Intercalation modeling

Fig. 12. Representation of the DNA-drug intercalation model showing locations of excluded sites which are not available for further intercalation, for (a) two separate mono-intercalators such as daunomycin 28 (b) one tris-intercalator such as compound 29...

In this regard, recent partial MM relaxation calculation on DNA and RNA intercalation models merit special attention. Kollman (309) performed preliminary studies on the interaction of cationic intercalators like ethidium bromide (118) with two base-paired dinucleoside monophosphates, CpG (119), and GpC. Their MM scheme minimizes 14 torsional (only for 119) and 12 intermolecular... 

Fig. 7.15 Band filling in an intercalation model according to Friedel s (1954) notion of screening. The upper panel shows the position of the bands at various degrees of filling the lower panel shows the corresponding values of the electron chemical potential (Fermi energy).

For quantitative structure-activity relationship (QSAR) studies a three-dimensional model of a DNA-quinoIone complex was built using molecular modeling techniques. It was based on the intercalation of quinolone into the double helix of DNA. It was concluded that the intercalation model is consistent with most available data on the structure of the quinolone complex. This predicted... 

Fig. 26. Intercalation model of the unit cell of iodine-PVA crystal in the a-c plane...

The evidence for a separate MoS2 phase being present on the catalyst has already been discussed under A above. There is scant evidence for the existence of an intercalation phase on the supported catalyst. Much of the argument is based on the intercalation model proposed for the bulk Ni-WS2 catalyst (108). Canesson and Grange (109) and Mone (55) have... 

One of the important tenets of the intercalation model is the role of Co in increasing the Mo3+ population, the presumed active site for HDS. Most workers have failed to detect Mo3+ by ESR or ESCA, but De Beer (41) cites ESR evidence for its presence on a reduced Mo/Al sample. Notwithstanding, its concentration must be extremely low not to be detected by others. However, even if this is the active site, an intercalation model need not be invoked to explain Co promotion. For example, the monolayer model could produce Mo3+ in reduction or sulfidation according to the structures,... 

The promoting action of cobalt on the activity for hydrodesulfurization has been shown already in the pioneering work of Byrns, Bradley and Lee (14). This promoting action might be linked with the sulfiding step, since the actual catalyst is the sulfided form of cobalt- or nickel-molybdenum-alumina. Voorhoeve and Stuiver (15) and Farragher and Cossee (16) demonstrated the promoting action for the unsupported Ni-WS2 system. Their intercalation model was based on these experiments. 

These observations are consistent with an intercalative mode of binding in the interaction of tilorone hydrochloride with double-helical DNA. These results were not examined in an attempt to verify whether they agree with measurements of the length increase on sonicated DNA. For this reason, the intercalation model of the DNA complex remains tentative. 

This model has been carried over to other p-doped systems. But the dimensions of ions such as AsFpolymer alternate can hardly occur. What is known is not inconsistent with the planar intercalation model. Finally, let us note that this model is also supported by the structure of doped oligomers, that is, of stoichiometric radical cation salts in which the cation is, for instance, that of quaterphenyle [65]. 

Structural information of HDT catalysts has been explained in terms of several models. These models are monolayer model, intercalation model, contact... 

Figure 1 shows the M0S2 structure with some of the possible locations. Position (a) represents the position proposed in the original intercalation model, (b) represents an edge or "pseudo-interca-lated Co atom, (c) Co substituting for Mo in the interior, (d) Co located at the edges of the slabs (e.g., at a surface substitutional site), and (e) Co at basal planes. 

Figure 1.27. Intercalation model proposed for the structure of heavily doped PPP. Phenyl rings arc stacked parallel with a 3 39 A spacing close to the 3.35 A spacings measured in lamellar graphite. A lateral dimension of 5.75 A for the phenyl ring is in agreement with the data available from the known structure of the oligomers and the value of 4.75 A corresponds to ihe value for a graphite/AsF6 intercalation structure. (Reproduced from ref. 194 with kind permission, Copyright (1988) Chapman Hall, UK.)...

Later on, they explored, using the same NMR technique, how a fluorine atom in position 3 affected the intercalation of IDA derivative 13 into the DNA major groove using a hexanucleotide duplex as an intercalation model (Fig. 4) [15]. 

Diffraction work on alkyl-substituted PTh doped with the same anions leads to an intercalation model similar to the simulated structures. 

For the so-called strong binding intercalation model, two models have been proposed. In the complete intercalation model, the dye molecule is totally enclosed inside the double helix between two consecutive base pairs. In the partial intercalation model, the dye lies between successive nucleotide bases on the same polynucleotide chain and the positive charge of the dye... 

The basic, classical interaction involves the insertion of the planar molecule between two neighboring base pairs of DNA to which it is held by Van der Waals forces [49]. A further weak interaction of an electrostatic type between the phosphate anions and charged groups of the molecule may also be present. A nonclassical intercalation model involving bending of the helix has also been proposed [50]. The models are outlined schematically ... 

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