1. Chemistry of natural products
Islamic University in Madinah
Department of Chemistry
CH-3
Chemistry of natural products
Prepared By
Dr. Khalid Ahmad Shadid
Chemistry Department – Islamic University in Madinah

2. ALKALOIDS
Alkaloids Chemistry: Sertuerner in 1806 laid the foundation of Alkaloids Chemistry. It is the branch of Pharma Phyto Chemistry, which deals with the study of Alkaloids. He reported isolation of Morphine from opium.
What is Alkaloids: Alkaloids means Alkali likes. The Pharmacist W.Meissner proposed the term Alkaloids in "Alkaloids (alkali = base, oid=like sub) are basic nitrogenous compd. of plant origin which have complex molecular structure & many pharmacological activity“
 Landenberg "Alkaloids are defined as natural plant compounds that have a basic character and contain at least one nitrogen atom in a heterocyclic ring and having biological activities."
Characteristic features Alkaloids are basic nitrogenous plant origin, mostly optically active & possessing nitrogen hetero cycles as there structural units with physiological action.

3. ALKALOIDS
The previous definitions not fully correct because not follow on all alkaloids for e.g.
Colchicine: Colchicine is regarded as an alkaloid although it is not Heterocyclic and is scarcely basic.
Thiamine: It is heterocyclic nitrogenous base but not as a alkaloid because it is universally distributed in living matter.
Nitrogen as side chain: Some compound is classed as in alkaloids but they do not contain nitrogen in heterocyclic ring, but contain nitrogen inside the chain e.g. ephedrine, hordenine, betanine, muscarine, strychnine & tryptamine etc.
Colchicine
Thiamine
Hordenine
Ephedrine
Muscarine

4. Naturally occurring open chain basic compound: These compounds have physiological activity but do not class in alkaloids e.g. Cholines, amino acid, phenylethylamines etc.
Piperine: It is neither basic character nor possessing any physiological activity but include in alkaloids.
Phenylethylamines
Cholines
Piperine
Purine
Xanthenes
Caffeine
Theobromine
Those compound, which fully satisfy the definitions, like physiological active, heterrocyclic basic nitrogenous ring but they do not classed in alkaloids e.g.- Thiamine, caffeine, purine, theobromine, and xanthenes.
Pelletier 1983 “an alkaloids is cyclic compounds containing nitrogen in negative of oxidation state. Which is of limited distribution in Living organisms”.

5. Occurrence of Alkaloids
 Alkaloids are chemically nitrogenous heterocyclic basic compound occur in nature, about 15% of vascular plant & widely distributed in higher plant e.g.. -Apocynace, papaveraceae, papilanaceae, rananeulaceae, solenaceae.
They are present in the form of salts of organic acid, like acetic acid, oxalic acid, malic, lactic, tartaric, tannic, aconitic acid, few are with sugar e.g. Solanum, veratrum groups. Acc. to parts of plants:
 Leaves: Nicotine
 Bark: Cinchonine, Quinine.
 Seeds: Strychnine, Nibidine.
 Roots: Rawelfinine, Glycyrrhizin, Punarnavine I & II

6. NOMENCLATURE
There was no systematic nomenclature. But there are some methods for nomenclature are mention below.
According to their source: There are named according to the family in which they are found e.g. papavarine, punarnavin, ephedrin.
According to their Physiological response: There are named according to their physiological response e.g.. Morphine means God of dreams, emetine means to vomit.
According to there discover: There are named according to there discover e.g.. pelletierine group has been named its discoverer, P.J. Pelletier.
4. Prefixes: There are named by some prefixes are fix in nomenclature of alkaloids, e.g. epi, iso, neo, pseudo, nor- CH3 group not attach to Nitrogen.
Pelletierine

7. CLASSIFICATION Alkaloids are classified as:
Taxonomic based: According to their family e.g. solanaceous, papilionaceous without reference their chemical type of alkaloids present & another according to genus. e.g.. ephedra, cinchona etc.
Pharmacological based: Their pharmacological activity or response. For example:
Analgesic alkaloids
Cardio active alkaloids etc. Do not have chemical similarity in their group.
 Bio Synthetic based: According to this alkaloids are classified on the basis of the type precursors or building block compounds used by plants to synthesise the complex structure. e.g.. Morphine, papaverine, narcotine, tubocurarine & calchicine in phenylalanine tyrosin derived base.

