Mechanisms of Photoisomerization of Polyenes in Confined Media: From Organic Glasses to Protein Binding Cavities^†

Abstract

Photochemical reactivities of model organic systems (stilbene and diphenylbutadiene) in organic glasses were first examined and compared with those in solution and in organized media. These observations were in turn compared with reactivities of polyene chromophores in protein binding cavities (specifically PYP, rhodopsin and bacteriorhodopsin). The obvious conclusion is that the preference for the most volume-conserving Hula-twist mechanism isomerization in organic glasses is because of the close interaction between the guest and the host molecules. In organized media (zeolites, crystals and protein binding cavities), the residual empty space coupled with any specific guest-host interactions that are characteristic of a given system, could lead to involvement of the more volume-demanding one-bond-flip (i.e. torsional relaxation) or bicycle-pedal or an extended HT process in photoisomerization.

Volume-conserving trans–cis isomerization pathways in photoactive yellow protein visualized by picosecond X-ray crystallography

“…When the chromophore is embedded in a cavity within a photoreceptor, this mechanism may no longer hold because interactions with the surrounding side chains of the protein, including hydrogen-bonding interactions and steric constraints, severely restrict the conformational mobility of the chromophore 1,2 . Instead, “volume-conserving” isomerization mechanisms 3,4 should be considered where the pathway of isomerization proceeds along a trajectory that minimizes the volume swept out by the atoms of the chromophore 5 (Fig. 1a).…”

Mechanism of Photoisomerization of 1‐Naphthyl‐2‐Phenylethylenes in Organic Glasses

“…The first example was reported by Matsumoto and coworkers on crystals of the muconate (cis,cis) salt (7). More recently there were similar reports on crystals of cis,cis-1,4-diphenyl-1,3-butadienes (2,8). All these examples showed direct formation of the more stable trans,trans isomer from the cis,cis isomer without detectable intermediacy of the cis,trans isomer.…”

“…Recently, there has been a renewed interest in search of the exact mechanism of photoisomerization in confined media (whether a chromophore embedded within a protein binding cavity or a simple organic molecule trapped within a rigid host, such as an organic glass or in a crystal). (See e.g., 1,2) The question was first raised when the photoisomerization of rhodopsin chromophore was found to be an extremely fast process (subpico seconds) (3,4) seemingly incompatible with the volume demanding, albeit commonly accepted, torsional relaxation (also known as one-bond-flip [OBF]) process taking place within a rigid binding cavity. Two volumeconserving processes have since been introduced: the bicyclepedal (BP) process in which the middle two CH fragments of a diene unit rotate simultaneously (5) and the Hula-twist (HT) process in which one CH unit transposes across the polyene skeleton (6) (Fig.…”

Investigation of Rhodopsin Chromophore Photoisomerization Based on the Quantum-Classical Model

“…В приближении данной квантово-классической модели первоначальное возмущение в первые пикосекунды локализовано строго в районе двойной связи C 11 = C 12 . На это указывает ряд литературных данных [5,18,[32][33][34][35][36][37]. Мы допускаем, что β-иононовое кольцо ретиналя и его хвост жёстко фиксированы.…”

“…Попытки решить данную задачу предпринимаются с 1971 года [5,[17][18][19][20][25][26][27][28][29][30][31]. В частности, предположение о локализации первичных изменений конформации ретиналя строго в районе двойной связи C 11 = C 12 , выдвигалось целым рядом исследователей [5,18,[32][33][34][35][36][37]. Однако, результаты квантово-классического моделирования являются одним из самых весомых доказательств элементарного характера фотореакции и узкой локализации конформационных изменений ретиналя [24].…”