701
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Alonso M, Pinter B, Woller T, Geerlings P, De Proft F. Scrutinizing ion-π and ion-σ interactions using the noncovalent index and energy decomposition analysis. COMPUT THEOR CHEM 2015. [DOI: 10.1016/j.comptc.2014.09.033] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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702
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Persch E, Dumele O, Diederich F. Molecular recognition in chemical and biological systems. Angew Chem Int Ed Engl 2015; 54:3290-327. [PMID: 25630692 DOI: 10.1002/anie.201408487] [Citation(s) in RCA: 424] [Impact Index Per Article: 47.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2014] [Indexed: 12/13/2022]
Abstract
Structure-based ligand design in medicinal chemistry and crop protection relies on the identification and quantification of weak noncovalent interactions and understanding the role of water. Small-molecule and protein structural database searches are important tools to retrieve existing knowledge. Thermodynamic profiling, combined with X-ray structural and computational studies, is the key to elucidate the energetics of the replacement of water by ligands. Biological receptor sites vary greatly in shape, conformational dynamics, and polarity, and require different ligand-design strategies, as shown for various case studies. Interactions between dipoles have become a central theme of molecular recognition. Orthogonal interactions, halogen bonding, and amide⋅⋅⋅π stacking provide new tools for innovative lead optimization. The combination of synthetic models and biological complexation studies is required to gather reliable information on weak noncovalent interactions and the role of water.
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Affiliation(s)
- Elke Persch
- Laboratorium für Organische Chemie, Departement Chemie und Angewandte Biowissenschaften, ETH Zürich, Vladimir-Prelog-Weg 3, 8093 Zürich (Switzerland)
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703
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Giust S, La Sorella G, Sperni L, Fabris F, Strukul G, Scarso A. Supramolecular Catalysis in the Synthesis of Substituted 1 H-Tetrazoles from Isonitriles by a Self-Assembled Hexameric Capsule. ASIAN J ORG CHEM 2015. [DOI: 10.1002/ajoc.201402229] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022]
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704
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Kumar PPP, Suresh CH, Haridas V. A supramolecular approach to metal ion sensing: cystine-based designer systems for Cu2+, Hg2+, Cd2+ and Pb2+ sensing. RSC Adv 2015. [DOI: 10.1039/c4ra14389b] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Here, we demonstrate an emergent property from a mixture of two simple cystine containing molecules. The 1 : 1 mixture of pyrene-labelled S1 and tryptophan appended S2 form the heterodimeric system S1 : S2, which shows a unique metal binding ability.
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Affiliation(s)
- P. P. Praveen Kumar
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
| | - Cherumuttathu H. Suresh
- Inorganic and Theoretical Chemistry Section
- CSTD
- CSIR-National Institute for Interdisciplinary Science and Technology
- Thiruvananthapuram 695019
- India
| | - V. Haridas
- Department of Chemistry
- Indian Institute of Technology Delhi
- New Delhi 110016
- India
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705
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Lima CFRAC, Fernandes AM, Melo A, Gonçalves LM, Silva AMS, Santos LMNBF. Diarylferrocene tweezers for cation binding. Phys Chem Chem Phys 2015; 17:23917-23. [DOI: 10.1039/c5cp04530d] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Diarylferrocenes can act as molecular tweezers of cations. Their unique molecular shape and low torsional potentials allow for strong binding of small cations in the gas phase.
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Affiliation(s)
- Carlos F. R. A. C. Lima
- CIQ
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | - Ana M. Fernandes
- Department of Chemistry & QOPNA
- University of Aveiro
- Aveiro
- Portugal
| | - André Melo
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | - Luís M. Gonçalves
- LAQV-REQUIMTE
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
| | | | - Luís M. N. B. F. Santos
- CIQ
- Departamento de Química e Bioquímica
- Faculdade de Ciências da Universidade do Porto
- Porto
- Portugal
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706
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Shaw JW, Grayson DH, Rozas I. Synthesis of Guanidines and Some of Their Biological Applications. TOPICS IN HETEROCYCLIC CHEMISTRY 2015. [DOI: 10.1007/7081_2015_174] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
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707
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Arias S, Freire F, Quiñoá E, Riguera R. The leading role of cation–π interactions in polymer chemistry: the control of the helical sense in solution. Polym Chem 2015. [DOI: 10.1039/c5py00587f] [Citation(s) in RCA: 49] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cation–π interactions determine the helical sense adopted by a polyphenylacetylene bearing (R)-α-methoxy-α-phenylacetamide as a pendant group (poly-1).
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Affiliation(s)
- Sandra Arias
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Félix Freire
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Emilio Quiñoá
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
| | - Ricardo Riguera
- Department of Organic Chemistry and Center for Research in Biological Chemistry and Molecular Materials (CIQUS)
- University of Santiago de Compostela
- E-15782 Santiago de Compostela
- Spain
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708
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McGovern RE, Snarr BD, Lyons JA, McFarlane J, Whiting AL, Paci I, Hof F, Crowley PB. Structural study of a small molecule receptor bound to dimethyllysine in lysozyme. Chem Sci 2015; 6:442-449. [PMID: 25530835 PMCID: PMC4266562 DOI: 10.1039/c4sc02383h] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Lysine is a ubiquitous residue on protein surfaces. Post translational modifications of lysine, including methylation to the mono-, di- or trimethylated amine result in chemical and structural alterations that have major consequences for protein interactions and signalling pathways. Small molecules that bind to methylated lysines are potential tools to modify such pathways. To make progress in this direction, detailed structural data of ligands in complex with methylated lysine is required. Here, we report a crystal structure of p-sulfonatocalix[4]arene (sclx4) bound to methylated lysozyme in which the lysine residues were chemically modified from Lys-NH3+ to Lys-NH(Me2)+. Of the six possible dimethyllysine sites, sclx4 selected Lys116-Me2 and the dimethylamino substituent was deeply buried in the calixarene cavity. This complex confirms the tendency for Lys-Me2 residues to form cation-π interactions, which have been shown to be important in protein recognition of histone tails bearing methylated lysines. Supporting data from NMR spectroscopy and MD simulations confirm the selectivity for Lys116-Me2 in solution. The structure presented here may serve as a stepping stone to the development of new biochemical reagents that target methylated lysines.