8. CLASSIFICATION
Chemical classification: It is based on the chemical structure of the alkaloid. The chemical classification of alkaloids is universally adopted and depends on the basic ring structure present. For example, atropine is a tropane alkaloid; quinine is considered as a quinolinetype alkaloid; papaverine is an isoquinoline and reserpine, strychnine and ergometrine are indole alkaloids.
papaverine
atropine
tropane alkaloid
isoquinoline
Based on the chemical nature, alkaloids are further classified into two major groups as mentioned below: 1. Heterocyclic or typical alkaloids 2. Nonheterocyclic or atypical alkaloids [protoalkaloids (or) biological amines] They are further subdivided as follows:

9. Heterocyclic Alkaloids
1. Pyridines and piperidines
Pyridines
piperidines

10. Heterocyclic Alkaloids
2. Quinolines

11. Heterocyclic Alkaloids
3. Isoquinolines

12. Heterocyclic Alkaloids
4. Phenanthrenes

13. Heterocyclic Alkaloids
5. Indole alkaloids

14. Heterocyclic Alkaloids
6. Pyrrole and pyrrolidines
7. Tropane alkaloids

15. Heterocyclic Alkaloids
8. Imidazole or glyoxalines
9. Purines

16. Heterocyclic Alkaloids
10. Terpenoid alkaloids
11. Steroidal alkaloids

17. Nonheterocyclic Alkaloids

18. QUALITATIVE CHEMICAL TESTS FOR ALKALOIDS
General tests answered by all alkaloids are as follows: 1. Dragendorff’s test: To 2–3 mL of the alkaloid solution add few drops of Dragendorff’s reagent (potassium bismuth iodide solution). An orange brown precipitate is formed. 2. Mayer’s test: To 2–3 mL of the alkaloid solution add few drops of Mayer’s reagent (potassium mercuric iodide solution). White brown precipitate is formed. 3. Wagner’s test: To 2–3 mL of the alkaloid solution add few drops of Wagner’s reagent (iodine-potassium iodide solution). Reddish brown precipitate is formed. 5. For opium alkaloids: These alkaloids are present as salts of meconic acid. Opium is dissolved in water, filtered and to the filtrate, ferric chloride solution is added by which deep reddish purple colour is obtained. The colour persists even upon adding hydrochloric acid. 7. For purine alkaloids (murexide colour reaction): Caffeine is taken in a Petri dish to which hydrochloric acid and potassium chlorate KClO3 are added and heated to dryness. A purple colour is obtained by exposing the residue to vapour of dilute ammonia. The purple colour is lost upon addition of alkali. Caffeine (and other purine alkaloids) gives murexide colour reaction.

19. ISOLATION OR PRODUCTION OF ALKALOIDS
Alkaloid bearing plant usually contains a complex mixture of alkaloids The steps involved in the isolation of an alkaloid may be summarized as follows:
1. The presence of an alkaloid in a plant is ascertained by using the various alkaloidal reagents. (Refer the qualitative tests mentioned above.)
2. The next step is the separation of relatively small amount of alkaloids from large amount of extraneous plant materials.
3. The final step is the separation and purification of individual alkaloids from the crude mixture.

21. CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
Extraction: - The plants is dried, then finally powdered and extracted with boiling methanol. The solvent is distilled off and the residue treated with inorganic acids, when the bases (alkaloids) are extracted as their soluble salts. The aqueous layer containing the salt of alkaloids and soluble plant impurities is made basic with NaOH. The insoluble alkaloids are set free precipitate out. The solid mass (ppt.) so obtained is then extracted with ether when alkaloid pass into solution and impurity left behind.
Separation of Alkaloids: After detection, next step is separation of a relatively small percentage of alkaloids from large amount of crude drugs. E.g.- Opium contains 10% Morphine, Chincona contains 5-8 % Quinine, Belladona- 0.2% of Hyoscyamine.
02/08/1438
The required alkaloid is separated from the mixture from fractional, crystallization, chromatography and ion exchange method.
Flow Chart of extraction

