351
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Cutini M, Civalleri B, Corno M, Orlando R, Brandenburg JG, Maschio L, Ugliengo P. Assessment of Different Quantum Mechanical Methods for the Prediction of Structure and Cohesive Energy of Molecular Crystals. J Chem Theory Comput 2016; 12:3340-52. [DOI: 10.1021/acs.jctc.6b00304] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Michele Cutini
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Bartolomeo Civalleri
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Marta Corno
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Roberto Orlando
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Jan Gerit Brandenburg
- Mulliken
Center of Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn, Beringstraße
4, 53115 Bonn, Germany
| | - Lorenzo Maschio
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
| | - Piero Ugliengo
- Department
of Chemistry and NIS (Nanostructured Interfaces and Surfaces) Center, University of Turin, Via P. Giuria 7, 10125 Turin, Italy
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352
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Tan R, Zheng X, Qu B, Sader CA, Fandrick KR, Senanayake CH, Zhang X. Tunable P-Chiral Bisdihydrobenzooxaphosphole Ligands for Enantioselective Hydroformylation. Org Lett 2016; 18:3346-9. [DOI: 10.1021/acs.orglett.6b01452] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Renchang Tan
- Department
of Chemistry and Chemical Biology and Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Xin Zheng
- Department
of Chemistry and Chemical Biology and Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
| | - Bo Qu
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - C. Avery Sader
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Keith R. Fandrick
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Chris H. Senanayake
- Chemical
Development, Boehringer Ingelheim Pharmaceuticals, Inc., 900 Ridgebury Road, Ridgefield, Connecticut 06877, United States
| | - Xumu Zhang
- Department
of Chemistry and Chemical Biology and Department of Medicinal Chemistry, Rutgers, The State University of New Jersey, Piscataway, New Jersey 08854, United States
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353
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Rasmussen TH, Wang YM, Kjærgaard T, Kristensen K. The explicitly correlated same number of optimized parameters (SNOOP-F12) scheme for calculating intermolecular interaction energies. J Chem Phys 2016; 144:204102. [DOI: 10.1063/1.4950846] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Troels Hels Rasmussen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Yang Min Wang
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Thomas Kjærgaard
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Kasper Kristensen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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354
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Bauer CA, Grimme S. How to Compute Electron Ionization Mass Spectra from First Principles. J Phys Chem A 2016; 120:3755-66. [DOI: 10.1021/acs.jpca.6b02907] [Citation(s) in RCA: 72] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie
der Rheinischen Friedrich-Wilhelms, Universität Bonn, Beringstr. 4, D-53115 Bonn, Germany
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355
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Masnyk M, Butkiewicz A, Górecki M, Luboradzki R, Bannwarth C, Grimme S, Frelek J. Synthesis and Comprehensive Structural and Chiroptical Characterization of Enones Derived from (−)-α-Santonin by Experiment and Theory. J Org Chem 2016; 81:4588-600. [DOI: 10.1021/acs.joc.6b00416] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
Affiliation(s)
- Marek Masnyk
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Aleksandra Butkiewicz
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Marcin Górecki
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Roman Luboradzki
- Institute
of Physical Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
| | - Christoph Bannwarth
- Mulliken
Center for Theoretical Chemistry, Institute of Physical and Theoretical
Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken
Center for Theoretical Chemistry, Institute of Physical and Theoretical
Chemistry, University of Bonn, Beringstr. 4, 53115 Bonn, Germany
| | - Jadwiga Frelek
- Institute
of Organic Chemistry, Polish Academy of Sciences, Kasprzaka 44/52, 01-224 Warsaw, Poland
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356
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Christensen A, Kubař T, Cui Q, Elstner M. Semiempirical Quantum Mechanical Methods for Noncovalent Interactions for Chemical and Biochemical Applications. Chem Rev 2016; 116:5301-37. [PMID: 27074247 PMCID: PMC4867870 DOI: 10.1021/acs.chemrev.5b00584] [Citation(s) in RCA: 246] [Impact Index Per Article: 30.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Indexed: 12/28/2022]
Abstract
Semiempirical (SE) methods can be derived from either Hartree-Fock or density functional theory by applying systematic approximations, leading to efficient computational schemes that are several orders of magnitude faster than ab initio calculations. Such numerical efficiency, in combination with modern computational facilities and linear scaling algorithms, allows application of SE methods to very large molecular systems with extensive conformational sampling. To reliably model the structure, dynamics, and reactivity of biological and other soft matter systems, however, good accuracy for the description of noncovalent interactions is required. In this review, we analyze popular SE approaches in terms of their ability to model noncovalent interactions, especially in the context of describing biomolecules, water solution, and organic materials. We discuss the most significant errors and proposed correction schemes, and we review their performance using standard test sets of molecular systems for quantum chemical methods and several recent applications. The general goal is to highlight both the value and limitations of SE methods and stimulate further developments that allow them to effectively complement ab initio methods in the analysis of complex molecular systems.
