201
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Abstract
Interest in molecular crystals has grown thanks to their relevance to pharmaceuticals, organic semiconductor materials, foods, and many other applications. Electronic structure methods have become an increasingly important tool for modeling molecular crystals and polymorphism. This article reviews electronic structure techniques used to model molecular crystals, including periodic density functional theory, periodic second-order Møller-Plesset perturbation theory, fragment-based electronic structure methods, and diffusion Monte Carlo. It also discusses the use of these models for predicting a variety of crystal properties that are relevant to the study of polymorphism, including lattice energies, structures, crystal structure prediction, polymorphism, phase diagrams, vibrational spectroscopies, and nuclear magnetic resonance spectroscopy. Finally, tools for analyzing crystal structures and intermolecular interactions are briefly discussed.
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Affiliation(s)
- Gregory J O Beran
- Department of Chemistry, University of California , Riverside, California 92521, United States
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202
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Sedlak R, Stasyuk OA, Fonseca Guerra C, Řezáč J, Růžička A, Hobza P. New Insight into the Nature of Bonding in the Dimers of Lappert's Stannylene and Its Ge Analogs: A Quantum Mechanical Study. J Chem Theory Comput 2016; 12:1696-704. [PMID: 26953594 DOI: 10.1021/acs.jctc.6b00065] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The strength and nature of the connection in Lappert's stannylene dimer ({Sn[CH(SiMe3)2]2}2) and its smaller analogs, simplified stannylenes, as well as similar Ge complexes were studied by means of DFT-D3 calculations, energy decomposition analysis (EDA), electrostatic potential (ESP), and natural population analysis. The trans-bent structure of the investigated molecules was rationalized by means of EDA, ESP, and molecular orbital (MO) analyses. The different ESPs for the monomers studied are a result of different hybridization of the Sn (Ge) atoms. The comparably strong stabilization in the largest and the smallest systems with a dramatically different substituent size is explained by the different nature of the binding between monomers. For all complexes, it has been found that the total attractive interaction is mostly provided by the electrostatic component (>50%), followed by orbital interaction and dispersion. In the largest molecule (Lappert's stannylene), the dispersion interaction plays a more significant role in stabilization and its magnitude is comparable to that of orbital interaction; on the other hand in the smallest molecule (SnH2), where bulky substituents are replaced by H only, the dispersion energy is less important and the E-E bond is more of a charge-transfer character, caused by donor-acceptor orbital interactions. The charge transfer in Ge dimers is greater than in the Sn ones due to shorter distances between monomers, which cause better ⟨HOMO/LUMO⟩ overlaps. The easier dimerization of Lappert's stannylene as compared to Kira's ({Sn[(Me3Si)2CHCH2CH2CH(SiMe3)2-κ(2)C,C']}) stannylene is explained by the different orientation of their substituents-asymmetry promotes dimerization.
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Affiliation(s)
- Robert Sedlak
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic
| | - Olga A Stasyuk
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Célia Fonseca Guerra
- Department of Theoretical Chemistry and Amsterdam Center for Multiscale Modeling, VU Amsterdam , De Boelelaan 1083, 1081 HV Amsterdam, The Netherlands
| | - Jan Řezáč
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry, Faculty of Chemical Technology, University of Pardubice , Studentská 573, CZ-532 10, Pardubice, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry , Academy of Sciences of the Czech Republic, 166 10 Prague 6, Czech Republic.,Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University , 771 46 Olomouc, Czech Republic
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203
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Abstract
Symmetry-adapted perturbation theory (SAPT) provides a unique set of advantages for parameterizing next-generation force fields from first principles. SAPT provides a direct, basis-set superposition error free estimate of molecular interaction energies, a physically intuitive energy decomposition, and a seamless transition to an asymptotic picture of intermolecular interactions. These properties have been exploited throughout the literature to develop next-generation force fields for a variety of applications, including classical molecular dynamics simulations, crystal structure prediction, and quantum dynamics/spectroscopy. This review provides a brief overview of the formalism and theory of SAPT, along with a practical discussion of the various methodologies utilized to parameterize force fields from SAPT calculations. It also highlights a number of applications of SAPT-based force fields for chemical systems of particular interest. Finally, the review ends with a brief outlook on the future opportunities and challenges that remain for next-generation force fields based on SAPT.
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Affiliation(s)
- Jesse G McDaniel
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706;
| | - J R Schmidt
- Theoretical Chemistry Institute and Department of Chemistry, University of Wisconsin-Madison, Madison, Wisconsin 53706;
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204
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Scherrer A, Sebastiani D. Moment expansion of the linear density-density response function. J Comput Chem 2016; 37:665-74. [DOI: 10.1002/jcc.24248] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2015] [Revised: 10/19/2015] [Accepted: 10/21/2015] [Indexed: 12/31/2022]
Affiliation(s)
- Arne Scherrer
- Institute of Theoretical Chemistry, Martin-Luther-University Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
| | - Daniel Sebastiani
- Institute of Theoretical Chemistry, Martin-Luther-University Halle-Wittenberg; Von-Danckelmann-Platz 4 06120 Halle (Saale) Germany
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205
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Vazhappilly T, Marjolin A, Jordan KD. Theoretical Characterization of the Minimum-Energy Structure of (SF6)2. J Phys Chem B 2016; 120:1788-92. [PMID: 26619257 DOI: 10.1021/acs.jpcb.5b09419] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
MP2 and symmetry-adapted perturbation theory calculations are used in conjunction with the aug-cc-pVQZ basis set to characterize the SF6 dimer. Both theoretical methods predict the global minimum structure to be of C2 symmetry, lying 0.07-0.16 kJ/mol below a C2h saddle point structure, which, in turn, is predicted to lie energetically 0.4-0.5 kJ/mol below the lowest-energy D2d structure. This is in contrast with IR spectroscopic studies that infer an equilibrium D2d structure. It is proposed that the inclusion of vibrational zero-point motion gives an averaged structure of D2d symmetry.
