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Diethyl pyrocarbonate

Diethyl pyrocarbonate (DEPC), also known as diethyl dicarbonate, is an with the molecular formula C₆H₁₀O₅ that serves as the diethyl of dicarbonic acid. It appears as a colorless with a density of 1.101 g/mL at 25°C and a of 93–94°C at 18 mmHg, decomposing at 155°C into and . Sensitive to moisture and pH changes, DEPC is widely used in to inactivate (RNase) enzymes and was formerly employed as a in beverages such as wines, soft drinks, and fruit juices (banned by the FDA in 1972 and prohibited in the due to urethane formation), where it hydrolyzes into non-toxic products. In laboratory settings, DEPC's primary application is the preparation of nuclease-free solutions for RNA handling, achieved by adding 0.1% (v/v) DEPC to deionized or buffers, followed by autoclaving to remove residual reagent through decomposition into and CO₂. This treatment effectively inhibits RNases by carbethoxylating residues in their active sites, preventing RNA degradation during experiments like , dot blot hybridization, and RNA purification. Beyond RNase inhibition, DEPC acts as a covalent labeling agent in protein , selectively modifying and residues to probe higher-order structures, protein-protein interactions, and conformational changes via . It also serves as a chemical probe for structures, reacting with bases (e.g., N-7 and N-6 positions) to detect distortions like or A-tracts in double-stranded DNA. Chemically, DEPC functions as a gentle esterifying in and has been used historically for preservation through cross-linking. In the , it was formerly used as a , stemming from slow decomposition in aqueous environments containing , yielding and without leaving harmful residues, but banned in the (1972) and EU due to regulatory concerns over potential urethane formation, a . considerations are critical: DEPC is classified as acutely toxic if ingested (Acute Tox. 4 Oral) and a skin/eye irritant, with a of 69°C necessitating storage at 2–8°C in a cool, dry place and handling under fume hoods with appropriate including gloves, eyewear, and respirators.

Chemical identity

Nomenclature and synonyms

Diethyl pyrocarbonate is the accepted for this , reflecting its structure as a pyrocarbonate . Its official IUPAC name is ethoxycarbonyl ethyl carbonate, also known systematically as diethyl dicarbonate. Common synonyms include DEPC, DEP, diethyl oxydiformate, and Baycovin, with DEPC being particularly prevalent in biochemical and industrial contexts. The is assigned the 1609-47-8. As a member of the pyrocarbonic acid family, diethyl pyrocarbonate is the ethyl homolog of dimethyl pyrocarbonate, differing in the alkyl chain length of the groups.

Molecular formula and structure

Diethyl pyrocarbonate has the molecular C₆H₁₀O₅ and a molecular weight of 162.14 g/. The compound's is (C₂H₅O–C(O)–O–)₂O, depicting it as ethoxyformic anhydride, a mixed anhydride derived from . This relates to its naming as a pyrocarbonate, reflecting the diethyl of pyrocarbonic acid (dicarbonic acid), the formal anhydride of two molecules. The canonical SMILES notation is CCOC(=O)OC(=O)OCC.

Physical and chemical properties

Physical properties

Diethyl pyrocarbonate is a clear, colorless at . Its is 1.101 g/mL at 25 °C and 1.121 g/mL at 20 °C. The is 93–94 °C at 24 hPa (18 mmHg). As a under standard conditions, it has no distinct . The is 69 °C (closed cup). It exhibits a of 1.398 (n20D). The dynamic is 1.97 mPa·s at 20 °C. Diethyl pyrocarbonate is soluble in and , with limited in (approximately 0.1 g/100 ) owing to its instability in aqueous environments.

