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ORGANIC CHEMISTRY
For Dentistry students
Ďuračková Zdeňka
2018
Institute of Medical Chemistry, Biochemistry and Clinical Biochemistry
Medical School UK
Structure of organic compounds(relation between structure and properties and functions of biologically important
organic compounds)
Organic chemistry – chemistry of hydrocarbons and their derivatives
6C 1s2 2s2 2px12py
1 C = O
Carbon in basic state
6C 1s2 2s1 2px1 2py
1 2pz1 O = C = O
Carbon in excited stateC
Basic principle of the structure of organic
compounds- carbon forms four covalent bonds C
- all 4 bonds are equivalant (hybridization s-, and p-orbitals
on valence layer of carbon atom)
- between carbons can be simple, double, or triple bond
(σ and π bound)
– C – C – – C = C – – C = C –
- atoms of carbon form chains – simple straight, branched and
cyclic forms
- between of carbon atoms, atoms of oxygen, nitrogen or
sulphur can be bound
Types of hydrocarbon structures
HYDROCARBONS
Heterocyclic compounds (O, S, N,)
Acyclic
(non-cyclic)
Cyclic
Saturated
Non-saturated
Alkenes
Alkynes
Alicyclic
Aromatic
Cycloalkanes
Cycloalkenes
STRUCTURE of ORGANIC COMPOUNDS
1. Acyclic (non-cyclic)
unbranched (straight chain)
CH3-CH2-CH3
Branched chain
CH3-CH-CH3
CH3
2. Cyclic
alicyclic (cyclic)
aromatic (arenes)
heterocyclic
Organic compounds – according hydrocarbone chain arrangement
N
Isomerism of organic compounds
(two or more compounds with identical molecular formula,
but different structure)
Types of isomerism
• Constitutional (n-propanol, 2-propanol)
• Configuration (stereoisomerism)
- geometrical (cis-, trans-) (fumaric, maleinic acids)
- optical (chirality, D/L - isomers) (D-AA, L-AA)
• Conformation of molecules (chair, boat)
REACTIONS of ORGANIC COMPOUNDS
1. Addition
2. Substitution (displacement of atom/atom group)
3. Elimination
2H
CH2 = CH2 --------> CH3 – CH3
CH3 – CH2 – Cl + OH- --------> CH3 – CH2 – OH + Cl-
- H2O
CH3 – CH – CH – CH2 ---------> CH3 – CH = CH – CH3
| |
OH H
2 – butanol 2 – butene 8
Acyclic (aliphatic) hydrocarbons
Alkanes:
Saturated hydrocarbons, simple () bonds, binding angle 109°
homologic chain, -CH2- homologic increase, sum formula CnH2n+2
Non-polar compounds, soluble in non-polar solvents, non-soluble
in H2O
Small reactivity, characteristic reaction - substitution (temperature,
UV radiation)
- example: methane, ethane, propane, butane, pentane,
hexane…, isobutane
HYDROCARBONS
Alkenes
non-saturated hydrocarbons, double bond (), binding angle 120°
homological chain, sum formula CnH2n
high reactivity, characteristic reaction – addition
(Markovnik rul)
CH2 = CH2 + HOH CH2 – CH2
OH H
ethene (ethylene) ethanol
catalyst
CH2 = CH2 + H2 CH3 – CH3
ethene ethane
Dienes (2 double bonds)
cummulated, conjugated or isolated double bonds
high reactivity, important reaction – addition polymerisation
n CH2 = C – CH = CH2 ----- --CH2 - C = CH – CH2-n-
CH3 CH3
2-metyl-1,3-butadiene natural rubber
isoprene polymer of isoprene
- Isoprenoids (for example: terpenes, steroids)
Alkynes