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Affiliation(s)
- Róise E McGovern
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
| | - Brendan D Snarr
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Joseph A Lyons
- School of Biochemistry and Immunology, Trinity College Dublin, Dublin, Ireland
| | - James McFarlane
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Amanda L Whiting
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Irina Paci
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Fraser Hof
- Department of Chemistry, University of Victoria, British Columbia, V8W 3V6, Canada
| | - Peter B Crowley
- School of Chemistry, National University of Ireland Galway, University Road, Galway, Ireland
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709
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Wilson KA, Wetmore SD. A Survey of DNA–Protein π–Interactions: A Comparison of Natural Occurrences and Structures, and Computationally Predicted Structures and Strengths. CHALLENGES AND ADVANCES IN COMPUTATIONAL CHEMISTRY AND PHYSICS 2015. [DOI: 10.1007/978-3-319-14163-3_17] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
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710
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Hussain HB, Wilson KA, Wetmore SD. Serine and Cysteine π-Interactions in Nature: A Comparison of the Frequency, Structure, and Stability of Contacts Involving Oxygen and Sulfur. Aust J Chem 2015. [DOI: 10.1071/ch14598] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
Despite many DNA–protein π-interactions in high-resolution crystal structures, only four X–H···π or X···π interactions were found between serine (Ser) or cysteine (Cys) and DNA nucleobase π-systems in over 100 DNA–protein complexes (where X = O for Ser and X = S for Cys). Nevertheless, 126 non-covalent contacts occur between Ser or Cys and the aromatic amino acids in many binding arrangements within proteins. Furthermore, Ser and Cys protein–protein π-interactions occur with similar frequencies and strengths. Most importantly, due to the great stability that can be provided to biological macromolecules (up to –20 kJ mol–1 for neutral π-systems or –40 kJ mol–1 for cationic π-systems), Ser and Cys π-interactions should be considered when analyzing protein stability and function.
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711
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Hussain MA, Mahadevi AS, Sastry GN. Estimating the binding ability of onium ions with CO2 and π systems: a computational investigation. Phys Chem Chem Phys 2015; 17:1763-75. [DOI: 10.1039/c4cp03434a] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/21/2022]
Abstract
The impact of increasing methyl substitution on onium ions in their complexes with CO2 and aromatic systems has been analyzed using DFT calculations.
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Affiliation(s)
- M. Althaf Hussain
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - A. Subha Mahadevi
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
| | - G. Narahari Sastry
- Center for Molecular Modeling
- Indian Institute of Chemical Technology
- Hyderabad 500607
- India
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712
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Zhang J, Zhou B, Sun ZR, Wang XB. Photoelectron spectroscopy and theoretical studies of anion–π interactions: binding strength and anion specificity. Phys Chem Chem Phys 2015; 17:3131-3141. [DOI: 10.1039/c4cp04687k] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Direct experimental measurements of non-covalent interactions between various anions and a π-electron-deficient cavity show significant binding strength and anion specificity.
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Affiliation(s)
- Jian Zhang
- State Key Laboratory of Precision Spectroscopy
- East China Normal University
- Shanghai 200062
- China
- Physical Sciences Division
| | - Bin Zhou
- State Key Laboratory of Precision Spectroscopy
- East China Normal University
- Shanghai 200062
- China
| | - Zhen-Rong Sun
- State Key Laboratory of Precision Spectroscopy
- East China Normal University
- Shanghai 200062
- China
| | - Xue-Bin Wang
- Physical Sciences Division
- Pacific Northwest National Laboratory
- Richland
- USA
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713
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Liu H, Zhang J, Ngo HH, Guo W, Wu H, Guo Z, Cheng C, Zhang C. Effect on physical and chemical characteristics of activated carbon on adsorption of trimethoprim: mechanisms study. RSC Adv 2015. [DOI: 10.1039/c5ra17968h] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Five different types of activated carbon varying in porosity, structure, and functional groups were prepared and used as adsorbents.
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Affiliation(s)
- Hai Liu
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- China
| | - Jian Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- China
| | - Huu Hao Ngo
- School of Civil and Environmental Engineering
- University of Technology Sydney
- Australia
| | - Wenshan Guo
- School of Civil and Environmental Engineering
- University of Technology Sydney
- Australia
| | - Haiming Wu
- College of Resources and Environment
- Northwest A & F University
- China
| | - Zizhang Guo
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- China
| | - Cheng Cheng
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- China
| | - Chenglu Zhang
- Shandong Key Laboratory of Water Pollution Control and Resource Reuse
- School of Environmental Science and Engineering
- Shandong University
- Jinan 250100
- China
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714
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. On the interaction between the imidazolium cation and aromatic amino acids. A computational study. Org Biomol Chem 2015; 13:7961-72. [DOI: 10.1039/c5ob01108f] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Phe, Tyr and Trp form parallel complexes with cation⋯π interactions. His complexes are the strongest, but without making contact with the aromatic cloud.
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Affiliation(s)
- Ana A. Rodríguez-Sanz
- Departamento de Química Física
- Facultade de Ciencias
- Universidade de Santiago de Compostela
- Lugo
- Spain
| | | | - Jesús Rodríguez-Otero
- Centro de investigación en Química Biolóxica e Materiais Moleculares
- CIQUS
- Universidade de Santiago de Compostela
- Santiago de Compostela
- Spain
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715
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Holland MC, Metternich JB, Mück-Lichtenfeld C, Gilmour R. Cation–π interactions in iminium ion activation: correlating quadrupole moment & enantioselectivity. Chem Commun (Camb) 2015; 51:5322-5. [DOI: 10.1039/c4cc08520e] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
A cation–π interaction is operational in the addition of uncharged nucleophiles to iminium salts derived from MacMillan's 1st generation catalyst.
