A study has been made of the structures and stabilities of copper and gold clusters and copper–gold nanoalloy clusters, with up to 56 atoms, modeled by the many-body Gupta potential. For pure copper clusters, the lowest energy structures are found to be based on icosahedral packing, while pure gold clusters tend to form less symmetrical (often amorphous) structures. In a number of cases, the replacement of a single gold atom by copper is found to be sufficient to convert the structure to that of the more symmetrical copper cluster. The lowest energy clusters are generally more difficult to find for the bimetallic clusters than for the pure metallic clusters, due to the presence of homotops (related by permuting Cu and Au atoms), as well as geometrical isomers. The structures of the lowest energy bimetallic clusters exhibit primarily icosahedral packing, with (CuAu)M and (CuAu3)M clusters tending to form layered structures and (Cu3Au)M clusters showing greater Cu–Au mixing.

The stabilities of all possible purine/pyrimidine pairings between the isomeric nucleobases isocytosine (iso-C) and isoguanine (iso-G) and standard genomic bases are reported for two independent oligonucleotide duplexes. Additionally, results are given from ab initio calculations performed on iso-C and iso-G. The calculations are used as an aid in the interpretation of thermodynamic data obtained from duplex denaturation studies. The unnatural iso-C/iso-G pair is found to be as stable as a C/G Watson-Crick pair in both duplex systems. The next most stable unnatural pair is that formed by C/iso-G and is observed to be isoenergetic with a U/A Watson-Crick pair. Ab initio data suggest iso-G may adopt an unprecedented imino oxo tautomer which could explain the unusual stability of the C/iso-G pair. The stability of the other possible unnatural pairs are reported and similarly interpreted in terms of ab initio and other available experimental data. Finally, the fitness is discussed of a six-component genetic system that includes iso-C, iso-G, and four standard genomic bases.

The application of a genetic algorithm, for optimizing the geometries of stoichiometric and non-stoichiometric MgO clusters, bound by a simple Coulomb-plus-BornÀMayer potential, is investigated. The genetic algorithm is shown to be ecient and reliable for ®nding, reproducibly the global minima for these clusters. The variation of the structures of MgO clusters are investigated as a function of the formal charges (q) on the ionsÐranging from q 1 to q 2. In agreement with previous studies, lower charges are found to favour compact, rocksalt-like cuboidal clusters, while the higher formal charges favour hollow pseudo-spherical structures. Hexagonal stacks are also found to be stable for small (MgO) N clusters with N 3n. Comparisons are made with experimental mass spectral abundances and the results of previous empirical calculations, as well as with more sophisticated model potential and ab initio calculations. Finally, possible ways in which the genetic algorithm search method could be coupled with more accurate calculation methods are discussed.

The growth, surface composition, and chemical activity of bimetallic Pt-Au clusters on TiO 2 (110) have been investigated. Scanning tunneling microscopy (STM) experiments demonstrate that the deposition of Au on Pt clusters results in the formation of bimetallic Pt-Au clusters due to the seeding of the mobile Au atoms at existing Pt nuclei. The composition of the top surface layer of the clusters was studied by low energy ion scattering (LEIS) for bulk compositions ranging from 25%-87.5% Pt with total metal coverages of 0.25 and 0.50 ML. For both coverages, the cluster surfaces consisted of nearly pure Au at Pt compositions of 50% and lower; however, a mix of Au and Pt atoms were found at the cluster surfaces at higher fractions of deposited Pt. These results are consistent with bulk thermodynamics, which predicts a Pt core-Au shell structure based on the lower surface free energy of Au compared to Pt and the large bulk miscibility gap for the two metals. The adsorption of CO on the Pt-Au clusters at room temperature promotes the diffusion of Pt to the surface of the clusters, and this phenomena is most pronounced for the clusters that are initially pure Au at the surface. Density functional theory calculations demonstrate that it is thermodynamically favorable for Pt to diffuse to the cluster surface in order to bind to CO. In contrast, the extent of CO 2 production via sequential adsorption of O 2 and CO on the Pt-Au clusters reflects the surface Pt content before adsorption. For CO oxidation, the first step in the reaction is the dissociation of O 2 at Pt sites. Since this process requires more than one contiguous Pt site, it is not surprising that O 2 dissociation cannot occur on the Pt-Au clusters that are ∼100% Au at the surface before CO exposure, given the low probability for ensembles of Pt sites to form at the surface.

The questions of whether different tautomeric forms of nucleic acid bases exist to any significant extent in DNA, or what their possible roles in mutation may be, are under intense scrutiny. 2'-Deoxyisoguanosine (iG) has been suggested to have a propensity to adopt the enol form. Isoguanine (also called 2-hydroxyadenine) can be found in oxidatively damaged DNA generated from treating DNA with a Fenton-type reactive oxygen-generating system and is known to cause mutation. We have analyzed the three-dimensional structure of the DNA dodecamer d(CGC[iG]AATTTGCG) (denoted iG-DODE) by X-ray crystallography and NMR. The crystal structure of the iG-DODE complexed with the minor groove binder Hoechst 33342, refined to 1.4 A resolution, showed that the two independent iG.T base pairs in the dodecamer duplex adopt different (one in Watson-Crick and the other in wobble) conformations. The high-resolution nature of the structure also affords unprecedented clear information about the conformation and interactions of the Hoechst drug. The Hoechst 33342 binds in the narrow minor groove at the iGAATT site, with the N-methylpiperazine ring near the iG4.T21 base pair. Three hydrogen bonds are found between the NH of the Hoechst ligand and T-O2 DNA atoms. In solution, the two iG.T base pairs in iG-DODE predominantly are in the wobble form at 2 degreesC. At higher temperatures, another duplex form (likely involving the enol form of iG) is in slow exchange with the keto form and becomes significantly populated, reaching approximately 40% at 40 degreesC. Our data support the conclusion that iG pairs with T in a Watson-Crick configuration to a significant extent at physiological temperature (37 degreesC), which may explain the facile incorporation rate of T across from an iG during in vitro DNA replication.