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Singh MP, Tarai A, Baruah JB. Neutral, Zwitterion, Ionic Forms of 5‐Aminoisophthalic Acid in Cocrystals, Salts and Their Optical Properties. ChemistrySelect 2019. [DOI: 10.1002/slct.201901111] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
Affiliation(s)
- Munendra Pal Singh
- Department of ChemistryIndian Institute of Technology Guwahati, Guwahati - 781 039 Assam India
| | - Arup Tarai
- Department of ChemistryIndian Institute of Technology Guwahati, Guwahati - 781 039 Assam India
| | - Jubaraj Bikash Baruah
- Department of ChemistryIndian Institute of Technology Guwahati, Guwahati - 781 039 Assam India
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2
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Ilawe NV, Schweitzer-Stenner R, DiGuiseppi D, Wong BM. Is a cross-β-sheet structure of low molecular weight peptides necessary for the formation of fibrils and peptide hydrogels? Phys Chem Chem Phys 2019; 20:18158-18168. [PMID: 29696249 DOI: 10.1039/c8cp00691a] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Short peptides have emerged as versatile building blocks for supramolecular structures and hydrogels. In particular, the presence of aromatic amino acid residues and/or aromatic end groups is generally considered to be a prerequisite for initiating aggregation of short peptides into nanotubes or cross β-sheet type fibrils. However, the cationic GAG tripeptide surprisingly violates these rules. Specifically, in water/ethanol mixtures, GAG peptides aggregate into very long crystalline fibrils at temperatures below 35 °C where they eventually form a spanning network structure and, thus, a hydrogel. Two gel phases are formed in this network, and they differ substantially in chirality and thickness of the underlying fibrils, their rheological parameters, and the kinetics of oligomerization, fibrilization, and gel formation. The spectroscopic data strongly suggests that the observed fibrils do not exhibit canonical cross β-sheet structures and are indicative of a yet unknown secondary conformation. To complement our unusual experimental observations in this perspective article, we performed large-scale DFT calculations to probe the geometry and spectroscopic properties of these GAG oligomers. Most importantly, our experimental and computational results yield rather unconventional structures that are not reminiscent of classical cross-β-sheet structures, and we give two extremely likely candidates for oligomer structures that are consistent with experimental amide I' profiles in IR and vibrational circular dichroism (VCD) spectra of the two gel phases.
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Affiliation(s)
- Niranjan V Ilawe
- Department of Chemical & Environmental Engineering, and Materials Science & Engineering Program, University of California-Riverside, Riverside, CA 92521, USA.
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3
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Radlow M, Czjzek M, Jeudy A, Dabin J, Delage L, Leblanc C, Hartung J. X-ray Diffraction and Density Functional Theory Provide Insight into Vanadate Binding to Homohexameric Bromoperoxidase II and the Mechanism of Bromide Oxidation. ACS Chem Biol 2018; 13:1243-1259. [PMID: 29665335 DOI: 10.1021/acschembio.8b00041] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
X-ray diffraction of native bromoperoxidase II (EC 1.11.1.18) from the brown alga Ascophyllum nodosum reveals at a resolution of 2.26 Å details of orthovanadate binding and homohexameric protein organization. Three dimers interwoven in contact regions and tightened by hydrogen-bond-clamped guanidinium stacks along with regularly aligned water molecules form the basic structure of the enyzme. Intra- and intermolecular disulfide bridges further stabilize the enzyme preventing altogether the protein from denaturing up to a temperature of 90 °C, as evident from dynamic light scattering and the on-gel ortho-dianisidine assay. Every monomer binds one equivalent of orthovanadate in a cavity formed from side chains of three histidines, two arginines, one lysine, serine, and tryptophan. Protein binding occurs primarily through hydrogen bridges and superimposed by Coulomb attraction according to thermochemical model on density functional level of theory (B3LYP/6-311++G**). The strongest attractor is the arginine side chain mimic N-methylguanidinium, enhancing in positive cooperative manner hydrogen bridges toward weaker acceptors, such as residues from lysine and serine. Activating hydrogen peroxide occurs in the thermochemical model by side-on binding in orthovanadium peroxoic acid, oxidizing bromide with virtually no activation energy to hydrogen bonded hypobromous acid.