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Affiliation(s)
- M. C. Holland
- Organisch Chemisches Institut
- and Excellence Cluster EXC 1003
- Cells in Motion
- Westfälische Wilhelms-Universität Münster
- Münster
| | - J. B. Metternich
- Organisch Chemisches Institut
- and Excellence Cluster EXC 1003
- Cells in Motion
- Westfälische Wilhelms-Universität Münster
- Münster
| | - C. Mück-Lichtenfeld
- Organisch Chemisches Institut
- and Excellence Cluster EXC 1003
- Cells in Motion
- Westfälische Wilhelms-Universität Münster
- Münster
| | - R. Gilmour
- Organisch Chemisches Institut
- and Excellence Cluster EXC 1003
- Cells in Motion
- Westfälische Wilhelms-Universität Münster
- Münster
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716
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Abstract
A series of crown ether based iodidobismuthates explores the influence of increasing I/Bi ratio and I⋯I interactions on the compounds’ optical properties. This includes [(Dibenzo-18-crown-6)Na(MeCN)2]21∞[Bi6I20], which contains a strand-like anion with an unprecedentedly low I/Bi ratio.
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Affiliation(s)
- Johanna Heine
- Fachbereich Chemie and Wissenschaftliches Zentrum für Materialwissenschaften (WZMW)
- Philipps-Universität Marburg
- 35043 Marburg
- Germany
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717
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Giust S, La Sorella G, Sperni L, Strukul G, Scarso A. Substrate selective amide coupling driven by encapsulation of a coupling agent within a self-assembled hexameric capsule. Chem Commun (Camb) 2015; 51:1658-61. [DOI: 10.1039/c4cc08833f] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Encapsulation of a cationic carbodiimide condensing agent within a self-assembled hexameric capsule made of resorcin[4]arene units provides a nano-environment that efficiently steers the substrate selectivity in the amide synthesis reaction between carboxylic acids and primary amines.
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Affiliation(s)
- Sonia Giust
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Giorgio La Sorella
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Laura Sperni
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Giorgio Strukul
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
| | - Alessandro Scarso
- Dipartimento di Scienze Molecolari e Nanosistemi
- Università Ca' Foscari di Venezia
- Venezia
- Italy
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718
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Chan CH, Tsai CJ, Chiang YW. Side-Chain Packing Interactions Stabilize an Intermediate of BAX Protein against Chemical and Thermal Denaturation. J Phys Chem B 2014; 119:54-64. [DOI: 10.1021/jp5091334] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Affiliation(s)
- Chun-Hui Chan
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Chia-Jung Tsai
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
| | - Yun-Wei Chiang
- Department of Chemistry and
Frontier Research Center on Fundamental and Applied Sciences of Matters, National Tsing Hua University, Hsinchu 30013, Taiwan
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719
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Shi L, Zhang W, Yang K, Shi H, Li D, Liu J, Ji J, Chu PK. Antibacterial and osteoinductive capability of orthopedic materials via cation-π interaction mediated positive charge. J Mater Chem B 2014; 3:733-737. [PMID: 32262162 DOI: 10.1039/c4tb01924e] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Both implant centered infection and deficient osteoinduction are pivotal issues for orthopedic implants in early and long-term osseointegration, but constructing a functional bio-interface that can overcome these two problems is highly challenging. Our study reveals that a bio-interface with promoted positive charges plays an active role in simultaneously enhancing the antibacterial and osteoinductive capability of orthopedic implants. The positively charged bio-interface is fabricated by a simple dipping method, in which the cationic polymer (polyhexamethylene biguanidine, PHMB) is immobilized in the conjugated polydopamine coating. Mediated by the cation-π interaction, the immobilized PHMB elevates the surface potential resulting in excellent antibacterial efficacy corresponding to 5 ppm of free PHMB. The materials exhibit far better cytocompatibility than free PHMB at the dose which kills over 50% of the cells. Most importantly, the cationic surface can function as a bioelectrical microenvironment to guide bone mesenchymal stem cells and consequently, enhanced cellular viability and proliferation together with upregulated osteogenesis are achieved. The cation-π interaction mediated cationic surface overcomes the disadvantages plaguing the immobilized cationic antibacterial compounds prepared by other methods and is applicable to different types of biomedical materials requiring antibacterial and osteoinductive bio-interfaces.
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Affiliation(s)
- Lianxin Shi
- Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, 29 Zhongguancun East Road, Haidian District, Beijing, 100190, P.R. China.
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720
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He Z, Ye G, Jiang W. Imine Macrocycle with a Deep Cavity: Guest-Selected Formation ofsyn/antiConfiguration and Guest-Controlled Reconfiguration. Chemistry 2014; 21:3005-12. [DOI: 10.1002/chem.201405912] [Citation(s) in RCA: 47] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2014] [Indexed: 12/15/2022]
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721
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La Sorella G, Sperni L, Strukul G, Scarso A. Supramolecular Encapsulation of Neutral Diazoacetate Esters and Catalyzed 1,3-Dipolar Cycloaddition Reaction by a Self-Assembled Hexameric Capsule. ChemCatChem 2014. [DOI: 10.1002/cctc.201402631] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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722
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Murakami K, Sasano Y, Tomizawa M, Shibuya M, Kwon E, Iwabuchi Y. Highly Enantioselective Organocatalytic Oxidative Kinetic Resolution of Secondary Alcohols Using Chiral Alkoxyamines as Precatalysts: Catalyst Structure, Active Species, and Substrate Scope. J Am Chem Soc 2014; 136:17591-600. [DOI: 10.1021/ja509766f] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Keiichi Murakami
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yusuke Sasano
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Masaki Tomizawa
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Masatoshi Shibuya
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Eunsang Kwon
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
| | - Yoshiharu Iwabuchi
- Department of Organic Chemistry,
Graduate School of Pharmaceutical
Sciences and ‡Research and Analytical Center for Giant Molecules, Graduate School
of Science, Tohoku University, 6-3 Aoba, Aramaki, Aoba-ku, Sendai 980-8578, Japan
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723
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Grubel K, Brennessel W, Mercado BQ, Holland PL. Alkali metal control over N-N cleavage in iron complexes. J Am Chem Soc 2014; 136:16807-16. [PMID: 25412468 PMCID: PMC4277784 DOI: 10.1021/ja507442b] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2014] [Indexed: 01/22/2023]
Abstract
Though N2 cleavage on K-promoted Fe surfaces is important in the large-scale Haber-Bosch process, there is still ambiguity about the number of Fe atoms involved during the N-N cleaving step and the interactions responsible for the promoting ability of K. This work explores a molecular Fe system for N2 reduction, particularly focusing on the differences in the results obtained using different alkali metals as reductants (Na, K, Rb, Cs). The products of these reactions feature new types of Fe-N2 and Fe-nitride cores. Surprisingly, adding more equivalents of reductant to the system gives a product in which the N-N bond is not cleaved, indicating that the reducing power is not the most important factor that determines the extent of N2 activation. On the other hand, the results suggest that the size of the alkali metal cation can control the number of Fe atoms that can approach N2, which in turn controls the ability to achieve N2 cleavage. The accumulated results indicate that cleaving the triple N-N bond to nitrides is facilitated by simultaneous approach of least three low-valent Fe atoms to a single molecule of N2.
