Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**
Consortium leader
PETER PAZMANY CATHOLIC UNIVERSITY
Consortium members
SEMMELWEIS UNIVERSITY, DIALOG CAMPUS PUBLISHER
The Project has been realised with the support of the European Union and has been co-financed by the European Social Fund ***
**Molekuláris bionika és Infobionika Szakok tananyagának komplex fejlesztése konzorciumi keretben
***A projekt az Európai Unió támogatásával, az Európai Szociális Alap társfinanszírozásával valósul meg.
Aliphatic and aromatic hydrocarbons
(Alifás és aromás szénhidrogének)
Organic and Biochemistry
(Szerves és Biokémia )
Compiled by dr. Péter Mátyus
with contribution by dr. Gábor Krajsovszky
Formatted by dr. Balázs Balogh
Table of Contents
1. Alkanes 6 – 20
2. Alkenes 21 – 42
3. Alkynes 43 – 53
4. Cyclic Compounds 54 – 55
5. Annulanes 56 – 58
6. Aromatic compounds 59 – 75
7. Antiaromatic compounds 76 – 82
8. Reactivity of aromatic compounds 83 – 107 9. Fused polycyclic aromatic hydrocarbons 108 – 116 10. Isolated polycyclic aromatic compounds 117 – 121
Topics
Hydrocarbons
Alkanes Alkenes Alkynes
Aromatic compounds carboaromatic
heteroaromatic compounds
Substituted hydrocarbons
(discussed according to functional goups) Chemical structure
Reactivity
(Biological function)
Hydrocarbons
paraffin hydrocarbons or alkanes or acyclic saturated hydrocarbons
n=1, 2, 3...
olefins and cycloalkanes n=2, 3, 4...
acetylenes, diolefins, cycloalkenes n=2, 3, 4...
benzene and its homologues n=6, 7, 8...
CnH2n+2 CnH2n CnH2n-2 CnH2n-6
Alkanes (paraffins)
n-alkanes
The stems of the names are of Greek and Latin origin isoalkanes
(alkyl group)
• Isomerism
Homologous series: any two neighboring members of the series differ by a CH2 group from each other
• chemical properties are rather similar
• physical properties are gradually changing
• Nomenclature
All carbon-carbon bonds are single bonds
many trivial or common names
Ending for all names: -ane
m.p.
n even
odd
v a n d e r W a a l s forces
( n - a l k a ne ) > ( i s o - a l k a ne )
b.p. b.p.
b.p.
(°C) 0
5 n
gas liquid
t r a n s methyl groups
c i s methyl groups
even: carbon atoms pack more closely
Alkanes
- Oxidation-reduction (in general) - Some synthetic methods
- Reactivity
oxidation reduction e
-releasing accepting O accepting releasing H releasing accepting e.g.,
CH4 electron density is shifted towards the carbon: C is reduced formally
or CH4 could be oxidised (C4- character) (is to be burned).
CCl4 C4+ character, i.e., fully oxidised, CCl4 can not be burned.
Oxidation and reduction (general remarks)
Oxidation levels of carbon: C
EA C IP
reduction oxidation C
+ 4 + 3
+ 2 + 1 C C C C
2
3
4
- 1 - 2 - 3 - 4
C
C C
C C
2
3 4
red.
oxid.
fully oxidised
fully reduced
(formal)
the lowest oxidation level (R2 = H, alkyl...)
