported by Quantum-Mechanical Methods. Chem Rev 2016; 116:5520-66. [DOI: 10.1021/acs.chemrev.5b00630] [Citation(s) in RCA: 175] [Impact Index Per Article: 21.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Ulf Ryde
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
| | - Pär Söderhjelm
- Department of Theoretical
Chemistry and ‡Department of Biophysical Chemistry, Lund University, Chemical Centre, P.O. Box 124, SE-221 00 Lund, Sweden
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158
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Grimme S, Hansen A, Brandenburg JG, Bannwarth C. Dispersion-Corrected Mean-Field Electronic Structure Methods. Chem Rev 2016; 116:5105-54. [DOI: 10.1021/acs.chemrev.5b00533] [Citation(s) in RCA: 799] [Impact Index Per Article: 99.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
| | | | - Christoph Bannwarth
- Mulliken Center for Theoretical
Chemistry, Universität Bonn, 53113 Bonn, Germany
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159
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Trouillas P, Sancho-García JC, De Freitas V, Gierschner J, Otyepka M, Dangles O. Stabilizing and Modulating Color by Copigmentation: Insights from Theory and Experiment. Chem Rev 2016; 116:4937-82. [PMID: 26959943 DOI: 10.1021/acs.chemrev.5b00507] [Citation(s) in RCA: 299] [Impact Index Per Article: 37.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Natural anthocyanin pigments/dyes and phenolic copigments/co-dyes form noncovalent complexes, which stabilize and modulate (in particular blue, violet, and red) colors in flowers, berries, and food products derived from them (including wines, jams, purees, and syrups). This noncovalent association and their electronic and optical implications constitute the copigmentation phenomenon. Over the past decade, experimental and theoretical studies have enabled a molecular understanding of copigmentation. This review revisits this phenomenon to provide a comprehensive description of the nature of binding (the dispersion and electrostatic components of π-π stacking, the hydrophobic effect, and possible hydrogen-bonding between pigment and copigment) and of spectral modifications occurring in copigmentation complexes, in which charge transfer plays an important role. Particular attention is paid to applications of copigmentation in food chemistry.
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Affiliation(s)
- Patrick Trouillas
- INSERM UMR 850, Univ. Limoges , Faculty of Pharmacy, 2 rue du Dr. Marcland, F-87025 Limoges, France.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Juan C Sancho-García
- Departamento de Química Física, Universidad de Alicante , Apartado de Correos 99, E-03080 Alicante, Spain
| | - Victor De Freitas
- REQUIMTE/LAQV - Research Unit, Faculty of Science, Porto University , Rua do Campo Alegre, 4169-007 Porto, Portugal
| | - Johannes Gierschner
- Madrid Institute for Advanced Studies - IMDEA Nanoscience , C/Faraday 9, Ciudad Universitaria de Cantoblanco, E-28049 Madrid, Spain
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacký University Olomouc , tr. 17. listopadu 12, 771 46 Olomouc, Czech Republic
| | - Olivier Dangles
- University of Avignon, INRA, UMR408 SQPOV , F-84000 Avignon, France
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160
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Dral P, Wu X, Spörkel L, Koslowski A, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Benchmarks for Ground-State Properties. J Chem Theory Comput 2016; 12:1097-120. [PMID: 26771261 PMCID: PMC4785506 DOI: 10.1021/acs.jctc.5b01047] [Citation(s) in RCA: 62] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2015] [Indexed: 11/30/2022]
Abstract
The semiempirical orthogonalization-corrected OMx methods (OM1, OM2, and OM3) go beyond the standard MNDO model by including additional interactions in the electronic structure calculation. When augmented with empirical dispersion corrections, the resulting OMx-Dn approaches offer a fast and robust treatment of noncovalent interactions. Here we evaluate the performance of the OMx and OMx-Dn methods for a variety of ground-state properties using a large and diverse collection of benchmark sets from the literature, with a total of 13035 original and derived reference data. Extensive comparisons are made with the results from established semiempirical methods (MNDO, AM1, PM3, PM6, and PM7) that also use the NDDO (neglect of diatomic differential overlap) integral approximation. Statistical evaluations show that the OMx and OMx-Dn methods outperform the other methods for most of the benchmark sets.
