Prochiral and pseudoasymmetric centers: Implications of recent definitions

New definitions of prochiral and of pseudoasymmetric elements have been proposed by Prelog and Helmchen [Helv. Chim. Acta55, 2581 (1972)]. The revised definition of prochiral centers would fail to identify many centers bearing like ligands that can be distinguished experimentally. The new definition of the pseudoasymmetric center would cause some that were previously so designated to be considered chiral. Whenever this occurs, concepts like retention and inversion of configuration would no longer have their customary meaning. Concomitant changes in the sequence subrules would not always provide reliable information about the possibilities of stereoisomerism. A modification of the rules is outlined which would avoid this, but secure similar benefits.     

Summary of ISO/TC 201 standard: XXXIII,ISO 18115:2001/Amd. 2:2007—Surface Chemical Analysis—Vocabulary—Amendment 2

This International Standard adds a further 87 terms to this Vocabulary series, many for secondary ion mass spectrometry, elastic peak electron spectroscopy and reflected electron energy loss spectroscopy, together with 76 acronyms for scanned probes, 33 definitions of scanned probe techniques, 6 terms for contact mechanics and 147 terms for concepts in scanned probe analysis. This brings the total number of terms and acronyms to over 750 in these documents. The terms cover words or phrases used in describing the samples, instruments and theoretical concepts involved in surface chemical analysis. Copyright © 2008 John Wiley & Sons, Ltd.     

Absolute and/or relative detection limits in laser-based analysis: the end justifies the means

The absolute limit of detection usually expresses the minimum amount of analyte detectable, while the relative limit of detection refers to the minimum concentration of analyte detectable. These concepts and their differences are obviously familiar to all analytical spectroscopists. Nevertheless, the two definitions are used liberally in the literature. For example, it is not uncommon to refer to exceptional sub-femtograms detection limits for a technique used to analyse ultratrace levels of an element in water and to a modest part per million detection limit of another technique used to characterise the microdistribution of an element in a sample mass of about one microgram. In this paper, an attempt is made to point out that the terms "ultratrace analysis" and "microanalysis" must refer to two conceptually different approaches and that there are cases in which one definition is more appropriate than the other. It is argued that, while there is no objection in reporting both detection limits when a single technique is evaluated, one has to be careful in choosing the most appropriate definition when different analytical techniques are compared.     

Absolute and/or relative detection limits in laser-based analysis: the end justifies the means

The absolute limit of detection usually expresses the minimum amount of analyte detectable, while the relative limit of detection refers to the minimum concentration of analyte detectable. These concepts and their differences are obviously familiar to all analytical spectroscopists. Nevertheless, the two definitions are used liberally in the literature. For example, it is not uncommon to refer to exceptional sub-femtograms detection limits for a technique used to analyse ultratrace levels of an element in water and to a modest part per million detection limit of another technique used to characterise the microdistribution of an element in a sample mass of about one microgram. In this paper, an attempt is made to point out that the terms ultratrace analysis and microanalysis must refer to two conceptually different approaches and that there are cases in which one definition is more appropriate than the other. It is argued that, while there is no objection in reporting both detection limits when a single technique is evaluated, one has to be careful in choosing the most appropriate definition when different analytical techniques are compared.     

Alphabetical index of defined terms and where they can be found Part I: A–F

 This paper, the first of a series of three, presents the first part of an alphabetical index of approximately 1400 terms taken from various international official standards, protocols and guides. The terms listed include those encountered in the analytical sector, related to sampling, quality, conformity assessment, standardisation, measurement and related statistics. The definitions themselves are not included. The purpose of the index is to provide the user with a ready means of establishing whether a particular term has an official definition and if so where it is located. In doing so it makes location of officially defined terms more straightforward and so encourages their use. It also highlights those terms which are defined in several places, indicating the degree of equivalence between the definitions from the different sources. This first part of the index covers A–F and additionally lists terms regularly encountered but thought to have no officially recognised definition.     

Estimation of the limit of detection using information theory measures

Definitions of the limit of detection (LOD) based on the probability of false positive and/or false negative errors have been proposed over the past years. Although such definitions are straightforward and valid for any kind of analytical system, proposed methodologies to estimate the LOD are usually simplified to signals with Gaussian noise. Additionally, there is a general misconception that two systems with the same LOD provide the same amount of information on the source regardless of the prior probability of presenting a blank/analyte sample. Based upon an analogy between an analytical system and a binary communication channel, in this paper we show that the amount of information that can be extracted from an analytical system depends on the probability of presenting the two different possible states. We propose a new definition of LOD utilizing information theory tools that deals with noise of any kind and allows the introduction of prior knowledge easily. Unlike most traditional LOD estimation approaches, the proposed definition is based on the amount of information that the chemical instrumentation system provides on the chemical information source. Our findings indicate that the benchmark of analytical systems based on the ability to provide information about the presence/absence of the analyte (our proposed approach) is a more general and proper framework, while converging to the usual values when dealing with Gaussian noise.     

