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Taras Shevchenko National University of Kyiv the Institute of Biology and Medicine Taras Shevchenko National University of Kyiv The Institute of Biology and Medicine METHODICAL POINTING from the course “Biological and bioorganic chemistry” (part 5. Classification, structure and biological role of heterocyclic compounds) for the studens of a 1 course with English of educating Compiler – the candidate of biological sciences, the associate professor Synelnyk Tatyana Borysivna Readers: It is ratified to printing by meeting of scientific advice of The Institute of Biology and Medicine (“____”________________ 2018, protocol №____) Kyiv-2018 2 CONTENT 5.1. General information ………………………………………………. 3 5.2. Heterocyclic compounds classification ……………………. 4 5.3. Nomenclature of heterocyclic compounds ………………… 6 5.4. Five-membered heterocyclic compounds with one heteroatom …………………….…………………….………………………….. 9 5.4.1. Physical properties of furan, pyrrole, thiophene .. 9 5.4.2. Chemical properties of furan, pyrrole, thiophene . 9 5.4.3. The important derivatives of pyrrole, furan and thiophene …………………….…………………….………………… 11 5.4.3.1. Pyrrole derivatives …………………….…………… 11 5.4.3.2. Furan and thiophene derivatives ……………… 22 5.5. Five-membered heterocyclic compounds with two or more heteroatoms …………………….…………………….…………… 23 5.5.1. Pyrazole derivatives …………………….………………… 24 5.5.2. Imidazole derivatives …………………….………………… 24 5.5.3. Thiazole derivatives …………………….………………… 25 5.6. Six-membered heterocyclic compounds with one heteroatoms …………………….…………………….………………………… 26 5.6.1. Chemical properties of pyridine ……………………….. 26 5.6.2. Pyridine and piperidine derivatives …………………… 27 5.7. Six-membered heterocycles with two heteroatoms …… 29 5.8. Test questions …………………….…………………….………….. 32 3 5.1. General information Heterocyclic compounds are the organic compounds contain one or more aromatic or non-aromatic rings with at least one atom (called heteroatom ) in the ring being an element other than carbon (C), most frequently oxygen (O), nitrogen (N), or sulfur (S). These compounds belong to different classes of molecules. Two thirds of all organic compounds are aromatic heterocycles. Heterocyclic compounds include many of the biochemical material essential to life. For example, nucleic acids - the chemical substances that carry the genetic information controlling inheritance – are built from nucleotides that contain heterocyclic compounds - purine and pyrimidine bases (Fig. 5.1). Fig, 5.1. The structure of adenine nucleotide – adenosine-5’-monophosphate (AMP) In addition, many naturally occurring pigments , vitamins , and antibiotics belong to this class of organic compounds. Most pharmaceuticals are heterocycles. In particular, quinine , whose formula is shown in Fig. 5.2, is used for malaria treatment for 400 years. Quinine Fig, 5.2. The structure of quinine Heteroatom can be represented by N, О, S, В, Al, Si, P, Sn, As, Cu, but more often - by N, О, or S (Fig. 5.3). 4 Fig, 5.3. The structures of the most widespread heterocyclic compounds 5.2. Heterocyclic compounds classification There are two main ways of heterocyclic compounds classifying: • By ring size • Aromatic/non aromatic When classification based on the ring size is used, heterocyclic compounds can be divided into three-, four-, five- and six-membered ones (Tab. 5.1). Seven-, eight- or more-membered heterocyclic compounds are less common. Table 5.1. The examples of three-, four-, five- and six-membered heterocyclic compounds Three-membered Four-membered Five-membered Six-membered In addition there are the fused rings-containing heterocyclic compounds (they have two ore more rings joined at two adjacent atoms) (Fig. 5.4). 5 Fig, 5.4. The formulas of the heterocyclic compounds with fused rings in their structures Nonaromatic heterocyclic compounds have physical and chemical properties that are typical of the particular hetero atom (Fig. 5.5): • tetrahydrofurane and 1,4-dioxane are typical ethers • 1,3,5-trioxane behaves as an acetal • pyrrolidine and piperidine are typical secondary amines • the bicyclic compound quinuclidine is а tertiary amine . Fig, 5.4. The structures of some nonaromatic heterocyclic compounds Aromatic heterocyclic compounds include such compounds as pyridine , where nitrogen replaces one of the СН groups in benzene, and pyrrole , in which the aromatic sextet is supplied by the four electrons of the two double bonds and the lone pair on nitrogen: Other aromatic heterocycles contain more than one hetero atom, and still others contain fused aromatic rings. Examples which we will treat in more detail later include oxazole , indole and purine : 6 5.3. Nomenclature of heterocyclic compounds Systematic nomenclature system is used for naming 3-10-membered monocyclic heterocyclics of various degree of the unsaturation containing