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Del Conte A, Camagni GF, Clementel D, Minervini G, Monzon AM, Ferrari C, Piovesan D, Tosatto SE. RING 4.0: faster residue interaction networks with novel interaction types across over 35,000 different chemical structures. Nucleic Acids Res 2024; 52:W306-W312. [PMID: 38686797 PMCID: PMC11223866 DOI: 10.1093/nar/gkae337] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/09/2024] [Accepted: 04/19/2024] [Indexed: 05/02/2024] Open
Abstract
Residue interaction networks (RINs) are a valuable approach for representing contacts in protein structures. RINs have been widely used in various research areas, including the analysis of mutation effects, domain-domain communication, catalytic activity, and molecular dynamics simulations. The RING server is a powerful tool to calculate non-covalent molecular interactions based on geometrical parameters, providing high-quality and reliable results. Here, we introduce RING 4.0, which includes significant enhancements for identifying both covalent and non-covalent bonds in protein structures. It now encompasses seven different interaction types, with the addition of π-hydrogen, halogen bonds and metal ion coordination sites. The definitions of all available bond types have also been refined and RING can now process the complete PDB chemical component dictionary (over 35000 different molecules) which provides atom names and covalent connectivity information for all known ligands. Optimization of the software has improved execution time by an order of magnitude. The RING web server has been redesigned to provide a more engaging and interactive user experience, incorporating new visualization tools. Users can now visualize all types of interactions simultaneously in the structure viewer and network component. The web server, including extensive help and tutorials, is available from URL: https://ring.biocomputingup.it/.
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Affiliation(s)
- Alessio Del Conte
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Giorgia F Camagni
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | - Damiano Clementel
- Department of Biomedical Sciences, University of Padova, Padova, Italy
| | | | | | - Carlo Ferrari
- Department of Information Engineering, University of Padova, Padova, Italy
| | - Damiano Piovesan
- Department of Biomedical Sciences, University of Padova, Padova, Italy
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Groß P, Ihmels H. Studies About the Effect of Halogenated Solvents on the Fluorescence Properties of 9-Aryl-Substituted Isoquinolinium Derivatives - A Case Study. J Fluoresc 2024:10.1007/s10895-024-03691-z. [PMID: 38598108 DOI: 10.1007/s10895-024-03691-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/15/2024] [Accepted: 03/23/2024] [Indexed: 04/11/2024]
Abstract
It was demonstrated that 9-aryl-substituted isoquinolinium derivatives have significantly increased fluorescence quantum yields in halogenated solvents, mostly pronounced in chloroalkanes, which appears to be specific for this type of solvents. Further analysis with selected halogenated solvents revealed that the type and number of halogen substituents and the dielectric constant of the solvent have a distinct impact on the emission quantum yield. The solvent effect is explained by a solvation of the charge shift (CS) state by attractive halogen-π interactions (halogen bond), which impedes the torsional relaxation of the excited state.
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Affiliation(s)
- Philipp Groß
- Department of Chemistry and Biology, Center of Micro- and Nanochemistry and (Bio)Technology (Cµ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany
| | - Heiko Ihmels
- Department of Chemistry and Biology, Center of Micro- and Nanochemistry and (Bio)Technology (Cµ), University of Siegen, Adolf-Reichwein-Str. 2, 57068, Siegen, Germany.
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3
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Persistent prevalence of non-covalent interaction in pyrimidine containing sulfonamide derivative: A quantum computational analysis. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133378] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
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4
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Taylor CM, Kilah NL. Synthesis of [2+2] Schiff base macrocycles by a solvent templating strategy and halogen bonding directed assembly. J INCL PHENOM MACRO 2022. [DOI: 10.1007/s10847-022-01137-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
AbstractSchiff base imine condensations are a useful tool for macrocycle synthesis and applications within supramolecular chemistry. Here we address the mixtures of products that can arise from template free synthesis using dicarbonylheterocycles and diamines, and look to develop metal-free template methods for selective macrocycle formation. A range of alkyl α,ω-diamines were combined with phenanthroline and pyridine heterocyclic dicarbaldehydes under standard literature conditions. The reaction conditions were modified to demonstrate a relationship between choice of solvent and product equilibria. It was observed that benzene and toluene could shift a mixture of products and unreacted starting materials to form predominantly one imine product for a number of systems. Once the macrocyclic products had been characterized in selected solvents, iodinated halogen bonding guest molecules were added to direct macrocycle assemblies using non-covalent interactions. Studies to investigate host – guest suitability and halogen bond interactions were conducted, and it was found that tetraiodoethylene had an influence on the formation of a phenanthroline based macrocycle. Proof of concept experiments were performed to show the influence of the guest molecule, tetraiodoethylene, on the macrocyclic products formed under competitive dynamic combinatorial chemistry conditions.