The most typical oxidating agents: KMnO4; OsO4; CrO3; H2O2; peracids Reducing agents:
• Catalytic hydrogenation
Ni, Pd, Pt / H2 2 H homolytic reaction in heterogeneous phase (solid + gas) alkene/alkyne: easy reduction
benzene: difficult reduction
• Chemical
LiAlH4, NaBH4 H is of nucleophilic character (ethylene, benzene: do not react)
Alkanes: syntheses
- Reduction
- Carbon-carbon bond formation
Synthesis of alkanes:
Fischer-Tropsch synthesis exothermic reaction
Reduction by ‘nascent’
hydrogen
Wurtz reaction
(coupling of alkyl halides) C C
H 2
c a t . C C H H
C Cl Na
2 C C
R X
2 Zn
2 H
2R H
n C O + ( 2 n + 1 ) H 2 catalyst D C n H 2 n + 2 + n H 2 O Reduction
Synthesis of alkanes:
Kishner-Wolff- Huang-Minlon reduction
Clemmensen reduction
C O H 2 N N H 2 C H 2
C N N H 2 - H 2 O
D base R B r L i A l H 4
R H + L i B r + A l H 3 R M g X + H 2 O R H + M g ( O H ) X R L i + H 2 O R H + L i O H
Reduction
C O C
- H Zn-Hg H 2
Alkanes: reactions
Reactions of alkanes
„Parum affinis” = bonds with low polarity, and they are less polarizable
1. Substitution reactions
halogenation (Cl2 and Br2)
nitration
2. Oxidation
heat of combustion: ~ 157 kcal ( C H 2 )
H3C CH3 HNO3
H3C CH2 NO2 + H3C NO2
2 CnH2n+2 + (3n+1) O2 2nCO2 + (2n+2) H2O C l
C H 4 2 H 3 C C l + H C l C C l 4 D or hn
Heat of combustion is the enthalpy change for the complet
oxidation of the compound (under standard conditions)
3. Isomerisation
cf., with data of heat of combustion
H3C CH2 CH2 CH3
AlCl3
HCl H3C CH CH3 CH3
20% 80%
+ 6.5 O2 + 6.5 O2
2 kcal/mol
- 685.5 kcal/mol - 687.5 kcal/mol
4 CO2 + 5 H2 O
Alkanes: as fuels
CH3 C H CH3
CH3
mágikus sav
CH3 C H CH3
CH3 H
CH C CH3 CH3
CH3 C CH2 CH3
CH3
CH CH3
CH3 + H
izooktán magic acid
isooctane
Alkenes (olefines)
CnH2n double bond H2C CH CH3
Nomenclature: - the longest carbon chain containing the double bond(s) - double bond(s)
- branching
Groups: H2C CH ethenyl (vinyl)
H2C CH CH2 2-propenyl (allyl) H2C C
CH3
1-methyl-ethenyl
alkylidene H3C CH CH3
CH 2-methyl-propylidene E, Z isomers
alkenyl
Relative stability: enthalpy of hydrogenation (kcal/mol)
H3C CH2
C CH2
H C C
H3C H
CH3 H
C C H3C
H
H CH3
CH2
H3C CH2
CH3 - 30.3
1.7
- 28.6
1.0
- 27.6
1. The disubstituted double bond is more stable, than the monosubstituted one
2. The trans-isomer is more stable, than the cis
3. The compound having polysubstituted double bond is more stable, than the one with less substituents reasons:
a) hyperconjugation (σ - π conjugation) is less important
H C C C
b) more sp3 - sp2 bonds are in the more substituted olefin
(delocalisation)
H3C CH3 CH2 CH
H3C
H3C
C H3C
H3C
average bond energy
bond energy
C C 82.6 kcal/mol C C 145.8 kcal/mol
60 kcal/mol
bond ~ ~
C C 1 . 3 3 Å
C C 1 . 5 4 Å
Temperature (°C) Energy content (kcal/mol)
at room temperature ~ 25
by heating 25 - 50
~ 500 60
π bond: ~ 60 kcal/mol
cis-trans isomerisation usually does not happen, but ‘push-pull’ or ‘captodative’ ethenes
(activation free enthalpy ≈ 15 kcal/mol)
C C
A E
B D B D
A E
C C
A, B electron-withdrawing, E, D electron-releasing
atoms marked by red color are in the same plane cis double bond
a.) planar b.) not planar
C C
C C C
C
H H
H H H
H
Alkenes: Syntheses
Preparation 1. Elimination
X = Cl, Br, NMe3 E2 or E1
E2 E 1
( or ) I CH3COOH
Zn/
H C C
Br
Br C C
C C OH
H H
X C
C base
2. Formation of new carbon-carbon double bonds:
Wittig reaction
Ph3P=CHR C O
R1 R2
C CHR R1
R2
3. Reduction Syn addition
Ni2B H2
Pd/CaCO3 H2
C C
R R
cis C C R
H H
R Lindlar
Li/EtNH2 anti addit ion trans olefin
Alkenes: Reactions
1. Addition reactions (a molecule is added to an another, and nothing is cleaved)
Electrophilic addition AdE
v = k 2 [ a l k e ne ] [ X 2 ] v = k 2 [ a l k e ne ] [ H X ] a l k e ne k 2 ( r e l a t i ve )
X 2 H X
Two-steps reactions
Alkene
C X
C X
X2
C C HX C C H
X
CH2 = CH2 CH = CH2 Et
Me2C = CMe2
1 102 106
Stereochemistry: Anti addition (X = Cl, Br)
C H 3
C H 3
B r 2 + H 3 C B r
C H 3 B r
B r B r + B r B r B d r B d r . . . . . . . . . . . . . . B d r B d r
B r B r
C C B r
B r C C
B r B r C C
d
H H
H 3 C
B r
H C C B r
B r C H 3 C H
C H 2
d
B r C C
H 3 C
B r H
H B H r
Addition reactions of olefins
Addition of hydrogen
CH3
CH3
CH3 H
CH3 H2 (cat). H
syn addition
CH3
CH3
O CH3
O C H3
Met O- O- OsO4 (25 °C) or MnO4-
(hydrogen)
syn addition OH
H
OH H
Met: Os, Mn K salt H
H CH3
C H3
Ar
OOH
O O
CH3 H C
H3 H
ArCOOH
+
syn addition
+ 1.
