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At least 19 records
All sourcesNASA NTRSDOE OSTI
DOE OSTI2023

Combinatorial gene inactivation of aldehyde dehydrogenases mitigates aldehyde oxidation catalyzed by E. coli resting cells

Aldehydes are attractive chemical targets both as end products in the flavors and fragrances industry and as synthetic intermediates due to their propensity for C–C bond formation. Here, in this study, we identify and address unexpected oxidation of a model collection of aromatic aldehydes, including many that originate from biomass degradation. When diverse aldehydes are supplemented to E. coli cells grown under aerobic conditions, as expected they are either reduced by the wild-type MG1655 strain or stabilized by a strain engineered for reduced aromatic aldehyde reduction (the E. coli RARE strain). Surprisingly, when these same aldehydes are supplemented to resting cell preparations of either E. coli strain, under many conditions we observe substantial oxidation. By performing combinatorial inactivation of six candidate aldehyde dehydrogenase genes in the E. coli genome using multiplexed automatable genome engineering (MAGE), we demonstrate that this oxidation can be substantially slowed, with greater than 50% retention of 6 out of 8 aldehydes when assayed 4 h after their addition. Given that our newly engineered strain exhibits reduced oxidation and reduction of aromatic aldehydes, we dubbed it the E. coli ROAR strain. We applied the new strain to resting cell biocatalysis for two kinds of reactions – the reduction of 2-furoic acid to furfural and the condensation of 3-hydroxybenzaldehyde and glycine to form a non-standard β-hydroxy-α-amino acid. In each case, we observed substantial improvements in product titer 20 h after reaction initiation (9-fold and 10-fold, respectively). Moving forward, the use of this strain to generate resting cells should allow aldehyde product isolation, further enzymatic conversion, or chemical reactivity under cellular contexts that better accommodate aldehyde toxicity.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2024

Reductive Dynamic and Static Excited State Quenching of a Homoleptic Ruthenium Complex Bearing Aldehyde Groups

A new homoleptic Ru polypyridyl complex bearing two aldehyde groups on each bipyridine ligand, [Ru(dab) 3 ](PF 6 ) 2 , where dab is 4,4′-dicarbaldehyde-2,2′-bipyridine, was synthesized, characterized, and utilized for iodide photo-oxidation studies. In acetonitrile (CH 3 CN) solution, the complex displayed an intense metal-to-ligand charge transfer (MLCT) absorbance maximum at 475 nm (ε = 22,000 M –1 cm –1 ) and an infrared (IR) band at 1712 cm –1 assigned to the pendent aldehyde groups. Visible light excitation in air-saturated solution resulted in room temperature photoluminescence (PL) with a maximum at 675 nm, a quantum yield, ϕ PL = 0.048, and an excited state lifetime, τ ο = 440 ns, from which radiative and nonradiative relaxation rate constants were extracted, k r = 9.1 × 10 4 s –1 and knr = 1.8 × 10 6 s –1 . Pulsed visible light excitation yielded transient UV–vis and IR absorption spectra consistent with an MLCT excited state; relaxation occurred with the maintenance of two isosbestic points in the visible region, and a lifetime that agreed with that measured by time-resolved PL. Cyclic voltammetry studies in a CH 3 CN solution with 0.1 M TBAPF 6 electrolyte revealed a quasi-reversible oxidation, E°(Ru III/II ) = +1.25 V vs. Fc +/0 , and three sequential one-electron reductions at −1.10, −1.25, and −1.54 V vs. Fc +/0 . Here, an excited state reduction potential of E°(Ru *2+/+ ) = +0.89 V vs. Fc +/0 was estimated with the Rehm–Weller expression. Titration of tetrabutylammonium iodide, TBAI, into a CD 3 CN solution of [Ru(dab) 3 ](PF 6 ) 2 resulted in significant shifts in the aldehyde H atom and 3,3′-biypridyl resonances that were analyzed with a 1:1 equilibrium model, from which K eq = 460 M –1 was extracted, increasing to 5800 M –1 when the solvent was changed to acetone-d 6 . Iodide titrations resulted in a significant quenching of the [Ru(dab) 3 ] *2+ lifetime and quantum yield in both CH 3 CN and acetone solvents. In CH 3 CN, the quenching was mainly dynamic and well described by the Stern–Volmer model, from which a quenching rate constant, k q , of 4.5 × 10 10 M –1 s –1 and an equilibrium constant, K eq , of 8.3 × 10 3 M –1 were obtained. In acetone, the static quenching pathway by iodide was greatly enhanced, with a K eq of 1.2 × 10 4 M –1 and a higher k q of 9.2 × 10 10 M –1 s –1 .

