Deuterium Labeling Research Articles

Mechanism of Z-Selective Allylic Functionalization via Thianthrenium Salts.

A detailed mechanistic study of the Z-selective allylic functionalization via thianthrenium salts is presented. Kinetic analyses, deuterium labeling experiments, and computational methods are used to rationalize the observed reactivity and selectivity. We find that the reaction proceeds via a rate-determining and stereodetermining allylic deprotonation of an alkenylthianthrenium species. The Z-configuration of the resultant allylic ylide is translated into the Z-allylic amine product through a sequence of subsequent fast and irreversible steps: protonation to form a Z-allylic thianthrenium electrophile and then regioselective substitution by the nucleophile. In the stereodetermining deprotonation step, computational studies identified a series of stabilizing nonbonding interactions in the Z-alkene-forming transition state that contribute to the stereoselectivity.

Chemoselective Hydrogenation of α,β-Unsaturated Ketones Catalyzed by a Manganese(I) Hydride Complex.

Here, we report the chemoselective hydrogenation of α,β-unsaturated ketones catalyzed by a well-defined Mn(I) PCNHCP pincer complex [(PCNHCP)Mn(CO)2H] (1). The reaction is compatible with a wide variety of functional groups that include halides, esters, amides, nitriles, nitro, alkynes, and alkenes, and for most substrates occurs readily at ambient hydrogen pressure (1-2 bar). Mechanistic studies and deuterium labeling experiments reveal a non-cooperative mechanism, which is further discussed in this report.

Efficient and economic protein labeling for NMR in mammalian expression systems: Application to a preT-cell and T-cell receptor protein.

Protein nuclear magnetic resonance(NMR) spectroscopy relies on the ability to isotopically label polypeptides, which is achieved through heterologous expression in various host organisms. Most commonly, Escherichia coli is employed by leveraging isotopically substituted ammonium and glucose to uniformly label proteins with 15N and 13C, respectively. Moreover, E. coli can grow and express proteins in uniformly deuterium-substituted water (D2O), a strategy useful for experiments targeting high molecular weight proteins. Unfortunately, many proteins, particularly those requiring specific posttranslational modifications like disulfide bonding or glycosylation for proper folding and/or function, cannot be readily expressed in their functional forms using E. coli-based expression systems. One such class of proteins includes T-cell receptors and their related preT-cell receptors. In this study, we present an expression system for isotopic labeling of proteins using a nonadherent human embryonic kidney cell line, Expi293F, and a specially designed media. We demonstrate the application of this platform to the β subunit common to both receptors. In addition, we show that this expression system and media can be used to specifically label amino acids Phe, Ile, Val, and Leu in this system, utilizing an amino acid-specific labeling protocol that allows targeted incorporation at high efficiency without significant isotopic scrambling. We demonstrate that this system can also be used to express proteins with fluorinated amino acids. We were routinely able to obtain an NMR sample with a concentration of 200 μM from 30 mL of culture media, utilizing less than 20 mg of the labeled amino acids.

Enantioselective Synthesis of Phosphine Boranes via Crystallization-Induced Dynamic Resolution of Lithiated Intermediate by Understanding the Underlying Epimerization Process.

Described herein is the successful crystallization-induced dynamic resolution (CIDR) of an α-lithiated phosphine borane utilizing the easily accessible and inexpensive ligand (R,R)-TMCDA. Starting from the essential P-prochiral building block dimethyl phenyl phosphine borane we were able to obtain phosphine boranes in yields up to 80 % and e.r. up to 98 : 2 by crystallization of the lithiated intermediate prior to the trapping reaction. NMR-based deuterium labeling experiments indicate that the epimerization in solution is based on the intermolecular proton transfer between nonlithiated phosphine borane and the corresponding lithiated intermediate, rendering the presence of the remaining starting compound in an optimized solvent mixture the main factor for successful enantioselective synthesis. Quantum chemical calculations using different model systems based on solid state structures confirm these experimental results. By gaining insights into the epimerization mechanism, essential principles for CIDR of lithiated phosphine boranes are elucidated that may be expanded to other important P-stereogenic compounds and simple chiral amines.

