Organic Compounds: an Introduction

Organic Compounds: an Introduction Andrea Raffaelli CNR - Istituto di Fisiologia Clinica, Via Moruzzi, 1, 56124 Pisa E-Mail: andrea.raffaelli@cnr.it ; WEB: http://raffaelli.ifc.cnr.it Chemical Bond Low EN: Na: 0.93 K: 0.82 Ca: 1 High EN: F: 3.98 O: 3.44 Cl: 3.16

Octet and Octet Rule F. 1s 2 2s 2 2p 5 Fluorine bears 7 electrons in the outer shell. This originates a strong tendency to gain one more electron so that all the orbitals are filled with electrons. Fluorine is strongly electronegative. Ne 1s 2 2s 2 2p 6 Neon, a «noble» gas, bears 8 electrons in the outer shell. This is a very stable situation: all the orbitals are filled with electrons. Na. 1s 2 2s 2 2p 6 3s 1 Sodium bears only one electron in the outer shell. This electron can be lost very easily so that all the outer orbitals are filled with electrons: sodium is poorly electronegative. Completion of the Octet: the Chemical Bond The tendency to complete the octet, leads to the formation of chemical bonds. A chemical bond is a lasting attraction between atoms that enables the formation of chemical compounds. The bond may result from the electrostatic force of attraction between atoms with opposite charges, or through the sharing of electrons as in the covalent bonds.

Chemical Bond: Ionic vs. Covalent Bond Uncertain Zone Pure Covalent Polar Ionic Electronegativity Difference EN F-Fr NaCl: Ionic Bond NaCl Na + Cl - EN: 2.23

Covalent Bond CC C-C EN: 0 C : C Pure Covalent ClCl Cl-Cl EN: 0 Cl : Cl Pure Covalent CH C-H EN: 0.35 C : H Pure Covalent CO C-O EN: 0.89 C : O Polar OH O-H EN: 1.24 O : H Polar + - - + Organic Chemistry: the Chemistry of Carbon Carbon is one of the few elements capable to form long chains where different carbon atoms are bonded one after the other. One of the reasons for this behavior is the presence of four electrons in the outer shell. This allows, in principle, the formation of four bonds, in order to complete the octet around each carbon atom. To this purpose, however, all the electrons of the outer shell are shared. There are no residual vacancy or excess of electrons and this induces a very stable situation.

Organic Compounds Organic compounds are formed by the interaction of carbon with other elements of the periodic table. Mainly these elements are H, O, N, halogens, P, S and a few more. Strictly speaking, organic compounds are formed at least by carbon and hydrogen. Binary compounds with these two elements are called hydrocarbons. Beside hydrocarbons, other organic compounds contain at least three elements. Binary compounds of carbon and elements other than hydrogen are considered, usually, inorganic compounds. Organic Compounds: Hybrid Orbitals CH 4 Methane First term of saturated hydrocarbons H electron configuration: 1s 1 C electron configuration: 1s 1 2s 2 2p 2 CH 2??? 90??? 1s Orbital 2s Orbital 2p Orbitals

Methane Structure 109.5 sp 3 Hybridization Linear combinations of the functions representing the orbitals can explain the structure of methane.

sp 3 Hybridization and Structure of Ethane sp 2 Hybridization and Structure of Ethene (Ethylene) In alkenes the hybridization uses two p orbitals and a s orbital. The resulting sp2 orbitals contain one electron each, the fourth electron being in the residual p orbital.

sp Hybridization and Structure of Ethyne (Acetylene) In alkynes the hybridization uses one p orbitals and a s orbital. The resulting sp orbitals contain one electron each, the remaining two being in the residual two p orbitals. Summary of Bond lenght and Energy in Saturated and Unsaturated Hydrocarbons

sp 3 Hybridization with Heteroatoms sp 3 Hybridization with Heteroatoms

Functional Groups In organic chemistry, functional groups are specific groups (moieties) of atoms or bonds within molecules that are responsible for the characteristic chemical reactions of those molecules. The same functional group will undergo the same or similar chemical reaction(s) regardless of the size of the molecule it is a part of. However, its relative reactivity can be modified by other functional groups nearby. Combining the names of functional groups with the names of the parent alkanes generates a powerful systematic nomenclature for naming organic compounds. Substituents A substituent is an atom or group of atoms substituted in place of a hydrogen atom on the parent chain of a hydrocarbon, becoming a moiety of the resultant new molecule. The terms substituent, side chain, group, branch, or pendant group are used almost interchangeably to describe branches from a parent structure. The suffix yl is used when naming organic compounds that contain a single bond replacing one hydrogen; ylidene and ylidyne are used with double bonds and triple bonds, respectively. In addition, when naming hydrocarbons that contain a substituent, positional numbers are used to indicate which carbon atom the substituent attaches to when such information is needed to distinguish between isomers.

