Quantum chemical studies of intermediates and reaction pathways in selected enzymes and catalytic synthetic systems

Issues on DFT+U calculations of organic diradicals

The diradical state is an important electronic state for understanding molecular functions and should be elucidated for the in silico design of functional molecules and their application to molecular devices. The density functional theory calculation with plane-wave basis and correction of the on-site Coulomb parameter U (DFT+U/plane-wave calculation) is a good candidate of high-throughput calculations of diradical-band interactions. However, it has not been investigated in detail to what extent the DFT+U/plane-wave calculation can be used to calculate organic diradicals with a high degree of accuracy. In the present study, using typical organic diradical molecules (bisphenalenyl molecules) as model systems, the discrepancy in the optimum U values between the two electronic states (open-shell singlet and triplet) that compose the diradical state is detected. The calculated results show that the reason for this U value discrepancy is the difference in electronic delocalisation due to π-conjugation between the open-shell singlet and triplet states, and that the effect of U discrepancy becomes large as diradical character decreases. This indicates that it is necessary to investigate the U value discrepancy with reference to the calculated results by more accurate methods or to experimental values when calculating organic diradicals with low diradical character. For this investigation, the local magnetic moments, unpaired beta electron numbers, and effective magnetic exchange integral values can be used as reference values. For the effective magnetic exchange integral values, the effects of U discrepancy are partially cancelled out. However, because the effects may not be completely offset, care should be taken when using the effective magnetic exchange integral value as a reference. Furthermore, a comparison of DFT+U and hybrid-DFT calculations shows that the DFT+U underestimates the HOMO-LUMO gap of bisphenalenyls, although a qualitative discussion of the gap is possible.

Model calculations for the prediction of the diradical character of physisorbed molecules: p-benzyne/MgO and p-benzyne/SrO

The analysis of the diradical state of functional open-shell molecules is important for understanding their physical properties and chemical reactivity. The diradical character is an important factor in the functional elucidation and design of open-shell molecules. In recent years, attempts have been made to immobilise functional open-shell molecules on surfaces to form devices. However, the influence of surface interactions on the diradical state remains unclear. In this study, the physisorption structures of p-benzyne, which is a typical diradical molecule, on MgO(001) and SrO(001) surfaces are used as models to investigate how the diradical character is affected by physisorption. This is done using approximate spin-projected density functional theory calculations with dispersion correction and plane-wave basis (AP-DFT-D3/plane-wave calculations). The diradical character change (Δy) due to adsorption can be categorised into three factors, namely the change due to the distortion of the diradical molecule (Δydis), the interaction between neighbouring diradical molecules (Δycoh), and molecule-surface interactions (Δysurf). In all the calculated models, physisorption reduced the diradical character (Δy < 0), and the contribution of Δysurf was the largest among the three factors. The calculated results show that adsorption induces electron delocalisation to π-conjugated orbitals and intramolecular charge polarisation, both of which contribute to reducing the occupancy of singly occupied molecular orbitals. This indicates that the diradical character of p-benzyne is reduced by the stabilisation of the resonance structures. Furthermore, geometry optimisation of the surfaces shows that the chemical-soft surface (SrO) varies the diradical character more significantly than the chemical-hard surface (MgO). This study shows that the open-shell electronic state and stack structure of diradical molecules can be controlled through the analysis of the surface diradical state.

Alternations in interleukin-1β and nuclear factor kappa beta activity (NF-kB) in rat liver due to the co-exposure of Cadmium and Arsenic: Protective role of curcumin