2.
3.
HX: HCl, HBr (H3O+ + Cl–/Br–
Regiochemistry: Markovnikov's rule ≈ 1870
(H moves to the least, while X to the most substituted carbon.) Stability of the carbenium ions: 3° > 2° > 1°
P H X
C C H
R H
H
C C R
HH
H H
X C R
H
C H HH C C X
R H
H H H
Markovnikov’s adduct
R C H
2C H
2X
R C H
2C H
2C H C H
2R
+ H X
R C H C H
3X
R C H C H
3X
X
z z
E
Markovnikov's rule is valid:
C C R
H H H
Anti-Markovnikov orientation:
1.
C C H R
H H
H OH H B R'
R'
H2O2 H2O, HO C C
H
R H
H
H B
R' R' C CH2
H R
(where the X in HX is more electropositive, than H)
H X C CH3
X R H I Cl
C CH2I Cl
R H
Cl OH
C CH2Cl OH
R H
H OH2 C CH3
OH R H
H OSO3H
C CH3 OSO3H R
H
Substitution:
Addition vs. substitution
substitution addition
regioselective chlorination in allylic position
RCH2 CH CH2
SeO2 R C CH CH2
O oxidation
R=H
HOOC CH CH2
oxidation (catalytic) H2C
H2C N O
O
Br
CCl4
BrCH CH R
CH2 C H 3 C H C H 2
C l C l
C l 2
2 5 o C C H 3 C H C H 2 C l 2
5 0 0 o C C l C H 2 C H C H 2
2. Radical reaction AdR
Stability of radicals:
(c.p., with bond dissociation energies, BDE) HF does not react, since the bond dissociation energy is too high.
HI does not react, since I is not enough reactive.
Init. Br H Br
CH3 CH CH3 Br
CH3 CH2 CH2Br Br
HBr CH3 CH CH2
Br
CH3 CH CH2Br
CH3 CH CH2 Br main product
side product
3 o > 2 o > 1 o
Init.: radical-initiator
Radical polimerisation
Stabilisation, e.g.,
In CH2 CH2 In CH2 CH2
CH2 CH2
In CH2 CH2 CH2 CH2 ...
In (CH2 CH2)
n CH2 CH2 H2C (CH2 CH2)n CH2 In
In (CH2 CH2)n CH2 CH2 CH2 (CH2 CH2) CH2 In n
Nucleophilic addition to carbon - carbon multiple bond
Michael addition:
C C EWG H H
H
HY Y CH2 CH2 EWG base
EWG: C O
H , R
C O
, C O
OR , NH2
C O C N, NO2, SOR, SO2R ,
a.) H2C CH CN NaOEt
EtOH C2H5O CH2 CH2 CN C COOR1
HC R2NH R2N CH CHCOOR1 b.)
