General and BIOorganic chemistry

(lecture notes)

Part 2. Organic chemistry

For 1st year students of the Faculty of Medicine, specialty "Dentistry"

Publishing house of the Peoples' Friendship University of Russia,

APPROVED

RIS Academic Council

Peoples' Friendship University of Russia

Kovalchukova O.V., Avramenko O.V.

General and bioorganic chemistry (lecture notes). Part 2. Organic chemistry. For 1st year students of the Faculty of Medicine, specialty “Dentistry”. M.: Publishing house RUDN, 2010. 108 p.

Lecture notes given to 1st year students of the Faculty of Medicine, specialty “Dentistry”. Compiled in accordance with the course program "General and bioorganic chemistry".

Prepared at the Department of General Chemistry.

© Kovalchukova O.V., Avramenko O.V.

© Publishing house of the Peoples' Friendship University of Russia, 2010

INTRODUCTION

Bioorganic chemistry is a branch of chemistry that is closely related to such special disciplines of medical faculties of universities as biochemistry, pharmacology, physiology, molecular biology. It is a field of science that studies the structure and mechanisms of functioning of biologically active molecules from the perspective and ideas organic chemistry, which determines the patterns in the relationship between structure and reactivity organic compounds.

The main attention in this course of lectures is paid to the classification of organic compounds according to the structure of the carbon skeleton and the nature of functional groups, the laws connecting the chemical structure of organic molecules with the nature of their reaction centers, the connection of their electronic and spatial structure with the mechanisms of chemical transformations.

THEORY OF THE CHEMICAL STRUCTURE OF ORGANIC COMPOUNDS

Organic compounds- these are carbon compounds (except for the simplest ones) in which it exhibits valence IV.

Organic chemistry– this is the chemistry of hydrocarbons and their derivatives.

The carbon atom in organic compounds is in an excited state and has four unpaired electrons:

6 С 1s 2 2s 2 2p 2 → 6 С* 1s 2 2s 1 2p 3

A carbon atom in an excited state is capable of:

1) form strong bonds with other carbon atoms, which leads to the formation of chains and cycles;

2) due to various types hybridization of orbitals to form simple, double and triple bonds between carbon atoms and with other atoms (H, O, N, S, P, etc.);

3) combine with four different atoms, resulting in the formation of branched carbon chains.

Types of carbon atom hybridization in organic compounds

sp 3 – hybridization

All four valence orbitals are involved in hybridization. Bond angle 109 o 28’ (tetrahedron). Carbon atoms form only simple (σ) bonds - the compound is saturated.

sp 2 – hybridization

Three hybrid and one non-hybrid orbital are formed. Bond angle 120° (flat structures, regular triangle). Hybrid orbitals form σ bonds. Non-hybrid orbitals form p-bonds. sp 2–Hybridization is typical for unsaturated compounds with one p-bond.

sp – hybridization

Two hybrid and two non-hybrid orbitals are formed. Bond angle 180° (linear structures). The carbon atom is in the state sp-hybridization takes part in the formation of two double bonds or one triple bond.

Theory of the structure of organic compounds formulated in 1861 by A.M. Butlerov and includes the following provisions:

1. All atoms that make up the molecule are connected to each other in a strictly defined sequence in accordance with their valences. The order in which atoms are combined into a molecule determines its chemical structure .

2. The properties of organic compounds depend not only on the qualitative and quantitative composition of the substances, but also on the order of their connection (the chemical structure of the molecule).

3. Atoms in a molecule have a mutual influence on each other, i.e. the properties of groups of atoms in a molecule can change depending on the nature of other atoms that make up the molecule. The group of atoms that defines chemical properties organic molecules are called functional group .

4. Each organic compound has only one chemical formula. Knowing the chemical formula, you can predict the properties of a compound, and by studying its properties in practice, you can establish the chemical formula.

Organic molecule

Types of carbon skeleton:

Acyclic:

· branched;

· normal (linear).

