Active Site Model Research Articles

Electric fields imbue enzyme reactivity by aligning active site fragment orbitals

It is broadly recognized that intramolecular electric fields, produced by the protein scaffold and acting on the active site, facilitate enzymatic catalysis. This field effect can be described by several theoretical models, each of which is intuitive to varying degrees. In this contribution, we show that a fundamental effect of electric fields is to generate electrostatic potentials that facilitate the energetic alignment of reactant frontier orbitals. We apply this model to demystify the impact of electric fields on high-valent iron-oxo heme proteins: catalases, peroxidases, and peroxygenases/monooxygenases. Specifically, we show that this model easily accounts for the observed field-induced changes to the spin distribution within peroxidase active sites and explains the transition between epoxidation and hydroxylation pathways seen in Cytochrome P450 active site models. Thus, for the intuitive interpretation of the chemical effect of the field, the strategy involves analyzing the response of the orbitals of active site fragments, and their energetic alignment. We note that the energy difference between fragment orbitals involved in charge redistribution acts as a measure for the chemical hardness/softness of the reactive complex. This measure, and its sensitivity to electric fields, offers a single parameter model from which to quantitatively assess the effects of electric fields on reactivity and selectivity. Thus, the model provides an additional perspective to describe electrostatic preorganization and offers ways for its manipulation.

Development of Potential Slip Surface Identification Model for Active Deep-Seated Landslide Sites: A Case Study in Taiwan

Identifying locations of landslide slip surfaces provides critical information for understanding the volume of landslides and the scale of disasters, both of which are essential for formulating disaster preparedness and mitigation strategies. Based on hydrogeological survey data from 24 deep-seated landslide-prone sites in Taiwan’s mountainous regions, this study developed the hydraulic conductivity potential index (HCPI) using principal component analysis to quantify the hydraulic properties of disturbed rock formations with six geological factors. Then, regression analysis was performed to construct a permeability estimation model for the geological environment of landslides. Finally, the established model was utilized to develop an identification method for potential slip depths in landslide-prone sites. Results indicated a strong relation between HCPI and hydraulic conductivity with a determination coefficient of 0.895. The relation equation confirmed that the data it generated concerning the depths of significant changes in hydraulic conductivity could be used to identify potential slip surfaces. Additionally, this study successfully established a rule for identifying potential slip zones by summarizing data concerning the generated hydraulic conductivity profiles, stratigraphic lithology, existing inclinometer slip depth records, and groundwater level of landslide sites. This identification method was then applied to predict potential slip depths for ten landslide sites where slip surfaces have not yet occurred. These findings offer a new alternative to having early information on potential sliding depths for timely disaster management and control implementation.

On the Nature of HOPG-Supported Pt1Ti2O7 and its Decomposition of a Nerve Agent Simulant: A Cluster Model of a Single Atom Catalyst Active Site.

Chemical weapons, including hyper lethal nerve agents, are a persistently looming threat across the modern geopolitical landscape. There is a pressing need for the design and development of improved protective materials, which can be substantially aided by the cultivation of a fundamental molecular-level understanding of candidate systems and the corresponding decomposition chemistry. The emergence of the exciting new class of single atom catalyst (SAC) materials has enhanced the prospect of subnanoscale design tailoring in the hopes of optimizing activity and selectivity for a variety of chemical applications. Here, we apply our recently developed experimental technique for modeling the active sites of such SAC materials through the preparation of surface supported size-selected single metal-atom doped metal oxide clusters. The propensity for an SAC cluster model system for Pt1/TiO2 materials, Pt1Ti2O7 supported on highly oriented pyrolytic graphite (HOPG), to adsorb and decompose nerve agent simulant dimethyl methylphosphonate (DMMP) was investigated through a combination of temperature-programmed desorption/reaction (TPD/R) and X-ray photoelectron spectroscopy (XPS). XPS measurements of the as-prepared Pt1Ti2O7 clusters supported the successful isolation of single Pt atoms in clusters monodispersed across the HOPG surface. TPD/R experiments showed that the reactivity exhibited by the Pt1Ti2O7 clusters was distinct from that of Ti2O7 clusters lacking the single Pt atom. It was found that DMMP decomposed over Pt1Ti2O7 upon heating to as low as room temperature, and higher temperature treatments evolved exclusively H2O, CO, and H2, while decomposition over Ti2O7 evolved only methanol and formaldehyde at elevated temperatures. This indicated the promotion of C-H and PO-C bond cleavage within DMMP due to the presence of single Pt atoms in the clusters. Further, the Pt1Ti2O7 clusters were found to desorb P-containing decomposition species, preventing active site poisoning; however, a change of reactivity reflecting that of Ti2O7 was observed following a single TPD/R cycle. This suggested the encapsulation of active Pt sites by titanium oxide during high temperature treatment and is thus an issue deserving of serious attention in the study of Pt1/Ti2O7 SAC materials.

