0006 a Molekulak Vilaga II

8/10/2019 0006 a Molekulak Vilaga II

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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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0006 a Molekulak Vilaga II