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. * 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 * * Types of isomerism * Structural Isomerism 1. Нydrocarbon Chain isomerism butane 2-methylpropane 2. Position Chain isomerism 3. Functional Group isomerism propanal propanone 4. Tautomerism Aceto-acetic ester: keto-tautomer enol-tautomer OH propan-2-ol CH3 – CH – CH3 propan-1-ol CH3 – CH2 – CН2 – ОH * Stereoisomerism Optical isomerism mirror * 2. Cis-trans isomerism cis-isomer “adjacent” Maleic acid trans-isomer “across” Fumaric acid Classification of organic compounds * * Acyclic compounds Saturated Unsaturated pentane 2,3-dimethylbutane propylene acetylene * Carbocyclic compounds Alicyclic Aromatic H2C CH2 CH2 Cyclopropane Cyclobutane Cyclopentane Cyclohexane Benzene Naphthalene Phenanthrene * Heterocyclic compounds H H H H Pyran Furan 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 Name of class General formula –F, –Cl, –Br - halogens Halogen derivatives R – Hal –OH - hydroxyl Alcohols, phenols –OR - alkoxy –SH - thiol –SR - alkylthiol –SO3 - sulphonic –NH2, =NH2,≡N - amino –NO2 - nitro –C≡N - cyano - carboxyl -alkoxycarbonyl - carboxamide Ethers Thiols Thioethers (sulphides) Sulphoacids Amines Nitrocompounds Nitriles Aldehydes, ketones Carboxylic acids Esters Amides R – OH R – O – R R – SH R – S – R R – SO3H R – NH2, R2NH, R3N R – NO2 R – C ≡N C=O - carbonyl C O OH C O OR C O NH2 R – C – R O R C H , O R C O – R O R C NH2 O R C OH O * Nomenclature 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. Lactic acid CH3 – CH – COOH OH 3 2 1 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 C* Carbon atom in excited state 1s 2s 2p 2p 1s 2s * sp3-hybridization C* Methane CH4 Tetrahedron 2p 2s H s p sp3 + * Saturated compounds Alkanes (CnH2n+2) Ethane Pentane Methane H atom C atom σ-bond Alkanes * Structure and formulae * Naming alkanes CnH2n+2 * Naming branched-chain alkanes * * sp2-hybridization C* 120º s p sp2 Ethene C2H4 (CH2=CH2) σ-bond σ-bonds π-bond overlap 2p 2s Isomerism of alkanes * * How to obtain alkanes * Chemical properties of alkanes * Chemical properties of alkanes * Radical substitution - SR * Cycloalkanes CnH2n * Chemical properties of cycloalkanes Small cycles show some particular properties: * Unsaturated hydrocarbons * Structure of alkenes: σ- and π-bonds * Naming alkenes CnH2n * 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 * 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 Kekulé structure or Benzene C6H6 * C H C H C H 3 - C H = C H 2 C H 3 - C H - C H - C H 3 C H 3 C H 3 C H 3 - C H 2 - C H 2 - C H 2 - C H 3 O O S N N N S N N N N N N N N N N + UNKNOWN-0 UNKNOWN-1 UNKNOWN-2 UNKNOWN-3 UNKNOWN-4 UNKNOWN-5 UNKNOWN-6 UNKNOWN-7 UNKNOWN-8 UNKNOWN-9 UNKNOWN-10 UNKNOWN-11 UNKNOWN-12 UNKNOWN-13 UNKNOWN-14 UNKNOWN-15 UNKNOWN-16 UNKNOWN-17 UNKNOWN-18 UNKNOWN-19 UNKNOWN-20 UNKNOWN-21 UNKNOWN-22 UNKNOWN-23 UNKNOWN-24 UNKNOWN-25 UNKNOWN-26