101
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Barwell NP, Davis AP. Substituent Effects in Synthetic Lectins - Exploring the Role of CH−π Interactions in Carbohydrate Recognition. J Org Chem 2011; 76:6548-57. [DOI: 10.1021/jo200755z] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Nicholas P. Barwell
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, U.K. BS8 1TS
| | - Anthony P. Davis
- School of Chemistry, University of Bristol, Cantock’s Close, Bristol, U.K. BS8 1TS
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102
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Nishio M. The CH/π hydrogen bond in chemistry. Conformation, supramolecules, optical resolution and interactions involving carbohydrates. Phys Chem Chem Phys 2011; 13:13873-900. [PMID: 21611676 DOI: 10.1039/c1cp20404a] [Citation(s) in RCA: 633] [Impact Index Per Article: 48.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The CH/π hydrogen bond is an attractive molecular force occurring between a soft acid and a soft base. Contribution from the dispersion energy is important in typical cases where aliphatic or aromatic CH groups are involved. Coulombic energy is of minor importance as compared to the other weak hydrogen bonds. The hydrogen bond nature of this force, however, has been confirmed by AIM analyses. The dual characteristic of the CH/π hydrogen bond is the basis for ubiquitous existence of this force in various fields of chemistry. A salient feature is that the CH/π hydrogen bond works cooperatively. Another significant point is that it works in nonpolar as well as polar, protic solvents such as water. The interaction energy depends on the nature of the molecular fragments, CH as well as π-groups: the stronger the proton donating ability of the CH group, the larger the stabilizing effect. This Perspective focuses on the consequence of this molecular force in the conformation of organic compounds and supramolecular chemistry. Implication of the CH/π hydrogen bond extends to the specificity of molecular recognition or selectivity in organic reactions, polymer science, surface phenomena and interactions involving proteins. Many problems, unsettled to date, will become clearer in the light of the CH/π paradigm.
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Affiliation(s)
- Motohiro Nishio
- The CHPI Institute, 705-6-338 Minamioya, Machida-shi, Tokyo, 194-0031, Japan.
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103
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Salonen LM, Ellermann M, Diederich F. Aromatische Ringe in chemischer und biologischer Erkennung: Energien und Strukturen. Angew Chem Int Ed Engl 2011. [DOI: 10.1002/ange.201007560] [Citation(s) in RCA: 245] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
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104
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Salonen LM, Ellermann M, Diederich F. Aromatic rings in chemical and biological recognition: energetics and structures. Angew Chem Int Ed Engl 2011; 50:4808-42. [PMID: 21538733 DOI: 10.1002/anie.201007560] [Citation(s) in RCA: 1172] [Impact Index Per Article: 90.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2010] [Indexed: 12/12/2022]
Abstract
This review describes a multidimensional treatment of molecular recognition phenomena involving aromatic rings in chemical and biological systems. It summarizes new results reported since the appearance of an earlier review in 2003 in host-guest chemistry, biological affinity assays and biostructural analysis, data base mining in the Cambridge Structural Database (CSD) and the Protein Data Bank (PDB), and advanced computational studies. Topics addressed are arene-arene, perfluoroarene-arene, S⋅⋅⋅aromatic, cation-π, and anion-π interactions, as well as hydrogen bonding to π systems. The generated knowledge benefits, in particular, structure-based hit-to-lead development and lead optimization both in the pharmaceutical and in the crop protection industry. It equally facilitates the development of new advanced materials and supramolecular systems, and should inspire further utilization of interactions with aromatic rings to control the stereochemical outcome of synthetic transformations.