Enantioselektive Synthese von Phosphinoboranen via kristallisationsinduzierter dynamischer Racematspaltung des lithiierten Intermediates durch Verständnis des zugrunde liegenden Epimerisierungsprozesses

AbstractHier wird die erfolgreiche kristallisationsinduzierte dynamische Racematspaltung (CIDR) eines α‐lithiierten Phosphinoborans mithilfe des leicht zugänglichen und kostengünstigen chiralen Liganden (R,R)‐TMCDA beschrieben. Ausgehend von dem wichtigen P‐prochiralen Baustein Dimethylphenylphosphinoboran konnten Phosphinoborane in Ausbeuten von bis zu 80 % und Enantiomerenverhältnissen von bis zu 98 : 2 durch Kristallisation des lithiierten Zwischenprodukts erhalten werden. NMR‐basierte Deuterium‐Markierungsexperimente zeigen, dass die Epimerisierung in Lösung auf dem intermolekularen Protonentransfer zwischen dem nicht lithiierten Phosphinoboran und dem entsprechenden lithiierten Zwischenprodukt beruht, sodass die Anwesenheit überschüssigen Eduktes in einem optimierten Lösungsmittelgemisch der Hauptfaktor für eine erfolgreiche enantioselektive Synthese ist. Quantenchemische Berechnungen mit verschiedenen auf Festkörperstrukturen basierenden Modellsystemen bestätigen diese experimentellen Ergebnisse. Durch den Einblick in den Epimerisierungsmechanismus wurden wesentliche Prinzipien für die CIDR von lithiierten Phosphinoboranen aufgeklärt, die auf andere wichtige P‐stereogene Verbindungen und einfache chirale Amine erweitert werden könnten.

Inverse kinetic isotope effect in singlet-to-triplet intersystem crossing contributes to greater robustness of deuterated organocatalyst

Abstract Precisely defined deuterium labeling of simplified Maruoka Catalyst® markedly increases its robustness under basic conditions, but the reason for this has remained unclear. Based on multicomponent density functional theory (MC_DFT) calculations, we find that an inverse kinetic isotope effect in singlet-to-triplet intersystem crossing contributes to the greater robustness of the deuterated catalyst.

Challenging Task of Ni-Catalyzed Highly Regio-/Enantioselective Semihydrogenation of Racemic Tetrasubstituted Allenes via a Kinetic Resolution Process.

The first earth-abundant transition metal Ni-catalyzed highly regio- and enantioselective semihydrogenation of racemic tetrasubstituted allenes via a kinetic resolution process as a challenging task was well established. This protocol furnishes expedient access to a diversity of structurally important enantioenriched tetrasubstituted allenes and chiral allylic molecules with high regio-, enantio-, and Z/E-selectivity. Remarkably, this semihydrogenation proceeded with one carbon-carbon double bond of allenes, which was regioselective complementary to the Rh-catalyzed asymmetric version. Deuterium labeling experiments and density functional theory (DFT) calculations were carried out to reveal the reasonable reaction mechanism and explain the regio-/stereoselectivity.

An Intermolecular Hydroarylation of Unactivated Arylcyclopropane via Re2O7/HFIP-Mediated Ring Opening.

In this paper, we describe a Re2O7-mediated ring-opening arylation of unactivated arylcyclopropane because of its functionalization with various arenes via Friedel-Crafts-type reactivity. This protocol allows facile access to functionalized 1,1-diaryl alkanes and is characterized by a broad substrate scope, mild reaction conditions, high efficiency, and high atom economy. Both density functional theory calculations and deuterium labeling experiments were carried out to justify the indispensable role of HFIP in this transformation and pointed to Re2O7-mediated ring opening being the rate-determining step.

