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Development of Complex Curricula for Molecular Bionics and Infobionics Programs within a consortial* framework**
Consortium leader
PETER PAZMANY CATHOLIC UNIVERSITYConsortium 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 ***
**Molekulris bionika s Infobionika Szakok tananyagnak komplex fejlesztse konzorciumi keretben
***A projekt az Eurpai Uni tmogatsval, az Eurpai Szocilis Alap trsfinanszrozsval valsul meg.
PETER PAZMANY
CATHOLIC UNIVERSITY
SEMMELWEIS
UNIVERSITY
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Organic compounds and nomenclature: whyorganic, conventions and rules
(Szerves vegyletek s elnevezsk: mirt 'szerves', konvencik, szablyok)
World of Molecules(Molekulk Vilga )
Compiled by dr. Pter Mtyus
with contribution by dr. Gbor Krajsovszky
Formatted by dr. Balzs Balogh
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World of Molecules: Organic compounds and nomenclature
Table of Contents
1. Nomenclature of Organic Compounds 4 8
2. Additive names 9 103. Radiofunctional names 11 12
4. Fusion and Hantschz-Widman names 13 13
5. Replacement names 14 146. Conjuctive names 15 15
7. Multiplying names 16 16
8. Substitutive names 17 179. Substractive names 18 21
10. Chemistry everywhere 22 27
11. Organic Compounds 28 37
semmelweis-egyetem.hu
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IUPAC Nomenclature of OrganicCompounds
According to the recommendation of the Commission onNomenclature of Organic Chemistry 1993
(IUPAC:International Union of Pure andAppliedChemistry)
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Purpose of naming:clear identification, e.g., one compound must have one name, or one name mustcorrespond to one structure
Problems:Many types of naming do existChemical names (IUPAC) are complicated, too longsystematic semi-trivial trivial names
Artificial names:
1. Generic name: made by the abbreviation of the full chemical namee.g.,p-acetylaminophenol paracetamol
2. International registered names : a) proposed nameb) recommended name3. Registered / trade names: in many cases, these are fantasy names e.g., Panadol
4. Names used in Pharmacopoeias
OH
NH CH3
O
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Name Construction of organic compounds
1. Determining the type(s) of nomenclature operations to be used dependingon the type of compounds- most frequently: by substitutive nomenclature
2. Determining the principal group:- aprincipal group is a characteristic group, which should be named as suffixat the end of the name of the principal chain (only one kind of the functionalgroups must be cited as suffix, with the highest ranking)
3. The principal chain or ring (system) as well as the prefixes:
- theprincipal chain or ring (system)
is such alinear chain without branching
or cyclic structure, or such an acyclic or cyclic structure with a hemisystematicor trivial name, which has only hydrogen atoms attached and does not containany characteristic groups
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- principal chain, preferred ring or ring system: the one with the highestranking among many possible chains or ring systems-non-detachable prefixes: such an atom or group that substitutes one or more
hydrogen atoms of a principal chain-detachable prefixes: indicates modification(s) of the skeleton of the principalchain; to be listed immediately before the name of the principal chain
4. Numbering of the principal chain, preferred ring orring system:- in regarding to theprincipal group,prefixes, etc.,
5. Composition of the whole name:
- list prefixes in alphabetic order, with multiplying prefixes if these are to beapplied
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NOMENCLATURE SYSTEMS
1. ADDITIVE name2. RADICOFUNCTIONAL name3. FUSION name4. HANTZSCH-WIDMAN name5. REPLACEMENT name6. CONJUNCTIVE name7. MULTIPLYING name8. SUBSTITUTIVE name9. SUBTRACTIVE name
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ADDITIVE names:a) The name of the compound is
made by formal attachments of
the name of the components,without loss of atoms or groupsstyrene oxyde
HC CH2O
HC CH2
styrene
b) Marking addition or insertion of atoms or groups:
Hydro prefixO
1
2
3
4
5
6O
1
2
3
4
5
6
2,3-dihydropyranepyrane
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Homoprefix (skeleton modifying name)
Secoprefix (skeleton modifying name)
COOH
CH2COOH
COOH
COOH
homophthalic acid phthalic acid
H
CH3
CH3
H H
H1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
H3C
H3C
H
CH3
CH3
H H
H12
34
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
5-androstane 2,3-seco-5-androstane
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RADICOFUNCTIONAL name- Expresses a charasteristic group as a class term written as a separate word following thename of a parent structure or a name derived from a parent structure
- applied only for simple, acyclic compounds with halogen, or pseudohalogen groups, orfor ethers, alcohols, or oxo compounds
H3C H2C OH H3C I H3C H2C C
O
CH3
H3C H2C O CH3 C NH3C CH3C
O
Cl
methyl iodide
methyl cyanide
ethyl alcohol
ethyl methyl ether
ethyl methyl ketone
acetyl chloride
- Indicating the modification of a functional group
CH2C
O
H
H3C CH2C
N
H
H3C
NH2
propanal propanal hydrazone
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Functional group Radicofunctional name-CN, -NC cyanide, isocyanide
-S-CN, -N=C=S thiocyanate, isothiocyanate
>C=O ketone
-OH alcohol-SH hydrosulfide
-O-OH hydroperoxide
>O ether, oxide>SO2, >SO, >S sulfone, sulfoxide, sulfide
-F, -Cl, -Br, -I, -N3 fluoride, chloride, bromide, iodide, azide
- The functional group with the highest priority would be the principal groupexpressed by a suffix, the others might be mentioned in the name as prefixes- Decreasing order of seniority of functional groups:
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FUSION name- A composite name having the maximum number of noncumulative double bondsand at least oneortho fusion.- Dissection of the structure into contiguous component having recognized trivial or
semisystematic names, one of which is selected as the base component. Attachmentof the other component(s) is described by prefix(es).
