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Molina-Paredes AA, Lara-Cerón JA, Ibarra-Rodríguez M, del Angel-Mosqueda C, Dias HR, Jiménez-Pérez VM, Muñoz-Flores BM. Supramolecular interactions in X-ray structures of oxalamides: Green synthesis and characterization. J Mol Struct 2022. [DOI: 10.1016/j.molstruc.2022.133144] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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2
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Accorsi G, Capodilupo AL, Claramunt RM, Clarkson GJ, Farrán A, Gatti FG, León S, Venturi S. Studies of novel trifluoroacetylated diaryl hydrazone molecular photoswitches in solution and in the solid state. NEW J CHEM 2021. [DOI: 10.1039/d1nj01677f] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022]
Abstract
Photoisomerization of trifluoroacetylated diaryl hydrazones induces a change in color due to the formation of a new hydrogen bond in solution and in the solid state.
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Affiliation(s)
- Gianluca Accorsi
- CNR NANOTEC – Institute of Nanotechnology c/o Campus Ecotekne
- University of Salento
- 73100 Lecce
- Italy
| | - Agostina-Lina Capodilupo
- CNR NANOTEC – Institute of Nanotechnology c/o Campus Ecotekne
- University of Salento
- 73100 Lecce
- Italy
| | - Rosa María Claramunt
- Departamento de Química Orgánica y Bio-Orgánica
- Facultad de Ciencias
- Universidad Nacional de Educación a Distancia
- E-28040 Madrid
- Spain
| | | | - A. Farrán
- Departamento de Química Orgánica y Bio-Orgánica
- Facultad de Ciencias
- Universidad Nacional de Educación a Distancia
- E-28040 Madrid
- Spain
| | - Francesco G. Gatti
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
| | - Salvador León
- Departamento de Ingeniería Química
- Universidad Politécnica de Madrid
- ETSIIM
- 28006 Madrid
- Spain
| | - Silvia Venturi
- Dipartimento di Chimica
- Materiali ed Ingegneria Chimica “Giulio Natta”
- Politecnico di Milano
- 20131 Milano
- Italy
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3
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Srivastava R, Gupta SK, Naaz F, Sen Gupta PS, Yadav M, Singh VK, Singh A, Rana MK, Gupta SK, Schols D, Singh RK. Alkylated benzimidazoles: Design, synthesis, docking, DFT analysis, ADMET property, molecular dynamics and activity against HIV and YFV. Comput Biol Chem 2020; 89:107400. [PMID: 33068917 PMCID: PMC7537607 DOI: 10.1016/j.compbiolchem.2020.107400] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2020] [Revised: 09/22/2020] [Accepted: 10/02/2020] [Indexed: 12/12/2022]
Abstract
New benzimidazole analogs synthesized as antivirals against HIV-1 and yellow fever virus. Molecular dynamics simulation studies indicated a stable ligand-protein complex of compound 3a within NNIBP of HIV-RT. DFT analysis confirmed the stability of hydrogen bonding interaction between the TRP 229 residue of HIV-RT and compound 3a. Molecules were tested for their anti-HIV and broad spectrum antiviral properties against different DNA and RNA viruses. Antiviral properties and cytotoxicity determined using MTT assay. Compound 3a showed anti-HIV activity and compound 2b showed excellent inhibition property against yellow fever virus.
A series of alkylated benzimidazole derivatives was synthesized and screened for their anti-HIV, anti-YFV, and broad-spectrum antiviral properties. The physicochemical parameters and drug-like properties of the compounds were assessed first, and then docking studies and MD simulations on HIV-RT allosteric sites were conducted to find the possible mode of their action. DFT analysis was also performed to confirm the nature of the hydrogen bonding interaction of active compounds. The in silico studies indicated that the molecules behaved like possible NNRTIs. The nature – polar or non-polar and position of the substituent present at fifth, sixth, and N-1 positions of the benzimidazole moiety played an important role in determining the antiviral properties of the compounds. Among the various compounds, 2-(5,6-dibromo-2-chloro-1H-benzimidazol-1-yl)ethan-1-ol (3a) showed anti-HIV activity with an appreciably low IC50 value as 0.386 × 10−5μM. Similarly, compound 2b, 3-(2-chloro-5-nitro-1H-benzimidazol-1-yl) propan-1-ol, showed excellent inhibitory property against the yellow fever virus (YFV) with EC50 value as 0.7824 × 10−2μM.
