Key facts
- Example
- BPC-157: C62H98N16O22
- Writing order
- Hill system: C, then H, then other elements alphabetically
- Shows
- Which elements are present and how many atoms of each
- Does not show
- Connectivity, sequence or stereochemistry
- Same formula, different molecules
- Leucine and isoleucine, both C6H13NO2
- KPV
- C16H30N4O4
What is a molecular formula?
A molecular formula says exactly which atoms make up one molecule of a substance. Each element appears as its chemical symbol, followed by a subscript giving the number of atoms of that element. If there's no subscript, there's one atom.
Take C62H98N16O22 for BPC-157. That's 62 carbon atoms, 98 hydrogen, 16 nitrogen and 22 oxygen, 198 atoms altogether. Those counts are all you need to calculate the molecular weight (1419.5 g/mol) and the monoisotopic mass (1418.70 Da), which is why compound records print the formula right next to them [1].
How is a molecular formula written?
Most databases, PubChem included, use Hill order: carbon first, hydrogen second, and then every other element alphabetically by symbol [1]. If a compound has no carbon, all its elements go in alphabetical order.
- Sermorelin: C149H246N44O42S. Sulfur sorts last and appears once, from a single methionine residue.
- MOTS-c: C101H152N28O22S2. Here there are two sulfur atoms, from two methionines.
- GHK-Cu: C14H23CuN6O4+. Copper (Cu) lands between H and N because "Cu" sorts ahead of "N", and the plus sign at the end tells you the species carries a positive charge.
Why insist on one order? Formulas get used as search keys, and the same composition written two ways would otherwise look like two different substances in a database.
Molecular formula vs. empirical and structural formulas
A molecular formula gives real atom counts. An empirical formula gives only the simplest whole-number ratio. A structural representation shows how the atoms are bonded to each other.
| Type | What it shows | Example |
|---|---|---|
| Empirical formula | Simplest ratio of atoms | Glucose: CH2O |
| Molecular formula | Actual number of each atom | Glucose: C6H12O6; KPV: C16H30N4O4 |
| Sequence notation | Order of amino acid residues | KPV: Lys-Pro-Val |
| Structural formula or line structure | Every bond and atom position | Drawn structure |
| Machine-readable identifiers | Full structure as text | SMILES, InChI |
With peptides, the empirical formula rarely helps. You get a far more complete description from the molecular formula, the peptide sequence and a structure-derived identifier like the IUPAC InChI, taken together. InChI encodes connectivity, charge and stereochemistry in layers, which no molecular formula can [2].
How do you work out the molecular formula of a peptide?
Add up the formulas of the free amino acids, then subtract one H2O for every peptide bond. Each peptide bond forms by condensation and gives off one water molecule.
| Component | Formula |
|---|---|
| L-Lysine | C6H14N2O2 |
| L-Proline | C5H9NO2 |
| L-Valine | C5H11NO2 |
| Sum | C16H34N4O6 |
| Minus 2 H2O (two peptide bonds) | -H4O2 |
| KPV | C16H30N4O4 |
That result matches the PubChem record for KPV (CID 125672) [1]. Modifications work the same way. A C-terminal amide swaps one O for one N and adds one H, and N-terminal acetylation adds C2H2O.
What can a molecular formula not tell you?
It can't tell isomers apart, meaning different molecules built from the same atoms. Of all its limits, this is the one to keep in mind whenever a formula is offered as identity information.
- Constitutional isomers. Leucine and isoleucine are both C6H13NO2 (131.17 g/mol), yet their side chains are shaped differently and they have different CAS numbers (61-90-5 and 73-32-5).
- Sequence isomers. Lys-Pro-Val and Val-Pro-Lys have the same residues and the same formula, C16H30N4O4, but they are different peptides.
- Stereoisomers. L- and D-amino acids have identical formulas. Ipamorelin includes D-amino acids by design, and you would never know it from the formula alone.
Isomers also share a mass, so a correct mass in mass spectrometry fits the formula without settling how the atoms are arranged. That gap is filled by sequence-level evidence, chromatographic behavior against a reference, and fragmentation data, as HPLC vs. mass spectrometry describes.