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Abstract
A halogen-bonded complex containing a pair of anions can be made more stable than the isolated anions if the Lewis acid is a long carbon chain, fully substituted by CN groups, with an I atom on one end and a COO− group on the other, with Cl− as base.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, Utah 84322-0300, USA
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6
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Dong Y, Gao M, Qiu W, Song Z. The influence of humic and fulvic acids on polytetrafluoroethylene-adsorbed arsenic: a mechanistic study. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2021; 28:64503-64515. [PMID: 34308520 DOI: 10.1007/s11356-021-15376-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/23/2020] [Accepted: 07/06/2021] [Indexed: 06/13/2023]
Abstract
The large-scale use of polytetrafluoroethylene has resulted in ever-increasing amounts of polytetrafluoroethylene (PTFE) microplastic particles entering the environment. Given that the environment is polluted with arsenic (As(III)), and that the environment contains significant levels of humic acid (HA) and fulvic acid (FA), how PTFE and As(III) in water interacting in the presence of HA and FA needs to be urgently investigated. The results showed that As(III) was adsorbed by PTFE in the presence of HA and FA more markedly than the absence of them Adsorption equilibrium was reached at approximately 960 min and the adsorption isotherms were found to be best fitted by the Toth model. An increase in temperature was found to destroy hydrogen bonds, resulting in inhibited, non-spontaneous adsorption; a higher pH inhibited adsorption in the range 3-7. Computational and mechanistic studies revealed that PTFE formed π complexes with HA units, which increased the number of oxygen-containing functional groups on its surface. The surface of the PTFE-HA π complex was mostly negatively charged; however, the hydrogen atoms of the hydroxyl and carboxylic acid groups exhibited large positive potentials that enabled the adsorption of As(III). When the oxygen atom on As was close to the oxygen-containing functional group on PTFE-HA, the more electronegative oxygen atom forms a special intermolecular interaction in the form of O-H···O through the medium of hydrogen, which makes As adsorb on the surface of PTFE. Pore filling, hydrogen bonding, and covalent bonding are the main ways in which PTFE adsorbs As(III) in the presence of HA and FA. PTFE also adsorbed more As(III) in the presence of HA than in the presence of FA.
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Affiliation(s)
- Youming Dong
- Agro-Environmental Protection Institute, Ministry of Agriculture of China, Tianjin, 300191, China
| | - Minling Gao
- Department of Civil and Environmental Engineering, Shantou University, Shantou, 515063, China
| | - Weiwen Qiu
- The New Zealand Institute for Plant and Food Research Limited, Private Bag 4704, Christchurch, 8140, New Zealand
| | - Zhengguo Song
- Department of Civil and Environmental Engineering, Shantou University, Shantou, 515063, China.
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7
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Holthoff JM, Weiss R, Rosokha SV, Huber SM. "Anti-electrostatic" Halogen Bonding between Ions of Like Charge. Chemistry 2021; 27:16530-16542. [PMID: 34409662 PMCID: PMC9293363 DOI: 10.1002/chem.202102549] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Indexed: 12/15/2022]
Abstract
Halogen bonding occurs between molecules featuring Lewis acidic halogen substituents and Lewis bases. It is often rationalized as a predominantly electrostatic interaction and thus interactions between ions of like charge (e. g., of anionic halogen bond donors with halides) seem counter-intuitive. Herein, we provide an overview on such complexes. First, theoretical studies are described and their findings are compared. Next, experimental evidences are presented in the form of crystal structure database analyses, recent examples of strong "anti-electrostatic" halogen bonding in crystals, and the observation of such interactions also in solution. We then compare these complexes to select examples of "counter-intuitive" adducts formed by other interactions, like hydrogen bonding. Finally, we comment on key differences between charge-transfer and electrostatic polarization.
