Natural Product Chemistry (Chm3202)Revised (1) (2)

7/23/2019 Natural Product Chemistry (Chm3202)Revised (1) (2)

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NATURAL

PRODUCTCHEMISTRY



Examples of important

drugs obtained from plants



Is the study of natural extracts which are

obtained from natural resources.

Natural product chemists extract, purify,and finally analyse compounds which are

obtained from living cells.



Techniques used are:

1. Column chromatography, CC2. Gas chromatography, GC

3. Thin layer chromatography, TLC

4. High pressure liquid chromatography,

HPLC

5. Paper chromatography

6. Electrophoresis

7. Ion exchange chromatography



These techniques allow for the separation

and purification of compounds which are

present in very small quantities. Structural elucidation of the unknown

compounds are usually carried out using

spectroscopic techniques such as:



Ultraviolet spectroscopy (UV)

Infra red spectroscopy (IR)

Nuclear magnetic resonance spectroscopy

(NMR) and

Mass spectroscopy (MS)



Primary and Secondary

Metabolism Primary metabolites are carboxylic acids

of the Krebs cycle, a-amino acids,

carbohydrates, fats and proteins. Hence, primary metabolism refers to the

photosynthesis process producing these

low molecular weight compounds. These are the starting materials – the

precursors – of the secondary metabolites.



Principal Pathways

The main streams of secondary

metabolism is outlined in the chart.

Most metabolites originate from a verylimited number of precursors.

They are linked to primary metabolism.



Acetic acid has a central position in the form of

its thioester acetyl, CoA.

It is produced in the cell, from pyruvic acid orfatty acids,or it may be directly formed from

acetate and coenzyme A with ATP.

C6H12O6 CH3CCOOH

O

CH3CHCO2H

OH

C6H12O6 + 6O2 6CO2 + H2O + energy

Glucose

Glucose Pyruvic acid Lactic acid



From acetic acid, mevalonic acid is

derived, from which via 3,3-dimethylallyl

pyrophosphate and the isomeric

isopentenyl pyrophosphate – the isoprene

unit – the terpenoids are formed.



From carbohydrates, shikimic acid is

derived which is the key to a wealth of

aromatics.

It is also important to note that amino acid

is the important precursor to a great

variety of nitrogen containing compounds.



Major Pathways:

• Shikimic acid – aromatic acids

• Acetate / polyketide –fats, oils,

aromatic and poly aromatic compounds• Mevalonic acid – Terpenoid: mono-,

sequi-, di-, triterpenoids.

• Mixed pathway

• Alkaloid

• Miscellaneous



Several groups of metabolites have mixedbiogenesis; i.e. an intermediate or

metabolite from one principal pathway acts

as a substrate for another metabolite from

a different pathway.

Thus, flavonoids are derived from a

polyketide (three acetate units) and a

cinnamic acid (shikimic acid)



The indole alkaloid comes from shikimateand a monoterpene (loganin)

In the past natural products were classified

according to structure or biological origin.

The biosynthetic scheme groups the

compounds according to the synthetic

route employed by the cell. There is

overlap.



There are 3 principal pathways: shikimic,

polyketide, and mevalonic pathways.



The Shikimic Acid Pathway

A very large number of compounds exhibit

a characteristic C6-aromatic-C3-side chain

structure. E.g. aromatic amino acids,

cinnamic acids, coumarins, flavonoids,lignin constituents, etc.

These come from a common origin.

It was found that erythrose-4-phosphate

starts the biosynthetic pathway leading to

shikimic acid.



The biosynthesis of these compounds was

elucidated by mutant studies of E.coli by

Davis and Sprinson.

Shikimic acid was isolated as early as1885 by Eykman from the Japanese plant,

Illicium anisatum long before we were

aware of its biosynthetic significance.



The biosynthesis pathway begins with

D-erythrosephosphate and

phosphoenolpyruvate (PEP) combining via

an aldol condensation.

Both these compounds were initially

derived from D-glucose.

The aldol condensation is aided by an

enzyme which adds on to the

phosphoenolpyruvate molecule to form 3-deoxy-D-arabinoheptulosonate-7-

phosphate (DAHP)



Ring closure of the heptulose derivative

(3,7-dideoxy-D-arabino-2,6-diulosonicacid) gives 3-dehydroquinic acid.

