Coupling and mixing times in a Markov chain

The derivation of the expected time to coupling in a Markov chain and its relation to the expected time to mixing (as introduced by the author [J.J. Hunter, Mixing times with applications to perturbed Markov chains, Linear Algebra Appl. 417 (2006) 108-123] are explored. The two-state cases and three-state cases are examined in detail.     

Ultra-rapid separation of an angiotensin mixture in nanochannels using shear-driven chromatography

The present paper reports on the separation of a mixture of fluorescein isothiocyanate-labeled angiotensin I and II peptides in a shear-driven nanochannel with a C18-coating and using an eluent consisting of 5% acetonitrile in 0.02 M aqueous phosphate buffer at pH 6.5. The flat-rectangular nanochannel in fused silica consisted of an etched structure in combination with a flat moving wall. The very fast separation kinetics that can be achieved in a nanochannel allowed to separate the angiotensin peptides in less then 0.2 s in a distance of only 1.8 mm. Plate heights as small as 0.4 microm were calculated after substraction of the injection effect.     

CO2 Hydroboration: Impact of the Boryl Moieties on the Reactivity of Four Bis(boryl)acetal Compounds toward 2,6-Diisopropylaniline

The hydroboration of CO₂ into bis(boryl)acetal (BBA) compounds is an important transformation, since it enabled to selectively reduce CO₂ by 4e^- and to subsequently use the BBA compounds as C₁ and C_n sources. However, the influence of the nature of the boryl moieties on the reactivity of BBA compounds has not been evaluated so far. In the present study, four BBA compounds – including two new ones – were reacted with 2,6-diisopropylaniline to afford the expected imine. Significant differences in the rate of the reaction from minutes to weeks have been observed depending on the BBA used, showing the importance of the nature of the boryl moieties. Theoretical investigations enabled to propose a mechanism involving the addition of the aniline to the BBA as the rate-determining step and to determine that the steric hindrance of the BBA compounds is the main factor driving the rate of this condensation reaction.     

Kinetic stability of complex molecular clusters

This investigation is concerned with modeling the evaporation, or decay, of n-nonane molecular clusters. We use a unique cluster decay model that was first developed to estimate the decay time scale of argon clusters using molecular-dynamics simulations. In this study we seek to enhance the model so that it represents a more complex cluster decay dynamic, suitable for n-nonane clusters. Experimental measurements of nucleation rates of n-nonane droplets have been used to deduce the rate at which a molecule escapes from the cluster. Typically for an n-nonane cluster containing 40 molecules, at an experimental temperature of 225 K, the empirical decay time, which is the inverse of the decay rate, is estimated to be 50 ns. For this time scale, the direct observation of n-nonane cluster decay from a molecular-dynamics trajectory is not feasible, since decay events are so rare. However, the cluster decay model uses a combination of molecular dynamics and stochastic dynamics in order to resolve the problem associated with long decay time scales. The model is based on a Langevin treatment that views cluster decay as single-particle escape from a confining potential of mean force. It is used to predict kinetic decay times of n-nonane clusters. We discover this result differs significantly from a classically derived decay time scale determined from a continuum thermodynamic treatment of the population balance equations of clusters. However, the dynamically generated results obtained from the kinetic decay model compare more favorably than the classical results with the empirical decay times that are deduced from experimental measurements of n-nonane clusters.     

Natural products as an inspiration in the diversity-oriented synthesis of bioactive compound libraries

The purpose of diversity-oriented synthesis is to drive the discovery of small molecules with previously unknown biological functions. Natural products necessarily populate biologically relevant chemical space, since they bind both their biosynthetic enzymes and their target macromolecules. Natural product families are, therefore, libraries of pre-validated, functionally diverse structures in which individual compounds selectively modulate unrelated macromolecular targets. This review describes examples of diversity-oriented syntheses which have, to some extent, been inspired by the structures of natural products. Particular emphasis is placed on innovations that allow the synthesis of compound libraries that, like natural products, are skeletally diverse. Mimicking the broad structural features of natural products may allow the discovery of compounds that modulate the functions of macromolecules for which ligands are not known. The ability of innovations in diversity-oriented synthesis to deliver such compounds is critically assessed.     

Progressive-convergent elucidation of stereochemistry in complex polyols. The absolute configuration of (-)-sagittamide A

The absolute stereostructure of sagittamide A (1), a O-hexacetyl long-chain hexahydroxy-alpha,omega-dicarboxylic acid, was assigned using a progressive-convergent approach that integrates three powerful regimens for stereochemical analysis of acyclic natural products: J-based analysis, 13C NMR universal database comparisons, and exciton coupling circular dichroism.     

