Volume 1 Chapter 7 Handling Structure Inversion

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7.14 Searching for Non-Bonded Contacts

So far in this chapter we have been concerned with geometrical calculations and geometrical searching applied to a single substructural fragment. In this section, these concepts are extended to examine relationships between multiple substructural fragments. These relationships will be refered to as non-bonded contacts.

Several examples of non-bonded contacts are shown below. In general, there are two types of contacts: intramolecular and intermolecular. When the two fragments are in the same molecule they form an intramolecular contact as shown in (a) and (b). Pharmacophores are a common example of searching for intramolecular contacts (b). If the fragments are in separate molecules then they are intermolecular, as illustrated in (c), (d), and (e). Analysis of hydrogen bonding is an obvious example of intermolecular searches. It is even possible in QUEST3D to search for a mixture of contact types like (f).

Many of the examples in this section deal with the location of hydrogen bonds. These examples are for illustration only, as it is a matter of opinion in many cases as to whether a distance should be classified as a 'hydrogen bond'. For guidelines the user should consult the review literature on the topic, a recommended monograph being G.A. Jeffrey and W. Saenger, 'Hydrogen Bonding in Biological Structures', Springer-Verlag, 1991.

The ability to search for such a variety of contact types is due to the crystallographic origin of the structural

data stored in the CSD. The CSD stores not only the atomic coordinates that represent the crystal chemical unit, but also the space group symmetry operations through which the extended crystal structure may be reconstructed. It is this information that makes it possible to search for intermolecular contacts.

It is these intermolecular non-bonded interactions that govern molecular aggregation in the crystal and, in a broader context, these interactions play a significant role in the phenomena that are now described as 'molecular recognition'. The crystallographic origin of the data means that the CSD is unique in containing experimental observations of intermolecular interactions, and the CSD System is unique in providing software tools for the search and analysis of this vitally important information.

In this Section we examine the facilities for searches involving non-bonded interactions. The definition and refinement of non-bonded searches is controlled by the buttons of the NON-BONDED section of the 3D CONSTRAIN sub-menu. The section button is Carolina Blue on colour displays.

Although the non-bonded search utility was designed so that no crystallographic knowledge is required for its use, it may be helpful to briefly describe how crystallographic data are stored and used to generate extended crystal structures.


(a)

ALPDLM


(b)

ALPALC10


(c)

DERZAB


(d)

AMBNZA


(e)

MORPHM


(f)

CITNOI10


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Volume 1 Chapter 7 The CSD Reference Molecules and the Extended Crystal Structure.