A GGA+U approach to effective electronic correlations in thiolate-ligated iron-oxo (IV) porphyrin

Contrasting Photochemical Activity of Two Sub-layers for Natural 2D Nanoclay with an Asymmetric Layer Structure

The two-dimensional (2D) materials with asymmetric sub-layers have recently attracted tremendous interest in many fields, and investigating the structure-performance relationship of different sub-layers is critical but challenging. Herein, we report that natural kaolinite (Kaol) nanosheets with an asymmetric layer structure possess a contrasting photocatalytic activity on its Al-O and Si-O sub-layers. The experimental and theoretical results reveal that the ion isovalent structure of Fe³⁺ and Al³⁺ not only results in a high iron doping concentration in the Al-O sub-layer but also causes superb intrinsic photochemical activity of the Al-O sub-layer compared with the Si-O sub-layer. Thus, the Al-O sub-layers of Kaol NSs have more excellent photogenerated charge generation and separation efficiency than Si-O sub-layers, resulting in about 1-2 orders of magnitude higher photocatalytic performance. This study not only unravels the structure-performance relationship of different sub-layers of 2D nanoclay but also sheds new light on the design of 2D materials with the asymmetric sub-layer.

Theoretical analysis of pressure induced spin crossover phenomenon in a di-nuclear Fe(II) molecular complex

We have studied a Fe-based di-nuclear molecular complex having the chemical formula [{Fe(bpp)(NCS)₂}₂([Formula: see text]'-bipy)]·2MeOH (where bpp  =  [Formula: see text]-bis(pyrazol-3-yl) pyridine and [Formula: see text]'-bipy  =  [Formula: see text]'-bipyridine, 1) using density functional theory and model Hamiltonian approach. Our study provides insight to the pressure driven spin-crossover (SCO) phenomena observed experimentally in these systems. Upon increasing the pressure, the spin state of Fe(II) cation gradually changes from a high spin state (S  =2) to a low spin (LS) state (S  =0) accompanied by volume contraction. The gradual increase in pressure shrinks Fe-N bond length and also causes angular deviation of the FeN₆ octahedron leading to full conversion to the LS state without global structural phase transition. We have carried out exact diagonalization study of an effective single site Hamiltonian and confirmed the importance of intramolecular interaction for SCO phenomena. We have investigated the cooperativity of the observed SCO phenomena. We have also studied the effect of Co doping on the spin state of Fe and find that the spin state of Fe has a subtle dependency on the concentration of dopant atoms. Excess Co doping pave the way towards the possibility of an intermediate spin state for Fe and can give rise to a bistable spin transition process.

Ab initio dynamics of the cytochrome P450 hydroxylation reaction

The iron(IV)-oxo porphyrin π-cation radical known as Compound I is the primary oxidant within the cytochromes P450, allowing these enzymes to affect the substrate hydroxylation. In the course of this reaction, a hydrogen atom is abstracted from the substrate to generate hydroxyiron(IV) porphyrin and a substrate-centered radical. The hydroxy radical then rebounds from the iron to the substrate, yielding the hydroxylated product. While Compound I has succumbed to theoretical and spectroscopic characterization, the associated hydroxyiron species is elusive as a consequence of its very short lifetime, for which there are no quantitative estimates. To ascertain the physical mechanism underlying substrate hydroxylation and probe this timescale, ab initio molecular dynamics simulations and free energy calculations are performed for a model of Compound I catalysis. Semiclassical estimates based on these calculations reveal the hydrogen atom abstraction step to be extremely fast, kinetically comparable to enzymes such as carbonic anhydrase. Using an ensemble of ab initio simulations, the resultant hydroxyiron species is found to have a similarly short lifetime, ranging between 300 fs and 3600 fs, putatively depending on the enzyme active site architecture. The addition of tunneling corrections to these rates suggests a strong contribution from nuclear quantum effects, which should accelerate every step of substrate hydroxylation by an order of magnitude. These observations have strong implications for the detection of individual hydroxylation intermediates during P450 catalysis.

Cytochrome P450 compound I in the plane wave pseudopotential framework: GGA electronic and geometric structure of thiolate-ligated iron(IV)-oxo porphyrin

The cytochromes P450 constitute a ubiquitous family of metalloenzymes, catalyzing manifold reactions of biological and synthetic importance via a thiolate-ligated iron-oxo (IV) porphyrin radical species denoted compound I (Cpd I). Experimental investigations have implicated this intermediate in a broad spectrum of biophysically interesting phenomena, further augmenting the importance of a Cpd I model system. Ab initio molecular dynamics, including Car-Parrinello and path integral methods, conjoin electronic structure theory with finite temperature simulation, affording tools most valuable to approach such enzymes. These methods are typically driven by density functional theory (DFT) in a plane-wave pseudopotential framework; however, existing studies of Cpd I have been restricted to localized Gaussian basis sets. The appropriate choice of density functional and pseudopotential for such simulations is accordingly not obvious. To remedy this situation, a systematic benchmarking of thiolate-ligated Cpd I is performed using several generalized-gradient approximation (GGA) functionals in the Martins-Troullier and Vanderbilt ultrasoft pseudopotential schemes. The resultant electronic and structural parameters are compared to localized-basis DFT calculations using GGA and hybrid density functionals. The merits and demerits of each scheme are presented in the context of reproducing existing experimental and theoretical results for Cpd I.