A resonance-assisted intramolecular hydrogen bond in compounds containing 2-hydroxy-3,5-dinitrobenzoic acid and its various deprotonated forms: redetermination of several related structures

A large number of structural determinations of compounds containing 2-hydroxy-3,5-dinitrobenzoic acid (I) and its various deprotonated forms, 2-hydroxy-3,5-dinitrobenzoate (II) or 2-carboxy-4,6-dinitrophenolate (III), are biased. The reason for the bias follows from incorrectly applied constraints or restraints on the bridging hydrogen, which is involved in the intramolecular hydrogen bond between the neighbouring carboxylic/carboxylate and oxo/hydroxy groups. This hydrogen bond belongs to the category of resonance-assisted hydrogen bonds. The present article suggests corrections for the following structure determinations that have been published in Acta Crystallographica: DUJZAK, JEVNAA, LUDFUL, NUQVEB, QIQJAD, SAFGUD, SEDKET, TIYZIM, TUJPEV, VABZIJ, WADXOR, YAXPOE [refcodes are taken from the Cambridge Structural Database [CSD; Groom et al. (2016). Acta Cryst. B72, 171–179]. The structural features of the title molecules in all the retrieved structures, together with structures that contain 3,5-dinitro-2-oxidobenzoate (IV), are discussed. Attention is paid to the localization of the above-mentioned bridging hydrogen, which can be situated closer to the O atom of the carboxylate/carboxylic group or that of the hydroxy/oxo group. In some cases, it is disordered between the two O atoms. The position of the bridging hydrogen seems to be dependent on the pK a (base) although with exceptions. A stronger basicity enhances the probability of the presence of a phenolate (III). The present article examines the problem of the refinement of such a bridging hydrogen as well as that of the hydrogen atoms involved in the hydroxy and primary and secondary amine groups. It appears that the best model, in many cases, is obtained by fixing the hydrogen-atom position found in the difference electron-density map while refining its isotropic displacement parameter.

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True symmetry or pseudosymmetry: 5-amino-1-(4-methylphenylsulfonyl)-4-pyrazolin-3-one and a comparison with its 1-phenylsulfonyl analogue

Acta Crystallographica Section C Crystal Structure Communications ◽

10.1107/s0108270112049906 ◽

2012 ◽

Vol 69 (1) ◽

pp. 90-92 ◽

Cited By ~ 2

Author(s):

Galal H. Elgemeie ◽

Shahinaz H. Sayed ◽

Peter G. Jones

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Intramolecular Hydrogen Bond ◽

Title Compound ◽

Acta Cryst ◽

Interplanar Angle ◽

Phenyl Derivative ◽

Compound C ◽

Independent Molecules ◽

Intramolecular Hydrogen

The title compound, C10H11N3O3S, (I), crystallizes as the NH tautomer. The two rings subtend an interplanar angle of 72.54 (4)°. An intramolecular hydrogen bond is formed from the NH2group to a sulfonyl O atom. The molecular packing involves layers of molecules parallel to thebcplane atx≃ 0, 1etc., with two classical linear hydrogen bonds (amino–sulfonyl and pyrazoline–carbonyl N—H...O) and a further interaction (amino–sulfonyl N—H...O) completing a three-centre system with the intramolecular contact. The analogous phenyl derivative, (II) [Elgemeie, Hanfy, Hopf & Jones (1998).Acta Cryst.C54, 136–138], crystallizes with essentially the same unit cell and packing pattern, but with two independent molecules that differ significantly in the orientation of the phenyl groups. The space group isP21/cfor (I) butP21for (II), which is thus a pseudosymmetric counterpart of (I).

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Dipole moment of the intramolecular hydrogen bond. 2-Nitrophenol and its derivatives

Collection of Czechoslovak Chemical Communications ◽

10.1135/cccc19830735 ◽

1983 ◽

Vol 48 (3) ◽

pp. 735-747 ◽

Cited By ~ 3

Author(s):

Otto Exner ◽

Juraj Koudelka ◽

Soňa Vašíčková

Keyword(s):

