Dissociation behavior of doubly-charged tryptic peptides: correlation of gas-phase cleavage abundance with ramachandran plots

Analysis of fragmentation patterns from 5654 unique doubly charged tryptic peptides is obtained. Great variability of average relative abundance of bond cleavage is found between different amino acid combinations. There exist similarities as well as differences between b and y ions. Strong enhancement or suppression of cleavage gives insight into possible chemical interactions at reactive conformations formed by preferred phi-psi angles.     

Asymmetric synthesis and applications of beta-amino Weinreb amides: asymmetric synthesis of (S)-coniine

Conjugate addition of lithium (S)-N-benzyl-N-alpha-methylbenzylamide to a range of alpha, beta-unsaturated Weinreb amides proceeds with high levels of diastereoselectivity (>95% de). The beta-amino Weinreb amide products may be transformed into beta-amino ketones via reactions with Grignard reagents, while treatment with DIBAL-H furnishes beta-amino aldehydes. Trapping of the aldehyde via Wadsworth-Emmons reaction and subsequent manipulation offers an efficient route to homochiral delta-amino acid derivatives and 2-substituted piperidines. The application of this methodology for the synthesis of (S)-coniine is demonstrated.     

Surface amplification of invasive cleavage products

A major focus of current efforts in genomics is to elucidate the genetic variations extent within the human population, and to study the effects of these variations upon the human system. The most common type of genetic variations are the single nucleotide polymorphisms (SNPs), which occur every 500-1000 nt in the genome. Large-scale population association studies to study the biological or medical significance of such variations may require the analysis of hundreds of thousands of SNPs on thousands of individuals. We are pursuing development of an approach to large-scale SNP analysis that combines the specificity of invasive cleavage reactions with the parallelism of high density DNA arrays. A surface-immobilized probe oligonucleotide is specifically cleaved in the presence of a complementary target sequence in unamplified human genomic DNA, yielding a 5' phosphate group. High sensitivity detection of this reaction product on the surface is achieved by the use of rolling circle amplification, with an approximate concentration detection limit of 10 fM target DNA. This combination of very specific surface cleavage and highly sensitive surface detection will make possible the rapid and parallel analysis of genetic variations across large populations.     

An automated instrument for human STR identification: design, characterization, and experimental validation

The microfluidic integration of an entire DNA analysis workflow on a fully integrated miniaturized instrument is reported using lab‐on‐a‐chip automation to perform DNA fingerprinting compatible with CODIS standard relevant to the forensic community. The instrument aims to improve the cost, duration, and ease of use to perform a “sample‐to‐profile” analysis with no need for human intervention. The present publication describes the operation of the three major components of the system: the electronic control components, the microfluidic cartridge and CE microchip, and the optical excitation/detection module. Experimental details are given to characterize the level of performance, stability, reliability, accuracy, and sensitivity of the prototype system. A typical temperature profile from a PCR amplification process and an electropherogram of a commercial size standard (GeneScan 500?, Applied Biosystems) separation are shown to assess the relevance of the instrument to forensic applications. Finally, we present a profile from an automated integrated run where lysed cells from a buccal swab were introduced in the system and no further human intervention was required to complete the analysis.     

Structural effects in pyrazolidinone-mediated organocatalytic Diels-Alder reactions

A range of pyrazolidin-3-ones have been prepared and their activity as catalysts for iminium-ion promoted Diels-Alder reactions evaluated. Systematic variation of the C(5)- and N(2)-substituents indicates that the incorporation of an electron withdrawing substitutent at N(2) and either a Ph or CF₃ substitution at C(5) results in optimal catalytic activity. The diastereoisomeric resolution of a model C(5)-Ph substituted pyrazolidinone and its ability to impart modest levels of asymmetric induction in the organocatalytic Diels-Alder reaction is also demonstrated.     

