1H NMR studies of nickel(II) complexes bound to oligonucleotides: a novel technique for distinguishing the binding locations of metal complexes in DNA

The selective paramagnetic relaxation of oligonucleotide proton resonances of d(GTCGAC)(2) and d(GTGCAC)(2) by Ni(phen)(2)(L)(2+) where L = dipyridophenazine (dppz), dipyrido[3,2-d:2',3'-f]quinoxaline (dpq), and phenanthrenequinone (phi) has been examined to obtain structural insight into the noncovalent binding of these metal complexes to DNA. In the oligonucleotide d(GTCGAC)(2), preferential broadening of the G1H8, G4H8, T2H6, and C3H6 proton resonances was observed with Ni(phen)(2)(dppz)(2+), Ni(phen)(2)(dpq)(2+), and Ni(phen)(2)(phi)(2+). In the case of the sequence d(GTGCAC)(2), where the central two bases are juxtaposed from the previous one, preferential broadening was observed instead for the A5H2 proton resonance. Thus, a subtle change in the sequence of the oligonucleotide can cause significant change in the binding location of the metal complex in the oligonucleotide. Owing to comparable changes for all metal complexes and sequences in broadening of the thymine methyl proton resonances, we attribute the switch in preferential broadening to a change in site location within the oligomer rather than to an alteration of groove location. Therefore, even for DNA-binding complexes of low sequence-specificity, distinct variations in binding as a function of sequence are apparent.     

A coupled reference interaction site model/molecular dynamics study of the potential of mean force curve of the SN2 Cl- + CH3Cl reaction in water

An application of the coupled reference interaction site model (RISM)/simulation methodology to the calculation of the potential of mean force (PMF) curve in aqueous solution for the identity nucleophilic substitution reaction Cl(-) + CH(3)Cl is performed. The free energy of activation is calculated to be 27.1 kcal/mol which compares very well with the experimentally determined barrier height of 26.6 kcal/mol. Furthermore, the calculated PMF is almost superimposed with that previously calculated using the computationally rigorous Monte Carlo with importance sampling method (Chandrasekhar, J.; Smith, S. F.; Jorgensen, W. L. J. Am. Chem. Soc. 1985, 107, 154). Using the calculated PMF, a crude estimate of the solvated kinetic transmission coefficient also compares well with that of previous more accurate simulations. These results indicate that the coupled RISM/simulation method provides a cost-effective methodology for studying reactions in solution.     

Electrostatic contributions to indole-lipid interactions

The role of electrostatic forces in indole-lipid interactions was studied by (1)H and (2)H NMR in ether- and ester-linked phospholipid bilayers with incorporated indole. Indole-ring-current-induced (1)H NMR chemical shifts of lipid resonances in bilayers of 1-palmitoyl-2-oleoyl-sn-glycero-3-phosphocholine, 1,2-dioleoyl-sn-glycero-3-phosphocholine, 1,2-di-O-octadecenyl-sn-glycero-3-phosphocholine, and 1,2-di-O-octadecenyl-sn-glycero-3-phosphomethanol show a bimodal indole distribution, with indole residing at the upper hydrocarbon chain/glycerol region of the lipid and near the choline group, when present. (2)H NMR of indole-d(7)-incorporated lipid bilayers reveals that the former site is occupied by about two-thirds of the indole, which adopts a distinct preferred orientation with respect to the bilayer normal. The results suggest that the upper hydrocarbon chain/glycerol location is dictated by many factors, including interactions with the electric charges and dipoles, van der Waals interactions, entropic contributions, and hydrogen bonding. Indole diffusion rates are higher in lipids with ester bonds and lower in choline-containing lipids, suggesting that interactions between indole and carbonyl groups are of minor importance for lipid-indole association and that cation-pi interactions with choline drive the second indole location. Nuclear Overhauser effect spectroscopy cross-relaxation rates suggest a 30-ns lifetime for indole-lipid associations. These results may have important implications for sidedness and structural transitions in tryptophan-rich membrane proteins.     

