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Selected Lectures in Organic and Bioorganic Chemistry

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Selected Lectures in Organic and Bioorganic Chemistry M. M. MELKONYAN SELECTED LECTURES IN ORGANIC AND BIOORGANIC CHEMISTRY Handbook YEREVAN 2016 1 YEREVAN STATE MEDICAL UNIVERSITY AFTER M.HERATSI M. M. MELKONYAN SELECTED LECTURES IN ORGANIC AND BIOORGANIC CHEMISTRY This handout is adopted by the Methodical Council of Foreign Students of the University YEREVAN 2016 1 YEREVAN STATE MEDICAL UNIVERSITY AFTER M.HERATSI Department of General and Bioorganic Chemistry MAGDA MHER MELKONYAN Professor, Head of Department of General and Bioorganic Chemistry SELECTED LECTURES IN ORGANIC AND BIOORGANIC CHEMISTRY The handbook ”SELECTED LECTURES IN ORGANIC AND BIOORGANIC CHEMISTRY” is intended to be studied by YSMU students of General medicine, Stomatological, Pharmacy facultes as well as those of Medical and Biological colleges. The present handbook includes all the chapters of Bioorganic Chemistry (in the frames of curriculum). Electronic and Steric constructions of organic compounds and the links between organic compounds structures and their biological activity is systematized in the textbook. The structure of the main compounds taking part in metabolism (static Biochemistry), widely recognized commonly used drugs are given in the textbook as well as a special place is devoted to the discussion of chemical properties and main principles of reactive ability of organic compounds. The teaching material is illustrated by tables and pictures. Yerevan, YSMU, 2016, p. 224. Ø.Ø. Ø»ÉùáÝÛ³Ý §úñ·³Ý³Ï³Ý ¨ λÝë³ûñ·³Ý³Ï³Ý ùÇÙdzÛÇ ¹³ë³ËáëáõÃÛáõÝ- Ý»ñÇ Ñ³í³ù³Íáõ¦: Ò»éݳñÏ Ý³Ë³ï»ëí³Í ºä´Ð ÁݹѳÝáõñ µÅßÏáõÃÛ³Ý ¨ ëïáÙ³ïáÉá·Ç³Ï³Ý ý³ÏáõÉï»ïÝ»ñÇ áõë³ÝáÕÝ»ñÇ, ÇÝãå»ë ݳ¨ Ï»Ýë³µ³Ý³Ï³Ý ¨ µÅßÏ³Ï³Ý Ã»ùáõÙáí áõëáõÙݳñ³ÝÝ»ñÇ, ùáÉ»çÝ»ñÇ áõë³ÝáÕÝ»ñÇ Ñ³Ù³ñ: ºñ¨³Ý, ºä´Ð, 2016, 224 ¿ç: ISBN 99941- 40 -12 - 4 © Melkonyan M.M. 2 BIOORGANIC CHEMISTRY Introduction According to the simplest definition, organic chemistry is the study of the compounds of carbon. Perhaps the most remarkable feature of organic chemistry is that it is the chemistry of carbon and only a few other elements-chiefly, hydrogen, oxygen, nitrogen, rare sulfur and phosphorus. Chemists have discovered or made well over ten million compounds composed of carbon and these three other elements. Organic compounds are every where around us—in our foods, flavors, and fragrances; in our medicines, toiletries, and cosmetics; in our plastics, films, fibers, and resins; in our paints and varnishes; in our glues and adhesives; and, of course, in our bodies and those of all living things. Organic chemistry has a long tradition of relating the properties of a substance to its molecular structure and, more than anything else, the relationship between how a substance behaves and the way its atoms are connected. Extremely important are problems, concerning biological and physiological activity of organic compounds. Therefore this part of organic chemistry, which studies structure and function of compounds, which are compulsory and necessary for normal functioning of living bodies and especially and particularly human body, used to call bioorganic chemistry. The main goals of subject are: 1.To study the structure of all organic compounds from living sources, including biopolymers, such as proteins, nucleic acids, polysaccharides and bioregulators, other metabolites and reveal connection between structure and function of these compounds. 2. Once a structure is known, to synthesize the compound in the laboratory and manufacture the compound if it is more economical, than to isolate from a natural sources. 3. To isolate, purify, identify and study the structure of active ingredients from remedies using in folk medicines and to synthesize the compound in the laboratory. 4. To synthesize the synthetic compounds with expected properties, much more efficient than analogues from natural sources. Unlike the course in general chemistry where topics often appear unrelated, each new topic in organic chemistry builds on what has come before. At the beginning let us revise the nature of chemical bonds. 3 Formation of chemical bonds. According to Lewis' model, atoms bond together in such a way that each atom participating in a chemical bond acquires a completed outer-shell electron configuration resembling that of the noble gas nearest it in the Periodic Table. Atoms acquire completed outer shells in two ways. 1. An atom may lose or gain enough electrons to acquire a completely filled outer shell. An atom that gains electrons becomes an anion (a negatively charged ion), and an atom that loses electrons becomes a cation (a positively charged ion). A chemical bond between a positively charged ion and a negatively charged ion is called an ionic bond. 2. An atom may share electrons with one or more other atoms to complete its outer shell. A