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© Institute of Medical Biochemistry and Laboratory Diagnostics of the General University Hospital and of The First Faculty of Medicine of Charles University in Prague - 2005-2016

Introduction to Medical Introduction to Medical Chemistry and BiochemistryChemistry and Biochemistry

Medical Chemistry and Biochemistry

Winter term – 2nd year

3

Chemistry

Organic chemistry

Biochemistry

Inorganic chemistry

Synthesis of urea (Wöhler 1828) (Thermic rearrangement)

Friedrich Wöhler (1800-1882): Organic compound formed from inorganic compoundsJan Horbaczewski (1854-1942): He graduated on the Faculty of Medicine in Wienna by prof. Ludwig; Founder of the Department of Medical Chemistry

O NH4CNNH2

NH2

TeploO C

Heat

Synthesis of uric acid Synthesis of uric acid (Horbaczewski 1882 – age of 28)

O CNH2

NH2

+ H2C C

NH2

O

OH

Teplo

NH

NH

NH

NH

O

O

O

Urea + Glycine + (heat) = Uric acid(very low efficiency)

(discovered by Schulz 1776)

heat

4

During further experiments he proved that uric acid is formed by decomposition of nucleus-containing cells only, this process was not observed in cells without nucleus (e.g., erythrocytes)He successfully separated uric acid from xanthine and other purine bases and correctly supposed that uric acid is formed from these substances.

NH

NH

NH

NH

O

O

O

Acrylic acid Uric acid

Synthesis of uric acid (Horbaczewski 1882)

OHO

C

HC

CH2

5

6

Professor M.D. Ivan HorbačevskýFounder of the Czech medical chemistry and biochemistry

•Born May 15, 1854 in Zarubince by Tarnopol (Ukraine)

•Medical faculty in Vienna (Austria) (graduated 1880)

•Assistant in Laboratory for applied chemistry in Vienna (1880-1883)

•Professor (1883 in Prague)

•Head of the ”Department of medical chemistry” in Prague (1883-1917)

•Dean of the Czech medical faculty (1890, 1894, 1904, 1911)

•Rector of the Czech university in Prague

•Professor of Ukrainian Free University (1920-1939)

•Died May 24, 1942 in PragueIntrod.Gen.Med. 2015/16

7Introd.Gen.Med. 2015/16

8Introd.Gen.Med. 2015/16

The bond polarity depends on the difference of electronegativities. Presence of polar and non-polar bonds significantly affects the resulting character of the organic compound:

Bind distance and binding energy - examples

Bonds in organic compounds

Bond Energy [kJ.mol-1] Distance [pm]

C-C 347 154

C=C 611 133

CC 837 120

C-H 414 106

C-N 293 147

CN 891 116

C-O 352 143

C=O 732 122

N-H 389 101

O-H 464 100

Values of energy are approximate („average“). In molecules are influenced by surrounding structures, i.e., by other parts of the molecule. There are s. c. hybrid (partial) bonds (e.g., benzene – 1.5). 9

Constitution: Inner structure of the molecule of organic compounds

Stereochemistry (Three-dimensional structure of organic compounds) – Formulas of organic compounds

Molecular formulas are in organic chemistry practically inapplicable, because they do not yield the most important information about the inner structure of the molecule.

e.g., C2H6O can be :

1) Ethanol (CH3-CH2-OH)

2) Dimethylether (CH3-O-CH3) Therefore, the structural formulas are used, because they show all bonds among atoms. Disadvantage of such formulas consists in their complicity in case of more complicated compounds. Most frequently the rational formulas are used, in which are marked out only such bonds, which are necessary for unambiguous determination of the constitution – three dimensional configuration. For absolutely exact definition of 3D organization of the organic molecule, it is necessary to use perspective formulas (the bonds aiming upwards and downwards, forwards, backwards are differentiated). The use of models, which can help by solving of e.g. DNA structure (Watson and Crick - Nobel prize for chemistry), seems to be optimal. The computers can simplify significantly the work with such models.

10

Why are isomers important in biochemistry ?

