Ligand-receptor interactions in chains of colloids: when reactions are limited by rotational diffusion

We discuss the theory of ligand receptor reactions between two freely rotating colloids in close proximity to one other. Such reactions, limited by rotational diffusion, arise in magnetic bead suspensions where the beads are driven into close contact by an applied magnetic field as they align in chainlike structures. By a combination of reaction-diffusion theory, numerical simulations, and heuristic arguments, we compute the time required for a reaction to occur in a number of experimentally relevant situations. We find in all cases that the time required for a reaction to occur is larger than the characteristic rotation time of the diffusion motion tau(rot). When the colloids carry one ligand only and a number n of receptors, we find that the reaction time is, in units of tau(rot), a function simply of n and of the relative surface alpha occupied by one reaction patch alpha = pirC2/(4pir2), where rC is the ligand receptor capture radius and r is the radius of the colloid.     

Surface chemistry of Cu in the presence of CO2 and H2O

The chemical nature of copper and copper oxide (Cu 2O) surfaces in the presence of CO 2 and H 2O at room temperature was investigated using ambient pressure X-ray photoelectron spectroscopy. The studies reveal that in the presence of 0.1 torr CO 2 several species form on the initially clean Cu, including carbonate CO 3 (2) (-), CO 2 (delta-) and C (0), while no modifications occur on an oxidized surface. The addition of 0.1 ML Zn to the Cu results in the complete conversion of CO 2 (delta-) to carbonate. In a mixture of 0.1 torr H 2O and 0.1 torr CO 2, new species are formed, including hydroxyl, formate and methoxy, with H 2O providing the hydrogen needed for the formation of hydrogenated species.     

The first silicon-based cationic clathrate III with high thermal stability: Si172-xPxTey (x=2y, y>20)

A new representative of a very rare clathrate III family, Si130P42Te21, has been synthesized from the elements. It crystallizes in the tetragonal space group P4(2)/mnm (no. 136) with the unit cell parameters a=19.2632(3) angstroms, c=10.0706(2) angstroms. Single crystal X-ray diffraction and solid state 31P NMR revealed a non-random distribution of phosphorus atoms over the framework positions. The crystal structure features a peculiar packing of large polyhedra Te@(Si/P)(n) never observed before for cationic clathrates. Despite the structural complexity, the composition of the novel clathrate Is in accordance with the Zintl rule, which was confirmed by a combination of optical metallography, scanning electron microscopy (SEM) and wavelength dispersive X-ray spectroscopy (WDXS), as well as by diamagnetic and semiconducting behavior of the synthesized phase. Clathrate Si130P42Te21 exhibits the highest reported thermal stability for this class of materials, it decomposes at 1510 K. This opens new perspectives for the creation of clathrate-based materials for high-temperature applications.     

Role of backbone-solvent interactions in determining conformational equilibria of intrinsically disordered proteins

Intrinsically disordered proteins (IDPs) are functional proteins that do not fold into well-defined three-dimensional structures under physiological conditions. IDP sequences have low hydrophobicity, and hence, recent experiments have focused on quantitative studies of conformational ensembles of archetypal IDP sequences such as polyglutamine and glycine-serine block copolypeptides. Results from these experiments show that, despite the absence of hydrophobic residues, polar IDPs prefer ensembles of collapsed structures in aqueous milieus. Do these preferences originate in interactions that are unique to polar sidechains? The current study addresses this issue by analyzing conformational equilibria for polyglycine and a glycine-serine block copolypeptide in two environments, namely, water and 8 M urea. Polyglycine, a poly secondary-amide, has no sidechains and is a useful model system for generic polypeptide backbones. Results based on large-scale molecular dynamics simulations show that polyglycine forms compact, albeit disordered, globules in water and swollen, disordered coils in 8 M urea. There is minimal overlap between conformational ensembles in the two environments. Analysis of order parameters derived from theories for flexible polymers show that water at ambient temperatures is a poor solvent for generic polypeptide backbones. Therefore, the experimentally observed preferences for polyglutamine and glycine-serine block copolypeptides must originate, at least partially, in polypeptide backbones. A preliminary analysis of the driving forces that lead to distinct conformational preferences for polyglycine in two different environments is presented. Implications for describing conformational ensembles of generic IDP sequences are also discussed.     

Ab initio modeling of protein/biomaterial interactions: glycine adsorption at hydroxyapatite surfaces

How does glycine adsorb at hydroxyapatite surfaces? Ab initio simulations based on periodic B3LYP GTO calculations reveal the detailed mechanism of binding to the (001) and (010) surfaces by shedding light on how acid and basic amino acid residues of proteins interact with hydroxyapatite based biomaterials.     

Total synthesis and biological mode of action of largazole: a potent class I histone deacetylase inhibitor

The efficient total synthesis of the recently described natural substance largazole (1) and its active metabolite largazole thiol (2) is described. The synthesis required eight linear steps and proceeded in 37% overall yield. It is demonstrated that largazole is a pro-drug that is activated by removal of the octanoyl residue from the 3-hydroxy-7-mercaptohept-4-enoic acid moiety to generate the active metabolite 2, which is an extraordinarily potent Class I histone deacetylase inhibitor. Synthetic largazole and 2 have been evaluated side-by-side with FK228 and SAHA for inhibition of HDACs 1, 2, 3, and 6. Largazole and largazole thiol were further assayed for cytotoxic activity against a panel of chemoresistant melanoma cell lines, and it was found that largazole is substantially more cytotoxic than largazole thiol; this difference is attributed to differences in the cell permeability of the two substances.     

