Open-path FT-IR spectrometry: is completely unattended operation feasible?

Most protocols used for open-path Fourier transform infrared spectrometry (OP/FT-IR) require that spectra be measured at a resolution of 1 cm(-1) and that the concentrations of the analytes be calculated by classical least squares regression (CLS). These specifications were largely developed for monitoring light molecules with easily resolvable rotational fine structure. For most volatile organic compounds in air, the rotational fine structure is not resolvable and better accuracy can be obtained when the spectrum is measured at lower resolution (typically 8 cm(-1)), provided that the algorithm used for quantification is partial least squares regression (PLS). By measuring the spectrum at low resolution, the need for a liquid-nitrogen-cooled mercury cadmium telluride detector is reduced and a pyroelectric detector operating at ambient temperature can be used instead. By using PLS rather than CLS, spectral features due to water vapor do not have to be compensated and a short-path background spectrum can be used, greatly simplifying field measurements.     

A new plasmid display technology for the in vitro selection of functional phenotype-genotype linked proteins

BACKGROUND: Display technologies which allow peptides or proteins to be physically associated with the encoding DNA are central to procedures which involve screening of protein libraries in vitro for new or altered function. Here we describe a new system designed specifically for the display of libraries of diverse, functional proteins which utilises the DNA binding protein nuclear factor kappa B (NF-kappa B) p50 to establish a phenotype-genotype link between the displayed protein and the encoding gene. RESULTS: A range of model fusion proteins to either the amino- or carboxy-terminus of NF-kappa B p50 have been constructed and shown to retain the picomolar affinity and DNA specificity of wild-type NF-kappa B p50. Through use of an optimal combination of binding buffer and DNA target sequence, the half-life of p50-DNA complexes could be increased to over 47 h, enabling the competitive selection of a variety of protein-plasmid complexes with enrichment factors of up to 6000-fold per round. The p50-based plasmid display system was used to enrich a maltose binding protein complex to homogeneity in only three rounds from a binary mixture with a starting ratio of 1:10(8) and to enrich to near homogeneity a single functional protein from a phenotype-genotype linked Escherichia coli genomic library using in vitro functional selections. CONCLUSIONS: A new display technology is described which addresses the challenge of functional protein display. The results demonstrate that plasmid display is sufficiently sensitive to select a functional protein from large libraries and that it therefore represents a useful addition to the repertoire of display technologies.     

Relationship between side chain structure and 14-helix stability of beta3-peptides in water

Folded polymers are used in Nature for virtually every vital process. Nonnatural folded polymers, or foldamers, have the potential for similar versatility, and the design and refinement of such molecules is of considerable current interest. Here we report a complete and systematic analysis of the relationship between side chain structure and the 14-helicity of a well-studied class of foldamers, beta(3)-peptides, in water. Our experimental results (1) verify the importance of macrodipole stabilization for maintaining 14-helix structure, (2) provide comprehensive evidence that beta(3)-amino acids branched at the first side chain carbon are 14-helix-stabilizing, (3) suggest a novel role for side chain hydrogen bonding as an additional stabilizing force in beta(3)-peptides containing beta(3)-homoserine or beta(3)-homothreonine, and (4) demonstrate that diverse functionality can be incorporated into a stable 14-helix. Gas- and solution-phase calculations and Monte Carlo simulations recapitulate the experimental trends only in the context of oligomers, yielding insight into the mechanisms behind 14-helix folding. The 14-helix propensities of beta(3)-amino acids differ starkly from the alpha-helix propensities of analogous alpha-amino acids. This contrast informs current models for alpha-helix folding, and suggests that 14-helix folding is governed by different biophysical forces than is alpha-helix folding. The ability to modulate 14-helix structure through side chain choice will assist rational design of 14-helical beta-peptide ligands for macromolecular targets.     

Ion/molecule reactions of ammonia and methylamine with chloro- and nitrobenzene. A comparison of chemical ionization and ion cyclotron resonance experiments

It is shown by ion cyclotron resonance measurements that ion/molecule reactions, leading to substitution or reduction product ions from chloro- and nitrobenzene with the title amines, are those between the molecular ions [RNH₂]⁺ or [C₆H₅X]⁺˙ and their respective counterparts C₆H₅X or RNH₂. The protonated reagent gas ions [RNH₃]⁺ are not involved in these reactions. In the case of nitrobenzene, adduct ions [C₆H₅NO₂·RNH₃]⁺ do not decompose within the time scale of the measurements. The results obtained are compared with those found under chemical ionization conditions.     

Flow-injection technique for the determination of low levels of phosphorus in natural waters

An inexpensive flow-injection instrument for determining low concentrations of dissolved reactive phosphorus in natural waters is reported. The unique feature is the use of an inexpensive detector consisting of a flow cell and a simple photometer that incorporates a super-bright light-emitting diode as the source and a photodiode as the detector. The tin(II) chloride-molybdate method was optimized using a modified simplex optimization method. Silicate interference up to 5 mg Si l^?1 was removed by addition of 0.10% (w/v) tartaric acid. Using the tartaric acid-modified optimized reagents, a detection limit of 0.6 μg P l^?1 was achieved. The method was linear over the range 0–100 μg P l^?1 with an excellent precision (r.s.d. 2.9% at 2.0 and 0.5% at 50 μg P l^?1). An in-line pre-concentration anion-exchange column was used to obtain an even lower detection limit of 0.1 μg P l^?1 and applied to the analysis of real samples.     

The E.S.R. and electronic absorption spectra of Chichibabin's biradical

The absorption spectra of a number of saturated hydrocarbons in the vacuum ultra-violet region have been examined and compared with their photoelectron and electron-loss spectra. Important conclusions about the quantum defect associated with the excited electrons and the nature of the excited states have been drawn from the relative positions of these spectra. The Rydberg bands of ethane, which were initially thought to originate in the C-C bond, have been shown to be associated with an electron largely localized in the CH₃ group.     

A Gibbs Approach to Chargaff’s Second Parity Rule

Chargaff’s second parity rule (CSPR) asserts that the frequencies of short polynucleotide chains are the same as those of the complementary reversed chains. Up to now, this hypothesis has only been observed empirically and there is currently no explanation for its presence in DNA strands. Here we argue that CSPR is a probabilistic consequence of the reverse complementarity between paired strands, because the Gibbs distribution associated with the chemical energy between the bonds satisfies CSPR. We develop a statistical test to study the validity of CSPR under the Gibbsian assumption and we apply it to a large set of bacterial genomes taken from the GenBank repository.