1.1. INTRODUCTION TO ORGANIC CHEMISTRY

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1 1.1. INTRODUCTION TO ORGANIC CHEMISTRY Everybody might know C as the symbol of carbon. However, it is not only a symbol but also a special key for about known compounds. Organic chemistry is chemistry of carbon atom, a huge branch of the chemistry tree and it can be said that we live in an Organic Chemistry Age in the 21 th century. The substances studied in organic chemistry are called organic compounds and they are vital for all living things on this planet. Petroleum, natural gas and coal are the main sources of organic compounds. All living systems obtain their energy from organic compounds like carbohydrates (sugars) and fats, using amino acids and proteins (organic) to grow. They transmit genetic information from one generation to the next through organic compounds called nucleic acids. The clothes we wear are of natural fibers like cotton, while wool or silk or synthetic materials like polyester are organic compounds. Most of the drugs and pharmaceuticals are also organic compounds. In agriculture too, organic chemistry is well represented. Fertilizers like urea, pesticides and plant growth regulators are all organic chemicals. Among various energy sources, fossil fuels like coal, lignite, petroleum and natural gas are of organic origin. Commonly used polymers natural and synthetic like wood, rubber, paper and plastics are again organic compounds. Thus, organic compounds play an important part in our daily lives. Figure 1.1. All organic compounds contain carbon and most are formed by living things, although they are also formed by geological and artificial processes. Carbon s ability to form diverse structures and an endless number of molecules make it an important building block in the living cells and tissues. It is interesting to know how every chemical in our body is produced, moved, modified and used by a sequence of amino acids that are related to DNA. The more we understand about how the chemistry of our body works the better our chance of keeping everything working, as it should. 1

2 1.2. A BRIEF HISTORY OF ORGANIC CHEMISTRY For over hundreds of years chemists have classified compounds as coming either from minerals (non-living origin) or from plants and animals (living origin). Alexander Mikhaylovich Butlerov September 15, 1828 August 17, 1886 Alexander Butlerov was born in Chistopol into a landowning family, was a Russian chemist, one of the principal creators of the theory of chemical structure ( ), the first to incorporate double bonds into structural formulas, the discoverer of hexamine (1859), the discoverer of formaldehyde (1859) and the discoverer of the formose reaction (1861). In 1807, Jacob Berzelius ( ) divided all the chemicals into two groups based on their reaction on heating. He classified the substances, which burnt or charred on heating as organic chemicals, which were mostly in living things. The substances, which melted or vaporized on heating but then returned to their original state, were classified under inorganic chemicals. He proposed a theory that: organic compounds are only found in living animals and plants because live forces or vital force is present in them. It was popularly known as vital force theory which summarizes that organic chemistry is the chemistry of life. In 1828, Friedrich Wohler ( ) reacted ammonia with cyanic acid, and obtained the well known organic compound, urea, instead of the expected ammonium cyanate: NH 3 + HNCO NH 2 CONH 2 Cyanic acid Urea This famous experiment proved to be the end of the theory called vitalism. In 1853, the English chemist Edward Frankland used the term valency (latin word valentia force). In 1857, two German scientists Kekule and Adolf Korbe explained the tetravalency of carbon. Between , August Kekule, Archibald Scott Couper and Alexander Mikhaylovich Butlerov independently established one of the fundamental theories in organic chemistry: The Structural Theory of Organic Compounds. In 1874, structural formulae were proposed by Van t Hoff to represent organic compounds methane, carbon in the center and hydrogen at the corners. 2

3 1.3. DIFFERENCES BETWEEN ORGANIC AND INORGANIC COMPOUNDS Carbon has the highest bonding capacity of all elements. Therefore, more than 5 million organic compounds have already been synthesized or isolated from natural sources. But there are about 400,000 inorganic compounds reported until now. The composition, the molecular structure and properties of organic compounds are highly different from those of inorganic compounds. Organic compounds 1. Organic compounds are formed from only a few elements, mainly C, H, O, N, S, P and halogens 2. There are covalent bonds between the atoms of organic molecules and these molecules are large, containing long chains and rings Inorganic compounds 1. Inorganic compounds are formed from more than 100 different elements 2. Ionic bonds are used in inorganic molecules to form simple and small molecules DEFINITIONS Volatile means to be turned into a vapor easily. The volatility of a covalent liquid depends on the strength of the intermolecular forces, as these must be overcome in order for the particles to change from liquid state to gaseous state. 3. Organic compounds are in the state of gases and volatile liquids and their solids have low melting points 4. Many organic compounds have their characteristic color and odor 5. They are insoluble in water, but soluble in organic solvents 6. Organic reactions are slow and complicated 3. Most of inorganic compounds are nonvolatile solids and they have very high melting and boiling points 4. Most of inorganic compounds, except a few metallic salts, are colorless and odorless 5. They are generally soluble in water, but insoluble in organic solvents 6. Inorganic reactions are fast, but simple Table 1.1. Differences between organic and inorganic compounds 3