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Affiliation(s)
- Laura M Salonen
- Laboratory of Organic Chemistry, Department of Chemistry and Applied Biosciences, ETH Zurich, Hönggerberg, HCI, 8093 Zurich, Switzerland
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105
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Kumari M, Balaji PV, Sunoj RB. Quantification of binding affinities of essential sugars with a tryptophan analogue and the ubiquitous role of C-H···π interactions. Phys Chem Chem Phys 2011; 13:6517-30. [PMID: 21369604 DOI: 10.1039/c0cp02559c] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The role of noncovalent interactions in carbohydrate recognition by aromatic amino acids has long been reported. To develop a molecular understanding of noncovalent interactions in the recognition process, we have examined a series of binary complexes between 3-methylindole (3-MeIn) and sugars. In particular, the geometries and binding affinities of 3-MeIn with α/β-D-glucose, β-D-galactose, α-D-mannose and α/β-L-fucose are obtained using the MP2(full)/6-31G(d,p) and the M06/TZV2D//MP2/6-31G(d,p) level of theories. The conventional hydrogen bonding such as N-H···O and C-H···O as well as nonconventional O-H···π and C-H···π type of interactions is, in general, identified as responsible for the moderately strong interaction energies. Large variations in the position-orientations of 3-MeIn with respect to saccharide are noticed, within the same sugar family, as well as across different sugar series. Furthermore, complexes with large differences in their geometries are recognized as capable of exhibiting very similar interaction energies, underscoring the significance of exhaustive conformation sampling, as carried out in the present study. These observations are readily attributed to the differences in the efficiency of the type of interactions enlisted above. The highest and lowest interaction energies, upon inclusion of 50% BSSE correction, are found to be -16.02 and -6.22 kcal mol(-1), respectively, for α-D-glucose (1a) and α-L-fucose (5j). While more number of prominent conventional hydrogen bonding contacts remains as a characteristic feature of the strongly bound complexes, the lower end of the interaction energy spectrum is dominated by multiple C-H···π interactions. The complexes exhibiting as many as four C-H···π contacts are identified in the case of α/β-D-glucose, β-D-galactose, and α/β-L-fucose with an interaction energy hovering around -8 kcal mol(-1). The presence of effective C-H···π interactions is found to be dependent on the saccharide configuration as well as the area of the apolar patch constituted by the C-H groups. The study offers a comprehensive set of binary complexes, across different saccharides, which serves as an illustration of the significance and ubiquitous nature of C-H···π interactions in carbohydrate binding in saccharide-protein complexes.
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Affiliation(s)
- Manju Kumari
- Department of Biosciences and Bioengineering, Indian Institute of Technology Bombay, Powai, Mumbai 400076, India
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106
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Zwier MC, Kaus JW, Chong LT. Efficient Explicit-Solvent Molecular Dynamics Simulations of Molecular Association Kinetics: Methane/Methane, Na+/Cl−, Methane/Benzene, and K+/18-Crown-6 Ether. J Chem Theory Comput 2011; 7:1189-97. [DOI: 10.1021/ct100626x] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Matthew C. Zwier
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Joseph W. Kaus
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
| | - Lillian T. Chong
- Department of Chemistry, University of Pittsburgh, Pittsburgh, Pennsylvania 15260, United States
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107
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Riley KE, Hobza P. Noncovalent interactions in biochemistry. WILEY INTERDISCIPLINARY REVIEWS-COMPUTATIONAL MOLECULAR SCIENCE 2011. [DOI: 10.1002/wcms.8] [Citation(s) in RCA: 157] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Kevin E. Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center for Biomolecules and Complex Molecular Systems, Prague, Czech Republic
- Department of Physical Chemistry, Palacky University, Olomouc, Czech Republic
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108
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Takahashi O, Kohno Y, Nishio M. Relevance of weak hydrogen bonds in the conformation of organic compounds and bioconjugates: evidence from recent experimental data and high-level ab initio MO calculations. Chem Rev 2011; 110:6049-76. [PMID: 20550180 DOI: 10.1021/cr100072x] [Citation(s) in RCA: 447] [Impact Index Per Article: 34.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Osamu Takahashi
- Department of Chemistry, Graduate School of Science, Hiroshima University, Kagamiyama, Higashi-Hiroshima, 739-8526, Japan.
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109
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Fujii A, Hayashi H, Park JW, Kazama T, Mikami N, Tsuzuki S. Experimental and theoretical determination of the accurate CH/π interaction energies in benzene–alkane clusters: correlation between interaction energy and polarizability. Phys Chem Chem Phys 2011; 13:14131-41. [DOI: 10.1039/c1cp20203k] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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110
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Geronimo I, Jiten Singh N, Kim KS. Nature of anion-templated π+–π+ interactions. Phys Chem Chem Phys 2011; 13:11841-5. [DOI: 10.1039/c1cp20348g] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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111
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Riley KE, Pitonák M, Jurecka P, Hobza P. Stabilization and structure calculations for noncovalent interactions in extended molecular systems based on wave function and density functional theories. Chem Rev 2010; 110:5023-63. [PMID: 20486691 DOI: 10.1021/cr1000173] [Citation(s) in RCA: 562] [Impact Index Per Article: 40.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, Rio Piedras, Puerto Rico 00931
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112
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Hohenstein EG, Sherrill CD. Density fitting of intramonomer correlation effects in symmetry-adapted perturbation theory. J Chem Phys 2010; 133:014101. [PMID: 20614953 DOI: 10.1063/1.3451077] [Citation(s) in RCA: 204] [Impact Index Per Article: 14.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023] Open
Abstract
Symmetry-adapted perturbation theory (SAPT) offers insight into the nature of intermolecular interactions. In addition, accurate energies can be obtained from the wave function-based variant of SAPT provided that intramonomer electron correlation effects are included. We apply density-fitting (DF) approximations to the intramonomer correlation corrections in SAPT. The introduction of this approximation leads to an improvement in the computational cost of SAPT by reducing the scaling of certain SAPT terms, reducing the amount of disk I/O, and avoiding the explicit computation of certain types of MO integrals. We have implemented all the intramonomer correlation corrections to SAPT through second-order under the DF approximation. Additionally, leading third-order terms are also implemented. The accuracy of this truncation of SAPT is tested against the S22 test set of Hobza and co-workers [Phys. Chem. Chem. Phys. 8, 1985 (2006)]. When the intramonomer corrections to dispersion are included in SAPT, a mean absolute deviation of 0.3-0.4 kcal mol(-1) is observed for the S22 test set when using an aug-cc-pVDZ basis. The computations on the adenine-thymine complexes in the S22 test set with an aug-cc-pVDZ basis represent the largest SAPT computations to date that include this degree of intramonomer correlation. Computations of this size can now be performed routinely with our newly developed DF-SAPT program.