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Affiliation(s)
- Katarzyna Grubel
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - William
W. Brennessel
- Department
of Chemistry, University of Rochester, Rochester, New York 14627, United States
| | - Brandon Q. Mercado
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
| | - Patrick L. Holland
- Department
of Chemistry, Yale University, New Haven, Connecticut 06511, United States
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724
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész Á, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite Aromatic Boxes for Enzymatic Transformations of Quaternary Ammonium Substrates. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201408246] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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725
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Wixe T, Christensen NJ, Lidin S, Fristrup P, Wärnmark K. A short designed semi-aromatic organic nanotube--synthesis, chiroptical characterization, and host properties. Org Biomol Chem 2014; 12:8930-41. [PMID: 25271821 DOI: 10.1039/c4ob01683a] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The first generation of an organic nanotube based on the enantiomerically pure bicyclo[3.3.1]nonane framework is presented. The helical tube synthesised is the longest to date having its aromatic systems oriented parallel to the axis of propagation (length ∼26 Å and inner diameter ∼11 Å according to molecular dynamics simulations in chloroform). The synthesis of the tube, a heptamer, is based on a series of Friedländer condensations and the use of pyrido[3,2-d]pyrimidine units as masked 2-amino aldehydes, as a general means to propagate organic tubular structures and the introduction of a methoxy group for modification toward solubility and functionalization are described. The electronic CD spectra of the tube and molecular intermediates are correlated with theoretical spectra calculated with time-dependent density functional theory to characterize the chirality of the tube. Both experimental (NMR-titrations) and theoretical (molecular dynamics simulations) techniques are used to investigate the use of the tube as a receptor for the acetylcholine and guanidinium cations, respectively.
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Affiliation(s)
- Torbjörn Wixe
- Centre for Analysis and Synthesis, Department of Chemistry, Lund University, P.O. Box 124, SE-221 00, Lund, Sweden.
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726
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Aliev AE, Arendorf JRT, Pavlakos I, Moreno RB, Porter MJ, Rzepa HS, Motherwell WB. Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201409672] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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727
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Aliev AE, Arendorf JRT, Pavlakos I, Moreno RB, Porter MJ, Rzepa HS, Motherwell WB. Surfing π Clouds for Noncovalent Interactions: Arenes versus Alkenes. Angew Chem Int Ed Engl 2014; 54:551-5. [DOI: 10.1002/anie.201409672] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2014] [Indexed: 11/07/2022]
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728
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Dulin F, Zatylny-Gaudin C, Ballandonne C, Guillet B, Bonafos R, Bureau R, Halm MP. Protecting honey bees: identification of a new varroacide by in silico, in vitro, and in vivo studies. Parasitol Res 2014; 113:4601-10. [PMID: 25358237 DOI: 10.1007/s00436-014-4150-z] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2014] [Accepted: 09/23/2014] [Indexed: 11/28/2022]
Abstract
Varroa destructor is the main concern related to the gradual decline of honeybees. Nowadays, among the various acaricides used in the control of V. destructor, most presents increasing resistance. An interesting alternative could be the identification of existent molecules as new acaricides with no effect on honeybee health. We have previously constructed the first 3D model of AChE for honeybee. By analyzing data concerning amino acid mutations implicated in the resistance associated to pesticides, it appears that pirimicarb should be a good candidate for varroacide. To check this hypothesis, we characterized the AChE gene of V. destructor. In the same way, we proposed a 3D model for the AChE of V. destructor. Starting from the definition of these two 3D models of AChE in honeybee and varroa, a comparison between the gorges of the active site highlighted some major differences and particularly different shapes. Following this result, docking studies have shown that pirimicarb adopts two distinct positions with the strongest intermolecular interactions with VdAChE. This result was confirmed with in vitro and in vivo data for which a clear inhibition of VdAChE by pirimicarb at 10 μM (contrary to HbAChE) and a 100% mortality of varroa (dose corresponding to the LD50 (contact) for honeybee divided by a factor 100) were observed. These results demonstrate that primicarb could be a new varroacide candidate and reinforce the high relationships between in silico, in vitro, and in vivo data for the design of new selective pesticides.
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729
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Shi G, Shen Y, Liu J, Wang C, Wang Y, Song B, Hu J, Fang H. Molecular-scale hydrophilicity induced by solute: molecular-thick charged pancakes of aqueous salt solution on hydrophobic carbon-based surfaces. Sci Rep 2014; 4:6793. [PMID: 25348642 PMCID: PMC4210940 DOI: 10.1038/srep06793] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2014] [Accepted: 10/08/2014] [Indexed: 12/14/2022] Open
Abstract
We directly observed molecular-thick aqueous salt-solution pancakes on a hydrophobic graphite surface under ambient conditions employing atomic force microscopy. This observation indicates the unexpected molecular-scale hydrophilicity of the salt solution on graphite surfaces, which is different from the macroscopic wetting property of a droplet standing on the graphite surface. Interestingly, the pancakes spontaneously displayed strong positively charged behavior. Theoretical studies showed that the formation of such positively charged pancakes is attributed to cation–π interactions between Na+ ions in the aqueous solution and aromatic rings on the graphite surface, promoting the adsorption of water molecules together with cations onto the graphite surface; i.e., Na+ ions as a medium adsorbed to the graphite surface through cation–π interactions on one side while at the same time bonding to water molecules through hydration interaction on the other side at a molecular scale. These findings suggest that actual interactions regarding carbon-based graphitic surfaces including those of graphene, carbon nanotubes, and biochar may be significantly different from existing theory and they provide new insight into the control of surface wettability, interactions and related physical, chemical and biological processes.
