Molecular structure terms Links

In terms of their molecular structures, the nucleotide and protein realms are usually considered to be rather independent of each other. However, these two families of molecules are covalently linked in the translational aminoacyl- RNAs and ribonucleoproteins as well as in the nucleoproteins involved in cellular and viral replication. In these hybrid biomolecules, a (deoxy)ribose phosphate moiety serves as the structural connection between the nucleoside and peptide moieties. 

In 1861 the Russian chemist A. M. Butlerov, Z. Chem. Pharm. 4, 540 (1861), used the term chemical structure11 for the first time and stated that it is essential to express the structure by a single formula. winch should show how each atom is linked to other atoms in the molecule of the substance. He stated clearly that all properties of a compound are determined by the molecular structure of the substance and suggested that it should be possible to find the correct structural formula of a substance by studying the ways in which it can be synthesized. 

One may however consider that the integrated operation of its individual components confers to a molecular (covalently linked) device a flavour of supramolecular nature, since its function extends over the whole device in a sort of superstructure fashion. It then would appear justified to include in the domain of supramolecular chemistry systems that bear relation to supramolecular species on functional grounds, systems whose function is of supramolecular nature although they are clearly molecular in terms of structure and bonding. A further reason for not excluding such a possibility lies in the considerable enrichment that such an open view brings to the field ... 

Theoretical chemistry has two problems that remain unsolved in terms of fundamental quantum theory the physics of chemical interaction and the theoretical basis of molecular structure. The two problems are related but commonly approached from different points of view. The molecular-structure problem has been analyzed particularly well and eloquent arguments have been advanced to show that the classical idea of molecular shape cannot be accommodated within the Hilbert-space formulation of quantum theory [161, 2, 162, 163]. As a corollary it follows that the idea of a chemical bond, with its intimate link to molecular structure, is likewise unidentified within the quantum context [164]. In essence, the problem concerns the classical features of a rigid three-dimensional arrangement of atomic nuclei in a molecule. There is no obvious way to reconcile such a classical shape with the probability densities expected to emerge from the solution of a molecular Hamiltonian problem. The complete molecular eigenstate is spherically symmetrical [165] and resists reduction to lower symmetry, even in the presence of a radiation field. 

It is to be stressed that a bond path is not to be understood as representing a ond . The presence of a bond path linking a pair of nuclei implies that the corresponding atoms are bonded to one another. As demonstrated later, the interaction can be characterized and classified in terms of the properties of the charge density at its associated (3, — 1) critical point. The complete description of the interaction, however, requires the evaluation of operators over the associated interatomic surface. These are the topics of later discussions At this point we continue with the identification of the elements of molecular structure with the topological properties of the remaining stable critical points, (3, + 1) and (3, + 3) critical points. 

All these results taken together allow us to visualize a likely mechanism for the catalytic cycle as a rotation in terms ofthe ye-subunit domain within the [a p]3in F, as illustrated in Fig. 33. After many enzyme turnovers and the rotation ofthe ye subunit domain has stopped, 1/3 ofthe ye subunit domains are expected to end up at each of the three a p pairs, consistent with the finding of approximately equal amounts of a 8 y, a 8 and a 5 e in the cross-linked products. The functional roles of these three small subunits will be discussed in Section I V.C. 1. below on the basis of their molecular structures. 

The term half-space concisely represents the region in space, either above or below a flat molecular moiety. Stereotopic or paired half-spaces are separated by a surface that may or may not be planar. The alternative term molecular face is more descriptive of a given molecular structure. Two stereotopic molecular faces are separated by a surface that is assumed to coincide with the plane of a finite, flat molecular framework. We use molecular face, in preference to half-space, as it is intimately linked to the term facioselectivity. Ring systems in carbohydrates, heterocyclic bases, steroids, porphyrins (see refs. 129(a), 129(b) above) are also said to have molecular faces, albeit in a generalized sense. 

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