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Affiliation(s)
- Edward G Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA
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113
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Sedlák R, Fanfrlík J, Hnyk D, Hobza P, Lepšík M. Interactions of Boranes and Carboranes with Aromatic Systems: CCSD(T) Complete Basis Set Calculations and DFT-SAPT Analysis of Energy Components. J Phys Chem A 2010; 114:11304-11. [DOI: 10.1021/jp104411x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Affiliation(s)
- Róbert Sedlák
- Center for Biomolecules and Complex Systems and Institute of Organic Chemistry and Biochemistry, 16610, Prague 6, Institute of Inorganic Chemistry, 250 68, Rez near Prague, Academy of Sciences of the Czech Republic, and Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Jindřich Fanfrlík
- Center for Biomolecules and Complex Systems and Institute of Organic Chemistry and Biochemistry, 16610, Prague 6, Institute of Inorganic Chemistry, 250 68, Rez near Prague, Academy of Sciences of the Czech Republic, and Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Drahomír Hnyk
- Center for Biomolecules and Complex Systems and Institute of Organic Chemistry and Biochemistry, 16610, Prague 6, Institute of Inorganic Chemistry, 250 68, Rez near Prague, Academy of Sciences of the Czech Republic, and Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Pavel Hobza
- Center for Biomolecules and Complex Systems and Institute of Organic Chemistry and Biochemistry, 16610, Prague 6, Institute of Inorganic Chemistry, 250 68, Rez near Prague, Academy of Sciences of the Czech Republic, and Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
| | - Martin Lepšík
- Center for Biomolecules and Complex Systems and Institute of Organic Chemistry and Biochemistry, 16610, Prague 6, Institute of Inorganic Chemistry, 250 68, Rez near Prague, Academy of Sciences of the Czech Republic, and Department of Physical Chemistry, Palacky University, 771 46, Olomouc, Czech Republic
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114
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Sanders JM. Optimal π-Stacking Interaction Energies in Parallel-Displaced Aryl/Aryl Dimers are Predicted by the Dimer Heavy Atom Count. J Phys Chem A 2010; 114:9205-11. [DOI: 10.1021/jp912094q] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- John M. Sanders
- Department of Chemistry Modeling and Informatics, Merck Research Laboratories, West Point, Pennsylvania 19486
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115
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Hohenstein EG, Sherrill CD. Density fitting and Cholesky decomposition approximations in symmetry-adapted perturbation theory: Implementation and application to probe the nature of π-π interactions in linear acenes. J Chem Phys 2010. [DOI: 10.1063/1.3426316] [Citation(s) in RCA: 231] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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116
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Li Q, Yuan H, Jing B, Liu Z, Li W, Cheng J, Gong B, Sun J. Theoretical study of halogen–hydride halogen bonds in F3CL ··· HM (L=Cl, Br; M=Li, BeH, MgH) complexes. Mol Phys 2010. [DOI: 10.1080/00268971003630703] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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117
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Geng Y, Takatani T, Hohenstein EG, Sherrill CD. Accurately Characterizing the π−π Interaction Energies of Indole−Benzene Complexes. J Phys Chem A 2010; 114:3576-82. [DOI: 10.1021/jp9099495] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yue Geng
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - Tait Takatani
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - Edward G. Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
| | - C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, and College of Computing, Georgia Institute of Technology, Atlanta, Georgia 30332-0280
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118
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Sherrill CD, Sumpter BG, Sinnokrot MO, Marshall MS, Hohenstein EG, Walker RC, Gould IR. Assessment of standard force field models against high-quality ab initio potential curves for prototypes of pi-pi, CH/pi, and SH/pi interactions. J Comput Chem 2010; 30:2187-93. [PMID: 19242959 DOI: 10.1002/jcc.21226] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
Several popular force fields, namely, CHARMM, AMBER, OPLS-AA, and MM3, have been tested for their ability to reproduce highly accurate quantum mechanical potential energy curves for noncovalent interactions in the benzene dimer, the benzene-CH(4) complex, and the benzene-H(2)S complex. All of the force fields are semi-quantitatively correct, but none of them is consistently reliable quantitatively. Re-optimization of Lennard-Jones parameters and symmetry-adapted perturbation theory analysis for the benzene dimer suggests that better agreement cannot be expected unless more flexible functional forms (particularly for the electrostatic contributions) are employed for the empirical force fields.