Cadmium chloride (Cd) and sodium arsenite (As) are two prominent examples of non-biodegradable substances that accumulate in ecosystems, pose a serious risk to human health and are not biodegradable. Although the toxicity caused by individual use of Cd and As is known, the toxicity of combined use (Cd+As) to mammals is poorly understood. The present study aims to investigate the hepatoprotective effect of curcumin (CUR), a naturally occurring bioactive component isolated from the root stem of Curcuma longa Linn., in preventing liver damage caused by a Cd+As mixture. A group of 30 Sprague-Dawley rats were subjected to intraperitoneal administration of Cd+As (0.44 mg/kg+5.55 mg/kg i.p.) and CUR (100 or 200 mg/kg) for a period of 14 days. The experimental results showed that the animals treated with Cd+As exhibited changes in liver biochemical parameters, inflammation and oxidative stress at the end of the experiment. Administration of CUR significantly reduced inflammation, oxidative stress and lipid peroxidation in the Cd+As plus CUR groups compared to the Cd+As group. Furthermore, histological examination of the liver tissue showed that administration of CUR had led to a significant reduction in the liver damage observed in the Cd+As group. The present study provides scientific evidence for the protective effects of CUR against lipid peroxidation, inflammation, oxidative stress and liver damage induced by Cd+As in the liver of rats. The results of our in vivo experiments were confirmed by those of our molecular modelling studies, which showed that CUR can enhance the diminished antioxidant capacity caused by Cd+As.

Stereoselective amino acid synthesis by synergistic photoredox-pyridoxal radical biocatalysis

Developing synthetically useful enzymatic reactions that are not known in biochemistry and organic chemistry is an important challenge in biocatalysis. Through the synergistic merger of photoredox catalysis and pyridoxal 5'-phosphate (PLP) biocatalysis, we developed a pyridoxal radical biocatalysis approach to prepare valuable noncanonical amino acids, including those bearing a stereochemical dyad or triad, without the need for protecting groups. Using engineered PLP enzymes, either enantiomeric product could be produced in a biocatalyst-controlled fashion. Synergistic photoredox-pyridoxal radical biocatalysis represents a powerful platform with which to discover previously unknown catalytic reactions and to tame radical intermediates for asymmetric catalysis.

Sequential C-H Methylation Catalyzed by the B12 -Dependent SAM Enzyme TokK: Comprehensive Theoretical Study of Selectivities

TokK is a B₁₂ -dependent radical SAM enzyme involved in the biosynthesis of the β-lactam antibiotic asparenomycin A. It can catalyze three methylations on different sp³ -hybridized carbon positions to introduce an isopropyl side chain at the β-lactam ring of pantetheinylated carbapenem. Herein, we report a quantum chemical study of the reaction mechanism of TokK. A stepwise ''push-pull'' radical relay mechanism is proposed for each methylation: a 5'-deoxyadenosine radical first abstracts a hydrogen atom from the substrate in the active site, then methylcobalamin directionally donates a methyl group to the substrate. More importantly, calculations were able to uncover the origin of observed chemoselectivity and stereoselectivity for the first methylation and regioselectivity for the following two methylations. Further detailed distortion/interaction analysis can help to unravel the main factors controlling the selectivities. Our findings of sequential methylations by TokK could have profound implications for studying other B₁₂ -dependent radical SAM enzymes.

DFT insight into asymmetric alkyl-alkyl bond formation via nickel-catalysed enantioconvergent reductive coupling of racemic electrophiles with olefins

A DFT study has been conducted to understand the asymmetric alkyl–alkyl bond formation through nickel-catalysed reductive coupling of racemic alkyl bromide with olefin in the presence of hydrosilane and K₃PO₄. The key findings of the study include: (i) under the reductive experimental conditions, the Ni(ii) precursor is easily activated/reduced to Ni(0) species which can serve as an active species to start a Ni(0)/Ni(ii) catalytic cycle. (ii) Alternatively, the reaction may proceed via a Ni(i)/Ni(ii)/Ni(iii) catalytic cycle starting with a Ni(i) species such as Ni(i)–Br. The generation of a Ni(i) active species via comproportionation of Ni(ii) and Ni(0) species is highly unlikely, because the necessary Ni(0) species is strongly stabilized by olefin. Alternatively, a cage effect enabled generation of a Ni(i) active catalyst from the Ni(ii) species involved in the Ni(0)/Ni(ii) cycle was proposed to be a viable mechanism. (iii) In both catalytic cycles, K₃PO₄ greatly facilitates the hydrosilane hydride transfer for reducing olefin to an alkyl coupling partner. The reduction proceeds by converting a Ni–Br bond to a Ni–H bond via hydrosilane hydride transfer to a Ni–alkyl bond via olefin insertion. On the basis of two catalytic cycles, the origins for enantioconvergence and enantioselectivity control were discussed.

