PART 0 An Advanced Introduction to Organic Chemistry

Organic chemical history, bonding, variety and complexity of compounds

Doc Brown's Chemistry Advanced Level Pre-University Chemistry Revision Study Notes for UK KS5 A/AS GCE level organic chemistry students US K12 grade 11 grade 12 organic chemistry

Sub-index for Part 0

0.1 A brief history of organic chemistry

0.2 The basis of organic chemistry - variety and complexity

0.3 Bonding theory and examples of the ways bonds surround a carbon atom

0.4 Representation of organic molecular formulae and structures and definitions

General Organic Chemistry Indexes

All Advanced Organic Chemistry Notes

Index of GCSE/IGCSE Oil - Useful Products Chemistry Revision Notes

0.1 A brief history of organic chemistry (advanced AS/A level chemistry revision notes)

The word 'organic' historically refers to chemical materials pertaining to plant or animal or animal organisms. The term organic was used as a convenient classification for substances derived from plant or animal materials.

In this sense organic substances go back to prehistoric times e.g. making wines by fermentation of sugary fruit materials (alcohol, ethanol solution) and the souring of wine to make vinegar (acetic acid/ethanoic acid solution).

Methods of using vegetable oils and animal fats to make soap have been known since Roman times,

and methods of applying the vegetable dye indigo and dyeing with madder root (alizarin) were also developed by both Roman and Egyptian civilisations. The production of dyed fabrics was an important commercial venture and some dyes were highly prized and the resulting fabrics very costly - purple only for very high status citizens! From these humble origins from the late 19th century to the present day the development and production of synthetic dyes shows no sign of slowing down!

By AD 900 the Islamic civilisation had developed a crude distillation process to increase the concentration of alcohol and produce oil of terpentine from pine resin. The words alchemy and chemistry are derived from Arabic words such as Al-Kimiya (which effectively means chemistry in Arabic today). The word alkaline is derived from the Arabic word Al-Qali which referred to substances derived from calcined ashes of the glass-wort plant that the Arabs used to make soap and glass. In medieval English it became 'alkali'. The names of substances like benzoin and benzene are derived from the Arabic phrase 'Luban Jawi' meaning substances derived from a natural 'aromatic' resin Arabic traders brought from Indonesia. Later benzoic acid was derived from benzoin resin and in turn benzene was synthesised from benzoic acid in the 19th century. In Victorian times dyes were made from aniline (phenylamine, aminobenzene), the Arabic word for dyes from indigo was annil. The word 'alcohol' is derived from the Arabic 'Al-khul' which mean body eating fluid! (it may also be the origin of the word ghoul!), but we are getting ahead of ourselves in the development of organic chemistry.

In the 16th and 17th century other products were made by pyrolysis e.g. the dry distillation of wood that yielded a variety-mixture of organic liquids including acetone (propanone). In the 18th century the technique of solvent extraction was used to obtain substances from plant and animal materials. In the years 1769-1785 the great Swedish chemist Scheele did many investigations that effectively prepared the way for the chemistry of studying biological products e.g. he isolated tartaric acid (2,3-dihydroxybutanedioic acid) as the sour taste of the grape, citric acid (2-hydroxypropane-1,2,3-tricarboxylic acid) from lemon, malic acid (2-hydroxybutanedioic acid) from apples, lactic acid (2-hydroxypropanoic acid) from sour milk, uric acid from urine and oxalic acid (ethanedioic acid) from wood sorrel, and he also prepared the latter by oxidation of sugar with concentrated nitric acid (a powerful oxidising agent). This was impressive work, but he had no idea what the molecular structure of these compounds was, but YOU can now work them out from the IUPAC systematic names in brackets.

Back to the late 18th century and early 19th century; from 1772-1777 the French chemist Lavoisier conducted some combustion analysis of organic compounds by measuring the amounts of water and carbon dioxide formed and was able to deduce the percentage of carbon and hydrogen in organic compounds. He produced the best results of his time, but they far from accurate, but it was recognised that organic compounds seemed to consist of carbon, hydrogen only, or these two elements combined with oxygen or nitrogen or both. unfortunately atomic theory and accurate atomic masses ('atomic weights') were still a few decades in the future.

The term 'organic'  as a branch of the study of chemistry, was used by the Swedish chemist Berzelius in 1807, and it was believed that these substance derived from once living material had some kind of 'vital force' associated with them. Organic compounds seemed more 'reactive', 'sensitive' or 'less stable' and so different from inorganic compounds e.g. they were combustible or readily transformed into different materials, especially by the application of heat and most organic compounds were liquids and low melting solids, compared to most inorganic compounds like salts which seemed so stable and high melting.

