HOME

TheInfoList



OR:

The skeletal formula, or line-angle formula or shorthand formula, of an
organic compound In chemistry, organic compounds are generally any chemical compounds that contain carbon-hydrogen or carbon-carbon bonds. Due to carbon's ability to catenate (form chains with other carbon atoms), millions of organic compounds are known. T ...
is a type of molecular structural formula that serves as a shorthand representation of a
molecule A molecule is a group of two or more atoms held together by attractive forces known as chemical bonds; depending on context, the term may or may not include ions which satisfy this criterion. In quantum physics, organic chemistry, and bioche ...
's bonding and some details of its
molecular geometry Molecular geometry is the three-dimensional arrangement of the atoms that constitute a molecule. It includes the general shape of the molecule as well as bond lengths, bond angles, torsional angles and any other geometrical parameters that dete ...
. A skeletal formula shows the skeletal structure or skeleton of a molecule, which is composed of the skeletal atoms that make up the molecule. It is represented in two dimensions, as on a piece of paper. It employs certain conventions to represent
carbon Carbon () is a chemical element with the symbol C and atomic number 6. It is nonmetallic and tetravalent—its atom making four electrons available to form covalent chemical bonds. It belongs to group 14 of the periodic table. Carbon mak ...
and
hydrogen Hydrogen is the chemical element with the symbol H and atomic number 1. Hydrogen is the lightest element. At standard conditions hydrogen is a gas of diatomic molecules having the formula . It is colorless, odorless, tasteless, non-toxic ...
atoms, which are the most common in organic chemistry. An early form of this representation was first developed by organic chemist
August Kekulé Friedrich August Kekulé, later Friedrich August Kekule von Stradonitz ( , ; 7 September 1829 – 13 July 1896), was a German organic chemist. From the 1850s until his death, Kekulé was one of the most prominent chemists in Europe, especially ...
, while the modern form is closely related to and influenced by the
Lewis structure Lewis structures, also known as 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 t ...
of molecules and their valence electrons. Hence they are sometimes termed Kekulé structures or Lewis–Kekulé structures. Skeletal formulae have become ubiquitous in
organic chemistry 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.Clayden, ...
, 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 In chemistry, delocalized electrons are electrons in a molecule, ion or solid metal that are not associated with a single atom or a covalent bond.IUPAC Gold Boo''delocalization''/ref> The term delocalization is general and can have slightly dif ...
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 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 ...
, 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 skeleton


Terminology

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
heteroatom In chemistry, a heteroatom () is, strictly, any atom that is not carbon or hydrogen. Organic chemistry In practice, the term is usually used more specifically to indicate that non-carbon atoms have replaced carbon in the backbone of the molecula ...
s. 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 Nitrogen is the chemical element with the symbol N and atomic number 7. Nitrogen is a nonmetal and the lightest member of group 15 of the periodic table, often called the pnictogens. It is a common element in the universe, estimated at se ...
, "O" for
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as ...
, 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 group In organic chemistry, a functional group is a substituent or moiety in a molecule that causes the molecule's characteristic chemical reactions. The same functional group will undergo the same or similar chemical reactions regardless of the re ...
s, 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 In organic chemistry, a hydrocarbon is an organic compound consisting entirely of hydrogen and carbon. Hydrocarbons are examples of group 14 hydrides. Hydrocarbons are generally colourless and hydrophobic, and their odors are usually weak or ...
of the organic compound.


Basic structure

As in Lewis structures, covalent bonds are indicated by line segments, with a doubled or tripled line segment indicating double or
triple bond 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 o ...
ing, respectively. Likewise, skeletal formulae indicate
formal charges In chemistry, a formal charge (F.C. or q), in the covalent view of chemical bonding, is the charge assigned to an atom in a molecule, assuming that electrons in all chemical bonds are shared equally between atoms, regardless of relative electroneg ...
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: *Carbon atoms are represented by the vertices (intersections or termini) of line segments. For clarity, methyl groups are often explicitly written out as Me or CH3, while (hetero)
cumulene In organic chemistry, a cumulene is a compound having three or more ''cumulative'' (consecutive) double bonds. They are analogous to allenes, only having a more extensive chain. The simplest molecule in this class is butatriene (), which is al ...
carbons are frequently represented by a heavy center dot. * Hydrogen atoms attached to carbon are implied. An unlabeled vertex is understood to represent a carbon attached to the number of hydrogens required to satisfy the
octet rule The octet rule is a chemical rule of thumb that reflects the theory that main-group elements tend to bond in such a way that each atom has eight electrons in its valence shell, giving it the same electronic configuration as a noble gas. The rul ...
, while a vertex labeled with a formal charge and/or nonbonding electron(s) is understood to have the number of hydrogen atoms required to give the carbon atom these indicated properties. Optionally, acetylenic and formyl hydrogens can be shown explicitly for the sake of clarity. * Hydrogen atoms attached to a heteroatom are shown explicitly. The heteroatom and hydrogen atoms attached thereto are usually shown as a single group (e.g., OH, NH2) without explicitly showing the hydrogen–heteroatom bond. Heteroatoms with simple alkyl or aryl substituents, like methoxy (OMe) or dimethylamino (NMe2), are sometimes shown in the same way, by analogy. * Lone pairs on carbene carbons must be indicated explicitly while lone pairs in other cases are optional and are shown only for emphasis. In contrast, formal charges and unpaired electrons on main-group elements are always explicitly shown. In the standard depiction of a molecule, the
canonical form In mathematics and computer science, a canonical, normal, or standard form of a mathematical object is a standard way of presenting that object as a mathematical expression. Often, it is one which provides the simplest representation of an ...
(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.


