NH/jt interactions

Side chain-side chain (SC-SC) interactions also play an important role in the backbone folding. In the presence of a workable vibrational probe in the side-chain (NH in Trp, OH in Tyr, OH in Ser or Thr, SH in Cys, CONH2 in Asp or Glu, etc.), SC-SC interactions can be directly monitored. For instance, the moderate red-shifts simultaneously observed for both OH(phenol) and NH(indole) bands in the capped Trp-Tyr dipeptide revealed, respectively, the OH-jc and NH-Jt interactions characteristic of the face-to-face arrangement of the aromatic side-chains [112]. Beyond H-bonding, IR spectroscopy is also sensitive to other interactions. A spectacular one is the formation of an intramolecular salt bridge, correspraiding to an intramolecular zwitterion formation after an intramolecular proton transfer between an acidic (Glu) and a basic side chain (Arg) [105, 141], revealed by the spectral carbonyl signatures. 

Interestingly, residue chirality can also contribute to backbone flexibility [92] through slight modifications of hindrance effects and NH-Jt interactions between homochiral and heterochiral sequences. Thus the type (I vs II ) of p-tum in Xxx-Phe sequences is controlled by the chirality of Xxx while both forms coexist in the... 

A series of simple amino amides has been synthesized and analyzed by Faggi et with a goal to study the conformational effects introduced by the corresponding side chains. The careful analysis of the experimental /hh couplings measured in several solvents at ambient temperature has been supported by DFT calculations leading the authors to the conclusion that the aromatic derivatives are characterized by a preferred folding of the side chain toward the polar amino amide moiety. These trends have been explained by a stabilizing NH- Jt interaction. 

Weakly polar interactions in proteins and protein-ligand complexes are frequently phenomenologically analyzed and classified in terms of the interacting partners [29]. This especially includes interactions with Jt-systems, such as the NH-jt, OH-jt, or CH-Jt interaction [30, 31], aromatic-aromatic interactions (parallel jt-jt stacking versus edge-to-face interaction), and the cation-jt interaction [32]. All of these can... 

Fig. 30 CPK representation of the single-crystal X-ray structure of the pentafluorophenyl receptor. The receptor adopts in the solid-state a conformation that is adequate to interact simultaneously through hydrogen-bonding (sulfonamide NH) and anion-jt interaction with an halide located on top of the pentafluorophenyl ring...

As illustrated in Scheme 2, aU NH and O-C sites of ima ligands form intermolecular NH O-C hydrogen bonds with adjacent units. These interactions yielded onedimensional hydrogen-bonded framework along the -axis. These chains are further associated with jt-jt interactions between phen ligands in the adjacent chains. Their chains... 

Additionally, the UV spectra might reveal the cmiformational abundances present in the molecular beam expansion. However, this information ought to be interpreted with care, since specific detection schemes may introduce a quantitative bias. For REMPI detection, the photo-ionization efficiency can be conformer-dependent [75], decreasing for instance in the presence of NH-jt intramolecular interactions [76]. When employing fluorescence detection, strongly fluorescent conformers may be overestimated, while poorly fluorescent crmformers are underestimated. 

Phe-Phe sequence in a He/Ne carrier gas mixture, together with an extensive theoretical conformational analysis, have revealed how specific NH-Jt and it-it interactiOTis stabilise other stmctures than p-tums, namely ji-ji-7 and 5-Jt-7 backbone forms (Fig. 9) [112]. This picture of ancillary interactions governing conformational distribution seems to hold on larger species, as testified by the systematic study of capped tripeptides, Phe-Ala-Ala, Ala-Phe-Ala and Ala-Ala-Phe, which shows how the presence of an NH-jr interaction can guide the backbone overall folding, and in this case control the formation of an incipient heUx [85]. 

Interestingly, gas-phase studies of NH b-Jt bonds enable tme to tackle general trends which are usually deduced from data mining. In proteins of the Protein Data Bank, the phenyl ring of the Phe residue (/), binds twice as frequently to the NH i +1) as to the NH(t) group. As a matter of fact, the conformation of the isolated Ac-Phe-NH2 residue characterised by a C5 interaction stabilised by such a NH i + i)-Phe interaction is by far the most stable [83]. 

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