Correcting density-driven errors in projection-based embedding.

Projection-based embedding provides a simple and numerically robust framework for multiscale wavefunction-in-density-functional-theory (WF-in-DFT) calculations. The approach works well when the approximate DFT is sufficiently accurate to describe the energetics of the low-level subsystem and the coupling between subsystems. It is also necessary that the low-level DFT produces a qualitatively reasonable description of the total density, and in this work, we study model systems where delocalization error prevents this from being the case. We find substantial errors in embedding calculations on open-shell doublet systems in which self-interaction errors cause spurious delocalization of the singly occupied orbital. We propose a solution to this error by evaluating the DFT energy using a more accurate self-consistent density, such as that of Hartree-Fock (HF) theory. These so-called WF-in-(HF-DFT) calculations show excellent convergence towards full-system wavefunction calculations.

A Projector-Embedding Approach for Multiscale Coupled-Cluster Calculations Applied to Citrate Synthase.

Projector-based embedding has recently emerged as a robust multiscale method for the calculation of various electronic molecular properties. We present the coupling of projector embedding with quantum mechanics/molecular mechanics modeling and apply it for the first time to an enzyme-catalyzed reaction. Using projector-based embedding, we combine coupled-cluster theory, density-functional theory (DFT), and molecular mechanics to compute energies for the proton abstraction from acetyl-coenzyme A by citrate synthase. By embedding correlated ab initio methods in DFT we eliminate functional sensitivity and obtain high-accuracy profiles in a procedure that is straightforward to apply.

A radical rebound mechanism for the methane oxidation reaction promoted by the dicopper center of a pMMO enzyme: a computational perspective.

In this article, we investigated the hydroxylation of methane catalyzed by the binuclear copper site of a pMMO enzyme, through a radical rebound mechanism. All intermediates and transition states along the reaction coordinate were located and the energies involved in the mechanism calculated using the B3LYP functional including dispersion effects. Our B3LYP-D2 results show that the singlet state of the (µ-1,2-peroxo)Cu(II)2 complex plays an important role as the lowest energy species prior to C-H bond activation. A crossing between the singlet and triplet PES is suggested to occur before the cleavage of the C-H bond of methane, where the triplet (bis-µ-oxo)Cu(III)2 is very reactive towards activation of the strong C-H bond of methane. The C-H bond activation is the rate-determining step of the reaction, with an activation energy of 18.6 kcal mol(-1) relative to the singlet (µ-1,2-peroxo)Cu(II)2 species. Comparison with previous theoretical results for a non-synchronous concerted mechanism suggests the radical rebound mechanism as a possible alternative pathway.

Electronic structure and formation of simple ferryloxo complexes: mechanism of the Fenton reaction.

The Fenton reaction is a famous reaction in inorganic chemistry, with relevance to topics such as bioinorganic oxidation and fundamental redox chemistry of water and oxygen. It is also a reaction concerning which there has been very extensive mechanistic debate, with experimental and computational work leading to extensive evidence concerning its mechanism-not all of which is consistent. Here, we use this reaction as a challenge to modern electronic structure theory methods and show that density functional theory, when validated by accurate ab initio methods, can yield a picture of this reaction that is consistent with experiment. The article also highlights some of the challenges in accurate studies of reaction mechanisms of ionic species in water solution.