Contemporary graphical conventions

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 ChemDraw is a molecule editor first developed in 1985 by David A. Evans and Stewart Rubenstein (later by the cheminformatics company CambridgeSoft). The company was sold to PerkinElmer in the year 2011. ChemDraw, along with Chem3D and ChemFinde ...
software package as a ''de facto'' industry standard (by
American Chemical Society The American Chemical Society (ACS) is a scientific society based in the United States that supports scientific inquiry in the field of chemistry. Founded in 1876 at New York University, the ACS currently has more than 155,000 members at all ...
,
Royal Society of Chemistry The Royal Society of Chemistry (RSC) is a learned society (professional association) in the United Kingdom with the goal of "advancing the chemical sciences". It was formed in 1980 from the amalgamation of the Chemical Society, the Royal Instit ...
, and
Gesellschaft Deutscher Chemiker The German Chemical Society (German: ', GDCh) is a learned society and professional association founded in 1949 to represent the interests of German chemists in local, national and international contexts. GDCh "brings together people working in che ...
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. 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.


Implicit carbon and hydrogen atoms

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 Lewis structures, also known as 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 t ...
(middle) and
ball-and-stick model In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods ...
(bottom) of the actual molecular structure of hexane, as determined by
X-ray crystallography X-ray crystallography is the experimental science determining the atomic and molecular structure of a crystal, in which the crystalline structure causes a beam of incident X-rays to diffract into many specific directions. By measuring the angles ...
, 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.


Explicit heteroatoms and hydrogen atoms

All atoms that are not carbon or hydrogen are signified by their
chemical symbol Chemical symbols are the abbreviations used in chemistry for chemical elements, functional groups and chemical compounds. Element symbols for chemical elements normally consist of one or two letters from the Latin alphabet and are written with ...
, for instance Cl for
chlorine Chlorine is a chemical element with the symbol Cl and atomic number 17. The second-lightest of the halogens, it appears between fluorine and bromine in the periodic table and its properties are mostly intermediate between them. Chlorine i ...
, O for
oxygen Oxygen is the chemical element with the symbol O and atomic number 8. It is a member of the chalcogen group in the periodic table, a highly reactive nonmetal, and an oxidizing agent that readily forms oxides with most elements as ...
, Na for
sodium Sodium is a chemical element with the symbol Na (from Latin ''natrium'') and atomic number 11. It is a soft, silvery-white, highly reactive metal. Sodium is an alkali metal, being in group 1 of the periodic table. Its only stable ...
, 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 Ethanol (abbr. EtOH; also called ethyl alcohol, grain alcohol, drinking alcohol, or simply alcohol) is an organic compound. It is an alcohol with the chemical formula . Its formula can be also written as or (an ethyl group linked to a ...
, 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 In chemistry, a hydroxy or hydroxyl group is a functional group with the chemical formula and composed of one oxygen atom covalently bonded to one hydrogen atom. In organic chemistry, alcohols and carboxylic acids contain one or more hydro ...
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 Lewis structures, also known as 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 t ...
(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 Microwave spectroscopy is the spectroscopy method that employs microwaves, i.e. electromagnetic radiation at GHz frequencies, for the study of matter. History The ammonia molecule NH3 is shaped like a pyramid 0.38 Å in height, with an equilatera ...
.


