Fundamentals of Bioorganic Chemistry (Study Guide) - H. O. Syrova - 2018

Topic

Classification, Nomenclature, and Isomerism of Bioorganic Compounds

Nature of the Chemical Bond

Relevance of the Topic. Bioorganic chemistry studies substances involved in vital processes in direct correlation with their biological Functions. The primary challenge for biology and medicine is elucidating the relationship between a compound's Structure and The Mechanism of its biological function, namely the structure-function relationship.

Due to The unique ability of the carbon atom to form numerous carbon-carbon bonds, there are already over 10 million known Organic compounds. To navigate this vast diversity of substances, it is essential to understand their scientific Classification and Nomenclature. Comprehending The Nature of the chemical bond in bioorganic compounds establishes the foundation for mastering The chemical properties of these substances and, consequently, for predicting their behavior in biochemical transformations.

This topic serves as a fundamental basis for studying bioorganic chemistry, biological chemistry, pharmacology, and other biomedical disciplines, given that organic substances found in nature are widely utilized as Pharmaceuticals.

General Objective: to master the fundamental principles of the scientific classification and nomenclature of bioorganic compounds; to be able to characterize the types of chemical bonds present in these compounds.

Specific Objectives:

1. To know the classification of organic compounds based on the carbon Skeleton Structure and Functional groups.

2. To master the principles of IUPAC substitutive nomenclature.

3. To be able to write structural formulas of bioorganic substances based on their systematic names.

4. To study the isomerism of bioorganic substances.

5. To explain the mechanism of chemical bonding in bioorganic compounds depending on the valence state of the carbon atom.

Theoretical Questions

1. Classification of organic compounds by the Nature of the carbon skeleton.

2. Classification of organic compounds by functional groups.

3. Nomenclature of organic compounds:

a) trivial names.

b) IUPAC substitutive nomenclature.

c) radicofunctional (rational) nomenclature.

4. Electronic STRUCTURE OF THE carbon atom in organic compounds. The nature of chemical bonding in organic compounds.

5. Isomerism in organic compounds. A.M. Butlerov's contribution to The Development of the fundamental principles of isomerism.

1. Based on the nature of the carbon skeleton, organic compounds are broadly divided into:

1. Acyclic compounds possessing open chains of carbon atoms:

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2. Carbocyclic compounds, containing rings formed exclusively by carbon atoms:

3. Heterocyclic compounds, containing rings whose formation involves atoms of other elements (heteroatoms: N, O, S) In addition to carbon atoms:

2. Within each group, there are classes of compounds whose properties are determined by the presence of specific groups of atoms called functional groups. The functional groups, their corresponding classes, and general formulas are presented in the table.

Functional groups and corresponding classes of compounds

The compounds shown in the table contain a single functional group and are therefore monofunctional.

However, a hallmark of physiological activity is polyfunctionality, meaning the presence of several identical (homopolyfunctional) or distinct (heteropolyfunctional) functional groups within the same molecule. Examples include:

Compounds of each organic class can be arranged into homologous series—families of related compounds with similar properties, where each successive member differs from the previous one by a -СН₂- group

(the Homology increment).

3. Nomenclature is a system of rules that provides an unambiguous name for every individual substance. Several types of nomenclature exist: trivial nomenclature, substitutive nomenclature (Geneva nomenclature, IUPAC international nomenclature), and functional-class (rational) nomenclature.

Trivial names arose historically, haphazardly, and unsystematically. These names often reflect the sources from which the substances were isolated (citric acid, lactic acid, formic acid, etc.), their Methods of preparation (pyruvic acid, obtained by the pyrolysis of tartaric acid), their fields of application (ascorbic acid—derived from "scorbutus," meaning scurvy), and so forth.

The most informative system is the modern IUPAC substitutive nomenclature. When constructing names using this system, The concepts of radical, parent structure, characteristic group, and substituent are employed.

A radical is a species with unpaired electrons, formed by the removal of one or more hydrogen atoms from a hydrocarbon molecule. Most commonly, names utilize radicals derived from the first four members of the saturated hydrocarbon homologous series:

"Prim." – primary; the free valence is located at a primary carbon atom, which is bonded to only one adjacent carbon atom.

"Sec." – secondary; the free valence is located at a secondary carbon atom, which is bonded to two adjacent carbon atoms.

"Tert." – tertiary; the free valence is located at a tertiary carbon atom, which is bonded to three adjacent carbon atoms.

The parent structure is the chemical framework that forms The basis of the named compound (the principal carbon chain or ring).

