What is OPSIN?

OPSIN is a freely available software that interprets systematic IUPAC nomenclature for chemistry and biochemistry and converts it into chemical structures reported as SMILES, InChI and CML (Chemical Markup Language). OPSIN was originally developed at the University of Cambridge. This website is hosted by the Chemical Biology Services Team at EMBL-EBI in collaboration with the developer of OPSIN, Dr Daniel Lowe. It allows users to easily run this software online as an aid to chemical and biochemical curation. In addition, web services are provided to facilitate usage from scripts.

Specifying Non-ASCII Characters

Greek characters may be specified by:

• The appropriate Unicode character, e.g. λ
• The romanised name for the letter, e.g. lambda
• The romanised name for the letter surrounded by dots, e.g. .lambda.
• The corresponding modern letter prefixed with a dollar, e.g. $l

Superscripts may be specified by:

• A carat with or without bracketing, e.g. N^(2) or N^2
• Bracketing on its own, e.g. N(2)
• Tildes or asterisks, e.g. N~2~ or N*2*
• Angle brackets, e.g. N<2>

Note that for locants OPSIN will be able to infer that N2 means N^2, and for von Baeyer systems OPSIN will intelligently guess what should have been superscripted. However, for spiro systems superscripts need to be indicated.

Supported Nomenclature

The goal of OPSIN is to interpret the entirety of IUPAC nomenclature. However since this is a large and ever-expanding set, there are still gaps in that coverage. The table below provides examples of classes of nomenclature supported.

Nomenclature	Examples
Alk/ane/ene/yne	hexane hex-1-ene hex-1-yne
Heteroatom chains	tetrasilane tetrasiloxane
Cyclised chains	cyclohexane cyclotriborazane
Trivial acids and derivatives	maleic acid maleamic acid maleamide maleimide
Hantzsch-Widman rings	1,3-oxazole
Spiro compounds	spiro[4.5]decane pentaspiro[2.0.24.1.1.210.0.213.18.23]octadecane 1H,1'H-2,2'-spirobi[naphthalene] 2λ6,2',2''-spiroter[[1,3,2]benzodioxathiole] 1'H,1''H,2H,8'H-1,2':7',2''-dispiroter[naphthalen]-1'-one spiro[1,2-benzodithiole-3,2'-[1,3]benzodithiole]
von Baeyer systems	pentacyclo[13.7.4.33,8.018,20.113,28]triacontane
Hydro/dehydro	2,3-dihydropyridine 1,2-didehydrobenzene
Indicated hydrogen	1H-benzoimidazole phosphinin-2(1H)-one
Heteroatom replacement	3-aza-pentane 3-azonia-pentane 3-azanylia-pentane 3-azanida-pentane 3-azanuida-pentane
Specification of charge: ium/ide/ylium/uide	azanium boranuide
Multiplicative nomenclature	ethylenediaminetetraacetic acid 3,3'-[ethane-1,2-diylbis(oxy)]bis{4-[2-(furan-3-yloxy)ethoxy]furan}
Conjunctive nomenclature	1,3,5-benzenetriacetic acid
Fused ring systems	imidazo[4,5-d]pyridine phenothiazino[3',4':5,6][1,4]oxazino[2,3-i]benzo[5,6][1,4]thiazino[3,2-c]phenoxazine phenanthro[4,5-bcd:1,2-c']difuran
Simple bridges	2,3-methanoindene 3,4-methylenedioxy-β-methoxyphenethylamine 3,4-epoxy-3,4-dihydrophenanthrene
Ring assemblies	biphenyl 2,2':6',2''-terpyridine
Prefix functional replacement	peroxybenzoic acid
Infix functional replacement	benzoperoxoic acid
Lambda convention	λ5-phosphane
Perhalogenation	perchloro-3,4-dimethylenecyclobutene
Radicofunctional nomenclature	acetals, acids, alcohols, amides, anhydrides, anilides, azetidides, azides, bromides, chlorides, cyanates, cyanides, esters, di/tri/tetra esters, ethers, fluorides, fulminates, glycol ethers, glycols, hemiacetals, hemiketal, hydrazides, hydrazones, hydrides, hydroperoxides, hydroxides, imides, iodides, isocyanates, isocyanides, isoselenocyanates, isothiocyanates, ketals, ketones, lactams, lactims, lactones, mercaptans, morpholides, oxides, oximes, peroxides, piperazides, piperidides, pyrrolidides, selenides, selenocyanates, selenoketones, selenolsselenosemicarbazones, selenones, selenoxides, selones, semicarbazones, sulfides, sulfones, sulfoxides, sultams, sultims, sultines, sultones, tellurides, telluroketones, tellurones, tellurosemicarbazones, telluroxides, thiocyanates, thioketones, thiols and thiosemicarbazones
Amino Acids and derivatives	glycinol L-2-aminobutyric acid L-alanyl-L-glutaminyl-L-arginyl-O-phosphono-L-seryl-L-alanyl-L-proline
Nucleosides, nucleotides and their esters	adenosine 5'-(tetrahydrogen triphosphate)
Steroids including alpha/beta stereochemistry	(3β)-cholest-5-en-3-ol
Open-chain monosaccharides	4-amino-4,6-dideoxy-3-C-methyl-2-O-methyl-L-mannose
Cyclised monosaccharides and glycosides	β-D-ribofuranose β-D-fructofuranosyl α-D-glucopyranosyl-(1->4)-α-D-glucopyranoside
Deoxy and anhydro	5-acetamido-2,7-anhydro-3,5-dideoxy-D-glycero-α-D-galacto-non-2-ulopyranosonic acid
Basic inorganic support	aluminium(3+) chloride mercury(II) chloride
Isotope specification	(2H6)propan-2-one acetone-d6 hexadeuterioacetone
R/S stereochemistry	(1R,3S)-3-amino-3-methylcyclohexanecarboxylic acid
E/Z stereochemistry	(2Z)-but-2-ene
cis/trans indicating relative stereochemistry on rings	cis-1,4-dimethylcyclohexane
Structure-based polymer names	poly(2,2'-diamino-5-hexadecylbiphenyl-3,3'-diyl)

