SEMMELWEIS

PETER PAZMANY

UNIVERSITY

CATHOLIC UNIVERSITY

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 ***

**Molekulris bionika s Infobionika Szakok tananyagnak komplex fejlesztse konzorciumi keretben

***A projekt az Eurpai Uni tmogatsval, az Eurpai Szocilis Alap trsfinanszrozsval valsul meg.

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World of Molecules
(Molekulk Vilga )

Organic compounds and nomenclature: why

organic, conventions and rules
(Szerves vegyletek s elnevezsk: mirt 'szerves', konvencik, szablyok)

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

semmelweis-egyetem.hu

Table of Contents
1.

Nomenclature of Organic Compounds

2.

Additive names

10

3.

Radiofunctional names

11

12

4.

Fusion and Hantschz-Widman names

13

13

5.

Replacement names

14

14

6.

Conjuctive names

15

15

7.

Multiplying names

16

16

8.

Substitutive names

17

17

9.

Substractive names

18

21

10. Chemistry everywhere

22

27

11. Organic Compounds

28

37

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IUPAC Nomenclature of Organic

Compounds
According to the recommendation of the Commission on
Nomenclature of Organic Chemistry 1993
(IUPAC: International Union of Pure and Applied
Chemistry)
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Purpose of naming:
clear identification, e.g., one compound must have one name, or one name must
correspond to one structure
O
Problems:
Many types of naming do exist
Chemical names (IUPAC) are complicated, too long
systematic semi-trivial trivial names

HN

CH3

OH
Artificial names:
1. Generic name: made by the abbreviation of the full chemical name
e.g., p-acetylaminophenol paracetamol
2. International registered names : a) proposed name
b) recommended name
3. Registered / trade names: in many cases, these are fantasy names e.g., Panadol
4. Names used in Pharmacopoeias

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Name Construction of organic compounds

1. Determining the type(s) of nomenclature operations to be used depending
on the type of compounds
- most frequently: by substitutive nomenclature
2. Determining the principal group:
- a principal group is a characteristic group, which should be named as suffix
at the end of the name of the principal chain (only one kind of the functional
groups must be cited as suffix, with the highest ranking)
3. The principal chain or ring (system) as well as the prefixes:
- the principal chain or ring (system) is such a linear chain without branching
or cyclic structure, or such an acyclic or cyclic structure with a hemisystematic
or trivial name, which has only hydrogen atoms attached and does not contain
any characteristic groups
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- principal chain, preferred ring or ring system: the one with the highest
ranking 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 principal
chain; to be listed immediately before the name of the principal chain
4. Numbering of the principal chain, preferred ring or ring system:
- in regarding to the principal group, prefixes, etc.,
5. Composition of the whole name:
- list prefixes in alphabetic order, with multiplying prefixes if these are to be
applied

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NOMENCLATURE SYSTEMS
1.
2.
3.
4.
5.
6.
7.
8.
9.

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ADDITIVE name
RADICOFUNCTIONAL name
FUSION name
HANTZSCH-WIDMAN name
REPLACEMENT name
CONJUNCTIVE name
MULTIPLYING name
SUBSTITUTIVE name
SUBTRACTIVE name

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O

ADDITIVE names:
a) The name of the compound is
made by formal attachments of
the name of the components,
without loss of atoms or groups

HC

CH2

styrene oxyde

HC

CH2

styrene

b) Marking addition or insertion of atoms or groups:

Hydro prefix

2
3

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2
3

pyrane

2,3-dihydropyrane

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Homo prefix (skeleton modifying name)

COOH

COOH

CH2COOH

COOH

homophthalic acid

phthalic acid

Seco prefix (skeleton modifying name)

18
12
11

19

CH3

1
2

10
5

12

17
16

14

5-androstane
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18

13

7
4

CH3

15

11

19

CH3

H3C

10
5

H3C

CH3

17

13

16

14
8

15

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 the
name of a parent structure or a name derived from a parent structure
- applied only for simple, acyclic compounds with halogen, or pseudohalogen groups, or
for ethers, alcohols, or oxo compounds
O
H3C

