Gradient elution isotachophoresis with direct ultraviolet absorption detection for sensitive amino acid analysis

This work demonstrates coupling of the newly described electrophoretic enrichment technique of gradient elution isotachophoresis (GEITP) to a low-cost, conventional ultraviolet absorbance detector to realize sensitive measurements with a universal detector, eliminating the need for fluorescent analytes or derivatization. The effects of various parameters on enrichment were studied, including current density varied by leading electrolyte concentration, current density varied by applied electric field, and counter-flow acceleration across varying capillary inner diameters. Optimized parameters were applied to the enrichment and separation of the amino acids tryptophan (Trp) and tyrosine (Tyr). Limits of detection for Trp and Tyr were 51 and 215 nM, respectively, reflecting sensitivity enhancements of 860- and 1900-fold. Analysis times were less than 6 min, and peak height RSDs were less than 4%. A demonstration of enrichment and separation of these amino acids from artificial cerebrospinal fluid is additionally shown as a first step to realizing biochemical monitoring by GEITP.     

Expedient synthesis of N-methyl tubulysin analogues with high cytotoxicity

An optimized and highly efficient synthesis of potent, bioactive N-methyl tubulysin analogues 2 and 4 has been achieved with > 40% overall yields. This synthesis represents a significant improvement over previously reported syntheses of these and related tubulysin analogues. The stereoselective synthesis of the unnatural amino acid tubuvaline is accomplished using tert-butanesulfinamide chemistry. N-Alkylation to form N-methyl tubuvaline is performed without protection of the tubuvaline alcohol by implementing a unique N-methylation strategy via formation and reduction of a 1,3-tetrahydrooxazine heterocycle. Acylation of the hindered N-methyl tubuvaline amine utilizes a novel sequence of O-acylation followed by an O- to N-acyl transfer to form the hindered amide bond between N-methyl tubuvaline and isoleucine. This high-yielding synthesis should enable the production of large quantities of material for biological studies.     

Conformational arm-wrestling: battles for stereochemical control in benzamides bearing matched and mismatched chiral 2- and 6-substituents

The orientation of a tertiary amide group adjacent to an aromatic ring may be governed by the stereochemistry of an adjacent chiral substituent. With a chiral substituent in both ortho positions, matched/mismatched pairs of isomers result. Evidence for matched stereochemistry is provided by the clean NMR spectra of single conformers, while mismatching gives poor or unexpected selectivities in the formation of chiral substituents, or mixtures of amide conformers. Attempts to use the match-mismatch effect to select for racemic pairs of enantiomeric substituents, and hence develop a "racemate-sequestering" reagent, are described, along with the use of "matching" to scavenge a single enantiomer of a diamine from material of incomplete enantiomeric purity.     

Synthesis and excited-state photodynamics of a chlorin-bacteriochlorin dyad--through-space versus through-bond energy transfer in tetrapyrrole arrays.

Understanding energy transfer among hydroporphyrins is of fundamental interest and essential for a wide variety of photochemical applications. Toward this goal, a synthetic free base ethynylphenylchlorin has been coupled with a synthetic free base bromobacteriochlorin to give a phenylethyne-linked chlorin-bacteriochlorin dyad (FbC-pe-FbB). The chlorin and bacteriochlorin are each stable toward adventitious oxidation because of the presence of a geminal dimethyl group in each reduced pyrrole ring. A combination of static and transient optical spectroscopic studies indicate that excitation into the Qy band of the chlorin constituent (675 nm) of FbC-pe-FbB in toluene results in rapid energy transfer to the bacteriochlorin constituent with a rate of approximately (5 ps)(-1) and efficiency of >99%. The excited bacteriochlorin resulting from the energy-transfer process in FbC-pe-FbB has essentially the same fluorescence characteristics as an isolated monomeric reference compound, namely a narrow (12 nm fwhm) fluorescence emission band at 760 nm and a long-lived (5.4 ns) Qy excited state that exhibits a significant fluorescence quantum yield (Phif=0.19). F?rster calculations are consistent with energy transfer in FbC-pe-FbB occurring predominantly by a through-space mechanism. The energy-transfer characteristics of FbC-pe-FbB are compared with those previously obtained for analogous phenylethyne-linked dyads consisting of two porphyrins or two oxochlorins. The comparisons among the sets of dyads are facilitated by density functional theory calculations that elucidate the molecular-orbital characteristics of the energy donor and acceptor constituents. The electron-density distributions in the frontier molecular orbitals provide insights into the through-bond electronic interactions that can also contribute to the energy-transfer process in the different types of dyads.     

