Molecular Visualiser

We will have a look at some widely used free and commercial software for crystallography and molecular visualisation and analysis Mercury, Diamond, CrystalMaker and RPluto. This section should not be seen as a complete review of these programs, if you are in the process of choosing such software ensure that you consult other sources and review other properties as well. 

Moreland, J., Gramada, A., Buzko, O. V., Zhang, Q., Bourne, P. E. (2005). The molecular biology toolkit (MBT) A modular platform for developing molecular visualisation applications. BMC Bioinformatics, 6,21. 

A hands-on experience with the method is possible via the SPINUS web service [48. This service uses a client-server model. The user can draw a molecular structure within the web browser workspace (the client), and send it to a server where the predictions are computed by neural networks. The results are then sent back to the user in a few seconds and visualised with the same web browser. Several operations and different types of technology arc involved in the system ... 

M, J P Bielawski, J C Hempel and M Waldman 1996. Optimisation and Visualisation of ecular Diversity of Combinatorial Libraries. Molecular Diversity 2 64-74. 

At any interface between two different phases there will be a redistribution of charge in each phase at the interface with a consequent loss of its electroneutrality, although the interface as a whole remains electrically neutral. (Bockris considers an interface to be sharp and definite to within an atomic layer, whereas an interphase is less sharply defined and may extend from at least two molecular diameters to tens of thousands of nanometres the interphase may be regarded as the region between the two phases in which the properties have not yet reached those of the bulk of either phase .) In the simplest case the interface between a metal and a solution could be visualised as a line of excess electrons at the surface of the metal and an equal number of positive charges in the solution that are in contact with the metal (Fig. 20.2). Thus although each phase has an excess charge the interface as a whole is electrically neutral. 

Head, J., Bucat, B. (2002). Visualisation and mental manipulation of molecular structures. Australian Journal of Education in Chemistry, 59, 25-29. 

Seddon, G. M., Tariq, R. H., Dos Santos Viega, A. (1982). The visualisation of spatial transformations in diagrams of molecular structures. European Journal of Science Education, 4, 409 20. 

A more sophisticated understanding is linked to an appreciation of the interaction of thermodynamic and kinetic considerations and is likely to be dependent upon the ability to visualise some form of mental model involving molecular collisions and interactions (Gilbert, 2005). This allows the student to see that two reactions are occurring simultaneously ... 

While Kozma and Russell (2005) recommend the use of visualisation resources, the value of the various formats for various topics is debatable. Kozma and Russell confirm we are not able to say, given the state of the research, for which topics or students it is best to use animations versus still pictures or models (p. 330). Ardac and Akaygun (2005) on the other hand favour the use of dynamic visuals (preferably on an individual basis) over static visuals when presenting molecular representations, confirming that dynamic visuals can be more effective than static visuals in fostering molecular understanding about the changes in matter (p. 1295). Obviously both static and dynamic forms are valuable and can be nsed to complement each other. 

Hassan M, Bielawski JP, Hempel JC, Waldman M. Optimisation and visualisation of molecular diversity of combinatorial libraries. Mol Diversity 1996 2 64-74. 

In our discussion so far we have used a group of spatial symmetries as an easily-visualised example. It is possible to put all the symmetries of the molecular Hamil-... 

Another way of visualising the potential energy of a molecular system is in terms of the potential-energy changes that occur during a chemical reaction. This is represented by means of a reaction profile where the potential energy values of the reactants, products, transition states and intermediates are plotted against the reaction coordinate (the lowest... 

Among the many microscopy-based techniques for the study of biomolecular interactions on surfaces, scanning probe microscopies, and especially the atomic force microscopies (AFM), are the most used because of their molecular and sub-molecular level resolution and in situ imaging capability. Apart from the high resolution mapping of siuface nanotopographies, AFM can be used for the quantification and visualisation of the distribution of chemistry, hydrophobicity and local mechanical properties on surfaces, and for the fabrication of nanostructmes on surfaces. 

Whilst the conditions of equilibrium for such systems were clearly enunciated by J. Willard Gibbs and Sir J. J. Thomson a great impetus was given to the subject by supplementing the formal thermodynamic treatment with a clearer visualisation of the molecular structure of surfaces by Sir W. B. Hardy and I. Langmuir. 

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