STRUCTURE, CHEMICAL PROPERTIES OF HETEROCYCLIC COMPOUNDS. STRUCTURE, COMPOSITION AND PROPERTIES OF NUCLEOSIDES, NUCLEOTIDES AND NUCLEIC ACIDS.

STRUCTURE, COMPOSITION AND PROPERTIES NUCLEIC ACIDS. HETEROCYCLIC COMPOUNDS. COMPARISON WITH CARBOCYCLIC COMPOUNDS

 

 

n  Heterocyclic compounds are cyclic compounds in which one or more ring atoms are not carbon (that is hetero atoms).

As hetero atom can be N, О, S, В, Al, Si, P, Sn, As, Cu. But common is N, О, or S.  

Heterocycles are conveniently grouped into two classes, nonaromatic and aromatic

 

n  By size of ring

Three-membered

Four-membered

 

Five-membered

 

Six-membered

 

The molecules of organic chemical compounds are built up from a framework or backbone of carbon atoms to which are attached hydrogen (H), oxygen, or other heteroatoms. Carbon atoms have the unique property of being able to link with one another to form chains of atoms. When the ends of the chains are joined together into a ring, cyclic compounds result; such substances often are referred to as carbocyclic or alicyclic compounds. Substitution of one or more of the ring carbon atoms in the molecules of a carbocyclic compound with a heteroatom gives a heterocyclic compound.

Five - membered heterocyclic compounds with one heteroatom.

The structures of these three heterocyclic would suggest that they have highly reactive diene character.

These heterocyclic have characteristics associated with aromaticity.

 

A typical carbocyclic compound is cyclopentane (C₅H₁₀), the molecular structure of which is indicated by the formula

 

in which the chemical symbols represent atoms of the elements and the lines represent bonds (see covalent bond) between the atoms. For convenience such formulas are often written in simplified polygonal form, such as

 

for cyclopentane, in which each corner of the polygon represents a carbon atom (it being understood that hydrogen atoms are joined to the carbon atoms as required).

When one of the carbon atoms of cyclopentane is replaced with an atom of nitrogen, the compound pyrrolidine, a chemical relative of pyrrole, is produced. The structural formula of pyrrolidine is written:

 

Other heterocyclic compounds can be envisioned similarly as derivatives of cyclopentane by substitution with other heteroatoms or of other carbocyclic compounds by substitution with nitrogen or other heteroatoms.

The simplest organic compounds are the hydrocarbons, compounds of carbon and hydrogen only. Hydrocarbons are classified as saturated if all four possible bonds of every carbon atom are joined singly to another carbon atom or to a hydrogen atom. They are classified as unsaturated if they contain a double or triple bond between any two of the carbon atoms, and they are classed as aromatic if they contain at least one ring, all atoms of which are joined by alternating double and single bonds. Nonaromatic unsaturated compounds are highly reactive—that is, they readily undergo additions of atoms or groups of atoms to the carbon atoms of their double bonds, giving each carbon four substituents. Aromatic compounds, though having double bonds, are extremely stable and do not readily undergo the addition reactions characteristic of other unsaturated compounds. The stability and unreactivity of, for instance, a six-membered aromatic ring are associated with the presence of three pairs of electrons, called pi (π) electrons, associated with the three double bonds of the ring. Together these electrons, constituting the so-called aromatic sextet, form an unusually stable structure associated with the aromatic ring as a whole rather than with the individual pairs of atoms.

Heterocycles too may be classified as saturated, unsaturated, or aromatic. Thus, as shown in the following structural formulas, pyrrolidine is a saturated heterocyclic compound containing no double bond; 4,5-dihydrofuran is an unsaturated heterocyclic compound; and pyridine is a typical heterocyclic aromatic, or heteroaromatic, substance. In the two structural formulas given for pyridine, the first shows the double bonds, whereas the second represents the aromatic sextet with a circle.

 

This classification relates the chemistry of heterocycles directly with that of carbocyclic derivatives, which are usually better known. In general, synthetic methods and physical and chemical properties of the saturated and the partly unsaturated heterocyclic compounds closely resemble those for their acyclic (noncyclic, or open-chain) analogs. Thus, pyrrolidine may be considered as a cyclic secondary amine and has much in common with the corresponding acyclic amine, diethylamine, which is represented by the formula:

Similarly, 4,5-dihydrofuran mirrors many of the properties of the corresponding unsaturated ether, ethyl vinyl ether, which has the formula:

Nomenclature of heterocyclic compounds

 

Naming heterocyclic compounds is complicated because of the existence of many common names in addition to the internationally agreed-upon systematic nomenclature. (A brief account of systematic nomenclature is given here; for more information, see below Major classes of heterocyclic compounds.)

The types of heteroatoms present in a ring are indicated by prefixes; in particular, oxa-, thia-, and aza- denote oxygen, sulfur, and nitrogen atoms, respectively. The numbers of heteroatoms of a particular kind are indicated by number prefixes joined to the heteroatom prefixes, as dioxa- and triaza-. The presence of different kinds of heteroatoms is indicated by combining the above prefixes, using the following order of preference: oxa- first, followed by thia- and then aza-.

In addition, partially saturated rings are indicated by the prefixes dihydro-, tetrahydro-, and so on, according to the number of “extra” hydrogen atoms bonded to the ring atoms. The positions of heteroatoms, extra hydrogen atoms, and substituents are indicated by Arabic numerals, for which the numbering starts at an oxygen atom, if one is present, or at a sulfur or nitrogen atom and continues in such a way that the heteroatoms are assigned the lowest possible numbers. Other things being equal, numbering starts at a nitrogen atom that carries a substituent rather than at a multiply bonded nitrogen. In compounds with maximum unsaturation, if the double bonds can be arranged in more than one way, their positions are defined by indicating the nitrogen or carbon atoms that are not multiply bonded and that consequently carry an extra hydrogen atom (or substituent), as follows: 1H-, 2H-, and so on.

Physical properties of heterocyclic compounds

Physical properties are important as criteria for judging the purity of heterocycles just as for other organic compounds. Organic compounds generally show great regularity in their physical properties, and heterocycles are no exception.

The melting point was once a widely used criterion for purity, but it has been increasingly superseded by optical spectra, based on light absorption; mass spectra, based on relative masses of molecular fragments; and magnetic resonance spectra, based on nuclear properties (see spectroscopy). Nevertheless, knowledge of melting and boiling points is still helpful for judging the purity of a compound.

 

Introduction to Heterocyclic Compounds

Heterocyclic compounds are cyclic compounds that contain atoms other than carbon in their ring. The figure above shows just a few single-ring heterocyclic compounds. The ones shown are simply 5 and 6 membered rings. There are smaller and larger rings and there are also multiple ring heterocycles.

Heterocyclic compounds play a big role in organic chemistry and because they have different electron configurations from carbon, they react differently from carbon rings and differently from each other. Later in this book we will discuss several specific heterocyclic compounds that are very commonly used in organic chemistry and we'll discuss their individual characteristics.

For now, it's simply important to know what a heterocyclic compound is.

 

Chemical properties of organic compounds

 

Chemical properties of furan, pyrrole, thiophene

   The typical reaction of furan, pyrrole, and thiophene is electrophilic substitution. All three heterocycles are much more reactive than benzene. The reactivity order being is:

 

To give some idea of the magnitude of this reactivity order, partial rate factors (activities related to benzene) for tritium exchange with fluoroacetic acid.

Reciprocal transformation of furan, pyrrole, thiophene (Yurie`s cycle reactions)

1. Interaction with dilute mineral acids

         Pyrroles are polymerized by even dilute acids by a mechanism such as the following .

 

 

2. Reactions of electrophilic substitution:

         This orientation is understandable in terms of the mechanism of electrophilic aromatic substitution. The a/b ratio is determined by the relative energies of the transition states leading to the two isomers. As in the case of substituted benzenes, we may estimate the relative energies of these two transition states by considering the actual reaction intermediates produced by attack at the a-or b-positions.

 

Nitration

Sulfonation

Acylation

 

Of these structures, the most important are the two with the positive charge on sulfur because, in these two sulfonium cation structures, all atoms have octets of electrons. Nevertheless, as the sets of resonance structures show, the charge on the cation resulting from attack at the a-position is more extensively delocalized than that for the cation resulting from attack at the b-position. The following examples demonstrate the generality of a-attack.

 

Halogenation

Reactions of oxidation

 

Properties

For identification of pyrrole and furan used the method coloring of a pine chip. 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.

The chemical reactivity of the saturated members of this class of heterocycles: tetrahydropyran, thiane and piperidine, resemble that of acyclic ethers, sulfides, and 2º-amines, and will not be described here. 1,3-Dioxanes and dithianes are cyclic acetals and thioacetals. These units are commonly used as protective groups for aldehydes and ketones, as well as synthetic intermediates, and may be hydrolyzed by the action of aqueous acid. The reactivity of partially unsaturated compounds depends on the relationship of the double bond and the heteroatom (e.g. 3,4-dihydro-2H-pyran is an enol ether).