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Affiliation(s)
- Jana M. Holthoff
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
| | - Robert Weiss
- Institut für Organische ChemieFriedrich-Alexander-Universität Erlangen-NürnbergHenkestraße 4291054ErlangenGermany
| | | | - Stefan M. Huber
- Fakultät für Chemie und BiochemieRuhr-Universität BochumUniversitätsstraße 15044801BochumGermany
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Loy C, Holthoff JM, Weiss R, Huber SM, Rosokha SV. "Anti-electrostatic" halogen bonding in solution. Chem Sci 2021; 12:8246-8251. [PMID: 34194716 PMCID: PMC8208320 DOI: 10.1039/d1sc01863a] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2021] [Accepted: 05/08/2021] [Indexed: 01/14/2023] Open
Abstract
Halogen-bonded (XB) complexes between halide anions and a cyclopropenylium-based anionic XB donor were characterized in solution for the first time. Spontaneous formation of such complexes confirms that halogen bonding is sufficiently strong to overcome electrostatic repulsion between two anions. The formation constants of such "anti-electrostatic" associations are comparable to those formed by halides with neutral halogenated electrophiles. However, while the latter usually show charge-transfer absorption bands, the UV-Vis spectra of the anion-anion complexes examined herein are determined by the electronic excitations within the XB donor. The identification of XB anion-anion complexes substantially extends the range of the feasible XB systems, and it provides vital information for the discussion of the nature of this interaction.
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Affiliation(s)
- Cody Loy
- Department of Chemistry, Ball State University Muncie Indiana 47306 USA
| | - Jana M Holthoff
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum Universitätsstr. 150 44801 Bochum Germany
| | - Robert Weiss
- Institut für Organische Chemie, Friedrich-Alexander-Universität Erlangen-Nürnberg Henkestr. 42 91054 Erlangen Germany
| | - Stefan M Huber
- Fakultät für Chemie und Biochemie, Ruhr-Universität Bochum Universitätsstr. 150 44801 Bochum Germany
| | - Sergiy V Rosokha
- Department of Chemistry, Ball State University Muncie Indiana 47306 USA
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Li T, Liang K, Tang J, Ding Y, Tong X, Xia C. A photoexcited halogen-bonded EDA complex of the thiophenolate anion with iodobenzene for C(sp 3)–H activation and thiolation. Chem Sci 2021; 12:15655-15661. [PMID: 35003596 PMCID: PMC8654056 DOI: 10.1039/d1sc03667j] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2021] [Revised: 11/23/2021] [Accepted: 10/20/2021] [Indexed: 01/26/2023] Open
Abstract
A direct photochemical thiolation of C(sp3)–H bond-containing substrates with thiophenol was developed. A halogen bonding-type EDA complex was found to trigger the downstream single electron transfer and hydrogen atom transfer process.
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Affiliation(s)
- Tao Li
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Kangjiang Liang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Jiaying Tang
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Yuzhen Ding
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Xiaogang Tong
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
| | - Chengfeng Xia
- Key Laboratory of Medicinal Chemistry for Natural Resource, Ministry of Education, Yunnan Provincial Center for Research & Development of Natural Products, School of Chemical Science and Technology, Yunnan University, Kunming 650091, China
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Zhu Z, Xu Z, Zhu W. Interaction Nature and Computational Methods for Halogen Bonding: A Perspective. J Chem Inf Model 2020; 60:2683-2696. [DOI: 10.1021/acs.jcim.0c00032] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China
- University of Chinese Academy of Sciences, Beijing 100049, China
- Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao 266237, China
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Phosphine Oxides as Spectroscopic Halogen Bond Descriptors: IR and NMR Correlations with Interatomic Distances and Complexation Energy. Molecules 2020; 25:molecules25061406. [PMID: 32204523 PMCID: PMC7144381 DOI: 10.3390/molecules25061406] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Revised: 03/14/2020] [Accepted: 03/16/2020] [Indexed: 02/07/2023] Open
Abstract
An extensive series of 128 halogen-bonded complexes formed by trimethylphosphine oxide and various F-, Cl-, Br-, I- and At-containing molecules, ranging in energy from 0 to 124 kJ/mol, is studied by DFT calculations in vacuum. The results reveal correlations between R–X⋅⋅⋅O=PMe3 halogen bond energy ΔE, X⋅⋅⋅O distance r, halogen’s σ-hole size, QTAIM parameters at halogen bond critical point and changes of spectroscopic parameters of phosphine oxide upon complexation, such as 31P NMR chemical shift, ΔδP, and P=O stretching frequency, Δν. Some of the correlations are halogen-specific, i.e., different for F, Cl, Br, I and At, such as ΔE(r), while others are general, i.e., fulfilled for the whole set of complexes at once, such as ΔE(ΔδP). The proposed correlations could be used to estimate the halogen bond properties in disordered media (liquids, solutions, polymers, glasses) from the corresponding NMR and IR spectra.