non-saturated hydrocarbons, triple bond (), binding angle 180°
homological chain, sum formula CnH2n-2
high reactivity, characteristic reaction – adition
CH CH + HCl CH2 = CH – Cl
Ethyne (acethylene) chloroethene (vinylchloride)
CH CH + HOH CH2 = CH – OH CH3 – C = OH
Ethyne (acetylene) vinylalcohol ethanal (acetaldehyde)
Tautomerism :enol- oxo-
Cyclic hydrocarbons
ALICYCLIC
For ex.: cyclopentane, cyclohexane, cyclohexene, cyclohexadiene,
cyclopentanoperhydrophenantrene
Stereochemistry cyclohexane
chair and boat form (bound angle 109°)
Chair Boat
AROMATIC hydrocarbons (ARENS)
basic hydrocarbon – benzene (benzol)
aromatic character – plane structure (120°bound angle)
π – electrons are delocalized arround whole circle
polycyclic arens
NAPHTHALEN E
ANTHRACENE
five- or six-membered rings with one or more heteroatoms
condensed heterocyclic compounds with two or more heteroatoms
HETEROCYCLIC COMPOUNDS
O NH S
N
NH
N
S
furane pyrrole thiophene
imidazole thiazole
N
N
N
pyridine pyrimidine pyran
(2H-pyran)
N
N NH
N
O
purine indole
pyrimidine + imidazole benzpyrole
NH
DERIVATIVES of HYDROCARBONS
replacing hydrogen atom/atoms in hydrocarbons with another atom
or a group of atoms, so called functional group
CHARACTERISTIC GROUPS and their marking
Compound Characteristic
group
Prefix Affix
Halogenhydrocarbons F
Cl
Br
I
Fluoro-
Chloro-
Bromo-
Iodo-
Nitroderivatives NO2 Nitro-
Nitrosoderivatives NO Nitróso-
Aldehydes HC=O Oxo- - e
Ketons C=O
Oxo- -on
Carboxylic acid COOH Carboxy- -ic acid
Alcohols OH Hydroxy- -ol
Thiols SH Merkapto-
Thio-
-tiol
Ethers O-R R-oxy
Sulphides S-R R-thio
Disulphides S-S
Sulphonic acids SO3 H Sulpho- Sulphonic acid
Amines NH2 Amino- - amine
Imines =NH Imino- - imine
Oxims =N-OH Hydroxylimino- - oxime
Nitrils CN Cyano- - nitril
HALOGENDERIVATIVES
Tyroxine – Tetraiodothyronine T4
– Triiodothyronine T3
nucleophilic substitution
׀
C X δ- + OH-
↔ H-C-OH + X-
19
δ+
High TOXICITY
HALOGENEDERIVATIVES of HYDROCARBONS
- insoluble in water, soluble in alcohols and ethers
- polar covalent bond between – C halogene
• characteristic reaction
- substitution (heterolytical termination of bound), as alkylation reagents
• practical use
solvents for non-polar compounds (CCl4)
monomers for preparation of macromolekular compounds (PVC, artificial rubber,
tephlon),
in refrigerator industry (freons – dichloro-difluoromethane)
iodoform CHI3 – disinfection effects
insecticides
dioxins
narcotiks (halotan, CF3-CHBrCl)
• toxicity
influence on central nerves system (CNS)
tetrachlorodibenzodioxin – carcinogenic, teratogenic, mutagenic effects
(c 1mg.l-1) (dioxins)
cancerogens or suspect carcinogens (CHCl3 , CCl 4)
Toxicity of halogenederivatives
DDT – insecticide DichloroDiphenylTrichlorethane
(1948 Paul Hermann Müller won Nobel Price for DDT discovering)
Dioxin
1. ALCOHOLS
Polarity of bond R O H - reactivity of hydroxyderivatives
Association of molecules of alcohols with hydrogene bounds =
increasing of boiling and melting point)
Dividing:
1. according place of -OH group bounding in the chain
- primary ( 1- butanol) CH3 – CH2 – CH2 – CH2 – OH