Fully unsaturated six-membered nitrogen heterocycles, such as pyridine, pyrazine, pyrimidine and pyridazine, have stable aromatic rings. Oxygen and sulfur analogs are necessarily positively charged, as in the case of 2,4,6-triphenylpyrylium tetrafluoroborate.

 

From heat of combustion measurements, the aromatic stabilization energy of pyridine is 21 kcal/mole. The resonance description drawn at the top of the following diagram includes charge separated structures not normally considered for benzene. The greater electronegativity of nitrogen (relative to carbon) suggests that such canonical forms may contribute to a significant degree. Indeed, the larger dipole moment of pyridine compared with piperidine supports this view. Pyridine and its derivatives are weak bases, reflecting the sp2 hybridization of the nitrogen. From the polar canonical forms shown here, it should be apparent that electron donating substituents will increase the basicity of a pyridine, and that substituents on the 2 and 4-positions will influence this basicity more than an equivalent 3-substituent. The pKa values given in the table illustrate a few of these substituent effects. Methyl substituted derivatives have the common names picoline (methyl pyridines), lutidine (dimethyl pyridines) and collidine (trimethyl pyridines). The influence of 2-substituents is complex, consisting of steric hindrance and electrostatic components. 4-Dimethylaminopyridine is a useful catalyst for acylation reactions carried out in pyridine as a solvent. At first glance, the sp3 hybridized nitrogen might appear to be the stronger base, but it should be remembered that N,N-dimethylaniline has a pKa slightly lower than that of pyridine itself. Consequently, the sp2 ring nitrogen is the site at which protonation occurs.

 

 

Nucleotides

Nucleotides consist of two parts: A base and a sugar, linked together by an N-glycosidic bond. The base can take two major forms, that of a purine or of a pyrimidine:

The numbering will be important later, and it follows the numbering scheme of heterocycles. There are 5 major bases that we will see. These are adenine, (A), guanine (G), cytosine (C), thymine (T), and uracil (U):

As most heterocyclic compounds, bases are pretty funky molecules. Although there are many natural sources for similar bases (xanthines), they are made from scratch by the organisms that use them. This means that these molecules connect all organisms in the very early stages of evolution. The same goes for DNA and RNA - They are the same in all organisms, so they link all evolution at a certain point in time - Everything came from a primordial bug that already made DNA and RNA. Pretty spooky.

In any case, the bases are highly congujated rings. If you analyze them, you will recognize that almost all the carbons are in sp2 hybridization, and form part of congujated systems. Even those that are sp3 (like the N9 in purines) are sharing their electron to form aromatic systems. Other nitrogens are either sp2 or form part of amide bonds (partial sp2 character). This means that this molecules will absorb UV-visible radiation, will be flat or almost flat, and they are pretty non-polar (except for the exocyclic amines in A and C).

Furthermore, since they have clouds of p-electrons, they will form favourable p-p stacking interactions with one another. This, as we will see later on, is a very important force that stabilizes polynucleotides like DNA and RNA. The bases will place on top of one another due to the favourable p-p stacking interactions, increasing the stability of the molecules they form part of.

Finally, the functional groups of the bases, carbonyls (C=O) and amines (-NH2) and amides (NH-CO), will participate in h-bonds. These h-bonds can be to water, or more importantly, between them - The second important interaction in molecules like DNA or RNA:

As we will see later, h-bonding will be between A and T or U, and G and C. Another property of the bases is they can form tautomers (not the same as resonant forms). We can have in many of them keto-enol equilibria:

The position of the equilibria (that is, which form will predominate) will depend on the pH of the solution (if in aqueous solution). In phisyological conditions (than is, pH = 7), the ones drawn at the top will predominate.

Heterocyclic Bases

Uracil                                         thymine                             cytosine

 

One particular group of hetero cyclic compounds are the heterocyclic bases. These examples are extremely important compounds. Look at the names of these compounds. If you have studied any biology, you will probably recognize these names as being very important parts of DNA and RNA molecules. The ones shown here are uracil, thymine, and cytosine.

In the biochemistry lesson on nucleic acids, you will learn about how these heterocyclic bases bond to sugar molecules and phosphate groups to form DNA and RNA. You will also learn about how they can bond to one another to pull the two strands of the DNA together.

Heterocyclic compounds

When the ring system in an organic compounds contains at least one other element (e.g. N, O, S, B, Si) other than carbon, it is classified as heterocyclic.  At least one heterocyclic ring component is found in about 50% of known organic compounds.

The most common heterocyclic systems contain heteroatoms N, O or S and good examples of these are six-membered heterocycle pyridine and five-membered heterocycles pyrrole, furan and thiophene. Pyridine is one of the most common and best known heterocycles. It is an excellent polar solvent and act as a donor ligand in metal complexes. In a nicotinamide, pyridine is a structural part of an important coenzyme, and the tobacco alkaloid nicotine is perhaps the best known naturally occurring pyridine derivative. Pyrrole occurs widely in nature and is a structural part of porphyrin haeme, chlorophyll and vitamin B₁₂. Furan is found in coal tar, and some terpenoids such as rose oil, contain the furan ring in their chemical structure. The reduction of furan leads to the heterocyclic ether tetrahydrofuran (THF), which is widely used as an organic solvent. Thiophene, which is a sulfur containing heterocycle, occurs in nature in some plant products but its greater importance is as an ingredient in synthetic pharmaceuticals and dyestuffs.

N−Heterocycles were involved at the very beginning of life in the genesis of DNA and play an essential role in many living systems. The nucleic acid bases adenine (A), guanine (G), cytosine (C) and thymine (T) are derivatives of the aromatic N−heterocycles pyrimidine and purine. The base-pairing of DNA by H-bonding is illustrated in Fig. Proteins, which are linear chains of α-amino acids are other important biological macromolecules. One of the essential amino acids, histidine, contains a heterocyclic imidazole ring in its chemical structure. Also histamine, which is a decarboxylation product of histidine has an important role in living systems, e.g. as a contracting agent of smooth muscles and as a substance involved in allergic reactions. The other important amino acid tryptophan and many naturally occuring alkaloids are indole derived structures. In tryptophane the heteroaromatic indole residue has appeared preference for cation−π and π −π interactions.

Most of the important heterocycles mentioned here are aromatic. According to the Hückel rule a monocyclic system containing 4n+2 π -electrons (n=0,1,2,… ) is classified as aromatic. Figure  shows the orbital structure of the five-membered aromatic system imidazole. Other criteria of aromaticity are bond lengths, ring current effects and chemical shifts in ¹H NMR spectra. All the heterocycles selected for study in this work are aromatic 6π -electron systems.

The H-bonding systems of DNA base-pairs between guanine (G) and cytosine (C), and adenine (A) and thymine (T). In addition the chemical structures of histidine and tryptophan proteins are shown. Histamine is a decarboxylation product of histidine.

An example of a five-memberered N-heteroaromatic 6π -electron system. Protonation of imidazole occurs on the lone pair of the nitrogen (in the plane of the ring) and does not change the number of π -electrons.

Five-membered rings with one heteroatom

                        

The parent aromatic compounds of this family—pyrrole, furan, and thiophene—have the structures shown.

The saturated derivatives are called pyrrolidine, tetrahydrofuran, and thiophane, respectively. The bicyclic compounds made of a pyrrole, furan, or thiophene ring fused to a benzene ring are called indole (or isoindole), benzofuran, and benzothiophene, respectively.

As mentioned in the introductory section, the nitrogen heterocycle pyrrole occurs in bone oil, in which it is formed by the decomposition of proteins upon strong heating. Pyrrole rings are found in the amino acids proline and hydroxyproline, which are components of many proteins and which are present in particularly high concentrations in collagen, the structural protein of bones, tendons, ligaments, and skin.

Pyrrole derivatives are widespread in the living world. Pyrrole compounds are found among the alkaloids, a large class of alkaline organic nitrogen compounds produced primarily by plants. Nicotine is the best-known pyrrole-containing alkaloid. The heme group of the oxygen-carrying protein hemoglobin and of related compounds such as myoglobin; the chlorophylls, which are the light-gathering pigments of green plants and other photosynthetic organisms; and vitamin B12 are all formed from four pyrrole units joined in a larger ring system known as a porphyrin, such as that of chlorophyll b, shown below.

The bile pigments are formed by decomposition of the porphyrin ring and contain a chain of four pyrrole rings. Bilirubin, for example, the brownish yellow pigment that gives feces its characteristic colour, is the end product of the breakdown of heme from destroyed red blood cells.

 

The phthalocyanines are a group of synthetic pigments that contain four isoindole units linked together in a large ring. A typical member of the family is phthalocyanine blue (Monastral Fast Blue).

Numerous compounds produced in plants or animals contain one or more indole units in their molecular structure. The important vat dye indigo, which contains two indole units, has been used for thousands of years and was formerly obtained from plants, but it is now synthesized on a large scale.

The closely related Tyrian purple, a dye obtained from species of snail and used in classical times, is 6,6′-dibromoindigo (with bromine atoms bonded to the numbered carbons in the structure above).