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Affiliation(s)
- Tijo Vazhappilly
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Aude Marjolin
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
| | - Kenneth D Jordan
- Department of Chemistry, University of Pittsburgh , Pittsburgh, Pennsylvania 15260, United States
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206
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Affiliation(s)
- Michal H. Kolář
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Institute
of Neuroscience and Medicine (INM-9) and Institute for Advanced Simulations
(IAS-5), Forschungszentrum Jülich GmbH, 52428 Jülich, Federal Republic of Germany
| | - Pavel Hobza
- Institute
of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, Flemingovo nám. 2, 16610 Prague, Czech Republic
- Department
of Physical Chemistry, Regional Centre of Advanced Technologies and
Materials, Palacky University, 771 46 Olomouc, Czech Republic
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207
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Berg L, Mishra BK, Andersson CD, Ekström F, Linusson A. The Nature of Activated Non-classical Hydrogen Bonds: A Case Study on Acetylcholinesterase-Ligand Complexes. Chemistry 2016; 22:2672-81. [DOI: 10.1002/chem.201503973] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2015] [Indexed: 01/25/2023]
Affiliation(s)
- Lotta Berg
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
| | | | | | - Fredrik Ekström
- CBRN Defense and Security; Swedish Defense Research Agency; 906 21 Umeå Sweden
| | - Anna Linusson
- Department of Chemistry; Umeå University; 901 87 Umeå Sweden
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208
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McDaniel JG, Choi E, Son CY, Schmidt JR, Yethiraj A. Conformational and Dynamic Properties of Poly(ethylene oxide) in an Ionic Liquid: Development and Implementation of a First-Principles Force Field. J Phys Chem B 2016; 120:231-43. [DOI: 10.1021/acs.jpcb.5b10065] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Jesse G. McDaniel
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Eunsong Choi
- Department
of Physics, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Chang-Yun Son
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - J. R. Schmidt
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- Department
of Chemistry, University of Wisconsin, Madison, Wisconsin 53706, United States
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209
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Abstract
David Craig (1919–2015) left us with a lasting legacy concerning basic understanding of chemical spectroscopy and bonding. This is expressed in terms of some of the recent achievements of my own research career, with a focus on integration of Craig’s theories with those of Noel Hush to solve fundamental problems in photosynthesis, molecular electronics (particularly in regard to the molecules synthesized by Maxwell Crossley), and self-assembled monolayer structure and function. Reviewed in particular is the relation of Craig’s legacy to: the 50-year struggle to assign the visible absorption spectrum of arguably the world’s most significant chromophore, chlorophyll; general theories for chemical bonding and structure extending Hush’s adiabatic theory of electron-transfer processes; inelastic electron-tunnelling spectroscopy (IETS); chemical quantum entanglement and the Penrose–Hameroff model for quantum consciousness; synthetic design strategies for NMR quantum computing; Gibbs free-energy measurements and calculations for formation and polymorphism of organic self-assembled monolayers on graphite surfaces from organic solution; and understanding the basic chemical processes involved in the formation of gold surfaces and nanoparticles protected by sulfur-bound ligands, ligands whose form is that of Au0-thiyl rather than its commonly believed AuI-thiolate tautomer.
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210
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Lo R, Švec P, Růžičková Z, Růžička A, Hobza P. On the nature of the stabilisation of the E⋯π pnicogen bond in the SbCl3⋯toluene complex. Chem Commun (Camb) 2016; 52:3500-3. [DOI: 10.1039/c5cc10363k] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The characteristic features of pnicogen bonding are due to the concert action of attractive dispersion and electrostatic interactions.
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Affiliation(s)
- Rabindranath Lo
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6
- Czech Republic
| | - Petr Švec
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- Pardubice
- Czech Republic
| | - Zdeňka Růžičková
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- Pardubice
- Czech Republic
| | - Aleš Růžička
- Department of General and Inorganic Chemistry
- Faculty of Chemical Technology
- University of Pardubice
- Pardubice
- Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry
- Academy of Sciences of the Czech Republic
- 166 10 Prague 6
- Czech Republic
- Regional Centre of Advanced Technologies and Materials
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211
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Parrish RM, Parker TM, Sherrill CD. Chemical Assignment of Symmetry-Adapted Perturbation Theory Interaction Energy Components: The Functional-Group SAPT Partition. J Chem Theory Comput 2015; 10:4417-31. [PMID: 26588139 DOI: 10.1021/ct500724p] [Citation(s) in RCA: 87] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Recently, we introduced an effective atom-pairwise partition of the many-body symmetry-adapted perturbation theory (SAPT) interaction energy decomposition, producing a method known as atomic SAPT (A-SAPT) [Parrish, R. M.; Sherrill, C. D. J. Chem. Phys. 2014, 141, 044115]. A-SAPT provides ab initio atom-pair potentials for force field development and also automatic visualizations of the spatial contributions of noncovalent interactions, but often has difficulty producing chemically useful partitions of the electrostatic energy, due to the buildup of oscillating partial charges on adjacent functional groups. In this work, we substitute chemical functional groups in place of atoms as the relevant local quasiparticles in the partition, resulting in a functional-group-pairwise partition denoted as functional-group SAPT (F-SAPT). F-SAPT assigns integral sets of local occupied electronic orbitals and protons to chemical functional groups and linking σ bonds. Link-bond contributions can be further assigned to chemical functional groups to simplify the analysis. This approach yields a SAPT partition between pairs of functional groups with integral charge (usually neutral), preventing oscillations in the electrostatic partition. F-SAPT qualitatively matches chemical intuition and the cut-and-cap fragmentation technique but additionally yields the quantitative many-body SAPT interaction energy. The conceptual simplicity, chemical utility, and computational efficiency of F-SAPT is demonstrated in the context of phenol dimer, proflavine(+)-DNA intercalation, and a cucurbituril host-guest inclusion complex.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - Trent M Parker
