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Deb B, Mahanta H, Baruah NP, Khardewsaw M, Paul AK. On the intramolecular vibrational energy redistribution dynamics of aromatic complexes: A comparative study on C6H6-C6H5Cl, C6H6-C6H3Cl3, C6H6-C6Cl6 and C6H6-C6H5F, C6H6-C6H3F3, C6H6-C6F6. J Chem Phys 2024; 160:024307. [PMID: 38197444 DOI: 10.1063/5.0174748] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2023] [Accepted: 12/17/2023] [Indexed: 01/11/2024] Open
Abstract
Chemical dynamics Simulation studies on benzene dimer (Bz2) and benzene-hexachlorobenzene (Bz-HCB) as performed in the past suggest that the coupling between the monomeric (intramolecular) vibrational modes and modes generated due to the association of two monomers (intermolecular) has to be neither strong nor weak for a fast dissociation of the complex. To find the optimum coupling, four complexes are taken into consideration in this work, namely, benzene-monofluorobenzene, benzene-monochlorobenzene, benzene-trifluorobenzene (Bz-TFB), and benzene-trichlorobenzene. Bz-TFB has the highest rate of dissociation among all seven complexes, including Bz2, Bz-HCB, and Bz-HFB (HFB stands for hexafluorobenzene). The set of vibrational frequencies of Bz-TFB is mainly the reason for this fast dissociation. The mass of chlorine in Bz-HCB is optimized to match its vibrational frequencies similar to those of Bz-TFB, and the dissociation of Bz-HCB becomes faster. The power spectrum of Bz-TFB, Bz-HCB, and Bz-HCB with the modified mass of chlorine is also computed to understand the extent of the said coupling in these complexes.
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Affiliation(s)
- Basudha Deb
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Himashree Mahanta
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
- Department of Chemistry, Assam Kaziranga University, Koraikhowa, NH-37, Jorhat 785006, India
| | - Netra Prava Baruah
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Maitjingshai Khardewsaw
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
| | - Amit Kumar Paul
- Department of Chemistry, National Institute of Technology Meghalaya Bijni Complex, Laitumkhrah, Shillong 793003, India
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2
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Quesada-Moreno MM, Pinacho P, Pérez C, Šekutor M, Schreiner PR, Schnell M. Do Docking Sites Persist Upon Fluorination? The Diadamantyl Ether-Aromatics Challenge for Rotational Spectroscopy and Theory. Chemistry 2021; 27:6198-6203. [PMID: 33512017 PMCID: PMC8048501 DOI: 10.1002/chem.202100078] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Indexed: 12/28/2022]
Abstract
Fluorinated derivatives of biological molecules have proven to be highly efficient at modifying the biological activity of a given protein through changes in the stability and the kind of docking interactions. These interactions can be hindered or facilitated based on the hydrophilic/hydrophobic character of a particular protein region. Diadamantyl ether (C20H30O) possesses both kinds of docking sites, serving as a good template to model these important contacts with aromatic fluorinated counterparts. In this work, an experimental study on the structures of several complexes between diadamantyl ether and benzene as well as a series of fluorinated benzenes is reported to analyze the effect of H→F substitution on the interaction and structure of the resulting molecular clusters using rotational spectroscopy. All experimentally observed complexes are largely dominated by London dispersion interactions with the hydrogen‐terminated surface areas of diadamantyl ether. Already single substitution of one hydrogen atom with fluorine changes the preferred docking site of the complexes. However, the overall contributions of the different intermolecular interactions are similar for the different complexes, contrary to previous studies focusing on the difference in interactions using fluorinated and non‐fluorinated molecules.
