Computational Evidence for the Catalytic Mechanism of Human Glutathione S Transferase A3-3. A QM/MM Investigation

A Quantum Mechanics/Molecular Mechanics (QM/MM) computational investigation of the catalytic mechanism of the human glutathione transferase A3-3 (hGSTA3-3) has been carried out. The results demonstrate that the isomerization reaction is concerted, but highly asynchronous: in the first reaction phase the glutathione (GSH) negative sulfur (thiolate) acts as a base and deprotonates carbon C4 of the substrate Delta(5)-androstene-3,17-dione (Delta(5)-AD); in the second reaction phase the hydroxyl proton of the tyrosine fragment Y9 is AD). The initial state of the enzyme is subsequently restored by transferred to C6 affording the Delta(4)-androstene-3,17-dione product (Delta(4)-transferring a proton from the GSH sulfur to the tyrosine negative oxygen. There is no evidence for a "genuine" stepwise mechanism involving the formation of a real dienolate intermediate as suggested in previous papers. Furthermore, our computations have evidenced that, when we consider the whole process (including the restoring of the enzyme), GSH behaves as a base/acid catalyst (as hypothesized by some authors), but it requires the participation of the tyrosine Y9 acting as a proton shuttle. A "fingerprint analysis" has been used to rank the electrostatic effects on the catalysis of the various residues surrounding the active site. This analysis highlights the role played by the arginine residue R15 in stabilizing the initial complex in agreement with previous suggestions based on-crystal structures

Spectroscopic Properties of Formaldehyde in Aqueous Solution: Insights from Car−Parrinello and TDDFT/CASPT2 Calculations

We present Car-Parrinello and Car-Parrinello/molecular mechanics simulations of the structural, vibrational, and electronic properties of formaldehyde in water. The calculatedproperties of the molecule reproduce experimental values and previous calculations. The n->π* excitation energy, calculated with TDDFT and CASPT2, agrees with experimental data.In particular, it shows a blue shift on going from the gas phase to aqueous solution. Temperature and wave function polarization contributions have been disentangled

Conical intersection dynamics of the primary photoisomerization event in vision.

Ever since the conversion of the 11-cis retinal chromophore to its all-trans form in rhodopsin was identified as the primary photochemical event in vision, experimentalists and theoreticians have tried to unravel the molecular details of this process. The high quantum yield of 0.65 (ref. 2), the production of the primary ground-state rhodopsin photoproduct within a mere 200 fs (refs 3-7), and the storage of considerable energy in the first stable bathorhodopsin intermediate all suggest an unusually fast and efficient photoactivated one-way reaction. Rhodopsin's unique reactivity is generally attributed to a conical intersection between the potential energy surfaces of the ground and excited electronic states enabling the efficient and ultrafast conversion of photon energy into chemical energy. But obtaining direct experimental evidence for the involvement of a conical intersection is challenging: the energy gap between the electronic states of the reacting molecule changes significantly over an ultrashort timescale, which calls for observational methods that combine high temporal resolution with a broad spectral observation window. Here we show that ultrafast optical spectroscopy with sub-20-fs time resolution and spectral coverage from the visible to the near-infrared allows us to follow the dynamics leading to the conical intersection in rhodopsin isomerization. We track coherent wave-packet motion from the photoexcited Franck-Condon region to the photoproduct by monitoring the loss of reactant emission and the subsequent appearance of photoproduct absorption, and find excellent agreement between the experimental observations and molecular dynamics calculations that involve a true electronic state crossing. Taken together, these findings constitute the most compelling evidence to date for the existence and importance of conical intersections in visual photochemistry