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology , Atlanta, Georgia 30332-0400, United States
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212
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Rodríguez-Cantano R, Pérez de Tudela R, Bartolomei M, Hernández MI, Campos-Martínez J, González-Lezana T, Villarreal P, Hernández-Rojas J, Bretón J. Coronene molecules in helium clusters: Quantum and classical studies of energies and configurations. J Chem Phys 2015; 143:224306. [DOI: 10.1063/1.4936414] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | | | - Marta I. Hernández
- Instituto de Física Fundamental, IFF-CSIC, Serrano 123, 28006 Madrid, Spain
| | | | | | - Pablo Villarreal
- Instituto de Física Fundamental, IFF-CSIC, Serrano 123, 28006 Madrid, Spain
| | | | - José Bretón
- Departamento de Física and IUdEA, Universidad de La Laguna, 38205 Tenerife, Spain
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213
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Šebesta F, Burda JV. Reduction Process of Tetraplatin in the Presence of Deoxyguanosine Monophosphate (dGMP): A Computational DFT Study. Chemistry 2015; 22:1037-47. [PMID: 26663432 DOI: 10.1002/chem.201503555] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2015] [Revised: 10/15/2015] [Indexed: 01/01/2023]
Abstract
The reduction mechanism of [Pt(IV) (dach)Cl4 ] (dach=diaminocyclohexyl) in the presence of dGMP was studied. The first step is substitution of a chloro ligand by dGMP, followed by nucleophilic attack of a phosphate or sugar oxygen atom to the C8-position of guanine. Subsequent reduction forms the [Pt(II) (dach)Cl2 ] complex. The whole process is completed by a hydrolysis. Two different pathways for the substitution reaction were examined: a direct associative and a Basolo-Pearson autocatalytic mechanism. All the explored structures were optimized at the B3LYP-D3/6-31G(d) level and by using the COSMO solvation model with Klamt's radii. Single-point energetics was determined at the B3LYP-GD3BJ/6-311++G(2df,2pd)/PCM/scaled-UAKS level. Activation barriers were used for an estimation of the rate constants and these were compared with experimental values. It was found that the rate-determining step is the nucleophilic attack with a slightly faster performance in the 3'-dGMP branch than in the case of 5'-dGMP with activation barriers of 21.1 and 20.4 kcal mol(-1) (experimental: 23.8 and 23.2 kcal mol(-1) ). The reduction reaction is connected with an electron flow from guanine. The product of the reduction reaction is a chelate structure, which dissociates within the last reaction step, that is, a hydrolysis reaction. The whole redox process (substitution, reduction, and hydrolysis) is exergonic by 34 and 28 kcal mol(-1) for 5'-dGMP and 3'-dGMP, respectively.
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Affiliation(s)
- Filip Šebesta
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic
| | - Jaroslav V Burda
- Department of Chemical Physics and Optics, Faculty of Mathematics and Physics, Charles University, Ke Karlovu 3, 121 16, Prague 2, Czech Republic.
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214
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Podeszwa R, Bukowski R, Szalewicz K. Density-Fitting Method in Symmetry-Adapted Perturbation Theory Based on Kohn-Sham Description of Monomers. J Chem Theory Comput 2015; 2:400-12. [PMID: 26626527 DOI: 10.1021/ct050304h] [Citation(s) in RCA: 144] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We present a new implementation of symmetry-adapted perturbation theory of intermolecular interactions based on Kohn-Sham description of monomers. With density-fitting of molecular integrals, the scaling of the computational cost of the method is reduced from the sixth to the fifth power of the system size. Computational requirements of some operations scaling as the fifth power have also been significantly reduced. The new method allows an accurate treatment of molecules consisting of as many as a few dozen of atoms, using both nonhybrid and hybrid density functionals.
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Affiliation(s)
- Rafał Podeszwa
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716
| | - Robert Bukowski
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716
| | - Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716
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215
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Cybulski H, Sadlej J. Symmetry-Adapted Perturbation-Theory Interaction-Energy Decomposition for Hydrogen-Bonded and Stacking Structures. J Chem Theory Comput 2015; 4:892-7. [PMID: 26621230 DOI: 10.1021/ct800067m] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
This letter reports the computational ab initio studies on the stacked and hydrogen-bonded geometries of the uracil dimer and pyrimidine···p-benzoquinone complex with a special regard to the ratios of different interaction-energy terms calculated by means of the symmetry-adapted perturbation theory (SAPT). In the hydrogen-bonded systems the absolute value of the dispersion term constitutes approximately half of the absolute value of the total SAPT0 interaction energy, while in the stacking complexes the ratio of the dispersion to the total interaction energy is much larger, ca. 1.2-2.0. Our SAPT results are compared with the DFT-SAPT results published recently by the Hobza group (J. Chem. Phys. 2007, 127, 075104), and the role of the dispersion contribution in stacking and hydrogen-bonded arrangements is discussed. The methodological part of this letter presents the influence of counterpoise corrections in the optimization procedure on the geometries of the systems and the calculated SAPT contributions.
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Affiliation(s)
- Hubert Cybulski
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
| | - Joanna Sadlej
- Department of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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216
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Misquitta AJ, Stone AJ. Accurate Induction Energies for Small Organic Molecules: 1. Theory. J Chem Theory Comput 2015; 4:7-18. [PMID: 26619975 DOI: 10.1021/ct700104t] [Citation(s) in RCA: 63] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
The induction energy often plays a very important role in determining the structure and properties of clusters of organic molecules, but only in recent years has an effort been made to include this energy in such calculations, notably in the field of organic crystal structure prediction. In this paper and the following one in this issue we provide ab initio methods suitable for the accurate inclusion of the induction energy for molecules containing as many as 30 atoms or so. These techniques are based on Symmetry-Adapted Perturbation Theory using Density Functional Theory [SAPT(DFT)] and use distributed polarizabilities computed using the recently developed density-fitting algorithm with constrained refinement. With this approach we are able to obtain induction models of varying complexity and study the effects of overlap and related numerical issues. Basis set effects on the exact and asymptotic induction energies are investigated, and the roles of higher-order induction energies and many-body effects are explored.