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Affiliation(s)
- Pavlo
O. Dral
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Lasse Spörkel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für
Kohlenforschung, Kaiser-Wilhelm-Platz
1, 45470 Mülheim
an der Ruhr, Germany
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161
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Dral PO, Wu X, Spörkel L, Koslowski A, Weber W, Steiger R, Scholten M, Thiel W. Semiempirical Quantum-Chemical Orthogonalization-Corrected Methods: Theory, Implementation, and Parameters. J Chem Theory Comput 2016; 12:1082-96. [PMID: 26771204 PMCID: PMC4785507 DOI: 10.1021/acs.jctc.5b01046] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
![]()
Semiempirical orthogonalization-corrected
methods (OM1, OM2, and
OM3) go beyond the standard MNDO model by explicitly including additional
interactions into the Fock matrix in an approximate manner (Pauli
repulsion, penetration effects, and core–valence interactions),
which yields systematic improvements both for ground-state and excited-state
properties. In this Article, we describe the underlying theoretical
formalism of the OMx methods and their implementation
in full detail, and we report all relevant OMx parameters
for hydrogen, carbon, nitrogen, oxygen, and fluorine. For a standard
set of mostly organic molecules commonly used in semiempirical method
development, the OMx results are found to be superior
to those from standard MNDO-type methods. Parametrized Grimme-type
dispersion corrections can be added to OM2 and OM3 energies to provide
a realistic treatment of noncovalent interaction energies, as demonstrated
for the complexes in the S22 and S66×8 test sets.
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Affiliation(s)
- Pavlo O Dral
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Xin Wu
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Lasse Spörkel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Axel Koslowski
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Weber
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Rainer Steiger
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Mirjam Scholten
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung , Kaiser-Wilhelm-Platz 1, 45470 Mülheim an der Ruhr, Germany
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162
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Nikiforov A, Gamez JA, Thiel W, Filatov M. Computational Design of a Family of Light-Driven Rotary Molecular Motors with Improved Quantum Efficiency. J Phys Chem Lett 2016; 7:105-10. [PMID: 26670164 PMCID: PMC4707559 DOI: 10.1021/acs.jpclett.5b02575] [Citation(s) in RCA: 60] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Two new light-driven molecular rotary motors based on the N-alkylated indanylidene benzopyrrole frameworks are proposed and studied using quantum chemical calculations and nonadiabatic molecular dynamics simulations. These new motors perform pure axial rotation, and the photochemical steps of the rotary cycle are dominated by the fast bond-length-alternation motion that enables ultrafast access to the S1/S0 intersection. The new motors are predicted to display a quantum efficiency higher than that of the currently available synthetic all-hydrocarbon motors. Remarkably, the quantum efficiency is not governed by the topography (peaked versus sloped) of the minimum-energy conical intersection, whereas the S1 decay time depends on the topography as well as on the energy of the intersection relative to the S1 minimum. It is the axial chirality (helicity), rather than the point chirality, that controls the sense of rotation of the motor.
