3.2 Lots of carbon compounds seem to be isomers. What is an isomer?

In organic chemistry, there are many examples of different compounds which have the same molecular formula as each other, but different arrangements of the atoms in their molecules, (different structural formulae). These compounds are said to be isomers of one another. Isomerism also occurs in inorganic chemistry, but it is less common.

There are two types of isomerism common in organic chemistry: structural isomerism and stereo isomerism.

Structural isomers of a compound have the atoms of their molecules linked in a different order. This can come about in one of three ways:

+ different carbon skeletons in the molecule (chain isomerism),

+ functional group linked to different carbon atoms (positional isomerism),

+ different functional groups (functional group isomerism).

Examples are shown below:

Stereo isomers of a compound have the same structural formula as one another, but the atoms of their molecules are orientated differently in space. Two common forms of stereo isomerism are:

+ geometric isomerism (also called cis /trans isomerism), which occurs due to lack of free rotation about double bonds,

+ optical isomerism, which occurs because of an asymmetry of a carbon atom with four different groups attached to it.

Alkane Isomers

Department of Chemistry: CAL

Suitable for use by students in CM1003, CM1004 and CM1504.

Alkane Isomers is a student tutorial for one of the first problems encountered in Organic Chemistry, isomerism and nomenclature of saturated hydrocarbons; i.e., finding the longest chain, determining whether two differently written structures are the same compound and finding the total number of isomers for a given formula.

In addition to providing text-based tutorials on naming alkanes and determining the number of isomers of an alkane of a specified number of carbons, Alkane Isomers provides three interactive practice modules. In two of these modules, the computer generates random exercises that the student can provide the answers or let the computer provide them. When an incorrect answer is given, intelligent analysis of the answer is done and appropriate feedback given to the student.

The program is completely menu-driven and is easy to use. On-line help is provided and easily accessible to aid the student in using the program.

Alkane Isomers should begin with a title screen. Press any key to get the seven-item menu and a boxed legend of instructions at the bottom of the screen.


For all menus and submenus, the selected option is denoted by the highlighted colour of the option. You can change the selection using the corresponding function key or the arrow keys. Pressing Enter activates the selection. Esc returns control to the immediately previous menu of submenu or, in the case of the main menu, ends the program. If on-line help is available, this is indicated in the prompt area at the bottom of the screen and is obtained by holding down Shift and pressing F1 .

The Main Menu

The main menu provides options to display the isomers of the alkanes methane to decane, view explanations of the elementary and intermediate naming rules for alkanes, practice finding the longest chain and naming alkanes, view rules for determining the number of isomers of an alkane, practice spotting identical isomers, and turn the sound off and on. Items from the main menu are selected as explained in the Navigation section above.


Alkane Isomers provides a help option at every menu and submenu. To view the help information, hold down the Shift key while pressing F1. The help information consists of a sequence of screen pages. You may terminate help and return to the menu at any point by pressing Esc, Page Up (previous page) and Page Down (next page) page through the help screens. Use Enter to view the next page of the help information.

The Tutorials

Alkane Isomers provides tutorials on the rules used to name alkanes (at the elementary and intermediate levels) and on how to determine the number of isomers of an alkane of a specified number of carbons.

To view one of these tutorials choose the corresponding item (2, 3 or 5) from the main menu. The tutorials consist of a sequence of screen pages. You may terminate a tutorial and return to the main menu at any point by pressing Esc. Page Up(previous page) and Page Down (next page) page through the screens. Use Enter to view the next page in the tutorial.


If you are working in an area with others nearby, you may wish to turn the sound off to avoid disturbing them. If you are working alone and enjoy the audio feedback provided by the program, you will want to turn on the sound. Choose item 7 from the main menu to turn the sound on, if it is currently off, or off, if it is currently on.

Display of Isomers

To see the isomers of an alkane from methane to decane, choose Display of Isomers from the main menu. A submenu is presented that offers the choices of methane to decane. Choosing an item from this submenu displays the isomers for that item. For example, choose heptane and the isomers of heptane are displayed (see Figure 1). Of course, for CH4 to C3H8 there is only one isomer. For C4H10 to C7H16 the number of isomers is small enough that all can be displayed on one screen. You are encouraged to guess the total number of isomers before they are displayed. With eight carbons or more, there are too many isomers to display all at once and they are instead shown by category. For example, for C8H18, methylheptane, then dimethylhexanes, ethylhexanes, etc. are displayed on consecutive screens. You are challenged to guess the number in each category, but not the overall total.

Finding the Longest Chain

To practice finding the longest chain and naming alkanes select Finding the longest chain from the main menu. Alkane Isomers generates a random carbon skeleton, displays it, and challenges you to number the longest chain correctly and then to name the alkane (see Figure 2). There is an initial submenu offering three levels of difficulty: Novice, Intermediate, and Expert. The Novice skeletons have a longest chain no greater that eight and no branched substituents, those of the Intermediate category may be up to undecanes and have isopropyl substituents. The only limitation on Expert is that branched substituents may have no more than four carbons.

The program will both number and name the alkanes if you decline to do so. If you number or name the alkane incorrectly, the program attempts to analyse your error and provide constructive error messages as well as the correct answers.

Spot the Duplicates

To gain practice in identifying identical structures, choose Spot the duplicates from the main menu. Six randomly generated structures are displayed, each next to a small box, as shown in Figure 3. You are asked to identify those structures which are actually the same compound and colour their boxes with the same colour. Follow the directions at the bottom of the screen to do so. There may be more than one set of duplicates or none at all. The program will identify the duplicates if you decline to do so or if you make any errors.

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Two compounds are considered isomers if they have the same molecular formula (i.e. the same numbers and types of atoms) but different structures.