Tryptophan, an indole-containing essential amino acid found in most proteins, is used by the body to make several important substances, including the neurotransmitter serotonin and the B-complex vitamin niacin (see below Six-membered rings with one heteroatom). Skatole, a degradation product of tryptophan that retains the indole unit, contributes much of the strong odour of mammalian feces. Indole-3-acetic acid (heteroauxin or β-indolylacetic acid) is a plant-growth regulator and the most important member of the auxin family of plant hormones (see hormone: The hormones of plants). The structures of these compounds are:

Probably the best-known indole-containing compounds are the indole alkaloids, which have been isolated from plants representing more than 30 families. The mushroom hallucinogens psilocin and psilocybin, the ergot fungus alkaloids, the drugs reserpine and yohimbine, and the poison strychnine all belong to this group.

The simplest member of the furan family of oxygen heterocycles, furan itself, is converted industrially by hydrogenation to tetrahydrofuran. Tetrahydrofuran is used as a solvent and for the production of adipic acid and hexamethylenediamine, the raw materials for nylon-6,6, the most common form of nylon. Other furan derivatives of industrial importance are maleic anhydride and phthalic anhydride, which are constituents of resins and plastics. These compounds are prepared in bulk by the oxidation of benzene and naphthalene, respectively, as shown (V2O5 is a vanadium catalyst).

All carbohydrates, the biochemical family that includes the sugars and starches, are composed of one or more simple sugar (monosaccharide) units. These sugars are polyhydroxy aldehydes or polyhydroxy ketones that in aqueous solution exist as equilibrium mixtures of their open-chain and cyclized forms. Frequently the cyclized form of the sugar is a five-membered tetrahydrofuran ring called a furanose, as shown below for fructose, or fruit sugar, as a cyclized isomer (called a fructofuranose).

Other important examples of tetrahydrofuran ring systems are the sugars ribose and deoxyribose, which are present in furanose form in, respectively, RNA and DNA, the heredity-controlling components of all living organisms.

Dehydration of certain carbohydrates yields furan derivatives. Of great commercial importance is the conversion of a carbohydrate in corncobs, oat husks, and other agricultural waste into furan-2-aldehyde, or furfural, which is used extensively as a solvent, in the manufacture of plastics, and in the preparation of other furan derivatives. Many other furan derivatives occur naturally, including vitamin C. The structures of furfural and vitamin C are:

The sulfur heterocycle thiophene and related compounds are found in coal tar and crude petroleum. The most important biologically occurring thiophene derivative is the B-complex vitamin biotin.

Six-membered rings with one heteroatom

 

The nomenclature used for the various monocyclic nitrogen-containing six-membered ring compounds is given below. Positions on the ring are shown for pyridine, Arabic numerals being preferred to Greek letters, although both systems are used. The pyridones are aromatic compounds because of contributions to the resonance hybrid from charged resonance forms such as that shown for 4-pyridone.

Mono-, di-, and trimethylpyridines—that is, pyridines with one, two, or three attached methyl groups, respectively—are called picolines, lutidines, and collidines, respectively, with the position of the methyl groups denoted by numbers—e.g., 2,4,6-collidine. Pyridine-2-, -3-, and -4-carboxylic acids also have widely used trivial names: picolinic, nicotinic (derived from nicotine, of which it is an oxidation product), and isonicotinic acid, respectively. Pyridine itself and the picolines, lutidines, and collidines occur in coal tar and bone oil. Pyridine derivatives are also of great biological importance. For example, nicotinic acid is more commonly known as the B-complex vitamin niacin; a nutritionally equivalent form of niacin is nicotinamide, or niacinamide. Pyridoxine is another member of the B complex, vitamin B6. The structures of pyridoxine and nicotinamide are:

Two coenzymes involved in many important metabolic reactions in living cells, nicotinamide adenine dinucleotide (NAD, also called coenzyme I) and nicotine adenine dinucleotide phosphate (NADP, coenzyme II), are derived from nicotinamide, and the coenzyme pyridoxal phosphate (codecarboxylase) is a physiologically active form of pyridoxine. Many alkaloids contain a pyridine or piperidine ring structure, among them nicotine (mentioned in the previous section for its pyrrole ring) and piperine (one of the sharp-tasting constituents of white and black pepper, from the plant species Piper nigrum), with the structures shown.

Pyridine, which once was extracted commercially from coal tar but now is prepared catalytically from tetrahydrofurfuryl alcohol and ammonia, is an important solvent and intermediate used to make other compounds. Vinylpyridines such as

are important monomer building blocks for plastics, and fully saturated pyridine, piperidine, is used in rubber processing and as a chemical raw material.

 

Pharmaceutically important pyridines include the tuberculostat isoniazid (isonicotinic acid hydrazide), the anti-AIDS-virus drug nevirapine, the vasodilator nicorandil, used for treating angina, the urinary-tract analgesic phenazopyridine, and the anti-inflammatory sulfa drug. 1-(1-phenylcyclohexyl) piperidine (PCP, phencyclidine) was originally used as an anesthetic, but its powerful hallucinogenic properties have led to abuse. Diquat, paraquat, clopyralid, and diflufenican are well-known pyridine derivatives used as herbicides.

Shown in the structural formulas below are two isomeric benzopyridines (upper pair) and two isomeric dibenzopyridines (lower pair), with their common names and accepted numberings. All four compounds and some of their alkyl derivatives have been obtained from coal tar. Each of them is also the parent substance of a class of alkaloids. Of these, the quinolines (e.g., quinine and other derivatives, still obtained from the Cinchona tree) and the isoquinoline (e.g., morphine) groups are particularly well-known.

Quinoline itself can be used to manufacture nicotinic acid and other compounds such as drugs and dyes. The production of synthetic quinoline far exceeds that from coal tar. Morphine, codeine, and thebaine—all containing partially reduced isoquinoline rings—are alkaloids of the opium poppy and have been used for many centuries as hypnotics and analgesics. The semisynthetic derivative of morphine, heroin, is an even more powerful hypnotic and a highly addictive drug.

Important synthetic derivatives of the benzo- and dibenzopyridines include cyanine dyes, used as sensitizers in silver halide photographic emulsions, and quinophthalone dyes, applied in plastics, polymer textiles, paper, cosmetics, transfer-printing processes, electronic photography, and laser dyes. Other derivatives are useful bacteria-staining agents for microscopy, antiseptics such as the coal-tar dye acriflavine, antimalarial agents such as mepacrine (quinacrine) and chloroquine, antibacterial agents such as ciprofloxacin, trypanocides (drugs that destroy trypanosomes, which are parasitic protozoans responsible for Chagas disease, sleeping sickness, and other serious infectious illnesses) such as ethidium bromide, and the reagent oxine (8-hydroxyquinoline or 8-quinolinol), used in analytical chemistry.

Positively charged ions (cations) of pyrylium and thiopyrylium are the parent six-membered, aromatic, monocyclic oxygen and sulfur compounds of their respective groups.

An uncharged aromatic (completely conjugated) six-membered ring containing an oxygen or sulfur atom is possible only if the ring contains a carbonyl group (i.e., a ring carbon atom linked by a double bond to an oxygen atom not in the ring), as in the pyrones.

The pyrans contain extra hydrogen atoms, the position of which is indicated in structural diagrams by a number followed by an H. Certain sugars—a typical example is the monosaccharide glucose—are called pyranoses because they contain six-membered tetrahydropyran rings, with the structure:

Pyrone derivatives are present in natural products. Kojic acid, for example, is an antibiotic derived by action of certain molds on starches or sugars. The steroid bufotalin and its poisonous ester bufotoxin are obtained from the skin glands of toads (genus Bufo; see steroid: Structural relationships of the principal categories of steroids).

The benzopyrylium cation is the parent of a large number of natural products. Chroman, or 3,4-dihydro-2H-1-benzopyran, is itself not found in nature, but the chroman unit is present in many natural products. Vitamin E (α-tocopherol), a substituted chroman, is found in plant oils and the leaves of green vegetables, whereas coumarin, or 2H-1-benzopyran-2-one, used in perfumes and flavourings, and its derivative dicoumarin (dicumarol, or discoumarol), a blood anticoagulant, are products of living organisms.

The flavylium cation is the parent of the anthocyanidines, substances that in chemical combination with sugars form the anthocyanin pigments, the common red and blue colouring matters of flowers and fruits. The colour range from yellow to reddish orange is provided by anthoxanthins, which constitute a subgroup of flavonoids. The latter are derivatives of flavone (2-phenyl-4-pyrone) in which one or more hydrogen atoms are replaced by hydroxy or methoxy groups. The flavylium ion has the structure:

Five- and six-membered rings with two or more heteroatoms

The names and numbering systems for the five-membered heteroaromatic rings with two heteroatoms are:

Few pyrazoles occur naturally; the compounds of this class are usually prepared by the reaction of hydrazines with 1,3-diketones. Many synthetic pyrazole compounds are of importance as dyes and medicinals. Among them are the fever-reducing analgesic aminopyrine, the anti-inflammatory drug phenylbutazone, used in treating arthritis, the yellow food colour and fibre dye tartrazine, and a series of dyes used as sensitizing agents in colour photography.