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Affiliation(s)
- Alexander Nikiforov
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jose A. Gamez
- Institute
of Technical and Macromolecular Chemistry, RWTH Aachen University, Worringerweg 1, 52074 Aachen, Germany
| | - Walter Thiel
- Max-Planck-Institut
für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Michael Filatov
- Department
of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, Texas 75275-0314, United States
- Department of Chemistry, School
of Natural Sciences, Ulsan National Institute
of Science and Technology (UNIST), Ulsan 689-798, Korea
- E-mail:
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163
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164
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Shift-and-invert parallel spectral transformation eigensolver: Massively parallel performance for density-functional based tight-binding. J Comput Chem 2015; 37:448-59. [DOI: 10.1002/jcc.24254] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2015] [Revised: 10/15/2015] [Accepted: 10/25/2015] [Indexed: 01/12/2023]
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165
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Tuna D, Lefrancois D, Wolański Ł, Gozem S, Schapiro I, Andruniów T, Dreuw A, Olivucci M. Assessment of Approximate Coupled-Cluster and Algebraic-Diagrammatic-Construction Methods for Ground- and Excited-State Reaction Paths and the Conical-Intersection Seam of a Retinal-Chromophore Model. J Chem Theory Comput 2015; 11:5758-81. [PMID: 26642989 DOI: 10.1021/acs.jctc.5b00022] [Citation(s) in RCA: 107] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
As a minimal model of the chromophore of rhodopsin proteins, the penta-2,4-dieniminium cation (PSB3) poses a challenging test system for the assessment of electronic-structure methods for the exploration of ground- and excited-state potential-energy surfaces, the topography of conical intersections, and the dimensionality (topology) of the branching space. Herein, we report on the performance of the approximate linear-response coupled-cluster method of second order (CC2) and the algebraic-diagrammatic-construction scheme of the polarization propagator of second and third orders (ADC(2) and ADC(3)). For the ADC(2) method, we considered both the strict and extended variants (ADC(2)-s and ADC(2)-x). For both CC2 and ADC methods, we also tested the spin-component-scaled (SCS) and spin-opposite-scaled (SOS) variants. We have explored several ground- and excited-state reaction paths, a circular path centered around the S1/S0 surface crossing, and a 2D scan of the potential-energy surfaces along the branching space. We find that the CC2 and ADC methods yield a different dimensionality of the intersection space. While the ADC methods yield a linear intersection topology, we find a conical intersection topology for the CC2 method. We present computational evidence showing that the linear-response CC2 method yields a surface crossing between the reference state and the first response state featuring characteristics that are expected for a true conical intersection. Finally, we test the performance of these methods for the approximate geometry optimization of the S1/S0 minimum-energy conical intersection and compare the geometries with available data from multireference methods. The present study provides new insight into the performance of linear-response CC2 and polarization-propagator ADC methods for molecular electronic spectroscopy and applications in computational photochemistry.
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Affiliation(s)
- Deniz Tuna
- Max-Planck-Institut für Kohlenforschung , 45470 Mülheim an der Ruhr, Germany
| | - Daniel Lefrancois
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Łukasz Wolański
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Samer Gozem
- Department of Chemistry, University of Southern California , Los Angeles, California 90089, United States
| | - Igor Schapiro
- Institut de Physique et Chimie des Matériaux de Strasbourg & Labex NIE, Université de Strasbourg, CNRS UMR 7504 , Strasbourg 67034, France
| | - Tadeusz Andruniów
- Department of Chemistry, Wrocław University of Technology , 50370 Wrocław, Poland
| | - Andreas Dreuw
- Interdisciplinary Center for Scientific Computing, University of Heidelberg , 69120 Heidelberg, Germany
| | - Massimo Olivucci
- Department of Chemistry, Bowling Green State University , Bowling Green, Ohio 43402, United States.,Dipartimento di Biotecnologie, Chimica e Farmacia, Universitá de Siena , 53100 Siena, Italy
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166
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Shepard R, Brozell SR, Gidofalvi G. The Representation and Parametrization of Orthogonal Matrices. J Phys Chem A 2015; 119:7924-39. [PMID: 25946418 DOI: 10.1021/acs.jpca.5b02015] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Four representations and parametrizations of orthogonal matrices Q ∈ R(m×n) in terms of the minimal number of essential parameters {φ} are discussed: the exponential representation, the Householder reflector representation, the Givens rotation representation, and the rational Cayley transform representation. Both square n = m and rectangular n < m situations are considered. Two separate kinds of parametrizations are considered: one in which the individual columns of Q are distinct, the Stiefel manifold, and the other in which only span(Q) is significant, the Grassmann manifold. The practical issues of numerical stability, continuity, and uniqueness are discussed. The computation of Q in terms of the essential parameters {φ}, and also the extraction of {φ} for a given Q are considered for all of the parametrizations. The transformation of gradient arrays between the Q and {φ} variables is discussed for all representations. It is our hope that developers of new methods will benefit from this comparative presentation of an important but rarely analyzed subject.