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Affiliation(s)
| | - Pablo Pinacho
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Cristóbal Pérez
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany
| | - Marina Šekutor
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Peter R Schreiner
- Institute of Organic Chemistry, Justus Liebig University, Heinrich-Buff-Ring 17, 35392, Giessen, Germany
| | - Melanie Schnell
- Deutsches Elektronen-Synchrotron (DESY), Notkestr. 85, 22607, Hamburg, Germany.,Institute of Physical Chemistry, Christian-Albrechts-Universität zu Kiel, Max-Eyth-Str. 1, 24118, Kiel, Germany
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3
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Kosikowska U, Wujec M, Trotsko N, Płonka W, Paneth P, Paneth A. Antibacterial Activity of Fluorobenzoylthiosemicarbazides and Their Cyclic Analogues with 1,2,4-Triazole Scaffold. Molecules 2020; 26:E170. [PMID: 33396536 PMCID: PMC7796209 DOI: 10.3390/molecules26010170] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 12/18/2020] [Accepted: 12/28/2020] [Indexed: 11/17/2022] Open
Abstract
The development of drug-resistant bacteria is currently one of the major challenges in medicine. Therefore, the discovery of novel lead structures for the design of antibacterial drugs is urgently needed. In this structure-activity relationship study, a library of ortho-, meta-, and para-fluorobenzoylthiosemicarbazides, and their cyclic analogues with 1,2,4-triazole scaffold, was created and tested for antibacterial activity against Gram-positive bacteria strains. While all tested 1,2,4-triazoles were devoid of potent activity, the antibacterial response of the thiosemicarbazides was highly dependent on substitution pattern at the N4 aryl position. The optimum activity for these compounds was found for trifluoromethyl derivatives such as 15a, 15b, and 16b, which were active against both the reference strains panel, and pathogenic methicillin-sensitive and methicillin-resistant Staphylococcus aureus clinical isolates at minimal inhibitory concentrations (MICs) ranging from 7.82 to 31.25 μg/mL. Based on the binding affinities obtained from docking, the conclusion can be reached that fluorobenzoylthiosemicarbazides can be considered as potential allosteric d-alanyl-d-alanine ligase inhibitors.
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Affiliation(s)
- Urszula Kosikowska
- Department of Pharmaceutical Microbiology, Faculty of Pharmacy, Medical University of Lublin, Chodźki 1, 20-093 Lublin, Poland;
| | - Monika Wujec
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
| | - Nazar Trotsko
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
| | | | - Piotr Paneth
- Institute of Applied Radiation Chemistry, Faculty of Chemistry, Lodz University of Technology, Żeromskiego 116, 90-924 Lodz, Poland;
| | - Agata Paneth
- Department of Organic Chemistry, Faculty of Pharmacy, Medical University of Lublin, Chodźki 4a, 20-093 Lublin, Poland; (M.W.); (N.T.)
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4
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Kazim M, Siegler MA, Lectka T. Close Amide NH···F Hydrogen Bonding Interactions in 1,8-Disubstituted Naphthalenes. J Org Chem 2020; 85:6195-6200. [PMID: 32227992 DOI: 10.1021/acs.joc.0c00553] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
Abstract
In this note, we present a series of N-(8-fluoronaphthalen-1-yl)benzamide derivatives designed to maximize amide-NH···F hydrogen bond interactions therein. A combination of IR and NMR spectroscopy indicates a linear correlation between the high energy shift in NH stretching frequency and the electron withdrawing nature of the substituent, consistent with the trend predicted by DFT calculations. Additionally, a limiting case of hydrogen bonding is observed when the benzamide derivatives are replaced with trifluoroacetamide, causing an additional red shift of 44 cm-1 in the NH stretching frequency. Most importantly, 1H-19F coupling constants in this series are among the largest measured for amide-NH···F interactions. X-ray crystallography reveals face-to-face alignment of naphthalene rings in these derivatives resulting in part from the NH···F hydrogen bonds. This motif also dictates the formation of sheets composed of stacked naphthalene rings in the crystal structure as opposed to unfluorinated analogues wherein NH···OC hydrogen-bonding interactions force benzamide and naphthalene rings to engage in T-shaped π-π interactions instead. Additionally, the NH proton in the trifluoroacetamide derivative engages in extended H-bond interactions in its crystal structure.