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Affiliation(s)
- Guosheng Shi
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Yue Shen
- 1] Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China [2] Salt Lake Resources and Chemistry Laboratory, Qinghai Institute of Salt Lakes, Chinese Academy of Sciences, Xining 810008, China
| | - Jian Liu
- 1] Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China [2] University of Chinese Academy of Sciences, Beijing 100049, China
| | - Chunlei Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Ying Wang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Bo Song
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Jun Hu
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
| | - Haiping Fang
- Division of Interfacial Water and Key Laboratory of Interfacial Physics and Technology, Shanghai Institute of Applied Physics, Chinese Academy of Sciences, Shanghai 201800, China
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730
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Ohtake K, Saito N, Shibuya S, Kobayashi W, Amano R, Hirai T, Sasaki S, Nakano C, Hoshino T. Biochemical characterization of the water-soluble squalene synthase fromMethylococcus capsulatusand the functional analyses of its two DXXD(E)D motifs and the highly conserved aromatic amino acid residues. FEBS J 2014; 281:5479-97. [DOI: 10.1111/febs.13090] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2014] [Revised: 09/12/2014] [Accepted: 09/30/2014] [Indexed: 11/27/2022]
Affiliation(s)
- Kana Ohtake
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Naoki Saito
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Satoshi Shibuya
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Wakako Kobayashi
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Ryosuke Amano
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Takumi Hirai
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Shinji Sasaki
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Chiaki Nakano
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
| | - Tsutomu Hoshino
- Department of Applied Biological Chemistry; Faculty of Agriculture and Graduate School of Science and Technology; Niigata University; Japan
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731
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Nagy GN, Marton L, Contet A, Ozohanics O, Ardelean LM, Révész A, Vékey K, Irimie FD, Vial H, Cerdan R, Vértessy BG. Composite aromatic boxes for enzymatic transformations of quaternary ammonium substrates. Angew Chem Int Ed Engl 2014; 53:13471-6. [PMID: 25283789 DOI: 10.1002/anie.201408246] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2014] [Indexed: 11/07/2022]
Abstract
Cation-π interactions to cognate ligands in enzymes have key roles in ligand binding and enzymatic catalysis. We have deciphered the key functional role of both charged and aromatic residues within the choline binding subsite of CTP:phosphocholine cytidylyltransferase and choline kinase from Plasmodium falciparum. Comparison of quaternary ammonium binding site structures revealed a general composite aromatic box pattern of enzyme recognition sites, well distinguished from the aromatic box recognition site of receptors.
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Affiliation(s)
- Gergely N Nagy
- Department of Applied Biotechnology and Food Science, Budapest University of Technology and Economics, 1111 Budapest (Hungary); Institute of Enzymology, Research Centre of National Sciences, HAS, 1117 Budapest (Hungary).
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732
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Talotta C, Gaeta C, Neri P. Endo-Complexation of Alkylammonium Ions by Calix[4]arene Cavity: Facilitating Cation−π Interactions through the Weakly Coordinating Anion Approach. J Org Chem 2014; 79:9842-6. [DOI: 10.1021/jo5016689] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Carmen Talotta
- Dipartimento
di Chimica e
Biologia, Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Carmine Gaeta
- Dipartimento
di Chimica e
Biologia, Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
| | - Placido Neri
- Dipartimento
di Chimica e
Biologia, Università di Salerno, Via Giovanni Paolo II 132, I-84084 Fisciano, Salerno, Italy
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733
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Affiliation(s)
- François N. Miros
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Guangxi Huang
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Yingjie Zhao
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Naomi Sakai
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
| | - Stefan Matile
- Department of Organic Chemistry, University of Geneva, Geneva, Switzerland
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734
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Rodríguez-Sanz AA, Cabaleiro-Lago EM, Rodríguez-Otero J. Interaction between the guanidinium cation and aromatic amino acids. Phys Chem Chem Phys 2014; 16:22499-512. [DOI: 10.1039/c4cp02630f] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
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735
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Fujisawa K, Beuchat C, Humbert-Droz M, Wilson A, Wesolowski TA, Mareda J, Sakai N, Matile S. Anion-π and Cation-π Interactions on the Same Surface. Angew Chem Int Ed Engl 2014; 53:11266-9. [DOI: 10.1002/anie.201407161] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2014] [Revised: 07/30/2014] [Indexed: 12/12/2022]
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736
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Fujisawa K, Beuchat C, Humbert-Droz M, Wilson A, Wesolowski TA, Mareda J, Sakai N, Matile S. Anion-π and Cation-π Interactions on the Same Surface. Angew Chem Int Ed Engl 2014. [DOI: 10.1002/ange.201407161] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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737
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Indra Neela Y, Narahari Sastry G. Theoretical investigation of anion (F−, Cl−) and cation (Na+) interactions with substituted benzene [C6H6 −nYn(Y = –F, –CN, –NO2;n= 1–6)]. Mol Phys 2014. [DOI: 10.1080/00268976.2014.948940] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/24/2022]
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738
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Zhang H, Li C, Yang F, Su J, Tan J, Zhang X, Wang C. Cation-pi interactions at non-redundant protein-RNA interfaces. BIOCHEMISTRY (MOSCOW) 2014; 79:643-52. [DOI: 10.1134/s0006297914070062] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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739
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Chiavarino B, Crestoni ME, Schütz M, Bouchet A, Piccirillo S, Steinmetz V, Dopfer O, Fornarini S. Cation-π interactions in protonated phenylalkylamines. J Phys Chem A 2014; 118:7130-8. [PMID: 25061749 DOI: 10.1021/jp505037n] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
Abstract
Phenylalkylamines of the general formula C6H5(CH2)nNH2 (n = 1-4) have been delivered to the gas phase as protonated species using electrospray ionization. The ions thus formed have been assayed by IRMPD spectroscopy in two different spectroscopic domains, namely, the 600-1800 and the 3000-3500 cm(-1) regions using either an IR free electron laser or a tabletop OPO/OPA laser source. The interpretation of the experimental spectra is aided by density functional theory calculations of candidate species and vibrational frequency analyses. Protonated benzylamine presents a relatively straightforward instance of a single stable conformer, providing a trial case for the adopted approach. Turning to the higher homologues, C6H5(CH2)nNH3(+) (n = 2-4), more conformations become accessible. For each C6H5(CH2)nNH3(+) ion (n = 2-4), the most stable geometry is characterized by cation-π interactions between the positively charged ammonium group and the aromatic π-electronic system, permitted by the folding of the polymethylene chain. The IRMPD spectra of the sampled ions confirm the presence of the folded structures by comparison with the calculated IR spectra of the various possible conformers. An inspection of the NH stretching region is helpful in this regard.
