Enzymatic Conversion of CO2: From Natural to Artificial Utilization

Multi-module engineering to guide the development of an efficient L-threonine-producing cell factory

The rapid development of high-productivity strains is fundamental for bio-manufacture in industry. Here, Multi-module metabolic engineering was implemented to reprogram Escherichia coli, enabling it to rapidly transitioning from zero-producer to hyperproducer of L-threonine. Firstly, the synthesis pathway of L-threonine was rationally divided into five modules, and the rapid production of L-threonine was achieved by optimizing the expression of genes in each module. Subsequently, the capture and fixation of CO2 was enhanced to improve L-threonine yield. Dynamically balancing cell growth and yield by quorum-sensing system resulted in the accumulation of L-threonine up to 34.24 g/L. Ultimately, the THR36-L19 strain accumulated 120.1 g/L L-threonine with 0.425 g/g glucose in a 5 L bioreactor. This is the highest yield for de novo producing L-threonine reported to date and without the use of exogenous inducers and antibiotics in the fermentation process. It also provided an effective technological guidence for the zero-to-overproduction of other chemicals.

Redistribution of Electron Density for Promoting CO2 Conversion Capacity

There is a need to design substrate-supported catalysts for the heterogeneous fields, especially with large porosity, which can facilitate mass transport. Herein, aiming at enhancing the performance of CO2 fixation, a hollow carbon sphere-supported catalyst of FeNPs/HCS (FeNPs, Fe nanoparticles; HCS, hollow carbon sphere) is facilely designed and fabricated. Excitingly, the experimental and calculation results reveal that FeNPs/HCS displays an ultrahigh activity with almost complete conversions in CO2 cycloaddition, surpassing the performance of FeNPs/CS (CS, carbon sphere); this demonstrates that the HCS plays a key role, which may be attributed to the hollow structure tuning the electron density and enhancing the enrichment of the substrate and CO2, consequently lowering the barrier associated with mass transfer. The work not only provides a novel strategy to construct an efficient catalyst but also proposes, for the first time, an electron redistribution tactic to influence the catalytic process for CO2 cycloaddition.

Molecular Heterogeneous Photocatalysts for Visible-Light-Driven CO2 Reduction

Photoreduction of CO2 to high-value chemical fuels presents an effective strategy to reduce reliance on fossil fuels and mitigate climate change. The development of a photocatalyst characterized by superior activity, high selectivity, and good stability is a critical issue for PCR. Molecular heterogeneous photocatalytic systems integrate the advantages of both homogeneous and heterogeneous catalysts, creating a synergistic enhancement effect that increases photocatalytic performance. This review summarizes recent advancements in molecular heterogeneous photocatalysts for CO2 reduction. Much of the discussion focuses on the types of molecular heterogeneous photocatalysts, and their photocatalytic performance in CO2 reduction is summarized. The synthesis strategies for molecular heterogeneous photocatalysts are thoroughly discussed. Finally, the challenges and future prospects of molecular heterogeneous photocatalysts for PCR are addressed.

Harnessing noncanonical redox cofactors to advance synthetic assimilation of one-carbon feedstocks

One-carbon (C1) feedstocks, such as carbon monoxide (CO), formate (HCO2H), methanol (CH3OH), and methane (CH4), can be obtained either through stepwise electrochemical reduction of CO2 with renewable electricity or via processing of organic side streams. These C1 substrates are increasingly investigated in biotechnology as they can contribute to a circular carbon economy. In recent years, noncanonical redox cofactors (NCRCs) emerged as a tool to generate synthetic electron circuits in cell factories to maximize electron transfer within a pathway of interest. Here, we argue that expanding the use of NCRCs in the context of C1-driven bioprocesses will boost product yields and facilitate challenging redox transactions that are typically out of the scope of natural cofactors due to inherent thermodynamic constraints.

Closing the Loop in the Carbon Cycle: Enzymatic Reactions Housed in Metal-Organic Frameworks for CO2 Conversion to Methanol

The preparation of value-added chemicals from carbon dioxide (CO2) can act as a way of reducing the greenhouse gas from the atmosphere. Industrially significant C1 chemicals like methanol (CH3OH), formic acid (HCOOH), and formaldehyde (HCHO) can be formed from CO2. One sustainable way of achieving this is by connecting the reactions catalyzed by the enzymes formate dehydrogenase (FDH), formaldehyde dehydrogenase (FALDH), and alcohol dehydrogenase (ADH) into a single cascade reaction where CO2 is hydrogenated to CH3OH. For this to be adaptable for industrial use, the enzymes should be immobilized in materials that are extraordinarily protective of the enzymes, inexpensive, stable, and of ultra-large surface area. Metal-organic frameworks (MOFs) meet these criteria and are expected to usher in the much-awaited dispensation of industrial biocatalysis. Unfortunately, little is known about the molecular behaviour of MOF-immobilized FDH, FALDH, and ADH. It is also yet not known which MOFs are most promising for industrial enzyme-immobilization since the field of reticular chemistry is growing exponentially with millions of hypothetical and synthesized MOF structures reported at present. This review initially discusses the properties of the key enzymes required for CO2 hydrogenation to methanol including available cofactor regeneration strategies. Later, the characterization techniques of enzyme-MOF composites and the successes or lack thereof of enzyme-MOF-mediated CO2 conversion to CH3OH and intermediate products are discussed. We also discuss reported multi-enzyme-MOF systems for CO2 conversion cognizant of the fact that at present, these systems are the only chance of housing cascade-type biochemical reactions where strict substrate channelling and operational conditions are required. Finally, we delve into future perspectives.

