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© 2000-2015   Gérard P. Michon, Ph.D.    

Organic Chemistry  

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 International Year 
 of Chemistry - 2011

Organic Chemistry

 Coat-of-arms of 
 Justus von Liebig (1803-1873)  Coat-of-arms of 
 August Wilhelm von Hofmann (1818-1892)  Coat-of-arms of 
 August Kekule (1829-1896)
 Coat-of-arms of 
 James Dewar (1842-1929)  Coat-of-arms of 
 Juan Oro (1923-2004)
 Urea
(2010-01-20)   Birth of Organic Chemistry  (1824 or 1828)
The synthesis of  urea  by Friedrich Wöhler, in 1828.
 Friedrich Woehler 
 1800-1882
Friedrich Wöhler
  Organic compounds  are so named because they were first  exclusively  observed as products or constituents of living  organisms.  Early chemists could not synthesize any of them from inorganic compounds using chemical procedures.
 
That feat was first achieved by  Friedrich Wöhler (1800-1882)  when he accidentally synthesized  urea  CO (NH2)2  in 1828.

Arguably, Wöhler had founded organic chemistry 4 years earlier,  when he synthesized oxalic acid  (COOH)2  from inorganic precursors, in 1824.

The work of Wöhler marked the beginning of the end for the doctrine of vitalism which argued that a mysterious  vital force  in living things would distinguish its constituents qualitatively from inorganic chemical compounds.

Today,  organic chemistry  is essentially synonymous with  carbon chemistry.  The tetravalence of carbon leads to the tremendous diversity of carbon-based compounds which makes life possible.  Biochemistry is just a part of organic chemistry.  Organic chemistry is more broadly concerned with the study of many synthetic compounds which are unrelated to biological organisms.

ThioUrea is structurally similar to urea, with the central atom of oxygen replaced by an atom of sulfur.  It's widely used in organic synthesis and has found a direct application as a photographic fixer in Diazo photosensitive silk-screens.

The Building Blocks of Organic Compounds  by  Ken Costello   (Chemistryland)


(2010-01-20)   Saturated hydrocarbons:  Alkanes and cycloalkanes.
Compounds of carbon and hydrogen atoms featuring  only  single bonds.

The structure of a saturated hydrocarbon is described by a  connected  simple graph where each node  (representing a carbon atom)  is connected  [ by an  edge  representing a single bond ]  to at most  4  other nodes.  It's understood that every carbon atom is bonded to  4  atoms  (of either carbon or hydrogen).

A molecule whose atoms do not form any cycles is called  aliphatic.  Their carbon skeletons are  acyclic  graphs  (technically called  trees).  All the other saturated hydrocarbons are called  cycloalkanes  (although that term is often understood to denote a saturated hydrocarbon where the carbon atoms form a single cycle).

Alkanes  (Aliphatic Saturated Hydrocarbons)  CnH2n+2

All alkanes burn in air to form carbon dioxide and water:

CnH2n+2  +   3n+1   O2   ®   n CO2  +  (n+1) H2O
vinculum
2

Methane  (1 carbon atom)  is represented by a graph of one node and no edges.  Ethane  (2 carbon atoms)  corresponds to a graph of two nodes connected by one edge.  Propane  (3 carbons)  is three nodes connected by two edges.

There are two kinds of butane  (4 carbons)  corresponding either to a chain of  4  nodes or to a central node connected to the other three.  The latter is called  isobutane  (or  methylpropane, according to the IUPAC nomenclature).

There are  3  kinds of pentane  (5 carbons)  including  isopentane  (methylbutane)  and  neopentane  (dimethylpropane).

Structurally, there are  5  hexanes,  9  heptanes,  18  octanesetc.

Number of distinct n-carbon alkanes :
n 12345678 9101112 ...
 Structural Isomers  111235918 3575159355 A000602
Stereoisomers 1112351124 55136345900 A000628

Chiral molecules are optically active :

Starting with heptane, the possibility exists that a single skeleton corresponds to several spatial configurations.  In particular, this happens whenever the molecule includes just  one  so-called  chiral carbon,  namely a carbon atom bonded to  4  different  ligands.  In that case, we are faced with a chiral compound with two different possible configurations which are mirror images of each other  (they are called enantiomers).  As it is traversed by a ray of polarized light, a pure enantiomer in fluid form (or in a solution) will rotate the angle of polarization by a angle proportional to the molar density and the distance travelled.

Such an  optical activity  is observed for the following two types of heptane.  Each of these has two enantiomers because each has a single  chiral atom :

The fact that either of those yields a pair of enantiomers is the reason why there are  11  stereoisomers of heptane for only  9  structural isomers.

It's often the case that a molecule with  k  chiral carbons  has  2k  stereoisomers.  The simplest exception among alkanes is the following octane, featuring two chiral carbons but only  3  (not  4)  stereoisomers; a pair of optically active enantiomers and one inactive  meso compound.  (HINT:  As the two halves may rotate around the axis of the two chiral carbons, the meso isomer is center-symmetric.)

