Side-chains

Hammen equation A correlation between the structure and reactivity in the side chain derivatives of aromatic compounds. Its derivation follows from many comparisons between rate constants for various reactions and the equilibrium constants for other reactions, or other functions of molecules which can be measured (e g. the i.r. carbonyl group stretching frequency). For example the dissociation constants of a series of para substituted (O2N —, MeO —, Cl —, etc.) benzoic acids correlate with the rate constant k for the alkaline hydrolysis of para substituted benzyl chlorides. If log Kq is plotted against log k, the data fall on a straight line. Similar results are obtained for meta substituted derivatives but not for orthosubstituted derivatives. 

The term vitamin K2 was applied to 2-methyl-3-difarnesyl-l,4-naphthoquinone, m.p. 54 C, isolated from putrefied fish meal. It now includes a group of related natural compounds ( menaquinones ), differing in the number of isoprene units in the side chain and in their degree of unsaturation. These quinones also appear to be involved in the electron transport chain and oxidative phosphorylation. 

Some of the common aromatics found in crude oil are the simple derivatives of benzene in which one or more alkyl groups (CHg) are attached to the basic benzene molecule as a side chain which takes the place of a hydrogen atom. These arenes are either liquids or solids under standard conditions. 

Fig. XV-16. A schematic drawing of the arrangement of polyglutamates having alkyl side chains in an LB film. The circles represent the rodlike polyglutamate backbone oriented perpendicular to the page the wiggly lines are the alkyl sidechains. (From Ref. 182.)...

A unique but widely studied polymeric LB system are the polyglutamates or hairy rod polymers. These polymers have a hydrophilic rod of helical polyglutamate with hydrophobic alkyl side chains. Their rigidity and amphiphilic-ity imparts order (lyotropic and thermotropic) in LB films and they take on a F-type stmcture such as that illustrated in Fig. XV-16 [182]. These LB films are useful for waveguides, photoresists, and chemical sensors. LB films of these polymers are very thermally stable, as was indicated by the lack of interdiffusion up to 414 K shown by neutron reflectivity of alternating hydrogenated and deuterated layers [183]. AFM measurements have shown that these films take on different stmctures if directly deposited onto silicon or onto LB films of cadmium arachidate [184]. 

The Fe-N mode is at 222 in the R state and 207 cnY in the T state for the a subunits, but only shifted to 218 T state for the (3 subunits. This is consistent with the interpretation that the Fe-imidazole interations are weakened more in the T state of the a subunits than p subunits. Time-resolved resonance Raman studies have shown that the R T switch is complete on a 10 ps tuuescale [38]. Finally, UV excitation of the aromatic protein side chains yields... 

Schneider J, Erdelen C, Ringsdorf H and Rabolt J F 1989 Structural studies of polymers with hydrophilic spacer groups. 2. Infrared-spectroscopy of Langmuir-Blodgett multilayers of polymers with fluorocarbon side-chains at ambient and elevated temperatures Macromolecules 22 3475-80... 

A likely exit path for the xenon was identified as follows. Different members of our research group placed the exit path in the same location and were able to control extraction of the xenon atom with the tug feature of the steered dynamics system without causing exaggerated perturbations of the structure. The exit path is located between the side chains of leucines 84 and 118 and of valine 87 the flexible side chain of lysine 83 lies just outside the exit and part of the time is an obstacle to a linear extraction (Fig. 1). 

P. E. Smith and B. M. Pettitt. Amino acid side-chain populations in aqueous and saline solution Bis(penicillamine) enkephalin. Biopolymers, 32 1623-1629,... 

Levitt Warshel [17, 18] were the first to show that reduced representations may work they used Ca atoms and virtual atoms at side chain centroids. OOBATAKE Crippen [24] simplified further by only considering the Ca atoms. This is snfficient since there are reasonably reliable methods (Holm Sander [11, 12]) that compute a full atom geometry from the geometry of the Ca atoms. (All atom representations are used as well, but limited to the prediction of tiny systems such as enkephalin.)... 

L. Holm and C. Sander, Database algorithm for generating protein backbone and side-chain co-ordinates from a trace, J. Mol. Biol. 218 (1991), 183-194. 

L. Holm and C. Sander, Fast and simple Monte Carlo algorithm for side chain optimization in proteins. Proteins 14 (1992), 213-223. 

By using an effective, distance-dependent dielectric constant, the ability of bulk water to reduce electrostatic interactions can be mimicked without the presence of explicit solvent molecules. One disadvantage of aU vacuum simulations, corrected for shielding effects or not, is the fact that they cannot account for the ability of water molecules to form hydrogen bonds with charged and polar surface residues of a protein. As a result, adjacent polar side chains interact with each other and not with the solvent, thus introducing additional errors. 

The comparison of both data sources qualitatively shows a similar picture. Regions of high mobflity are located especially between the secondary structure elements, which are marked on the abscissa of the plot in Figure 7-17. Please remember that the fluctuations plotted in this example also include the amino acid side chains, not only the protein backbone. This is the reason why the side chains of large and flexible amino acids like lysine or arginine can increase the fluctuations dramatically, although the corresponding backbone remains almost immobile. In these cases, it is useful to analyze the fluctuations of the protein backbone and side chains individually. 

Including solvent in a rn olecu lar dy ri arn ics sim illation creates a friction a I force that dam ps some motion of th e solti te. Tti is affects in particular th e m otion s of exposed side chain in proteins. 

Fig. 9.25 If the leucine side chain interconverts rapidly between too conprmations then the NMR spectrum will he an average of them. With a traditional refinement this leads to a structure that sirmltaiieausly tries to satisfy all restraints and is at the top of the energy barrier between the two minima.

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