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Affiliation(s)
- Anders
S. Christensen
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Tomáš Kubař
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
| | - Qiang Cui
- Department
of Chemistry and Theoretical Chemistry Institute, University of Wisconsin—Madison, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Marcus Elstner
- Institute of Physical
Chemistry & Center for Functional Nanostructures and Institute of Physical
Chemistry, Karlsruhe Institute of Technology, Kaiserstrasse 12, 76131 Karlsruhe, Germany
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357
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Structural diversity, spectral characterization and computational studies of Cu(I) complexes with pyridylamide ligands. Inorganica Chim Acta 2016. [DOI: 10.1016/j.ica.2016.03.011] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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358
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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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359
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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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360
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Sure R, Brandenburg JG, Grimme S. Small Atomic Orbital Basis Set First-Principles Quantum Chemical Methods for Large Molecular and Periodic Systems: A Critical Analysis of Error Sources. ChemistryOpen 2016; 5:94-109. [PMID: 27308221 PMCID: PMC4906470 DOI: 10.1002/open.201500192] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 11/12/2022] Open
Abstract
In quantum chemical computations the combination of Hartree-Fock or a density functional theory (DFT) approximation with relatively small atomic orbital basis sets of double-zeta quality is still widely used, for example, in the popular B3LYP/6-31G* approach. In this Review, we critically analyze the two main sources of error in such computations, that is, the basis set superposition error on the one hand and the missing London dispersion interactions on the other. We review various strategies to correct those errors and present exemplary calculations on mainly noncovalently bound systems of widely varying size. Energies and geometries of small dimers, large supramolecular complexes, and molecular crystals are covered. We conclude that it is not justified to rely on fortunate error compensation, as the main inconsistencies can be cured by modern correction schemes which clearly outperform the plain mean-field methods.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
| | - Stefan Grimme
- Mulliken Center for Theoretical ChemistryInstitut für Physikalische und Theoretische ChemieUniversität BonnBeringstr. 453115BonnGermany
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361
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Gkionis K, Kruse H, Šponer J. Derivation of Reliable Geometries in QM Calculations of DNA Structures: Explicit Solvent QM/MM and Restrained Implicit Solvent QM Optimizations of G-Quadruplexes. J Chem Theory Comput 2016; 12:2000-16. [DOI: 10.1021/acs.jctc.5b01025] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Affiliation(s)
- Konstantinos Gkionis
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Holger Kruse
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
| | - Jiří Šponer
- Institute of Biophysics,
Academy of Sciences of the Czech Republic, Královopolská 135, 612
65 Brno, Czech Republic
- CEITEC
− Central European Institute of Technology, Masaryk University, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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362
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Brandenburg JG, Maas T, Grimme S. Benchmarking DFT and semiempirical methods on structures and lattice energies for ten ice polymorphs. J Chem Phys 2016; 142:124104. [PMID: 25833562 DOI: 10.1063/1.4916070] [Citation(s) in RCA: 71] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Water in different phases under various external conditions is very important in bio-chemical systems and for material science at surfaces. Density functional theory methods and approximations thereof have to be tested system specifically to benchmark their accuracy regarding computed structures and interaction energies. In this study, we present and test a set of ten ice polymorphs in comparison to experimental data with mass densities ranging from 0.9 to 1.5 g/cm(3) and including explicit corrections for zero-point vibrational and thermal effects. London dispersion inclusive density functionals at the generalized gradient approximation (GGA), meta-GGA, and hybrid level as well as alternative low-cost molecular orbital methods are considered. The widely used functional of Perdew, Burke and Ernzerhof (PBE) systematically overbinds and overall provides inconsistent results. All other tested methods yield reasonable to very good accuracy. BLYP-D3(atm) gives excellent results with mean absolute errors for the lattice energy below 1 kcal/mol (7% relative deviation). The corresponding optimized structures are very accurate with mean absolute relative deviations (MARDs) from the reference unit cell volume below 1%. The impact of Axilrod-Teller-Muto (atm) type three-body dispersion and of non-local Fock exchange is small but on average their inclusion improves the results. While the density functional tight-binding model DFTB3-D3 performs well for low density phases, it does not yield good high density structures. As low-cost alternative for structure related problems, we recommend the recently introduced minimal basis Hartree-Fock method HF-3c with a MARD of about 3%.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Tilo Maas
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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363
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Sperger T, Fisher HC, Schoenebeck F. Computationally deciphering palladium-catalyzed reaction mechanisms. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2016. [DOI: 10.1002/wcms.1244] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Affiliation(s)
- Theresa Sperger
- Institute of Organic Chemistry; RWTH Aachen University; Aachen Germany
| | - Henry C. Fisher
- Institute of Organic Chemistry; RWTH Aachen University; Aachen Germany
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364
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Liu W, Peck EM, Smith BD. High Affinity Macrocycle Threading by a Near-Infrared Croconaine Dye with Flanking Polymer Chains. J Phys Chem B 2016; 120:995-1001. [PMID: 26807599 DOI: 10.1021/acs.jpcb.5b11961] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
Croconaine dyes have narrow and intense absorption bands at ∼800 nm, very weak fluorescence, and high photostabilities, which combine to make them very attractive chromophores for absorption-based imaging or laser heating technologies. The physical supramolecular properties of croconaine dyes have rarely been investigated, especially in water. This study focuses on a molecular threading process that encapsulates a croconaine dye inside a tetralactam macrocycle in organic or aqueous solvent. Macrocycle association and rate constant data are reported for a series of croconaine structures with different substituents attached to the ends of the dye. The association constants were highest in water (Ka ∼ 10(9) M(-1)), and the threading rate constants (kon) increased in the solvent order H2O > MeOH > CHCl3. Systematic variation of croconaine substituents located just outside the croconaine/macrocycle complexation interface hardly changed Ka but had a strong influence on kon. A croconaine dye with N-propyl groups at each end of the structure exhibited a desirable mixture of macrocycle threading properties; that is, there was rapid and quantitative croconaine/macrocycle complexation at relatively high concentrations in water, and no dissociation of the preassembled complex when it was diluted into a solution of fetal bovine serum, even after laser-induced photothermal heating of the solution. The combination of favorable near-infrared absorption properties and tunable mechanical stability makes threaded croconaine/macrocycle complexes very attractive as molecular probes or as supramolecular composites for various applications in absorption-based imaging or photothermal therapy.
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Affiliation(s)
- Wenqi Liu
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Evan M Peck
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
| | - Bradley D Smith
- Department of Chemistry and Biochemistry, University of Notre Dame , 236 Nieuwland Science Hall, Notre Dame, Indiana 46556, United States
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365
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Nunes Dos Santos Comprido L, Klein JEMN, Knizia G, Kästner J, Hashmi ASK. Gold(I) Vinylidene Complexes as Reactive Intermediates and Their Tendency to π-Backbond. Chemistry 2016; 22:2892-5. [PMID: 26711532 DOI: 10.1002/chem.201504511] [Citation(s) in RCA: 56] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2015] [Indexed: 11/10/2022]
Abstract
We herein report a computational study of the bonding in gold(I) vinylidene complexes and compare them to their carbene and CO analogues. The relevance of these intermediates is analysed for the intramolecular cyclisation leading to vinyl sulfonates.
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Affiliation(s)
| | - Johannes E M N Klein
- Department of Chemistry, University of Minnesota, 207 Pleasant St SE, Minneapolis, MN, 55455, USA
| | - Gerald Knizia
- Department of Chemistry, Pennsylvania State University, 401A Chemistry Bldg, University Park, PA, 16802, USA
| | - Johannes Kästner
- Institut für Theoretische Chemie, Universität Stuttgart, Pfaffenwaldring 55, 70569, Stuttgart, Germany
| | - A Stephen K Hashmi
- Organisch-Chemisches Institut, Ruprecht-Karls-Universität Heidelberg, Im Neuenheimer Feld 270, 69120, Heidelberg, Germany. .,Chemistry Department, Faculty of Science, King Abdulaziz University, Jeddah, 21589, Saudi Arabia.
