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Khan HM, Grauffel C, Broer R, MacKerell AD, Havenith RWA, Reuter N. Improving the Force Field Description of Tyrosine-Choline Cation-π Interactions: QM Investigation of Phenol-N(Me) 4+ Interactions. J Chem Theory Comput 2016; 12:5585-5595. [PMID: 27682345 PMCID: PMC5148683 DOI: 10.1021/acs.jctc.6b00654] [Citation(s) in RCA: 35] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cation-π interactions between tyrosine amino acids and compounds containing N,N,N-trimethylethanolammonium (N(CH3)3) are involved in the recognition of histone tails by chromodomains and in the recognition of phosphatidylcholine (PC) phospholipids by membrane-binding proteins. Yet, the lack of explicit polarization or charge transfer effects in molecular mechanics force fields raises questions about the reliability of the representation of these interactions in biomolecular simulations. Here, we investigate the nature of phenol-tetramethylammonium (TMA) interactions using quantum mechanical (QM) calculations, which we also use to evaluate the accuracy of the additive CHARMM36 and Drude polarizable force fields in modeling tyrosine-choline interactions. We show that the potential energy surface (PES) obtained using SAPT2+/aug-cc-pVDZ compares well with the large basis-set CCSD(T) PES when TMA approaches the phenol ring perpendicularly. Furthermore, the SAPT energy decomposition reveals comparable contributions from electrostatics and dispersion in phenol-TMA interactions. We then compared the SAPT2+/aug-cc-pVDZ PES obtained along various approach directions to the corresponding PES obtained with CHARMM, and we show that the force field accurately reproduces the minimum distances while the interaction energies are underestimated. The use of the Drude polarizable force field significantly improves the interaction energies but decreases the agreement on distances at energy minima. The best agreement between force field and QM PES is obtained by modifying the Lennard-Jones terms for atom pairs involved in the phenol-TMA cation-π interactions. This is further shown to improve the correlation between the occupancy of tyrosine-choline cation-π interactions obtained from molecular dynamics simulations of a bilayer-bound bacterial phospholipase and experimental affinity data of the wild-type protein and selected mutants.
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Affiliation(s)
- Hanif M Khan
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
| | - Cédric Grauffel
- Institute of Biomedical Sciences, Academia Sinica , Taipei 11529, Taiwan
| | | | - Alexander D MacKerell
- Department of Pharmaceutical Sciences, University of Maryland School of Pharmacy , Baltimore, Maryland 21201, United States
| | - Remco W A Havenith
- Ghent Quantum Chemistry Group, Department of Inorganic and Physical Chemistry, Ghent University , 9000 Ghent, Belgium
| | - Nathalie Reuter
- Department of Molecular Biology, University of Bergen , N-5020 Bergen, Norway
- Computational Biology Unit, Department of Informatics, University of Bergen , N-5020 Bergen, Norway
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2
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Shishido R, Kawai Y, Fujii A. Infrared Spectroscopy of Protonated Trimethylamine–(Benzene)n (n = 1–4) as Model Clusters of the Quaternary Ammonium–Aromatic Ring Interaction. J Phys Chem A 2014; 118:7297-305. [DOI: 10.1021/jp4115157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Affiliation(s)
- Ryunosuke Shishido
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Yuki Kawai
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
| | - Asuka Fujii
- Department of Chemistry,
Graduate School of Science, Tohoku University, Sendai 980-8578, Japan
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3
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Mahadevi AS, Sastry GN. Cation-π interaction: its role and relevance in chemistry, biology, and material science. Chem Rev 2012; 113:2100-38. [PMID: 23145968 DOI: 10.1021/cr300222d] [Citation(s) in RCA: 719] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Affiliation(s)
- A Subha Mahadevi
- Molecular Modeling Group, CSIR-Indian Institute of Chemical Technology Tarnaka, Hyderabad 500 607, Andhra Pradesh, India
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4
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Gresh N, Audiffren N, Piquemal JP, de Ruyck J, Ledecq M, Wouters J. Analysis of the Interactions Taking Place in the Recognition Site of a Bimetallic Mg(II)−Zn(II) Enzyme, Isopentenyl Diphosphate Isomerase. A Parallel Quantum-Chemical and Polarizable Molecular Mechanics Study. J Phys Chem B 2010; 114:4884-95. [DOI: 10.1021/jp907629k] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Affiliation(s)
- Nohad Gresh
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Nicole Audiffren
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jean-Philip Piquemal