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Affiliation(s)
- Ritika Srivastava
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Sunil K Gupta
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Farha Naaz
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Parth Sarthi Sen Gupta
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | - Madhu Yadav
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Vishal Kumar Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Anuradha Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India
| | - Malay Kumar Rana
- Department of Chemical Sciences, Indian Institute of Science Education and Research Berhampur, Odisha 760010, India
| | | | | | - Ramendra K Singh
- Bioorganic Research Laboratory, Department of Chemistry, University of Allahabad, Allahabad, 211002, India.
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4
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Dhar J, Kishore R, Chakrabarti P. Delineation of a new structural motif involving NHN γ-turn. Proteins 2019; 88:431-439. [PMID: 31587358 DOI: 10.1002/prot.25820] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/16/2019] [Revised: 09/17/2019] [Accepted: 09/18/2019] [Indexed: 10/25/2022]
Abstract
Macromolecules are characterized by distinctive arrangement of hydrogen bonds. Different patterns of hydrogen bonds give rise to distinct and stable structural motifs. An analysis of 4114 non-redundant protein chains reveals the existence of a three-residue, (i - 1) to (i + 1), structural motif, having two hydrogen-bonded five-membered pseudo rings (the first, an NH···OC involving the first residue, and the second being NH∙∙∙N involving the last two residues), separated by a peptide bond. There could be an additional hydrogen bond between the side-chain at (i-1) and the main-chain NH of (i + 1). The average backbone torsion angles of -76(±21)° and - 12(±17)° at i creates a tight turn in the polypeptide chain, akin to a γ-turn. Indeed, a search of three-residue fragments with restriction on the terminal Cα ···Cα distance and the existence of the two pseudo rings on either side revealed the presence 14 846 cases of a variant, termed NHN γ-turn, distinct from the NHO γ-turn (2032 cases) that has traditionally been characterized by the presence of NHO hydrogen bond linking the terminal main-chain atoms. As in the latter, the newly identified γ-turns are also of two types-classical and inverse, occurring in the ratio of 1:6. The propensities of residues to occur in these turns and their secondary structural features have been enumerated. An understanding of these turns would be useful for structure prediction and loop modeling, and may serve as models to represent some of the unfolded state or disordered region in proteins.