Thermodynamics and statistical mechanics of the ideally polarisable electrode: Gibbs isotherm and surface tension

A definition of the ideally polarisable electrode which allows a general statistical mechanical treatment is given, comparisons with the usual thermodynamic approach being made. It is shown that, with this definition, the system behaves as a pure capacitance to an imposed alternating potential of sufficiently low frequency. The equilibrium states of the system are described by the grand canonical distribution. Thermodynamic functions, given in terms of the grand canonical partition function, can be computed in molecular terms. In particular, general expressions for the surface tension and the pressure are obtained, and compared to those proposed by various authors. The separation of the pressure into electrical and non-electrical parts is analyzed. Expressions are given for the electrochemical potentials of charged and of dipolar species. With these microscopic definitions, the Gibbs adsorption isotherms and the Lippmann equation are derived. For several simple models, including that of Gouy and Chapman for an ionic solution and a metal electrode, these relations are explicity considered. The inadmissability, in a coherent model, of reducing the solvent to a medium of fixed dielectric constant, is emphasized.     

Systems theory in analysis-I: definitions and interpretations in the basic terms of systems theory

The twelve basic terms of systems theory-system, element, relation, function, structure, organization, feedback, Black Box, model, input-output analysis, trial-and-error method, simulation-are given general definitions and are also interpreted in terms of chemical analysis. The distinction between a generally acceptable brief and precise definition and an interpretation peculiar to one particular specialized field avoids, in the case of universally used terms, a biased view and conception. Simple systems are deliberately chosen and the terms used are clarified by means of diagrams. A system-oriented approach is outlined, with feedback-coupled stages (defining the problems, setting the limits, designing the model, simulation) which has proved useful in practical systems analysis and in systems design. The working group will report, in subsequent publications, on specific analytical systems which are of considerable importance in automation. Those with special interests in these fields are warmly invited to communicate their critical opinions, suggestions, and examples of interpretations based on these definitions.     

Hydrogen bonding definitions and dynamics in liquid water

X-ray and neutron diffractions, vibrational spectroscopy, and x-ray Raman scattering and absorption experiments on water are often interpreted in terms of hydrogen bonding. To this end a number of geometric definitions of hydrogen bonding in water have been developed. While all definitions of hydrogen bonding are to some extent arbitrary, those involving one distance and one angle for a given water dimer are unnecessarily so. In this paper the authors develop a systematic procedure based on two-dimensional potentials of mean force for defining cutoffs for a given pair of distance and angular coordinates. They also develop an electronic structure-based definition of hydrogen bonding in liquid water, related to the electronic occupancy of the antibonding OH orbitals. This definition turns out to be reasonably compatible with one of the distance-angle geometric definitions. These two definitions lead to an estimate of the number of hydrogen bonds per molecule in liquid simple point charge/extended (SPC/E) water of between 3.2 and 3.4. They also used these and other hydrogen-bond definitions to examine the dynamics of local hydrogen-bond number fluctuations, finding an approximate long-time decay constant for SPC/E water of between 0.8 and 0.9 ps, which corresponds to the time scale for local structural relaxation.     

Reflections About Mathematical Chemistry

A personal account is presented for the present status of mathematical chemistry, with emphasis on non-numerical applications. These use mainly graph-theoretical concepts. Most computational chemical applications involve quantum chemistry and are therefore largely reducible to physics, while discrete mathematical applications often do not. A survey is provided for opinions and definitions of mathematical chemistry, and then for journals, books and book series, as well as symposia of mathematical chemistry.     

Alphabetical index of defined terms and where they can be found Part III: R–Z

 This paper, the third of a series of three, presents the final part of an alphabetical index of approximately 1400 terms taken from various international official standards, protocols and guides. The terms listed are those encountered in the analytical sector, related to sampling, quality, conformity assessment, standardisation, measurement and related statistics. The definitions themselves are not included. The purpose of the index is to provide the user with a ready means of establishing whether a particular term has an official definition and if so where it is located. In doing so it makes location of officially defined terms more straightforward and so encourages their use. It also highlights those terms which are defined in several places, indicating the degree of equivalence between the definitions from the different sources. This third part of the index covers R–Z.     

