CLASSIFICATION, STRUCTURE AND REACTIVITY OF BIOORGANIC COMPOUNDS Kharkiv National Medical University Department of Medical and Bioorganic chemistry «Biological and Bioorganic Chemistry» Lecture № 1 CLASSIFICATION, STRUCTURE AND REACTIVITY OF BIOORGANIC COMPOUNDS Lecturer: As. Professor, Department of Medical and Bioorganic Chemistry,, Ph.D. Lukianova L.V.

Plan of lecture 1. Main principles of organic chemistry. 2. Classification of organic compounds. 2. Isomerism of organic compounds. 3. Nomenclature of organic compounds. 4. Structure and properties of saturated hydrocarbons. 4. Structure and properties of unsaturated hydrocarbons.

Organic chemistry is the chemistry of the compounds of carbon. Bioorganic chemistry is based on Organic chemistry. Organic chemistry is the chemistry of the compounds of carbon. Carbon forms more compounds than any other element.

Main principles of organic chemistry

Organic vs. Inorgaic

Theory of chemical structure Alexander M.Butlerov (1828-1886) Eminent Russian chemist, one of the founders of the theory of chemical structure. First scientist to introduce double bonds in structural formulae

A. M. Butlerov's Theory of Chemical Structure Atoms of elements, which form molecules, are combined in definite order according to their valence and all valences should be used to combine each other. 2. Properties of organic compound depend not only on its composition but on its structure as well, i. e. on the order of combining of atoms in a molecule and a character of bonds. 3. Atoms in a molecule influence each other and especially those, which are directly combined.

Isomerism Isomers have identical qualitative and quantitative composition but different physical and chemical properties. Compounds that have: The same molecular formula. Similar or different types of structural formulas. Different arrangement of atoms. Isomerism of organic compounds is explained by the Theory of chemical structure given by A. M. Butlerov in 1861

Structural or constitutional Types of isomerism Isomerism Structural or constitutional Hydrocarbon Chain Tauto-merism Position Chain Functional Group Stereoisomerism Optical Cis-trans

Structural Isomerism 2. Position Chain isomerism 1. Нydrocarbon Chain isomerism 2-methylpropane butane 2. Position Chain isomerism propan-1-ol CH3 – CH2 – CН2 – ОH OH propan-2-ol CH3 – CH – CH3 3. Functional Group isomerism propanal propanone 4. Tautomerism Aceto-acetic ester: keto-tautomer enol-tautomer

Stereoisomerism Optical isomerism mirror

cis-isomer “adjacent” trans-isomer “across” 2. Cis-trans isomerism cis-isomer “adjacent” Maleic acid trans-isomer “across” Fumaric acid

Classification of organic compounds

Acyclic compounds pentane 2,3-dimethylbutane propylene acetylene Saturated 2,3-dimethylbutane pentane Unsaturated acetylene propylene

Carbocyclic compounds Alicyclic Aromatic H2C CH2 Cyclopropane Cyclobutane Cyclopentane Cyclohexane Benzene Naphthalene Phenanthrene

Heterocyclic compounds Pyran Furan H Pyrrol Thiophene Thiazole Imidazole Pyridine Pyrimidine Indole Quinoline Purine

Classification on the basis of nature of functional group

Classification of organic compounds Halogen derivatives Oxygen-containing: Alcohols & ethers Aldehydes & ketones Carboxylic acids & esters Nitrogen-containing: Amines Nitriles Mixed: Aminoacids Peptides Nitro compounds

Functional group General formula Halogen derivatives Thiols Esters Name of class General formula –F, –Cl, –Br - halogens Halogen derivatives R – Hal –OH - hydroxyl Alcohols, phenols R – OH –OR - alkoxy Ethers R – O – R –SH - thiol R – SH Thiols –SR - alkylthiol Thioethers (sulphides) R – S – R –SO3 - sulphonic Sulphoacids R – SO3H –NH2, =NH2,≡N - amino Amines R – NH2, R2NH, R3N –NO2 - nitro Nitrocompounds R – NO2 –C≡N - cyano Nitriles R – C ≡N O R C H , R – C – R O C=O - carbonyl Aldehydes, ketones C O OH O R C OH - carboxyl Carboxylic acids C O OR -alkoxycarbonyl O R C O – R Esters C O NH2 Amides O R C NH2 - carboxamide

Nomenclature 2 – hydroxypropanoic acid Lactic acid For a long time, organic compounds were named by common names, generally given after the name of source from which they were obtained (Trivial nomenclature): Citric acid, Lactic acid. Now IUPAC has developed a new system of naming compounds which is known as IUPAC Nomenclature. CH3 – CH – COOH OH 3 2 1 Lactic acid 2 – hydroxypropanoic acid prefix root primary suffix secondary suffix

What makes carbon so special? It has a “central” role in all living organisms. It has 4 valence electrons. It makes 4 covalent bonds. It can bond with any element, but really loves to bond with other carbon atoms and make long chains

Lots of ways to draw this…

Structure of organic compounds Types of hybridization C6 1s22s22p2 Ground state of carbon atom 2p 1s 2s C* Carbon atom in excited state

sp3-hybridization 2p 2s C* s p sp3 + Tetrahedron H Methane CH4

Saturated compounds Alkanes (CnH2n+2) Methane H atom C atom σ-bond Pentane Ethane

Alkanes

Structure and formulae

Naming alkanes CnH2n+2

Naming branched-chain alkanes

sp2-hybridization C* 2p 2s 120º s p sp2 Ethene C2H4 (CH2=CH2) σ-bond σ-bonds π-bond overlap

Isomerism of alkanes

How to obtain alkanes

Chemical properties of alkanes

Chemical properties of alkanes

Radical substitution - SR

CnH2n Cycloalkanes

Chemical properties of cycloalkanes Small cycles show some particular properties:

Unsaturated hydrocarbons

Structure of alkenes: σ- and π-bonds

CnH2n Naming alkenes

Naming branched-chain alkenes

Isomerism of alkenes

Isomerism of alkenes

Addition to the double bond – AdE reactions Markovnikov rule

Naming and properties of alkynes CnH2n-2

Structure of alkynes: σ- and π-bonds

carbon skeleton branching interclass isomerism: alkadienes Isomerism of alkynes triple bond position in alkyne molecule carbon skeleton branching interclass isomerism: alkadienes cycloalkenes

Synthesis and reactions of alkynes

Carbon forms Rings Carbon-based molecules also can be shaped like rings. Most carbon rings contain 5 or 6 carbon atoms. One of the most important carbon rings is benzene. It has 6 carbons & 6 hydrogens, with alternating double bonds. All carbon atoms are sp2-hybridized.

Carbon forms Rings Many compounds are based on Benzene. They often have very strong smells or aromas, so they are called aromatic compounds. An example of one aromatic compound is a molecule called vanillin.

Aromatic compounds All carbon atoms are sp2-hybridized Benzene C6H6 or Kekulé structure

Thank you for your attention!