Aldehydes↗
DOE OSTI2021

In-depth understanding of molecular mechanisms of aldehyde toxicity to engineer robust Saccharomyces cerevisiae

Aldehydes are ubiquitous electrophilic compounds that ferment microorganisms including Saccharomyces cerevisiae encounter during the fermentation processes to produce food, fuels, chemicals, and pharmaceuticals. Aldehydes pose severe toxicity to the growth and metabolism of the S. cerevisiae through a variety of toxic molecular mechanisms, predominantly via damaging macromolecules and hampering the production of targeted compounds. Compounds with aldehyde functional groups are far more toxic to S. cerevisiae than all other functional classes, and toxic potency depends on physicochemical characteristics of aldehydes. The yeast synthetic biology community established a design–build–test–learn framework to develop S. cerevisiae cell factories to valorize the sustainable and renewable biomass, including the lignin-derived substrates. However, thermochemically pretreated biomass-derived substrate streams contain diverse aldehydes (e.g., glycolaldehyde and furfural), and biological conversions routes of lignocellulosic compounds consist of toxic aldehyde intermediates (e.g., formaldehyde and methylglyoxal), and some of the high-value targeted products have aldehyde functional group (e.g., vanillin and benzaldehyde). Numerous studies comprehensively characterized both single and additive effects of aldehyde toxicity via systems biology investigations, and novel molecular approaches have been discovered to overcome the aldehyde toxicity. Based on those novel approaches, researchers successfully developed synthetic yeast cell factories to convert lignocellulosic substrates to valuable products, including aldehyde compounds. Here, we highlight the salient relationship of physicochemical charac- teristics and molecular toxicity of aldehydes, the molecular detoxification and macromolecules protection mechanisms of aldehydes, and the advances of engineering robust S. cerevisiae against complex mixtures of aldehyde inhibitors.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

The plant pathogen enzyme AldC is a long-chain aliphatic aldehyde dehydrogenase

Aldehyde dehydrogenases are versatile enzymes that serve a range of biochemical functions. Although traditionally considered metabolic housekeeping enzymes because of their ability to detoxify reactive aldehydes, like those generated from lipid peroxidation damage, the contributions of these enzymes to other biological processes are widespread. For example, the plant pathogen Pseudomonas syringae strain PtoDC3000 uses an indole-3-acetaldehyde dehydrogenase to synthesize the phytohormone indole-3-acetic acid to elude host responses. In this work we investigate the biochemical function of AldC from PtoDC3000. Analysis of the substrate profile of AldC suggests that this enzyme functions as a long-chain aliphatic aldehyde dehydrogenase. The 2.5 Å resolution X-ray crystal of the AldC C291A mutant in a dead-end complex with octanal and NAD + reveals an apolar binding site primed for aliphatic aldehyde substrate recognition. Functional characterization of site-directed mutants targeting the substrate- and NAD(H)-binding sites identifies key residues in the active site for ligand interactions, including those in the “aromatic box” that define the aldehyde-binding site. Overall, this study provides molecular insight for understanding the evolution of the prokaryotic aldehyde dehydrogenase superfamily and their diversity of function.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Reactivity of net-zero carbon alcohol fuels and their corresponding aldehyde intermediates on PGM-based commercial oxidation catalysts for lean-burn emissions control

