Mechanisms and Opportunities for Rational In Silico Design of Enzymes to Degrade Per- and Polyfluoroalkyl Substances (PFAS)

Per and polyfluoroalkyl substances (PFAS) present a unique challenge to remediation techniques because their strong carbon-fluorine bonds make them difficult to degrade. This review explores the use of in silico enzymatic design as a potential PFAS degradation technique. The scope of the enzymes included is based on currently known PFAS degradation techniques, including chemical redox systems that have been studied for perfluorooctanesulfonic acid (PFOS) and perfluorooctanoic acid (PFOA) defluorination, such as those that incorporate hydrated electrons, sulfate, peroxide, and metal catalysts. Bioremediation techniques are also discussed, namely the laccase and horseradish peroxidase systems. The redox potential of known reactants and enzymatic radicals/metal-complexes are then considered and compared to potential enzymes for degrading PFAS. The molecular structure and reaction cycle of prospective enzymes are explored. Current knowledge and techniques of enzyme design, particularly radical-generating enzymes, and application are also discussed. Finally, potential routes for bioengineering enzymes to enable or enhance PFAS remediation are considered as well as the future outlook for computational exploration of enzymatic in situ bioremediation routes for these highly persistent and globally distributed contaminants.

Benchmarking Density Functional Theory Methods for Metalloenzyme Reactions: The Introduction of the MME55 Set

We present a new benchmark set of metalloenzyme model reaction energies and barrier heights that we call MME55. The set contains 10 different enzymes, representing eight transition metals, both open and closed shell systems, and system sizes of up to 116 atoms. We use four DLPNO-CCSD(T)-based approaches to calculate reference values against which we then benchmark the performance of a range of density functional approximations with and without dispersion corrections. Dispersion corrections improve the results across the board, and triple-ζ basis sets provide the best balance of efficiency and accuracy. Jacob's ladder is reproduced for the whole set based on averaged mean absolute (percent) deviations, with the double hybrids SOS0-PBE0-2-D3(BJ) and revDOD-PBEP86-D4 standing out as the most accurate methods for the MME55 set. The range-separated hybrids ωB97M-V and ωB97X-V also perform well here and can be recommended as a reliable compromise between accuracy and efficiency; they have already been shown to be robust across many other types of chemical problems, as well. Despite the popularity of B3LYP in computational enzymology, it is not a strong performer on our benchmark set, and we discourage its use for enzyme energetics.

DFT and TDDFT exploration on the role of pyridyl ligands with copper toward bonding aspects and light harvesting

CONTEXT

Schiff base-containing metal complexes have been the subject of extensive research. In this work, a coordination polymer-derived complex called [Cu(L)] that is solution-stable (L = 2-(2-hydroxybenzylidene-amino)phenol) has been explored theoretically with five different pyridyl-based ligands using DFT/TDDFT in order to understand the structural-functional and electronic transitions of these five complexes. Frontier molecular orbital (FMO) analysis was carried out to assess the reactivity behavior of all five complexes. For the purpose of studying the charge energy distribution over complexes, electrostatic potential maps were also drawn. Furthermore, in order to identify any stabilizing interactions that may be present in the given complexes, an NBO analysis was studied. To learn more about any potential correlations between the properties of these five complexes, a comparative analysis was explored. Our calculations demonstrate that complex 3 having pyridine-4-carboxamide as a ligand has a lower energy gap and a higher negative electrostatic potential which may indicate its higher reactivity and this may be due to the electron withdrawing group (carboxamide). TDDFT results show that the highest light harvesting efficiency (LHE) of all the studied complexes is found in the range of 440-448 nm. Complexes 1, 2, and 4 show the higher light harvesting efficiency as compared to complexes 3 and 5. Our findings are in good accordance with the available experimental data.

METHODS

All DFT computations were performed using the Gaussian16 with unrestricted B3LYP-D2 functional with the basis sets 6-31G(d,p) for O, N, C, and H while LanL2DZ for Cu. The polarized continuum model (PCM) was used for the solvation. The software GaussView6.1 was utilized for the modeling of initial geometries and the plotting of MEP maps. The NBO6.0 program which is incorporated in Gaussian16 was utilized to investigate the bonding nature and stabilization energies of the complexes. The ORCA program was used to simulate the absorption spectra.

