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Saturday, 25 June 2011

Organic Chemistry An Introduction

Organic Chemistry

An Introduction

by Anthony Carpi, Ph.D.
To understand life as we know it, we must first understand a little bit of organic chemistry. Organic molecules contain both carbon and hydrogen. Though many organic chemicals also contain other elements, it is the carbon-hydrogen bond that defines them as organic. Organic chemistry defines life. Just as there are millions of different types of living organisms on this planet, there are millions of different organic molecules, each with different chemical and physical properties. There are organic chemicals that make up your hair, your skin, your fingernails, and so on. The diversity of organic chemicals is due to the versatility of the carbon atom. Why is carbon such a special element? Let's look at its chemistry in a little more detail.
Carbon (C) appears in the second row of the periodic table and has four bonding electrons in its valence shell (see our Periodic Table module for more information). Similar to other non-metals, carbon needs eight electrons to satisfy its valence shell. Carbon therefore forms four bonds with other atoms (each bond consisting of one of carbon's electrons and one of the bonding atom's electrons). Every valence electron participates in bonding, thus a carbon atom's bonds will be distributed evenly over the atom's surface. These bonds form a tetrahedron (a pyramid with a spike at the top), as illustrated below:
carbon bonds - Carbon forms 4 bonds
Carbon forms 4 bonds
Organic chemicals get their diversity from the many different ways carbon can bond to other atoms. The simplest organic chemicals, called hydrocarbons, contain only carbon and hydrogen atoms; the simplest hydrocarbon (called methane) contains a single carbon atom bonded to four hydrogen atoms:
carbon-methane - Methane - a carbon atom bonded to 4 hydrogen atoms 
Methane - a carbon atom bonded to 4 hydrogen atoms 
But carbon can bond to other carbon atoms in addition to hydrogen, as illustrated in the molecule ethane below:
carbon-ethane - Ethane - a carbon-carbon bond
Ethane - a carbon-carbon bond
In fact, the uniqueness of carbon comes from the fact that it can bond to itself in many different ways. Carbon atoms can form long chains:
carbon-hexane - Hexane - a 6-carbon chain
Hexane - a 6-carbon chain
branched chains:
carbon-isohexane - Isohexane - a branched-carbon chain
Isohexane - a branched-carbon chain
rings:
carbon-cyclohexane - Cyclohexane - a ringed hydrocarbon
Cyclohexane - a ringed hydrocarbon
There appears to be almost no limit to the number of different structures that carbon can form.  To add to the complexity of organic chemistry, neighboring carbon atoms can form double and triple bonds in addition to single carbon-carbon bonds:
c-ethane c-ethene c-ethyne
Single bonding 
Double bonding
Triple bonding
Keep in mind that each carbon atom forms four bonds. As the number of bonds between any two carbon atoms increases, the number of hydrogen atoms in the molecule decreases (as can be seen in the figures above).

Simple hydrocarbons

The simplest hydrocarbons are those that contain only carbon and hydrogen. These simple hydrocarbons come in three varieties depending on the type of carbon-carbon bonds that occur in the molecule. Alkanes are the first class of simple hydrocarbons and contain only carbon-carbon single bonds. The alkanes are named by combining a prefix that describes the number of carbon atoms in the molecule with the root ending "ane". The names and prefixes for the first ten alkanes are given in the following table.
Carbon
Atoms
Prefix
Alkane
Name
Chemical
Formula
Structural
Formula
1 Meth Methane CH 4 CH4
2 Eth Ethane C2H6 CH3CH3
3 Prop Propane C3H8 CH3CH2CH3
4 But Butane C4H10 CH3CH2CH2CH3
5 Pent Pentane C5H12 CH3CH2CH2CH2CH3
6 Hex Hexane C6H14 ...
7 Hept Heptane C7H16
8 Oct Octane C8H18
9 Non Nonane C9H20
10 Dec Decane C10H22