An innovative guanidinium-based ionic covalent organic frameworks with abundant aromatic rings for high-efficiency naproxen removal: Adsorption behavior, mechanisms, and density functional theory calculations

In recent years, naproxen (NPX) has raised significant environmental concerns requiring urgent attention. This study presents an innovative guanidinium-based ionic covalent organic framework (TFPB-TgCl), containing abundant aromatic rings, which was successfully synthesized via Schiff base reaction for the efficient and selective removal of NPX. Remarkably, TFPB-TgCl manifested a maximal NPX adsorption capacity of 308 mg/g at pH = 5. The adsorption on the active site (AOAS) model highlighted the simultaneous occurrence of both physical and chemical adsorption during the NPX uptake. The coefficients of the physical adsorption rates (5.6479, 1.9224, and 1.9224 min−1 for NPX concentrations of 20, 50, and 100 mg/L, respectively) were significantly higher than those of the chemical adsorption rates (0.1759, 0.0681, and 0.0567 g·mg−1·min−1 for the same concentrations), indicating the predominance of physical adsorption. Furthermore, the multilayer adsorption (MLA) model suggested that an adsorption site can interact with more NPX molecules, benefiting from various electrostatic and π-π interactions. The negative values of enthalpy change (ΔH° = −11.956 kJ/mol) and Gibbs free energy (ΔG < 0) confirmed the exothermic and spontaneous nature of the adsorption process. Additionally, in the optimal adsorption configuration (−131.57 kcal/mol), the Independent Gradient Model based on Hirshfeld partition (IGMH) was utilized to identify interaction sites between the guanidinium group of TFPB-TgCl and the carboxyl group of NPX, with subsequent electrostatic potential (ESP) analysis emphasizing their crucial role in electrostatic adsorption. Overall, the adsorption mechanism of electrostatic and π-π interactions in TFPB-TgCl highlights the significant contribution of its guanidinium and aromatic rings in facilitating NPX adsorption.

Discussing the Terms Biomimetic and Bioinspired within Bioinorganic Chemistry.

The terms biomimetic and bioinspired are very relevant in the field of bioinorganic chemistry and have been widely applied. Although they were defined by the International Organization for Standardization in 2015, these terms have at times been used rather ambiguously in the literature. This may be due to the inherent complexity of bioinorganic systems where, for example, a structural model of an enzyme active site may not replicate its function. Conversely, the function of an enzyme may be reproduced in a system where the structure does not resemble the enzyme's active site. To address this, we suggest definitions for the terms biomimetic and bioinspired wherein structure and function have been decoupled. With the help of some representative case studies we have outlined the challenges that may arise and make suggestions on how to apply terminology with careful intention.

Bidentate Substrate Binding Mode in Oxalate Decarboxylase.