Engineered metallobiocatalysts for energy-relevant reactions

Engineering metallobiocatalysts is a promising approach to addressing challenges in energy-relevant electrocatalysis and photocatalysis. The design freedom provided by semisynthetic and fully synthetic approaches to catalyst design allows researchers to demonstrate how structural modifications can improve selectivity and activity of biocatalysts. Furthermore, the provision of a superstructure in many metallobiocatalysts facilitates active-site microenvironment engineering. Recurring themes include the role of the biomolecular scaffold in enhancing reactivity in water and catalyst robustness, the impact of the outer sphere on reactivity, and the importance of tuning system components in full system optimization. In this perspective, recent strategies to design and modify novel biocatalysts, understand proton and electron transfer mechanisms, and tune system activity by modifying catalysts and system conditions are highlighted within the field of energy-related catalysis. Opportunities in this field include developing robust structure-function relationships to support approaches to engineering second-sphere interactions and identifying ways to enhance biocatalyst activity over time.

A Comprehensive Review of CO2 Hydrogenation into Formate/Formic Acid Catalyzed by Whole Cell Bacteria

The increasing levels of carbon dioxide (CO2) in the atmosphere, primarily due to the use of fossil fuels, pose a significant threat to the environment and necessitate urgent action to mitigate climate change. Carbon capture and utilization technologies that can convert CO2 into economically valuable compounds have gained attention as potential solutions. Among these technologies, biocatalytic CO2 hydrogenation using bacterial whole cells shows promise for the efficient conversion of CO2 into formate, a valuable chemical compound. Although it was discovered nearly a century ago, comprehensive reviews focusing on the utilization of whole-cell bacteria as the biocatalyst in this area remain relatively limited. Therefore, this review provides an analysis of the progress, strategies, and key findings in this field. It covers the use of living cells, resting cells, or genetically modified bacteria as biocatalysts to convert CO2 into formate, either naturally or with the integration of electrochemical and protochemical techniques as sources of protons and electrons. By consolidating the current knowledge in this field, this review article aims to serve as a valuable resource for researchers and practitioners interested in understanding the recent progress, challenges, and potential applications of bacterial whole cell catalyzed CO2 hydrogenation into formate.

Low-valent group 6 metals/Al(C6F5)3 donor-acceptor systems for CO2 activation and cleavage

Donor-acceptor systems for CO2 activation combining a formally zero-valent group 6 metal as the donor with the Lewis acid Al(C6F5)3 (AlCF) are reported. They were obtained from AlCF adducts of N2-complexes by N2-to-CO2 substitution. One species was capable of C-O cleavage. The boron analogues led to intractable mixtures.

Computational methods for the study of carboxylases: The case of crotonyl-CoA carboxylase/reductase

The rising levels of atmospheric CO2 and its impact on climate change call for new methods to transform this greenhouse gas into beneficial compounds. Carboxylases have a significant role in the carbon cycle, converting gigatons of CO2 into biomass annually. One of the most effective and fastest carboxylases is crotonyl-CoA carboxylase/reductase (Ccr). To understand its underlying mechanism, we have developed computational methods and protocols based on all-atom molecular dynamics simulations. These methods provide the CO2 binding locations and free energy inside the active site, dependent on different conformations adopted by Ccr and the presence of the crotonyl-CoA substrate. Furthermore, the adaptive string method and quantum mechanics/molecular mechanics (QM/MM) molecular dynamics simulations outline the CO2 fixation reaction via two different mechanisms. The direct mechanism involves a hydride transfer creating a reactive enolate, which then binds the electrophilic CO2 molecule, resulting in the carboxylated product. Alternatively, another mechanism involves the formation of a covalent adduct. Our simulations suggest that this adduct serves to store the enolate in a much more stable intermediate avoiding its reduction side reaction, explaining the enzyme's efficiency. Overall, this work presents computational methods for studying carboxylation reactions using Ccr as a model, providing general principles that can be applied to modeling other carboxylases.

Constructing an artificial in vitro multi-enzyme cascade pathway to convert glycerol and CO2 into L-aspartic acid

Developing utilization technologies for biomass resources, exploring their applications in the fields of energy and chemical engineering, holds significant importance for promoting sustainable development and constructing a green, low-carbon society. In this study, we designed a non-natural in vitro multi-enzyme system for converting glycerol and CO2 into L-aspartic acid (L-Asp). The coupled system utilized eight enzymes, including alditol oxidase (ALDO), catalase-peroxidase (CAT), lactaldehyde dehydrogenase (ALDH), glycerate 2-kinase (GK), phosphopyruvate hydratase (PPH), phosphoenolpyruvate carboxylase (PPC), L-aspartate dehydrogenase (ASPD), and polyphosphate kinase (PPK), to convert the raw materials into L-Asp in one-pot coupled with NADH and ATP regeneration. Under optimal reaction conditions, 18.6 mM of L-Asp could be produced within 2.0 h at a total enzyme addition of 4.85 mg/mL, demonstrating the high efficiency and productivity characteristics of the designed system. Our technological application provides new insights and methods for the development of biomass resource utilization technologies.