Saturated Hydrocarbons: Alkanes General formula: C n H 2n+2 Functional group: None: just single C-C and C-H bonds ( bonds). Nomenclature Suffix: -ane. Reactivity: Relatively inert. Can undergo oxidation (combustion) and other radical reactions. Also called paraffins. H CH 4 H C H H Methane C 2 H 6 ; CH 3 -CH 3 H H H C C H H H Ethane Isomers Isomers are compounds having the same molecular formula (that is the same elemental composition) but different structure. Two isomers may belong to the same chemical class or be of different type compounds. In the previous example, butane and isobutane, both are alkanes, but, for instance, C 2 H 6 O can have two different structures, CH 3 -CH 2 -OH (an alcohol) and CH 3 -O-CH 3 (an ether). There are different kinds of isomerism, as we will see.

Saturated Hydrocarbons: Cycloalkanes General formula: C n H 2n Functional group: None: just single C-C and C-H bonds ( bonds). Nomenclature Prefix: Cyclo; Nomenclature Suffix: -ane. Reactivity: relatively inert. Can undergo oxidation (combustion) and other radical reactions. Unsaturated Hydrocarbons: Alkenes General formula: C n H 2n Functional group: C=C double bond. Nomenclature Suffix: -ene. Reactivity: the presence of electrons induces reactivity towards electrophilic reagents.

Geometric Isomers When the double C=C bond is situated internally in the carbon atoms chain there is the possibility of geometric isomerism. If two similar groups are on the same side we say the isomer is cis, if on opposite sites we indicate it as trans. There is also a better defined notation, Z or E (initials of the German words Zusammen (meaning Together ) and Entgegen (meaning Opposite ). cis-but-2-ene (or Z-But-2-ene) trans-but-2-ene (or E-But-2-ene) Unsaturated Hydrocarbons: Dienes and Polyenes General formula: C n H 2n-2x Functional group: two or more C=C double bonds. Nomenclature Suffix: -diene, -triene, Reactivity: the presence of electrons induces reactivity towards electrophilic reagents.

Dienes and Polyenes: Relative Positions of Double Bonds Dienes show quite different chemical properties depending on the relative positions of the C=C double bonds. In isolated dienes the two double bonds are far away one from the other: -C=C-(C-) n C=C-. At least two single bonds separate the two double bonds. In conjugated dienes the two double bonds are separated by only one single bond: -C=C-C=C-. In cumulated dienes (also called allenes) the two double bonds are adjacent: -C=C=C-. The central carbon atom is hybridized sp, the side ones are sp 2. Conjugated Dienes: Resonance Single C-C bond length in ethane is 1.54 Å. Double C=C bond length in ethane is 1.33 Å. Single C-C bond length in buta-1,3-diene is 1.48 Å. Double C=C bond lengths in buta-1,3-diene is 1.34 Å.

Unsaturated Hydrocarbons: Alkynes General formula: C n H 2n-2 Functional group: C C triple bond. Nomenclature Suffix: -yne. Reactivity: the presence of electrons induces reactivity towards electrophilic reagents. CH CH From Resonance to Aromaticity: Benzene Molecular formula: C 6 H 6 Functional group: Benzene (aromatic) ring. Cyclic, alternation of single and double bonds. Nomenclature: Benzene. Reactivity: the presence of electrons induces reactivity towards electrophilic reagents. All the C-C bonds have the same length of 1.39Å Resonance Energy: 36 kcal/mole 150.7 kj/mol)

Polycyclic Aromatic Hydrocarbons Molecular formula: C 10 H 8, C 14 H 10,, C 20 H 12, Functional group: Condensed benzene rings. Cyclic, alternation of single and double bonds. Nomenclature: current names used. Reactivity: the presence of electrons induces reactivity towards electrophilic reagents. Phenanthrene Halogenated compounds General formula: C n H 2n+2-m X m X = F, Cl, Br, I Functional group: C-X bond. Nomenclature Substituent; -fluoro, -chloro, -bromo, -iodo. Reactivity: Relatively inert. Polar C-X bond induces some electron deficiency on the carbon atom, which can react with nucleophilic reagents.

