Targeting Intermediates of [FeFe]-Hydrogenase by CO and CN Vibrational Signatures

Abstract

In this work we employ density functional theory to assign vibrational signatures of [FeFe]-hydrogenase intermediates to molecular structures. For this purpose, we perform an exhaustive analysis of structures and harmonic vibrations of a series of CN and CO containing model clusters of the [FeFe]-hydrogenase enzyme active site considering also different charges, counter ions and solvents. The pure density functional BP86 in combination with a triple-zeta polarized basis set produce reliable molecular structures as well as harmonic vibrations. Calculated CN and CO stretching vibrations are analyzed separately. Our results are discussed in close comparison to previous studies. Finally, we apply the scaled vibrational frequencies to assign intermediates in [FeFe]-hydrogenase's reaction cycle.

Stepwise isotope editing of [FeFe]-hydrogenases exposes cofactor dynamics

“…Only these models reproduced the altered origin of the pCO vibrational frequency and inverted band intensities for species including d 1 13 CO and d 2 13 CO. Improved correlation of experimental and calculated IR data for H ox -CO with apical dCN − has been discussed before, but evaluated against insufficiently small experimental IR datasets (39,47,48). We prove the effect for 16 H ox -CO species, three phylogenetically distinct [FeFe]-hydrogenases, and varying computational approaches.…”

“…13 CO editing of the H-cluster has been achieved using 13 C-precursors during H-cluster assembly or exposure of [FeFe]-hydrogenases to 13 CO gas (18,(24)(25)(26)33 CO groups also facilitates analysis of structure-function relationships using quantum chemical calculations. However, relatively few computational studies to calculate vibrational modes of the diatomic ligands have been carried out (35)(36)(37)(38)(39).We compared three different [FeFe]-hydrogenase proteins, HYDA1, from the green alga Chlamydomonas reinhardtii, and the bacterial enzymes CPI from Clostridium pasteurianum and DDH from Desulfovibrio desulfuricans. HYDA1 represents the "minimal unit" of biological hydrogen turnover as it exclusively binds the H-cluster, whereas CPI and DDH hold accessory iron-sulfur clusters (3,40).…”

“…13 CO editing of the H-cluster has been achieved using 13 C-precursors during H-cluster assembly or exposure of [FeFe]-hydrogenases to 13 CO gas (18,(24)(25)(26)33 CO groups also facilitates analysis of structure-function relationships using quantum chemical calculations. However, relatively few computational studies to calculate vibrational modes of the diatomic ligands have been carried out (35)(36)(37)(38)(39).…”

“…Introduction of 13 CO groups also facilitates analysis of structure-function relationships using quantum chemical calculations. However, relatively few computational studies to calculate vibrational modes of the diatomic ligands have been carried out (35)(36)(37)(38)(39).…”

MOVIPAC: Vibrational spectroscopy with a robust meta‐program for massively parallel standard and inverse calculations

“…[14] If this is not the case, scaling factors may be used; note that the so-called scaled quantum mechanical force fields are one particular ' 'flavor' ' of these techniques. [14,[20][21][22][23][24][25] In 2002, we presented a seminumerical, massively parallel implementation for quantum chemical calculations of molecular vibrations in the harmonic approximation which has become known as the SNF program. [26] SNF was based on earlier work in the 1990s by Grimme and Marian [27] and its structure has been under constant development.…”