Zn(II)‐Stabilized Azo‐Anion Radical Catalyzed Sustainable C−C Bond Formation: Regioselective Alkylation of Fluorene, Oxindole, and Indoles

AbstractHerein we report a sustainable approach for the alkylation of ketones, 9H‐fluorene, oxindole, and indole using alcohols as the alkylating agent catalyzed by a well‐defined air‐stable zinc catalyst (1 a) of a tridentate redox non‐innocent arylazo ligand, 2‐((4‐chlorophenyl)diazenyl)‐1,10‐phenanthroline (La). 2–3 mol % of 1 a efficiently produces substituted α‐alkylated ketones, 9‐alkylated fluorenes, C3‐alkylated oxindoles, and C3‐alkylated indoles in moderate to good isolated yields. In aerial condition, the formation of bis(indolyl)methane (BIMs) derivatives were observed when indoles were subjected to alkylation by primary alcohols. A few drug molecules containing BIMs were prepared in good isolated yields. The catalyst 1 a exhibited good chemoselectivity during the functionalization of fluorene and indole with oleyl alcohol and β‐citronellol. A few control experiments, including deuterium labeling experiments, performed to unveil the reaction mechanism indicate that the one‐electron reduced azo‐anion radical species [1 a]‐formed in situ, acts as the active catalyst. All the redox events occur at the redox‐active aryl‐azo ligand, which acts as the reservoir of hydrogen and electrons throughout the catalytic cycle, keeping the Zn(II)‐center as a template.

Differentiation of isomeric chalcone and dihydroflavone using liquid chromatography coupled with hydrogen-deuterium exchange tandem mass spectrometry (HDX-MS/MS): An application for flavonoids-focused characterization of Snow chrysanthemum

Although the co-occurrences of isomeric chalcones and dihydroflavones widely appear in medicinal plants, the differentiation of such isomerism seldom succeeds using MS/MS, attributing to totally identical MS/MS spectra. Here, efforts were paid to pursue an eligible tool allowing to address the technical challenge. Being inspired by that one more proton signal is observed in 1H NMR spectrum of isoliquiritigenin than liquiritigenin when employing DMSO‑d6 as solvent, hydrogen-deuterium exchange (HDX)-MS/MS was evaluated towards differentiating isomeric chalcones and dihydroflavones through replacing H2O with D2O to prepare the mobile phase. As a result, differences were observed for either MS1 or MS2 spectrum when comparing two pairs of isomers, such as liquiritigenin vs. isoliquiritigenin and liquiritin vs. isoliquiritin, because the isomeric precursor and fragment ion species owned different amounts of hydroxyl protons and those reactive protons could be partially or completely substituted by deuterium protons at the exposure in D2O to result in n × 1.006 mass increments. Moreover, utmost four hydrogen/deuterium exchanges occurred for a single glucosyl moiety. Thereafter, HDX-MS/MS was applied to characterize the flavonoids of Snow chrysanthemum, a precious edible herbal medicine that is rich in isomeric chalcones and dihydroflavones. Through paying special attention to the deuterium labeling styles of (de)protonated molecules as well as those featured fragment ions, five pairs of isomeric chalcones and dihydroflavones were confirmatively differentiated, in addition to that 28 flavonoids were structurally annotated by applying those well-defined mass fragmentation rules. Hence, this study offered an in-depth insight towards the flavonoids-focused characterization of Snow chrysanthemum, and more importantly, HDX-MS/MS is a superior tool to differentiate, but not limited to, isomeric chalcones and dihydroflavones.