Oxygenated Compounds: Alcohols General formula: C n H 2n+2 O Functional group: -OH, Hydroxyl group. Nomenclature Suffix: -ol. Reactivity: Polar C-O bond induces a weak electron deficiency on the carbon atom, which can react with nucleophilic reagents. Alcohols: Primary, Secondary and Tertiary Depending on the carbon atom bearing the hydroxyl group, an alcohol is defined: Primary if the OH group is on a primary carbon; Secondary if the OH group is on a secondary carbon; Tertiary if the OH group is on a tertiary carbon. Primary Alcohols Secondary Alcohols Tertiary Alcohols OH Tert-Butanol OH 2-Methylbutan-2-ol

General formula: nn Oxygenated Compounds: Phenols Functional group: -OH, Hydroxyl group, directly linked to a benzene ring. Nomenclature Phenol. Reactivity: The hydroxyl group linked to an aromatic systems induces some acidity to the H atom. Phenols are weak acids. Oxygenated Compounds: Ethers General formula: C n H 2n+2 O Functional group: Oxygen bridge O- linking two carbon atoms. Nomenclature Suffix: -ether. Reactivity: Relatively inert. Often used as solvents.

Unsaturated Oxygenated Compounds: Carbonyl Derivatives Carbonyl derivatives contain a C=O double bond. Such a functional group, capable to link to two atoms or chains, is named Carbonyl. Strictly speaking, carbonyl derivatives are Aldehydes and Ketones. + - Carbonyl Derivatives: Aldehydes General formula: C n H 2n O Functional group: -CHO. Carbonyl links at least one H Nomenclature Suffix: -al. Reactivity: Carbon atom of the carbonyl group is quite electrophilic: tends to undergo attack by nucleophilic reagents. Oxidizes readily.

Carbonyl Derivatives: Ketones General formula: C n H 2n O (n 3) Functional group: >C=O. Carbonyl bridge linking two carbon atoms. Nomenclature Suffix: -one. Reactivity: Carbon atom of the carbonyl group is quite electrophilic: tends to undergo attack by nucleophilic reagents. Oxygenated Compounds: Carboxylic Acids General formula: C n H 2n O 2 Functional group: -COOH. Carboxylic group. Nomenclature Suffix: -oic Acid. Reactivity: Carboxylic Acids are (weak) acids. Carbon atom of the carbonyl group is quite electrophilic: tends to undergo attack by nucleophilic reagents.

Derivatives of Carboxylic Acids: Acyl Compounds Acyl compounds, where the carbonyl group is linked to an alkyl group (or an hydrogen) and to a polar group can be considered derivatives of the carboxylic acids. Acyl compounds and carboxylic acids, indeed, can be readily interconverted. General structure of these compounds is: Also nitriles, R-C N, are considered part of this class, due to the fact that they are easily hydrolyzed to carboxylic acids and easily synthesized from them. Acyl Compounds O O O Acetic Anhydride (An Anhydride) O NH 2 Benzamide (An Amide)

Compounds Containing the Carbonyl Group And so on ; S can replace O; P can replace N; Nitrogen Compounds: Amines General formula: C n H 2n+3 N Functional group: -NH 2, -NHR, NR R, Amino group. Nomenclature Suffix: -amine. Reactivity: Amines are (weak) bases. The presence of the free doublet on the nitrogen atom allows to act as nucleophilic reagents. N Triethylamine (a tertiary amine)

Sulfur Compounds Oxygen atoms can be replaced by sulfur atoms. The SH functional group is present in thiols (or mercaptans). The S- atom linked to two carbon atom is present in sulfides. The prefix thio is used to indicate these compounds. SH Thiophenol Phosphorus Compounds The nitrogen atoms of amines can be replaced by a phosphorus atom forming phosphines. Organic esters of phosphoric acid (organic phosphates) are an important class of organic pollutants. P Triphenylphosphine

Names of Organic Compounds In origin organic compounds were named as soon as they were discovered. Names were originated in a completely random way. Sometimes they reflected the origin of the compound. For instance, formic acid was isolated from the secretions of ants, acetic acid was one of the main components of vinegar, cadaverine is one of the biogenic amines coming from the decomposition of animals, and so on. Several natural terpenoids use this approach. Considering that nowadays there are millions of known organic compounds, it is not possible to invent (and remember) the names for each of them. It is necessary a rationale and systematic approach. IUPAC Nomenclature Basics: Priority of Functional Groups Priority Functional group Formula Prefix Suffix 1 Carboxylic acids COOH carboxy- -oic acid 2 Esters Acyl halides Amides COOR COX CONH 2 R-oxycarbonylhalocarbonylcarbamoyl- -R-oate -oyl halide -amide 3 Nitriles CN cyano- -nitrile 4 Aldehydes CHO formyl- -al 5 Ketones =O (-CO) oxo- -one 6 Alcohols OH hydroxy- -ol 7 Amines NH 2 amino- -amine -imine -hydrazine