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Affiliation(s)
- Madlen Radlow
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
| | - Mirjam Czjzek
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Alexandra Jeudy
- Sorbonne Université, CNRS, FR 2424, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Jerome Dabin
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Ludovic Delage
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Catherine Leblanc
- Sorbonne Université, CNRS, UMR 8227, Integrative Biology of Marine Models, Station Biologique de Roscoff, CS 90074, F-29688 Roscoff cedex, France
| | - Jens Hartung
- Fachbereich Chemie, Organische Chemie, Technische Universität Kaiserslautern, Erwin-Schrödinger-Straße, D-67663 Kaiserslautern, Germany
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4
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Pari S, Wang IA, Liu H, Wong BM. Sulfate radical oxidation of aromatic contaminants: a detailed assessment of density functional theory and high-level quantum chemical methods. ENVIRONMENTAL SCIENCE. PROCESSES & IMPACTS 2017; 19:395-404. [PMID: 28229155 DOI: 10.1039/c7em00009j] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/06/2023]
Abstract
Advanced oxidation processes that utilize highly oxidative radicals are widely used in water reuse treatment. In recent years, the application of sulfate radical (SO4˙-) as a promising oxidant for water treatment has gained increasing attention. To understand the efficiency of SO4˙- in the degradation of organic contaminants in wastewater effluent, it is important to be able to predict the reaction kinetics of various SO4˙--driven oxidation reactions. In this study, we utilize density functional theory (DFT) and high-level wavefunction-based methods (including computationally-intensive coupled cluster methods), to explore the activation energies of SO4˙--driven oxidation reactions on a series of benzene-derived contaminants. These high-level calculations encompass a wide set of reactions including 110 forward/reverse reactions and 5 different computational methods in total. Based on the high-level coupled-cluster quantum calculations, we find that the popular M06-2X DFT functional is significantly more accurate for OH- additions than for SO4˙- reactions. Most importantly, we highlight some of the limitations and deficiencies of other computational methods, and we recommend the use of high-level quantum calculations to spot-check environmental chemistry reactions that may lie outside the training set of the M06-2X functional, particularly for water oxidation reactions that involve SO4˙- and other inorganic species.
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Affiliation(s)
- Sangavi Pari
- Department of Chemical & Environmental Engineering, University of California-Riverside, Riverside, California, USA.
| | - Inger A Wang
- Department of Chemical & Environmental Engineering, University of California-Riverside, Riverside, California, USA.
| | - Haizhou Liu
- Department of Chemical & Environmental Engineering, University of California-Riverside, Riverside, California, USA.
| | - Bryan M Wong
- Department of Chemical & Environmental Engineering, University of California-Riverside, Riverside, California, USA. and Materials Science & Engineering Program, University of California-Riverside, Riverside, California, USA.
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5
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Hoque MN, Das G. Overview of the strategic approaches for the solid-state recognition of hydrated anions. CrystEngComm 2017. [DOI: 10.1039/c6ce02438f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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6
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Li B, Sun X. Water clusters with anion templates in cucurbit[6]uril supramolecular pseudorotaxanes. INORG CHEM COMMUN 2016. [DOI: 10.1016/j.inoche.2016.10.026] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
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7
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Li B, Li X, Sun X, Wang N. Halide-Anion Water Clusters in Cucurbit[6]uril Supramolecular Systems. CHINESE J CHEM 2016. [DOI: 10.1002/cjoc.201600384] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022]
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8
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Ilawe NV, Raeber AE, Schweitzer-Stenner R, Toal SE, Wong BM. Assessing backbone solvation effects in the conformational propensities of amino acid residues in unfolded peptides. Phys Chem Chem Phys 2016; 17:24917-24. [PMID: 26343224 DOI: 10.1039/c5cp03646a] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Conformational ensembles of individual amino acid residues within model GxG peptides (x representing different amino acid residues) are dominated by a mixture of polyproline II (pPII) and β-strand like conformations. We recently discovered rather substantial differences between the enthalpic and entropic contributions to this equilibrium for different amino acid residues. Isoleucine and valine exceed all other amino acid residues in terms of their rather large enthalpic stabilization and entropic destabilization of polyproline II. In order to shed light on these underlying physical mechanisms, we performed high-level DFT calculations to explore the energetics of four representative GxG peptides where x = alanine (A), leucine (L), valine (V), and isoleucine (I) in explicit water (10 H2O molecules with a polarizable continuum water model) and in vacuo. We found that the large energetic contributions to the stabilization of pPII result, to a major extent, from peptide-water, water-water interactions, and changes of the solvent self-energy. Differences between the peptide-solvent interaction energies of hydration in pPII and β-strand peptides are particularly important for the pPII ⇌ β equilibria of the more aliphatic peptides GIG and GLG. Furthermore, we performed a vibrational analysis of the four peptides in both conformations and discovered a rather substantial mixing between water motions and peptide vibrations below 700 cm(-1). We found that the respective vibrational entropies are substantially different for the considered conformations, and their contributions to the Gibbs/Helmholtz energy stabilize β-strand conformations. Taken together, our results underscore the notion of the solvent being the predominant determinant of peptide (and protein) conformations in the unfolded state.
