Structure of chemical compounds Bonds and isomery Richard Vytášek 2008 Presentation is only for...

Structure of chemical compoundsStructure of chemical compounds

Bonds and isomery

Richard Vytášek 2008 Presentation is only for internal purposes of 2nd Medical faculty

Lewis octet ruleAtoms combine and form bonds by

transferring or sharing electrons until each atom is surrounded by eight valence electrons

Types of chemical bonds• covalent bonds

• ionic bonds

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)

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

Fajans´ rulespredict whether a chemical bond will be covalent or ionic

Covalent• 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)

Ionic compounds dissociate in water to cations and anions

The change of water structure nearby the ion

Types of noncovalent intaractions

Influence of the hydrogen bond on

biomolecules

Nucleobase pairing

by hydrogen bonds

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

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

Carbon - hybrid orbitals sp3

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

Carbon - hybrid orbitals sp2

• the three hybrid orbitals sp2 are formed by linear combination of orbital 2s and two orbitals 2p

Forming of bond and bond

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 bonds - triple bond

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

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

Conformation of cyclohexane• two stabile conformations - chair and boat - are in

equilibrium• chair conformation is more abundant because its

energy is slightly lower

Conformation of glucose is similar to conformation of cyclohexane

IsomersIsomers are compounds with the same Isomers are compounds with the same

molecular formula but different molecular formula but different structurestructure

• 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

Skeletal isomers

differ in their carbon

skeleton

Functional group isomers

isomers with different functional group(s)

Positional isomers

• different location of the same functional group or double (triple) bond

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

Stereochemistry

• studies spatial arrangement of molecules

• configuration isomers (stereoisomers) :

geometric isomers

optic isomers

Geometric isomerscis/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

1,2-dichlorocyklohexane

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

Enantiomers• optic stereoisomers which are mirro-images (e.g. D,L forms of

sugars or amino acids)

Diastereoisomers

• stereoisomers which contain multiple chiral centers and are not enantiomers

• in the case of sugars they differ in the name

Anomers• stereoisomers of sugars in hemiacetal form differing

by orientation of hydroxyl group on carbon 1

Meso compounds• contains multiple chiral centers but are

nevertheless symetrical