one/more heteroatoms. It specifies the following characters such as: - the ring size (3-, 4-, 5-, 6-, 7-, 8-membered ) - the type of heteroatom - the position of heteroatom - one/more heteroatom etc. The commonly used names for heterocyclic compounds are their trivial names. Systematic nomenclature of heterocyclic compounds: the Hantzsch- Widman system The compound formed by replacing а carbon by а hetero atom is named by an appropriate prefix (Tab. 5.2): • aza for nitrogen (N), • оха for oxygen (O), • thia for sulfur (S). Table 5.2. The principle of heterocyclic compounds names forming_1 Heteroatom Prefix O oxa S thia N aza Saturated and unsaturated monocyclic rings are named according to ring size (Tab. 5.3). Table 5.3. The principle of heterocyclic compounds names forming_2 Ring Size 3 4 5 6 Suffix Unsaturated irene ete ole ine Saturated irane etane olane inane 7 When two or more the same heteroatoms are present, the prefixes “di”, “tri” , etc. are used: When a maximally unsaturated ring includes a saturated atom, its location may be designated by a "# H" prefix to avoid ambiguity. The examples of systematic and trivial names of some heterocyclic compounds with one heteroatom are given on Fig. 5.5. Fig, 5.5. Trivial (black) and systematic (blue) names of some heterocyclic compounds with one heteroatom In a monocyclic compounds that contain only one heteroatom numbering starts at this atom. When more than one heteroatoms are present , the ring is numbered to give the substituents or other heteroatoms the lowest number possible with the ending : If the heteroatoms are different they are named in the order of “O, S, N,” etc. by combining the prefixes (Tab. 5.2) in the order of preference: oxygen is considered to be older, then sulfur and then nitrogen Therefore, in the presence of oxygen and nitrogen in the ring, numbering begins with oxygen): 8 Exceptions and modifications of nomenclature of the Hantzsch- Widman system Saturated 5-membered heterocycles with nitrogen as heteroatom should use respectively the traditional " olidine " suffix. Established use of oxine and azine for other compounds prohibits their use for pyran and pyridine respectively. Trivial names are also often used for fused aromatic rings-contained heterocyclic compounds (Fig. 5.6). Fig, 5.6. Trivial (black) and systematic (blue) names of some fused aromatic rings- contained heterocyclic compounds 9 5.4. Five-membered heterocyclic compounds with one heteroatom The main examples of five-membered heterocyclic compounds are aromatic heterocycles pyrrole, furan and thiophene: 5.4.1. Physical properties of furan, pyrrole, thiophene At room temperature, thiophene is a colorless liquid with a mildly pleasant odor reminiscent of benzene, with which thiophene shares some similarities. Like benzene, thiophene forms an azeotrope with water. Furan is typically derived by the thermal decomposition of pentose-containing materials, cellulosic solids especially pine-wood. Furan is a colorless, flammable, highly volatile liquid with a boiling point close to room temperature. It is toxic and may be carcinogenic. Pyrrole is a heterocyclic aromatic organic compound. Substituted derivatives are also called pyrroles . Porphobilinogen is a trisubstituted pyrrole, which is the biosynthetic precursor to many natural products. 5.4.2. Chemical properties of furan, pyrrole, thiophene The most typical reaction of furan, pyrrole and thiophene is electrophilic substitution. All three heterocycles are much more reactive than benzene, the reactivity order being: The most reactive The less reactive 10 1. Interaction with mineral acids: Pyrroles are polymerized by even mineral acids, probably by such mechanism as the following: 2. Reduction reactions for furan, pyrrole and thiophene follow the scheme : Pyrrole Pyrrolidine Ni 2 H + 2 O O tetrahydrofuran furan Pd 2 H + 2 S S thiophene tetrahydrothiophene 3. Reactions of oxidation – their examples for furan and pyrrole are given below: O O O O O V2O5 furan maleinic anhydride O O NH O H2Cr 2O4 NH maleinmide pyrrole 4. Reactions of electrophilic substitution are typical for all of these aromatic heterocycles: 11 For furan: For thiophene : Nitration Acetylation Sulfonation Bromination Polyhalogenation 5. Reciprocal transformation of furan, pyrrole and thiophene (Yurie`s cycle reactions): Pyrrol H2S NH 3 NH 3 H2O H2S H2O Thiophene Furan For identification of pyrrole and furan the method coloring of a pine chip is used. Couples of pyrrole painted a pine chip soaked in hydrochloric acid in the red colour and furan - in the green colour. Qualitative reaction on thiophene is indophenin`s reaction: a mixture of izathine with concentrated sulfuric acid painted in the blue colour. 5.4.3. The important derivatives of pyrrole, furan and thiophene 5.4.3.1. Pyrrole derivatives The main
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