Specific protonation

In an isolated two-spin system, the NOE (or, more accurately, the slope of its buildup) depends simply on where d is the distance between two protons. The difficulties in the interpretation of the NOE originate in deviations from this simple distance dependence of the NOE buildup (due to spin diffusion caused by other nearby protons, and internal dynamics) and from possible ambiguities in its assignment to a specific proton pair. Mofec-ufar modeling methods to deaf with these difficulties are discussed further below. 

The change in mechanism with pH for compound 1 gives rise to the pH-rate profile shown in Fig. 8.7. The rates at the extremities pH < 2 and pH > 9 are proportional to [H+] and [ OH], respectively, and represent the specific proton-catalyzed and hydroxide-catalyzed mechanisms. In the absence of the intramolecular catalytic mechanisms, the... 

The 1H NMR spectrum shown is that of 3-methyl-3-buten-l-ol. Assign all the observed resonance peaks to specific protons, and account for the splitting... 

Besides, information on intermolecular interactions has been derived in these studies from complexation-induced shifts (CIS). The chemical shift is an indicator for the shielding of a nucleus and thus for the electronic state of a specific proton. Since the electronic environment may change on complexation, CIS can be used to monitor where host-guest contacts may take place. If these interactions occur stereoselectively, the CIS will be different for the two guest enantiomers (AS distinct from 0) giving possibly some insight into the chiral recognition mechanism. 

The NMR spectrum given by a globular protein with a well-defined tertiary structure differs from that of the same protein under denaturing conditions in two respects. First, the reduction in mobility of residues when the protein folds into a stable tertiary structure produces a broadening of resonances. Second, alterations in resonances caused by chemical shifts arise due to the stable placement of specific protons in unique chemical environments which leads to the appearance of resonances in new positions. 

Figure 9.8 Simple diagram of mitochondrial H -ion movement and axonal K -ion movement to establish membrane potentials across membranes. Note that H movement from the mitochondrial matrix to the outer surface of the inner membrane requires a specific proton pump that requires energy, which is transferred from electron transfer, whereas the K ion movement occurs via an ion channel with energy provided from the concentration difference of K ions on either side of the membrane (approximately 100-fold). The movement of both the protons and K ions generates a membrane potential. The potential across the membrane of the nerve axon provides the basis for nervous activity (see Chapter 14).

R.E. Hurd, D.M. Freeman, Metabolite specific proton magnetic-resonance imaging, Proc. Natl. Acad. Sci. USA 86 (1989) 4402-4406. 

The novel heterocyclic system 92 has been prepared by reaction of 2-amino-1,3,4-thiadiazoles 91 with either l-(haloalkyl)pyridinium halides 89 or N,N -methylenebis(pyridinium) dihalides 90. A mechanism for the formation of 92 was proposed and involved a series of specific proton migrations, bond-breaking and bond-forming processes <98EJOC2923>. 

The pH sensitivity of the Nef-reaction (general vs. specific protonation. Section 4.1.1) becomes obvious when the concave pyridine 3j was used instead of 3c. Both concave pyridines 3c and j have the same structure the only difference is the 4-substitution by a methoxy group leading to another basicity. Therefore with the same buffer concentration, the pH of the 3j-buffer is higher leading to more C-protonation. 

The term general and specific protonation is used in the same sense as the terms general and specific acid catalyses are used specific means a specific protonated solvent molecule is the reacting species while general means that in general all acids in solution contribute to the reaction... 

In gramicidin SA four protons were shown to have very slow deuterium-proton exchange rates which could be assigned to specific protons. 

J. Yarger, R. Nieman, and A. Bieber,/. Chem. Educ. 74,243-246 (1997). NMRTitration Used to Observe Specific Proton Dissociation in Polyprotic Tripeptides. ... 

The adjacent mechanism for step 1 would involve the 02 attack opposite X (or Y) and this would require protonation of X (or Y) so that it could be apical in the intermediate. Pseudorotation would then be required to allow 05" to become apical preparatory to leaving, and 03 would also become apical. Either group could then leave and specific protonation of 05" would be required to explain the lack of 2, 5"-diester formation. 

In the following the proton NMR spectra of some low spin ferric compounds are presented, and the assignment of the resonances to specific protons in the molecules will be discussed. 

The previous section describes methods that can provide an enormous amount of chemical-shift and coupling information about a protein. Recall that our goal is to determine the protein s conformation. We hope that we can use couplings to decide which pairs of hydrogens are neighbors, and that this information will restrict our model s conformations to one or a few similar possibilities. But before we can use the couplings, we must assign all the resonances in the 1-D spectrum to specific protons on specific residues in the sequence. This is usually the most laborious task in NMR structure determination, and I will provide only a brief sketch of it here. 

Advances in NMR instrumentation and methodology have now made it possible to determine site-specific proton chemical shift assignments for a large number of proteins and nucleic acids (1,2). It has been known for some time that in proteins the "structural" chemical shifts (the differences between the resonance positions in a protein and in a "random coil" polypeptide (3-5),) carry useful structural information. We have previously used a database of protein structures to compare shifts calculated from simple empirical models to those observed in solution (6). Here we demonstrate that a similar analysis appears promising for nucleic acids as well. Our conclusions are similar to those recently reported by Wijmenga et al (7),... 

Figure 5.19 Portions of NOESY spectra of kinaseX inhibitor 1 in complex with residue type specifically protonated samples of kinaseX. Intra-ligand cross peaks are circled in both spectra. (A) KinaseX inhibitor 1 in complex with p ]Leu (otherwise 2 - -labeled) kinaseX. Concentrations of both the protein and the inhibitor used were 140 pM. (B) KinaseX inhibitor 1 in complex with p H ]Val (otherwise2 - -labeled) kinaseX. Concentrations of both the protein and the inhibitor were 90 pM. Both spectra (A) and (B) were recorded at 15 °C, 600 MHz 1 H frequency, using a NOESY mixing time of 60 ms.

A new experimental approach has been developed to study the distribution of local electrostatic potential around specific protons in biologically important molecules. The approach is the development of a method denoted as "spin label/spin-probe" proposed in... 

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