Removal of 1 H2O molecule from

3-dehydroquinic acid yields 3-dehydroshikimic acid; this acid is reduced

to shikimic acid.

At the pH of living organism, this acidexists in its anionic form, the shikimate ion.



OH

OH

HO

HO O

Shikimic acid



Phosphorylation of the shikimate anion

with adenosine triphosphate gives

shikimate-3-phosphate which then reactswith another molecule of

phosphoenolpyruvate (PEP) to yield

5-enolpyruvylshikimate-3-phosphate



OH

OH

O

O O-

P

shikimate-3-phosphate

-H+

enzyme

surface O-

OH

O

O O-

P

O

CH2

O-

O

P

H

+

PEP

O-

OO

HH

H

O

P

EnzOH

O

O O-

P

O-

O

O

OH

O

O O-

P CH2

enzyme





converts to chorismate by elimination (1,4

with respect to Hydrogen and Phosphate) Enzyme assistance is once more involved

in this conversion.



We now have the starting material for the biosynthesis ofnatural aromatic compounds.



Shikimic Acid

The structure of shikimic acid wasdetermined chemically through the

following methods:



The acid was optically active and formed

the triacetate when reacted with acetic

anhydride.

This reaction indicated the presence ofthree hydroxyl groups in the molecule.

It reacted with Br 2 (1 mole) and also with

H2 to form dehydroshikimic acid (A).



HO O

OH

OH

HO

1

2

3

45

6 H2 / Pt

HO O

OH

OH

HO

Shikimic acid 1,2-dehydroshikimic acid

(A)



HO O

OH

OH

HO

1

2

3

45

6

HO O

OH

OH

HO

Shikimic acid 1,2-dibromoshikimic acid

Br2

Br

Br

HO O

OH

OH

HO

1

2

3

45

6

HO O

OAc

OAc

AcO

Shikimic acid Triacetate shikimic acid

Ac2O



All the 3 hydroxy groups were shown to be

next to each other by oxidising the methyl

ester of the trihydroxy dehydroshikimicacid with 2 moles of periodic acid to give

the dialdehyde (B).

HO O OH C O



HO O

OH

OH

HO

OH3C O

OH

OH

HO

CH3OH

H

+

OH3C O

OO

HIO4

dialdehyde

(B)



The dialdehyde reacts with Bromine water to

give the diacid (C).

OH3C O

OO

OH3C

OO OH

Br2 water

OH



The diacid is hydrolysed by alkali to give the

triacid (D), tricarbalic (tricarboxylic acid)

OH3C

OO OH

OH

HO O

OO OHHO

Tricarbalic acid(D)

OH



Methylshikimate reacts with periodic acidunder carefully controlled conditions to

form the dialdehyde (E), which in turn is

oxidised to the unsaturated tri-acid (F),transaconitic acid by oxidation with

peroxypropionic acid and followed by

hydrolysis with base.



OH3C O

OH

OH

HO

OH3C O

OO

HO O

OO OH

HIO4

C2H5C

OOH

O

2 mol then OH-

MethylshikimateDialdehyde

(E)

Trans-aconitic

acid

(F)

OH



The C7 skeleton of shikimic acid is the

precursor in the biosynthesis of various

natural products. This include importantamino acids such as p-aminobenzoic acid,

heterocyclic amino acids such as

tryptophan and galotanin and depsideswhich involve galic acid.

COOH



OH

OH

HO

COOH

NH2

p-aminobenzoicacid

Folic acid

COOH

NH2

anthranilate(B)

N

COOH

NH2

H

Indole

C2N

Tryptophan

(A)

COOH

OH

OH

HO

Galic acid

Galotanin



The amino acid tryptophan (A) isnecessary for the metabolism processes in

mammals.

In plants tryptophan is formedbiosynthetically from anthranilate (B) by

the addition of a 5C chain.

Tryptophan is an indole derivative.



Melanin is a dark pigment present in

plants and animals.

This pigment is responsible for the colourof the hair and the skin colour of human

beings.



Another class of dark coloured pigment in

plants is catechol which is derived from

the oxidation of phenol. This pigment is referred to as catechol

melanin and is responsible for the brown

colour of cut apples and pears.



Indoliacetic acid (heteroauxin) is a plant

growth regulator.