• isomers (tautomers, e.g.) have different chemical features

• differ in their actions in biological systems• all the enzymes are specific to structure of all the

compounds in reactions which are catalysed by them – stereochemistry is substantial property of all processes

in biological systems

11

Introd.Gen.Med. 2015/16 12

Isomers

Isomers: Isomers are molecules, which have the same molecular formula, but they have a different arrangement of the atoms in space.

Isomers I. Basic types of isomerism:

Constitutional (Structural) isomerism: Isomers have different constitution, i.e., they have a different arrangement of the atoms in space or in molecule.Chain: Butane, isobutene (arrangement of chain)Position: chains have variable amounts of branching

(groups: 1-propanol, 2-propanol)(bonds: 1-buten, 2-buten)

Tautomerism - Isomers differs in the position of the hydrogen and double bond, e.g., acetamide (Amide of acetic acid)

The dynamic equilibrium is established between both tautomers.

H3C CO

NH2N

OCH3C

H

H

13

Constitution isomers

• Citric acid

• Isocitric acid

OH

OO

HO

O

OH

OH

OH

OH

O

OH

O

O

OH

14

Tautomerism• Tautomers – isomers differing in the position of hydrogen

and double bond

– C2H4O gives either :

acetaldehyde

or vinylalcohol :

oxo – enol tautomerism, Typical for aldehydes a ketonesstabilization by mesomery

more stable

less stable

COHC

H

H

H

COC

H

HH

H

15

Tautomerism

CH3

CCH2

C

O O

O- CH3

CCH

C

OH O

O-

tautomerism of acetoacetic acid esters

16

Tautomerism in uracil

N

N

OH

OH NH

N

OH

O NH

NH

O

O

17

Isomers II.

Keto (oxo) form Acetoacetic acid enol form

Keto-enol-tautomerism is best known

CH3 C CH2 COOH

O

CH3 C CH COOH

OH

Conformation of the molecule is given by the free rotation of molecules along single bonds. There are (theoretically) possible (by more complicated molecules) large amounts of conformations; they are limited by energy of the positions and by weak bonds (hydrogen bridges, ionic and non-polar interactions).

18

Introd.Gen.Med. 2015/16 19

Isomers III. Stereoisomerism (spatial): the bond structure is the same, but the geometrical positioning of atoms and functional groups in space differs.Various configurations are given by double bond (cis-trans isomers) or by presence of a chiral center (an asymmetric carbon C*).

cis-trans (geometric) isomerism is a result of the impossibility of the rotation along the double bond (it is caused by binding-orbitals).

cis-2-butene trans-2-butene

CH3C C

CH3

H H

H

H CH3CC

CH3

Stereochemistry• Describes the ways atoms are organized in

three-dimensional arrangement as well as relationships between different compounds

• Configuration– Geometric isomerism (cis-trans)– Optical isomerism and chirality

• Conformation– Rotation isomerism– Non-covalent and trans-annular interactions

20

Stereochemistry – basic terms

• Configuration – the way atoms in molecule are arranged one to another in space– always only single possibility – cannot be changed without bound breakage

• Conformation – groups of atoms are arranged in molecules that enables free rotation along single bonds– Free rotation can be disabled due to the size of the

functional groups=steric strain or weak bonds (e.g., hydrogen bridges)

21

Conformation

• No conformation structure is the only possible arrangement of the compound

• It is only one of the possible existing states in which higher or lower number of molecules of the compound can exist in– All those states can rearrange one to another without

breakage of any bond

22

Conformation of aliphatic compounds

• One compound can in theory give uninfinitive amount of conformers

• Conformers cannot be isolated neither by chemical nor physical techniques

• They differ only in their energy

23

Visual representation of molecules

• Perspective drawings provide a visual representation of stereochemistry

• different kinds of projections – Newman projection for conformation isomers

• molecular models

24

Molecular models

• Molecular models serve for visualisation of the three-dimensional arrangement of one or more molecules

• Mechanical models– wire models– Kalotte models

• Computer modelling – can also provide properties of the molecule based on molecular calculation methods which can be used e.g. for new drug syntheses