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Affiliation(s)
- Muhammad Kazim
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Maxime A Siegler
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
| | - Thomas Lectka
- Department of Chemistry, Johns Hopkins University, 3400 North Charles Street, Baltimore, Maryland 21218, United States
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5
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Investigating the impact of aromatic ring substitutions on selectivity for a multimodal anion exchange prototype library. J Chromatogr A 2018; 1569:101-109. [DOI: 10.1016/j.chroma.2018.07.049] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2018] [Revised: 07/08/2018] [Accepted: 07/15/2018] [Indexed: 11/17/2022]
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6
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Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017. [DOI: 10.1002/ange.201700520] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Drug Discovery and Development Centre (H3D); Department of Chemistry; University of Cape Town; Rondebosch 7701 South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
- Max-Planck-Institut für Kolloid- und Grenzflächenforschung; Am Mühlenberg 1 14476 Potsdam Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL); Chemical Biology Core Facility; Meyerhofstrasse 1 69117 Heidelberg Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie; Anorganische Chemie; Freie Universität Berlin; Fabeckstrasse 34-36 14195 Berlin Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology; Leibniz-Institut fϋr Molekulare Pharmakologie (FMP); Campus Berlin-Buch; Robert-Roessle-Strasse 10 13125 Berlin Germany
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7
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Sun H, Horatscheck A, Martos V, Bartetzko M, Uhrig U, Lentz D, Schmieder P, Nazaré M. Direct Experimental Evidence for Halogen-Aryl π Interactions in Solution from Molecular Torsion Balances. Angew Chem Int Ed Engl 2017; 56:6454-6458. [PMID: 28452102 DOI: 10.1002/anie.201700520] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Indexed: 12/24/2022]
Abstract
We dissected halogen-aryl π interactions experimentally using a bicyclic N-arylimide based molecular torsion balances system, which is based on the influence of the non-bonded interaction on the equilibria between folded and unfolded states. Through comparison of balances modulated by higher halogens with fluorine balances, we determined the magnitude of the halogen-aryl π interactions in our unimolecular systems to be larger than -5.0 kJ mol-1 , which is comparable with the magnitude estimated in the biomolecular systems. Our study provides direct experimental evidence of halogen-aryl π interactions in solution, which until now have only been revealed in the solid state and evaluated theoretically by quantum-mechanical calculations.
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Affiliation(s)
- Han Sun
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - André Horatscheck
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Drug Discovery and Development Centre (H3D), Department of Chemistry, University of Cape Town, Rondebosch, 7701, South Africa
| | - Vera Martos
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Max Bartetzko
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany.,Max-Planck-Institut für Kolloid- und Grenzflächenforschung, Am Mühlenberg 1, 14476, Potsdam, Germany
| | - Ulrike Uhrig
- European Molecular Biology Laboratory (EMBL), Chemical Biology Core Facility, Meyerhofstrasse 1, 69117, Heidelberg, Germany
| | - Dieter Lentz
- Institut für Chemie und Biochemie, Anorganische Chemie, Freie Universität Berlin, Fabeckstrasse 34-36, 14195, Berlin, Germany
| | - Peter Schmieder
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
| | - Marc Nazaré
- Departments of Chemical Biology and Structural Biology, Leibniz-Institut fϋr Molekulare Pharmakologie (FMP), Campus Berlin-Buch, Robert-Roessle-Strasse 10, 13125, Berlin, Germany
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8
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Landeros-Rivera B, Moreno-Esparza R, Hernández-Trujillo J. Theoretical study of intermolecular interactions in crystalline arene–perhaloarene adducts in terms of the electron density. RSC Adv 2016. [DOI: 10.1039/c6ra14957j] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The intermolecular interactions in C6X6–arene crystals (X = F, Cl) and the halogen substitution effect can be quantified by the electron density.
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9
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Liu L, Jalili N, Baergen A, Ng S, Bailey J, Derda R, Klassen JS. Fluorine bonding enhances the energetics of protein-lipid binding in the gas phase. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2014; 25:751-757. [PMID: 24658801 DOI: 10.1007/s13361-014-0837-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/15/2013] [Revised: 01/13/2014] [Accepted: 01/15/2014] [Indexed: 06/03/2023]
Abstract
This paper reports on the first experimental study of the energies of noncovalent fluorine bonding in a protein-ligand complex in the absence of solvent. Arrhenius parameters were measured for the dissociation of gaseous deprotonated ions of complexes of bovine β-lactoglobulin (Lg), a model lipid-binding protein, and four fluorinated analogs of stearic acid (SA), which contained (X =) 13, 15, 17, or 21 fluorine atoms. In all cases, the activation energies (E(a)) measured for the loss of neutral XF-SA from the (Lg + XF-SA)⁷⁻ ions are larger than for SA. From the kinetic data, the average contribution of each > CF₂ group to E(a) was found to be ~1.1 kcal mol⁻¹, which is larger than the ~0.8 kcal mol⁻¹ value reported for > CH₂ groups. Based on these results, it is proposed that fluorocarbon–protein interactions are inherently stronger (enthalpically) than the corresponding hydrocarbon interactions.
