1. 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.

2. 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.

3. 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.

4. Main principles of organic chemistry

5. Organic vs. Inorgaic

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

7. 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.

8. 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

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

10. 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

11. Stereoisomerism
Optical isomerism
mirror

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

13. Classification of organic compounds

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

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

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

17. Classification
on the basis
of nature
of functional group

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

19. 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
–SO sulphonic
Sulphoacids
R – SO3H
–NH2, =NH2,≡N - amino
Amines
R – NH2, R2NH, R3N
–NO 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

20. 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
Lactic acid
2 – hydroxypropanoic acid
prefix root
primary suffix
secondary suffix

21. 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

23. Lots of ways to draw this…

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

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

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

27. Alkanes

28. Structure and formulae

29. Naming alkanes
CnH2n+2

30. Naming branched-chain alkanes

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

32. Isomerism of alkanes

34. How to obtain alkanes

35. Chemical properties of alkanes

36. Chemical properties of alkanes

37. Radical substitution - SR

38. CnH2n
Cycloalkanes

39. Chemical properties of cycloalkanes
Small cycles show some particular properties:

40. Unsaturated
hydrocarbons

41. Structure of alkenes: σ- and π-bonds

42. CnH2n
Naming alkenes

43. Naming branched-chain alkenes

44. Isomerism of alkenes

45. Isomerism of alkenes

47. Addition to the double bond – AdE reactions
Markovnikov rule

48. Naming and properties of alkynes
CnH2n-2

49. Structure of alkynes: σ- and π-bonds

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

51. Synthesis and reactions of alkynes

52. 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.

53. 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.

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

55. Thank you for your attention!