This compound controls the formation ofthe new cells in plants and at the growing

tips.



The Acetate Pathway

C6H12O6 CH3CCOH + CH3CHCOHOO OH

O

glucose pyruvic acid lactic acid

In biochemical situations, the pH of the

media is ~7; hence, the carboxylic acidexists in its conjugate base form.



Therefore,Pyruvic acid pyruvate and

Lactic acid lactate

Pyruvate then acetate

Acetate is the starting material for the

biosynthesis of complex compounds.



Acetyl coenzyme A, CH3COSCoA

Plays an important role in many metabolicprocesses.

OO

O

CH3CCOH + CoASH + NAD+

pyruvicacid

coenzymeA

nicotinamideadenine dinucleotide

CH3CSCoA + NADH + CO2 + H+

acetyl coenzyme

A

reduced form

of NAD



Acetyl coenzyme A is the basic unit for thesynthesis of complex natural products.



Fatty acid

Fats was one of the first natural products

to be studied by chemists.

Fats are glycerol esters. A big part of the natural fatty acid are

straight chain alkanoic acids with an even

number of C atoms.



They also have double or triple bonds,

hydroxy groups or epoxy or carboxylic acidgroups.

Common fatty acids in living tissues are

stearic acid, oleic acid,palmitic acid andlinoleic acid.

Alternate arrangements (ie at 1, 4, 7) of

the cis-double bonds on these acids areespecially for most of the unsaturated fatty

acids.



COOH

Palmitic acid (C16)

COOH

Stearic acid (C18)

COOH

Oleic acid (C18)

cis-octadec-9-enoic acid

COOH

Linoleic acidcis,cis-octadec-9,12-dienoic acid

COOH

Arachidonic acid (C20)



Fatty acids usually exist as glycerol esters

(triglyceride and lecitin) or cholesterol

esters or wax esters. All these compounds are derived from

long chain fatty acids and are known as

lipids.



Lipid chemists have a special way todenote these fatty acids:

Palmitic acid = 16:0

Stearic acid = 18:0Oleic acid = 18:1 (9C)

Linoleic acid = 18:2 (9C, 12C)

Arachidonic acid = 20:4 (5C, 8C, 11C, 4C)



CH2 O

CH

CO(CH2)14CH3

O CO(CH2)12CH3

CH2 O CO(CH2)16CH3

A triglyceride

Natural fats are mixtures of triglycerides

like the one shown above and maybe with

di- and mono-glyceride.



Biosynthesis of Fatty Acids

Acetic acid is the precursor for the synthesis offatty acids.

Acetic acid is first converted to a more reactive

form, the acetylcoenzyme A.

CH3CSCoA + HS-ACP

O

CH3CSACP

O

Acetyl coenzymeA

Acyl

carrierprotein

s-acetyl acylcarrier protein

+ HSCoA

coenzyme A



A second molecule of acetylcoenzyme A reacts

with HCO3-

(bicarbonate) to yield malonylcoenzyme A.

CH3CSCoA + HCO3-

O

Acetyl coenzyme

A

-OCCH2CSCoA

O O

+ H2OX

Malonylcoenzyme A

X



The formation of malonyl coenzyme A is

followed by an acyl transfer reaction whichbonds the malonyl group to an acyl carrier

protein.

-OCCH2CSCoA

O O

Malonylcoenzyme A

+ HS-ACP

Acylcarrierprotein

-OCCH2CS-ACP

O O

s-malonyl acylcarrier protein

+ HSCoA

coenzyme A



A C-C bond is formed between the a-carbon in

the malonyl group and the carbonyl carbon ofthe acetyl group.



Reduction of the C=O group of the acetoacetyl



Dehydration of the b-hydroxy group of the acyl



Thus, the biosynthesis of hexadecanoic acid

(palmitic) can be represented by the followingequation:

Details are:



Details are:

CH3CSACP + COOHCH2CSACP

O O

CH3CCH2CSACP

O O

+ CO2 + -SACP

CH3CH2CH2CSACP

COOHCH2CSACP

CH3CH2CH2CCH2CSACP + CO2 + -SACP

O

O

OO

CH CH CH CH CH CSACP

O



CH3CH2CH2CH2CH2CSACP

COOHCH2CSACP

CH3(CH2)4CCH2CSACP + CO2 + -SACP

CH3(CH2)4CH2CH2CSACP

COOHCH2CSACP


O

OO

O

O

OO

O



COOHCH2CSACP




COOHCH2CSACP

O

OO

O

O

CH (CH ) CCH CSACP + CO + -SACP

OO



CH3(CH2)10CCH2CSACP + CO2 + SACP


COOHCH2CSACP


CH3(CH2)12CH2CH2CSACP CH3(CH2)14CSACP

S-Hexadecanoyl acyl

carrier protein

O

O

OO

O O



Flavonoid

The name flavon is given to compounds whichcontain the phenylbenzopyrone skeleton as

shown below:



Hence, flavons are heterocyclic compunds

of oxygen.

They are an important group of

compounds in the natural yellow pigment.

Flavonols (3-hydroxyflavon) and flavanons

(2,3-dihydroxyflavon) as well as

anthocyanin (flavilium salt) usually exist

together with flavon in the same plant.



This group of compounds is calledflavonoid.

Flavonoids are present in the ferns as well

as in higher plants.

It usually has hydroxyl groups at 3,5,7,3’

and 4’ as in quercetin and also usually

exists as glycosides like

Kaempherol-7-rhamnoside.



Flavonoids contribute to the beauty and

splendour of flowers and fruits in nature.

The flavones give yellow or orangecolours, the athocyanins red, violet, or

blue colours i.e. all the colours of the

rainbow but green.



The flavonoids play a major role in relation

to insects pollinating or feeding on plants

but some flavonoids have a bitter taste,repelling certain caterpillars from feeding

on leaves.



The flavonoids are structurally

characterized by having two hydroxylated

aromatic rings A and B joined by a 3C

fragment.

One OH group is often linked to a sugar.

Several substructures can be

distinguished: chalcones, flavones,

isoflavones, aurones, and anthocyanidins.



Structures of Flavonoid Compounds

HO OH

O

OH

OH

B

A

Butein (a chalcone)

2'

3'

4'

5'

6'

1

2

3

4

5

6

HO O

O

OH

OH1'

6'

5'

4'

3'

2'

OH

8

7

6

5 4

3

2

1

Luteolin (a flavone)



HO O

O

OH

Daidzein (Isoflavone)

HOO

CH

OH

OH

O

Sulphuretin (Aureone)

HO O

OH

OH

OH

OH

Cyanidin (Anthocyanidin)

2’-Hydroxy-substituted chalcones cyclize easily



2 Hydroxy substituted chalcones cyclize easily

to flavones, the structure of which is stabilized

by hydrogen bonding at C-4O and C-5O.

HO OH

O

OH

a chalcone

2'

OH

HO O

O

OH

O5 4

H

Naringenin (a flavanone)



The structural determination of Chalcone

was accomplished by alkaline degradation

which gave acetophlorophenone, p-hydroxybenzaldehyde, phloroglucinol, and

acetic acid.

OH



HO OH

O

a chalcone

2'

OH

HO OH

C

OH

CH3

O

acetophlorophenone

+

OH

OHC

p-hydroxybenzaldehyde

OH

-



HO OH

C

OH

CH3

O

OH-

OHHO

OH

+ CH3COOH

Phloroglucinol

acetic acid

Acetophlorophenone



Anthocyanidins were related to 3-

hydroxyflavones by reduction of the

carbonyl group followed by treatment withacid.

OH OH



HO O

O

OH

OH

OH

LiAlH4

HO O

OH

OH

OH

3

OH

HO O

OH

OH

OH

H+

cyanidin (an anthocyanidin)



The structure of flavone was initially

determined using alkaline hydrolysis

(Kostanecki, 1893). Chrisin (C) C15H10O4 when heated with

KOH gave phloroglucinol, acetic acid,

benzoic acid and benzophenone.



HO O

OOH

OH-

Chrisin (C)(a flavone)

OHHO

OH

Phloroglucinol

+ CH3COOH

acetic acid

+COOH

benzoic acid

+

C

O

benzophenone



For polyhydroxyflavones, methylation ofthe hydroxyl groups before hydrolysis is

important because phenol is easily

oxidised in alkaline medium.

New flavones are usually identified by

comparing their spectra with spectra of

known flavones or by comparison of the

colours with that of known flavones.

