Substructure Codes

¹³C chemical shift searching is initiated with the command JJ.  Searching from a displayed molfile is in development.

The substructure code is a simple, text-based system for classifying carbons by their type, nearest neighbors and next nearest neighbors.   Each different type of carbon (methyl, carbonyl, phenyl, etc) is assigned a number.  Its substituents are indicated by upper case letters, usually alphabetically.  For each substituent, its substituents are, in turn, indicated by lower case letters, usually listed alphabetically.

For main groups and their substituents that are part of a ring, the number or upper-case letter is enclosed in parentheses.  This does not apply to the ring systems designated explicitly (numbers 10-15).  See examples below.

The following 2 tables show the numbers for each type of carbon, and the letters for each substituent. 

Partial codes can be entered for searching.  For example, 2-B will return all CH₂s which have at least one CH₂ substituent.

For olefin, phenyl and pyridine (types 5, 10 and 11, respectively), it is necessary to use * as a "wildcard".  For example, 10-E*** will return all chloro-substituted phenyl carbons.

Try doing a Ref # or Range search first, and look at the codes returned to get a better idea of how the coding works.

Main Groups

Group	Example	Code and Comments
1.  CH3--R1	CH3-CH2-OH	1-Bp
2.  CH2--R1,2	CH3-CH2-OH	2-AP    list substituents alphabetically
3.  CH--R1,2,3	(CH3-CH2)2-CH-OH	3-BaBaP  list substituents alphabetically
4.  C--R1,2,3,4	(CH3)3-C-OH	4-AAAP   list substituents alphabetically
5.		List substituents starting with directly bonded groups, alphabetically, then gem, cis and trans to the first group, in that order *5-ABaEH   and   5-EHABa
6.		List directly bonded substituents first, alphabetically, then N substituent 6-ABaH   for C=N carbon methyl:  1-Mb ethyl:   1-Bm and 2-AMa
7.		List directly bonded substituent first *7-AH    and    7-HA methyl:  1-Th
8.    R--CN	CH3-CH2-CN	8-Ba   for the cyano C ethyl:  1-Bm   and   2-AM
9.		9-ABa  for the carbonyl methyl:  1-Jb ethyl:   1-Bj   and    2-AJa
10.		List directly bonded substituent, then ortho substituents, alphabetically, then para substituent *10-EAPF The other ring carbons are, clockwise: 10-PEHH 10-HFPA 10-FHHE 10-HAFP 10-AEHH
11.		List directly bonded substituent first, followed by ortho substituents, alphabetically.  (The report will include a lower case letter (a, b or g) following the number indicating alpha, beta or gamma.  Don't use this a, b or g in searching.) 11-AH    for C alpha to N 11-HAE  for C beta to N   11-EHH  for C gamma to N report will show 11-a-AH, 11-b-HAE and 11-g-EHH
12.		*12-JhH List directly bonded substituent first, followed by ortho substituents, alphabetically.  The report will include lower case letter (a or b) following the number indicating alpha or beta  (12-a-JhH in this case).
13.		*13-AHH List directly bonded substituent first, followed by ortho substituents, alphabetically.  The report will include lower case letter (a or b) following the number indicating alpha or beta (13-b-AHH in this case).
14.		*14-HEH List directly bonded substituent first, followed by ortho substituents, alphabetically.  The report will include lower case letter (a or b) following the number indicating alpha or beta (14-b-HEH in this case).
15.  Miscellaneous aromatic		*15-(quinolyl-4)-H List directly bonded substituent only.  Indicate ring system and position after number, in parentheses.

Substituent Groups

A.  --CH3	J.	S.   --S--
B.  --CH2--R1	K.	T.
C.  --CH--R1,2	L.    --C=	U.  --CN
D.  --C--R1,2,3	M.   --C=N	V.  phenyl
E.  --Cl	N.   --N=	W.  Misc. aromatic
F.  --F	O.  --O--  or  --O-->	X.   P
G.  --Br	P.  --OH	Y.   Si
H.  --H	Q.	Z.   Misc. atom
I.   --I	R.   --NO2

For a phenyl substituent, V, list its two ortho substituents in lower case letters, alphabetically.

Note that K and Q are different, as illustrated below:

Cyclic structures

Some rings are encoded explicitly (groups 10-15, above).  Other rings are indicated using the codes described above, but using parentheses to indicate that the atom is part of a ring.  Only main group numbers and nearest neighbors (upper case letters) are so indicated.  

  
The CH is coded as 3-ABaBa  (A for methly, Ba for each CH₂-CH₃)

The indicated CH has the similar substituents as above (one methyl, 2 methylenes) but they are now in a ring.  The CH is encoded as   (3)-A(B)b(B)b     Note that lower case letters are not in parentheses.

If a methylene is in a ring, by definition, both of its substituents are in the ring.  Methyls can never be part of a ring.

Another example:

The indicated carbon is coded as   5-(C)bbHHH   because the attached CH is part of a ring.  The olefinic CH₂ is    5-HHH(C)bb

The other carbons in this molecule are coded as:

methyl    1-(L)bl

Ring carbons, starting with C bearing methyl and proceeding clockwise:

(5)-A(B)bH(B)c    olefinic Cs are coded with attached, gem, cis and trans, respectively

(2)-(B)c(L)al

(2)-(B)l(C)bl

(3)-(B)b(B)lLhl    C bearing the olefinic substituent

(2)-(C)bl(L)hl

(5)-(B)cH(B)bA

Last updated: 2/10/04