Pseudoelement symbols

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. A list of common pseudoelement symbols:


General symbols

*X for any (
pseudo The prefix pseudo- (from Greek ψευδής, ''pseudes'', "false") is used to mark something that superficially appears to be (or behaves like) one thing, but is something else. Subject to context, ''pseudo'' may connote coincidence, imitation, ...
) halogen atom (in the related MLXZ notation, X represents a one-electron donor ligand) *L ''or'' L''n'' for a
ligand In coordination chemistry, a ligand is an ion or molecule ( functional group) that binds to a central metal atom to form a coordination complex. The bonding with the metal generally involves formal donation of one or more of the ligand's elec ...
or ligands (in the related MLXZ notation, L represents a two-electron donor ligand) *M ''or'' Met for any
metal A metal (from Greek μέταλλον ''métallon'', "mine, quarry, metal") is a material that, when freshly prepared, polished, or fractured, shows a lustrous appearance, and conducts electricity and heat relatively well. Metals are typicall ...
atom ( is used to indicate a ligated metal, ML''n'', when the identities of the ligands are unknown or irrelevant) *E ''or'' El for any
electrophile In chemistry, an electrophile is a chemical species that forms bonds with nucleophiles by accepting an electron pair. Because electrophiles accept electrons, they are Lewis acids. Most electrophiles are positively charged, have an atom that carrie ...
(in some contexts, E is also used to indicate any p-block element) *Nu for any nucleophile *Z for conjugating electron-withdrawing groups (in the related MLXZ notation, Z represents a zero-electron donor ligand; ''in unrelated usage, Z is also an abbreviation for the carboxybenzyl group''.) *D for
deuterium Deuterium (or hydrogen-2, symbol or deuterium, also known as heavy hydrogen) is one of two stable isotopes of hydrogen (the other being protium, or hydrogen-1). The nucleus of a deuterium atom, called a deuteron, contains one proton and one ...
(2H) *T for
tritium Tritium ( or , ) or hydrogen-3 (symbol T or H) is a rare and radioactive isotope of hydrogen with half-life about 12 years. The nucleus of tritium (t, sometimes called a ''triton'') contains one proton and two neutrons, whereas the nucleus of ...
(3H)


Alkyl groups

*R for any alkyl group or even any organyl group (Alk can be used to unambiguously indicate an alkyl group) *Me for the
methyl group In organic chemistry, a methyl group is an alkyl derived from methane, containing one carbon atom bonded to three hydrogen atoms, having chemical formula . In formulas, the group is often abbreviated as Me. This hydrocarbon group occurs in ma ...
*Et for the ethyl group *Pr, ''n''-Pr, ''or'' ''n''Pr for the (''normal'') propyl group (''Pr is also the symbol for the element
praseodymium Praseodymium is a chemical element with the symbol Pr and the atomic number 59. It is the third member of the lanthanide series and is considered to be one of the rare-earth metals. It is a soft, silvery, malleable and ductile metal, valued for i ...
. However, since the propyl group is monovalent, while praseodymium is nearly always trivalent, ambiguity rarely, if ever, arises in practice.'') *''i''-Pr ''or'' ''i''Pr for the isopropyl group *All for the allyl group (uncommon) *Bu, ''n''-Bu ''or'' ''n''Bu for the (''normal'') butyl group *''i''-Bu ''or'' ''i''Bu (''i'' often italicized) for the
isobutyl In organic chemistry, butyl is a four-carbon alkyl radical or substituent group with general chemical formula , derived from either of the two isomers (''n''-butane and isobutane) of butane. The isomer ''n''-butane can connect in two ways, givi ...
group *''s''-Bu ''or'' ''s''Bu for the ''secondary'' butyl group *''t''-Bu ''or'' ''t''Bu for the ''tertiary'' butyl group *Pn for the
pentyl Pentyl is a five-carbon alkyl group or substituent with chemical formula -C5H11. It is the substituent form of the alkane pentane. In older literature, the common non-systematic name amyl was often used for the pentyl group. Conversely, the name ...
group (''or'' Am for the synonymous
amyl Amyl may refer to: * Amylum or starch, a carbohydrate ** Amylopectin, a polymer of glucose found in plants; one of two components of starch ** Amylose, a helical polymer made of α-D-glucose units; one of two components of starch * Pentyl, a five- ...
group, ''although Am is also the symbol for americium.'') *Np ''or'' Neo for the
neopentyl Pentyl is a five-carbon alkyl group or substituent with chemical formula -C5H11. It is the substituent form of the alkane pentane. In older literature, the common non-systematic name amyl was often used for the pentyl group. Conversely, the name ...
group (''Warning: Organometallic chemists often use Np for the related neophyl group, PhMe2C–. Np is also the symbol for the element
neptunium Neptunium is a chemical element with the symbol Np and atomic number 93. A radioactive actinide metal, neptunium is the first transuranic element. Its position in the periodic table just after uranium, named after the planet Uranus, led to it bein ...
.'') *Cy ''or'' Chx for the
cyclohexyl Cyclohexane is a cycloalkane with the molecular formula . Cyclohexane is non-polar. Cyclohexane is a colorless, flammable liquid with a distinctive detergent-like odor, reminiscent of cleaning products (in which it is sometimes used). Cyclohexan ...
group *Ad for the 1- adamantyl group *Tr ''or'' Trt for the
trityl Triphenylmethane, or triphenyl methane, is the hydrocarbon with the formula (C6H5)3CH. This colorless solid is soluble in nonpolar organic solvents and not in water. Triphenylmethane is the basic skeleton of many synthetic dyes called triarylmetha ...
group