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Affiliation(s)
- Barbara Chiavarino
- Dipartimento di Chimica e Tecnologie del Farmaco, Università degli Studi di Roma La Sapienza , P. le A. Moro 5, I-00185 Roma, Italy
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740
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Najor MS, Olsen KW, Graham DJ, Mota de Freitas D. Contribution of each Trp residue toward the intrinsic fluorescence of the Giα1 protein. Protein Sci 2014; 23:1392-402. [PMID: 25044474 DOI: 10.1002/pro.2523] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2014] [Revised: 07/10/2014] [Accepted: 07/13/2014] [Indexed: 12/27/2022]
Abstract
Giα1 is the inhibitory G-protein that, upon activation, reduces the activity of adenylyl cyclase. Comparison of the crystal structures of Giα1 bound to GDP•AMF or GTPγS with that of the inactive, GPD-bound protein indicates that a conformational change occurs in the activation step centered on three switch regions. The contribution of each tryptophan residue (W211 in the switch II region, W131 in the α-helical domain, and W258 in the GTPase domain) toward the intrinsic protein fluorescence was evaluated by using W211F, W131F, and W258F mutants. All three tryptophan residues contributed significantly toward the emission spectra regardless of the conformation. When activated by either GDP•AMF or GTPγS, the observed maximal-fluorescence scaled according to the solvent accessibilities of the tryptophan residues, calculated from molecular dynamics simulations. In the GDP•AMF and GTPγS, but not in the GDP, conformations, the residues W211 and R208 are in close proximity and form a π-cation interaction that results in a red shift in the emission spectra of WT, and W131F and W258F mutants, but a blue shift for the W211F mutant. The observed shifts did not show a relationship with the span of the W211-R208 bridge, but rather with changes in the total interaction energies. Trypsin digestion of the active conformations only occurred for the W211F mutant indicating that the electrostatic π-cation interaction blocks access to R208, which was consistent with the molecular dynamics simulations. We conclude that solvent accessibility and interaction energies account for the fluorescence features of Giα1 .
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Affiliation(s)
- Matthew S Najor
- Department of Chemistry and Biochemistry, Loyola University Chicago, Chicago, Illinois
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741
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AFAL: a web service for profiling amino acids surrounding ligands in proteins. J Comput Aided Mol Des 2014; 28:1069-76. [PMID: 25085083 PMCID: PMC4241235 DOI: 10.1007/s10822-014-9783-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2014] [Accepted: 07/23/2014] [Indexed: 10/25/2022]
Abstract
With advancements in crystallographic technology and the increasing wealth of information populating structural databases, there is an increasing need for prediction tools based on spatial information that will support the characterization of proteins and protein-ligand interactions. Herein, a new web service is presented termed amino acid frequency around ligand (AFAL) for determining amino acids type and frequencies surrounding ligands within proteins deposited in the Protein Data Bank and for assessing the atoms and atom-ligand distances involved in each interaction (availability: http://structuralbio.utalca.cl/AFAL/index.html ). AFAL allows the user to define a wide variety of filtering criteria (protein family, source organism, resolution, sequence redundancy and distance) in order to uncover trends and evolutionary differences in amino acid preferences that define interactions with particular ligands. Results obtained from AFAL provide valuable statistical information about amino acids that may be responsible for establishing particular ligand-protein interactions. The analysis will enable investigators to compare ligand-binding sites of different proteins and to uncover general as well as specific interaction patterns from existing data. Such patterns can be used subsequently to predict ligand binding in proteins that currently have no structural information and to refine the interpretation of existing protein models. The application of AFAL is illustrated by the analysis of proteins interacting with adenosine-5'-triphosphate.
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742
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Bania KK, Guha AK, Bhattacharyya PK, Sinha S. Effect of substituent and solvent on cation-π interactions in benzene and borazine: a computational study. Dalton Trans 2014; 43:1769-84. [PMID: 24248426 DOI: 10.1039/c3dt52081a] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
A DFT and ab initio quantum chemical study has been carried out at different theoretical levels to delve into the role of the cation-π interaction within the main group metal cations (Li(+), Na(+) and K(+)), substituted benzene and borazine. The effects of electron withdrawing and electron donating groups on these non-covalent forces of interaction were also studied. The excellent correlation between Hammett constants and binding energy values indicates that the cation-π interaction is influenced by both inductive and resonance effects. Electron donating groups (EDG) such as -CH3 and -NH2 attached to benzene at the 1, 3 and 5 position and the three boron atoms of borazine were found to strengthen these interactions, while electron withdrawing groups (EWG) such as -NO2 did the reverse. These results were further substantiated by topological analysis using the quantum theory of atoms in molecules (QTAIM). The polarized continuum model (PCM) and the discrete solvation model were used to elucidate the effect of solvation on the cation-π interaction. The size of the cations and the nature of the substituents were found to influence the enthalpy and binding energy of the systems (or complex). In the gas phase, the cation-π interaction was found to be exothermic, whereas in the presence of a polar solvent the interaction was highly endothermic. Thermochemical analysis predicts the presence of thermodynamic driving forces for borazine and benzene substituted with EDG. DFT based reactivity descriptors, such as global hardness (η), chemical potential (μ) and the electrophilicity index (ω) were used to elucidate the effect of the substituent on the reactivity of the cation-π complexes.