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Affiliation(s)
- Niranjan V Ilawe
- Department of Chemical & Environmental Engineering, and Materials Science & Engineering Program, University of California, Riverside, 900 University Avenue, Riverside, CA 92521, USA.
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9
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Ghosh S, Mandal L, Mohanta S. Exploration of weak interaction directed self-assemblies on reacting mononuclear copper(II)/nickel(II)⋯water host⋯guest systems of a double-compartment ligand with mono/di/tricarboxylic acids. Polyhedron 2015. [DOI: 10.1016/j.poly.2015.04.033] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Chakraborty S, Arunachalam M, Dutta R, Ghosh P. Arene platform based hexa-amide receptors for anion recognition: single crystal X-ray structural and thermodynamic studies. RSC Adv 2015. [DOI: 10.1039/c5ra08747c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
Compartmental recognition of [Cl2(inf>O/inf>O)2]2− in the cavity of p-fluoro-phenyl substituted hexa-amide receptor.
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Affiliation(s)
- Sourav Chakraborty
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - M. Arunachalam
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Ranjan Dutta
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science
- Kolkata 700032
- India
| | - Pradyut Ghosh
- Department of Inorganic Chemistry, Indian Association for the Cultivation of Science
- Kolkata 700032
- India
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11
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Chakraborty P, Jana A, Mohanta S. Surprising difference between two closely similar O(phenoxo)2O(ether)2 compartments as hosts for an aquated proton and a novel type of host–guest system. Polyhedron 2014. [DOI: 10.1016/j.poly.2014.03.054] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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12
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Pati A, Athilakshmi J, Ramkumar V, Chand DK. A two-dimensional polydodecameric water–chloride cluster enfolding (Hg–Cl–Hg)+concealed cascade cryptate. CrystEngComm 2014. [DOI: 10.1039/c4ce00802b] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
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13
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Rhaman MM, Ahmed L, Wang J, Powell DR, Leszczynski J, Hossain MA. Encapsulation and selectivity of sulfate with a furan-based hexaazamacrocyclic receptor in water. Org Biomol Chem 2014; 12:2045-8. [PMID: 24554233 PMCID: PMC4428163 DOI: 10.1039/c4ob00116h] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A furan-based hexaazamacrocycle encapsulates a sulfate anion in its cavity showing strong affinity and selectivity for sulfate in water over a wide range of inorganic anions. The DFT calculations demonstrate that the receptor provides binding sites as hydrogen bonding donors and electrostatic positive charges for the strong binding of sulfate.
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Affiliation(s)
- Md Mhahabubur Rhaman
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212, USA;
| | - Lucky Ahmed
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212, USA;
| | - Jing Wang
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212, USA;
| | - Douglas R. Powell
- Department of Chemistry and Biochemistry, University of Oklahoma, Norman, OK 73019, USA;
| | - Jerzy Leszczynski
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212, USA;
| | - Md. Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, MS 39212, USA;
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14
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Ivanov AS, Frenking G, Boldyrev AI. Stabilization of a Cl––Cl– Anion Pair in the Gas Phase: Ab Initio Microsolvation Study. J Phys Chem A 2014; 118:7375-84. [DOI: 10.1021/jp4123997] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Alexander S. Ivanov
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
| | - Gernot Frenking
- Fachbereich
Chemie, Philipps-Universitat Marburg, Hans-Meerwein-Strasse, D-35043 Marburg, Germany
| | - Alexander I. Boldyrev
- Department
of Chemistry and Biochemistry, Utah State University, 0300 Old
Main Hill, Logan, Utah 84322, United States
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15
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Basu A, Chutia R, Das G. Dual modes of binding on the hexafluorosilicate anion by a C3v symmetric flexible tripodal amide ligand in solid state. CrystEngComm 2014. [DOI: 10.1039/c4ce00529e] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
A para-nitrophenyl functionalized C3v symmetric flexible tripodal amide ligand, L, shows remarkable solvent dependent dual binding behaviour towards the octahedral hexafluorosilicate anion in solid state.