4 Ethyl alcohol, C 2 H 6 O 1.4. STRUCTURAL THEORY OF ORGANIC COMPOUNDS The way in which component atoms of an organic substance are bod between them and influence each other, defines the chemical structure. This fundamental idea has been developed within "Theory of organic compounds' structure" of A.M.Butlerov (1861). Being enriched with new remarkable theoretical gains such as stereochemical theory, electronic theory in organic chemistry and others, the theory of structure of the organic compounds allowed scientific systematization of the wide experimental material of organic chemistry, correct explanation of the already known phenomenons and getting to discover new ones. On the foundation offered by this theory, through the tireless work of thousands of scientists, the modern organic chemistry has been created and developed. Structural theory of organic compounds 1. Atoms in compounds connect one to another according to valency concept. Carbon is tetra covalent in compounds; it means it forms four bonds. The order of connection of atoms in a molecule and the character of bonds is called as chemical structure. Valency of elements is shown by dash. Representation of molecules structure is known as structural formula. Dimethyl ether, C 2 H 6 O Figure 1.2. Ethyl alcohol and dimethyl ether 2. Properties of compounds determined not only by their composition but also with chemical structure (the order of connecting atoms in molecule). By using the structural formulas, the existence of isomers is explained. Isomers are compounds, which have the same molecular formula, but different structural formulas. Chemical and physical properties of isomers are different. For instance, to use a very simple case, ethyl alcohol and dimethyl either, although possessing widely different properties, have the same empirical formula: C 2 H 6 O (Fig. 1.2.) 3. The structure of molecule can be determined by using the properties of compound and vice versa by using the structure of molecule the properties of compound can be predicted. 4. Atoms and group of atoms influence each other. 4

5 1.5. ORGANIC STRUCTURE Carbon atoms possesses some remarkable properties: They can form strong, stable covalent bonds to other carbon atoms and many different types of atom. They can build up chains of carbon atoms to form a carbon 'skeleton'. They can form multiple bonds, both with other carbon atoms or chains, and with other elements. These three factors allow carbon to produce, literally, millions of different compounds, many of which are found in living systems. The definition of organic compound is now taken to mean a compound of carbon that is not a simple mineral compound. Again, this is pretty vague, but means that carbonates, hydrogen carbonates and oxides are excluded from the definition. Carbon is often bonded to hydrogen and oxygen in its compounds. Those compounds that contain carbon and hydrogen only are called hydrocarbons. Bonding in carbon compounds Carbon has four electrons in its highest energy level (outer shell). It must share four more electrons to attain a full outer shell. There are four ways that carbon atoms can do this. By forming four covalent bonds to four other atoms. By bonding covalently to two other atoms using one shared pair of electrons and a third atom using two shared pairs of electrons (a double bond). By bonding covalently to two other atoms by means of two shared pairs of electrons (two double bonds - this is unusual). By bonding covalently to two other atoms, one using a single bond and to the other by means of a triple bond (three shared pairs) Carbon single bonds are the type of sigma bond, caused by direct orbital overlap along a linear axis. (Figure 1.3.) KEY POINT The ability of carbon to form strong bonds to four other atoms, including carbon atoms, results in a huge range of organic compounds. DEFINITION Hydrocarbons compounds containing carbon hydrogen. are only and 5

6 Figure 1.3. Formation of sigma bond. Carbon double bonds consist of one sigma bond and one 'pi' bond, caused by lateral (sideways) overlap of two parallel orbitals. Notice that the overlap happens above and below the sigma bond. These two overlaps constitute only one pi bond. (Figure 1.4.) Figure 1.4. Formation of π-bond 6

