Alhamdullilah, praise to be upon HIM, The Most Gracious and Merciful Lord. Today, we are fortunate to learn new things that practically can be apply in our daily life. Our new lessons for Computer in Science is related with S.M.I.L.E.
The simplified molecular input line entry specification or SMILES is a
specification for unambiguously describing the structure of chemical
molecules using short ASCII strings. SMILES strings can be imported by
most molecule editors for conversion back into two-dimensional drawings
or three-dimensional models of the molecules. For further clarification, click here.
Examples of chemical campound in S.M.I.L.E:
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Ethanol
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CCO
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Acetic acid
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CC(=O)O
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Cyclohexane
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C1CCCCC1
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Pyridine
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c1cnccc1
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Trans-2-butene
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C/C=C/C
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L-alanine
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N[C@@H](C)C(=O)O
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Sodium chloride
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[Na+].[Cl-]
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Displacement reaction
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C=CCBr>>C=CCI
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SMILES Symbols
· String of alphanumeric
characters and certain punctuation symbols
· Terminates at the first space encountered when read left to
right
· The organic subset are B,C,N,O,P and others
Other SMILES Atoms
Aliphatic or nonaromatic
carbon: C. Atom in aromatic ring: lowercase letter. Designate
ring closure with pairs of matching digits.
For example, C1CCCCC1 is Cyclohexane
SMILES Charges
l. Specify attached hydrogens
and charges in square brackets
2. Number of
attached hydrogens is the symbol H followed by optional digit.
SMILES Cyclic Structures
: Break one single or one aromatic bond
in each ring
: Number in any order
–Designate ring-breaking atoms by the
same digit following the atomic symbol
Cyclic Structures
Numbers indicate start and stop of ring
Same number indicates start and end of
the ring, entered immediately following the start/end atoms
Further Restrictions
A
branch cannot begin a SMILES notation - A branch cannot immediately follow
a double- or triple-bond symbol-Example: C=(CC)C is invalid, butlC(=CC)C or
C(CC)=C are valid SMILES
Disconnected Structures
Tetramethyl ammonium bromide
C[N+]C(C)C.[Br-]
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