H2C

OH

H3C

ethyl alcohol

H3C

methyl iodide

H2C

CH3

ethyl methyl ketone

O

H3C

H2C

CH3

H3C

ethyl methyl ether

H3C

Cl

methyl cyanide

acetyl chloride

- Indicating the modification of a functional group

O
H3C

H2C

propanal
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N
H3C

H2C

NH2

C
H

propanal hydrazone

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- The functional group with the highest priority would be the principal group
expressed by a suffix, the others might be mentioned in the name as prefixes
- Decreasing order of seniority of functional groups:
Functional group
-CN, -NC
-S-CN, -N=C=S
>C=O
-OH
-SH
-O-OH
>O
>SO2, >SO, >S
-F, -Cl, -Br, -I, -N3
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Radicofunctional name
cyanide, isocyanide
thiocyanate, isothiocyanate
ketone
alcohol
hydrosulfide
hydroperoxide
ether, oxide
sulfone, sulfoxide, sulfide
fluoride, chloride, bromide, iodide, azide

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FUSION name
- A composite name having the maximum number of noncumulative double bonds
and at least one ortho fusion.
- Dissection of the structure into contiguous component having recognized trivial or
semisystematic names, one of which is selected as the base component. Attachment
of the other component(s) is described by prefix(es).

b
O

dibenzo[b,e]oxepine

HANTZSCH-WIDMAN name
- For heteromonocyclic parent structure having no
more than 10 ring members
- one or more heteroatoms

1
2

3
5

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
3
number of hydrogen atoms is indicated by nondetachable prefixes.
4
N2
Proper number -O- oxa; -S- thia; -NH- aza, respectively:
5
O

H3C

NH

oxacyclohexane

CH2 CH2 O

CH3

2-oxa-5-azahexane

N
8

10
9

2,7,9-triazaphenanthrene

b) Functional replacement name: replacement of an oxygen atom or hydroxy

group by another atom or group:
O
H3C

H3C
SH

thioacetic-S-acid
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S
C

S
H3C

OH

thioacetic-O-acid

S
C

SH

dithioacetic acid

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OH

hexanethio-O-acid
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World of Molecules: Organic compounds and nomenclature

CONJUNCTIVE name:
Assembling cyclic systems with acyclic side chain.
Implying the loss of an appropriate number of hydrogen atoms from
each.
CH2 OH

cyclohexanemethanol

CH2 COOH

benzene-1,3,5-triacetic acid
HOOC

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H2C

CH2 COOH

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MULTIPLYING name:
Expresses multiple occurence of identical parent structures skeletons.
These are attached symmetrically, or the same rings are attached.
N

1'

2 2'

2,2-bipyridine

3
2'

HOOC

1'

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3'

O
4'

2
1

COOH

4,4-peroxydibenzoic acid

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Organic and Biochemistry: Nomenclature of Organic Compounds

SUBSTITUTIVE name (details of this nomenclature system see in

advance part of nomenclature):
The most important names, that are recommended by IUPAC.
Substitutive name indicates the exchange of one or more hydrogen
atoms attached to a skeletal atom of a parent structure, which may be
expressed by a suffix or by prefixes.
The parent chain or ring (system) is such a linear chain without
branching or cyclic structure, or such an acyclic or cyclic structure
with 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 as parent
chain, if it is cyclic, then the ring of the highest priority would make
the parent ring.
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SUBTRACTIVE name:
Made by removal of atoms or groups from the parent structure, shown by prefixes
and/or suffixes. The added hydrogens are also indicated in the names.
a) By prefix: methyl group

hydrogen: demethyl
HO

HO

morphine

H
N

CH3

NH

HO

HO

hydroxyl group

hydrogen: deoxy
5'

5'

1'

4'

OH

OH

O
3'

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HO

HO

ribose

N-demethylmorphine

2'

OH

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1'

4'
3'

OH

2'

deoxyribose

OH

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World of Molecules: Organic compounds and nomenclature

