Droplet evaporation study applied to DNA chip manufacturing

DNA chips are potentially powerful technologies for genotyping and gene expression profiling that rely on comparative analyses of up to thousands of "spots of analysis" on a glass support. The spot quality throughout the support influences spot-to-spot variations within an array and the repeatability of data across experiments. For glass slide DNA microarrays, droplets of DNA solution are deposited on functionalized glass slides and left to react through complete evaporation of the droplet. On hydrophobic flat surfaces, different modes of droplet evaporation can be attained. Under atmospheric pressure, water droplets tend to evaporate under two main regimes. Initially, the droplet flattens with a constant contact area, and then the droplet shrinks at a constant contact angle. As a result, the diameter and morphology of thousands of spots on microarrays are not uniform. This leads to poor and unreliable data processing results. In this work, we report the evaporation of an aqueous solution under a constant contact area mode. Evaporation under reduced pressure and the effect of reagent additives to the solution have been investigated. Video microscopy and digital image analysis techniques were applied to monitor the evaporation of the droplets. A mixture of surfactants was developed to maintain a constant area regime during evaporation and to form homogeneous spots. The control of some physicochemical properties (wetting, evaporation rate) of the droplet allows the formation of well-controlled spots compatible with DNA grafting. The influence of surfactant molecules on the mechanisms of evaporation is also discussed.     

Stereoselective synthesis of a new perhydroindole derivative of chiral iminodiacid,a potent inhibitor of angiotensin converting enzyme

The stereoselective synthesis of N-[(s) 1 - carbethoxybutyl)] (s) alanine and of (2S, 3aS, 7aS) 2-t.butoxycarbonyl perhydroindole are described. Their coupling produces the title compound     

Reactivity of peroxo forms of the vanadium haloperoxidase cofactor. A DFT investigation

Density functional theory has been used to investigate structural, electronic and reactivity properties of complexes related to the peroxo forms of vanadium haloperoxidases (VHPO). In particular, the reactivity of the cofactor as a function of protonation state and environment, which are two factors thought to be crucial in modulating the activity of the enzyme, has been examined. In full agreement with experimental data, results highlight the role of protonation in the activation of the peroxo-vanadium complexes and show that the oxo-transfer step involves the unprotonated axial peroxo oxygen atom, which is easily accessible to substrates in the peroxo form of the enzyme. The role of Lys353, which in the X-ray structure of the peroxide-bound form of vanadium chloroperoxidase is hydrogen bonded to the equatorial oxygen atom of the peroxo group, has been also explored. It is concluded that Lys353 can play a role similar to a H+ in the activation of the peroxo form of the cofactor.     

The unexpected rearrangement of 1,5‐benzodiazepin‐2,4‐dione to a benzimidazol‐2‐one derivative during N,N'‐diglucosylation

Reaction of 1,5‐benzodiazepin‐2,4‐dione with 3‐O‐substituted‐5,6‐anhydro‐1,2‐isopropylidene‐α‐D‐glucofuranose gave the unexpected N,N'‐di‐glucofuranosyl benzimidazol‐2‐one by a novel rearrangement and ring closure reaction. A mechanism is proposed.     

Polystyrene nanoparticles based on poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers

The solubilization of styrene by poly(butyl methacrylate-g-methoxypoly(ethylene glycol)) and poly(methyl methacrylate-g-methoxypoly(ethylene glycol)) graft copolymers has been examined. From turbidity measurements the solubility limit of the monomer in the micelles was obtained and the distribution coefficients were evaluated. Dynamic light scattering revealed that below the solubility limit, solubilization leads to a slight increase in micelle size, while above the solubility limit, there is a dramatic increase in particle size and turbidity as oil-in-water emulsions are formed through coalescence of monomer-swollen micelles. Polymerizations carried out below the solubility limit using the graft copolymer micelles as templates resembled microemulsion polymerizations in nature and led to very fine sterically stabilized polystyrene latex particles. Through careful control of the monomer concentration and the polymerization temperature it was possible to obtain spherical nanosize latex particles with similar size to those of the micelle precursors (10 nm) up to 11% monomer by weight. Polymerizations above the solubility limit, on the other hand, showed similarities with emulsion polymerizations and resulted in larger particles with higher polydispersity.     

Double proton transfer in the isolated and DNA-embedded guanine-cytosine base pair

The energetics and dynamics of double proton transfer (DPT) is investigated theoretically for the Watson-Crick conformation of the guanine-cytosine (GC) base pair. Using semiempirical density functional theory the isolated and DNA-embedded GC pair is considered. Differences in the energetics and dynamics of DPT thus addresses the question of how relevant studies of isolated base pairs are for the understanding of processes occurring in DNA. Two-dimensional potential energy surfaces involving the transferring hydrogen atoms and the proton donors and acceptors are presented for both systems. The DPT reaction is accompanied by a contraction of the distance between the two bases with virtually identical energetic barriers being 18.8 and 18.7 kcal/mol for the isolated and DNA-embedded system, respectively. However, the transition state for DPT in the DNA-embedded GC pair is offset by 0.1 A to larger N-H separation compared to the isolated GC pair. Using activated ab initio molecular dynamics, DPT is readily observed for the isolated base pair with a minimal amount of 21.4 kcal/mol of initial average kinetic energy along the DPT normal mode vector. On a time scale of approximately 100 fs DPT has occurred and the excess energy is redistributed. For the DNA-embedded GC pair considerably more kinetic energy is required (30.0 kcal/mol) for DPT and the process is completed within one hydrogen vibration. The relevance of studies of isolated base pairs and base pair analogs in regard of reactions or properties involving DNA is discussed.     