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Affiliation(s)
- C David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry, Georgia Institute of Technology, Atlanta, Georgia 30332-0400, USA.
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119
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Nayak SK, Sathishkumar R, Row TNG. Directing role of functional groups in selective generation of C–H⋯π interactions: In situ cryo-crystallographic studies on benzyl derivatives. CrystEngComm 2010. [DOI: 10.1039/c001190h] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
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120
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Riley KE, Pitoňák M, Černý J, Hobza P. On the Structure and Geometry of Biomolecular Binding Motifs (Hydrogen-Bonding, Stacking, X-H···π): WFT and DFT Calculations. J Chem Theory Comput 2009; 6:66-80. [PMID: 26614320 DOI: 10.1021/ct900376r] [Citation(s) in RCA: 167] [Impact Index Per Article: 11.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The strengths of noncovalent interactions are generally very sensitive to a number of geometric parameters. Among the most important of these parameters is the separation between the interacting moieties (in the case of an intermolecular interaction, this would be the intermolecular separation). Most works seeking to characterize the properties of intermolecular interactions are mainly concerned with binding energies obtained at the potential energy minimum (as determined at some particular level of theory). In this work, in order to extend our understanding of these types of noncovalent interactions, we investigate the distance dependence of several types of intermolecular interactions, these are hydrogen bonds, stacking interactions, dispersion interactions, and X-H···π interactions. There are several methods that have traditionally been used to treat noncovalent interactions as well as many new methods that have emerged within the past three or four years. Here we obtain reference data using estimated CCSD(T) values at the complete basis set limit (using the CBS(T) method); potential energy curves are also produced using several other methods thought to be accurate for intermolecular interactions, these are MP2/cc-pVTZ, MP2/aug-cc-pVDZ, MP2/6-31G*(0.25), SCS(MI)-MP2/cc-pVTZ, estimated MP2.5/CBS, DFT-SAPT/aug-cc-pVTZ, DFT/M06-2X/6-311+G(2df,2p), and DFT-D/TPSS/6-311++G(3df,3pd). The basis set superposition error is systematically considered throughout the study. It is found that the MP2.5 and DFT-SAPT methods, which are both quite computationally intensive, produce potential energy curves that are in very good agreement to those of the reference method. Among the MP2 techniques, which can be said to be of medium computational expense, the best results are obtained with MP2/cc-pVTZ and SCS(MI)-MP2/cc-pVTZ. DFT-D/TPSS/6-311++G(3df,3pd) is the DFT-based method that can be said to give the most well-balanced description of intermolecular interactions.
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Affiliation(s)
- Kevin E Riley
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Michal Pitoňák
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Jiří Černý
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
| | - Pavel Hobza
- Department of Chemistry, University of Puerto Rico, P.O. Box 23346, Rio Piedras, Puerto Rico 00931, Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic and Center of Biomolecules and Complex Molecular Systems, Flemingovo nam. 2, 166 10 Prague 6, Czech Republic, Department of Physical and Theoretical Chemistry, Faculty of Natural Sciences, Comenius University, Mlynska Dolina CH-1, 842 15 Bratislava, Slovak Republic, Institute of Biotechnology, Academy of Sciences of the Czech Republic, 142 00 Prague 4, Czech Republic, and Department of Physical Chemistry, Palacký University, Olomouc, 771 46 Olomouc, Czech Republic
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121
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Li W, Gahungu G, Zhang J, Hao L. Design of an Organic Zeolite toward the Selective Adsorption of Small Molecules at the Dispersion Corrected Density Functional Theory Level. J Phys Chem B 2009; 113:16472-8. [DOI: 10.1021/jp905471d] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Wenliang Li
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Godefroid Gahungu
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Jingping Zhang
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
| | - Lizhu Hao
- Faculty of Chemistry, Northeast Normal University, Changchun 130024, China, and Key Laboratory for Applied Statistics of MOE, Northeast Normal University, Changchun 130024, China
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122
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Prakash M, Samy KG, Subramanian V. Benzene−Water (BZWn (n = 1 − 10)) Clusters. J Phys Chem A 2009; 113:13845-52. [DOI: 10.1021/jp906770x] [Citation(s) in RCA: 88] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- M. Prakash
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - K. Gopal Samy
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
| | - V. Subramanian
- Chemical Laboratory, Central Leather Research Institute, Council of Scientific and Industrial Research, Adyar, Chennai 600 020, India
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123