First-Generation Organic Reaction Intermediates in Zeolite Chemistry and Catalysis

Zeolite chemistry and catalysis are expected to play a decisive role in the next decade(s) to build a more decentralized renewable feedstock-dependent sustainable society owing to the increased scrutiny over carbon emissions. Therefore, the lack of fundamental and mechanistic understanding of these processes is a critical "technical bottleneck" that must be eliminated to maximize economic value and minimize waste. We have identified, considering this objective, that the chemistry related to the first-generation reaction intermediates (i.e., carbocations, radicals, carbenes, ketenes, and carbanions) in zeolite chemistry and catalysis is highly underdeveloped or undervalued compared to other catalysis streams (e.g., homogeneous catalysis). This limitation can often be attributed to the technological restrictions to detect such "short-lived and highly reactive" intermediates at the interface (gas-solid/solid-liquid); however, the recent rise of sophisticated spectroscopic/analytical techniques (including under in situ/operando conditions) and modern data analysis methods collectively compete to unravel the impact of these organic intermediates. This comprehensive review summarizes the state-of-the-art first-generation organic reaction intermediates in zeolite chemistry and catalysis and evaluates their existing challenges and future prospects, to contribute significantly to the "circular carbon economy" initiatives.

Single Atom Catalysts for Selective Methane Oxidation to Oxygenates

Direct conversion of methane (CH₄) to C_1-2 liquid oxygenates is a captivating approach to lock carbons in transportable value-added chemicals, while reducing global warming. Existing approaches utilizing the transformation of CH₄ to liquid fuel via tandemized steam methane reforming and the Fischer-Tropsch synthesis are energy and capital intensive. Chemocatalytic partial oxidation of methane remains challenging due to the negligible electron affinity, poor C-H bond polarizability, and high activation energy barrier. Transition-metal and stoichiometric catalysts utilizing harsh oxidants and reaction conditions perform poorly with randomized product distribution. Paradoxically, the catalysts which are active enough to break C-H also promote overoxidation, resulting in CO₂ generation and reduced carbon balance. Developing catalysts which can break C-H bonds of methane to selectively make useful chemicals at mild conditions is vital to commercialization. Single atom catalysts (SACs) with specifically coordinated metal centers on active support have displayed intrigued reactivity and selectivity for methane oxidation. SACs can significantly reduce the activation energy due to induced electrostatic polarization of the C-H bond to facilitate the accelerated reaction rate at the low reaction temperature. The distinct metal-support interaction can stabilize the intermediate and prevent the overoxidation of the reaction products. The present review accounts for recent progress in the field of SACs for the selective oxidation of CH₄ to C_1-2 oxygenates. The chemical nature of catalytic sites, effects of metal-support interaction, and stabilization of intermediate species on catalysts to minimize overoxidation are thoroughly discussed with a forward-looking perspective to improve the catalytic performance.

Refining details of the structural and electronic properties of the CuB site in pMMO enzyme through sequential molecular dynamics/CPKS-EPR calculations

This work investigated the structural and electronic properties of the copper mononuclear site of the PmoB part of the pMMO enzyme at the molecular level. We propose that the Cu_B catalytic site in the soluble portion of pMMO at room temperature and under physiological conditions is a mononuclear copper complex in a distorted octahedral arrangement with the residues His³³, His¹³⁷, and His¹³⁹ on the equatorial base and two water molecules on the axial axis. Our view was based on the molecular dynamics results and DFT calculations of the electronic paramagnetic resonance parameters and comparisons with experimental EPR data. This new proposed model for the Cu_B site brings additional support concerning the recent experimental evidence, which pointed out that a saturated coordination sphere of the copper ion in the Cu_B center is an essential factor that makes it less efficient than the Cu_C site in the methane oxidation. Therefore, according to the Cu_B site model proposed here, an additional step involving a displacement of at least one water molecule of the copper coordination sphere by the O₂ molecule prior to its activation must be necessary. This scenario is less likely to occur in the Cu_C center once this one is buried in the alpha-helices, which are part of the pMMO structure bound to the membrane wall, and consequently located in a less solvent-exposed region. In addition, we also present a simple and efficient sequential S-MD/CPKS protocol to compute EPR parameters that can, in principle, be expanded for the study of other copper-containing proteins.

