5'-Thymidylic acid (365-07-1) Physical and Chemical Properties
5'-Thymidylic acid
A deoxythymidine monophosphate nucleotide used as a reagent and analytical standard in molecular biology, enzymology and nucleotide synthesis workflows.
| CAS Number | 365-07-1 |
| Family | Pyrimidine nucleotides / nucleoside monophosphates |
| Typical Form | Powder or crystalline solid |
| Common Grades | EP |
5'-Thymidylic acid is a pyrimidine nucleotide (a thymine nucleoside 5'-monophosphate) belonging to the class of nucleic acid derivatives. Structurally it comprises a 5-methylpyrimidine base (thymine) N‑linked to a 2'-deoxyribofuranose and a monoesterified phosphate at the 5' position. The molecule contains multiple hydrogen-bond donors and acceptors and three defined stereocenters on the sugar ring, producing a compact, highly polar organic phosphate that is characteristic of deoxynucleotide monophosphates.
Electronically the compound presents a conjugated heterocyclic base with carbonyl functions and an electron-withdrawing phosphate moiety. The phosphate group confers pronounced acidity at the 5' position (exists in protonation states that depend on pH) and dominates the molecule's aqueous ionization and solvation behavior; the deoxyribose provides the stereochemical framework that determines biological recognition. The combination of a charged phosphate, multiple hydroxyl groups and polar carbonyls yields low lipophilicity and strong water solvation, while the lack of a 2'-hydroxyl (deoxy sugar) reduces susceptibility to certain hydrolytic pathways relative to ribonucleotides.
Biologically and industrially, 5'-thymidylic acid is a fundamental cellular metabolite and a common reagent/standard in biochemical, enzymology and analytical workflows involving nucleotides and nucleic acids. It is frequently encountered as a substrate or product in nucleotide metabolism and in assays for polymerases, kinases and phosphatases. 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
5'-Thymidylic acid is reported as a solid and is highly water‑soluble owing to the charged phosphate group and multiple polar functional groups (hydroxyl and carbonyl). The compound dissolves readily in aqueous buffers at neutral pH (spectroscopic and mass‑spectrometric data are commonly recorded in water or D2O at physiologic pH), and is effectively insoluble in nonpolar organic solvents. In solution the molecule exists in pH-dependent protonation states of the phosphate; at neutral to alkaline pH the phosphate is predominantly ionized, increasing hydrophilicity and interaction with cations.
Reactivity and Stability
As a monoesterified phosphate of a deoxynucleoside, the principal chemical liabilities are hydrolysis of the phosphate ester under strongly acidic or strongly basic conditions and enzymatic cleavage by phosphatases and nucleases under biological conditions. The deoxyribose–base glycosidic bond and the thymine ring are generally stable under mild laboratory conditions but can undergo enzymatic or chemical transformation (e.g., phosphorolysis, deamination under harsh oxidative conditions). The compound is relatively nonvolatile; thermal decomposition and hydrolytic cleavage become relevant under prolonged exposure to extremes of pH, temperature or enzymatic activity. Standard precautions to avoid contamination with nucleases and phosphatases (use of nuclease-free reagents and glassware) are recommended to preserve sample integrity.
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: C10H15N2O8P
- Molecular weight: 322.21 \(\mathrm{g}\,\mathrm{mol}^{-1}\)
- Exact mass / Monoisotopic mass: 322.05660244 (Da)
- Heavy atom count: 21
LogP and Polarity
- XLogP3 (computed): -2.8 (low lipophilicity)
- Topological polar surface area (TPSA): 146 \(\text{Å}^2\)
- Hydrogen bond donors: 4
- Hydrogen bond acceptors: 8
- Rotatable bond count: 4
- Molecular complexity (computed): 529
These descriptors are consistent with a small, highly polar, hydrogen‑bonding molecule that partitions strongly to aqueous phases and has limited membrane permeability in its ionized forms.
Structural Features
5'-Thymidylic acid consists of three principal substructures: a thymine pyrimidine base (5‑methyluracil), a 2′‑deoxyribofuranose sugar bearing three stereocenters (defined atom stereocenter count = 3), and a 5′‑linked dihydrogen phosphate (phosphoric monoester). The phosphate imparts the principal negative charge in deprotonated forms and is the primary site for enzyme recognition and chemical modification.