The enantioconvergent alkyl–alkyl coupling involves two competitive catalytic cycles with nickel(0) and nickel(i) active catalysts, respectively. K₃PO₄ plays a crucial role to enable the hydride transfer from hydrosilane to nickel–bromine species.

Computational Study revealed a “Pull-Push” Radical Transfer Mechanism of Mmp10-Catalyzed Cδ-methylation of Arginine

Mmp10 is a B12-dependent SAM radical enzyme that catalyzes Cδ-methylation of arginine. The quantum chemical cluster calculations of Mmp10 revealed a “Pull-Push” radical transfer mechanism in which 5’-deoxyadenosine radical first...

Density functional theory study of transition metal single-atoms anchored on graphyne as efficient electrocatalysts for the nitrogen reduction reaction

Ammonia (NH3) is the main raw material for the organic chemical industry and a critical feedstock for the fertilizer industry with great significance for the global economy. The NH3 demand has gradually increased with modern society development. Moreover, the electrocatalytic nitrogen reduction reaction (NRR) is a promising NH3 synthesis technology. However, the design of efficient electrocatalysts for the NRR is still challenging. In this study, we systematically analyzed transition metal (TM) single-atoms (Ti, V, Cr, Mn, Zr, Nb, and Mo) anchored on graphyne (GY) as NRR catalysts using density functional theory calculations. The calculation results for the first and last hydrogenation steps (*NNH formation and *NH3 desorption, respectively) revealed that Mn@GY (with an end-on configuration) and V@GY (with a side-on configuration) were the most suitable catalytic substrates for the NRR. The free-energy profiles of the TM@GY catalysts indicated that Mn@GY was the best NRR electrocatalyst owing to its distal pathway with a minimum free-energy barrier of 0.36 eV. In addition, the electronic properties, namely the Bader charge, charge density difference, partial density of states, and crystal orbital Hamilton population, of the TM@GY catalysts were analyzed in detail, and the results further confirmed that Mn@GY was an efficient electrocatalyst. The insights obtained from this comprehensive study can provide useful guidelines for designing new and efficient electrocatalysts.

Direct detection of coupled proton and electron transfers in human manganese superoxide dismutase

Human manganese superoxide dismutase is a critical oxidoreductase found in the mitochondrial matrix. Concerted proton and electron transfers are used by the enzyme to rid the mitochondria of O₂^•−. The mechanisms of concerted transfer enzymes are typically unknown due to the difficulties in detecting the protonation states of specific residues and solvent molecules at particular redox states. Here, neutron diffraction of two redox-controlled manganese superoxide dismutase crystals reveal the all-atom structures of Mn³⁺ and Mn²⁺ enzyme forms. The structures deliver direct data on protonation changes between oxidation states of the metal. Observations include glutamine deprotonation, the involvement of tyrosine and histidine with altered pK_as, and four unusual strong-short hydrogen bonds, including a low barrier hydrogen bond. We report a concerted proton and electron transfer mechanism for human manganese superoxide dismutase from the direct visualization of active site protons in Mn³⁺ and Mn²⁺ redox states.

Human manganese superoxide dismutase (MnSOD) is an oxidoreductase that uses concerted proton and electron transfers to reduce the levels of superoxide radicals in mitochondria, but mechanistic insights into this process are limited. Here, the authors report neutron crystal structures of Mn³⁺SOD and Mn²⁺SOD, revealing changes in the protonation states of key residues in the enzyme active site during the redox cycle.

Spin controlled surface chemistry: alkyl desorption from Si(100)-2×1 by nonadiabatic hydrogen elimination

An understanding of the role that spin states play in semiconductor surface chemical reactions is currently limited. Herein, we provide evidence of a nonadiabatic reaction involving a localized singlet to triplet thermal excitation of the Si(100) surface dimer dangling bond. By comparing the β-hydrogen elimination kinetics of ethyl adsorbates probed by thermal desorption experiments to electronic structure calculation results, we determined that a coverage-dependent change in mechanism occurs. At low coverage, a nonadiabatic, inter-dimer mechanism is dominant, while adiabatic mechanisms become dominant at higher coverage. Computational results indicate that the spin crossover is rapid near room temperature and the nonadiabatic path is accelerated by a barrier that is 40 kJ mol^-1 less than the adiabatic path. Simulated thermal desorption reactions using nonadiabatic transition state theory (NA-TST) for the surface dimer intersystem crossing are in close agreement with experimental observations.

