▪ Abstract We describe large scale ab initio quantum chemical and mixed quantum mechanics/molecular mechanics (QM/MM) methods for studying enzymatic reactions. First, technical aspects of the methodology are reviewed, including the hybrid density functional theory (DFT) methods that are typically employed for the QM aspect of the calculations, and various approaches to defining the interface between the QM and MM regions in QM/MM approaches. The modeling of the enzymatic catalytic cycle for three examples—methane monooxygenase, cytochrome P450, and triose phosphate isomerase—are discussed in some depth, followed by a brief summary of other systems that have been investigated by ab initio methods over the past several years. Finally, a discussion of the qualitative and quantitative conclusions concerning enzymatic catalysis that are available from modern ab initio approaches is presented, followed by a conclusion briefly summarizing future prospects.

Esterases receive special attention because their wide distribution in biological systems and environments and their importance for physiology and chemical synthesis. The prediction of esterases substrate promiscuity level from sequence data and the molecular reasons why certain such enzymes are more promiscuous than others, remain to be elucidated. This limits the surveillance of the sequence space for esterases potentially leading to new versatile biocatalysts and new insights into their role in cellular function. Here we performed an extensive analysis of the substrate spectra of 145 phylogenetically and environmentally diverse microbial esterases, when tested with 96 diverse esters. We determined the primary factors shaping their substrate range by analyzing substrate range patterns in combination with structural analysis and protein-ligand simulations. We found a structural parameter that helps ranking (classifying) promiscuity level of esterases from sequence data at 94% accuracy. This parameter, the active site effective volume, exemplifies the topology of the catalytic environment by measuring the active site cavity volume corrected by the relative solvent accessible surface area (SASA) of the catalytic triad. Sequences encoding esterases with active site effective volumes (cavity volume/SASA) above a threshold show greater substrate spectra, which can be further extended in combination with phylogenetic data. This measure provides also a valuable tool for interrogating substrates capable of being converted. This measure, found to be transferred to phosphatases of the haloalkanoic acid dehalogenase superfamily and possibly other enzymatic systems, represents a powerful tool for low-cost bioprospecting for esterases with broad substrate ranges, in large scale sequence datasets.

An ab initio excited state potential energy surface is constructed for describing excited state double proton transfer in the tautomerization reaction of photo-excited 7-azaindole dimers, and the ultrafast dynamics is simulated using the semiclassical (SC) initial value representation (IVR). The potential energy surface, determined in a reduced dimensionality, is obtained at the CIS level of quantum chemistry, and an approximate version of the SC-IVR approach is introduced which scales linearly with the number of degrees of freedom of the molecular system. The accuracy of this approximate SC-IVR approach is verified by comparing our semiclassical results with full quantum mechanical calculations. We find that proton transfer usually occurs during the first intermonomer symmetric-stretch vibration, about 100 fs after photoexcitation of the system, and produces an initial 15 percent population decay of the reactant base-pair, which is significantly reduced by isotopic substitution.

We elucidate the hydroxylation of camphor by cytochrome P450 with the use of density functional and mixed quantum mechanics/molecular mechanics methods. Our results reveal that the enzyme catalyzes the hydrogen-atom abstraction step with a remarkably low free-energy barrier. This result provides a satisfactory explanation for the experimental failure to trap the proposed catalytically competent high-valent heme Fe(IV) oxo (oxyferryl) species responsible for this hydroxylation chemistry. The primary and previously unappreciated contribution to stabilization of the transition state is the interaction of positively charged residues in the active-site cavity with carboxylate groups on the heme periphery. A similar stabilization found in dioxygen binding to hemerythrin, albeit with reversed polarity, suggests that this mechanism for controlling the relative energetics of redox-active intermediates and transition states in metalloproteins may be widespread in nature.