Reliable and efficient reaction path and transition state finding for surface reactions with the growing string method.

The computational challenge of fast and reliable transition state and reaction path optimization requires new methodological strategies to maintain low cost, high accuracy, and systematic searching capabilities. The growing string method using internal coordinates has proven to be highly effective for the study of molecular, gas phase reactions, but difficulties in choosing a suitable coordinate system for periodic systems has prevented its use for surface chemistry. New developments are therefore needed, and presented herein, to handle surface reactions which include atoms with large coordination numbers that cannot be treated using standard internal coordinates.

Dynamic Flexibility of Hydrogenase Active Site Models Studied with 2D-IR Spectroscopy.

Hydrogenase enzymes enable organisms to use H as an energy source, having evolved extremely efficient biological catalysts for the reversible oxidation of molecular hydrogen. Small-molecule mimics of these enzymes provide both simplified models of the catalysis reactions and potential artificial catalysts that might be used to facilitate a hydrogen economy. We have studied two diiron hydrogenase mimics, μ-pdt-[Fe(CO)] and μ-edt-[Fe(CO)] (pdt = propanedithiolate, edt = ethanedithiolate), in a series of alkane solvents and have observed significant ultrafast spectral dynamics using two-dimensional infrared (2D-IR) spectroscopy.

PCR-Free, Multiplexed Expression Profiling of microRNAs Using Silicon Photonic Microring Resonators.

We describe an approach for multiplexed microRNA analysis using silicon photonic microring resonators to detect cDNA reverse transcription products via a subsequent enzymatic signal enhancement strategy. Key to this method is a modified stem loop primer that facilitates downstream signal amplification via enzymatic turnover and improves the sensor signal 20-fold when compared to traditional stem loop primers. This approach facilitates targeted microRNA quantification in only 2.

Molecular Mechanism for Isoform-Selective Inhibition of Acyl Protein Thioesterases 1 and 2 (APT1 and APT2).

Post-translational S-palmitoylation directs the trafficking and membrane localization of hundreds of cellular proteins, often involving a coordinated palmitoylation cycle that requires both protein acyl transferases (PATs) and acyl protein thioesterases (APTs) to actively redistribute S-palmitoylated proteins toward different cellular membrane compartments. This process is necessary for the trafficking and oncogenic signaling of S-palmitoylated Ras isoforms, and potentially many peripheral membrane proteins. The depalmitoylating enzymes APT1 and APT2 are separately conserved in all vertebrates, suggesting unique functional roles for each enzyme.

Design and microfabrication of a miniature fiber optic probe with integrated lenses and mirrors for Raman and fluorescence measurements.

Fiber optics coupled to components such as lenses and mirrors have seen extensive use as probes for Raman and fluorescence measurements. Probes can be placed directly on or into a sample to allow for simplified and remote application of these optical techniques. The size and complexity of such probes however limits their application.

MOF-5-Polystyrene: Direct Production from Monomer, Improved Hydrolytic Stability, and Unique Guest Adsorption.

An unprecedented mode of reactivity of Zn4 O-based metal-organic frameworks (MOFs) offers a straightforward and powerful approach to polymer-hybridized porous solids. The concept is illustrated with the production of MOF-5-polystyrene wherein polystyrene is grafted and uniformly distributed throughout MOF-5 crystals after heating in pure styrene for 4-24 h. The surface area and polystyrene content of the material can be fine-tuned by controlling the duration of heating styrene in the presence of MOF-5.

Formation and Trapping of Azafulvene Intermediates Derived from Manganese-Mediated Oxidative Malonate Coupling.

The one-pot, three-component, coupling reaction of indoles/pyrroles, dimethyl malonate, and acetic acid was performed using Mn(III) acetate as an oxidant. In the presence of Mn(OAc), indole-2, and indole-3-carbonyl compounds were alkylated at the 3- and 2- positions, respectively, with subsequent oxidation and nucleophilic capture occurring at the newly formed benzylic carbon. In contrast, oxidation of 2- and 3-indole carboxylic acids afforded the corresponding 2-oxindol-3-ylidenes and 3-oxindol-2-ylidenes.

Probing the Biexponential Dynamics of Ring-Opening in 7-Dehydrocholesterol.

Our prior discovery of a novel biexponential photochemical ring-opening in 7-dehydrocholesterol (DHC) to previtamin D3 [ Tang J. Chem. Phys.

