101
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McGrath MJ, Kuo IFW, Ghogomu JN, Mundy CJ, Siepmann JI. Vapor–Liquid Coexistence Curves for Methanol and Methane Using Dispersion-Corrected Density Functional Theory. J Phys Chem B 2011; 115:11688-92. [DOI: 10.1021/jp205072v] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Matthew J. McGrath
- Department of Physics, University of Helsinki, P.O. Box 64, FI-00014 Helsinki, Finland
| | - I.-F. Will Kuo
- Physical and Life Sciences Directorate, Lawrence Livermore National Laboratory, California 94550, United States
| | - Julius N. Ghogomu
- Department of Chemistry, University of Dschang, B.P. 67, Dschang, Cameroon
- Departments of Chemistry and Chemical Engineering and Materials Science and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
| | - Christopher J. Mundy
- Chemical and Materials Sciences Division, Pacific Northwest National Laboratory, P.O. Box 999, Washington 99352, United States
| | - J. Ilja Siepmann
- Departments of Chemistry and Chemical Engineering and Materials Science and Chemical Theory Center, University of Minnesota, Minneapolis, Minnesota 55455, United States
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102
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Mutter ST, Platts JA. Density Functional Theory Studies of Interactions of Ruthenium–Arene Complexes with Base Pair Steps. J Phys Chem A 2011; 115:11293-302. [DOI: 10.1021/jp2049487] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Affiliation(s)
- Shaun T. Mutter
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
| | - James A. Platts
- School of Chemistry, Cardiff University, Park Place, Cardiff CF10 3AT, U.K
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103
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Convex–concave stacking of curved conjugated networks: Benchmark calculations on the corannulene dimer. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.07.030] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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104
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Ajitha MJ, Suresh CH. A higher energy conformer of (S)-proline is the active catalyst in intermolecular aldol reaction: Evidence from DFT calculations. ACTA ACUST UNITED AC 2011. [DOI: 10.1016/j.molcata.2011.05.016] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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105
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Neves AR, Fernandes PA, Ramos MJ. The Accuracy of Density Functional Theory in the Description of Cation-π and π-Hydrogen Bond Interactions. J Chem Theory Comput 2011; 7:2059-67. [PMID: 26606477 DOI: 10.1021/ct2001667] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cation-π and π-hydrogen bond interactions are ubiquitous in protein folding, molecular recognition, and ligand-receptor associations. As such systems are routinely studied at the DFT level, it becomes essential to understand the underlying accuracy of the plethora of density functionals currently available for the description of these interactions. For that purpose, we carried out theoretical calculations on two small model systems (benzene-Na(+) and benzene-H2O) that represent a paradigm for those intermolecular interactions and systematically tested 46 density functionals against the results of high-level post-HF methods, ranging from MP2 to extrapolated CCSD(T)/CBS. A total of 13 basis sets were also tested to examine the convergence of the interaction energy with basis set size. The convergence was surprisingly fast, with deviations below 0.2 kcal/mol for double-ζ polarized basis sets with diffuse functions. Concerning functional benchmarking, the Truhlar group functionals were particularly well suited for the description of the π-hydrogen bond interactions. In the case of cation-π interactions, there was not a clear correlation between accuracy and functional sophistication. Despite the large number of functionals predicting interaction energies within chemical accuracy (five for π-hydrogen bond and 20 for cation-π interactions), not a single functional has shown chemical accuracy in both cases. Moreover, if we calculate the average error for these two interactions, only two density functionals resulted in an average error below 1.0 kcal/mol (M06 and HCTH, with average errors of 0.6 and 0.8 kcal/mol). The obtained results serve as a guide for future computer simulations on this kind of system.