Aromatic and unsaturated substituents

*Ar for any aromatic substituent ''(Ar is also the symbol for the element
argon Argon is a chemical element with the symbol Ar and atomic number 18. It is in group 18 of the periodic table and is a noble gas. Argon is the third-most abundant gas in Earth's atmosphere, at 0.934% (9340 ppmv). It is more than twice as ...
. 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 In chemistry, aromaticity is a chemical property of cyclic compound, cyclic (ring (chemistry), ring-shaped), ''typically'' plane (geometry), planar (flat) molecular structures with pi bonds in Resonance (chemistry), resonance (those containing ...
substituent *Bn ''or'' Bzl for the
benzyl In organic chemistry, benzyl is the substituent or molecular fragment possessing the structure . Benzyl features a benzene ring () attached to a methylene group () group. Nomenclature In IUPAC nomenclature, the prefix benzyl refers to a substi ...
group (''not to be confused with Bz for benzoyl group; However, old literature may use Bz for benzyl group.'') *Dipp for the 2,6-diisopropylphenyl group *Mes for the mesityl group *Ph, Φ, ''or'' φ for the phenyl group (''the use of
phi Phi (; uppercase Φ, lowercase φ or ϕ; grc, ϕεῖ ''pheî'' ; Modern Greek: ''fi'' ) is the 21st letter of the Greek alphabet. In Archaic and Classical Greek (c. 9th century BC to 4th century BC), it represented an aspirated voicele ...
for phenyl has been in decline'') *Tol for the tolyl group, usually the ''para'' isomer *Is ''or'' Tipp for the 2,4,6-triisopropylphenyl group (''the former symbol is derived from the synonym'' ''isityl'') *An for the anisyl group, usually the ''para'' isomer (''An is also the symbol for a generic actinoid element. However, since the anisyl group is monovalent, while the actinides are usually divalent, trivalent, or even higher valency, ambiguity rarely, if ever, arises in practice.'') *Cp for the cyclopentadienyl group (''Cp was the symbol for cassiopeium, a former name for
lutetium Lutetium is a chemical element with the symbol Lu and atomic number 71. It is a silvery white metal, which resists corrosion in dry air, but not in moist air. Lutetium is the last element in the lanthanide series, and it is traditionally counted am ...
'') *Cp* for the pentamethylcyclopentadienyl group *Vi for the vinyl group (uncommon)


Functional groups

*Ac for the acetyl group ''(Ac is also the symbol for the element
actinium Actinium is a chemical element with the symbol Ac and atomic number 89. It was first isolated by Friedrich Oskar Giesel in 1902, who gave it the name ''emanium''; the element got its name by being wrongly identified with a substance An ...
. 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; OBz is the benzoate group *Piv for the pivalyl (''t''-butylcarbonyl) group; OPiv is the pivalate group *Bt for the 1-benzotriazolyl group *Im for the 1-imidazolyl group *NPhth for the phthalimide-1-yl group


