Download Structure of chemical compounds

Structure of chemical compounds
Bonds and isomery
Richard Vytášek 2008
Presentation is only for internal purposes of 2nd Medical faculty
Lewis octet rule
Atoms 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´ rules
predict 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
3
sp
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 s
and
bond p
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
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
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
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 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
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