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Zou J, Zhang D, Thi QH, Chen W, Xu G, Lu Z, Ly TH, Luo J. Exploring Favorable Supramolecular Interactions of Multifluorinated Aromatics in Dendronized Push-Pull Chromophores for Electro-Optics. Chempluschem 2024; 89:e202400320. [PMID: 38853751 DOI: 10.1002/cplu.202400320] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2024] [Revised: 06/09/2024] [Accepted: 06/10/2024] [Indexed: 06/11/2024]
Abstract
Multifluorinated aromatics serve as supramolecular synthons in the research of organic electro-optic (EO) materials by exploiting π-π stacking interaction between the aromatic hydrocarbon and multifluorinated aromatic groups for performance improvement. However, non-classical hydrogen bonding remains largely unexplored in fluorinated EO dendrimers. In this study, three Fréchet-type generation 1 benzyl ether co-dendrons were synthesized by replacing one benzyl group with 2,3,5,6-tetrafluorobenzyl (p-HF4Bz), pentafluorobenzyl (C6F5Bz), and 2,3,4,5-tetrafluorobenzyl (o-HF4Bz) groups, to afford the benzoic acid derivatives D1, D2, and D3, which were further bonded to the donor and π-bridge moieties to afford three co-dendronized push-pull phenyltetraene chromophores EOD1, EOD2, and EOD3, respectively. The weak C-H⋅⋅⋅X (X=O, F) interactions in the crystal structure of D1 cumulatively add to the benzoic acid dimers to form an extended hydrogen-bonded network, while D2 is crystallized into a centric one-dimensional chain with strong intermolecular interactions. The poled films of EOD1 with PMMA exhibited the largest and most stable EO activity with optical homogeneity among the series. The results identify the effectiveness of weak but favorable hydrogen bonds enabled by the enhanced carbon acidity of p-HF4Bz synthon in D1, over the interactions in D2 and D3, for the rational design of supramolecular EO dendrimers.
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Affiliation(s)
- Jie Zou
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Di Zhang
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Quoc Huy Thi
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Center of Super-Diamond & Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, China
| | - Weilong Chen
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
| | - Gan Xu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Zhenpin Lu
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
| | - Thuc Hue Ly
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Center of Super-Diamond & Advanced Films (COSDAF), City University of Hong Kong, Hong Kong SAR, China
| | - Jingdong Luo
- Department of Chemistry, City University of Hong Kong, Hong Kong SAR, China
- Shenzhen Research Institute, City University of Hong Kong, Shenzhen, China
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2
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Thermodynamics of chlorobenzene, or bromobenzene, or 1-chloronaphthalene or 1,2,4-trichlorobenzene + alkane mixtures. J Mol Liq 2022. [DOI: 10.1016/j.molliq.2021.118282] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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Smith RS, Kay BD. Desorption of Benzene, 1,3,5-Trifluorobenzene, and Hexafluorobenzene from a Graphene Surface: The Effect of Lateral Interactions on the Desorption Kinetics. J Phys Chem Lett 2018; 9:2632-2638. [PMID: 29724099 DOI: 10.1021/acs.jpclett.8b00986] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/08/2023]
Abstract
The desorption of benzene, 1,3,5-trifluorobenzene (TFB), and hexafluorobenzene (HFB) from a graphene covered Pt(111) substrate was investigated using temperature-programmed desorption (TPD). All three species have well-resolved monolayer and second-layer desorption peaks. The desorption spectra for submonolayer coverages of benzene and HFB are consistent with first-order desorption kinetics. In contrast, the submonolayer TPD spectra for TFB align on a common leading-edge, which is indicative of zero-order desorption kinetics. The desorption behavior of the three molecules can be correlated with the strength of the quadrupole moments. Calculations (second-order Møller-Plesset perturbation and density functional theory) show that the potential minimum for coplanar TFB dimers is more than a factor of 2 greater than that for either benzene or HFB dimers. The calculations support the interpretation that benzene and HFB are less likely to form the two-dimensional islands that are needed for submonolayer zero-order desorption kinetics.