Chemical vapor discrimination using a compact and low-power array of piezoresistive microcantilevers

A compact and low-power microcantilever-based sensor array has been developed and used to detect various chemical vapor analytes. In contrast to earlier micro-electro-mechanical systems (MEMS) array sensors, this device uses the static deflection of piezoresistive cantilevers due to the swelling of glassy polyolefin coatings during sorption of chemical vapors. To maximize the sensor response to a variety of chemical analytes, the polymers are selected based on their Hildebrand solubility parameters to span a wide range of chemical properties. We utilize a novel microcontact spotting method to reproducibly coat a single side of each cantilever in the array with the polymers. To demonstrate the utility of the sensor array we have reproducibly detected 11 chemical vapors, representing a breadth of chemical properties, in real time and over a wide range of vapor concentrations. We also report the detection of the chemical warfare agents (CWAs) VX and sulfur mustard (HD), representing the first published report of CWA vapor detection by a polymer-based, cantilever sensor array. Comparisons of the theoretical polymer/vapor partition coefficient to the experimental cantilever deflection responses show that, while general trends can be reasonably predicted, a simple linear relationship does not exist.     

New ruthenium(II) complexes with enantiomerically pure bis- and tris(pinene)-fused tridentate ligands. Synthesis, characterization and stereoisomeric analysis

A new set of Ru-Cl complexes containing either the pinene[5,6]bpea ligand (L1) or the C3 symmetric pinene[4,5]tpmOMe (L2) tridentate ligand in combination with the bidentate (B) 2,2'-bipyridine (bpy) or 1,2-diphenylphosphinoethane (dppe) with general formula [RuCl(L1 or L2)(B)](+) have been prepared and thoroughly characterized. In the solid state, X-ray diffraction analysis techniques have been used. In solution, cyclic voltammetry (CV) and 1D and 2D NMR spectroscopy have been employed. DFT calculations have been also performed on these complexes and their achiral analogues previously reported in our group, to interpret and complement experimental results. Whereas isomerically pure complexes ([Ru(II)Cl(L2)(bpy)](BF4), 5 and [Ru(II)Cl(L2)(dppe)](BF4), 6) are obtained when starting from the highly symmetric [Ru(III)Cl3(L2)], 2, isomeric mixtures of cis, fac-[Ru(II)Cl(L1)(bpy)](BF4) (3b/3b'), trans,fac- (3a) and up/down,mer- (3c, 3d) isomers are formed when bpy is added to the less symmetric [Ru(III)Cl3(L1)], 1, in contrast to the case of the bulky dppe ligand that, upon coordination to 1, leads to the trans,fac-[Ru(II)Cl(L1)(dppe)](BF4) (4a) complex as a sole isomer due to steric factors.     

Effects of surface passivation on the exciton dynamics of CdSe nanocrystals as observed by ultrafast fluorescence upconversion spectroscopy

The exciton dynamics of CdSe nanocrystals are intimately linked to the surface morphology. Photo-oxidation of the selenium surfaces of the nanocrystal leads to an increase in radiative decay efficiency from both the band edge and deep trap emission states. The addition of the primary amine hexadecylamine curtails nonradiative excitonic decay attributed to the dangling surface selenium orbitals by passivation of those trap sites by the methylene protons on the amine, leading to enhanced band edge emission and the absence of deep trap emission. Furthermore, CdSeZnSe core/shell nanocrystals are not immune from contributions from surface states because of the alignment of the band structures of the core and shell materials.     

Ortho-Alkoxy-benzamide Directed Formation of a Single Crystalline Hydrogen-bonded Crosslinked Organic Framework and Its Boron Trifluoride Uptake and Catalysis

Boron trifluoride (BF₃) is a highly corrosive gas widely used in industry. Confining BF₃ in porous materials ensures safe and convenient handling and prevents its degradation. Hence, it is highly desired to develop porous materials with high adsorption capacity, high stability, and resistance to BF₃ corrosion. Herein, we designed and synthesized a Lewis basic single-crystalline hydrogen-bond crosslinked organic framework (H_COF-50) for BF₃ storage and its application in catalysis. Specifically, we introduced self-complementary ortho-alkoxy-benzamide hydrogen-bonding moieties to direct the formation of highly organized hydrogen-bonded networks, which were subsequently photo-crosslinked to generate H_COFs. The H_COF-50 features Lewis basic thioether linkages and electron-rich pore surfaces for BF₃ uptake. As a result, H_COF-50 shows a record-high 14.2 mmol/g BF₃ uptake capacity. The BF₃ uptake in H_COF-50 is reversible, leading to the slow release of BF₃. We leveraged this property to reduce the undesirable chain transfer and termination in the cationic polymerization of vinyl ethers. Polymers with higher molecular weights and lower polydispersity were generated compared to those synthesized using BF₃ ⋅ Et₂O. The elucidation of the structure–property relationship, as provided by the single-crystal X-ray structures, combined with the high BF₃ uptake capacity and controlled sorption, highlights the molecular understanding of framework-guest interactions in addressing contemporary challenges.