Search

The region encompassing residues 13-23 of the amyloid beta peptide (Aβ(13-23)) of Alzheimer’s disease is the self-recognition site that initiates toxic oligomerization and fibrillization, and also is the site of interaction of Aβ with many other proteins. Peptidic compounds intended to act as β-sheet inhibitors targeted to Aβ(13-23) have been shown to inhibit fibrillization of Aβ and also to reduce its neurotoxicity. We describe herein a study by molecular dynamics (MD) of the complexes between Aβ(13-23) and three (pseudo)peptidic βsheet inhibitors, as well as its homodimer. The monomers of all systems exist predominantly as extended β-strands, with Aβ(13-23) having the greatest flexibility to adopt other conformations. The dimers of all systems exist almost exclusively as stable antiparallel β-sheets anchored at the C-terminus of Aβ(13-23) by salt bridges to the C-terminal residues, Glu22 and Asp23. We also employ an MD technique called “atomic force microscopy” (AFM) to examine the dynamics of dissociation of the complexes in water. Each ligand attached to Aβ(13-23) begins dissociation by peeling back from its C-terminus, breaking interstrand H-bonds, and losing the β-sheet character. The salt bridges are the last to release, and presumably are the first to form in the reverse process of aggregation. The free energy profiles of the dissociation as a function of the separation of the centers-of-mass of all systems show plateau regions in which separation takes place with relatively little or no rise in free energy. For each system the dissociation profile does not have a maximum and reaches a flat plateau. By implication, the reverse process of assembly does not have a barrier. This and the plateau regions in the dissociation profile are examples of entropy-enthalpy compensation that arise naturally during the AFM-MD simulation.

The Paal–Knorr pyrrole synthesis, which involves the reaction of 1,4-dicarbonyls with amines, is among the most classical methods of heterocyclic pyrrole ring synthesis. The detailed sequence and the nature of the intermediates that occur in the Paal–Knorr reaction mechanism are not well understood. Density functional theory methods have been employed to investigate the nature of the intermediates and transition states in the Paal–Knorr pyrrole mechanism. Two mechanistic pathways for the reaction were examined: hemiaminal cyclization vs. enamine cyclization. Our calculated reaction potential energy surfaces suggest that the hemiaminal cyclization is the preferred pathway for the reaction both in gas phase and in solution. This conclusion is consistent with the experimental results which suggest that the hemiaminal intermediate undergoes cyclization in the rate-limiting step in the Paal–Knorr reaction mechanism. The preferred mechanism for the Paal–Knorr reaction consists of hemiaminal formation, hemiaminal cyclization and a dehydration step to form the pyrrole ring. Water and hydrogen-bonding interactions play a key role in catalyzing the hydrogen-transfer steps of the reaction.

The performance of the DFT functionals B3LYP, B3PW91 and PBE1PBE in conjunction with selected basis sets for the prediction of 15N and 13C nuclear shieldings for small nitrogen-containing molecules is assessed. For molecules containing only singly bonded nitrogen and carbon atoms, the PBE1PBE/6-311+G(2df,p) level of theory is shown to provide reliable 15N and 13C nuclear shieldings. For the triply bonded nitrogen-containing molecules N2, CH3CN and HCN, all three levels of theory are much less satisfactory.

An interesting aspect of the ring-opening of thiamine and certain other thiazolium ions is the biphasic kinetics of the ring reclosure process. It has previously been proposed that the two amide rotamers of the ring-opened amidoenethiolates are responsible for the two kinetic processes. We have carried out Hartree-Fock and density functional theory calculations on a series of amidoenethiolates and their corresponding tetrahedral intermediates. The corrected gas phase energy difference of 14.6 kJ/mol between 1′c and 2′c supports the notion that the two rotamers can exist in solution in sufficient quantities to give rise to two kinetic processes. The major enethiolate conformer should cyclize more rapidly (after protonation) than the minor conformer in agreement with previous observations. The most stable tetrahedral intermediate has a geometry that suggests stabilization by the anomeric effect.

Ab initio molecular orbital theory has been used to investigate a series of possible chlorosulfonium ylides to assess the potential for ylide intermediacy in the chlorination of organic sulfides. The majority of optimized structures are best viewed as thionium salts. Only ylide structures in which the putative carbanionic centre bears a powerful anion stabilizer (e.g. cyano or carbomethoxy) survive optimization.