Water-assisted Proton Transfer in Ferredoxin I

Abstract

The role of water molecules in assisting proton transfer (PT) is investigated for the proton-pumping protein ferredoxin I (FdI) from Azotobacter vinelandii. , a larger barrier than for the forward reaction is correctly predicted, but it is quantitatively overestimated (23.1 kcal/mol from simulations versus 14.1 from experiment). Possible reasons for this discrepancy are discussed. Compared with the water-assisted process (⌬E ≈ 10 kcal/mol), water-unassisted proton transfer yields a considerably higher barrier of ⌬E ≈ 35 kcal/mol.

Reduction of CO2 to Methanol Catalyzed by a Biomimetic Organo-Hydride Produced from Pyridine

“…This view is also supported by the prior configuration of the water molecules in the aqueous solution solvating the reactant complex and the widespread occurrence of proton relays in other processes, [55][56][57]59,60,[64][65][66][67] including water oxidation 54,58 and enzymatic reactions. [61][62][63] In any event, the ∆G ‡ HT's reported in Table 1 show that the reaction is viable even without involvement of any proton relay chain.…”

“…In addition to stabilizing the TS, these water molecules also intimately participate in the reaction by acting as a proton relay chain during the proton transfer event. 47,[54][55][56][57][58][59][60][61][62][63][64][65][66][67] We calculate vibrational force constants at the M06/6-31+G** level of theory to: 1) verify that the reactant and product structures have only positive vibrational modes, 2) confirm that each TS has only one imaginary mode and that it connects the desired reactant and product structures via Intrinsic Reaction Coordinate (IRC) calculations, and 3) compute entropies, zero-point energies (ZPE) and thermal corrections included in the reported free energies at 298K.…”

“…99 In particular, using a hybrid explicit/implicit solvent model, we calculated low enthalpic barriers with respect to the complexed reactants of 13.6-18.5 kcal/mol (depending on the number of solvating waters) for PyCOOH 0 formation via a proton relay mechanism; the importance of proton relays have been extensively described in assorted chemical reactions. [54][55][56][57][58][59][60][61][62][63][64][65] Charge analysis on CO2 and PyH 0 along the reaction coordinate reveals that PyH 0 's propensity to recover its aromaticity drives the sequence of ET to CO2 followed by PT (mediated by a proton relay) to ultimately form PyCOOH 0 . 47,100 While this particular reaction is not of direct interest in the present work, 101 we will see that the themes of aromaticity recovery and proton relay mechanisms also prove to be important for our three HTPT step reduction of CO2 to CH3OH.…”

Atomistic simulations of reactive processes in the gas- and condensed-phase

“…During the past few years, a force field-based method -Molecular Mechanics with Proton Transfer (MMPT) -has been developed and successfully applied to a variety of chemical and biological systems [51,[54][55][56][57][58][59][60]. MMPT has been applied to several model PT systems.…”

“…unassisted process is found to have a barrier of DE % 35 kcal/mol [58] and therefore can be ruled out.…”