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Sherrill CD, Takatani T, Hohenstein EG. An Assessment of Theoretical Methods for Nonbonded Interactions: Comparison to Complete Basis Set Limit Coupled-Cluster Potential Energy Curves for the Benzene Dimer, the Methane Dimer, Benzene−Methane, and Benzene−H2S. J Phys Chem A 2009; 113:10146-59. [DOI: 10.1021/jp9034375] [Citation(s) in RCA: 339] [Impact Index Per Article: 22.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- C. David Sherrill
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia, 30332-0400
| | - Tait Takatani
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia, 30332-0400
| | - Edward G. Hohenstein
- Center for Computational Molecular Science and Technology, School of Chemistry and Biochemistry and College of Computing, Georgia Institute of Technology, Atlanta, Georgia, 30332-0400
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124
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Churchill CDM, Navarro-Whyte L, Rutledge LR, Wetmore SD. Effects of the biological backbone on DNA-protein stacking interactions. Phys Chem Chem Phys 2009; 11:10657-70. [PMID: 20145810 DOI: 10.1039/b910747a] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
The pi-pi stacking (face-to-face) interactions between the five natural DNA or RNA nucleobases and the four aromatic amino acids were compared using three different types of dimers: (1) a truncated nucleoside (nucleobase) stacked with a truncated amino acid; (2) a truncated nucleoside (nucleobase) stacked with an extended amino acid; and (3) a nucleoside (extended nucleobase) stacked with a truncated amino acid. Systematic (MP2/6-31G*(0.25)) potential energy surface scans reveal important information about the effects of the deoxyribose sugar and protein backbone on the structure and binding energy between truncated nucleobase and amino acid models that are typically implemented in the literature. Most notably, electrostatic and steric interactions arising from the bulkiness of the biological backbones can change the preferred relative orientations of DNA and protein pi-systems. More importantly, the protein backbone can strengthen the stacking energy (by up to 10 kJ mol(-1)), while the deoxyribose moiety can strengthen or weaken the stacking interaction depending on the positioning of the amino acid relative to the sugar residue. These effects are likely due to additional interactions between the amino acid or nucleobase ring and the backbone in the extended monomer rather than significant changes in the properties of the biological pi-systems upon model extension. Since the present work reveals that all calculated DNA-protein stacking interactions are significant and approach the strength of other noncovalent interactions between biomolecules, both pi-pi and backbone-pi interactions must be considered when attempting to gain a complete picture of DNA-protein binding.
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Affiliation(s)
- Cassandra D M Churchill
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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125
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Dey RC, Seal P, Chakrabarti S. CH/π Interaction in Benzene and Substituted Derivatives with Halomethane: A Combined Density Functional and Dispersion-Corrected Density Functional Study. J Phys Chem A 2009; 113:10113-8. [DOI: 10.1021/jp905078p] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Ram Chandra Dey
- Department of Chemistry, University of Calcutta, 92, A. P. C. Ray Road, Kolkata - 700 009, India
| | - Prasenjit Seal
- Department of Chemistry, University of Calcutta, 92, A. P. C. Ray Road, Kolkata - 700 009, India
| | - Swapan Chakrabarti
- Department of Chemistry, University of Calcutta, 92, A. P. C. Ray Road, Kolkata - 700 009, India
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126
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Imai Y, Inoue Y, Nakanishi I, Kitaura K. Cl-π Interactions in Protein-Ligand Complexes. ACTA ACUST UNITED AC 2009. [DOI: 10.1002/qsar.200860168] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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127
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Trung NT, Hue TT, Nguyen MT. Remarkable blue shifts of C-H and N-H stretching frequencies in the interaction of monosubstituted formaldehyde and thioformaldehyde with nitrosyl hydride. J Phys Chem A 2009; 113:3245-53. [PMID: 19256510 DOI: 10.1021/jp810826z] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Weak interactions of monosubstituted formaldehydes and thioformaldehydes with nitrosyl hydride were investigated by using ab initio MO calculations at the MP2/aug-cc-pVTZ level. Thirty two equilibrium structures having different complex forms were located on the corresponding potential energy surfaces (all having C(s) symmetry). Obtained binding energies, which include both ZPE and BSSE corrections, range from 7 to 14 kJ x mol(-1) and 6 to 12 kJ x mol(-1) for complexes of substituted formaldehydes and thioformaldehydes, respectively. In each geometrical structure, the (XCHO,HNO) complex is consistently more stable than the (XCHS,HNO) complex. The H-bond strength significantly increases when one H atom is replaced by a methyl group in both formaldehyde and thioformaldehyde. When replacing H by a halogen atom, the binding energy tends to decrease. It is remarkable that all the C-H and N-H bonds are shortened upon complexation, resulting in an increase of their stretching frequencies. Furthermore, the blue shifts are consistently observed for the interacting N-H bonds in N-H...X, Z, with X = F, Cl, Br, and Z = O, S; such contraction of a covalent N-H bond is extremely rare. In addition, the N-H bond length contraction and its frequency blue shift in the N-H...S complex have been revealed for the first time.
