- Hex-3-ene has an internal carbon–carbon double bond
- Hex-1-ene has a terminal double bond
- Hex-3-yne has an internal carbon–carbon triple bond
- Hex-1-yne has a terminal triple bond
The skeletal formula, line-angle formula, bond-line 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 piece of paper. It employs certain conventions to represent carbon and hydrogen atoms, which are the most common in organic chemistry.
An early form of this representation was first developed by organic chemist August Kekulé, while the modern form is closely related to and influenced by the Lewis structure of molecules and their valence electrons. Hence they are sometimes termed Kekulé structures [a] or Lewis–Kekulé structures. Skeletal formulae have become ubiquitous in organic chemistry, partly because they are relatively quick and simple to draw, and also because the curved arrow notation used for discussions of reaction mechanisms and electron delocalization can be readily superimposed.
Several other ways of depicting chemical structures are also commonly used in organic chemistry (though less frequently than skeletal formulae). For example, conformational structures look similar to skeletal formulae and are used to depict the approximate positions of atoms in 3D space, as a perspective drawing. Other types of representation, such as Newman projection, Haworth projection or Fischer projection, also look somewhat similar to skeletal formulae. However, there are slight differences in the conventions used, and the reader needs to be aware of them in order to understand the structural details encoded in the depiction. While skeletal and conformational structures are also used in organometallic and inorganic chemistry, the conventions employed also differ somewhat.
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 "C"), whereas heteroatoms are always explicitly noted as such ("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 collectively called "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.
As in Lewis structures, covalent bonds are indicated by line segments, with a doubled or tripled line segment indicating double or triple bonding, respectively. Likewise, skeletal formulae indicate formal charges associated with each atom (although lone pairs are usually optional, see below). In fact, skeletal formulae can be thought of as abbreviated Lewis structures that observe the following simplifications:
In the standard depiction of a molecule, the canonical form (resonance structure) with the greatest contribution is drawn. However, the skeletal formula is understood to represent the "real molecule" – that is, the weighted average of all contributing canonical forms. Thus, in cases where two or more canonical forms contribute with equal weight (e.g., in benzene, or a carboxylate anion) and one of the canonical forms is selected arbitrarily, the skeletal formula is understood to depict the true structure, containing equivalent bonds of fractional order, even though the delocalized bonds are depicted as nonequivalent single and double bonds.
Since skeletal structures were introduced in the latter half of the 19th century, their appearance has undergone considerable evolution. The graphical conventions in use today date to the 1980s. Thanks to the adoption of the ChemDraw software package as a de facto industry standard (by American Chemical Society, Royal Society of Chemistry, and Gesellschaft Deutscher Chemiker publications, for instance), these conventions have been nearly universal in the chemical literature since the late 1990s. A few minor conventional variations, especially with respect to the use of stereobonds, continue to exist as a result of differing US, UK and European practice, or as a matter of personal preference. [3] As another minor variation between authors, formal charges can be shown with the plus or minus sign in a circle (⊕, ⊖) or without the circle. The set of conventions that are followed by most authors is given below, along with illustrative examples.
For example, the skeletal formula of hexane (top) is shown below. 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 Lewis structure (middle) and ball-and-stick model (bottom) of the actual molecular structure of hexane, as determined by X-ray crystallography, are shown for comparison.
It does not matter which end of the chain one starts numbering from, as long as consistency is maintained when drawing diagrams. The condensed formula or the IUPAC name will confirm the orientation. Some molecules will become familiar regardless of the orientation.
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. In the context of organic chemistry, these atoms are commonly known as heteroatoms (the prefix hetero- comes from Greek ἕτερος héteros, meaning "other").
Any hydrogen atoms bonded to heteroatoms 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 skeletal formula (top), its Lewis structure (middle) and its ball-and-stick model (bottom) of the actual 3D structure of the ethanol molecule in the gas phase, as determined by microwave spectroscopy.
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 called pseudoelement symbols or organic elements and are treated like univalent "elements" in skeletal formulae. [4] A list of common pseudoelement symbols:
Sulfonate esters are often leaving groups in nucleophilic substitution reactions. See the articles on sulfonyl and sulfonate groups for further information.
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.
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.
In recent years, benzene is generally depicted as a hexagon with alternating single and double bonds, much like the structure Kekulé originally proposed in 1872. As mentioned above, the alternating single and double bonds of "1,3,5-cyclohexatriene" are understood to be a drawing of one of the two equivalent canonical forms of benzene (the one explicitly shown and the one with the opposite pattern of formal single and double bonds), in which all carbon–carbon bonds are of equivalent length and have a bond order of exactly 1.5. For aryl rings in general, the two analogous canonical forms are almost always the primary contributors to the structure, but they are nonequivalent, so one structure may make a slightly greater contribution than the other, and bond orders may differ somewhat from 1.5.