Proton-Electron Transfer to the Active Site Is Essential for the Reaction Mechanism of Soluble Δ9-Desaturase

A full understanding of the catalytic action of non-heme iron (NHFe) and non-heme diiron (NHFe₂) enzymes is still beyond the grasp of contemporary computational and experimental techniques. Many of these enzymes exhibit fascinating chemo-, regio-, and stereoselectivity, in spite of employing highly reactive intermediates which are necessary for activations of most stable chemical bonds. Herein, we study in detail one intriguing representative of the NHFe₂ family of enzymes: soluble Δ⁹ desaturase (Δ⁹D), which desaturates rather than performing the thermodynamically favorable hydroxylation of substrate. Its catalytic mechanism has been explored in great detail by using QM(DFT)/MM and multireference wave function methods. Starting from the spectroscopically observed 1,2-μ-peroxo diferric P intermediate, the proton-electron uptake by P is the favored mechanism for catalytic activation, since it allows a significant reduction of the barrier of the initial (and rate-determining) H-atom abstraction from the stearoyl substrate as compared to the "proton-only activated" pathway. Also, we ruled out that a Q-like intermediate (high-valent diamond-core bis-μ-oxo-[Fe^IV]₂ unit) is involved in the reaction mechanism. Our mechanistic picture is consistent with the experimental data available for Δ⁹D and satisfies fairly stringent conditions required by Nature: the chemo-, stereo-, and regioselectivity of the desaturation of stearic acid. Finally, the mechanisms evaluated are placed into a broader context of NHFe₂ chemistry, provided by an amino acid sequence analysis through the families of the NHFe₂ enzymes. Our study thus represents an important contribution toward understanding the catalytic action of the NHFe₂ enzymes and may inspire further work in NHFe₍₂₎ biomimetic chemistry.

Machine learning dihydrogen activation in the chemical space surrounding Vaska's complex

A machine learning exploration of the chemical space surrounding Vaska's complex.

Homogeneous catalysis using transition metal complexes is ubiquitously used for organic synthesis, as well as technologically relevant in applications such as water splitting and CO₂ reduction. The key steps underlying homogeneous catalysis require a specific combination of electronic and steric effects from the ligands bound to the metal center. Finding the optimal combination of ligands is a challenging task due to the exceedingly large number of possibilities and the non-trivial ligand–ligand interactions. The classic example of Vaska's complex, trans-[Ir(PPh₃)₂(CO)(Cl)], illustrates this scenario. The ligands of this species activate iridium for the oxidative addition of hydrogen, yielding the dihydride cis-[Ir(H)₂(PPh₃)₂(CO)(Cl)] complex. Despite the simplicity of this system, thousands of derivatives can be formulated for the activation of H₂, with a limited number of ligands belonging to the same general categories found in the original complex. In this work, we show how DFT and machine learning (ML) methods can be combined to enable the prediction of reactivity within large chemical spaces containing thousands of complexes. In a space of 2574 species derived from Vaska's complex, data from DFT calculations are used to train and test ML models that predict the H₂-activation barrier. In contrast to experiments and calculations requiring several days to be completed, the ML models were trained and used on a laptop on a time-scale of minutes. As a first approach, we combined Bayesian-optimized artificial neural networks (ANN) with features derived from autocorrelation and deltametric functions. The resulting ANNs achieved high accuracies, with mean absolute errors (MAE) between 1 and 2 kcal mol^–1, depending on the size of the training set. By using a Gaussian process (GP) model trained with a set of selected features, including fingerprints, accuracy was further enhanced. Remarkably, this GP model minimized the MAE below 1 kcal mol^–1, by using only 20% or less of the data available for training. The gradient boosting (GB) method was also used to assess the relevance of the features, which was used for both feature selection and model interpretation purposes. Features accounting for chemical composition, atom size and electronegativity were found to be the most determinant in the predictions. Further, the ligand fragments with the strongest influence on the H₂-activation barrier were identified.

