2-Deoxyribose, D- (533-67-5) Physical and Chemical Properties
2-Deoxyribose, D-
A deoxy pentose monosaccharide used as a biochemical building block and reagent for nucleotide synthesis, analytical standards, and research applications.
| CAS Number | 533-67-5 |
| Family | Deoxy sugars (deoxypentose) |
| Typical Form | Powder or crystalline solid |
| Common Grades | EP |
2-Deoxy-D-ribose is a deoxypentose carbohydrate (a reduced ribose) belonging to the aldopentose structural class; its molecular formula is \(\ce{C5H10O4}\). Structurally it is an open‑chain aldose with three secondary alcohol functions and one aldehyde in the linear form, and it readily cyclizes to form intramolecular hemiacetals (furanose and pyranose ring forms). The defined stereochemistry is described by the IUPAC condensed name (3S,4R)-3,4,5-trihydroxypentanal; two defined stereocenters are present in the canonical structure. The molecule is neutral (formal charge 0) and contains multiple hydrogen‑bond donors and acceptors, which dominates its condensed‑phase behavior.
Electronically, the combination of a formal aldehyde group and multiple hydroxyl groups makes 2‑deoxyribose a classical reducing sugar: the aldehyde is nucleophilic and prone to oxidation and Schiff‑base formation under appropriate conditions, while the hydroxyls confer high polarity and extensive hydrogen bonding. The substance is highly hydrophilic (computed XLogP3‑AA = -2.3) and has a large topological polar surface area (TPSA = 77.8 Ų), predicting strong aqueous solvation and poor partitioning into nonpolar solvents. Under acidic or high‑temperature conditions the sugar backbone is susceptible to dehydration, acid‑catalyzed cleavage and other degradation pathways typical of aldoses.
In biological and industrial contexts, 2‑deoxyribose is primarily important as the sugar component of DNA and as a metabolite in cellular biochemistry; it is therefore widely encountered in biochemical manufacturing, nucleoside/nucleotide synthesis, and analytical workflows (metabolomics). Common commercial grades reported for this substance include: EP.
Basic Physical Properties
Density
No experimentally established value for this property is available in the current data context.
Melting Point
No experimentally established value for this property is available in the current data context.
Boiling Point
No experimentally established value for this property is available in the current data context.
Vapor Pressure
No experimentally established value for this property is available in the current data context.
Flash Point
No experimentally established value for this property is available in the current data context.
Chemical Properties
Solubility and Phase Behavior
2‑Deoxyribose is strongly polar and therefore highly soluble in water and other protic solvents; the computed descriptors support this behavior (XLogP3‑AA = -2.3; Hydrogen Bond Donor Count = 3; Hydrogen Bond Acceptor Count = 4; TPSA = 77.8). In aqueous solution the compound exists in an equilibrium between the open‑chain aldehyde form and cyclic hemiacetal forms (both furanose and pyranose ring conformations can be present); the cyclic hemiacetal forms are usually dominant under neutral conditions. Because of its reducing aldehyde functionality the compound will participate in common wet‑chemistry reactions of reducing sugars (e.g., reductive amination, formation of Schiff bases) and will complex strongly with polar matrices and chromatographic stationary phases designed for hydrophilic interaction.
Reactivity and Stability
Chemically, the aldehyde group confers reducing properties and sensitivity to oxidation by mild oxidants; the molecule can be converted to corresponding acids or lactones under oxidative conditions. The multiple hydroxyl groups render the compound susceptible to acid‑catalyzed dehydration and cleavage at elevated temperature or under strongly acidic conditions. In synthetic contexts 2‑deoxyribose can participate in glycosylation and derivatization chemistries, and care is required to avoid uncontrolled oxidation or condensation. Storage under dry, cool conditions and exclusion of strong oxidants/strong acids minimizes degradation.
Thermodynamic Data
Standard Enthalpies and Heat Capacity
No experimentally established value for this property is available in the current data context.