Increasing unsaturation:
didehydro
H3C
H
18
CH3
12
11
19
1

CH3

10
5

HO

13

8
7

cholesterol
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20
17

24
23

H3C
H
18
CH3
12

CH3
25

CH3

11
19

16

14

21 22

1
2

15

HO

CH3
10

13
9

20
17

24
23

CH3
25

CH3
16

14
8

21 22

15

7
4

7,8-didehydrocholesterol
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World of Molecules: Organic compounds and nomenclature

removal of a methyl group:

nor

CH2 NH
CH

CH3

CH2 NH2

OH

CH

OH

adrenaline

noradrenaline
OH

OH

OH

OH

removal of water from two hydroxyl groups:

COOH
COOH
anhydro
ascorbinic acid

OH

OH

HO
H

HO

OH
CH2OH

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anhydroascorbinic acid
H
OH
CH2OH
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World of Molecules: Organic compounds and nomenclature

b) By suffix: removal of two or four hydrogen atoms:

-ene / -yne
H3C

CH3

ethane

H2C

CH2

ethene

HC

CH

ethyne

Loss of a hydrid anion, a proton, a hydrogen radical:

-ilium / -ide / -yl
H3C

CH2

ethylium

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H3C

CH2

ethanide

H3C

CH2

ethyl

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World of Molecules: Organic compounds and nomenclature

A Rational Chemical Synthesis of C60, the smallest stable fullarene.

A molecular polycyclic aromatic precursor bearing chlorine subtituents at key

positions forms C60 when subjected to flash vacuum pyrolysis at 1100oC.
Scott L. T. et al.: Science 295, 1500 (2002)
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World of Molecules: Organic compounds and nomenclature

Final step in the synthesis of C60.

Curved lines indicate where the
new bonds are formed in the
molecular precursor 2 (C60H27Cl3).

X
*

*
X

1 X=H

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2 X = Cl

Scott L. T. et al.: Science 295, 1500 (2002)

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World of Molecules: Organic compounds and nomenclature

The best-selling anticancer drug ever.

O

CH3
O OH

O
H3C
O
H
N

O
OH HO

O
O
O

O
CH3

Taxol
Isolated from the pacific yew tree, total synthesis
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World of Molecules: Organic compounds and nomenclature

Chemistry
Chemical substance:
Nuclei + electrons
Types
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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World of Molecules: Organic compounds and nomenclature

Subject of Organic Chemistry

- 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
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Topics of Organic Chemistry

Chemical bond
- MO
- Hybridization
- Resonance theory
- Lewis
- Ionic bond

Stability - reactivity
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core structure (molecule structure)

Structure

electronic structure

- Molecular formula
- 2D description by classic structural formula
- 3D (stereochemistry)
Chemical reactivity
biological reactivity are dependent on the structure
other properties
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)

Hydrocarbons
Substituted derivatives of hydrocarbons
Heterocyclic compounds
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Organic compounds

Acyclic compounds

Cyclic compounds

Carbocycles

Saturated:
alkanes

Unsaturated:
alkenes, alkynes

Alicycles

Heterocycles

Aromatic
compounds

Saturated
Unsaturated
Aromatic

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Unsaturated compounds

Containing C=C
double bonds

Alkenes
H3C

CH

propene

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Containing CC
triple bonds

Polyenes
CH2 H2C

CH

CH

Alkynes
CH2

HC

buta-1,3-diene

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CH

ethyne

Polyynes
HC

CH

buta-1,3-diyne

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World of Molecules: Organic compounds and nomenclature

Alicyclic compounds

Cycloalkanes

cyclohexane
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Polycyclic
alkanes

Cycloalkenes

spiropentane

cyclohexene

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Cycloalkynes

cyclooctyne

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World of Molecules: Organic compounds and nomenclature

Aromatic
compounds

Monocycles

Monosubstituted
benzene derivatives

Fused (condensed) cyclic

compounds

Polysubstituted
benzene derivatives

Linear
anellation

Angular
anellation

naphthalene

phenanthrene

1
6

3
4

ortho

meta

para
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Heterocyclic
compounds
saturated
O

tetrahydrofurane

monocycles

unsaturated
(monocycles and
polycycles)

pyridine

5
6

NH
S

6H-2,3-dihidro-[1,3]-thiazine

fused
ring systems

N
H

indole

H
N

3
2

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aromatic

N
H

imidazole

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purine
37