Chemical File Formats

There are a number of file formats that can be used for storing chemical structures. One of the simplest is a tab or CSV file containing SMILES, but it is also possible to store explicitly the connection table. The slides below describe some of the more common of these, such as the SDfile , MOL file, and MOL2 File. These formats are very rich formats and can represent the stereochemistry as well as the 2D and 3D chemical structure information.


Before checking the video you should have a general idea about SMARTS . You will get all the information and examples here and here

The SMILES used in the video are:

CC(=O)Nc1ccc(O)cc1 Acetaminophen
CC(C)NCC(O)COc1ccccc1CC=C Alprenolol
CC(N)Cc1ccccc1 Amphetamine
CC(CS)C(=O)N1CCCC1C(=O)O Captopril
CN(C)CCCN1c2ccccc2Sc3ccc(Cl)cc13 Chlorpromazine
OC(=O)Cc1ccccc1Nc2c(Cl)cccc2Cl Diclofenac
NCC1(CC(=O)O)CCCCC1 Gabapentin
COC(=O)c1ccccc1O Salicylate
Nc1ccc(N=Nc2ccccc2)c(N)n1 PHENAZOPYRIDINE
C1=CC=C(C(=C1)C(=O)OC2=CC=CC(=C2)CO[N+](­=O)[O-])O AC1L1DBO
IC(=O)c1ccccc1 Benzoyl Iodide
CCOP(=S)(OCC)Oc1cc(Cl)cc(Cl)c1 Dichlofenthion

Example SMARTS used in the Video

Any atom in a ring that is not aliphatic Carbon
Hydroxyl group (-OH)
Two carbons separated by aromatic bond
Carbon and nitrogen attached by any bond
Carboxyl Group
carboxyl attached to a ring
Hits conjugate bases of carboxylic, carbamic, and carbonic acids.
Carbonyl with Carbon. Hits aldehyde, ketone, carboxylic acid (except formic), anhydride (except formic), acyl halides. Won't hit carbamic acid/ester, carbonic acid/ester.
Won't hit aldehyde or ketone.
Thiol group
Any carbon attached to any halogen
Acyl halide
Ether aliphatic O with 0 futher total connections
Amide Aliphatic N with 2 further total connections and aliphatic C with 0 further total connections
Primary or secondary amine, not amide.Aliphatic N with 1 or 2 futher total connections with 1,2 further hydrogen
Nitrate group
Azo Nitrogen.diazene
Hydroxyl ,
Hydroxyl in alcohol ,
Hydroxyl in Carboxylic Acid
Phenol Aliphatic O with 0 further total connections with 1 further hydrogen.
H-bond Acceptor where C is not in a ring and N not in a ring.double bonded to an oxygen
Aliphatic carbon that is ortho to an O and meta to an N