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743
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Green BT, Lee ST, Welch KD, Panter KE. Plant alkaloids that cause developmental defects through the disruption of cholinergic neurotransmission. ACTA ACUST UNITED AC 2014; 99:235-46. [PMID: 24339035 DOI: 10.1002/bdrc.21049] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Revised: 10/24/2013] [Accepted: 10/24/2013] [Indexed: 12/26/2022]
Abstract
The exposure of a developing embryo or fetus to alkaloids from plants, plant products, or plant extracts has the potential to cause developmental defects in humans and animals. These defects may have multiple causes, but those induced by piperidine and quinolizidine alkaloids arise from the inhibition of fetal movement and are generally referred to as multiple congenital contracture-type deformities. These skeletal deformities include arthrogyrposis, kyposis, lordosis, scoliosis, and torticollis, associated secondary defects, and cleft palate. Structure-function studies have shown that plant alkaloids with a piperidine ring and a minimum of a three-carbon side-chain α to the piperidine nitrogen are teratogenic. Further studies determined that an unsaturation in the piperidine ring, as occurs in gamma coniceine, or anabaseine, enhances the toxic and teratogenic activity, whereas the N-methyl derivatives are less potent. Enantiomers of the piperidine teratogens, coniine, ammodendrine, and anabasine, also exhibit differences in biological activity, as shown in cell culture studies, suggesting variability in the activity due to the optical rotation at the chiral center of these stereoisomers. In this article, we review the molecular mechanism at the nicotinic pharmacophore and biological activities, as it is currently understood, of a group of piperidine and quinolizidine alkaloid teratogens that impart a series of flexure-type skeletal defects and cleft palate in animals.
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Affiliation(s)
- Benedict T Green
- United States Department of Agriculture, Poisonous Plant Research Laboratory, Agricultural Research Service, 1150 E 1400 N, Logan, Utah, 84321
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744
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Synergy of aromatic residues and phosphoserines within the intrinsically disordered DNA-binding inhibitory elements of the Ets-1 transcription factor. Proc Natl Acad Sci U S A 2014; 111:11019-24. [PMID: 25024220 DOI: 10.1073/pnas.1401891111] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The E26 transformation-specific (Ets-1) transcription factor is autoinhibited by a conformationally disordered serine-rich region (SRR) that transiently interacts with its DNA-binding ETS domain. In response to calcium signaling, autoinhibition is reinforced by calmodulin-dependent kinase II phosphorylation of serines within the SRR. Using mutagenesis and quantitative DNA-binding measurements, we demonstrate that phosphorylation-enhanced autoinhibition requires the presence of phenylalanine or tyrosine (ϕ) residues adjacent to the SRR phosphoacceptor serines. The introduction of additional phosphorylated Ser-ϕ-Asp, but not Ser-Ala-Asp, repeats within the SRR dramatically reinforces autoinhibition. NMR spectroscopic studies of phosphorylated and mutated SRR variants, both within their native context and as separate trans-acting peptides, confirmed that the aromatic residues and phosphoserines contribute to the formation of a dynamic complex with the ETS domain. Complementary NMR studies also identified the SRR-interacting surface of the ETS domain, which encompasses its positively charged DNA-recognition interface and an adjacent region of neutral polar and nonpolar residues. Collectively, these studies highlight the role of aromatic residues and their synergy with phosphoserines in an intrinsically disordered regulatory sequence that integrates cellular signaling and gene expression.
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745
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Abadie MA, Trivelli X, Medina F, Capet F, Roussel P, Agbossou-Niedercorn F, Michon C. Asymmetric Intramolecular Hydroamination of Alkenes in Mild and Wet Conditions-Structure and Reactivity of Cationic Binuclear Gold(I) Catalysts. ChemCatChem 2014. [DOI: 10.1002/cctc.201402350] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/27/2023]
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746
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Dougherty DA, Van Arnam EB. In vivo incorporation of non-canonical amino acids by using the chemical aminoacylation strategy: a broadly applicable mechanistic tool. Chembiochem 2014; 15:1710-20. [PMID: 24990307 DOI: 10.1002/cbic.201402080] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2014] [Indexed: 01/05/2023]
Abstract
We describe a strategy for incorporating non-canonical amino acids site-specifically into proteins expressed in living cells, involving organic synthesis to chemically aminoacylate a suppressor tRNA, protein expression in Xenopus oocytes, and monitoring protein function, primarily by electrophysiology. With this protocol, a very wide range of non-canonical amino acids can be employed, allowing both systematic structure-function studies and the incorporation of reactive functionalities. Here, we present an overview of the methodology and examples meant to illustrate the versatility and power of the method as a tool for investigating protein structure and function.
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Affiliation(s)
- Dennis A Dougherty
- Division of Chemistry and Chemical Engineering, California Institute of Technology, 1200 E. California Blvd., Pasadena, CA 91125 (USA).