Oxidation and Reduction

Oxidation and Reduction

Kiyotomi Kaneda of Osaka University devised (Angew. Chem. Int. Ed. 2010, 49, 5545. DOI: 10.1002/anie.201001055) gold nanoparticles that efficiently deoxygenated an epoxide 1 to the alkene 2. Robert G. Bergman of the University of California, Berkeley and Jonathan A. Ellman, now of Yale University, reported (J. Am. Chem. Soc. 2010, 132, 11408. DOI: 10.1021/ja103436v) a related protocol for deoxygenating 1,2-diols. Dennis A. Dougherty of Caltech established (Org. Lett. 2010, 12, 3990. DOI: 10.1021/ol1015493) that an acid chloride 3 could be reduced to the phosphonate 4.
Pei-Qiang Huang of Xiamen University effected (Synlett 2010, 1829. DOI: 10.1055/s-0030-1258111) reduction of an amide 5 by activation with Tf2O followed by reduction with NaBH4. André B. Charette of the Université de Montreal described (J. Am. Chem. Soc. 2010, 132, 12817. DOI: 10.1021/ja105194s) parallel results with Tf2O/Et3SiH. David Milstein of the Weizmann Institute of Science devised (J. Am. Chem. Soc. 2010, 132, 16756. DOI: 10.1021/ja1080019) a Ru catalyst for the alternative reduction of an amide 7 to the amine 8 and the alcohol 9.
Shi-Kai Tian of the University of Science and Technology of China effected (Chem. Commun. 2010, 46, 6180. DOI: 10.1039/C0CC00765J) reduction of a benzylic sulfonamide 10 to the hydrocarbon 11. Thirty years ago, S. Yamamura of Nagoya University reported (Chem. Commun. 1967, 1049. DOI: 10.1039/C19670001049) the efficient reduction of a ketone to the corresponding methylene with Zn/HCl. Hirokazu Arimoto of Tohoku University established (Tetrahedron Lett. 2010, 51, 4534. DOI: 10.1016/j.tetlet.2010.06.102) that a modified Zn/TMSCl protocol could be used following ozonolysis to effect conversion of an alkene 12 to the methylene 13.
José Barluenga and Carlos Valdés of the Universidad de Oviedo effected (Angew. Chem. Int. Ed. 2010, 49, 4993. DOI: 10.1002/anie.201001704) reduction of a ketone to the ether 16 by way of the tosylhydrazone 14. Kyoko Nozaki and Makoto Yamashita of the University of Tokyo and Dennis P. Curran of the University of Pittsburgh found (J. Am. Chem. Soc. 2010, 132, 11449. DOI: 10.1021/ja105277u) that the hydride 18 (actually a complex dimer) could effect the direct reduction of a halide 17, and also function as the hydrogen atom donor for free radical reduction, and as the hydride donor for the Pd-mediated reduction of an aryl halide.
Masayuki Inoue, also of the University of Tokyo used (Org. Lett. 2010, 12, 4195. DOI: 10.1021/ol1018079) Cl3CCN to promote MCPBA oxidation of an ether 20 to the ketone 21. Kandikere Ramaiah Prabhu of the Indian Institute of Technology, Bangalore oxidized (Angew. Chem. Int. Ed. 2010, 49, 6622. DOI: 10.1002/anie.201002635) a primary azide 22 to the nitrile 23 using commercial aqueous t-BuOOH. Debashis Chakraborty of the Indian Institute of Technology, Madras found (Tetrahedron Lett. 2010, 51, 3521. DOI: 10.1016/j.tetlet.2010.04.101) that commercial aqueous t-BuOOH could also be used to oxidize an aldehyde 24 to the acid 25. Masahito Ochiai of the University of Tokushima and Waro Nakanishi of Wakayama University devised (J. Am. Chem. Soc. 2010, 132, 9236. DOI: 10.1021/ja104330g) the reagent 26 to effect oxidation of the aldehyde 24 to the Baeyer-Villiger product 27.
Jonathan M. J. Williams of the University of Bath used (Org. Lett. 2010, 12, 5096. DOI: 10.1021/ol101978h) hydroxylamine to oxidize an aldehyde 28 to the amide 30. Jörg Sedelmeier, Steven V. Ley and Marcus Baumann of the University of Cambridge established (Org. Lett. 2010, 12, 3618. DOI: 10.1021/ol101345z) that flow conditions could be used to oxidize a nitro derivative 31 to the aldehyde 32, or (not illustrated) to the corresponding carboxylic acid or (from a secondary nitro) the ketone.

Neighbouring group participation

Neighbouring group participation

The stereochemical outcome of a glycosylation reaction may in certain cases be affected by the type of protecting group employed at position 2 of the glycosyl donor. A participating group, typically one with a carboxyl group present, will predominantly result in the formation of a β-glycoside. Whereas a non-particiapting group, a group usually without a carboxyl group, will often result in an α-glycoside.
Below it can be seen that having an acetyl protecting group at position 2 allows for the formation for an acetoxonium ion intermediate that blocks attack to the bottom face of the ring therefore allowing for the formation of the β-glycoside predominantly.
NGPAcetoxoniumIon.gif
Alternatively, the absence of a participating group at position 2, allows for either attack from the bottom or top face. Since the α-glycoside product will be favoured by the anomeric effect, the α-glycoside usually predominates.
NGPBenzylExample.gif