An alternate representation that emphasizes this delocalization uses a circle, drawn inside the hexagon of single bonds, to represent the delocalized pi orbital. This style, based on one proposed by Johannes Thiele, used to be very common in introductory organic chemistry textbooks and is still frequently used in informal settings. However, because this depiction does not keep track of electron pairs and is unable to show the precise movement of electrons, it has largely been superseded by the Kekuléan depiction in pedagogical and formal academic contexts. [f]
Stereochemistry is conveniently denoted in skeletal formulae: [5]
The relevant chemical bonds can be depicted in several ways:
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 solid and hashed wedges were introduced in the 1940s by Giulio Natta to represent the structure of high polymers, and extensively popularised in the 1959 textbook Organic Chemistry by Donald J. Cram and George S. Hammond. [6]
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 tetrahedral stereocenters). A crossed double-bond has been used sometimes; it is no longer considered an acceptable style for general use but may still be required by computer software. [5]
Hydrogen bonds are generally denoted by dotted or dashed lines. In other contexts, dashed lines may also represent partially formed or broken bonds in a transition state.
Aromatic compounds or arenes are organic compounds "with a chemistry typified by benzene" and "cyclically conjugated." The word "aromatic" originates from the past grouping of molecules based on odor, before their general chemical properties were understood. The current definition of aromatic compounds does not have any relation to their odor. Aromatic compounds are now defined as cyclic compounds satisfying Hückel's Rule. Aromatic compounds have the following general properties:
A chemical formula is a way of presenting information about the chemical proportions of atoms that constitute a particular chemical compound or molecule, using chemical element symbols, numbers, and sometimes also other symbols, such as parentheses, dashes, brackets, commas and plus (+) and minus (−) signs. These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a chemical name since it does not contain any words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulae can fully specify the structure of only the simplest of molecules and chemical substances, and are generally more limited in power than chemical names and structural formulae.
Organic chemistry is a subdiscipline within chemistry involving the scientific study of the structure, properties, and reactions of organic compounds and organic materials, i.e., matter in its various forms that contain carbon atoms. Study of structure determines their structural formula. Study of properties includes physical and chemical properties, and evaluation of chemical reactivity to understand their behavior. The study of organic reactions includes the chemical synthesis of natural products, drugs, and polymers, and study of individual organic molecules in the laboratory and via theoretical study.
In chemistry, a structural isomer of a compound is another compound whose molecule has the same number of atoms of each element, but with logically distinct bonds between them. The term metamer was formerly used for the same concept.
In stereochemistry, stereoisomerism, or spatial isomerism, is a form of isomerism in which molecules have the same molecular formula and sequence of bonded atoms (constitution), but differ in the three-dimensional orientations of their atoms in space. This contrasts with structural isomers, which share the same molecular formula, but the bond connections or their order differs. By definition, molecules that are stereoisomers of each other represent the same structural isomer.
The Simplified Molecular Input Line Entry System (SMILES) is a specification in the form of a line notation for describing the structure of chemical species 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.
Stereochemistry, a subdiscipline of chemistry, studies the spatial arrangement of atoms that form the structure of molecules and their manipulation. The study of stereochemistry focuses on the relationships between stereoisomers, which are defined as having the same molecular formula and sequence of bonded atoms (constitution) but differing in the geometric positioning of the atoms in space. For this reason, it is also known as 3D chemistry—the prefix "stereo-" means "three-dimensionality". Stereochemistry applies to all kinds of compounds and ions, organic and inorganic species alike. Stereochemistry affects biological, physical, and supramolecular chemistry.
The structural formula of a chemical compound is a graphic representation of the molecular structure, showing how the atoms are possibly arranged in the real three-dimensional space. The chemical bonding within the molecule is also shown, either explicitly or implicitly. Unlike other chemical formula types, which have a limited number of symbols and are capable of only limited descriptive power, structural formulas provide a more complete geometric representation of the molecular structure. For example, many chemical compounds exist in different isomeric forms, which have different enantiomeric structures but the same molecular formula. There are multiple types of ways to draw these structural formulas such as: Lewis structures, condensed formulas, skeletal formulas, Newman projections, Cyclohexane conformations, Haworth projections, and Fischer projections.
In chemistry, a double bond is a covalent bond between two atoms involving four bonding electrons as opposed to two in a single bond. Double bonds occur most commonly between two carbon atoms, for example in alkenes. Many double bonds exist between two different elements: for example, in a carbonyl group between a carbon atom and an oxygen atom. Other common double bonds are found in azo compounds (N=N), imines (C=N), and sulfoxides (S=O). In a skeletal formula, a double bond is drawn as two parallel lines (=) between the two connected atoms; typographically, the equals sign is used for this. Double bonds were introduced in chemical notation by Russian chemist Alexander Butlerov.