7 Triple bonds formed by carbon atoms comprise one 'sigma' and two 'pi' bonds. The 'pi' bonds are at right angles to one another. In a triple bond with two 'pi' bonds there are four regions of overlap corresponding to the two pi bonds and one region of overlap along the axis joining the two atoms corresponding to the sigma bond. Shapes of organic molecules The shape of a molecule depends on the geometry of the bonding electrons that join all of the atoms together. Carbon atoms may adopt one of three geometries depending on the number of atoms to which they are bonded. (Figures 1.5., 1.6., 1.7.) Figure 1.5. The geometry of a fourbonded carbon is tetrahedral with bond angles of 109.5º. Functional groups The average bond strength of a carbon - carbon single bond is 346 kj/mole and a C=C double bond has a bond strength of 602 kj/mole. To break carbon-carbon bonds requires large amounts of energy, meaning that the carbon skeleton is particularly stable. Organic compounds react in many different ways, but the carbon skeleton is rarely broken. For this reason, the atoms that are attached to the carbon skeleton are very important as they often confer reactivity to the molecule. Such atom or groups are called 'functional groups' - they give the molecule functionality. Common functional groups are given in table 1.2. Atom or grouping -Cl -F, -Cl, -Br, -I -OH -CHO -COOH -NH 2 -CONH 2 -CN Table 1.2. Common functional groups Name Chlorine atom Halide group Alcohol group Aldehyde group (Carbonyl group) Carboxyl group Amine group Amide group Nitrile group Figure 1.6. The geometry of carbon bonded to three other atoms is trigonal planar (bond angle 120º) Figure 1.7. The geometry of carbon bonded to two other atoms is linear (bond angle 180º) 7

8 DEFINITIONS The empirical formula shows the simplest whole number ratio for the atoms of each element in a compound. The molecular formula shows the actual number of atoms of each element in one molecule of the compound. The structural formula shows how the different atoms are joined together, and the positions of functional groups FORMULA REPRESENTATION Representation of chemical formula in organic chemistry must leave the structure unambiguous. There are several accepted ways to do this. Empirical formula The empirical formula is the simplest ratio of the atoms within a molecule of the compound. It emerges from calculations of formula using a consideration of the percentage composition by mass of each element. Traditionally, the method of determining the nature of a substance was based on a direct analysis of the elements within the compound, taking advantage of the fact that most organic compounds are flammable. When burnt, all of the carbon turns to carbon dioxide and all of the hydrogen turns to water. Thus, if the mass of carbon dioxide produced from a known mass of an unknown compound is found, the actual mass of carbon and hence the percentage carbon in the original compound can be calculated. Worked problem 1.1.: 5g of an unknown organic compound produced 11.0g of carbon dioxide on complete combustion in excess air. Calculate the percentage carbon in the compound. Solution: m (CO 2 ) = 11.0g, M (CO 2 ) = 44.0 g/mole First, we can find mole number of CO 2 n (CO 2 ) = m M = 11 g 44 g = 0.25 mole mol n (CO 2 ) = n (C) = 0.25 mole m (C) = n (C) A(C) = 0.25 mole 12 g/mole = 3.0 g w% (C) = m (C) m (comp) Answer: w% (C) = 60% 100% = % = 60% 8

9 Worked problem 1.2: 5g of an unknown organic compound produced 3.3g of water on complete combustion in excess air. Calculate the percentage carbon in the compound. Solution: m (H 2 O) = 3.3 g, M (H 2 O) = 18.0 g/mole First, we can find mole number of H 2 O n (H 2 O) = m M = 3.3 g 18 g = mole mol n (H) = 2 n (H 2 O) = = mole m (H) = n (H) A(H) = mole 1 g/mole = g m (C) = m(organic compound) m (H), m (C) = = g w% (C) = Answer: w% (C) = 92.68% Molecular formula m (C) % = m (comp) % = 92.68% The molecular formula shows the actual number of atoms of each type in the molecule. For example, the molecular formula of ethanol is C 2 H 6 O. There are two fundamental problems with using the molecular formulae to represent molecules: They give no indication as to the actual arrangement of the atoms within the molecule. There may be many different molecules with the same molecular formula. The mass spectrometer is an instrument, which turns atoms and molecules into ions and measures their mass. When an organic compound passes through a mass spectrometer, its molecules get broken into positively charged particles. These fragments provide useful information. Each fragment gives a corresponding line in the mass spectrum. From the position of the line, we can find the relative mass of the fragment, and use this to work out its formula. By piecing together the fragments, we can deduce the structure of the parent molecule. 9

