Quantum Chemical Cluster Approach Research Articles

Mechanistic Insights into the electron‐transfer driven substrate activation by [4Fe‐4S]‐dependent Enzymes

Abstract[4Fe‐4S]‐dependent enzymes catalyze many different types of biological reactions. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics approach, with the broken symmetry approach, are powerful tools for understanding the reaction mechanism in enzymes. This review discusses examples of the computational studies on [4Fe‐4S]‐dependent enzymes, focusing on the electron‐transfer driven substrate activation.

Quantum chemical modeling of enantioselective sulfoxidation and epoxidation reactions by indole monooxygenase VpIndA1.

Indole monooxygenases (IMOs) are enzymes from the family of Group E monooxygenases, requiring flavin adenine dinucleotide (FAD) for their activities. IMOs play important roles in both sulfoxidation and epoxidation reactions. The broad substrate range and high selectivity of IMOs make them promising biocatalytic tools for synthesizing chiral compounds. In the present study, quantum chemical calculations using the cluster approach were performed to investigate the reaction mechanism and the enantioselectivity of the IMO from Variovorax paradoxus EPS (VpIndA1). The sulfoxidation of methyl phenyl sulfide (MPS) and the epoxidation of indene were chosen as the representative reactions. The calculations confirmed that the FADOOH intermediate is the catalytic species in the VpIndA1 reactions. The oxidation of MPS adopts a one-step mechanism involving the direct oxygen-transfer from FADOOH to the substrate and the proton transfer from the -OH group back to FAD, while the oxidation of indene follows a stepwise mechanism involving a carbocation intermediate. It was computationally predicted that VpIndA1 prefers the formation of (S)-product for the MPS sulfoxidation and (1S,2R)-product for the indene epoxidation, consistent with the experimental observations. Importantly, the factors controlling the stereo-preference of the two reactions are identified. The findings in the present study provide valuable insights into the VpIndA1-catalyzed reactions, which are essential for the rational design of this enzyme and other IMOs for industrial applications. It is also worth emphasizing that the quantum chemical cluster approach is again demonstrated to be powerful in studying the enantioselectivity of enzymatic reactions.

Quantum chemical studies of the reaction mechanisms of enzymatic CO2 conversion.

Enzymatic capture and conversion of carbon dioxide (CO2) into value-added chemicals are of great interest in the field of biocatalysis and have a positive impact on climate change. The quantum chemical methods, recognized as valuable tools for studying reaction mechanisms, have been widely employed in investigating the reaction mechanisms of the enzymes involved in CO2 utilization. In this perspective, we review the mechanistic studies of representative enzymes that are either currently used or have the potential for converting CO2, utilizing the quantum chemical cluster approach and the quantum mechanical/molecular mechanical (QM/MM) method. We begin by summarizing current trends in enzymatic CO2 conversion, followed by a brief description of the computational details of quantum chemical methods. Then, a series of representative examples of the computational modeling of biocatalytic CO2 conversion are presented, including the reduction of CO2 to C1 species (carbon monoxide and formate), and the fixation of CO2 to form aliphatic and aromatic carboxylic acids. The microscopic views of reaction mechanisms obtained from these studies are helpful in guiding the rational design of current enzymes and the discovery of novel enzymes with enhanced performance in converting CO2. Additionally, they provide key information for the de novo design of new-to-nature enzymes. To conclude, we present a perspective on the potential combination of machine learning with quantum description in the study of enzymatic conversion of CO2.

Theoretical study on the mechanism of tryptophan methylation catalyzed by the cobalamin-dependent radical enzyme TsrM

TsrM is a radical S-adenosylmethionine (SAM) methylase that catalyzes the C2 methylation of L-tryptophan to produce 2-methyltryptophan, an intermediate in the biosynthesis of the antibiotic thiostrepton A. The mechanism of TsrM is investigated through the quantum chemical cluster approach. The calculations suggested an expanded ‘ping-pong’ mechanism that requires the participation of two SAM molecules. In the first half-reaction, one SAM molecule binds to the active site of TsrM and delivers its methyl group to the CoI ion of the cobalamin, leading to the generation of methylcobalamin. With the subsequent dissociation of a SAH molecule, another SAM molecule binds into the active site, which facilitates the transfer of the methyl group from methylcobalamin to the C2 of tryptophan via a non-radical mechanism. The resulting carbon cation intermediate then readily undergoes facile deprotonation to yield the final product 2-methyltryptophan. Our proposed mechanism also rationalizes the reactivity trends observed among four substrates with different substitutions.

