Effect of a Hydrogen Bonding Carboxamide Group on Universal Bases

2006 ◽  
Vol 71 (6) ◽  
pp. 899-911 ◽  
Author(s):  
Kathleen Too ◽  
Daniel M. Brown ◽  
Philipp Holliger ◽  
David Loakes
Keyword(s):  
Hydrogen Bonding ◽  
Nitro Group ◽  
Pyrrole Ring ◽  
Major Groove ◽  
Duplex Stability ◽  
Universal Bases

A number of aromatic universal base analogues have been described in the literature, but most are non-hydrogen bonding. We have examined the effect of introducing hydrogen bonding carboxamide groups onto the pyrrole ring of 5-nitroindole. The modified analogues retain universal base features, but there are no overall effects on duplex stability. This leads to the suggestion that the nitro group is within the hydrogen bonding face of the duplex, and the hydrogen bonding carboxamide group is in the duplex major groove.

Hydrogen Bonding in organic compounds. 1. o-Nitroanilines

1958 ◽  
Vol 11 (4) ◽  
pp. 513 ◽  
Author(s):  
LK Dyall ◽  
AN Hambly
Keyword(s):  
Hydrogen Bonding ◽  
Nitro Group ◽  
Organic Compounds ◽  
Intramolecular Hydrogen Bonding ◽  
Amino Group ◽  
Infra Red ◽  
Sterically Hindered ◽  
Intramolecular Hydrogen

The infra-red spectra of o-nitroanilines do not indicate any intramolecular hydrogen bonding unless there are nitro groups in both positions 2 and 6 to the amino group. An examination of the literature shows that there is no unambiguous evidence from other sources of such bonding in simple o-nitroanilines. An explanation is given of the variation of the stretching frequencies of the nitro group in sterically hindered compounds and in those with electron-donating ortho- and para-substituents.

Nitric acid promoted formation of an N-confused porphyrin-derived porphodimethene and a violinoid

2006 ◽  
Vol 10 (07) ◽  
pp. 953-961 ◽  
Author(s):  
Chen-Hsiung Hung ◽  
Chia-Chi Liaw ◽  
Wei-Ming Chin ◽  
Gao-Fong Chang ◽  
Chuan-Hung Chuang
Keyword(s):  
Crystal Structure ◽  
Nitro Group ◽  
Nucleophilic Addition ◽  
Ring Opening ◽  
Pyrrole Ring ◽  
Hydroxyl Group ◽  
Parallel Reaction ◽  
Free Base ◽  
Hydrogen Bonding Interactions ◽  
Open Ring

The nitration of free-base N -confused porphyrin led to a novel 5,10-meso-dihydroxy- N -confused porphodimethene and an open-ring N -confused violinoid. The results support nitration occurring first, followed by nucleophilic addition of a hydroxyl group and a parallel reaction of oxygenolysis to cause the ring-opening. The nitro group substituted at the inner carbon of the inverted pyrrole ring is located on both the porphodimethene and violinoid. In the case of the porphodimethene, two dihydroxyl groups with υ( OH ) at 3404 cm−1 are arranged in a syn conformation at the same side with the nitro group. The violinoid exhibits υ( C = O ) at 1659 cm−1. NMR and structure determination suggest that oxygenolysis occurs selectively at the C=C bond between the α-pyrrole and meso carbon closest to the amino NH of the inverted pyrrole ring. The single crystal structure of porphodimethene gave a 50% disorder between the peripheral nitrogen and carbon atom on the inverted pyrrole ring, while a dimeric structure assembled through hydrogen bonding interactions was observed in the crystal lattice of the violinoid.

scholarly journals The role of nitro groups in the binding of nitroaromatics to protein MOPC 315

1978 ◽  
Vol 173 (3) ◽  
pp. 713-722 ◽  
Author(s):  
P Gettins ◽  
D Givol ◽  
R A Dwek
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonding ◽  
High Resolution ◽  
Hydrogen Bonds ◽  
Fluorescence Quenching ◽  
Nitro Group ◽  
Protein Interactions ◽  
Chemical Shifts ◽  
Binding Constants

Two series of dinitrophenyl haptens, in which chlorine replaces one or both nitro groups, were used to investigate, by a combination of high-resolution 1H n.m.r. and fluorescence quenching, the presence of groups in the combining site of protein MOPC 315, which form hydrogen bonds to the aromatic-ring substituents of the hapten. The large differences in binding constants on successive replacement of nitro groups were shown to be due to specific hapten-substituent-protein interactions by (a) showing that there was little difference in the interaction between these haptens and 3-methylindole (a model for the residue tryptophan-93L with which the hapten stacks in protein MOPC 315), (b) proving by 1H n.m.r. that the mode of hapten binding is constant and (c) showing that the differences in Kd were consistent with the relative hydrogen-bonding capacities of chlorine and the nitro moiety. In this way it was established that each nitro group forms a hydrogen bond. Furthermore, from consideration of the 1H n.m.r. chemical shifts of several dinitrophenyl haptens and their trinitrophenyl analogues, it was shown that there is no distortion of the o-nitro group on binding to the variable fragment of protein MOPC 315.