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Affiliation(s)
- Alston J Misquitta
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, U.K., and University College London, 20 Gordon Street, London WC1H 0AJ, U.K
| | - Anthony J Stone
- University Chemical Laboratory, Lensfield Road, Cambridge CB2 1EW, U.K., and University College London, 20 Gordon Street, London WC1H 0AJ, U.K
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217
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Berka K, Laskowski R, Riley KE, Hobza P, Vondrášek J. Representative Amino Acid Side Chain Interactions in Proteins. A Comparison of Highly Accurate Correlated ab Initio Quantum Chemical and Empirical Potential Procedures. J Chem Theory Comput 2015; 5:982-92. [PMID: 26609607 DOI: 10.1021/ct800508v] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
Abstract
Interactions between amino acid side chains play a crucial role both within a folded protein and between the interacting protein molecules. Here we have selected a representative set of 24 of the 400 (20 × 20) possible interacting side chain pairs based on data from Atlas of Protein Side-Chain Interactions. For each pair, we obtained its most favorable interaction geometry from the structural data and computed the interaction energy in the gas phase using several different, commonly used, ab initio and force field methods, namely Møller-Plesset perturbation theory (MP2), density functional theory combined with symmetry-adapted perturbation theory (DFT-SAPT), density functional theory empirically augmented with an empirical dispersion term (DFT-D), and empirical potentials using the OPLS-AA/L and Amber03 force fields. All the methods were compared against a reference method taken to be the CCSD(T) level of theory extrapolated to the complete basis set limit. We found a high degree of agreement between the different methods, even though the range of binding energies obtained was extremely large. The most computationally intensive methods yielded the best results. Among the less computationally time-consuming methods, the DFT-D method as well as parm03 force field provided consistently good results when compared to the reference values. We also tested how representative the chosen geometries of the side chains were and investigated the effect on the binding energies of the dielectric constant of the surrounding medium.
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Affiliation(s)
- Karel Berka
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Roman Laskowski
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Kevin E Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
| | - Jiří Vondrášek
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Complex Molecular Systems and Biomolecules, Flemingovo náměstí 2, Prague 6, 166 10 Czech Republic, Department of Physical and Macromolecular Chemistry, Faculty of Natural Sciences, Charles University in Prague, Hlavova 8, Prague 2, 128 43 Czech Republic, EMBL Outstation - Hinxton, European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, U.K., and Department of Chemistry, P.O. Box 23346, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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218
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Abstract
The role of π-π interactions in controlling the reactivity and selectivity of a chemical reaction is only recently being explored, even though their ubiquitous role in the structural aspects is well known. We have studied Bergman cyclisation focusing on the effect of π-π interactions on the activation barrier and the variation of π-π interactions along the reaction coordinate. We used enediyne substrates that contain phenyl groups connected to the reaction centres (C1 and C6 atoms), separated by 0, 1 and 2 linker groups. The main difference between the substrates is that the Ph groups enjoy different flexibility to accommodate the changes occurring during the progress of the reaction. The path length of the minimum energy path is increased - shortest in the least flexible substrate (a) and longer in the more flexible ones (c, d and e). We calculated the interaction between the Ph groups, the π-π interaction, using BP86-D3BJ, B3LYP-D3BJ, M06-2X, B2PLYP-D3BJ, SCS-MP2, and SAPT. The BP86-D3BJ was found to be sufficiently accurate with a mean absolute deviation of 0.26 kcal mol(-1) with respect to the SAPT2+3 values. The variation in the π-π interaction shows different behaviour in a-e, and this can be correlated with the flexibility of the Ph groups to orient themselves to maintain the optimal relative orientation while conforming to the changes in the reaction coordinate. We analysed the relative orientation of the phenyl groups using certain geometric parameters that showed that when Ph groups can attain a relative orientation close to that of the free dimer, the interaction is maximum. Energy decomposition analysis using SAPT showed that the dispersive interaction is the major contributor (50-60%) to the attractive forces. The π-π interactions influenced the overall activation energy, either by destabilising the substrates or by stabilising the TS - resulting in a variation of about 3.5 kcal mol(-1) in activation energies in a-e. The effect of substituents of different electronic nature was assessed which showed that electron donating and electron withdrawing substituents increase the π-π interactions; however, the TS is more stabilised and hence activation energies are increased.
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Affiliation(s)
- Saibal Jana
- Department of Chemistry, Indian Institute of Technology Kharagpur, Kharagpur 721302, India.
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219
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de Lara-Castells MP, Bartolomei M, Mitrushchenkov AO, Stoll H. Transferability and accuracy by combining dispersionless density functional and incremental post-Hartree-Fock theories: Noble gases adsorption on coronene/graphene/graphite surfaces. J Chem Phys 2015; 143:194701. [DOI: 10.1063/1.4935511] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
| | | | - Alexander O. Mitrushchenkov
- Laboratoire Modélisation et Simulation Multi Echelle, Université Paris-Est, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Hermann Stoll
- Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart, Germany
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220
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de Lara-Castells MP, Mitrushchenkov AO. Nuclear Bound States of Molecular Hydrogen Physisorbed on Graphene: An Effective Two-Dimensional Model. J Phys Chem A 2015; 119:11022-32. [DOI: 10.1021/acs.jpca.5b09208] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
| | - Alexander O. Mitrushchenkov
- Laboratoire
Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, Université Paris-Est, 5 bd Descartes, 77454 Marne-la-Vallée, France
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221
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de Lara-Castells MP, Mitrushchenkov AO, Stoll H. Combining density functional and incremental post-Hartree-Fock approaches for van der Waals dominated adsorbate-surface interactions: Ag2/graphene. J Chem Phys 2015; 143:102804. [DOI: 10.1063/1.4919397] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Affiliation(s)
| | - Alexander O. Mitrushchenkov
- Université Paris-Est, Laboratoire Modélisation et Simulation Multi Echelle, MSME UMR 8208 CNRS, 5 bd Descartes, 77454 Marne-la-Vallée, France
| | - Hermann Stoll
- Institut für Theoretische Chemie, Universität Stuttgart, D-70550 Stuttgart, Germany
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222
