An independently addressable microbiosensor array: what are the limits of sensing element density?

A microdisc sensor array, prepared by thin film technology, has been used as a model for miniaturized multi-functional biosensors. It consists of a series of wells, 20 microns in diameter, possessing a 1000 A Pt layer at the bottom that serves as the indicating electrode. The depth of the wells ranged from 2.3-24 microns, depending on the photoresist employed and the spinning speed used to coat the electrode interconnect grid. Ten such wells were arranged in a circular array within an area of radius 130 microns. The center to center distance between any two of the discs ranged from 30 to 155 microns. Each disc is connected by a conductive film line to corresponding pads on the side of the sensor chip. A cylinder placed on top of the chip array formed the electrochemical cell into which a common reference and counter electrode were placed. The reference electrode was operated at ground potential. Prior to the evaluation of enzyme sensors, an assessment of "chemical cross-talk", the perturbation of sensor response resulting from the overlap of proximal diffusion layers, was made using Fe(CN)6(4-). The preliminary conclusion is that the sensing elements probably must be separated by about 100 microns in order to avoid interference from adjacent sensors. A technique was developed for the precision delivery of enzyme and cross-linking agent to the 2.3 microns cavity, having a capacity of 4 pL. This procedure makes possible the preparation of sensor arrays capable of detecting different analytes by employing different enzymes. The sensors gave reasonably rapid (2-4 s) response with linearity (up to about 10 mM. However, the sensors in the center of the array clearly showed the effects of depletion of substrates by the surrounding sensors.     

Carbohydrate-pi interactions: what are they worth?

Protein-carbohydrate interactions play an important role in many biologically important processes. The recognition is mediated by a number of noncovalent interactions, including an interaction between the alpha-face of the carbohydrate and the aromatic side chain of the protein. To elucidate this interaction, it has been studied in the context of a beta-hairpin in aqueous solution, in which the interaction can be investigated in the absence of other cooperative noncovalent interactions. In this beta-hairpin system, both the aromatic side chain and the carbohydrate were varied in an effort to gain greater insight into the driving force and magnitude of the carbohydrate-pi interaction. The magnitude of the interaction was found to vary from -0.5 to -0.8 kcal/mol, depending on the nature of the aromatic ring and the carbohydrate. Replacement of the aromatic ring with an aliphatic group resulted in a decrease in interaction energy to -0.1 kcal/mol, providing evidence for the contribution of CH-pi interactions to the driving force. These findings demonstrate the significance of carbohydrate-pi interactions within biological systems and also their utility as a molecular recognition element in designed systems.     

O-alkyl resorcarenes: where are we now?

This review describes the current position in the emerging field of direct synthesis of O-alkyl resorcarenes through the use of O-protected precursors. The use of this approach for the selective synthesis of the diastereoisomers of resorc[4]arenes, the synthesis of parent resorcarenes and pyrogalloranes and the preparation of chiral partially alkylated resorc[4]arenes are highlighted. The applications of such molecules, with regard to their role as ligand platforms, for binding of cations, organic electron acceptors and in chiral discrimination are discussed.     

Speciation and legislation – Where are we today and what do we need for tomorrow?

In international legislation concerning trace elements in food, in the environment or in occupational health most regulations are based on the total element contents, and are frequently given as maximum limits or guideline levels. In contrast, only few regulations pay attention to the molecular species in which the elements are bound. The international legislation concerning contaminants in food is presently being established in the Codex Alimentarius, which is an independent United Nations organisation under the joint FAO/WHO Food Standards Programme. Development of the Codex General Standard for Contaminants and Toxins in Food provides the framework for future international legislation on metals as contaminants in food. For certain food additives, which include some essential minerals, speciation is an integral part of the set of specification criteria, because only certain defined chemical compounds are permitted as sources of the essential element. The development of more species-specific analytical and toxicological data, and improved communication with legislators will be necessary before it will become possible to lay down species-specific regulations in all the cases where the specialised scientist will consider it reasonable.     

Designing higher surface area metal-organic frameworks: are triple bonds better than phenyls?

We have synthesized, characterized, and computationally validated the high Brunauer-Emmett-Teller surface area and hydrogen uptake of a new, noncatenating metal-organic framework (MOF) material, NU-111. Our results imply that replacing the phenyl spacers of organic linkers with triple-bond spacers is an effective strategy for boosting molecule-accessible gravimetric surface areas of MOFs and related high-porosity materials.     