Understanding the CH4 Conversion over Metal Dimers from First Principles

Inspired by the advantages of bi-atom catalysts and recent exciting progresses of nanozymes, by means of density functional theory (DFT) computations, we explored the potential of metal dimers embedded in phthalocyanine monolayers (M₂-Pc), which mimics the binuclear centers of methane monooxygenase, as catalysts for methane conversion using H₂O₂ as an oxidant. In total, 26 transition metal (from group IB to VIIIB) and four main group metal (M = Al, Ga, Sn and Bi) dimers were considered, and two methane conversion routes, namely *O-assisted and *OH-assisted mechanisms were systematically studied. The results show that methane conversion proceeds via an *OH-assisted mechanism on the Ti₂-Pc, Zr₂-Pc and Ta₂-Pc, a combination of *O- and *OH-assisted mechanism on the surface of Sc₂-Pc, respectively. Our theoretical work may provide impetus to developing new catalysts for methane conversion and help stimulate further studies on metal dimer catalysts for other catalytic reactions.

Microbial oxidation of atmospheric trace gases

The atmosphere has recently been recognized as a major source of energy sustaining life. Diverse aerobic bacteria oxidize the three most abundant reduced trace gases in the atmosphere, namely hydrogen (H₂), carbon monoxide (CO) and methane (CH₄). This Review describes the taxonomic distribution, physiological role and biochemical basis of microbial oxidation of these atmospheric trace gases, as well as the ecological, environmental, medical and astrobiological importance of this process. Most soil bacteria and some archaea can survive by using atmospheric H₂ and CO as alternative energy sources, as illustrated through genetic studies on Mycobacterium cells and Streptomyces spores. Certain specialist bacteria can also grow on air alone, as confirmed by the landmark characterization of Methylocapsa gorgona, which grows by simultaneously consuming atmospheric CH₄, H₂ and CO. Bacteria use high-affinity lineages of metalloenzymes, namely hydrogenases, CO dehydrogenases and methane monooxygenases, to utilize atmospheric trace gases for aerobic respiration and carbon fixation. More broadly, trace gas oxidizers enhance the biodiversity and resilience of soil and marine ecosystems, drive primary productivity in extreme environments such as Antarctic desert soils and perform critical regulatory services by mitigating anthropogenic emissions of greenhouse gases and toxic pollutants.

A framework for constructing linear free energy relationships to design molecular transition metal catalysts

A computational framework for ligand-driven design of transition metal complexes is presented in this work. We propose a general procedure for the construction of active site-specific linear free energy relationships (LFERs), which are inspired from Hammett and Taft correlations in organic chemistry and grounded in the activation strain model (ASM). Ligand effects are isolated and quantified in terms of their contribution to interaction and strain energy components of ASM. Scalar descriptors that are easily obtainable are then employed to construct the complete LFER. We successfully demonstrate proof-of-concept by constructing and applying an LFER to CH activation with enzyme-inspired [Cu2O2]2+ complexes. The key benefit of using ASM is a built-in compensation or error cancellation between LFER prediction of interaction and strain terms, resulting in accurate barrier predictions for 37 of the 47 catalysts examined in this study. The LFER is also transferable with respect to level of theory and flexible towards the choice of reference system. The absence of interaction-strain compensation or poor model performance for the remaining systems is a consequence of the approximate nature of the chosen interaction energy descriptor and LFER construction of the strain term, which focuses largely on trends in substrate and not catalyst strain.