Quantum chemical studies of the reaction mechanisms of enzymatic CO2 conversion

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

Computational Study on Flavin-Catalyzed Aerobic Dioxygenation of Alkenyl Thioesters: Decomposition of Anionic Peroxides

Flavin-dependent catalysts are widely applied to aerobic monooxygenation/oxidation reactions. In contrast, flavin-catalyzed aerobic dioxygenation reactions exhibit higher atomic economy but are less reported, not to mention the relevant mechanistic studies. Herein, a density functional theory study on flavin-catalyzed aerobic epoxidation-oxygenolysis of alkenyl thioesters was performed for the first time. Different from the previous mechanistic proposal, a pathway featuring two catalytic stages, monoanionic flavin-C(4a)-peroxide/oxide intermediates, and a reverse reaction sequence (epoxidation goes prior to oxygenolysis) was revealed. In comparison, the pathways involving dianionic flavin catalysts, monoanionic flavin-N(5)-(hydro)peroxide/C(10a)-peroxide, or neutral flavin-C(4a)-hydroperoxide/hydroxide/N(5)-oxide, and the pathways where oxygenolysis goes prior to epoxidation are less favored. Epoxidation goes through intramolecular substitution of the O-O bond of anionic flavin-C(4a)-peroxide by β-carbon, while the resulting flavin-C(4a)-oxide accomplishes the oxygenolysis. Furthermore, two other reaction modes, i.e., concerted O-O cleavage/1,2-shift of α-substituents and dyotropic rearrangement were discovered for the decomposition of other anionic peroxides, and preliminary rules were summarized for understanding the chemoselectivity for this process. This study sheds light on the different reaction features of numerous flavin-dioxygen derivatives, providing deeper insights into flavin-catalyzed dioxygenation reactions, and is expected to inspire experimental design based on unconventional anionic peroxides.

Enzymatic CO2 reduction catalyzed by natural and artificial Metalloenzymes

The continuously increasing level of atmospheric CO2 in the atmosphere has led to global warming. Converting CO2 into other carbon compounds could mitigate its atmospheric levels and produce valuable products, as CO2 also serves as a plentiful and inexpensive carbon feedstock. However, the inert nature of CO2 poses a major challenge for its reduction. To meet the challenge, nature has evolved metalloenzymes using transition metal ions like Fe, Ni, Mo, and W, as well as electron-transfer partners for their functions. Mimicking these enzymes, artificial metalloenzymes (ArMs) have been designed using alternative protein scaffolds and various metallocofactors like Ni, Co, Re, Rh, and FeS clusters. Both the catalytic efficiency and the scope of CO2-reduction product of these ArMs have been improved over the past decade. This review first focuses on the natural metalloenzymes that directly reduce CO2 by discussing their structures and active sites, as well as the proposed reaction mechanisms. It then introduces the common strategies for electrochemical, photochemical, or photoelectrochemical utilization of these native enzymes for CO2 reduction and highlights the most recent advancements from the past five years. We also summarize principles of protein design for bio-inspired ArMs, comparing them with native enzymatic systems and outlining challenges and opportunities in enzymatic CO2 reduction.

Atomically Dispersed Metal Catalysts for the Conversion of CO2 into High-Value C2+ Chemicals

The conversion of carbon dioxide (CO2) into value-added chemicals with two or more carbons (C2+) is a promising strategy that cannot only mitigate anthropogenic CO2 emissions but also reduce the excessive dependence on fossil feedstocks. In recent years, atomically dispersed metal catalysts (ADCs), including single-atom catalysts (SACs), dual-atom catalysts (DACs), and single-cluster catalysts (SCCs), emerged as attractive candidates for CO2 fixation reactions due to their unique properties, such as the maximum utilization of active sites, tunable electronic structure, the efficient elucidation of catalytic mechanism, etc. This review provides an overview of significant progress in the synthesis and characterization of ADCs utilized in photocatalytic, electrocatalytic, and thermocatalytic conversion of CO2 toward high-value C2+ compounds. To provide insights for designing efficient ADCs toward the C2+ chemical synthesis originating from CO2, the key factors that influence the catalytic activity and selectivity are highlighted. Finally, the relevant challenges and opportunities are discussed to inspire new ideas for the generation of CO2-based C2+ products over ADCs.

Multi-scale reactor designs extend the physical limits of CO 2 fixation

CO 2 valorization is a promising strategy for climate adaptation and transitioning towards a circular carbon economy. Here, we present a multi-scale, integrated systems approach for designing biomanufacturing systems that can utilizeCO 2 as a feedstock, focusing on the Wood-Ljungdahl and reductive glycine pathways. This approach relies on first principles, coupling the optimization of pathway and process variables. We examine theCO 2 -fixation capacity of both pathways in single- and multi-compartment reactor systems, demonstrating that the reductive glycine pathway has the potential to fixCO 2 at significantly higher rates than photosynthetic organisms. We show that small differences in the energy-dissipative and stoichiometric structures of carbon-fixation pathways could significantly impact optimal designs and feasible design spaces. Our first-principle, systems-level approach quantifies these differences and uncovers strategies to expand the design space and extend the physical limits of carbon fixation, offering insights into pathway selection and process configurations for efficient biomanufacturing.