Quantum Chemical and QM/MM Models in Biochemistry

Quantum chemical (QC) calculations provide a basis for deriving a microscopic understanding of enzymes and photobiological systems. Here we describe how QC models can be used to explore the electronic structure, dynamics, and energetics of biomolecules. We introduce the hybrid quantum mechanics/classical mechanics (QM/MM) approach, where a quantum mechanically described system of interest is embedded in a classically described force field representation of the biochemical surroundings. We also discuss the QM cluster model approach, as well as embedding theories, that provide complementary methodologies to model quantum mechanical effects in biomolecules. The chapter also provides some practical guides for building quantum biochemical models using the quinone reduction catalysis in respiratory complex I and a model reaction in solution as examples.

Catalytic performance of Pdn (n = 1, 2, 3, 4 and 6) clusters supported on TiO2-V for the formation of dimethyl oxalate via the CO catalytic coupling reaction: a theoretical study

The formation of dimethyl oxalate (DMO) via CO catalytic coupling on a series of catalysts including Pdn (n = 1, 2, 3, 4 and 6) clusters loaded on TiO2-V has been explored by density functional theory (DFT) calculation. The results show that different Pdn clusters have a remarkable influence on DMO formation. The Pd1/TiO2-V catalyst is not suitable for the CO catalytic coupling reaction since CO is easily bound to the O atom on the surface of TiO2-V leading to the formation of CO2. The activity of four catalysts complies with the following order of Pd4/TiO2-V > Pd6/TiO2-V > Pd2/TiO2-V > Pd3/TiO2-V by comparing the activation energy barriers of the rate-determining steps in the optimal paths. Charge analysis implies that less charge is transferred from the Pd4/TiO2-V and Pd6/TiO2-V catalysts to CO than on the other catalysts, which leads to the relatively weak adsorption of CO, and therefore CO has a greater tendency to react with other species on the surface. In addition, Pd6/TiO2-V also exhibits relatively higher selectivity toward DMO than the other three catalysts. Therefore, Pd6 is regarded as a suitable cluster, which is supported on TiO2-V demonstrating high catalytic activity and selectivity to DMO.

How does the nickel catalyst control the doubly enantioconvergent coupling of racemic alkyl nucleophiles and electrophiles? The rebound mechanism

DFT mechanistic study unveils that the rebound mechanism is the key to the nickel-catalyzed doubly enantioconvergent C(sp³)–C(sp³) coupling of racemic alkyl nucleophiles and electrophiles.

Investigation of different photochemical reactions of avobenzone derivatives by ultrafast transient absorption spectroscopy

Avobenzone (AB) is one of the most widely used UVA sunscreens, and it is viewed as a model compound for studying the photoisomerization process. In recent years, Miranda and co-workers studied photophysical and photochemical reactions of several AB derivatives. However, there is still a gap in the data of these compounds in the ultrafast time region. To get a better understanding of the photophysical and photochemical reaction mechanisms, selected AB derivatives of AB-Me, AB-Pr, AB-Br and AB-Cl were studied using ultrafast transient absorption spectroscopy and density functional theory calculations in the present study. It is unravelled that alkylated substituted AB compounds of AB-Me and AB-Pr exhibit an efficient intersystem crossing with the generation of the corresponding triplet state species, which further leads to the Norrish type II reaction for AB-Pr. On the other hand, AB-Br and AB-Cl prefer photochemical reactions via the singlet state surface. Based on the DFT calculations, the spin-orbit coupling constant between the singlet and triplet states, the energy difference between the singlet and triplet states and the natural transition orbital separations of the studied AB compounds were found to be the leading reasons accounting for their corresponding photochemical activities via singlet and triplet states.