dibenzo[b,e]oxepineO
be
HANTZSCH-WIDMAN name
- For heteromonocyclic parent structure having nomore than 10 ring members- one or more heteroatoms
S
N
1
2
3
45
6
7
1,4-thiazepine
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REPLACEMENT name:Replacement of one atom or group of a parent structure by another atom or group.a) Skeletal replacement name: the replacement of skeletal atoms and their associated hydrogen atoms of a parent hydride by other atoms with the appropriate
number of hydrogen atoms is indicated by nondetachable prefixes.Proper number -O- oxa; -S- thia; -NH- aza, respectively:
N
N
N
3
4
6
2
15
78 9
10
O
oxacyclohexane 2,7,9-triazaphenanthrene
b) Functional replacement name: replacement of an oxygen atom or hydroxy
group by another atom or group:
dithioacetic acid
H3C C
O
SH
H3C C
S
OH
H3C C
S
SH
thioacetic-S-acid thioacetic-O-acid
2-oxa-5-azahexane
H3C NH CH2 CH2 O CH3
hexanethio-O-acid
COH
S
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CONJUNCTIVE name:Assembling cyclic systems with acyclic side chain.Implying the loss of an appropriate number of hydrogen atoms fromeach.
CH2 OH cyclohexanemethanol
CH2
H2C CH2 COOHOOC
COOH
benzene-1,3,5-triacetic acid
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MULTIPLYING name:Expresses multiple occurence of identical parent structures skeletons.These are attached symmetrically, or the same rings are attached.
2N N1 1'
2'2,2-bipyridine
OOC O
O COOH1'
2' 3'
4'
1
23
4
4,4-peroxydibenzoic acid
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SUBSTITUTIVE name (details of this nomenclature system see inadvance part of nomenclature):
The most important names, that are recommended by IUPAC.Substitutive name indicates the exchange of one or more hydrogenatoms attached to a skeletal atom of a parent structure, which may beexpressed by a suffix or by prefixes.The parent chain or ring (system) is such a linear chain withoutbranching orcyclic structure, or such anacyclic orcyclic structurewith a semisystematic or trivial name, which has only hydrogen
atoms attached and does not contain any functional groups.If the main skeleton is linear, than this should be chosen asparentchain, if it is cyclic, then the ring of the highest priority would make
theparent ring.
Organic and Biochemistry: Nomenclature of Organic Compounds
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SUBTRACTIVE name:Made by removal of atoms or groups from the parent structure, shown by prefixesand/or suffixes. The added hydrogens are also indicated in the names.
