Skeletal formula

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The skeletal formula of the antidepressant drug escitalopram, featuring skeletal representations of heteroatoms, a triple bond, phenyl groups and stereochemistry

The skeletal formula, also called line-angle formula or shorthand formula, of an organic compound is a type of molecular structural formula that serves as a shorthand representation of a molecule's bonding and some details of its molecular geometry. A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule.[1] It is represented in two dimensions, as on a page of paper. It employs certain conventions to represent carbon and hydrogen atoms, which are the most common in organic chemistry.

The technique was developed by the organic chemist Friedrich August Kekulé von Stradonitz. Skeletal formulae have become ubiquitous in organic chemistry, partly because they are relatively quick and simple to draw. They can be thought of as abbreviated Lewis structures observing the following conventions: (1) a carbon atom is indicated as the terminus of a line segment or the meeting point of line segments; (2) hydrogen atoms connected to carbon atoms are not shown but are implied, such that each carbons atom is bonded to the number of hydrogen atoms that would satisfy the octet rule, or otherwise maintain consistency with the formal charge and the number of explicitly indicated nonbonding electrons on the carbon; (3) heteroatoms and hydrogen atoms attached thereto are shown as a single group (e.g., OH, NH2) without explicitly showing the heteroatom–hydrogen bonds; (4) nonbonding electron pairs on heteroatoms are optionally shown. As in a Lewis structure, a doubled or tripled line segment indicates double or triple bonding, respectively.

Although Haworth projections and Fischer projections look somewhat similar to skeletal formulae, there are differences in the conventions used, which the reader needs to be aware of in order to understand the details of a molecule.

The skeleton[edit]

The skeletal structure of an organic compound is the series of atoms bonded together that form the essential structure of the compound. The skeleton can consist of chains, branches and/or rings of bonded atoms. Skeletal atoms other than carbon or hydrogen are called heteroatoms.[2]

The skeleton has hydrogen and/or various substituents bonded to its atoms. Hydrogen is the most common non-carbon atom that is bonded to carbon and, for simplicity, is not explicitly drawn. In addition, carbon atoms are not generally labelled as such directly (i.e. with a "C"), whereas heteroatoms are always explicitly noted as such (i.e. using "N" for nitrogen, "O" for oxygen, etc.)

Heteroatoms and other groups of atoms that give rise to relatively high rates of chemical reactivity, or introduce specific and interesting characteristics in the spectra of compounds are called functional groups, as they give the molecule a function. Heteroatoms and functional groups are known collectively as "substituents", as they are considered to be a substitute for the hydrogen atom that would be present in the parent hydrocarbon of the organic compound in question.

Implicit carbon and hydrogen atoms[edit]

For example, in the image below, the skeletal formula of hexane is shown. The carbon atom labeled C1 appears to have only one bond, so there must also be three hydrogens bonded to it, in order to make its total number of bonds four. The carbon atom labelled C3 has two bonds to other carbons and is therefore bonded to two hydrogen atoms as well. A ball-and-stick model of the actual molecular structure of hexane, as determined by X-ray crystallography, is shown for comparison, in which carbon atoms are depicted as black balls and hydrogen atoms as white ones.

The skeletal formula of hexane, with carbons number one and three labelled
The 3d ball representation of hexane, with carbon (black) and hydrogen (white) shown explicitly.

NOTE: It doesn't matter which end of the chain you start numbering from, as long as you're consistent when drawing diagrams. The condensed formula or the IUPAC name will confirm the orientation. Some molecules will become familiar regardless of the orientation.

Any hydrogen atoms bonded to non-carbon atoms are drawn explicitly. In ethanol, C2H5OH, for instance, the hydrogen atom bonded to oxygen is denoted by the symbol H, whereas the hydrogen atoms which are bonded to carbon atoms are not shown directly. Lines representing heteroatom-hydrogen bonds are usually omitted for clarity and compactness, so a functional group like the hydroxyl group is most often written −OH instead of −O−H. These bonds are sometimes drawn out in full in order to accentuate their presence when they participate in reaction mechanisms.

Shown below for comparison are a ball-and-stick model of the actual three-dimensional structure of the ethanol molecule in the gas phase (determined by microwave spectroscopy, left), the Lewis structure (centre) and the skeletal formula (right).

Ethanol-CRC-MW-trans-3D-balls.png Ethanol-structure.svg Ethanol-2D-skeletal.svg

Explicit heteroatoms[edit]

All atoms that are not carbon or hydrogen are signified by their chemical symbol, for instance Cl for chlorine, O for oxygen, Na for sodium, and so forth. These atoms are commonly known as heteroatoms in the context of organic chemistry.