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Jerome de Ruyck
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Marie Ledecq
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
| | - Johan Wouters
- Laboratoire de Pharmacochimie Moléculaire et Cellulaire, U648 INSERM, UFR Biomédicale, Université Paris Descartes, 45 rue des Saints-Pères, 75006 Paris, France, Centre Informatique National de l’Enseignement Supérieur, 950, rue de Saint Priest, 34097 Montpellier, France, Laboratoire de Chimie Théorique, Centre National de la Recherche Scientifique, UMR 7616, Université Pierre et Marie Curie, 4 place Jussieu, 75252 Paris Cedex 05, France, and Laboratoire de Chimie Biologique Structurale, FUNDP, 61 Rue de
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5
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Dubis AT, Domagała M, Grabowski SJ. Spectroscopic and theoretical studies on some new pyrrol-2-yl-chloromethyl ketones. NEW J CHEM 2010. [DOI: 10.1039/b9nj00507b] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Chen SC, Kuo SW, Liao CS, Chang FC. Syntheses, Specific Interactions, and pH-Sensitive Micellization Behavior of Poly[vinylphenol-b-2-(dimethylamino)ethyl methacrylate] Diblock Copolymers. Macromolecules 2008. [DOI: 10.1021/ma801546z] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Shih-Chien Chen
- Institute of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan, and Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Shiao-Wei Kuo
- Institute of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan, and Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Chun-Syong Liao
- Institute of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan, and Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
| | - Feng-Chih Chang
- Institute of Applied Chemistry, National Chiao Tung University, Hsinchu 300, Taiwan, and Department of Materials and Optoelectronic Science, Center for Nanoscience and Nanotechnology, National Sun Yat-Sen University, Kaohsiung 804, Taiwan
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7
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Soteras I, Orozco M, Luque FJ. Induction effects in metal cation–benzene complexes. Phys Chem Chem Phys 2008; 10:2616-24. [DOI: 10.1039/b719461g] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023]
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8
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SINGH NJITEN, LEE HANMYOUNG, HWANG INCHUL, KIM KWANGS. Designing Ionophores and Molecular Nanotubes Based on Molecular Recognition. Supramol Chem 2007. [DOI: 10.1080/10610270701294480] [Citation(s) in RCA: 59] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Affiliation(s)
- N. JITEN SINGH
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - HAN MYOUNG LEE
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - IN-CHUL HWANG
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
| | - KWANG S. KIM
- a Department of Chemistry , Center for Superfunctional Materials, Pohang University of Science and Technology , Pohang, 790-784, South Korea
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9
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Liu Y, Hu X. Molecular determinants for binding of ammonium ion in the ammonia transporter AmtB-A quantum chemical analysis. J Phys Chem A 2007; 110:1375-81. [PMID: 16435797 DOI: 10.1021/jp054261c] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The transport of ammonium across the cell membrane represents an important biological process in all living organisms. The mechanisms for ammonium translocation were analyzed by computer simulations based on first principles. Intermolecular interaction energies between the differentially methylated ammonium and the ammonium channel protein AmtB were calculated by means of the supermolecular approach at the MP2/6-311+G* level based on the high-resolution crystal structures of ligand-bound protein complexes. Our analysis attributes the molecular determinants for protein-ligand recognition in ammonium transporter AmtB to the aromatic cage formed by three aromatic residues Phe103, Phe107, and Trp148, as well as Ser219. The former residues are involved in cation-pi interactions with the positively charged methylated ammoniums. The latter residue acts as a hydrogen bond acceptor to ammonium. Thus, this work provides directly the missing evidence for the hypothesized role played by the wider vestibule site of AmtB at the periplasmic side of the membrane in "recruiting" NH(4)(+) or methylammonium ions as proposed by Khademi et al. (Science 2004, 305, 1587). In addition, a hybrid quantum mechanics/molecular mechanics scheme was applied to optimize the structures of differentially methylated ammoniums in the AmtB protein, which generated structural and energetic data that provide a satisfactory explanation to the experimental observation that tetramethylammonium is not inhibitory to conducting ammonium and methylammonium in the ammonium transport channel.