There are two types of isomers, structural isomers and stereoisomers .

Two compounds are considered structural isomers is they have the same molecular formula but different connections between atoms (bonding).

Two compounds are considered stereoisomers if they have the same molecular formula, the same connections between atoms, but different arrangements of the atoms in three dimensional space.

, in chemistry, one of two or more compounds having the same molecular formula but different structures (arrangements of atoms in the molecule). Isomerism is the occurrence of such compounds. Isomerism was first recognized by J. J. Berzelius in 1827. Early work with stereoisomers was carried out by Louis Pasteur, who separated racemic acid into its two optically active tartaric acid components by crystallization (1848). Pasteur s results were given theoretical basis by J. H. Van t Hoff and independently by J. A. le Bel (1864). 1

General Characteristics

Isomers have the same number of atoms of each element in them and the same atomic weight but differ in other properties. For example, there are two compounds with the molecular formula C2H6O. One is ethanol (also called ethyl alcohol), CH3CH2OH, a colorless liquid alcohol; the other is dimethyl ether, CH3OCH3, a colorless gaseous ether. Among their different properties, ethanol has a boiling point of 78.5.C and a freezing point of -117.C; dimethyl ether has a boiling point of -25.C and a freezing point of -138.C. Ethanol and dimethyl ether are isomers because they differ in the way the atoms are joined together in their molecules: 2

Isomers are classified as structural isomers, which have the same number of atoms of each element and molecular weight but different bonding patterns (see chemical bond), or as stereoisomers, which have the same number of atoms of each element, molecular weight, and bonding pattern but in which the atoms have different spatial relationships. Tautomers are structural isomers that readily convert from one isomeric form to another and therefore exist in equilibrium. 3

Structural Isomers

Structural isomers are subdivided as chain, position, and functional group. Chain isomers occur among the alkanes. For example, there are two chain isomers of butane, C4H10. In n-butane, CH3CH2CH2CH3, the carbon atoms are joined in a so-called straight, or unbranched, chain. In isobutane, CH3CH(CH3)2, the carbon atoms are joined in a branched chain; the isobutane molecule can be visualized as a carbon atom bonded to one hydrogen atom and to three methyl (CH3) groups. 4

Position isomers occur among substituted alkanes and other compounds. For example, 1-propanol, CH3CH2CH2OH, and 2-propanol, CH3CH(OH)CH3, are position isomers, as are 1-butene, CH2[symbol]CHCH2CH3, and 2-butene, CH3CH[symbol]CHCH3. Position isomers have similar chemical properties since they differ only in the location of the functional group (e.g., the OH in an alcohol or the double bond in an alkene). 5

Functional group isomers, on the other hand, have very different chemical properties because differences in their structure give rise to different functional groups. Ethanol and dimethyl ether (see the example, above) are functional group isomers. 6


Stereoisomerism occurs when two or more molecules have the same basic arrangement of atoms in their molecules but differ in the way the atoms are arranged in space. There are two types of stereoisomerism. The first type, geometric isomerism, may occur when a compound contains a double bond or some other feature that gives the molecule a certain amount of structural rigidity. Geometric isomers differ in physical properties such as melting point and boiling point. For example, there are two geometric isomers of 2-butene, CH3CH[symbol]CHCH3:The prefix cis- means same side and trans- means opposite side ; they are used when the groups on either side of the double bond are identical or closely related, e.g., methyl and ethyl. Syn- and anti- have similar meanings but are used when the groups are not identical or closely related. 7

The second type of stereoisomerism is optical isomerism. When plane-polarized light is passed through an optical isomer it is rotated into a different plane of polarization. Optical isomers exhibit this optical activity in varying degrees. Optical isomers of a given compound are often identical in all physical properties except the direction in which they rotate light. The molecules of optical isomers are asymmetrical. The simplest optical isomers have a single asymmetrical carbon atom in their molecules. An asymmetrical carbon atom has four different atoms or radicals bonded to it, arranged approximately at the corners of a tetrahedron centered on the carbon atom. For example, there are two optical isomers of lactic acid:The atom and radical to either side of the carbon atom are visualized as being above the plane of the paper, the central carbon atom in the plane of the paper, and the radicals above and below the central carbon atom below the plane of the paper. Thus it is seen that the two molecules are mirror images of each other and, each being asymmetrical, cannot be superposed on each other. The d- and l- prefixes stand for dextro (right) and levo (left). Two optical isomers, such as these, whose molecules are asymmetrical and are mirror images of each other, are called enantiomorphs. When equal amounts of d- and l-enantiomorphs are mixed, the mixture has no effect on polarized light; such a mixture is called racemic. 8

When there is more than one asymmetrical carbon atom, there may be more than two optical isomers. For example, tartaric acid has two asymmetrical carbon atoms and three optical isomers:The d- and l-tartaric acids are enantiomorphs; each molecule is asymmetrical and is the mirror image of the other. There are two asymmetrical carbon atoms in meso-tartaric acid, but the molecule is symmetrical and does not exhibit optical activity; the optical activity is internally compensated, the effect of one asymmetrical carbon atom balancing the effect of the other. A pair of optical isomers such as d-tartaric acid and meso-tartaric acid, which are not enantiomorphs, are called diastereoisomers. Molecular disymmetry in optical isomers may come from some source other than an asymmetrical carbon atom, e.g., structural rigidity resulting from double bonds or ring structures within a molecule. 9

Stereoisomers are important in metabolism; in many cases only one of several isomeric forms of a compound can take part in biochemical reactions. For example, there are 16 stereoisomers of a simple sugar whose molecular formula is C6H12O4. Of these, only d-glucose is readily utilized in human metabolism.

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