Biocatalytic cascade to polysaccharide amination

BackgroundChitin, the main form of aminated polysaccharide in nature, is a biocompatible, polycationic, and antimicrobial biopolymer used extensively in industrial processes. Despite the abundance of chitin, applications thereof are hampered by difficulties in feedstock harvesting and limited structural versatility. To address these problems, we proposed a two-step cascade employing carbohydrate oxidoreductases and amine transaminases for plant polysaccharide aminations via one-pot reactions. Using a galactose oxidase from Fusarium graminearum for oxidation, this study compared the performance of CvATA (from Chromobacterium violaceum) and SpATA (from Silicibacter pomeroyi) on a range of oxidized carbohydrates with various structures and sizes. Using a rational enzyme engineering approach, four point mutations were introduced on the SpATA surface, and their effects on enzyme activity were evaluated.ResultsHerein, a quantitative colorimetric assay was developed to enable simple and accurate time-course measurement of the yield of transamination reactions. With higher operational stability, SpATA produced higher product yields in 36 h reactions despite its lower initial activity. Successful amination of oxidized galactomannan by SpATA was confirmed using a deuterium labeling method; higher aminated carbohydrate yields achieved with SpATA compared to CvATA were verified using HPLC and XPS. By balancing the oxidase and transaminase loadings, improved operating conditions were identified where the side product formation was largely suppressed without negatively impacting the product yield. SpATA mutants with multiple alanine substitutions besides E407A showed improved product yield. The E407A mutation reduced SpATA activity substantially, supporting its predicted role in maintaining the dimeric enzyme structure.ConclusionsUsing oxidase–amine transaminase cascades, the study demonstrated a fully enzymatic route to polysaccharide amination. Although the activity of SpATA may be further improved via enzyme engineering, the low operational stability of characterized amine transaminases, as a result of low retention of PMP cofactors, was identified as a key factor limiting the yield of the designed cascade. To increase the process feasibility, future efforts to engineer improved SpATA variants should focus on improving the cofactor affinity, and thus the operational stability of the enzyme.Graphical

Deuterium Labeling of Isoaspartic and Isoglutamic Acids for Mass Spectrometry Analysis.

Isoaspartic acid (isoAsp) is a common protein modification that spontaneously arises from asparagine or aspartic acid and has been linked to various diseases and health conditions. However, current methods for identifying isoAsp sites in proteins often suffer from ambiguity and have not gained widespread adoption. We developed a novel method that exclusively labels isoAsp with deuterium. This method capitalizes on the unique structural characteristics of isoAsp residues, which possess a free α-carboxyl group and can form an oxazolone ring. Once the oxazolone ring forms, it facilitates racemization at the Cα-position, incorporating a deuteron from a D2O solvent. The sites of deuterium-incorporated isoAsp in proteins can be unequivocally determined by comparing the precursor and product ion masses of the peptides from proteins reacted in H2O and D2O. The effectiveness of this method has been demonstrated through its application to model proteins lysozyme and rituximab. Furthermore, we have confirmed that the isoAsp deuterium-labeling reaction efficiently labels both l- and d-isoAsp without distinction, as well as isoglutamic acid (isoGlu), for which no effective detection methods currently exist.

Tritium and deuterium labelling of a kainate receptor antagonist and evaluation as a radioligand.

Kainate receptors play a crucial role in mediating synaptic transmission within the central nervous system. However, the lack of selective pharmacological tool compounds for the GluK3 subunit represents a significant challenge in studying these receptors. Recently presented compound 1 stands out as a potent antagonist of GluK3 receptors, exhibiting nanomolar affinity at GluK3 receptors and strongly inhibiting glutamate-induced currents at homomeric GluK1 and GluK3 receptors in HEK293 cells with Kb values of 65 and 39 nM, respectively. This study presents the synthesis of two potent GluK3-preferring iodine derivatives of compound 1, serving as precursors for radiolabelling. Furthermore, we demonstrate the optimisation of dehalogenation conditions using hydrogen and deuterium, resulting in [2H]-1, and demonstrate the efficient synthesis of the radioligand [3H]-1 with a specific activity of 1.48 TBq/mmol (40.1Ci/mmol). Radioligand binding studies conducted with [3H]-1 as a radiotracer at GluK1, GluK2, and GluK3 receptors expressed in Sf9 and rat P2 membranes demonstrated its potential applicability for selectively studying native GluK3 receptors in the presence of GluK1 and 2-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) receptor-blocking ligands.