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Affiliation(s)
- Yuemin Liu
- Department of Chemistry, University of Toledo, Toledo, Ohio 43606, USA
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10
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Ghoufi A, Archirel P, Morel JP, Morel-Desrosiers N, Boutin A, Malfreyt P. Methodology for the Calculation of the Potential of Mean Force for a Cation–π Complex in Water. Chemphyschem 2007; 8:1648-56. [PMID: 17583904 DOI: 10.1002/cphc.200700197] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
We report potential of mean force (PMF) calculations on the interaction between the p-sulfonatocalix[4]arene and a monovalent cation (Cs(+)). It has been recently shown from microcalorimetry and (133)Cs NMR experiments that the association with Cs(+) is governed by favourable cation-pi interactions and is characterized by the insertion of the cation into the cavity of the macrocycle. We show that the PMF calculation based upon a classical model is not able to reproduce both the thermodynamic properties of association and the insertion of the cation. In order to take into account the different contributions of the cation-pi interactions, we develop a new methodology consisting of changing the standard PMF by an additional contribution resulting from quantum calculations. The calculated thermodynamic properties of association are thus in line with the microcalorimetry and (133)Cs NMR experiments and the structure of the complex at the Gibbs free-energy minimum shows the insertion of the cation into the cavity of the calixarene.
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Affiliation(s)
- Aziz Ghoufi
- Laboratoire de Thermodynamique des Solutions et des Polymères, UMR CNRS 6003, Université Blaise Pascal, 63177 Aubière Cedex, France
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11
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Yang CM, Li X, Wei W, Li Y, Duan Z, Zheng J, Huang T. Dissecting the General Physicochemical Properties of Noncovalent Interactions Involving Tyrosine Side Chain as a Second-Shell Ligand in Biomolecular Metal-Binding Site Mimetics: An Experimental Study Combining Fluorescence,13C NMR Spectroscopy and ESI Mass Spectrometry. Chemistry 2007; 13:3120-30. [PMID: 17201001 DOI: 10.1002/chem.200600661] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022]
Abstract
Detailed physicochemical features inherent in the dynamic cation-pi interactions of aromatic amino acid side chains in the secondary coordination spheres around metal ions were extracted and mapped by intrinsic tyrosine fluorescence titration experiments with two homologous, artificially engineered metal-binding scaffolds which mimic metal-binding sites in metalloproteins. A newly formulated method for the treatment of fluorescence titration data allows straightforward assessment of both the magnitudes and properties of metal-chelation-assisted cation-aromatic interactions (K2) underlying a proposed two-step metallosupramolecular association process. The unprecedented linear platform-motif correlations between the two contrasting scaffolds in their changes in tyrosine fluorescence on binding of 3d metal cations help to elucidate the properties of general cation-arene recognition corresponding to the metal-responsive characteristics of the second-shell Tyr residue surrounding the metal-binding sites in the supramolecular context, and thereby define a new noncovalent design principle for metal-ion recognition in aqueous solution. As supported by NMR spectroscopic and ESI-MS analyses and molecular mechanics force field calculations, the systematic study exemplifies the concept of using steady-state tyrosine fluorescence as a powerful tool for comprehensive descriptions of cation-pi interactions in the extended environment of a metal-binding site. We established that the physicochemical properties pertaining to indirect metal-arene interactions are highly dependent on the electronic properties of the metal ions. This work suggests that second-shell cation-pi interactions may play more diverse roles, including modulation of structure, reactivity, and function of metal-binding sites, than the previously well-established direct cation-pi interactions involving hard cations (e.g., alkali metal ions). Moreover, such a study will continue to complement theoretical predications and/or the early experimental investigations in organic solvents.
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Affiliation(s)
- Chi Ming Yang
- Neurochemistry and Physical Organic Chemistry, Nankai University, Tianjin 300071, China.