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Affiliation(s)
- Ana Rute Neves
- REQUIMTE, Faculdade de Ciências do Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
| | | | - Maria João Ramos
- REQUIMTE, Faculdade de Ciências do Porto, Rua do Campo Alegre S/N, 4169-007, Porto, Portugal
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106
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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107
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1170] [Impact Index Per Article: 90.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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108
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Wu J, Walker VE, Boyd RJ. A theoretical study of the structure and conductivity of polycytosineacetylene. Chem Phys Lett 2011. [DOI: 10.1016/j.cplett.2011.03.018] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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109
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Ghigo G, Osella S, Maranzana A, Tonachini G. The Mechanism of the Acid-Catalyzed Benzidine Rearrangement of Hydrazobenzene: A Theoretical Study. European J Org Chem 2011. [DOI: 10.1002/ejoc.201001636] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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110
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Wu J, Walker VEJ, Boyd RJ. Theoretical study of polaron formation in poly(G)-poly(C) cations. J Phys Chem B 2011; 115:3136-45. [PMID: 21384938 DOI: 10.1021/jp108818u] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Polaron formation in poly(G)-poly(C) cations is investigated with density functional theory (DFT) and molecular mechanics (MM) employing a two-layer ONIOM method. In these calculations, the high layer, composed of all complementary base pairs, is treated by a DFT method, while the low layer, which includes the sugar-phosphate backbone, counterions and water molecules, is described by the AMBER force field. The high layer is the model system in which the charge transfer takes place. According to our calculations, three or four guanines move in a paddle-like fashion when an electron is removed from the neutral model system. In the cation model system, about 80% of the charge is delocalized onto the guanine residues, and the remaining charge is delocalized onto the cytosine residues. This happens because guanine has a lower ionization potential (IP) than cytosine. The counterions and water molecules in the low layer are important in the geometry optimization. The optimized geometry of the model system is closer to the standard B-form structure when counterions and water molecules are included than when they are omitted. Comparison of the optimized neutral and cationic model systems reveals a polaron in poly(G)-poly(C) cations extending from the first to the third guanine. It is demonstrated that the position of counterions and the number of surrounding water molecules can affect polaron formation.
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Affiliation(s)
- Jian Wu
- Department of Chemistry, Dalhousie University, Halifax, Nova Scotia, Canada
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111
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112
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Josa D, Otero JR, Cabaleiro Lago EM. A DFT study of substituent effects in corannulene dimers. Phys Chem Chem Phys 2011; 13:21139-45. [DOI: 10.1039/c1cp23021b] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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113
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Liakos DG, Hansen A, Neese F. Weak Molecular Interactions Studied with Parallel Implementations of the Local Pair Natural Orbital Coupled Pair and Coupled Cluster Methods. J Chem Theory Comput 2010; 7:76-87. [DOI: 10.1021/ct100445s] [Citation(s) in RCA: 135] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Dimitrios G. Liakos
- Lehrstuhl für Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
| | - Andreas Hansen
- Lehrstuhl für Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
| | - Frank Neese
- Lehrstuhl für Theoretische Chemie, Universität Bonn, Wegelerstrasse 12, D-53115 Bonn, Germany
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114
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Filatov AS, Petrukhina MA. Probing the binding sites and coordination limits of buckybowls in a solvent-free environment: Experimental and theoretical assessment. Coord Chem Rev 2010. [DOI: 10.1016/j.ccr.2010.05.004] [Citation(s) in RCA: 116] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
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115
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Ducháčková L, Kadlčíková A, Kotora M, Roithová J. Oxygen Superbases as Polar Binding Pockets in Nonpolar Solvents. J Am Chem Soc 2010; 132:12660-7. [DOI: 10.1021/ja103744f] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lucie Ducháčková
