Jeremy G. Frey

Infrared predissociation spectra of water dimer in a supersonic molecular-beam

The infrared absorption spectrum of the hydrogen-bonded water dimer, (H2O)2, formed in a supersonic expansion, was recorded in the region of th

Breaking the book: translating the chemistry lab book into a pervasive computing lab environment

The UK e-Science programme is relying on the evolution of the paper lab book into a pervasive data gathering lab system. To date take up of existing commercial or research lab book replacement systems has not been great. In this paper, we reconsider both the role of the lab book in the experimental cycle, as well as its affective and experiential properties as an artefact, in order to design an e-Science lab book that will be acceptable to the scientists who will use it. To this end we combined and extended existing design analysis models in order to assess the artefact functionally and experientially. We present the approach we developed, the prototype we designed based on our analysis, and the results of the formative study we performed of the artefact in real use. We show that our design elicitation method strongly contributed to the success of our prototypes take up.

Enzyme Accessibility and Solid Supports: Which Molecular Weight Enzymes Can Be Used on Solid Supports? An Investigation Using Confocal Raman Microscopy

The accessibility of various solid supports (TentaGel, PEGA 1900, and beaded controlled pore glasses (CPGs)) to a range of enzymes was investigated. The different beaded materials were loaded with the peptide 4-cyanobenzamide-Gly-Pro-Leu-Gly-Leu-Phe-Ala-Arg-OH and incubated with the enzymes MMP-12 (22 kDa), thermolysin (35 kDa), MMP-13 (42.5 kDa), clostridium collagenase (68 kDa), and NEP (90 kDa). The absence/presence of the cyano stretching frequency was measured by means of confocal Raman microscopy. It was found that none of the investigated enzymes could enter the polymer matrices of TentaGel. PEGA 1900 was compatible only with the two smallest enzymes, while beaded CPG was successful even with NEP (90 kDa), proving its superiority over other materials in terms of bio-compatibility.

Towards predictable transmembrane transport: QSAR analysis of anion binding and transport

The transport of anions across biological membranes by small molecules is a growing research field due to the potential therapeutic benefits of these compounds. However, little is known about the exact mechanism by which these drug-like molecules work and which molecular features make a good transporter. An extended series of 1-hexyl-3-phenylthioureas were synthesized, fully characterized (NMR, mass spectrometry, IR and single crystal diffraction) and their anion binding and anion transport properties were assessed using 1H NMR titration techniques and a variety of vesicle-based experiments. Quantitative structure–activity relationship (QSAR) analysis revealed that the anion binding abilities of the mono-thioureas are dominated by the (hydrogen bond) acidity of the thiourea NH function. Furthermore, mathematical models show that the experimental transmembrane anion transport ability is mainly dependent on the lipophilicity of the transporter (partitioning into the membrane), but smaller contributions of molecular size (diffusion) and hydrogen bond acidity (anion binding) were also present. Finally, we provide the first step towards predictable anion transport by employing the QSAR equations to estimate the transmembrane transport ability of four new compounds.

The semantic smart laboratory: a system for supporting the chemical eScientist

One goal of eScience is to enable the end-to-end publication of experiments and results. In the Combechem project we have developed an innovative human-centred system which captures the process of a chemistry experiment from plan to execution. The system comprises an electronic lab book replacement, which has been successfully trialled in a synthetic organic chemistry laboratory, and a flexible back-end storage system. Working closely with the users, we found that a light touch and a high degree of flexibility was required in the user interface. In this paper, we concentrate on the representation and storage of human-scale experiment metadata, introducing an ontology to describe the record of an experiment, and a storage system for the data from our lab book software. Just as the interfaces need to be flexible to cope with whatever a chemist wishes to record, so the back end solutions need to be similarly flexible to store any metadata that may be created. The storage system is based on Semantic Web technologies, such as RDF, and Web Services. It gives a much higher degree of flexibility to the type of metadata it can store, compared to the use of rigid relational databases.

Soft-x-ray wavelength shift induced by ionization effects in a capillary

Coherent soft x rays are produced by high-harmonic generation in a capillary filled with Ar gas. We demonstrate that the tuning of the harmonic wavelengths with intensity and chirp arises from changes in the Ar ionization level. Control over the tuning can be achieved either by changing the average intensity of the laser pulse or by varying the quadratic spectral phase of the laser pulse. We observe an ionization-dependent blueshift of the fundamental wavelength that is directly imprinted on the harmonic wavelengths. The harmonic tuning is shown to depend on nonlinear spectral shifts of the fundamental laser pulse that are due to the plasma created by ionization, rather than directly on any chirp imposed on the fundamental wavelength.

Bringing Chemical Data onto the Semantic Web

Present chemical data storage methodologies place many restrictions on the use of the stored data. The absence of sufficient high-quality metadata prevents intelligent computer access to the data without human intervention. This creates barriers to the automation of data mining in activities such as quantitative structure-activity relationship modelling. The application of Semantic Web technologies to chemical data is shown to reduce these limitations. The use of unique identifiers and relationships (represented as uniform resource identifiers, URIs, and resource description framework, RDF) held in a triplestore provides for greater detail and flexibility in the sharing and storage of molecular structures and properties.

Second harmonic generation from the air/water interface of an aqueous solution of the dipeptide Boc-Trp-Trp

Abstract The air/water interface of aqueous ( t -butyloxycarbonyl) -tryptophan-tryptophan (Boc-Trp-Trp) has been studied by surface second harmonic generation (SHG). The SHG signals obtained with a linearly polarised fundamental indicate a Langmuir-like adsorption isotherm. Wavelength-dependent circularly differential harmonic generation (SHG-CD) was observed together with SHG optical rotation. The SHG signals from the LL and DD enantiomer show equal but opposite dependence on the handedness of the fundamental radiation and the DL diastereoisomer gave rise to a different spectrum.

Anion-directed assembly: the first fluoride-directed double helix

The crystal structures of anion complexes of two nitroaromatic functionalised isophthalamides are reported; the structures reveal assembly around anions in the solid-state and in the case of the fluoride complex of receptor 2, the formation of a double helix.

The calculation of the ground state energy of weakly bound van der Waals trimers using the method of hyperspherical harmonics. I: The Born-Oppenheimer and adiabatic approximations

Abstract The method of hyperspherical harmonics is applied to the calculation of the vibrational energy levels of the three-particle weakly bound van der Waals complexes. (H 2 ) 3− (D 2 ) 3 and Ne 3 . Hyperspherical coordinates and the properties of the associated hyperspherical harmonic functions are discussed. These functions are used as an angular basis in which to expand the wavefunction for the three-particle system. A Born—Oppenheimer-type separation of the angular and hyper-radial motion is made. permitting a lower bound (Born—Oppenheimer approximation) and an upper bound (adiabatic approximation) to the energy of the clusters to be calculated.