Oxalate decarboxylase is an Mn- and O2-dependent enzyme in the bicupin superfamily that catalyzes the redox-neutral disproportionation of the oxalate monoanion to form carbon dioxide and formate. Its best-studied isozyme is from Bacillus subtilis where it is stress-induced under low pH conditions. Current mechanistic schemes assume a monodentate binding mode of the substrate to the N-terminal active site Mn ion to make space for a presumed O2 molecule, despite the fact that oxalate generally prefers to bind bidentate to Mn. We report on X-band 13C-electron nuclear double resonance (ENDOR) experiments on 13C-labeled oxalate bound to the active-site Mn(II) in wild-type oxalate decarboxylase at high pH, the catalytically impaired W96F mutant enzyme at low pH, and Mn(II) in aqueous solution. The ENDOR spectra of these samples are practically identical, which shows that the substrate binds bidentate (κO, κO') to the active site Mn(II) ion. Domain-based local pair natural orbital coupled cluster singles and doubles (DLPNO-CCSD) calculations of the expected 13C hyperfine coupling constants for bidentate bound oxalate predict ENDOR spectra in good agreement with the experiment, supporting bidentate bound substrate. Geometry optimization of a substrate-bound minimal active site model by density functional theory shows two possible substrate coordination geometries, bidentate and monodentate. The bidentate structure is energetically preferred by ~4.7 kcal/mol. Our results revise a long-standing hypothesis regarding substrate binding in the enzyme and suggest that dioxygen does not bind to the active site Mn ion after substrate binds. The results are in agreement with our recent mechanistic hypothesis of substrate activation via a long-range electron transfer process involving the C-terminal Mn ion.

Mol-ecular structure of tris-[(6-bromo-pyridin-2-yl)meth-yl]amine.

Coordination compounds of polydentate nitro-gen ligands with metals are used extensively in research areas such as catalysis, and as models of complex active sites of enzymes in bioinorganic chemistry. Tris(2-pyridyl-meth-yl)amine (TPA) is a tripodal tetra-dentate ligand that is known to form coordination compounds with metals, including copper, iron and zinc. The related compound, tris-[(6-bromo-pyridin-2-yl)meth-yl]amine (TPABr3), C18H15Br3N4, which possesses a bromine atom on the 6-position of each of the three pyridyl moieties, is also known but has not been heavily investigated. The mol-ecular structure of TPABr3 as determined by X-ray diffraction is reported here. The TPABr3 molecule belongs to the triclinic, P space group and displays interesting intermolecular Br⋯Br interactions that provide a stabilizing influence within the molecule.

Modeling of Active Sites and Mechanism of Oxidative Coupling of Methane over Alkali Tungstate Catalysts

Modeling of Active Sites and Mechanism of Oxidative Coupling of Methane over Alkali Tungstate Catalysts

Performant automatic differentiation of local coupled cluster theories: Response properties and ab initio molecular dynamics

In this work, we introduce a differentiable implementation of the local natural orbital coupled cluster (LNO-CC) method within the automatic differentiation framework of the PySCFAD package. The implementation is comprehensively tuned for enhanced performance, which enables the calculation of first-order static response properties on medium-sized molecular systems using coupled cluster theory with single, double, and perturbative triple excitations [CCSD(T)]. We evaluate the accuracy of our method by benchmarking it against the canonical CCSD(T) reference for nuclear gradients, dipole moments, and geometry optimizations. In addition, we demonstrate the possibility of property calculations for chemically interesting systems through the computation of bond orders and Mössbauer spectroscopy parameters for a [NiFe]-hydrogenase active site model, along with the simulation of infrared spectra via ab initio LNO-CC molecular dynamics for a protonated water hexamer.

Structure Activity of β-Amidomethyl Vinyl Sulfones as Covalent Inhibitors of Chikungunya nsP2 Cysteine Protease with Anti-alphavirus Activity.

Despite their widespread impact on human health there are no approved drugs for combating alphavirus infections. The heterocyclic β-aminomethyl vinyl sulfone RA-0002034 (1a) is a potent irreversible covalent inhibitor of the alphavirus nsP2 cysteine protease with broad spectrum antiviral activity. Analogs of 1a that varied each of three regions of the molecule were synthesized to establish structure-activity relationships for inhibition of Chikungunya (CHIKV) nsP2 protease and viral replication. The covalent warhead was highly sensitive to modifications of the sulfone or vinyl substituents. However, numerous alterations to the core 5-membered heterocycle and its aryl substituent were well tolerated and several analogs were identified that enhanced CHIKV nsP2 binding. For example, the 4-cyanopyrazole analog 8d exhibited a kinact /Ki ratio >10,000 M-1s-1. 3-Arylisoxazole was identified an isosteric replacement for the 5-membered heterocycle, which circumvented the intramolecular cyclization that complicated the synthesis of pyrazole-based inhibitors like 1a. The accumulated structure-activity data was used to build a ligand-based model of the enzyme active site, which can be used to guide the design of covalent nsP2 protease inhibitors as potential therapeutics against alphaviruses.

