Centre, reaction

Figure Bl.15.16. Two-pulse ESE signal intensity of the chemically reduced ubiqumone-10 cofactor in photosynthetic bacterial reaction centres at 115 K. MW frequency is 95.1 GHz. One dimension is the magnetic field value Bq, the other dimension is the pulse separation x. The echo decay fiinction is anisotropic with respect to the spectral position.

From SCRP spectra one can always identify the sign of the exchange or dipolar interaction by direct exammation of the phase of the polarization. Often it is possible to quantify the absolute magnitude of D or J by computer simulation. The shape of SCRP spectra are very sensitive to dynamics, so temperature and viscosity dependencies are infonnative when knowledge of relaxation rates of competition between RPM and SCRP mechanisms is desired. Much use of SCRP theory has been made in the field of photosynthesis, where stnicture/fiinction relationships in reaction centres have been connected to their spin physics in considerable detail [, Mj. 

So far we have exclusively discussed time-resolved absorption spectroscopy with visible femtosecond pulses. It has become recently feasible to perfomi time-resolved spectroscopy with femtosecond IR pulses. Flochstrasser and co-workers [M, 150. 151. 152. 153. 154. 155. 156 and 157] have worked out methods to employ IR pulses to monitor chemical reactions following electronic excitation by visible pump pulses these methods were applied in work on the light-initiated charge-transfer reactions that occur in the photosynthetic reaction centre [156. 157] and on the excited-state isomerization of tlie retinal pigment in bacteriorhodopsin [155]. Walker and co-workers [158] have recently used femtosecond IR spectroscopy to study vibrational dynamics associated with intramolecular charge transfer these studies are complementary to those perfomied by Barbara and co-workers [159. 160], in which ground-state RISRS wavepackets were monitored using a dynamic-absorption technique with visible pulses. 

Many key protein ET processes have become accessible to theoretical analysis recently because of high-resolution x-ray stmctural data. These proteins include the bacterial photosynthetic reaction centre [18], nitrogenase (responsible for nitrogen fixation), and cytochrome c oxidase (the tenninal ET protein in mammals) [19, 20]. Although much is understood about ET in these molecular machines, considerable debate persists about details of the molecular transfonnations. 

Figure C3.2.6. Zones associated witlr the distinctive decay of electronic coupling tlrrough a-helical against p-sheet stmctures in proteins. Points shown refer to specific rates in mtlrenium-modified proteins aird in tire photosyntlretic reaction centre. From Gray H B aird Wiirkler J R 1996 Electron trairsfer in proteins A . Rev. Biochem. 65 537.

With tlie development of femtosecond laser teclmology it has become possible to observe in resonance energy transfer some apparent manifestations of tire coupling between nuclear and electronic motions. For example in photosyntlietic preparations such as light-harvesting antennae and reaction centres [32, 46, 47 and 49] such observations are believed to result eitlier from oscillations between tire coupled excitonic levels of dimers (generally multimers), or tire nuclear motions of tire cliromophores. This is a subject tliat is still very much open to debate, and for extensive discussion we refer tire reader for example to [46, 47, 50, 51 and 55]. A simplified view of tire subject can nonetlieless be obtained from tire following semiclassical picture. 

Comparison of the water-induced acceleration of the reaction of 2.4a with the corresponding effect on 2.4g is interesting, since 2.4g contains an ionic group remote from the reaction centre. The question arises whether this group has an influence on the acceleration of the Diels-Alder reaction by water. Comparison of the data in Table 2.1 demonstrates that this is not the case. The acceleration upon going from ethanol to water amounts a factor 105 ( 10) for 2.4a versus 110 ( 11) for 2.4g. Apparently, the introduction of a hydrophilic group remote from the reaction centre has no effect on the aqueous acceleration of the Diels-Alder reaction. 

Studies of the Diels-Alder reaction of the ionic dienophile 2.4g have demonstrated that the acpieous acceleration of the uncatalysed reaction as well as the catalysed reaction is not significantly affected by the presence of the ionic group at a site remote from the reaction centre. 

The observation that in the activated complex the reaction centre has lost its hydrophobic character, can have important consequences. The retro Diels-Alder reaction, for instance, will also benefit from the breakdown of the hydrophobic hydration shell during the activation process. The initial state of this reaction has a nonpolar character. Due to the principle of microscopic reversibility, the activated complex of the retro Diels-Alder reaction is identical to that of the bimoleciilar Diels-Alder reaction which means this complex has a negligible nonpolar character near the reaction centre. O nsequently, also in the activation process of the retro Diels-Alder reaction a significant breakdown of hydrophobic hydration takes placed Note that for this process the volume of activation is small, which implies that the number of water molecules involved in hydration of the reacting system does not change significantly in the activation process. 