Enzyme-Immobilized Porous Crystals for Environmental Applications

Developing efficient technologies to eliminate or degrade contaminants is paramount for environmental protection. Biocatalytic decontamination offers distinct advantages in terms of selectivity and efficiency; however, it still remains challenging when applied in complex environmental matrices. The main challenge originates from the instability and difficult-to-separate attributes of fragile enzymes, which also results in issues of compromised activity, poor reusability, low cost-effectiveness, etc. One viable solution to harness biocatalysis in complex environments is known as enzyme immobilization, where a flexible enzyme is tightly fixed in a solid carrier. In the case where a reticular crystal is utilized as the support, it is feasible to engineer next-generation biohybrid catalysts functional in complicated environmental media. This can be interpreted by three aspects: (1) the highly crystalline skeleton can shield the immobilized enzyme against external stressors. (2) The porous network ensures the high accessibility of the interior enzyme for catalytic decontamination. And (3) the adjustable and unambiguous structure of the reticular framework favors in-depth understanding of the interfacial interaction between the framework and enzyme, which can in turn guide us in designing highly active biocomposites. This Review aims to introduce this emerging biocatalysis technology for environmental decontamination involving pollutant degradation and greenhouse gas (carbon dioxide) conversion, with emphasis on the enzyme immobilization protocols and diverse catalysis principles including single enzyme catalysis, catalysis involving enzyme cascades, and photoenzyme-coupled catalysis. Additionally, the remaining challenges and forward-looking directions in this field are discussed. We believe that this Review may offer a useful biocatalytic technology to contribute to environmental decontamination in a green and sustainable manner and will inspire more researchers at the intersection of the environment science, biochemistry, and materials science communities to co-solve environmental problems.

A Blueprint for Secondary Coordination Sphere Editing: Approaches Toward Lewis-Acid Assisted Carbon Dioxide Co-Activation

Carbon dioxide (CO2) is a potent greenhouse gas of environmental concern. Seeking to offer a solution to the "CO2-problem", the chemistry community has turned a focus toward transition metal complexes which can activate, reduce, and convert CO2 into carbon-based products. The design of such systems involves judicious selection of both metal and accompanying donor ligand; in part, these efforts are motivated by biological metalloenzymes that undertake similar transformations. As a design element, metal-ligand cooperativity, which leverages intramolecular interactions between a transition metal and an adjacent secondary ligand site, has been acknowledged as a vitally important component by the CO2 activation community. These systems offer a "push-pull" style of activation where electron density is chaperoned onto CO2 with an accompanying electrophile, such as a Lewis-acid, playing the role of acceptor. This pairing allows for the stabilization of reactive CxHyOz-containing intermediates and can bias CO2 product selectivity. In the laboratory, chemists can test hypotheses and ideas, enabling rationalization of why a given pairing of transition metal/Lewis-acid leads to selective CO2 reduction outcomes. This Concept identifies literature examples and highlights key design properties, allowing interested contributors to design, create, and implement novel systems for productive transformations of a small molecule (CO2) with huge potential impact.

Tailoring Cu-Based Electrocatalysts for Enhanced Electrochemical CO2 Reduction to Alcohols: Structure-Selectivity Relationship

The use of CO2 as a feedstock for the production of carbon-based fuels and value-added chemicals offers a promising route toward carbon neutrality. In this study, two Cu-based electrocatalysts, namely, Cu24/N-C and Cu2/N-C, are successfully prepared by thermal treatment of Cu24 metal-organic polyhedron-loaded zeolitic imidazolate framework-8 (ZIF-8) nanocrystals (Cu24/ZIF-8) and Cu2 dinuclear compound-loaded ZIF-8 nanocrystals (Cu2/ZIF-8), respectively. Extensive structural and compositional analyses were conducted to confirm the formation of Cu nanocluster-loaded N-doped porous carbon supports in both Cu24/N-C and Cu2/N-C and Cu nanoparticles encapsulated by graphitic carbons in Cu2/N-C as well. These two Cu-based electrocatalysts exhibited different behaviors in the electrochemical CO2 reduction reaction (CO2RR). The Cu24/N-C electrocatalyst showed high selectivity for CO production, while Cu2/N-C showed a preference for alcohol generation. The excellent stability of Cu2/N-C over a 30 h continuous electrochemical reduction further highlights its potential for practical applications. The difference in electrocatalytic performance observed in the two catalysts for CO2RR was attributed to distinct catalytic sites associated with Cu nanoclusters and nanoparticles. This research reveals the significance of their structures and compositions for the development of highly selective electrocatalysts for CO2 reduction.

Molecular Environment Modulates CO2 Liberation from Carboxy-Biotin

Carboxy-biotin serves as a coenzyme in certain carboxylases, exhibiting the remarkable capability to transfer a carboxy group to specific substrates. This process is made possible by the presence of biotin, a unique molecule that consists of a sulfur-containing tetrahydrothiophene ring fused to a ureido group. It is covalently attached to the enzyme via a flexible linker, allowing for its functionality. Biotin-dependent carboxylases consist of two distinct domains. The first domain (BC) facilitates biotin carboxylation by utilizing ATP, while the second domain (CT) transfers CO2 to the substrate. The process of ATP-dependent carboxylation using bicarbonate in the biotin carboxylase domain (BC) is well-known. However, the precise mechanism by which CO2 is released in the carboxyltransferase domain (CT) is still not fully understood. We employed advanced computational chemistry methods to investigate the decarboxylation process of carboxy-biotin in various molecular environments and different protonation states. Regardless of the polarity of the molecular surroundings, decarboxylation only occurs spontaneously in the protonated form. To determine the protonation state of biotin in different environments, we established an accurate computational chemistry method for calculating the pKa value of carboxy-biotin, reaching sub-kcal/mol accuracy. Based on our findings, nonpolar environments, such as the active site of the carboxyltransferase domain, have the ability to cause the spontaneous release of CO2 from carboxy-biotin. The CO2 release takes place spontaneously from protonated carboxy-biotin, promoting the carboxylation of substrates.