Recent Advances in Deuteration Reactions†

Comprehensive SummaryThe deuteration of organic compounds has attracted more attentions in recent years for the potential applications in new drug discovery and synthetic chemistry. For this purpose, many efficient deuterium labeling methodologies have been developed, including hydrogen isotope exchange (HIE), reductive deuteration, and dehalogenative deuteration that allow for the synthesis of selectively deuterated compounds. In the last few years, great breakthroughs in selective isotope labeling have been achieved and the interest in new methodologies for the deuteration of organic molecules is rising. In this review, we summarized the recent developments in the selective deuteration of organic molecules since 2021. Several types of key processes in deuterium incorporation reactions, including H/D exchange, reductive deuteration and dehalogenative deuteration, are introduced and discussed. Key ScientistsIn the 2000s, Derdau and Atzrodt's group have made great contributions to the directing group assisted noble‐metal catalyzed hydrogen isotope exchange of arenes and applications of labeled compounds. During the same period, Sajiki and co‐workers completed a series of deuteration reactions by heterogeneous platinum‐group metal catalysts. Since 2015, Gregory Pieters and co‐workers have developed ruthenium catalysts for selective hydrogen isotope exchange. In 2016, Chirik's group achieved hydrogen isotope exchange in the presence of a homogeneous iron complex. David MacMillan and coworkers have made breakthroughs in photocatalyzed HIE reactions for α‐amino C(sp3)–H bonds. From 2020, a series of nanoelectrodes were designed for selective dehalogenative deuterations and reductive deuteration of unactivated unsaturated bonds by Zhang's group. Recently, Beller's group developed several efficient strategies for isotopic labeling using heterogeneous earth‐abundant catalysts. Our review summarized the latest and important developments since 2021.

Hydroxyl transport mechanisms upon passivation of Cr-Fe-Co-Ni-Mo multi-principal element alloy surfaces investigated by isotopic labelling

Time-of-flight secondary ion mass spectrometry (ToF-SIMS) combined with deuterium labelling (D2O), and X-ray photoelectron spectroscopy (XPS) were applied to investigate the interfacial transport mechanisms of hydroxyls between aqueous electrolyte and outer part of the protective oxide film during passivation of Cr15Fe10Co5Ni60Mo10 multi-principal element alloy surfaces. A ToF-SIMS signal treatment methodology was developed to retrieve the in-depth distribution of deuterated hydroxides in the nanometer-thick surface oxide film. After immersion at free potential or anodic passivation in acidified D2O, the initial bilayer structure is retained. The use of heavy water electrolyte has no effect on the composition alterations induced by passivation. Deuterated species were detected mostly in the outer layer of the surface oxide film. Pure inward hydroxyl diffusion from electrolyte/oxide to oxide/metal interface is excluded from being primarily responsible for oxide film growth induced by anodic passivation. The hydroxyls from the dissolving hydroxide species are retained in the oxide film and participate in forming Cr hydroxide, thus reducing the hydroxyl surface uptake from the electrolyte. This work provides deeper insight into the mechanisms of oxide growth and corrosion protection induced by anodic passivation.

Propargylic Dialkyl Effect for Cyclobutene Formation through Ir(III)-Catalyzed Cycloisomerization of 1,6-Enynes.

The propargylic dialkyl effect (PDAE) has a significant impact on the cyclization reaction of enynes, partly reflected in changing the types of products. Herein, we described the influence of the propargylic dialkyl effect on the Ir(III)-catalyzed cycloisomerization of 1,6-enynes to provide strained cyclobutenes. A series of substituted 1,6-enynes were proved to be excellent substrate candidates in the presence of [Cp*IrCl2]2 in toluene. Mechanistic investigation, based on deuterium labeling experiments and control experiments, indicated that the propargylic dialkyl effect might boost C(sp)-H activation by preventing the coordination of active iridium species to the C(sp)≡C(sp) bond of enynes. This finding contributes to the fundamental understanding of enyne cyclization reactions and offers valuable insight into the propargylic dialkyl effect.

Optimization of a Hydrogen Exchange-Mass Spectrometry Robotic Liquid Handler Using Tracers.