Chemical reactivity and stability

Diethyl pyrocarbonate (DEPC) undergoes in aqueous environments, decomposing to and . The reaction proceeds via nucleophilic attack on the carbonyl groups, with the overall given by: (\ce{EtOCO})_2\ce{O} + \ce{H2O} -> 2 \ce{EtOH} + 2 \ce{CO2} This process is accelerated by the presence of nucleophiles, which facilitate the breakdown by enhancing the electrophilic character of the central oxygen atom. DEPC exhibits high reactivity toward nucleophilic sites, particularly through carbethoxylation, where it transfers an ethoxycarbonyl group to amines, including the imidazole ring of histidines and other protein residues such as lysines and tyrosines. This modification involves nucleophilic addition to the carbonyl, leading to stable carbamate derivatives. The compound's electrophilic nature, stemming from its pyrocarbonate structure, enables selective interactions with nucleophilic heteroatoms in biological molecules. Thermally, DEPC is unstable above 155 °C, decomposing to and under heating conditions. This thermal instability limits its use in high-temperature processes and underscores the need for controlled storage below . DEPC shows pronounced sensitivity to pH and moisture, with rapid decomposition in basic or aqueous conditions; for instance, its half-life in phosphate buffer at 25 °C is 4 minutes at 6 and 9 minutes at 7.4, shortening further under alkaline conditions due to increased nucleophilic activity. Moisture alone triggers slow , generating pressure from CO₂ evolution. In terms of buffer compatibility, DEPC is incompatible with amine-containing buffers like Tris and , which accelerate through nucleophilic reaction; however, it remains stable in non-amine buffers such as or , allowing its use in those systems without significant degradation.

Synthesis

Laboratory preparation

Diethyl pyrocarbonate is commonly prepared in the laboratory by reacting with sodium ethyl carbonate, which is generated from and under an inert atmosphere to prevent by moisture. is first prepared by dissolving sodium metal in anhydrous , followed by bubbling dry through the solution at to form the sodium ethyl carbonate intermediate. The subsequent addition of to this intermediate proceeds as follows: \ce{NaO(CO)OEt + ClCO2Et -> (EtOCO)2O + NaCl} This reaction is typically conducted at low temperatures, between -10°C and 0°C, to minimize side reactions and decomposition, with stirring under nitrogen or argon. After the reaction, the mixture is filtered to remove the precipitated sodium chloride, and the crude product is dried over a dehydrating agent such as magnesium sulfate. Purification is achieved by distillation under reduced pressure (e.g., boiling point 83–84°C at 11 mm Hg) to isolate the clear, colorless to light yellow liquid, avoiding higher temperatures that could lead to thermal decomposition into ethanol and carbon dioxide. Typical yields range from 70% to 80%.

Industrial production

Diethyl pyrocarbonate is commercially manufactured via the reaction of with , summarized by the equation COCl₂ + 2 EtOH → (EtOCO)₂O + 2 HCl. This process proceeds through the intermediate formation of (EtOCOCl) from phosgene and ethanol, followed by condensation of the chloroformate, often with aqueous (35–50% concentration) in the presence of a catalytic amount (0.1–1.0 %) of a such as bis[poly(oxy(C₂–C₄)alkylene)] C₆–C₂₀ aliphatic amine (e.g., PEG-15 stearamine). The reaction is conducted at low temperatures (0–20°C, preferably 5–10°C) to control exothermicity and ensure selectivity, typically in a solvent-free system to reduce environmental impact. Given phosgene's extreme and corrosivity, incorporates closed-loop systems for its handling and to prevent leaks and exposure, along with integrated neutralization of byproducts such as using bases like . These measures comply with rigorous safety protocols, including automated monitoring and containment to mitigate risks during the exothermic steps. Yields in this process reach up to 85–98%, depending on the specific variant, with final purification via to achieve greater than 97% purity, aligning with commercial standards for laboratory and pharmaceutical applications. Historical developments have emphasized solvent-free and catalyst-optimized methods to improve efficiency and reduce , evolving from earlier solvent-based approaches. Due to its susceptibility to hydrolysis, diethyl pyrocarbonate produced industrially is handled and stored under conditions to maintain stability. Cost factors are primarily influenced by the availability and price fluctuations of precursor , derived from renewable sources, and , which requires careful owing to its regulated status.