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366
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Silva NJ, Machado FBC, Lischka H, Aquino AJA. π–π stacking between polyaromatic hydrocarbon sheets beyond dispersion interactions. Phys Chem Chem Phys 2016; 18:22300-10. [DOI: 10.1039/c6cp03749f] [Citation(s) in RCA: 52] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
A slipped parallel structure of a stacked graphene flake showing a biconcave curvature.
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Affiliation(s)
- Nadeesha J. Silva
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
| | | | - Hans Lischka
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
- Institute for Theoretical Chemistry
| | - Adelia J. A. Aquino
- Department of Chemistry and Biochemistry
- Texas Tech University
- Lubbock Texas 79409
- USA
- School of Pharmaceutical Sciences and Technology
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367
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Marin-Montesinos I, Paniagua JC, Peman A, Vilaseca M, Luis F, Van Doorslaer S, Pons M. Paramagnetic spherical nanoparticles by the self-assembly of persistent trityl radicals. Phys Chem Chem Phys 2016; 18:3151-8. [DOI: 10.1039/c5cp05767a] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The self-association of a water-soluble persistent trityl radical gives rise to paramagnetic nanoparticles: a new class of non-metallic high spin systems.
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Affiliation(s)
- I. Marin-Montesinos
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
| | - J. C. Paniagua
- Department of Physical Chemistry
- University of Barcelona
- Martí i Franquès
- 1-11 08028-Barcelona
- Spain
| | - Alejandro Peman
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
| | - M. Vilaseca
- Mass Spectrometry Core Facility
- Institute for Research in Biomedicine (IRB Barcelona)
- 10-12 08028 Barcelona
- Spain
| | - F. Luis
- Instituto de Ciencia de Materiales de Aragón
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | | | - M. Pons
- Biomolecular NMR Laboratory
- Department of Organic Chemistry
- University of Barcelona
- 10-12 08028 Barcelona
- Spain
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368
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Sukhikh TS, Bashirov DA, Ogienko DS, Kuratieva NV, Sherin PS, Rakhmanova MI, Chulanova EA, Gritsan NP, Konchenko SN, Zibarev AV. Novel luminescent β-ketoimine derivative of 2,1,3-benzothiadiazole: synthesis, complexation with Zn(ii) and photophysical properties in comparison with related compounds. RSC Adv 2016. [DOI: 10.1039/c6ra06547c] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
2,1,3-Benzothiadiazoles and their Zn complexes show fluorescence in different wavelength regions, one of the complexes reveals white emission.
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369
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Wang H, Liu J, Xu H, Ma Z, Jia W, Ren S. Demulsification of heavy oil-in-water emulsions by reduced graphene oxide nanosheets. RSC Adv 2016. [DOI: 10.1039/c6ra18898b] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The purpose of this work is to investigate the relationship between the chemical structure of the GO materials and the demulsification performance.
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Affiliation(s)
- Huanjiang Wang
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Juan Liu
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Haiyan Xu
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Zhanwei Ma
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Weihong Jia
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
| | - Sili Ren
- State Key Laboratory of Solid Lubrication
- Lanzhou Institute of Chemical Physics
- Chinese Academy of Sciences
- Lanzhou
- P. R. China
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370
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Brandenburg JG, Caldeweyher E, Grimme S. Screened exchange hybrid density functional for accurate and efficient structures and interaction energies. Phys Chem Chem Phys 2016; 18:15519-23. [DOI: 10.1039/c6cp01697a] [Citation(s) in RCA: 42] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
HSE-3c: a computationally efficient and numerically robust screened hybrid functional that can be applied to periodic small gap systems.
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Affiliation(s)
| | - Eike Caldeweyher
- Mulliken Center for Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- University of Bonn
- 53115 Bonn
- Germany
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371
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Yoshida T, Hayashi T, Mashima A, Sasahara K, Chuman H. A simple and efficient dispersion correction to the Hartree–Fock theory (3): A comprehensive performance comparison of HF-Dtq with MP2 and DFT-Ds. Bioorg Med Chem Lett 2016; 26:589-593. [DOI: 10.1016/j.bmcl.2015.11.061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Revised: 11/14/2015] [Accepted: 11/19/2015] [Indexed: 11/25/2022]
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372
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Grimme S, Brandenburg JG, Bannwarth C, Hansen A. Consistent structures and interactions by density functional theory with small atomic orbital basis sets. J Chem Phys 2015; 143:054107. [PMID: 26254642 DOI: 10.1063/1.4927476] [Citation(s) in RCA: 531] [Impact Index Per Article: 59.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
A density functional theory (DFT) based composite electronic structure approach is proposed to efficiently compute structures and interaction energies in large chemical systems. It is based on the well-known and numerically robust Perdew-Burke-Ernzerhoff (PBE) generalized-gradient-approximation in a modified global hybrid functional with a relatively large amount of non-local Fock-exchange. The orbitals are expanded in Ahlrichs-type valence-double zeta atomic orbital (AO) Gaussian basis sets, which are available for many elements. In order to correct for the basis set superposition error (BSSE) and to account for the important long-range London dispersion effects, our well-established atom-pairwise potentials are used. In the design of the new method, particular attention has been paid to an accurate description of structural parameters in various covalent and non-covalent bonding situations as well as in periodic systems. Together with the recently proposed three-fold corrected (3c) Hartree-Fock method, the new composite scheme (termed PBEh-3c) represents the next member in a hierarchy of "low-cost" electronic structure approaches. They are mainly free of BSSE and account for most interactions in a physically sound and asymptotically correct manner. PBEh-3c yields good results for thermochemical properties in the huge GMTKN30 energy database. Furthermore, the method shows excellent performance for non-covalent interaction energies in small and large complexes. For evaluating its performance on equilibrium structures, a new compilation of standard test sets is suggested. These consist of small (light) molecules, partially flexible, medium-sized organic molecules, molecules comprising heavy main group elements, larger systems with long bonds, 3d-transition metal systems, non-covalently bound complexes (S22 and S66×8 sets), and peptide conformations. For these sets, overall deviations from accurate reference data are smaller than for various other tested DFT methods and reach that of triple-zeta AO basis set second-order perturbation theory (MP2/TZ) level at a tiny fraction of computational effort. Periodic calculations conducted for molecular crystals to test structures (including cell volumes) and sublimation enthalpies indicate very good accuracy competitive to computationally more involved plane-wave based calculations. PBEh-3c can be applied routinely to several hundreds of atoms on a single processor and it is suggested as a robust "high-speed" computational tool in theoretical chemistry and physics.