Building blocks

[edit] Building blocks

Common donors in oligosaccharide synthesis are glycosyl halides, glycosyl acetates, thioglycosides, trichloroacetimidates, pentenyl glycosides, and glycals. Of all these donors, glycosyl halides are classic donors, which played a historical role in the development of glycosylation reactions. Thioglycoside and trichloroacetimidate donors are used more than others in contemporary glycosylation methods. When it comes to the trichloroacetimidate method, one of the advantages is that there is no need to introduce heavy metal reagents in the activation process. Moreover, using different bases can selectively lead to different anomeric configurations. (Scheme 2) As to the thioglycosides, the greatest strength is that they can offer a temporary protection to the anomeric centre because they can survive after most of the activation processes.[3] Additionally, a variety of activation methods can be employed, such as NIS/ AgOTf, NIS/ TfOH, IDCP (Iodine dicollidine perchlorate), iodine, and Ph2SO/ Tf2O. Furthermore, in the preparation of 1, 2-trans glycosidic linkage, using thioglycosides and imidates can promote the rearrangement of the orthoester byproducts, since the reaction mixtures are acidic enough.
Scheme2(Lu).gif

Oligosaccharide synthesis

Oligosaccharide synthesis

Oligosaccharides have diverse structures. The number of monosaccharides, ring size, the different anomeric stereochemistry, and the existence of the branched-chain sugars all contribute to the amazing complexity of the oligosaccharide structures. The essence of the reducing oligosaccharide synthesis is connecting the anomeric hydroxyl of the glycosyl donors to the alcoholic hydroxyl groups of the glycosyl acceptors. Protection of the hydroxyl groups of the acceptor with the target alcoholic hydroxyl group unprotected can assure the regiochemical control. Additionally, factors such as the different protecting groups, the solvent, and the glycosylation methods can influence the anomeric configurations. This concept is illustrated by an oligosaccharide synthesis in Scheme 1. Oligosaccharide synthesis normally consists of four parts: preparation of the glycosyl donors, preparation of the glycosyl acceptors with a single unprotected hydroxyl group, the coupling of them, and the deprotection process.
Scheme1(Lu).gif

Classification of organic compounds

Classification of organic compounds

[edit] Functional groups

The family of carboxylic acids contains a carboxyl (-COOH) functional group. Acetic acid is an example.
The concept of functional groups is central in organic chemistry, both as a means to classify structures and for predicting properties. A functional group is a molecular module, and the reactivity of that functional group is assumed, within limits, to be the same in a variety of molecules. Functional groups can have decisive influence on the chemical and physical properties of organic compounds. Molecules are classified on the basis of their functional groups. Alcohols, for example, all have the subunit C-O-H. All alcohols tend to be somewhat hydrophilic, usually form esters, and usually can be converted to the corresponding halides. Most functional groups feature heteroatoms (atoms other than C and H). Organic compounds are classified according to functional groups, alcohols, carboxylic acids, amines, etc.

[edit] Aliphatic compounds

The aliphatic hydrocarbons are subdivided into three groups of homologous series according to their state of saturation:
  • paraffins, which are alkanes without any double or triple bonds,
  • olefins or alkenes which contain one or more double bonds, i.e. di-olefins (dienes) or poly-olefins.
  • alkynes, which have one or more triple bonds.
The rest of the group is classed according to the functional groups present. Such compounds can be "straight-chain," branched-chain or cyclic. The degree of branching affects characteristics, such as the octane number or cetane number in petroleum chemistry.
Both saturated (alicyclic) compounds and unsaturated compounds exist as cyclic derivatives. The most stable rings contain five or six carbon atoms, but large rings (macrocycles) and smaller rings are common. The smallest cycloalkane family is the three-membered cyclopropane ((CH2)3). Saturated cyclic compounds contain single bonds only, whereas aromatic rings have an alternating (or conjugated) double bond. Cycloalkanes do not contain multiple bonds, whereas the cycloalkenes and the cycloalkynes do.

Nomenclature

Nomenclature

Various names and depictions for one organic compound.‎
The names of organic compounds are either systematic, following logically from a set of rules, or nonsystematic, following various traditions. Systematic nomenclature is stipulated by specifications from IUPAC. Systematic nomenclature starts with the name for a parent structure within the molecule of interest. This parent name is then modified by prefixes, suffixes, and numbers to unambiguously convey the structure. Given that millions of organic compounds are known, rigorous use of systematic names can be cumbersome. Thus, IUPAC recommendations are more closely followed for simple compounds, but not complex molecules. To use the systematic naming, one must know the structures and names of the parent structures. Parent structures include unsubstituted hydrocarbons, heterocycles, and monofunctionalized derivatives thereof.
Nonsystematic nomenclature is simpler and unambiguous, at least to organic chemists. Nonsystematic names do not indicate the structure of the compound. Nonsystematic names are common for complex molecules, which includes most natural products. Thus, the informally named lysergic acid diethylamide is systematically named (6aR,9R)-N,N-diethyl-7-methyl-4,6,6a,7,8,9-hexahydroindolo-[4,3-fg] quinoline-9-carboxamide.
With the increased use of computing, other naming methods have evolved that are intended to be interpreted by machines. Two popular formats are SMILES and InChI.