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Affiliation(s)
- Ron Shepard
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Scott R Brozell
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
| | - Gergely Gidofalvi
- Chemical Sciences and Engineering Division, Argonne National Laboratory, Argonne, Illinois 60439, United States.,Department of Chemistry and Biochemistry, Gonzaga University, 502 East Boone Avenue, Spokane, Washington 99258-0102, United States
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167
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Nikiforov A, Gamez JA, Thiel W, Huix-Rotllant M, Filatov M. Assessment of approximate computational methods for conical intersections and branching plane vectors in organic molecules. J Chem Phys 2015; 141:124122. [PMID: 25273427 DOI: 10.1063/1.4896372] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023] Open
Abstract
Quantum-chemical computational methods are benchmarked for their ability to describe conical intersections in a series of organic molecules and models of biological chromophores. Reference results for the geometries, relative energies, and branching planes of conical intersections are obtained using ab initio multireference configuration interaction with single and double excitations (MRCISD). They are compared with the results from more approximate methods, namely, the state-interaction state-averaged restricted ensemble-referenced Kohn-Sham method, spin-flip time-dependent density functional theory, and a semiempirical MRCISD approach using an orthogonalization-corrected model. It is demonstrated that these approximate methods reproduce the ab initio reference data very well, with root-mean-square deviations in the optimized geometries of the order of 0.1 Å or less and with reasonable agreement in the computed relative energies. A detailed analysis of the branching plane vectors shows that all currently applied methods yield similar nuclear displacements for escaping the strong non-adiabatic coupling region near the conical intersections. Our comparisons support the use of the tested quantum-chemical methods for modeling the photochemistry of large organic and biological systems.
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Affiliation(s)
- Alexander Nikiforov
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Jose A Gamez
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Walter Thiel
- Max-Planck-Institut für Kohlenforschung, Kaiser-Wilhelm-Platz 1, D-45470 Mülheim an der Ruhr, Germany
| | - Miquel Huix-Rotllant
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt, Max-von-Laue-Str. 7, D-60438 Frankfurt am Main, Germany
| | - Michael Filatov
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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168
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Nishino S, Fujiwara T, Watanabe N, Yamamoto S. Parameter determination procedure for extended Hückel approximation and its application for solid-state electrolytes. J Mol Model 2015; 21:169. [PMID: 26058735 DOI: 10.1007/s00894-015-2694-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2014] [Accepted: 05/03/2015] [Indexed: 11/25/2022]
Abstract
A determination procedure of transferable tight-binding parameters of extended Hückel approximation with charge self-consistency is explained, which is applicable to both molecules and crystalline solids. The parameters are adjusted by optimizing evaluation functions, compared with reference results of energy levels or band structure calculated by, for example, the density functional theory. By introducing the evaluation function, the automatic optimization of the parameters for small molecules and clusters is achieved, which makes it easy to determine an accurate parameter set and a wide application of the TB scheme. A practical procedure of parameter optimization is demonstrated for solid-state electrolytes of Li4GeS4 and Li3PS4.
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Affiliation(s)
- Shinya Nishino
- Center for Research and Development of Higher Education, The University of Tokyo, Bunkyo-ku, Tokyo, 113-0033, Japan,
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169
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Marion A, Monard G, Ruiz-López MF, Ingrosso F. Water interactions with hydrophobic groups: assessment and recalibration of semiempirical molecular orbital methods. J Chem Phys 2015; 141:034106. [PMID: 25053300 DOI: 10.1063/1.4886655] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
In this work, we present a study of the ability of different semiempirical methods to describe intermolecular interactions in water solution. In particular, we focus on methods based on the Neglect of Diatomic Differential Overlap approximation. Significant improvements of these methods have been reported in the literature in the past years regarding the description of non-covalent interactions. In particular, a broad range of methodologies has been developed to deal with the properties of hydrogen-bonded systems, with varying degrees of success. In contrast, the interactions between water and a molecule containing hydrophobic groups have been little analyzed. Indeed, by considering the potential energy surfaces obtained using different semiempirical Hamiltonians for the intermolecular interactions of model systems, we found that none of the available methods provides an entirely satisfactory description of both hydrophobic and hydrophilic interactions in water. In addition, a vibrational analysis carried out in a model system for these interactions, a methane clathrate cluster, showed that some recent methods cannot be used to carry out studies of vibrational properties. Following a procedure established in our group [M. I. Bernal-Uruchurtu, M. T. C. Martins-Costa, C. Millot, and M. F. Ruiz-López, J. Comput. Chem. 21, 572 (2000); W. Harb, M. I. Bernal-Uruchurtu, and M. F. Ruiz-López, Theor. Chem. Acc. 112, 204 (2004)], we developed new parameters for the core-core interaction terms based on fitting potential energy curves obtained at the MP2 level for our model system. We investigated the transferability of the new parameters to describe a system, having both hydrophilic and hydrophobic groups, interacting with water. We found that only by introducing two different sets of parameters for hydrophilic and hydrophobic hydrogen atom types we are able to match the features of the ab initio calculated properties. Once this assumption is made, a good agreement with the MP2 reference is achieved. The results reported in this work provide therefore a direction for future developments of semiempirical approaches that are still required to investigate chemical processes in biomolecules and in large disordered systems.