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Affiliation(s)
- Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Christoph Bannwarth
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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373
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Kumbhar S, Jana S, Anoop A, Waller MP. Cooperativity in bimetallic glutathione complexes. J Mol Graph Model 2015; 62:1-10. [DOI: 10.1016/j.jmgm.2015.05.003] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/18/2015] [Revised: 04/30/2015] [Accepted: 05/05/2015] [Indexed: 01/03/2023]
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374
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Yoshida T, Hayashi T, Mashima A, Chuman H. A simple and efficient dispersion correction to the Hartree-Fock theory (2): Incorporation of a geometrical correction for the basis set superposition error. Bioorg Med Chem Lett 2015; 25:4179-84. [PMID: 26292629 DOI: 10.1016/j.bmcl.2015.08.008] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 07/29/2015] [Accepted: 08/04/2015] [Indexed: 02/02/2023]
Abstract
One of the most challenging problems in computer-aided drug discovery is the accurate prediction of the binding energy between a ligand and a protein. For accurate estimation of net binding energy ΔEbind in the framework of the Hartree-Fock (HF) theory, it is necessary to estimate two additional energy terms; the dispersion interaction energy (Edisp) and the basis set superposition error (BSSE). We previously reported a simple and efficient dispersion correction, Edisp, to the Hartree-Fock theory (HF-Dtq). In the present study, an approximation procedure for estimating BSSE proposed by Kruse and Grimme, a geometrical counterpoise correction (gCP), was incorporated into HF-Dtq (HF-Dtq-gCP). The relative weights of the Edisp (Dtq) and BSSE (gCP) terms were determined to reproduce ΔEbind calculated with CCSD(T)/CBS or /aug-cc-pVTZ (HF-Dtq-gCP (scaled)). The performance of HF-Dtq-gCP (scaled) was compared with that of B3LYP-D3(BJ)-bCP (dispersion corrected B3LYP with the Boys and Bernadi counterpoise correction (bCP)), by taking ΔEbind (CCSD(T)-bCP) of small non-covalent complexes as 'a golden standard'. As a critical test, HF-Dtq-gCP (scaled)/6-31G(d) and B3LYP-D3(BJ)-bCP/6-31G(d) were applied to the complex model for HIV-1 protease and its potent inhibitor, KNI-10033. The present results demonstrate that HF-Dtq-gCP (scaled) is a useful and powerful remedy for accurately and promptly predicting ΔEbind between a ligand and a protein, albeit it is a simple correction procedure.
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Affiliation(s)
- Tatsusada Yoshida
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Takahisa Hayashi
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Akira Mashima
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan
| | - Hiroshi Chuman
- Institute of Biomedical Sciences, Tokushima University, Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan.
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375
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Kruse H, Mladek A, Gkionis K, Hansen A, Grimme S, Sponer J. Quantum chemical benchmark study on 46 RNA backbone families using a dinucleotide unit. J Chem Theory Comput 2015; 11:4972-91. [PMID: 26574283 DOI: 10.1021/acs.jctc.5b00515] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
We have created a benchmark set of quantum chemical structure-energy data denoted as UpU46, which consists of 46 uracil dinucleotides (UpU), representing all known 46 RNA backbone conformational families. Penalty-function-based restrained optimizations with COSMO TPSS-D3/def2-TZVP ensure a balance between keeping the target conformation and geometry relaxation. The backbone geometries are close to the clustering-means of their respective RNA bioinformatics family classification. High-level wave function methods (DLPNO-CCSD(T) as reference) and a wide-range of dispersion-corrected or inclusive DFT methods (DFT-D3, VV10, LC-BOP-LRD, M06-2X, M11, and more) are used to evaluate the conformational energies. The results are compared to the Amber RNA bsc0χOL3 force field. Most dispersion-corrected DFT methods surpass the Amber force field significantly in accuracy and yield mean absolute deviations (MADs) for relative conformational energies of ∼0.4-0.6 kcal/mol. Double-hybrid density functionals represent the most accurate class of density functionals. Low-cost quantum chemical methods such as PM6-D3H+, HF-3c, DFTB3-D3, as well as small basis set calculations corrected for basis set superposition errors (BSSEs) by the gCP procedure are also tested. Unfortunately, the presently available low-cost methods are struggling to describe the UpU conformational energies with satisfactory accuracy. The UpU46 benchmark is an ideal test for benchmarking and development of fast methods to describe nucleic acids, including force fields.
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Affiliation(s)
- Holger Kruse
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Arnost Mladek
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic
| | - Konstantinos Gkionis
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
| | - Andreas Hansen
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstr. 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie der Universität Bonn , Beringstr. 4, D-53115 Bonn, Germany
| | - Jiri Sponer
- Institute of Biophysics, Academy of Sciences of the Czech Republic , Královopolská 135, 612 65 Brno, Czech Republic.,CEITEC-Central European Institute of Technology, Campus Bohunice, Kamenice 5, 625 00 Brno, Czech Republic
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376
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Chen GQ, Türkyilmaz F, Daniliuc CG, Bannwarth C, Grimme S, Kehr G, Erker G. Enamine/butadienylborane cycloaddition in the frustrated Lewis pair regime. Org Biomol Chem 2015; 13:10477-86. [PMID: 26330093 DOI: 10.1039/c5ob01602a] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
Abstract
The dienylborane 2a was prepared by regioselective alkyne hydroboration of the conjugated enyne 1a with Piers' borane [HB(C6F5)2]. Its reaction with a series of acetophenone derived enamines 3 resulted in the formation of the strong enamine β-carbon adduct with the borane Lewis acid (4). In contrast B-C adduct formation between the dienylborane 2a and a series of much more bulky cyclohexanone derived enamines (6) is rapidly reversible above ca.-30 °C and then leads to the formation of the [4 + 2]cycloaddition products 8. A DFT study revealed that this reaction is probably taking a stepwise route, proceeding by means of enamine addition to the dienylborane terminus to generate a zwitterionic borata-alkene/iminium ion intermediate that undergoes rapid subsequent ring closure. Heating of the products 8 led to amidoborane elimination from the vicinal amino/borane pair at the product framework to give the respective hexahydronaphthalene product 10. Subsequent treatment with TEMPO (2 equiv.) resulted in selective oxidation of the unsaturated ring to give the respective tetrahydronaphthalene derivative 12.