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12
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De novo design approach based on nanorecognition toward development of functional molecules/materials and nanosensors/nanodevices. PURE APPL CHEM 2007. [DOI: 10.1351/pac200779061057] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
For the design of functional molecules and nanodevices, it is very useful to utilize nanorecognition (which is governed mainly by interaction forces such as hydrogen bonding, ionic interaction, π-H/π-π interactions, and metallic interactions) and nanodynamics (involving capture, transport, and release of electrons, photons, or protons). The manifestation of these interaction forces has led us to the design and realization of diverse ionophores/receptors, organic nanotubes, nanowires, molecular mechanical devices, molecular switches, enzyme mimetics, protein folding/unfolding, etc. In this review, we begin with a brief discussion of the interaction forces, followed by some of our representative applications. We discuss ionophores with chemo-sensing capability for biologically important cations and anions and explain how the understanding of hydrogen bonding and π-interactions has led to the design of self-assembled nanotubes from calix[4]hydroquinone (CHQ). The binding study of neutral and cationic transition metals with the redox system of hydroquinone (HQ) and quinone (Q) predicts what kind of nanostructures would form. Finally, we look into the conformational changes between stacked and edge-to-face conformers in π-benzoquinone-benzene complexes controlled by alternating electrochemical potential. The resulting flapping motion illustrates a promising pathway toward the design of mobile nanomechanical devices.
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13
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Majumdar D, Roszak S, Leszczynski J. Probing the Acetylcholinesterase Inhibition of Sarin: A Comparative Interaction Study of the Inhibitor and Acetylcholine with a Model Enzyme Cavity. J Phys Chem B 2006; 110:13597-607. [PMID: 16821887 DOI: 10.1021/jp061497n] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Interaction energies have been estimated between sarin and a model enzyme cavity of acetylcholinesterase (ACHE) using the density functional and Møller-Plesset second-order perturbation (MP2) levels of theories. The calculated interaction energies have been compared with those of acetylcholine and the same model ACHE cavity. The ACHE...sarin and ACHE...acetylcholine (Ach) structures have been optimized using DFT based two-layer ONIOM hybrid calculations. The nature of interactions has been investigated in detail using an interaction energy partitioning technique. The effects of solvation on the interaction energies have also been taken into account. An inhibition mechanism during the uptake of sarin inside the ACHE cavity has been proposed from the comparison of the energetics of the ACHE...sarin and ACHE...Ach complexes.
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Affiliation(s)
- D Majumdar
- Computational Center for Molecular Structure and Interactions, Department of Chemistry, Jackson State University, Jackson, Mississippi 39217, USA
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14
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Pratuangdejkul J, Jaudon P, Ducrocq C, Nosoongnoen W, Guerin GA, Conti M, Loric S, Launay JM, Manivet P. Cation-π Interactions in Serotonin: Conformational, Electronic Distribution, and Energy Decomposition Analysis. J Chem Theory Comput 2006; 2:746-60. [DOI: 10.1021/ct0600316] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Jaturong Pratuangdejkul
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Pascale Jaudon
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Claire Ducrocq
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Wichit Nosoongnoen
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Georges-Alexandre Guerin
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Marc Conti
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Sylvain Loric
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Jean-Marie Launay
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
| | - Philippe Manivet
