Optimized structures of transition state

Fig. 2 Optimized structures of transition states and intermediates corresponding to Fig. 1 (Bond...

In [NiFe] hydrogenase, catalyzation does not necessarily occur in the neutral state of the active site. Therefore we have to consider electron transfer during catalyzation. Hence, we calculated the energy of the anion and dianion complexes in the catalytic reaction, where the structures of each state are assumed to be optimized structures and transition states of the neutral state. This is the starting point in the analysis of the string model.105-107... 

Fig. 37 More O Ferrall-Jencks diagram for the Menschutkin reactions of 1-phenylethy] and benzyl chlorides with pyridine. The structures of transition states were optimized by ab initio MO calculation (RHF/b-Sf G ). O, substituted 1-phenylethyl chlorides with pyridine , benzyl chlorides with pyrindine , with 4-nitropyridine O, methyl and A, ethyl chlorides with pyridine (Fujio et al, unpublished).

A. Komornicki and J. W. Mclver, Chem. Phys. Lett., 10, 303 (1971). Rapid Geometry Optimization for Self-Consistent Molecular Orbital Methods. A. Komornicki and J. W. Mclver, / Am. Chem. Soc., 94, 2625 (1971). Structures of Transition States in Organic Reactions. General Theory and an Application to the Cyclobutene-Butadiene Isomerization Using a Self-Consistent Molecular Orbital Method. 

Jensen has carried out detailed studies on the dissociation of phosphine from metathesis precatalysts, using BLYP-D-CP (with Grimme s dispersion corrections and counterpoise correction, to reduce basis set superposition error). This functional was selected after a brief benchmarking study. Relaxed potential energy surface scans were carried out, where the ruthenium-phosphorus distances in complexes 3 and 8 were stepped in increments (Figure 2.33). Maxima were observed at c. 4 A, which were used to obtain optimized structures for transition states with Ru-P distances of 3.95 A (for 3) and 3.97 A (for 8), and concomitant benzylidene rotation. Weakly bound complexes resulted from dissociation, with Ru-P distances of 5-7 A. Notably, there existed a significant difference in energy between the dissociation transition state and the infinitely separated products (c. 15—16 kcal mol ), and therefore the association of phosphine is not barrierless. 

Scheme 53 Optimized locaUzed stracture of 5-la, optimized delocalized structure of S-la , and optimized stracture of transition-state 5-la at the B3LYP/6-31G level. Selected bond length (A) and angles (°) of all stractures ate also shown. Reprinted with the permission from ref. [25]. Copyright 2012 American Chemical Society...

The catalytically active enzyme substrate complex is an interactive structure in which the enzyme causes the substrate to adopt a form that mimics the transition-state intermediate of the reaction. Thus, a poor substrate would be one that was less effective in directing the formation of an optimally active enzyme transition-state intermediate conformation. This active conformation of the enzyme molecule is thought to be relatively unstable in the absence of substrate, and free enzyme thus reverts to a conformationally different state. 

Fan, L., and T. Ziegler. 1990. The application of density functional theory to the optimization of transition state structures. I. Organic migration reactions. J. Chem. Phys. 92, 3645. 

Figure 4.77 The optimized structure of the transition state II for the ethylene-insertion reaction II III (4.106), with forward activation energy A > = 6.90 kcalmol-1 relative to the metal-ethylene complex II.

Figure 4.80 Optimized structures of (a) the transition state (IIpri ) and (b) the product (IIpri) of the model propylene-insertion reaction (4.107b).

Mandelate racemase, another pertinent example, catalyzes the kinetically and thermodynamically unfavorable a-carbon proton abstraction. Bearne and Wolfenden measured deuterium incorporation rates into the a-posi-tion of mandelate and the rate of (i )-mandelate racemi-zation upon incubation at elevated temperatures. From an Arrhenius plot, they obtained a for racemization and deuterium exchange rate was estimated to be around 35 kcal/mol at 25°C under neutral conditions. The magnitude of the latter indicated mandelate racemase achieves the remarkable rate enhancement of 1.7 X 10, and a level of transition state affinity (K x = 2 X 10 M). These investigators also estimated the effective concentrations of the catalytic side chains in the native protein for Lys-166, the effective concentration was 622 M for His-297, they obtained a value 3 X 10 M and for Glu-317, the value was 3 X 10 M. The authors state that their observations are consistent with the idea that general acid-general base catalysis is efficient mode of catalysis when enzyme s structure is optimally complementary with their substrates in the transition-state. See Reference Reaction Catalytic Enhancement... 

Fig. 18. Optimized structure of the FeIV=0 complex with benzene (13a) and the transition state for the C-0 bond formation (TS[13a-14b] ). Distances are given in angstroms.

Figure 8.4. Optimal structure of the transition state for addition of an X -substituted nucleophile to a carbonyl group according to orbital interaction considerations.

H, Me, r-Bu, or Ph or R = H and R = Me, r-Bu, or Ph), was performed. Two possible reactions were investigated (a) the reactions suitable for the gas-phase interactions, which start from a 1 1 Br2-alkyne r-complex and do not enter into a 2 1 Br2-alkyne jt-complex and (b) the processes passing through a 2 1 Br2-alkyne 7r-complex, which appear more realistic for the reactions in solutions. The structures of the reactants and (g) the final products and also the possible stable intermediates have been optimized and the transition states for the predicted process have been found. Both trans- and cw-dibromoalkenes may ensue without the formation of ionic intermediates from a n-complex of two bromine molecules with the alkyne (solution reactions). The geometry around the double bond formed in dibromoalkenes strongly depends on the nature of the substituents at the triple bond. The cluster model was used for the prediction of the solvent influence on the value of the activation barrier for the bromination of the but-2-yne.35... 

Optimized structure of the F3Si-0-0 radical in ground state (Cs symmetry), modeling the site in silica, is shown in the Figure 7.16d. The unpaired electron occupies the 2px atomic orbital of the terminal oxygen atom (the X-axis is perpendicular to the plane of symmetry). The first electronically excited state (2A ) of the radical is related to the electronic transition of the lone pair of the terminal O atom to the 2px atomic orbital of the same atom. The energy of this vertical transition was found to be equal to AE — 0.5 eV. 

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