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Affiliation(s)
- Guo-Qiang Chen
- Organisch-Chemisches Institut, Universität Münster, Corrensstraβe 40, 48149 Münster, Germany.
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377
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Kang F, Hu X, Liu J, Gao Y. Noncovalent Binding of Polycyclic Aromatic Hydrocarbons with Genetic Bases Reducing the in Vitro Lateral Transfer of Antibiotic Resistant Genes. ENVIRONMENTAL SCIENCE & TECHNOLOGY 2015; 49:10340-10348. [PMID: 26262891 DOI: 10.1021/acs.est.5b02293] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
In current studies of noncovalent interactions of polycyclic aromatic hydrocarbons (PAHs) with genetic units, the impact of such interactions on gene transfer has not been explored. In this study, we examined the association of some widely occurring PAHs (phenanthrene, pyrene, benzo[g,h,i]perylene, and other congeners) with antibiotic resistant plasmids (pUC19). Small molecular PAHs (e.g., phenanthrene) bind effectively with plasmids to form a loosely clew-like plasmid-PAH complex (16.5-49.5 nm), resulting in reduced transformation of ampicillin resistance gene (Ampr). The in vitro transcription analysis demonstrated that reduced transformation of Ampr in plasmids results from the PAH-inhibited Ampr transcription to RNA. Fluorescence microtitration coupled with Fourier transform infrared spectroscopy (FTIR) and theoretical interaction models showed that adenine in plasmid has a stronger capacity to sequester small Phen and Pyre molecules via a π-π attraction. Changes in Gibbs free energy (ΔG) suggest that the CT-PAH model reliably depicts the plasmid-PAH interaction through a noncovalently physical sorption mechanism. Considering the wide occurrence of PAHs and antibiotic resistant genes (ARGs) in the environment, our findings suggest that small-sized PAHs can well affect the behavior of ARGs via above-described noncovalent interactions.
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Affiliation(s)
- Fuxing Kang
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Xiaojie Hu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Juan Liu
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
| | - Yanzheng Gao
- Institute of Organic Contaminant Control and Soil Remediation, College of Resources and Environmental Sciences, Nanjing Agricultural University , Nanjing, Jiangsu 210095, China
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378
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379
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Kristensen K, Ettenhuber P, Eriksen JJ, Jensen F, Jørgensen P. The same number of optimized parameters scheme for determining intermolecular interaction energies. J Chem Phys 2015; 142:114116. [DOI: 10.1063/1.4915141] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Affiliation(s)
- Kasper Kristensen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Patrick Ettenhuber
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Janus Juul Eriksen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Frank Jensen
- Department of Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
| | - Poul Jørgensen
- Department of Chemistry, qLEAP Center for Theoretical Chemistry, Aarhus University, Langelandsgade 140, DK-8000 Aarhus C, Denmark
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380
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Beckmann PA, Mallory CW, Mallory FB, Rheingold AL, Wang X. Methoxy and Methyl Group Rotation: Solid-State NMR1H Spin-Lattice Relaxation, Electronic Structure Calculations, X-ray Diffractometry, and Scanning Electron Microscopy. Chemphyschem 2015; 16:1509-19. [DOI: 10.1002/cphc.201402716] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2014] [Revised: 02/17/2015] [Indexed: 11/05/2022]
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381
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Ranta J, Niskanen M, Kaunisto K, Manninen V, Mundy ME, Virkki K, Hakola H, Hukka TI, Lemmetyinen H. Monoisomeric phthalocyanine-fullerene dyads with e- and cis-3 addition pattern; synthesis, modeling, photovoltage and solar cell experiments. J PORPHYR PHTHALOCYA 2015. [DOI: 10.1142/s1088424614500928] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Synthesis and characterization of two A 2 B 2-type monoisomeric phthalocyanines and phthalocyanine-fullerene (Pc- C 60) dyads, in which fullerene is regioselectively attached to phthalocyanine with two linkers, are described. 1 H NMR spectroscopy results clearly indicate an e addition pattern of the fullerene moiety in trans-dyad 9, and apparently a cis-3 addition pattern in cis-dyad 10. The possible spatial arrangements of 9 and 10 were further examined by molecular modeling. The dyads have polar (– OH ) side chains on the fullerene side of the dyad providing a possibility to produce oriented donor–acceptor (D–A) Langmuir monolayers on aqueous subphase, which can be shifted onto a solid surface. When deposited on a solid electrode material, parallel vertical alignment of the phthalocyanine and fullerene moieties in 100% dyad monolayer was obtained and vertical electron transfer from Pc to C 60 upon photoexcitation was demonstrated. Introduction of the dyads as an oriented interfacial monolayer between the photoactive layer and metal anode improved the power conversion efficiency in inverted organic solar cells.
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Affiliation(s)
- Jenni Ranta
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Mika Niskanen
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Kimmo Kaunisto
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Venla Manninen
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - M. Elizabeth Mundy
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Kirsi Virkki
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Hanna Hakola
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Terttu I. Hukka
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
| | - Helge Lemmetyinen
- Department of Chemistry and Bioengineering, Tampere University of Technology, P. O. Box 541, FIN-33101 Tampere, Finland
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382
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Conrad JA, Gordon MS. Modeling Systems with π–π Interactions Using the Hartree–Fock Method with an Empirical Dispersion Correction. J Phys Chem A 2015; 119:5377-85. [DOI: 10.1021/jp510288k] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Justin A. Conrad
- Department
of Chemistry and
Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
| | - Mark S. Gordon
- Department
of Chemistry and
Ames Laboratory, Iowa State University, Ames, Iowa 50011, United States
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383
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Darvish Ganji M, Hosseini-khah SM, Amini-tabar Z. Theoretical insight into hydrogen adsorption onto graphene: a first-principles B3LYP-D3 study. Phys Chem Chem Phys 2015; 17:2504-11. [DOI: 10.1039/c4cp04399e] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
This work investigates hydrogen adsorption onto graphene flakes as suitable models of graphene within the framework of the B3LYP-D3 method.