Deposition of DNA-functionalized gold nanospheres into nanoporous surfaces

We report the deposition of DNA-conjugated gold nanospheres into arrays of surface nanopores obtained from hexagonally ordered thin polystyrene-b-poly(methyl methacrylate) (PS-b-PMMA) diblock copolymer films on silicon. The deposition occurs spontaneously from aqueous solution and is driven by either electrostatic interactions or specific DNA hybridization events between the DNA nanospheres and the surface nanopores. To mitigate this spontaneous deposition, we have chemically modified the nanopores with either positively charged aminosilanes or oligonucleotide probe sequences. The deposition of DNA nanospheres into the surface nanopores was characterized by atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS). We have observed preferential immobilization of individual DNA nanospheres within the nanopores, based on the size matching between the two entities. The inclusion density and selectivity of DNA nanosphere deposition into the surface nanopores was found to depend predominantly on the methods through which the nanoporous surfaces were prepared and chemically functionalized.     

High-density targeting of a viral multifunctional nanoplatform to a pathogenic, biofilm-forming bacterium

Nanomedicine directed at diagnosis and treatment of infections can benefit from innovations that have substantially increased the variety of available multifunctional nanoplatforms. Here, we targeted a spherical, icosahedral viral nanoplatform to a pathogenic, biofilm-forming bacterium, Staphylococcus aureus. Density of binding mediated through specific protein-ligand interactions exceeded the density expected for a planar, hexagonally close-packed array. A multifunctionalized viral protein cage was used to load imaging agents (fluorophore and MRI contrast agent) onto cells. The fluorescence-imaging capability allowed for direct observation of penetration of the nanoplatform into an S. aureus biofilm. These results demonstrate that multifunctional nanoplatforms based on protein cage architectures have significant potential as tools for both diagnosis and targeted treatment of recalcitrant bacterial infections.     

Theoretical analysis of initial adsorption of high-κ metal oxides on In(x)Ga(1-x)As(0 0 1)-(4×2) surfaces

Ordered, low coverage to monolayer, high-κ oxide adsorption on group III rich InAs(0 0 1)-(4×2) and In(0.53)Ga(0.47)As(0 0 1)-(4×2) was modeled via density functional theory (DFT). Initial adsorption of HfO(2) and ZrO(2) was found to remove dangling bonds on the clean surface. At full monolayer coverage, the oxide-semiconductor bonds restore the substrate surface atoms to a more bulklike bonding structure via covalent bonding, with the potential for an unpinned interface. DFT models of ordered HfO(2)/In(0.53)Ga(0.47)As(0 0 1)-(4×2) show it fully unpins the Fermi level.     

Second-Generation Covalent TMP-Tag for Live Cell Imaging

Chemical tags are now viable alternatives to fluorescent proteins for labeling proteins in living cells with organic fluorophores that have improved brightness and other specialized properties. Recently, we successfully rendered our TMP-tag covalent with a proximity-induced reaction between the protein tag and the ligand-fluorophore label. This initial design, however, suffered from slow in vitro labeling kinetics and limited live cell protein labeling. Thus, here we report a second-generation covalent TMP-tag that has a fast labeling half-life and can readily label a variety of intracellular proteins in living cells. Specifically, we designed an acrylamide-trimethoprim-fluorophore (A-TMP-fluorophore v2.0) electrophile with an optimized linker for fast reaction with a cysteine (Cys) nucleophile engineered just outside the TMP-binding pocket of Escherichia coli dihydrofolate reductase (eDHFR) and developed an efficient chemical synthesis for routine production of a variety of A-TMP-probe v2.0 labels. We then screened a panel of eDHFR:Cys variants and identified eDHFR:L28C as having an 8-min half-life for reaction with A-TMP-biotin v2.0 in vitro. Finally, we demonstrated live cell imaging of various cellular protein targets with A-TMP-fluorescein, A-TMP-Dapoxyl, and A-TMP-Atto655. With its robustness, this second-generation covalent TMP-tag adds to the limited number of chemical tags that can be used to covalently label intracellular proteins efficiently in living cells. Moreover, the success of this second-generation design further validates proximity-induced reactivity and organic chemistry as tools not only for chemical tag engineering but also more broadly for synthetic biology.