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10
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Gardarsson H, Schweizer WB, Trapp N, Diederich F. Structures and Properties of Molecular Torsion Balances to Decipher the Nature of Substituent Effects on the Aromatic Edge-to-Face Interaction. Chemistry 2014; 20:4608-16. [DOI: 10.1002/chem.201304810] [Citation(s) in RCA: 54] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Indexed: 11/10/2022]
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11
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Ebrahimi A, Karimi P, Akher FB, Behazin R, Mostafavi N. Investigation of the π–π stacking interactions without direct electrostatic effects of substituents: the aromatic∥aromatic and aromatic∥anti-aromatic complexes. Mol Phys 2013. [DOI: 10.1080/00268976.2013.830784] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/26/2022]
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12
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Riley KE, Hobza P. On the importance and origin of aromatic interactions in chemistry and biodisciplines. Acc Chem Res 2013; 46:927-36. [PMID: 22872015 DOI: 10.1021/ar300083h] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Aromatic systems contain both σ- and π-electrons, which in turn constitute σ- and π-molecular orbitals (MOs). In discussing the properties of these systems, researchers typically refer to the highest occupied and lowest unoccupied MOs, which are π MOs. The characteristic properties of aromatic systems, such as their low ionization potentials and electron affinities, high polarizabilities and stabilities, and small band gaps (in spectroscopy called the N → V1 space), can easily be explained based on their electronic structure. These one-electron properties point to characteristic features of how aromatic systems interact with each other. Unlike hydrogen bonding systems, which primarily interact through electrostatic forces, complexes containing aromatic systems, especially aromatic stacked pairs, are predominantly stabilized by dispersion attraction. The stabilization energy in the benzene dimer is rather small (~2.5 kcal/mol) but strengthens with heteroatom substitution. The stacked interaction of aromatic nucleic acid bases is greater than 10 kcal/mol, and for the most stable stacked pair, guanine and cytosine, it reaches approximately 17 kcal/mol. Although these values do not equal the planar H-bonded interactions of these bases (~29 kcal/mol), stacking in DNA is more frequent than H-bonding and, unlike H-bonding, is not significantly weakened when passing from the gas phase to a water environment. Consequently, the stacking of aromatic systems represents the leading stabilization energy contribution in biomacromolecules and in related nanosystems. Therefore stacking (dispersion) interactions predominantly determine the double helical structure of DNA, which underlies its storage and transfer of genetic information. Similarly, dispersion is the dominant contributor to attractive interactions involving aromatic amino acids within the hydrophobic core of a protein, which is critical for folding. Therefore, understanding the nature of aromatic interactions, which depend greatly on quantum mechanical (QM) calculations, is of key importance in biomolecular science. This Account shows that accurate binding energies for aromatic complexes should be based on computations made at the (estimated) CCSD(T)/complete basis set limit (CBS) level of theory. This method is the least computationally intensive one that can give accurate stabilization energies for all common classes of noncovalent interactions (aromatic-aromatic, H-bonding, ionic, halogen bonding, charge-transfer, etc.). These results allow for direct comparison of binding energies between different interaction types. Conclusions based on lower-level QM calculations should be considered with care.
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Affiliation(s)
- Kevin E. Riley
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
| | - Pavel Hobza
- Institute of Organic Chemistry and Biochemistry, Academy of Sciences of the Czech Republic, 166 10 Prague, Czech Republic
- Regional Centre of Advanced Technologies and Materials, Department of Physical Chemistry, Faculty of Science, Palacky University, 771 46 Olomouc, Czech Republic
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13
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Effects of fluorines on nonsecosteroidal vitamin D receptor agonists. Bioorg Med Chem 2013; 21:712-21. [DOI: 10.1016/j.bmc.2012.11.029] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2012] [Revised: 11/20/2012] [Accepted: 11/21/2012] [Indexed: 11/17/2022]
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14
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Bloom JWG, Raju RK, Wheeler SE. Physical Nature of Substituent Effects in XH/π Interactions. J Chem Theory Comput 2012; 8:3167-74. [DOI: 10.1021/ct300520n] [Citation(s) in RCA: 79] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jacob W. G. Bloom
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Rajesh K. Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
| | - Steven E. Wheeler
- Department of Chemistry, Texas A&M University, College Station, Texas 77843, United States
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Raju RK, Bloom JWG, An Y, Wheeler SE. Substituent effects on non-covalent interactions with aromatic rings: insights from computational chemistry. Chemphyschem 2011; 12:3116-30. [PMID: 21928437 DOI: 10.1002/cphc.201100542] [Citation(s) in RCA: 107] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Indexed: 02/01/2023]
Abstract
Non-covalent interactions with aromatic rings pervade modern chemical research. The strength and orientation of these interactions can be tuned and controlled through substituent effects. Computational studies of model complexes have provided a detailed understanding of the origin and nature of these substituent effects, and pinpointed flaws in entrenched models of these interactions in the literature. Here, we provide a brief review of efforts over the last decade to unravel the origin of substituent effects in π-stacking, XH/π, and ion/π interactions through detailed computational studies. We highlight recent progress that has been made, while also uncovering areas where future studies are warranted.