In the case of the retro Diels-Alder reaction, the nature of the activated complex plays a key role. In the activation process of this transformation, the reaction centre undergoes changes, mainly in the electron distributions, that cause a lowering of the chemical potential of the surrounding water molecules. Most likely, the latter is a consequence of an increased interaction between the reaction centre and the water molecules. Since the enforced hydrophobic effect is entropic in origin, this implies that the orientational constraints of the water molecules in the hydrophobic hydration shell are relieved in the activation process. Hence, it almost seems as if in the activated complex, the hydrocarbon part of the reaction centre is involved in hydrogen bonding interactions. Note that the... 

Kranss, N., et al., 1996. Photosystem I at 4 A resolution represents the first structural model of a joint photosynthedc reaction centre and core antenna system. Nature Structural Biology 3 965-973. 

The proximity of the reaction centre to the second phenyl ring makes the aryl cation, formed by heterolytic dediazoniation, a serious competitor to the aryl radical. This is evident in Table 10-6 from various examples where the yield obtained in aqueous mineral acid (varying from 0.1 m to 50% H2S04) is higher than in the presence of an electron-transfer reagent. This competition was studied in three types of product analyses by Cohen s group (Lewin and Cohen, 1967 Cohen et al., 1977), by Huisgen and Zahler (1963 a, 1963 b), and by Bolton et al. (1986). 

In the same manner, the rc-electron densities of the monomer and the cation are affected. Substituents, which decrease the electron density at the P-C-atom, that is, the place of the primary attack on the double bond, increase the positive charge at the a-C-atom of the cation and therefore its electrostatic interaction with a negative reaction centre (qa(cation) = —2.08 + 2.53qp(monomer) r = 0.93 n = 13). The previous equation shows that the electron density of the cation is more influenced than that of the monomer (Aqp(monomer) = 0.1 and Aqjcation) = 0.25).. 

The steric environment of the atoms in the vicinity of the reaction centre will change in the course of a chemical reaction, and consequently the potential energy due to non-bonded interactions will in general also change and contribute to the free energy of activation. The effect is mainly on the vibrational energy levels, and since they are usually widely spaced, the contribution is to the enthalpy rather than the entropy. When low vibrational frequencies or internal rotations are involved, however, effects on entropy might of course also be expected. In any case, the rather universal non-bonded effects will affect the rates of essentially all chemical reactions, and not only the rates of reactions that are subject to obvious steric effects in the classical sense. 

The Holy Grail of catalysis has been to identify what Taylor described as the active site that is, that ensemble of atoms which is responsible for the surface reactions involved in catalytic turnover. With the advent of atomically resolving techniques such as scanning tunnelling microscopy it is now possible to identify reaction centres on planar surfaces. This gives a greater insight also into reaction kinetics and mechanisms in catalysis. In this paper two examples of such work are described, namely CO oxidation on a Rh(llO) crystal and methanol selective oxidation to formaldehyde on Cu(llO). 

Thus crx can be regarded as a measure of the overall polar effect exerted by a substituent, X, on the reaction centre. Its sign indicates the direction (-ve = electron-donating +ve = electron-withdrawing), and its magnitude the extent, of the effect that X exerts—compared, of course, with the effect exerted by H. Indeed, the assumed constancy of a substituent s absolute polar effect of X always remains constant, but only that its effect relative to H remains constant. 

This has p value of +2-51, the known slow, rate-limiting step in this reaction is attended by the development of -ve charge adjacent to the reaction centre in the transition state leading to the intermediate (12), and the overall reaction is, as we have already seen (p. 365),... 

On this basis, it might well be expected that the p value, of otherwise similar reactions, would decrease as the reaction centre is moved further away from the substituents that are exerting a polar, electronic effect upon it. This is borne out by the p values for the aqueous ionisation of the acids (13)—(16) ... 

For each species, the inductive effect of the p-N02 substituent— which will be essentially similar in each of the sets of species—has been omitted, but the mesomeric or conjugative effect has been included. In (18a) = (18b), the standard reaction that was used to evaluate conjugative effect of the p-NOz substituent is transmitted ultimately to the reaction centre only through an inductive effect operating on the C02H, or CO , group from the ring carbon atom to which it is attached. In (19a) (19b), however, the... 

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