This doctrine of an essential vital force remained unchallenged until the German chemist Wohler, by chance discovery in 1828, that an inorganic salt (of non-plant/non-animal origin) was converted into a well known organic compound urea

All you do is evaporate ammonium cyanate solution ===> urea crystals;   NH₄OCN  ===> CO(NH₂)₂

This is actually an (the first known?) example of an isomerisation reaction, in this case based on the formula CH₄N₂O

Clearly the inorganic salt had no 'vital force', and as Wohler said in a letter to Berzelius "I must tell you that I can prepare urea without requiring a kidney of an animal, either man or dog". Nearly the end of 'vital force' theory, but still no molecular structures known!

However, the term organic chemistry, has been universally accepted as the chemistry of carbon compounds bar carbon oxides and inorganic carbonates.

Further syntheses e.g. Kolbe's synthesis of ethanoic acid (acetic acid) from its elements in 1845, further proved that no vital force was needed to make vinegar, identical to that formed by the souring of fermented sugar solution!

The pioneering work of Lavoisier was continued by the German chemist Liebig (of condenser fame) who improved combustion analysis apparatus so that the  technique of burning organic compounds was producing quite accurate data by 1838. It actually took until 1911 via the work of the chemists like the Austrian Pregl to perfect the technique of semi-micro analysis on small samples of highly purified samples of organic compounds to give % composition to at least 3 significant figures. During the same period techniques for determining the percentage of nitrogen were also developed (by the French chemist Dumas 1830 and more accurately by the Danish chemist Kjeldahl in 1883 (a technique I was taught to do in the 1960s). This meant by the end of the 19th century the majority of organic compounds could now be analysed accurately, and from patterns in formula the idea of 'valency' or 'combining power' was beginning to shape (see work of Kekule below). Atomic masses e.g. of carbon, hydrogen, oxygen and nitrogen were now accurately known.

By the mid 19th century different substances with the same empirical formula were being recognised

e.g. alcohol (ethanol) and dimethylether (methoxymethane), both having an empirical formula C₂H₆O, but at that time, all they really knew that these compounds contained the same % of carbon, hydrogen and oxygen but were obviously different chemicals but of unknown structure.

From the increasing accurate and widening analysis of organic compounds, the idea of 'valency' ('combing power') of carbon, hydrogen, oxygen and nitrogen atoms was beginning to emerge and thanks to the brilliance of chemists like the German chemist Kekule, a solution to explaining the different formulae began to emerge.

Remarkably, as early as 1859 Kekule proposed that that carbon could form four bonds in a variety of ways, and added a similar idea for oxygen and hydrogen and came up with the following 'bonding' situations:

>C< (4 single),   =C= (two double),   -C (single plus triple),   -O- (two single),   =O (one double)  and   -H (one single)

Recognise this lot, not bad for a graphical representations of 1859, and it meant that Kekule could write out simple structures like

methane ,  carbon dioxide O=C=O,  ammonia ,  hydrogen cyanide (methanenitrile) H-CN

and the structures of hydrocarbons like ethane   and   propane which fitted the analytical data.

Therefore organic chemists now had a way of writing out formula and explore possible structures based on empirical formula analysis and of course be able to explain isomerism (different molecular structures with the same molecular formula).

e.g.   and 

We of course now take these structures to another level and draw electronic dot and cross diagrams, but they only emerged in the 1920s via the electron octet theory of compound structure!

So, it was only by the late 19th century the concept of 'homologous series' and 'functional group' were beginning to be recognised!

BUT, although structural formulae could now be correctly written down, the actual 3D shape of molecules was still a mystery.

Stereochemistry, 'three dimensional chemistry', didn't begin with organic molecules, but from 1812 to 1820 it was noticed that hemihedral quartz crystals seem to occur in two forms that were mirror images of each other. It was also demonstrated that each crystal form rotated plane polarised light in opposite directions. This occurs when molecular structures exhibit a centre of asymmetry. From 1820 to 1854 via the work of scientists like Louis Pasteur and Biot , crystals of some organic acid salts like ammonium tartrate could be separated into two forms with the same chemical formula, that were chemically and physically identical except that the solution of each form rotated plane polarised light in equal but opposite directions.

To explain the two different forms, which we now know as optical isomers (enantiomers), Kekule's valency theory offered a solution by presenting his 2D structures in a 3D way. The brilliant Dutch scientist van't Hoff proposed in 1874 that the four valencies of the 'central carbon' (we know call this the asymmetric or chiral carbon), pointed to the corners of a tetrahedron. Therefore with a molecule Cabcd, where a, b, c and d are different atoms or groups of atoms, it is possible to construct two models of the compound which are non-superimposable mirror image forms. These forms cannot have a plane of symmetry, whereas Ca₄, Ca₃b, Ca₂b₂, and Ca₂bc all have a plane of symmetry . Unknown to van't Hoff, the French chemist Le Bel had come to the same theoretical proposition (hypothesis). We now know that from x-ray diffraction studies of optically active organic compounds, that both of these great scientists were absolutely correct, but that was about 40 years later in the early 20th century!