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12
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Balmohammadi Y, Khavasi HR, Naghavi SS. Existence of untypical halogen-involving interactions in crystal packings: a statistical and first-principles study. CrystEngComm 2020. [DOI: 10.1039/c9ce01885a] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
There is a common perception by the scientific community that a halogen-involving interaction forms when the distance between the donor atom and the acceptor atom is less than the sum of their van der Waals (vdW) radii.
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Affiliation(s)
- Yaser Balmohammadi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
| | - Hamid Reza Khavasi
- Department of Inorganic Chemistry and Catalysis
- Shahid Beheshti University
- Tehran 1983963113
- Iran
| | - S. Shahab Naghavi
- Department of Physical and Computational Chemistry
- Shahid Beheshti University
- 1983963113 Tehran
- Iran
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Oliveira VP, Marcial BL, Machado FBC, Kraka E. Metal-Halogen Bonding Seen through the Eyes of Vibrational Spectroscopy. MATERIALS 2019; 13:ma13010055. [PMID: 31861904 PMCID: PMC6982077 DOI: 10.3390/ma13010055] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/24/2019] [Revised: 12/09/2019] [Accepted: 12/15/2019] [Indexed: 11/17/2022]
Abstract
Incorporation of a metal center into halogen-bonded materials can efficiently fine-tune the strength of the halogen bonds and introduce new electronic functionalities. The metal atom can adopt two possible roles: serving as halogen acceptor or polarizing the halogen donor and acceptor groups. We investigated both scenarios for 23 metal–halogen dimers trans-M(Y2)(NC5H4X-3)2 with M = Pd(II), Pt(II); Y = F, Cl, Br; X = Cl, Br, I; and NC5H4X-3 = 3-halopyridine. As a new tool for the quantitative assessment of metal–halogen bonding, we introduced our local vibrational mode analysis, complemented by energy and electron density analyses and electrostatic potential studies at the density functional theory (DFT) and coupled-cluster single, double, and perturbative triple excitations (CCSD(T)) levels of theory. We could for the first time quantify the various attractive contacts and their contribution to the dimer stability and clarify the special role of halogen bonding in these systems. The largest contribution to the stability of the dimers is either due to halogen bonding or nonspecific interactions. Hydrogen bonding plays only a secondary role. The metal can only act as halogen acceptor when the monomer adopts a (quasi-)planar geometry. The best strategy to accomplish this is to substitute the halo-pyridine ring with a halo-diazole ring, which considerably strengthens halogen bonding. Our findings based on the local mode analysis provide a solid platform for fine-tuning of existing and for design of new metal–halogen-bonded materials.
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Affiliation(s)
- Vytor P. Oliveira
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Bruna L. Marcial
- Núcleo de Química, Instituto Federal Goiano (IF Goiano), Campus Morrinhos, 75650-000 Goiás, Brazil;
| | - Francisco B. C. Machado
- Departamento de Química, Instituto Tecnológico de Aeronáutica (ITA), São José dos Campos, 12228-900 São Paulo, Brazil; (V.P.O.); (F.B.C.M.)
