CID 1135

C₅H₆N₂O₂

Thymine

Ball-and-stick Stick Space-filling

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15 atoms, 15 bonds.

IUPAC name: 5-methyl-1H-pyrimidine-2,4-dione
Molar mass: 126.115(15) g/mol
Atoms: 15
SMILES: CC1=CNC(=O)NC1=O
InChIKey: RWQNBRDOKXIBIV-UHFFFAOYSA-N
PubChem CID: 1135

Made of

Structural formula of thymine. Each unlabelled corner is a carbon atom, and the one hydrogen on carbon is not drawn. It shows which atoms are joined to which, not the shape. The model above shows the shape.

One methyl group at ring position 5 is all that separates thymine from uracil, the base RNA uses instead, in the definition of ChEBI (Chemical Entities of Biological Interest). Every T in a written DNA sequence stands for thymine. It is one of the four nucleotide bases whose order encodes the information in DNA, according to the National Human Genome Research Institute (NHGRI). A nucleotide, the building block of DNA and RNA, joins a sugar, a phosphate group and a base.

The IUPAC name, 5-methyl-1H-pyrimidine-2,4-dione, spells out the rest. A pyrimidine ring of four carbon and two nitrogen atoms carries oxygen double-bonded at positions 2 and 4, with the methyl at 5. Its formula, C₅H₆N₂O₂, gives a molar mass of 126.12 g/mol.

Structure and bonding

The viewer draws 15 atoms and 15 bonds around one six-membered ring. With Labels on, the two N atoms flank a single ring carbon, which carries an O through a double bond. A second C=O stands two places further round, next to the carbon holding the methyl group. Of the two ring bonds between carbons, the one from the methyl-bearing carbon to the carbon beside a nitrogen is drawn double; the other is single. Each nitrogen carries one hydrogen.

Turned edge-on, PubChem’s computed 3D model is flat: all nine carbon, nitrogen and oxygen atoms and the three hydrogens on the ring share one plane. Only the methyl group breaks it, with two of its hydrogens about 0.89 Å above and below. In Ball-and-stick the ring reads as a slightly uneven hexagon, its angles running from 114° to 126°. In Stick the short C=O rods, 1.23 Å in the model, sit beside the ring C=C at 1.34 Å. Space-filling merges the spheres into a thin slab with one knob, the methyl.

The model shows a free molecule. In DNA the same ring is joined to a deoxyribose sugar and paired with adenine through hydrogen bonds, and the viewer draws neither.

Where it turns up

Medical Subject Headings (MeSH) describes thymine as one of four constituent bases of DNA. Among the nucleic acids it belongs to DNA alone: in RNA, the NHGRI glossary states, uracil takes its place. Each DNA strand has a backbone of alternating deoxyribose sugar and phosphate groups, and every sugar carries one base. The backbones lie on the outside of the double helix, as Chem1 describes it, leaving the bases inside and facing one another.

That is where a thymine on one strand meets an adenine on the other, the pair forming one rung of the twisted ladder.

Thymine also occurs outside the human body. The LOTUS database reports it in Huperzia serrata and Streptomyces piomogenus among other organisms. As a pure compound, thymine is a laboratory chemical, used in biochemical research according to Haz-Map, a US occupational health database. The US Environmental Protection Agency lists it as active on the Toxic Substances Control Act (TSCA) inventory.

Why it matters

Hydrogen bonds join a nitrogen atom of one strand’s nucleotide to a nitrogen or oxygen atom of the base opposite, in Chem1’s account.

Inside the helix, hydrogen bonding is efficient only between A and T and between C and G, so thymine always faces adenine. Because one base fixes its partner, scientists need not report both, and DNA is written as one string of letters.

Working out that string, the exact order of base pairs along a stretch of DNA or a whole genome, is DNA sequencing, as NHGRI describes it. The Human Genome Project read over 90 per cent of the human genome this way, and the remaining parts took nearly two more decades. These hydrogen bonds are weaker than covalent bonds. Water molecules hydrogen-bonded to the outside of the helix help to stabilise it.

The swap between thymine and uracil marks the line between DNA and RNA. On NHGRI’s account, uracil in RNA helps RNA to be broken down easily, which lets a cell change which genes it reads to build proteins.

