QM Cluster Model Research Articles

Mechanistic insights into the catalytic reaction of plant allene oxide synthase (pAOS) via QM and QM/MM calculations

QM cluster and QM/MM protein models have been employed to understand aspects of the reaction mechanism of plant allene oxide synthase (pAOS). In this study we have investigated two reaction mechanisms for pAOS. The standard pAOS mechanism was contrasted with an alternative involving an additional active site molecule which has been shown to facilitate proton coupled electron transfer (PCET) in related systems. Firstly, we found that the results from QM/MM protein model are comparable with those from the QM cluster model, presumably due to the large active site used. Furthermore, the results from the QM cluster model show that the FeIII and FeIV pathways for the standard mechanism have similar energetic and structural properties, indicating that the reaction mechanism may well proceed via both pathways. However, while the PCET process is facilitated by an additional active site bound water in other related families, in pAOS it is not, suggesting this type of process is not general to all closely related family members.

Convergence of QM/MM and Cluster Models for the Spectroscopic Properties of the Oxygen-Evolving Complex in Photosystem II.

The latest crystal structure of photosystem II at 1.9 Å resolution, which resolves the topology of the Mn4CaO5 oxygen evolving complex (OEC) at atomistic detail, enables a better correlation between structural features and spectroscopic properties than ever before. Building on the refined crystallographic model of the OEC and the protein, we present combined quantum mechanical/molecular mechanical (QM/MM) studies of the spectroscopic properties of the natural catalyst embedded in the protein matrix. Focusing on the S2 state of the catalytic cycle, we examine the convergence of not only structural parameters but also of the intracluster magnetic interactions in terms of exchange coupling constants and of experimentally relevant (55)Mn, (17)O, and (14)N hyperfine coupling constants with respect to QM/MM partitioning using five QM regions of increasing size. This enables us to assess the performance of the method and to probe second sphere effects by identifying amino acid residues that principally affect the spectroscopic properties of the OEC. Comparison between QM-only and QM/MM treatments reveals that whereas QM/MM models converge quickly to stable values, the QM cluster models need to incorporate significantly larger parts of the second coordination sphere and surrounding water molecules to achieve convergence for certain properties. This is mainly due to the sensitivity of the QM-only models to fluctuations in the hydrogen bonding network and ligand acidity. Additionally, a hydrogen bond that is typically omitted in QM-only treatments is shown to determine the hyperfine coupling tensor of the unique Mn(III) ion by regulating the rotation plane of the ligated D1-His332 imidazole ring, the only N-donor ligand of the OEC.

Skeletal Isomerization of Butene in Ferrierite: Assessing the Energetic and Structural Differences between Carbenium and Alkoxide Based Pathways

In this study, the results from a systematic analysis of two different mechanisms for the skeletal isomerization of cis-butene to isobutene in ferrierite (FER) are presented. One involves a conventional mechanism that proceeds via stable alkoxide intermediates and the other is one which proceeds via carbenium ions only. A 27T QM cluster model has been used in this study, which is described using the M06-2X DFT functional. It is found that the alkoxide intermediates formed over the course of the conventional pathway are considerably lower in energy than the carbenium ion formed over the course of the alternate pathway. However, the rate determining step in the latter pathway is predicted to be almost 10 kcal/mol lower in energy. The higher barrier for the latter process is due to the inherent stability of the alkoxide intermediates formed within FER. These results appear to suggest that while these intermediates are formed over the course of the reaction, the skeletal isomerization of linear butenes to form isobutene in FER may occur via a carbenium based mechanism. This proposal is consistent with experimental results that show alkoxide intermediates are experimentally observed species.

Effect of the size of the quantum region in a hybrid embedded-cluster scheme for zeolite systems

Recently we presented an improved scheme for constructing the border region within the covEPE hybrid quantum mechanics/molecular mechanics (QM/MM) embedded cluster approach for zeolites and covalent oxides in the framework of the elastic polarizable environment method. In the present study we explored how size and shape of the embedded QM cluster affect the results for structural features, energies, and characteristic vibrational frequencies of two model systems, adsorption complexes of H 2O and Rh 6 in faujasite frameworks that contain Brønsted acid sites. Comparison of calculated characteristics of different QM cluster models suggests that the local structure and vibrational frequencies of acid sites in adsorbate-free zeolite are well reproduced with all embedded QM clusters, which contain from 5T to 14T atoms. A proper description of systems with an H 2O adsorbate requires larger QM clusters, with at least 8T atoms, whereas vibrational frequencies of OH groups participating in hydrogen bonds demand even larger quantum clusters, preferably with 12T or 14T atoms. The structure of the metal particle in adsorbed rhodium species is well reproduced with all QM clusters scrutinized, from 12T atoms. Larger QM models, with 18T or 24T atoms, are recommended when one aims at a high accuracy of Rh–O and Rh–H distances and characteristic energies.