Synthesis of flavones & flavanone



Synthesis of flavones & flavanone

OHHO

OH

Phloroglucinol

+

C

CH2

Ar

C OEt

O

O

A keto ester

vacuum

C

HO Ar

OH O

OH O

HO

OH

O Ar

O

a flavone

Rearrangement (intramolecular) within molecule



Rearrangement (intramolecular) within molecule

of o-benzoyloxyacetophenone

O

C

C

O

Ar

CH2

H

O

OH

C

C

H

H

Ar O

O

O Ar

H

O

A Flavone



2’-hydroxy-substituted chalcones cyclize easily

to flavanones.

OH

OOH

H

OH

HO2'

Isomerase

O

OO

H

OH

HO

H

H

Naringenin(a flavanone)

4



Anthocyanin

Red colour, purple and blue colours of

flowers, berries, and leaves during autumn

are all due to the anthocyanin such ascyanin.

Anthocyanin are glycosides of flavilium

salts.

OH



O

Oglucose

Oglucose

HO

OH

Cyanin (an anthocyanin)

Contains the basic skeleton of flavone and was

formed by the reduction of quercetin to cyanidin.



O

O

OH

OH

OH

OH

HO

O

OH

OH

OH

OH

HO

Quercetin

Cyanidin(an anthocyanin)

Anthocyanin is biosynthesized from a flavanonethrough dihydroflavanol



through dihydroflavanol.

O

OH

O

OH

OH

OH

HO

O

OH

OH

OH

OH

HO

H

H+

OH

H+

O

OH

OH

OH

OH

HO

Cyanidin



TERPENES

We have already looked at how some

secondary metabolites were

biosynthesized from acetate through thecondensation of linear C2 units.

We shall now look at how the acetate units

are combined in a different form to yieldmevalonic acid which is then converted to

different products such as terpenes.



These compounds are found naturally in

living organisms.

They were first isolated from plants and

flowers which possess a fragrant smell.

These have long been of interest in the

olden days.

Since the 19th century, the structures of

some components of the essential oils

isolated from plants have been

discovered.



Most of these components were

unsaturated C10H16 hydrocarbons.

These compounds were named terpenes.

Apart from hydrocarbons, there were also

alcohols and ketones with similar

skeletons.

All these compounds are called

terpenoids.

These compounds have a carbon skeleton



These compounds have a carbon skeleton

which can be split into two C5 units.

These C5 units are called isopentene units orisoprene units.

Two isopreneunits

Limonene



C10 compunds are known as

monoterpenes. C15 compounds are called sesquiterpenes,

C20 as diterpenes, C30 as triterpenes, and

C40 as tetraterpenes. These compounds are classified under

terpenes (or terpenoid or isoprenoids) if

their structures can be divided into

isoprene units.

CH



C CH

CH3

CH2H2C

Isoprene(2-methyl-1,3-butadiene)

tail

head

Two isoprene units joined head to tail.



Isoprene units in farnesol

OH



Most terpenes contain one or more rings.

For e.g. a-selinene has 3 isoprene units.

CH3

CH2CH2

H3C



12

13

tail

head

Isoprene units in squalene (C30-triterpene)

Other examples of terpenes are as follows:



-phellandrene

(monoterpene)

OH

Methol (peppermint)(monoterpene)

C H

O

Citral (lemon grass)

(monoterpene)



Sesquiterpenes (C15)

HCH2CH2

OH

-selinene

(celery)

Farnesol



Diterpene (C20)

OH

Vitamin A



Triterpene (C30)

Squalene(shark liver oil)



Tetraterpene

-carotene

(

-carotene Vitamin A)

C40 2 x C20

The Biosynthesis of Terpenes



The Biosynthesis of Terpenes All terpenes and steroids have the same

biosynthetic sources.

Terpenes can be said to be biosynthesized from

mevalonate (mevalonic acid) via isopentenyl

pyrophosphate.