The reactive chemisorption of alkyl iodides at Cu(110) and Ag(111) surfaces: a combined STM and XPS study

The chemisorption of methyl and phenyl iodide has been studied at Cu(110) and Ag(111) surfaces at 290 K with STM and XPS. At both surfaces dissociative adsorption of both molecules leads to chemisorbed iodine, with the STM showing c(2 x 2) and (square root 3 x square root 3)R30 structures at the Cu(110) and Ag(111) surfaces, respectively. At the Cu(110) surface a comparison of coexisting c(2 x 2) I(a) and p(2 x 1) O(a) domains shows the iodine adatoms to be chemisorbed in hollow sites with evidence at low coverage for diffusion in the (110) direction. In the case of methyl iodide no carbon adsorption is observed at either the silver or the copper surfaces, but chemisorbed phenyl groups are imaged at the Cu(110) surface after exposure to phenyl iodide. The STM images show the phenyl groups as bright features approximately 0.7 nm in diameter and 0.11 nm above the iodine adlayer, reaching a maximum surface concentration after approximately 6 Langmuir exposure. However, the phenyl coverage decreases with subsequent exposures to PhI and is negligible by approximately 1000 L exposure, consistent with the formation and desorption of biphenyl. The adsorbed phenyls are located above hollow sites in the substrate, they are stabilized at the top and bottom of step edges and in paired chains (1.1 nm apart) on the terraces with a regular interphenyl spacing within the chains of 1.0 nm in the (110) direction. The interphenyl ring spacing and diffusion of individual phenyls from within the chains shows that the chains do not consist of biphenyl species but may be a precursor to their formation. Although the XPS data shows carbon present at the Ag(111) surface after exposure to PhI, no features attributable to phenyl groups were observed by STM.     

Structure of ethnic violence in Sudan: a semi-automated network analysis of online news (2003–2010)

Mining textual sources of data can be used to design studies and test theories at temporal and spatial scales unheard of in the past. This opens up new opportunities for conflict studies and ethnographic research. We conducted a semi-automated network analysis of the 2003–2010 Sudan Tribune online news articles and modeled ethnic-group conflict in Sudan. We tested whether an ethnic group’s connections to the environment (livestock, biomes, and other resources) and other ethnic groups was associated with severe conflict and peace terms and whether ethnic-group richness at a given geospatial location was associated with severe conflict. Ethnic groups with more connections to livestock, environmental resources, and those ethnic groups with denser environmental–resource networks in their sphere of influence had more co-occurrences with severe conflict terms. Ethnic groups that had more connections to biomes in their sphere of influence were co-associated with peace terms. Locations that had high ethnic-group richness were associated with a higher frequency of severe conflict terms.     

Measuring CMOT’s intellectual structure and its development

Computational Organization Theory is often described as a multidisciplinary and fast-moving field which can make it difficult to keep track of it. The recent inclusion of Computational and Mathematical Organization Theory (CMOT) into the Social Science Citation Index offers a good reason to take stock of what has happened since the foundation of the journal and to analyze its intellectual structure and development from 1995 to 2008. We identify the most influential publications by means of citation analysis and show that a core of codified knowledge has developed over time. Additionally, we provide empirical support for the characteristics generally ascribed to the journal such as multidisciplinarity. Finally, we depict the main research foci in CMOT’s intellectual structure employing a co-citation analysis of publications and investigate their development over time. Overall, our quantitative review shows CMOT to be thematically focused on organizations, groups and networks while being remarkably diverse in terms of theoretical approaches and methods used.     

Proton spin-spin relaxation study of hydration of a model nanopore

The hydration pattern of controlled pore glass, with pore diameter of 237 Å, was investigated using nuclear magnetic resonance. Water proton spin–spin relaxation decay curves were monitored and modeled as two-component exponential decays as a function of hydration. The results are consistent with a geometric model involving a surface water layer and a bulk-like liquid fraction in the form of a plug. The amount of surface water increases as the sample hydrates, until hydration reached approximately a monolayer, at which point a water plug starts to form in the pore, and grow in length at the expense of the surface layer. The results are also analyzed in terms of, and compared to, a recently developed puddle pore-filling model [S.G. Allen, et al. J. Chem. Phys. 106 (1997) 7802–7809].