Applications

In

Diethyl pyrocarbonate (DEPC) is widely employed in to inactivate ribonucleases (RNases), thereby preventing RNA degradation during experimental procedures. Its primary role involves the covalent modification of essential residues in the active sites of RNases, such as RNases A, B, and C, which disrupts their catalytic activity and renders them inactive. This -specific ensures irreversible inhibition, making DEPC a reliable tool for maintaining integrity in sensitive assays. A standard for preparing RNase-free solutions entails treating or buffers with 0.1% v/v DEPC, followed by incubation for approximately 2 hours at 37 °C to allow sufficient reaction time for RNase inactivation. Subsequent autoclaving for 15 minutes is critical to hydrolyze residual DEPC into and , eliminating any unreacted compound. This treatment is also applied to glassware by soaking in 0.1% DEPC overnight at 37 °C before autoclaving or , ensuring contamination-free surfaces for handling. In practice, DEPC-treated solutions are integral to RNA extraction protocols, where they form the basis for buffers and steps to protect isolated from . Similarly, DEPC is used in preparing buffers and reaction mixes to safeguard RNA templates or cDNA during amplification, minimizing false negatives due to activity. These applications extend to routine lab preparations, such as DEPC-treated water stocks, which serve as a foundational for diluting RNA samples and reagents in downstream analyses like Northern blotting or RT-qPCR. Despite its efficacy, DEPC has limitations, as residual unhydrolyzed DEPC can react with nucleic acids or inhibit enzymes such as reverse transcriptase and Taq polymerase, potentially compromising assay performance. Autoclaving is thus essential for complete removal, though over-treatment or incomplete hydrolysis may still introduce artifacts in enzyme-dependent reactions. In post-2012 molecular biology workflows, DEPC treatment remains a standard for custom RNase-free solutions, even as commercial RNase-free kits (e.g., from Thermo Fisher or QIAGEN) provide pre-treated reagents; however, DEPC is preferred for in-house preparations due to its cost-effectiveness and reliability in diverse protocols.

In protein modification and chemical research

Diethyl pyrocarbonate (DEPC) serves as a key reagent in protein modification studies, particularly for targeting the ring of residues under mildly acidic to neutral conditions. At 6-7, DEPC selectively carbethoxylates the unprotonated of the imidazole , forming an N-carbethoxyhistidine adduct that disrupts protein function and enables site-specific probing. The reaction proceeds as follows: \text{His} + (\ce{EtOCO})_2\text{O} \rightarrow \text{His-CO}_2\text{Et} + \text{EtOH} + \text{CO}_2 This modification is particularly useful for identifying catalytically important histidines in enzyme active sites, as demonstrated in early studies on ribonuclease where DEPC inactivation revealed essential histidine involvement in catalysis. Under controlled conditions, DEPC can also modify other nucleophilic residues such as lysine (via ε-amino groups), cysteine (thiol), and tyrosine (phenolic hydroxyl), though these reactions typically require higher pH or concentrations and are less specific than histidine carbethoxylation. The histidine modification by DEPC is reversible, allowing for controlled experiments in chemical research. Treatment of the carbethoxylated protein with 0.5 M at pH 7.2 hydrolyzes the ethoxycarbonyl group, restoring the native and activity, which confirms the specificity of the modification.86123-9/fulltext) This reversibility has been exploited in probing active sites of various , such as the Rieske iron-sulfur protein, where DEPC modification of ligating 154 reduced the [2Fe-2S] cluster potential, highlighting its role in . Beyond proteins, DEPC facilitates structural probing of DNA by carbethoxylating the N7 positions of and , which are more accessible in non-B-form conformations like cruciforms or . This reaction enhances reactivity in distorted regions, enabling analysis with single-nucleotide resolution, as shown in studies of negatively supercoiled plasmids. Modification progress is commonly monitored by UV , where carbethoxylation produces a characteristic increase at 240 nm (extinction coefficient ≈ 3200 M⁻¹ cm⁻¹), allowing quantification of modified residues without disrupting the sample.55762-3/pdf)