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128
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Dinadayalane TC, Leszczynski J. In the pursuit of small "red shift" of C-H stretching vibrational frequency of C-H...pi interactions for benzene dimer: How to amend MP2 calculations to reproduce the experimental results. J Chem Phys 2009; 130:081101. [PMID: 19256586 DOI: 10.1063/1.3085815] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
For the bent T-shaped benzene dimer, the vibrational frequencies at the MP2/aug-cc-pVDZ level with counterpoise correction reproduce experimental results of the small "red shifts" of C-H stretching, while those without counterpoise correction yield considerable "blue shift." Counterpoise correction also affects the C-H bond distances of C-H...pi interactions as well as intermoiety distances.
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Affiliation(s)
- T C Dinadayalane
- Department of Chemistry, Interdisciplinary Center for Nanotoxicity, Jackson State University, Jackson, Mississippi 39217, USA
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129
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Shi Y, Sitkoff D, Zhang J, Klei HE, Kish K, Liu ECK, Hartl KS, Seiler SM, Chang M, Huang C, Youssef S, Steinbacher TE, Schumacher WA, Grazier N, Pudzianowski A, Apedo A, Discenza L, Yanchunas J, Stein PD, Atwal KS. Design, structure-activity relationships, X-ray crystal structure, and energetic contributions of a critical P1 pharmacophore: 3-chloroindole-7-yl-based factor Xa inhibitors. J Med Chem 2009; 51:7541-51. [PMID: 18998662 DOI: 10.1021/jm800855x] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
An indole-based P1 moiety was incorporated into a previously established factor Xa inhibitor series. The indole group was designed to hydrogen-bond with the carbonyl of Gly218, while its 3-methyl or 3-chloro substituent was intended to interact with Tyr228. These interactions were subsequently observed in the X-ray crystal structure of compound 18. SAR studies led to the identification of compound 20 as the most potent FXa inhibitor in this series (IC(50) = 2.4 nM, EC(2xPT) = 1.2 microM). An in-depth energetic analysis suggests that the increased binding energy of 3-chloroindole-versus 3-methylindole-containing compounds in this series is due primarily to (a) the more hydrophobic nature of chloro- versus methyl-containing compounds and (b) an increased interaction of 3-chloroindole versus 3-methylindole with Gly218 backbone. The stronger hydrophobicity of chloro- versus methyl-substituted aromatics may partly explain the general preference for chloro- versus methyl-substituted P1 groups in FXa, which extends beyond the current series.
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Affiliation(s)
- Yan Shi
- Bristol-Myers Squibb Research & Development, P.O. Box 5400, Princeton, New Jersey 08543-5400, USA.
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130
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Rutledge LR, Durst HF, Wetmore SD. Evidence for Stabilization of DNA/RNA−Protein Complexes Arising from Nucleobase−Amino Acid Stacking and T-Shaped Interactions. J Chem Theory Comput 2009; 5:1400-10. [DOI: 10.1021/ct800567q] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Holly F. Durst
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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131
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Imai YN, Ryu S, Oiki S. Docking Model of Drug Binding to the Human Ether-à-go-go Potassium Channel Guided by Tandem Dimer Mutant Patch-Clamp Data: A Synergic Approach. J Med Chem 2009; 52:1630-8. [DOI: 10.1021/jm801236n] [Citation(s) in RCA: 40] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Yumi N. Imai
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Sunghi Ryu
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
| | - Shigetoshi Oiki
- Discovery Research Center, Pharmaceutical Research Division, Takeda Pharmaceutical Company Ltd., Osaka 532-8686, Japan, and Department of Molecular Physiology and Biophysics, Faculty of Medical Sciences, University of Fukui, Fukui 910-1193, Japan
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132
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Raju RK, Ramraj A, Hillier IH, Vincent MA, Burton NA. Carbohydrate-aromatic pi interactions: a test of density functionals and the DFT-D method. Phys Chem Chem Phys 2009; 11:3411-6. [PMID: 19421542 DOI: 10.1039/b822877a] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023]
Abstract
The performance of a number of computational approaches based upon density functional theory (DFT) for the accurate description of carbohydrate-pi interactions is described. A database containing interaction energies of a small number of representative complexes, computed at a high ab initio level, is described, and is used to judge 18 different density functionals including the M05 and M06 families as well as the DFT method augmented with empirical dispersive corrections (DFT-D). The DFT-D method and the M06 functionals are found to perform particularly well, whilst traditional functionals such as B3LYP perform poorly. The interaction energies for 23 sugar-aromatic complexes calculated by the DFT-D method are compared with the values from the 18 functionals. Again, the M06 class of functional is found to be superior.