Cyclical:

· carbocyclic (a cycle of only carbon atoms);

· heterocyclic (in addition to carbon atoms, the cycle includes some other atoms - nitrogen, oxygen, sulfur).

Types of carbon atoms in a hydrocarbon chain:

H 3 C-CH 2 -CH-C- CH 3

Primary carbon atoms (connected in a chain with only one carbon atom, is terminal);

Secondary carbon atom (connected to two neighboring carbon atoms, located in the middle of the chain);

Tertiary carbon atom (located on a branch of the carbon chain, connected to three carbon atoms);

Quaternary carbon atom (has no substituents other than carbon atoms).

Functional group– special group atoms, which determines the chemical properties of compounds.

Examples functional groups:

-HE–hydroxyl group (alcohols, phenols);

C=O– carbonyl group (ketones, aldehydes);

WITH- carboxyl group ( carboxylic acids);

-NH 2 – amino group (amines);

-SH – thiol group (thioalcohols)

organic compound

compound

properties

chemical structure

The atoms that make up organic compound, can be combined into molecules in different ways. For example, a compound with the composition C 2 H 6 O may have two chemical compounds, having different physical and chemical properties:

Compound organic compound - number of atoms various elements included in its molecule. Isomers– compounds that have the same composition, but different chemical structures. Isomers have different chemical properties.

Types of isomerism

STRUCTURAL ISOMERISM

Carbon chain isomerism:

Isomerism of the position of multiple bonds:

Interclass isomerism:

STEREOISOMERISM

Geometric(spatial, cis-trans-isomerism of compounds with double bonds):

cis-butene-2	trance-butene-2

Geometric isomerism is possible if each of the carbon atoms involved in the formation of a double bond has different substituents. Thus, for butene-1 CH 2 =CH–CH 2 –CH 3 geometric isomerism is impossible, since one of the carbon atoms at the double bond has two identical substituents (hydrogen atoms).

Geometric(spatial, cis-trans-isomerism of cyclic limit compounds):

Geometric isomerism is possible if at least two carbon atoms forming a ring have different substituents.

Optical:

Optical isomerism is a type of stereoisomerism caused by the chirality of molecules. In nature there are connections that are related like two hands of one person. One of the properties of these compounds is their incompatibility with their mirror image. This property is called chirality (from the Greek. « With heir"- hand).

The optical activity of molecules is detected when they are exposed to polarized light. If a polarized beam of light is passed through a solution of an optically active substance, the plane of its polarization will rotate. Optical isomers are designated using prefixes d-

Sp-hybridization

sp-hybridization occurs, for example, during the formation of Be, Zn, Co and Hg (II) halides. In the valence state, all metal halides contain s and p-unpaired electrons at the appropriate energy level. When a molecule is formed, one s and one p orbital form two hybrid sp orbitals at an angle of 180 degrees.

Fig.3 sp hybrid orbitals

Experimental data show that Be, Zn, Cd and Hg(II) halides are all linear and both bonds are of the same length.

sp 2 hybridization

As a result of the hybridization of one s-orbital and two p-orbitals, three hybrid sp 2 orbitals are formed, located in the same plane at an angle of 120 o to each other. This is, for example, the configuration of the BF 3 molecule:

Fig.4 sp 2 hybridization

sp 3 hybridization

sp 3 hybridization is characteristic of carbon compounds. As a result of the hybridization of one s orbital and three

p-orbitals, four hybrid sp 3 orbitals are formed, directed towards the vertices of the tetrahedron with an angle between the orbitals of 109.5 o. Hybridization is manifested in the complete equivalence of the bonds of the carbon atom with other atoms in compounds, for example, in CH 4, CCl 4, C(CH 3) 4, etc.