Novel bismuth and lead coordination polymers synthesized with pyridine-2,5-dicarboxylates: two single component "white" light emitting phosphors

New two-dimensional (2D) bismuth and three-dimensional (3D) lead based coordination polymers containing pyridine-2,5-dicarboxylate ligands (H(2)pydc) have been synthesized hydrothermally and characterized by single crystal X-ray diffraction. Bi(3)(μ(3)-O)(2)(pydc)(2)(Hpydc)(H(2)O)(2) (1), which crystallizes in the space group P1? (a = 8.7256(5) ?, b = 11.1217(7) ?, c = 14.0933(9) ?, α = 85.239(1)°, β = 98.582(1)°, γ = 71.106(1)°), has a 3D structure that contains Bi(6)O(4) clusters that connect into 2D sheets via linking ligands. The sheets form a 3D supramolecular structure via hydrogen bonding along the z-axis. Pb(pydc)(H(2)O) (2), which crystallizes in the space group P2(1)/c (a = 10.8343(14) ?, b = 11.2099(15) ?, c = 6.6573(9) ?, β = 90.697(2)°), contains 1D chains of corner-sharing distorted face capped trigonal prisms that are connected into a 3D framework via the pydc ligand. In addition, the ligands are hydrogen bonded to each other. Both 1 and 2 are single component "white" light emitting phosphors and are shown to exhibit "white" luminescence that covers a much wider spectral range than is observed for the as received H(2)pydc ligand.     

A 93Nb Solid‐State NMR and Density Functional Theory Study of Four‐ and Six‐Coordinate Niobate Systems

A variable B₀ field static (broadline) NMR study of a large suite of niobate materials has enabled the elucidation of high‐precision measurement of ⁹³Nb NMR interaction parameters such as the isotropic chemical shift (δ_iso), quadrupole coupling constant and asymmetry parameter (C_Q and η_Q), chemical shift span/anisotropy and skew/asymmetry (Ω/Δδ and κ/η_δ) and Euler angles (α, β, γ) describing the relative orientation of the quadrupolar and chemical shift tensorial frames. These measurements have been augmented with ab initio DFT calculations by using WIEN2k and NMR‐CASTEP codes, which corroborate these reported values. Unlike previous assertions made about the inability to detect CSA (chemical shift anisotropy) contributions from Nb^V in most oxo environments, this study emphasises that a thorough variable B₀ approach coupled with the VOCS (variable offset cumulative spectroscopy) technique for the acquisition of undistorted broad (?1/2?+1/2) central transition resonances facilitates the unambiguous observation of both quadrupolar and CSA contributions within these ⁹³Nb broadline data. These measurements reveal that the ⁹³Nb electric field gradient tensor is a particularly sensitive measure of the immediate and extended environments of the Nb^V positions, with C_Q values in the 0 to >80 MHz range being measured; similarly, the δ_iso (covering an approximately 250 ppm range) and Ω values (covering a 0 to approximately 800 ppm range) characteristic of these niobate systems are also sensitive to structural disposition. However, their systematic rationalisation in terms of the Nb? O bond angles and distances defining the immediate Nb^V oxo environment is complicated by longer‐range influences that usually involve other heavy elements comprising the structure. It has also been established in this study that the best computational method(s) of analysis for the ⁹³Nb NMR interaction parameters generated here are the all‐electron WIEN2k and the gauge included projector augmented wave (GIPAW) NMR‐CASTEP DFT approaches, which account for the short‐ and long‐range symmetries, periodicities and interaction‐potential characteristics for all elements (and particularly the heavy elements) in comparison with Gaussian 03 methods, which focus on terminated portions of the total structure.     

Infrared spectroscopy and optical constants of porous amorphous solid water

Reflection-absorption infrared spectra (RAIRS) of amorphous solid water (ASW) films grown at 20 K on a Pt(111) substrate at various angles (theta(Beam) = 0-85 degrees ) using a molecular beam are reported. They display complex features arising from the interplay between refraction, absorption within the sample, and interference effects between the multiple reflections at the film-substrate and film-vacuum interfaces. Using a simple classical optics model based on Fresnel equations, we obtain optical constants [i.e., n(omega) and k(omega)] for porous ASW in the 1000-4000 cm(-1) (10-2.5 microm) range. The behavior of the optical properties of ASW in the intramolecular OH stretching region with increasing theta(Beam) is shown to be strongly correlated with its decreasing density and increasing surface area. A direct comparison between the RAIRS and calculated vibrational spectra shows a large difference ( approximately 200 cm(-1)) in the position of the coupled H-bonded intramolecular OH stretching vibrations spectral feature. Moreover, this band shifts in opposite directions with increasing theta(Beam) in RAIRS and vibrational spectra demonstrating RAIRS spectra cannot be interpreted straightforwardly as vibrational spectra due to severe optical distortions from refraction and interference effects.