10 STUDY TIP Do not forget that carbon always forms four bonds. This can help when drawing a structure. If you end up with carbons with 3 or 5 bonds then you have done it However, in analysis the molecular formula is a good start when working out the identity of a compound. A high definition Mass Spectrometer can determine the relative formula mass of a compound to such a high degree of accuracy that the molecular formula can be obtained directly. It is then up to other techniques to identify the actual arrangement of the atoms within the molecule. Structural formula The structural formula shows the actual arrangement of the atoms in a molecule by drawing the bonds as lines between letters representing the atoms. A single bond is shown as one line only and a double bond is shown as a double line. Structural formula of ethanol is: Condensed formula The condensed formula is a shorthand method of representing the structural formula which relies on some knowledge of chemical structures. The structure is written starting at one end of the chain with each carbon shown along with any attachments. There are no single bonds shown between carbon atoms, as it is assumed that the reader understands that the atoms must be joined together in the chain, using at least one bond. Where groups are attached to the carbons in the chain they can be show by using brackets immediately after the carbon to which they are attached. CH 3 CH(OH)CH 2 CH 3 In this case there is an -OH group attached to carbon number 2 in the chain. 10

11 Skeletal formula This is another way to represent the molecular structure. In a skeletal formula each carbon is represented by an angle, or termination in a line and the hydrogen atoms are just assumed. Double bonds are shown as a double line and heteroatoms are draw as usual. A certain amount of logical reasoning must be used to understand the structure from a skeletal representation. This type of representation is very useful when the molecule is large and the number of atoms becomes too unwieldy for other representations. Lewis structure These are structural formula in which the bonds are not represented by lines, but rather by the electron pairs that make up the bonds. Any lone (non-bonding) electron pairs must also be shown. The electron pairs may be shown as two dots, or two crosses, or even a line. The Lewis structure of ethanol C 2 H 6 O is represented as follows: Butane Skeletal formula Butane Structural formula Benzene Skeletal formula Notice that the two lone pairs on the oxygen are also shown. When drawing Lewis structures there are nearly always eight electrons around each atom (except hydrogen). There are some exceptions, but not in organic chemistry. Benzene Structural formula Figure 1.8. Skeletal and structural formulas of butane and benzene 11

12 1.7. HYBRIDIZATION The Valence Shell Electron Pair Repulsion (VSEPR) model is based on the idea that electron pairs will repel each other electrically and will seek to minimize this repulsion. To accomplish this minimization, the electron pairs will be arranged around a central atom as far apart as possible. Covalent bonds are formed when atomic orbitals overlap. There are two types of orbital overlap that an organic chemist needs to be familiar with. Sigma, s, overlap occurs when there is one bonding interaction that results from the overlap of two orbitals. Pi, p, overlap occurs when two bonding interactions result from the overlap of orbitals. Figure 1.9. Sigma and pi overlap of orbitals The organic chemist also needs to realize how these orbital overlaps relate to the type of bonding that is occurring between atoms: single bond double bond triple bond s overlap s and p overlaps s and two p overlaps sp 3 Hybridization Unfortunately, overlap of existing atomic orbitals (s, p, etc.) is not sufficient to explain some of the bonding and molecular geometries that are observed. Consider the element carbon and the methane (CH 4 ) molecule. A carbon atom has the electron configuration of 1s 2 2s 2 2p 2, meaning that it has two unpaired electrons in its 2p orbitals, as shown in Figure Figure Orbital configuration for carbon atom. 12