A characteristic group is a functional group attached to the parent structure or partially incorporated into it.

A substituent is any characteristic group or radical attached to the parent structure.

The name of an organic compound according to substitutive nomenclature is formed According to the following rules:

1) identify the principal characteristic group, if present (see table). This group is indicated by the suffix in the name;

2) determine the parent structure. This must be the longest carbon chain containing the maximum number of multiple bonds and characteristic groups;

3) number the parent chain such that the principal characteristic group receives the lowest possible locant;

4) name junior characteristic groups, non-carbon characteristic groups, and hydrocarbon radicals as prefixes in alphabetical order, indicating their positions with appropriate numbers;

5) name the parent structure using the name of the hydrocarbon corresponding to the number of carbon atoms and append the suffix for the principal characteristic group.

The degree of unsaturation of the parent structure is indicated by suffixes: a saturated hydrocarbon skeleton by -an; the presence of a double bond by -en; and a triple bond by -in (-yn).

Locants are placed before prefixes and after suffixes or endings. If a compound contains multiple identical substituents or multiple bonds, a multiplying prefix—such as di-, tri-, tetra-, penta-, etc.—is placed before the respective term.

Some non-carbon characteristic groups indicated only as prefixes

Order of seniority of characteristic groups indicated both as prefixes and suffixes

1 - the carbon atom enclosed in parentheses is part of the carbon chain;

2 - in Russian-language literature, the -OH group is also referred to as an oxy group.

Examples of nomenclature:

Monofunctional compounds:

Homopolyfunctional compounds

Polyhydric alcohols:

Dicarboxylic acids:

Heteropolyfunctional compounds

Amino alcohols

Hydroxy acids

Oxo acids (aldehyde and keto acids)

Aldehyde and keto alcohols

Amino Acids

The application of the radical-functional nomenclature is more limited. It is used to name simple mono- and bifunctional compounds as well as certain classes of natural substances (e.g., hydroxy acids, oxo acids, amino acids).

If a compound contains a single characteristic group, its name is constructed from the names of the radicals and the characteristic group or compound class:

For more complex substances, a parent chain or ring is selected, and the positions of substituents are designated by Greek letters: α, β, γ, δ, ε, etc.

For disubstituted benzenes, the positions of substituents are indicated by the prefixes: ortho- (o-), meta- (m-), para- (p-).

4. The properties of organic compounds are largely determined by the electronic structure of the carbon atom and the nature of its chemical bonds. In the excited state (1s² 2s¹ 2p³ ), the carbon atom has four unpaired electrons and, consequently, can form four covalent bonds. In this case, all bonds in structures of the CX₄ type are equivalent. To explain this phenomenon, L. Pauling introduced METABOLISM/2.html">THE CONCEPT OF Hybridization—a peculiar interaction of orbitals with similar energies, resulting in The formation of so-called hybrid orbitals of lower energy.

Three Different types of hybridization are possible for the carbon atom.

1. sp³ hybridization, in which one s- and three p-orbitals interact to form four energetically equivalent hybrid orbitals shaped like lobed dumbbells with unequal lobes (Fig. 1). The maximum electron Separation corresponds to the orientation of the hybrid orbitals toward the vertices of a regular tetrahedron at an angle of 109°28'. Carbon atoms not bonded to other atoms via multiple bonds are in an sp³-hybridized state, and their orbitals exhibit a specific spatial configuration. Chemical bonds in this case are formed through the axial overlap of the carbon atom's hybrid orbitals with the orbitals of adjacent atoms. This results in the formation of σ-bonds, where the maximum electron density is located between the atomic nuclei on the straight line connecting them. Typical compounds in which the carbon atom is in the sp³-hybridized state are saturated Hydrocarbons (hydrocarbons), i.e., alkanes.

Fig. 1

2. sp² hybridization, in which one s- and two p-orbitals interact to form three hybrid orbitals whose axes lie in the same plane and are directed from the center of a triangle to its vertices at an angle of 120° (Fig. 2).

Fig. 2

The direction of the unhybridized p-orbital is perpendicular to the plane containing the hybrid orbitals. In sp² hybridization, there is an axial overlap of hybrid orbitals between carbon atoms and a lateral overlap of unhybridized p-orbitals (Fig. 3).

Fig. 3

In the latter case, a π-bond is formed, with its electron cloud located above and below the plane of the σ-bonds. Typical compounds in which carbon atoms exhibit sp² hybridization include Ethylene and its homologues (alkenes).