3,4-Dimethylhexane   =   ( C* H CH3 C2H5 ) 2

A star superscript  ( C* )  is used to indicate that a given carbon is chiral.

On the limited usefulness of the  "chiral carbon"  concept :

Spiranes are cycloalkanes which contain two cycles that share a  single  carbon atom.  At that central atom, the two pairs of bonds that define the planes of the two cycles are perpendicular.  The simplest example of a spirane is  spiroheptane, which consists of 2 carbon quadrilaterals sharing one vertex.

Spiranes can illustrate some of the difficulties associated with  chiral carbons  in the analysis of delicate cases.  For example, consider the following pair of enantiomers for dimethylspiroheptane  C9H16

 Dimethylspiroheptane    Dimethylspiroheptane

This is clearly a  chiral compound  because those two mirror images cannot be superposed.  Such molecules are sometimes  wrongly  heralded as having no chiral carbons.  A close examination reveals that this is not the case; the above chiral molecule does feature  3  chiral carbons  (the central carbon and the two carbons attached to methyl groups).

Indeed, a carbon is  chiral  whenever it's attached to  4  different ligands.  Two chiral ligands that are enantiomers of each other  are  different!  When two ligands are interconnected by a structurally symmetrical chain, the case may not be obvious to settle.  In the case of a carbon attached to a methyl group in the aforementioned molecule of dimethylspiroheptane, the chain that goes from one bond to the other and the chain that goes back have different chiralities  (otherwise the whole molecule would not be chiral).  Both of those carbons are therefore  chiral.

The case of the central atom is even trickier.  It belongs to two oriented 4-cycles which are symmetrical but chiral  (we may decide to observe from the side of the methyl group and describe unambiguously a direction as either clockwise or counterclockwise).  Some thinking is needed to realize that two  identical chiral loops meeting perpendicularly at one point form a chiral configuration  (the two chirality do not cancel, so to speak).  The central carbon is thus chiral as well.

Alkyl Groups :

Removing an hydrogen atom from an alkane yields an active chemical entity called an  alkyl group  (it's eager to combine with some other "free" group, as the two unpaired electrons from both groups tend to form a  covalent  bond).

As already illustrated above, such groups are commonly named after the simple alkane they are derived from  (by removing an hydrogen from a carbon atom at the end of a chain):  Methyl, ethyl, propyl, butyl, etc.

-CH3       -C2H5       -C3H7       -C4H9       ...

In the standard nomenclature used to describe "branched" alkanes, the longest carbon chain is used along with the names and numeric positions of the akyl groups borne by carbons on that chain.  Symmetries are usually taken advantage of, in order to make the numeric positions as small as possible.

For example, a descriptive name for  isobutane  is  methylpropane:  A methyl group attached to the middle atom  (position 2)  in the 3-chain of propane...  The position is not explicited in this case because there's only one possibility which does not yield a compound with a simpler name  (namely, straight  butane ).

Several akyl groups may be attached to the same carbon atom.  For example, dimethylpropane  properly describes a pentane  (also called  neopentane)  consisting of a central carbon atom attached to  4  identical methyl groups.

Wikipedia :   Alkanes   |   Cubane   |   Dodecahedrane   |   Cahn-Ingold-Prelog convention


(2010-02-05)   Unsaturated Hydrocarbons
They feature at least one pair of carbon atoms tied by multiple bonds.

 Come back later, we're
 still working on this one...


(2015-08-14)   Triple Bonds
The simplest  alkyne  is acetylene  (or  ethyne,  C2H2 ).

 Come back later, we're
 still working on this one...

Wikipedia :   Acetylene   |   Acetylene


 Coat-of-arms of 
 August Kekule (1829-1896)  Coat-of-arms of 
 von Hofmann (1818-1892)  Coat-of-arms of 
 Michel de Nostredame (1503-1566) (2011-09-04)   Aromatic compounds
Unsaturated ring of 6 coplanar carbons.

The simplest aromatic compound is  benzene  C6H.

Toluene  is  CH3C6H.

 Come back later, we're
 still working on this one...

Gum benzoin   |   Beinzoic acid   |   Benzene   |   Phenyl (Ph)   |   Aromatic   |   Cahn-Ingold-Prelog convention


(2011-08-05)   Carbohydrates = Saccharides  (Glucides)   CmH2nOn

 Come back later, we're
 still working on this one...

Wikipedia :   Carbohydrate   |   Monosaccharide   |   Disaccharide   |   Oligosaccharide   |   Polysaccharide


(2010-01-23)   Functional Groups
Groups of atoms that determine a class of molecular reactions.