Sulfonyl/sulfonate groups

Sulfonate esters are often leaving groups in nucleophilic substitution reactions. ''See the articles on
sulfonyl In organosulfur chemistry, a sulfonyl group can refer either to a functional group found primarily in sulfones, or to a substituent obtained from a sulfonic acid by the removal of the hydroxyl group, similarly to acyl groups. Sulfonyl groups c ...
and
sulfonate In organosulfur chemistry, a sulfonate is a salt or ester of a sulfonic acid. It contains the functional group , where R is an organic group. Sulfonates are the conjugate bases of sulfonic acids. Sulfonates are generally stable in water, non-o ...
groups for further information.'' *Bs for the brosyl (''p''-bromobenzenesulfonyl) group; OBs is the brosylate group *Ms for the mesyl (methanesulfonyl) group; OMs is the mesylate group *Ns for the nosyl (''p''-nitrobenzenesulfonyl) group ''(Ns was the former chemical symbol for bohrium, then called nielsbohrium)''; ONs is the nosylate group *Tf for the triflyl (trifluoromethanesulfonyl) group; OTf is the
triflate In organic chemistry, triflate ( systematic name: trifluoromethanesulfonate), is a functional group with the formula and structure . The triflate group is often represented by , as opposed to −Tf, which is the triflyl group, . For example, ...
group *Nf for the nonaflyl (nonafluorobutanesulfonyl) group, CF3(CF2)3SO2; ONf is the nonaflate group *Ts for tosyl (''p-''toluenesulfonyl) group ''(Ts is also the symbol for the element
tennessine Tennessine is a synthetic chemical element with the symbol Ts and atomic number 117. It is the second-heaviest known element and the penultimate element of the 7th period of the periodic table. The discovery of tennessine was officially anno ...
. However, tennessine is never encountered in organic chemistry, so the use of Ts to represent tosyl never causes confusion)''; OTs is the
tosylate In organic chemistry, a toluenesulfonyl group (tosyl group, abbreviated Ts or Tos) is a univalent functional group with the chemical formula –. It consists of a tolyl group, –, joined to a sulfonyl group, ––, with the open valence on s ...
group


Protecting groups

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. *Boc for the ''t-''butoxycarbonyl group *Cbz ''or'' Z for the carboxybenzyl group *Fmoc for the fluorenylmethoxycarbonyl group *Alloc for the allyloxycarbonyl group *Troc for the trichloroethoxycarbonyl group *TMS, TBDMS, TES, TBDPS, TIPS, ... for various silyl ether groups *PMB for the 4-methoxybenzyl group *MOM for the methoxymethyl group *THP for the 2-tetrahydropyranyl group


Multiple bonds

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 An integer is the number zero (), a positive natural number (, , , etc.) or a negative integer with a minus sign ( −1, −2, −3, etc.). The negative numbers are the additive inverses of the corresponding positive numbers. In the languag ...
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.


Benzene rings

In recent years,
benzene Benzene is an organic chemical compound with the molecular formula C6H6. The benzene molecule is composed of six carbon atoms joined in a planar ring with one hydrogen atom attached to each. Because it contains only carbon and hydrogen atoms ...
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 1,3,5- and 2,4,6-isomers), 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 In chemistry, pi bonds (π bonds) are covalent chemical bonds, in each of which two lobes of an orbital on one atom overlap with two lobes of an orbital on another atom, and in which this overlap occurs laterally. Each of these atomic orbitals ...
. 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.


Stereochemistry

Stereochemistry is conveniently denoted in skeletal formulae: Image:Stereochemistry-example-3D-balls.png,
Ball-and-stick model In chemistry, the ball-and-stick model is a molecular model of a chemical substance which displays both the three-dimensional position of the atoms and the bonds between them. The atoms are typically represented by spheres, connected by rods ...
of
(''R'')-2-chloro-2-fluoropentane
Image:(R)-2-Chloro-2-fluoropentane.svg,
Skeletal formula of
(''R'')-2-chloro-2-fluoropentane
Image:(S)-2-Chloro-2-fluoropentane.svg,
Skeletal formula of
(''S'')-2-chloro-2-fluoropentane
Image:Amphetamine-2D-skeletal.svg,
Skeletal formula of amphetamine, indicating a mixture of two stereoisomers: (''R'')- and (''S'')-
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 obsolescent depiction of hydrogen stereochemistry that used to be common in steroid chemistry is the use of a filled circle centered on a vertex (sometimes called H-dot/H-dash/H-circle, respectively) for an upward pointing hydrogen atom and two hash marks next to vertex or a hollow circle for a downward pointing hydrogen atom. 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 Giulio Natta (26 February 1903 – 2 May 1979) was an Italian chemical engineer and Nobel laureate. He won a Nobel Prize in Chemistry in 1963 with Karl Ziegler for work on high polymers. He also received a Lomonosov Gold Medal in 1969. Biograph ...
to represent the structure of high
polymer A polymer (; Greek '' poly-'', "many" + ''-mer'', "part") is a substance or material consisting of very large molecules called macromolecules, composed of many repeating subunits. Due to their broad spectrum of properties, both synthetic a ...
s, and extensively popularised in the 1959 textbook ''Organic Chemistry'' by Donald J. Cram and George S. Hammond. 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; is no longer considered an acceptable style for general use, but may still be required by computer software.


Hydrogen bonds

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.


Notes


References


External links


Drawing organic molecules
from ''chemguide.co.uk'' {{Visualization Organic chemistry Chemical formulas Chemical structures