Substrate Promiscuity of Thermoplasma acidophilum Malic Enzyme for CO2 Fixation Reaction

CO2 fixation technology has gained attention as a method to effectively utilize the abundant CO2 in the atmosphere by converting it into useful chemicals. However, since CO2 is a highly stable molecule, many of the currently developed methods for chemical CO2 fixation require harsh conditions and reactive reagents. The establishment of efficient and sustainable processes is eagerly awaited. In this study, we investigated a biocatalytic process and achieved a carboxylation reaction under mild conditions (37 °C, 0.1 MPa CO2) using a biocatalyst, Thermoplasma acidophilum NADP+-malic enzyme (TaME), and gaseous CO2 by coupling enzymatic coenzyme regeneration. We also demonstrated for the first time that the carboxylation reaction by ME proceeds not only with pyruvate, a natural substrate, but also with 2-ketoglutarate.

Synergistic effects of core-shell poly(ionic liquids)@ZIF-8 nanocomposites for enhancing additive-free CO2 conversion

The present study, for the first time, reports the fabrication of core-shell poly(ionic liquids)@ZIF-8 nanocomposites through a facile in-situ polymerization strategy. These composites exhibited exceptional structural characteristics including high specific surface areas and the integration of high-density Lewis acid/base and nucleophilic active sites. The structure-activity relationship, reusability, and versatility of the poly(ionic liquids)@ZIF-8 composites were investigated for the cycloaddition reaction between CO2 and epoxide. By optimizing the composites structures and their catalytic performance, PIL-Br@ZIF-8(2:1) was identified as an exciting catalyst that exhibits high activity and selectivity in the synthesis of various cyclic carbonates under mild or even atmospheric pressure or simulated flue gas conditions. Moreover, the catalyst demonstrated excellent structural stability while maintaining its catalytic activity throughout multiple usage cycles. By combining DFT calculations, we investigated the transition states and intermediate geometries of the cycloaddition reaction in different coordination microenvironments, thereby proposing a synergistic catalytic mechanism involving multiple active sites.

Photocatalytic CO2 Reduction Using CO2-Binding Enzymes

Novel concepts to utilize carbon dioxide are required to reach a circular carbon economy and minimize environmental issues. To achieve these goals, photo-, electro-, thermal-, and biocatalysis are key tools to realize this, preferentially in aqueous solutions. Nevertheless, catalytic systems that operate efficiently in water are scarce. Here, we present a general strategy for the identification of enzymes suitable for CO2 reduction based on structural analysis for potential carbon dioxide binding sites and subsequent mutations. We discovered that the phenolic acid decarboxylase from Bacillus subtilis (BsPAD) promotes the aqueous photocatalytic CO2 reduction selectively to carbon monoxide in the presence of a ruthenium photosensitizer and sodium ascorbate. With engineered variants of BsPAD, TONs of up to 978 and selectivities of up to 93 % (favoring the desired CO over H2 generation) were achieved. Mutating the active site region of BsPAD further improved turnover numbers for CO generation. This also revealed that electron transfer is rate-limiting and occurs via multistep tunneling. The generality of this approach was proven by using eight other enzymes, all showing the desired activity underlining that a range of proteins is capable of photocatalytic CO2 reduction.

Exploring Emergent Properties in Enzymatic Reaction Networks: Design and Control of Dynamic Functional Systems

The intricate and complex features of enzymatic reaction networks (ERNs) play a key role in the emergence and sustenance of life. Constructing such networks in vitro enables stepwise build up in complexity and introduces the opportunity to control enzymatic activity using physicochemical stimuli. Rational design and modulation of network motifs enable the engineering of artificial systems with emergent functionalities. Such functional systems are useful for a variety of reasons such as creating new-to-nature dynamic materials, producing value-added chemicals, constructing metabolic modules for synthetic cells, and even enabling molecular computation. In this review, we offer insights into the chemical characteristics of ERNs while also delving into their potential applications and associated challenges.

Reactivity of metal dioxo complexes

Metal dioxo chemistry and its diverse reactivity are presented with an emphasis on the mechanisms of reactivity. Work from approximately the last decade is surveyed and organized by metal. In particular, the chemistry of cis-dioxo metal complexes is discussed at length. Reactions are grouped by generic type, including addition across a metal oxo bond, oxygen atom transfer, and radical atom transfer reactions. Attention is given to advances in deoxygenation chemistry, oxidation chemistry, and reductive transformations.

Creating new-to-nature carbon fixation: A guide

Synthetic biology aims at designing new biological functions from first principles. These new designs allow to expand the natural solution space and overcome the limitations of naturally evolved systems. One example is synthetic CO2-fixation pathways that promise to provide more efficient ways for the capture and conversion of CO2 than natural pathways, such as the Calvin Benson Bassham (CBB) cycle of photosynthesis. In this review, we provide a practical guideline for the design and realization of such new-to-nature CO2-fixation pathways. We introduce the concept of "synthetic CO2-fixation", and give a general overview over the enzymology and topology of synthetic pathways, before we derive general principles for their design from their eight naturally evolved analogs. We provide a comprehensive summary of synthetic carbon-assimilation pathways and derive a step-by-step, practical guide from the theoretical design to their practical implementation, before ending with an outlook on new developments in the field.