Imidazoles are most important biologically; histidine, for example, is an essential amino acid of particular importance in enzyme reactions. A breakdown product of histidine, called histamine, has a variety of functions in different organisms; in the human body it plays a crucial role in the immune response, including allergic reactions—hence the importance of antihistamine drugs. Histidine and histamine have the structures:

Among other naturally occurring compounds with an imidazole nucleus are hydantoin, which is found in beet sap, and allantoin, which is related to the metabolic product uric acid. Hydantoin derivatives, in particular phenytoin, are important antiepileptic drugs. The imidazole ring is also present in the B vitamin biotin (mentioned above for its thiophene unit; see above Five-membered rings with one heteroatom).

The antibiotic cycloserine, produced by a bacterium, is one of the few naturally occurring isoxazoles. A synthetic isoxazole, hymexazol, has found practical use as soil and seed fungicide.

Thiazoles are of great biological importance. This ring system occurs in thiamin (thiamine, vitamin B1), the bacitracin and penicillin antibiotics (from a bacterium and a mold, respectively), and in numerous synthetic drugs, dyes, and industrial chemicals. Synthetic drugs belonging to the thiazole family include the antimicrobial agents sulfathiazole and acinitrazole, the antidepressant pramipexole, and the antiasthmatic drug cinalukast. Sulfathiazole has the structure:

Other thiazole compounds include rhodanine, the dye rhodanine red derived from it, and the yellow dye primuline.

Most bicyclic systems derived from these five-membered rings are named systematically—that is, by use of the prefix benz- or benzo- to indicate the presence of the benzene ring. Benzimidazole, for example, is the name for the compound:

A benzimidazole unit occurs in vitamin B₁₂. Benzothiazole derivatives are used for accelerating the vulcanization of rubber (2-mercaptobenzothiazole), as herbicides (benazolin, mefenacet), and as fungicides and antihelminthic drugs (thiabendazole).

The three monocyclic diazines—six-membered ring compounds with two nitrogen heteroatoms—are named and numbered as shown.

The pyridazine derivative maleic hydrazide is a herbicide, and some pyrazines occur naturally—the antibiotic aspergillic acid, for example. The structures of the aforementioned compounds are:

The pyrazine ring is a component of many polycyclic compounds of biological or industrial significance. Important members of the pyrazine family include pteridines, alloxazines, and phenazines, which are discussed below in this section.

Biologically and pharmacologically, however, the most important diazines are the pyrimidines. Uracil, thymine, and cytosine, for example, with the structures shown, are three of the five nucleotide bases that constitute the genetic code in DNA and RNA.

The vitamin thiamin contains a pyrimidine ring (in addition to the five-membered thiazole ring mentioned above), and synthetic barbiturates such as amobarbital (amylobarbitone) are widely used drugs.

Various oxazine and thiazine derivatives are known, but monocyclic thiazines are as yet of little importance. The parent tetrahydro-1,4-oxazine, commonly called morpholine, is produced on a large scale for use as a solvent, corrosion inhibitor, and fungicide. The morpholine ring is also present in the sedative-hypnotic drug trimetozine and in some fungicides such as tridemorph and fenpropimorph. The structural formula for morpholine is:

The benzodiazines are polycyclic compounds containing one or more benzene rings fused to a diazine ring. Many have common names—e.g., cinnoline, quinazoline, and phenazine.

Five other polycyclic systems in this general family are of significance, their names, structures, and numbering systems being:

Quinoxaline alkaloids exist, and there are some phenazine natural products. Phenazine dyes are used for fabrics (for example, indanthrones and anthraquinone vat dyes; see anthraquinone dye) and for inks and printer toners (nigrosines). The first synthetic phenazine dye, mauve (aniline purple), is historically important; its structure is:

The phenoxazine system is a chromophoric (colour-imparting) part of the molecular structures of the naturally occurring actinomycin antibiotics, which are yellow-red in colour. Many polycyclic compounds containing a phenoxazine ring are used as biological stains, fabric dyes, and light-emitting materials in dye lasers (e.g., cresyl violet and nile blue).

Phenothiazine has been used as a worming agent for livestock and as an insecticide. Drugs of the phenothiazine type include the antipsychotic agents chlorpromazine and thioridazine, the long-acting antihistamine promethazine, and ethopropazine, used in treatment of parkinsonism. A large group of dyes have the phenothiazine structure, including methylene blue, a substance widely used as a biological stain and an oxidation-reduction indicator. The structure of methylene blue is:

Biologically, the purines and pteridines are the most important polycyclic diazines. Purine itself is not common, but the purine structure is present in many natural substances. Two purine nucleotide bases, adenine and guanine, occur together with the pyrimidine bases in DNA and RNA mentioned above.

Other natural purines include the alkaloids xanthine and caffeine (found in tea, coffee, and cocoa), the alkaloid theobromine (found in cocoa), and uric acid. The structures of caffeine, theobromine, and uric acid are:

Adenosine monophosphate, diphosphate, and triphosphate (AMP, ADP, and ATP, respectively) are important participants in energy processes in the living cell. Each of the compounds is composed of the nucleotide base adenine linked to the sugar ribose, which in turn is linked to a linear “tail” of one, two, or three phosphate groups, respectively, as shown.

Folic acid, also a pteridine, is a B-complex vitamin and an important growth factor.

Rings with seven or more members

 

As the size of the ring increases, the range of compounds that can be obtained by varying the number, type, and location of the heteroatoms increases enormously. Nevertheless, the chemistry of heterocyclic compounds with rings seven-membered or larger is much less developed than that of five- and six-membered ring heterocycles, although these compounds are usually stable and some of them have found practical application. Of the seven-membered ring compounds, one-heteroatom heterocycles—azepines, oxepines, and thiepines—and their derivatives are the most comprehensively studied.

The increase in ring size constrains these compounds to be nonplanar in order to lessen the ring strain. Nonplanarity, however, affects aromaticity, so these heterocycles react as cyclic polyenes (compounds with noninteracting, alternating single and double bonds). Azepine and oxepine rings are important constituents of numerous naturally occurring alkaloids and metabolic products of marine organisms. The azepine derivative caprolactam is produced commercially in bulk for use as an intermediate in the manufacture of nylon-6 and in production of films, coatings, and synthetic leather. Seven-membered heterocycles with one or two nitrogen atoms in the ring are structural units of widely used psychopharmaceuticals such as imipramine (trade name Prazepine)—the first of the tricyclic antidepressants—and the tranquilizer diazepam (trade name Valium).

Of the larger ring heterocycles, the most important are the crown ethers, which contain one or more heterocyclic rings comprising 12 or more ring atoms and involving a number of various heteroatoms, usually nitrogen, oxygen, or sulfur. The heteroatoms are usually separated by two-carbon or three-carbon units (ethylene or propylene units, respectively). The first crown ether, dibenzo-18-crown-6, was synthesized in 1960.

The first number in a crown ether name indicates the total number of atoms involved in the macrocycle (i.e., the large ring), while the second indicates the number of heteroatoms in that ring. The remarkable feature of crown ethers, which stimulated the explosive development of their chemistry, is their ability to selectively bind the ions of metal elements (e.g., potassium and sodium) and whole organic molecules inside their cavities, the selectivity for a particular ion or molecule being directly related to the size of the macrocycle. Because of this feature, crown ethers have found wide application as ion transporters, as materials for ion-selective electrodes used in environmental testing for various metal ions, as sensitizers in photography, in medical diagnostics, and for the separation of radioactive isotopes.

Although crown ethers are not found in nature, some larger ring heterocycles that possess similar pronounced binding abilities exist as natural products. An example is the porphyrins, which are widely distributed as biological pigments—e.g., the magnesium-binding chlorophylls and the iron-binding heme groups of hemoglobin and myoglobin (see above Five-membered rings with one heteroatom; see also chelate).

Structure and Properties of Nucleosides and Nucleotides

Now we join one of the purines or pyrimidines to the sugar (an N-glycosidic bond to the 1' carbon of the sugar). These structures are called nucleosides:

Notice that the numbering convention for the sugar is now 1' through 5'.

When phosphates are now added to the 5' carbon, we have the final structures to consider, the nucleotides:

We now add the final bit of nomenclature convention. The phosphates are designated, moving out from the 5' carbon, as alpha, beta, and gamma. This is very important to remember, since the position of radiolabeled phosphorous in experimental protocols will determine the outcome.

The nomenclature of the nucleosides found in RNA and DNA are:

 

For thymidine the deoxy is understood. In fact in the rare occurrence of T in RNA (in some transfer RNAs) the nucleoside is called ribothymidine.

The nomenclature of the nucleotides use the names of the nucleosides plus the number of phosphates.

A nucleotide is a substance that, on hydrolysis, yields per mole at least 1 mole of a nitrogenous base, a sugar, and orthophosphate. A nucleoside yields 1 mole each of a nitrogenous base and a sugar. The term nucleobase refers to those nucleotides found in nucleic acids—adenine, guanine, cytosine, and uracil in RNA, and adenine, guanine, cytosine, and thymine in DNA, plus the quantitatively minor bases found in both nucleic acids. Other bases, such as the nicotinamide found in NAD+ and NADP+, occur as parts of coenzymes or as parts of metabolically activated biosynthetic intermediates, such as uridine diphosphate glucose.

