ACD/Name
Generate Name from Structure

VI. NATURAL PRODUCTS AND BIOCHEMISTRY

Although ACD/Name is designed to name general organic structures, some of the most important classes of biochemicals and natural products are recognized and added on a continuous basis.

The current version supports carbohydrate, amino acid, and peptide nomenclatures and can also treat derivatives of basic steroids, alkaloids, and terpenes.

VI.1. α-Amino Acids, Peptides and Derivatives

ACD/Name allows the generation of names for various derivatives of common α-amino acids and peptides.

Cyclic peptides composed of common amino acids can also be named.

For example:

IUPAC Name	(4R,5S)-4-methyl-5-phenyl-D-prolyl-L-valyl-D-cysteinyl-L-alanine
Index Name	L-alanine, (4R,5S)-4-methyl-5-phenyl-D-prolyl-L-valyl-D-cysteinyl-
IUPAC Name	cyclo(glycyl-L-prolyl-L-leucylglycyl-L-prolyl-L-leucyl)
Index Name	cyclo(glycyl-L-prolyl-L-leucylglycyl-L-prolyl-L-leucyl)

VI.2. Natural Product Parent Structures and Derivatives

ACD/Name IUPAC naming algorithm recognizes approximately 130 basic tri- and more cyclic parent structures of natural product derivatives. ACD/Name conventions for naming of these classes are based on the published IUPAC and IUBMB recommendations, mainly on chapter F of refs.[1] and [5].

ACD/Name Index naming algorithm recognizes approximately 70 basic 3- and more cyclic parent structures of natural product derivatives.

For example:

IUPAC Name	(7β,16R)-morphinan-7,16-diol
Index Name	morphinan-7,16-diol, (7β,16R)-
IUPAC Name	3β,5β,25R)-spirost-8(14)-en-3-ol
Index Name	spirost-8(14)-en-3-ol, (3β,5β,25R)-

Supported Natural Product Naming Operations

The following operations in the Natural product parent structures are supported:

1. Retained numbering scheme;
2. Substitution, i.e. 3-chloro-2-methylcholane or cholane, 3-chloro-2-methyl-;
3. Functional derivatives, i.e. gonane-6-carboxylic acid;
4. Modification of unsaturation degree; (-ene and -yne modifications; dehydro- and hydro- modifications), e.g., androst-9(11)-ene;
5. Stereochemical modifications, (α/β, R/S, cis/trans, E/Z), e.g., (3R,11cis)-3-chlororetinal
6. Substituent names for non-functional parent structures; and
7. Cyclo- and epoxy-modifications

For example:

IUPAC Name	(11cis)-retinol
Index Name	retinol, (11cis)-
IUPAC Name	(3α,5β,6β)-5,6-epoxypregnan-3-ol
Index Name	pregnan-3-ol, 5,6-epoxy-, (3α,5β,6β)-

Note: All stereo descriptors are cited in accordance with the general organic practice.
For example: (3β,5β)-3-bromoandrostane not 3β-bromo-5β-androstane.

Non-supported Natural Product Naming Operations

1. Cyclic modifications - nor, and homo in cyclic part, fusion, and fission of rings.
2. Lengthening and shortening of side chains (homo and nor modifications in acyclic parts).
3. Replacements of elements with other elements-"a"-modifications.

All structures with modifications mentioned above are refused to be named or are named according to general organic rules.

VI.3. Carbohydrates

Supported Carbohydrate Derivatives

Carbohydrate nomenclature for most of carbohydrate derivatives is supported according to Ref. [6]. The following types of carbohydrates are supported by ACD/Name in cyclic and acyclic forms:

ACD/Name supports naming of N-glycosyl derivatives of heterocycles that were previously refused.

For example:

IUPAC Name	2-chloro-2,3-dideoxy-α-D-lyxo-hexofuranosyl 4,6-O-(1-methylethylidene)-β-D-idopyranoside
Index Name	β-D-idopyranoside, 2-chloro-2,3-dideoxy-α-D-lyxo-hexofuranosyl 4,6-O-(1-methylethylidene)-
IUPAC Name	1-β-L-ribofuranosyl-1,5-dihydro-4H-imidazo[4,5-c]pyridin-4-one
Index Name	4H-imidazo[4,5-c]pyridin-4-one, 1,5-dihydro-1-β-L-ribofuranosyl-

Note: The most correct carbohydrate names can be generated for wedge-bond specified stereochemical configurations only - not for Haworth, Chair, or Fisher presentations.

Non-supported Carbohydrate Derivatives

The following types of carbohydrates are not supported:

For each structure which contains such fragments the following warning is generated: "Structure contains unsupported carbohydrate derivative". To generate the non-carbohydrate name for such compounds, the user needs to switch off the check box on the Custom tab in the Preferences dialog box.

Carbohydrate Representations

ACD/Name supports three main types of structure presentations: Haworth, Fisher and general stereo representations. An easy way to view these is in the Templates Window, which can be accessed through the ChemSketch Window.

Common Stereo Representation

This is a preferred method for the designation of stereo configuration and is treated in accordance with ACD/Name stereoconventions described in the Stereochemistry chapter of this document.
For example:

IUPAC Name	3-deoxy-3-methyl-β-D-gulopyranosyl bromide
Index Name	β-D-gulopyranosyl bromide, 3-deoxy-3-methyl-

Haworth and Fisher representations are less preferred as soon as they need more careful designation of stereoconfigurations.
The following four possible Haworth structures lead to the generation of the same name:

IUPAC Name	methyl 6-deoxy-β-D-idopyranoside
Index Name	β-D-idopyranoside, methyl 6-deoxy-

Fisher representation is supported for acyclic carbohydrates only.

For example:

IUPAC Name	2-bromo-2-deoxy-D-xylaric acid
Index Name	D-xylaric acid, 2-bromo-2-deoxy-

VI.4 Nucleotides and Nucleosides

The new version of ACD/Name recognizes nucleosides, nucleotides, and some of their derivatives. The following seven basic nucleosides and their derivatives are supported:

The following procedures are supported for parent nucleosides: substitution, deoxy modifications, hydro- and dehydro prefixes, cyclic acetals, 3'- and 5'-tri, di, and monophosphate esters.

For example:

IUPAC Name	2'-deoxy-2'-fluoro-8-methyladenosine 5'- (trihydrogen diphosphate)	5'-O-acetyl-5-methyl-2',3'-O-(1 -methylethylidene)cytidine
Index Name	adenosine, 2'-deoxy-2'-fluoro-8-methyl-, 5'-(trihydrogen diphosphate)	cytidine, 5-methyl-2',3'-O- (1-methylethylidene)-, 5'-acetate

VI.5 Porphyrin-like structures

ACD/Name supports naming of porphyrin, phthalocyanine, porphyrazine, and phorbine derivatives according to IUPAC and CAS nomenclature rules.

Note: IUPAC recommends the use of porphyrin as a parent while CAS recommends the use of porphine for the same structure.

For example:

IUPAC Name	dimethyl 3,3'-(7,12-diethyl-3,8,13,17-tetramethyl-2,18-porphyrindiyl)dipropanoate
Index Name	21H,23H-porphine-2,18-dipropanoic acid, 7,12-diethyl-3,8,13,17- tetramethyl-, dimethyl ester