chemical bond formed by sharing electrons is called a covalent bond. The main type of chemical bond in organic compounds is a covalent bond. 1. CLASSIFICATION OF ORGANIC COMPOUNDS The classes of hydrocarbons are alkanes, alkenes, alkynes, and arenes. Alkanes are hydrocarbons in which all of the bonds are single bonds and are characterized by the molecular formula CnH2n+2. Functional groups are the structural units responsible for the characteristic reactions of a molecule. The functional groups in an alkane are its hydrogen substituents. Families of organic compounds are listed in Table 1. The simplest alkane is methane, CH4; ethane is C2H6, and propane is C3H8. Constitutional isomers are possible for alkanes with four or more carbons. Thus there are two isomers of molecular formula C4H10. One of these has an unbranched carbon chain (СН3СН2СН2СН3) and is called n-butane; the other has a branched chain [(CH3)3CH)] and is called isobutane. n-Butane and isobutane are common names. Unbranched alkanes are sometimes called normal alkanes and are designated by the prefix n- in their common name . The prefixes n- and "iso" are joined by "neo" in the common names of the three isomeric C5H12 alkanes: CH3CH2CH2CH2CH3 (CH3)2CHCH2CH3 (CH3)4C n-Pentane Isopentane Neopentane A single alkane may have different names; a name may be a common name or it may be a systematic name developed by a well-defined set of rules. The system that is the most widely used in chemistry is IUPAC nomenclature. Cycloalkanes are alkanes in which a ring is present; they have the molecular formula CnH2n. The IUPAC rules for alkanes and cycloalkanes the rules for alkyl groups are given below. 4 Alkanes and cycloalkanes are essentially nonpolar and are insoluble in water. The only forces of attraction between nonpolar molecules are relatively weak induced dipole-induced dipole attractions. These forces are variously referred to as van der Waals attractions, London forces, or dispersion forces. Carbon combines with other atoms (e.g., C, H, N, O, S, halogens) to form structural units called functional groups-an atom or group of atoms within a molecule that shows a characteristic set of physical and chemical properties. Classification of organic compounds is based both on the structure of the chain and on the nature of functional groups existing in the compounds. Table 1. Some important families of organic molecules Functional Group Names of Common Family name Name Structures Functional formula ending Groups Contains only C-C and Alkane -ane C-H single bonds R-CH=CH-R Alkene -ene C = C –C C– R-CC-R Alkyne -yne Phenyl Arene none -F, -Cl, -Br, -I (Hal) Halides R– Hal Alkyl Halide none –OH Hydroxyl R–OH Alcohol, Phenol -ol –OR alkoxy R–OR Ether none –SH Mercapto R–SH Thiol, Mercaptan Thiol –SR Alkylthio R–S—R, Sulfide Amine –NH R–NH 2 primary 2 >NH R –NH Amine -amine secondary 2 >N- R N tertiary 3 –CN Cyano R—C N Nitrile Aldehyde >C=O Carbonyl -one Ketone carboxyl (carbonyl Carboxylic -ic acid (-CO2H) +hydroxyl) Carboxylic Acids -ate Ester Ester Amide Amide -amide 5 2. IUPAC NOMENCLATURE 2.1. IUPAC nomenclature of alkanes and cycloalkanes 2. 1. 1. Naming Alkanes (main rules). 1. Find the longest continuous chain of carbon atoms and assign a basis name to the compound corresponding to the IUPAC name of the unbranched alkane having the same number of carbons. The longest continuous chain in the alkane shown is six carbons. This alkane is named as a derivative of hexane. 2. List the substituents attached to the longest continuous chain in alphabetical order. Use the prefixes di-,tri-, tetra-, etc., when the same substituent appears more than once. Ignore these prefixes when alphabetizing. The alkane bears two methyl groups and an ethyl group. It is an ethyldimethylhexane. 3. Number the chain in the direction that giwes the lower locant to a substituent at the first point of difference. When numbering from left to right, the substituents appear at carbons 3,3, and 4. When numbering from right to left the locants are 3, 4, and 4. Therefore, number from left to right Correct Incorrect The correct name is 4-ethyl-3,3-dimethylhexane. 4. When two different numbering schemes give equivalent sets of locants, choose the direction that gives the lower locant to the group that appears first in the name. In the following example, the substituents are located at carbons 3 and 4 regardless of the direction in which the chain is numbered. 6 Correct Incorrect Ethyl precedes methyl in the name; therefore 3-ethyl-4-methylhexane is correct. 2.1.2. Cycloalkanes 5. Count the number of carbons in the ring and assign a basis name to the cycloalkane corresponding to the IUPAC name of the unbranched alkane having the same number of carbons. The compound shown contains five carbons in its ring. It is named as a derivative of cyclopentane. 6. Name the alkyl group and append it as a prefix to the cycloalkane.
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