IUPAC Nomenclature Basics Identification of the parent functional group, if any, with the highest order of precedence. Identification of the parent hydrocarbon chain containing the parent functional group. It must be the longest present in the structure. Identification of the side-chains. Side chains are the carbon chains that are not in the parent chain, but are branched off from it. Identification of the remaining functional groups, if any, and naming them by their ionic prefixes (such as hydroxy for -OH, oxy for =O, oxyalkane for O-R, etc.). Identification of double/triple bonds. IUPAC Nomenclature Basics Numbering of the chain. This is done by first numbering the chain in both directions (left to right and right to left), and then choosing the numbering which follows these rules, in order of precedence Has the lowest-numbered locant (or locants) for the suffix functional group. Locants are the numbers on the carbons to which the substituent is directly attached. Has the lowest-numbered locants for multiple bonds (The locant of a multiple bond is the number of the adjacent carbon with a lower number). Has the lowest-numbered locants for prefixes. Numbering of the various substituents and bonds with their locants. If there is more than one of the same type of substituent/double bond, a prefix is added showing how many there are ( di 2 tri 3 tetra 4 then as for the number of carbons below with 'a' added)

IUPAC Nomenclature Basics Arrangement in this form: Group of side chains and secondary functional groups with numbers made in step 3 + prefix of parent hydrocarbon chain (eth, meth) + double/triple bonds with numbers (or "ane") + primary functional group suffix with numbers. Wherever it says "with numbers", it is understood that between the word and the numbers, the prefix(di-, tri-) is used. Adding of punctuation: Commas are put between numbers (2 5 5 becomes 2,5,5); Hyphens are put between a number and a letter (2 5 5 trimethylheptane becomes 2,5,5-trimethylheptane); Successive words are merged into one word (trimethyl heptane becomes trimethylheptane). IUPAC Nomenclature Basics The finalized name should look like this: #,#-di<side chain>-#-<secondary functional group>-#-<side chain>- #,#,#-tri<secondary functional group><parent chain prefix><if all bonds are single bonds, use "ane">-#,#-di<double bonds>-#-<triple bonds>-#- <primary functional group> Note: # is used for a number. The group secondary functional groups and side chains may not look the same as shown here, as the side chains and secondary functional groups are arranged alphabetically. The di- and trihave been used just to show their usage. (di- after #,#, tri- after #,#,#, etc.)

Particular Cases In some instances the structure is such that it is very clear to say which is the parent functional group, but it is not easy to insert it into the parent carbon chain. This happens when an high priority functional group is present as a side chain of a cyclic moiety. In this cases the nomenclature is peculiar: Cyclohexancarboxaldehyde Cyclohexancarbonitrile Cyclohexancarboxylic Acid Ethyl Cyclohexancarboxylate More Clear with Some Examples No functional group: it s an alkane 9 Carbon chain 1 Ethyl, 1 Methyl, 1 Ethyl groups Numbering: 3,4,6 (wrong: 4,6,7) 4-Ethyl-3-methyl-6-propylnonane

Another Example 9 Carbon chain 1 Double bond in position 2 (not 7) 3 Methyl groups 4,6,8-Trimethylnon-2-ene Numbering: 4,6,8 (wrong: 2,4,6) (Tetrapropylene) More - 7 Carbon chain - Alcohol with OH in position 3 (not 5) - Double Bond in position 4 (not 3), Z configuration (Z)-Ept-4-en-3-olo

Another one 8 Carbon chain OH in position 1 (not 8) 2 Methyl groups in position 3,7 (not 2,6) 2 Double bonds in position 2,6 (anyway) The double bond in 6 position is symmetric, the one in 2 position has E configuration (the two heavier groups are in opposite positions). (E)-3,7-Dimethylocta-2,6-dien-1-ol Geraniol The last Example Citronellal 8 Carbon chain Carbonyl group in position 1 (ABSOLUTELY!) 2 Methyl groups in position 3,7 1 Double bond in position 6 (symmetric) 3,7-dimethyloct-6-enal

IUPAC Names Are They Comfortable? Retinal Cholesterol