Strategies for computational design and discovery of two-dimensional transition-metal-free materials for electro-catalysis applications

In this perspective, we review two new strategies for computational design and discovery of two-dimensional (2D) transition-metal (TM) free electro-catalysts for the oxygen reduction reaction (ORR) and the nitrogen reduction reaction (NRR). The "2D binary compound" strategy for designing ORR electro-catalysts shows promising applications, which benefits from abundant intrinsic catalytic sites for the adsorption of reaction intermediates. And with the "activated B site" strategy for designing NRR electro-catalysts, several novel NRR electro-catalysts with extremely low limiting potential are developed. Computational-simulation-driven material design from a bottom-up method could not only provide rational strategies, but also accelerate the discovery of novel materials.

Hierarchy of Commonly Used DFT Methods for Predicting the Thermochemistry of Rh-Mediated Chemical Transformations

The accuracy and reliability of 17 commonly used density functionals in conjunction with Poisson-Boltzmann finite solvation model were gauged for predicting the free energy of Rh(I)- and Rh(III)-mediated chemical transformations such as ligand exchange, hydride elimination, dihydrogen elimination, chloride affinity, and silyl hydride bond activation reactions. In total, six Rh-mediated reactions were examined, and the computed density functional theory results were then subjected to comparison with the experimentally reported values. For reaction A, involving replacement of N₂ with η²-H₂ over Rh(I), MPWB1K-D3, B3PW91, B3LYP, and BHandHYLP emerged to be the best functionals of all the tested methods in terms of their deviations ≤2 kcal mol^-1 from experimental data. For reaction B, in which exchange of η²-C₂H₄ with N₂ over Rh(I) takes place, MPWB1K-D3 and M06-2X-D3 functionals performed the best, while as for reaction C (hydride elimination reaction in Rh(III) complex), it is PBE functional that showed impressive performance. Similarly, for reaction D (H₂ elimination reaction in Rh(III) complex), PBE0-D3 and PBE-D3 showed exceptional results compared to other functionals. For reaction E (H₂O/Cl^- exchange), the PBE0 again shows impressive performance as compared to other functionals. For reaction F (Si-H activation), M06-2X-D3, PBE0-D3, and MPWB1K-D3 functionals are undoubtedly the best functionals. Overall, PBE0-D3 and MPWB1K-D3 functionals were impressive in all cases with lowest mean unsigned errors (3.2 and 3.4 kcal mol^-1, respectively) with respect to experimental Gibbs free energies. Thus, these two functionals are recommended for studying Rh-mediated chemical transformations.

Extent of Spin Contamination Errors in DFT/Plane-wave Calculation of Surfaces: A Case of Au Atom Aggregation on a MgO Surface

The aggregation of Au atoms onto a Au dimer (Au₂) on a MgO (001) surface was calculated by restricted (spin-un-polarized) and unrestricted (spin-polarized) density functional theory calculations with a plane-wave basis and the approximate spin projection (AP) method. The unrestricted calculations included spin contamination errors of 0.0⁻0.1 eV, and the errors were removed using the AP method. The potential energy curves for the aggregation reaction estimated by the restricted and unrestricted calculations were different owing to the estimation of the open-shell structure by the unrestricted calculations. These results show the importance of the open-shell structure and correction of the spin contamination error for the calculation of small-cluster-aggregations and molecule dimerization on surfaces.

How does Mo-dependent perchlorate reductase work in the decomposition of oxyanions?

The mechanisms of Mo-dependent perchlorate reductase (PcrAB)-catalyzed decomposition of perchlorate, bromate, iodate, and nitrate were revealed by density functional calculations.

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.

Redox manipulation of the manganese metal in human manganese superoxide dismutase for neutron diffraction

Human manganese superoxide dismutase (MnSOD) is one of the most significant enzymes in preventing mitochondrial dysfunction and related diseases by combating reactive oxygen species (ROS) in the mitochondrial matrix. Mitochondria are the source of up to 90% of cellular ROS generation, and MnSOD performs its necessary bioprotective role by converting superoxide into oxygen and hydrogen peroxide. This vital catalytic function is conducted via cyclic redox reactions between the substrate and the active-site manganese using proton-coupled electron transfers. Owing to protons being difficult to detect experimentally, the series of proton transfers that compose the catalytic mechanism of MnSOD are unknown. Here, methods are described to discern the proton-based mechanism using chemical treatments to control the redox state of large perdeuterated MnSOD crystals and subsequent neutron diffraction. These methods could be applicable to other crystal systems in which proton information on the molecule in question in specific chemical states is desired.

