Metrology and protometrology: the ordinal question

Laboratory medicine provides results for quantities as well as for properties having no magnitude. The terminology of the latter is less well established and sources are contradictory. Two recent papers on “protometrology” published in this journal offer an opportunity to discuss the necessary concept systems. The delineations of “metrology” versus “protometrology”, “observation” versus “measurement”, and the generic division of “property” are examined with emphasis on avoiding conflict with the International Vocabulary of Metrology. It is suggested that having “examination” as a top generic concept coupled with systematic modifiers for division, especially ‘nominal’ and ‘ordinal’, is a preferable terminological solution.

The meaning of ‘concentration’

Terminology within a small laboratory community can be informal without danger of misunderstanding, but communication with a wider audience and not least in publications, needs unequivocal terms for defined concepts. As an example, the many meanings of “concentration” are explored to present a systematic nomenclature, including a concept diagram.

A novel Ce<Superscript>III</Superscript>-cyclam type complex and its redox chemistry in aqueous solutions

A new Ce^III complex was synthesized by mixing the ligand “dioxocyclam” with Ce^III ions at pH 8.0 and its redox properties were investigated.

Hermann Jahn and Rudolf Renner of the Jahn–Teller and Renner–Teller effects

Vibronic interactions have received increasing attention in modern structural chemistry. Edward Teller played a pioneering role in understanding and describing them during the “molecular physics” period of his scientific career. Very little is known about the two scientists who contributed significantly to our knowledge about these effects and whose names have become associated with Teller’s. This Editorial is devoted to Hermann Jahn and Rudolf Renner and attempts to lift them out of oblivion by paying them tribute for their contributions.

Introduction

These are the proceedings of an international meeting on “Structural Aspects of the Intercellular Matrices of Plants and Animals”, June 23–26, 2008 in St. Tropez, France. The meeting was sponsored by the Matrix Biology Institute (Edgewater, New Jersey, USA) and Phillips Hydrocolloids Research Ltd, London, UK, and organized by Janet Denlinger and Glyn Phillips (co-editors of this Special Issue), with Endre A. Balazs at Villas Nifnaha and Hylan, Parc de la Moutte, St. Tropez, France.

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Why take chemistry stoically? The case of Posidonius

This paper analyzes views of the Stoic philosopher Posidonius (1st century BC) in the light of modern Chemistry. I propose that Posidonius’ account on “generation and destruction” bears noteworthy similarities to the scientific notions of chemical elements, chemical species, nuclear reactions, and the law of conservation of mass. I find that his views compare favorably also with our understanding of chemical change at solid surfaces. Provided his thought is correctly placed in the cultural context of his day, I argue that Posidonius deserves a previously un-acknowledged consideration in the historical background of modern Chemistry.

How chemistry shifts horizons: element, substance, and the essential

In 1931 eminent chemist Fritz Paneth maintained that the modern notion of “element” is closely related to (and as “metaphysical” as) the concept of element used by the ancients (e.g., Aristotle). On that basis, the element chlorine (properly so-called) is not the elementary substance dichlorine, but rather chlorine as it is in carbon tetrachloride. The fact that pure chemicals are called “substances” in English (and closely related words are so used in other European languages) derives from philosophical compromises made by grammarians in the late Roman Empire (particularly Priscian [fl. ~520 CE]). When the main features of the constitution of isotopes became clear in the first half of the twentieth century, the formal (IUPAC) definition of a “chemical element” was changed. The features that are “essential” to being an element had previously been “transcendental” (“beyond the sphere of consciousness”) but, by the mid-twentieth century the defining characteristics of elements, as such, had come to be understood in detail. This amounts to a shift in a “horizon of invisibility” brought about by progress in chemistry and related sciences. Similarly, chemical insight is relevant to currently-open philosophical problems, such as the status of “the bundle theory” of the coherence of properties in concrete individuals.

A model for high-surface-area porous Nafion™-bonded cathodes operating in hydrogen–oxygen proton exchange membrane fuel cells (PEMFCs)

A critical discussion of dioxygen reduction kinetics using the Tafel (for the irreversible cathode process) and the Butler–Volmer (anode process) rate equations has been used to evaluate the accuracy of “standard” modeling interpretations of experimental cell potential current (E–I) plots. The potential–current curve for what is believed to be an optimized Nafion™-bonded fuel cell cathode was analyzed. It appears to behave as a well-ordered diffusional system and shows high electrocatalyst utilization based on its electrocatalytic and gas diffusion characteristics. The electrode appears to perform as expected, without any anomalous characteristics showing any lower than expected electrocatalyst utilization. Any improvement in electrode performance, which is certainly desirable, seems to demand an improved diffusional structure, barring any potential (although unlikely) change in electrochemical kinetic characteristics.

Metrological traceability: I make it 42; you make it 42; but is it the same 42?