| | - Elfi Kraka
- Department of Chemistry, Southern Methodist University, 3215 Daniel Avenue, Dallas, TX 75275-0314, USA
- Correspondence: ; Tel.: +1-214-768-2611
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14
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Islam MT. Antipyretic effect of phytol, possibly via 5KIR-dependent COX-2 inhibition pathway. Inflammopharmacology 2019; 27:857-862. [PMID: 30778877 DOI: 10.1007/s10787-019-00574-9] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2019] [Accepted: 02/04/2019] [Indexed: 12/14/2022]
Abstract
AIMS This study is aimed at the evaluation of antipyretic effect of PHY in yeast-induced hyperthermia rats. Additionally, possible mechanism of antipyretic action of PHY has been also studied by molecular docking study. METHODS Adult male Wistar albino rats were treated with PHY at 100, 150 and 200 mg/kg in 0.05% Tween-80 dissolved in 0.9% NaCl solution. PHY was also given at 200 mg/kg with ibuprofen (IBU) 12.5 mg/kg (p.o.) or paracetamol (PARA) 100 mg/kg (p.o.) to see the combined effect of PHY in animals. In silico study of PHY was performed against cyclooxygenase (COX) enzymes (COX-1 and -2) proteins. RESULTS PHY exhibited the antipyretic effect in febrile rats in a dose and time dependent manner. PHY 200 mg/kg co-treated with IBU12.5 or PARA100 exhibited greater antipyretic effect than the PHY or NSAIDs individual groups. Data from the computational study reveal that 5KIR of COX-2 is the most efficient receptor protein to which PHY interacts. CONCLUSION PHY attributed an antipyretic effect, possibly via 5KIR-dependent COX-2 inhibition pathway.
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Affiliation(s)
- Muhammad Torequl Islam
- Department for Management of Science and Technology Development, Ton Duc Thang University, Ho Chi Minh City, 700000, Vietnam. .,Faculty of Pharmacy, Ton Duc Thang University, Ho Chi Minh City, 700000, Vietnam.
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Differential Binding of Tetrel-Bonding Bipodal Receptors to Monatomic and Polyatomic Anions. Molecules 2019; 24:molecules24020227. [PMID: 30634503 PMCID: PMC6358819 DOI: 10.3390/molecules24020227] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2018] [Revised: 01/05/2019] [Accepted: 01/05/2019] [Indexed: 11/22/2022] Open
Abstract
Previous work has demonstrated that a bidentate receptor containing a pair of Sn atoms can engage in very strong interactions with halide ions via tetrel bonds. The question that is addressed here concerns the possibility that a receptor of this type might be designed that would preferentially bind a polyatomic over a monatomic anion since the former might better span the distance between the two Sn atoms. The binding of Cl− was thus compared to that of HCOO−, HSO4−, and H2PO4− with a wide variety of bidentate receptors. A pair of SnFH2 groups, as strong tetrel-binding agents, were first added to a phenyl ring in ortho, meta, and para arrangements. These same groups were also added in 1,3 and 1,4 positions of an aliphatic cyclohexyl ring. The tetrel-bonding groups were placed at the termini of (-C≡C-)n (n = 1,2) extending arms so as to further separate the two Sn atoms. Finally, the Sn atoms were incorporated directly into an eight-membered ring, rather than as appendages. The ordering of the binding energetics follows the HCO2− > Cl− > H2PO4− > HSO4− general pattern, with some variations in selected systems. The tetrel bonding is strong enough that in most cases, it engenders internal deformations within the receptors that allow them to engage in bidentate bonding, even for the monatomic chloride, which mutes any effects of a long Sn···Sn distance within the receptor.
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Chakraborty S, Maji S, Ghosh R, Jana R, Datta A, Ghosh P. Aryl-platform-based tetrapodal 2-iodo-imidazolium as an excellent halogen bond receptor in aqueous medium. Chem Commun (Camb) 2019; 55:1506-1509. [DOI: 10.1039/c8cc09937e] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023]
Abstract
The graphic shows a halogen bonding interaction between a tetrapodal platform attached to a 2-iodo-imidazole unit and bromide in water.