22. DETERMINATION OF MOLECULAR STRUCTURE OF ALKALOIDS: GENERAL METHODS
CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
02/08/1438
DETERMINATION OF MOLECULAR STRUCTURE OF ALKALOIDS: GENERAL METHODS
Molecular Formula Determination: The first step in structural elucidation is the determination of molecular formula and optical rotatory power. Elemental composition and hence the empirical formula is found by combustion analysis.
Determination of Unsaturation The unsaturation can be determined by adding bromine, halogen acids or by hydroxylation with KMnO4 or by reduction (using either LiAlH4 or NaBH4).
Number of Double bond: - Number of Rings present in an alkaloids can be determine by following formula- Ca Hb Nc Od  
Then number of double bond present =
no. of hydrogen in alkane – no.of hydrogen in formula / 2 =

23. Functional Group Determination By using the usual standard chemical tests or by infrared (IR) spectroscopy, functional nature of the alkaloids is determined. (1) Hydroxyl group: - Formation of Acetate on treatment with Acetic anhydride /Acetyl chloride or benzoate on treatment with Benzyl chloride.
Then check (alcoholic-OH or phenolic –OH) + FeCl3 = color phenolic –OH
Or if Soluble in NaOH = phenolic – OH
If not Phenolic –OH:
Alkaloid +H2SO4 -> unsaturated + KMNO4 -> aldehyde or ketone or acid
By determining the amount of Acetic anhydride /Acetyl chloride or benzoate that reacted with alcohol to form an ester, the number of hydroxyl groups is determined.
If Primary amines are present in an alkaloids also give this test. Then Hydroxyl group is can be determined:
Excess of Alkali is estimated by titration with standard HCl. Number of -OH group can be calculated from the volume of Alkali used for Hydrolysis.

24. (2) Carboxylic group: - soluble in aqueous solution sodium carbonate Na2CO3 or ammonia NH3 , on treat with alcohol form ester (Esterification). Specific IR and NMR signals. - Number of -COOH group can be determined by volumetrically by titration against a standard. Ba(OH)2 or NaOH solution by using phenolphthalein as an indicator. (3) Carbonyl group: The presence of aldehydes and ketones is detected by their reaction with hydroxylamine to form the corresponding oxime
The aldehydes and ketones are distinguished by their oxidation or reduction products. The carbonyl groups of aldehydes, ketones and carboxyl are further confirmed by their spectral data such as IR, ultraviolet (UV) and NMR.

25. (4) Methoxyle group: - BY Zeisel determination method
(4) Methoxyle group: - BY Zeisel determination method. When methoxy group present in a alkaloids treated with HI at 1260C perform methyl iodide which can treated further with silver nitrites to perform silver iodide precipitate. Which estimated gravimetrically
e.g.. Papavarine.
5) Nature of Nitrogen
 Majority of nitrogen presence in alkaloids are secondary and tertiary: If tertiary when treated with H2O2 (50%) form.
Yellow ppt
Papavarine
If alkaloids react with one molecule of methyl-iodide to form N-methyl derivative, it means secondary e.g.

26. the nature of ‘N’ is confirmed by degradation methods such as Hoffmann Exhaustive Methylation (HEM). The N-alkyl groups are estimated by Herzig–Meyer method:
From the amount of silver iodide formed, the number of N-alkyl groups is calculated.

27. Degradation of Alkaloids
Degradation of Alkaloids: For discovering the structural system which incorporate these substituents groups & is tackled by degradation of the molecules by following methods:
1. Hoffmann's exhaustive methylation: - This is a composite reaction of alkaloid (Heterocyclic amines). This involves following steps:
a) The alkaloid is treated with excess of CH3I to form quartertionarey -ammoniumiodide.
Piperidine
b) 40-ammonium iodide is converted to the hydroxide and heated. The -OH of hydroxide extracts hydrogen atom from beta position and eliminate a water molecule and also the ring is cleaved at the N-atom to give an open chain 30-amine.

28. CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
02/08/1438
c) The step Ist and IInd are repeated when a second cleavage at the N-atom given an unsaturated hydrocarbon which isomerase’s to conjugated derivative.
Piperyline
The exhaustive methylation of an alkaloid is an important method for the investigation of the nature of the C-skeleton in the heterocyclic system.
2. Zinc distillation: Distillation of alkaloid over zinc dust degrades it into a stable aromatic derivative.
Zinc dust
distillation
Phenanthrene
Morphine

29. CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
02/08/1438
Papaverine
Papaverine: C20H21NO4, m.p. 147°C
UV (HC1, MeOH): λ max 325, 312, 283 and 238 nm (log 4.08, 4.12, 4.13, and 4.81 respectively). IR: υ max 3020, 2965, 2940 (CH), 2845 (OCH3), 1635 (C = N), 1520, 1510, 1485 (C = N, conjugated cyclic system), 1610, 1595 (C = C, Ar) cm-1.
1H NMR. δ 8.24 (d, H2), 7.54 (d, H1, H14,), 8.31 (s, H7,), 7.03 (s, H16), (s, H12, H13), 4.48 (s, H10 x 2), 3.90 (s, 2 x OMe), 3.68, 3.87 (s, 2 x OMe, C-17, C-18). 13C NMR: δ (d, C-l), (d, C-2), , (s, C-3), (d, C-4), (s, C-5), (s, C-6), (d, C-7), (s, C-8), (s, C-9), (t, C-10), (s, C-11), (d, C-12), (d, C-13), (s, C-14), (s, C- 15), (d, C-16), (q, C-17), (q, C-18), (q, C-19), (q, C-20).
MS: m/z 340 (12.9), 339 (69.3), 338 (95.2), 324 (100), 322 (15.0), 305 (29.0), 294 (13.4), 393 (19.5).

30. Structure of Papaverine
CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
02/08/1438
Structure of Papaverine
One of the opium constituents, papaverine has been studied particularly intensively because it has a clinical use as antispasmolytic agent. Papaverine is an optically inactive 1-benzyl-isoquinoline derivative.
1. Methoxyl determination: established that all four oxygen atoms are present as methoxyl groups proved by Zeisel determination method.
2. The structure was further elucidated from cleavage reactions leading to identifiable fragments. Thus, alkali fusion gives two fragments that account for all of the carbon atoms, a C-11-base identified as 6,7-dimethoxylisoquinoline and a C-9 ether identified as 4- methylcatechol dimethyl ether.

31. Structure of Papaverine
CHAPTER-3 CHEMISTRY OF NATURAL PRODUCTS, Prepared by Dr. Khalid Shadid
02/08/1438
Structure of Papaverine
3. The point of linkage in the isoquinoline fragment was revealed by permanganate oxidation of papaverine, which results in attack at the methylene group to give ketone papaveraldine which on heating with potassium hydroxide degrades further into 1-4 four products. 1 2
KMnO4 4 3
The position of carboxyl group in compounds 1 and 2 above, indicated that the isoquinoline unit is linked to dimethylcatechol unit at the position C1 through methylene bridge.

32. PYRIDINE ALKALOIDS OF TOBACCO
Most of these compounds are 3-pyridyl-derivatives. The main species used commercially for the production of tobacco is Nicotiana tabacum.
The main alkaloid found in almost all species of Nicotiana is: nicotine
3(1’methyl-pyrrolidin-2’-yl)-pyridine, which is levorotatory as free base.
The configuration at the C (2’) chiral center is S. Nornicotine usually accompanies nicotine as a minor alkaloid and its main origin is by the demethylation of nicotine, which occurs both in the living plant and during the curing of tobacco leaves.
The proportions of the alkaloids found using separation by TLC (thin layer chromatography) were nicotine (93%), anatabine (3.9%), nornicotine (2.4%) and anabasine (0.5%).
In recent years, using modern analytical techniques, especially gas chromatography coupled mass spectrometry (GC-MS) a large number of related alkaloids have been identified in tobacco.
Nicotine is widely distributed (24 genera, 12 families) in nature, though the amount of nicotine found in some of the species is extremely small. For example Datura stramonium was reported to contain % nicotine.
Nicotiana tabacum
nicotine