CH3 – CH2 – CH – CH3
OH
CH3
CH3 – C – CH3
OH
- secondary (2-butanol)
- tertiary (tert. butanol)
HYDROXYDERIVATIVES of HYDROCARBONS
2. According to a number of –OH groups
- monohydroxyderivatives (monohydric)
- dihydroxyderivatives (diols) (dihydric), ethanediol (ethyleneglycol)
- trihydroxyderivatives (triols) (trihydric), propanetriol (glycerol)
- polyhydroxyderivatives (polyols) (saccharides)
CH2 – OH
CH2 – OH
CH2 – OH
CH – OH
CH2 – OH
O
CH2OH
OH
OH
OH
OH
ethyleneglycol glycerol glucose
R-CH2-OH R-CH=O R-COOH
R R
CH-OH C=O
R R
R - alcohol R – OH
Ar – phenol Ar – OH
H H- O -
Ether R – O – R
HYDROXYDERIVATIVES
(alcohols a phenols)
ox
-2H
ox
-2H
ox
H2O
bond cleavage
between carbon atoms
ox
Oxidation of alcohols
Oxidation of diols
CH2 – OH COOH COOH COOH
CH2 – OH CH2 – OH HC=O COOH
Ethylene glycol
Ethane diole glycolic acid glyoxalic acid oxalic acid
Oxidation of triols
CH2 – OH CH2 – OH HC = O COOH
ox. ox ox
C = O CH – OH CH – OH CH – OH
CH2 – OH CH2 – OH CH2 – OH CH2 – OH
dihydroxyacetone glycerol glyceraldehyde glyceric acid
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- Acidic character of phenols and alcohols
- Toxicity of alcoholate and phenols
O - + Na+ + H2OOH + NaOH Sodium phenolate
CH3- CH2-O-H + NaOH CH3- CH2-O- + Na+ + H2O
Sodium alcoholate
Alkaline character of alcohols and ethers
CH3- CH2-O-H + H+ Cl- CH3- CH2- O-H Cl-
H +
Alcoxonic salt
Alcoxonic salt
H
CH3 – O – CH3 + H+ Cl- CH3 – O – CH3 Cl-
+
Hydrogene bond formation
R – O Hδ- δ+
δ-δ+
H O – R
Higher boiling
point
cca 80°C
Esterifikacion with organic acids
R – OH + HOOC – R
ester
+ H2OR – O – CO – R
Reactions with inorganic phosphoric acid
OH OH
R – OH + HO – P = O R – O – P = O
OH OH
- H2O
monoester
Reaction with inorganic acids
OH OH
R – OH + HO – P = O R – O – P = O
OH OH
OH + HO – R
R – O – P = O
OH
- H2O
monoester
- H2O
Reaction with inorganic acids
OH OH
R – OH + HO – P = O R – O – P = O
OH OH
OH + HO – R O – R
R – O – P = O R – O – P = O
OH OH
- H2O
diester
monoester
- H2O
Esterification of glycerol with phosphoric acid
H3PO4
CH2 – OH CH2 – OH
CH – OH OH CH – OH OH + H2O
CH2 – OH + H – O – P = O CH2 – O – P = O
OH OH
1-glycerolphosphoric acid (phosphatidic acid)
( unit of complex lipids)
- in the form of ions at different pH values of body fluids:
O O
- H+ - H+
R-O – P – OH R-O – P – O- R-O – P – O-
+ H+ + H+
OH OH O-
pH << 7 pH 7 pH 7
= = =
o
phosphoanhydric arrangement
O O
R – O - P – O ~ P – OH
protone-donoric
OH OH groups
phosphoester bound
ATP + H2O ADP + Pi G0 - 32 kJ.mol-1
PHENOLS
- one or more - OH groups are linked directly to aromatic ring
- higher acidity of phenols in comparison to alcohols
- chemical reactions
COOH
OH
Salicylic acid
OH
OH
Hydroquinone
OH
Phenol
Oxidation of dihydroxyarenes – diphenols
- formation of quinones, cyclical conjugated diketons
OH
OH
O
O
-2H
+2H
p-dihydroxybenzene p-benzoquinone
( hydroquinone) (1,4-benzoquinone)
- antioxidant function of phenols is related to reversible oxidation of
diphenols to quinones (CoQ – ubiquinone in mitochondria)
-Desinfective properties of phenols (carbolic acid)
