Reaction center polarity

The crystallization and X-ray diffraction analysis of the reaction center from the bacterium Rb. sphaeroides R-26 has revealed the three-dimensional structure of the protein and bound cofactors to atomic resolution (Allen et al., 1986 Allen et al., 1987 Yeates et al., 1987 Yeates et al., 1988 Allen et al., 1988 Komiya et al., 1988 Chang et al., 1991 El-Kabbani et al., 1991). With this information available, it is of interest to ask how the spectroscopic properties of the reaction center correlate with the structural features. Ultimately this correlation will allow an elucidation of the molecular details that control the spectral features and relate to the primary photochemical events carried out by the reaction center. Polarized light absorption is one technique for correlating the spectroscopic features with its molecular structure (Breton, 1985). In order to make the correlation more precise, it is distinctly advantageous to carry out the spectroscopic experiments directly on the crystalline samples used in the X-ray diffraction analyses. In this way the clearest link between the structure of the complex and its photochemical properties will emerge. 

The functional reaction center contains two quinone molecules. One of these, Qb (Figure 12.15), is loosely bound and can be lost during purification. The reason for the difference in the strength of binding between Qa and Qb is unknown, but as we will see later, it probably reflects a functional asymmetry in the molecule as a whole. Qa is positioned between the Fe atom and one of the pheophytin molecules (Figure 12.15). The polar-head group is outside the membrane, bound to a loop region, whereas the hydrophobic tail is... 

In general, the dissection of substituertt effects need not be limited to resonance and polar components, vdiich are of special prominence in reactions of aromatic compounds.. ny type of substituent interaction with a reaction center could be characterized by a substituent constant characteristic of the particular type of interaction and a reaction parameter indicating the sensitivity of the reaction series to that particular type of interactioa For example, it has been suggested that electronegativity and polarizability can be treated as substituent effects separate from polar and resonance effects. This gives rise to the equation... 

A few comments on the polar effects of the substituents reported in Tables IX—XI are now relevant. With the exception of 4-chloro-5-nitroquinoline (see Section IV, C, l,c), they involve only positions not subject to primary steric effects. The relations to the reaction center are of the conjugative cata, amphi) as well as of the non-conjugative class meta, epi, pros) as shown in Chart 3 by structures 45 and 46. 

The direction of addition, verified by acetylene oxidation into a known acid, proves that the nitiilimine carbon atom adds to the terminal atom of the enyne system, which is inconsistent with the assumed polarization of the unsaturated compound H2C=CH—C=C—R from the vinyl group towardR. The authors explain this by a possible transfer of the reaction center in nitrilimine as a particle with a nucleophilic center on a carbon Ph—C=N" —N —Ph Ph—C =N =N—Ph (63ZOB3558). 

A different picture is observed when a polar radical reacts with a C—H bond of a polar molecule. For example, the reaction of an oxygen atom with the methane C—H bond is characterized by the activation energy of thermoneutral reaction /ic0 54.6 kJ mol-1 and parameter bre= 13.11 (kJ mol-1)172 while the reaction with the methanol C—H bond is characterized by Ed) 50 kJ mol-1 and parameter brc 12.55 (kJ mol-1)172 [30]. For these values of bre, the difference between the activation energies is 4.6 kJ mol-1. The decrease in the activation energy can be explained by the fact that the polar O—H group in the O H C—OH transition state interacts with the O H C polar reaction center. 

The polar effect involved in radical addition has been repeatedly discussed in the scientific literature. The parabolic model opens up new prospects for the correct estimation of the polar effect (see Section 6.2.7). It permits one to determine the contribution of this effect to the activation energy using experimental data. This contribution (AE ) is estimated by choosing a reference reaction that involves the same reaction center but in which one or both reactants... 

An additional polar interaction called multidipole interaction is observed in reactions of peroxyl radicals with polyatomic alcohols [55], A few polar O—H groups interact with the polar reaction center C H O in such systems. A few examples of such interaction are given here [17]. Multidipole interaction sufficiently changes the thermoneutral activation energy of the reaction HOO + alcohol [54] and can be characterized by increment A A E. ... 

In addition to the enthalpy and polar interaction, the following factors influence the activation energy of these reactions triplet repulsion, electron affinity of atoms C and O in the TS, radii of C and O atoms, and n-bonds in the vicinity of the reaction center. These factors were discussed in Chapter 6 in application to the reaction of peroxyl radicals with hydrocarbons. 

Another factor that influences the reactivity of two polar reactants, acylperoxyl radical with aldehyde, is the polar interaction of carbonyl group with reaction center in the transition state. Aldehydes are polar compounds, their dipole moments are higher than 2.5 Debye (see Section 8.1.1). The dipole moment of the acylperoxyl radical is about 4 Debye (/jl = 3.87 Debye for PhC(0)00 according to the quantum-chemical calculation [54]). Due to this, one can expect a strong polar effect in the reaction of peroxyl radicals with aldehydes. The IPM helps to evaluate the increment Ain the activation energy Ee of the chosen reaction using experimental data [1], The results of Acalculation are presented in Table 8.10. 

The values of Aare negative and varies from —1.6 to —11 kJ mol-1. The reaction center C H O for the reaction of the peroxyl radical with the C—H bond of the hydrocarbon has a nearly linear geometry (see Chapter 2). The polar interaction changes the geometry of the TS (see Chapter 7). The geometric parameters for the reactions of peroxyl radicals with aldehydes... 

The polar interaction changes the geometry of the transition state of the reaction R02 + RH. Atoms C, H, O of the reaction center O H C of this reaction are in a straight line for the reaction of the peroxyl radical with a hydrocarbon. The reaction center O H C has an angular geometry in the reaction of the polar peroxyl radical with a polar molecule of the ketone. The interatomic distances rc H and i o n and angles peroxyl radical reactions with ketones calculated by the IPM method [79,80] are given in Table 8.15. 

The reaction constant p depends on nature of reaction, solvent and temperature. It is a measure of the susceptibility of the reaction to polar effect. A positive value of p for a reaction shows that the reaction is accelerated by electron withdrawing substituents (o = + 1.0). Thus a positive value of p indicates the reaction center has higher electron density in the transition state than in the starting material. While negative value of p indicates that the reaction center has a lower electron density in the transition state than in the starting material and the reaction is accelerated by electron donating... 

The limited kinetic data for reactions of tin hydride with nitrogen-centered radicals apparently demonstrates the combined effects of the enthalpies of the reactions and polarization in the transition states for H-atom transfer. The aminyl and iminyl radicals are electron-rich, and the N-H bonds formed are relatively weak these radicals react relatively slowly with tin hydride. On the other hand, the electrophilic amidyl and aminium cation radicals form strong N-H bonds and react rapidly with the tin hydride reagents. 

Another important result that was obtained recently concerns the evaluation of the contribution to the reorganization energy arising from the polarization of the medium, protein and solvent from a microscopic model including the residual charges and induced dipoles of the protein as well as bound water molecules, a value of about 0.2 eV was calculated for different eleetron transfer processes [97], This weak value results from the apolar character of the medium, and is compatible with the kinetic data which indicate that reorganization energies are small in the reaction center (Sect. 3.2.2)... 

The effect of the relative electronegativity of a substituent (R) and/or the delocalization of electrons on a chemical property of a substance. Thus, for a molecule R—R, the polar effect refers to all nonsteric influences and modifications of electrostatic forces operating at the reaction center (R ), relative to some standard molecule, Rq—R. Hence, the term is synonymous with the electronic effect. 

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