Physical properties of alkenes
Biological importance:
- fixing conformation - form homologous series
C n C 5 - -
liquids boiling point alkanes
dipole moment of the cis isomer is higher
H
3C
S CH
2CH NH
3COO
H
2C C
NH
3COO H
2C
H
2C CH
2methionine
enzyme
enzyme
Diolefins
Cumulated:
Allenes: in two planes perpendicular to each other Conjugated:
butadiene isoprene
H2C C CH2 H3C C CH
H2C C CH CH2 CH3
H2C CH CH CH2
Br2 1,2 1,4 BrH2C CH CH CH2
Br
BrCH2 CH CH CH2Br 5°C
H2C CH CH CH2
C C C
B
A B
A
C C C
Alkynes
Acetylenes (Alkynes): Structure
Bond energy is 200 kcal/mol
CnH2n-2
1.2 A° C C
H H
sp sp
Nomenclature of hydrocarbons
Principal chain: must be chosen according to the following priority:
1. must contain the most unsaturated (double and triple) bonds 2. the carbon chain must be the longest
3. must contain the most double bonds
4. unsaturated bonds must get the lowest locants
5. a double bond must get lower locant, than a triple bond, if there are alternatives
6. must contain the most substituents, those can be named as prefixes
C H3C
CH C
CH3 CH2 CH2
CH2 CH2CH3
3 2 4
6 5 7
2-ethyl 4-methylhepta-1,3-diene
1 2 3 4 5
H
2C CH CH
2C CH
pent-1-en-4-yne
2 1 4 3
6 5
H3C CH CH3
CH2 CH2 C CH
5-methylhex-1-yne
Groups with one valence (univalent groups)
numbering starts from the carbon with free valence:
H2C CH vinyl (ethenyl)
HC C CH2 2-propynyl
H2C CH CH2 allyl (2-propenyl)
choosing the principal chain happens according to the usual method Groups with more, than one valence (polyvalent groups)
-ylidene H3C CH2 CH propylidene -ylidyne H3C CH2 C H propylidyne
Alkynes: syntheses
- Elimination reaction
- Carbon-carbon bond formation: alkylation of alkyne
carbon
Preparation
2. HC C R
1. NaNH2
2. R Br, ,
C C
R R
1.
KOH, R CH2 CX2 R,
R C C R,
KOH, R CH CH R,
X X
R , = H
NaNH2 R C CH if
Alkynes: Reactions
- Addition - Substitution - Oxidation
Reactions
I. Addition
1. Electrophilic addition: HX → ‘Markovnikov's rule’
HBr HBr
CH3C O Br Al2O3 CH2Cl2
H2O
Br2C R
CH3 C CH
R C CH2
Br R
C CH2 Br
R
‘Anti-Markovnikov’: by initiation with peroxides or with light
HBr H2O2 C CH
R RHC CHBr
X2 (X = Cl, Br)
t r a n s Addition of an organic acid
Addition of water
H low temperature
stoichiometric amount of bromine
vinyl acetate
HC CH CH3COOH Zn2 ,
CH3 C O
O CH CH2 D
Br2
C C Br C C
Br
H C C H H 2 C C H O H H
3 C C H 2 SO 4 O
HgSO 4
tautomerisation
H 3 C H 3 C C C H 2 O H
H 3 C C C H
3
O C C H H 2 SO 4
HgSO 4
tautomerisation
2. Nucleophilic addition
In the case of olefins, it works only in the presence of a strong
electron withdrawing group in α position (if the olefin is activated).
3. Hydrogenation - Reduction by active catalysts
in the case of a deactivated catalyst: olefin is produced II. Substitution: - alkylation
III. Oxidative cleavage: - Oxidation
KOH ROH
HC CH RO C C
H RO
H
RO CH CH2 vinyl ether R1 C C R H2
R1 CH2 CH2 R
100 °C KMnO4
R1 C C R
O O pH ~ 7 R1 C C R R1 COOH R COOH KMnO4
Cyclic Compounds
- Monocyclic - Polycyclic
- Isolated cyclic - Fused polycyclic
- ortho
- ortho and peri fused
- Bridged cyclic
(contains bridge head atoms) - Spirocyclic
isolated ring systems no common atom in the rings number of connections is less by one than the
number of cycles
ortho-condensed/fused two common atoms in the rings
n common edges and 2n common atoms
ortho and peri-fused n common edges and less than 2n common atoms
CH2 CH2 CH2
CH2
CH2
CH CH2
CH CH2
CH2 CH2 H2C
H2C
CH
CH2 CH2
CH CH2
CH2 CH2
H2C
H2C C CH2
4. Spirocyclic one common atom
Polycyclic compounds:
1. 2.a 2.b
3. Bridged
more than 2 common atoms
Annulenes
Unsubstituted monocyclic hydrocarbons with the greatest possible number of noncumulated double bonds. Their general formulae
CnHn (n>6, even number) CnHn+1 (n>6, odd number)
1
2 3 4
6 5 7
8
9 10
[10]annulene
9 8
7 6
5
4 3
2 1
1H-[9]annulene
‘[6]annulene’
benzene
Heterocyclic compounds
They contain carbon atom(s) and heteroatom(s) atoms in the ring
- Saturated - Unsaturated
- Partially saturated Classification:
- number of the ring member atoms - heteroatoms
- number of the heteroatoms - quality of the heteroatoms
Heteroannulenes
(compounds with the greatest possible number of non-cumulated double bonds)
These can be derived from annulenes:
- if a CH group is replaced by an X (the same ring size)
- if a HC=CH group is replaced by an X (next lower ring size).