Cyclic,
nonsaturated
di-keton
OXO-compounds (aldehydes and ketons)(polarisation of bound to oxygen)
R – Cδ+ Cδ+ = Oδ-
Oδ-
H
R
R
Aldehydes Ketons
+
Carbonyl group (oxo-group) - C = O
- all three atoms linked to carbonyl carbon form angle 120°
- they lie in one plane
R R
Aldehydes C = O Ketons C = O
H R
- polarisation of group – reactivity of aldehydes and ketons
OXO-compounds
Chemical reactions of oxo-compounds
Oxidation and reduction
aldehyde
reductionR – CH2 –OH
primary alcohol
O
R – C – H
oxidationO
R – C –OH
carboxylic acid
+2H (Ni)
or donor H atom
- 2H
O
R – C – R
Ketone
Reduction
catalyst Ni
or donor H atoms
relatively stable against oxidation
OH
R – CH – R
secondary alcohol
Oxidation
- 2H
Addition and condensation reactions
- formation of hemiacetals and acetals
Aldehyde Alcohol Hemiacetal Acetal
- hemiacetal in cyclic form (cyclic monosaccharides - relatively stable
intermediates at the formation of acetals - glycosides)
R – C – H + CH3 – OH R– C – H + CH3OH R – C –H + H2O
O – CH3 O – CH3
O – CH3
hemiacetal
hydroxyl
OHO
- hemiacetals are unstable
O OH
OH
CH3 – C – H + CH3 – CH2– C – H CH3 – CH – CH – C – H
O OCH3
Aldol condensation (aldehydes with - hydrogene)
3- hydroxyaldehyde = aldol
O OH
OH
CH3 – C – H + CH3 – C – CH3 CH3 – CH – CH2 – C – CH3
4-hydroxy-2-pentanone
O O
1
3
Condensation with primary amines -
Formation of imines (Schiff bases)
R – CH = O + H2N – CH3 R – CH = N – CH3
• aldimine
R – C = O + H2N – CH3 R – C = N – CH3
| |
R ketone R ketimine
Schiff bases
- important intermediators of biochemical reactions
- binding of carbonyl compounds to free aminogroups of proteins
CARBOXYLIC ACIDS
C
O
OH
120°
120°
120°
- Shift of - elektrons in group C = O
- Polarisation of – O H bound
O H
R – C = OR – C
O
O
+ H+
- Mostly weak acids, K(ionis.const.) = neer to 10-5
- According to number of – COOH groups:
mono-, di- and tricarboxylic acids
- Saturated and unsaturated
Monocarboxylic acids Dicarboxylic acids
formula
Name
formula
Name
substitutio
nal
common substitutional common
HCOOH Metanoic Formic
CH3 COOH Ethanoic Acetic HOOC–COOH Ethanedionic Oxalic
CH3 CH2 COOH Propanoic Propionic HOOC– CH2 –COOH Propanedioic Malonic
CH3(CH2)2 COOH Butanoic Butyric HOOC–(CH2)2 COOH Butanedioic Succinic
CH3(CH2)3 COOH Pentanoic Valeric HOOC–(CH2)3COOH Pentanedioic Glutaric
CH3(CH2)4 COOH Hexanoic Caproic HOOC–(CH2)4COOH Hexanedioic Adipic
Examples of saturated mono- and dicarboxylic acids
Acid name formula R-COOH salt name R-COO
Oxalic HOOC–COOH Oxalate
Malonic HOOC–CH2–COOH Malonate
Succinic HOOC– (CH2)2–COOH Succinate
Glutaric HOOC– (CH2)3–COOH Glutarate
Fumaric (trans- form) HOOC–CH=CH-COOH Fumarate Maleinic (cis-
form) Maleinate
Lactic CH3–CH–COOH Lactate
OH
Important dicarboxylic and hydroxy-acids
Important dicarboxylic, hydroxy- and oxo- acids II
Tartaric HOOC–CH–CH–COOH Tartarate
Acid name formula R-COOH salt name R-COO
3-Hydroxybutyric CH3–CH–CH2–COOH 3-Hydroxybutyrate
OH
Malic HOOC–CH–CH2–COOH Malate
OH
OH OH
Citric CH2–COOH Citrate
HO–C–COOH
CH2–COOH
Pyruvic CH3–CO–COOH Pyruvate