Theoretical Study of the Catalytic Mechanism of the Cu-Only Superoxide Dismutase.

The catalytic mechanisms for the wild-type and the mutated Cu-only superoxide dismutase were studied using the hybrid density functional B3LYP and a quantum chemical cluster approach. Optimal protonation states of the active site were examined for each stage of the catalytic cycle. For both the reductive and the oxidative half-reactions, the arrival of the substrate was found to be accompanied by a charge-compensating H+ with exergonicities of -15.4 kcal·mol and -4.7 kcal·mol, respectively. The second-sphere Glu-110 and first-sphere His-93 were suggested to be the transient protonation site for the reductive and the oxidative half-reactions, respectively, which collaborates with the hydrogen bonding water chain to position the substrate near the redox-active copper center. For the reductive half-reaction, the rate-limiting step was found to be the inner-sphere electron transfer from the partially coordinated to CuII with a barrier of 8.1 kcal·mol. The formed O2 is released from the active site with an exergonicity of -14.9 kcal·mol. For the oxidative half-reaction, the inner-sphere electron transfer from CuI to the partially coordinated was found to be accompanied by the proton transfer from the protonated His-93 and barrierless. The rate-limiting step was found to be the second proton transfer from the protonated Glu-110 to with a barrier of 7.3 kcal·mol. The barriers are reasonably consistent with experimental activities, and a proton-transfer rate-limiting step in the oxidative half-reaction could explain the experimentally observed pH-dependence. For the E110Q CuSOD, Asp-113 was suggested to be likely to serve as the transient protonation site in the reductive half-reaction. The rate-limiting barriers were found to be 8.0 and 8.6 kcal·mol, respectively, which could explain the slightly lower performance of E110X mutants. The results were found to be stable, with respect to the percentage of exact exchange in B3LYP.

The Quantum Chemical Cluster Approach in Biocatalysis

The quantum chemical cluster approach has been used for modeling enzyme active sites and reaction mechanisms for more than two decades. In this methodology, a relatively small part of the enzyme around the active site is selected as a model, and quantum chemical methods, typically density functional theory, are used to calculate energies and other properties. The surrounding enzyme is modeled using implicit solvation and atom fixing techniques. Over the years, a large number of enzyme mechanisms have been solved using this method. The models have gradually become larger as a result of the faster computers, and new kinds of questions have been addressed. In this Account, we review how the cluster approach can be utilized in the field of biocatalysis. Examples from our recent work are chosen to illustrate various aspects of the methodology. The use of the cluster model to explore substrate binding is discussed first. It is emphasized that a comprehensive search is necessary in order to identify the lowest-energy binding mode(s). It is also argued that the best binding mode might not be the productive one, and the full reactions for a number of enzyme-substrate complexes have therefore to be considered to find the lowest-energy reaction pathway. Next, examples are given of how the cluster approach can help in the elucidation of detailed reaction mechanisms of biocatalytically interesting enzymes, and how this knowledge can be exploited to develop enzymes with new functions or to understand the reasons for lack of activity toward non-natural substrates. The enzymes discussed in this context are phenolic acid decarboxylase and metal-dependent decarboxylases from the amidohydrolase superfamily. Next, the application of the cluster approach in the investigation of enzymatic enantioselectivity is discussed. The reaction of strictosidine synthase is selected as a case study, where the cluster calculations could reproduce and rationalize the selectivities of both the natural and non-natural substrates. Finally, we discuss how the cluster approach can be used to guide the rational design of enzyme variants with improved activity and selectivity. Acyl transferase from Mycobacterium smegmatis serves as an instructive example here, for which the calculations could pinpoint the factors controlling the reaction specificity and enantioselectivity. The cases discussed in this Account highlight thus the value of the cluster approach as a tool in biocatalysis. It complements experiments and other computational techniques in this field and provides insights that can be used to understand existing enzymes and to develop new variants with tailored properties.

QM Calculations Revealed that Outer-Sphere Electron Transfer Boosted O-O Bond Cleavage in the Multiheme-Dependent Cytochrome bd Oxygen Reductase.