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Affiliation(s)
- Rajesh K Raju
- Department of Chemistry, Texas A&M University, College Station, Texas 77842, USA
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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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17
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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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18
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Albrecht M, Müller M, Valkonen A, Rissanen K. Weak non-covalent interactions control the relative molecular orientation in the crystals of N-pentafluorobenzyl aniline derivatives. CrystEngComm 2010. [DOI: 10.1039/c003636f] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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19
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Zhou P, Zou J, Tian F, Shang Z. Fluorine Bonding — How Does It Work In Protein−Ligand Interactions? J Chem Inf Model 2009; 49:2344-55. [DOI: 10.1021/ci9002393] [Citation(s) in RCA: 207] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Peng Zhou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Jianwei Zou
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Feifei Tian
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
| | - Zhicai Shang
- Department of Chemistry, Zhejiang University, Hangzhou 310027, China, Key Laboratory for Molecular Design and Nutrition Engineering, Ningbo Institute of Technology, Zhejiang University, Ningbo 315100, China, College of Bioengineering, Chongqing University, Chongqing 400044, China, and Center for Heterocyclic Compounds, Department of Chemistry, University of Florida, Gainesville, Florida 32611
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Hohenstein EG, Sherrill CD. Effects of heteroatoms on aromatic pi-pi interactions: benzene-pyridine and pyridine dimer. J Phys Chem A 2009; 113:878-86. [PMID: 19132847 DOI: 10.1021/jp809062x] [Citation(s) in RCA: 250] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Heteroatoms are found in many noncovalent complexes which are of biological importance. The effect of heteroatoms on pi-pi interactions is assessed via highly accurate quantum chemical computations for the two simplest cases of interactions between aromatic molecules containing heteroatoms, namely, benzene-pyridine and pyridine dimer. Benchmark quality estimated coupled-cluster through perturbative triples [CCSD(T)] binding energies are computed near the complete basis set limit. Comparisons to the benzene dimer are made to determine the contributions from heteroatoms. The presence of a heteroatom reduces the spatial extent of the pi-electron cloud and polarizability of pyridine as compared to benzene. As a result, the magnitude of the dispersion, exchange, and induction interactions in benzene-pyridine and pyridine dimer is generally reduced as compared to those for the benzene dimer. Benzene-pyridine and pyridine dimer bind more strongly than the benzene dimer in several configurations, and in contrast to the benzene dimer, parallel-displaced configurations can be significantly preferred over T-shaped configurations. Hydrogens para to a heteroatom are more effective "pi-hydrogen bond" donors, but aromatic rings with heteroatoms are worse "pi-hydrogen bond" acceptors.
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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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21
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Dinadayalane TC, Leszczynski J. Geometries and stabilities of various configurations of benzene dimer: details of novel V-shaped structure revealed. Struct Chem 2009. [DOI: 10.1007/s11224-009-9411-6] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
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22
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Caramori GF, Galembeck SE. A Computational Study of Tetrafluoro-[2.2]Cyclophanes. J Phys Chem A 2008; 112:11784-800. [DOI: 10.1021/jp805125r] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Giovanni F. Caramori
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto—SP, Brazil
| | - Sérgio E. Galembeck
- Departamento de Química, Faculdade de Filosofia, Ciências e Letras de Ribeirão Preto, Universidade de São Paulo, 14040-901, Ribeirão Preto—SP, Brazil
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23
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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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25
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Rutledge LR, Durst HF, Wetmore SD. Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases. Phys Chem Chem Phys 2008; 10:2801-12. [DOI: 10.1039/b718621e] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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26
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Arnstein SA, Sherrill CD. Substituent effects in parallel-displaced π–π interactions. Phys Chem Chem Phys 2008; 10:2646-55. [DOI: 10.1039/b718742d] [Citation(s) in RCA: 142] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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27
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Morgado CA, Hillier IH, Burton NA, McDouall JJW. A QM/MM study of fluoroaromatic interactions at the binding site of carbonic anhydrase II, using a DFT method corrected for dispersive interactions. Phys Chem Chem Phys 2008; 10:2706-14. [DOI: 10.1039/b715514j] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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28
