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| − | + | This page is a sandbox for the upcoming guide for SMILES. | |
| − | This | + | ; Symbols |
| + | {| class="wikitable sortable" | ||
| + | ! Name !! SMILES !! Example name !! Example SMILES | ||
| + | |- | ||
| + | | Zero bond || <code>.</code> || XKCD Oxygen crystal || <pre>[O].[O]</pre> | ||
| + | |- | ||
| + | | Single bond || <code>-</code><ref name="singlebond" group="note"/> || Ethane || <pre>C-C</pre> | ||
| + | |- | ||
| + | | Double bond || <code>=</code> || Ethene || <pre>C=C</pre> | ||
| + | |- | ||
| + | | [[Linguistics Club|Sesqui]] bond || <code>:</code> || Benzene (sesqui bond notation) || <pre>C1:C:C:C:C:C:1</pre> | ||
| + | |- | ||
| + | | Triple bond || <code>#</code> || Ethyne || <pre>C#C</pre> | ||
| + | |- | ||
| + | | Branch group R || <code>(<i>R</i>)</code> || Isobutane || <pre>CC(C)C</pre> | ||
| + | |- | ||
| + | | Branch group R via double bond || <code>(=<i>R</i>)</code> || Acetic acid || <pre>CC(=O)O</pre> | ||
| + | |- | ||
| + | | Teleport bond || <code><i>1</i></code> || Cyclohexane || <pre>C1CCCCC1</pre> | ||
| + | |- | ||
| + | | Teleport bond with multiple-digit ID such as "12" || <code>%<i>12</i></code> || tricyclo[2.1.0.0<sup>1,3</sup>]pentane || <pre>C1%12CC2%12CC12</pre> | ||
| + | |- | ||
| + | | Aromatic carbon atom || <code>c</code> || Benzene (lowercase notation) || <pre>c1ccccc1</pre> | ||
| + | |- | ||
| + | | Aromatic nitrogen atom || <code>n</code> || Pyridine (lowercase notation) || <pre>n1ccccc1</pre> | ||
| + | |- | ||
| + | | Aromatic oxygen atom || <code>o</code> || Furan (lowercase notation) || <pre>o1cccc1</pre> | ||
| + | |- | ||
| + | | Element "A" with mass number b || <code>[<i>bA</i>]</code> || Deuterium gas || <pre>[2H][2H]</pre> | ||
| + | |- | ||
| + | | An "A" ion with positive charge b || <code>[<i>A</i>+<i>b</i>]</code> || Sodium ion || <pre>[Na+1]</pre> | ||
| + | |- | ||
| + | | An "A" ion with negative charge b || <code>[<i>A</i>-<i>b</i>]</code> || Chlorine ion || <pre>[Cl-1]</pre> | ||
| + | |- | ||
| + | | <pre>A D | ||
| + | \ / | ||
| + | C = C | ||
| + | / \ | ||
| + | B E</pre><ref group="note" name="cistrans"/> || <code><i>A</i>/C(<i>B</i>)=C(<i>D</i>)/<i>E</i></code> || Cis-but-2-ene || <pre>[H]/C(C)=C([H])/C</pre> | ||
| + | |- | ||
| + | | <pre>D B | ||
| + | \ / | ||
| + | A | ||
| + | | | ||
| + | E</pre><ref group="note" name="chirality"/> || <code><i>A</i>[C@](<i>B</i>)(<i>D</i>)<i>E</i></code> || L-alanine || <pre>N[C@](C)([H])C(=O)O</pre> | ||
| + | |} | ||
| + | |||
| + | ; Useful substrings | ||
| + | {| class="wikitable sortable" | ||
| + | ! Name !! SMILES | ||
| + | |- | ||
| + | | Osazone || <code>C(=NNC1=CC=CC=C1)C(=NNC1=CC=CC=C1)</code> | ||
| + | |} | ||
| + | |||
| + | == Notes == | ||
| + | <references group="note"> | ||
| + | <ref name="singlebond">Single bond <code>-</code> is often omitted.</ref> | ||
| + | <ref name="cistrans">You can also use the <code>\</code> character. In this case, Cis-but-2-ene can be represented as <code>C/C=C\C</code>.<br>If A is larger than B and D is larger than E, this is called a "Z-" structure. If A is smaller than B and D is larger than E, this is called a "E-" structure.</ref> | ||
| + | <ref name="chirality">This is a top view of the molecule, with the carbon atom obscured under the "A" with a single bond in between.<br>The structure can also be represented as <code><i>A</i>[C@@](<i>D</i>)(<i>B</i>)<i>E</i></code>.</ref> | ||
| + | </references> | ||
| + | |||
| + | httpd://conwaylife.com/forums/viewtopic.php?f=12&t=4249&p=144482#p144482 | ||
| + | [[:Category:Chemistry]] | ||
Latest revision as of 12:42, 5 May 2023
This page is a sandbox for the upcoming guide for SMILES.
- Symbols
| Name | SMILES | Example name | Example SMILES |
|---|---|---|---|
| Zero bond | . |
XKCD Oxygen crystal | [O].[O] |
| Single bond | -[note 1] |
Ethane | C-C |
| Double bond | = |
Ethene | C=C |
| Sesqui bond | : |
Benzene (sesqui bond notation) | C1:C:C:C:C:C:1 |
| Triple bond | # |
Ethyne | C#C |
| Branch group R | (R) |
Isobutane | CC(C)C |
| Branch group R via double bond | (=R) |
Acetic acid | CC(=O)O |
| Teleport bond | 1 |
Cyclohexane | C1CCCCC1 |
| Teleport bond with multiple-digit ID such as "12" | %12 |
tricyclo[2.1.0.01,3]pentane | C1%12CC2%12CC12 |
| Aromatic carbon atom | c |
Benzene (lowercase notation) | c1ccccc1 |
| Aromatic nitrogen atom | n |
Pyridine (lowercase notation) | n1ccccc1 |
| Aromatic oxygen atom | o |
Furan (lowercase notation) | o1cccc1 |
| Element "A" with mass number b | [bA] |
Deuterium gas | [2H][2H] |
| An "A" ion with positive charge b | [A+b] |
Sodium ion | [Na+1] |
| An "A" ion with negative charge b | [A-b] |
Chlorine ion | [Cl-1] |
A D \ / C = C / \ B E[note 2] |
A/C(B)=C(D)/E |
Cis-but-2-ene | [H]/C(C)=C([H])/C |
D B \ / A | E[note 3] |
A[C@](B)(D)E |
L-alanine | N[C@](C)([H])C(=O)O |
- Useful substrings
| Name | SMILES |
|---|---|
| Osazone | C(=NNC1=CC=CC=C1)C(=NNC1=CC=CC=C1)
|
Notes[edit]
- ↑ Single bond
-is often omitted. - ↑ You can also use the
\character. In this case, Cis-but-2-ene can be represented asC/C=C\C.
If A is larger than B and D is larger than E, this is called a "Z-" structure. If A is smaller than B and D is larger than E, this is called a "E-" structure. - ↑ This is a top view of the molecule, with the carbon atom obscured under the "A" with a single bond in between.
The structure can also be represented asA[C@@](D)(B)E.
httpd://conwaylife.com/forums/viewtopic.php?f=12&t=4249&p=144482#p144482 Category:Chemistry