H4(+): what do we know about it?

The potential energy surface of H(4)(+) has been analyzed and stationary points and minima of intersections characterized by benchmark multireference configuration interaction calculations with basis sets as large as augmented septuble zeta. No evidence for minima other than those of the well established stable C(2v) configuration has been found. Some of the results obtained previously at a lower level of ab initio theory had to be revised.     

Detection techniques in ion analysis: what are our choices?

Trends in detection techniques for ion analysis by ion-exchange chromatography and capillary zone electrophoresis are reviewed. Special attention is paid to conductivity, UV-Vis absorbance, amperometric and potentiometric detection, mass spectrometry (including inductively coupled plasma MS and atmospheric pressure ionization MS) and post-separation reaction detection. Applications reported within the last few years are summarized.     

Metrology for metalloproteins—where are we now, where are we heading?

The use of the amount of certain proteins in biological samples as markers for distinguishing between a healthy and a diseased state has become increasingly important in clinical diagnosis. As about 30 % of all proteins contain metals in one form or another, either as a cofactor or covalently bound as part of the protein, some of these proteins are regularly analyzed in clinical laboratories. With the increasing number of measurements of those proteins performed all over the world, the necessity of obtaining reliable and comparable results is becoming a focal point for scientists and politicians. Directives such as the EC directive covering in vitro diagnostic medical devices (Directive 98/79/EC) and standards such as EN ISO 17511:2003 demand the traceability of the results obtained for analytes in samples of human origin. However, no reference measurement procedures with results traceable to the SI exist for many metalloproteins. In this article, the situation for a few important metalloproteins, such as hemoglobin, transferrin, superoxide dismutase, ceruloplasmin, and C-reactive protein, for which specific efforts have been made in recent years to achieve comparable and traceable results worldwide, is discussed. These proteins also serve as examples of the difficulties scientists face when they wish to quantify proteins and the pitfalls they should avoid to achieve reliable results.

Computational strategies for predicting free radical scavengers' protection against oxidative stress: Where are we and what might follow?

Oxidative stress, which is frequently induced by an overproduction of free radicals (FR), poses a high risk to human health. Thus, finding efficient strategies for scavenging FR is a research area of current interest. Among many other aspects, this involves identifying chemical compounds capable of offering antioxidant protection (AOP) and quantifying such protection. This review summarizes different computational approaches that can contribute to gain a deeper knowledge on this subject. Several reaction mechanisms that may contribute to AOP are discussed, as well as some key factors influencing their relative importance including the chemical nature of the reacting FR, the polarity of the environment and the pH in aqueous solution. Kinetics-based analyses to characterize antioxidants, through their FR scavenging activity, are presented. Trends in such activity, from the data currently available in the literature are provided. Some key aspects, regarding AOP, that still deserves further investigation, are discussed.     

Fracture of polymer interfaces: what are the relevant length scales?

While it is tempting to relate directly the molecular structure of an interface (between glassy or between semi‐cristalline polymers) with its fracture toughness, these two parameters are simply the two end‐points of a complex network which needs to be understood in order to control the mechanical strength of the interface. The important mechanisms occur at three different length scales: the molecular scale (stress‐transfer across the interface), the microscopic scale (plastic deformation at the crack tip) and the macroscopic scale (loading geometry and elastic constants of the polymers). The couplings existing between these length scales in glassy polymer interfaces are reviewed in this paper in light of the latest experimental studies.     

Overview of the SAMPL5 host–guest challenge: Are we doing better?

The ability to computationally predict protein-small molecule binding affinities with high accuracy would accelerate drug discovery and reduce its cost by eliminating rounds of trial-and-error synthesis and experimental evaluation of candidate ligands. As academic and industrial groups work toward this capability, there is an ongoing need for datasets that can be used to rigorously test new computational methods. Although protein–ligand data are clearly important for this purpose, their size and complexity make it difficult to obtain well-converged results and to troubleshoot computational methods. Host–guest systems offer a valuable alternative class of test cases, as they exemplify noncovalent molecular recognition but are far smaller and simpler. As a consequence, host–guest systems have been part of the prior two rounds of SAMPL prediction exercises, and they also figure in the present SAMPL5 round. In addition to being blinded, and thus avoiding biases that may arise in retrospective studies, the SAMPL challenges have the merit of focusing multiple researchers on a common set of molecular systems, so that methods may be compared and ideas exchanged. The present paper provides an overview of the host–guest component of SAMPL5, which centers on three different hosts, two octa-acids and a glycoluril-based molecular clip, and two different sets of guest molecules, in aqueous solution. A range of methods were applied, including electronic structure calculations with implicit solvent models; methods that combine empirical force fields with implicit solvent models; and explicit solvent free energy simulations. The most reliable methods tend to fall in the latter class, consistent with results in prior SAMPL rounds, but the level of accuracy is still below that sought for reliable computer-aided drug design. Advances in force field accuracy, modeling of protonation equilibria, electronic structure methods, and solvent models, hold promise for future improvements.     

