Organic compounds and nomenclature: why

(1)

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.

PETER PAZMANY CATHOLIC UNIVERSITY SEMMELWEIS

UNIVERSITY

(2)

Organic compounds and nomenclature: why

‘organic’, conventions and rules

(Szerves vegyületek és elnevezésük: miért 'szerves', konvenciók, szabályok)

World of Molecules

(Molekulák Világa )

Compiled by dr. Péter Mátyus

with contribution by dr. Gábor Krajsovszky

Formatted by dr. Balázs Balogh

(3)

World of Molecules: Organic compounds and nomenclature

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)

(5)

Purpose of naming:

clear identification, e.g., one compound must have one name, or one name must correspond to one structure

Problems:

Many types of naming do exist

Chemical names (IUPAC) are complicated, too long systematic – semi-trivial – trivial names

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

OH N

H CH₃ O

(6)

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

(7)

- 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

(8)

NOMENCLATURE SYSTEMS

1. ADDITIVE name

2. RADICOFUNCTIONAL name 3. FUSION name

4. HANTZSCH-WIDMAN name 5. REPLACEMENT name

6. CONJUNCTIVE name 7. MULTIPLYING name 8. SUBSTITUTIVE name 9. SUBTRACTIVE name

(9)

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

styrene oxyde

HC CH₂ O

HC CH₂

styrene

b) Marking addition or insertion of atoms or groups:

Hydro prefix

O¹

2 3 4

5

O¹ 6 2 3 4

5 6

2,3-dihydropyrane pyrane

(10)

Homo prefix (skeleton modifying name)

Seco prefix (skeleton modifying name)

COOH

CH₂COOH

COOH

homophthalic acid phthalic acid

H CH₃

CH₃

H H

1 H

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

1 H

2

3 4 5

6 7

8 9 10

11 12

13 14

15 16 17 18

19

5β-androstane 2,3-seco-5β-androstane

(11)

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

H₃C H₂C OH H₃C I H₃C H₂C C O

CH₃

H₃C H₂C O CH₃ H₃C C N H₃C C O

Cl

methyl iodide

methyl cyanide ethyl alcohol

ethyl methyl ether

ethyl methyl ketone

acetyl chloride - Indicating the modification of a functional group

C H₂C

O

H

H₃C H₂C C

N

H H₃C

NH₂

propanal propanal hydrazone

(12)

Functional group Radicofunctional name -C≡N, -NC cyanide, isocyanide

-S-C≡N, -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 group expressed by a suffix, the others might be mentioned in the name as prefixes

- Decreasing order of seniority of functional groups:

(13)

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).

dibenzo[b,e]oxepine

O

b e

HANTZSCH-WIDMAN name

- For heteromonocyclic parent structure having no more than 10 ring members

- one or more heteroatoms

S

N

1 2

3 4 5

6 7

1,4-thiazepine World of Molecules: Organic compounds and nomenclature

(14)

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

5 1

7

8 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

C OH S

(15)

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

H₂C CH₂ COOH HOOC

COOH

benzene-1,3,5-triacetic acid

(16)

MULTIPLYING name:

Expresses multiple occurence of identical parent structures skeletons.

These are attached symmetrically, or the same rings are attached.

2

N ¹ ^1' N

2'

2,2’-bipyridine

HOOC O

O COOH

1'

2' 3'

4'

1 2 3

4

4,4’-peroxydibenzoic acid

(17)

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.

Organic and Biochemistry: Nomenclature of Organic Compounds

(18)

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

hydroxyl group → hydrogen: deoxy

ribose deoxyribose

morphine N-demethyl-

morphine

O

N O

H

O H

CH₃

H O

NH O

H

O H

H

3' 2'

1'

O

4'

OH

OH OH

5'

O H

3' 2'

1'

O

4'

OH OH

5'

O H

(19)

didehydro

CH₃

H H

H

HO

CH₃ CH₃ HH₃C

1 2 3

4 5

6

7 8 9 10

11 12

13 14

15 16 17 18

19

20 21

23

22 24

25

CH₃

H H

HO

CH₃ CH₃ HH₃C

1 2 3

4 5

6

7 8 9 10

11 12

13 14

15 16 17 18

19

20 21

23

22 24

25

cholesterol 7,8-didehydrocholesterol Increasing unsaturation:

(20)

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

HO H

H OH

CH OH

COOH H

H

HO H

H OH

CH OH O

adrenaline noradrenaline

ascorbinic acid anhydroascorbinic acid

(21)

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 CH₂ H₃C CH₂

ethylium ethanide ethyl

(22)

(23)

(24)

2 3 1

(25)

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 key positions forms C₆₀ when subjected to flash vacuum pyrolysis at 1100^oC.