- Service de Biochimie et de Biologie Moléculaire, IFR 139, Hôpital Lariboisière, 2, rue Ambroise Paré, 75475 Paris Cedex 10, France, E.A. 3621, Laboratoire de Biologie Cellulaire, UFR des Sciences Pharmaceutiques et Biologiques, 4 Avenue de l'Observatoire, 75270 Paris, Cedex 06, France, I.C.M.M.O. Laboratoire de Chimie Structurale Organique, Université Paris-Sud, Bat. 410, 91405 Orsay, Cedex, France, Institut de Chimie des Substances Naturelles, CNRS, F-91198 Gif-sur-Yvette, France, BioQuanta Corp., 2850
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15
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Ruan C, Yang Z, Hallowita N, Rodgers MT. Cation−π Interactions with a Model for the Side Chain of Tryptophan: Structures and Absolute Binding Energies of Alkali Metal Cation−Indole Complexes†. J Phys Chem A 2005; 109:11539-50. [PMID: 16354046 DOI: 10.1021/jp053830d] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Threshold collision-induced dissociation techniques are employed to determine bond dissociation energies (BDEs) of mono- and bis-complexes of alkali metal cations, Li+, Na+, K+, Rb+, and Cs+, with indole, C8H7N. The primary and lowest energy dissociation pathway in all cases is endothermic loss of an intact indole ligand. Sequential loss of a second indole ligand is observed at elevated energies for the bis-complexes. Density functional theory calculations at the B3LYP/6-31G level of theory are used to determine the structures, vibrational frequencies, and rotational constants of these complexes. Theoretical BDEs are determined from single point energy calculations at the MP2(full)/6-311+G(2d,2p) level using the B3LYP/6-31G* geometries. The agreement between theory and experiment is very good for all complexes except Li+ (C8H7N), where theory underestimates the strength of the binding. The trends in the BDEs of these alkali metal cation-indole complexes are compared with the analogous benzene and naphthalene complexes to examine the influence of the extended pi network and heteroatom on the strength of the cation-pi interaction. The Na+ and K+ binding affinities of benzene, phenol, and indole are also compared to those of the aromatic amino acids, phenylalanine, tyrosine, and tryptophan to elucidate the factors that contribute to the binding in complexes to the aromatic amino acids. The nature of the binding and trends in the BDEs of cation-pi complexes between alkali metal cations and benzene, phenol, and indole are examined to help understand nature's preference for engaging tryptophan over phenylalanine and tyrosine in cation-pi interactions in biological systems.
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Affiliation(s)
- Chunhai Ruan
- Department of Chemistry, Wayne State University, Detroit, Michigan 48202, USA
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Xu Y, Shen J, Zhu W, Luo X, Chen K, Jiang H. Influence of the Water Molecule on Cation−π Interaction: Ab Initio Second Order Møller−Plesset Perturbation Theory (MP2) Calculations. J Phys Chem B 2005; 109:5945-9. [PMID: 16851648 DOI: 10.1021/jp044568w] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The influence of introducing water molecules into a cation-pi complex on the interaction between the cation and the pi system was investigated using the MP2/6-311++G method to explore how a cation-pi complex changes in terms of both its geometry and its binding strength during the hydration. The calculation on the methylammonium-benzene complex showed that the cation-pi interaction is weakened by introducing H(2)O molecules into the system. For example, the optimized interaction distance between the cation and the benzene becomes longer and longer, the transferred charge between them becomes less and less, and the cation-pi binding strength becomes weaker and weaker as the water molecule is introduced one by one. Furthermore, the introduction of the third water molecule leads to a dramatic change in both the complex geometry and the binding energy, resulting in the destruction of the cation-pi interaction. The decomposition on the binding energy shows that the influence is mostly brought out through the electrostatic and induction interactions. This study also demonstrated that the basis set superposition error, thermal energy, and zero-point vibrational energy are significant and needed to be corrected for accurately predicting the binding strength in a hydrated cation-pi complex at the MP2/6-311++G level. Therefore, the results are helpful to better understand the role of water molecules in some biological processes involving cation-pi interactions.