Fig.5 sp 3 hybridization

If all hybrid orbitals are connected to the same atoms, then the bonds are no different from each other. In other cases, slight deviations from standard bond angles occur. For example, in the water molecule H 2 O, oxygen - sp 3 -hybrid, is located in the center of an irregular tetrahedron, at the vertices of which two hydrogen atoms and two lone pairs of electrons “look” (Fig. 2). The shape of the molecule is angular when viewed from the centers of the atoms. The HOH bond angle is 105°, which is quite close to the theoretical value of 109°.

Fig.6 sp 3 - hybridization of oxygen and nitrogen atoms in molecules a) H 2 O and b) NCl 3.

If there were no hybridization (“alignment” O-H bonds), the bond angle of HOH would be 90° because the hydrogen atoms would be attached to two mutually perpendicular p orbitals. In this case, our world would probably look completely different.

The hybridization theory explains the geometry of the ammonia molecule. As a result of the hybridization of the 2s and three 2p orbitals of nitrogen, four sp 3 hybrid orbitals are formed. The configuration of the molecule is a distorted tetrahedron, in which three hybrid orbitals participate in the formation of a chemical bond, but the fourth with a pair of electrons does not. Angles between N-H bonds not equal to 90° as in a pyramid, but also not equal to 109.5°, corresponding to a tetrahedron.

Fig.7 sp 3 - hybridization in an ammonia molecule

When ammonia interacts with a hydrogen ion, as a result of donor-acceptor interaction, an ammonium ion is formed, the configuration of which is a tetrahedron.

Hybridization also explains the difference in angle between O-H connections in the corner water molecule. As a result of the hybridization of the 2s and three 2p orbitals of oxygen, four sp 3 hybrid orbitals are formed, of which only two are involved in the formation of a chemical bond, which leads to a distortion of the angle corresponding to the tetrahedron.

Fig.8 sp 3 hybridization in a water molecule

Hybridization can involve not only s- and p-orbitals, but also d- and f-orbitals.

With sp 3 d 2 hybridization, 6 equivalent clouds are formed. It is observed in such compounds as 4-, 4-. In this case, the molecule has an octahedral configuration.

Problem 261.
What types of carbon AO hybridization correspond to the formation of CH molecules 4, C 2 H 6, C 2 H 4, C 2 H 2?
Solution:
a) In CH molecules 4 and C 2 H 6 The valence electron layer of a carbon atom contains four electron pairs:

Therefore, the electron clouds of the carbon atom in the CH 4 and C 2 H 6 molecules will be maximally distant from each other during sp3 hybridization, when their axes are directed towards the vertices of the tetrahedron. In this case, in the CH4 molecule, all the vertices of the tetrahedron will be occupied by hydrogen atoms, so that the CH4 molecule has a tetrahedral configuration with a carbon atom in the center of the tetrahedron. In the C 2 H 6 molecule, hydrogen atoms occupy three vertices of the tetrahedron, and the common electron cloud of another carbon atom is directed towards the fourth vertex, i.e. two carbon atoms are connected to each other. This can be represented by diagrams:

b) In the C 2 H 4 molecule there is a valence electron layer of the carbon atom, as in the CH 4 and C 2 H 6 molecules. contains four electron pairs:

When C 2 H 4 is formed, three covalent bonds are formed according to the usual mechanism, i.e. are - connections, and one - - connection. When a C 2 H 4 molecule is formed, each carbon atom has two hydrogen atoms - bonds and two bonds to each other, one - and one - bonds. Hybrid clouds corresponding to this type of hybridization are located in the carbon atom so that the interaction between electrons is minimal, i.e. as far apart as possible. This arrangement of carbon atoms (two double bonds between carbon atoms) is characteristic of sp 2 hybridization of carbon AO. During sp 2 hybridization, the electron clouds in carbon atoms are oriented in directions lying in the same plane and making angles of 120 0 with each other, i.e. in directions to the vertices of a regular triangle. In the ethylene molecule, the formation of - bonds involves three sp 2 -hybrid orbitals of each carbon atom, two between two hydrogen atoms and one with the second carbon atom, and - the bond is formed due to the p-electron clouds of each carbon atom. The structural formula of the C 2 H 4 molecule will look like:

c) In the C 2 H 2 molecule, the valence electron layer of the carbon atom contains four pairs of electrons:

The structural formula of C 2 N 2 is:

Each carbon atom is connected by one electron pair to a hydrogen atom and three electron pairs to another carbon atom. Thus, in an acetylene molecule, the carbon atoms are connected to each other by one -bond and two -bonds. Each carbon atom is connected to hydrogen by an - bond. The formation of - bonds involves two sp-hybrid AOs, which are located relative to each other so that the interaction between them is minimal, i.e. as far apart as possible. Therefore, during sp-hybridization, the electron clouds between carbon atoms are oriented in opposite directions relative to each other, i.e. angle between C-C connections is 180 0. Therefore, the C 2 H 2 molecule has a linear structure:

Problem 262.
Indicate the type of hybridization of silicon AO in SiH 4 and SiF 4 molecules. Are these molecules polar?
Solution:
In SiH 4 and SiF 4 molecules, the valence electron layer contains four pairs of electrons:

Therefore, in both cases, the electron clouds of the silicon atom will be maximally distant from each other during sp 3 hybridization, when their axes are directed towards the vertices of the tetrahedron. Moreover, in the SiH 4 molecule all the vertices of the tetrahedron are occupied by hydrogen atoms, and in the SiF 4 molecule - by fluorine atoms, so that these molecules have a tetrahedral configuration with a silicon atom in the center of the tetrahedron:

In tetrahedral molecules SiH 4 and SiF 4, the dipole moments of the Si-H and Si-F bonds mutually cancel each other, so that the total dipole moments of both molecules will be equal to zero. These molecules are non-polar, despite the polarity of the Si-H and Si-F bonds.

Problem 263.
In SO 2 and SO 3 molecules, the sulfur atom is in a state of sp 2 hybridization. Are these molecules polar? What is their spatial structure?
Solution:
During sp 2 hybridization, hybrid clouds are located in the sulfur atom in directions lying in the same plane and making angles of 120 0 with each other, i.e. directed towards the vertices of a regular triangle.

a) In the SO 2 molecule, two sp 2 -hybrid AOs form a bond with two oxygen atoms, the third sp 2 -hybrid orbital will be occupied by a free electron pair. This electron pair will shift the electron plane and the SO 2 molecule will take the shape of an irregular triangle, i.e. angle OSO will not be equal to 120 0. Therefore, the SO 2 molecule will have an angular shape with sp 2 hybridization of the atomic orbitals structure:

In the SO 2 molecule, mutual compensation of dipole moments S-O connections doesn't happen; the dipole moment of such a molecule will have a value greater than zero, i.e. the molecule is polar.

b) In the corner SO 3 molecule, all three sp2-hybrid AOs form a bond with three oxygen atoms. The SO3 molecule will have the shape of a flat triangle with sp2 hybridization of the sulfur atom:

In a triangular SO 3 molecule, the dipole moments of the S-O bonds cancel each other out, so that the total dipole moment will be zero, the molecule is polar.

Problem 264.
When SiF4 interacts with HF, a strong acid H 2 SiF 6 is formed, which dissociates into H + and SiF 6 2- ions. Can the reaction between CF 4 and HF proceed in a similar way? Indicate the type of hybridization of silicon AO in the SiF 6 2- ion.
Solution:
a) When excited, a silicon atom goes from the state 1s 2 2s 2 2p 6 3s 2 3p 3 to the state 1s 2 2s 2 2p 6 3s 1 3p 4 3d 0, and electronic structure valence orbitals corresponds to the diagram:

Four unpaired electrons of an excited silicon atom can participate in the formation of four covalent bonds according to the usual mechanism with fluorine atoms (1s 2 2s 2 2p 5), each having one unpaired electron, to form a SiF 4 molecule.