Acetoacetate CH3–CO-CH2-COOH Acetoacetate
Oxalacetic HOOC-CO–CH2-COOH Oxalacetate
2-Oxoglutaric HOOC–(CH2)2–CO–COOH 2-Oxoglutarate
(α-ketoglutaric) (α-ketoglutarate)
Oxalosuccinic HOOC–CO–CH(COOH)CH2(COOH) Oxalosuccinate
DERIVATIVES of CARBOXYLIC ACIDS
1. Functional derivatives
- substitution of – H or - OH group of carboxyl by another atom
or atom group
- esters, thioesters, halogenides, amides, anhydrides
2. Substitutional derivatives
- substitution of hydrogen atom/s in side chain of carboxylic acid
by another atom or atom group
- hydroxyacids, oxoacids, aminoacids, halogeneacids
DERIVATIVES of CARBOXYLIC ACIDS
O
R – C – O – H
- M (salt) –––––––––––––––––
– X (halogenides)
– NH2 (amides)
– O – R (esters)
– O – CO – R (anhydrides)
≡ N (nitrils)
Function derivatives
Acyl-
Chemical reactions
1. Neutralisation - salt formation
CH3 – COOH + NaOH CH3 – COO- Na+ + H2O
Acetic acid sodium acetate
Sodium and potassium salts – good soluble in water
(COOH)2 + Ca(OH)2 (COO)2 Ca + H2O
Oxalic acid calcium oxalate - insoluble (urine stons)
- organic acids at pH near to 7,4 form in cells salts
- dissociated in the form of anions R – COO-
- soaps – sodium and potassium salts of fatty acids
- palmitic acid CH3–(CH2)14 - COONa
- stearic acid CH3–(CH2)16 - COOK
Esterifikation)
H+
H – COOH + HO – CH3 H – CO – O –CH3 + H2O
Formic acid Methyl formiate
Methylester of formic acid
Hydrolyses of esters
R – CO – O – R1 + H2O R – COOH + R1 – OH
R – rest of fatty acid Salt of fatty acid
Alcaline hydrolyse of esters, so called as saponification:
R – CO – OR1 + NaOH R – COO Na+ + R1 – OH
Ester Acid Alcohol
Soap – sodium or potassium salt of fatty acids
-Transport of acyl in biochemical reactions
coenzyme A, (CoA SH)
- activation of carboxylic acid in v metabolic pathways:
R – COOH + HS – CoA R – CO ~ SCoA + H2O
thioester
- thioesters – activ form of carbocylic acids (acyls) in cells
CH3– CO ~ S-CoA acetyl – CoA
CH3 – CO ~ CoA the key intermediate of metabolism
of lipids, saccharides and proteins
- substrate for Krebs cycle (citric acid cycle) 56
Acyl-
Amides of carboxylic acid
O
R – C – O – H
O
R – C – NH2+ NH3 + H2O
Amide of carboxylic acid
Amid of nicotic acid
Niacine
Vitamin PP
- Substitutional derivatives
γ(4) β(3) α(2) 1 O
R – CH2 – CH2 – CH – C
OH
- X (halogene of carboxylic acid)
- OH (hydroxyacids)
- NH2 (aminoacids)
= O (aldehyde- and oxo-acids)
H
!
Hydroxyacids
CH3 – CH CO O
O CO CH –CH3
lactid
CH3 – CH – COOH HO
OH HOOC+
CH – CH3
- 2 H2O
α –hydroxyacids eliminate water to lactids at higher temperature
Hydroxyacids
–hydroxyacids eliminate water (dehydrated) to unsaturated acids at
higher temperaturae:
-H2O
CH3 3CH – CH2 – 1COOH CH3 CH = CH COOH
T
OH
3–Hydroxybutanoic acid 2- Butenoic acid
λ –hydroxyacids dehydrated to lactons at higher temperaturae:
R – CH – CH2 – CH2 – C
O H OH
γ β α
R–CH–CH2–CH2–C=O
O
γ – hydroxyacid γ – lacton
-H2OO
Synthesis of ascorbic acid
O = C
HO – CH
HO – CH
HO – CH2
HC
O
HO – CH
L-gulono-
lacton
L-gulonoic
acid
D – glukuronic
acid
COOH
HO – CH
HO – CH
HO – CH2
HC – OH
HO – CH
+ 2H
L-gulonolacton dehydrogenase
O
=O
