Supramolecular assembly of strongly chemisorbed size- and shape-defined chiral clusters: S- and R-alanine on Cu(110)

The bonding and self-assembly of a chirally organized monolayer of alanine on the Cu(110) surface has been investigated using reflection-absorption infrared spectroscopy, low-energy electron diffraction (LEED), and scanning tunneling microscopy (STM). This multitechnique approach has enabled an in-depth understanding of the hierarchy of chirality transfer: from a single adsorbed molecule, to size-defined chiral clusters, and then to an overall chiral assembly. The data have indicated that the alanine is in its anionic form, bound to the copper surface through the oxygens of the ionized carboxylate group and the nitrogen of the neutral amino group. Importantly, the methyl group is held away from the surface, resulting in direct chirality transfer into the footprint of the adsorbed alanine molecules, with the local adsorption motif for S-alanine being the mirror image of that created for R-alanine. STM has shown that S-alanine molecules self-organize to form size-defined chiral clusters of six or eight molecules at the surface, interspersed with chiral channels of bare metal. Together, these clusters and channels further self-assemble into a chiral array with one unique chiral domain sustained across the entire surface. A similar chiral assembly, but with the mirror organization, has been observed for R-alanine. Structural models for the individual clusters are proposed, and in conjunction with LEED data, overall models for these chiral phases of both S- and R-alanine have been constructed. Overall, this adsorption system has been found to be both strongly chemisorbed and capable of extensive intermolecular H-bonding, causing stresses that lead not only to the chiral self-organization of molecules but also to a specific self-organization of the empty chiral channels and spaces that intersperse the structure which, in turn, chirally assemble across macroscopic length scales to give a surface with global organizational chirality.     

Determination of sugar structures in solution from residual dipolar coupling constants: methodology and application to methyl beta-D-xylopyranoside

We have developed methodology for the determination of solution structures of small molecules from residual dipolar coupling constants measured in dilute liquid crystals. The power of the new technique is demonstrated by the determination of the structure of methyl beta-d-xylopyranoside (I) in solution. An oriented sample of I was prepared using a mixture of C(12)E(5) and hexanol in D(2)O. Thirty residual dipolar coupling constants, ranging from -6.44 to 4.99 Hz, were measured using intensity-based J-modulated NMR techniques. These include 15 D(HH), 4 (1)D(CH), and 11 (n)D(CH) coupling constants. The accuracy of the dipolar coupling constants is estimated to be < +/- 0.02 Hz. New constant-time HMBC NMR experiments were developed for the measurement of (n)D(CH) coupling constants, the use of which was crucial for the successful structure determination of I, as they allowed us to increase the number of fitted parameters. The structure of I was refined using a model in which the directly bonded interatom distances were fixed at their ab initio values, while 16 geometrical and 5 order parameters were optimized. These included 2 CCC and 6 CCH angles, and 2 CCCC and 6 CCCH dihedral angles. Vibrationally averaged dipolar coupling constants were used during the refinement. The refined solution structure of I is very similar to that obtained by ab initio calculations, with 11 bond and dihedral angles differing by 0.8 degrees or less and the remaining 5 parameters differing by up to 3.3 degrees . Comparison with the neutron diffraction structure showed larger differences attributable to crystal packing effects. Reducing the degree of order by using dilute liquid crystalline media in combination with precise measurement of small residual dipolar coupling constants, as shown here, is a way of overcoming the limitation of strongly orienting liquid crystals associated with the complexity of (1)H NMR spectra for molecules with more than 12 protons.     

Hydroxyl radical is the active species in photochemical DNA strand scission by bis(peroxo)vanadium(V) phenanthroline

Bis(peroxo)vanadium(V) complexes are widely investigated as anticancer agents. They exert their antitumor and cyctotoxic effects through inhibition of tyrosine phosphatases and DNA cleavage, respectively. The latter process remains poorly understood. The mechanism of DNA cleavage by NH(4)[(phen)V(O)(eta(2)-O(2))(2)] (phen = 1,10-phenanthroline) was investigated. Kinetic studies on DNA cleavage revealed that the complex is a single-strand nicking agent with no specificity. EPR experiments using 2,2,6,6-tetramethyl-4-piperidone (TMP) and 5,5'-dimethyl-1-pyrroline-N-oxide (DMPO) as spin-traps for singlet oxygen and hydroxyl radical, respectively, implicated hydroxyl radical production upon photodecomposition of bis(peroxo)vanadium(V). This was corroborated by benzoate inhibition of DNA strand scission and stoichiometric oxidation of 2-propanol to acetone upon irradiation of bis(peroxo)vanadium(V) phenanthroline. High-resolution polyacrylamide gel analysis of the vanadium cleavage reaction and [Fe(II)EDTA](2)(-)/H(2)O(2) resulted in comigration of "ladder" pattern bands, which superimposed when both reactions were run on the same lane. These findings identify hydroxyl radical produced from the photooxidation of the peroxo ligand on vanadium as the active species in DNA cleavage.     

Plutonium Isotopes in Sediments from the Sudanese Coast of the Red Sea

This paper presents the activity concentrations of Pu isotopes in surface marine sediments collected from the Sudanese coast of the Red Sea. The following concentration ranges were determined: ²³⁸Pu, 4.7–28.6 mBq/kg; ^239+240Pu, 53–343 mBq/kg dry weight. The average activity ratios of ²³⁸Pu/^239+240Pu (0.075±0.045 mBqk/kg) and ^239+240Pu/¹³⁷Cs (0.026±0.025 mBq/kg) are appropriately comparable to the literature values that are characteristic of the global fallout from the atmospheric nuclear weapon tests. However, ^239+240Pu/¹³⁷Cs ratio in sediments collected from the biologically rich fringing reef is an order of magnitude higher compared to other sampling locations.     