Shifting the scaling relations of single-atom catalysts for facile methane activation by tuning the coordination number

We investigate oxidative methane activation on a wide range of single transition metal atom catalysts embedded on N-doped graphene derivatives using density functional theory calculations. An inverse scaling relationship between *O formation and its hydrogen affinity is observed, consistent with a previous report. However, we find that the latter scaling line can be shifted towards a more reactive region by tuning the coordination number (CN) of the active metal sites. Specifically, we find that lowering the CN plays an important role in increasing the reactivity for methane activation via a radical-like transition state by moving the scaling lines. Thus, in the new design strategy suggested here, different from the conventional efforts focusing mainly on breaking the scaling relations, one maintains the scaling relations but moves them towards more reactive regions by controlling the coordination number of the active sites. With this design principle, we suggest several single atom catalysts with lower C-H activation barriers than some of the most active methane activation catalysts in the literature such as Cu-based zeolites.

The Chemistry, Biology, and Modulation of Ammonium Nitrification in Soil

Approximately two percent of the world's energy is consumed in the production of ammonia from hydrogen and nitrogen gas. Ammonia is used as a fertilizer ingredient for agriculture and distributed in the environment on an enormous scale to promote crop growth in intensive farming. Only 30-50 % of the nitrogen applied is assimilated by crop plants; the remaining 50-70 % goes into biological processes such as nitrification by microbial metabolism in the soil. This leads to an imbalance in the global nitrogen cycle and higher nitrous oxide emissions (a potent and significant greenhouse gas) as well as contamination of ground and surface waters by nitrate from the nitrogen-fertilized farmland. This Review gives a critical overview of the current knowledge of soil microbes involved in the chemistry of ammonia nitrification, the structures and mechanisms of the enzymes involved, and phytochemicals capable of inhibiting ammonia nitrification.

Computational Approach to Molecular Catalysis by 3d Transition Metals: Challenges and Opportunities

Computational chemistry provides a versatile toolbox for studying mechanistic details of catalytic reactions and holds promise to deliver practical strategies to enable the rational in silico catalyst design. The versatile reactivity and nontrivial electronic structure effects, common for systems based on 3d transition metals, introduce additional complexity that may represent a particular challenge to the standard computational strategies. In this review, we discuss the challenges and capabilities of modern electronic structure methods for studying the reaction mechanisms promoted by 3d transition metal molecular catalysts. Particular focus will be placed on the ways of addressing the multiconfigurational problem in electronic structure calculations and the role of expert bias in the practical utilization of the available methods. The development of density functionals designed to address transition metals is also discussed. Special emphasis is placed on the methods that account for solvation effects and the multicomponent nature of practical catalytic systems. This is followed by an overview of recent computational studies addressing the mechanistic complexity of catalytic processes by molecular catalysts based on 3d metals. Cases that involve noninnocent ligands, multicomponent reaction systems, metal-ligand and metal-metal cooperativity, as well as modeling complex catalytic systems such as metal-organic frameworks are presented. Conventionally, computational studies on catalytic mechanisms are heavily dependent on the chemical intuition and expert input of the researcher. Recent developments in advanced automated methods for reaction path analysis hold promise for eliminating such human-bias from computational catalysis studies. A brief overview of these approaches is presented in the final section of the review. The paper is closed with general concluding remarks.

Methane selective oxidation to methanol by metal-exchanged zeolites: a review of active sites and their reactivity

A review of the recent progress in revealing the structures, formation, and reactivity of the active sites in Fe-, Co-, Ni- and Cu-exchanged zeolites as well as outlooks on future research challenges and opportunities is presented.

Computational strategies to probe CH activation in dioxo-dicopper complexes

We employ density functional theory and energy decomposition analysis to probe the mechanism of CH activation in dioxo-dicopper complexes. The electrophilicity of monodentate N-donor ligands coordinated to Cu is systematically varied to examine the response of barriers to the two proposed pathways - one-step oxo-insertion and two-step radical recombination. Electron-withdrawing ligand stabilize the oxo-insertion transition state via charge transfer interactions, and therefore lead to lower barriers. On the other hand, barriers to the CH activation step in the radical recombination mechanism exhibit almost no dependence on N-donor electrophilicity. Based on the similarities between calculated and experimental Hammett relationships, the oxo-insertion pathway appears to be the preferred mechanism of CH activation in dioxo-dicopper catalysts.