A mononucleotide is a nucleotide that, on hydrolysis, yields 1 mole each of a base and a sugar plus at least 1 mole of orthophosphate. The term nucleoside diphosphate usually refers to a mononucleotide which, on hydrolysis, yields 1 mole each of a base and a sugar plus 2 moles of orthophosphate; similarly, a nucleoside triphosphate yields 3 moles of orthophosphate per mole of nucleotide. A dinucleotide yields, on complete hydrolysis, 2 moles each of base and sugar, plus at least 1 mole of orthophosphate; a trinucleotide yields 3 moles each of base and sugar, plus 2 or more moles of orthophosphate.

Figure 1 shows the structures of the five common nucleobases (in their most frequent tautomeric configuration) and several nucleosides, mononucleotides, and oligonucleotides, as well as the numbering systems used. Note that, in all nucleotides found in nucleic acids, a glycosidic bond links N-9 of a purine base or N-1 of a pyrimidine base to C-1, the carbonyl carbon, of either ribose or 2-deoxyribose. By convention, all positions in the sugar of a nucleoside or nucleotide are given primed numbers. Thus, the adenine nucleotide recovered from digestion of DNA with certain enzymes would be named 2′-deoxyadenosine 5′-monophosphate, identifying the position of the phosphate esterified to the sugar, as well as the carbon of the sugar that is in the reduced, or deoxy, configuration. Note that some modes of nucleic acid digestion will yield 2′- or 3′-nucleotides, in which the phosphate is esterified to positions 2′ or 3′ of the sugar, respectively. Also, in the 3′,5′-cyclic nucleotides, cyclic AMP and cyclic GMP, which play multiple roles in biological signal transduction, the phosphate is esterified simultaneously to carbons 3′ and 5′. Because the nucleic acid biosynthetic intermediates are nucleoside 5′-phosphates, or 5′-nucleotides, these structures are shown predominantly.

Structures of the five common nucleobases and representative nucleosides and nucleotides.

Names and Abbreviations of the Nucleotide Constituents of Nucleic Acids and of Cyclic Nucleotides

One additional structural feature of nucleotides relates to the somewhat hindered rotation about the glycosidic bond, which leads to two rather stable orientations of bases with respect to the sugar, termed syn and anti. Because it is more compact to draw, most of the structures shown here are represented as syn, but the anti configuration predominates in nucleic acids (see Z-DNA).

 

dAMP in the syn and anti configurations.

The important derivatives of pyrrole, furan and thiophene.

             

The important derivatives of pyrrole, furan and thiophene.

             

Five-membered heterocyclec with two heteroatoms

         

 

Six-membered heterocycles with two heteroatoms

           

 

Nucleic acids

A Nucleic acids are polymers of nucleotides joined by 3',5' -phosphodiester bonds; that is, a phosphate group links the 3' carbon of a sugar to the 5' carbon of the next sugar in the chain. A phosphate group is often found at the 5' end, and a hydroxyl group is often found at the 3' end.

 

Types of nucleic acids.

Two types of nucleic acids are found within cells of higher organisms: deoxyribonucleic acid (DNA) and ribonucleic acid (RNA). Nearly all the DNA is found in the cell nucleus. Its primary function is the storage and transfer of genetic information. This information is used (indirectly) to control many functions of a living cell. In addition, DNA is passed from existing cell to new cells during cell division RNA occurs in all parts of a cell. It functions primarily in synthesis of proteins, the molecules that carry out essential cellular functions.

DNA has only one biological role, but it is the more central one. The information to make all the functional macromolecules of the cell (even DNA itself) is preserved in DNA and accessed through transcription of the information into RNA copies. Coincident with its singular purpose, there is only a single DNA molecule (or “chromosome”) in simple life forms such as viruses or bacteria. Such DNA molecules must be quite large in order to embrace enough information for making the macromolecules necessary to maintain a living cell RNA has a number of important biological functions, and on this basis, RNA molecules are categorized into several major types: messenger RNA, ribosomal RNA, and transfer RNA. Eukaryotic cells contain an additional type, small nuclear RNA (snRNA). 

The DNA isolated from different cells and viruses consists of two polynucleotide strands wound together to form a long, slender, helical molecule, the DNA double helix. The strands run in opposite directions; that is, they are antiparallel and are held together in the double helical structure through interchain hydrogen bonds

n  DNA molecules are the carriers of the genetic information within а cell; that is, they the molecules of heredity. Each time а cell divides, an exact copy of the DNA of the present cell is needed for the new daughter cell. The process by which new DNA molecule generated is DNA replication. DNA replication is the process by which DNA molecules produce exact duplicates of themselves. The key concept in understanding DNA replication is the base pairing associated with the DNA double helix.

n  We can divide the overall process of protein synthesis into two steps. The first step is called transcription and the second translation. Transcription is the process by which DNA directs the synthesis of RNA molecules that carry the coded information needed for protein synthesis. Translation is the process by which the codes within RNA molecules are deciphered and а particular protein molecule is formed.

Ribonucleic acids (RNA).

Four major differences exist between RNA molecules and DNA molecules.

1.     The sugar unit in the backbone of RNA is ribose; it is deoxyribose in DNA.

2.     The base thymine found in DNA is replaced by uracil in RNA. Uracil, instead of thymine, pairs with (forms hydrogen bonds with) adenine in RNA.

3.     RNA is а single-stranded molecule; DNA is double-stranded (double helix). Thus RNA, unlike DNA, does not contain equal amounts of specific bases.

RNA molecules are much smaller than DNA molecules, ranging from as few as 75 nucleotides to а few thousand nucleotides.

 

 

The monomers for nucleic acid polymers, nucleotides, have а more complex structure than polysaccharide monomers (monosacharides) or protein monomers (amino acids). Within each nucleotide monomer are three subunits. А nucleotide is, а molecule composed of a pentose sugar bonded to both a group and a nitrogen-containing hetero-cyclic base.

            

A nucleotide results when phosphoric acid is esterified to a sugar OOH group of a nucleoside. The nucleoside ribose ring has three OOH groups available for esterification, at C-2, C-3, and C-5 (although 2-deoxyribose has only two). The vast majority of monomeric nucleotides in the cell are ribonucleotides having 5-phosphate groups.

Nucleotide formation.

The formation of а nucleotide from sugar, base, and phosphate can be visualized as occurring in the following manner:

 

 

 

Heterocyclic compound, also called heterocycle,  any of a major class of

organic chemical compounds characterized by the fact that some or all of the atoms in their molecules are joined in rings containing at least one atom of an element other than carbon (C). The cyclic part (from Greek kyklos, meaning “circle”) of heterocyclic indicates that at least one ring structure is present in such a compound, while the prefix hetero- (from Greek heteros, meaning “other” or “different”) refers to the noncarbon atoms, or heteroatoms, in the ring. In their general structure, heterocyclic compounds resemble cyclic organic compounds that incorporate only carbon atoms in the rings—for example, cyclopropane (with a three-carbon-atom ring) or benzene (with a six-carbon-atom ring)—but the presence of the heteroatoms gives heterocyclic compounds physical and chemical properties that are often quite distinct from those of their all-carbon-ring analogs.

 

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, consist of long chains of heterocyclic units held together by other types of materials. Many naturally occurring pigments, vitamins, and antibiotics are heterocyclic compounds, as are most hallucinogens. Modern society is dependent on synthetic heterocycles for use as drugs, pesticides, dyes, and plastics

General aspects of heterocyclic compounds

The most common heterocycles are those having five- or six-membered rings and containing heteroatoms of nitrogen (N), oxygen (O), or sulfur (S). The best known of the simple heterocyclic compounds are pyridine, pyrrole, furan, and thiophene. A molecule of pyridine contains a ring of six atoms—five carbon atoms and one nitrogen atom. Pyrrole, furan, and thiophene molecules each contain five-membered rings, composed of four atoms of carbon and one atom of nitrogen, oxygen, or sulfur, respectively.

 

Pyridine and pyrrole are both nitrogen heterocycles—their molecules contain nitrogen atoms along with carbon atoms in the rings. The molecules of many biological materials consist in part of pyridine and pyrrole rings, and such materials yield small amounts of pyridine and pyrrole upon strong heating. In fact, both of these substances were discovered in the 1850s in an oily mixture formed by strong heating of bones. Today, pyridine and pyrrole are prepared by synthetic reactions.Their chief commercial interest lies in their conversion to other substances, chiefly dyestuffs and drugs. Pyridine is used also as a solvent, a waterproofing agent, a rubber additive, an alcohol denaturant, and a dyeing adjunct.

 

Furan is an oxygen-containing heterocycle employed primarily for conversion to other substances (including pyrrole). Furfural, a close chemical relative of furan, is obtained from oat hulls and corncobs and is used in the production of intermediates for nylon. Thiophene, a sulfur heterocycle, resembles benzene in its chemical and physical properties. It is a frequent contaminant of the benzene obtained from natural sources and was first discovered during the purification of benzene. Like the other compounds, it is used primarily for conversion to other substances. Furan and thiophene were both discovered in the latter part of the 19th century.