In both cases, the resulting heteroannulene is isoelectronic with the corresponding annulene.
[6]annulene benzene X
X = N pyridine
NH pyrrole
Aromatic compounds: monocyclic, fused and isolated carboaromatics
- Aromaticity and antiaromaticity
- Aromatic electophilic and nucleophilic substitution
Benzene
1.
hypothetic cyclohexatriene
alternating single and double bonds
2. Resonance structures
Benzene
1H NMR:
d aromatic H : ~ 7-8 ppm d olefinic H : ~ 5-6 ppm
Outside magnetic field induced space
H H
Bond dissociation energy (BDE)
The energy necessary for the cleavage of a bond resulting in radicals.
118 kcal/mol 100 kcal/mol Bonding energy (BE)
(average bonding energy) bonding energy for the
O—H bond of water: 118 + 100
2 = 109 kcal/mol For a molecule having more than two atoms: BDE BE
Determination of BE:
from atomisation heat, that is calculated from combustion heat
H2O H + H2O H +
HO O
Bond energies (25°C) (average values)
bond kcal/mol kJ/mol
C-H 96-99 400-415
C-C 83-85 345-355
C-Cl 79 330
C-Br 66 275
C-I 52 220
C=C 146-151 610-630
CC 199-200 835
Resonance energy:
measured energy - resonance structure with the lowest energy Atomisation heat for benzene : 1323 kcal/mol (measured)
calculated from bonding energies: 1289 kcal/mol (A or B)
A B
Resonance energy: 1289-1323 =
= - 34 kcal/mol Empirical resonance energy:
3 x (-120) - (-210) = - 150 kJ/mol = - 35.9 kcal/mol
H2
- 120 kJ/mol
H2
- 210 kJ/mol
H2
2 H2 2 H2
DH = -30.3 kcal/mol
DH = -60.7 kcal/mol Estimated value from other unconjugated dienes or twice the value for 1-butene
DH = -57.1 kcal/mol experimental value
About 3.6 kcal/mol stabilization owing to conjugation
DH H2
length (Å) energy (kcal/mol)
biligand sp (acetylene) 1.057 120
triligand sp2 (ethene) 1.079 106
quadriligand sp3 (ethane) 1.094 101
120 °
sp2
90 °
180 ° pz
px
sp 109.5 °
sp3
An sp2 orbital has more s character than an sp3 orbital, and bonds made from sp2-sp2 overlap will be stronger and shorter than those made from sp3-sp3 overlap.
H2
2H2
3H2 3H2
Energy
The value for the special stability of benzene as derived from measured and calculated heats of hydrogenation.
Predicted effect of adding one more double bond
(–82.2 kcal/mol)
–32.9 kcal/mol delocalization energy of benzene
ΔH = –82.2 kcal/mol estimated for hypothetical
1,3,5-cyclohexatriene Experimental effect of
adding one double bond (–26.8 kcal/mol)
ΔH = –55.4 kcal/mol ΔH = – 28.6 kcal/mol
Energy of cyclohexane ΔH = –49.3 kcal/mol
measured for the real benzene
antibonding orbitals
bonding orbitals
The relative energies of the molecular orbitals of benzene derived from a Frost circle.