1. 3 CH3COH

oseveral

steps HOCCH2CCH2CH2OH

O CH3

OH

acetic acid mevalonic acid

In the 2nd step, mevalonic acid is converted to 3-

th l 3 b t l h h t (i t l



methyl-3-butenylpyrophosphate (isopentenyl

pyrophosphate)

HOCCH2CCH2CH2OH

O CH3

OH

Mevalonic acid

several

stepsCCH2CH2OPOPOH

CH3

H2C

O O

OHOH

OPP

Isopentenyl pyrophosphate(a biological isoprene unit)



Isopentenyl pyrophosphate undergoes an

enzyme catalyzed reaction and getsconverted to dimethylpyrophosphate.

OPP

H+

-H+OPP

H H

H+

-H+

OPP

Dimethylpyrophosphate



Dimethylpyrophosphate is more reactive

than isopentenylpyrophosphate tonuclephilic reagents.



Formation of C-C bond in terpenebiosynthesis.

OPP

OPP

x

-(OPP-)

OPPx

10-C CarbocationDimethylpyrophosphate

Isopentenylpyrophosphate



Loss of a proton from the carbocation to

give an alkene.

OPP

H H

OPP

Geranylpyrophosphate



Hydrolysis of the ester group yields

geraniol, a monoterpene which exists inthe rose essential oil.

OPP


H2O

OH

Geraniol



Geranylpyrophosphate is an allylicpyrophosphate and likedimethylallylpyrophosphate can react as

an alkylation reagent to isopentenylpyrophosphate.

OPP

+




xOPP

+

Isopentenylpyrophosphate

OPP

x

H H

-H+



OPP

Farnesyl pyrophosphate

H2O

OH

Farnesol

Questions:



Questions:

Write the steps for the biosynthesis of

geranylgeraniol from farnesyl

pyrophosphate

OPP

Farnesyl pyrophosphate



Higher terpenes are not formed by the

continuous addition of C5 units but bycoupling of simple terpenes.

Therefore, triterpenes are formed by the

coupling of two farnesyl pyrophosphatewhile tetraterpenes (C40) from two

molecules of

geranylgeranilpyrophosphate.



The formation of the C-C bond is a

complex process and involves the joining

of tail to tail.

The formation of geraniol and farnesol can

be said to be a dimerization of alkenes.

We now look at the formation of a cyclic

monoterpene.



OPP

OPP

+ OPP-

Geranylpyrophosphate Nerylpyrophosphate

a tertiarycarbocation

-H+



H2O HO

Limonene

-terpineol



Loss of a H+ gives Limonene a natural

product present in citrus.

Addition of H2O to the carbocation gives a-terpineol a natural product also.

The same carbocation can also give

bicyclic monoterpenes.



x x x

xxx

x

y

y

y

yy

y y



H3C

xH

H

-H+

x

H

x

+

-Pinene -Pinene



O

HH

O

HH

OH

Borneol

Formation of isopentenyl



p y

pyrophosphate

CH3CSCoA + -OOCCH2CSCoA

O O

CH3CCH2CSCoA + CO2

O O

AcetylCoenzyme A

MalonylCoenzyme A

AcetoacetylCoenzyme A



We have seen how mevalonic acid is

formed from 3 molecules of acetic acid. From mevalonic acid isopentenyl

pyrophosphate is formed.

Isopentenyl pyrophosphate is used in thebiosynthesis of terpenes.

We now look at how mevalonic acid is

formed from acetate.

CH3CSCoA

O

CH3CCH2CSCoA

O O

+



CH3CSCoACH3CCH2CSCoA

Acetyl

Coenzyme A

Acetoacetyl

Coenzyme A

+

CH3C CH2CSCoA

OH

CH2COH

O

O

-hydroxy- -methylglutaryl

coenzyme A (HMG CoA)

CoASH +

coenzyme A



CH3C CH2CSCoA

OH

CH2COH

O

O

-hydroxy- -methylglutaryl

coenzyme A (HMG CoA)

CH3C CH2CH2OH

OH

CH2COH

O

O

Mevalonic acid

Mevalonic acid has 6C.

Loss of a C atom changes it to isopentenyl



Loss of a C atom changes it to isopentenyl

pyrophosphate

C CH2

COHH3C

CH2CH2OH

-O

O

Mevalonate

C CH2

COPO3

2-H3C

CH2CH2OPP

-O

O

-PO43-

-CO2

CCH2CH2OPP

H3C

H2C

Natural Product Chemistry (Chm3202)Revised (1) (2)

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Transcript of Natural Product Chemistry (Chm3202)Revised (1) (2)