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Affiliation(s)
- Antoine Marion
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | - Gérald Monard
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
| | | | - Francesca Ingrosso
- Université de Lorraine, SRSMC UMR 7565, Vandœuvre-lès-Nancy F-54506, France
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170
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Computational modeling of photoexcitation in DNA single and double strands. Top Curr Chem (Cham) 2015; 356:89-122. [PMID: 24647841 DOI: 10.1007/128_2014_533] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
The photoexcitation of DNA strands triggers extremely complex photoinduced processes, which cannot be understood solely on the basis of the behavior of the nucleobase building blocks. Decisive factors in DNA oligomers and polymers include collective electronic effects, excitonic coupling, hydrogen-bonding interactions, local steric hindrance, charge transfer, and environmental and solvent effects. This chapter surveys recent theoretical and computational efforts to model real-world excited-state DNA strands using a variety of established and emerging theoretical methods. One central issue is the role of localized vs delocalized excitations and the extent to which they determine the nature and the temporal evolution of the initial photoexcitation in DNA strands.
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171
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Chung LW, Sameera WMC, Ramozzi R, Page AJ, Hatanaka M, Petrova GP, Harris TV, Li X, Ke Z, Liu F, Li HB, Ding L, Morokuma K. The ONIOM Method and Its Applications. Chem Rev 2015; 115:5678-796. [PMID: 25853797 DOI: 10.1021/cr5004419] [Citation(s) in RCA: 752] [Impact Index Per Article: 83.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Lung Wa Chung
- †Department of Chemistry, South University of Science and Technology of China, Shenzhen 518055, China
| | - W M C Sameera
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Romain Ramozzi
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Alister J Page
- §Newcastle Institute for Energy and Resources, The University of Newcastle, Callaghan 2308, Australia
| | - Miho Hatanaka
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
| | - Galina P Petrova
- ∥Faculty of Chemistry and Pharmacy, University of Sofia, Bulgaria Boulevard James Bourchier 1, 1164 Sofia, Bulgaria
| | - Travis V Harris
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan.,⊥Department of Chemistry, State University of New York at Oswego, Oswego, New York 13126, United States
| | - Xin Li
- #State Key Laboratory of Molecular Reaction Dynamics, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian 116023, China
| | - Zhuofeng Ke
- ∇School of Chemistry and Chemical Engineering, Sun Yat-sen University, Guangzhou 510275, China
| | - Fengyi Liu
- ○Key Laboratory of Macromolecular Science of Shaanxi Province, School of Chemistry and Chemical Engineering, Shaanxi Normal University, Xi'an, Shaanxi 710119, China
| | - Hai-Bei Li
- ■School of Ocean, Shandong University, Weihai 264209, China
| | - Lina Ding
- ▲School of Pharmaceutical Sciences, Zhengzhou University, 100 Kexue Avenue, Zhengzhou, Henan 450001, China
| | - Keiji Morokuma
- ‡Fukui Institute for Fundamental Chemistry, Kyoto University, 34-4 Takano Nishihiraki-cho, Sakyo, Kyoto 606-8103, Japan
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172
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Yilmazer ND, Korth M. Enhanced semiempirical QM methods for biomolecular interactions. Comput Struct Biotechnol J 2015; 13:169-75. [PMID: 25848495 PMCID: PMC4372622 DOI: 10.1016/j.csbj.2015.02.004] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2015] [Revised: 02/17/2015] [Accepted: 02/19/2015] [Indexed: 12/21/2022] Open
Abstract
Recent successes and failures of the application of 'enhanced' semiempirical QM (SQM) methods are reviewed in the light of the benefits and backdraws of adding dispersion (D) and hydrogen-bond (H) correction terms. We find that the accuracy of SQM-DH methods for non-covalent interactions is very often reported to be comparable to dispersion-corrected density functional theory (DFT-D), while computation times are about three orders of magnitude lower. SQM-DH methods thus open up a possibility to simulate realistically large model systems for problems both in life and materials science with comparably high accuracy.