A Structurally Characterized CuIII Complex Supported by a Bis(anilido) Ligand and Its Oxidative Catalytic Activity

Three copper(II) complexes of the (R,R)-N,N'-bis(3,5-di-tert-butyl-2-aminobenzylidene)-1,2-diaminocyclohexane ligand, namely [Cu(^N L)], [Cu(^N LH)]⁺ and [Cu(^N LH₂ )]²⁺ , were prepared and structurally characterized. In [Cu(^N LH₂ )]²⁺ the copper ion lies in an octahedral geometry with the aniline groups coordinated in equatorial positions. In [Cu(^N L)] the anilines are deprotonated (anilido moieties) and coordinated to an almost square-planar metal ion. Complex [Cu(^N L)] displays two oxidation waves at E_1/2^ox, 1 =-0.14 V and E_1/2^ox, 2 =0.36 V vs. Fc⁺ /Fc in CH₂ Cl₂ . Complex [Cu(^N LH₂ )]²⁺ displays an irreversible oxidation wave at high potential (1.21 V), but shows a readily accessible and reversible metal-centered reduction at E_1/2^red =-0.67 V (Cu^II /Cu^I redox couple). Oxidation of [Cu(^N L)] by AgSbF₆ produces [Cu(^N L)](SbF₆ ), which was isolated as single crystals. X-ray structure analysis discloses a contraction of the coordination sphere by 0.05 Å upon oxidation, supporting a metal-centered process. Complex [Cu(^N L)](SbF₆ ) displays an intense NIR band at 1260 nm corresponding to an anilido-to-copper(III) charge transfer transition. This compound slowly evolves in CH₂ Cl₂ solution towards [Cu(^N LH)](SbF₆ ), which is a copper(II) complex comprised of both anilido and aniline groups coordinated to the metal center. The copper(III) complex [Cu(^N L)](SbF₆ ) is an efficient catalyst for benzyl alcohol oxidation, with 236 TON in 24 h at 298 K, without additives other than oxygen and a base.

Copper-Oxygen Complexes Revisited: Structures, Spectroscopy, and Reactivity

A longstanding research goal has been to understand the nature and role of copper-oxygen intermediates within copper-containing enzymes and abiological catalysts. Synthetic chemistry has played a pivotal role in highlighting the viability of proposed intermediates and expanding the library of known copper-oxygen cores. In addition to the number of new complexes that have been synthesized since the previous reviews on this topic in this journal (Mirica, L. M.; Ottenwaelder, X.; Stack, T. D. P. Chem. Rev. 2004, 104, 1013-1046 and Lewis, E. A.; Tolman, W. B. Chem. Rev. 2004, 104, 1047-1076), the field has seen significant expansion in the (1) range of cores synthesized and characterized, (2) amount of mechanistic work performed, particularly in the area of organic substrate oxidation, and (3) use of computational methods for both the corroboration and prediction of proposed intermediates. The scope of this review has been limited to well-characterized examples of copper-oxygen species but seeks to provide a thorough picture of the spectroscopic characteristics and reactivity trends of the copper-oxygen cores discussed.

Understanding trends in C-H bond activation in heterogeneous catalysis

While the search for catalysts capable of directly converting methane to higher value commodity chemicals and liquid fuels has been active for over a century, a viable industrial process for selective methane activation has yet to be developed. Electronic structure calculations are playing an increasingly relevant role in this search, but large-scale materials screening efforts are hindered by computationally expensive transition state barrier calculations. The purpose of the present letter is twofold. First, we show that, for the wide range of catalysts that proceed via a radical intermediate, a unifying framework for predicting C-H activation barriers using a single universal descriptor can be established. Second, we combine this scaling approach with a thermodynamic analysis of active site formation to provide a map of methane activation rates. Our model successfully rationalizes the available empirical data and lays the foundation for future catalyst design strategies that transcend different catalyst classes.