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Sign Up Sign In. Lobby Slots Table Live. Show me the Mummy. Tournament Dragon King Tournament Read more. An additional type of bond is a "non-bond", indicated with.
An aromatic "one and a half" bond may be indicated with: Ring structures are written by breaking each ring at an arbitrary point although some choices will lead to a more legible SMILES than others to make an acyclic structure and adding numerical ring closure labels to show connectivity between non-adjacent atoms.
For a second ring, the label will be 2. SMILES does not require that ring numbers be used in any particular order, and permits ring number zero, although this is rarely used.
Also, it is permitted to reuse ring numbers after the first ring has closed, although this usually makes formulae harder to read. Multiple digits after a single atom indicate multiple ring-closing bonds.
Either or both of the digits may be preceded by a bond type to indicate the type of the ring-closing bond. The first form is preferred.
Ring-closing bonds may not be used to denote multiple bonds. However, they may be used with non-bonds; C1. C12 is a peculiar but legal alternative way to write propane , more commonly written CCC.
For example, cyclohexane-1,2-diol is most simply written as OC1CCCCC1O ; choosing a different ring-break location produces a branched structure that requires parentheses to write.
Aromatic rings such as benzene may be written in one of three forms:. In the latter case, bonds between two aromatic atoms are assumed if not explicitly shown to be aromatic bonds.
When aromatic atoms are singly bonded to each other, such as in biphenyl , a single bond must be shown explicitly: This is one of the few cases where the single bond symbol - is required.
In fact, most SMILES software can correctly infer that the bond between the two rings cannot be aromatic and so will accept the nonstandard form c1ccccc1c2ccccc2.
The first atom within the parentheses, and the first atom after the parenthesized group, are both bonded to the same branch point atom. Branches may be written in any order.
Generally, a SMILES form is easiest to read if the simpler branch comes first, with the final, unparenthesized portion being the most complex.
The only caveats to such rearrangements are:. The one form of branch which does not require parentheses are ring-closing bonds. Choosing ring-closing bonds appropriately can reduce the number of parentheses required.
For example, toluene is normally written as Cc1ccccc1 or c1ccccc1C , avoiding the parentheses required if written as c1ccc C ccc1 or c1ccc ccc1 C.
Bond direction symbols always come in groups of at least two, of which the first is arbitrary. When alternating single-double bonds are present, the groups are larger than two, with the middle directional symbols being adjacent to two double bonds.
Configuration at tetrahedral carbon is specified by or. Looking toward the central carbon from the perspective of the first bond, the other three are either clockwise or counter-clockwise.
These cases are indicated with and , respectively because the symbol itself is a counter-clockwise spiral. For example, consider the amino acid alanine.
While the order is which branches are specified in SMILES is normally unimportant, in this case it matters; swapping any two groups requires reversing the chirality indicator.
The SMILES specification includes elaborations on the symbol to indicate stereochemistry around more complex chiral centers, such as trigonal bipyramidal molecular geometry.
Isotopes are specified with a number equal to the integer isotopic mass preceding the atomic symbol. Benzene in which one atom is carbon is written as [14c]1ccccc1 and deuterochloroform is [2H]C Cl Cl Cl.
To illustrate a molecule with more than 9 rings, consider cephalostatin -1,  a steroidic ringed pyrazine with the empirical formula C 54 H 74 N 2 O 10 isolated from the Indian Ocean hemichordate Cephalodiscus gilchristi:.
While it uses many of the same symbols as SMILES, it also allows specification of wildcard atoms and bonds, which can be used to define substructural queries for chemical database searching.
Atoms can additionally be identified with a number e. This conversion is not always unambiguous. Conversion to three-dimensional representation is achieved by energy-minimization approaches.
There are many downloadable and web-based conversion utilities. From Wikipedia, the free encyclopedia. For other uses, see Smiles disambiguation.
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