Alanine racemase free energy profiles from global analyses of progress curves

Free energy profiles for alanine racemase from Bacillus stearothermophilus have been determined at pH 6.9 and 8.9 from global analysis of racemization progress curves. This required a careful statistical design due to the problems in finding the global minimum in mean square for a system with eight adjustable parameters (i.e., the eight rate constants that describe the stepwise chemical mechanism). The free energy profiles obtained through these procedures are supported by independent experimental evidence: (1). steady-state kinetic constants, (2). solvent viscosity dependence, (3). spectral analysis of reaction intermediates, (4). equilibrium overshoots for progress curves measured in D(2)O, and (5). the magnitudes of calculated intrinsic kinetic isotope effects. The free energy profiles for the enzyme are compared to those of the uncatalyzed and the PLP catalyzed reactions. At pH 6.9, PLP lowers the free energy of activation for deprotonation by 8.4 kcal/mol, while the inclusion of apoenzyme along with PLP additionally lowers it by 11 kcal/mol.     

Competitive decay at two- and three-state conical intersections in excited-state intramolecular proton transfer

We demonstrate the existence of a simultaneous degeneracy (not required by symmetry) of three electronic states in malonaldehyde. This is one of the first reports of such a triple degeneracy involving S0, S1, and S2 in a molecule with a closed-shell ground state. We further report on a two-state S2/S1 conical intersection which is higher in energy than the three-state intersection, but closer to the Franck-Condon point. First-principles quantum dynamics calculations of the photochemistry after excitation to S2 show that there is a competition between these intersections, with more than half of the population decaying to S1 through the higher energy S2/S1 intersection. Surprisingly, much of the population which makes it to the triple degeneracy point is not funneled directly to S0, but rather remains trapped on S1. We attribute this to the large dimensionality of the branching plane at a three-state intersection (the degeneracy is lifted along at least five distinct molecular displacements).     

The practical synthesis of a novel and highly potent analogue of bryostatin

Macrocycle 1 is a new highly potent analogue of bryostatin 1, a promising anti-cancer agent currently in human clinical trials. In vitro, 1 displays picomolar affinity for PKC and exhibits over 100-fold greater potency than bryostatin 1 when tested against various human cancer cell lines. Macrocycle 1 can be generated in clinically required amounts by chemical synthesis in only 19 steps (LLS) and represents a new clinical lead for the treatment of cancer.     

Interfacial micellar structures from novel amphiphilic star polymers

An amphiphilic heteroarm star polymer containing 12 alternating hydrophobic/hydrophilic arms of polystyrene (PS) and poly(acrylic acid) (PAA) connected to a well-defined rigid aromatic core was studied at the air-water and the air-solid interfaces. At the air-water interface, the molecules spontaneously form pancakelike micellar aggregates which measure up to several microns in diameter and 5 nm in thickness. Upon reduction of the surface area per molecule to 7 nm2, the two-dimensional micelles merged into a dense monolayer. We suggest that confined phase separation of dissimilar polymer arms occurred upon their segregation on the opposite sides of the rigid disklike aromatic core, forcing the rigid cores to adopt a face-on orientation with respect to the interface. Upon transfer onto solid supports the PS chains face the air-film interface making it completely hydrophobic, and the PAA chains were found to collapse and form a thin flattened underlayer. This study points toward new strategies to create large 2D microstructures with facial amphiphilicity and suggests a profound influence of star molecular architecture on the self-assembly of amphiphiles at the air-water interface.     

Charge transport in DNA via thermally induced hopping.

In this contribution we advance and explore the thermally induced hopping (TIH) mechanism for long-range charge transport (CT) in DNA and in large-scale chemical systems. TIH occurs in donor-bridge-acceptor systems, which are characterized by off-resonance donor-bridge interactions (energy gap DeltaE > 0), involving thermally activated donor-bridge charge injection followed by intrabridge charge hopping. We observe a "transition" from superexchange to TIH with increasing the bridge length (i.e., the number N of the bridge constituents), which is manifested by crossing from the exponential N-dependent donor-acceptor CT rate at low N (< N(X)) to a weakly (algebraic) N-dependent CT rate at high N (>N(X)). The "critical" bridge size N(X) is determined by the energy gap, the nearest-neighbor electronic couplings, and the temperature. Experimental evidence for the TIH mechanism was inferred from our analysis of the chemical yields for the distal/proximal guanine (G) triplets in the (GGG)(+)TTXTT(GGG) duplex (X = G, azadine (zA), and adenine (A)) studied by Nakatani, Dohno and Saito [J. Am. Chem. Soc. 2000, 122, 5893]. The TIH sequential model, which involves hole hopping between (GGG) and X, is analyzed in terms of a sequential process in conjunction with parallel reactions of (GGG)(+) with water, and provides a scale of (free) energy gaps (relative to (GGG)(+)) of Delta = 0.21-0.24 eV for X = A, Delta = 0.10-0.14 eV for X = zA, and Delta = 0.05-0.10 eV for X = G. We further investigated the chemical yields for long-range TIH in (G)l(+)Xn(G)l (l = 1-3) duplexes, establishing the energetic constraints (i.e., the donor - bridge base (X) energy gap Delta), the bridge structural constraints (i.e., the intrabridge X-X hopping rates k(m)), and the kinetic constraints (i.e., the rate k(d) for the reaction of with water). Effective TIH is expected to prevail for Delta less than or approximately equal to 0.20 eV with a "fast" water reaction (k(d)/k(m) approximately 10(-3)) and for Delta < 0.30 eV with a "slow" water reaction (k(d)/k(m) approximately 10(-5)). We conclude that (T)n bridges (for which Delta approximately equals 0.6 eV) cannot act in TIH of holes. From an analysis based on the energetics of the electronic coupling matrix elements in G(+)(T-A)n(GGG) duplexes we conclude that the superexchange mechanism is expected to dominate for n = 1-4. For long (A)n bridges (n > or approximately equal to 4) the TIH prevails, provided that the water side reaction is slow, raising the issue of chemical control of TIH through long (A)n bridges in DNA attained by changing the solution composition.     