In general, the physical and chemical properties of heterocyclic compounds are best understood by comparing them with ordinary organic compounds that do not contain heteroatoms.

The nature of heteroaromaticity

Aromaticity denotes the significant stabilization of a ring compound by a system of alternating single and double bonds—called a cyclic conjugated system—in which six π electrons generally participate. A nitrogen atom in a ring can carry a positive or a negative charge, or it can be in the neutral form. An oxygen or sulfur atom in a ring can either be in the neutral form or carry a positive charge. A fundamental distinction is usually made between (1) those heteroatoms that participate in a cyclic conjugated system by means of a lone, or unshared, pair of electrons that are in an orbital perpendicular to the plane of the ring and (2) those heteroatoms that do so because they are connected to another atom by means of a double bond.

 

An example of an atom of the first type is the nitrogen atom in pyrrole, which is linked by single covalent bonds to two carbon atoms and one hydrogen atom. Nitrogen has an outermost shell of five electrons, three of which can enter into three covalent bonds with other atoms. After the bonds are formed, as in the case of pyrrole, there remains an unshared electron pair that can engage in cyclic conjugation. The aromatic sextet in pyrrole is made up of two electrons from each of the two carbon-carbon double bonds and the two electrons that compose the unshared electron pair of the nitrogen atom. As a consequence, there tends to be a net flow of electron density from the nitrogen atom to the carbon atoms as the nitrogen’s electrons are drawn into the aromatic sextet. Alternatively, the pyrrole molecule may be described as a resonance hybrid—that is, a molecule whose true structure can only be approximated by two or more different forms, called resonance forms.

 

An example of a heteroatom of the second type is the nitrogen atom in pyridine, which is linked by covalent bonds to only two carbon atoms. Pyridine also has a π-electron sextet, but the nitrogen atom contributes only one electron to it, one additional electron being contributed by each of the five carbon atoms in the ring. In particular, the unshared electron pair of the nitrogen atom is not involved. Moreover, because nitrogen’s attraction for electrons (its electronegativity) is greater than that of carbon, electrons tend to move toward the nitrogen atom rather than away from it, as in pyrrole.

 

Quite generally, heteroatoms may be referred to as pyrrolelike or pyridine-like, depending on whether they fall into the first or second class described above. The pyrrolelike heteroatoms −NR− (R being hydrogen or a hydrocarbon group), −N−−, −O−, and −S− tend to donate electrons into the π-electron system, whereas the pyridine-like heteroatoms −N=, −N+R=, −O+=, and −S+= tend to attract the π electrons of a double bond.

 

In six-membered heteroaromatic rings, the heteroatoms (usually nitrogen) are pyridine-like—for example, the compounds pyrimidine, which contains two nitrogen atoms, and 1,2,4-triazine, which contains three nitrogen atoms.

 

Six-membered heteroaromatic compounds cannot normally contain pyrrolelike heteroatoms. Five-membered heteroaromatic rings, however, always contain one pyrrolelike nitrogen, oxygen, or sulfur atom, and they may also contain up to four pyridine-like heteroatoms, as in the compounds thiophene (with one sulfur atom), 1,2,4-oxadiazole (with one oxygen atom and two nitrogen atoms), and pentazole (with five nitrogen atoms).

 

The quantitative measurement of aromaticity—and even its precise definition—has challenged chemists since German chemist August Kekule formulated the ring structure for benzene in the mid-19th century. Various methods based on energetic, structural, and magnetic criteria have been widely used to measure the aromaticity of carbocyclic compounds. All of them, however, are difficult to apply quantitatively to heteroaromatic systems because of complications arising from the presence of heteroatoms.

 

Chemical reactivity can provide a certain qualitative insight into aromaticity. The reactivity of an aromatic compound is affected by the extra stability of the conjugated system that it contains; the extra stability in turn determines the tendency of the compound to react by substitution of hydrogen—i.e., replacement of a singly bonded hydrogen atom with another singly bonded atom or group—rather than by addition of one or more atoms to the molecule via the breaking of a double bond (see substitution reaction; addition reaction). In terms of reactivity, therefore, the degree of aromaticity is measured by the relative tendency toward substitution rather than addition. By this criterion, pyridine is more aromatic than furan, but it is difficult to say just how much more aromatic.

 

Ultraviolet, infrared, nuclear magnetic resonance, and mass spectra

Spectroscopic studies of heterocyclic compounds, like those of other organic compounds, have became of great importance as means of identification of unknown materials, as criteria for purity, and as probes for investigating the electronic structures of molecules, thereby explaining and helping to predict their reactions. The ultraviolet spectrum of an organic compound (the pattern of its light absorption in the ultraviolet region of the spectrum) is characteristic of the π-electron system of the molecule—i.e., of the arrangement of double bonds within the structure. The ultraviolet spectra of heteroaromatic compounds show general similarity to those of benzenoid compounds (compounds with one or more benzene rings), and the effects of substituents can usually be rationalized in a similar way.

 

The infrared spectrum of an organic compound, with its complexity of bands, provides an excellent “fingerprint” of the compound—far more characteristic than a melting point. It also can be used to identify certain common groups, such as carbonyl (C=O) and imino, as well as various heterocyclic ring systems.

 

Magnetic resonance spectra are indispensable today for studies in heterocyclic chemistry. Proton resonance spectra, the most common type, yield information regarding the number of hydrogen atoms in the molecule, their chemical environment, and their relative orientation in space. Mass spectra are used to determine not only the complete molecular formula of the compound but also the molecular structure from the way the molecule fragments.

Synthesis and modification of heterocyclic rings

The important methods for synthesizing heterocyclic compounds can be classified under five headings. Three are ways of forming new heterocyclic rings from precursors containing either no rings (acyclic precursors) or one fewer ring than the desired product; one is a way of obtaining a heterocyclic ring from another heterocyclic ring or from a carbocyclic ring; and one involves the modification of substituents on an existing heterocyclic ring.

 

In the formation of rings from acyclic precursors, the key step is frequently the formation of a carbon-heteroatom linkage (C−Z, in which Z represents an atom of nitrogen, oxygen, sulfur, or a more unusual element). The actual ring closure, or cyclization, however, may involve the formation of a carbon-carbon bond. In any case, ring formation reactions are divided into three general categories according to whether the cyclization reaction occurs primarily as a result of nucleophilic or electrophilic attack or by way of a cyclic transition state.

 

Nucleophilic ring closure

To prepare compounds containing one heteroatom, an open-chain hydrocarbon derivative containing two halogen element atoms—specifically, chlorine, bromine (Br), or iodine (I)—either as halides (in which the halogen atoms are attached directly to the hydrocarbon chain) or as acyl halides (in which the halogen atoms belong to derivatives of carboxylic acids) is reacted with the dihydro form of the heteroatom (ZH2, or an equivalent reagent) to give nonaromatic heterocycles.

 

Diketones also can react with dihydro Z compounds to give heterocycles. (A ketone is an organic compound that contains a carbonyl group, the carbon atom of which is linked to two other carbon atoms belonging to hydrocarbon groups. Diketones contain two such carbonyl groups.) Diketones with the carbonyl groups separated by two carbon atoms, for example, can be cyclized to form five-membered aromatic pyrroles, furans, and thiophenes. In the case of diketones whose carbonyl groups are separated by three carbons, six-membered rings may be formed.

 

In each of these reactions the heteroatom Z acts as a nucleophile—an atom or a molecule that seeks a positively charged centre, such as a partly unprotected atomic nucleus. The heteroatom attacks the positively charged carbon atom produced by electron withdrawal because of the presence of the halogen atom (in the first two reactions above) or of the oxygen atom (in the last reaction).

 

Usually, such reactions proceed by means of intermediates in which only one of the two C−Z bonds has formed. In reactions involving halogens as halides, for instance, a compound such as HZ−CH2−(CH2)n−CH2Br may form first. This fact can be applied to heterocycle synthesis in that it is frequently possible to make such intermediate compounds by other routes; these intermediates then cyclize readily to form the desired ring. One procedure for pyridine synthesis, for example, involves a condensation reaction employing an intermediate with the carbon-nitrogen bond already formed.

 

Heterocycles containing two adjacent nitrogen atoms, two oxygen atoms, or adjacent nitrogen and oxygen atoms also may be prepared from precursors by the use of hydrazine (N2H4), hydroxylamine (NH2OH), or hydrogen peroxide (H2O2) in place of the dihydro Z compound. Similarly, two adjacent heteroatoms can be introduced by employing one of the reagents in the reactions with diketones, discussed earlier in this section.

 

When a compound containing two nonadjacent heteroatoms is desired, appropriate components can be put together, as in the synthesis of a pyrimidine. Ring synthesis reactions in which the heteroatom acts as a nucleophile can also employ precursors containing a ring, resulting in two-ring compounds. These reactions involve the use of ortho-disubstituted benzenes (ortho substituents being groups attached to adjacent carbon atoms in the benzene ring). The formation of quinoline and quinazoline rings (see below Major classes of heterocyclic compounds: Six-membered rings with one heteroatom) is an example of this reaction type.

