Subsections

A.11 Lexichem v1.0b2, August 2004

On a benchmark of 250251 compounds in the NCI00 database, mol2nam is able to convert 208378 structures (83.27%) to names without BLAH. Of these 208378 names, nam2mol is able to convert 139100 (66.75%) back into structures.

A.11.1 OEParseIUPACName Improvements

Support for parsing substituents (name fragments) by generating a wildcard atom in SMILES, for example, ``methyl'' returns *C and ``hydroxy'' returns *O. Adds support for parenthesized indicated hydrogens, e.g. ``naphthalen-1(2H)-one''. Tweaks to support names, such as ``9,10-anthracene-dicarboxylic acid'', where the hyphen after the stem would cause the parser to expect a list of locants. Fixes to multipliers of ``oxy'' (and related) linkers, so that ``dineopentyloxybenzene'' is correctly considered two copies of the prefix ``neopentoxy''. Added support for ``...ic aldehyde'' and ``..ic acid aldehyde'' as synonyms of ``...aldehyde''. Added support for both ``yl'' and ``oyl'' variants of traditional acid stems, i.e. both ``crontonoyl'' and ``crotonyl'', and both ``acryloyl'' and ``acrylyl''. Adds support for ``...amido'' as a traditional linker, e.g. ``propanamido'', ``acrylamido'' and ``benzamido''. Added support for traditional bivalent imides, e.g. ``succinimide'', including N-substituted forms, e.g. ``N-iodosuccinimide''. Fixes parsing of salt multipliers, e.g. ``benzene trihydrate''. Fixes nitrogenous linker processing, e.g. ``N,N-dimethylsulfamoyl chloride''. Adds support for locants alpha, beta and gamma (as written in english), allowing us to handle ``alpha,alpha,alpha-trichlorotoluene'' and ``beta-mercaptoethanol''. Improvements to handle unspecified locants, e.g. ``chlorophenyl'' and ``pentachlorophenyl''. Support for substitutions on ``benzoyl'' and ``benzamido'' prefixes, e.g. ``4-nitrobenzoyl chloride''. Handling of names using di, tri etc. incorrectly when bis, tris etc. should have been used, e.g. ``2,4-di(t-butylperoxy)hexane''. Improvements to ring locant numbers on ``benzophenone'' and ``benzidine'', and support for primed locants on ring system parents. Adds N and N' locants to the hydrazine stem, e.g. ``4-(N',N'-dihydroxyhydrazino)benzoic acid''.

Treat ``imidamide'' as a synonym for ``amidine'', and ``hydrazinyl'' as a synonym for ``hydrazino''.

Adds suppprt for the element ``columbium'' (more commonly known as ``niobium'').

Adds support for the prefixes ``keto'' (synonym for ``oxo''), ``allophanoyl'', ``hydantoyl'', ``ureido'', ``carbamido'', ``lauryl'', ``myrsityl'', ``palmityl'', ``stearyl', ``carbamimidoyl'', ``sulfinamoyl'', ``thiocarbamoyl'', ``carbamothioyl'', ``carbamoyl'', ``guanyl'', ``morpholino'', ``oxycyano'', ``sulfinyl'', ``sulfonyl'' and ``fulminato''.

Added support for ``acetonyl'' and ``phenacyl'' as vinyl-like prefixes, including their ``...idene'' and ``..idyne'' variants.

Added support for the traditional stems ``vanillic acid'', ``isovanillic acid'', ``syringic acid'', ``arachidic acid'', ``behenic acid'', ``carboceric acid'', ``cerinic acid'', ``ceromelissic acid'', ``ceroplastic acid'', ``cerotic acid'', ``daturic acid'', ``enanthic acid'', ``geddic acid'', ``gheddic acid'', ``japanic acid'', ``lacceric acid'', ``lignoceric acid'', ``margaric acid'', ``melissic acid'', ``montanic acid'', ``pelargonic acid'', ``psylic acid'', ``thapsic acid'', ``brassylic acid'' and ``pyruvic acid''.

Added support for the stems ``ketene'', ``thioketene'', ``vanillin'', ``isovanillin'', ``rhodanine'', ``allophanic acid'', ``hydantoic acid'', ``picoline'', ``borate'' [BH4-], ``fulvene'', ``isobutene'', ``isoprene'', ``alloxane'', ``barbituric acid'', ``hydantoin'', ``cytosine'', ``guanine'', ``hydroxylamine'' and the common amino acids.

Adds support for the ring systems ``benzimidazole'', ``benzoimidazole'', ``benzothiophene'', ``benzoxazole'', ``benzooxazole'', ``benzothiazole'', ``benzotriazole'', ``benzotrioxazole'', ``pyrene'', ``perylene'', ``as-indacene'', ``s-indacene'', ``pyrrolizine'' and ``quinolizine''.

Added support for the ring suffix ``carbonyl chloride'' (and other acid halides).

