Prototype, topological

Here, the topological nature of the tori will be discussed briefly. Figure 1 shows the five possible prototypes of toroidal forms that are considered to be related to fullerenes. These structures are classified by the ratios of the inner and outer diameters r, and r, and the height of the torus, h. (Note that is larger than / ,) As depicted in Fig. 1, if r, = r, and h r, and h = — r,) then the toroidal forms are of type... 

Anderson J.R., Chiu D.T., Jackman R.J., Chemiavskaya O., McDonald J.C., Wu H.K., Whitesides S.H., Whitesides G.M., Fabrication of topologically complex three-dimensional microfluidic systems in PDMS by rapid prototyping, Anal. Chem. 2000 72 3158-3164. 

The basic perovskite structure ABX3 forms the prototype for a wide range of other structures related to it by combinations of topological distortions, substitution of the A, B and X ions, and intergrowth with other structure types. These compounds exhibit a range of magnetic, electrical, optical, and catalytic properties of potential application in solid state physics, chemistry, and materials science. 

There are five classes of flavin-binding structural folds presented in Table 1 that are identified by the prototype protein in which they were first discovered. These are flavodoxin (FDX), ferredoxin reductase (FNR), triosephosphate isomerase (TIM), glutathione reductase (GR) and p-cresol methylhydroxylase (PCMH). The topologies of four of these five domains are shown in Figure 2. There are also four classes of primary acceptor/donor domain folds that are identified by the prototype protein where they were first discovered. They are cytochrome P450BMP (BMP), cytochrome b5 (CYTB5), cytochrome c (CYTC) and the 2Fe-2S plant-type ferredoxin (FDN). 

In the present article, we report a study concerning the reaction mechanism of a prototype reaction using both static and dynamic approaches to explore a DFT potential surface. The static approach is the standard IRC model, while the dynamic one is based on a Carr-Parrinello method performed with localized (Gaussian) orbitals, the so-called atom-centered density matrix propagation (ADMP) model.25 Our aim is to elucidate the differences, and the common aspects, between the two approaches in the analysis of bond breaking/formation. To this end, we have chosen topological quantities as probe molecular descriptors. 

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