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Affiliation(s)
- Rajesh K Raju
- School of Chemistry, University of Manchester, Oxford Road, M13 9PL, Manchester, UK
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133
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Singh NJ, Min SK, Kim DY, Kim KS. Comprehensive Energy Analysis for Various Types of π-Interaction. J Chem Theory Comput 2009; 5:515-29. [PMID: 26610219 DOI: 10.1021/ct800471b] [Citation(s) in RCA: 218] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Affiliation(s)
- N. Jiten Singh
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Seung Kyu Min
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Dong Young Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
| | - Kwang S. Kim
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, Pohang 790-784, Korea
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134
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Crittenden DL. A Systematic CCSD(T) Study of Long-Range and Noncovalent Interactions between Benzene and a Series of First- and Second-Row Hydrides and Rare Gas Atoms. J Phys Chem A 2009; 113:1663-9. [DOI: 10.1021/jp809106b] [Citation(s) in RCA: 53] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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135
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Wu J, Yan H, Cao W. Study on the nature of unusual hydrogen-bonded complexes FClHX and halogen-bonded complexes FClClF. ACTA ACUST UNITED AC 2009. [DOI: 10.1016/j.theochem.2008.09.039] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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136
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Nishio M, Umezawa Y, Honda K, Tsuboyama S, Suezawa H. CH/π hydrogen bonds in organic and organometallic chemistry. CrystEngComm 2009. [DOI: 10.1039/b902318f] [Citation(s) in RCA: 481] [Impact Index Per Article: 32.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
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137
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Raju RK, Ramraj A, Vincent MA, Hillier IH, Burton NA. Carbohydrate-protein recognition probed by density functional theory and ab initio calculations including dispersive interactions. Phys Chem Chem Phys 2008; 10:6500-8. [PMID: 18979035 DOI: 10.1039/b809164a] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
Abstract
Carbohydrate-protein recognition has been studied by electronic structure calculations of complexes of fucose and glucose with toluene, p-hydroxytoluene and 3-methylindole, the latter aromatic molecules being analogues of phenylalanine, tyrosine and tryptophan, respectively. We use mainly a density functional theory model with empirical corrections for the dispersion interactions (DFT-D), this method being validated by comparison with a limited number of high level ab initio calculations. We have calculated both binding energies of the complexes as well as their harmonic vibrational frequencies and proton NMR chemical shifts. We find a range of minimum energy structures in which the aromatic group can bind to either of the two faces of the carbohydrate, the binding being dominated by a combination of OH-pi and CH-pi dispersive interactions. For the fucose-toluene and alpha-methyl glucose-toluene complexes, the most stable structures involve OH-pi interactions, which are reflected in a red shift of the corresponding O-H stretching frequency, in good quantitative agreement with experimental data. For those structures where CH-pi interactions are found we predict a corresponding blue shift in the C-H frequency, which parallels the predicted proton NMR shift. We find that the interactions involving 3-methylindole are somewhat greater than those for toluene and p-hydroxytoluene.
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Affiliation(s)
- Rajesh K Raju
- School of Chemistry, University of Manchester, Oxford Road, Manchester, UKM13 9PL
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138
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Lait LA, Rutledge LR, Millen AL, Wetmore SD. yDNA versus xDNA Pyrimidine Nucleobases: Computational Evidence for Dependence of Duplex Stability on Spacer Location. J Phys Chem B 2008; 112:12526-36. [DOI: 10.1021/jp805547p] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Linda A. Lait
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Andrea L. Millen
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, T1K 3M4, Canada
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139
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Rutledge LR, Wetmore SD. Remarkably Strong T-Shaped Interactions between Aromatic Amino Acids and Adenine: Their Increase upon Nucleobase Methylation and a Comparison to Stacking. J Chem Theory Comput 2008; 4:1768-80. [DOI: 10.1021/ct8002332] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Lesley R. Rutledge
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
| | - Stacey D. Wetmore
- Department of Chemistry and Biochemistry, University of Lethbridge, 4401 University Drive, Lethbridge, Alberta, Canada T1K 3M4
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140
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Cabaleiro-Lago EM, Rodríguez-Otero J, Peña-Gallego Á. Computational Study on the Characteristics of the Interaction in Naphthalene···(H2X)n=1,2 (X = O, S) Clusters. J Phys Chem A 2008; 112:6344-50. [DOI: 10.1021/jp8021979] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- 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, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
| | - Jesús Rodríguez-Otero
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
| | - Ángeles Peña-Gallego
