Software and internet resources for capillary electrophoresis and micellar electrokinetic capillary chromatography

The purpose of the contribution is to show how software and the internet have changed the way in which we carry out research, and what additional possibilities these new resources and tools provide. The internet and e-mail broaden our horizon for cooperation. There are no borders for information exchange: our library is a virtual one, electronic databases are at our fingertips. E-mail discussion groups provide an electronic community of CE users. Such forums have provided a basis for worldwide scientific cooperation amongst scientists; the present contribution is only one of several examples. Estimation software provides us with estimates of component properties in those cases where this information is not available from literature or from experiments (an estimated value is better than no value). Several examples will illustrate the use of estimation software in capillary zone electrophoresis and micellar electrokinetic capillary chromatography. Simulation software presents visualization of experimental results to be expected, both as a training tool and as the first step in method development. Other simulations yield valuable insights into phenomena that are not readily accessible experimentally for reasons of size or time-scale.     

Automated protein design and sequence optimisation: scoring functions and the search problem

Advances in molecular biology may mean that almost any protein sequence can be synthesised, but perhaps this has served to highlight the inadequacy of theoretical work. For a given protein fold, it is probably not possible to reliably predict an "ideal" sequence. We identify and survey several aspects of the problem. Firstly, it is not clear what is the best way to score a sequence-structure pair. Secondly, there is no consensus as to what the score function should represent (free energy or some abstract measure of sequence-structure compatibility). Finally, the number of possible sequences is astronomical and searching this space poses a daunting optimisation problem. These problems are discussed in the light of recent experimental successes.     

Methodology for the Study of Toxicology in Combustion: Application to PVC

I will try to give some idea of how we study toxicology, what it means, and I will then discuss some aspects of our recent studies with polyvinyl chloride) polymers. I should like also to discuss briefly the analytical methods used. May I point out that during the last three and a half years, we have investigated about 500 fire injuries and deaths. This work is done in collaboration with the city and county fire services by using two-way radio. Two months ago, we began what is probably the most important aspect of this work: paramedical teams arriving at the scene of the fires now take blood and breath samples from the fire victims the moment that they are removed from the fire scene, thus enabling us to get some idea of the immediate effects. Previously, we have been obtaining this sort of information after the individuals have reached the hospital, by which time they have been put on oxygen and hyperventilated so that it does not reflect what happens during the fire.     

Concepts of photochemical damage of Photosystem II and the role of excessive excitation

Photoinhibition is one of the most controversial topics in photophysiology. Well into the 21 st century, scientists have not agreed on the mechanism of action, primary site, and roles of excess energy absorbed by photosynthetic pigments. It is recognized that Photosystem II is the most fragile component during photoinhibition and that excess excitation absorbed by the photosynthetic pigments has a strong impact on it. Consensus is yet to come on terminology, guidelines to study photoinhibition, or boundaries of what can be considered photodamage. Some of these controversies are the result of how we understand the phenomenon of photoinhibition, as this is what determines a given experimental design. Thus, how we understand photodamage depends on the philosophical approach of each group. While some efforts have been made in the parametrization of Photosystem II photoinhibition, an updated review about the concepts of photoinhibition of Photosystem II and how to study it is still pending. In this work, a review of the concepts used in the field of photoinhibition is presented, accompanied by a synopsis on the history and mechanisms of action.     

Blood glucose monitoring with smartphone as glucometer

In this short communication, we redefine smartphone and enable it to monitor blood glucose as glucometer. The proposed smartphone is not only a mobile phone but also a medical device‐glucometer. An electrometer module, acquiring the electrochemical current from the disposable enzymatic test strip on which a 0.5 μL human peripheral whole blood drop is placed, was integrated in the smartphone. The medical smartphone is capable of directly measuring blood glucose concentration and uploading into personal health center by the 4G mobile communication internet.     

Avoiding pitfalls in electrokinetic remediation: robust design and operation criteria based on first principles for maximizing performance in a rectangular geometry

The role of the symmetrical conditions on the temperature field is studied in a capillary of rectangular geometry. By using the generalized flux, i.e., Robin-type of boundary conditions for the heat transfer in such a capillary domain, it is possible to identify clearly conditions under which the velocity field will depend crucially on the basic parameters and, therefore, what types of flow regimes may arise in the capillary channel. In addition, it is possible to conclude under what conditions the velocity field will not at all depend on some of these. The behavior is intimately tied to the symmetrical conditions associated with the temperature field in the system. A "skew" or asymmetrical parameter, W infinity, has been identified in the temperature profiles; this parameter is useful for studying the role of the symmetrical conditions on the hydrodynamics field and in determining a set of a priori design criteria that limits the range of values of the parameters. Several numerical examples are presented to show the flow situations found in the system.     