Added support for the suffixes ``thioketone'', ``sulfide'', ``nitrite'', ``azanium'', ``thial'', ``diazonium'', ``arsonic acid'', ``peroxoic acid'', ``carboperoxoic acid'', ``carbothioamide'', ``carboximidamide'', ``carboxamidine'', ``aldehyde oxime'' ``one oxime''.

Added support for the linkers ``mercuri'', ``carbamimidoyl'', ``sulfinamoyl'', ``sulfamoyl'', ``thiocarbamoyl'', ``carbamothioyl'', ``carbonimidoyl'', and ``thioyl'' (as in ``ethanethioylbenzene'').

Added support for the salts ``hydrobromide'', ``hydrofluoride'', ``hydroiodide'', ``triiodide'', ``hydrotriiode'', ``sulfite'', ``peroxide'', ``perchlorate'', ``perbromate'', ``periodate'', ``hydrate'', ``nitrite'', ``hypochlorite'', ``chlorite'', ``chlorate'', ``bromate'', ``iodate'', ``nitrate'', ``cyanide'' and ``cyanate'' (including iso and thio variants).

Added support for ``hydrochloric acid'', ``hydrobromic acid'', ``hydrofluoric acid'', ``hydroiodic acid'', ``hydrotriiodic acid'', and ``tetronic acid''.

A.11.2 OECreateIUPACName Improvements

Added support for spiro, bicyclo and large simple heterocycle naming, all with hetero replacement nomenclature. No longer elide ring system prefix locants, which fixes the ambiguity with ``N-tetlinylacetamide'' which should be ``N-tetralin-1-ylacetamide''. Improvements to indicated hydrogen perception (a nitrogen with three ring bonds doesn't require an indicated hydrogen), improving our naming of ``indolizine'', ``pyrrolizine'' and ``quionlizine''. Improvements to naming cycloalkane rings attached via an oxygen linker, i.e. ``cyclopropoxy'' instead of ``cylopropyloxy''. Improvements in the handling of substituted linkers, ``carbamoyl'', ``thiocarbamoyl'', ``carbamimidoyl'', ``sulfamoyl'' and ``sulfinamoyl''. Improvements to alkyl chain termination, for example ``carboxymethyl'' instead of ``2-hydroxy-2-oxo-ethyl'' and ``cyanomethyl'' instead of ``nitridoethyl''. Improvements to amide, thioamide and sulfonamide atom typing to allow *C(=O)N=C* to be considered an N-substituted amide. Added support for more phosphane variants; *=P-*, *=PH and *#P. Add ``oxamide'' as a contraction of ``oxalamide''.

Fixes in multiple suffix processing, e.g. ``cyclohexane-1,4-diamine''. Fixes to the prefixes ``acryloyl'' and ``proprioloyl'' (and their acid halides) which were previously incorrectly named ``acrylyl'' and ``propiolyl''. Fixed handling of atom typed metals, fixing ``trichloromagnessium''. Corrected names for bivalent acid halides, e.g. ``malonyl dichloride''. Made ``benzoyl chloride'' the preferred name for ``benzenecarbonyl chloride'' and likewise for other benzoic acid halides. Fix spelling typos in ``acenaphthene'' and ``isothiazolidine''.

Added support for the parents ``heptalene'', ``octalene'', ``hydroxylamine'', ``hexahydropyrimidine'' (formerly ``1,2-diazinane''), and ``hexahydropyridazine'' (formerly ``1,3-diazinane'').

Added support for the prefixes ``acetonyl'', ``aceonylidene'', ``phenacyl'', ``phenacylidene'', ``ureido'', ``anilino'', ``hydantoyl'', ``allophanoyl'', ``amidino'', ``acetoxy'', ``isopropoxy'', ``isobutoxy'', ``sec-butoxy'', ``tert-butoxy'', ``morpholino'' (formerly ``morpholin-4-yl''), ``oxycyano'', ``sulfinyl'' (*=S=O), ``sulfonyl'' (*=S(=O)=O), and ``methylene'' (formerly ``methylidene'').

Added support for the linkers ``carbonimidoyl'', ``mercuri'' and ``benzoyl'' (replacing ``phenylcarbonyl'').

Add support for the suffixes ```amidine'', `ohydrazide'', ``carbohydrazide'', ``...one oxime'', ``...al oxime'', ``aldehyde oxime'' and ``nitrile oxide'' (note we consider both *C#N=O and *C#[N+][O-] nitrile oxides).

Added support for the salts ``triiodide'', ``hydrotriiodide'', ``hydrogen triiodide'', ``perbromate'', ``periodate'', ``sulfide'', ``sulfite'', ``peroxide'', ``iodate'', ``nitrite'' and ``hypochlorite''.

Added support for the molecule ``fulvene''.

				Lexichem Chemical Name to Structure and Structure to Name Conversion