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Rutledge LR, Campbell-Verduyn LS, Hunter KC, Wetmore SD. Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme. J Phys Chem B 2007; 110:19652-63. [PMID: 17004834 DOI: 10.1021/jp061939v] [Citation(s) in RCA: 67] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladenine due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage. The MP2 potential energy surfaces of the stacked dimers are considered as a function of four variables (vertical displacement, angle of rotation, horizontal displacement, and tilt angle) using a variety of basis sets. It is found that the maximum stacking interaction energy decreases with the amino acid according to TRP > TYR approximately HIS > PHE for both nucleobases. However, the magnitude of the stacking interaction significantly increases upon alkylation (by 50-115%). Comparison of the stacking energies calculated using our surface scans to those estimated from experimental crystal structures indicates that the stacking interactions within the active site of 3-methyladenine DNA glycosylase can account for 65-75% of the maximum possible stacking interaction between the relevant molecules. The decrease in stacking in the crystal structure arises due to significant differences in the relative orientations of the nucleobase and amino acid. Nevertheless, alkylation is found to significantly increase the stacking energy when the crystal structure geometries are considered. Our calculations provide computational support for suggestions that alkylation enhances the stacking interactions within the active site of DNA repair enzymes, and they give a measure of the magnitude of this enhancement. Our results suggest that alkylation likely plays a more important role in substrate identification and removal than the nature of the aromatic amino acid that interacts with the substrate via stacking interactions.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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29
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Jack E, Newsome M, Stockley PG, Radford SE, Middleton DA. The organization of aromatic side groups in an amyloid fibril probed by solid-state 2H and 19F NMR spectroscopy. J Am Chem Soc 2007; 128:8098-9. [PMID: 16787049 DOI: 10.1021/ja0581898] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Some 25 diseases are associated with proteins and peptides that assemble into amyloid fibrils composed of beta-strands connected by hydrogen bonds oriented parallel to the fiber long axis. There is mounting evidence that amyloid formation involves specific interactions between amino acid side groups, which bring together beta-sheets to form layers with buried and exposed faces. This work demonstrates how a combination of solid-state 2H and 19F NMR experiments can provide constraints on fibril architecture by probing the environment and spatial organisation of aromatic side groups. It is shown that phenylalanine rings within fibrils formed by a decapeptide fragment of the islet amyloid polypeptide, amylin, are highly motionally restrained and are situated within 6.5 A of one another. Taken together with existing structural constraints for this peptide, these results are consistent with a fibril architecture that comprises layers of two or more beta-sheets, with the aromatic residues facing into the inter-sheet space and possibly engaged in pi-pi interactions. The methods presented will be of general utility in exploring the architecture of fibrils of larger, full-length peptides and proteins, including amylin itself.
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Affiliation(s)
- Edward Jack
- Faculty of Life Sciences, University of Manchester, P.O. Box 88, Manchester M60 1QD, United Kingdom
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30
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Fernández B, Pedersen TB, Sánchez de Merás A, Koch H. Coupled cluster calculations of interaction energies in benzene–fluorobenzene van der Waals complexes. Chem Phys Lett 2007. [DOI: 10.1016/j.cplett.2007.05.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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31
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Riley KE, Cui G, Merz KM. An ab Initio Investigation of the Interactions Involving the Aromatic Group of the Set of Fluorinated N-(4-Sulfamylbenzoyl)benzylamine Inhibitors and Human Carbonic Anhydrase II. J Phys Chem B 2007; 111:5700-7. [PMID: 17474767 DOI: 10.1021/jp067313m] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
In this work we investigate the interactions that occur between the aromatic portion of the set of fluorinated N-(4-sulfamylbenzoyl)benzylamine (SBB) inhibitors and two residues of Human Carbonic Anhydrase II (HCAII), namely Phe-131 and Pro-202. Calculations were carried out at the MP2/aug-cc-pVDZ level of theory and the counterpoise scheme of Boys and Bernardi was employed to account for the basis set superposition error. The most striking result obtained here is that the SBB phenyl ring interacts at least as strongly with the proline pyrrolidine ring as with the phenylalanine phenyl ring, which is surprising because aromatic-aromatic interactions have long been thought to be particularly favorable in protein and protein-ligand structure. Comparison of the MP2 binding energies to those obtained with the Hartree-Fock method indicates that the attraction between the proline pyrrolidine ring and the SBB phenyl ring is largely attributable to dispersion forces. These favorable interactions between pyrrolidine and phenyl rings may have important implications in protein structure because there is potential for proline residues to interact with phenylalanine residues in a fashion analogous to that seen here. A preliminary protein data bank search indicates that the proline-phenylalanine contacts are about 40% as common as those between two phenylalanines. It is also found here that the number and pattern of fluorine substituents on the SBB phenyl ring is much less important in determining the SBB-HCAII binding energy than the relative geometric configuration of the interacting pairs.