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Usvyat D. High precision quantum-chemical treatment of adsorption: Benchmarking physisorption of molecular hydrogen on graphane. J Chem Phys 2015; 143:104704. [DOI: 10.1063/1.4930851] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Denis Usvyat
- Institute for Physical and Theoretical Chemistry, Universität Regensburg, Universitätsstrasse 31, D-93040 Regensburg, Germany
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223
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Bharti A, Banerjee T. Solubility prediction of bio-oil derived chemicals in aqueous media by Localized Molecular Orbital-Energy Decomposition Analysis (LMO-EDA) and COSMO-RS predictions. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2015.05.019] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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224
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Thirman J, Head-Gordon M. An energy decomposition analysis for second-order Møller–Plesset perturbation theory based on absolutely localized molecular orbitals. J Chem Phys 2015; 143:084124. [DOI: 10.1063/1.4929479] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Affiliation(s)
- Jonathan Thirman
- Department of Chemistry, Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
| | - Martin Head-Gordon
- Department of Chemistry, Kenneth S. Pitzer Center for Theoretical Chemistry, University of California, Berkeley, Berkeley, California 94720, USA
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225
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Yourdkhani S, Korona T, Hadipour NL. Structure and Energetics of Complexes of B12N12 with Hydrogen Halides—SAPT(DFT) and MP2 Study. J Phys Chem A 2015; 119:6446-67. [DOI: 10.1021/acs.jpca.5b01756] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Sirous Yourdkhani
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Tatiana Korona
- Faculty
of Chemistry, University of Warsaw, ul. Pasteura 1, 02-093 Warsaw, Poland
| | - Nasser L. Hadipour
- Department
of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran
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226
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Parrish RM, Sherrill CD. Spatial assignment of symmetry adapted perturbation theory interaction energy components: The atomic SAPT partition. J Chem Phys 2015; 141:044115. [PMID: 25084889 DOI: 10.1063/1.4889855] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/14/2023] Open
Abstract
We develop a physically-motivated assignment of symmetry adapted perturbation theory for intermolecular interactions (SAPT) into atom-pairwise contributions (the A-SAPT partition). The basic precept of A-SAPT is that the many-body interaction energy components are computed normally under the formalism of SAPT, following which a spatially-localized two-body quasiparticle interaction is extracted from the many-body interaction terms. For electrostatics and induction source terms, the relevant quasiparticles are atoms, which are obtained in this work through the iterative stockholder analysis (ISA) procedure. For the exchange, induction response, and dispersion terms, the relevant quasiparticles are local occupied orbitals, which are obtained in this work through the Pipek-Mezey procedure. The local orbital atomic charges obtained from ISA additionally allow the terms involving local orbitals to be assigned in an atom-pairwise manner. Further summation over the atoms of one or the other monomer allows for a chemically intuitive visualization of the contribution of each atom and interaction component to the overall noncovalent interaction strength. Herein, we present the intuitive development and mathematical form for A-SAPT applied in the SAPT0 approximation (the A-SAPT0 partition). We also provide an efficient series of algorithms for the computation of the A-SAPT0 partition with essentially the same computational cost as the corresponding SAPT0 decomposition. We probe the sensitivity of the A-SAPT0 partition to the ISA grid and convergence parameter, orbital localization metric, and induction coupling treatment, and recommend a set of practical choices which closes the definition of the A-SAPT0 partition. We demonstrate the utility and computational tractability of the A-SAPT0 partition in the context of side-on cation-π interactions and the intercalation of DNA by proflavine. A-SAPT0 clearly shows the key processes in these complicated noncovalent interactions, in systems with up to 220 atoms and 2845 basis functions.
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Affiliation(s)
- Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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227
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Heßelmann A, Korona T. Intermolecular symmetry-adapted perturbation theory study of large organic complexes. J Chem Phys 2015; 141:094107. [PMID: 25194364 DOI: 10.1063/1.4893990] [Citation(s) in RCA: 67] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
Binding energies for the complexes of the S12L database by Grimme [Chem. Eur. J. 18, 9955 (2012)] were calculated using intermolecular symmetry-adapted perturbation theory combined with a density-functional theory description of the interacting molecules. The individual interaction energy decompositions revealed no particular change in the stabilisation pattern as compared to smaller dimer systems at equilibrium structures. This demonstrates that, to some extent, the qualitative description of the interaction of small dimer systems may be extrapolated to larger systems, a method that is widely used in force-fields in which the total interaction energy is decomposed into atom-atom contributions. A comparison of the binding energies with accurate experimental reference values from Grimme, the latter including thermodynamic corrections from semiempirical calculations, has shown a fairly good agreement to within the error range of the reference binding energies.
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Affiliation(s)
- Andreas Heßelmann
- Lehrstuhl für Theoretische Chemie, Universität Erlangen-Nürnberg, Egerlandstr. 3, D-91058 Erlangen, Germany
| | - Tatiana Korona
- Faculty of Chemistry, University of Warsaw, Pasteura 1, 02-093 Warsaw, Poland
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228
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Hughes ZE, Walsh TR. Computational chemistry for graphene-based energy applications: progress and challenges. NANOSCALE 2015; 7:6883-6908. [PMID: 25833794 DOI: 10.1039/c5nr00690b] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Research in graphene-based energy materials is a rapidly growing area. Many graphene-based energy applications involve interfacial processes. To enable advances in the design of these energy materials, such that their operation, economy, efficiency and durability is at least comparable with fossil-fuel based alternatives, connections between the molecular-scale structure and function of these interfaces are needed. While it is experimentally challenging to resolve this interfacial structure, molecular simulation and computational chemistry can help bridge these gaps. In this Review, we summarise recent progress in the application of computational chemistry to graphene-based materials for fuel cells, batteries, photovoltaics and supercapacitors. We also outline both the bright prospects and emerging challenges these techniques face for application to graphene-based energy materials in future.
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Affiliation(s)
- Zak E Hughes
- Institute for Frontier Materials, Deakin University, Geelong, VIC 3216, Australia.