25

Butane - projections

CH3

CH2

CH2

CH3

butane

CH3

CH3

CH3

CH3

H CH3

H CH3

H

H

H

H

H

H

H

H

HCH3

HCH3

H

H

H

H

H

HH

H

Newman projectionsighting along C2-C3bond

26

Butan – 4 different conformation isomers • Anti-conformation has less

energy of all and therefore it is the most probable conformation

A Eclipsed

H CH3H CH

3

HH

HH

B G auche

H CH3 H CH

3

H

HH

H

C Eclipsed

H CH3

H

HH

H

H CH3

D Anti

H CH3

H

H

H

H CH3

H

H CH3

H CH3

H

H

HH

E G auche

E

Degrees of Rotation

A A

E

CC

D

B

30060 120 180 2400 360

27

Conformation of cyclic compounds

• Cyklopropane – planar molecule, diminished bond angle – higher energy

• Cycles with six or more carbon atoms – non planar conformations, lower energy

• free of angle strain

Introd.Gen.Med. 2015/16 28

chair, boat, twisted form

low energy, the most stable high energy, less stable conformation

29

Cyklohexane, chair conformation, low energy, favorable

• Axial bounds– perpendicular to the

cycle plane (vertical)• Equatorial bounds

H

HH

H

H

H

H

H

H

H

H

H

H

HH

H

H

H

H

H

H

H

H

H

All of them having antiperiplanar butane interactions30

Geometric isomers in cyclic compounds

• Substituents can be situated on the same side of the cycle plane or on opposite sides

• Cis ….on the same side • Trans….opposite

H

HH

H

H

H

H

H

H

H

H

H

31

Cis-trans isomerscyclohexane

H

HH

H

H

H

H

H

H

R1

H

R2

R1

HR2

H

H

H

H

H

H

H

H

H

(ee) (aa)

1,2 – trans - isomer

32

Cis - trans isomers• occur not only in cyclic compounds• whenever we can find out a reference plane • double bonds : π bound is the reference

– Substituents on the same sides…cis– Different sides……………… trans

C C

CH2

CH3 CH2

CH3

CH3

CH3

(3E)-3,4-dimethylhex-3-ene

C C

CH2

CH3

CH2

CH3 CH3

CH3

(3Z)-3,4-dimethylhex-3-ene33

Example

• maleic acid – Cis, Z isomer

• fumaric acid– Trans, E isomer

H

OH

O

H

OH

O

H

OH

OH

OH

O

34

Is that of any use in medicine ?• Steroids : on cis or trans mutual configuration of

A and b cycles depends biological activity

O

OH

5α – Androstan-17-ol-3-onStanolon, StanazolOne of the most potent anabolicsKonfiguration trans (between A and B)

5ß-androstan-3,17-dionexcreten by urineMetabolite free of any androgenic acticitykonfiguration cis between A and B

Podle Pádr Z., Hanč O.: Hormony, Academia, 1982

O

O

35

Peptides

• Amides with trans configuration of side chains towards plane of the amide bound

• Why trans ? – Steric effect

• In cases when side chain is “small” cis configuration is also possible

36

Tripeptide

O

NH2

OH

NHO

NH2

CH3

O

OH

NH

Ala-Tyr-Lys

37

Isomers VI.

Asymmetric carbon has each bond occupied by completely different single-bonded atom or group of atoms, therefore the structure has not any symmetry plane. There exit two possible space arrangements: subject and its mirror image. By their differentiation we go out from structure of glyceraldehyde:

D- and L- isomers are characterized by equal chemical reactivity, but biochemically can differ mutually substantially (reactions with enzymes or antibodies)

C

C

CH2OH

O H

OHH HO H

HO

CH2OH

C

C

D- L-Compounds containing asymmetric carbon show optical rotation and they form optical antipodes - enantiomeres. Rotation is labeled: (+) – to the right and (-) – to the left. The aim of light rotation is not connected with the D- and L- labeling!!!!!