Estimation of exposure levels by measurements and models

Summary Results from environmental and biological monitoring programs are abundant, but it is a question to what extent such data can be used for exposure assessments. The quality of such data depends not only on sampling and analytical errors, but also, and probably more, on the sampling strategy used. Therefore, uncritically use of such results can be biased and associated with large variations. The size of bias between two studies carried out in the same industry was found to be a factor of 5–7. Samples that are not representative of the exposed population studied are misleading. An estimation of exposure to cobalt in the porcelain industry illustrates the distinction between biological measurement data and air cobalt measurement data done on selected individuals. Following improvement of the working environment during the period 1983–1990, the change of cobalt concentration in urine indicates a reduction of cobalt exposure with a factor of 10, but air monitoring data do not verify that figure. Furthermore, results must always be interpreted with caution, when used beyond the purpose for what they were originally made. Great care should be taken to secure that data are representative and a quality assurance-quality control program should be used to ensure data quality.     

Special Collection: Computational Chemistry

Chemists know well the value of an experimental or a theoretical result, but what is the value of a computational result? Simulation is neither theory nor experience, nor a mere calculation tool, but a genuine way of approaching reality that is transforming the scientific method. In some cases, it offers explanations to observations or experiments that seem incomprehensible because they are too complex. In this case, the computation serves as a relief. An experiment that converges with a certain computation has more scientific value than an experiment that does not converge with anything at all. In other cases, contribution of computational chemistry is essential because there is no experimental manner to determine what happens during a chemical process; for instance, in the path from reactants to products in (fast) reactions. Now, computational chemistry provides additional information that is not possible to obtain from experiments, so it is a valuable complement to them. Indeed, fruitful synergy between computation and experiment has led to the approach of theory-driven experimentation. Finally, computational chemistry helps to legitimize models or theories that have little opportunity to be contrasted with reality. In this situation, computational chemistry is not experience, but it does substitute it in relation to theory. In the present special collection, we have examples of the different ways computational chemistry helps chemists to interpret the electronic and molecular structure of molecules and their reactivity.     

Does a molecule have structure?

The classical model of the molecule assumes that it has a definite shape and structure like a mechanical object in the world of possible experience. This study deals with this assumption so as to shed some light on the foundations of the model. Arguments based on Kant’s theory of transcendental idealism suggest that neither shape nor structure are attributes of the molecule, but are rather contributions of the subject. This claim has great relevance to the questions of (1) whether or not a quantum treatment of the molecule can derive structure without recourse to any approximation, and (2) the possible existence of emergence and downward causation. The answer to the first question is in the negative, and to the second is that agnosticism is the only possible attitude to have toward this problem. We are creatures who can only imagine what is going on by observing phenomena. All that is accessible to us is the modal structure of the model. The causal structure of the real system is not. From the same point of view and taking the concept of the affordance into account, the adequacy of the concept of molecular structure will be argued. The point is to specify what objects the concept can legitimately be applied to. Also briefly discussed in relation to shape and structure is the idea that molecular chirality might be a probe to reveal the nature of space.     

Control of Nanospaces with Molecular Devices

Cavitands and capsules define nanoliter spaces for recognition, isolation and reactions of small molecules. These systems are usually self-assembled and factors such as solvent size, stoichiometry, and packing factors determine what goes into the spaces. Here we examine two switching devices to control what and when guests get in and out of these hosts: bipyridyl-metal chelation and azobenzene photoisomerization. The effects are reversible by treatment with conventional chelating agents and brief heating, respectively. Accordingly, it is possible to trigger reactions that take place within a cylindrical capsule by light, even though the reaction process is not photochemical by nature. Likewise the presence of metals can regulate reactions without acting as direct catalysts.     

On the nature of intramolecular dephasing processes in polyatomic molecules

Intramolecular dephasing processes in polyatomic molecules are discussed with relation to coherent transient spectroscopy, radiationless transitions, multiphoton molecular processes, and overtone spectroscopy. A distinction is made between proper and improper dephasing processes (PDP, IDP) depending on whether they arise due to changes in populations or not. It is shown that the type of experiment and, consequently, the way we partition the hamiltonian are closely related to this distinction. We consider several experimental and theoretical approaches for studying intramolecular dynamics and discuss under what conditions it is necessary and useful to introduce explicitly dephasing interactions.     

New insights into the meaning and usefulness of principal component analysis of concatenated trajectories

A comparison between different conformations of a given protein, relating both structure and dynamics, can be performed in terms of combined principal component analysis (combined‐PCA). To that end, a trajectory is obtained by concatenating molecular dynamics trajectories of the individual conformations under comparison. Then, the principal components are calculated by diagonalizing the correlation matrix of the concatenated trajectory. Since the introduction of this approach in 1995 it has had a large number of applications. However, the interpretation of the eigenvectors and eigenvalues so obtained is based on intuitive foundations, because analytical expressions relating the concatenated correlation matrix with those of the individual trajectories under consideration have not been provided yet. In this article, we present such expressions for the cases of two, three, and an arbitrary number of concatenated trajectories. The formulas are simple and show what is to be expected and what is not to be expected from a combined‐PCA. Their correctness and usefulness is demonstrated by discussing some representative examples. The results can be summarized in a simple sentence: the correlation matrix of a concatenated trajectory is given by the average of the individual correlation matrices plus the correlation matrix of the individual averages. From this it follows that the combined‐PCA of trajectories belonging to different free energy basins provides information that could also be obtained by alternative and more straightforward means. © 2014 Wiley Periodicals, Inc.     

