WOLFRAM NOTEBOOK

Chemical Representations

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For each molecular entity a wide range of properties can be measured and stored. Since only a subset of those properties are required to answer any particular chemical question, many different chemical representations have been developed in chemistry. These representations allow one to quickly communicate just the right amount of information. Knowing which chemical representation is relevant in a given chemical context is the foundation of good chemical intuition and computation.

Atomic

If only atomic or isotopic properties are required an
Atom
is the necessary representation.
A seaborgium atom:
Atom["Sg"]
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Atom[Sg]

Mass Composition

When only mass, charge and elemental composition properties are required a
ChemicalFormula
is the correct representation.
The chemical formula for uranyl tetrahydroxide dianion:
ChemicalFormula["UO2(OH)4-2"]
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2-
U
O
2
(OH)
4

Structural

If both structural information and mass composition properties are required a
Molecule
is the necessary representation.
A molecule of bromobenzene:
Molecule["bromobenzene"]
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Molecule
Formula:
C
6
H
5
Br
Atoms: 12 Bonds: 12
When multiple molecules are connected together to form DNA, RNA or peptides a
BioSequence
is the correct representation.
A peptide sequence containing sixty-three amino acids:
BioSequence["Peptide","ITGTSTVGVGRGVLGDQKNINTTYSTYYYLQDNTRGNGIFTYDAKYRTTLPGSLWADADNQFF"]
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BioSequence
Type: Peptide Sequence
Content: ITGTST…QFF 
(63 letters)

Experimental

If experimentally measured properties are necessary then a built in
Entity
is the necessary representation.
The melting point of fructose:
D-(-)-fructose
CHEMICAL
melting point
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105.
°C

Mixed

When how much of a molecular entity is present or properties from different representations are needed use a
ChemicalInstance
.
An experimentally measured melting point:
ChemicalInstance[ChemicalFormula["H2Se"],<|QuantityVariable["MeltingTemperature"]->Quantity[Around[-63.73,0.01],"DegreesCelsius"]|>]
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ChemicalInstance
H
2
Se
,
MeltingTemperature
(-63.730
±
0.010
)
°C
A measured amount of ferrocene:
ChemicalInstance
ferrocene
CHEMICAL
,Quantity[Around[930.1,0.1],"Milligrams"]
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ChemicalInstance
ferrocene
,
(930.10
±
0.10
)
mg
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