The cytochrome bd oxygen reductase catalyzes the four-electron reduction of dioxygen to two water molecules. The structure of this enzyme reveals three heme molecules in the active site, which differs from that of heme-copper cytochrome c oxidase. The quantum chemical cluster approach was used to uncover the reaction mechanism of this intriguing metalloenzyme. The calculations suggested that a proton-coupled electron transfer reduction occurs first to generate a ferrous heme b595. This is followed by the dioxygen binding at the heme d center coupled with an outer-sphere electron transfer from the ferrous heme b595 to the dioxygen moiety, affording a ferric ion superoxide intermediate. A second proton-coupled electron transfer produces a heme d ferric hydroperoxide, which undergoes efficient O-O bond cleavage facilitated by an outer-sphere electron transfer from the ferrous heme b595 to the O-O σ* orbital and an inner-sphere proton transfer from the heme d hydroxyl group to the leaving hydroxide. The synergistic benefits of the two types of hemes rationalize the highly efficient oxygen reduction repertoire for the multi-heme-dependent cytochrome bd oxygen reductase family.

Modeling Enzymatic Enantioselectivity using Quantum Chemical Methodology

The computational study of enantioselective reactions is a challenging task that requires high accuracy, as very small energy differences have to be reproduced. Quantum chemical methods, most commonly density functional theory, are today an important tool in this pursuit. This Perspective describes recent efforts in modeling asymmetric reactions in enzymes by means of the quantum chemical cluster approach. The methodology is described briefly and a number of illustrative case studies performed recently at our laboratory are presented. The reviewed enzymes are limonene epoxide hydrolase, soluble epoxide hydrolase, arylmalonate decarboxylase, phenolic acid decarboxylase, benzoylformate decarboxylase, secondary alcohol dehydrogenase, acyl transferase, and norcoclaurine synthase. The challenges encountered in each example are discussed, and the modeling lessons learned are highlighted.

Computational Understanding of the Selectivities in Metalloenzymes.

Metalloenzymes catalyze many different types of biological reactions with high efficiency and remarkable selectivity. The quantum chemical cluster approach and the combined quantum mechanics/molecular mechanics methods have proven very successful in the elucidation of the reaction mechanism and rationalization of selectivities in enzymes. In this review, recent progress in the computational understanding of various selectivities including chemoselectivity, regioselectivity, and stereoselectivity, in metalloenzymes, is discussed.

Theoretical study of the mechanism of the manganese catalase KatB.

The mechanism of the H2O2 disproportionation catalyzed by the manganese catalase (MnCat) KatB was studied using the hybrid density functional theory B3LYP and the quantum chemical cluster approach. Compared to the previous mechanistic study at the molecular level for the Thermus thermophilus MnCat (TTC), more modern methodology was used and larger models of increasing sizes were employed with the help of the high-resolution X-ray structure. In the reaction pathway suggested for KatB using the Large chemical model, the O-O homolysis of the first substrate H2O2 occurs through a μ-η1:η1 coordination mode and requires a barrier of 10.9kcal/mol. In the intermediate state of the bond cleavage, two hydroxides form as terminal ligands of the dimanganese cluster at the Mn2(III,III) oxidation state. One of the two Mn(III)-OH- moieties and a second-sphere tyrosine stabilize the second substrate H2O2 in the second-sphere of the active site via hydrogen bonding interactions. The H2O2, unbound to the metals, is first oxidized into HO2· through a proton-coupled electron transfer (PCET) step with a barrier of 9.5kcal/mol. After the system switches to the triplet surface, the uncoordinated HO2· replaces the product water terminally bound to the Mn(II) and is then oxidized into O2 spontaneously. Transition states with structural similarities to those obtained for TTC, where μ-η2-OH-/O2- groups play important roles, were found to be higher in energy.

Empirical Valence Bond Simulations Suggest a Direct Hydride Transfer Mechanism for Human Diamine Oxidase.