Alcohol net-zero carbon fuels will play a significant role in decarbonization of the hard-to-electrify transportation sectors. However, the combustion process in alcohol-fueled engines generate toxic aldehydes. For commercialization of net-zero carbon fuels on engines, compliance with the stringent U.S. EPA regulations is necessary. Here, this contribution focuses on reactivity of alcohols and aldehydes on commercial diesel oxidation catalysts (DOC) to inform selection of future net-zero carbon fuels. Alcohol (and aldehyde) light-off temperatures were measured on aged DOCs under full synthetic engine-exhaust conditions. Methanol was the most reactive, while ethanol completely oxidized at higher temperatures. Alcohols typically formed less reactive aldehyde intermediates. DRIFTS revealed strongly adsorbing surface formates and acetates during methanol and ethanol oxidation, respectively, resulting in inhibition effects. Preliminary alcohol oxidation mechanisms combining flow reactor and DRIFTS observations are presented. Aldehydes inhibited CO oxidation. Minimal N 2 O formation was observed for the alcohols investigated.

Alcohol oxidation↗
DOE OSTI2025

An electron-bifurcating “plug” to a protein nanowire in tungsten-dependent aldehyde detoxification

Members of the tungsten-containing oxidoreductase (WOR) family, which contain a tungstopyranopterin (Tuco) cofactor, are typically either monomeric (WorL) or heterodimeric (WorLS). These enzymes oxidize aldehydes to the corresponding acids while reducing the redox protein ferredoxin. They have been structurally characterized mainly using WORs from hyperthermophilic archaea. The WORs of some bacteria contain three additional subunits of the BfuABC family and these chimeric WorABCSL enzymes catalyze an electron-bifurcating reaction in which aldehyde oxidation is coupled to the simultaneous reduction of ferredoxin and nicotinamide adenine dinucleotide. In human gut microbes, electron bifurcation by WorABSL is proposed to enable the detoxification of aldehydes generated from cooked foods and in the tungstocentric production of beneficial short chain fatty acids from lactate, potentially impacting health. Herein we present the high-resolution cryogenic electron microscopy (cryo-EM) structure of the WorABCSL purified from the bacteriumAcetomicrobium mobile.The structure reveals a surprising 1:3 stoichiometry between WorABC and WorSL, with the WorSL units forming a nanowire-like architecture leading from three Tuco-containing catalytic sites in WorL via strings of multiple iron-sulfur clusters in WorS to a single bifurcating WorABC core. Our structure uncovers a distinct domain arrangement that links three Tuco-dependent aldehyde oxidation sites with the bifurcation process and potentially facilitates environmental aldehyde oxidation.

Science & Technology - Other Topics↗
DOE OSTI2021

Reactions of NO 3 with aromatic aldehydes: gas-phase kinetics and insights into the mechanism of the reaction

Rate coefficients for the reaction of NO3 radicals with a series of aromatic aldehydes were measured in a 7300 L simulation chamber at ambient temperature and pressure by relative and absolute methods. The rate coefficients for benzaldehyde (BA), ortho-tolualdehyde (O-TA), meta-tolualdehyde (M-TA), para-tolualdehyde (P-TA), 2,4-dimethyl benzaldehyde (2,4-DMBA), 2,5-dimethyl benzaldehyde (2,5-DMBA) and 3,5-dimethyl benzaldehyde (3,5-DMBA) were k 1 = 2.6 ± 0.3, k 2 = 8.7 ± 0.8, k 3 = 4.9 ± 0.5, k 4 = 4.9 ± 0.4, k 5 = 15.1 ± 1.3, k 6 = 12.8 ± 1.2 and k 7 = 6.2 ± 0.6, respectively, in the units of 10 -15 cm 3 molec. -1 s -1 at 298 ± 2 K. The rate coefficient k 13 for the reaction of the NO 3 radical with deuterated benzaldehyde (benzaldehyde-d1) was found to be half that of k 1 . The end product of the reaction in an excess of NO 2 was measured to be C 6 H 5 C(O)O 2 NO 2 . Furthermore, theoretical calculations of aldehydic bond energies and reaction pathways indicate that the NO 3 radical reacts primarily with aromatic aldehydes through the abstraction of an aldehydic hydrogen atom. The atmospheric implications of the measured rate coefficients are briefly discussed.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Simultaneous electrocatalytic hydrogenation of aldehydes and phenol over carbon-supported metals