Rendering non-energetic microporous coordination polymers explosive.

Adsorption of oxidizing guest molecules into a non-energetic microporous coordination polymer produces explosives with desirable oxygen balance, high heat released upon decomposition, and suppressed vapor pressure of the guest. Here, this results in primary explosives, materials very sensitive to impact, that have the potential to be used as replacements for lead-based initiators.

Protein Cross-Linking Capillary Electrophoresis for Protein-Protein Interaction Analysis.

Capillary electrophoresis (CE) has been identified as a useful platform for detecting, quantifying, and screening for modulators of protein-protein interactions (PPIs). In this method, one protein binding partner is labeled with a fluorophore, the protein binding partners are mixed, and then, the complex is separated from free protein to allow direct determination of bound to free ratios. Although it possesses many advantages for PPI studies, the method is limited by the need to have separation conditions that both prevent protein adsorption to capillary and maintain protein interactions during the separation.

Efficient implementation of constant pH molecular dynamics on modern graphics processors.

The treatment of pH sensitive ionization states for titratable residues in proteins is often omitted from molecular dynamics (MD) simulations. While static charge models can answer many questions regarding protein conformational equilibrium and protein-ligand interactions, pH-sensitive phenomena such as acid-activated chaperones and amyloidogenic protein aggregation are inaccessible to such models. Constant pH molecular dynamics (CPHMD) coupled with the Generalized Born with a Simple sWitching function (GBSW) implicit solvent model provide an accurate framework for simulating pH sensitive processes in biological systems.

Exploring the relationship between vibrational mode locality and coupling using constrained optimization.

The use of alternate coordinate systems as a means to improve the efficiency and accuracy of anharmonic vibrational structure analysis has seen renewed interest in recent years. While normal modes (which diagonalize the mass-weighted Hessian matrix) are a typical choice, the delocalized nature of this basis makes it less optimal when anharmonicity is in play. When a set of modes is not designed to treat anharmonicity, anharmonic effects will contribute to inter-mode coupling in an uncontrolled fashion.

Correlated S-palmitoylation profiling of Snail-induced epithelial to mesenchymal transition.

Epithelial cells form spatially-organized adhesion complexes that establish polarity gradients, regulate cell proliferation, and direct wound healing. As cells accumulate oncogenic mutations, these key tumor suppression mechanisms are disrupted, eliminating many adhesion complexes and bypassing contact inhibition. The transcription factor Snail is often expressed in malignant cancers, where it promotes transcriptional reprogramming to drive epithelial-mesenchymal transition (EMT) and establishes a more invasive state.

Asymmetric Palladium-Catalyzed Alkene Carboamination Reactions for the Synthesis of Cyclic Sulfamides.

The synthesis of cyclic sulfamides by enantioselective Pd-catalyzed alkene carboamination reactions between N-allylsulfamides and aryl or alkenyl bromides is described. High levels of asymmetric induction (up to 95:5 e.r.

Palladium-catalysed transannular C-H functionalization of alicyclic amines.

Discovering pharmaceutical candidates is a resource-intensive enterprise that frequently requires the parallel synthesis of hundreds or even thousands of molecules. C-H bonds are present in almost all pharmaceutical agents. Consequently, the development of selective, rapid and efficient methods for converting these bonds into new chemical entities has the potential to streamline pharmaceutical development.

A Perylene-Based Microporous Coordination Polymer Interacts Selectively with Electron-Poor Aromatics.

The design, synthesis, and properties of the new microporous coordination polymer UMCM-310 are described. The unique electronic character of the perylene-based linker enables selective interaction with electron-poor aromatics leading to efficient separation of nitroaromatics. UMCM-310 possesses high surface area and large pore size and thus permits the separation of large organic molecules based on adsorption rather than size exclusion.

Other species in the aqueous environment of a peptide can invert its intrinsic solvated polyproline II/beta propensity: Implications for amyloid formation.

As we have previously shown, the predominance of the polyproline II conformation in the circular dichroism spectra of aqueous polypeptides is related to its lower energy than that of the beta conformation. To test whether this is still the case in the presence of additional components in the medium, we have calculated the energy difference between these two conformations in an alanine-dipeptide/12-water system without and with the addition of an HCl molecule. We find in the latter case that the beta conformer is of lower energy than the polyproline II.

Parallelization and improvements of the generalized born model with a simple sWitching function for modern graphics processors.