- Departamento de Química Física, Facultade de Ciencias, Universidade de Santiago de Compostela, Campus de Lugo, Avda. Alfonso X El Sabio s/n 27002 Lugo, Galicia, Spain, and Departamento de Química Física, Facultade de Química, Universidade de Santiago de Compostela, Avda. das Ciencias, s/n 15706 Santiago de Compostela, Galicia, Spain
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141
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Cabaleiro-Lago EM, Peña-Gallego Á, Rodríguez-Otero J. Study of the interaction in clusters formed by phenol and CH3X (X=CN,F,Cl) molecules. J Chem Phys 2008; 128:194311. [DOI: 10.1063/1.2919128] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
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142
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Wang ZX, Zheng BS, Yu XY, Yi PG. Characteristics and nature of the intermolecular interactions between thiophene and XY(X, Y=F, Cl, Br): A theoretical study. ACTA ACUST UNITED AC 2008. [DOI: 10.1016/j.theochem.2008.01.032] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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143
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Imai YN, Inoue Y, Nakanishi I, Kitaura K. Cl-pi interactions in protein-ligand complexes. Protein Sci 2008; 17:1129-37. [PMID: 18434503 DOI: 10.1110/ps.033910.107] [Citation(s) in RCA: 159] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
During systematic analysis of nonbonded contacts in protein-ligand complexes derived from crystal structures in the Protein Data Bank, Cl-pi interactions have been found, not only in the well-documented serine proteases but also, to a lesser extent, in other proteins. From geometric analysis of such Cl-pi interactions in the crystal structures, two distinct geometries were found: the "edge-on" approach of a Cl atom to a ring atom or C-C bond and the "face-on" approach toward the ring centroid with an average interatomic distance of 3.6 A. High-level ab initio calculations using benzene-chlorohydrocarbon model systems elucidated that the calculated Cl-pi interaction energy is -2.01 kcal/mol, and the dispersion force is the major source of attraction. We also discussed the geometric flexibility in Cl-pi interactions and a relationship between the intensity of the pi density in an aromatic ring and the interaction position of the Cl atom.
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Affiliation(s)
- Yumi N Imai
- Department of Theoretical Drug Design, Graduate School of Pharmaceutical Sciences, Kyoto University, Kyoto 606-8501, Japan.
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144
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Hooper J, Cooper VR, Thonhauser T, Romero NA, Zerilli F, Langreth DC. Predicting CH/π Interactions with Nonlocal Density Functional Theory. Chemphyschem 2008; 9:891-5. [DOI: 10.1002/cphc.200700715] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
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145
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Takatani T, Hohenstein EG, Sherrill CD. Improvement of the coupled-cluster singles and doubles method via scaling same- and opposite-spin components of the double excitation correlation energy. J Chem Phys 2008; 128:124111. [DOI: 10.1063/1.2883974] [Citation(s) in RCA: 120] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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146
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Cohen M, Reichmann D, Neuvirth H, Schreiber G. Similar chemistry, but different bond preferences in inter versus intra-protein interactions. Proteins 2008; 72:741-53. [DOI: 10.1002/prot.21960] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
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147
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Tsuzuki S, Honda K, Fujii A, Uchimaru T, Mikami M. CH/π interactions in methane clusters with polycyclic aromatic hydrocarbons. Phys Chem Chem Phys 2008; 10:2860-5. [DOI: 10.1039/b718550b] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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148
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Fujii A, Shibasaki K, Kazama T, Itaya R, Mikami N, Tsuzuki S. Experimental and theoretical determination of the accurate interaction energies in benzene–halomethane: the unique nature of the activated CH/π interaction of haloalkanes. Phys Chem Chem Phys 2008; 10:2836-43. [DOI: 10.1039/b717053j] [Citation(s) in RCA: 74] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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149
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Tsuzuki S, Fujii A. Nature and physical origin of CH/π interaction: significant difference from conventional hydrogen bonds. Phys Chem Chem Phys 2008; 10:2584-94. [DOI: 10.1039/b718656h] [Citation(s) in RCA: 288] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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150
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Abstract
The importance of stacking interactions for the Twist and stability of DNA is investigated using the fully ab initio van der Waals density functional (vdW-DF). Our results highlight the role that binary interactions between adjacent sets of base pairs play in defining the sequence-dependent Twists observed in high-resolution experiments. Furthermore, they demonstrate that additional stability gained by the presence of thymine is due to methyl interactions with neighboring bases, thus adding to our understanding of the mechanisms that contribute to the relative stability of DNA and RNA. Our mapping of the energy required to twist each of the 10 unique base pair steps should provide valuable information for future studies of nucleic acid stability and dynamics. The method introduced will enable the nonempirical theoretical study of significantly larger pieces of DNA or DNA/amino acid complexes than previously possible.
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