Electrocatalytic hydrogenation of furfural, benzaldehyde, and phenol was studied on carbon-supported Rh, Ru, Pd, and Cu catalysts. All metals were active for hydrogenation of the carbonyl group in furfural and benzaldehyde, but only Rh/C was active for phenol hydrogenation. The intrinsic activities for furfural and benzaldehyde conversion were Pd/C < Ru/C ? Rh/C < Cu/C and Ru/C < Rh/C < Pd/C < Cu/C, respectively. While the trend in furfural hydrogenation remained the same in the presence of phenol, the trend in benzaldehyde hydrogenation in the presence of phenol changed to Rh/C < Ru/C < Pd/C < Cu/C. The Faradaic efficiencies for hydrogenation of both furfural (in the 10–40% range) and benzaldehyde (in the 45–100% range) followed the trend: Cu/C < Rh/C < Ru/C < Pd/C. When phenol and an aldehyde were present in the reactant solution, phenol hydrogenation (only observed on Rh) was suppressed. In contrast, enhancements in the rates of carbonyl reduction were observed for both aldehydes in presence of phenol. Such enhancements depend on both the aldehyde and the metal catalyst. The enhancing factors for hydrogenation of furfural and benzaldehyde were in the 1.5–2 and 2–4 ranges, respectively. We conclude that intermolecular interactions between adsorbed phenol and the aldehydes is a general phenomenon that can potentially enhance the rates of carbonyl hydrogenation. This work highlights co-adsorption effects that pose both challenges and advantages for electrocatalytic reduction of organic compounds.

Electrocatalytic hydrogenation, metal catalysts, p↗
DOE OSTI2020

Guidelines to Achieving High Selectivity for the Hydrogenation of α,β-Unsaturated Aldehydes with Bimetallic and Dilute Alloy Catalysts: A Review

Selective hydrogenation of unsaturated aldehydes to unsaturated alcohols is a challenging class of reactions, yielding valuable intermediates for the production of pharmaceuticals, perfumes, and flavorings. On monometallic heterogeneous catalysts, the formation of the unsaturated alcohols is thermodynamically disfavored over the saturated aldehydes. Hence, new catalysts are required to achieve the desired selectivity. In this work, the literature of three major research areas in catalysis is integrated as a step toward establishing the guidelines for enhancing the selectivity: reactor studies of complex catalyst materials at operating temperature and pressure, surface science studies of crystalline surfaces in ultrahigh vacuum, and first-principles modeling using density functional theory calculations. Aggregate analysis shows that bimetallic and dilute alloy catalysts significantly enhance the selectivity to the unsaturated alcohols compared to monometallic catalysts. This comprehensive review focuses primarily on the role of different metal surfaces as well as the factors that promote the adsorption of the unsaturated aldehyde via its C=O bond, most notably by electronic modification of the surface and formation of the electrophilic sites. Furthermore, challenges, gaps, and opportunities are identified to advance the rational design of efficient catalysts for this class of reactions, including the need for systematic studies of catalytic processes, theoretical modeling of complex materials, and model studies under ambient pressure and temperature.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2024

Impacts of Hydrogen Bond Donor Structures in Phenolic Aldehyde Deep Eutectic Solvents on Pretreatment Efficiency

As a green solvent for biomass processing, deep eutectic solvents (DESs) have shown effectiveness in biomass processing. Here, in this study, phenolic aldehydes with different numbers of methoxy groups, including 4-hydroxybenzaldehyde (HBA, no methoxy), vanillin (VA, monomethoxy), and syringaldehyde (SA, dimethoxy) were employed to synthesize DESs with choline chloride (ChCl). The presence of methoxy groups in the hydrogen bond donor structure affected DES properties, as well as biomass pretreatment performance. The high thermal stability of phenolic aldehyde DESs was shown with over 225 °C onset temperature. The hydrogen bond donor with one aldehyde and one hydroxyl group at the para position without a methoxy group (ChCl-HBA) showed the highest xylan removal and delignification, reaching 59.3 and 88.0%, respectively, leading to the highest enzymatic hydrolysis yield. Sonication after pretreatment further enhanced the hydrolysis yields, achieving 83.3% glucan conversion and 50.1% xylan conversion. In the lignin-rich fraction, the recovered lignin showed a low weight–average molecular weight under 2100 g/mol with a relatively uniform molecular weight dispersity below 1.5. This study provides insights into how the chemical structure of hydrogen bond donors in DESs affects biomass processing and paves the way for designing effective lignin-derived DES in future biorefinery processes.