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Affiliation(s)
| | - Martin Korth
- Institute of Theoretical Chemistry, Ulm University, D-89069 Ulm, Germany
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173
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Chaudret R, Kiss CF, Subramanian L. Prediction of absorption wavelengths using a combination of semi-empirical quantum mechanics simulations and quantitative structure–property relationship modeling approaches. J Photochem Photobiol A Chem 2015. [DOI: 10.1016/j.jphotochem.2014.11.020] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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174
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Voityuk AA. INDO/X: A New Semiempirical Method for Excited States of Organic and Biological Molecules. J Chem Theory Comput 2014; 10:4950-8. [DOI: 10.1021/ct500717u] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Affiliation(s)
- Alexander A. Voityuk
- Institució
Catalana de Recerca i Estudis Avançats (ICREA), 08010 Barcelona, Barcelona, Spain
- Institut
de Química Computacional i Catàlisi (IQCC), Universitat de Girona, Campus de Montilivi, 17071 Girona, Girona, Spain
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175
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Zhou Y, Pu J. Reaction Path Force Matching: A New Strategy of Fitting Specific Reaction Parameters for Semiempirical Methods in Combined QM/MM Simulations. J Chem Theory Comput 2014; 10:3038-54. [PMID: 26588275 DOI: 10.1021/ct4009624] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
We present a general strategy of reparametrizing semiempirical (SE) methods against ab initio (AI) methods for combined quantum mechanical and molecular mechanical (QM/MM) simulations of specific chemical reactions in condensed phases. The resulting approach, designated Reaction Path Force Matching (RP-FM), features cycles of sampling configurations along a reaction path on an efficient SE/MM potential energy surface (PES) and adjusting specific reaction parameters (SRPs) in the SE method such that the atomic forces computed at the target AI/MM level are reproduced. Iterative applications of the RP-FM cycle make possible achieving the accuracy of AI/MM simulations without explicitly sampling the computationally expensive AI/MM PES. The bypassed sampling, nevertheless, is implicitly accomplished through the aid of the efficient SE-SRP/MM PES, on which the target-level reaction path is expected to be obtained upon convergence. We demonstrate the effectiveness of the RP-FM procedure for a symmetric proton transfer reaction in the gas phase and in solution. The remarkable agreements between the RP-FM optimized SE-SRP methods and the target AI method on various properties, including energy profiles, potential of mean force free energy profiles, atomic forces, charge populations, and solvation effects, suggest that RP-FM can be used as an efficient and reliable strategy for simulating condensed-phase chemical reactions.
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Affiliation(s)
- Yan Zhou
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , 402 N. Blackford St., LD326, Indianapolis, Indiana 46202, United States
| | - Jingzhi Pu
- Department of Chemistry and Chemical Biology, Indiana University-Purdue University Indianapolis , 402 N. Blackford St., LD326, Indianapolis, Indiana 46202, United States
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176
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The singlet–triplet energy splitting of π-nucleophiles as a measure of their reaction rate with electrophilic partners. Chem Phys Lett 2014. [DOI: 10.1016/j.cplett.2014.05.040] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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177
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Thiel W. Computational Catalysis-Past, Present, and Future. Angew Chem Int Ed Engl 2014; 53:8605-13. [DOI: 10.1002/anie.201402118] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Indexed: 01/03/2023]
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178
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