Hydrogen Bond ◽

Electron Transfer ◽

Dipole Moment ◽

Intramolecular Hydrogen Bond ◽

Dipole Moments ◽

Charge Redistribution ◽

Experimental Dipole Moment ◽

Mndo Calculations ◽

The Difference ◽

Intramolecular Hydrogen

Dipole moments of substituted 2-nitrophenols VIa-VIf and substituted 2-nitroanisoles VIIa to VIIf were measured in benzene and dioxan solutions. Infrared spectroscopy confirmed that nitrophenols VI exist either solvent and at different concentrations as non-associated molecules with an intramolecular hydrogen bond. Therefore, the difference between the experimental dipole moment and that calculated from group moments can be attributed to charge redistribution raised by the hydrogen bond. Only a minute part of it may be due to electron transfer through the ring (conjugation of the functional groups) as follows particularly from he comparison with nitroanisoles VII. Nevertheless, the charge transfer, expressed as the vector μH, amounts only 1.7 . 10-30 Cm (at an angle of 138° to the H-O bond), i.e. several times less than observed previously in compounds with more powerful hydrogen acceptors. CNDO/2 and MNDO calculations agree fairly with the gross dipole moments of the compounds investigated but are unable to predict μH, not even as far as its direction is concerned.

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Accurate location of hydrogen atoms in hydrogen bonds of tizoxanide from the combination of experimental and theoretical models

RSC Advances ◽

10.1039/d0ra10609g ◽

2021 ◽

Vol 11 (13) ◽

pp. 7644-7652

Author(s):

Ana L. Reviglio ◽

Fernando A. Martínez ◽

Marcos D. A. Montero ◽

Yamila Garro-Linck ◽

Gustavo A. Aucar ◽

...

Keyword(s):

Hydrogen Bond ◽

Hydrogen Bonds ◽

Intramolecular Hydrogen Bond ◽

Theoretical Models ◽

Full Description ◽

Hydrogen Atoms ◽

Theoretical Methods ◽

Intramolecular Hydrogen

In this work, we present a combination of ssNMR spectroscopy and two different theoretical methods to get a full description of an intramolecular hydrogen bond in tizoxanide.

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Competition between the intramolecular hydrogen bond and the π-electron delocalization in some RAHB systems: A theoretical study

Журнал структурной химии ◽

10.26902/jsc_id40420 ◽

2019 ◽

Vol 60 (5) ◽

Keyword(s):

Hydrogen Bond ◽

Intramolecular Hydrogen Bond ◽

Theoretical Study ◽

Electron Delocalization ◽

Intramolecular Hydrogen

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Effect of the intramolecular hydrogen bond in the active metabolite analogs of leflunomide for blocking the Plasmodium falciparum dihydroorotate dehydrogenase enzyme: QTAIM, NBO, and docking study

Current Computer - Aided Drug Design ◽

10.2174/1573409916666200527133126 ◽

2020 ◽

Vol 16 ◽

Author(s):

Reihaneh Heidarian ◽

Mansoureh Zahedi-Tabrizi

Keyword(s):

Hydrogen Bond ◽

Plasmodium Falciparum ◽

Molecular Orbital ◽

Intramolecular Hydrogen Bond ◽

Active Metabolite ◽

Chemical Hardness ◽

Dihydroorotate Dehydrogenase ◽

Molecular Orbital Analysis ◽

Intramolecular Hydrogen ◽

Orbital Analysis

: Leflunomide (LFM) and its active metabolite, teriflunomide (TFM), have drawn a lot of attention for their anticancer activities, treatment of rheumatoid arthritis and malaria due to their capability to inhibit dihydroorotate dehydrogenase (DHODH) and Plasmodium falciparum dihydroorotate dehydrogenase (PfDHODH) enzyme. In this investigation, the strength of intramolecular hydrogen bond (IHB) in five analogs of TFM (ATFM) has been analyzed employing density functional theory (DFT) using B3LYP/6-311++G (d, p) level and molecular orbital analysis in the gas phase and water solution. A detailed electronic structure study has been performed using the quantum theory of atoms in molecules (QTAIM) and the hydrogen bond energies (EHB) of stable conformer obtained in the range of 76-97 kJ/mol, as a medium hydrogen bond. The effect of substitution on the IHB nature has been studied by natural bond orbital analysis (NBO). 1H NMR calculations show an upward trend in the proton chemical shift of the enolic proton in the chelated ring (14.5 to 15.7ppm) by increasing the IHB strength. All the calculations confirmed the strongest IHB in 5-F-ATFM and the weakest IHB in 2-F-ATFM. Molecular orbital analysis, including the HOMO-LUMO gap and chemical hardness, was performed to compare the reactivity of inhibitors. Finally, molecular docking analysis was carried out to identify the potency of inhibition of these compounds against PfDHODH enzyme.

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