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Affiliation(s)
- M. Darvish Ganji
- Nanoscale Simulation Group
- Nanotechnology Research Institute
- Babol Noshirvani University of Technology
- Babol
- Iran
| | | | - Z. Amini-tabar
- Department of Chemistry
- Islamic Azad University
- Qaemshahr
- Iran
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384
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Marin-Montesinos I, Paniagua JC, Vilaseca M, Urtizberea A, Luis F, Feliz M, Lin F, Van Doorslaer S, Pons M. Self-assembled trityl radical capsules – implications for dynamic nuclear polarization. Phys Chem Chem Phys 2015; 17:5785-94. [DOI: 10.1039/c4cp05225k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The OX63 radical forms supramolecular capsules hosting tetraalkylammonium cations. Extensive self-association is also observed under standard dynamic nuclear polarization conditions.
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Affiliation(s)
- I. Marin-Montesinos
- Biomolecular NMR laboratory
- Department of Organic Chemistry
- University of Barcelona
- Cluster Building, Barcelona Science Park
- 08028 Barcelona
| | - J. C. Paniagua
- Department of Physical Chemistry
- University of Barcelona
- 08028 Barcelona
- Spain
- Institute of Theoretical and Computational Chemistry
| | - M. Vilaseca
- Mass Spectrometry Core Facility
- Institute for Research in Biomedicine (IRB Barcelona)
- 08028 Barcelona
- Spain
| | - A. Urtizberea
- Instituto de Ciencia de Materiales de Aragón
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - F. Luis
- Instituto de Ciencia de Materiales de Aragón
- CSIC-Universidad de Zaragoza
- 50009 Zaragoza
- Spain
| | - M. Feliz
- Unitat de RMN
- Centres Científics i Tecnològics
- Universitat de Barcelona
- 08028 Barcelona
- Spain
| | - F. Lin
- Department of Physics
- University of Antwerp
- B-2610 Wilrijk
- Belgium
| | | | - M. Pons
- Biomolecular NMR laboratory
- Department of Organic Chemistry
- University of Barcelona
- Cluster Building, Barcelona Science Park
- 08028 Barcelona
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385
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Duan RF, Cheng L, Zhang QC, Ma LS, Ma HY, Yang JC. Mechanistic insight into the aerobic oxidation of benzyl alcohol catalyzed by the CuII–TEMPO catalyst in alkaline water solution. RSC Adv 2015. [DOI: 10.1039/c5ra18083j] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The benzyl alcohol oxidation to benzaldehyde in the alkaline water solution catalyzed by CuII/L–TEMPO catalyst is investigated by density functional method. The favorable mechanisms and the role for the water have also been predicted.
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Affiliation(s)
- R. F. Duan
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
| | - L. Cheng
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
| | - Q. C. Zhang
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
| | - L. S. Ma
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
| | - H. Y. Ma
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
| | - J. C. Yang
- Key Laboratory of Industrial Catalysis of the Inner Mongolia Autonomous Region
- Inner Mongolia University of Technology
- Huhhot 010051
- China
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386
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Hitaoka S, Chuman H, Yoshizawa K. A QSAR study on the inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs based on molecular orbital calculations. Org Biomol Chem 2015; 13:793-806. [DOI: 10.1039/c4ob01843e] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The inhibition mechanism of matrix metalloproteinase-12 by arylsulfone analogs is revealed using a comprehensive computational approach including docking simulations, molecular orbital calculations, and QSAR.
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Affiliation(s)
- Seiji Hitaoka
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
| | - Hiroshi Chuman
- Institute of Health Biosciences
- The University of Tokushima Graduate School
- Tokushima 770-8505
- Japan
| | - Kazunari Yoshizawa
- Institute for Materials Chemistry and Engineering and International Research Center for Molecular System
- Kyushu University
- Fukuoka 819-0395
- Japan
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387
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Tasinato N, Grimme S. Unveiling the non-covalent interactions of molecular homodimers by dispersion-corrected DFT calculations and collision-induced broadening of ro-vibrational transitions: application to (CH2F2)2 and (SO2)2. Phys Chem Chem Phys 2015; 17:5659-69. [DOI: 10.1039/c4cp05680a] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
(CH2F2)2 and (SO2)2 are investigated using DFT-D3 computations, and experimental dissociation energies are determined by TDL-IR spectroscopy. DFT-D3 dramatically improves over uncorrected DFT.
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Affiliation(s)
- Nicola Tasinato
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari Venezia
- I-30123 Venezia
- Italy
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry
- Institut für Physikalische und Theoretische Chemie der Universität Bonn
- D-53115 Bonn
- Germany
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388
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Sladek V, Holka F, Tvaroška I. Ab initio modelling of the anomeric and exo anomeric effects in 2-methoxytetrahydropyran and 2-methoxythiane corrected for intramolecular BSSE. Phys Chem Chem Phys 2015; 17:18501-13. [DOI: 10.1039/c5cp02191j] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Oxygen substitution in 2-methoxytetrahydropyran by sulphur in 2-methoxythiane approximately doubles the anomeric effect, which slows down enzymatic processing of 2-methoxythiane.