Structural identifiers (plain text): - SMILES: CC1=CN(C(=O)NC1=O)[C@H]2CC@@HO - InChI: InChI=1S/C10H15N2O8P/c1-5-3-12(10(15)11-9(5)14)8-2-6(13)7(20-8)4-19-21(16,17)18/h3,6-8,13H,2,4H2,1H3,(H,11,14,15)(H2,16,17,18)/t6-,7+,8+/m0/s1 - InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
Experimental collision cross section (CCS) measurements (reported values):
- 163.84 \(\text{Å}^2\) [M+H]+ [CCS Type: DT; Method: stepped-field]
- 166.26 \(\text{Å}^2\) [M-H]- [CCS Type: DT; Method: stepped-field]
- 169.74 \(\text{Å}^2\) [M+Na]+ [CCS Type: DT; Method: stepped-field]
- 173.1 \(\text{Å}^2\) [M+Na]+ [CCS Type: DT; Method: single field calibrated with Agilent tune mix (Agilent)]
- 170 \(\text{Å}^2\) [M+Na]+ [CCS Type: TW; Method: calibrated with polyalanine]
- Additional reported CCS variants: 176.2, 173.5, 163.1, 162.8, 167.7, 163.8 \(\text{Å}^2\) with specified adduct/ion types.
Chemical class: nucleic acids and derivatives; pyrimidine nucleosides.
Identifiers and Synonyms
Registry Numbers and Codes
- CAS number: 365-07-1
- UNII: 43W3021X6C
- ChEBI: CHEBI:17013
- ChEMBL: CHEMBL394429
- DrugBank: DB01643
- HMDB: HMDB0001227
- KEGG: C00364
- InChIKey: GYOZYWVXFNDGLU-XLPZGREQSA-N
Synonyms and Structural Names
Selected synonyms and names reported for this substance include:
- Thymidine Monophosphate; DTMP; Thymidylic Acid; TMP
- Thymidylate; 5'-TMP; Deoxythymidine 5'-monophosphate; Deoxythymidylic acid; Thymidine 5'-phosphate
- IUPAC: [(2R,3S,5R)-3-hydroxy-5-(5-methyl-2,4-dioxopyrimidin-1-yl)oxolan-2-yl]methyl dihydrogen phosphate
Industrial and Commercial Applications
Representative Uses and Industry Sectors
5'-Thymidylic acid is primarily of interest in biochemical, molecular biology and analytical laboratories. Representative uses include:
- Reagent and substrate in enzymology (polymerases, kinases, phosphatases) and nucleotide metabolism studies.
- Analytical standard for mass spectrometry and chromatographic assays targeting nucleotides and nucleotide metabolites.
- Reference material in metabolomics and biochemical profiling workflows.
These uses reflect the compound's role as a core metabolite and as a standardized biochemical building block.
Role in Synthesis or Formulations
In synthetic and preparative contexts, 5'-thymidylic acid acts as a nucleotide monomer or intermediate for enzymatic incorporation and for construction of oligonucleotides in research settings. It is also used as a calibration or quality control compound in assays that quantify nucleotide pools or enzyme activities. No specific formulation recipes or proprietary grade specifications are provided here.
Safety and Handling Overview
Acute and Occupational Toxicity
No experimentally established acute toxicity values (e.g., LD50) are available in the current data context. The substance is reported to cause irritation on contact, consistent with many low‑molecular‑weight polar organics and inorganic phosphates. Standard occupational precautions should be applied: avoid inhalation of dust, skin and eye contact; use appropriate personal protective equipment (gloves, eye protection, lab coat) and engineering controls (local exhaust, dust containment) when handling powders.
Storage and Handling Considerations
As a solid, 5'-thymidylic acid should be stored in a tightly closed container in a dry environment to minimize hydrolysis and contamination with nucleases or moisture. Where long‑term stability is required, keeping material refrigerated and protected from repeated freeze–thaw cycles and from exposure to strong acids, bases or oxidants is prudent. Use nuclease‑free consumables when preparing aqueous solutions for biochemical applications. For detailed hazard, transport and regulatory information, users should refer to the product‑specific Safety Data Sheet (SDS) and applicable local legislation.