The paper reproduces a talk given at a 2-day symposium on quality assurance in chemistry held in Brisbane, Australia in 2005. Intended for an audience of analysts in the field, the theme of the symposium drew inspiration from the series of books by Douglas Adams “The Hitchhiker's Guide to the Galaxy”. An introduction to basic concepts of metrological traceability is followed by a discussion of practical steps to ensure metrological traceability of field measurement results. The relationship between metrological traceability and comparability of measurement results is discussed. To achieve metrological traceability in the field, the use of appropriate certified reference materials for calibration is recommended. Examples of atmospheric carbon dioxide and roadside breathalyzer measurements are given.

Interaction force diagrams: new insight into ligand-receptor binding

A method is described to calculate and visualize the interaction forces of ligand-receptor complexes. Starting from an X-ray crystallographic structure, a “thawing” procedure results in a force-field energy-minimized geometry which is close to the crystallographic starting point. By subtracting non-bonded interactions of the ligand with each amino acid residue and using the resulting force vectors to describe the slope of the remaining potential, two types of interaction force diagrams are created; the first shows the direction of the force vectors in 3D and the second shows the magnitude of the force vectors. The latter representation leads to definition of an ‘Interaction Force Fingerprint’ (IFFP) which is characteristic of the ligand-receptor binding. IFFPs are used to discuss ligand binding in the human estrogen receptors ERα and ERβ, and provide new insight into ligand selectivity between receptor isoforms. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.

Shape selectivity in embedded polar group stationary phases for liquid chromatography

Seven columns with embedded polar functionality were evaluated for use in liquid chromatography with a focus on molecular shape recognition. Tests based on Standard Reference Material 869b Column Selectivity Test Mixture for Liquid Chromatography and the Tanaka test indicate that only two of the phases are slightly shape selective at 20 °C. The shape recognition characteristics of the phases appear to be directly related to the density of the embedded polar ligands and the temperature of the separation, consistent with trends observed with conventional hydrocarbon phases.

Electron free energy levels in oxidic solutions: relating oxidation potentials in aqueous and non-aqueous systems

We provide background to the problem of describing the state of redox couples in different types of solvent media ranging from acidic aqueous solutions to high temperature molten silicates, pointing out the essential similarity between these solvent media in Lewis acid–base terms. We review the adaptation of the Gurney proton energy level diagram approach to the case of electron transfer processes. Using data from various spectroscopic and analytical chemistry sources, we review the construction of electron free energy level diagrams for redox couples in aqueous and non-aqueous systems using, as a common reference, the potential of the oxygen gas (1 atm)/oxide ion couple in the solution of interest. We emphasize the anomalous effect of “oxide ion activity” (mean ionic activity of alkali oxide) on the state of equilibrium and interpret this in terms of oxide ion transfers that accompany electron transfers. After showing the essential agreement between recent direct electrochemical assessments of the energy levels and those deduced in our original analysis of oxidic melts of different glass formers, we provide an interpretation of the apparent “oxide ion transfer” in terms of the differential medium polarization by the two redox species involved in the equilibrium. We anticipate the extension of these ideas to redox chemistry in the currently burgeoning field of “ionic liquids” in its recent ambient temperature liquid incarnation. Dedicated to the 85th birthday of John O’M. Bockris.

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Encapsulating of single quantum dots into polymer particles

Single semiconductor quantum dots were embedded into polymer particles with diameters below 0.1 μm by an emulsion polymerization procedure or via a secondary dispersion approach. The photoluminescence properties of the nanocrystals are retained upon encapsulation, as demonstrated by fluorescence confocal microscopy.

The effect of cationic disorder on the optical and electrochemical behavior of nanocrystalline ZnO preparedfrom peroxide precursors

The relation between particle size and the optical and electrochemical behavior of nanocrystalline ZnO was studied on materials prepared by the thermal decomposition of zinc peroxide. The formation of zinc oxide starts at 180°C and yields particles of characteristic size bigger than 10 nm. Smaller particles (r∼2–5 nm) may be prepared at reduced pressure and at a temperature of 150°C. The particle radius of synthesized nanocrystals increases proportionally to synthesis temperature. Regardless of actual particle size, synthesized ZnO samples show cationic disorder, with Zn distributed between 2b and 2a sites. The fraction of “octahedrally” coordinated Zn in 2a position decreases with increasing synthesis temperature. Zn disorder causes a narrowing of band gap, which results in the “red shift” of the absorption edge in the UV–Vis spectra of prepared samples with respect to bulk ZnO. The effect of the disorder on the band gap width is partially compensated by quantum size effects when the characteristic particle size drops below 5 nm. A decrease in particle size results in an asymmetric shift of valence and conduction band edges, which can be assigned to uneven effective masses of electrons and holes in nanocrystalline ZnO. Prepared nanocrystalline samples were (photo)electrochemically active; their activity, however, decreases with particle size.

