Data manipulation, molecular

Open-access LC/MS formats have spawned new dimensions in access and data management. The use of a direct exposure probe (DEP) for automated sample introduction has been developed for quick (ca. 3 min) molecular weight determination of new lead compounds and quantitative analysis. Fig. 7 illustrates an automated direct probe system for molecular weight determination. Versatile software packages for data manipulation and processing has been a popular... 

Good, A.C. (1992). The Calculation of Molecular Similarity Alternative Formulas, Data Manipulation and Graphical Display. J.Mol.Graphics, 10,144-151. 

Good, A.C. (1992) The calculation of molecular similarity alternative formulas, data manipulation and graphical display. J. Mol. Graph., 10,... 

The current practice of size exclusion chromatography has been described in Chapter 2. In contrast to the early application of this technique, the experimental practice is now often relatively straightforward. Also, the complex data manipulation is now normally carried out using a dedicated data-handling system which produces the calculated molecular mass averages and distributions at the touch of a few keys. Unfortunately, this apparent ease of operation and calculation tends to conceal the real complexity of the situation, and the results are often treated as more definitive than they in fact are. 

SEC is a particularly valuable tool for examining the molecular mass distributions (MMDs) of polymers. However, appropriate levels of caution are required in the interpretation of the results. There are many difficulties in obtaining the best applicable calibration of an SEC system, and even if this is achieved, the data manipulation can introduce further uncertainty. This is well illustrated by pointing out that many computer programs for SEC contain an error in the calculation (see section 3.3). 

It is likely that the main variations in calculated molecular masses are due to the data manipulation and the actual SEC columns. There must be potential for imposing common methods of data manipulation but, with the range of data handling systems available, this would be difficult. Unfortunately, the contribution of the SEC columns is complex and not well appreciated. It is quite easy to compound these problems by an inappropriate selection of columns. 

Experience with the pattern recognition technique points out that even the most elaborate QSAR study backed by all sorts of data manipulation and statistical analysis can bear little fruit if the molecular properties do not have some rational, causal connection with the biological effect under consideration. In seeking correlations with biological data the molecular features must have some relevance to the biochemistry involved in the drug eliciting its biological response. 

The isothermal curves of mechanical properties in Chap. 3 are actually master curves constructed on the basis of the principles described here. Note that the manipulations are formally similar to the superpositioning of isotherms for crystallization in Fig. 4.8b, except that the objective here is to connect rather than superimpose the segments. Figure 4.17 shows a set of stress relaxation moduli measured on polystyrene of molecular weight 1.83 X 10 . These moduli were measured over a relatively narrow range of readily accessible times and over the range of temperatures shown in Fig. 4.17. We shall leave as an assignment the construction of a master curve from these data (Problem 10). 

But a computer simulation is more than a few clever data structures. We need algorithms to manipulate our system. In some way, we have to invent ways to let the big computer in our hands do things with the model that is useful for our needs. There are a number of ways for such a time evolution of the system the most prominent is the Monte Carlo procedure that follows an appropriate random path through configuration space in order to investigate equilibrium properties. Then there is molecular dynamics, which follows classical mechanical trajectories. There is a variety of dissipative dynamical methods, such as Brownian dynamics. All these techniques operate on the fundamental degrees of freedom of what we define to be our model. This is the common feature of computer simulations as opposed to other numerical approaches. 

---