Zirconium-mediated conversion of homoallylic ethers into cyclopropane derivatives

Homoallylic ethers react with Cp₂ZrCl₂/2 n-BuLi reagent to afford cyclopropane derivatives. Cyclopropylcarbinyl-homoallyl rearrangements involving zirconium species are observed depending on the substrate structure.     

Morphological characterization of elastin-mimetic block copolymers utilizing cryo- and cryoetch-HRSEM.

Elastin-mimetic block copolymers were produced by genetic engineering. Genetically driven synthesis permitted control of the final physiochemical characteristics of the block copolymers. We designed BB and BAB block copolymers in which the A-block was hydrophilic and the B-block was hydrophobic. By designing the copolymers in this manner, it was proposed that they would self-assemble into micellar aggregates that, at high concentration, would form thermoreversible hydrogels. To analyze the three-dimensional fine surface morphology of the copolymers, to the resolution level of a few nanometers, we employed cryo-HRSEM. This method provided vast expanses of the specimen in its frozen hydrated state for survey. In our initial cryo-HRSEM studies, we observed the protein filaments and micelles surrounded by lakes of vitreous ice. Upon examination at low and intermediate magnifications, there was an extensive honeycomb-like filamentous network. To delineate the fine morphology of the hydrogel network at high magnification and to greater depths, we cryoetched away unbound water from the sample surface, in high vacuum, prior to chromium deposition. By using this technique, we were able to visualize for characterization purposes the fine fibril networks formed from the micellar aggregates over the surface of the hydrogel.     

Mixed-metal cluster chemistry. 19. Crystallographic, spectroscopic, electrochemical, spectroelectrochemical, and theoretical studies of systematically varied tetrahedral group 6-iridium clusters

A systematically varied series of tetrahedral clusters involving ligand and core metal variation has been examined using crystallography, Raman spectroscopy, cyclic voltammetry, UV-vis-NIR and IR spectroelectrochemistry, and approximate density functional theory, to assess cluster rearrangement to accommodate steric crowding, the utility of metal-metal stretching vibrations in mixed-metal cluster characterization, and the possibility of tuning cluster electronic structure by systematic modification of composition, and to identify cluster species resultant upon electrochemical oxidation or reduction. The 60-electron tetrahedral clusters MIr(3)(CO)(11-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (5), C(5)HMe(4) (6), C(5)Me(5) (7); M = W, Cp = C(5)H(4)Me, x = 1 (13), x = 2 (14)] and M(2)Ir(2)(CO)(10-x)(PMe(3))(x)(eta(5)-Cp) [M = Mo, x = 0, Cp = C(5)H(4)Me (8), C(5)HMe(4) (9), C(5)Me(5) (10); M = W, Cp = C(5)H(4)Me, x = 1 (15), x = 2 (16)] have been prepared. Structural studies of 7, 10, and 13 have been undertaken; these clusters are among the most sterically encumbered, compensating by core bond lengthening and unsymmetrical carbonyl dispositions (semi-bridging, semi-face-capping). Raman spectra for 5, 8, WIr(3)(CO)(11)(eta(5)-C(5)H(4)Me) (11), and W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(4)Me)(2) (12), together with the spectrum of Ir(4)(CO)(12), have been obtained, the first Raman spectra for mixed-metal clusters. Minimal mode-mixing permits correlation between A(1) frequencies and cluster core bond strength, frequencies for the A(1) breathing mode decreasing on progressive group 6 metal incorporation, and consistent with the trend in metal-metal distances [Ir-Ir < M-Ir < M-M]. Cyclic voltammetric scans for 5-15, MoIr(3)(CO)(11)(eta(5)-C(5)H(5)) (1), and Mo(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (3) have been collected. The [MIr(3)] clusters show irreversible one-electron reduction at potentials which become negative on cyclopentadienyl alkyl introduction, replacement of molybdenum by tungsten, and replacement of carbonyl by phosphine. These clusters show two irreversible one-electron oxidation processes, the easier of which tracks with the above structural modifications; a third irreversible oxidation process is accessible for the bis-phosphine cluster 14. The [M(2)Ir(2)] clusters show irreversible two-electron reduction processes; the tungsten-containing clusters and phosphine-containing clusters are again more difficult to reduce than their molybdenum-containing or carbonyl-containing analogues. These clusters show two one-electron oxidation processes, the easier of which is reversible/quasi-reversible, and the more difficult of which is irreversible; the former occur at potentials which increase on cyclopentadienyl alkyl removal, replacement of tungsten by molybdenum, and replacement of phosphine by carbonyl. The reversible one-electron oxidation of 12 has been probed by UV-vis-NIR and IR spectroelectrochemistry. The former reveals that 12(+) has a low-energy band at 8000 cm(-1), a spectrally transparent region for 12, and the latter reveals that 12(+) exists in solution with an all-terminal carbonyl geometry, in contrast to 12 for which an isomer with bridging carbonyls is apparent in solution. Approximate density functional calculations (including ZORA scalar relativistic corrections) have been undertaken on the various charge states of W(2)Ir(2)(CO)(10)(eta(5)-C(5)H(5))(2) (4). The calculations suggest that two-electron reduction is accompanied by W-W cleavage, whereas one-electron oxidation proceeds with retention of the tetrahedral core geometry. The calculations also suggest that the low-energy NIR band of 12(+) arises from a sigma(W-W) --> sigma*(W-W) transition.