Effects of viscosity on droplet formation and mixing in microfluidic channels

This paper characterizes the conditions required to form nanoliter-sized droplets (plugs) of viscous aqueous reagents in flows of immiscible carrier fluid within microfluidic channels. For both non-viscous (viscosity of 2.0 mPa s) and viscous (viscosity of 18 mPa s) aqueous solutions, plugs formed reliably in a flow of water-immiscible carrier fluid for Capillary number less than 0.01, although plugs were able to form at higher Capillary numbers at lower ratios of the aqueous phase flow rate to the flow rate of the carrier fluid (in all the experiments performed, the Reynolds number was less than 1). The paper also shows that combining viscous and non-viscous reagents can enhance mixing in droplets moving through straight microchannels by providing a nearly ideal initial distribution of reagents within each droplet. The study should facilitate the use of this droplet-based microfluidic platform for investigation of protein crystallization, kinetics, and assays.     

Intermediate level structure in the s2 state of the isolated ultracold ovalene molecule

Spectroscopic information pertaining to interstate coupling between the S₂ and S₁ electronic states of ovalene, whose electronic origins are separated by ≈ 1800 cm^?1, has been obtained by the interrogation of the fluorescence action spectrum and of the energy-resolved fluorescence in seeded supersonic beams.     

Molybdenum-phosphorus triple bond stabilization by ancillary alkoxide ligation: synthesis and structure of a terminal phosphide tris-1-methylcyclohexanoxide complex

Using alcoholysis, we converted terminal phosphide PMo(N[i-Pr]Ar)3 into a new, monomeric terminal phosphide PMo(OR)3, where R = 1-methylcyclohexyl or 1-adamantyl. Dimerization of the PMo unit was observed upon alcoholysis with 2,6-dimethylphenol, and the dimer [PMo(N[i-Pr]Ar)(O-2,6-C6H3Me2)2]2 was isolated and characterized by X-ray crystallography.     

Formation of Bi-Sb, Bi-Sn, and Bi-Sb-Sn Nanoclusters in Silica Xerogel Matrices from Mixed-Metal Oxide Precursors

Homogeneous mixed-metal oxides of the general formula (Bi/E/Si)O _x , where E represents a dopant element (E=Sb, Sn, or Sb/Sn), can be prepared using typical sol-gel processing techniques. Reduction of the in-situ Bi(III) and E ions by hydrogen affords nanocomposites of Bi-Sb, Bi-Sn, or Bi-Sb-Sn widely dispersed throughout the silica xerogel matrix. The materials prepared have high Bi-E metal loading of 52–60 wt. % containing Bi-E alloy nanoclusters of 12–15 nm average diameter. These results demonstrate a convenient method for the production of practical quantities of nanostructured bismuth alloy ceramic composites at high metal content.     

Functionalized nanoparticles for liquid atmospheric pressure matrix-assisted laser desorption/ionization peptide analysis

Nanoparticles for the extraction of peptides and subsequent analysis using atmospheric pressure matrix-assisted laser desorption/ionization (APMALDI) have been evaluated. The atmospheric pressure source allows for particles to be directly introduced in the liquid matrix, minimizing sample loss and analysis time. Described in this work are two sample preparation procedures for liquid APMALDI analysis: a C18 functionalized silica nanoparticle for hydrophobic extractions, and an aptamer functionalized magnetite core nanoparticle for rapid, affinity extractions. The C18 particles provide a non-selective support for rapid profiling applications, while the aptamer particles are directed towards reducing the complexity in biological samples. The aptamer functionalized particles provide a more selective analyte-nanoparticle interaction whereby the tertiary structure of the analyte becomes more critical to the extraction. In both cases, the liquid APMALDI matrix provides a support for ionization, and acts as the releasing agent for the analyte-particle interaction. Additionally, analyte enrichment was possible due to the large surface-to-volume ratio of the particles. The experiments conducted with functionalized nanoparticles, in an atmospheric pressure liquid matrix, present a basis for further methodologies and utilities of silica nanoparticles to be developed.