In organic chemistry, some common chemical reactions involve only certain well-known groups of atoms within molecules.  Those are called  functional groups.  The nature of the aforementioned reactions is determined by the functional groups, but the rest of the molecule  (abbreviated R in the following tables)  may influence reactivity.  Here are a few frequently encountered groups:

Some Functional Groups Based on Oxygen
Group  Structure     Compound  FormulaExample
Hydroxyl -OH AlcoholR-OH Ethanol
C2H5 OH
   - O - Ether  R-O-R'   Diethyl Ether
C2H5 O C2H5
  Carboxyl    - COOH Acid  R-COOH   Acetic acid
  CH3 COOH  
   - COO - Ester  R-COO-R'   n-Octyl Acetate
CH3 COO C8H17
Aldehyl  - CHO Aldehyde  R-CHO    Methanal (Formol) 
CH2O
   - CO - Ketone  R-CO-R'   Acetone
CH3 CO CH3
 Perhydroxyl  -O-OH  Hydroperoxide   R-HOO   Methyl peroxide
CH3 OOH
  -O-O- PeroxideR-OO-R'  Dimethyl peroxide 
(CH3 O)2

  • Esterification :   Alcohol  +  Acid   ®   Ester  +  Water
  • Etherification :   Alcohol  +  Alcohol   ®   Ether  +  Water
  • Saponification :   Fatty Acid  +  Base   ®   Soap  +  Alcohol

 Epoxide

Epoxides  (with the structure depicted at left)  are commonly obtained industrially by the catalytic oxidation of alkenes, especially ethylene  (ethylene oxide is known as oxirane)  and propylene  (propylene epoxide).

Wikipedia :   Functional group   |   Organic chemistry   |   Dehydration reactions   |   Cumene process


(2015-09-02)   Oxocarbons = Oxides of Carbon
Compounds of carbon and oxygen  (without hydrogen).

The lightest oxide of carbon is  carbon monoxide  ( CO )  a toxic gas produced by incomplete combustion of carbon.  The triple bond between the two atoms of the carbon monoxide molecule is the  strongest  known chemical bond  (1072 kJ/mol).  It consists of two ordinary covalent bonds and one  dative bond  (where both electrons originate from the carbon atom).

The most common oxide of carbon is  carbon dioxide  ( CO or  O=C=O )  which is an essential trace component of the atmosphere  (0.04%)  and the primary source of carbon for all plants.

Polycarbon Dioxides :   O=(C=)n=O

Carbon dioxide is just the simplest example of a whole series of  rectilinear  molecules  CnO  consisting of a chain of double-bonded carbon atoms, terminated by two oxygen atoms.

For theoretical reasons, such a chain is inherently unstable if there are an even number of carbon atoms in it.

 Coat-of-arms of 
 Benjamin C. Brodie, Jr. (1817-1880) Tricarbon dioxide  is better known as  carbon suboxide  ( C3O).  It's a metastable gas discovered in 1873 by  Benjamin C. Brodie, Jr. (1817-1880). 

Günther Maier,  from  the  University of Giessen,  was involved in the discovery of two other polycarbon dioxides:

The elusive existence of  dicarbon dioxide  or  ethylenedione  ( C2O or  OCCO )  had been conjectured since 1913.  In 2015,  a team from the University of Arixona at Tucson  (Andrew R. Dixon and Tian Xue, supervised by Andrei Sanov)  found it to be a transient molecule with an approximate lifetime of  0.5 ns  (which they detected spectroscopically).
 Coat-of-arms of 
 Justus von Liebig (1803-1873)

Exotic Oxides of Carbon :

Mellitic anhydride  ( C12O)  is a sublimable solid, first obtained in 1830 by  Justus von Liebig (1803-1873)  and Friedrich Wöhler (1800-1882)  as part of their study of  mellite.  They attributed it, tentatively, the formula  C4O.

Mellite  is the  honeystone  mineral, originally discovered at Artern in 1789.  Mellitic acid  C12H6O12  was obtained from that mineral in 1799 by Martin Klaproth (1753-1817) discoverer of uranium.

The beautiful structure of the molecule of  mellitic anhydride  ( C12O)  was first characterized in 1913 by Hans Meyer and Karl Steiner.  It has a ternary symmetry around a central benzene ring which gives it aromatic properties:

 Mellitic Anydride, C12O9

Ethylenetetracarboxylic dianhydride  ( C6O)  was studied in 1967 and reportedly synthesized in 1981 and 2009.

1,2-Dioxetanedione  ( C2O)  is an unstable  dimer  of  carbon dioxide  which can be viewed as a double ketone of 1,2-dioxetane.  It has been detected by mass spectrometry.

Oxalic anhydride  ( C2O)  has never been observed.

Wikipedia :   Oxocarbons   |   Hypothetical chemical compounds   |   Cyclohexanehexone

 Coat-of-arms of 
 Justus von Liebig (1803-1873)
(2015-09-18)   Simplest compounds containing  C, H, O and N.
Isocyanic acid,  fulminic acid,  hydrogen cyanate.

In 1830,  Friedrich Wöhler (1800-1882)  and Justus von Liebig (1803-1873) 

Isocyanic acid (HNCO). 

Fulminic acid (HCNO). 

Hydrogen cyanate (HOCN)

Wikipedia :   Oxocarbons   |   Hypothetical chemical compounds   |   Cyclohexanehexone

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