Diamine oxidase (DAO) is an enzyme involved in the regulation of cell proliferation and the immune response. This enzyme performs oxidative deamination in the catabolism of biogenic amines, including, among others, histamine, putrescine, spermidine, and spermine. The mechanistic details underlying the reductive half-reaction of the DAO-catalyzed oxidative deamination which leads to the reduced enzyme cofactor and the aldehyde product are, however, still under debate. The catalytic mechanism was proposed to involve a prototropic shift from the substrate–Schiff base to the product–Schiff base, which includes the rate-limiting cleavage of the Cα–H bond by the conserved catalytic aspartate. Our detailed mechanistic study, performed using a combined quantum chemical cluster approach with empirical valence bond simulations, suggests that the rate-limiting cleavage of the Cα–H bond involves direct hydride transfer to the topaquinone cofactor—a mechanism that does not involve the formation of a Schiff base. Additional investigation of the D373E and D373N variants supported the hypothesis that the conserved catalytic aspartate is indeed essential for the reaction; however, it does not appear to serve as the catalytic base, as previously suggested. Rather, the electrostatic contributions of the most significant residues (including D373), together with the proximity of the Cu2+ cation to the reaction site, lower the activation barrier to drive the chemical reaction.

Recent Trends in Quantum Chemical Modeling of Enzymatic Reactions.

The quantum chemical cluster approach is a powerful method for investigating enzymatic reactions. Over the past two decades, a large number of highly diverse systems have been studied and a great wealth of mechanistic insight has been developed using this technique. This Perspective reviews the current status of the methodology. The latest technical developments are highlighted, and challenges are discussed. Some recent applications are presented to illustrate the capabilities and progress of this approach, and likely future directions are outlined.

A DFT study on the chiral synthesis of R-phenylacetyl carbinol within the quantum chemical cluster approach

The reaction pathway leading to R-phenylacetyl carbinol within the quantum chemical cluster approach is addressed by means of density functional theory (DFT) calculations. The study includes calculation of Fukui functions, activation free energies, and potential energy surface scans, both in gas and solution phase. The protonation states of the nitrogen atoms of the pyrimidine moiety are determined. The reaction appears to be slightly exergonic (ΔG0=−5.6 and −4.0kcal/mol for gas and solution phase, respectively) following a concerted synchronous mechanism having activation free energy barriers of 16.2 and 13.3kcal/mol, in gas phase and solution phase, respectively.

Which Oxidation State Initiates Dehalogenation in the B12-Dependent Enzyme NpRdhA: CoII, CoI, or Co0?

The quantum chemical cluster approach was used to elucidate the reaction mechanism of debromination catalyzed by the B12-dependent reductive dehalogenase NpRdhA. Various pathways, involving different oxidation states of the cobalt ion and different protonation states of the model, have been analyzed in order to find the most favorable one. We find that the reductive C–Br cleavage takes place exclusively at the CoI state via a heterolytic pathway in the singlet state. Importantly, the C–H bond formation and the C–Br bond cleavage proceeds via a concerted transition state, as opposed to the stepwise pathway suggested before. C–Br cleavage at the CoII state has a very high barrier, and the reduction of CoI to Co0 is associated with a very negative potential; thus, reductive dehalogenation at CoII and Co0 can be safely ruled out. Examination of substrates with different halogen substitutions (F, Cl, Br, I) shows that the dehalogenation reactivity follows the order C–I > C–Br > C–Cl > C–F, and the barrier for ...

Revealing Monoamine Oxidase B Catalytic Mechanisms by Means of the Quantum Chemical Cluster Approach.

Two of the possible catalytic mechanisms for neurotransmitter oxidative deamination by monoamine oxidase B (MAO B), namely, polar nucleophilic and hydride transfer, were addressed in order to comprehend the nature of their rate-determining step. The Quantum Chemical Cluster Approach was used to obtain transition states of MAO B complexed with phenylethylamine (PEA), benzylamine (BA), and p-nitrobenzylamine (NBA). The choice of these amines relies on their importance to address MAO B catalytic mechanisms so as to help us to answer questions such as why BA is a better substrate than NBA or how para-substitution affects substrate's reactivity. Transition states were later validated by comparison with the experimental free energy barriers. From a theoretical point of view, and according to the our reported transition states, their calculated barriers and structural and orbital differences obtained by us among these compounds, we propose that good substrates such as BA and PEA might follow the hydride transfer pathway while poor substrates such as NBA prefer the polar nucleophilic mechanism, which might suggest that MAO B can act by both mechanisms. The low free energy barriers for BA and PEA reflect the preference that MAO B has for hydride transfer over the polar nucleophilic mechanism when catalyzing the oxidative deamination of neurotransmitters.