Artificial Photosynthesis for Regioselective Reduction of NAD(P)+ to NAD(P)H Using Water as an Electron and Proton Source

In photosynthesis, four electrons and four protons taken from water in photosystem II (PSII) are used to reduce NAD(P)+ to produce NAD(P)H in photosystem I (PSI), which is the most important reductant to reduce CO2. Despite extensive efforts to mimic photosynthesis, artificial photosynthesis to produce NAD(P)H using water electron and proton sources has yet to be achieved. Herein, we report the photocatalytic reduction of NAD(P)+ to NAD(P)H and its analogues in a molecular model of PSI, which is combined with water oxidation in a molecular model of PSII. Photoirradiation of a toluene/trifluoroethanol (TFE)/borate buffer aqueous solution of hydroquinone derivatives (X-QH2), 9-mesityl-10-methylacridinium ion, cobaloxime, and NAD(P)+ (PSI model) resulted in the quantitative and regioselective formation of NAD(P)H and p-benzoquinone derivatives (X-Q). X-Q was reduced to X-QH2, accompanied by the oxidation of water to dioxygen under the photoirradiation of a toluene/TFE/borate buffer aqueous solution of [(N4Py)FeII]2+ (PSII model). The PSI and PSII models were combined using two glass membranes and two liquid membranes to produce NAD(P)H using water as an electron and proton source with the turnover number (TON) of 54. To the best of our knowledge, this is the first time to achieve the stoichiometry of photosynthesis, photocatalytic reduction of NAD(P)+ by water to produce NAD(P)H and O2.

Electroenzymatic cascade reaction on a biohybrid boosts the chiral epoxidation reaction

The chiral epoxidation of styrene and its derivatives is an important transformation that has attracted considerable scientific interest in the chemical industry. Herein, we integrate enzymatic catalysis and electrocatalysis to propose a new route for the chiral epoxidation of styrene and its derivatives. Chloroperoxidase (CPO) functionalized with 1-ethyl-3-methylimidazolium bromide (ILEMB) was loaded onto cobalt nitrogen-doped carbon nanotubes (CoN@CNT) to form a biohybrid (CPO-ILEMB/CoN@CNT). H2O2 species were generated in situ through a two-electron oxygen reduction reaction (2e-ORR) at CoN@CNT to initiate the following enzymatic epoxidation of styrene by CPO. CoN@CNT had high electroactivity for the ORR to produce H2O2 at a more positive potential, prohibiting the conversion of FeIII to FeII in the heme of CPO to maintain enzymatic activity. Meanwhile, CoN@CNT could serve as an ideal carrier for the immobilization of CPO-ILEMB. Hence, the coimmobilization of CPO-ILEMB and CoN@CNT could facilitate the diffusion of intermediate H2O2, which achieved 17 times higher efficiency than the equivalent amounts of free CPO-ILEMB in bulk solution for styrene epoxidation. Notably, an enhancement (∼45%) of chiral selectivity for the epoxidation of styrene was achieved.

Valorization of single-carbon chemicals by using carboligases as key enzymes

Single-carbon (C1) biorefinery plays a key role in the consumption of global greenhouse gases and a circular carbon economy. Thereby, we have focused on the valorization of C1 compounds (e.g. methanol, formaldehyde, and formate) into multicarbon products, including bioplastic monomers, glycolate, and ethylene glycol. For instance, methanol, derived from the oxidation of CH4, can be converted into glycolate, ethylene glycol, or erythrulose via formaldehyde and glycolaldehyde, employing C1 and/or C2 carboligases as essential enzymes. Escherichia coli was engineered to convert formate, produced from CO via CO2 or from CO2 directly, into glycolate. Recent progress in the design of biotransformation pathways, enzyme discovery, and engineering, as well as whole-cell biocatalyst engineering for C1 biorefinery, was addressed in this review.

Photosynthesis 2.0: Realizing New-to-Nature CO2-Fixation to Overcome the Limits of Natural Metabolism

Synthetic biology provides opportunities to realize new-to-nature CO2-fixation metabolisms to overcome the limitations of natural photosynthesis. Two different strategies are currently being pursued: One is to realize engineered plants that feature carbon-neutral or carbon-negative (i.e., CO2-fixing) photorespiration metabolism, such as the tatronyl-CoA (TaCo) pathway, to boost CO2-uptake rates of photosynthesis between 20% and 60%. Another (arguably more radical) is to create engineered plants in which natural photosynthesis is fully replaced by an alternative CO2-fixation metabolism, such as the CETCH cycle, which carries the potential to improve CO2 uptake rates between 20% and 200%. These efforts could revolutionize plant engineering by expanding the capabilities of plant metabolism beyond the constraints of natural evolution to create highly improved crops addressing the challenges of climate change in the future.

Paired Electrosynthesis of Formaldehyde Derivatives from CO2 Reduction and Methanol Oxidation

Utilizing CO2 -derived formaldehyde derivatives for fuel additive or polymer synthesis is a promising approach to reduce net carbon dioxide emissions. Existing methodologies involve converting CO2 to methanol by thermal hydrogenation, followed by electrochemical or thermochemical oxidation to produce formaldehyde. Adding to the conventional methanol oxidation pathway, we propose a new electrochemical approach to simultaneously generate formaldehyde derivatives at both electrodes by partial methanol oxidation and the direct reduction of CO2 . To achieve this, a method to directly reduce CO2 to formaldehyde at the cathode is required. Still, it has been scarcely reported previously due to the acidity of the formic acid intermediate and the facile over-reduction of formaldehyde to methanol. By enabling the activation and subsequent stabilization of formic acid and formaldehyde respectively in methanol solvent, we were able to implement a strategy where formaldehyde derivatives were generated at the cathode alongside the anode. Further mechanism studies revealed that protons supplied from the anodic reaction contribute to the activation of formic acid and the stabilization of the formaldehyde product. Additionally, it was found that the cathodic formaldehyde derivative Faradaic efficiency can be further increased through prolonged electrolysis time up to 50 % along with a maximum anodic formaldehyde derivative Faradaic efficiency of 90 %.