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Affiliation(s)
- Yechun Xu
- Center for Drug Discovery and Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 555 Zuchongzhi Road, Shanghai 201203, People's Republic of China
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17
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Song J, Gordon MS, Deakyne CA, Zheng W. Theoretical Investigations of Acetylcholine (ACh) and Acetylthiocholine (ATCh) Using ab Initio and Effective Fragment Potential Methods. J Phys Chem A 2004. [DOI: 10.1021/jp0406013] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- Jie Song
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Mark S. Gordon
- Department of Chemistry, Iowa State University, Ames, Iowa 50011
| | - Carol A. Deakyne
- Department of Chemistry, University of MissouriColumbia, Columbia, Missouri 65211
| | - Wencui Zheng
- Department of Chemistry, Eastern Illinois University, Charleston, Illinois 61920
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18
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Liu T, Zhu W, Gu J, Shen J, Luo X, Chen G, Puah CM, Silman I, Chen K, Sussman JL, Jiang H. Additivity of Cation−π Interactions: An ab Initio Computational Study on π−Cation−π Sandwich Complexes. J Phys Chem A 2004. [DOI: 10.1021/jp0476850] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Tong Liu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Weiliang Zhu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jiandu Gu
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jianhua Shen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiaomin Luo
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Gang Chen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Chum Mok Puah
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Israel Silman
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Kaixian Chen
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Joel L. Sussman
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hualiang Jiang
- Center for Drug Discovery and Design, State Key Laboratory of New Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 555 Zu Chong Zhi Road, Shanghai, 201203, P. R. China, Technology Centre for Life Sciences, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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19
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Yun S, Kim YO, Kim D, Kim HG, Ihm H, Kim JK, Lee CW, Lee WJ, Yoon J, Oh KS, Yoon J, Park SM, Kim KS. Rational design of biologically important chemosensors: a novel receptor for selective recognition of acetylcholine over ammonium cations. Org Lett 2003; 5:471-4. [PMID: 12583746 DOI: 10.1021/ol0273203] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
[structure: see text] In consideration of competition between cation-pi and hydrogen bond interaction forces, we designed a novel receptor, 1,3,5-tris(pyrrolyl)benzene, which shows high selectivity for acetylcholine (ACh). The selectivity of the receptor for ACh over other ammonium cations is demonstrated by the ion-selective electrode (ISE) method in buffer solution. The binding free energy of the receptor with ACh in chloroform solution is measured to be 3.65 kcal/mol in the presence of chloride anion by nuclear magnetic resonance spectroscopy, and that in water is estimated to be much greater ( approximately 6 kcal/mol).
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Affiliation(s)
- Sunggoo Yun
- National Creative Research Initiative Center for Superfunctional Materials, Department of Chemistry, Division of Molecular and Life Sciences, Pohang University of Science and Technology San 31, Hyojadong, Namgu, Pohang, 790-784, Korea
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20
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Ribas J, Cubero E, Luque FJ, Orozco M. Theoretical study of alkyl-pi and aryl-pi interactions. Reconciling theory and experiment. J Org Chem 2002; 67:7057-65. [PMID: 12354000 DOI: 10.1021/jo0201225] [Citation(s) in RCA: 97] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Quantum mechanical and quantum mechanical/molecular mechanical calculations in conjunction with continuum solvation models have been used to analyze CH-pi interactions in model systems of aryl- and alkyl-aromatic interactions, as well as in a model folding system designed to study those interactions. High level calculations reproduced accurately the interaction of CH-pi interactions in both alkyl- and aryl-based model systems. Dispersion effects dominate the interaction, but the electrostatics term is also relevant for aryl CH-pi interactions. Theoretical calculations were also used to examine the influence of CH-pi interactions in determining the conformational flexibility of folding models. Finally, a critical comparison of the results obtained from high level calculations on model systems and the experimental data derived for folding models in apolar solvents was carried out, which allowed us to reconcile the apparent discrepancy found between both data.