Selection of aptamers for signal transduction proteins by capillary electrophoresis

High‐affinity aptamers for important signal transduction proteins, i.e. Cdc42‐GTP, p21‐activated kinase1 (PAK1) and MRCK (myotonic dystrophy kinase‐related Cdc42‐binding kinase) α were successfully selected in the low micro‐ to nanomolar range using non‐systematic evolution of ligands by exponential enrichment (SELEX) with at least three orders of magnitude enhancement from their respective bulk affinity of naïve DNA library. In the non‐SELEX procedure, CE was used as a highly efficient affinity method to select aptamers for the desired molecular target through a process that involved repetitive steps of partitioning, known as non‐equilibrium CE of equilibrium mixtures with no PCR amplification between successive steps. Various non‐SELEX conditions including the type, concentration and pH of the run buffer were optimized. Other considerations such as salt composition of selection buffer, protein concentration and sample injection size were also studied for high stringency during selection. After identifying the best enriched aptamer pool, randomly selected clones from the aptamer pool were sequenced to obtain the individual DNA sequences. The dissociation constants (K_d) of these sequences were in the low micromolar to nanomolar range, indicating high affinity to the respective proteins. The best binders were also subjected to sequence alignment to generate a phylogenetic tree. No significant consensus region based on approximately 50 sequences for each protein was observed, suggesting the high efficiency of non‐SELEX for the selection of numerous unique sequences with high selectivity.     

Steric factors override thermodynamic driving force in regioselectivity of proline hydroxylation by prolyl-4-hydroxylase enzymes

Prolyl-4-hydroxylase is an important nonheme iron-containing dioxygenase in humans involved in the regioselective hydroxylation of a proline residue in a peptide chain on the C(4) position. In biosystems this process is important to create collagen cross-linking and cellular responses to hypoxia. We have performed a series of density functional theory (DFT) studies into the origin of the regioselectivity of proline hydroxylation by P4H enzymes using a minimal active site model (where substrate is unhindered in the binding site) and a larger active site model that incorporates steric hindrance of the substrate by several secondary sphere aromatic residues. Our studies show that thermodynamically the most favorable hydrogen atom abstraction position of proline is from the C(5) position; hence, the small model gives a low reaction barrier and large exothermicity for this process. However, stereochemical repulsions of the substrate with aromatic residues of Tyr(140) and Trp(243) in the second coordination sphere prevent C(5) hydroxylation and make C(4) hydroxylation the dominant mechanism, despite a lesser driving force for the reaction. These studies explain the remarkable regioselectivity of proline hydroxylation by P4H enzymes and show that the regioselectivity is kinetically controlled but not thermodynamically. In addition, we calculated spectroscopic parameters and found good agreement with experimental data.     

Silylene extrusion from organosilanes via double geminal Si-H bond activation by a Cp*Ru(kappa2-P,N)+ complex: observation of a key stoichiometric step in the glaser-tilley alkene hydrosilylation mechanism

Treatment of Cp*RuCl(kappa2-P,N-2b) (2b = 2-NMe2-3-PiPr2-indene) with TlSO3CF3 produced the cyclometalated complex [4]+SO3CF3- in 94% isolated yield. Exposure of [4]+X- (X = B(C6F5)4 or SO3CF3) to Ph2SiH2 (10 equiv) or PhSiH3 afforded the corresponding [Cp*(mu-P,N-2b)(H)2Ru=SiRPh]+X- complexes, [5]+X- (R = Ph; X = B(C6F5)4, 82%; X = SO3CF3, 39%) and [6]+X- (R = H; X = B(C6F5)4, 94%; X = SO3CF3, 95%). Notably, these transformations represent the first documented examples of Ru-mediated silylene extrusion via double geminal Si-H bond activation of an organosilane-a key step in the recently proposed Glaser-Tilley (G-T) alkene hydrosilylation mechanism. Treatment of [5]+B(C6F5)4- with KN(SiMe3)2 or [6]+SO3CF3- with NaN(SiMe3)2 afforded the corresponding zwitterionic Cp*(mu-2-NMe2-3-PiPr2-indenide)(H)2Ru=SiRPh complex in 69% (R = Ph, 7) or 86% (R = H, 8) isolated yield. Both [6]+X- and 8 proved unreactive toward 1-hexene and styrene and provided negligible catalytic turnover in the attempted metal-mediated hydrosilylation of these substrates with PhSiH3, thereby providing further empirical evidence for the required intermediacy of base-free Ru=Si species in the G-T mechanism. Isomerization of the P,N-indene ligand backbone in [6]+X-, giving rise to [Cp*(mu-1-PiPr2-2-NMe2-indene)(H)2Ru=SiHPh]+X- ([9]+X-), was observed. In the case of [9]+SO3CF3-, net intramolecular addition of the Ru=Si-H group across the styrene-like C=C unit within the ligand backbone to give 10 (96% isolated yield) was observed. Crystallographic characterization data are provided for [4]+X-, [5]+X-, [6]+X-, 8, and 10.     

Synthesis of monofluorinated 1-(naphthalen-1-yl)piperazines

A series of regioisomerically monofluorinated 1-(naphthalen-1-yl)piperazines is described.