09 BIOMASS FUELS↗
DOE OSTI2025

Chemistry of Sugar Formation in the Gas Phase: Following the Activated Aldehyde

Sugars are produced by living organisms, and are required building blocks for life as we know it, which raises the foundational question of how sugars formed in a prebiotic environment. The abiotic formose reaction produces sugars from formaldehyde, but our understanding of its initiation step remains murky, with chemists invoking the concept of an “activated aldehyde” to seed this reaction. Singlet hydroxycarbenes, high-energy isomers of aldehydes, were recently reported to facilitate sugar formation under cold, nonaqueous conditions relevant to interstellar environments. Here, we generate singlet methylhydroxycarbene ( 1 CH 3 –C̈–OH) from the photodissociation of pyruvic acid and experimentally measure its gas-phase reaction with d 4 -acetaldehyde using multiplexed photoionization mass spectrometry. The C 4 H 4 D 4 O 2 isomer d 4 -acetoin is the sole product, which we kinetically link to the reactant CH 3 –C̈–OH, and attribute to a carbonyl-ene formation mechanism. We see no evidence of 3-hydroxybutanal, the C–H insertion product expected in carbene chemistry. Using automated exploration we calculate stationary points on the potential energy surface and report master equation rate coefficients from T = 20–600 K, providing quantitative kinetics of this fast reaction for use in chemical models. The prereactive complex in this reaction is stabilized by both hydrogen bonding and electrophilic carbene C═O interactions. These effects create a short-range dynamical bottleneck for the reaction besides the long- and midrange barrierless bottlenecks. Combined with recent reports of 1 HC̈OH production from methanol photodissociation and pyruvic acid production in cold irradiated ices, this work provides evidence that singlet hydroxycarbene + aldehyde chemistry is a feasible path to prebiotic sugar formation.

aldehydes↗
DOE OSTI2023

Aldehyde and Ketone Hydroboration Mediated by a Heterogeneous Single–Site Molybdenum–Dioxo Catalyst: Scope and Mechanistic Implications

Efficient hydroboration of aldehydes and ketones is demonstrated using a single-site MoO 2 catalyst supported on activated carbon. Under mild conditions with low catalytic loadings, the reaction exhibits chemoselectivity towards carbonyl reduction over halides, alkene, alkyne, nitrile, and ester groups, affording high yields of desired products. Furthermore, competition studies between aldehyde and ketone reduction using HBpin and HBcat indicate that HBpin preferably functionalizes aldehydes, while HBcat can functionalize either substrate under specific conditions. Mechanistic studies suggest that the reaction proceeds via the initial formation of a molybdenum-hydride species upon B–H activation and subsequent molybdenum-alkoxide species upon carbonyl activation by the Mo center. The experimental activation energy of 14.3 kcal/mol alignssatisfactorily with the DFT computed ΔH ≠ of 18.7 kcal/mol, further supporting the proposed mechanism. Combined experimental/computational analyses reveal that excess HBpin can possibly deactivate the catalyst. The presence of excess benzaldehyde efficiently mitigates deactivation by HBpin, providing significantly higher catalyst recyclability. Altogether, this non-toxic, air- and moisture-stable, active, and selective catalyst demonstrates significant potential for green processes.

08 HYDROGEN↗
DOE OSTI2025

The structural basis for the broad aldehyde specificity of the aminoaldehyde dehydrogenase PauC from the human pathogen Pseudomonas aeruginosa