Engineering of two thiamine diphosphate-dependent enzymes for the regioselective condensation of C1-formaldehyde into C4-erythrulose

A number of carboligases, which catalyze condensation of C1- and/or C2-aldehydes into multi-carbon products, have been reported. However, their catalytic activities and/or regioselectivities remained rather low. Thereby, this study has focused on engineering of C1 and C2 carboligases for the regioselective condensation of C1-formaldehyde into C4-erythrulose via C2-glycolaldehyde. The crystal structure of the glyoxylate carboligase from Escherichia coli (EcGCL) was elucidated in complex with glycolaldehyde. A structure-guided rationale generated several mutants, one of whose catalytic activity reached 15.6 M-1·s-1, almost 10 times greater than the wild-type enzyme. Another variant (i.e., EcGCL_R484M/N283Q/L478M/M488L/R284K) has shown significantly increased stability to the glycolaldehyde toxicity, enabling production of glycolaldehyde to 31 mM from 75 mM formaldehyde (conversion: 83 %). Besides, the E1 subunit of α-ketoglutarate dehydrogenase complex from Vibrio vulnificus (VvSucA) was engineered as a regiospecific C2 carboligase for condensation of glycolaldehyde into erythrulose. The combination of EcGCL_R484M/N283Q/L478M/M488L/R284K and VvSucA_K228L led to the cascade production of erythrulose to 8 mM from 90 mM formaldehyde via glycolaldehyde without byproduct formation. This study will contribute to valorization of C1 gases into industrially relevant multi-carbon products in an environment-friendly way.

Conformational Dynamics of the Most Efficient Carboxylase Contributes to Efficient CO2 Fixation

Crotonyl-CoA carboxylase/reductase (Ccr) is one of the fastest CO2 fixing enzymes and has become part of efficient artificial CO2-fixation pathways in vitro, paving the way for future applications. The underlying mechanism of its efficiency, however, is not yet completely understood. X-ray structures of different intermediates in the catalytic cycle reveal tetramers in a dimer of dimers configuration with two open and two closed active sites. Upon binding a substrate, this active site changes its conformation from the open state to the closed state. It is challenging to predict how these coupled conformational changes will alter the CO2 binding affinity to the reaction's active site. To determine whether the open or closed conformations of Ccr affect binding of CO2 to the active site, we performed all-atom molecular simulations of the various conformations of Ccr. The open conformation without a substrate showed the highest binding affinity. The CO2 binding sites are located near the catalytic relevant Asn81 and His365 residues and in an optimal position for CO2 fixation. Furthermore, they are unaffected by substrate binding, and CO2 molecules stay in these binding sites for a longer time. Longer times at these reactive binding sites facilitate CO2 fixation through the nucleophilic attack of the reactive enolate in the closed conformation. We previously demonstrated that the Asn81Leu variant cannot fix CO2. Simulations of the Asn81Leu variant explain the loss of activity through the removal of the Asn81 and His365 binding sites. Overall, our findings show that the conformational dynamics of the enzyme controls CO2 binding. Conformational changes in Ccr increase the level of CO2 in the open subunit before the substrate is bound, the active site closes, and the reaction starts. The full catalytic Ccr cycle alternates among CO2 addition, conformational change, and chemical reaction in the four subunits of the tetramer coordinated by communication between the two dimers.

Machine Learning-Supported Enzyme Engineering toward Improved CO2-Fixation of Glycolyl-CoA Carboxylase

Glycolyl-CoA carboxylase (GCC) is a new-to-nature enzyme that catalyzes the key reaction in the tartronyl-CoA (TaCo) pathway, a synthetic photorespiration bypass that was recently designed to improve photosynthetic CO2 fixation. GCC was created from propionyl-CoA carboxylase (PCC) through five mutations. However, despite reaching activities of naturally evolved biotin-dependent carboxylases, the quintuple substitution variant GCC M5 still lags behind 4-fold in catalytic efficiency compared to its template PCC and suffers from futile ATP hydrolysis during CO2 fixation. To further improve upon GCC M5, we developed a machine learning-supported workflow that reduces screening efforts for identifying improved enzymes. Using this workflow, we present two novel GCC variants with 2-fold increased carboxylation rate and 60% reduced energy demand, respectively, which are able to address kinetic and thermodynamic limitations of the TaCo pathway. Our work highlights the potential of combining machine learning and directed evolution strategies to reduce screening efforts in enzyme engineering.