Now we can confidently draw structures such as  for alpha amino acids, and deduce bond angles from electron pair repulsion theory, no problem!

So, by the end of the 19th century the basic structure of thousands of organic molecules was understood and ideas on the 3D structure of them too. Atomic masses were accurately known and methods of molecular mass determination were also developed so that the relationship between empirical formula and molecular formula were now clearly understood.

By 1899 full commercial production of the sedative aspirin (acetylsalicylic acid, 2-ethanoylhydroxybenzoic acid), a medication used to treat pain, fever, or inflammation, was in full commercial production but the original molecules with these medicinal properties were obtained from plants such as willow and had been known in ancient Greece as early as 400 BC from the writings of Hippocrates, who describes the preparation of willow herb tea! This was one of many developments that 2300 years on from the ancient Greeks that has contributed to the development of the pharmaceutical industry.

The pain killer codeine is derived from morphine, the chief alkaloid molecule in opium. There are many instances where a whole series of drugs are developed from a starter molecule from a plant resource including analgesics, blood pressure controls, Statins to control cholesterol levels in the blood etc. etc. The skill of organic chemists is such that very complicated naturally occurring molecules can be synthesised in the laboratory by amazing multi-stage preparations from indigo like dyes to chlorophyll.

However, the spatial arrangement of atoms in organic molecules was not clear, so the idea of bond angles and 3D shape was still very much in its infancy and the propositions of van't Hoff and Le Bel, although correct, were not proven. The development of X-ray crystallography to get to the 3D molecular structure of organic molecules began in 1912-1914 with the work of Bragg (Cambridge, England) and the German Max von Laue. Initially they worked with inorganic crystals but as the x-ray diffraction analysis techniques improved, crystals of organic compounds were analysed. At the same time the electronic theory of atomic and molecular structure was developing and bond angles measured and compared with bonding theory predictions.

X-ray crystallography of biological molecules progressed e.g. with the remarkable and pioneering work of the English woman Professor Dorothy Hodgkin, who solved the structures of cholesterol (1937), penicillin (1946) and vitamin B12 (1956), for which she was awarded the Nobel Prize in Chemistry in 1964 (apart from mother Marie and daughter Irene, the Curies were the only other women to get a Nobel prize in chemistry). In 1969, she succeeded in solving the structure of insulin, on which she had  worked for over thirty years!

In 1952 Rosalind Franklin and others working at Kings College, London and Cambridge, obtained crucial x-ray diffraction photographs (crystallographic data) that would help lead to the recognition of the double helix structure of DNA. Her work was not fully recognised at the time and she should have got a Nobel Prize in 1962 with the likes of Crick, Watson and Wilkins (who also used x-ray diffraction), but she tragically died of cancer in 1958 at the age of 37.

One of the problems was the complex mathematics needed to analyse x-ray diffraction data. What might take months in the 1950s can be done in minutes today with modern high speed computers. IT is now a powerful too in the development of chemistry.

The structure of many essential molecules such as vitamins are known and many can be synthesised in the laboratory. Synthetic proteins can be made and manipulation of DNA genetic material is nothing short of amazing.

From the mid 19th century to the early 20th century, particularly in the USA, the commercial usefulness of crude oil was recognised and so the petrochemical industry was born from which, to this day, we derive a variety of hydrocarbon products ranging from fuels to polymers (the latter via alkenes from cracking) and a host of other organic molecules including the synthesis of many pharmaceutical products once derived from natural plant and animal sources.

In the late 19th century plastics were produced by modifying natural polymers e.g. celluloid by reacting cellulose from plants with nitric acid. The first truly synthetic plastic was the hard brown material known as Bakelite, patented in 1910. All the well known plastics like nylon, Terylene, poly(ethene) - discovered by accident in 1933, poly(propene), PVC, polystyrene, Perspex and polyurethanes were developed through 1930s to the 1960s. Crude oil has become the largest source of organic chemicals and we are very much dependent on its products.

World War II lead to many technological developments in radar and electronics. This in turn lead to major advances in spectroscopic techniques for investigating the structure of organic molecules. Techniques like infra-red spectroscopy and mass spectroscopy are quite limited but nuclear magnetic resonance spectroscopy (proton NMR and C-13 NMR) is the most powerful molecular technique apart from x-ray diffraction analysis.

¹H proton NMR is so sophisticated now, you can deduce the whole structure of quite complex organic molecules from the NMR spectra alone, it is an amazing technique. I presume you still need x-ray diffraction analysis to get the full 3D structure?

