1. Structure of chemical compounds
Bonds and isomery
Richard Vytášek 2008
Presentation is only for internal purposes of 2nd Medical faculty

2. Lewis octet rule
Atoms combine and form bonds by transferring or sharing electrons until each atom is surrounded by eight valence electrons
(valence subshells s and p of inert gas)

3. Types of chemical bonds
covalent bonds
ionic bonds

4. Covalent bonds
electron pair (bonding electrons) is shared between two atoms
molecular orbital is formed by ovelapping of atomic orbitals of two atoms
electronegativity of atoms must be similar : nonpolar covalent bond – both atoms are equally electronegative
polar covalent bond – one atom is more electronegative and attracts more electrons
a coordinate covalent bond – both electrons of bonding pair are provided by the same atom (complexes, transition metals)
center of negarive as well as positive charge is in the middle of atoms
atomic orbital is a region about the nucleus of an atom where electron or two electrons my be found
interpenetration of one atomic orbital by another

5. Ionic bonds
strong polarization leads to formation relatively high partial charge on both atoms – the bond becames electrostatic
if the character of a bond is mainly electrostatic we call this bond ionic
between a polar covalent bond and an ionic bond is continous transition

6. Fajans´ rules predict whether a chemical bond will be covalent or ionic
Large anion
Small cation
High positive charge
Nonstabile electron structure
Ionic
Low positive charge
Large cation
Small anion
Stabile electron structure (configuration of noble gas)

7. Ionic compounds dissociate in water to cations and anions

8. The change of water structure nearby the ion

9. Types of noncovalent intaractions

10. Influence of the hydrogen bond on biomolecules

11. Nucleobase pairing by hydrogen bonds

12. The unique carbon atom Carbon
forms very stable single, double and triple covalent bonds
forms strong covalent bonds with many other atoms (hydrogen, nitrogen, oxygen, sulfur)
atoms form chains of atoms bonded to each other

13. Carbon elektron structure 1s2 2s2 2p2
the energy of elektrons of valence shell is different (2p > 2s)
hybrid atomic orbitals are formed by linear combination of original atomic orbitals and the energy of all hydrid orbitals is equal

14. Carbon - hybrid orbitals sp3
the four hybrid orbitals sp3 are formed by linear combination of orbital 2s and three orbitals 2p

15. Carbon - hybrid orbitals sp2
the three hybrid orbitals sp2 are formed by linear combination of orbital 2s and two orbitals 2p

16. Forming of bond s and bond p

17. Carbon - hybrid orbitals sp and formation of triple bond
the two hybrid orbitals sp are formed by linear combination of orbital 2s and one orbital 2p
remaining two orbitals 2p take part in formation of two p bonds - triple bond

18. Conformation orientation of a molecule in space (3D)
a molecule can exist in many various conformations
various conformations are formed by rotation about single bond

19. Rotation about single bond C-C
individual conformation formed by rotation about single bond C-C (rotamers) is indistinguishing but various conformations can exibit various reactivity

20. Conformation of cyclohexane
two stabile conformations - chair and boat - are in equilibrium
chair conformation is more abundant because its energy is slightly lower

21. Conformation of glucose is similar to conformation of cyclohexane

22. Isomers
Isomers are compounds with the same molecular formula but different structure
constitutive – different order of atoms or different position of double (triple) bond or different site of linking of functional group (skeletal , positional , functional group isomers, tautomers)
configuration

23. differ in their carbon skeleton
Skeletal isomers
differ in their carbon skeleton

24. Functional group isomers
isomers with different functional group(s)

25. Positional isomers
different location of the same functional group or double (triple) bond

26. Tautomeric isomers (tautomers)
specific case of the constitutive isomery
change in the location of a hydrogen and a double bond, both tautomers are in a dynamic equilibrium (individual tautomer can´t be isolated)
typical example is enol and keto form of carbonyl group

27. Stereochemistry studies spatial arrangement of molecules
configuration isomers (stereoisomers) :
geometric isomers
optic isomers

28. Geometric isomers cis/trans isomers
contain the bond which is unable of rotation (usually double or triple bond but also single bond of cyclic compounds)
two different substituents on the first carbon and two different substituents on the second carbon

29. 1,2-dichlorocyklohexane

30. Asymmetric (chiral) carbon
is attached to four different substituents
causes the optical activity - the rotation of the plane of polarized light
is responsible for optic isomery

31. Enantiomers
optic stereoisomers which are mirro-images (e.g. D,L forms of sugars or amino acids)
dextrorotatory and levorotatory

32. Diastereoisomers
stereoisomers which contain multiple chiral centers and are not enantiomers
in the case of sugars they differ in the name
do not have mirror-image relationship

33. Anomers
stereoisomers of sugars in hemiacetal form differing by orientation of hydroxyl group on carbon 1

34. Meso compounds
contains multiple chiral centers but are nevertheless symetrical