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Affiliation(s)
- Jordi Ribas
- Departament de Bioquímica, Facultat de Química, Universitat de Barcelona, Martí i Franquès 1, Barcelona 08028, Spain
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Bartoli S, Roelens S. Binding of acetylcholine and tetramethylammonium to a cyclophane receptor: anion's contribution to the cation-pi interaction. J Am Chem Soc 2002; 124:8307-15. [PMID: 12105911 DOI: 10.1021/ja025884w] [Citation(s) in RCA: 95] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The interaction of the lipophilic cyclophane 1 with several acetylcholine (ACh) and tetramethylammonium (TMA) salts has been investigated in deuteriochloroform to ascertain the influence of the counterion on the cation-pi interaction. Reliable association constants have been measured for 17 salts of commonly used anions; corresponding binding free energies -DeltaG degrees ranged from over 8 kJ mol(-1) down to the limit of detection. The dramatic dependence of the binding energy on the anion showed that the latter takes part in the process with a passive and adverse contribution, which inhibits cation binding even to complete suppression in unfavorable cases. Thermodynamic parameters for the association of 1 with TMA picrate demonstrate that binding is enthalpic in origin, showing a substantial enthalpy gain (DeltaH degrees = -16.7 kJ mol(-1)) and an adverse entropic contribution (DeltaS degrees = -27.9 J mol(-1) K(-1)). A correlation has been found between the "goodness" of anions as binding partners and the solubility of their salts. Conversion of the anion into a more charge-dispersed species, for example, conversion of chloride into dialkyltrichlorostannate, improves cation binding substantially, indicating that charge dispersion is a main factor determining the influence of the anion on the cation-pi interaction. DFT computational studies show that the variation of the binding free energy of TMA with the counterion is closely accounted for by the electrostatic potential (EP) of the ion pair: guest binding appears to respond to the cation's charge density exposed to the receptor, which is determined by the anion's charge density through a polarization mechanism. A value of -DeltaG degrees = 38.6 kJ mol(-1) has been extrapolated for the free energy of binding of TMA to 1 in chloroform but in the absence of a counterion. The transmission of electrostatic effects from the ion pair to the cation-pi interaction demonstrates that host-guest association is governed by Coulombic attraction, as long as factors (steric, entropic, solvation, etc.) other than pure electrostatics are not prevalent.
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Affiliation(s)
- Sandra Bartoli
- CNR, Istituto di Chimica dei Composti Organometallici, Dipartimento di Chimica Organica, Università di Firenze, Polo Scientifico, I-50019 Sesto Fiorentino, Firenze, Italy
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22
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Aschi M, Mazza F, Di Nola A. Cation–π interactions between ammonium ion and aromatic rings: an energy decomposition study. ACTA ACUST UNITED AC 2002. [DOI: 10.1016/s0166-1280(02)00112-4] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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23
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Liu T, Gu J, Tan XJ, Zhu WL, Luo XM, Jiang HL, Ji RY, Chen KX, Silman I, Sussman JL. The Relationship between Binding Models of TMA with Furan and Imidazole and the Molecular Electrostatic Potentials: DFT and MP2 Computational Studies. J Phys Chem A 2001. [DOI: 10.1021/jp0113275] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Tong Liu
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jiande Gu
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiao-Jian Tan
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Wei-Liang Zhu
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiao-Min Luo
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hua-Liang Jiang
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ru-Yun Ji
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Kai-Xian Chen
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Israel Silman
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Joel L. Sussman
- Center for Drug Discovery & Design and State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel
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24
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Liu T, Gu J, Tan XJ, Zhu WL, Luo XM, Jiang HL, Ji RY, Chen KX, Silman I, Sussman JL. Theoretical Insight into the Interactions of TMA-Benzene and TMA-Pyrrole with B3LYP Density-Functional Theory (DFT) and ab Initio Second Order Møller−Plesset Perturbation Theory (MP2) Calculations. J Phys Chem A 2001. [DOI: 10.1021/jp003098c] [Citation(s) in RCA: 39] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Tong Liu
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Jiande Gu
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiao-Jian Tan
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Wei-Liang Zhu
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Xiao-Min Luo
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Hua-Liang Jiang
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Ru-Yun Ji
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Kai-Xian Chen
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Israel Silman
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
| | - Joel L Sussman