Analysis of computational models for an accurate study of electronic excitations in GFP.

Using the chromophore of the green fluorescent protein (GFP), the performance of a hybrid RI-CC2/polarizable embedding (PE) model is tested against a quantum chemical cluster approach. Moreover, the effect of the rest of the protein environment is studied by systematically increasing the size of the cluster and analyzing the convergence of the excitation energies. It is found that the influence of the environment of the chromophore can accurately be described using a polarizable embedding model with only a minor error compared to a full quantum chemical description. It is also shown that the treatment of only a small region around the chromophore is only by coincidence a good approximation. Therefore, such cluster approaches should be used with care. Based on our results, we suggest that polarizable embedding models, including a large part of the environment to describe its effect on biochromophores on top of an accurate way of describing the central subsystem, are both accurate and computationally favourable in many cases.

Theoretical Study of Reaction Mechanism and Stereoselectivity of Arylmalonate Decarboxylase

The reaction mechanism of arylmalonate decarboxylase is investigated using density functional theory calculations. This enzyme catalyzes the asymmetric decarboxylation of prochiral disubstituted malonic acids to yield the corresponding enantiopure carboxylic acids. The quantum chemical cluster approach is employed, and two different models of the active site are designed: a small one to study the mechanism and characterize the stationary points and a large one to study the enantioselectivity. The reactions of both α-methyl-α-phenylmalonate and α-methyl-α-vinylmalonate are considered, and different substrate binding modes are assessed. The calculations overall give strong support to the suggested mechanism in which decarboxylation of the substrate first takes place, followed by a stereoselective protonation by a cysteine residue. The enediolate intermediate and the transition states are stabilized by a number of hydrogen bonds that make up the dioxyanion hole, resulting in feasible energy barriers. It is f...

Quantum Chemistry as a Tool in Asymmetric Biocatalysis: Limonene Epoxide Hydrolase Test Case

Cluster model: Large active-site models (see figure) are used to investigate the selectivity of limonene epoxide hydrolase, both the wild type and mutants optimized through directed evolution. Good agreement is found between theory and the experimental data, thus demonstrating that the quantum chemical cluster approach can be a powerful tool in the field of asymmetric biocatalysis.

Nuclear magnetic resonance predictions for graphenes: concentric finite models and extrapolation to large systems

Nuclear magnetic resonance (NMR) data for graphenes are mainly lacking in the literature. We provide quantitative first-principles quantum-chemical calculations of NMR chemical shifts and shielding anisotropies as well as spin-spin couplings and anisotropies for increasingly large, hexagon-like fragments of graphene, hydrogenated graphene (graphane) and fluorinated graphene (fluorographene). Due to the rapid convergence of finite molecular model results, the parameter values in the innermost region of large flakes of these materials approach the bulk limit. For nuclear shieldings in the finite band-gap graphane and fluorographene systems, as well as deuterium quadrupole couplings in graphane, these limiting values are verified by periodic gauge-including projector augmented wave (PAW) calculations at corresponding theoretical levels. The periodic PAW wave method was used for all systems to obtain periodic structures. A quantum-chemical cluster approach was used with novel completeness-optimised basis sets to calculate both the shielding and coupling tensors for planar carbon nanoflakes of increasing size. The geometry of the innermost part of the nanoflakes as well as the nuclear shieldings converge toward the periodic counterparts. The cluster method allows the calculation of the spin-spin coupling tensors of all the graphenes and--in contrast to the periodic approach--all the NMR properties for the zero-band-gap graphene itself. The obtained parameters provide a plausible starting point for experimental NMR investigations of graphenes.

Quantum Chemical Modeling of Enzymatic Reactions: The Case of Decarboxylation.

We present a systematic study of the decarboxylation step of the enzyme aspartate decarboxylase with the purpose of assessing the quantum chemical cluster approach for modeling this important class of decarboxylase enzymes. Active site models ranging in size from 27 to 220 atoms are designed, and the barrier and reaction energy of this step are evaluated. To model the enzyme surrounding, homogeneous polarizable medium techniques are used with several dielectric constants. The main conclusion is that when the active site model reaches a certain size, the solvation effects from the surroundings saturate. Similar results have previously been obtained from systematic studies of other classes of enzymes, suggesting that they are of a quite general nature.