Web service

The OPSIN web service is accessed using the base URL https://www.ebi.ac.uk/opsin/ws.

To use it, send a GET request to https://www.ebi.ac.uk/opsin/ws/CHEMICAL_NAME.EXTENSION. For example, accessing https://www.ebi.ac.uk/opsin/ws/benzene.png will return a PNG depiction of benzene, while accessing https://www.ebi.ac.uk/opsin/ws/benzene.smi will return a SMILES string. Note that the chemical name must be URL-encoded. The list of supported extensions is as follows:

.smi

A SMILES string.

.cml and .no2d.cml

CML with(out) 2D coordinates

.stdinchi, .stdinchikey and .inchi

A standard InChI(Key) or a non-standard tautomer-specific InChI

.png and .svg

A PNG or SVG depiction.

.json

A JSON string with keys cml, inchi, stdinchi, stdinchikey, smiles, message and status (plus warnings where applicable).

Bulk conversion

If you need to convert large numbers of IUPAC names to structures, we recommend that you use a local installation of OPSIN rather than use the web service. This will yield faster results while ensuring that the web site is not impacted for other users. Here are two ways to do this:

1. Download the latest version of OPSIN and follow the instructions on the OPSIN GitHub page to run it at the command-line
2. Use a third-party Python integration such as pyopsin, py2opsin or MoleculeResolver.

Contact

For questions about this website, please contact opsin-website@ebi.ac.uk.

For questions about OPSIN, or to report a bug, please file an issue on OPSIN's GitHub page.

For questions about IUPAC Nomenclature, users are referred to the IUPAC documentation.

How to cite

If you use OPSIN via this website please consider citing:

• Daniel M. Lowe, Peter T. Corbett, Peter Murray-Rust, Robert C. Glen. J. Chem. Inf. Model. 2011, 51, 739. (Link)
• OPSIN webserver. https://www.ebi.ac.uk/opsin (accessed DATE)