- Center for Drug Discovery & Design, State Key Laboratory of Drug Research, Shanghai Institute of Materia Medica, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 294 Taiyuan Road, Shanghai 200031, P. R. China, Chemical Process & Biotechnology Department, Singapore Polytechnic, 500 Dover Road, Singapore 139651, Department of Neurobiology, Weizmann Institute of Science, 76100 Rehovot, Israel, and Department of Structural Biology, Weizmann Institute of Science, 76100 Rehovot, Israel
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25
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Mavri J, Hadži D. Modelling of ligand–receptor interactions: ab-initio and DFT calculations of solvent reaction field effects on methylated ammonium–π and –acetate complexes. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00733-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
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26
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Pullman A, Berthier G, Savinelli R. Components of the interaction energy of benzene with Na+ and methylammonium cations. ACTA ACUST UNITED AC 2001. [DOI: 10.1016/s0166-1280(00)00673-4] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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27
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Bessis AS, Bertrand HO, Galvez T, De Colle C, Pin JP, Acher F. Three-dimensional model of the extracellular domain of the type 4a metabotropic glutamate receptor: new insights into the activation process. Protein Sci 2000; 9:2200-9. [PMID: 11152130 PMCID: PMC2144486 DOI: 10.1110/ps.9.11.2200] [Citation(s) in RCA: 43] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/21/2022]
Abstract
Metabotropic glutamate receptors (mGluRs) belong to the family 3 of G-protein-coupled receptors. On these proteins, agonist binding on the extracellular domain leads to conformational changes in the 7-transmembrane domains required for G-protein activation. To elucidate the structural features that might be responsible for such an activation mechanism, we have generated models of the amino terminal domain (ATD) of type 4 mGluR (mGlu4R). The fold recognition search allowed the identification of three hits with a low sequence identity, but with high secondary structure conservation: leucine isoleucine valine-binding protein (LIVBP) and leucine-binding protein (LBP) as already known, and acetamide-binding protein (AmiC). These proteins are characterized by a bilobate structure in an open state for LIVBP/LBP and a closed state for AmiC, with ligand binding in the cleft. Models for both open and closed forms of mGlu4R ATD have been generated. ACPT-I (1-aminocyclopentane 1,3,4-tricarboxylic acid), a selective agonist, has been docked in the two models. In the open form, ACPT-I is only bound to lobe I through interactions with Lys74, Arg78, Ser159, and Thr182. In the closed form, ACPT-I is trapped between both lobes with additional binding to Tyr230, Asp312, Ser313, and Lys317 from lobe II. These results support the hypothesis that mGluR agonists bind a closed form of the ATDs, suggesting that such a conformation of the binding domain corresponds to the active conformation.
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Affiliation(s)
- A S Bessis
- Laboratoire de Chimie et Biochimie Pharmacologiques et Toxicologiques, UMR8601-CNRS, Université René Descartes-Paris V, France
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Minoux H, Chipot C. Cation−π Interactions in Proteins: Can Simple Models Provide an Accurate Description? J Am Chem Soc 1999. [DOI: 10.1021/ja990914p] [Citation(s) in RCA: 169] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Hervé Minoux
- Contribution from the Laboratoire de Chimie Théorique, Unité Mixte de Recherche CNRS 7565, Université Henri Poincaré, Nancy I, B.P. 239, 54506 Vandœ uvre-lès-Nancy, France
| | - Christophe Chipot
- Contribution from the Laboratoire de Chimie Théorique, Unité Mixte de Recherche CNRS 7565, Université Henri Poincaré, Nancy I, B.P. 239, 54506 Vandœ uvre-lès-Nancy, France
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Ryzhov V, Dunbar RC. Interactions of Phenol and Indole with Metal Ions in the Gas Phase: Models For Tyr and Trp Side-Chain Binding. J Am Chem Soc 1999. [DOI: 10.1021/ja983272z] [Citation(s) in RCA: 97] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Norrby PO, Liljefors T. Strong Decrease of the Benzene−Ammonium Ion Interaction upon Complexation with a Carboxylate Anion. J Am Chem Soc 1999. [DOI: 10.1021/ja984076v] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Per-Ola Norrby
- Contribution from the Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
| | - Tommy Liljefors
- Contribution from the Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark
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Deakyne CA, Meot-Ner (Mautner) M. Ionic Hydrogen Bonds in Bioenergetics. 4. Interaction Energies of Acetylcholine with Aromatic and Polar Molecules. J Am Chem Soc 1999. [DOI: 10.1021/ja982549s] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Carol A. Deakyne
- Contribution from the Department of Chemistry, Eastern Illinois University, Charleston, Illinois 61920, and Chemical Kinetics and Thermodynamics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
| | - Michael Meot-Ner (Mautner)
- Contribution from the Department of Chemistry, Eastern Illinois University, Charleston, Illinois 61920, and Chemical Kinetics and Thermodynamics Division, National Institute of Standards and Technology, Gaithersburg, Maryland 20899
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