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Affiliation(s)
- Vladimir Sladek
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
| | - Filip Holka
- Faculty of Materials Science and Technology in Trnava
- Slovak University of Technology in Bratislava
- SK-917 24 Trnava
- Slovakia
| | - Igor Tvaroška
- Institute of Chemistry
- Slovak Academy of Sciences
- SK-845 38 Bratislava
- Slovakia
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389
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Brandenburg JG, Hochheim M, Bredow T, Grimme S. Low-Cost Quantum Chemical Methods for Noncovalent Interactions. J Phys Chem Lett 2014; 5:4275-4284. [PMID: 26273974 DOI: 10.1021/jz5021313] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The efficient and reasonably accurate description of noncovalent interactions is important for various areas of chemistry, ranging from supramolecular host-guest complexes and biomolecular applications to the challenging task of crystal structure prediction. While London dispersion inclusive density functional theory (DFT-D) can be applied, faster "low-cost" methods are required for large-scale applications. In this Perspective, we present the state-of-the-art of minimal basis set, semiempirical molecular-orbital-based methods. Various levels of approximations are discussed based either on canonical Hartree-Fock or on semilocal density functionals. The performance for intermolecular interactions is examined on various small to large molecular complexes and organic solids covering many different chemical groups and interaction types. We put the accuracy of low-cost methods into perspective by comparing with first-principle density functional theory results. The mean unsigned deviations of binding energies from reference data are typically 10-30%, which is only two times larger than those of DFT-D. In particular, for neutral or moderately polar systems, many of the tested methods perform very well, while at the same time, computational savings of up to 2 orders of magnitude can be achieved.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Manuel Hochheim
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Thomas Bredow
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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390
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Goerigk L, Collyer CA, Reimers JR. Recommending Hartree–Fock Theory with London-Dispersion and Basis-Set-Superposition Corrections for the Optimization or Quantum Refinement of Protein Structures. J Phys Chem B 2014; 118:14612-26. [DOI: 10.1021/jp510148h] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lars Goerigk
- School
of Chemistry, The University of Melbourne, Parkville, Victoria 3010, Australia
| | - Charles A. Collyer
- School
of Molecular Bioscience, The University of Sydney, Sydney, New South Wales 2006, Australia
| | - Jeffrey R. Reimers
- Centre
for Quantum and Molecular Structure, College of Sciences, Shanghai University, Shanghai 200444, China
- School
of Physics and Advanced Materials, The University of Technology, Sydney, New South Wales 2007, Australia
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391
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Bauer CA, Grimme S. Elucidation of Electron Ionization Induced Fragmentations of Adenine by Semiempirical and Density Functional Molecular Dynamics. J Phys Chem A 2014; 118:11479-84. [DOI: 10.1021/jp5096618] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Christoph Alexander Bauer
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical
Chemistry, Institut für Physikalische und Theoretische Chemie der Rheinischen Friedrich-Wilhelms-Universität Bonn, Beringstrasse 4, D-53115 Bonn, Germany
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392
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Mashima A, Kurahashi M, Sasahara K, Yoshida T, Chuman H. Connecting Classical QSAR and LERE Analyses Using Modern Molecular Calculations, LERE-QSAR (VI): Hydrolysis of Substituted Hippuric Acid Phenyl Esters by Trypsin. Mol Inform 2014; 33:802-14. [PMID: 27485426 DOI: 10.1002/minf.201400099] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/14/2014] [Indexed: 11/08/2022]
Abstract
The reaction mechanism of trypsin was studied by applying DFT and ab initio molecular orbital (MO) calculations to complexes of trypsin with a congeneric series of eight para-substituted hippuric acid phenyl esters, for which a previous quantitative structureactivity relationship (QSAR) study revealed nice linearity of Hammett substitution constant σ(-) with logarithmic values of the MichaelisMenten and catalytic rate constants. Based on the LERE procedure, we performed QSAR analyses on each elementary reaction step during the acylation process. The present calculations showed that the rate-determining step during the acylation process is the transition state (TS) between the enzymesubstrate complex (ES) and tetrahedral intermediate (TET), and that the proton transfer occurs from Ser195 to His57, not between His57 and Asp102. The LERE-QSAR analysis statistically suggested that the variation of overall free-energy changes leading to formation of TS is governed mostly by that of activation energies required to form TS from ES. In spite of a very limited number of congeneric ligands in the current work, it is critically essential to clarify and verify physicochemical meanings of a typical QSAR/Chemoinformatics parameter, Hammett σ(-) based on quantum chemical calculations on the proteinligand kinetics; how Hammett σ(-) behaves in terms of proteinligand interaction energies.
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Affiliation(s)
- Akira Mashima
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Masahiro Kurahashi
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Katsunori Sasahara
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Tatsusada Yoshida
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508
| | - Hiroshi Chuman
- Institute of Health Biosciences, The University of Tokushima Graduate School, 1-78 Shomachi, Tokushima 770-8505, Japan phone/fax: +81-88-633-7257/+81-88-633-9508.
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393
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Lorenz M, Civalleri B, Maschio L, Sgroi M, Pullini D. Benchmarking dispersion and geometrical counterpoise corrections for cost-effective large-scale DFT calculations of water adsorption on graphene. J Comput Chem 2014; 35:1789-800. [DOI: 10.1002/jcc.23686] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 06/20/2014] [Accepted: 06/27/2014] [Indexed: 01/22/2023]
Affiliation(s)
- Marco Lorenz
- Dipartimento di Chimica; Università di Torino; Via P. Giuria 5 I-10125 Torino Italy
| | - Bartolomeo Civalleri
- Dipartimento di Chimica; Università di Torino; Via P. Giuria 5 I-10125 Torino Italy
| | - Lorenzo Maschio
- Dipartimento di Chimica; Università di Torino; Via P. Giuria 5 I-10125 Torino Italy
| | - Mauro Sgroi
- Group Materials Lab, Centro Ricerche FIAT; Strada Torino 50, 10043 Orbassano Torino Italy
| | - Daniele Pullini
- Group Materials Lab, Centro Ricerche FIAT; Strada Torino 50, 10043 Orbassano Torino Italy
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394
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Brandenburg JG, Grimme S. Accurate Modeling of Organic Molecular Crystals by Dispersion-Corrected Density Functional Tight Binding (DFTB). J Phys Chem Lett 2014; 5:1785-1789. [PMID: 26273854 DOI: 10.1021/jz500755u] [Citation(s) in RCA: 122] [Impact Index Per Article: 12.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The ambitious goal of organic crystal structure prediction challenges theoretical methods regarding their accuracy and efficiency. Dispersion-corrected density functional theory (DFT-D) in principle is applicable, but the computational demands, for example, to compute a huge number of polymorphs, are too high. Here, we demonstrate that this task can be carried out by a dispersion-corrected density functional tight binding (DFTB) method. The semiempirical Hamiltonian with the D3 correction can accurately and efficiently model both solid- and gas-phase inter- and intramolecular interactions at a speed up of 2 orders of magnitude compared to DFT-D. The mean absolute deviations for interaction (lattice) energies for various databases are typically 2-3 kcal/mol (10-20%), that is, only about two times larger than those for DFT-D. For zero-point phonon energies, small deviations of <0.5 kcal/mol compared to DFT-D are obtained.