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229
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Hongo K, Watson MA, Iitaka T, Aspuru-Guzik A, Maezono R. Diffusion Monte Carlo Study of Para-Diiodobenzene Polymorphism Revisited. J Chem Theory Comput 2015; 11:907-17. [DOI: 10.1021/ct500401p] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Affiliation(s)
- Kenta Hongo
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
| | - Mark A. Watson
- Department
of Chemistry, Princeton University, Princeton, New Jersey 08540, United States
| | - Toshiaki Iitaka
- Computational
Astrophysics Laboratory, RIKEN, 2-1 Hirosawa, Wako, Saitama 351-0198, Japan
| | - Alán Aspuru-Guzik
- Department
of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, United States
| | - Ryo Maezono
- School
of Information Science, JAIST, Asahidai 1-1, Nomi, Ishikawa 923-1292, Japan
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230
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Shirkov L, Makarewicz J. Does DFT-SAPT method provide spectroscopic accuracy? J Chem Phys 2015; 142:064102. [DOI: 10.1063/1.4907204] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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231
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Pecina A, Lepšík M, Hnyk D, Hobza P, Fanfrlík J. Chalcogen and Pnicogen Bonds in Complexes of Neutral Icosahedral and Bicapped Square-Antiprismatic Heteroboranes. J Phys Chem A 2015; 119:1388-95. [DOI: 10.1021/jp511101n] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Adam Pecina
- Gilead
Sciences and IOCB Research Center and Institute of Organic Chemistry
and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Martin Lepšík
- Gilead
Sciences and IOCB Research Center and Institute of Organic Chemistry
and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
| | - Drahomír Hnyk
- Institute
of Inorganic Chemistry, Academy of Sciences of the Czech Republic, v.v.i., 250 68 Řež near Prague, Czech Republic
| | - Pavel Hobza
- Gilead
Sciences and IOCB Research Center and Institute of Organic Chemistry
and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
- Regional
Center of Advanced Technologies and Materials, Department of Physical Chemistry, Palacký University, 77146 Olomouc, Czech Republic
| | - Jindřich Fanfrlík
- Gilead
Sciences and IOCB Research Center and Institute of Organic Chemistry
and Biochemistry (IOCB), Academy of Sciences of the Czech Republic, v.v.i., Flemingovo nám. 2, 16610 Prague 6, Czech Republic
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232
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Riley KE, Ford CL, Demouchet K. Comparison of hydrogen bonds, halogen bonds, C H⋯π interactions, and C X⋯π interactions using high-level ab initio methods. Chem Phys Lett 2015. [DOI: 10.1016/j.cplett.2014.12.040] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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233
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Sharma B, Srivastava HK, Gayatri G, Sastry GN. Energy decomposition analysis of cation-π, metal ion-lone pair, hydrogen bonded, charge-assisted hydrogen bonded, and π-π interactions. J Comput Chem 2015; 36:529-38. [DOI: 10.1002/jcc.23827] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2014] [Revised: 12/04/2014] [Accepted: 12/05/2014] [Indexed: 01/09/2023]
Affiliation(s)
- Bhaskar Sharma
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Hemant Kumar Srivastava
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Gaddamanugu Gayatri
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
| | - Garikapati Narahari Sastry
- Centre for Molecular Modeling, CSIR-Indian Institute of Chemical Technology; Tarnaka Hyderabad 500 607 India
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234
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Kocman M, Jurečka P, Dubecký M, Otyepka M, Cho Y, Kim KS. Choosing a density functional for modeling adsorptive hydrogen storage: reference quantum mechanical calculations and a comparison of dispersion-corrected density functionals. Phys Chem Chem Phys 2015; 17:6423-32. [DOI: 10.1039/c4cp04354e] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Various dispersion-corrected density functionals are compared with high level QM data for several model complexes for adsorptive hydrogen storage.
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Affiliation(s)
- Mikuláš Kocman
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Petr Jurečka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Matúš Dubecký
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Michal Otyepka
- Regional Centre of Advanced Technologies and Materials
- Department of Physical Chemistry
- Faculty of Science
- Palacky University
- 77146 Olomouc
| | - Yeonchoo Cho
- Center for Superfunctional Materials
- Department of Chemistry and Department of Physics
- Pohang University of Science and Technology
- Pohang 790-784
- Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
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235
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236
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Lee HM, Youn IS, Saleh M, Lee JW, Kim KS. Interactions of CO2with various functional molecules. Phys Chem Chem Phys 2015; 17:10925-33. [DOI: 10.1039/c5cp00673b] [Citation(s) in RCA: 82] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
We report the CO2-interactions with diverse functional molecules. Useful functional molecules such as melamine showing very large adsorption enthalpy for CO2are reported.
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Affiliation(s)
- Han Myoung Lee
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
| | - Il Seung Youn
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
| | - Muhammad Saleh
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
| | - Jung Woo Lee
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials
- Department of Chemistry
- Ulsan National Institute of Science and Technology (UNIST)
- Ulsan 689-798
- Korea
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237
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Manukyan A, Tekin A. First principles potential for the cytosine dimer. Phys Chem Chem Phys 2015; 17:14685-701. [DOI: 10.1039/c5cp00553a] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A new first principles potential for the cytosine dimer.
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Affiliation(s)
- Artür Manukyan
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
| | - Adem Tekin
- Informatics Institute
- Istanbul Technical University
- Istanbul
- Turkey
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238
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Phipps MJS, Fox T, Tautermann CS, Skylaris CK. Energy decomposition analysis approaches and their evaluation on prototypical protein–drug interaction patterns. Chem Soc Rev 2015; 44:3177-211. [DOI: 10.1039/c4cs00375f] [Citation(s) in RCA: 226] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
The partitioning of the interaction energy into chemical components such as electrostatics, polarization, and charge transfer is possible with energy decomposition analysis approaches. We review and evaluate these for biomolecular applications.