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747
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Zhai X, Go M, O’Donoghue AC, Amyes TL, Pegan SD, Wang Y, Loria JP, Mesecar A, Richard JP. Enzyme architecture: the effect of replacement and deletion mutations of loop 6 on catalysis by triosephosphate isomerase. Biochemistry 2014; 53:3486-501. [PMID: 24825099 PMCID: PMC4051426 DOI: 10.1021/bi500458t] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/07/2023]
Abstract
Two mutations of the phosphodianion gripper loop in chicken muscle triosephosphate isomerase (cTIM) were examined: (1) the loop deletion mutant (LDM) formed by removal of residues 170-173 [Pompliano, D. L., et al. (1990) Biochemistry 29, 3186-3194] and (2) the loop 6 replacement mutant (L6RM), in which the N-terminal hinge sequence of TIM from eukaryotes, 166-PXW-168 (X = L or V), is replaced by the sequence from archaea, 166-PPE-168. The X-ray crystal structure of the L6RM shows a large displacement of the side chain of E168 from that for W168 in wild-type cTIM. Solution nuclear magnetic resonance data show that the L6RM results in significant chemical shift changes in loop 6 and surrounding regions, and that the binding of glycerol 3-phosphate (G3P) results in chemical shift changes for nuclei at the active site of the L6RM that are smaller than those of wild-type cTIM. Interactions with loop 6 of the L6RM stabilize the enediolate intermediate toward the elimination reaction catalyzed by the LDM. The LDM and L6RM result in 800000- and 23000-fold decreases, respectively, in kcat/Km for isomerization of GAP. Saturation of the LDM, but not the L6RM, by substrate and inhibitor phosphoglycolate is detected by steady-state kinetic analyses. We propose, on the basis of a comparison of X-ray crystal structures for wild-type TIM and the L6RM, that ligands bind weakly to the L6RM because a large fraction of the ligand binding energy is utilized to overcome destabilizing electrostatic interactions between the side chains of E168 and E129 that are predicted to develop in the loop-closed enzyme. Similar normalized yields of DHAP, d-DHAP, and d-GAP are formed in LDM- and L6RM-catalyzed reactions of GAP in D2O. The smaller normalized 12-13% yield of DHAP and d-DHAP observed for the mutant cTIM-catalyzed reactions compared with the 79% yield of these products for wild-type cTIM suggests that these mutations impair the transfer of a proton from O-2 to O-1 at the initial enediolate phosphate intermediate. No products are detected for the LDM-catalyzed isomerization reactions in D2O of [1-(13)C]GA and HPi, but the L6RM-catalyzed reaction in the presence of 0.020 M dianion gives a 2% yield of the isomerization product [2-(13)C,2-(2)H]GA.
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Affiliation(s)
- Xiang Zhai
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14221, United States
| | - Maybelle
K. Go
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14221, United States
| | | | - Tina L. Amyes
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14221, United States
| | - Scott D. Pegan
- Department
of Pharmaceutical and Biomedical Sciences, University of Georgia, Athens, Georgia 30602, United States
| | - Yan Wang
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States
| | - J. Patrick Loria
- Department
of Chemistry, Yale University, New Haven, Connecticut 06520, United States,Department
of Chemistry and Molecular Biophysics and Biochemistry, Yale University, New Haven, Connecticut 06520, United States
| | - Andrew
D. Mesecar
- Departments
of Biological Sciences and Chemistry, Purdue
University, West Lafayette, Indiana 47907, United States
| | - John P. Richard
- Department
of Chemistry, University at Buffalo, Buffalo, New York 14221, United States,E-mail: . Telephone: (716) 645-4232. Fax: (716) 645-6963
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748
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Zhao Y, Sakai N, Matile S. Enolate chemistry with anion–π interactions. Nat Commun 2014; 5:3911. [DOI: 10.1038/ncomms4911] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2014] [Accepted: 04/17/2014] [Indexed: 12/12/2022] Open
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749
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Sarmah N, Bhattacharyya PK, Bania KK. Substituent and Solvent Effects on the Absorption Spectra of Cation-π Complexes of Benzene and Borazine: A Theoretical Study. J Phys Chem A 2014; 118:3760-3774. [PMID: 24801959 DOI: 10.1021/jp5021966] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Time-dependent density functional theory (TDDFT) has been used to predict the absorption spectra of cation-π complexes of benzene and borazine. Both polarized continuum model (PCM) and discrete solvation model (DSM) and a combined effect of PCM and DSM on the absorption spectra have been elucidated. With decrease in size of the cation, the π → π* transitions of benzene and borazine are found to undergo blue and red shift, respectively. A number of different substituents (both electron-withdrawing and electron-donating) and a range of solvents (nonpolar to polar) have been considered to understand the effect of substituent and solvents on the absorption spectra of the cation-π complexes of benzene and borazine. Red shift in the absorption spectra of benzene cation-π complexes are observed with both electron-donating groups (EDGs) and electron-withdrawing groups (EWGs). The same trend has not been observed in the case of substituted borazine cation-π complexes. The wavelength of the electronic transitions corresponding to cation-π complexes correlates well with the Hammet constants (σp and σm). This correlation indicates that the shifting of spectral lines of the cation-π complexes on substitution is due to both resonance and inductive effect. On incorporation of solvent phases, significant red or blue shifting in the absorption spectra of the complexes has been observed. Kamlet-Taft multiparametric equation has been used to explain the effect of solvent on the absorption spectra of complexes. Polarity and polarizability are observed to play an important role in the solvatochromism of the cation-π complexes.
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750
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Myslinski JM, Clements JH, Martin SF. Protein-ligand interactions: probing the energetics of a putative cation-π interaction. Bioorg Med Chem Lett 2014; 24:3164-7. [PMID: 24856058 DOI: 10.1016/j.bmcl.2014.04.114] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2014] [Revised: 04/25/2014] [Accepted: 04/28/2014] [Indexed: 01/01/2023]
Abstract
In order to probe the energetics associated with a putative cation-π interaction, thermodynamic parameters are determined for complex formation between the Grb2 SH2 domain and tripeptide derivatives of RCO-pTyr-Ac6c-Asn wherein the R group is varied to include different alkyl, cycloalkyl, and aryl groups. Although an indole ring is reputed to have the strongest interaction with a guanidinium ion, binding free energies, ΔG°, for derivatives of RCO-pTyr-Ac6c-Asn bearing cyclohexyl and phenyl groups were slightly more favorable than their indolyl analog. Crystallographic analysis of two complexes reveals that test ligands bind in similar poses with the notable exception of the relative orientation and proximity of the phenyl and indolyl rings relative to an arginine residue of the domain. These spatial orientations are consistent with those observed in other cation-π interactions, but there is no net energetic benefit to such an interaction in this biological system. Accordingly, although cation-π interactions are well documented as important noncovalent forces in molecular recognition, the energetics of such interactions may be mitigated by other nonbonded interactions and solvation effects in protein-ligand associations.
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Affiliation(s)
- James M Myslinski
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - John H Clements
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA
| | - Stephen F Martin
- The Department of Chemistry, The Institute of Cellular and Molecular Biology, and the Texas Institute of Drug and Diagnostic Development, The University of Texas, Austin, TX 78712, USA.
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