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Organic Chemistry  

 Michon
 
 

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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)  
The synthesis of urea  by Friedrich Wöhler, in 1828.
 Organic compounds  are so named because they werefirst exclusively  observed as products or constituents of living organisms. Early chemists could not synthesize any of themfrom inorganic compounds using chemical procedures.
 
That feat was first achieved by Friedrich Wöhler(1800-1882)  when heaccidentallysynthesized urea CO (NH2)2  in 1828.

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

The work of Wöhler was the beginning of the end for thevitalism doctrine, which held that some mysterious vital force  in living tissue could make biologicalstuff qualitatively  distinct from inorganic chemical compounds.

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

ThioUrea is structurallysimilar 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 aphotographic fixer in Diazo photosensitive silk-screens.


(2010-01-20)  
Compounds of carbon and hydrogen atoms featuring only  single bonds.

The structure of a saturated hydrocarbon is described bya connected simple graphwhere each node (representing a carbon atom)  is connected [ by an edge  representing asinglebond ] 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 hydrocarbonwhere 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 nodeand 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 ofbutane  (4 carbons) corresponding either to a chain of  4  nodes or to a central nodeconnected to the other three.  The latter is called isobutane  (or methylpropane, according to the IUPAC nomenclature).

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

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

Number of distinct n-carbon alkanes :
n123456789101112...
 Structural Isomers 1112359183575159355A000602
Stereoisomers111235112455136345900A000628

Chiral molecules are optically active :

Starting with heptane, the possibility exists that a single skeletoncorresponds 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 achiral compoundwith two different possible configurations which are mirror images of each other (they are calledenantiomers). As it is traversed by a ray of polarized light,a pure enantiomer in fluid form (or in a solution) will rotatethe angle of polarization by a angle proportional to the molar density and the distancetravelled.

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'softenthe 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 ofoptically active enantiomers and one inactive meso compound. (:  As the two halves may rotate around the axis ofthe 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 pairsof 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 enantiomersfordimethylspiroheptane C9H16

 Dimethylspiroheptane   Dimethylspiroheptane

This is clearly a chiral compound  because those two mirror images cannot be superposed. Such molecules are sometimes wrongly  heralded as havingno chiral carbons. A close examination reveals that this is not the case; the above chiralmolecule does feature  3  chiral carbons  (the central carbon and the twocarbons attached to methyl groups).

Indeed, a carbon is chiral  whenever it's attached to 4  different ligands.  Two chiral ligands that are enantiomers of eachother 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 ofdimethylspiroheptane, the chain that goes fromone bond to the other and the chain that goes back have different chiralities (otherwise the whole molecule would not be chiral).  Both of those carbonsare 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 unambiguouslya direction as either clockwise or counterclockwise). Some thinking is needed to realize that two identical chiral loops meeting perpendicularly at one point form a chiralconfiguration  (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 activechemical 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 commonlynamed after thesimple alkane they are derived from  (by removing an hydrogen froma 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 chainis used along with the names and numeric positions of the akyl groups borneby 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'sonly one possibility which does not yield a compound with asimpler 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 attachedto  4  identical methyl groups.


(2010-02-05)  
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)  
The simplest alkyne  is acetylene (or ethyne,  C2H2).

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


 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)  
Unsaturated ring of 6 coplanar carbons.

The simplest aromatic compound is benzene C6H  whose cyclic structure wasfirst proposed in 1865 by August Kekulé (1829-1896)the father of structural chemistry.

Phenyl  -C6H5 (symbol Ph, formerly )  consists of six carbonsin a circle, all bonded to an hydrogen with at most one exception (no exception in the case of benzene, which may be denoted by the formula PhH). All six carbon atoms are equally spaced, regardless of their positions withrespect to the substituent.

Toluene  (PhCH3)  is also known as phenyl methane. as it consists of a phenyl group and a methy group, the IUAPC recommends the systematic name methylbenzene.

Phenol  (PhOH).  Also called carbolic acid. It consists of a phenyl group and an hydroxyl group  (-OH). As such, it's also known as phenyl hydroxide.

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


(2011-08-05)  

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


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

Inorganic chemistry, some common chemical reactionsinvolve 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-OHAlcoholR-OHEthanol
C2H5OH
Methoxyl-OCH3EtherR-OCH3Methoxypropane
C3H7OCH3
Ethoxyl-OCH5R-OCH5Ethoxypropane
C3H7OCH5
Alkoxyl - O -   R-O-R'  Diethyl Ether
C2H5O C2H5
  Carboxyl   - COOH Acid  R-COOH  Acetic acid
  CH3COOH  
Carboxylate - COO - Ester  R-COO-R'  n-Octyl Acetate
CH3COO C8H17
Aldehyl - CHO Aldehyde  R-CHO   Methanal(Formol)  CH2O
Carbonyl - CO - Ketone  R-CO-R'  Acetone
CH3CO CH3
 Perhydroxyl -O-OH Hydroperoxide   R-HOO  Methyl peroxide
CH3OOH
 -O-O-PeroxideR-OO-R'Dimethyl peroxide
(CH3O)2
-CH(NH2)-COOHAmino-acidR-CH(NH2)-COOHGlycine  [R=H]
NH2CH2COOH

  • :  Alcohol  +  Acid   Ester  +  Water
  • :  Alcohol  +  Alcohol   Ether  +  Water
  • :  Fatty Acid  +  Base   Soap  +  Alcohol

 Epoxide

Epoxides  (with the structure depicted at left) are commonly obtained industrially by the catalytic oxidation of alkenes,especiallyethylene (ethylene oxide is known asoxirane) andpropylene (propylene epoxide).


(2022-09-09)  
Living organisms synthesize proteins from only 20 different amino-acids.

The 20+2 proteinogenic amino-acids.
NameSymbolsSide ChainFormula / Note
GlycineGlyG-HNH2CH2COOH
ProlineProP-C4NH4
CysteineCysC-CH2SH
SelenocysteineSecU-CH2SeH
PyrrolysinePylO

A protein is a peptide with at least about 50 amino-acids in it. About eighty million different proteins exist on Earth. 

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


(2015-09-02)  
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 moleculeis the strongest  known chemical bond (1072 kJ/mol).  It consists of two ordinary covalent bondsand one dativebond  (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 theprimary source of carbon for all plants.

Polycarbon Dioxides :   O=(C=)n=O

Carbon dioxide is just the simplest example of a whole seriesof 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 thereare 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 BenjaminC. 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. In2015, a team from the University of Arixona at Tucson (Andrew R. Dixon and Tian Xue, supervised by Andrei Sanov)  found it to be a transientmolecule 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)  andFriedrich Wöhler (1800-1882)  as part of their study of mellite. They attributed it, tentatively, the formula  C4O.

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 ringwhich gives itaromatic properties:

 Mellitic Anydride, C12O9

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

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

Oxalic anhydride ( C2O)  has never been observed.

 Coat-of-arms of  Justus von Liebig (1803-1873)
(2015-09-18)  
Isocyanic acid,  fulminic acid,  hydrogen cyanate.

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

Isocyanic acid  (HNCO). 

Fulminic acid (HCNO). 

Hydrogen cyanate (HOCN)

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 (c) Copyright 2000-2023, Gerard P. Michon, Ph.D.

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