Active Sites of Mixed-Metal Core-Shell Oxygen Evolution Reaction Catalysts: FeO4 Sites on Ni Cores or NiN4 Sites in C Shells?

Water electrolysis for clean hydrogen production requires high-activity, high-stability, and low-cost catalysts for its particularly sluggish half-reaction, the oxygen evolution reaction (OER). Currently, the most promising of such catalysts working in alkaline conditions is a core-shell nanostructure, NiFe@NC, whose Fe-doped Ni (NiFe) nanoparticles are encapsulated and interconnected by N-doped graphitic carbon (NC) layers, but the exact OER mechanism of these catalysts is still unclear, and even the location of the OER active site, either on the core side or on the shell side, is still debated. Therefore, we herein derive a plausible active-site model for each side based on various experimental evidence and density functional theory calculations and then build OER free-energy diagrams on both sides to determine the active-site location. The core-side model is an FeO4-type (rather than NiO4-type) active site where an Fe atom sits on Ni oxide layers grown on top of the core surface during catalyst activation, whose facile dissolution provides an explanation for the activity loss of such catalysts directly exposed to the electrolyte. The shell-side model is a NiN4-type (rather than FeN4-type) active site where a Ni atom is intercalated into the porphyrin-like N4C site of the NC shell during catalyst synthesis. Their OER free-energy diagrams indicate that both sites require similar amounts of overpotentials, despite a complete shift in their potential-determining steps, i.e., the final O2 evolution from the oxophilic Fe on the core and the initial OH adsorption to the hydrophobic shell. We conclude that the major active sites are located on the core, but the NC shell not only protects the vulnerable FeO4 active sites on the core from the electrolyte but also provides independent active sites, owing to the N doping.

HPLC with chiral stationary phase for separation and kinetics study of aspartic acid epimerization in Peroxiredoxin 2 active site peptide

Amino acid epimerization, a process of converting L-amino acids to D-amino acids, will lead to modification in the protein structure and, subsequently, its biological function. This modification causes no change in protein m/z and may be overlooked during protein analysis. Aspartic Acid Epimerization (AAE) is faster than other amino acids and could be accelerated by free radicals and peroxides. In this work, a novel and site-specific HPLC method using a chiral stationary phase for determining the AAE in the active site model peptide (AP) of Peroxiredoxin 2 has been developed and validated. The developed method showed good linearity (1 – 200 μg/mL) and recoveries of the limit of quantification (LOQ), low, medium, and high concentrations were between 85% and 115%. The Kinetics of AAE in AP were studied using the developed method, and the results showed that when ascorbic acid and Cu2+ coexisted, the AP epimerized rapidly. The AAE extent increased with time and was positively correlated with hydrogen peroxide generation.

A novel loofah-like chitosan/alginate composite aerogels prepared for efficient removal of perchlorate: Experimental and DFT study

Perchlorate, an emerging contaminant in drinking water, has attracted global attention. In this study, a novel loofah-like porous chitosan/alginate composite aerogel (CTS/SA-m) was fabricated using ionotropic pregelation and freeze-dried technology to effectively adsorb perchlorate. The performance, isotherms, thermodynamics, and kinetics of perchlorate adsorption by CTS/SA-m were systematically discussed. The results showed that the loofah-like CTS/SA-m with high hydrophilicity exhibited excellent adsorption properties. Over 95 % of the removal rate in 10 min can be achieved, with initial concentration of perchlorate and CTS/SA-m dosage of 10 mg/L and 2 g/L, respectively. And 70.15 mg/g of equilibrium adsorption capacity of perchlorate could be reached at pH 5 and 298 K. pH had little effect on the removal rate of perchlorate, the removal rate surpassed 85 % over a wide pH range of 3.0–11.0. Multilayer adsorption (MLA), intraparticle diffusion (IPD), and adsorption on the active site (AOAS) models were employed to discuss the adsorption mechanism of perchlorate. It was confirmed that double-layer chemisorption played a dominant role. Density functional theory (DFT) analysis of binding energy revealed the effect of functional groups on the ClO4− adsorption strength in the order of –NH3+ > –COOH > –NH2 > –OH. Furthermore, electrostatic potential and the independent gradient model confirmed that electrostatic interactions, hydrogen bonding, and van der Waals forces contributed to the highly efficient adsorption of perchlorate. These findings have a vital promoting effect on perchlorate removal technology in water treatment. Moreover, the loofah-like CTS/SA-m aerogel material, exhibiting outstanding performance, shows great potential in effectively in trapping perchlorate anions from aquatic systems.

