Organic molecules: the chemistry of carbon and hydrogen

chapter 3 Organic molecules: the chemistry of carbon and hydrogen



KEY POINTS


image Molecules can be categorised as inorganic or organic based on their elemental composition.

image Carbon–hydrogen bonds define molecules as organic.

image The simplest organic molecules are hydrocarbons which contain only carbon and hydrogen atoms.

image Alkanes are saturated hydrocarbons, alkenes have one or more double bonds and alkynes have one or more triple bonds.

image Alicyclic compounds have carbon atoms linked in cyclic structures.

image Aromatic compounds contain one or more benzene rings.

image Functional groups are added to hydrocarbon skeletons to give biologically functional molecules.

image Many hydrocarbons have multiple isomeric forms.

image Elements cannot be broken down into other substances by chemical reactions.

image A compound is made from two or more elements which are combined in a fixed ratio.

In the early 19th century, Swedish chemist Jöns Jacob Berzelius classified compounds into two categories. Those that were isolated from plants or animals were called organic, while those extracted from ores and minerals were inorganic. Later, in 1828, Friedrich Wöhler used an inorganic molecule (ammonium cyanate, NH4OCN) to synthesise urea (H2NCONH2), an organic molecule. This initiated the synthesis of organic molecules in the laboratory. Of the more than 10 million compounds that have been discovered, at least 90% are molecules that contain carbon. More than 1.5 million new molecules are discovered or synthesised each year and almost all of these are compounds of carbon. Just as there are millions of different types of living organisms on this planet, there are millions of different organic molecules, each with different chemical and physical properties.


Organic chemistry is often defined as the chemistry of carbon. However, this definition would include calcium carbonate (CaCO3) and graphite, which more closely resemble inorganic compounds. A more selective definition of organic chemistry is the study of compounds that contain both carbon and hydrogen, for example, formic acid (HCOOH), methane (CH4) and glucose (C6H12O6). Though many organic chemicals also contain other elements, it is the carbon–hydrogen bond that defines them as organic. The chemistry of organic molecules (biochemistry) defines life.



Why is carbon such a special element?


Carbon (C) appears in the second row of the periodic table and has four bonding electrons in its valence shell. Similarly to other non-metals, carbon needs eight electrons to satisfy its valence shell. Carbon therefore forms four bonds with other atoms (each bond consisting of one of carbon’s electrons and one of the bonding atom’s electrons). Every valence electron participates in bonding, thus the bonds made by a carbon atom will be distributed evenly over the atom’s surface. These bonds form a tetrahedron as described in Chapter 1.


The chemistry of carbon is dominated by three factors:


• Carbon forms very strong carbon–carbon single bonds (C–C), carbon–carbon double bonds (C=C), and carbon–carbon triple bonds (C≡C). Single bonds can rotate whereas double and triple bonds cannot. However, while carbon–carbon single and double bonds are common in biological molecules, the same cannot be said for triple bonds.

• The electronegativity of carbon is too low to allow carbon to form C4– ions with most metals and too large for carbon to form C4+ ions when it reacts with non-metals. It therefore forms covalent bonds.

• Carbon forms strong double and triple bonds with a number of other non-metals, including N, O, P and S.


Formulas used in organic chemistry


Three different types of formula are used when working with organic molecules (Fig 3-1). The simplest is referred to as the molecular formula and indicates the number of each type of atom in a molecule. However, this does not give any structural information, particularly when a large number of atoms are involved. To deal with this a condensed structural formula can be used which shows the number of hydrogen atoms bonded to each carbon atom in the molecule. The most information is shown using a structural formula which indicates how the hydrogen and carbon atoms are bonded and arranged, and uses dashes for bonds.


image

FIGURE 3-1 Three different types of formula that can be used to describe butane. Each gives progressively more information about the structure of the molecule.



Hydrocarbons


The simplest organic chemicals, called hydrocarbons, contain only carbon and hydrogen atoms (Fig 3-2). The simplest hydrocarbon (methane) contains a single carbon atom bonded to four hydrogen atoms. Aliphatic molecules have carbons linked in an open chain (acyclic) form, one in which the carbons are arranged in a linear manner. Alicyclic molecules have carbons linked in a cyclic structure in which the first and last carbon atoms of a chain are connected to one another. Aromatic molecules contain one or more benzene rings, an extremely stable type of cyclic structure.


image

FIGURE 3-2 Hydrocarbons can be divided into three major groups.



