Methylamine, model structure

The structures of PMs are trimeric, consisting of three molecules of PS and two molecules of methylamine that are condensed together (Table 9.5). In the structures of PMs, however, the bonds created by the condensation lack adjacent hydrogen atoms, making the connectivity assignment in 1H-NMR studies virtually impossible (see the 9-membered rings in Fig. 9.11). To circumvent this problem, a model compound of panal, K-l, having 13C-labeles at the C12 and C13 positions, has been synthesized at Kishi s laboratory (Harvard University) to make a model compound of PM (Stojanovic, 1995). 

Data on molecules containing nitrogen, oxygen, silicon, phosphorous and sulfur not only provide additional examples, but also allow assessment of the ability of the different models to reproduce known changes in dipole moments accompanying structural variations. For example, dipole moments in methylamines are known experimentally to decrease with increasing methyl substitution,... 

Computational approach. Lee and Houk conducted calculations using a methyl-ammonium ion to mimic the key lysine of the enzyme active site.16 They chose this model because, even though no crystal structures had been solved at the time, a lysine was known to be essential for catalysis.60 The reaction of orotate + CH3NH3 to form a carbene-methylamine complex was thus examined in various dielectrics using the SCI-PCM SCRF method in Gaussian 94.30 31 48 Solvation energies computed at the RHF/6-31 + G level were used to correct gas phase MP2/ 6-31 + G energies and obtain AH values for reaction in solution. 

Several different models of the active site were used, based on the reported crystal structures. In these, the OMP substrate (Scheme 1) was generally modeled as 1-methylorotate (lb), but in some calculations, parts of the ribose ring were also included. Lysine residues were modeled as methylamine, aspartate residues were... 

The carboxyl group occupies a prominent place in protein structure and function and is commonly taken to be ionized as a carboxylate, particularly when paired in a salt bridge with a Whereas this may be the case in a protein environment, it is not obvious that a —COOH group will donate its proton to a base to form an ion pair in the gas phase. For example, SCF calculations with a polarized 6-31G basis set indicate that neither methy-lamine nor an arginine model is able to extract a proton from acetic acid so as to form an ion pair. On the other hand, there is some indication that correlation might stabilize the ion pair for formic acid -f methylamine. ... 

You can examine the structure of methylamine, including its electrostatic potential, in more detail on Learning By Modeling. 

The availability of the crystal structure of the binary complex of these two proteins (92) adds to the impact of these studies, and provides a model to which current electron transfer theories can be applied. The theoretical results can then be compared with kinetic studies of electron transfer within the complex. Additional studies 185, 186) have focused on the electron transfer reaction between MADH, amicyanin, and c5rtochrome Cssu from P. denitrificans (as pointed out in Section II, MADH and amicyanin are induced by growth on methylamine, and cytochrome Cm is induced by growth on methanol). Again, a crystal structure is available for the complex of... 

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