- Department of Organic Chemistry, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Aneta Kadlčíková
- Department of Organic Chemistry, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Martin Kotora
- Department of Organic Chemistry, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
| | - Jana Roithová
- Department of Organic Chemistry, Charles University in Prague, Hlavova 8, 12843 Prague 2, Czech Republic
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116
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Peltier C, Adamo C, Lainé PP, Campagna S, Puntoriero F, Ciofini I. Theoretical Insights into Branched and Fused Expanded Pyridiniums by the Means of Density Functional Theory. J Phys Chem A 2010; 114:8434-43. [DOI: 10.1021/jp104439q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Cyril Peltier
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
| | - Carlo Adamo
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
| | - Philippe P. Lainé
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
| | - Sebastiano Campagna
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
| | - Fausto Puntoriero
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
| | - Ilaria Ciofini
- LECIME, Laboratoire d′Électrochimie, Chimie des Interfaces et Modélisation pour l′Énergie (CNRS UMR-7575), École Nationale Supérieure de Chimie de Paris—Chimie ParisTech, 11, rue Pierre et Marie Curie, F-75231 Paris Cedex 05, France, Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques (CNRS UMR-8601), Université Paris Descartes, 45, rue des Saints Pères, F-75270 Paris Cedex 06, France, and Dipartimento di Chimica Inorganica, Chimica Analitica e Chimica Fisica, Università di Messina, Via
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117
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Peverati R, Macrina M, Baldridge KK. Assessment of DFT and DFT-D for Potential Energy Surfaces of Rare Gas Trimers-Implementation and Analysis of Functionals and Extrapolation Procedures. J Chem Theory Comput 2010; 6:1951-65. [PMID: 26615924 DOI: 10.1021/ct100061f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Given the recent developments in methodology associated with the accurate computation of molecular systems with weak interactions, it is of particular interest to revisit systems that are notoriously challenging for determining reliable potential energy surface (PES) descriptions. Additionally, challenges associated with carrying out complete basis set extrapolation procedures and treatment of basis set superposition error (BSSE) are of importance in these descriptions. In this work, investigation into the ability to accurately predict the potential energy surfaces of the main Rg3 molecules (Rg = He, Ne, Ar) is made across a range of wave function types and large basis sets, including the use of several established extrapolation procedures and counterpoise corrections. Wave function types span most classes of density functional types, including the newest DFT-D schemes, and are benchmarked against high accuracy CCSD(T)/CBS methodology. Study of such systems is valuable, as they serve as simple models for many complex properties, most importantly n-body weak interaction energies.
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Affiliation(s)
- Roberto Peverati
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Marina Macrina
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Kim K Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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118
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Jenness GR, Karalti O, Jordan KD. Benchmark calculations of water-acene interaction energies: Extrapolation to the water-graphene limit and assessment of dispersion-corrected DFT methods. Phys Chem Chem Phys 2010; 12:6375-81. [PMID: 20414490 DOI: 10.1039/c000988a] [Citation(s) in RCA: 72] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a previous study (J. Phys. Chem. C, 2009, 113, 10242-10248) we used density functional theory based symmetry-adapted perturbation theory (DFT-SAPT) calculations of water interacting with benzene (C(6)H(6)), coronene (C(24)H(12)), and circumcoronene (C(54)H(18)) to estimate the interaction energy between a water molecule and a graphene sheet. The present study extends this earlier work by use of a more realistic geometry with the water molecule oriented perpendicular to the acene with both hydrogen atoms pointing down. We also include results for an intermediate C(48)H(18) acene. Extrapolation of the water-acene results gives a value of -3.0 +/- 0.15 kcal mol(-1) for the binding of a water molecule to graphene. Several popular dispersion-corrected DFT methods are applied to the water-acene systems and the resulting interacting energies are compared to results of the DFT-SAPT calculations in order to assess their performance.
