Chemical bonds between carbon and oxygen, and nitrogen and carbon with other atoms such as hydrogen, oxygen, sulphur,

Mitesh Shrestha

• Most of the molecules in living systems contain only six different atoms: hydrogen, carbon, nitrogen, phosphorus, oxygen, and sulfur.

• The outermost orbital of each atom has a characteristic number of electrons:

Table 3-l Elemental abundance in seawater , the human body, and the earth's crust*

Seawater (%) Human body (%) Earth's crust (%)

H 66 H 63 O 47

O 33 O 25.5 Si 28

Cl 0.33 C 9.5 Al 7.9

Na 0.28 N 1.4 Fe 4.5

Mg 0.033 Ca 0.31 Ca 3.5

S 0.017 P 0.22 Na 2.5

Ca 0.0062 Cl 0.08 K 2.5

K 0.0060 K 0.06 Mg 2.2

C 0.0014

Carbon

• Carbon is the most important element to living things because it can form many different kinds of bonds and form essential compounds.

Carbon and Oxygen

• Covalent bond between carbon and oxygen.

• Oxygen has 6 valence electrons and prefers to either share two electrons in bonding with carbon, leaving the 4 nonbonding electrons in 2 lone pairs :Ó: or to share two pairs of electrons to form the carbonyl functional group. =O:

• Simple representatives of these two bond types are the _OH in alcohols such as the ethanol in beverages and fuels and the C=O in ketones (as well as many other related carbonyl compounds).

Carbon and Oxygen

• The C–O bond is strongly polarized towards oxygen (electronegativity of C vs O, 2.55 vs 3.44).

• Bond lengths for paraffinic C–O bonds are in the range of 143 picometer – less than those of C–N or C–C bonds. Shortened single bonds are found with carboxylic acids (136 pm) due to partial double bond character and elongated bonds are found in epoxides (147 pm).

• The C–O bond strength is also larger than C–N or C–C. For example, bond strengths are 91 kilocalories (380 kJ)/mol (at 298 K) in methanol, 87 kilocalories (360 kJ)/mol in methylamine, and 88 kilocalories (370 kJ)/mol in ethane.

Carbon and Nitrogen

• Covalent bond between carbon and nitrogen and is one of the most abundant bonds in organic chemistry and biochemistry.

• A CN bond is strongly polarized towards nitrogen (the electronegativities of C and N are 2.55 and 3.04, respectively)

Carbon and Carbon

• covalent bond between two carbon atoms.

• Carbon is one of the few elements that can form long chains of its own atoms, a property called catenation. This coupled with the strength of the carbon–carbon bond gives rise to an enormous number of molecular forms, many of which are important structural elements of life.

• Branching is also common in C−C skeletons. Different carbon atoms can be identified with respect to the number of carbon neighbors:

• primary carbon atom: one carbon neighbor • secondary carbon atom: two carbon neighbors • tertiary carbon atom: three carbon neighbors • quaternary carbon atom: four carbon neighbors

Carbon and Carbon

Carbon and Hydrogen

• a covalent bond between carbon and hydrogen atoms that can be found in many organic compounds.

• C (2.55) and H (2.2)—the electronegativity difference between these two atoms is 0.35. Because of this small difference in electronegativities, the C−H bond is generally regarded as being non-polar.

• The C−H bond in general is very strong, so it is relatively unreactive

Carbon and Sulphur

• Carbonyl sulfide is the organic compound with the formula OCS. Commonly written as COS, it is a colourless flammable gas with an unpleasant odor. It is a linear molecule consisting of a carbonyl group double bonded to a sulfur atom.

• Carbonyl sulfide can be considered to be intermediate between carbon dioxide and carbon disulfide, both of which are valence isoelectronic with it.

• Carbonyl sulfide decomposes in the presence of humidity and bases to carbon dioxide and hydrogen sulfide.

• This compound is found to catalyze the formation of peptides from amino acids. This finding is an extension of the Miller–Urey experiment and it is suggested that carbonyl sulfide played a significant role in the origin of life.

O

H H

1 molecule of water is

made up of 2 hydrogen atoms

bonded with 1 oxygen atom

STRUCTURE OF WATER

O

STRUCTURE OF WATER

The bond that forms water

is a covalent bond

Properties of Water • Polar molecule

• Cohesion and adhesion

• High specific heat

• Density – greatest at 4oC

• Universal solvent of life

Polarity of Water

• In a water molecule two hydrogen atoms form single polar covalent bonds with an oxygen atom. Gives water more structure than other liquids – Because oxygen is more electronegative, the

region around oxygen has a partial negative charge.

– The region near the two hydrogen atoms has a partial positive charge.

• A water molecule is a polar molecule with opposite ends of the molecule with opposite charges.

• Water has a variety of unusual properties because of attractions between these polar molecules.

– The slightly negative regions of one molecule are attracted to the slightly positive regions of nearby molecules, forming a hydrogen bond.

– Each water molecule can form hydrogen bonds with up to four neighbors.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 3.1

HYDROGEN BONDS • Hold water molecules

together

• Each water molecule can form a maximum of 4 hydrogen bonds

• The hydrogen bonds joining water molecules are weak, about 1/20th as strong as covalent bonds.

• They form, break, and reform with great frequency

• Extraordinary Properties that are a result of hydrogen bonds. – Cohesive behavior

– Resists changes in temperature

– High heat of vaporization

– Expands when it freezes

– Versatile solvent

Organisms Depend on Cohesion

• Cohesion is responsible for the transport of the water column in plants

• Cohesion among water molecules plays a key role in the transport of water against gravity in plants

• Adhesion, clinging of one substance to another, contributes too, as water adheres to the wall of the vessels.

Hydrogen bonds hold the substance together, a phenomenon called cohesion

• Surface tension, a measure of the force necessary to stretch or break the surface of a liquid, is related to cohesion.

– Water has a greater surface tension than most other liquids because hydrogen bonds among surface water molecules resist stretching or breaking the surface.

– Water behaves as if covered by an invisible film.

– Some animals can stand, walk, or run on water without breaking the surface.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 3.3

Moderates Temperatures on Earth

Celsius Scale at Sea Level

100oC

Water boils

37oC

Human body temperature

23oC

Room temperature

0oC

Water freezes

Water stabilizes air temperatures by absorbing heat from warmer air and releasing heat to cooler air. Water can absorb or release relatively large amounts of heat with only a slight change in its own temperature.

Three-fourths of the earth is covered

by water. The water serves as a

large heat sink responsible for:

1. Prevention of temperature

fluctuations that are outside the

range suitable for life.

2. Coastal areas having a mild

climate

3. A stable marine environment

Specific Heat is the amount of heat that must be absorbed or lost for one gram of a substance to change

its temperature by 1oC.

Density of Water

• Most dense at 4oC

• Contracts until 4oC

• Expands from 4oC to 0oC

The density of water:

1. Prevents water from freezing from the bottom up.

2. Ice forms on the surface first—the freezing of the

water releases heat to the water below creating

insulation.

3. Makes transition between season less abrupt.

– When water reaches 0oC, water becomes locked into a crystalline lattice with each molecule bonded to to the maximum of four partners.

– As ice starts to melt, some of the hydrogen bonds break and some water molecules can slip closer together than they can while in the ice state.

– Ice is about 10% less dense than water at 4oC.

Copyright © 2002 Pearson Education, Inc., publishing as Benjamin Cummings

Fig. 3.5