Lipid peroxidation is an important part of the pathological pathway of membrane damage in membranes that have high levels of polyunsaturated fatty acids such as linoleic, linolenic, arachidonic, and docosahexaenoic acids. Neural membranes are particularly rich in polyunsaturated acids and such damage is implicated in neurological diseases, such as Alzheimer's disease. To obtain a bilayer model that represents the property of susceptibility to lipid peroxidation, we carried out molecular dynamics (MD) simulations of a bilayer of 1-palmitoyl-2-linoleyl-sn-glycero-3-phosphatidylcholine (PLPC). Parameters for the torsional potentials of the cis,cis-∆ 9,12 bis-allylic region of the linoleate chain were fitted to the results of high-level ab initio calculations on model compounds. The MD simulations of the bilayer provided the structural properties of the system and show that the unsaturation induces disorder and affects the physical properties of the membrane.

Two of the defining hallmarks of Alzheimer's disease (AD) are deposits of the beta-amyloid peptide, Abeta, and the generation of reactive oxygen species, both of which may be due to the Abeta peptide coordinating metal ions. The Cu2+ concentrations in cores of senile plaques are significantly elevated in AD patients. Experimental results indicate that Abeta1-42 in particular has a very high affinity for Cu2+, and that His13 and His14 are the two most firmly established ligands in the coordination sphere of the copper ion. Quantum chemical calculations using the unrestricted B3LYP hybrid density functional method with the 6-31G(d) basis set were performed for geometries, zero point energies and thermochemistry. The effects of solvation were accommodated using the CPCM method. The enthalpies were calculated with the 6-311+G(2df,2p) basis set. Calculations show that when Cu(H2O)(4)2+ combines with the model compound 1 (3-(1H-imidazol-5-yl)-N-[2-(1H-imidazol-5-yl)ethyl] propanamide) in the aqueous phase, the most stable binding site involves the Npi atoms of His13 and His14 as well as the carbonyl of the intervening backbone amide group. These structures are fairly rigid and the implications for conformational changes to the Abeta backbone are discussed. In solution at pH=7, Cu2+ promotes the deprotonation and involvement in the binding of the backbone amide nitrogen in a beta-sheet like structure. This geometry does not induce strain in the peptide backbone, making it the most likely representation of that portion of the Cu2+-Abeta complex monomer in aqueous solution.

The complexes between the radical cation of dimethyl sulfide 2 and models for eight biologically available electron pair donors, :X (:X = H2O (2a), H2CO (2b), HC(O)NH2 (2c), HC(O)NHCH3 (2d), HCO2 - (2e), HCO3 - (2f), H2PO4 - (2g), and CH3NH2 (2h)), were optimized at the B3LYP/6-31G(d) level of theory. S∴X bond dissociation enthalpies (BDEs) were determined by single point calculations at the CBS−RAD level, a method designed for quantitative thermochemistry of free radicals. The effect of solvation was determined by application of a polarizable continuum model. Only the amine complex is predicted to be stable in water. H2O and H2PO4 - make transient complexes, and the remaining complexes are predicted to dissociate spontaneously. The dissociation is driven by entropy and conformationally constrained complexes are predicted to be stable in water. Reduction potentials, E°, accurate to ±0.1 V were calculated for the complexes with dimethyl sulfide and for the amino acid, methionine, both as an isolated amino acid and incorporated into a polypeptide at the N- and C-terminals and midchain. Stabilization of the radical cation of Met by three-electron bonding is predicted if an S∴N bond can be formed to a free amino group, as in N-terminal Met or a nearby Lys. Likewise, Met oxidation is facilitated by phosphodiesters, but not by carboxylate groups or amide groups. No lowering of E° is predicted for C-terminal Met or for midchain Met. The implications of the results for the redox chemistry associated with Alzheimer's disease are discussed.

The intrinsic factors governing the diastereofacial selectivity of 2-methyl-5-X-2-adamantyl cations (X = F (I(F)), Si(CH(3))(3) (I(Si))) toward a representative nucleophile, i.e., methanol, have been investigated in the gas phase at 750 Torr and in the 20-80 degrees C temperature range. The kinetic results indicate that CH(3)OH addition to I(F) proceeds through tight transition structures (TS(F)(syn) and TS(F)(anti)) characterized by advanced C-O bonding. The same interactions are much less pronounced in the comparatively loose transition structures involved in the CH(3)OH addition to I(Si) (TS(Si)(syn) and TS(Si)(anti)). The experimental evidence indicates that the activation barriers for the anti addition to I(F) and I(Si) are invariably lower than those for the syn attack. Large adverse entropic factors account for the preferred syn diastereoselectivity observed in the reaction with I(F). Entropy plays a minor role in the much looser transition structures involved in the reaction with I(Si), which instead exhibits a preferred anti diastereoselectivity. Comparison of the above gas-phase results with related theoretical and solution data suggests that the diastereofacial selectivity of I(F) and I(Si) measured in solution arises in part from the differential solvation of the two faces of the pyramidalized ions.

A systematic study of the binding affinities of the model biological ligands X: = (CH3)2S, CH3S-, CH3NH2, 4-CH3-imidazole (MeImid), C6H5O-, and CH3CO2- to (NH3)i(H2O)3-iCu(II)-H2O (i = 3, 2, 1, 0) complexes has been carried out using quantum chemical calculations. Geometries have been obtained at the B3LYP/ 6-31G(d) level of theory, and binding energies, Delta, relative to H2O as a ligand, have been calculated at the B3LYP/6-311+G(2df,2p)//B3LYP/6-31G(d) level. Solvation effects have been included using the COSMO model, and the relative binding free energies in aqueous solution (Delta) have been determined at pH 7 for processes that are pH dependent. CH3S- (Delta = -16.0 to -53.5 kJ mol(-1)) and MeImid (Delta = -18.5 to -35.2 kJ mol(-1)) give the largest binding affinities for Cu(II). PhO- and (CH3)2S are poor ligands for Cu(II), Delta = 20.6 to -9.7 and 19.8 to -3.7 kJ mol(-1), respectively. The binding affinities for CH3NH2 range from -0.8 to -15.0 kJ mol(-1). CH3CO2- has Cu(II) binding affinities in the ranges Delta = -13.5 to -32.4 kJ mol(-1) if an adjacent OH bond is available for hydrogen bonding and Delta = 10.1 to -4.6 kJ mol(-1) if this interaction is not present. In the context of copper coordination by the Abeta peptide of Alzheimer's disease, the binding affinities suggest preferential binding of Cu(II) to the three histidine residues plus a lysine or the N-terminus. For a 3N1O Cu(II) ligand arrangement, it is more probable that the oxygen ligand comes from an aspartate/glutamate residue side chain than from the tyrosine at position 10. Methionine appears unlikely to be a Cu(II) ligand in Abeta.