Transition states five-coordinate

Two recent computational studies have examined the mechanism of crosscouplings involving aryl acetates, earbamates, and sulfamates. In a study of synthetic advances with aryl pivalates, oxidative addition of Ni(0) to the aryl acetate was found to proceed by a three-centered mechanism via an T arene complex. Alternatively, in a separate study, oxidative addition involving aryl carbamates and sulfamates was found to proceed by a five-centered transition state, with coordination of the carbonyl oxygen to nickel being a key interaction in the oxidative addition. ... 

To account for the course of this reaction theoretical calculations of the coordination of ketomalonate 37 to copper(II) and zinc(II) have revealed that the six-membered ring system is slightly more stable than the five-membered ring system (Scheme 4.30). The coordination of 37 to catalyst (l )-39 shows that the six-membered intermediate is C2-symmetric with no obvious face-shielding of the carbonyl functionality (top), while for the five-membered intermediate (bottom) the carbonyl is shielded by the phenyl substituent. Calculations of the transition-state energy for the reaction of the two intermediates with 1,3-cyclohexadiene leads to the lowest energy for the five-membered intermediate this approach is in agreement with the experimental results [45]. 

This coordination causes a cyclic five-membered ring transition state and effects an attack cis to the substituent in the 3-position. 

The replacement of five waters in [Cr(H20)6]3+ by NH3 in [Cr(NH3)5H20]3+ causes a 20-fold increase in the lability of the single remaining water (which is quite small by comparison with such replacement in [Ni(H20)6]2 +, as seen from Table V) and appears to decrease the importance of the a-activation mode in the approach to the transition state (see Section III,G). Assuming that the free radii (222) of H20 (138 pm) and NH3 (169 pm) reflect their relative electrostricted coordinated radii, it is anticipated that the first coordination sphere of [Cr(H20)6]3+ will be less crowded than that of [Cr(NH3)5H20]3+ and that the extent of a-activation character in the substitution of water in the latter species will decrease. 

A detailed examination of the kinetics of dimethylaminolysis of N3P3C16 by Krishnamurthy and co-workers has revealed that there is a gradual and subtle mechanistic change that occurs as the degree of replacement of chlorines increases (92). While the first chlorine replacement follows an Sn2 pathway involving the formation of a neutral five-coordinate intermediate [Fig. 8(A)], at the second stage the mechanism can be induced to follow a concerted path [Fig. 8(B)] by using acetonitrile as the solvent. The polar transition state of the concerted path reaction pathway is stabilized in acetonitrile. This postulate has sup-... 

There have been a number of hydrolysis studies. The mechanism of alkaline hydrolysis of phenyl dimethylthiophosphinate has been compared to that of phenyl acetate.27 Evidence for the formation of five coordinate oxyphosphorane intermediates in the alkaline hydrolysis of aryl diphenylthiophosphinates is based on the lack of development of negative charge on the leaving group in the transition state.279... 

Before our work [39], only one catalytic mechanism for zinc dependent HDACs has been proposed in the literature, which was originated from the crystallographic study of HDLP [47], a histone-deacetylase-like protein that is widely used as a model for class-I HDACs. In the enzyme active site, the catalytic metal zinc is penta-coordinated by two asp residues, one histidine residues as well as the inhibitor [47], Based on their crystal structures, Finnin et al. [47] postulated a catalytic mechanism for HDACs in which the first reaction step is analogous to the hydroxide mechanism for zinc proteases zinc-bound water is a nucleophile and Zn2+ is five-fold coordinated during the reaction process. However, recent experimental studies by Kapustin et al. suggested that the transition state of HDACs may not be analogous to zinc-proteases [48], which cast some doubts on this mechanism. 

Macrocycles attached to redox responsive groups such as ferrocene (78) can give selective transition metal ion receptors. The X-ray structure reveals a five-coordinate zinc with distorted square-pyramidal geometry bound to the four macrocycle nitrogens and an iodide. In the solid state the two ferrocenyl groups are positioned on the same side of the ligand with distances to the metal center of 5.347(7) and 6.120(8) A and these distances can be related to the redox behavior.689... 

The microwave-specific effect is more apparent in the case of demethylation (Sn2). The microwave acceleration clearly is more pronounced with the difficulty of the reaction, thus constituting a clear example of an increased microwave effect with a more difficult reaction, indicative of a later TS position along the reaction coordinate. The microwave effect may also be connected to the more localized charge in the Sn2 transition state (three centers) when compared to that of p-E2 (charge developed over five centers). 

If one end of a chelate ring on an octahedral complex is detached from the metal, the five-coordinate transition state can be considered as a fluxional molecule in which there is some interchange of positions. When the chelate ring reforms, it may be with a different orientation that could lead to racemization. If the chelate ring is not symmetrical (such as 1,2-diaminopropane rather than ethyl-enediamine), isomerization may also result. For reactions carried out in solvents that coordinate well, a solvent molecule may attach to the metal where one end of the chelating agent vacated. Reactions of this type are similar to those in which dissociation and substitution occur. 

Mechanistic details are very similar for DMSO and water exchange. The reaction proceeds through a distorted trigonal bipyramidal reactive intermediate [Li(DMSO)5]+ that is reached via a late transition state. The enthalpy profile (see Fig. 13) is in line with the experimentally observed very fast exchange process. The five-coordinate intermediate is computed to be 7.9kcalmol 1 less stable than [Li(DMS0)4]+ and free DMSO, while an overall activation barrier of only 8.4kcalmol 1 is computed. Obviously,... 

There have been other reports of transitions in related iron(III) systems [123] as well as in five-coordinate adducts of bis(ethylenedithiolato)iron(III) derivatives [124]. Remarkably, in these latter systems the transitions occur at extremely low temperatures and their observation at such temperatures is an indication of the relatively rapid inter-conversion of the spin states compared to iron(II) systems for which thermally-driven transitions are only rarely encountered below liquid nitrogen temperature. 

The comparison of Fe(III) spin transition systems with those of other metal ions reveals the greater variety of chromophores for which spin crossover is observed in iron(III). This is reflected in a generally more diverse coordination environment as well as a far broader range of donor atom sets. For six-coordinate systems the spin crossover generally involves an S=l/2<->S=5/2 change, whereas for five-coordinate materials an intermediate (quartet) spin state is involved in S=l/2<->S=3/2 transitions. There is just one report of such a transition in a six-coordinate system and that is considerably distorted [126]. 

Mechanistic interpretation of activation volumes on square-planar complexes is complicated by the geometry. The sterically less crowded complexes may have loosely bound solvent molecules occupying the axial sites above and below the plane. Replacing them in the formation of a five-coordinate transition state or intermediate may result by compensation in relatively small volume effects. It is therefore difficult to distinguish between Ia and A mechanisms from the value of the activation volume. Nevertheless, the AV values are negative and together with the second-order rate laws observed, point to an a-activation for those solvent exchange reactions. 

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