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Affiliation(s)
- Kevin E Riley
- Quantum Theory Project and Department of Chemistry, The University of Florida, Gainesville, Florida 32611-8435, USA
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32
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Lee EC, Kim D, Jurecka P, Tarakeshwar P, Hobza P, Kim KS. Understanding of Assembly Phenomena by Aromatic−Aromatic Interactions: Benzene Dimer and the Substituted Systems. J Phys Chem A 2007; 111:3446-57. [PMID: 17429954 DOI: 10.1021/jp068635t] [Citation(s) in RCA: 512] [Impact Index Per Article: 30.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interactions involving aromatic rings are important in molecular/biomolecular assembly and engineering. As a consequence, there have been a number of investigations on dimers involving benzene or other substituted pi systems. In this Feature Article, we examine the relevance of the magnitudes of their attractive and repulsive interaction energy components in governing the geometries of several pi-pi systems. The geometries and the associated binding energies were evaluated at the complete basis set (CBS) limit of coupled cluster theory with singles, doubles, and perturbative triples excitations [CCSD(T)] using a least biased scheme for the given data set. The results for the benzene dimer indicate that the floppy T-shaped structure (center-to-center distance: 4.96 A, with an axial benzene off-centered above the facial benzene) is isoenergetic in zero-point-energy (ZPE) corrected binding energy (D0) to the displaced-stacked structure (vertical interplanar distance: 3.54 A). However, the T-shaped structure is likely to be slightly more stable (D0 approximately equal to 2.4-2.5 kcal/mol) if quadruple excitations are included in the coupled cluster calculations. The presence of substituents on the aromatic ring, irrespective of their electron withdrawing or donating nature, leads to an increase in the binding energy, and the displaced-stacked conformations are more stabilized than the T-shaped conformers. This explains the wide prevalence of displaced stacked structures in organic crystals. Despite that the dispersion energy is dominating, the substituent as well as the conformational effects are correlated to the electrostatic interaction. This electrostatic origin implies that the substituent effect would be reduced in polar solution, but important in apolar media, in particular, for assembling processes.
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Affiliation(s)
- Eun Cheol Lee
- Center for Superfunctional Materials, Department of Chemistry, Pohang University of Science and Technology, San 31, Hyojadong, Namgu, Pohang 790-784, Korea
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33
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Allesch M, Schwegler E, Galli G. Structure of Hydrophobic Hydration of Benzene and Hexafluorobenzene from First Principles. J Phys Chem B 2007; 111:1081-9. [PMID: 17266261 DOI: 10.1021/jp065429c] [Citation(s) in RCA: 49] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
We report on the aqueous hydration of benzene and hexafluorobenzene, as obtained by carrying out extensive (>100 ps) first principles molecular dynamics simulations. Our results show that benzene and hexafluorobenzene do not behave as ordinary hydrophobic solutes, but rather present two distinct regions, one equatorial and the other axial, that exhibit different solvation properties. While in both cases the equatorial regions behave as typical hydrophobic solutes, the solvation properties of the axial regions depend strongly on the nature of the pi-water interaction. In particular, pi-hydrogen and pi-lone pair interactions are found to dominate in benzene and hexafluorobenzene, respectively, which leads to substantially different orientations of water near the two solutes. We present atomic and electronic structure results (in terms of Maximally Localized Wannier Functions) providing a microscopic description of benzene- and hexafluorobenzene-water interfaces, as well as a comparative study of the two solutes. Our results point at the importance of an accurate description of interfacial water to characterize hydration properties of apolar molecules, as these are strongly influenced by subtle charge rearrangements and dipole moment redistributions in interfacial regions.
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Affiliation(s)
- Markus Allesch
- Department of Theoretical and Computational Physics, Graz University of Technology, Graz, Austria
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34
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Rutledge LR, Wheaton CA, Wetmore SD. A computational characterization of the hydrogen-bonding and stacking interactions of hypoxanthine. Phys Chem Chem Phys 2007; 9:497-509. [PMID: 17216066 DOI: 10.1039/b606388h] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The hydrogen-bonding and stacking interactions of hypoxanthine, a potential universal nucleobase, were calculated using a variety of methodologies (CCSD(T), MP2, B3LYP, PWB6K, AMBER). All methods predict that the hydrogen-bonding interaction in the hypoxanthine-cytosine pair is approximately 25 kJ mol(-1) stronger than that in the other dimers. Although the calculations support suggestions from experiments that hypoxanthine preferentially binds with cytosine, the trend in the calculated hydrogen-bond strengths for the remaining natural nucleobases do not show a strong correlation with the experimentally predicted binding preferences. However, our calculations suggest that the stacking interactions of hypoxanthine are similar in magnitude to the hydrogen-bonding interactions at all levels of theory (with the exception of B3LYP, which incorrectly predicts stacked dimers to be unstable). Therefore, stacking interactions should also be considered when analyzing the stability of DNA helices containing hypoxanthine and the use of larger models that account for both hydrogen-bonding and stacking within DNA duplexes will likely result in better agreement with experimental observations. For the majority of the dimers, PWB6K and AMBER provide reasonable binding strengths at reduced computational costs, and therefore will be useful techniques for considering larger models.