33. Nicotine Isolation of Nicotine:
Nicotine, C10H14N2, b.p. 247°C, [α]D = °
UV (ethanol): λ max 261 nm ( 5.5 x 103) IR (KBr): υ max (C = C, C = N) cm-1. 1H-NMR (D2O): δ 7.3 (m, H5), 8.55 (m, H6), (m, H2), 7.75 (m, H4), 2.16 (s, N-Me).
Nicotine is a toxic and carcinogenic alkaloid. At one time it was in wide use as agricultural insecticide, but now has been largely replaced by other chemicals.
Isolation of Nicotine:
Dried and powdered leaves and stems of tobacco plant are heated with lime when nicotine distils over. The distillate is extracted with organic solvent and when the solvent is evaporated, nicotine is left as an oily liquid, which is further purified by repeated crystallization of its oxalate salt.

34. Structure of Nicotine
Both nitrogen atoms are present as tertiary amines and one bears a N-methyl group. Chromic acid oxidation of nicotine gave nicotinic acid, which in decarboxylation yield pyridine. While distillation from lime afforded pyrrole and methylamine.
Oxidation
Nicotinic acid
Decarboxylation
Pyridine
distillation
CH3NH2 methylamine
Pyrrole

35. Structure of Nicotine
Nicotine forms two different monomethiodides on treatment with one equivalent of methyl iodide, when the methiodide with pyridine ring quaternized was oxidized with ferricyanide and then with dichromate, (-) N-methylproline was formed. These reactions led to the structure of nicotine.
Nicotine
monomethiodides
(-) N-methylproline

36. PIPERINE PIPERINE, C17H19NO3, m.p. 128-129.5 °C
UV: λEtOH max 245 nm (log 4.4). IR (KBr): υ max 3000 (aromatic C-H stretching), 1635, 1608 (sym and asym C = C stretching of diene) 1608, 1580, 1495 (C = C stretching of phenyl ring), 1635 (amide carbonyl stretching), 2925, 2840 (CH2 asym and sym stretching), 1450 (CH2 bending), 995 (C-H bending of trans CH = CH-), 850, 830, 805 (out of plane C-H bending 1,2,4-trisubstituted phenyl group) cm-1.
1H NMR: δ 5.93 (2H, H-7), 7.40(1H, H-3), 6.43(1H, H-2), 3.57(4H, H-c), 1.62 (4H,H-b), 1.62 (2H,H-a).
13C NMR: δ (C-l), (C-2), (C-3), (C-4), (C-5), (C-1’), (C-2’), (C-3’), (C-4’), (C-5’), (C-6’) and (C-7’). MS: m/z 285 (M+, 65%), 202 (29%), 201 (100%), 174 (25%), 173 (42%), 171 (26%), 143 (32%), 115 (92%).

37. PIPERINE
Piperine occurs in black pepper (Piper nigrum, Fam. Piparaceae).
The piperine content of black pepper is 6 to 11%. It is present in relatively smaller amounts in other piper species, e.g. Piper longum (~5%), P nigrum (~1.5%) Black pepper is employed commercially as a condiment. It has been used as a stimulant and a febrifuge. Piperine has insecticidal activity.
Piper nigrum
Piper longum

38. Structure of PIPERINE
Piperine on hydrolysis yielded piperidine and piperic acid, indicating that the two fragments are linked with each other by means of an acid amide linkage.
further oxidation of which gave piperonylic acid and tartaric acid.
Piperic acid has trans, trans geometry of the double bonds. (2Br2 !?)
PIPERINE
Piperidine
Piperic acid
Piperonylic

39. Piperine was synthesized (Ladenburg, 1894) by the reaction of the piperic acid chloride with piperidine, which confirmed the structure of the molecule. The synthesis of piperic acid was achieved starting from piperonal, which was obtained from catechol using Reimer-Tiemann reaction followed by the condensation with diiodomethane in the presence of a base.
Piperonal was condensed with acetaldehyde in the presence of sodium hydroxide and the product obtained was then heated with acetic anhydride and sodium acetate to yield piperic acid.
Piperonal
Piperic acid
Synthesis of PIPERINE
piperidine
Piperic acid chloride

40. Purine Bases
The purine bases contain six membered pyrimidine ring fused to the five membered imidazole ring . Purine itself does not occur in nature, but numerous derivatives are biologically significant.
The pharmaceutically important bases of this group are N-methylated derivative of 2,6-dioxypurine (Xanthine 4.304). Caffeine is 1,3,7-trimethylxanthine, theophylline is 1,3-dimethylxanthine and theobromine is 3,7-dimethylxanthine. (Figure 4.60).

