Visualization, in chemistry

Hoffmann R (2003) Thoughts on aesthetics and visualization in chemistry. HYLE. 9 7-10. 

Spector, T. and Schummer, J. (eds.). 2003. Aesthetics and Visualization in Chemistry. Special issue of Hyle 9. 

Ratios in Chemistry Calculations Conceptual Chemistry Problems Visualization in Chemistry... 

The visualization of volumetric properties is more important in other scientific disciplines (e.g., computer tomography in medicine, or convection streams in geology). However, there are also some applications in chemistry (Figure 2-125d), among which only the distribution of water density in molecular dynamics simulations will be mentioned here. Computer visualization of this property is usually realized with two or three dimensional textures [203]. 

J. B. Foresman, "Ab Initio Techniques in Chemistry Interpretation and Visualization, Chapter 14 in What Every Chemist Should Know About Computing, Bd. M. L Swift and T. J. Zielinski (ACS Books, Washington, D.C., 1996). 

Ben-Zvi, R., Eylon, B.-S., Silberstein, J. (1987). Students visualization of some chemical reactions. Education in Chemistry, 24, 117-120. 

In chemistry, perhaps because of the significance in visualizing molecular strac-ture, there has been a focus on how students perceive three-dimensional objects from a two-dimensional representation and how students mentally manipulate rotated, reflected and inverted objects (Stieff, 2007 Tuckey Selvaratnam, 1993). Although these visualization skills are very important in chemistry, it is evident that they are not the only ones needed in school chemistry (Mathewson, 1999). For example, conceptual understanding of nature of different types of chemical bonding, atomic theory in terms of the Democritus particle model and the Bohr model, and... 

Methane is the simplest molecule with a tetrahedral shape, but many molecules contain atoms with tetrahedral geometry. Because tetrahedral geometry is so prevalent in chemistry, it is important to be able to visualize the shape of a tetrahedron. 

The probe molecules of greatest historical interest in catalysis are the Hammett indicators [13]. The difficulty of making reliable visual or spectrophotometric observations of the state of protonation of these species on solids is well known. We have recently carried out the first NMR studies of Hanunett indicators on solid acids [ 14]. This was also the occasion of the first detailed collaboration between the authors of this article, and theoretical methods proved to strongly compliment the NMR experiments. The Hanunett story is told after first reviewing the application of theoretical chemistry to such problems. Central to the application of any physical method in chemistry is the process of modeling the relationship between the observables and molecular structure. However often one does this, it is rarely an exact process. One can rationalize almost any trend in isotropic chemical shift as a function of some variation in molecular structure - after the fact, but the quantitative prediction of such trends in advance defies intuition in most nontrivial cases. Even though the NMR spectrum is a function... 

Confocal fluorescence microscopy has been extensively used in cell biology. Single living cells can indeed be studied by this technique visualization of organelles, distribution of electrical potential, pH imaging, Ca2+ imaging, etc. (Lemasters, 1996). Interesting applications in chemistry have also been reported in the fields of colloids, liquid crystals and polymer blends. 

A single CV as described gives n predictions. For many data sets in chemistry n is too small for a visualization of the error distribution. Furthermore, the obtained performance measure may heavily depend on the split of the objects into segments. It is therefore recommended to repeat the CV with different random splits into segments (repeated CV), and to summarize the results. Knowing the variability of MSEcv at different levels of model complexities also allows a better estimation of the optimum model complexity, see one standard error rule in Section 4.2.2 (Hastie et al. 2001). 

The microscopic world of atoms is difficult to imagine, let alone visualize in detail. Chemists and chemical engineers employ different molecular modelling tools to study the structure, properties, and reactivity of atoms, and the way they bond to one another. Richard Bader, a chemistry professor at McMaster University, has invented an interpretative theory that is gaining acceptance as an accurate method to describe molecular behaviour and predict molecular properties. According to Dr. Bader, shown below, small molecules are best represented using topological maps, where contour lines (which are commonly used to represent elevation on maps) represent the electron density of molecules. 

The current paradigm in chemistry celebrates the existence of physical entities called chemical atoms (now known simply as atoms). John Dalton (1766-1844) looked at the material world in which he hved and visualized it in terms of a set of different material objects of small size and combining capacity (7). He called these particles atoms in his New System of Chemical Philosophy (1808). Others, such as Humphry Davy (1778-1829), were not yet willing to see the world in this way. Dalton combined both a partictrlar theory of nature and specific observatiorrs to arrive at his views. The present paper will examine some episodes in the history of chemistry that enabled other chemists to see atoms as appropriate chemical constituents of our world. The view of what constitutes a chemical atom has changed during the time period from 1808 to 2008, but the common theme requires a context in which actual measurements can be viewed as evidence for atoms. ... 

The chemistry of flavins is complex, a fact that is reflected in the uncertainity that has accompanied efforts to understand mechanisms. For flavoproteins at least four mechanistic possibilities must be considered.1533 233 (a) A reasonable hydride-transfer mechanism can be written for flavoprotein dehydrogenases (Eq. 15-23). The hydride ion is donated at N-5 and a proton is accepted at N-l. The oxidation of alcohols, amines, ketones, and reduced pyridine nucleotides can all be visualized in this way. Support for such a mechanism came from study of the nonenzymatic oxidation of NADH by flavins, a reaction that occurs at moderate speed in water at room temperature. A variety of flavins and dihydropyridine derivatives have been studied, and the electronic effects observed for the reaction are compatible with the hydride ion mecha-nism.234 236... 

Molecule visualization adheres to the standard conventions for depicting molecules in chemistry by providing the usual display modes for molecules, using the standard colors for elements and so on. Additionally, it can optionally show context-related information in tool-tips (similar to additional information in user interfaces), and also provide means to interact with the molecule. 

Modem computer graphics have given visualization, the pictorial presentation of the results of calculations, a very important place in science. Not only in chemistry, but in physics, aerodynamics, meteorology, and even mathematics, the remarkable ability of the human mind to process visual information is being utilized [317]. Gone are the days when it was de rigeur to pore over tables of numbers to... 

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