On surface conduction and its role in electrokinetics

A review is given of the role of surface conduction in electrokinetics. Experimental evidence is considered to indicate when such conduction has to be considered and to what extent this conduction is carried by charges within the stagnant layer. For non-penetrable surfaces, lateral mobilities of monovalent ions in the stern layer are not much lower than those in bulk and under certain conditions conduction behind the slip plane may be of the same order of magnitude as that beyond it. New experiments on the conductivity of polystyrene latex plugs illustrate these phenomena.     

The flow analysis database on the World Wide Web

The field of flow injection analysis (FIA) is growing rapidly because much applied research is being conducted around the world. This creates a great need for information dissemination across the globe to keep researchers up to date on current research trends. With the internet becoming the tool for global communication, it seems appropriate that support of the growth in FIA should be via this medium. Thus, the flow analysis database (FAD) has been developed as a central resource for bibliographic information on the area of FIA and flow analysis in general.     

Changing Perspectives on the Strategic Use of Microwave Heating in Organic Synthesis

This Personal Account describes collaborative investigations into apocryphal microwave effects in organic chemistry. Focused research on microwave‐assisted organic synthesis has been fraught with confusion, controversy, and misinformation. Microwave heating is an undoubtedly useful tactic for organic synthesis, but whether or not it can offer strategic advantages remains an open question in the minds of many people. (Ironically, those who do not consider it an open question are split as to whether it has been resolved affirmatively or negatively.) Our research in this area is guided by the hypothesis that microwave heating can alter reaction kinetics in ways distinct from what is observable under conventional heating. Here we provide a succinct record of the origins of our interests, our initial queries and associated controversies, and recent efforts to identify, quantify, and begin to leverage selective microwave heating for strategic advantage in organic synthesis.     

Progress in Practice: The Synergy Derived From Knowing Pedagogy as Well as Chemistry

What is the value that comes from consciously and explicitly linking what we know about chemistry with what we do in the classroom? It is tempting to dismiss this question because we are uncomfortable with the implication that there are times when what we do in the classroom is not informed by our personal understanding of chemistry. Yet instructors of introductory chemistry courses often lack the personal understanding, especially the kind that comes from laboratory experience, for significant parts of the course. An experienced general chemistry instructor, for example, probably understands the practical expectations of teaching this subject better than anyone who has recently graduated with a Ph.D. in physical or inorganic chemistry. Although the merits of this situation are worth reflecting on at another time, a reasonable operational assumption is that a substantial portion of the introductory program is defined by its own existence rather than as an identifiable area of specialization. The general chemistry curriculum is flexible to the degree that it can accommodate a variety of backgrounds in its instructors, yet it is constrained by the historical inertia that has defined it. To a lesser yet still significant extent, beginning instructors of organic chemistry face the same problem when their understanding of more specialized topics (such as the synthesis of heterocyclic compounds, transition metal organometallics, carbohydrate and peptide chemistry) is limited by their inexperience in those areas. Organic chemists might have only studied these topics as a part of their own introductory or intermediate instruction, and the textbook in use could be their primary source of information. Consequently, introductory chemistry instruction is filled with its own “urban myths”, or perhaps they are parables [1] passed down from author to author, about chemical phenomena that may or may not stand up to the scrutiny of contemporary understanding. Sometimes this is by design; for instance, demonstrating some general features about macroscopic properties can be done by using simplifications like the ideal gas assumptions or with the use of concentration instead of activity. Intentional simplifications that use less sophisticated models to explain phenomena at an adequate level of complexity are commonplace (in fact, this is not a bad interpretation of Occam’s Razor as it applies to science in general). This may be analogous to the way our colleagues in physics begin college instruction with Newtonian mechanics, or the way chemists can successfully use valence bond models for molecular structure to do a prodigious amount of chemistry without ever invoking a Hamiltonian operator. Problems can arise, however, whenever an instructor’s depth of understanding of a subject is only marginally different than the simplified version of it. Agassi [2] offers a sobering view on the way some writers of introductory textbooks “mislead the innocent reader” (implying that unwary instructors will sometimes mislead learners). He laments that individuals who ultimately choose science do so in spite of their formal education and he refers to them as “those who survive the injury of the science textbook.”     

The Philosophy of Science: Its Possibilities and Limits

Science in the modern world has long since become a factor in the production and reproduction of goods and a condition of life in this world. At the same time, however, it is more than this. Science has therefore become caught-up in an orientation crisis ever since scientists became aware that science can no longer be pursued merely for the sake of pure knowledge, the ideal from ancient times which had been held to be the proper guide for science in its quest for self-understanding. Is the philosopher of science capable of providing the researcher with an answer to the questions what it is he does, and whether or not he is deceiving himself in regard to science and his relationship to it? The philosophy of science has revealed areas which demonstrate that our science is never the smooth and elegant construction composed of observation, experiments, and mathematical and formal techniques which it has often been held to be. It is not the least of the modern philosophy of science's achievements to have demonstrated that science cannot teach man what he should do with it and its results.