Dimer formation modeling

On the basis of the above dimer formation model, a time course of the absorbance of Y-Dye (/4(f)) produced in an individual droplet has been analyzed [104]. The coupling reaction between QDI and Y-Cp is assumed to proceed at the oil-droplet/water interface (rate constant, kt) and the association equilibrium between the Y-Dye monomer and dimer is attained immediately upon the dye formation. In the actual experiments, QDI is oxidized partly by 02 dissolved in the water phase, so that Y-Dye is produced in a DBP droplet even before electrolysis of QDI. To correct this contribution, [Y-Dye] is defined as [Y-Cp]0 — [Y-Cp]j exp( — fc,[QDI]wf), where [Y-Cp]0 and [Y-Cp], are the Y-Cp concentrations at the emulsion preparation and t = 0 (before electrolysis), respectively. According to the... 

Figure 39-15. The leucine zipper motif. A shows a helical wheel analysis of a carboxyl terminal portion of the DNA binding protein C/EBP. The amino acid sequence is displayed end-to-end down the axis of a schematic a-helix. The helical wheel consists of seven spokes that correspond to the seven amino acids that comprise every two turns of the a-helix. Note that leucine residues (L) occur at every seventh position. Other proteins with "leucine zippers" have a similar helical wheel pattern. B is a schematic model of the DNA binding domain of C/EBP. Two identical C/EBP polypeptide chains are held in dimer formation by the leucine zipper domain of each polypeptide (denoted by the rectangles and attached ovals). This association is apparently required to hold the DNA binding domains of each polypeptide (the shaded rectangles) in the proper conformation for DNA binding. (Courtesy ofS McKnight)...

With different pectins, one found that the activity coefficient of calcium has a value half that of magnesium this is interpreted as the basis of a dimer formation in presence of calcium. The specific interaction of calcium was described as the egg-box model first proposed for polyguluronate in which oxygen atoms coordinated to calcium [46]. Recently, the comparative behaviour of Mg and Ca with homogalacturonan was reexamined [47]. 

In other words, the homopolygalacturonic acids of the cell walls distribute in two equal amounts of high and low affinity exchange sites. This is compatible with the dimer formation predicted by the egg box model between pectin chains in the 2i helical conformation [9, 10]. According to this model, we would associate the high affinity sites with the inner faces of the dimers. 

In summary, researchers have found a number of methods for avoiding p-oxo dimer formation and preserving a five-coordinate Fe(II) in iron-containing model compounds, through ... 

Self-association of substances with acidic hydrogens82, including amines (to form, in a first approximate model, dimers mainly by hydrogen bonding interactions), is a long known problem. There are numerous reports in the literature on the thermodynamic, spectroscopic and structural aspects of self-association and dimer formation of water, alcohols, ammonia, amines and hydrogen sulphide83. 

Conditions such as DjDj+l = DjHj — D HJ+i = 0 follow immediately from the model. Let kx be the rate constant of dimer formation. Then the probability rates of dimer formation per radiation dose, PUi(Sj), which depend upon the nature of the occupation of a set of sites, Sj, are given in Table I. The probability of the reverse reaction of the dimer (jj + 1),... 

Mononuclear Mov complexes with sterically hindered monodentate thiolato ligands are of interest as models for special molybdenum enzymes (the Mo oxidases). Here dimer formation via thiolato bridges and sulfide formation by C—S bond cleavage do not occur. Such a ligand is TIPTH. The complex [Mo(CO)2(TIPT)3) (14), with essentially trigonal prismatic coordination about Mo and trans CO groups in the axial sites, can be obtained.91... 

H bonding. In a later study, Petersen et al. (1971) identified associated complexes of 2-quinolones with carboxylic acids. The 2-quinolones had been previously detected in petroleum heavy oils (Copelin, 1964 Snyder et al., 1968). Model compound studies (Petersen et al., 1971) of dimer and mixed dimer formation with 2-quinolone and carboxylic acids suggest strong association with enthalpies in the 8- to 10-kcal/mole range. 

In an infinite crystal, all units must be neutral. The small degree of charge transfer observed in the dimer supports the appropriateness of the dimer as a model for the crystal. In the cases where H-bonds to ortho hydrogens are implicated, the charge increases substantially on the ortho hydrogen upon dimer formation. 

One approach to limit dimer formation in model complexes involves the use of bulky ligands and weakly coordinating solvents. Holm and coworkers [196,198-201] have studied oxygen atom transfer reactions of 2,6-bis(2,2-diphe-nyl-2-thioethyl)pyridinate [2] molybdenum oxo complexes. In contrast to the structurally similar dithiocarbamate molybdenum complexes, the tendency of the 2,6-bis(2,2-dipheny 1-2-thioethy l)pyridinate MoIV monoxo complex to undergo di-... 

The minimal model comprises an uncatalyzed and unspecific direct formation of R and S (ko), a simple and unspecified description of the autocatalytic steps assuming monomers as catalytic species (k ), and the monomer-dimer equilibria (k2, M and (M M in which different rates of dimer formation for homochiral and heterochiral species is allowed. This model translates into the following set of differential equations ... 

The reduction of organic dye methyl orange (MO) over CdS colloids with the particles size d = 2R - 5 nm has appeared to be a convenient reaction for detail studying the kinetics of photocatalytic processes. This dye is readily reducible with no dimers formation. The MO adsorption spectrum in the pH range of 10-12, practically does not change. This allows simplifying the interpretation of the experiments on redox transformations of MO and considering the reaction of photostimulated reduction of MO as a model one. 

In typical surface science experiments as presented previously, oxide-supported metal nanoparticles are deposited onto a clean oxide surface by physical vapor deposition. The precursor in this process is metal atoms in the gas phase, which impinge on the surface, diffuse until they eventually get trapped (either at surface defects or by dimer formation), and then act as nuclei for the growth of larger particles. These processes are well understood for ideal model systems under ultrahigh vacuum (UHV) conditions [56, 57]. In contrast, most realistic supported metal catalyst... 

Another problem with small models is that molecules from the solution (e.g. water) may come in and stabilise tetragonal structures and higher coordination numbers [224]. It is illustrative that very few inorganic con5)lexes reproduce the properties of the blue copper proteins [66,67], whereas typical blue-copper sites have been constructed in several proteins and peptides by metal substitution, e.g. insulin, alcohol dehydrogenase, and superoxide dismutase [66]. This shows that the problem is more related to protection from water and dimer formation than to strain. 

In 1973, Baldwin and Huff [31] reported the synthesis of the iron(n) octaazamacrocycle (2) (Figure 2), the first nonporphyrin model which acts as a reversible dioxygen carrier at relatively low temperature. The sterically hindered substituents form a cavity in which the dioxygen is fixed and retard p-0x0 dimer formation. 

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