a) By prefix: methyl group hydrogen:demethyl
hydroxyl group hydrogen:deoxy
ribose deoxyribose
morphine N-demethyl-
morphine
O
N
OH
OH
CH3
H O
NH
OH
OH
H
3' 2'
1'
O
4'
OH
OHOH
5'OH
3' 2'
1'
O
4'
OHOH
5'
OH
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didehydro
CH3
CH3
H H
H
HO
CH3
CH3HH3C
1
2
3
4
5
6
7
8
9
10
1112
13
14
15
16
17
18
19
20
21
23
22 24
25
CH3
CH3
H H
HO
CH3
CH3HH3C
1
2
3
4
5
6
7
8
9
10
1112
13
14
15
16
17
18
19
20
21
23
22 24
25
cholesterol 7,8-didehydrocholesterol
Increasing unsaturation:
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removal of a methyl group:nor
removal of water from two hydroxyl groups:anhydro
OH
OH
CH OH
CH2 NH2
OH
OH
CH OH
CH2 NH CH3
COOH
H OH
H OHO H
H OH
CH2OH
COOH
H
HHO H
H OH
CH2OH
O
adrenaline noradrenaline
ascorbinic acid anhydroascorbinic acid
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b) By suffix: removal of two or four hydrogen atoms:-ene / -yne
Loss of a hydrid anion, a proton, a hydrogen radical:
-ilium / -ide / -yl
H3C CH3 H2C CH2 HC CH
ethane ethene ethyne
H3C CH2 H3C CH2H3C CH2
ethylium ethanide ethyl
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2 3
45
1
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Scott L. T. et al.: Science 295, 1500 (2002)
A Rational Chemical Synthesis of C60, the smallest stable fullarene.
A molecular polycyclic aromatic precursor bearing chlorine subtituents at keypositions forms C60 when subjected to flash vacuum pyrolysis at 1100oC.
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Scott L. T. et al.: Science 295, 1500 (2002)
Final step in the synthesis of C60.Curved lines indicate where thenew bonds are formed in the
molecular precursor 2 (C60H27Cl3).
X
X
X
X = H X = Cl1 2
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O
N
O O
OH
H3C
O
O CH3
O
HO
O
O
O
OCH3
O
OH
H
Taxol
Isolated from the pacific yew tree, total synthesis
The best-selling anticancer drug ever.
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ChemistryChemical substance:
Nuclei + electronsTypes
According to the type of interaction- Atomic single nucleus + electrons
- Molecular nuclei + electrons
- Macromolecular many nuclei + electrons
Chemical particles:
Molecules
Ions
Radicals
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- vis vitalis; 1824, Whler (Synthesis of an organic compound
from an inorganic compound) Organic Chemistry = Chemistry of Carbon Compounds
(except for the simplest carbon compounds,
e.g., carbon dioxide, hydrogen cyanide)
C, H, N, O, halogens, S, P (C + organogenic elements)
C +other elements Organoelement Chemistry> 14 Millions
Deals with structures and reactions of organic molecules
Subject of Organic Chemistry
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Topics of Organic Chemistry
Chemical bond
- MO
- Hybridization
- Resonance theory- Lewis
- Ionic bond
Stability - reactivity
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- Molecular formula
- 2D description by classic structural formula- 3D (stereochemistry)
Chemical reactivity
biological reactivity are dependent on the structure
other properties
Structurecore structure (molecule structure)electronic structure
Purpose: planning and prediction of the properties
Chemical reactions mechanism
- synthesis
- transformation: preparation of derivatives
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Classification of organic compounds
- characteristic groups- carbon skeleton
Acyclic (aliphatic)Cyclic
carbocyclic and heterocyclic compounds
monocycles polycycles- isolated polycycles- spirocycles (1 bridgehead atom)- condensed (2 bridgehead atoms)- bridged (more than 2 bridgehead atoms)
HydrocarbonsSubstituted derivatives of hydrocarbonsHeterocyclic compounds
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Organic compounds
Acyclic compounds Cyclic compounds
Saturated:
alkanes
Unsaturated:
alkenes, alkynes
Carbocycles Heterocycles
Alicycles Aromatic
compounds
Saturated
Unsaturated
Aromatic
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Unsaturated compounds
Containing C=Cdouble bonds
Containing CCtriple bonds
Alkenes Polyenes Alkynes Polyynes
H3C CH CH2 H2C CH CH CH2 HC CH HC C C CH
propene buta-1,3-diene ethyne buta-1,3-diyne
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Alicyclic compounds
Cycloalkanes Polycyclic
alkanes
Cycloalkenes Cycloalkynes
cyclohexane spiropentane cyclohexene cyclooctyne
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naphthalene phenanthrene
Aromaticcompounds
Monocycles Fused (condensed) cyclic
compounds
Monosubstituted
benzene derivatives
Polysubstituted
benzene derivatives
Linear
anellation
Angular
anellation
RR
12
3
4
5
6 ortho
meta
para
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saturated aromatic
monocycles fused
ring systems
tetrahydrofurane
unsaturated
(monocycles and
polycycles)
6H-2,3-dihidro-[1,3]-thiazine
pyridine
imidazole
indole
purine
O
S
NH
1
23
4
5
6
N
N
NH
NH
N
N
N
N
H
Heterocycliccompounds
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