Hydrogen exchange-mass spectrometry (HX-MS) is a valuable analytical technique that can provide insight into protein interactions and structure. The deuterium labeling necessary to gain this insight is affected by many physical and chemical factors, making it challenging to achieve high reproducibility. Poor precision during dispensing, transfer, and mixing of solutions during the experiment contributes substantially to the overall variability. While the use of a robotic liquid handler can potentially improve precision, its operation must be optimized. We observed poor precision in data collected using a robotic liquid handler to perform HX-MS. In this work, we describe how we were able to improve that system's precision considerably based on tracking performance using caffeine, caffeine-d3, and caffeine-d9 as tracers for the sample, label, and quench to report on each operation of the liquid handling workflow. The insights gained about liquid handler performance and the three-tracer approach can aid in optimizing HX-MS workflow operations, whether performed manually or when using a liquid handling system. Additionally, these tracers can be incorporated as internal tracers during an experiment to report on the labeling and quench operations of each sample throughout the run and, if desired, be used to implement an uptake correction described previously.

Noninnocent Azo-Aromatic Cobalt(II)-Catalyzed sp3 C-H Alkylation of Fluorenes with Alcohols.

Herein, employing well-defined redox noninnocent cobalt(II) complexes an efficient sp3 C-H alkylation of fluorenes using alcohols as alkylating agents to result in alkylated fluorenes is reported. The catalytic protocol was versatile with various fluorenes and benzyl alcohols. It also showed very good functional group tolerance with both alcohols and fluorenes. Moreover, an efficient single-step and simultaneous di C-C as well as both C-C and the C-N alkylation reaction of fluorenes was observed with this catalytic protocol. Such selective single-step dialkylation of fluorenes is indeed beneficial. Several control experiments, deuterium labeling, and 1H NMR kinetic studies have revealed a ligand radical-based borrowing hydrogen mechanism involving the azo-aromatic complexes of cobalt as catalysts for the alkylation of fluorenes.

Raman optical activity study of deuterated sugars: deuterium labelling as a tool for structural analysis.

Structural analyses using Raman optical activity (ROA) spectroscopy conventionally rely on vibrational signals in the fingerprint region ranging from 100 to 1800 cm-1. Use of deuterium labelling to observe ROA signals in the C-D stretching region provides additional information about a local structure of large molecular systems. So far, the potential of C-D stretching ROA signals for structural analysis has rarely been explored. In the present work, we synthesized model deuterated glucose monosaccharides and studied their ROA properties by employing molecular dynamics and density functional theory to interpret the spectra. A good agreement between the simulated and experimental spectra is achieved when the proper conformer ratios are considered. This shows the usefulness of ROA spectroscopy assisted by deuterium labelling for stereochemical and conformational analysis.

A millimeter water-in-oil droplet as an alternative back exchange prevention strategy for hydrogen/deuterium exchange mass spectrometry of peptides/proteins.

Hydrogen/deuterium exchange mass spectrometry (HDX-MS) is a versatile bioanalytical technique for protein analysis. Since the reliability of HDX-MS analysis considerably depends on the retention of deuterium labels in the post-labeling workflow, deuterium/hydrogen (D/H) back exchange prevention strategies, including decreasing the pH, temperature, and exposure time to protic sources of the deuterated samples, are widely adopted in the conventional HDX-MS protocol. Herein, an alternative and effective back exchange prevention strategy based on the encapsulation of a millimeter droplet of a labeled peptide solution in a water-immiscible organic solvent (cyclohexane) is proposed. Cyclohexane was used to prevent the undesirable uptake of water by the droplet from the atmospheric vapor through the air-water interface. Using the pepsin digest of deuterated myoglobin, our results show that back exchange kinetics of deuterated peptides is retarded in a millimeter droplet as compared to that in the bulk solution. Performing pepsin digestion directly in a water-in-oil droplet at room temperature (18-21 °C) was found to preserve more deuterium labels than that in the bulk digestion with an ice-water bath. Based on the present findings, it is proposed that keeping deuterated peptides in the form of water-in-oil droplets during the post-labelling workflow will facilitate the preservation of deuterium labels on the peptide backbone and thereby enhance the reliability of the H/D exchange data.