(26)

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

Final step in the synthesis of C₆₀. Curved lines indicate where the new bonds are formed in the

molecular precursor 2 (C₆₀H₂₇Cl₃).

X X

X

*

X = H X = Cl

1 2

(27)

O N

O O

OH H₃C

O

O CH₃ O

HO

O O

O

O CH₃ O OH

H

Taxol

Isolated from the pacific yew tree, total synthesis

The best-selling anticancer drug ever.

(28)

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

(29)

- vis vitalis; 1824, Wöhler (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

(30)

Topics of Organic Chemistry

Chemical bond - MO

- Hybridization

- Resonance theory - Lewis

- Ionic bond

Stability - reactivity

(31)

- Molecular formula

- 2D description by classic structural formula - 3D (stereochemistry)

Chemical reactivity

biological reactivity are dependent on the structure other properties

Structure

core structure („molecule structure”) electronic structure

Purpose: planning and prediction of the properties Chemical reactions – mechanism

- synthesis

- transformation: preparation of derivatives

(32)

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

(33)

Organic compounds

Acyclic compounds Cyclic compounds

Saturated:

alkanes

Unsaturated:

alkenes, alkynes

Carbocycles Heterocycles

Alicycles Aromatic compounds

Saturated Unsaturated Aromatic World of Molecules: Organic compounds and nomenclature

(34)

Unsaturated compounds

Containing C=C double bonds

Containing C≡C triple 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

(35)

Alicyclic compounds

Cycloalkanes Polycyclic alkanes

Cycloalkenes Cycloalkynes

cyclohexane spiropentane cyclohexene cyclooctyne

(36)

naphthalene phenanthrene

Aromatic compounds

Monocycles Fused (condensed) cyclic

compounds

Monosubstituted benzene derivatives

Polysubstituted benzene derivatives

Linear anellation

Angular anellation R

R

1 2 3 4 5

6 ortho

meta

(37)

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 2 3 4 5 6

N N NH

NH

N N

N N H

Heterocyclic compounds

Organic compounds and nomenclature: why

Organic compounds and nomenclature: why

‘organic’, conventions and rules

World of Molecules

Compiled by dr. Péter Mátyus

with contribution by dr. Gábor Krajsovszky

Formatted by dr. Balázs Balogh

Table of Contents

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)

NOMENCLATURE SYSTEMS

1. ADDITIVE name

2. RADICOFUNCTIONAL name 3. FUSION name

4. HANTZSCH-WIDMAN name 5. REPLACEMENT name

6. CONJUNCTIVE name 7. MULTIPLYING name 8. SUBSTITUTIVE name 9. SUBTRACTIVE name

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

b) Marking addition or insertion of atoms or groups:

Hydro prefix

Homo prefix (skeleton modifying name)

Seco prefix (skeleton modifying name)

CONJUNCTIVE name:

Assembling cyclic systems with acyclic side chain.

Implying the loss of an appropriate number of hydrogen atoms from each.

cyclohexanemethanol

benzene-1,3,5-triacetic acid

MULTIPLYING name:

Expresses multiple occurence of identical parent structures skeletons.

These are attached symmetrically, or the same rings are attached.

2,2’-bipyridine

4,4’-peroxydibenzoic acid

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.

didehydro

cholesterol 7,8-didehydrocholesterol Increasing unsaturation:

removal of a methyl group:

nor

removal of water from two hydroxyl groups:

anhydro

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

ethane ethene ethyne

ethylium ethanide ethyl

Taxol

The best-selling anticancer drug ever.

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

- vis vitalis; 1824, Wöhler (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

Topics of Organic Chemistry

Chemical bond - MO

- Hybridization

- Resonance theory - Lewis

- Ionic bond

Stability - reactivity

- Molecular formula

- 2D description by classic structural formula - 3D (stereochemistry)

Chemical reactivity

biological reactivity are dependent on the structure other properties

Structure

core structure („molecule structure”) electronic structure

Purpose: planning and prediction of the properties Chemical reactions – mechanism

- synthesis

- transformation: preparation of derivatives