41. Murexide test
A few crystals of caffeine and 3 drops of nitric acid are placed in a small porcelain dish and evaporated to dryness. Addition of two drops of ammonium hydroxide imparts a purple coloration.
The crude tea extract is spotted and developed (chloroform, ethanol, 9.5:0.5) on thin layer chromatography with silica gel (GF254 plate and sprayed with solution A [KI/I (1:2, w/w) in ethanol (100ml)] followed (after 1 min.) by solution B (25%HC1, ethanol, 1:1, v/v).
Theophylline gives a pink spot, (Rf 0.1), theobromine, a violet spot (Rf 0.2) and caffeine, yellow-brown spot, (Rf 0.6).
TLC

42. Caffeine
Caffeine, C8H10N4O2, m.p °C UV: λ max 278nm (log  4.03). IR(KBr): υ max 3034, 2950, 1700 (C = O stretch), 1660 (C = N stretch), 1604, 1548, 1440 (aromatic stretch pyrimidine moiety), 1230, 1197, 1020 (-C-N stretch) and 740 (C-H deformation) cm-1. 1H NMR: δ 3.53 (N1Me), 3.33 (N3Me), 3.98 (N7Me) and 7.54 (H-8). 13C NMR: δ (s, C-2), (s, C-4), (s, C-5), (s, C-6), (d, C-8), (q, N, Me), (q, N3-Me) and (q, N7-Me). MS: m/z 194 (M+ 100%, base peak), 165(M+-CO), 109 (C5H7N3, 66%), 82 (37%), 67(54%) and 55 (80%).

43. Structure Elucidation of Caffeine
Caffeine when subjected to Herzig Meyer’s method of N-methyl determination gives 3 moles of methyl iodide and xanthine, indicating the presence of 3-N-methyl groups.
Caffeine when oxidized with potassium chlorate in hydrochloric acid solution, yielded equimolar amounts of 1,3-dimethylalloxan, monomethyl urea, and N-methylhydantoin HI
CH3I
xanthine
1,3-dimethylalloxan

44. Structure Elucidation of Caffeine
1,3-Dimethyl alloxan on further hydrolysis gave N, N’-dimethyl urea and mesoxalic acid.
N-methylhydantoin on hydrolysis afforded N-methyl glycine together with CO2 and ammonia.
mesoxalic acid
N, N’-dimethyl urea
1,3-dimethylalloxan

45. Structure Elucidation of Caffeine
The formation of 1,3-dimethyl-alloxan indicated the presence of pyrimidine ring containing two methyl groups. Similarly formation of N-methylhydantoin revealed the presence of imidazole ring with one N-methyl substituent.
Thus oxidation studies established the position of two methyl groups at 1 and 3 positions of xanthine skeleton of caffeine.
The position of third methyl group, which may be at 7 or 9, was fixed from further oxidative degradation.
N,N′-Dimethyloxamide

46. Structure Elucidation of Caffeine
Caffeine on chlorination gave chloro-caffeine, which on nucleophilic displacement with methoxide ion yielded methoxycaffine the hydrolysis of the latter compound yields oxycaffeine.
methoxycaffine
chloro-caffeine
oxycaffeine

47. The structure of caffeine was further confirmed by total synthesis
The structure of caffeine was further confirmed by total synthesis. Traube synthesized caffeine starting from N, N’-dimethyllurea and ethylcyanoacetate.
The condensation of N, N’-dimethylurea with ethyl cyanoacetate in the presence of sodamide yields 4-amino-1,3-dimethyl-uracil 4.317, which on treatment with nitrous acid followed by reduction of the resulting compound in the presence of zinc/acid gave 1,3-drmethy -4.5-d,am,nourac,l The latter compound on treatment with formic acid underwent ring cyclization to yield theophylline. N-Methylation of theophylline yielded caffeine. (Book; Chemistry of Natural Products- Bhat.)

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