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Affiliation(s)
- R Scott Smith
- Physical and Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
| | - Bruce D Kay
- Physical and Computational Sciences Directorate , Pacific Northwest National Laboratory , Richland , Washington 99352 , United States
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Smith RS, Kay BD. Desorption Kinetics of Benzene and Cyclohexane from a Graphene Surface. J Phys Chem B 2017; 122:587-594. [DOI: 10.1021/acs.jpcb.7b05102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- R. Scott Smith
- Physical and Computational
Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
| | - Bruce D. Kay
- Physical and Computational
Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352, United States
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Giroud M, Harder M, Kuhn B, Haap W, Trapp N, Schweizer WB, Schirmeister T, Diederich F. Fluorine Scan of Inhibitors of the Cysteine Protease Human Cathepsin L: Dipolar and Quadrupolar Effects in the π-Stacking of Fluorinated Phenyl Rings on Peptide Amide Bonds. ChemMedChem 2016; 11:1042-7. [DOI: 10.1002/cmdc.201600132] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2016] [Revised: 03/23/2016] [Indexed: 11/10/2022]
Affiliation(s)
- Maude Giroud
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Michael Harder
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Bernd Kuhn
- Small Molecule Research; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124, Building 92 4070 Basel Switzerland
| | - Wolfgang Haap
- Small Molecule Research; Roche Innovation Center Basel; F. Hoffmann-La Roche AG; Grenzacherstrasse 124, Building 92 4070 Basel Switzerland
| | - Nils Trapp
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - W. Bernd Schweizer
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
| | - Tanja Schirmeister
- Institut für Pharmazie und Biochemie; Johannes Gutenberg-Universität Mainz; Staudinger Weg 5 55128 Mainz Germany
| | - François Diederich
- Laboratorium für Organische Chemie; ETH Zürich; Wolfgang-Pauli-Strasse 10, HCI 8093 Zürich Switzerland
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Kim JS, Jeon HG, Jeong KS. Modulation of helix stability of indolocarbazole–pyridine hybrid foldamers. Chem Commun (Camb) 2016; 52:3406-9. [DOI: 10.1039/c6cc00045b] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
The kinetic stabilities of the helical conformations of indolocarbazole–pyridine hybrid foldamers were modulated through single site modification.
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Kirimli HE, Ovalioglu H. 19F Dynamic Nuclear Polarization and SEM in Suspensions Consisting of Fluorobenzene Derivatives and Asphaltene Extracted from MC-800 Liquid Asphalt. J DISPER SCI TECHNOL 2014. [DOI: 10.1080/01932691.2013.767208] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Bretschneider A, Andrada DM, Dechert S, Meyer S, Mata RA, Meyer F. Preorganized Anion Traps for Exploiting Anion-π Interactions: An Experimental and Computational Study. Chemistry 2013; 19:16988-7000. [DOI: 10.1002/chem.201302598] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2013] [Indexed: 12/17/2022]
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10
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Alparone A. Nonlinear optical properties of fluorobenzenes: A Time-Dependent Hartree–Fock study. COMPUT THEOR CHEM 2013. [DOI: 10.1016/j.comptc.2013.03.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Ader L, Jones DNM, Lin H. Alcohol binding to the odorant binding protein LUSH: multiple factors affecting binding affinities. Biochemistry 2010; 49:6136-42. [PMID: 20550105 DOI: 10.1021/bi100540k] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023]
Abstract
Density function theory (DFT) calculations have been carried out to investigate the binding of alcohols to the odorant binding protein LUSH from Drosophila melanogaster. LUSH is one of the few proteins known to bind to ethanol at physiologically relevant concentrations and where high-resolution structural information is available for the protein bound to alcohol at these concentrations. The structures of the LUSH-alcohol complexes identify a set of specific hydrogen-bonding interactions as critical for optimal binding of ethanol. A set of truncated models based on the structure of the LUSH-butanol complex were constructed for the wild-type and mutant (T57S, S52A, and T57A) proteins in complexes with a series of n-alcohols and for the apoprotein bound to water and for the ligand-free protein. Using both gas-phase calculations and continuum solvation model calculations, we found that the widely used DFT model, B3LYP, failed to reproduce the experimentally observed trend of increasing binding affinity with the increasing length of the alkyl chain in the alcohol. In contrast, the recently developed M05-2X DFT model successfully reproduced this subtle trend. Analysis of the results indicated that multiple factors contribute to the differences in alcohol binding affinity: the H-bonding with Thr57 and Ser52 (4-5 kcal/mol per H-bond), the desolvation contribution (4-6 kcal/mol for alcohols and 8-10 kcal/mol for water), and the other noncovalent interaction (1.2 kcal/mol per CH(2) group of the alcohol alkyl chain). These results reveal the outstanding potential for using the M05-2X model in calculations of protein-substrate complexes where noncovalent interactions are important.