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Affiliation(s)
- Sourav Chakraborty
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
| | - Siddhartha Maji
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
| | - Rajib Ghosh
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
| | - Rajkumar Jana
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
| | - Ayan Datta
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
| | - Pradyut Ghosh
- School of Chemical Science
- Indian Association for the Cultivation of Science
- Kolkata – 700032
- India
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17
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Zhu Z, Wang G, Xu Z, Chen Z, Wang J, Shi J, Zhu W. Halogen bonding in differently charged complexes: basic profile, essential interaction terms and intrinsic σ-hole. Phys Chem Chem Phys 2019; 21:15106-15119. [PMID: 31241121 DOI: 10.1039/c9cp01379b] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/03/2023]
Abstract
Studies on halogen bonds (XB) between organohalogens and their acceptors in crystal structures revealed that the XB donor and acceptor could be differently charged, making it difficult to understand the nature of the interaction, especially the negatively charged donor's electrophilicity and positively charged acceptor's nucleophilicity. In this paper, 9 XB systems mimicking all possibly charged halogen bonding interactions were designed and explored computationally. The results revealed that all XBs could be stable, with binding energies after removing background interaction as strong as -1.2, -3.4, and -8.3 kcal mol-1 for Cl, Br, and I involved XBs respectively. Orbital and dispersion interactions are found to be always attractive while unidirectional intermolecular electron transfer from a XB acceptor to a XB donor occurs in all XB complexes. These observations could be attributed to the intrinsic σ-hole of the XB donor and the intrinsic electronic properties of the XB acceptor regardless of their charge states. Intramolecular charge redistribution inside both the donor and the acceptor is found to be system-dependent but always leads to a more stable XB. Accordingly, this study demonstrates that the orbital-based origin of halogen bonds could successfully interpret the complicated behaviour of differently charged XB complexes, while electrostatic interaction may dramatically change the overall bonding strength. The results should further promote the application of halogens in all related areas.
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Affiliation(s)
- Zhengdan Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Guimin Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhijian Xu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhaoqiang Chen
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jinan Wang
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China
| | - Jiye Shi
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China.
| | - Weiliang Zhu
- CAS Key Laboratory of Receptor Research, Drug Discovery and Design Center, Shanghai Institute of Materia Medica, Chinese Academy of Sciences, Shanghai 201203, China. and University of Chinese Academy of Sciences, Beijing 100049, China and Open Studio for Druggability Research of Marine Natural Products, Pilot National Laboratory for Marine Science and Technology (Qingdao), 1 Wenhai Road, Aoshanwei, Jimo, Qingdao, 266237, China
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18
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Wang H, Shen QJ, Wang W. Weakening and Leveling Effect of Solvent Polarity on Halogen Bond Strength of Diiodoperfluoroalkane with Halide. J SOLUTION CHEM 2017. [DOI: 10.1007/s10953-017-0623-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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19
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Scheiner S. Highly Selective Halide Receptors Based on Chalcogen, Pnicogen, and Tetrel Bonds. Chemistry 2016; 22:18850-18858. [PMID: 27740702 DOI: 10.1002/chem.201603891] [Citation(s) in RCA: 90] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2016] [Indexed: 11/09/2022]
Abstract
The interactions of halides with a number of bipodal receptors were examined by quantum chemical methods. The receptors were based on a dithieno thiophene framework in which two S atoms can engage in a pair of chalcogen bonds with a halide. These two S atoms were replaced by P and As atoms to compare chalcogen with pnicogen bonding, and by Ge which engages in tetrel bonds with the receptor. Zero, one, and two O atoms were added to the thiophene S atom which is not directly involved in the interaction with the halides. Fluoride bound the most strongly, followed by Cl- , Br- , and I- , respectively. Replacing S by the pnicogen bonds of P strengthened the binding, as did moving down to As in the third row of the periodic table. A further large increment is associated with the switch to the tetrel bonds of Ge. Even though the thiophene S atom is remote from the binding site, each additional O atom added to it raises the binding energy, which can be quite large, as much as 63 kcal mol-1 for the Ge⋅⋅⋅F- interaction. The receptors have a pronounced selectivity for F- over the other halides, as high as 27 orders of magnitude. The data suggest that incorporation of tetrel atoms may lead to new and more powerful halide receptors.
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Affiliation(s)
- Steve Scheiner
- Department of Chemistry and Biochemistry, Utah State University, Logan, UT, 84322-0300, USA
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