Hydrogen bond nitrogen atom

Tab. 8.2 H NMR chemical shifts A and the distances between hydrogen-bonded nitrogen atoms (d) in several porphycenes and in 2.

In summary, both experiment and calculations demonstrate low barriers for tautomerization in porphycene as compared to porphyrin. This may explain the tunneling effects readily observed for 1 and its derivatives, as well as the change in the reaction mechanism, from stepwise in 2 towards synchronous in 1. Moreover, the cis structures, postulated, but never observed for porphyrin, may be present in porphycenes, their population increasing with the strength of the intramolecular hydrogen bond, i.e., with the decrease in the distance between hydrogen-bonded nitrogen atoms. 

The depolarization of fluorescence has been observed at temperatures around 100 K not only for 1, but also for the two derivatives, lb and Ic. in contrast, the measurements performed under the same conditions for le revealed no sign of depolarization. The textbook values of the anisotropy were obtained, i.e. 0.4 and about -0.2 for excitation into Sj and S2, respectively (Fig. 8.11). The octaethyl derivative le is the porphycene with the largest separation (2.80 A) between the hydrogen-bonded nitrogen atoms and should therefore exhibit the slowest tautomerization kinetics. It was thus concluded that the reduced anisotropy values observed in three different porphycenes are caused by excited state tautomerization [30, 80]. As shown in Fig. 8.12, the interconversion between the two trans tautomers changes the direction of the transition moment. Therefore, only a part of the excited state population emits fluorescence polarized parallel to that of the transition moment in Sg-Sj absorption (this fraction should approach 0.5 if the tautomerization is fast compared to the excited state lifetime). For the remaining frac-... 

Fig. 6 The packing of the terminally protected tripeptide Boc-Leu Aib-p-Ala-OMe, showing the formation of a continuous p sheet column along the crystallographic b axis via intermolecular hydrogen bonds and van der Waals interactions in the crystal. Dashed lines indicate hydrogen bonds. Nitrogen atoms are blue, oxygen atoms are red. carbon atoms are green, and hydrogen atoms are white. View this art in color, at www.dekker.com.)...

Fig. 2. The hydrogen bonding in crystalline 6-azauracil (Reference 16), showing that all potential donor and acceptor atoms except Ne participate in hydrogen bonding. Nitrogen atoms are shaded, oxygen atoms are shown as large open circles.

Ammonium salts contain a nitrogen atom with four bonds that has a positive charge. Four-bonded nitrogen atoms derived from amines are ammonium ions (if they re derived from aniline, they re anilinium ions). If the four bonds are all to carbon atoms, the nitrogen atom is quaternary. Salts contain a cation (named first) and an anion (named last). Typical anions include Cl (chloride), Bi" (bromide), HSO (hydrogen sulfate or bisulfate), and NOj-(nitrate). Figure 13-5 shows two examples of ammonium ions. 

PROBLEM 2.9 Draw the structural formula of methylamine, CH5N, a substance responsible for the odor of rotting fish. The carbon atom is bonded to the nitrogen atom and to three hydrogens. The nitrogen atom is bonded to the carbon and two hydrogens. 

In the crystal of 6-hydroxycrinamine, for example, there are two independent molecules of the alkaloid in each asymmetric unit, that is, the two molecules are not related by symmetry operations although the conformations of the two molecules are very similar (26). These pairs of molecules, shown in Fig. 7, occur as dimers, and each pair is held together by two hydrogen bonds between atoms N-5 0 6 and N -5 0-6, where the respective N O distances are 2.88 and 2.83 A. The hydrogen bonds to the nitrogen atoms N-5 and N -5 provide the fourth bond linkage in a tetrahedral configuration. 

C - For powder diffraction data determination the key step is the generation of reliable trial structures for final refinement. The subject of the study reported here is the pharmaceutical material anhydrous theophylline (3,7-dihydro-1,3-dimethyl-l//-purine-2,6-dione), which contains both oxygen and nitrogen as possible hydrogen bond acceptor atoms. Solid-state NMR spectra of a commercial sample not only confirmed immediately that there was only one molecule in the crystallographic asymmetric unit but also produced distinctive and chemical shifts. 

A flexible helix model in which the surfactant molecules form a flexible cylindrical micelle and the polypeptide chain of the protein wraps around it and is stabilized by hydrogen bonding between the surfactant head group and the peptide bond nitrogen atoms. 

The simplest diamine, hydrazine N2H4 (Table 3), is normally available as the monohydrate. An X-ray structure of the crystalline solid has been determined (there is some doubt as to the correct space group ) as well as an electron diffraction study of the vapor.The structxues of the di(hydrogen fluoride), di(hydrogen chloride) and monoperchlorate crown ether salts are also known. The N—N distance in hydrazine (1.499 A) is an important parameter, as one half this distance is used for the covalent radius of the single-bonded nitrogen atom. 

FIGURE 15.13 Helical protein structure. An illustration of how hydrogen bonding connects a peptide bond nitrogen atom to an oxygen atom in the third amino acid unit down the chain, resulting in a coiled structure. 

FQ [60]. Substitution of the hydrogen on nitrogen atom 11 by a methyl group prevents the formation of the hydrogen bond and thus allows studying its role in the antimalarial activity. The molecule was named methyl ferroquine (MeFQ). 

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