Molecular information content

It has often been mentioned in this chapter that many molecular descriptors can well be highly intcr-corrclatcd. Therefore, any significant information content of a... 

The relative molecular dynamics fluctuations shown in Figure 7-17 can be compared with the crystallographic B-factors, which are also called temperature factors. The latter name, especially, indicates the information content of these factors they show how well defined within the X-ray structure the position of an atom is. Atoms with high temperature have an increased mobility. In principle, this is the same information as is provided by the molecular dynamics fluctuations. Using Eq. (48), the RMS fluctuation of an atom j can be converted into a B-factor... 

The information content of a structure descriptor depends on two major factors a) the molecular representation of the compound b) the algorithm which is used for the calculation of the descriptor. 

Information may be stored in the architecture of the receptor, in its binding sites, and in the ligand layer surrounding the bound substrate such as specified in Table 1. It is read out at the rate of formation and dissociation of the receptor—substrate complex (14). The success of this approach to molecular recognition ties in estabUshing a precise complementarity between the associating partners, ie, optimal information content of a receptor with respect to a given substrate. 

The previous sections focused on the case of isolated atoms or molecules, where coherence is fully maintained on relevant time scales, corresponding to molecular beam experiments. Here we proceed to extend the discussion to dense environments, where both population decay and pure dephasing [77] arise from interaction of a subsystem with a dissipative environment. Our interest is in the information content of the channel phase. It is relevant to note, however, that whereas the controllability of isolated molecules is both remarkable [24, 25, 27] and well understood [26], much less is known about the controllability of systems where dissipation is significant [78]. Although this question is not the thrust of the present chapter, this section bears implications to the problem of coherent control in the presence of dissipation, inasmuch as the channel phase serves as a sensitive measure of the extent of decoherence. 

Measurements in the laboratory are much more sensitive to spectral separations and hence understanding the spectrum of a molecule uniquely for the purposes of identification. However, the astronomical observations are limited by the telescope resolution and the atmospheric shimmer but the intrinsic information content of microwave spectra provides the best method for molecular identification - the other regions of the spectrum have their uses, as we shall see. 

The pharmacophore concept, like that of molecular/chemical structure, assumes different meanings, and consequently different definitions, according to the accuracy and resolution level of its information content. 

Analytically, IR (FTIR) spectroscopy is unquestionably one of the most versatile techniques available for the measurement of molecular species in the laboratory today, and also for applications beyond the laboratory. A major benefit of the technique is that it may be used to study materials in almost any form, and usually without any modification all three physical states are addressed solids, liquids and gases. Also, it is a fundamental molecular property, and as such the information content can be considered to be absolute in terms of information content, and as such can be very diagnostic in terms of material purity and composition. Traces of impurities can be both uniquely detected and in most cases characterized. This is a very important attribute in a process analytical enviromnent. 

The authors feel that compounds need to be sufficiently complex in order to provide a significant level of information content. On the other hand, compounds that are too complex may be viewed as undesirable. A number of measures for characterizing molecular complexity have been developed over the years. Complexity has been defined in terms of size, elemental composition, topology, symmetry, and functional groups present in a molecule (17,18). In the present work, we have applied a simple, chemically intuitive measure developed by Barone and Channon (18). This approach is based on a simple additive model, where values are assigned to specific classes of molecular features such as the types of atoms and bonding patterns, and the number and types of rings. This is illustrated in Eq. 2.1 ... 

The SlogP, SMR, and PEOE VSA descriptors have rich information content and can be used in place of many traditional descriptors (13-17). Figure 5 presents the results of a collection of 64 linear models each of which approximates a traditional descriptor as a linear combination of the VSA descriptors (trained on approx 2,000 small molecules). Out of the 64 descriptors, 32 showed an r2 of 0.90 or better and 49 had an r2 of 0.80 or better, and 61 showed an r2 of 0.5 or better. Descriptors related to flexibility are poorly modeled. In particular, the Lipinksi parameters log/5, acceptor count, donor count, and molecular weight are... 

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