When SiF 4 interacts with HF, the acid H 2 SiF 6 is formed. This is possible because the SiF 4 molecule has free 3d orbitals, and the F- (1s 2 2s 2 2p 6) ion has free pairs of electrons. The connection is carried out according to the donor-acceptor mechanism due to a pair of electrons from each of the two F - (HF ↔ H + + F -) ions and the free 3d orbitals of the SiF 4 molecule. In this case, the SiF 6 2- ion is formed, which with the H + ions forms an acid molecule H 2 SiF 6.

b) Carbon (1s 2 2s 2 2p 2) can form, like silicon, a CF 4 compound, but the valence capabilities of the carbon atom will be exhausted (there are no unpaired electrons, free pairs of electrons and free valence orbitals at the valence level). The structure diagram of the valence orbitals of an excited carbon atom has the form:

When CF 4 is formed, all valence orbitals of carbon are occupied, so an ion cannot be formed.

In the SiF 4 molecule, the valence electron layer of the silicon atom contains four pairs of electrons:

The same is observed for the CF 4 molecule. therefore, in both cases, the electron clouds of silicon and carbon atoms will be as far apart as possible from each other during sp3 hybridization. When their axes are directed to the vertices of the tetrahedron:

In 1930, Slater and L. Pauling developed the theory of the formation of covalent bonds due to the overlap of electronic orbitals - the valence bond method. This method is based on the hybridization method, which describes the formation of molecules of substances due to the “mixing” of hybrid orbitals (“it is not the electrons that are mixed, but the orbitals”).

DEFINITION

Hybridization– mixing of orbitals and alignment of their shape and energy. Thus, when mixing s- and p-orbitals, we obtain the type of hybridization of sp, s- and 2 p-orbitals - sp 2, s- and 3 p-orbitals - sp 3. There are other types of hybridization, for example, sp 3 d, sp 3 d 2 and more complex ones.

Determination of the type of hybridization of molecules with a covalent bond

The type of hybridization can only be determined for molecules with covalent bond type AB n, where n is greater than or equal to two, A is the central atom, B is the ligand. Only the valence orbitals of the central atom undergo hybridization.

Let us determine the type of hybridization using the example of the BeH 2 molecule.

Initially, we write down the electronic configurations of the central atom and ligand and draw electron graphic formulas.

The beryllium atom (central atom) has vacant 2p orbitals, therefore, in order to accept one electron from each hydrogen atom (ligand) to form a BeH 2 molecule, it needs to go into an excited state:

The formation of the BeH 2 molecule occurs due to the overlap of the valence orbitals of the Be atom

* The electrons of hydrogen are indicated in red, and the electrons of beryllium in black.

The type of hybridization is determined by which orbitals overlap, i.e., the BeH 2 molecule is in sp - hybridization.

In addition to molecules of composition AB n, the method of valence bonds can determine the type of hybridization of molecules with multiple bonds. Let's look at the example of the ethylene molecule C 2 H 4 . The ethylene molecule has a multiple double bond, which is formed by and – bonds. To determine hybridization, we write down the electronic configurations and draw electron graphic formulas of the atoms that make up the molecule:

6 C 2s 2 2s 2 2p 2

The carbon atom has one more vacant p-orbital, therefore, in order to accept 4 hydrogen atoms it needs to go into an excited state:

One p-orbital is required to form a -bond (highlighted in red), since the -bond is formed by overlapping “pure” (non-hybrid) p-orbitals. The remaining valence orbitals go into hybridization. Thus, ethylene is in sp 2 hybridization.

Determination of the geometric structure of molecules

The geometric structure of molecules, as well as cations and anions of composition AB n, can be determined using the Gillespie method. This method is based on valence pairs of electrons. The geometric structure is influenced not only by the electrons involved in the formation of a chemical bond, but also by lone electron pairs. In Gillespie's method, each lone pair of electrons is designated E, the central atom is designated A, and the ligand is designated B.