3. sp-hybridization, in which one s- and one p-orbital interact to form two hybrid orbitals. They are arranged linearly at an angle of 180°. The two remaining unhybridized p-orbitals lie in mutually perpendicular planes. When two carbon atoms in the sp-hybridized state combine, they form one σ- and two π-bonds (Fig. 4). Carbon sp-hybridization is observed in acetylene and its homologues (alkynes).

Fig. 4

The key parameters characterizing bond strength are its energy and length. In general, the greater the bond energy and the shorter the bond length, the stronger the bond. The table below presents the energy and length values for several types of bonds.

A comparison of single and multiple bond energies shows that the energy of a π-bond is lower than that of a σ-bond, meaning that the π-bond is less strong.

Depending on the electronegativity of the atoms forming a covalent bond, it can be either nonpolar or polar. Electronegativity is the ability of an atom to attract the shared electron pair toward itself when forming a covalent bond with other atoms.

Bond polarity increases with a larger difference in electronegativity between the bonded atoms. Bond polarizability is a measure of the displacement of bonding electrons under The Influence of an external electric field, including that of an attacking species. Polarizability is characterized by electron mobility; highly mobile electrons are located farther from The Nucleus. The polarizability of a π-bond is higher than that of a σ-bond.

Hydrogen bonding plays a crucial role in shaping the Structure and properties of bioorganic compounds. It is a bond that forms between a hydrogen atom and another highly electronegative atom (N, O, F). It can be intramolecular or intermolecular and is represented by three dots:

The energy of Hydrogen Bonds is relatively low (10-40 kJ/mol), making these bonds weak; nevertheless, they significantly influence the properties of compounds, including their physiological activity.

5. A landmark event in the development of organic chemistry was the formulation of The Theory of Chemical Structure of organic compounds in the 1860s by the prominent Russian scientist A.M. Butlerov. One of the core principles of this theory states that the properties of a substance depend not only on the identity and number of atoms comprising its molecule, but also on the order in which they are interconnected—that is, the chemical structure of the molecule.

This principle of A.M. Butlerov’s theory of chemical structure explained the widespread phenomenon of isomerism among organic substances. Isomers are substances that have the same Qualitative and quantitative composition but differ in their structure and, consequently, in their properties.

Carbon skeleton isomerism is possible:

Some organic compounds differ in the arrangement of functional groups within the carbon chain or ring (positional isomerism):

Spatial isomerism (stereoisomerism) arises from the different spatial arrangement of parts of a molecule. One of its types is cis-trans isomerism in ethylene derivatives. A cis-isomer is a compound in which the substituents are located on the same side of the double-bond plane. Trans-isomers are compounds in which the substituents are located on opposite sides of the double-bond plane.

Trans-isomers are generally more stable.

Complete the tasks and check your Answers against the provided solution keys

Task № 1

1. Provide the correct IUPAC name for the substance:

A. Oxoethanoic acid.

B. Aldehyde acid.

C. Hydroxyethanoic acid.

D. Glyoxylic acid.

2. Local anesthetics, such as novocaine and benzocaine, are derivatives of p-aminobenzoic acid. Indicate its structure.

3. Specify the compound whose molecule contains carbon atoms in the sp-hybrid state:

Correct answers: 1 - A; 2 - B; 3 - C.

Task No. 2

1. Indicate the type of hybridization of atoms in the pyrrole molecule.

А. sp B. sp² C. sp³ D. spd²

2. Which of the following compounds are isomers:

A. Butanoic acid and butanol.

B. Diethyl ether and dimethyl ether.

C. Methyl acetate and propanoic acid.

D. Propene and propane.

3. Indicate the correct rational name of the substance:

А. 2,3-Dihydroxybutanedioic acid.

B. Tartaric acid.

C. Dihydroxybutanoic acid.

D. α,β-Dihydroxysuccinic acid.

Correct answers: 1 - B; 2 - C; 3 - D.

Task No. 3

1. What type of chemical bond is present in the substance shown below:

A. Nonpolar covalent.

B. Polar covalent.

C. Hydrogen.

D. Ionic.

2. To which class of compounds does the substance belong:

A. Aromatic amino acid.

B. Amino acid.

C. Aromatic amino alcohol.

D. Amino alcohol.

3. What type of isomerism is possible for butenedioic acid?

A. Carbon skeleton isomerism.

B. Cis-trans isomerism.

C. Position isomerism of the multiple bond.

D. Functional group isomerism.

Answer keys: 1 - C; 2 - A; 3 - B.