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Affiliation(s)
- Jesmita Dhar
- Bioinformatics Centre, Bose Institute, Kolkata, India
| | - Raghuvansh Kishore
- Department of Zoology and Department of Biotechnology, Mizoram University, Aizawl, India
| | - Pinak Chakrabarti
- Bioinformatics Centre, Bose Institute, Kolkata, India.,Department of Biochemistry, Bose Institute, Kolkata, India
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5
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Carvalho LC, Bueno MA, de Oliveira BG. The interplay and strength of the π⋯HF, C⋯HF, F⋯HF and F⋯HC hydrogen bonds upon the formation of multimolecular complexes based on C 2H 2⋯HF and C 2H 4⋯HF small dimers. SPECTROCHIMICA ACTA. PART A, MOLECULAR AND BIOMOLECULAR SPECTROSCOPY 2019; 213:438-455. [PMID: 30738351 DOI: 10.1016/j.saa.2019.01.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 12/20/2018] [Accepted: 01/01/2019] [Indexed: 06/09/2023]
Abstract
The conception of this theoretical research was idealized aiming to unveil the intermolecular structures of complexes formed by acetylene or ethylene and hydrofluoric acid. At light of computational calculations by using the B3LYP/6-311++G(d,p) method, the geometries of the C2H2⋯(HF), C2H2⋯2(HF), C2H2⋯4(HF), C2H4⋯(HF), C2H4⋯2(HF) and C2H4⋯4(HF) hydrogen-bonded complexes were fully optimized. Moreover, the Post-Hartree-Fock calculations MP2/6-311++G(d,p), MP2/aug-cc-pVTZ, MP4(SDQ)/6-311++G(d,p) and CCSD/6-311++G(d,p) also were also used. The infrared spectra were analyzed in order to identify the new vibrational modes and frequencies of the proton donors shifted to red region. Through the modeling of charge-fluxes on the basis of the Quantum Theory of Atoms In Molecules (QTAIM) and, by contradicting the expectation of the hydrofluorination mechanisms of acetylene or ethylene, C⋯HF was recognized as a new type of hydrogen bond instead of the already well known π⋯H. The calculations of the Natural Bonding Orbital (NBO) and Charges derived from the Electrostatic Potential Grid-based (ChElPG) were also applied to interpret the shifting frequencies as well as measuring of the punctual charge-transfer after the formation of the complexes. Finally, the determination of the stabilization energy was carried out through the arguments of the Fock matrix in NBO basis and through the supermolecule approach. Also it is worthwhile to notice that some algebraic formulations were used for determining the electronic cooperative effect (CE).
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Patel AK, Mishra SK, Krishnamurthy K, Suryaprakash N. Retention of strong intramolecular hydrogen bonds in high polarity solvents in binaphthalene–benzamide derivatives: extensive NMR studies. RSC Adv 2019; 9:32759-32770. [PMID: 35529738 PMCID: PMC9073135 DOI: 10.1039/c9ra07299c] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2019] [Accepted: 10/07/2019] [Indexed: 11/21/2022] Open
Abstract
Advanced multidimensional NMR techniques have been employed to investigate the intramolecular hydrogen bonds (HBs) in a series of N,N′-([1,1′-binaphthalene]-2,2′-diyl)bis(benzamide) derivatives, with the site-specific substitution of different functional groups. The existence of intramolecular HBs and the elimination of any molecular aggregation and possible intermolecular HBs are ascertained by various experimental NMR techniques, including solvent polarity dependent modifications of HB strengths. In the fluorine substituted derivative, direct evidence for the engagement of organic fluorine in HB is obtained by the detection of heteronuclear through-space correlation and the coupling between two NMR active nuclei where the transmission of spin polarization is mediated through HBs (1hJFH). The extent of reduction in the strength of 1hJFH on dilution with high polarity solvents directly provided the qualitative measure of HB strength. The HB, although becoming weakened, does not get nullified even in pure high polarity solvent, which is attributed to the structural constraints. The rate of exchange of a labile hydrogen atom with the deuterium of the solvent permitted the measurement of their half-lives, that are correlated to the relative strengths of HBs. The experimental NMR findings are further validated by XRD and DFT-based theoretical computations, such as, NCI and QTAIM. NMR studies reveal very strong hydrogen bond unbreakable even in high polarity solvents.![]()
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Affiliation(s)
- Arun Kumar Patel
- Solid State and Structural Chemistry Unit and NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- NMR Research Centre
| | | | | | - N. Suryaprakash
- Solid State and Structural Chemistry Unit and NMR Research Centre
- Indian Institute of Science
- Bangalore 560012
- India
- NMR Research Centre
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7
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O'Reilly D, Stein RS, Patrascu MB, Jana SK, Kurian J, Moitessier N, Damha MJ. Exploring Atypical Fluorine-Hydrogen Bonds and Their Effects on Nucleoside Conformations. Chemistry 2018; 24:16432-16439. [PMID: 30125398 DOI: 10.1002/chem.201803940] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2018] [Indexed: 12/16/2022]
Affiliation(s)
- Daniel O'Reilly
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Robin S. Stein
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Mihai Burai Patrascu
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Sunit Kumar Jana
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Jerry Kurian
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Nicolas Moitessier
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