Continuous kinetics of 2-hydroxyisobutryic acid esterification using solid acid granular and monolithic activated carbon catalysts

Kinetics of 2-hydroxyisobutyric acid (2-HIBA) esterification with ethanol was studied using sulfonated carbon catalysts in granular (sGAC) and monolith (sACM) forms in a continuous flow packed bed reactor. 2-HIBA is a potential biobased carboxylic acid and its ester a sustainably produced industrial solvent. The catalyst monolith form, made from renewable carbon, offers significantly higher space time yields and conversions, yet little kinetic data or models are available for its use, especially under non-ideal conditions. The effect of ethanol/2-HIBA molar ratio (44, 10, 3.6 and 1.5) at different liquid residence times (3–9 min) was investigated using sGAC. Kinetics of sACM esterifications were investigated at a molar ratio of 3.6 by varying the residence time (2–7 min) and compared with the sGAC. The sACM displayed higher ester yields, acid conversions, and significantly higher reaction rates and space–time-yields (2.1–2.8 ×) compared to the sGAC due to higher surface area to volume ratio. The sACM reaction rates and turnover frequency were comparable to solid acid resins and sulfated silica and zirconia. Pseudo-homogeneous, Eley-Rideal and Langmuir-Hinshelwood models were applied to fit the kinetic data, and the reaction system parameters were obtained through regression analysis. The LH dual active site model resulted in the lowest mean relative error for both 2-HIBA and ester concentration residuals. Adsorption/desorption equilibrium constants for 2-HIBA, ethanol, and ester, were higher compared to water suggesting hydrophobic regions in the sGAC/sACM. Estimation of the external and internal mass transfer criteria indicated negligible effects of mass transfer. With further development sACM and the kinetic model can be used for reactor design of continuous esterification processes using solid acid monolith catalysts.

Eliminating Imaginary Vibrational Frequencies in Quantum-Chemical Cluster Models of Enzymatic Active Sites.

In constructing finite models of enzyme active sites for quantum-chemical calculations, atoms at the periphery of the model must be constrained to prevent unphysical rearrangements during geometry relaxation. A simple fixed-atom or "coordinate-lock" approach is commonly employed but leads to undesirable artifacts in the form of small imaginary frequencies. These preclude evaluation of finite-temperature free-energy corrections, limiting thermochemical calculations to enthalpies only. Full-dimensional vibrational frequency calculations are possible by replacing the fixed-atom constraints with harmonic confining potentials. Here, we compare that approach to an alternative strategy in which fixed-atom contributions to the Hessian are simply omitted. While the latter strategy does eliminate imaginary frequencies, it tends to underestimate both the zero-point energy and the vibrational entropy while introducing artificial rigidity. Harmonic confining potentials eliminate imaginary frequencies and provide a flexible means to construct active-site models that can be used in unconstrained geometry relaxations, affording better convergence of reaction energies and barrier heights with respect to the model size, as compared to models with fixed-atom constraints.

How Do Differences in Electronic Structure Affect the Use of Vanadium Intermediates as Mimics in Nonheme Iron Hydroxylases?