Molecular formulas and accurate mass
An accurate mass measurement narrows the list of possible formulas but can't choose one by itself. Kind and Fiehn worked out that about eight billion C, H, N, S, O and P formulas are theoretically possible up to 2000 Da; apply chemical rules and isotope patterns and you are down to roughly 623 million plausible ones [3]. For a known peptide, the logic is reversed. You calculate the formula from the sequence and check the measurement against it.
Why does the salt form change the formula?
A salt form includes counter-ions, which makes its formula bigger than the free peptide's. Isolate a peptide as an acetate salt, for instance, and its full formula picks up one or more C2H4O2 units. Regulatory substance registries treat these forms as related but separate substances. The FDA's Global Substance Registration System describes substances to the ISO 11238 standard precisely so that forms don't get confused [4]. A product record ought to say which form its formula describes, and the Vinnix compound pages in the compound library do.
FAQFrequently asked questions
What does a molecular formula show?
It shows which elements are in one molecule and how many atoms of each. C62H98N16O22, for example, means 62 carbon, 98 hydrogen, 16 nitrogen and 22 oxygen atoms. What it leaves out is how those atoms are connected, the order of amino acids in a peptide, and the molecule's three-dimensional shape.
What is the molecular formula of BPC-157?
PubChem (CID 9941957) gives the molecular formula of BPC-157 as C62H98N16O22. That corresponds to the 15-residue sequence GEPPPGKPADDAGLV in its free form, with a molecular weight of 1419.5 g/mol. A salt form, such as an acetate salt, has a larger formula because the counter-ions are counted in.
What is the Hill system?
It is the standard order for writing molecular formulas: carbon first, hydrogen second, and every other element after that in alphabetical order of its symbol. A compound with no carbon simply lists all its elements alphabetically. PubChem and similar databases use it so that each composition has exactly one written, searchable form.
Can two compounds have the same molecular formula?
Yes, and such compounds are called isomers: same formula, different structure. Leucine and isoleucine are both C6H13NO2. In peptides, shuffling the same residues into a new order, or swapping an L-amino acid for its D form, leaves the formula unchanged. So a formula can support identity, but on its own it never proves it.
What is the difference between a molecular formula and an empirical formula?
A molecular formula gives the actual count of each atom in one molecule. An empirical formula boils those counts down to the simplest whole-number ratio. Glucose, for example, has the molecular formula C6H12O6 and the empirical formula CH2O. For peptides the empirical formula tells you very little, so compound records give the molecular formula instead.
Why does the GHK-Cu formula end with a plus sign?
The plus sign means the species carries a positive charge. PubChem lists GHK-Cu as C14H23CuN6O4+, a copper complex of the tripeptide Gly-His-Lys. That charge matters: it affects how the substance is registered and how its formula and mass line up with analytical results, especially in mass spectrometry, which measures charged ions.
How many atoms are in a BPC-157 molecule?
Going by its molecular formula, C62H98N16O22, one BPC-157 molecule has 198 atoms: 62 carbon, 98 hydrogen, 16 nitrogen and 22 oxygen. Hydrogen wins on count, but carbon contributes the most to the molecular weight. These numbers are for the free peptide. In a salt form, the counter-ions would add more atoms to the full formula.
REFScientific references
-
Kim S, Chen J, Cheng T, et al. PubChem 2025 update. Nucleic Acids Res. 2025;53(D1):D1516-D1525. PubMed 39558165
database (PubChem description) -
Heller SR, McNaught A, Pletnev I, et al. InChI, the IUPAC International Chemical Identifier. J Cheminform. 2015;7:23. PubMed 26136848
standards paper (chemical identifiers) -
Kind T, Fiehn O. Seven Golden Rules for heuristic filtering of molecular formulas obtained by accurate mass spectrometry. BMC Bioinformatics. 2007;8:105. PubMed 17389044
computational methods study -
Peryea T, Southall N, Miller M, et al. Global Substance Registration System: consistent scientific descriptions for substances related to health. Nucleic Acids Res. 2021;49(D1):D1179-D1185. PubMed 33137173
database (FDA/NCATS substance registry)
Research Library: Peptide Fundamentals
Research Library