Aliphatic compounds


Simple hydrocarbons are non-cyclic molecules that can be classified into three groups depending on the type of carbon–carbon bonds that occur in the molecule (Table 3-1).



TABLE 3-1 Hydrocarbons showing how names for the first ten simple hydrocarbons are derived

image

Alkanes have the general formula CnH2n+2, where ‘n’ is a whole number. All bonds between the carbon atoms are single bonds, and the molecule is saturated with hydrogen atoms. These molecules are named as follows:


• For a straight-chain alkane, define the longest continuous chain of carbon atoms using the stem and add the suffix ‘ane’ e.g. butane.

• For a branched chain alkane, number the carbon atoms of the longest continuous chain starting at the end closest to the branch; locate the branch by the number of the carbon atom to which it is attached on the main chain. Then name the branch. The branches are called alkyl groups and are named by using the appropriate stem plus the suffix ‘yl’. If more than one of the same alkyl group is present as a branch, then the number of these branches is indicated by the prefix multipliers. The location of a branch is identified with a number, using the lowest number. If different alkyl groups are present as branches, assign the lowest number possible to each branch. The order of the branches is arranged alphabetically regardless of their number on the longest chain (Fig 3-3).

image

FIGURE 3-3 Some examples of branched alkanes.


Alkanes burn in oxygen to produce carbon dioxide and water vapour. This means that alkanes are flammable, making them good fuels. For example, methane is the major component of natural gas, and butane is used in liquid form in lighters.



image

Alkenes are molecules that contain at least one double-bonded carbon pair, and have the general formula CnH2n. Alkenes follow a naming convention similar to that used for alkanes:


• For a straight-chain alkene, define the longest continuous chain of carbon atoms using the stem and add the suffix ‘ene’. This means that because one of the carbon pairs is double bonded, simple alkenes have two fewer hydrogen atoms than the corresponding alkanes.

• The rules for naming branched alkenes are similar to those for naming branched alkanes. The longest continuous chain must be chosen to contain both carbon atoms of the double bond, even if a longer chain could be found by choosing a different path. The chain must be numbered from the end closest to a double-bonded carbon atom. If there is no difference, then it is numbered from the end closest to an alkyl group. The position of the double bond is indicated by the lowest-numbered carbon atom in the double bond, and this number is placed immediately before the stem. The number is omitted if there is only one possible location for the double bond.

Alkynes contain at least one triple-bonded carbon pair, and have the general formula CnH2n–2. Alkynes follow a naming convention similar to that used for alkanes and alkenes:


• For a straight-chain alkyne, define the longest continuous chain of carbon atoms using the stem and add the suffix ‘yne’. This means that because one of the carbon pairs is double bonded, simple alkynes have four fewer hydrogen atoms than the corresponding alkanes, and two fewer than the corresponding alkenes.

• The rules for naming branched alkenes are similar to those for naming branched alkanes. The longest continuous chain must be chosen to contain both carbon atoms of the triple bond, even if a longer chain could be found by choosing a different path. The chain must be numbered from the end closest to a triple-bonded carbon atom. If there is no difference, then it is numbered from the end closest to an alkyl group. The position of the triple bond is indicated by the lowest-numbered carbon atom in the triple bond, and this number is placed immediately before the stem. The number is omitted if there is only one possible location for the triple bond.


Alicyclic compounds


Alicyclic compounds are aliphatic cyclic compounds, with at least some of their carbons arranged in a ring. Some typical alicyclic compounds are shown in Figure 3-4. Generally the smaller rings are less stable than the larger ones. These compounds are named as follows:


• The prefix ‘cyclo’ is added before the word root which has been determined by the number of carbon atoms in the ring.

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Jun 11, 2016 | Posted by in BIOCHEMISTRY | Comments Off on Organic molecules: the chemistry of carbon and hydrogen

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