In chemistry, resonance, also called mesomerism, is a way of describing bonding in certain molecules or polyatomic ions by the combination of several contributing structures into a resonance hybrid in valence bond theory. It has particular value for analyzing delocalized electrons where the bonding cannot be expressed by one single Lewis structure. The resonance hybrid is the accurate structure for a molecule or ion; it is an average of the theoretical contributing structures.
Lewis structures – also called Lewis dot formulas, Lewis dot structures, electron dot structures, or Lewis electron dot structures (LEDs) – are diagrams that show the bonding between atoms of a molecule, as well as the lone pairs of electrons that may exist in the molecule. Introduced by Gilbert N. Lewis in his 1916 article The Atom and the Molecule, a Lewis structure can be drawn for any covalently bonded molecule, as well as coordination compounds. Lewis structures extend the concept of the electron dot diagram by adding lines between atoms to represent shared pairs in a chemical bond.
In chemical nomenclature, the IUPAC nomenclature of organic chemistry is a method of naming organic chemical compounds as recommended by the International Union of Pure and Applied Chemistry (IUPAC). It is published in the Nomenclature of Organic Chemistry. Ideally, every possible organic compound should have a name from which an unambiguous structural formula can be created. There is also an IUPAC nomenclature of inorganic chemistry.
In organic chemistry, a nucleophilic addition (AN) reaction is an addition reaction where a chemical compound with an electrophilic double or triple bond reacts with a nucleophile, such that the double or triple bond is broken. Nucleophilic additions differ from electrophilic additions in that the former reactions involve the group to which atoms are added accepting electron pairs, whereas the latter reactions involve the group donating electron pairs.
In chemistry, the Fischer projection, devised by Emil Fischer in 1891, is a two-dimensional representation of a three-dimensional organic molecule by projection. Fischer projections were originally proposed for the depiction of carbohydrates and used by chemists, particularly in organic chemistry and biochemistry. The use of Fischer projections in non-carbohydrates is discouraged, as such drawings are ambiguous and easily confused with other types of drawing. The main purpose of Fischer projections is to show the chirality of a molecule and to distinguish between a pair of enantiomers. Some notable uses include drawing sugars and depicting isomers.
A triple bond in chemistry is a chemical bond between two atoms involving six bonding electrons instead of the usual two in a covalent single bond. Triple bonds are stronger than the equivalent single bonds or double bonds, with a bond order of three. The most common triple bond is in a nitrogen N2 molecule; the second most common is that between two carbon atoms, which can be found in alkynes. Other functional groups containing a triple bond are cyanides and isocyanides. Some diatomic molecules, such as diphosphorus and carbon monoxide, are also triple bonded. In skeletal formulae the triple bond is drawn as three parallel lines (≡) between the two connected atoms.
In organic chemistry, a substituent is one or a group of atoms that replaces atoms, thereby becoming a moiety in the resultant (new) molecule.
In a tetrahedral molecular geometry, a central atom is located at the center with four substituents that are located at the corners of a tetrahedron. The bond angles are arccos(−1/3) = 109.4712206...° ≈ 109.5° when all four substituents are the same, as in methane as well as its heavier analogues. Methane and other perfectly symmetrical tetrahedral molecules belong to point group Td, but most tetrahedral molecules have lower symmetry. Tetrahedral molecules can be chiral.
In organic chemistry, the anomeric effect or Edward-Lemieux effect is a stereoelectronic effect that describes the tendency of heteroatomic substituents adjacent to a heteroatom within a cyclohexane ring to prefer the axial orientation instead of the less-hindered equatorial orientation that would be expected from steric considerations. This effect was originally observed in pyranose rings by J. T. Edward in 1955 when studying carbohydrate chemistry.
A cyclic compound is a term for a compound in the field of chemistry in which one or more series of atoms in the compound is connected to form a ring. Rings may vary in size from three to many atoms, and include examples where all the atoms are carbon, none of the atoms are carbon, or where both carbon and non-carbon atoms are present. Depending on the ring size, the bond order of the individual links between ring atoms, and their arrangements within the rings, carbocyclic and heterocyclic compounds may be aromatic or non-aromatic; in the latter case, they may vary from being fully saturated to having varying numbers of multiple bonds between the ring atoms. Because of the tremendous diversity allowed, in combination, by the valences of common atoms and their ability to form rings, the number of possible cyclic structures, even of small size numbers in the many billions.
An electric effect influences the structure, reactivity, or properties of a molecule but is neither a traditional bond nor a steric effect. In organic chemistry, the term stereoelectronic effect is also used to emphasize the relation between the electronic structure and the geometry (stereochemistry) of a molecule.