Zwitterionic ALA

To convert the diprotected dipeptide Boc-Ala-Phe-OMe (10) into Ala-Phe, it is necessary to remove the protecting groups from the nitrogen atom of the N-terminal L-alanine and the carboxylic acid of the C-terminal L-phenylalanine. This might be accomplished by hydrolysis of both groups under acidic conditions. However, the zwitterionic Ala-Phe is difficult to isolate, so in this experiment you will only selectively remove the Boc group from the L-alanine residue to give... 

Lanthanide coordination chemistry is still not completely understood, and many attempts are usually required to design specific Inminescent lanthanide complexes. As an alternative to rational design, a combinatorial approach shows promise for the development of specific luminescent lanthanide materials. Shinoda et al. built a combinatorial library to optimize luminescent lanthanide complexes structurally for the selective detection of amino acids. The lanthanide complex library included 196 combinations of 4 lanthanide centers, 7 pyridine ligands, and 7 amino acid substrates (Figure 16.16). The luminescence responses for amino acids depended on the nature of the ligand used. A series of Tb + complexes typically exhibited interesting luminescence responses. The TV+-picolinic acid complex and Tb -pyrazinecar-boxylic acid complex preferred zwitterionic Ala, Val, Phe, and Gin, whereas the Tb complex with dipicolinic acid favored anionic Gin and Asp. 

As a simple example of a QM/MM Car-Parinello study, we present here results from a mixed simulation of the zwitterionic form of Gly-Ala dipeptide in aqueous solution [12]. In this case, the dipeptide itself was described at the DFT (BLYP [88, 89 a]) level in a classical solvent of SPC water molecules [89b]. The quantum solute was placed in a periodically repeated simple cubic box of edge 21 au and the one-particle wavefunctions were expanded in plane waves up to a kinetic energy cutoff of 70 Ry. After initial equilibration, a simulation at 300 K was performed for 10 ps. 

Tab. 1.3 Comparison between different sets of atomic point charges for a zwitterionic Gly-Ala dipeptide in aqueous solution. D-RESP electrostatic potential derived charges [12] fitted to all 36 configurations. Hirshfeld average value of the Hirshfeld charges [89c] along the full trajectory, Amber AMBER 1995 force field [86], Gromos GROMOS96 force field [85], The charges of equivalent atoms are imposed to be equal.

Figure 9 shows a comparison of the infrared absorption and VCD spectra of (L-Ala), n = 3 - 5. The spectra are normalized for equal absorption intensity at 1595 cm 1, which is the frequency of the carboxylate anion antisymmetric stretching mode. The data show that the amide I intensity increases roughly linearly with the number of peptide linkages in the molecule, and that the VCD intensity increases similarly. However, the positions of the infrared absorption maxima are shifted from about 1654 cm 1 in the trimer to 1648 cm 1 in the pentamer. Similarly, the VCD zero crossing in the trimer occurs at 10 cm 1 higher frequency than in the tetramer and pentamer. We have interpreted these results [48] in terms of different solution conformations of the peptides the trimer seems to be stabilized by zwitterionic interactions, as discussed before, whereas formation of extended helices seems to occur at the level of the tetramer. 

Fig. 3a, b. Structures of (gly-ala)7Cs+ obtained by molecular mechanics calculations a globular zwitterion structure b a-helical non-zwitterion structure... 

Structural formulae of L-alanyl-L-serine (ala-ser) and L-alanyl-L-histidine (ala-his) in their zwitterionic representation, and proposed structures of the predominant vanadate complexes. For the ala-ser complexes, see also the speciation diagram in Figure 2.16. 

Ans. Line up the amino acids in the order Phe Asp Ala left to right and then carry out dehydrations between adjacent carboxyl and amino groups. Show the product as the zwitterion ... 

Amino acids, the monomeric units of peptides and proteins. From analysis of the vast number of proteins, it follows that 20 proteinogenic or standard amino acids are the building blocks of aU proteins. These amino acids are specified by the genetic code. With selenocysteine and pyrrolysine two additional members have been identified. Besides the imino acid proline, all other building blocks are known as a-amino acids, H2N-CHR-COOH, but the zwitterion form, H3N+-CHR-C00, occurs at physiological pH values. The amino acids can therefore act as either acids or bases. Depending on the side-chain residue R, amino acids can be classified into those with (a) non polar side chains [Gly/G Ala/A Val/V Leu/L Ile/I Met/M Pro/P Phe/F Trp/W] ... 

The aliphatic amino acids present more complicated structure changes upon hydration of the deprotonated complexes. [Pb (Pro-H) H20] is assigned a carboxylate structure with a proton transferred from the water, which can be viewed as a PbOH-l- complexed to a Pro carboxylate zwitterion (Scheme 7a) [83]. For the hydrated Pb " complexes of the other aliphatic amino acids (Ala, Val, Leu, and lieu), it was suggested that a structure type with intact carboxylate was most consistent with experiment, although not the lowest in energy. They suggest the structure shown in Scheme 7b, which, interestingly, amounts to a PbOH cation complexed with the intact (un-deprotonated) amino acid [83]. 

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