13 According to the description of valence bond theory so far, carbon would be expected to form only two bonds, corresponding to its two unpaired electrons. However, methane is a common and stable molecule, with four equivalent C H bonds. To account for this, one of the 2s electrons is promoted to the empty 2p orbital (see Figure 1.11). Figure Promotion of carbon s electron to empty p orbital. Now, four bonds are possible. The promotion of the electron costs a small amount of energy, but recall that the process of bond formation is accompanied by a decrease in energy. The two extra bonds that can now be formed results in a lower overall energy and thus greater stability to the CH 4 molecule. Carbon normally forms four bonds in most of its compounds. The number of bonds is now correct, but the geometry is wrong. The three p orbitals (px, py, pz) are oriented at 90 o relative to one another. However, as was seen from VSEPR theory, the observed H C H bond angle in the tetrahedral CH 4 molecule is actually o. Therefore, the methane molecule cannot be adequately represented by simple overlap of the 2s and 2p orbitals of carbon with the 1s orbitals of each hydrogen atom. To explain the bonding in methane, it is necessary to introduce the concept of hybridization and hybrid atomic orbitals. Hybridization is the mixing of the atomic orbitals in an atom to produce a set of hybrid orbitals. When hybridization occurs, it must do so as a result of the mixing of nonequivalent orbitals. In other words, s and p orbitals can hybridize but p orbitals cannot hybridize with other p orbitals. Hybrid orbitals are the atomic orbitals obtained when two or more nonequivalent orbitals form the same atom combine in preparation for bond formation. In the current case of carbon, the single 2s orbital hybridizes with the three 2p orbitals to form a set of four hybrid orbitals, called sp 3 hybrids (Figure 1.12). DEFINITIONS Hybridization is the mixing of the atomic orbitals in an atom to produce a set of hybrid orbitals. Hybrid orbitals are the atomic orbitals obtained when two or more nonequivalent orbitals form the same atom combine in preparation for bond formation. 13

14 Figure Carbon sp 3 hybrid orbitals. The sp 3 hybrids are all equivalent to one another. Spatially, the hybrid orbitals point towards the four corners of a tetrahedron (Figure 1.13.). Figure The process of sp 3 hybridization is the mixing of an s orbital with a set of three p orbitals to form a set of four sp 3 hybrid orbitals. Each large lobe of the hybrid orbitals points to one corner of a tetrahedron. The four lobes of each of the sp 3 hybrid orbitals then overlap with the normal unhybridized 1s orbitals of each hydrogen atoms to form the tetrahedral methane molecule. 14

15 sp 2 Hybridization Ethene (C 2 H 4 ) has a double bond between the carbons. For this molecule, carbon will sp 2 hybridize. In sp 2 hybridization, the 2s orbital mixes with only two of the three available 2p orbitals, forming a total of 3 sp 2 orbitals with one p-orbital remaining. In ethylene (ethene), the two carbon atoms form a sigma bond by overlapping two sp 2 orbitals; each carbon atom forms two covalent bonds with hydrogen by s sp 2 overlapping all with 120 angles. The pi bond between the carbon atoms forms by a 2p-2p overlap. The hydrogen-carbon bonds are all of equal strength and length, which agrees with experimental data. The geometry of the sp2 hybrid orbitals is trigonal planar, with the large lobe of each orbital pointing toward one corner of an equilateral triangle. The angle between any two of the hybrid orbital lobes is 120. (Figure 1.13.) Carbon atoms make use of sp 2 hybrid orbitals not only in ethene, but also in much other type of compounds. The table 1.3. shows some of these compounds: Figure sp 2 hybridization Formaldehyde Ketene Acetic acid Benzene Acetone Table 1.3. Compounds, in which carbon atoms have sp 2 -hybridization. 15

16 sp hybridization When sp hybrid orbitals are used for the sigma bond, the two sigma bonds around the carbon is linear. Two other p orbitals are available for pi bonding, and a typical compound is the acetylene or ethyne HC CH. The three sigma and two pi bonds of this molecule from is shown in the figure Figure sp hybridization in acetylene molecule 16

17 SUPPLEMENTARY QUESTIONS 1. What are the differences between organic and inorganic compounds? 2. Why is organic chemistry considered the chemistry of Carbon compounds? 3. Give five examples of organic and inorganic compounds that you use at home. 4. Which properties of carbon make it unique? 5. Why is organic chemistry so important? 6. An organic compound was found to contain 10% hydrogen and 90% of carbon by mass. Find its empirical formula. 7. Find the empirical formula of the organic compound of which 3g contains 0,6 grams of hydrogen and 2,4 grams of carbon. 8. An organic compounds whose molar mass is 88 g/mol contains 55% C, 36% O and 9% H by mass. Find its molecular formula. 9. An organic compound contains only 1,5 grams hydrogen and 9 grams of carbon by mass. Find its molecular formula if its molar mass is 210 g/mol. 17