Select Functional Group Dialog Box

Select a functional group to use in the analysis of the input structures to find R groups.

To open this dialog box, click the Define button in the R-Group Creator panel.

Features
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Select Functional Group Dialog Box Features

Functional group to identify area
Selected functional group display

Functional group to identify area

Click on the functional group that you want to use to analyze the input structures for R groups. The bond that is broken to form the R group is indicated with a red line across the bond. The R group is shown in black, the part that is discarded is shown in red. When you click on a functional group in the table, the (long) name is shown below the functional group area.

The structures shown in this area are relatively common reagents used to synthesize organic molecules. They are listed below with their names and a description.

Table 1. Functional groups with definitions
Structure	Name	Definition of R, R', R", Alk, Ar, Vi, A
	Acid_Chloride_C_C	R can be anything with a carbon attached to the carbonyl.
	Acid_Chloride_C_Cl	See above
	Alcohol_C_O	R can be an alkyl or aryl group. R cannot have a carbonyl attached to the oxygen of the alcohol.
	Alcohol_O_H	See above
	Alkoxylamine_N_H	R can be H or anything with a carbon attached to the oxygen of the alkoxylamine.
	Alkoxylamine_O_N	See above
	Alkyl_Bromide_C_Br	R can be almost anything: H, alkyl, aryl, alkenyl, alkynyl; alkoxy, aryloxy, alkoxycarbonyl, or aryloxycarbonyl with oxygen attached to CH₂; silyl with silicon attached to CH₂; alkylamino, arylamino, alkylaminocarbonyl, or arylaminocarbonyl with nitrogen attached to CH₂; alkylthio, arylthio, alkylsulfinyl, arylsulfinyl, alkylsufonyl, or arylsulfonyl with sulfur attached to CH₂; ketone with carbonyl attached to CH₂; cyano. R cannot be chloro, iodo, chlorocarbonyl (carbonyl attached to CH₂).
	Alkyl_Iodide_C_I	Same as for alkyl bromides
	Alkyl_Sulfonate_C_O	Same as for alkyl bromides
	Any_Iodide_A_I	A can be any atom.
	Alkyne_C_H	R can be H, alkyl, aryl, silyl.
	Amine_General_N_H	R can be H, alkyl, aryl. R cannot have a carbonyl carbon attached to the nitrogen of the amine. R' can be H, alkyl, aryl. R' cannot have a carbonyl carbon attached to the nitrogen of the amine.
	Amine_General_Aryl_N_H	Ar can be aryl. R can be H, alkyl, aryl. R cannot have a carbonyl attached to the nitrogen of the amine.
	Amine_Primary_Alkyl_N_H	R can be H, alkyl. R cannot have a carbonyl attached to the nitrogen of the amine.
	Amine_Primary_Aryl_N_H	Ar can be aryl.
	Amine_Primary_General_N_H	R can be alkyl, aryl. R cannot have a carbonyl carbon attached to the nitrogen of the amine.
	Amine_Secondary_Alkyl_N_H	R can be alkyl. R cannot have a carbonyl carbon attached to the nitrogen of the amine. R' can be alkyl. R' cannot have a carbonyl carbon attached to the nitrogen of the amine.
	Amine_Secondary_Aryl_N_H	Ar can be aryl. R can be alkyl, aryl. R cannot have a carbonyl carbon attached to the nitrogen of the amine.
	Amine_Secondary_General_N_H	R can be alkyl, aryl. R cannot have a carbonyl carbon attached to the nitrogen of the amine. R' can be alkyl, aryl. R' cannot have a carbonyl carbon attached to the nitrogen of the amine.
	Amino_Acid_C_C	R can be H, alkyl, aryl.
	Aryl_or_Vinyl_Bromide_C_Br	Ar is an aryl group; Vi is a vinyl (C=C) group. The aryl or vinyl group must be directly attached to the Br.
	Aryl_or_Vinyl_Iodide_C_I	Ar is an aryl group; Vi is a vinyl (C=C) group. The aryl or vinyl group must be directly attached to the I.
	Aryl_or_Vinyl_Thiol_S_H	Ar is an aryl group; Vi is a vinyl (C=C) group. The aryl or vinyl group must be directly attached to the S.
	alphaBromocarbonyl_C_Br	R can be alkyl, aryl. R' can be H, alkyl, aryl.
	Carbamoyl_Chloride_C_Cl	R can be anything with a carbon attached to nitrogen. R' can be anything with a carbon attached to nitrogen.
	alphaCarbonyl_C_H	R can be H, alkyl, aryl, alkoxy with oxygen attached to carbonyl. R' can be H, alkyl, aryl, carbonyl with carbonyl carbon attached to CH, cyano. R" can be H, alkyl, aryl, carbonyl with carbonyl carbon attached to CH, cyano.
	Carboxylic_Acid_C_C	R can be anything with carbon attached to carbonyl.
	Carboxylic_Acid_C_O	See above
	Carboxylic_Acid_O_H	See above
	Carboxylic_Acid_Ester_C_O	R can be anything with carbon attached to carbonyl. R' can be anything with carbon attached to the oxygen except for a carbonyl carbon.
	Chloroformate_C_Cl	R can be anything with carbon attached to oxygen.
	Hydrazine_C_N	R can be H or anything with a carbon attached to the nitrogen of the hydrazine.
	Hydrazine_N_H	See above
	Hydrazine_N_N	See above
	Isocyanate_C_N	R can be anything with a carbon attached to the nitrogen of the NCO.
	Sulfonamide_N_H	R can be anything with a carbon attached to the sulfur of the SO₂.
	Sulfonyl_Chloride_S_Cl	R can be anything with a carbon attached to the sulfur of the SO₂.
	Thiol_S_H	R can be H, alkyl, aryl, vinyl. R cannot have the carbon of a carbonyl attached to the sulfur.
	Weinreb_Amide_C_N	R can be alkyl, aryl. R cannot have a carbonyl carbon attached to the amide carbonyl.
	Boronic_Acid/Ester_C_B	R can be alkyl, aryl.
	Grignard_Reagent_C_Mg	R can be alkyl, aryl.

Selected functional group display