One of the many hypotheses on the pathogenesis of Alzheimer's disease is that the amyloid-beta peptide (A beta) binds Cu(II) and can catalytically generate H(2)O(2), leading to oxidative damage in brain tissues. For a molecular level understanding of such catalysis it is critical to know the structure of the A beta-Cu(II) complex precisely. Unfortunately, no high-resolution structure is available to date and there is considerable debate over the copper coordination environment with no clear consensus on which residues are directly bound to Cu(II). Considering all plausible isomers of the copper-bound A beta 42 and A beta 40 using a combination of density functional theory and classical molecular dynamics methods, we report an atomic resolution structure for each possible complex. We evaluated the relative energies of these isomeric structures and surprisingly found that A beta 42 and A beta 40 display very different binding modes, suggesting that shorter peptides that are truncated at the C-terminus may not be realistic models for understanding the chemistry of the most neurotoxic peptide, A beta 42.