Mechanistic study of styrene aziridination by iron(iv) nitrides

A combined experimental and computational investigation reveals that styrene aziridination by an iron(iv) nitride occurs by a stepwise mechanism involving multistate character.

A combined experimental and computational investigation was undertaken to investigate the mechanism of aziridination of styrene by the tris(carbene)borate iron(iv) nitride complex, PhB(^tBuIm)₃Fe Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> N. While mechanistic investigations suggest that aziridination occurs via a reversible, stepwise pathway, it was not possible to confirm the mechanism using only experimental techniques. Density functional theory calculations support a stepwise radical addition mechanism, but suggest that a low-lying triplet (S = 1) state provides the lowest energy path for C–N bond formation (24.6 kcal mol^–1) and not the singlet ground (S = 0) state. A second spin flip may take place in order to facilitate ring closure and the formation of the quintet (S = 2) aziridino product. A Hammett analysis shows that electron-withdrawing groups increase the rate of reaction σ_p (ρ = 1.2 ± 0.2). This finding is supported by the computational results, which show that the rate-determining step drops from 24.6 kcal mol^–1 to 18.3 kcal mol^–1 when (p-NO₂C₆H₄)CH Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> CH₂ is used and slightly increases to 25.5 kcal mol^–1 using (p-NMe₂C₆H₄)CH Created by potrace 1.16, written by Peter Selinger 2001-2019 ]]> CH₂ as the substrate.

A Review of the Catalytic Mechanism of Human Manganese Superoxide Dismutase

Superoxide dismutases (SODs) are necessary antioxidant enzymes that protect cells from reactive oxygen species (ROS). Decreased levels of SODs or mutations that affect their catalytic activity have serious phenotypic consequences. SODs perform their bio-protective role by converting superoxide into oxygen and hydrogen peroxide by cyclic oxidation and reduction reactions with the active site metal. Mutations of SODs can cause cancer of the lung, colon, and lymphatic system, as well as neurodegenerative diseases such as Parkinson's disease and amyotrophic lateral sclerosis. While SODs have proven to be of significant biological importance since their discovery in 1968, the mechanistic nature of their catalytic function remains elusive. Extensive investigations with a multitude of approaches have tried to unveil the catalytic workings of SODs, but experimental limitations have impeded direct observations of the mechanism. Here, we focus on human MnSOD, the most significant enzyme in protecting against ROS in the human body. Human MnSOD resides in the mitochondrial matrix, the location of up to 90% of cellular ROS generation. We review the current knowledge of the MnSOD enzymatic mechanism and ongoing studies into solving the remaining mysteries.

Deciphering the chemoselectivity of nickel-dependent quercetin 2,4-dioxygenase

QM/MM calculations were performed to elucidate the reaction mechanism and chemoselectivity of 2,4-QueD. The protonation state of the first-shell ligand Glu74 plays an important role in dictating the selectivity.

Measurement and Prediction of Chlorine Kinetic Isotope Effects in Enzymatic Systems

Approaches to determine chlorine kinetic isotope effects (Cl-KIEs) on enzymatic dehalogenations are discussed and illustrated by representative examples. Three aspects are considered. First methodology for experimental measurement of Cl-KIEs, with stress being on FAB-IRMS technique developed in our laboratory, is described. Subsequently, we concentrate our discussion on the consequences of reaction complexity in the interpretation of experimental values, a problem especially important in cases of polychlorinated reactants. The most fruitful studies of enzymatic dehalogenations by Cl-KIEs require their theoretical evaluation, hence the computational focus of the second part of this chapter.

Quantum chemical modeling of the reaction path of chorismate mutase based on the experimental substrate/product complex

Chorismate mutase is a well-known model enzyme, catalyzing the Claisen rearrangement of chorismate to prephenate. Recent high-resolution crystal structures along the reaction coordinate of this enzyme enabled computational analyses at unprecedented detail. Using quantum chemical simulations, we investigated how the catalytic reaction mechanism is affected by electrostatic and hydrogen-bond interactions. Our calculations showed that the transition state (TS) was mainly stabilized electrostatically, with Arg90 playing the leading role. The effect was augmented by selective hydrogen-bond formation to the TS in the wild-type enzyme, facilitated by a small-scale local induced fit. We further identified a previously underappreciated water molecule, which separates the negative charges during the reaction. The analysis includes the wild-type enzyme and a non-natural enzyme variant, where the catalytic arginine was replaced with an isosteric citrulline residue.