Synthetic chlorins bearing auxochromes at the 3- and 13-positions

Synthetic chlorins bearing diverse auxochromes at the 3- and 13-positions of the macrocycle are valuable targets given their resemblance to chlorophylls a and b, which bear 3-vinyl and 13-keto groups. A de novo route has been exploited to construct nine zinc chlorins bearing substituents at the 3- and 13-positions and two benchmark zinc chlorins lacking such substituents. The chlorins are sterically uncongested and bear (1) a geminal dimethyl group in the reduced pyrroline ring, (2) a H, an acetyl, a triisopropylsilylethynyl (TIPS-ethynyl), or a vinyl at the 3-position, (3) a H, an acetyl, or TIPS-ethynyl at the 13-position, and (4) a H or a mesityl at the 10-position. The synthesis of the 13-substituted chlorins relied on p-TsOH x H2O-catalyzed condensation of an 8,9-dibromo-1-formyldipyrromethane (eastern half) and 2,3,4,5-tetrahydro-1,3,3-trimethyldipyrrin (western half), followed by metal-mediated oxidative cyclization, affording the 13-bromochlorin. Similar use of a bromo- or TIPS-ethynyl-substituted western half provided access to 3-substituted chlorins. A 3-bromo, 13-bromo, or 3,13-dibromochlorin was further transformed by Pd-coupling to introduce the vinyl group (via tributylvinyltin), TIPS-ethynyl group (via TIPS-acetylene), or acetyl group (via tributyl(1-ethoxyvinyl)tin, followed by acidic hydrolysis). In the 10-mesityl-substituted zinc chlorins, the series of substituents, 3-vinyl, 13-TIPS-ethynyl, 3-TIPS-ethynyl, 13-acetyl, 3,13-bis(TIPS-ethynyl), 3-TIPS-ethynyl-13-acetyl, or 3,13-diacetyl, progressively causes (1) a redshift in the absorption maximum of the B band (405-436 nm) and the Q(y) band (606-662 nm), (2) a relative increase in the intensity of the Q(y) band (I(B)/I(Q) = 4.2-1.5), and (3) an increase in the fluorescence quantum yield phi(f) (0.059-0.29). The zinc chlorins bearing a 3-TIPS-ethynyl-13-acetyl or a 3,13-diacetyl group exhibit a number of spectral properties resembling those of chlorophyll a or its zinc analogue. Taken together, this study provides access to finely tuned chlorins for spectroscopic studies and diverse applications.     

NMR method for the determination of solute hydrogen bond acidity

It is shown that the difference in the 1H NMR chemical shift of a protic hydrogen in DMSO and CDCl3 solvents is directly related to the overall, or summation, hydrogen bond acidity for a wide range of solutes. This provides a new and direct method of measuring the hydrogen bond acidity. For 54 compounds, the observed shifts for 72 protic hydrogens could be correlated to the Abraham solute hydrogen bond acidity parameter, A, with a correlation coefficient squared, R2, of 0.938 and a standard deviation, SD, of 0.054 units in A. A training equation that used half the data could predict A values for the remaining data with an average error of 0.001 and a standard deviation, SD, of 0.053 units, thus demonstrating the predictive power of the method. Unlike any previous method for the determination of solute hydrogen bond acidities, the NMR method allows the determination of A values for individual protic hydrogens in multifunctional solutes.     

A concise synthesis of butylcycloheptylprodigiosin

A short and efficient total synthesis of the tripyrrole alkaloid butylcycloheptylprodigiosin is described. Key to the brevity of the approach is a two-step synthesis of macrocyclic formylpyrrole 4 from cyclononenone 6.     

Classification of water molecules in protein binding sites

Water molecules play a crucial role in mediating the interaction between a ligand and a macromolecular receptor. An understanding of the nature and role of each water molecule in the active site of a protein could greatly increase the efficiency of rational drug design approaches: if the propensity of a water molecule for displacement can be determined, then synthetic effort may be most profitably applied to the design of specific ligands with the displacement of this water molecule in mind. In this paper, a thermodynamic analysis of water molecules in the binding sites of six proteins, each complexed with a number of inhibitors, is presented. Two classes of water molecules were identified: those conserved and not displaced by any of the ligands, and those that are displaced by some ligands. The absolute binding free energies of 54 water molecules were calculated using the double decoupling method, with replica exchange thermodynamic integration in Monte Carlo simulations. It was found that conserved water molecules are on average more tightly bound than displaced water molecules. In addition, Bayesian statistics is used to calculate the probability that a particular water molecule may be displaced by an appropriately designed ligand, given the calculated binding free energy of the water molecule. This approach therefore allows the numerical assessment of whether or not a given water molecule should be targeted for displacement as part of a rational drug design strategy.     

Enantiomerically enriched atropisomeric N,N′-diaryl ureas by oxidative kinetic resolution of their 2-sulfanyl derivatives

Atropisomeric N-methyl-N,N′-diaryl ureas may be obtained in enantiomerically enriched form by oxidative kinetic resolution of their sulfide derivatives. The atropisomeric sulfides may be obtained in up to 97:3 er and display high stability to racemisation (half-lives at 25 °C of up to 500 years). Unlike related fully alkylated ureas, the product sulfoxides exhibit relatively weak thermodynamic conformational selectivity.     

Polyglycerol-derived amphiphiles for the solubilization of single-walled carbon nanotubes in water: a structure-property study

A series of nonionic amphiphiles derived from polyglycerol dendrons were studied for their ability to solubilize and isolate single-walled carbon nanotubes. The amphiphiles possessed differently sized polar head groups, hydrophobic tail units, and various aromatic and non-aromatic groups between the head and tail groups. Absorbance analysis revealed that amphiphiles with anchor groups derived from pyrene were far inferior to those that possessed simple linear aliphatic tail groups. Absorbance and near-infrared fluorescence analyses revealed a weak dependence on the dendron size of the head group, but a strong positive trend in suspended nanotube density and fluorescence intensity for amphiphiles with longer tail units. Variations in the moieties linking the head and tail groups led to a range of effects on the suspensions, with linkers imparting flexibility and a bent shape that gave improved performance overall. This was illustrated most dramatically by a pair of benzamide-containing amphiphiles, the para isomer of which showed evidence in the fluorescence data of increased nanotube aggregate formation when compared with the meta isomer. In addition, statistical AFM was used to illustrate more directly the microscopic differences between amphiphiles that were effective at nanotube bundle disruption and those that were not.