We study active-site models of nonheme iron hydroxylases and their vanadium-based mimics using density functional theory to determine if vanadyl is a faithful structural mimic. We identify crucial structural and energetic differences between ferryl and vanadyl isomers owing to the differences in their ground electronic states, i.e., high spin (HS) for Fe and low spin (LS) for V. For the succinate cofactor bound to the ferryl intermediate, we predict facile interconversion between monodentate and bidentate coordination isomers for ferryl species but difficult rearrangement for vanadyl mimics. We study isomerization of the oxo intermediate between axial and equatorial positions and find the ferryl potential energy surface to be characterized by a large barrier of ca. 10 kcal/mol that is completely absent for the vanadyl mimic. This analysis reveals even starker contrasts between Fe and V in hydroxylases than those observed for this metal substitution in nonheme halogenases. Analysis of the relative bond strengths of coordinating carboxylate ligands for Fe and V reveals that all of the ligands show stronger binding to V than Fe owing to the LS ground state of V in contrast to the HS ground state of Fe, highlighting the limitations of vanadyl mimics of native nonheme iron hydroxylases.

Synthesis and Application of a Near-Infrared Light-Emitting Fluorescent Probe for Specific Imaging of Cancer Cells with High Sensitivity and Selectivity.

The preclinical diagnosis of tumors is of great significance to cancer treatment. Near-infrared fluorescence imaging technology is promising for the in-situ detection of tumors with high sensitivity. Here, a fluorescent probe was synthesized on the basis of Au nanoclusters with near-infrared light emission and applied to fluorescent cancer cell labeling. Near-infrared methionine-N-Hydroxy succinimide Au nanoclusters (Met-NHs-AuNCs) were prepared successfully by one-pot synthesis using Au nanoclusters, methionine, and N-Hydroxy succinimide as frameworks, reductants, and stabilizers, respectively. The specific fluorescence imaging of tumor cells or tissues by fluorescent probe was studied on the basis of SYBYL Surflex-DOCK simulation model of LAT1 active site of overexpressed receptor on cancer cell surface. The results showed that Met-NHs-AuNCs interacted with the surface of LAT1, and C_Score scored the conformation of the probe and LAT1 as five. Characterization and in vitro experiments were conducted to explore the Met-NHs-AuNCs targeted uptake of cancer cells. The prepared near-infrared fluorescent probe (Met-NHs-AuNCs) can specifically recognize the overexpression of L-type amino acid transporter 1 (LAT1) in cancer cells so that it can show red fluorescence in cancer cells. Meanwhile, normal cells (H9c2) have no fluorescence. The fluorescent probe demonstrates the power of targeting and imaging cancer cells.

Tools to Simulate Resonance Raman Spectra for in-Situ Studies of Electron Transport Mediators and Bioelectrocatalysts

Raman spectroscopy is widely applied as an in-situ probe of electrochemical processes. When the excitation light is resonant with an electronic transition, the detected signal can be enhanced by more than 1,000-fold. Resonance Raman (RR) spectroscopy has broad application in the study of common organic electron transport mediators (i.e., viologens, phenazines, photosynthetic pigments) and active sites of redox proteins (i.e., laccases, peroxidases, flavin-containing enzymes). To support investigations of bioelectrocatalytic membranes, we have been adapting RR spectroscopy to gain insights into the properties of immobilized redox mediators and biocatalyst active sites.1,2 Computational methods can be useful for guiding spectral interpretation. This poster reports on applications of recently advanced time-dependent density functional theory (TDDFT) codes that enable the simulation of RR spectra for small electron transport mediators (e.g., methyl viologen radical anion) and redox protein active site models (e.g., laccase T1 site mimics). The ORCA program suite3 was adapted. A series of Cu-centered compounds that model the T1 active site in laccases was studied along with the methyl viologen radical cation. The T1 site in laccases facilitates direct electron transport to an electrode and is a target for in-situ RR measurements. The reported work demonstrates careful selection of the functional (B3-LYP versus the long-range corrected hybrid exchange functional, ωB97X-D3) results in TDDFT-calculated electronic absorption and RR spectra that have features in excellent agreement with experiment. The results provide a foundation to build from in advancing models of small redox mediators and laccase catalytic active sites in support of sustainable technologies. Ozuguzel, U.; Aquino, A.J.A.; Nieman, R.; Minteer, S.D.; Korzeniewski, C. “Calculation of Resonance Raman Spectra and Excited State Properties for Blue Copper Protein Model Complexes” ACS Sustainable Chem. Eng. 2022, 10, 14614. Xu, J.; Koh, M.; Minteer, S. D.; Korzeniewski, C. “In Situ Confocal Raman Microscopy of Redox Polymer Films on Bulk Electrode Supports” ACS Measurement Science Au 2023 (DOI: 10.1021/acsmeasuresciau.2c00064). Neese, F.; Wennmohs, F.; Becker, U.; Riplinger, C. “ORCA Quantum Chemistry Program Package” J. Chem. Phys. 2020, 152, 224108.