Electrophilic ring closure

Heterocyclic ring-forming reactions in which the heteroatom acts as an electrophile—an electron-seeking atom or molecule—are rare, because nitrogen, oxygen, and sulfur atoms are themselves electron-rich centres that act generally as nucleophiles. Nevertheless, electrophilic ring closure reactions are known in which a heterocyclic ring is formed by a reaction in which a carbon atom of the future ring acts as an electrophile. Usually such reactions involve ring closure onto an existing benzene ring (or other aromatic system), an electron-rich system that is generally subject to attack by electrophilic reagents. An example of ring closures of this type is the formation of quinoline from aniline and acrolein, a dehydration product of glycerol. The initial heterocyclic product of the reaction is dihydroquinoline, which must be dehydrogenated (must undergo removal of two hydrogen atoms) to give the fully aromatic product, quinoline itself.

Ring closure by way of cyclic transition states

 

A most important method for the synthesis of carbocyclic six-membered rings is the Diels-Alder diene reaction, named for its Nobel Prize-winning discoverers, the German chemists Otto Diels and Kurt Alder. In this reaction, illustrated below, a diene—a compound with two double bonds—reacts with a dienophile (a diene-seeking reagent), which contains a pair of carbon atoms linked by a double or triple bond. The product is a cyclohexene, a compound with a six-membered ring containing a double bond.

Heterocycles likewise can be synthesized by the Diels-Alder reaction, in which the dienophile contains a pair of heteroatoms such as nitrogen linked by multiple bonds.

 

Of even greater use, however, is a related method called the Huisgen dipolar cycloaddition reaction. This reaction is an important means of preparing many types of five-membered rings, especially those containing several heteroatoms. Pyrazoles, isoxazoles (see below Major classes of heterocyclic compounds: Five- and six-membered rings with two or more heteroatoms), and many less-common heterocycles can be synthesized by this method.

 

Conversion of one heterocyclic ring into another

Although there are many reactions of theoretical importance in which one heterocyclic ring is converted into another, few are of practical use. The preparation of pyridine from tetrahydrofurfuryl alcohol and ammonia (see below Major classes of heterocyclic compounds: Six-membered rings with one heteroatom) and the conversion of pyrylium salts into pyridinium salts are good examples of such transformations. In addition, ring-atom rearrangement, or “shuffling,” can be brought about with light (see photochemical reaction) in five- and six-membered heteroaromatic compounds, and ring contraction by extrusion of an atom or a group can occur under certain conditions.

 

Modification of an existing ring

Dehydrogenation of saturated or partially saturated heterocyclic rings to thermodynamically more-stable heteroaromatic compounds by heating with sulfur or by treatment with a palladium catalyst is analogous to similar reactions involving carbocyclic compounds. The hydrogenation of (addition of hydrogen to) heteroaromatic rings is, by contrast, usually more difficult, for the heteroatoms tend to poison the catalyst. Finally, the modification of substituents on heterocyclic rings is of highest importance in synthesis, and reactions by which substituents may be altered are among the most useful in heterocyclic chemistry.

 

Major classes of heterocyclic compounds

The major classes of heterocycles containing the common heteroatoms—nitrogen, oxygen, and sulfur—are reviewed in order of increasing ring size, with compounds containing other heteroatoms left to a final section. Classification by ring size is convenient because heterocyclic rings of a given size have many common features. For heterocyclic (as for carbocyclic) rings, certain broad generalizations can be made. Three- and four-membered rings, because of their small size, are geometrically strained and thus readily opened; they are also readily formed. Such heterocycles are well-known reactive intermediates. Five- and six-membered rings are readily formed and are very stable; their sizes also allow the development of aromatic character. Seven-membered rings and larger are stable but less readily formed and relatively less well investigated.

Three-membered rings

The three-membered ring heterocycles containing single atoms of nitrogen, oxygen, and sulfur—aziridine, oxirane (or ethylene oxide), and thiirane, respectively—and their derivatives can all be prepared by nucleophilic reactions, of the type shown. Thus, aziridine is formed by heating β-aminoethyl hydrogen sulfate with a base (in this case Y is −OSO₃H).

A reaction of this type is involved in the pharmacological action of nitrogen mustards, which were among the first anticancer drugs developed (see drug: Cancer chemotherapy). Intramolecular ring closure, as in the case of the anticancer agent mechlorethamine, produces an intermediate aziridinium ion, the biologically active agent, which attacks rapidly proliferating cells such as cancer cells by inhibiting replication of their DNA (deoxyribonucleic acid). Nitrogen mustards linked to steroids also have been used as anticancer agents.

 

Commercially, oxirane and (to a lesser extent) aziridine are important bulk industrial chemicals. Oxirane is prepared on a large scale by the direct reaction of ethylene with oxygen.

 

The chemical reaction that is the most characteristic of these three-membered rings is susceptibility to attack by nucleophilic reagents to open the ring, as shown by:

The first step shown is the reverse of the formation reaction shown at the top of this section. As indicated, a second molecule of the three-membered ring may react with the first product. Further reaction leads to long chainlike molecules (polymers) of the type C2H5O(CH2CH2Z)nCH2CH2ZH. Polymers and copolymers of oxirane and aziridine are useful plastics.

 

The oxirane ring can also be opened by hydrolysis—i.e., the breaking of a bond accompanied by the addition of the elements of water (H and OH), which is similar to the first step of the ring-opening reaction illustrated above. The result of this reaction is ethylene glycol (HOCH2CH2OH), which serves as antifreeze in cooling and heating systems, in brake fluid, and as a solvent in the paints and plastics industries.

 

In medicine, aziridine derivatives are used for the treatment of cancer and in research as affinity probes (labeled chemicals that react selectively with biological molecules of interest) for detection and assay studies. The mitomycin family of antitumour antibiotics is the most well-known class of natural products containing the aziridine ring.

 

Naturally occurring compounds containing one or more oxirane rings are abundant. These molecules include insect juvenile hormones, pheromones, and products of marine organisms. Often they are biologically active and have promising therapeutic applications. For example, the fungal product (−)-ovalicin, which contains two oxirane rings, has potential for inhibiting development of solid tumours by cutting off their blood supply. An important synthetic oxirane having one ring is fosfomycin, used as an antibacterial drug, particularly in treating urinary tract infections.

 

Molecules containing thiirane rings are more bactericidal than those containing oxirane rings, and some thiirane derivatives have found application as tuberculostats (drugs that inhibit the growth of tuberculosis-causing bacteria), whereas thiirane 1 oxides have been reported to be insecticides, molluscicides, or herbicides.

 

Although aziridine, oxirane, and thiirane are saturated heterocycles, they are much more reactive than the corresponding open-chain amines, ethers, or sulfides because of the strain inherent in the three-membered ring. This behaviour reflects the comparable enhanced reactivity of the related three-membered carbocyclic compound cyclopropane.

 

Since 1950, five different classes of three-membered ring compounds with two heteroatoms have been discovered. They are derivatives of the parent ring systems diaziridine (containing N−N), oxaziridine (O−N), thiaziridine (S−N), dioxirane (O−O), and dithiirane (S−S). The oxathiirane system has no reported stable representatives in its class.

 

Except for diaziridine systems, which are used in the manufacture of plastic films and foamed plastics, as propellants and fuel stabilizers, and in the synthesis of anticancer drugs and psychopharmaceuticals, these compounds currently have limited practical importance, but they offer interesting possibilities for future applications.

Four-membered rings

Azetidine, oxetane, and thietane—four-membered rings containing, respectively, one nitrogen, oxygen, or sulfur atom—are prepared by nucleophilic displacement reactions similar to those used to prepare the corresponding three-membered rings.

(In the reaction above, Y is usually Cl, Br, or SO3H.) With four-membered rings, however, the reactions proceed less readily than do the analogous reactions for three-membered rings. The ring-opening reactions of four-membered heterocycles resemble qualitatively those of the corresponding three-membered rings, but they occur rather less readily.

 

The most important heterocycles with four-membered rings are two related series of antibiotics, the penicillins and the cephalosporins. Both series contain the azetidinone ring (the suffix -one indicating an oxygen atom linked with a double bond to a ring carbon atom). Another common name for the azetidinone ring is the β-lactam ring, which lends its name to the β-lactam antibiotics, the class to which the penicillins and cephalosporins belong. The chemistry of azetidinones was explored thoroughly during the intensive research into penicillin structure and synthesis that took place during World War II. A practical synthesis of penicillin was not achieved, however, until 1959.

 

Numerous oxetanes, the synthetic analogs of the antiviral natural product oxetanocin, are under investigation as antifungal, anti-inflammatory, anticancer, and antiviral agents. Oxetanones, whose ring structure is analogous to that of the azetidinones except that the heteroatom is oxygen, are widely applied in polymer manufacturing and in agriculture as herbicides, fungicides, and bactericides. The parent thietane was found in shale oil, whereas its odoriferous derivatives function as scent markers for minks, ferrets, and European polecats. Thietanes are used in the production of polymers, as bactericides and fungicides in paint, and as iron corrosion inhibitors.