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Affiliation(s)
| | - Thomas Fox
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
| | - Christofer S. Tautermann
- Lead Identification and Optimization Support
- Boehringer Ingelheim Pharma GmbH & Co. KG
- 88397 Biberach
- Germany
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239
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Kirchner B, Hollóczki O, Canongia Lopes JN, Pádua AAH. Multiresolution calculation of ionic liquids. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1212] [Citation(s) in RCA: 87] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Affiliation(s)
- Barbara Kirchner
- Mulliken Center for Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Bonn Germany
| | - Oldamur Hollóczki
- Mulliken Center for Theoretical Chemistry; Rheinische Friedrich-Wilhelms-Universität Bonn; Bonn Germany
| | - José Nuno Canongia Lopes
- Centro de Química Estrutural, Instituto Superior Técnico; Universidade de Lisboa; Lisboa Portugal
- Instituto de Tecnologia Química e Biológica; Universidade Nova de Lisboa; Lisboa Portugal
| | - Agílio A. H. Pádua
- Institut de Chimie de Clermont-Ferrand; Université Blaise Pascal and CNRS; Clermont-Ferrand France
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240
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Clark T, Politzer P, Murray JS. Correct electrostatic treatment of noncovalent interactions: the importance of polarization. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2014. [DOI: 10.1002/wcms.1210] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Timothy Clark
- Computer-Chemie-Centrum; Friedrich-Alexander-Universität Erlangen-Nürnberg; Erlangen Germany
| | - Peter Politzer
- Chemistry Department; University of New Orleans; New Orleans LA USA
| | - Jane S. Murray
- Chemistry Department; University of New Orleans; New Orleans LA USA
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241
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Szalewicz K. Determination of structure and properties of molecular crystals from first principles. Acc Chem Res 2014; 47:3266-74. [PMID: 25354310 DOI: 10.1021/ar500275m] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
CONSPECTUS: Until recently, it had been impossible to predict structures of molecular crystals just from the knowledge of the chemical formula for the constituent molecule(s). A solution of this problem has been achieved using intermolecular force fields computed from first principles. These fields were developed by calculating interaction energies of molecular dimers and trimers using an ab initio method called symmetry-adapted perturbation theory (SAPT) based on density-functional theory (DFT) description of monomers [SAPT(DFT)]. For clusters containing up to a dozen or so atoms, interaction energies computed using SAPT(DFT) are comparable in accuracy to the results of the best wave function-based methods, whereas the former approach can be applied to systems an order of magnitude larger than the latter. In fact, for monomers with a couple dozen atoms, SAPT(DFT) is about equally time-consuming as the supermolecular DFT approach. To develop a force field, SAPT(DFT) calculations are performed for a large number of dimer and possibly also trimer configurations (grid points in intermolecular coordinates), and the interaction energies are then fitted by analytic functions. The resulting force fields can be used to determine crystal structures and properties by applying them in molecular packing, lattice energy minimization, and molecular dynamics calculations. In this way, some of the first successful determinations of crystal structures were achieved from first principles, with crystal densities and lattice parameters agreeing with experimental values to within about 1%. Crystal properties obtained using similar procedures but empirical force fields fitted to crystal data have typical errors of several percent due to low sensitivity of empirical fits to interactions beyond those of the nearest neighbors. The first-principles approach has additional advantages over the empirical approach for notional crystals and cocrystals since empirical force fields can only be extrapolated to such cases. As an alternative to applying SAPT(DFT) in crystal structure calculations, one can use supermolecular DFT interaction energies combined with scaled dispersion energies computed from simple atom-atom functions, that is, use the so-called DFT+D approach. Whereas the standard DFT methods fail for intermolecular interactions, DFT+D performs reasonably well since the dispersion correction is used not only to provide the missing dispersion contribution but also to fix other deficiencies of DFT. The latter cancellation of errors is unphysical and can be avoided by applying the so-called dispersionless density functional, dlDF. In this case, the dispersion energies are added without any scaling. The dlDF+D method is also one of the best performing DFT+D methods. The SAPT(DFT)-based approach has been applied so far only to crystals with rigid monomers. It can be extended to partly flexible monomers, that is, to monomers with only a few internal coordinates allowed to vary. However, the costs will increase relative to rigid monomer cases since the number of grid points increases exponentially with the number of dimensions. One way around this problem is to construct force fields with approximate couplings between inter- and intramonomer degrees of freedom. Another way is to calculate interaction energies (and possibly forces) "on the fly", i.e., in each step of lattice energy minimization procedure. Such an approach would be prohibitively expensive if it replaced analytic force fields at all stages of the crystal predictions procedure, but it can be used to optimize a few dozen candidate structures determined by other methods.
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Affiliation(s)
- Krzysztof Szalewicz
- Department of Physics and Astronomy, University of Delaware, Newark, Delaware 19716, United States
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242
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Kennedy MR, McDonald AR, DePrince AE, Marshall MS, Podeszwa R, Sherrill CD. Communication: resolving the three-body contribution to the lattice energy of crystalline benzene: benchmark results from coupled-cluster theory. J Chem Phys 2014; 140:121104. [PMID: 24697416 DOI: 10.1063/1.4869686] [Citation(s) in RCA: 57] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Coupled-cluster theory including single, double, and perturbative triple excitations [CCSD(T)] has been applied to trimers that appear in crystalline benzene in order to resolve discrepancies in the literature about the magnitude of non-additive three-body contributions to the lattice energy. The present results indicate a non-additive three-body contribution of 0.89 kcal mol(-1), or 7.2% of the revised lattice energy of -12.3 kcal mol(-1). For the trimers for which we were able to compute CCSD(T) energies, we obtain a sizeable difference of 0.63 kcal mol(-1) between the CCSD(T) and MP2 three-body contributions to the lattice energy, confirming that three-body dispersion dominates over three-body induction. Taking this difference as an estimate of three-body dispersion for the closer trimers, and adding an Axilrod-Teller-Muto estimate of 0.13 kcal mol(-1) for long-range contributions yields an overall value of 0.76 kcal mol(-1) for three-body dispersion, a significantly smaller value than in several recent studies.
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Affiliation(s)
- Matthew R Kennedy
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Ashley Ringer McDonald
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - A Eugene DePrince
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Michael S Marshall
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Rafal Podeszwa
- Institute of Chemistry, University of Silesia, Szkolna 9, 40-006, Katowice, Poland
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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243
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Parker TM, Burns LA, Parrish RM, Ryno AG, Sherrill CD. Levels of symmetry adapted perturbation theory (SAPT). I. Efficiency and performance for interaction energies. J Chem Phys 2014; 140:094106. [PMID: 24606352 DOI: 10.1063/1.4867135] [Citation(s) in RCA: 545] [Impact Index Per Article: 49.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
A systematic examination of the computational expense and accuracy of Symmetry-Adapted Perturbation Theory (SAPT) for the prediction of non-covalent interaction energies is provided with respect to both method [SAPT0, DFT-SAPT, SAPT2, SAPT2+, SAPT2+(3), and SAPT2+3; with and without CCD dispersion for the last three] and basis set [Dunning cc-pVDZ through aug-cc-pV5Z wherever computationally tractable, including truncations of diffuse basis functions]. To improve accuracy for hydrogen-bonded systems, we also include two corrections based on exchange-scaling (sSAPT0) and the supermolecular MP2 interaction energy (δMP2). When considering the best error performance relative to computational effort, we recommend as the gold, silver, and bronze standard of SAPT: SAPT2+(3)δMP2/aug-cc-pVTZ, SAPT2+/aug-cc-pVDZ, and sSAPT0/jun-cc-pVDZ. Their respective mean absolute errors in interaction energy across the S22, HBC6, NBC10, and HSG databases are 0.15 (62.9), 0.30 (4.4), and 0.49 kcal mol(-1) (0.03 h for adenine·thymine complex).