Hexagon inscribed inside the Frost circle (relative energies of the molecular orbitals of planar, cyclic fully conjugated molecules): inscribe the polygon vertex down, the intersections with the circle will mark the positions of molecular orbitals
Nonbonding
Three antibonding orbitals
Three bonding orbitals will hold the six available π electrons
Energy
Radius = 2β 2b
1b 1b
Benzene
The effort to the lowest energy level forces the structure into the same plane.
Conditions for formation of aromatic systems:
1. There must be a continuously conjugated, cyclic delocalised system (using pz atomic orbitals).
2. Participation of 4n+2 electrons in the delocalisation (Hückel's rule).
3. The carbon skeleton constructing the cyclic system must be coplanar or approximately coplanar.
Conditions for formation of antiaromatic systems:
1. There must be a continuously conjugated, cyclic delocalised system (using pz atomic orbitals).
2. Participation of 4n electrons in the delocalisation.
3. The carbon skeleton constructing the cyclic system must be coplanar or approximately coplanar.
cis-1,3-Hexatriene is fully conjugated and can be planar, but the lack of a ring structure means that overlap between the 2p orbitals on C(1) and C(6) is essentially zero.
No strong overlap here;
the molecule is not aromatic
cis-1,3, 5-Hexatriene
Six-membered aromatic rings
Benzene
carbon-carbon bond distance: 1.40 Å
c.p., with Csp2-Csp2: 1.48 Å Csp2=Csp2: 1.32 Å Pyridine
Pyrilium cation
pyridinium cation
N
H
N H
N H
O
Other aromatic systems containing - sextet
Cyclopentadienide anion
Pyrrol, thiophene, furane
X: NH pyrrol S thiophene O furane
H H
pKa = 16
base H
H
X
Cyclopentadine is a quite strong acid. The cyclopentadienyl anion is an aromatic species. For an anion, it is extremely stable.
CH2 CH + B H
base,B
The cyclopentadienide anion is easily formed A pentagon inscribed in a circle (vertex down)
Antibonding molecular orbitals
Nonbonding Bonding
molecular orbitals pKa = 15
Energy
cycloheptatrienylium cation (tropylium cation)
aromatic OH
-OH
67 6
5 4
3 2
H
1Antiaromatic compounds
4 electrons
generally: 4n electron
Much less stable, than the appropriate non-aromatic compound!
Antiaromaticity: the electron circuit is destabilizing the system.
Paramagnetic circuit: the outer hydrogen atoms have lower chemical shifts, than of the appropriate non-aromatic system.
The relative energies of the molecular orbitals of cyclobutadiene derived from a Frost circle.
Energy
Nonbonding molecular orbital
Nonbonding molecular orbital
Bonding molecular orbital Antibonding molecular orbitals
Delocalized cyclobutadiene
A square inscribed in a circle (vertex down)
The electronic occupancy of the four molecular orbitals for square cyclobutadiene.
Energy
Nonbonding molecular orbital
Nonbonding molecular orbital
Bonding molecular orbital Antibonding molecular orbital
not biradical (since it is square- shaped); antiaromatic
antiaromatic
H H
H H
H I
H Ag
H HH
H H
HI HH H
Ag
H cyclooctatetraene
Homoaromatic compound (ions):
presence of one or more sp3 carbon in the conjugated cycle
H1 H7 Hb Ha 3 2
6 7
H H
H H H H
H H
1 2
8
Na 10
aromatic
d Hb = - 0.3 ppm
Ha = 5.1 H2-H6 = 8.5
ppm ppm d
d
Energy
The molecular orbitals of planar cyclooctatetraene.
Two electrons must occupy nonbonding orbitals.
Nonbonding molecular orbital
Nonbonding molecular orbital
Bonding molecular orbitals
Antibonding molecular orbitals
Delocalized cyclooctatetraene
An octagon inscribed in a circle (vertex down)
A O E
cyclooctatetraene 8 electrons
planar benzene
6 electrons cyclobutadiene
4 electrons
antibonding non-bonding bonding
1.33 A
o1.46 A
oReactivity:
substitution (electrophilic or nucleophilic depending on the substrate)
addition: very difficult, under harsh conditions
Aromatic electrophilic substitution (S
EAr)
X
X = mostly H
slow Y X
Y
X Y
X Y
X Y
fast Y - X