N.M.R. and absorption spectra of nitrotoluidines

1974 ◽  
Vol 27 (4) ◽  
pp. 915 ◽  
Author(s):  
T Yokoyama
Keyword(s):  
Hydrogen Bonding ◽  
Absorption Band ◽  
Nitro Group ◽  
Absorption Spectra ◽  
Long Range ◽  
Chemical Shifts ◽  
Intramolecular Hydrogen Bonding ◽  
Polar Solvents ◽  
Dimethylamino Group ◽  
Intramolecular Hydrogen

N.m.r. chemical shifts of ring protons and absorption spectra of 4-substituted 2-nitroaniline deriva- tives were investigated. It was ascertained that the rotations of dimethylamino and/or 2-nitro groups are influenced by the resonance interaction of the dimethylamino group with 4-substituents and the C1 → C2 absorption band is displaced bathochromically by resonance saturation with 4-substituents. The long-range coupling of NH with H5 in N-methyl-2-nitro-p-toluidine was found to be absent and it is considered that the intramolecular hydrogen bonding of amino hydrogen with the 2-nitro group is ruptured by ROH and polar solvents.

TheN1-(2′-deoxyribofuranoside) of 3-iodo-5-nitroindole: a universal nucleoside forming nitro–iodo interactions

2009 ◽  
Vol 65 (3) ◽  
pp. o100-o102 ◽  
Author(s):  
Simone Budow ◽  
Peter Leonard ◽  
Henning Eickmeier ◽  
Hans Reuter ◽  
Frank Seela
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonding ◽  
Hydrogen Bonds ◽  
Nitro Group ◽  
Hydroxy Group ◽  
Torsion Angle ◽  
Title Compound ◽  
Stacking Interactions ◽  
Sugar Moiety ◽  
Determining Factors

The title compound [systematic name: 1-(2-deoxy-β-D-erythro-pentofuranosyl)-3-iodo-5-nitro-1H-indole], C13H13IN2O5, exhibits anantiglycosylic bond conformation with a χ torsion angle of −114.9 (3)°. The furanose moiety shows a twisted C2′-endosugar pucker (S-type), withP= 141.3° and τm = 40.3°. The orientation of the exocyclic C4′—C5′ bond is +ap(gauche,trans), with a γ torsion angle of 177.4 (2)°. The extended crystal structure is stabilized by hydrogen bonding and I...O contacts, as well as by stacking interactions. The O atoms of the nitro group act as acceptors, forming bifurcated hydrogen bonds within theacplane. Additionally, the iodo substituent forms an interplanar contact with an O atom of the nitro group, and another contact with the O atom of the 5′-hydroxy group of the sugar moiety within theacplane is observed. These contacts can be considered as the structure-determining factors for the molecular packing in the crystal structure.

scholarly journals Crystallographic and spectroscopic characterization of 4-nitro-2-(trifluoromethyl)benzoic acid and 4-nitro-3-(trifluoromethyl)benzoic acid

2019 ◽  
Vol 75 (4) ◽  
pp. 524-528
Author(s):  
George L. Diehl III ◽  
Lisa Je ◽  
Joseph M. Tanski
Keyword(s):  
Hydrogen Bonding ◽  
Carboxylic Acid ◽  
Benzoic Acid ◽  
Nitro Group ◽  
Spectroscopic Characterization ◽  
Acid Group ◽  
Carboxylic Acid Group ◽  
Donor Acceptor ◽  
Graph Set

The title compounds, both C8H4F3NO4, represent two isomers of nitro trifluoromethyl benzoic acid. The compounds each contain a nitro functionality para to the carboxylic acid group, with the trifluoromethyl substituent ortho to the acid group in the 2-isomer and ortho to the nitro group in the 3-isomer. The regiochemistry with respect to the trifluoromethyl group results in steric interactions that rotate the carboxylic acid group or the nitro group out of the aromatic plane in the 2- and 3-isomer, respectively. Each molecule engages in intermolecular hydrogen bonding, forming head-to-tail dimers with graph-set notation R 2 2(8) and donor–acceptor hydrogen-bonding distances of 2.7042 (14) Å in the 2-isomer and 2.6337 (16) in the 3-isomer. Recrystallization attempts did not yield untwinned crystals.

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