OH OH
CH2 – OH
HO – CH
Kys. L-ascorbic
acid (vitamín C)
- 2H
Synthesis of aspirin
COOH
OH
+ CH3COOH- H2O
COOH
O CO CH3
2-Hydroxybenzoic acid (salicylic acid)
Acetic acid Acetylsalicylic acid
aspirin
esterification
CH3 – CH – COOH
OH
+2H
-2H
CH3 – C – COOH
O
Lactic acid Pyruvic acid
CH3 – CH – CH2 –COOH
+2H
-2H
CH3 – CO –CH2 –COOH
OH
αβ
β – hydroxybutiric acid Acetacetic acid
Oxidation of hydroxyacids
Dekarboxylation
- CO2CH3 – CH2 – COOH CH3 - CH3
propanoic acid etane
HOOC–CH2–CH2–CO–COOH (O)
– CO2
HOOC–CH2–CH2–COOH
Succinic acidOxoglutaric acid
– CO2
O=C–COOH
CH – COOH
CH2– COOH
Oxaljantaric acid
dehydrogenation
HOOC–CH=CH–COOH
Fumaric acid
Reaction of ß-oxoacidsimportant in the metabolism of fatt
CH3CCH2COOH
║
O
Acetoacetic acid
NADH + H+
hydrogenation
CO2 ketone
forming
cleavage
(OH- ) acid
forming cleavage
CH3CHCH2COOH
OH
-Hydroxybutyric acid
CH3COCH3
Acetone
2 CH3COOH
Acetic acid
CH3 – CH – CH2 COOH
OH
β – hydroxybutyric acid
CH3 – CO – CH2 – COOH acetoacetic acid
CH3 – CO –CH3 aceton
Ketone bodies in the organism
In trace amount in blood, urine
At higher concentration in urine – ketonuria (ketoacidosis) (starvation, diabetes)
Transamination
transaminases
Glutamic acid Phenylpyruvic acid 2-oxo-glutaric acid Phenylalanine
67
Citrate cycle
C4C6
C2
C5
C4
Nobel price for physiology and
medicine, 1953
Discovery of citric acid cycleHe was born in Hildesheimu (Germany) in the family of Judaic
physician. After studying of medicine he studied in Berlín also
chemistry one year.
His most important discovery was Citric cycle (Krebsov)
cyklus.
Krebs Hans Adolf (1900 - 1981)
Citrate formation from Oxylacetate and
Acetyl-CoA
- CoA-SH
H
Citrate/Isocitrate isomerisation
Oxalosuccinate and α-oxoglutarate formation
CO2
Succinyl-CoA formation
CO2
Fumarate formation
Malate formation through water addition
H2O
Malate dehydrogenation
H2O
O=C-COOH H2C-COOH
CH2-COOH + CH3-CO-S-CoA HO-C-COOH + CoA-SH
H2C-COOH
Oxalacetic acid Acetyl-CoA Citric acid
Synthesis of citric acid
Organic compounds of nitrogene
Amines - primare R-NH2
- secondary R-NH-R
- tertiare R-N-R
R – NH2 + H+ R – NH3+
Basic properties
Formation of amonium salts
Biological important amines formation
– CH2 – CH – COOH
NH2 – CO2
– CH2 –CH2 –NH2
HistamineHistidineN
H
N
N
H
N
HO CH2 CH
NH2
COOH HO CH2 CH2 NH2HO CH2 CH2 N
CH3
CH3
CH3
++ 3 CH3
cholínCO2
Serine EtanolamineCholine
ORGANIC COMPOUNDS OF SUPHUR
• Thiols R-SH (disulphides, thioesters)
• Sulphides R-S-R (sulphoxides, sulphons)
• Sulphonic acids, sulphonamides R – SO3H
• Heterocyclic compounds with suphur
(thiophene, thiazol)
S
N
S
thiophene thiazol
Redox reaction of thiols
R – SH + HS – R R – S – S – R + 2H
oxid
red
disulfid
Redox reactions of thiols – structure of proteins is
changed
Oxidation – 2H
Reduction + 2H
S
S
OOC-CH-CH2-CH2-CO-NH-CH-CO-NH-CH2-COO-
NH3+ CH2
SH
SH
NH3+ CH2
OOC-CH-CH2-CH2-CO-NH-CH-CO-NH-CH2-COO
dehydrogenation
- 2H
2 GSH GSSG + 2H
Oxidation of glutathione
Derivatives of sulfanilic acid
sulfonamides
Folic acid
Sulfanilic acid sulfonamid
Sulfanic acid
85
Thank you
for your attention.....