Molecules

Out[]=
The Wolfram|Alpha Chemistry Team
Molecules can be created in silico by passing a variety of information into the
Molecule
function.

Creation

Let’s consider propane which is the gas used in barbeque grills all over the world.
Build up a propane molecule atom by atom, bond by bond or use the corresponding chemical
Entity
:
propaneAtomBond=Molecule[{"C","H","H","H","C","H","H","C","H","H","H"},{Bond[{1,2},"Single"],Bond[{1,3},"Single"],Bond[{1,4},"Single"],Bond[{1,5},"Single"],Bond[{5,6},"Single"],Bond[{5,7},"Single"],Bond[{5,8},"Single"],Bond[{8,9},"Single"],Bond[{8,10},"Single"],Bond[{8,11},"Single"]}]
Out[]=
Molecule
Formula:
C
3
H
8
Atoms: 11 Bonds: 10

propaneEntity=Molecule
propane
CHEMICAL

Out[]=
Molecule
Formula:
C
3
H
8
Atoms: 11 Bonds: 10

Create propane from its common or Systematic International Union of Pure and Applied Chemistry (IUPAC) name:
propaneCommonName=Molecule["propane"]
Out[]=
Molecule
Formula:
C
3
H
8
Atoms: 11 Bonds: 10

propaneIUPACName=Molecule["Tricarbane"]
Out[]=
Molecule
Formula:
C
3
H
8
Atoms: 11 Bonds: 10

Create propane from identifiers such as SMILES (Simplified Molecular-Input Line-Entry System) or InChI (International Chemical Identifier):
propaneSMILES=Molecule["CCC"]
Out[]=
Molecule
Formula:
C
3
H
8
Atoms:
11
Bonds:
10

propaneInChI=Molecule["InChI=1S/C3H8/c1-3-2/h3H2,1-2H3"]
Out[]=
Molecule
Formula:
C
3
H
8
Atoms:
11
Bonds:
10

MoleculeMatchQ
combined with
AllTrue
can be used to verify that the different representations give the same molecule:
propaneList={propaneAtomBond,propaneEntity,propaneCommonName,propaneIUPACName,propaneSMILES,propaneInChI};​​AllTrue[propaneList,MoleculeMatchQ[propaneAtomBond,#]&]
Out[]=
True

Recognition

Chemists communicate chemical structure information with structure diagrams in the literature.
images=
images
;​​GraphicsRow[images]
Out[]=
Use
MoleculeRecognize
to make
Molecule
objects from such images.
Grid[Map[{#,MoleculeRecognize[#]}&,images]]
Out[]=
Molecule
Formula:
C
15
H
16
FN
O
2
Atoms:
35
Bonds:
36

Molecule
Formula:
C
37
H
45
N
5
O
2
S
Atoms:
90
Bonds:
96

Molecule
Formula:
C
22
H
28
N
2
O
4
S
Atoms:
57
Bonds:
59

Out[]=
Close
TOC