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Affiliation(s)
- Arghya Basu
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781039, India
| | - Romen Chutia
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781039, India
| | - Gopal Das
- Department of Chemistry
- Indian Institute of Technology Guwahati
- Guwahati 781039, India
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16
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Fu K, Ren CX, Chen C, Cai LX, Tan B, Zhang J. Auxiliary ligand-controlled photochromism and decolourization of two bipyridinium-based metal–organic hybrid materials with various water clusters. CrystEngComm 2014. [DOI: 10.1039/c4ce00295d] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
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17
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Han LL, Hu TP, Chen JS, Li ZH, Wang XP, Zhao YQ, Li XY, Sun D. Simultaneous encapsulation of an infinite T4(0)A(0)6(0) water tape and discrete water hexamers in a hydrogen-bonded Ag(i) supramolecular framework. Dalton Trans 2014; 43:8774-80. [DOI: 10.1039/c4dt00494a] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
In a one-dimensional mixed-ligand Ag(i) coordination polymer, an infinite 1D T4(0)A(0)6(0) water tape and discrete water hexamers were simultaneously encapsulated.
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Affiliation(s)
- Lu-Lu Han
- Key Lab of Colloid and Interface Chemistry, Ministry of Education, School of Chemistry and Chemical Engineering, Shandong University, Jinan, 250100, People's Republic of China.
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18
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Chakraborty S, Dutta R, Wong BM, Ghosh P. Anion directed conformational diversities of an arene based hexa-amide receptor and recognition of the [F4(H2O)6]4− cluster. RSC Adv 2014. [DOI: 10.1039/c4ra10795k] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The TOC shows difference in binding energies between different conformers after binding with anions of different dimensionalities and conformers A, B & C show structural diversities with anions in case of L.
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Affiliation(s)
- Sourav Chakraborty
- Department of Inorganic Chemistry Indian Association for the Cultivation of Science
- Kolkata 700032, India
| | - Ranjan Dutta
- Department of Inorganic Chemistry Indian Association for the Cultivation of Science
- Kolkata 700032, India
| | - Bryan M. Wong
- Department of Chemical & Environmental Engineering and Materials Science & Engineering Program
- University of California, Riverside
- Riverside, USA
| | - Pradyut Ghosh
- Department of Inorganic Chemistry Indian Association for the Cultivation of Science
- Kolkata 700032, India
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Basu A, Das G. Encapsulation of a discrete cyclic halide water tetramer [X2(H2O)2]2-, X = Cl-/Br- within a dimeric capsular assembly of a tripodal amide receptor. Chem Commun (Camb) 2013; 49:3997-9. [PMID: 23563509 DOI: 10.1039/c3cc40955d] [Citation(s) in RCA: 52] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
A conformationally flexible C3v symmetric N-bridged tripodal amide receptor encapsulates a tetrameric halide water cluster [X2(H2O)2](2-) (X = Cl(-)/Br(-)) within its dimeric capsular assembly and forms a non-capsular 1D polymeric assembly with higher homologous iodide anions upon protonation.
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Affiliation(s)
- Arghya Basu
- Department of Chemistry, Indian Institute of Technology Guwahati, Guwahati 781039, Assam, India
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20
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Structural and Infra Red Spectroscopic Aspects of Ion-Water Clusters: A Study Based on a Combined Stochastic and Quantum Chemical Approach. J CLUST SCI 2013. [DOI: 10.1007/s10876-013-0565-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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21
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Wang YC, Ju SP, Lee WJ, Chen HT, Hsieh JY. Effect of Au nanotube size on molecular behavior of water/ethanol mixtures. RSC Adv 2013. [DOI: 10.1039/c3ra22530e] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
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22
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Hossain MA, Saeed MA, Pramanik A, Wong BM, Haque SA, Powell DR. A self-assembled fluoride-water cyclic cluster of [F(H2O)]4(4-) in a molecular box. J Am Chem Soc 2012; 134:11892-5. [PMID: 22765503 PMCID: PMC3601558 DOI: 10.1021/ja3043855] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
We present an unprecedented fluoride-water cyclic cluster of [F(H(2)O)](4)(4-) assembled in a cuboid molecular box formed by two large macrocycles. Structural characterization reveals that [F(H(2)O)](4)(4-) is assembled by strong H-bonding interactions [OH···F = 2.684(3)-2.724(3) Å], where a fluoride anion plays the topological role of a water molecule in the classical cyclic water octamer. The interaction of fluoride was further confirmed by (19)F NMR and (1)H NMR spectroscopies, indicating the encapsulation of the anionic species within the cavity in solution. High-level DFT calculations and Bader topological analyses fully support the crystallographic results, demonstrating that the bonding arrangement in the fluoride-water cluster arises from the unique geometry of the host.
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Affiliation(s)
- Md Alamgir Hossain
- Department of Chemistry and Biochemistry, Jackson State University, Jackson, Mississippi 39217, USA.
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