Other uses

Diethyl pyrocarbonate (DEPC) was historically employed as an in beverages such as wine, soft drinks, and fruit juices during the and to inhibit microbial growth. Studies in 1971 revealed that DEPC decomposes to form (), a known , in treated beverages at concentrations up to 0.2 mg/L in . As a result, the U.S. banned its use in food and beverages in 1972 due to the cancer risk. In , DEPC serves as a protecting agent for amino groups during by forming derivatives that can be selectively removed. It also acts as a precursor for the preparation of β-ketoesters through reaction with active methylene compounds. As of 2025, DEPC finds limited application as an intermediate in pharmaceutical synthesis for producing organic compounds via its reactive pyrocarbonate group, though its use remains niche due to concerns. In discontinued research contexts, DEPC was used in early studies from the 1980s to probe inhibition mechanisms, such as binding to and modifying residues essential for activity in .

Safety and regulatory aspects

Toxicity and health hazards

Diethyl pyrocarbonate (DEPC) exhibits acute toxicity primarily through oral and inhalation routes, with an oral LD50 in rats of 850 mg/kg, classifying it as under GHS category 4 (H302). It is also harmful if inhaled (GHS H332), with vapors causing irritation at high concentrations. Chronic exposure to DEPC shows limited evidence of carcinogenic potential, attributed to its in vivo decomposition into urethane (ethyl carbamate), a known carcinogen, particularly in the presence of ammonia or biological amines. Animal studies have demonstrated pulmonary tumors in mice treated with DEPC and ammonia, though DEPC alone does not exhibit strong carcinogenic activity. DEPC has not been classified by the International Agency for Research on Cancer (IARC) with respect to its carcinogenicity to humans. Additionally, DEPC acts as an irritant to skin (GHS H315), eyes (GHS H319), and the respiratory system (GHS H335). The primary toxicity mechanisms involve carbethoxylation of nucleophilic sites, such as histidine, lysine, cysteine, and tyrosine residues in proteins, leading to functional disruptions, and ethoxycarbonylation of purine bases (e.g., at N-7 of adenine and guanine) in DNA. Hydrolysis products of DEPC, including ethanol and carbon dioxide, pose low toxicity risk compared to the parent compound. Exposure primarily occurs via of vapors or , resulting in symptoms such as eye and , respiratory distress, , and at elevated levels.

Handling precautions and environmental impact

Diethyl pyrocarbonate (DEPC) should be stored in a cool, dry place at 2-8°C under an inert atmosphere such as , in tightly sealed glass containers to prevent moisture ingress and pressure buildup from ; plastic containers should be avoided due to potential reactivity. Handling requires the use of appropriate (PPE), including or gloves, , and protective clothing, with all operations conducted in a well-ventilated to minimize vapor exposure and prevent accumulation. In the event of a spill, the area should be evacuated, ignition sources removed, and adequate ventilation ensured before containing the liquid with an inert absorbent material such as or sand; the absorbed material is then transferred to a suitable container for disposal, and any residues neutralized with a mild base like if necessary before cleanup. DEPC waste and DEPC-treated materials, such as laboratory solutions, are typically disposed of by incineration at an approved or, for biological waste, by autoclaving to inactivate residual DEPC prior to standard disposal protocols. Environmentally, DEPC exhibits low persistence owing to its rapid hydrolysis in aqueous environments, breaking down into ethanol and carbon dioxide, which aids in its natural degradation. It shows minimal bioaccumulation potential due to this hydrolysis and the small size of its degradation products, with no significant tendency to concentrate in organisms. In wastewater treatment, the ethanol byproduct is readily biodegradable through conventional microbial processes, facilitating effective removal without long-term ecological buildup. DEPC is listed on the EU EINECS inventory (EC 216-542-8) under REACH as a pre-registered substance, though full registration is not required due to low production volumes (<1 tonne/year); handlers must comply with general assessments. In the US, OSHA does not establish specific permissible limits for DEPC vapors, relying instead on general requirements and to maintain below hazardous levels.

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