Properties

Properties of thymine Molar mass summed from IUPAC/CIAAW 2024 standard atomic weights; formula, atom and bond counts and PubChem's molecular weight from PubChem CID 1135.
Property	Value	Unit	Source
Molecular formula (Hill order)	C₅H₆N₂O₂
Molar mass	126.115(15) g/mol	g/mol	IUPAC/CIAAW 2024
Carbon atoms	5
Hydrogen atoms	6
Nitrogen atoms	2
Oxygen atoms	2
Bonds	15
Single bonds	12
Double bonds	3
PubChem molecular weight	126.11 g/mol	g/mol	PubChem

Safety

Pure thymine is classed at most as an eye irritant, and most company reports find no hazard at all. In the European Chemicals Agency’s classification inventory, three of seven reports give the signal word Warning and the statement “Causes serious eye irritation”. The other four find that it meets no hazard criteria. The eye hazard concerns people who handle the pure powder, as in biochemical research, and PubChem’s Laboratory Chemical Safety Summary for thymine gives its handling data.

Questions

What does thymine pair with in DNA?

Thymine pairs with adenine, a base on the opposite strand, and the two together make one rung of the DNA ladder. Hydrogen bonds hold the pair in place. The partner is fixed by hydrogen bonding: within the helix, Chem1 explains, it works efficiently only between adenine and thymine or between cytosine and guanine. Those two pairings are the alphabet in which genetic information is written.

What is the difference between thymine and uracil?

Structurally, one methyl group. ChEBI defines thymine as uracil whose hydrogen at ring position 5 has been replaced by CH₃. Their jobs differ too: DNA uses thymine, while in RNA uracil takes its place, and uracil also pairs with adenine. The NHGRI glossary adds that keeping uracil in RNA and out of DNA helps RNA to be broken down easily, so a cell can change which genes it reads to build proteins.

What does the 3D model of thymine show?

It shows one molecule of C₅H₆N₂O₂, 126.12 g/mol, as 15 atoms and 15 bonds. A single six-membered ring holds four carbons and two nitrogens. Two oxygens hang from it by double bonds, a methyl group sticks out from one carbon, and each nitrogen carries a hydrogen. The model is the free base; in DNA the ring is also bonded to a sugar, which is not drawn.

Is thymine found only in DNA?

Thymine is one of the four bases of DNA, but that is not its only role. The NHGRI glossary notes that thymine, like several other nucleotides, also takes part in metabolism, with more roles than its place in DNA. ChEBI records it as a human metabolite, a mouse metabolite and an Escherichia coli metabolite. In the laboratory the pure compound serves biochemical research, according to Haz-Map.

Made of the same elements

C₄H₄N₂O₂ Uracil 12 atoms, 12 bonds.
C₃H₇NO₂ Alanine 13 atoms, 12 bonds.
C₄H₅N₃O Cytosine 13 atoms, 13 bonds.
C₂H₅NO₂ Glycine 10 atoms, 9 bonds.
C₅H₅N₅O Guanine 16 atoms, 17 bonds.
C₅H₄N₄O₃ Uric acid 16 atoms, 17 bonds.
C₅H₉NO₄ Glutamic acid 19 atoms, 18 bonds.
C₈H₉NO₂ Acetaminophen 20 atoms, 20 bonds.

All 25 compounds made of carbon, hydrogen, nitrogen and oxygen

CO(NH₂)₂ Urea 8 atoms, 7 bonds.
C₈H₁₀N₄O₂ Caffeine 24 atoms, 25 bonds.
C₈H₁₁NO₂ Dopamine 22 atoms, 22 bonds.
C₆H₁₃NO₂ Isoleucine 22 atoms, 21 bonds.
C₆H₁₃NO₂ Leucine 22 atoms, 21 bonds.
C₉H₁₁NO₂ Phenylalanine 23 atoms, 23 bonds.
C₉H₁₁NO₃ Tyrosine 24 atoms, 24 bonds.
C₁₀H₁₂N₂O Serotonin 25 atoms, 26 bonds.
C₁₁H₁₂N₂O₂ Tryptophan 27 atoms, 28 bonds.
C₉H₁₃NO₃ Epinephrine 26 atoms, 26 bonds.
C₁₃H₁₆N₂O₂ Melatonin 33 atoms, 34 bonds.
C₁₂H₁₇NO DEET 31 atoms, 31 bonds.
C₁₄H₁₈N₂O₅ Aspartame 39 atoms, 39 bonds.
C₁₃H₂₁NO₃ Albuterol 38 atoms, 38 bonds.
C₁₄H₂₂N₂O Lidocaine 39 atoms, 39 bonds.
C₁₇H₂₁NO Diphenhydramine 40 atoms, 41 bonds.
C₂₀H₂₄N₂O₂ Quinine 48 atoms, 51 bonds.