Exploring CPS-Extrapolated DLPNO-CCSD(T1) Reference Values for Benchmarking DFT Methods on Enzymatically Catalyzed Reactions.

Domain-based local pair natural orbital coupled-cluster singles doubles with perturbative triples [DLPNO-CCSD(T)] is regularly used to calculate reliable benchmark reference values at a computational cost significantly lower than that of canonical CCSD(T). Recent work has shown that even greater accuracy can be obtained at only a small additional cost through extrapolation to the complete PNO space (CPS) limit. Herein, we test two levels of CPS extrapolation, CPS(5,6), which approximates the accuracy of standard TightPNO, and CPS(6,7), which surpasses it, as benchmark values to test density functional approximations (DFAs) on a small set of organic and transition-metal-dependent enzyme active site models. Between the different reference levels of theory, there are changes in the magnitudes of the absolute deviations for all functionals, but these are small and there is minimal impact on the relative rankings of the tested DFAs. The differences are more significant for the metalloenzymes than the organic enzymes, so we repeat the tests on our entire ENZYMES22 set of organic enzyme active site models [Wappett, D. A.; Goerigk, L. J. Phys. Chem. A 2019, 123, 7057-7074] to confirm that using the CPS extrapolations for the reference values has negligible impact on the benchmarking outcomes. This means that we can particularly recommend CPS(5,6) as an alternative to standard TightPNO settings for calculating reference values, increasing the applicability of DLPNO-CCSD(T) in benchmarking reaction energies and barrier heights of larger models of organic enzymes. DLPNO-CCSD(T1)/CPS(6,7) energies for ENZYMES22 are finally presented as updated reference values for the set, reflecting the recent improvements in the method.

Catalytic Effects of Active Site Conformational Change in the Allosteric Activation of Imidazole Glycerol Phosphate Synthase.

Imidazole glycerol phosphate synthase (IGPS) is a class-I glutamine amidotransferase (GAT) that hydrolyzes glutamine. Ammonia is produced and transferred to a second active site, where it reacts with N1-(5'-phosphoribosyl)-formimino-5-aminoimidazole-4-carboxamide ribonucleotide (PrFAR) to form precursors to purine and histidine biosynthesis. Binding of PrFAR over 25 Å away from the active site increases glutaminase efficiency by ∼4500-fold, primarily altering the glutamine turnover number. IGPS has been the focus of many studies on allosteric communication; however, atomic details for how the glutamine hydrolysis rate increases in the presence of PrFAR are lacking. We present a density functional theory study on 237-atom active site cluster models of IGPS based on crystallized structures representing the inactive and allosterically active conformations and investigate the multistep reaction leading to thioester formation and ammonia production. The proposed mechanism is supported by similar, well-studied enzyme mechanisms, and the corresponding energy profile is consistent with steady-state kinetic studies of PrFAR + IGPS. Additional active site models are constructed to examine the relationship between active site structural change and transition-state stabilization via energy decomposition schemes. The results reveal that the inactive IGPS conformation does not provide an adequately formed oxyanion hole structure and that repositioning of the oxyanion strand relative to the substrate is vital for a catalysis-competent oxyanion hole, with or without the hVal51 dihedral flip. These findings are valuable for future endeavors in modeling the IGPS allosteric mechanism by providing insight into the atomistic changes required for rate enhancement that can inform suitable reaction coordinates for subsequent investigations.