Local similarity in organic crystals and the non-uniqueness of X-ray powder patterns.

Two new concepts for molecular solids, 'local similarity' and 'boundary-preserving isometry', are defined mathematically and a theorem which relates these concepts is formulated. 'Locally similar' solids possess an identical short-range structure and a 'boundary-preserving isometry' is a new mathematical operation on a finite region of a solid that transforms mathematically a given solid to a locally similar one. It is shown further that the existence of such a 'boundary-preserving isometry' in a given solid has infinitely many 'locally similar' solids as a consequence. Chemical implications, referring to the similarity of X-ray powder patterns and patent registration, are discussed as well. These theoretical concepts, which are first introduced in a schematic manner, are proved to exist in nature by the elucidation of the crystal structure of some diketopyrrolopyrrole (DPP) derivatives with surprisingly similar powder patterns. Although the available powder patterns were not indexable, the underlying crystals could be elucidated by using the new technique of ab initio prediction of possible polymorphs and a subsequent Rietveld refinement. Further ab initio packing calculations on other molecules reveal that 'local crystal similarity' is not restricted to DPP derivatives and should also be exhibited by other molecules such as quinacridones. The 'boundary-preserving isometry' is presented as a predictive tool for crystal engineering purposes and attempts to detect it in crystals of the Cambridge Structural Database (CSD) are reported.

Heterofullerenes: structure and property predictions, possible uses and synthesis proposals.

Substituting carbon atoms of fullerenes by heteroatoms and vacancies will lead to new and yet unknown spherical-shaped molecules termed hereafter as heterofullerenes. The enormous structural diversity of these molecules is investigated and their structural, electronic and thermochemical properties are predicted using semiempirical computations. Computational results for complexes with ions lead to the hypothesis that these molecules behave like microscopic Faraday cages in which the electrons concentrate on the outer side of the sphere. It is predicted that some of these heterofullerenes are structurally and electronically similar to phthalocyanines and related molecules but offer many additional advantages. Potential uses such as adding heterofullerenes to fullerene materials, as superior starting materials for the fabrication of diamonds, as catalysts in hydrogenation reactions, as components of materials dominated until now by phthalocyanines, etc., are discussed. Simple synthetic routes to these compounds that are based on minor alternations of existing methods for fullerene production are proposed. On the basis of the thermochemical calculations, we believe that the most promising possibility consists of using metal cyanide/graphite composite target rods instead of pure graphite rods as in a conventional fullerene synthesis.

A fast algorithm for the interactive docking maneuver with flexible macromolecules and probes.

A new algorithm for the interactive docking maneuver is presented. Full attention is given to the flexibility of both substrate and macromolecule, i.e., all the fragments are allowed to move. It is assumed that any numerical quantity which depends only on the isolated macromolecule at energy minimum is disposable when approximate expressions are derived. The central idea is the concept of relevant docking coordinates which reflect the essential features of the macromolecular deformations during the docking maneuver and which substantially diminish the number of considered degrees of freedom (DF). The conformational energy is divided into two parts. The first part, represented by condensed potential functions, needs no approximations. For the second part, termed Erest , a quadratic approximation in the subspace spanned by the relevant docking coordinates is used. All the pairwise interactions between the atoms of the macromolecule are eliminated. A simple computational example using the ECEPP force field is given. Atomic coordinate computations are simplified by the introduction of virtual rotation axes for the backbone. In connection with drug design the concept of pressure pattern is defined and related to quantities appearing in the energy gradient. Extensions to substrate induced allosteric transitions are discussed.

Excitable chemical reaction systems. II. Several pulses on the ring fiber.

The parameters of the Field, Noyes and Körös model for the Belousov-Zhabotinskii reaction were chosen in such a way that the given system is excitable. It is shown by simulation that several pulses on the ring fiber, contrary to experience with known excitable media, may arrange themselves in a non-symmetrical manner while the equilibrium distances are stable. The condition for such behavior is the non-monotonic dependence of the propagation velocity, v, on the time, T, elpased since the previous excitation at that point.