Two fundamental challenges of simulating biologically relevant systems are the rapid calculation of the energy of solvation and the trajectory length of a given simulation. The Generalized Born model with a Simple sWitching function (GBSW) addresses these issues by using an efficient approximation of Poisson-Boltzmann (PB) theory to calculate each solute atom's free energy of solvation, the gradient of this potential, and the subsequent forces of solvation without the need for explicit solvent molecules. This study presents a parallel refactoring of the original GBSW algorithm and its implementation on newly available, low cost graphics chips with thousands of processing cores.

Upgrading ethanol to 1-butanol with a homogeneous air-stable ruthenium catalyst.

An amide-derived N,N,N-Ru(ii) complex catalyzes the conversion of EtOH to 1-BuOH with high activity. Conversion to alcohol upgraded products exceeds 250 turnovers per hour (>50% conversion) with 0.1 mol% catalyst loading.

Identification of sirtuin 5 inhibitors by ultrafast microchip electrophoresis using nanoliter volume samples.

Sirtuin 5 (SIRT5) is a member of the sirtuin family of protein deacylases that catalyzes removal of post-translational modifications, such as succinyl and malonyl moieties, on lysine residues. In light of SIRT5's roles in regulating metabolism, and its reported oncogenic functions, SIRT5 modulators would be valuable tools for basic biological research and perhaps clinically. Several fluorescence assays for sirtuin modulators have been developed; however, the use of fluorogenic substrates has the potential to cause false positive results due to interactions of engineered substrates with enzyme or test compounds.

Palladium-Catalyzed Alkene Carboamination Reactions of Electron-Poor Nitrogen Nucleophiles.

Modified reaction conditions that facilitate Pd-catalyzed alkene carboamination reactions of electron-deficient nitrogen nucleophiles are reported. Pent-4-enylamine derivatives bearing -tosyl or -trifluoroacetyl groups are coupled with aryl triflates to afford substituted pyrrolidines in good yield. These reactions proceed via a mechanism involving -aminopalladation of the alkene, which differs from previously reported analogous reactions of -aryl and -boc pentenylamines.

Thermal Dehydrogenation of Base-Stabilized B2H5(+) Complexes and Its Role in C-H Borylation.

Thermally induced dehydrogenation of the H-bridged cation L2B2H5(+) (L=Lewis base) is proposed to be the key step in the intramolecular C-H borylation of tertiary amine boranes activated with catalytic amounts of strong "hydridophiles". Loss of H2 from L2B2H5(+) generates the highly reactive cation L2B2H3(+), which in its sp(2)-sp(3) diborane(4) form then undergoes either an intramolecular C-H insertion with B-B bond cleavage, or captures BH3 to produce L2B3H6(+). The effect of the counterion stability on the outcome of the reaction is illustrated by formation of LBH2C6F5 complexes through disproportionation of L2B2H5(+) HB(C6F5)3(-) .

Scattering based hyperspectral imaging of plasmonic nanoplate clusters towards biomedical applications.

A new optical scattering contrast-agent based on polymer-nanoparticle encapsulated silver nanoplates (PESNs) is presented. Silver nanoplates were chosen due to the flexibility of tuning their plasmon frequencies. The polymer coating preserves their physical and optical properties and confers other advantages such as controlled contrast agent delivery.

Development of Enantioselective Palladium-Catalyzed Alkene Carboalkoxylation Reactions for the Synthesis of Tetrahydrofurans.

The Pd-catalyzed coupling of γ-hydroxyalkenes with aryl bromides affords enantiomerically enriched 2-(arylmethyl)tetrahydrofuran derivatives in good yield and up to 96:4 e.r. This transformation was achieved through the development of a new TADDOL/2-arylcyclohexanol-derived chiral phosphite ligand.

Functionalization of Styrenes by Copper-Catalyzed Borylation/ ortho-Cyanation and Silver-Catalyzed Annulation Processes.

An efficient two-step method for the assembly of indanone derivatives starting from a simple vinyl arene has been developed. The sequence first involves addition of bis(pinacolato)diboron (B2 pin2 ) and N-cyano-N-phenyl-p-methylbenzenesulfonamide (NCTS) to a broad range of styrenes by utilizing IMesCuCl as catalyst. This step simultaneously accomplishes hydroboration of the alkene and ortho cyanation of the benzene unit.