One of the important specialized pathways of a number of amino acids is the synthesis of purine and pyrimidine nucleotides. These nucleotides are important for a number of reasons. Most of them, not just ATP, are the sources of energy that drive most of our reactions. ATP is the most commonly used source but GTP is used in protein synthesis as well as a few other reactions. UTP is the source of energy for activating glucose and galactose. CTP is an energy source in lipid metabolism. AMP is part of the structure of some of the coenzymes like NAD and Coenzyme A. And, of course, the nucleotides are part of nucleic acids. Neither the bases nor the nucleotides are required dietary components. We can both synthesize them de novo and salvage and reuse those we already have.

 

Nitrogen Bases

There are two kinds of nitrogen-containing bases - purines and pyrimidines. Purines consist of a six-membered and a five-membered nitrogen-containing ring, fused together. Pyridmidines have only a six-membered nitrogen-containing ring. There are 4 purines and 4 pyrimidines that are of concern to us.

 

 

Purines

http://www.youtube.com/watch?v=uOAsqECXVco

Adenine and guanine are found in both DNA and RNA. Hypoxanthine and xanthine are not incorporated into the nucleic acids as they are being synthesized but are important intermediates in the synthesis and degradation of the purine nucleotides.

http://www.youtube.com/watch?v=PHOjrY3zYdM

 

Pyrimidines

http://www.youtube.com/watch?v=KXr8bM69Nq4

 

Cytosine is found in both DNA and RNA. Uracil is found only in RNA. Thymine is normally found in DNA. Sometimes tRNA will contain some thymine as well as uracil.

Nucleosides

 

 

If a sugar, either ribose or 2-deoxyribose, is added to a nitrogen base, the resulting compound is called a nucleoside. Carbon 1 of the sugar is attached to nitrogen 9 of a purine base or to nitrogen 1 of a pyrimidine base. The names of purine nucleosides end in -osine and the names of pyrimidine nucleosides end in -idine. The convention is to number the ring atoms of the base normally and to use l', etc. to distinguish the ring atoms of the sugar. Unless otherwise specificed, the sugar is assumed to be ribose. To indicate that the sugar is 2'-deoxyribose, a d- is placed before the name.

·                    Adenosine

·                    Guanosine

·                    Inosine - the base in inosine is hypoxanthine

·                    Uridine

·                    Thymidine

·                    Cytidine

Nucleotides

Adding one or more phosphates to the sugar portion of a nucleoside results in a nucleotide. Generally, the phosphate is in ester linkage to carbon 5' of the sugar. If more than one phosphate is present, they are generally in acid anhydride linkages to each other. If such is the case, no position designation in the name is required. If the phosphate is in any other position, however, the position must be designated. For example, 3'-5' cAMP indicates that a phosphate is in ester linkage to both the 3' and 5' hydroxyl groups of an adenosine molecule and forms a cyclic structure. 2'-GMP would indicate that a phosphate is in ester linkage to the 2' hydroxyl group of a guanosine. Some representative names are:

·                    AMP = adenosine monophosphate = adenylic acid

·                    CDP = cytidine diphosphate

·                    dGTP = deoxy guanosine triphosphate

·                    dTTP = deoxy thymidine triphosphate (more commonly designated TTP)

·                    cAMP = 3'-5' cyclic adenosine monophosphate

NOMENCLATURE OF NUCLEIC BASES, NUCLEOSIDES, AND NUCLEOTIDES

 

 

Polynucleotides

 

Nucleotides are joined together by 3'-5' phosphodiester bonds to form polynucleotides. Polymerization of ribonucleotides will produce an RNA while polymerization of deoxyribonucleotides leads to DNA.

Hydrolysis of Polynucleotides

Most, but not all, nucleic acids in the cell are associated with protein. Dietary nucleoprotein is degraded by pancreatic enzymes and tissue nucleoprotein by lysosomal enzymes. After dissociation of the protein and nucleic acid, the protein is metabolized like any other protein.

 

The nucleic acids are hydrolyzed randomly by nucleases to yield a mixture of polynucleotides. These are further cleaved by phosphodiesterases (exonucleases) to a mixture of the mononucleotides. The specificity of the pancreatic nucleotidases gives the 3'-nucleotides and that of the lysosomal nucleotidases gives the biologically important 5'-nucleotides.

 

 

The nucleotides are hydrolyzed by nucleotidases to give the nucleosides and P_i. This is probably the end product in the intestine with the nucleosides being the primary form absorbed. In at least some tissues, the nucleosides undergo phosphorolysis with nucleoside phosphorylases to yield the base and ribose 1-P (or deoxyribose 1-P). Since R 1-P and R 5-P are in equilibrium, the sugar phosphate can either be reincorporated into nucleotides or metabolized via the Hexose Monophosphate Pathway. The purine and pyrimidine bases released are either degraded or salvaged for reincorporation into nucleotides.

There is significant turnover of all kinds of RNA as well as the nucleotide pool. DNA doesn't turnover but portions of the molecule are excised as part of a repair process.

Purine and pyrimidines from tissue turnover which are not salvaged are catabolized and excreted. Little dietary purine is used and that which is absorbed is largely catabolized as well. Catabolism of purines and pyrimidines occurs in a less useful fashion than did the catabolism of amino acids in that we do not derive any significant amount of energy from the catabolism of purines and pyrimidines. Pyrimidine catabolism, however, does produce beta-alanine, and the endproduct of purine catabolism, which is uric acid in man, may serve as a scavenger of reactive oxygen species.

 

The metabolic requirements for the nucleotides and their cognate bases can be met by both dietary intake or synthesis de novo from low molecular weight precursors. Indeed, the ability to salvage nucleotides from sources within the body alleviates any nutritional requirement for nucleotides, thus the purine and pyrimidine bases are not required in the diet. The salvage pathways are a major source of nucleotides for synthesis of DNA, RNA and enzyme co-factors.

Extracellular hydrolysis of ingested nucleic acids occurs through the concerted actions of endonucleases, phosphodiesterases and nucleoside phosphorylases. Endonucleases degrade DNA and RNA at internal sites leading to the production of oligonucleotides. Oligonucleotides are further digested by phosphodiesterases that act from the ends inward yielding free nucleosides. The bases are hydrolyzed from nucleosides by the action of phosphorylases that yield ribose-1-phosphate and free bases. If the nucleosides and/or bases are not re-utilized the purine bases are further degraded to uric acid and the pyrimidines to β-aminoiosobutyrate, NH₃ and CO₂.

Purine and pyrimidine bases which are not degraded are recycled - i.e. reincorporated into nucleotides. This recycling, however, is not sufficient to meet total body requirements and so some de novo synthesis is essential. There are definite tissue differences in the ability to carry out de novo synthesis. De novo synthesis of purines is most active in liver. Non-hepatic tissues generally have limited or even no de novo synthesis. Pyrimidine synthesis occurs in a variety of tissues. For purines, especially, non-hepatic tissues rely heavily on preformed bases - those salvaged from their own intracellular turnover supplemented by bases synthesized in the liver and delivered to tissues via the blood.

"Salvage" of purines is reasonable in most cells because xanthine oxidase, the key enzyme in taking the purines all of the way to uric acid, is significantly active only in liver and intestine. The bases generated by turnover in non-hepatic tissues are not readily degraded to uric acid in those tissues and, therefore, are available for salvage. The liver probably does less salvage but is very active in de novo synthesis - not so much for itself but to help supply the peripheral tissues.

De novo synthesis of both purine and pyrimidine nucleotides occurs from readily available components.

 

Phosphoribosyl pyrophosphate (PRPP) is important in both, and in these pathways the structure of ribose is retained in the product nucleotide, in contrast to its fate in the tryptophan and histidine biosynthetic pathways discussed earlier. An amino acid is an important precursor in each type of pathway: glycine for purines and aspartate for pyrimidines. Glutamine again is the most important source of amino groups — in five different steps in the de novo pathways. Aspartate is also used as the source of an amino group in the purine pathways, in two steps. Two other features deserve mention. First, there is evidence, especially in the de novo purine pathway, that the enzymes are present as large, multienzyme complexes in the cell, a recurring theme in our discussion of metabolism. Second, the cellular pools of nucleotides (other than ATP) are quite small, perhaps 1% or less of the amounts required to synthesize the cell’s DNA.

Therefore, cells must continue to synthesize nucleotides during nucleic acid synthesis, and in some cases nucleotide synthesis may limit the rates of DNA replication and transcription. Because of the importance of these processes in dividing cells, agents that inhibit nucleotide synthesis have become particularly important to modern medicine. We examine here the biosynthetic pathways of purine and pyrimidine nucleotides and their regulation, the formation of the deoxynucleotides, and the degradation of purines and pyrimidines to uric acid and urea. We end with a discussion of chemotherapeutic agentsthat affect nucleotide synthesis.

In the first committed step of the pathway, an amino group donated by glutamine is attached at C-1 of PRPP.

 

 

The resulting 5-phosphoribosylamine is highly unstable, with a half-life of 30 seconds at pH 7.5. The purine ring is subsequently built up on this structure. The pathway described here is identical in all organisms, with the exception of one step that differs in higher eukaryotes as noted below.