Visualization of Molecular Models

Since the early 20th century, chemists have represented molecular information by molecular models. The human brain comprehends these representations of graphical models with 3D relationships more effectively than numerical data of distances and angles in tabular form. Thus, visualization makes complex information accessible to human understanding easily and directly through the use of images. 

For all the different methods of chemical visualization, a lar e number of special techniques arc available, depending on the purpose of visualization. These software programs can be installed on a local computer or can be operated via the Internet. An ovemew of these programs is given in Section 2.12.3. 

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In the late 1960s, Langridge and co-workers developed methods, first at Princeton, then at UC San Francisco, to visualize 3D molecular models on the screens of cathode-ray tubes. At the same time Marshall, at Washington University St. Louis, MO, USA, started visuaHzing protein structures on graphics screens. 

We contend therefore that introduction of molecular modeling very early into the currieulum need not complicate or eonfuse the learning of organie chemistry, but rather assist the student in visualizing the structures of organic molecules and in learning the intimate connections between molecular structure and molecular properties. 

Whilst these difficulties do not invalidate application of molecular mechanics methods to such systems, they do mean that the interpretation of the results must be different from what is appropiate for small-molecule systems. For these reasons, the real value of molecular modeling of macromolecule systems emerges when the models are used to make predictions that can be tested experimentally or when the modeling is used as an adjunct to the interpretation of experiments. Alternatively, the relatively crude molecular mechanics models, while not of quantitative value, are an excellent aid to the visualization of problems not readily accessible in any other way. Molecular dynamics is needed, especially for large molecules, to scan the energy surface and find low-energy minima. The combination of computational studies with experimental data can help to assign the structure. 

Molecular modelling is not strictly an analytical tool that can be used directly. It is, however, a valuable way of visualizing supramolecular systems and predicting structures. The most sophisticated methods are able to predict properties associated with the model that can usefully be compared to data gathered on the real system. This is useful when several different interpretations of an experiment arise as one model may be shown to fit the data best and so be the most probable explanation. The main limitations of molecular modelling, and computational techniques in general, are the accuracy of the output and the the size of simulation that can usefully be attempted without recourse to a supercomputer or massively parallel facility. 

Extensive use of molecular models, both in-text and online, helps students visualize the shapes of compounds and how the molecules interact in three dimensions. In addition, Model-Building Problems are interspersed throughout the text to give students practice building handheld models. End-of-chapter problems based on online models are also included. 

In order to approach this problem, we must first identify the structure of the starting compound when the acidic proton is oriented fraws-periplanar to the bromide. The relevant configuration is illustrated below and can be visualized using molecular models. 

Any molecule of a given configuration can exist in different spatial arrangements (conformations) when the atoms or atomic groups are rotated or twisted with respect to each other within the limits permitted by the bonds. Although the concept of conformation in carbohydrate chemistry is old (Haworth, 1929), novel studies during the last three decades, especially by Barton and Hassel (Nobel Prize in 1969), have added clarity and important details to this concept. The conformations can best be visualized with the use of molecular models. 

M. Waldherr-Teschner, T. Goetze, W. Heiden, M. Knoblauch, H. Vollhardt, and J. Brickmann, MOLCAD—Computer Aided Visualization and Manipulation of Models in Molecular Science, in Advances in Scientific Visualisation (F. H. Post and A. J. S. Hin, eds.), pp. 58-67. Springer-Verlag, Berlin (1992) J. Brickmann, T. Goetze, W. Heiden, G. Moeckel, S. Reiling, H. Vollhardt, and C.-D. Zachmann, Interactive Visualization of Molecular Scenarios with MOLCAD/SYBYL, in Data Visualization in Molecular Science (J. E. Bowie, ed.), pp. 84-97. Addison-Wesley, Reading, MA, 1995. 

The above topological shape analysis techniques can replace visual shape comparisons of molecular models on the computer screen with precise, reliable, and reproducible numerical comparisons of topological shape codes. These comparisons and the similarity or complementarity rankings of molecular sequences can be performed by the computer automatically. This eliminates the subjective element of visual shape comparisons, a particularly important concern if large sequences (e.g. several thousands) of molecules are to be compared. In the data banks of most drug companies there is information stored on literally hundreds of thousands of molecules, and their detailed shape analysis by visual comparison on a computer screen is clearly not feasible. By contrast, automatic, numerical, topological shape analysis by computer is a viable alternative. 

Ans. This pair (III, IV) represents the same pair of enantiomers as pair I and n. Pair HI and IV are drawn from a different observation point than pair I and II. If you visualize yourself positioned midway behind the CH3 and Cl groups of I and n, you would then draw the molecules as III and IV, respectively. This imaginary visualization is not easy for the beginning student. Building and manipulation of molecular models of structures I, II, III, and IV is the surest way to verify that structure I = structure III and structure II = structure IV. 

We should actually build models of the molecules whose topicity we are exploring, because it is challenging to visualize molecules in three dimensions. Discussions are also much easier to carry out when we can point to specific parts of molecular models. Model kits range in size, complexity and price. One model kit that the author regards with particular esteem is the Molecular Visions model kits available from Darling Models (if searching online for "Darling Models," be sure the include the term "Chemistry"). 

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