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Affiliation(s)
- Jan Gerit Brandenburg
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
| | - Stefan Grimme
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Rheinische Friedrich-Wilhelms Universität Bonn, Beringstraße 4, 53115 Bonn, Germany
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395
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Wang X, Mallory FB, Mallory CW, Odhner HR, Beckmann PA. Solid state ¹H spin-lattice relaxation and isolated-molecule and cluster electronic structure calculations in organic molecular solids: the relationship between structure and methyl group and t-butyl group rotation. J Chem Phys 2014; 140:194304. [PMID: 24852535 DOI: 10.1063/1.4874157] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
We report ab initio density functional theory electronic structure calculations of rotational barriers for t-butyl groups and their constituent methyl groups both in the isolated molecules and in central molecules in clusters built from the X-ray structure in four t-butyl aromatic compounds. The X-ray structures have been reported previously. We also report and interpret the temperature dependence of the solid state (1)H nuclear magnetic resonance spin-lattice relaxation rate at 8.50, 22.5, and 53.0 MHz in one of the four compounds. Such experiments for the other three have been reported previously. We compare the computed barriers for methyl group and t-butyl group rotation in a central target molecule in the cluster with the activation energies determined from fitting the (1)H NMR spin-lattice relaxation data. We formulate a dynamical model for the superposition of t-butyl group rotation and the rotation of the t-butyl group's constituent methyl groups. The four compounds are 2,7-di-t-butylpyrene, 1,4-di-t-butylbenzene, 2,6-di-t-butylnaphthalene, and 3-t-butylchrysene. We comment on the unusual ground state orientation of the t-butyl groups in the crystal of the pyrene and we comment on the unusually high rotational barrier of these t-butyl groups.
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Affiliation(s)
- Xianlong Wang
- Key Laboratory for NeuroInformation of Ministry of Education, School of Life Science and Technology, University of Electronic Science and Technology of China, 4 North Jianshe Rd., 2nd Section, Chengdu 610054, China
| | - Frank B Mallory
- Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Clelia W Mallory
- Department of Chemistry, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Hosanna R Odhner
- Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
| | - Peter A Beckmann
- Department of Physics, Bryn Mawr College, 101 North Merion Ave., Bryn Mawr, Pennsylvania 19010-2899, USA
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396
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Kruse H, Havrila M, Šponer J. QM Computations on Complete Nucleic Acids Building Blocks: Analysis of the Sarcin–Ricin RNA Motif Using DFT-D3, HF-3c, PM6-D3H, and MM Approaches. J Chem Theory Comput 2014; 10:2615-29. [DOI: 10.1021/ct500183w] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Affiliation(s)
- Holger Kruse
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
| | - Marek Havrila
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
| | - Jiřı́ Šponer
- CEITEC
− Central European Institute of Technology, Campus Bohunice, Kamenice
5, 625 00 Brno, Czech Republic
- Institute
of Biophysics, Academy of Sciences of the Czech Republic, Královopolská
135, 612 65 Brno, Czech Republic
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397
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Peláez WJ, Pepino AJ, Argüello GA, Pinho e Melo TMVD. 1-Methyl-5-(trifluoromethyl)azafulvenium Methide, an Intermediate That Undergoes Reaction through “Unusual”cis-exo-1,3- andtrans-exo-1,7-Cycloadditions. European J Org Chem 2014. [DOI: 10.1002/ejoc.201301922] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
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398
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Sure R, Antony J, Grimme S. Blind prediction of binding affinities for charged supramolecular host-guest systems: achievements and shortcomings of DFT-D3. J Phys Chem B 2014; 118:3431-40. [PMID: 24588346 DOI: 10.1021/jp411616b] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Association free energies ΔGa are calculated for two different types of host-guest systems, the rigid cucurbit[7]uril (CB7) and the basket shaped octa-acid (OA), and a number of charged guest molecules each by quantum chemical methods from first principles in the context of a recent blind test challenge (SAMPL4). For CB7, the overall agreement between theory and experiment is excellent. In comparison with all other submitted calculated relative ΔGa,rel values for this part of the blind test, our results ranked on top. Modeling the binding free energy in the case of the OA host mainly suffers from the problem that the binding situation is undefined with respect to the charge state and due to its intrinsic flexibility the host-guest complex is not represented well by a single configuration, but qualitative features of the binding process such as the proper binding orientation and the order of magnitude of ΔGa are represented in accord with the experimental expectations even though an accurate ranking is not possible.
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Affiliation(s)
- Rebecca Sure
- Mulliken Center for Theoretical Chemistry, Institut für Physikalische und Theoretische Chemie, Universität Bonn , Beringstr. 4, D-53115 Bonn, Germany
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399
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Van Houteghem M, Ghysels A, Verstraelen T, Poelmans W, Waroquier M, Van Speybroeck V. Critical analysis of the accuracy of models predicting or extracting liquid structure information. J Phys Chem B 2014; 118:2451-70. [PMID: 24512612 DOI: 10.1021/jp411737s] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This work aims at a critical assessment of properties predicting or extracting information on the density and structure of liquids. State-of-the-art NVT and NpT molecular dynamics (MD) simulations have been performed on five liquids: methanol, chloroform, acetonitrile, tetrahydrofuran, and ethanol. These simulations allow the computation of properties based on first principles, including the equilibrium density and radial distribution functions (RDFs), characterizing the liquid structure. Refinements have been incorporated in the MD simulations by taking into account basis set superposition errors (BSSE). An extended BSSE model for an instantaneous evaluation of the BSSE corrections has been proposed, and their impact on the liquid properties has been assessed. If available, the theoretical RDFs have been compared with the experimentally derived RDFs. For some liquids, significant discrepancies have been observed, and a profound but critical investigation is presented to unravel the origin of these deficiencies. This discussion is focused on tetrahydrofuran where the experiment reveals some prominent peaks completely missing in any MD simulation. Experiments providing information on liquid structure consist mainly of neutron diffraction measurements offering total structure factors as the primary observables. The splitting of these factors in reciprocal space into intra- and intermolecular contributions is extensively discussed, together with their sensitivity in reproducing correct RDFs in coordinate space.
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Affiliation(s)
- Marc Van Houteghem
- Center for Molecular Modeling, QCMM Alliance Ghent-Brussels, Ghent University , Technologiepark 903, B-9052 Zwijnaarde, Belgium
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400
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Goerigk L. How Do DFT-DCP, DFT-NL, and DFT-D3 Compare for the Description of London-Dispersion Effects in Conformers and General Thermochemistry? J Chem Theory Comput 2014; 10:968-80. [DOI: 10.1021/ct500026v] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Affiliation(s)
- Lars Goerigk
- School
of Chemistry, The University of Sydney, New South Wales 2006, Australia
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