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Affiliation(s)
- Lesley R Rutledge
- Department of Chemistry, Mount Allison University, 63C York Street, Sackville, New Brunswick, Canada E4L 1G8
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35
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36
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Tsuzuki S, Honda K, Uchimaru T, Mikami M. Intermolecular interactions of nitrobenzene-benzene complex and nitrobenzene dimer: Significant stabilization of slipped-parallel orientation by dispersion interaction. J Chem Phys 2006; 125:124304. [PMID: 17014171 DOI: 10.1063/1.2354495] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
Abstract
The CCSD(T) level interaction energies of eight orientations of nitrobenzene-benzene complexes and nine orientations of nitrobenzene dimers at the basis set limit have been estimated. The calculated interaction energy of the most stable slipped-parallel (C(s)) nitrobenzene-benzene complex was -4.51 kcal/mol. That of the most stable slipped-parallel (antiparallel) (C(2h)) nitrobenzene dimer was -6.81 kcal/mol. The interaction energies of these complexes are significantly larger than that of the benzene dimer. The T-shaped complexes are substantially less stable. Although nitrobenzene has a polar nitro group, electrostatic interaction is always considerably weaker than the dispersion interaction. The dispersion interaction in these complexes is larger than that in the benzene dimer, which is the cause of the preference of the slipped-parallel orientation in these complexes.
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Affiliation(s)
- Seiji Tsuzuki
- National Institute of Advanced Industrial Science and Technology (AIST), Tsukuba, Ibaraki 305-8568, Japan.
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37
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Sinnokrot MO, Sherrill CD. High-Accuracy Quantum Mechanical Studies of π−π Interactions in Benzene Dimers. J Phys Chem A 2006; 110:10656-68. [PMID: 16970354 DOI: 10.1021/jp0610416] [Citation(s) in RCA: 588] [Impact Index Per Article: 32.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Although supramolecular chemistry and noncovalent interactions are playing an increasingly important role in modern chemical research, a detailed understanding of prototype noncovalent interactions remains lacking. In particular, pi-pi interactions, which are ubiquitous in biological systems, are not fully understood in terms of their strength, geometrical dependence, substituent effects, or fundamental physical nature. However, state-of-the-art quantum chemical methods are beginning to provide answers to these questions. Coupled-cluster theory through perturbative triple excitations in conjunction with large basis sets and extrapolations to the complete basis set limit have provided definitive results for the binding energy of several configurations of the benzene dimer, and benchmark-quality ab initio potential curves are being used to calibrate new density functional and force-field models for pi-pi interactions. Studies of substituted benzene dimers indicate flaws in the conventional wisdom about substituent effects in pi-pi interactions. Three-body and four-body interactions in benzene clusters have also been examined.
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Affiliation(s)
- Mutasem Omar Sinnokrot
- 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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38
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Ringer AL, Sinnokrot MO, Lively RP, Sherrill CD. The Effect of Multiple Substituents on Sandwich and T-Shaped π–π Interactions. Chemistry 2006; 12:3821-8. [PMID: 16514687 DOI: 10.1002/chem.200501316] [Citation(s) in RCA: 181] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
Abstract
Sandwich and T-shaped configurations of substituted benzene dimers were studied by second-order perturbation theory to determine how substituents tune pi-pi interactions. Remarkably, multiple substituents have an additive effect on the binding energy of sandwich dimers, except in some cases when substituents are aligned on top of each other. The energetics of substituted T-shaped configurations are more complex, but nevertheless a simple model that accounts for electrostatic and dispersion interactions (and direct contacts between substituents on one ring and hydrogen atoms on the other), provides a good match to the quantum mechanical results. These results provide insight into the manner by which substituents csan be utilized in supramolecular design.
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Affiliation(s)
- Ashley L Ringer
- 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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