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Affiliation(s)
- Trent M Parker
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Lori A Burns
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Robert M Parrish
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - Alden G Ryno
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
| | - C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, and School of Computational Science and Engineering, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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244
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Hapka M, Rajchel Ł, Modrzejewski M, Chałasiński G, Szczęśniak MM. Tuned range-separated hybrid functionals in the symmetry-adapted perturbation theory. J Chem Phys 2014; 141:134120. [DOI: 10.1063/1.4896608] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Affiliation(s)
- Michał Hapka
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Pasteura 1, Poland
| | - Łukasz Rajchel
- Faculty of Chemistry, University of Duisburg-Essen, Universitätsstraße 5, 45117 Essen, Germany
- Interdisciplinary Centre for Mathematical and Computational Modelling, University of Warsaw, 00-838 Warsaw, Prosta 69, Poland
| | - Marcin Modrzejewski
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Pasteura 1, Poland
| | - Grzegorz Chałasiński
- Faculty of Chemistry, University of Warsaw, 02-093 Warsaw, Pasteura 1, Poland
- Department of Chemistry, Oakland University, Rochester, Michigan 48309-4477, USA
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245
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Mikulski D, Eder K, Molski M. Quantum-chemical study on stacking interactions between bioactive polyphenols (trans-resveratrol, trans-piceatannol) and ribonucleosides. Insight into minimum energy geometries of π–π stacked systems. COMPUT THEOR CHEM 2014. [DOI: 10.1016/j.comptc.2014.08.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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246
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Mishra BK, Deshmukh MM, Venkatnarayan R. C-H···π interactions and the nature of the donor carbon atom. J Org Chem 2014; 79:8599-606. [PMID: 25157745 DOI: 10.1021/jo501251s] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The influence of multiple substituents (F, CH3, NO2, CN, Cl, OH and NH2) on the C-H···π interaction in benzene-ethylene complex was investigated using the estimated CCSD(T) method and complete basis set limit. The results were compared with our earlier reported complexes of benzene-acetylene and benzene-methane, thus completing the sp, sp(2) and sp(3) series of C-H donors. The stabilization energy values for multiple fluoro-substituted benzene-ethylene complexes are found to be very close to those of the multiple fluoro-substituted benzene-methane complexes. Expectedly, the stabilization energies for the multiple methyl-substituted benzene-ethylene complexes lie between those of the multiple methyl-substituted benzene-methane and benzene-acetylene complexes. Energy decomposition analysis using the DFT-SAPT method predicts the dispersion energy to be dominant, similar to the benzene-methane complexes. For the symmetrically disubstituted complexes (-OH, -Cl, -NH2, -CN and -NO2), additional C-H···X interaction was observed, possibly due to the angular orientation of the ethylene molecule. Multidimensional correlation analysis between the electrostatic, dispersion and exchange-repulsion with the C-H···π interaction distance (r), Hammett constant (σ) and the molar refractivity (MR) revealed strong correlation between dispersion energy and the C-H···π interaction distance (r) as well as molar refractivity (MR).
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Affiliation(s)
- Brijesh Kumar Mishra
- International Institute of Information Technology Bangalore , Bangalore 560100, Karnataka, India
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247
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Interaction between the guanidinium cation and aromatic amino acids. Phys Chem Chem Phys 2014; 16:22499-512. [DOI: 10.1039/c4cp02630f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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248
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Ahnen S, Hehn AS, Vogiatzis KD, Trachsel MA, Leutwyler S, Klopper W. Accurate computations of the structures and binding energies of the imidazole ⋯benzene and pyrrole ⋯benzene complexes. Chem Phys 2014. [DOI: 10.1016/j.chemphys.2014.05.023] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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249
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Choi E, McDaniel JG, Schmidt JR, Yethiraj A. First-Principles, Physically Motivated Force Field for the Ionic Liquid [BMIM][BF4]. J Phys Chem Lett 2014; 5:2670-2674. [PMID: 26277961 DOI: 10.1021/jz5010945] [Citation(s) in RCA: 48] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Molecular simulations play an important role in establishing structure-property relations in complex fluids such as room-temperature ionic liquids. Classical force fields are the starting point when large systems or long times are of interest. These force fields must be not only accurate but also transferable. In this work, we report a physically motivated force field for the ionic liquid 1-butyl-3-methylimidazolium tetrafluoroborate ([BMIM][BF4]) based on symmetry-adapted perturbation theory. The predictions (from molecular dynamics simulations) of the liquid density, enthalpy of vaporization, diffusion coefficients, viscosity, and conductivity are in excellent agreement with experiment, with no adjustable parameters. The explicit energy decomposition inherent in the force field enables a quantitative analysis of the important physical interactions in these systems. We find that polarization is crucial and there is little evidence of charge transfer. We also argue that the often used procedure of scaling down charges in molecular simulations of ionic liquids is unphysical for [BMIM][BF4]. Because all intermolecular interactions in the force field are parametrized from first-principles, we anticipate good transferability to other ionic liquid systems and physical conditions.
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Affiliation(s)
- Eunsong Choi
- †Department of Physics, University of Wisconsin, 1150 University Avenue, Madison, Wisconsin 53706, United States
| | - Jesse G McDaniel
- ‡Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - J R Schmidt
- ‡Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
| | - Arun Yethiraj
- ‡Department of Chemistry, University of Wisconsin, 1101 University Avenue, Madison, Wisconsin 53706, United States
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250
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Campo-Cacharrón A, Cabaleiro-Lago EM, González-Veloso I, Rodríguez-Otero J. Interaction of Anions with Substituted Buckybowls. The Anion’s Nature and Solvent Effects. J Phys Chem A 2014; 118:6112-24. [DOI: 10.1021/jp5058463] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Alba Campo-Cacharrón
- Departamento
de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X
El Sabio s/n, 27002 Lugo, Spain
| | - Enrique M. Cabaleiro-Lago
- Departamento
de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo. Avda. Alfonso X
El Sabio s/n, 27002 Lugo, Spain
| | - Iván González-Veloso
- Departamento
de Química Física, Centro de investigación en
Química Biolóxica e Materiais Moleculares, CIQUS, Universidade de Santiago de Compostela, Rúa Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
| | - Jesús Rodríguez-Otero
- Departamento
de Química Física, Centro de investigación en
Química Biolóxica e Materiais Moleculares, CIQUS, Universidade de Santiago de Compostela, Rúa Jenaro de la Fuente s/n, Santiago de Compostela 15782, Spain
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