If there are no lone electron pairs, then the composition of the molecules can be AB 2 (linear molecular structure), AB 3 (flat triangle structure), AB4 (tetrahedral structure), AB 5 (trigonal bipyramid structure) and AB 6 (octahedral structure). Derivatives can be obtained from basic structures if a lone electron pair appears instead of a ligand. For example: AB 3 E (pyramidal structure), AB 2 E 2 (angular structure of the molecule).

To determine the geometric structure (structure) of a molecule, it is necessary to determine the composition of the particle, for which the number of lone electron pairs (LEP) is calculated:

NEP = ( total number valence electrons – the number of electrons used to form bonds with ligands) / 2

The bond with H, Cl, Br, I, F requires 1 electron from A, the bond with O takes 2 electrons, and the bond with N takes 3 electrons from the central atom.

Let's look at the example of the BCl 3 molecule. The central atom is B.

5 B 1s 2 2s 2 2p 1

NEP = (3-3)/2 = 0, therefore there are no lone electron pairs and the molecule has the structure AB 3 - a flat triangle.

The detailed geometric structure of molecules of different compositions is presented in Table. 1.

Table 1. Spatial structure of molecules

Molecule formula	Hybridization type		Molecule type	Molecule geometry
				linear
				triangular
				tetrahedron
				trigonal pyramid
				trigonal bipyramid
				disphenoid
				T-shaped
				linear
				square pyramid

Examples of problem solving

EXAMPLE 1

Exercise	Using the valence bond method, determine the type of hybridization of the methane molecule (CH 4) and its geometric structure using the Gillespie method
Solution	6 C 2s 2 2s 2 2p 2

Atomic orbital hybridization is a process that allows us to understand how atoms modify their orbitals when forming compounds. So, what is hybridization, and what types of it exist?

General characteristics of hybridization of atomic orbitals

Atomic orbital hybridization is a process in which different orbitals of a central atom are mixed, resulting in the formation of orbitals with identical characteristics.

Hybridization occurs during the formation of a covalent bond.

A hybrid orbital has a handicap of an infinity sign or an asymmetrical inverted figure of eight, extended away from the atomic nucleus. This form causes a stronger overlap of hybrid orbitals with the orbitals (pure or hybrid) of other atoms than in the case of pure atomic orbitals and leads to the formation of stronger covalent bonds.

Rice. 1. Hybrid orbital appearance.

The idea of ​​hybridization of atomic orbitals was first put forward by the American scientist L. Pauling. He believed that those entering chemical bond an atom has different atomic orbitals (s-, p-, d-, f-orbitals), then as a result, hybridization of these orbitals occurs. The essence of the process is that atomic orbitals equivalent to each other are formed from different orbitals.

Types of atomic orbital hybridization

There are several types of hybridization:

• . This type of hybridization occurs when one s orbital and one p orbital mix. As a result, two full-fledged sp orbitals are formed. These orbitals are located towards the atomic nucleus in such a way that the angle between them is 180 degrees.

Rice. 2. sp-hybridization.

• sp2 hybridization. This type of hybridization occurs when one s orbital and two p orbitals mix. As a result, three hybrid orbitals are formed, which are located in the same plane at an angle of 120 degrees to each other.
• . This type of hybridization occurs when one s orbital and three p orbitals mix. As a result, four full-fledged sp3 orbitals are formed. These orbitals are directed towards the top of the tetrahedron and are located at an angle of 109.28 degrees to each other.

sp3 hybridization is characteristic of many elements, for example, the carbon atom and other substances of group IV (CH 4, SiH 4, SiF 4, GeH 4, etc.)

Rice. 3. sp3 hybridization.

More complex types of hybridization involving d-orbitals of atoms are also possible.

What have we learned?

Hybridization is a complex chemical process in which different orbitals of an atom form identical (equivalent) hybrid orbitals. The theory of hybridization was first voiced by the American L. Pauling. There are three main types of hybridization: sp-hybridization, sp2-hybridization, sp3-hybridization. There are also more complex types of hybridization that involve d orbitals.