Density functional theory study of nine-atom germanium clusters: effect of electron count on cluster geometry

Density functional theory (DFT) at the hybrid B3LYP level has been applied to the germanium clusters Ge(9)(z) clusters (z = -6, -4, -3, -2, 0, +2, and +4) starting from three different initial configurations. Double-zeta quality LANL2DZ basis functions extended by adding one set of polarization (d) and one set of diffuse (p) functions were used. The global minimum for Ge(9)(2)(-) is the tricapped trigonal prism expected by Wade's rules for a 2n + 2 skeletal electron structure. An elongated tricapped trigonal prism is the global minimum for Ge(9)(4)(-) similar to the experimentally found structure for the isoelectronic Bi(9)(5+). However, the capped square antiprism predicted by Wade's rules for a 2n + 4 skeletal electron structure is only 0.21 kcal/mol above this global minimum indicating that these two nine-vertex polyhedra have very similar energies in this system. Tricapped trigonal prismatic structures are found for both singlet and triplet Ge(9)(6)(-), with the latter being lower in energy by 3.66 kcal/mol and far less distorted. The global minimum for the hypoelectronic Ge(9) is a bicapped pentagonal bipyramid. However, a second structure for Ge(9) only 4.54 kcal/mol above this global minimum is the C(2)(v)() flattened tricapped trigonal prism structure found experimentally for the isoelectronic Tl(9)(9)(-). For the even more hypoelectronic Ge(9)(2+), the lowest energy structure consists of an octahedron fused to two trigonal bipyramids. For Ge(9)(4+), the global minimum is an oblate (squashed) pentagonal bipyramid with two pendant Ge vertices.     

Quantitative analysis of the low molecular weight serum proteome using 18O stable isotope labeling in a lung tumor xenograft mouse model

With advancements in the analytical technologies and methodologies in proteomics, there is great interest in biomarker discovery in biofluids such as serum and plasma. Current hypotheses suggest that the low molecular weight (LMW) serum proteome possesses an archive of clipped and cleaved protein fragments that may provide insight into disease development. Though these biofluids represent attractive samples from which new and more accurate disease biomarkers may be found, the intrinsic person-to-person variability in these samples complicates their discovery. Mice are one of the most extensively used animal models for studying human disease because they represent a highly controllable experimental model system. In this study, the LMW serum proteome was compared between xenografted tumor-bearing mice and control mice by differential labeling utilizing trypsin-mediated incorporation of the stable isotope of oxygen, 18O. The digestates were combined, fractionated by strong cation exchange chromatography, and analyzed by nanoflow reversed-phase liquid chromatography coupled online with tandem mass spectrometry, resulting in the identification of 6003 proteins identified by at least a single, fully tryptic peptide. Almost 1650 proteins were identified and quantitated by two or more fully tryptic peptides. The methodology adopted in this work provides the means for future quantitative measurements in comparative animal models of disease and in human disease cohorts.     

Cyclopentadienyl ruthenium, rhodium, and iridium vertices in metallaboranes: geometry and chemical bonding

Most cyclopentadienylmetallaboranes containing the vertex units CpM (M = Co, Rh, Ir; Cp = eta(5)-cyclopentadienyl ring, mainly eta(5)-Me(5)C(5)) and CpRu donating two and one skeletal electrons, respectively, have structures closely related to binary boranes or borane anions. Smaller clusters of this type, such as metallaborane analogues of arachno-B(4)H(10) (e.g., (CpIr)(2)B(2)H(8)), nido-B(5)H(9) (e.g., (CpRh)(2)B(3)H(7) and (CpRu)(2)B(3)H(9)), arachno-B(5)H(11) (e.g., CpIrB(4)H(10)), B(6)H(6)(2)(-) (e.g., (CpCo)(4)B(2)H(4)), nido-B(6)H(10) (e.g., CpIrB(5)H(9) and (CpRu)(2)B(4)H(10)), and arachno-B(6)H(12) (e.g., (CpIr)(2)B(4)H(10)), have the same skeletal electron counts as those of the corresponding boranes. However, such clusters with eight or more vertices, such as metallaborane analogues of B(8)H(8)(2)(-) (e.g., (CpCo)(4)B(4)H(4)), arachno-B(8)H(14) (e.g., (CpRu)(2)B(6)H(12)), and nido-B(10)H(14) (e.g., (CpRu)(2)B(8)H(12)), have two skeletal electrons less than those of the corresponding metal-free boranes, analogous to the skeletal electron counts of isocloso boranes relative to those of metal-free deltahedral boranes. Some metallaboranes have structures not analogous to metal-free boranes but instead analogous to metal carbonyl clusters such as 3-capped square pyramidal (CpRu)(2)B(4)H(8) and (CpRu)(3)B(3)H(8) analogous to H(2)Os(6)(CO)(16) and capped octahedral (CpRh)(3)B(4)H(4) analogous to Os(7)(CO)(21). In the metallaborane structures closely related to metal-free boranes, the favored degrees of BH and CpM vertices appear to be 5 and 6, respectively.