structure of chemical compounds bonds and isomery richard vytášek 2008 presentation is only for...
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Structure of chemical compoundsStructure of chemical compounds
Bonds and isomery
Richard Vytášek 2008 Presentation is only for internal purposes of 2nd Medical faculty
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Lewis octet ruleAtoms combine and form bonds by
transferring or sharing electrons until each atom is surrounded by eight valence electrons
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Types of chemical bonds• covalent bonds
• ionic bonds
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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)
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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
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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)
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Ionic compounds dissociate in water to cations and anions
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The change of water structure nearby the ion
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Types of noncovalent intaractions
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Influence of the hydrogen bond on
biomolecules
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Nucleobase pairing
by hydrogen bonds
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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
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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
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Carbon - hybrid orbitals sp3
the four hybrid orbitals sp3 are formed by linear combination of orbital 2s and three orbitals 2p
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Carbon - hybrid orbitals sp2
• the three hybrid orbitals sp2 are formed by linear combination of orbital 2s and two orbitals 2p
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Forming of bond and bond
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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
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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
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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
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Conformation of cyclohexane• two stabile conformations - chair and boat - are in
equilibrium• chair conformation is more abundant because its
energy is slightly lower
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Conformation of glucose is similar to conformation of cyclohexane
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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
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Skeletal isomers
differ in their carbon
skeleton
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Functional group isomers
isomers with different functional group(s)
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Positional isomers
• different location of the same functional group or double (triple) bond
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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
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Stereochemistry
• studies spatial arrangement of molecules
• configuration isomers (stereoisomers) :
geometric isomers
optic isomers
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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
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1,2-dichlorocyklohexane
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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
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Enantiomers• optic stereoisomers which are mirro-images (e.g. D,L forms of
sugars or amino acids)
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Diastereoisomers
• stereoisomers which contain multiple chiral centers and are not enantiomers
• in the case of sugars they differ in the name
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Anomers• stereoisomers of sugars in hemiacetal form differing
by orientation of hydroxyl group on carbon 1
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Meso compounds• contains multiple chiral centers but are
nevertheless symetrical