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Alkyl Halides and Substitution Reactions
Published in Michael B. Smith, A Q&A Approach to Organic Chemistry, 2020
When a radical removes a hydrogen atom from a carbon, the resulting carbon radical reacts with another molecule of halogen, and the overall process replaces a hydrogen of the alkane precursor with a halogen atom. This transformation is often called a radical substitutionreaction. In general, radical substitution is not a selective reaction unless the radical reacts faster with one type of hydrogen rather than another. This statement means that the rate of reaction of the radical with a primary hydrogen may be slower than the rate of reaction for a tertiary hydrogen. What is the product when diatomic chlorine or bromine is heated to 300°C or exposed to light?
Theory of chemical bonds in metalloenzymes XXIII fundamental principles for the photo-induced water oxidation in oxygen evolving complex of photosystem II
Published in Molecular Physics, 2020
K. Yamaguchi, S. Yamanaka, H. Isobe, M. Shoji, K. Miyagawa, T. Kawakami
The S4 intermediate with hydroxy radical •O(3)H coordinated to Ca ion may be a transient species. In fact, the proton shift from the inserted hydroxide anion to •O(3)H [145] was feasible to afford the Mn-oxyl radical intermediate, Ca(II)Mn(IV)4O5- O•. The L-opened Mn-oxyl radical intermediate was more stable by 3.1 kcal/mol than S4 intermediate with •O(3)H as shown in Table 4 [38,145,146]. Moreover, the R-opened Mn-oxyl radical intermediate was more stable by 5.4 kcal/mol than the L-opened one. The calculated spin density of the oxyl-radical (•O) was larger than 0.9 because of no participation of the Ca(II) ion in the minimal model. Therefore, the radical substitution reactions (RS) instead of the radical coupling (RC) in Equation (10) were feasible as follows. where the O(5) site was fixed by the Mn(IV)3 ion in the cubane structure of the CaMn4O5 cluster, affording the Mn(IV)3-O(5)-O(3)-Mn(IV)j. The activation energies for the RS5(L) and RS6(R) were calculated to be 12.3 and 6.8 (kcal/mol) for L- and R-opened Mn-oxyl radicals, respectively [38,145,146]. Thus, the activation barriers for three reaction patterns in the S4 state were lower in the R-opened pathways than in the corresponding L-opened pathways.
Theory of chemical bonds in metalloenzymes XXII: a concerted bond-switching mechanism for the oxygen–oxygen bond formation coupled with one electron transfer for water oxidation in the oxygen-evolving complex of photosystem II
Published in Molecular Physics, 2019
K. Yamaguchi, M. Shoji, H. Isobe, K. Miyagawa, K. Nakatani
Present computational results indicate the necessity of brief discussions on possible mechanisms of the O–O bond formation in artificial and native photosynthesis systems as illustrated in Figure 21. In several artificial systems, two high-valent Mn = O bonds are formed at the reaction site [138]. The spin polarisation (SP) effect (see Figure 11) occurs in the transition state region, providing two oxyl radical sites. Therefore, radical coupling (RC) reaction is facile, affording the O–O bond as shown in (A) of Figure 21. The RC mechanism is easily applicable for the O–O bond formation in the case of OEC of PSII if the SP effect of the Mn4–O(5) bond occurs in the TS region as illustrated in (B) of Figure 21. However, the NO analysis indicates no such SP effect of the Mn4–O(5) bond in the case of OEC of PSII. On the other hand, the negative spin densities might be regarded as a free radical substitution reaction as illustrated in (C) of Figure 21. However, the populations of spin density on the Mn1 and O(6) sites at TS were −0.5 and −0.3, respectively (see Equation (11)), indicating contributions of the charge polarised configurations like in the case of the SE2 reaction as illustrated in (D) of Figure 21. The NO analysis in Figures 15 and 16 indeed elucidated that the spin densities are mainly responsible for formation of the one-electron transfer (OET) diradical where the charge and spin separation are operative; •Mn(III)4 … O(5)- and +O(6)–Mn(IV)1•. The weak diradical character for the OET diradical, [Mn(III)4(−0.5) … O(5)- … +O(6)(−0.3)]-[Mn(IV)1](+0.8), at TS indicates contribution of such SE2 type character for the O(5)–O(6) bond formation in the confinement environment of OEC of PSII. The CBS-OET mechanism is acceptable instead of the simple radical substitution (SR) mechanism by free radical. The push–pull stabilisation by His332-Glu329 and Ca(II)–Mn(IV)3 should enhance such contributions (for example −0.7 on Mn(III)4 and −0.1 on O(6)) in the realistic QM/MM model (see Figure 21(D)).