Alphabetical index of defined terms and where they can be found¶Part II: G–Q

 This paper, the second of a series of three, presents the second part of an alphabetical index of approximately 1400 terms taken from various international official standards, protocols and guides. The terms listed are those encountered in the analytical sector, related to sampling, quality, conformity assessment, standardisation, measurement and related statistics. The definitions themselves are not included. The purpose of the index is to provide the user with a ready means of establishing whether a particular term has an official definition and if so where it is located. In doing so it makes location of officially defined terms more straightforward and so encourages their use. It also highlights those terms which are defined in several places, indicating the degree of equivalence between the definitions from the different sources. This second part of the index covers G–Q.     

Definitions and methods of calculation of the temperature-programmed retention index, ITP: II. Comparison of ITP values calculated according to different definitions

Temperature-programmed retention indices, I_TP, calculated according to three different definitions are compared. The advantages and shortcomings of these definitions are discussed in terms of their theoretical background, accuracy, ease of calculation and applicability. The Generalized Retention Index (GI) seems to be the best definition of I_TP, while Van den Dool's definition and the Extended Kováts Definition are approximate and can be applied only to simple temperature programme.     

Handling large amounts of chemical data

The main aspects of handling large amounts of complex information, in general, and spectroscopic data, in particular, are described and discussed. In the first part, the basic terms and procedures are defined and illustrated with examples from different spectrometries. The items such as the representation of complex data of different types, measurement — and information — pace, metrics of a multi-dimensional space, different types of transformations, information content of a given representation, the concept of a frame, the holistic and reductionistic aspect of information are explained in more detail.In the second part, the organization of complex data with the intention of forming an expert system is discussed. Emphasis is put on the clustering of data, on the criteria for clustering, and on the ways and means governing the formation of hierarchies of clusters and frames they represent. Furtheron, a model for an expert system (which is able to acquire new information, i. e. which is able to learn, and to use the acquired knowledge for predicting the structural features of unknown compounds) based on the hierarchical organization of a large amount of data is outlined.Finally, the prospects and limitations of expert systems based on the hierarchical clustering of large data collections are discussed.     

Temperature-dependent approach to chemical reactivity concepts in density functional theory

The chemical reactivity concepts of density functional theory are studied through a unified view in the temperature-dependent approach provided by the grand canonical ensemble. This procedure leads to a more general perspective that enriches our understanding of the behavior of the average energy and its derivatives with respect to the average number of electrons, provides alternative definitions for those quantities that are “ill defined” at zero temperature, and allows one to determine the relationships among reactivity concepts at any temperature. In particular, it has been found that at high temperatures the parabolic model for reactivity indicators may be justified through the electronic entropy term in the Helmholtz free energy, and that at nonzero temperatures there is an electronic heat capacity contribution to the average energy. In summary, the unified view of the temperature-dependent approach is an important complement to the zero-temperature formulation that clarifies fundamental issues therein.     

Quality and quantity within medicine

The concept of quality is placed both within a historical as well as philosophical light. It is argued that nowadays general and laboratory medicine is a logical extension of economical and social concepts which stem from the beginning of the twentieth century. However, it seems that medicine cannot be explained based entirely upon these concepts. The medical field has a variety of definitions of quality: all depending on the person and/or institution posing the questions. The quality concept sometimes concerns an individual and sometimes a group of individuals. The quality definition and indicator scores are then different. This quantified quality can also be looked upon from an eastern (i.e. Japanese, Chinese, ancient Greece) perspective. The ideal world, framed within a cyclic evaluation between well-defined static situations, does not relate easily with the individualized (quantified quality) western medical world. Nevertheless, we are in search of a quality concept that balances the western industrial model of medicine and the eastern, philosophical approach. Papers published in this section do not necessarily reflect the opinion of the Editors, the Editorial Board and the Publisher. Apart from exceptional circumstances, they are not submitted to the usual referee procedure and go essentially unaltered. Presented at the European Conference on Quality in the Spotlight in Medical Laboratories, 7–9 October 2001, Antwerp, Belgium     

Applicability domain: towards a more formal definition$

Abstract

In recent years the applicability domain (AD) of a prediction system has become an important concern in (Q)SAR modelling, especially in the context of human safety assessment. Today AD is an active research topic, and many methods have been designed to estimate the adequacy of a model and the confidence in its outcome for a given prediction task. Unfortunately, the wide spectrum of techniques developed for this purpose is based on various definitions of the concept of AD, often taking into account different types of information. This variety of methodologies confuses the end users and makes the comparison of the AD for different models almost impossible. In this article, we demonstrate that AD is not a monolithic concept and can be broken down into three well-defined sub-domains assessing confidence at the model, prediction and decision levels, respectively. By leveraging this separation of concerns we have an opportunity to clarify, formalize and extend the definition of AD. We propose a framework that captures this new vision with the aim to initiate a global effort to converge towards a common AD definition within the (Q)SAR community.