Wilhelm Ostwald’s energetics 3: energetic theory and applications,part II

This is the third of a series of essays on the development and reception of Wilhelm Ostwald’s energetics. The first essay described the chemical origins of Ostwald’s interest in the energy concept and his motivations for seeking a comprehensive science of energy. The second essay and the present one discuss his various attempts, beginning in 1891 and extending over almost 3 years, to develop a consistent and coherent energetic theory. A final essay will consider reactions to this work and Ostwald’s replies, and will also seek to evaluate his program of research. Ostwald’s project—to reconstruct physics and chemistry “as a pure energetics”—is worth attending to for several reasons: first, because Ostwald did ground-breaking work in chemistry (he was awarded a Nobel Prize in 1909 for his studies in catalysis and rates of reaction); second, because an important school of physical chemistry formed around him at Leipzig, a school that promoted his ideas; and, finally, because he was a prominent and vigorous participant in debates at the end of the nineteenth century concerning the proper course of physical theory.

The advent of chemical symbolism in the art of Sonya Rapoport

This paper explores the use of chemical symbolism in works by the new media artist Sonya Rapoport, with a focus on the pivotal Cobalt series from the late 1970s. These works, drawings on computer printouts generated by research at the Lawrence Berkeley Laboratory, respond to experiments in nuclear chemistry. They mark the beginning of three productive decades in which Rapoport produced a variety of images related to chemistry in her work. She states, “I looked for authentic research projects that were interesting to me, preferably with captivating pictorial subject matter. Then came the creative chaotic process of resolving a cohesive product that combined scientific research with art concept.” Rapoport had an unusual degree of access to scientific materials through her husband, organic chemist Henry Rapoport, a faculty member at the University of California, Berkeley. At the time of production, these works were outside mainstream art world interests and they have received little critical attention. This paper examines the development of Rapoport’s images and places her use of chemical references in context in her lifetime of work.

A century on from Dmitrii Mendeleev: tables and spirals,noble gases and Nobel prizes

Mendeleev’s failure to represent the periodic system as a continuum may have hidden from him the space for the noble gases. A spiral format might have revealed the significance of the wide gaps in atomic mass between his rows. Tables overemphasize the division of the sequence into ‘periods’ and blocks. Not only do spirals express the continuity; in addition they are more attractive visually. They also facilitate a new placing for hydrogen and the introduction of an ‘element of atomic number zero’.

Environmental metabolomics: new insights into earthworm ecotoxicity and contaminant bioavailability in soil

Environmental metabolomics is a growing and emerging sub-discipline of metabolomics. Studies with earthworms have progressed from the initial stages of simple contact exposure tests to detailed studies of earthworm responses in soil. Over the past decade, a variety of endogenous metabolites have been identified as potential biomarkers of contaminant exposure. Furthermore, metabolomic methods have delineated responses from sub-lethal exposure of earthworms to polycyclic aromatic hydrocarbons and metals in soil suggesting that environmental metabolomics may be used as a direct measure of contaminant bioavailability in soil. Environmental metabolomics has the potential to fill knowledge gaps related to earthworm toxicity and contaminant bioavailability. However, challenges with metabolite quantification and limited systems-level models of metabolic data require improvement before detailed models of “normal” responses can be developed and used routinely in assessment of contaminated sites. Nonetheless, environmental metabolomics is poised to improve our fundamental understanding of earthworm responses and toxicity to contaminants in soil. Figure Principal component analysis (PCA) scores plots of earthworm metabolic profiles measured by ¹H NMR spectroscopy after exposure to sub-lethal concentrations of phenanthrene in soil.

Spectrometric and theoretical investigation of the structures of Cu and Pb/DTPA complexes

Spectrometric and theoretical tools have been employed in this study in order to elucidate the structures of DTPA (diethylenetriaminepentaacetic acid) complexed to copper and lead. Mass spectrometry allowed determining the 1:1 stoichiometry of metal:ligand, while infrared spectroscopy demonstrated that both N and O are sites for complexation. ¹³C NMR analysis showed the existence of free and complexed carboxyl groups, due to a straight singlet at 180.7 ppm (free carboxylic ¹³C) and to a broad signal at 179.3 ppm (complexed carboxylic ¹³C, ² J _Pb…O=C). A distorted NMR signal were observed for the Cu–DTPA carboxyl group, due to the Cu²⁺ paramagnetism. Based on the spectrometric evidences for the metal–DTPA structures, DFT optimizations were carried out and an octahedral-like arrangement for the Cu complex and a “shell-like” arrangement for the Pb complex, both hexa-coordinated, were then proposed for the structures of the titled compounds.

A note on Michael Weisberg’s: challenges to the structural conception of chemical bonding

Michael Weisberg’s recent 2007 paper on the chemical bond makes the claim that the chemical notion of the covalent bond is in trouble. This note casts doubts on that claim.