| | - Masad J. Damha
- Department of Chemistry; McGill University; Otto Maass Chemistry Bldg.; 801 Sherbrooke St. West Montreal QC, H3C0B8 Canada
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Lakshmipriya A, Chaudhary M, Mogurampelly S, Klein ML, Suryaprakash N. Intramolecular Hydrogen Bonding Appetency for Conformational Penchants in Oxalohydrazide Fluoro Derivatives: NMR, MD, QTAIM, and NCI Studies. J Phys Chem A 2018; 122:2703-2713. [PMID: 29488767 DOI: 10.1021/acs.jpca.8b00913] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The conformational stability of synthesized diphenyloxalohydrazide and dibenzoyloxalohydrazide fluoro derivatives has been investigated by extensive NMR studies that are ascertained by various levels of theoretical calculations. Two-dimensional 1H-19F HOESY NMR experiments revealed the close spatial proximity between two NMR-active nuclei, confirming the hydrogen bond (HB)-mediated interaction between them, further aiding in establishing the probable stable conformations of these molecules. The relaxed potential energy scan disclosed the energy-minimized most stable structure among the several possible multiple conformations, which is in concurrence with NMR interpretations. Atomistic molecular dynamics simulations have been employed to unequivocally establish the conformational stability and the nature of HB formation at varied temperatures. With the possibility of occurrence of a number of probable conformations, the percentage of occurrences of different types of HBs in them was determined by MD simulations. Their population analysis was carried out using a Boltzmann distribution, in addition to deriving their Gibbs free energies. The molecular interactions governing the stable conformations have not only been ascertained by experimental NMR interpretations but also corroborated by other theoretical computations, viz., quantum theory of atoms in molecules (QTAIM) and noncovalent interaction (NCI).
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Affiliation(s)
- A Lakshmipriya
- NMR Research Centre , Indian Institute of Science , Bangalore , Karnataka 560012 , India.,Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore , Karnataka 560012 , India
| | - Madhusudan Chaudhary
- NMR Research Centre , Indian Institute of Science , Bangalore , Karnataka 560012 , India
| | - Santosh Mogurampelly
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - Michael L Klein
- Institute for Computational Molecular Science , Temple University , Philadelphia , Pennsylvania 19122 , United States
| | - N Suryaprakash
- NMR Research Centre , Indian Institute of Science , Bangalore , Karnataka 560012 , India.,Solid State and Structural Chemistry Unit , Indian Institute of Science , Bangalore , Karnataka 560012 , India
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9
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Dhanishta P, Mishra SK, Suryaprakash N. Intramolecular HB Interactions Evidenced in Dibenzoyl Oxalamide Derivatives: NMR, QTAIM, and NCI Studies. J Phys Chem A 2017; 122:199-208. [DOI: 10.1021/acs.jpca.7b10598] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- P. Dhanishta
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - Sandeep Kumar Mishra
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - N. Suryaprakash
- NMR Research Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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10
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Investigation of conventional and non-conventional hydrogen bonds: a comparison of fluorine-substituted and non-fluorine substituted compounds. MONATSHEFTE FUR CHEMIE 2017. [DOI: 10.1007/s00706-017-2044-3] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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11
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Mishra SK, Suryaprakash N. Intramolecular Hydrogen Bonding Involving Organic Fluorine: NMR Investigations Corroborated by DFT-Based Theoretical Calculations. Molecules 2017; 22:E423. [PMID: 28272370 PMCID: PMC6155419 DOI: 10.3390/molecules22030423] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2017] [Accepted: 03/02/2017] [Indexed: 01/24/2023] Open
Abstract
The combined utility of many one and two dimensional NMR methodologies and DFT-based theoretical calculations have been exploited to detect the intramolecular hydrogen bond (HB) in number of different organic fluorine-containing derivatives of molecules, viz. benzanilides, hydrazides, imides, benzamides, and diphenyloxamides. The existence of two and three centered hydrogen bonds has been convincingly established in the investigated molecules. The NMR spectral parameters, viz., coupling mediated through hydrogen bond, one-bond NH scalar couplings, physical parameter dependent variation of chemical shifts of NH protons have paved the way for understanding the presence of hydrogen bond involving organic fluorine in all the investigated molecules. The experimental NMR findings are further corroborated by DFT-based theoretical calculations including NCI, QTAIM, MD simulations and NBO analysis. The monitoring of H/D exchange with NMR spectroscopy established the effect of intramolecular HB and the influence of electronegativity of various substituents on the chemical kinetics in the number of organic building blocks. The utility of DQ-SQ technique in determining the information about HB in various fluorine substituted molecules has been convincingly established.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
| | - N Suryaprakash
- NMR Research Centre, Solid State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India.