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Affiliation(s)
- Lauren Ader
- Chemistry Department, University of Colorado Denver, Denver, Colorado 80217, USA
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Shimizu K, Costa Gomes MF, Pádua AAH, Rebelo LPN, Canongia Lopes JN. On the Role of the Dipole and Quadrupole Moments of Aromatic Compounds in the Solvation by Ionic Liquids. J Phys Chem B 2009; 113:9894-900. [DOI: 10.1021/jp903556q] [Citation(s) in RCA: 81] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Karina Shimizu
- Instituto de Tecnologia Química e Biológica, ITQB 2, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal, Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, and Laboratoire Thermodynamique et Interactions Moléculaires, CNRS/Université Blaise Pascal, Clermont-Ferrand, France
| | - Margarida F. Costa Gomes
- Instituto de Tecnologia Química e Biológica, ITQB 2, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal, Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, and Laboratoire Thermodynamique et Interactions Moléculaires, CNRS/Université Blaise Pascal, Clermont-Ferrand, France
| | - Agílio A. H. Pádua
- Instituto de Tecnologia Química e Biológica, ITQB 2, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal, Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, and Laboratoire Thermodynamique et Interactions Moléculaires, CNRS/Université Blaise Pascal, Clermont-Ferrand, France
| | - Luís Paulo N. Rebelo
- Instituto de Tecnologia Química e Biológica, ITQB 2, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal, Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, and Laboratoire Thermodynamique et Interactions Moléculaires, CNRS/Université Blaise Pascal, Clermont-Ferrand, France
| | - José N. Canongia Lopes
- Instituto de Tecnologia Química e Biológica, ITQB 2, Universidade Nova de Lisboa, Apartado 127, 2780-901 Oeiras, Portugal, Centro de Química Estrutural, Instituto Superior Técnico, 1049-001 Lisboa, Portugal, and Laboratoire Thermodynamique et Interactions Moléculaires, CNRS/Université Blaise Pascal, Clermont-Ferrand, France
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Thode AB, Kruse SW, Nix JC, Jones DNM. The role of multiple hydrogen-bonding groups in specific alcohol binding sites in proteins: insights from structural studies of LUSH. J Mol Biol 2008; 376:1360-76. [PMID: 18234222 PMCID: PMC2293277 DOI: 10.1016/j.jmb.2007.12.063] [Citation(s) in RCA: 61] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2007] [Revised: 12/21/2007] [Accepted: 12/21/2007] [Indexed: 11/16/2022]
Abstract
It is now generally accepted that many of the physiological effects of alcohol consumption are a direct result of binding to specific sites in neuronal proteins such as ion channels or other components of neuronal signaling cascades. Binding to these targets generally occurs in water-filled pockets and leads to alterations in protein structure and dynamics. However, the precise interactions required to confer alcohol sensitivity to a particular protein remain undefined. Using information from the previously solved crystal structures of the Drosophila melanogaster protein LUSH in complexes with short-chain alcohols, we have designed and tested the effects of specific amino acid substitutions on alcohol binding. The effects of these substitutions, specifically S52A, T57S, and T57A, were examined using a combination of molecular dynamics, X-ray crystallography, fluorescence spectroscopy, and thermal unfolding. These studies reveal that the binding of ethanol is highly sensitive to small changes in the composition of the alcohol binding site. We find that T57 is the most critical residue for binding alcohols; the T57A substitution completely abolishes binding, while the T57S substitution differentially affects ethanol binding compared to longer-chain alcohols. The additional requirement for a potential hydrogen-bond acceptor at position 52 suggests that both the presence of multiple hydrogen-bonding groups and the identity of the hydrogen-bonding residues are critical for defining an ethanol binding site. These results provide new insights into the detailed chemistry of alcohol's interactions with proteins.