Pseudoelement symbols[edit]

There are also symbols that appear to be chemical element symbols, but represent certain very common substituents or indicate an unspecified member of a group of elements. These are known as pseudoelement symbols or organic elements.[3] The most widely used symbol is Ph, which represents the phenyl group. A list of pseudoelement symbols is shown below:

General symbols[edit]

  • X for any (pseudo)halogen atom
  • L or Ln for a ligand
  • M or Met for any metal atom ([M] is used to indicate a ligated metal, MLn, when the identity of ligand is unknown or irrelevant)
  • E for any electrophile (in some contexts, it is also used to indicate a p-block element)
  • Nu for any nucleophile
  • D for a deuterium (2H) atom
  • T for a tritium (3H) atom

Alkyl groups[edit]

Aromatic substituents[edit]

  • Ar for any aromatic substituent (Ar is also the symbol for the element argon. However, argon is inert under all usual conditions encountered in organic chemistry, so the use of Ar to represent an aryl substituent never causes confusion.)
  • Het for any heteroaromatic substituent
  • Bn or Bzl for the benzyl group (not to be confused with Bz for benzoyl)
  • Mes for the mesityl group
  • Ph or Φ for the phenyl group
  • Tol for the tolyl group
  • Cp for the cyclopentadienyl group
  • Cp* for the pentamethylcyclopentadienyl group

Functional groups[edit]

  • Ac for the acetyl group (Ac is also the symbol for the element actinium. However, actinium is almost never encountered in organic chemistry, so the use of Ac to represent the acetyl group never causes confusion)
  • Bz for the benzoyl group
  • Piv for the pivaloyl group

Leaving groups[edit]

See the article leaving group for further information

  • Bs for the brosyl group
  • Ms for the mesyl group
  • Ns for the nosyl group
  • Tf for the trifyl group
  • Ts for tosyl group (Ts is also the symbol for the element tennessine. However, tennessine is never encountered in organic chemistry, so the use of Ts to represent the tosyl group never causes confusion)

Protecting groups[edit]

A protecting group or protective group is introduced into a molecule by chemical modification of a functional group to obtain chemoselectivity in a subsequent chemical reaction, facilitating multistep organic synthesis.

Multiple bonds[edit]

Two atoms can be bonded by sharing more than one pair of electrons. The common bonds to carbon are single, double and triple bonds. Single bonds are most common and are represented by a single, solid line between two atoms in a skeletal formula. Double bonds are denoted by two parallel lines, and triple bonds are shown by three parallel lines.

In more advanced theories of bonding, non-integer values of bond order exist. In these cases, a combination of solid and dashed lines indicate the integer and non-integer parts of the bond order, respectively.

Note: in the gallery above, double bonds have been shown in red and triple bonds in blue. This was added for clarity - multiple bonds are not normally coloured in skeletal formulae.

Benzene rings[edit]

Thiele diagram of a benzene ring with circle

Benzene rings are common in organic compounds. To represent the delocalization of electrons over the six carbon atoms in the ring, a circle is drawn inside the hexagon of single bonds. This style, based on one proposed by Johannes Thiele, is very common in introductory organic chemistry texts used in schools.

Kekulé structure of a benzene ring with alternating double bonds

An alternative style that is more common in academia is the Kekulé structure. Although it could be considered inaccurate as it implies three single bonds and three double bonds (benzene would therefore be cyclohexa-1,3,5-triene), all qualified chemists are fully aware of the delocalization in benzene. Kekulé structures are useful for drawing reaction mechanisms clearly.

Stereochemistry[edit]

Different depictions of chemical bonds in skeletal formulae

Stereochemistry is conveniently denoted in skeletal formulae:[4]

The relevant chemical bonds can be depicted in several ways:

  • Solid lines represent bonds in the plane of the paper or screen.
  • Solid wedges represent bonds that point out of the plane of the paper or screen, towards the observer.
  • Hashed wedges or dashed lines (thick or thin) represent bonds that point into the plane of the paper or screen, away from the observer.
  • Wavy lines represent either unknown stereochemistry or a mixture of the two possible stereoisomers at that point.

An early use of this notation can be traced back to Richard Kuhn who in 1932 used solid thick lines and dotted lines in a publication. The modern wedges were popularised in the 1959 textbook "Organic Chemistry" by Donald J. Cram and George S. Hammond [5]

Skeletal formulae can depict cis and trans isomers of alkenes. Wavy single bonds are the standard way to represent unknown or unspecified stereochemistry or a mixture of isomers (as with tetrahedeal stereocenters). A crossed double-bond has been used sometimes; is no longer considered an acceptable style for general use, but may still be required by computer software.[4]

Alkene stereochemistry

Hydrogen bonds[edit]

Using dashed lines (green) to show hydrogen bonding in acetic acid.

Hydrogen bonds are generally denoted by dotted or dashed lines.

References[edit]

  1. ^ General, Organic, and Biological Chemistry, H. Stephen Stoker 2012
  2. ^ IUPAC Recommendations 1999, Revised Section F: Replacement of Skeletal Atoms
  3. ^ Clayden, Jonathan; Greeves, Nick; Warren, Stuart; Wothers, Peter (2001). Organic Chemistry (1st ed.). Oxford University Press. p. 27. ISBN 978-0-19-850346-0. 
  4. ^ a b J. Brecher (2006). "Graphical representation of stereochemical configuration (IUPAC Recommendations 2006)" (PDF). Pure Appl. Chem. 78 (10): 1897–1970. doi:10.1351/pac200678101897. 
  5. ^ The Historical Origins of Stereochemical Line and Wedge Symbolism William B. Jensen Journal of Chemical Education 2013 90 (5), 676-677 doi:10.1021/ed200177u

External links[edit]