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Lakshmipriya A, Suryaprakash N. Two- and Three-Centered Hydrogen Bonds Involving Organic Fluorine Stabilize Conformations of Hydrazide Halo Derivatives: NMR, IR, QTAIM, NCI, and Theoretical Evidence. J Phys Chem A 2016; 120:7810-7816. [DOI: 10.1021/acs.jpca.6b06362] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- A. Lakshmipriya
- NMR Research
Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
| | - N. Suryaprakash
- NMR Research
Centre, Solid
State and Structural Chemistry Unit, Indian Institute of Science, Bangalore 560012, India
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14
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Shahi A, Arunan E. Microwave spectroscopic and theoretical investigations of the strongly hydrogen bonded hexafluoroisopropanol···water complex. Phys Chem Chem Phys 2015; 17:24774-82. [PMID: 26309125 DOI: 10.1039/c5cp03585f] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
This paper reports microwave spectroscopic and theoretical investigations on the interaction of water with hexafluoroisopropanol (HFIP). The HFIP monomer can exist in two conformations, antiperiplanar (AP) and synclinical (SC). The former is about 5 kJ mol(-1) more stable than the latter. Theoretical calculations predicted three potential minima for the complex, two having AP and one having SC conformations. Though, the binding energy for the HFIP(SC)···H2O turned out to be larger than that for the other two conformers having HFIP in the AP form, the global minimum for the complex in the potential energy hypersurface had HFIP in the AP form. Experimental rotational constants for four isotopologues measured using a pulsed nozzle Fourier transform microwave spectrometer, correspond to the global minimum in the potential energy hypersurface. The structural parameters and the internal dynamics of the complex could be determined from the rotational spectra of the four isotopologues. The global minimum has the HFIP(AP) as a hydrogen bond donor forming a strong hydrogen bond with H2O. To characterize the strength of the bonding and to probe the other interactions within the complex, atoms in molecules, non-covalent interaction index and natural bond orbital theoretical analyses have been performed.
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Affiliation(s)
- A Shahi
- Department of Inorganic and Physical Chemistry, Indian Institute of Science, Bangalore, 560012, India.
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15
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Mishra SK, Suryaprakash N. Organic fluorine involved intramolecular hydrogen bonds in the derivatives of imides: NMR evidence corroborated by DFT based theoretical calculations. RSC Adv 2015. [DOI: 10.1039/c5ra19537c] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
Abstract
The rare occurrence of intramolecular hydrogen bonds (HBs) of the type N–H⋯F–C is detected in the derivatives of imides in a low polarity solvent by using multi-dimensional and multinuclear NMR experiments.
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Affiliation(s)
- Sandeep Kumar Mishra
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
| | - N. Suryaprakash
- NMR Research Centre
- Solid State and Structural Chemistry Unit
- Indian Institute of Science
- Bangalore-560012
- India
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