Theoretical Study of the Mechanism of the Nonheme Iron Enzyme EgtB

EgtB is a nonheme iron enzyme catalyzing the C-S bond formation between γ-glutamyl cysteine (γGC) and N-α-trimethyl histidine (TMH) in the ergothioneine biosynthesis. Density functional calculations were performed to elucidate and delineate the reaction mechanism of this enzyme. Two different mechanisms were considered, depending on whether the sulfoxidation or the S-C bond formation takes place first. The calculations suggest that the S-O bond formation occurs first between the thiolate and the ferric superoxide, followed by homolytic O-O bond cleavage, very similar to the case of cysteine dioxygenase. Subsequently, proton transfer from a second-shell residue Tyr377 to the newly generated iron-oxo moiety takes place, which is followed by proton transfer from the TMH imidazole to Tyr377, facilitated by two crystallographically observed water molecules. Next, the S-C bond is formed between γGC and TMH, followed by proton transfer from the imidazole CH moiety to Tyr377, which was calculated to be the rate-limiting step for the whole reaction, with a barrier of 17.9 kcal/mol in the quintet state. The calculated barrier for the rate-limiting step agrees quite well with experimental kinetic data. Finally, this proton is transferred back to the imidazole nitrogen to form the product. The alternative thiyl radical attack mechanism has a very high barrier, being 25.8 kcal/mol, ruling out this possibility.

Metal Ion Modeling Using Classical Mechanics

Metal ions play significant roles in numerous fields including chemistry, geochemistry, biochemistry, and materials science. With computational tools increasingly becoming important in chemical research, methods have emerged to effectively face the challenge of modeling metal ions in the gas, aqueous, and solid phases. Herein, we review both quantum and classical modeling strategies for metal ion-containing systems that have been developed over the past few decades. This Review focuses on classical metal ion modeling based on unpolarized models (including the nonbonded, bonded, cationic dummy atom, and combined models), polarizable models (e.g., the fluctuating charge, Drude oscillator, and the induced dipole models), the angular overlap model, and valence bond-based models. Quantum mechanical studies of metal ion-containing systems at the semiempirical, ab initio, and density functional levels of theory are reviewed as well with a particular focus on how these methods inform classical modeling efforts. Finally, conclusions and future prospects and directions are offered that will further enhance the classical modeling of metal ion-containing systems.

Phosphoramidate hydrolysis catalyzed by human histidine triad nucleotide binding protein 1 (hHint1): a cluster-model DFT computational study

The histidine triad of hHint1 serves as a proton shuttle in the DFT proposed mechanism of the hydrolysis of phosphoramidate.

(19)F NMR and DFT Analysis Reveal Structural and Electronic Transition State Features for RhoA-Catalyzed GTP Hydrolysis

Molecular details for RhoA/GAP catalysis of the hydrolysis of GTP to GDP are poorly understood. We use (19)F NMR chemical shifts in the MgF3(-) transition state analogue (TSA) complex as a spectroscopic reporter to indicate electron distribution for the γ-PO3(-) oxygens in the corresponding TS, implying that oxygen coordinated to Mg has the greatest electron density. This was validated by QM calculations giving a picture of the electronic properties of the transition state (TS) for nucleophilic attack of water on the γ-PO3(-) group based on the structure of a RhoA/GAP-GDP-MgF3(-) TSA complex. The TS model displays a network of 20 hydrogen bonds, including the GAP Arg85' side chain, but neither phosphate torsional strain nor general base catalysis is evident. The nucleophilic water occupies a reactive location different from that in multiple ground state complexes, arising from reorientation of the Gln-63 carboxamide by Arg85' to preclude direct hydrogen bonding from water to the target γ-PO3(-) group.