Do we fully understand what controls chemical selectivity?

Reaction rates and product selectivity of kinetically controlled reactions are not always sufficiently described by standard RRKM or TST theory. Reactions taking place on potential energy surfaces featuring a valley ridge inflection point belong to this class of reactions. Though various research groups could show that reaction path bifurcations are far from being an exception in organic reactions the underlying principles that govern product distributions of those bifurcating reaction pathways are yet not fully understood. This Perspective has the intention to provide an overview of how far our understanding and the development of the theoretical foundation have progressed.     

A decade of yeast surface display technology: where are we now?

Yeast surface display has become an increasingly popular tool for protein engineering and library screening applications. Recent advances have greatly expanded the capability of yeast surface display, and are highlighted by cell-based selections, epitope mapping, cDNA library screening, and cell adhesion engineering. In this review, we discuss the state-of-the-art yeast display methodologies and the rapidly expanding set of applications afforded by this technology.     

Photochemical properties of carotenoids: what can we get from the VB model?

Photo-isomerization and anti-oxidation of carotenoids have been studied for many years be-cause of their diverse roles in photobiology, photochemistry and photomedicine[1—6]. The experi-mental works revealed that the changes in the geometry between S0 (the ground state) and T1 (the first triplet state) states are very important for the two processes. Meanwhile, theoretical studies have also been carried out to investigate these processes. The polyenes have usually been used as the models for…     

Paradigms and paradoxes: what are the 54 electron affinities of O2?

Only one electron affinity of oxygen, 43(1) kJ mol⁻¹ is generally cited since the molecular orbital theory anion bond order [3/4] gives an electron affinity, 14 kJ mol⁻¹. However, electron correlation rules predict 27 bonding and 27 antibonding spin orbital coupling states. The relative bond orders (RBOs), 12/13 to [1/4] and the 13 valence electrons of superoxide are used to calculate electron affinities 103 to −243 kJ mol⁻¹ consistent with experimental and theoretical values. These are used to construct 54 ionic Morse potentials.     

Structure and reactivity of the polarised liquid–liquid interface: what we know and what we do not

Charge transfer phenomena at the interface between two immiscible electrolyte solutions (ITIES) are electrochemical reactions taking place in soft media. Owing to their liquid nature, the ITIES shows a large panel of electrochemical reactions including electron transfer reactions, ion transfer reactions, coupled electron–ion transfer reactions or biomimetic redox reactions. Nevertheless, the mechanisms by which these reactions proceed are yet to be fully understood. The goal of this short review is to summarise the work accomplished over the past decades towards the elucidation of the structure and reactivity at the ITIES, highlighting the main questions still to be answered.     

What are we determining using gas chromatographic multiresidue methods: tralomethrin or deltamethrin?

The analytical behaviour of the relatively new pyrethroid insecticide tralomethrin has been evaluated by using gas chromatography (GC) with electron-capture and mass spectrometry (MS) detectors, and liquid chromatography (LC)-atmospheric pressure ionization mass spectrometry with electrospray interfacing. Under the GC conditions commonly used in pesticide residue analysis, it was found that tralomethrin is transformed into deltamethrin (in a reproducible way) in the injector port of the GC system. Results obtained in this work indicate that the GC multiresidue methodologies routinely applied in the analysis of pyrethroid pesticides in foods cannot distinguish between these two pesticides, and the chromatographic signal obtained at the retention time of deltamethrin/tralomethrin can be really quantified as either deltamethrin or tralomethrin, including when it is confirmed as deltamethrin by MS. Under the LC-MS conditions assessed in this work, deltamethrin and the two diasteroisomers of tralomethrin were well separated and identified.