Abstract Despite significant differences in size and formal charge, the aldehyde dehydrogenasePaPauC (PA5312) fromPseudomonas aeruginosaPAO1 efficiently catalyzes the NAD + ‐dependent oxidation of the aminoaldehydes formed in polyamines degradation. We report here thatPaPauC also oxidizes 4‐guanidinebutyraldehyde, formed in one arginine degradation pathway, trimethylaminobutyraldehyde, of unknown metabolic origin, and indole‐3‐acetaldehyde, a precursor of the plant growth‐promoting hormone indoleacetic acid.PaPauC has been proposed as a potential target for combatingP. aeruginosa. However, understanding its structure–function relationships, crucial for developing specific inhibitors, is lacking. Using X‐ray crystallography, we identified the structural characteristics that determinePaPauC broad aldehyde specificity: a spacious aldehyde‐entrance tunnel and six active‐site residues. Docking simulations, site‐directed mutagenesis, and kinetic analyses support the interactions of Lys479 with glutamylated aminoaldehydes; Phe169, Trp176, and Phe467 with amino and guanidinium groups through cation–π interactions and with the indole group via NH–π and CH–π interactions; Asp459 with amino and indole groups; and Thr303 with amide and guanidinium groups. Exploiting the distinctive structural features of thePaPauC active site could aid in developing specific inhibitors to combatP. aeruginosainfections in humans and animals, as well as in preventing its colonization of plants, which are abundantP. aeruginosareservoirs and, therefore, a significant source of human infections.

Biochemistry & Molecular Biology↗
DOE OSTI2022

A multi-pronged evaluation of aldehyde-based tripeptidyl main protease inhibitors as SARS-CoV-2 antivirals

As an essential enzyme of SARS-CoV-2, the COVID-19 pathogen, main protease (M Pro ) is a viable target to develop antivirals for the treatment of COVID-19. By varying chemical compositions at both P2 and P3 positions and the N-terminal protection group, we synthesized 18 tripeptidyl M Pro inhibitors that contained also an aldehyde warhead and β-(S-2-oxopyrrolidin-3-yl)-alaninal at the P1 position. Systematic characterizations of these inhibitors were conducted, including their in vitro enzymatic inhibition potency, X-ray crystal structures of their complexes with M Pro , their inhibition of M Pro transiently expressed in 293T cells, and cellular toxicity and SARS-CoV-2 antiviral potency of selected inhibitors. These inhibitors have a large variation of determined in vitro enzymatic inhibition IC 50 values that range from 4.8 to 650 nM. Here, the determined in vitro enzymatic inhibition IC 50 values reveal that relatively small side chains at both P2 and P3 positions are favorable for achieving high in vitro M Pro inhibition potency, the P3 position is tolerable toward unnatural amino acids with two alkyl substituents on the α-carbon, and the inhibition potency is sensitive toward the N-terminal protection group. X-ray crystal structures of M Pro bound with 16 inhibitors were determined. In all structures, the M Pro active site cysteine interacts covalently with the aldehyde warhead of the bound inhibitor to form a hemithioacetal that takes an S configuration. For all inhibitors, election density around the N-terminal protection group is weak indicating possible flexible binding of this group to M Pro . In M Pro , large structural variations were observed on residues N142 and Q189. Unlike their high in vitro enzymatic inhibition potency, most inhibitors showed low potency to inhibit M Pro that was transiently expressed in 293T cells. Inhibitors that showed high potency to inhibit M Pro transiently expressed in 293T cells all contain O-tert-butyl-threonine at the P3 position. These inhibitors also exhibited relatively low cytotoxicity and high antiviral potency. Overall, our current and previous studies indicate that O-tert-butyl-threonine at the P3 site is a key component to achieve high cellular and antiviral potency for tripeptidyl aldehyde inhibitors of M Pro .

60 APPLIED LIFE SCIENCES↗
DOE OSTI2023

Optical detection of alcohols with a Cu($\tiny{I}$)HETPHEN complex by reversible aldehyde to hemiacetal conversion

A heteroleptic copper(I) bis(phenanthroline) complex with aldehyde groups at the 4,7 positions of the phenanthroline ligand was synthesized. Here, the complex is responsive to alcohol, resulting in a distinct colour change caused by the facile reaction of the aldehyde group with alcohol, forming a hemiacetal product. The aldehyde species can be regenerated after heating the intermediate at 80 °C for 10 minutes, demonstrating the reusability of the complex for alcohol detection. This work presents a new strategy for applying transition metal complexes in small molecule sensing by installing functional groups in the secondary coordination sphere which reversibly react with analytes.

36 MATERIALS SCIENCE↗