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Affiliation(s)
- Glen R Jenness
- Department of Chemistry and Center for Molecular and Materials Simulations, University of Pittsburgh, Pittsburgh, PA 15260, USA
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119
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Vázquez-Mayagoitia Á, Sherrill CD, Aprà E, Sumpter BG. An Assessment of Density Functional Methods for Potential Energy Curves of Nonbonded Interactions: The XYG3 and B97-D Approximations. J Chem Theory Comput 2010; 6:727-34. [DOI: 10.1021/ct900551z] [Citation(s) in RCA: 80] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Álvaro Vázquez-Mayagoitia
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, and Computer Science and Mathematics Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, P.O. Box 2008, Building 6012, Oak Ridge, Tennessee 37831-6367
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, and Computer Science and Mathematics Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, P.O. Box 2008, Building 6012, Oak Ridge, Tennessee 37831-6367
| | - Edoardo Aprà
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, and Computer Science and Mathematics Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, P.O. Box 2008, Building 6012, Oak Ridge, Tennessee 37831-6367
| | - Bobby G. Sumpter
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, Chemistry Department, University of Tennessee, 1416 Circle Drive, 552 Dabney-Buehler Hall, Knoxville, Tennessee 37996-1600, and Computer Science and Mathematics Division and Center for Nanophase Materials Sciences, Oak Ridge National Laboratory, Bethel Valley Road, P.O. Box 2008, Building 6012, Oak Ridge, Tennessee 37831-6367
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120
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Shamov GA, Budzelaar PHM, Schreckenbach G. Performance of the Empirical Dispersion Corrections to Density Functional Theory: Thermodynamics of Hydrocarbon Isomerizations and Olefin Monomer Insertion Reactions. J Chem Theory Comput 2010; 6:477-90. [DOI: 10.1021/ct9005135] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Grigory A. Shamov
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Peter H. M. Budzelaar
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
| | - Georg Schreckenbach
- Department of Chemistry, University of Manitoba, Winnipeg, MB, R3T 2N2, Canada, and Dutch Polymer Institute (DPI), P.O. Box 902, 5600 AX Eindhoven, The Netherlands
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121
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Karim AR, Linden A, Baldridge KK, Siegel JS. Symmetry and polar-π effects on the dynamics of enshrouded aryl-alkyne molecular rotors. Chem Sci 2010. [DOI: 10.1039/c0sc00117a] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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122
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Riley KE, Pitoňák M, Černý J, Hobza P. On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations. J Chem Theory Comput 2009; 6:66-80. [PMID: 26614320 DOI: 10.1021/ct900376r] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H···π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
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Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Michal Pitoňák
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Jiří Černý
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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Peverati R, Baldridge KK. Implementation and Optimization of DFT-D/COSab with Respect to Basis Set and Functional: Application to Polar Processes of Furfural Derivatives in Solution. J Chem Theory Comput 2009; 5:2772-86. [DOI: 10.1021/ct900363n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Roberto Peverati
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
| | - Kim K. Baldridge
- University of Zürich, Winterthurerstrasse 190, CH-8057 Zürich, Switzerland
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124
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Minenkov Y, Occhipinti G, Jensen VR. Metal−Phosphine Bond Strengths of the Transition Metals: A Challenge for DFT. J Phys Chem A 2009; 113:11833-44. [DOI: 10.1021/jp902940c] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Yury Minenkov
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Giovanni Occhipinti
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
| | - Vidar R. Jensen
- Department of Chemistry, University of Bergen, Allégaten 41, N-5007 Bergen, Norway
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125
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Sancho-García JC, Pérez-Jiménez AJ. Assessment of double-hybrid energy functionals for π-conjugated systems. J Chem Phys 2009; 131:084108. [DOI: 10.1063/1.3212881] [Citation(s) in RCA: 71] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
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126
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Bauert T, Merz L, Bandera D, Parschau M, Siegel JS, Ernst KH. Building 2D Crystals from 5-Fold-Symmetric Molecules. J Am Chem Soc 2009; 131:3460-1. [DOI: 10.1021/ja8101083] [Citation(s) in RCA: 72] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tobias Bauert
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
| | - Leo Merz
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
| | - Davide Bandera
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
| | - Manfred Parschau
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
| | - Jay S. Siegel
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
| | - Karl-Heinz Ernst
- Empa, Swiss Federal Laboratories for Materials Testing and Research, Laboratory for Nanoscale Materials Science, Ueberlandstrasse 129, 8600 Dübendorf, Switzerland, and Organic Chemistry Institute, University of Zurich, Winterthurerstrasse 190, 8052 Zurich, Switzerland
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127
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Feng C, Lin CS, Fan W, Zhang RQ, Van Hove MA. Stacking of polycyclic aromatic hydrocarbons as prototype for graphene multilayers, studied using density functional theory augmented with a dispersion term. J Chem Phys 2009; 131:194702. [DOI: 10.1063/1.3251785] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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