Molecular Parameters
Molecular Weight and Formula
- Molecular formula: \(\ce{C5H10O4}\)
- Molecular weight: 134.13 \(\mathrm{g}\,\mathrm{mol}^{-1}\)
- Exact mass / Monoisotopic mass: 134.05790880 Da
Additional computed descriptors:
- XLogP3‑AA: -2.3
- Topological Polar Surface Area (TPSA): 77.8 Ų
- Heavy atom count: 9
- Formal charge: 0
- Complexity: 83
- Defined atom stereocenter count: 2
- Rotatable bond count: 4
- Hydrogen bond donor count: 3
- Hydrogen bond acceptor count: 4
LogP and Polarity
The computed partition coefficient descriptor XLogP3‑AA = -2.3 indicates pronounced hydrophilicity and very low affinity for nonpolar phases. The combination of low logP and substantial TPSA predicts strong aqueous solubility and limited membrane permeability in its neutral form.
Structural Features
2‑Deoxyribose contains an aldehyde carbonyl (reducing end) and three hydroxyl groups on a five‑carbon backbone; the absence of the C‑2 hydroxyl (relative to ribose) alters ring‑forming tendencies and conformational preferences compared with ribose. The molecule has two defined stereocenters (configuration indicated by the IUPAC name). In solution it interconverts between open‑chain and cyclic hemiacetal forms, and the cyclic furanose form is commonly encountered in nucleotide chemistry. Conformational flexibility is moderate (rotatable bond count = 4), but extensive hydrogen bonding governs solid and solution packing.
Identifiers and Synonyms
Registry Numbers and Codes
- CAS: 533-67-5
- European Community (EC) Number: 217-028-6
- UNII: LSW4H01241
- ChEBI: CHEBI:28816
- InChIKey: ASJSAQIRZKANQN-CRCLSJGQSA-N
- SMILES:
C(C=O)[C@@H]([C@@H](CO)O)O - InChI:
InChI=1S/C5H10O4/c6-2-1-4(8)5(9)3-7/h2,4-5,7-9H,1,3H2/t4-,5+/m0/s1 - LC‑MS precursor m/z (reported): 133.0495 [M−H]− and 135.0798 [M+H]+ (instrument details available in spectral datasets)
Synonyms and Structural Names
Depositor‑supplied synonyms (selection):
- 2‑Deoxy‑D‑ribose
- (3S,4R)-3,4,5‑trihydroxypentanal
- Thyminose
- 2‑Deoxy‑D‑erythro‑pentose
- D‑2‑Deoxyribose
- 2‑Deoxy‑D‑arabinose
(Additional synonyms and nomenclature variants exist in supplier and registry listings.)
Industrial and Commercial Applications
Representative Uses and Industry Sectors
2‑Deoxyribose is primarily of biochemical interest as the sugar component of DNA and as a common metabolite; accordingly it is used in academic and industrial molecular biology, nucleoside and nucleotide chemistry, metabolomics, and as a reference standard in analytical laboratories. Its role in synthesis is typically as a starting material or intermediate in preparation of nucleoside analogues and related derivatives, and it is encountered as an impurity or by‑product in certain nucleoside manufacturing processes.
Role in Synthesis or Formulations
In synthetic chemistry 2‑deoxyribose serves as a building block for glycosylation, protected sugar derivatives, and for construction of deoxyribonucleoside targets. Its reducing character requires protection or selective derivatization strategies when used in multistep syntheses. Commercial material is supplied for analytical use, cell culture suitability, and for reagent use in chemical and biochemical applications.
Commercial grades reported for this substance: - EP
Safety and Handling Overview
Acute and Occupational Toxicity
As a simple aldo‑sugar, 2‑deoxyribose is expected to have low acute systemic toxicity in comparison with many industrial organic chemicals; however, the aldehyde functionality can cause local irritation, and inhalation of fine particulate material should be avoided. Typical occupational controls include standard laboratory personal protective equipment (gloves, eye protection) and engineering controls to limit dust generation and inhalation exposure. Use of closed handling and good hygiene minimizes worker exposure.
Storage and Handling Considerations
Store in a cool, dry place in a tightly closed container, protected from strong oxidizing agents and strong acids. Avoid prolonged exposure to elevated temperature or acidic conditions to reduce the risk of dehydration and decomposition. For detailed hazard, transport and regulatory information, users should refer to the product‑specific Safety Data Sheet (SDS) and local legislation.