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Affiliation(s)
- Anna B. Thode
- Program in Biomolecular Structure, University of Colorado, Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
| | - Schoen W Kruse
- Department of Pharmacology, University of Colorado Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
| | - Jay C. Nix
- Molecular Biology Consortium, Advanced Light Source Beamline 4.2.2, Lawrence Berkeley National Laboratory, Berkeley, California 94720
| | - David N. M. Jones
- Department of Pharmacology, University of Colorado Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
- Program in Biomolecular Structure, University of Colorado, Denver School of Medicine, 12801 East 17 Avenue, MS 8303, PO Box 6511, Aurora, CO 80045
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Soave R, Barzaghi M, Destro R. Progress in the understanding of drug-receptor interactions, part 2: experimental and theoretical electrostatic moments and interaction energies of an angiotensin II receptor antagonist (C30H30N6(O)3S). Chemistry 2007; 13:6942-56. [PMID: 17539033 DOI: 10.1002/chem.200601516] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
A combined experimental and theoretical charge density study of an angiotensin II receptor antagonist (1) is presented focusing on electrostatic properties such as atomic charges, molecular electric moments up to the fourth rank and energies of the intermolecular interactions, to gain an insight into the physical nature of the drug-receptor interaction. Electrostatic properties were derived from both the experimental electron density (multipole refinement of X-ray data collected at T=17 K) and the ab initio wavefunction (single molecule and fully periodic calculations at the DFT level). The relevance of SO and SN intramolecular interactions on the activity of 1 is highlighted by using both the crystal and gas-phase geometries and their electrostatic nature is documented by means of QTAIM atomic charges. The derived electrostatic properties are consistent with a nearly spherical electron density distribution, characterised by an intermingling of electropositive and -negative zones rather than by a unique electrophilic region opposed to a nucleophilic area. This makes the first molecular moment scarcely significant and ill-determined, whereas the second moment is large, significant and highly reliable. A comparison between experimental and theoretical components of the third electric moment shows a few discrepancies, whereas the agreement for the fourth electric moment is excellent. The most favourable intermolecular bond is show to be an NHN hydrogen bond with an energy of about 50 kJ mol(-1). Key pharmacophoric features responsible for attractive electrostatic interactions include CHX hydrogen bonds. It is shown that methyl and methylene groups, known to be essential for the biological activity of the drug, provide a significant energetic contribution to the total binding energy. Dispersive interactions are important at the thiophene and at both the phenyl fragments. The experimental estimates of the electrostatic contribution to the intermolecular interaction energies of six molecular pairs, obtained by a new model proposed by Spackman, predict the correct relative electrostatic energies with no exceptions.
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Affiliation(s)
- Raffaella Soave
- CNR-ISTM, Istituto di Scienze e Tecnologie Molecolari, Via Golgi 19, 20133 Milano, Italy.
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