38

Assymetry and optical activity• Each carbon can have 4 substituents

– having 4 different substituents we speak about “assymetric carbon”=stereogenic center=chiral center

• molecule with at least one stereogenic center on it is called an optically active molecule– if you take the molecule, put it into a beaker and shine

plane polarized light the light will not come straight out but will be shifted

– optical activity is not only caused by assymetric carbon but depends whether molecule is chiral or not

39

Chirality, enantiomers

• When is a molecule chiral?– it has at least one center of chirality

– must be unsuperimposable with it`s mirror image

• Enantiomer– optical isomers that have almost all properties identical

(melting points, solubility, spectroscopic properties)

– BUT differ when interacting with plane-polarized light

– enantiomers have opposite directions of optical rotation

40

Assymetric carbon – example of enantiomersC2H5

i-Pr

Me

H

C2H5

i-Pr

Me

H

≠

Mixture 1:1 of both enantimers is called racemic mixture and is not optically active sign of optical rotation (+) or (-) is not related neither to L- or D- or R, S prefixes! There is no straightforward correlation betweenconfiguration and direction or magnitude of optical rotation!

41

Relative configuration – Fischer projection

• older way how to verbalize stereochemical configuration

• Two basic compounds which serve as reference for other – similar – compounds D(+) - glyceraldehyde – for configuration of carbohydrates

• L(+) – serine– for natural α-aminoacids

42

Glyceraldehyde and serine

• D(+) L(-) glyceraldehyde

• D (+) L (-) serine

O

OH

H OH

O

OH

HOH

O

NH2

OH

OH

H

O

NH2

OH

OH

H

Introd.Gen.Med. 2015/16 43

Absolute configuration at a chirality center

• verbal indication of the arrangement of atoms at a chirality center

• = configuration at a chirality center in the three-dimensional system

• Stereochemistry nomenclature and sequence rules according to Cahn, Ingold and Prelog

44

Sequence rules for specification of absolute configuration

• those rules are really abbreviated and do not cover all possibilities. Students wishing to have deeper knowledge should study textbook of organic chemistry.

• 1. assign priorities to all four atoms directly attached to chirality center. The highest atomic number is first, the last (priority 4) is the lowest atomic number.

• 2. Orient the molecule so that the group with lowest priority (=4) is pointing away from us

• 3. If a curved arrow, drawn from the highest to the lowest priority substituent goes counterclockwise, than it is R-configuration– of course, counterclockwise is S

45

3-methylhexane

• (R)- izomer

C2H5

i-Pr

Me

H

direction of the observation

1

2

3

46

Diastereomers• you always need more than one chirality center

in a molecule, when thinking about diastereomers

• diastereomers are two molecules that are nonsuperimposable , non-mirror images of one another

• In practice, you must calculate each chirality center's configuration in order to determine whether two molecules are diastereomers

• If on one center you have opposite configuration and the same on another, than you have diastereomers

• two opposite – enantiomers, two same – identical compound

47

Meso compounds

• as for diastereomers you need more than one chiral center

• if there are two centers,both having the same atoms or groups as substituents

• one beeing R and the second S,• 1. the molecule has the plane of symmetry• 2. it is not optically active compound• 3. it is only one compound (no pair of meso)• 4. IT IS a MESO COMPOUND

48

Enantiomers have different biological activity – an example

• Contergan – thalidomid

• Assymetric carbon marked with *

• R enantiomer …sedative and antiemetic activity• S enantiomer… inhibitor of angiogenesis• during yrs.1959-61 pregnant women from 28 countries were

treated in order to relief nausea and vomitting associated with pregnancy.Contergan,a drug used for this purpose, was a racemic mixture.

• Those women gived birth to more than 12 000 children with serious malformation

NHN

O

O

O

O

*

49

Classification of organic compoundsOrganic compounds

Aliphatic Cyclic

Saturated (single bonds)

Unsaturated (multiple bonds)

Isocyclic (carbocyclic,C only) Heterocyclic (in

ring are other atoms then C)

Alicyclic

Saturated Unsaturated

Aromatic (conjugated double bonds in ring)

Saturated Unsaturated Aromatic50

Most important arenes IBenzene

Naphtalene

Anthracene

Tetracene

(partly hydrogenated „tetracycline“)

Phenanthrene

Cyclopentano perhydrophenanthrene - base of steroids

51

Most important arenes II

Pyrene

Benzopyrene (carcinogenic)

Biphenyl (Polychlorated biphenyls

- toxic for CNS of children)

Diphenylmethane

Base of DDT –

p,p’-dichloro diphenyl trichloroethane

C

H

H

1,1,1-trichloro-2,2-bis(p-chlorophenyl) ethane

52