Current status of carbon monoxide dehydrogenases (CODH) and their potential for electrochemical applications

Anthropogenic carbon dioxide (CO2) levels are rising to alarming concentrations in earth's atmosphere, causing adverse effects and global climate changes. In the last century, innovative research on CO2 reduction using chemical, photochemical, electrochemical and enzymatic approaches has been addressed. In particular, natural CO2 conversion serves as a model for many processes and extensive studies on microbes and enzymes regarding redox reactions involving CO2 have already been conducted. In this review we focus on the enzymatic conversion of CO2 to carbon monoxide (CO) as the chemical conversion downstream of CO production render CO particularly attractive as a key intermediate. We briefly discuss the different currently known natural autotrophic CO2 fixation pathways, focusing on the reversible reaction of CO2, two electrons and protons to CO and water, catalyzed by carbon monoxide dehydrogenases (CODHs). We then move on to classify the different type of CODHs, involved catalyzed chemical reactions and coupled metabolisms. Finally, we discuss applications of CODH enzymes in photochemical and electrochemical cells to harness CO2 from the environment transforming it into commodity chemicals.

Mechanism of CO2 Reduction to Methanol with H2 on an Iron(II)-scorpionate Catalyst

CO2 utilization is an important process in the chemical industry with great environmental power. In this work we show how CO2 and H2 can be reacted to form methanol on an iron(II) center and highlight the bottlenecks for the reaction and what structural features of the catalyst are essential for efficient turnover. The calculations predict the reactions to proceed through three successive reaction cycles that start with heterolytic cleavage of H2 followed by sequential hydride and proton transfer processes. The H2 splitting process is an endergonic process and hence high pressures will be needed to overcome this step and trigger the hydrogenation reaction. Moreover, H2 cleavage into a hydride and proton requires a metal to bind hydride and a nearby source to bind the proton, such as an amide or pyrazolyl group, which the scorpionate ligand used here facilitates. As such the computations highlight the non-innocence of the ligand scaffold through proton shuttle from H2 to substrate as an important step in the reaction mechanism.

Changing the Electron Acceptor Specificity of Rhodobacter capsulatus Formate Dehydrogenase from NAD+ to NADP. Int J Mol Sci 2023;24:16067. [PMID: 38003259 PMCID: PMC10671435 DOI: 10.3390/ijms242216067] [Citation(s) in RCA: 0] [Impact Index Per Article: 0]

Formate dehydrogenases catalyze the reversible oxidation of formate to carbon dioxide. These enzymes play an important role in CO2 reduction and serve as nicotinamide cofactor recycling enzymes. More recently, the CO2-reducing activity of formate dehydrogenases, especially metal-containing formate dehydrogenases, has been further explored for efficient atmospheric CO2 capture. Here, we investigate the nicotinamide binding site of formate dehydrogenase from Rhodobacter capsulatus for its specificity toward NAD+ vs. NADP+ reduction. Starting from the NAD+-specific wild-type RcFDH, key residues were exchanged to enable NADP+ binding on the basis of the NAD+-bound cryo-EM structure (PDB-ID: 6TG9). It has been observed that the lysine at position 157 (Lys157) in the β-subunit of the enzyme is essential for the binding of NAD+. RcFDH variants that had Glu259 exchanged for either a positively charged or uncharged amino acid had additional activity with NADP+. The FdsBL279R and FdsBK276A variants also showed activity with NADP+. Kinetic parameters for all the variants were determined and tested for activity in CO2 reduction. The variants were able to reduce CO2 using NADPH as an electron donor in a coupled assay with phosphite dehydrogenase (PTDH), which regenerates NADPH. This makes the enzyme suitable for applications where it can be coupled with other enzymes that use NADPH.

Direct Biocatalytic Processes for CO2 Capture as a Green Tool to Produce Value-Added Chemicals

Direct biocatalytic processes for CO₂ capture and transformation in value-added chemicals may be considered a useful tool for reducing the concentration of this greenhouse gas in the atmosphere. Among the other enzymes, carbonic anhydrase (CA) and formate dehydrogenase (FDH) are two key biocatalysts suitable for this challenge, facilitating the uptake of carbon dioxide from the atmosphere in complementary ways. Carbonic anhydrases accelerate CO₂ uptake by promoting its solubility in water in the form of hydrogen carbonate as the first step in converting the gas into a species widely used in carbon capture storage and its utilization processes (CCSU), particularly in carbonation and mineralization methods. On the other hand, formate dehydrogenases represent the biocatalytic machinery evolved by certain organisms to convert CO₂ into enriched, reduced, and easily transportable hydrogen species, such as formic acid, via enzymatic cascade systems that obtain energy from chemical species, electrochemical sources, or light. Formic acid is the basis for fixing C₁-carbon species to other, more reduced molecules. In this review, the state-of-the-art of both methods of CO₂ uptake is assessed, highlighting the biotechnological approaches that have been developed using both enzymes.

Artificial Photosynthesis: Current Advancements and Future Prospects

Artificial photosynthesis is a technology with immense potential that aims to emulate the natural photosynthetic process. The process of natural photosynthesis involves the conversion of solar energy into chemical energy, which is stored in organic compounds. Catalysis is an essential aspect of artificial photosynthesis, as it facilitates the reactions that convert solar energy into chemical energy. In this review, we aim to provide an extensive overview of recent developments in the field of artificial photosynthesis by catalysis. We will discuss the various catalyst types used in artificial photosynthesis, including homogeneous catalysts, heterogeneous catalysts, and biocatalysts. Additionally, we will explore the different strategies employed to enhance the efficiency and selectivity of catalytic reactions, such as the utilization of nanomaterials, photoelectrochemical cells, and molecular engineering. Lastly, we will examine the challenges and opportunities of this technology as well as its potential applications in areas such as renewable energy, carbon capture and utilization, and sustainable agriculture. This review aims to provide a comprehensive and critical analysis of state-of-the-art methods in artificial photosynthesis by catalysis, as well as to identify key research directions for future advancements in this field.