Some of the most advanced chemical advances are now being made using computer databases of highly accurate 3D images of organic molecules. Even complex protein molecules like enzymes are being modelled and drugs can be designed to fit into the active site to inhibit their action, the basis of many medical treatments.

0.2 An advanced introduction to organic chemistry - VARIETY and COMPLEXITY

(advanced level chemistry revision notes)

More on WHY is there such a range of organic molecules and hence why the vast discipline of organic chemistry?

AND more on homologous series and functional groups.

• There are many possible series of organic molecules, so why such variety?

• Organic compounds belong to different families, though all organic compounds are based on carbon C, usually hydrogen H, and sometimes other elements such as oxygen, nitrogen, phosphorous and sulfur.

  • The chemistry of the oxides of carbon and carbonates is NOT considered part of organic chemistry.

• Most food is chemically organic in nature, apart from some minerals, and many drugs and plastic materials are composed of organic molecules, consequently, organic compounds and organic chemistry is rather important to us!

• The term organic compound comes from the fact that most of the original organic compounds studied by scientists-chemists came from plants or animals, i.e. of natural origin and contained the 'vital force' of mother nature!

  • Historically, for thousands of years, many organic compounds have been used indirectly in herbal preparations for healing and alleviating symptoms and in food materials such as honey.

  • Many natural products have proved precursors for the development of synthetic 'man-made' drugs manufactured by the pharmaceutical industry.

• These days most organic compounds are produced and synthesised from raw materials, in particular the physical separation and chemical manipulation of the products of fractionally distilling crude petroleum oil.

• However, this description of organic chemistry and its historical origins does NOT explain the vast range of organic molecules and their complex chemistry.

• The principal reason why the range of organic molecules is primarily due to the fact that carbon atoms have the ability to link together by strong covalent bonds to form linear chains, branched chains and cyclic chains and with considerable numbers of rearrangements to make different molecules of the same formula (isomers).

  • Carbon is in Group 4 of the periodic Table with four outer electrons (2.4 or 1s²2s²2p²) which readily pair with electrons from an atom like oxygen or nitrogen to give four stable covalent bonds (maybe 4 single bonds, 2 single and a double bond, two double bonds or a triple and a single bond), either way, the normal valency (combining power) of carbon in organic compounds is four.

  • The property of forming chains is called catenation and the C-C bonds are generally strong giving rise to whole groups (homologous series) of stable organic molecules.

  • To add to the complexity and variety of organic molecules, carbon can also form stable bonds with other elements, especially ...

    • oxygen as in alcohols like ethanol which is used in fuels, as a solvent and combined with organic acids to make esters used in flavourings and perfumes.

    • nitrogen as in amines like ethylamine   are organic bases and form alkaline solutions when dissolved in water.

    • nitrogen and oxygen in amino acids like aminoethanoic acid which is found combined with other amino acids in polypeptides - proteins.

    • halogens as in bromoethane is an 'intermediate' compound and used in the organic synthesis of more complex organic compounds.

    • and sulfur & phosphorus etc. by substituting a hydrogen atom with another element or group of atoms compared to hydrocarbon alkanes like butane which only consists of carbon and hydrogen atoms.

  • So, this leads to even more possible 'families' of organic compounds and many more individual different molecules.

  • There is no limit to the number of different organic molecules that can be made, though only a small percentage of them would be useful (others maybe unstable or very difficult to synthesise).

    • The molecular formula represents a summary of all the atoms in the molecule and a general formula sums up the formulae a series of compounds e.g. a homologous series of chemically similar compounds.

      • More on these terms later, but you need their basic definition to appreciate the next point I'm making.

    • Just to give you an idea of the limitlessness of organic chemistry, using some simple molecular formulae and general formulae, consider the table below of the number of molecules which can theoretically exist for a given molecular formula

      • The different structures with the same molecular formula are called isomers (see types of isomerism).

      • Isomers have the same molecular formula, but differ in the way the atoms are connected or how the atoms are spatially arranged.

      • Examples are shown in the diagram below, but don't worry about the details here, just appreciate what we mean by the concept of isomers and how it makes organic chemistry much more interesting!

      • You will appreciate more about the structures after studying section 0.4 Representation of organic molecules

      • The easiest example to appreciate is the two isomers of C₂H₆O, two completely different molecules from the same 9 atoms of the same molecular formula, you will understand the rest in time!

• The following table really brings home the possibilities and sheer huge variety of organic molecules.

• e.g. if n = 5 for the number of carbon atoms in the molecular formula you get ...

• alkanes of molecular formula C₅H₁₂  (3 isomers)

• alkenes/cycloalkanes of molecular formula C₅H₁₀  (5 isomers)

• alcohols/ethers of molecular formula C₅H₁₂O  (14 isomers)

• and amines of molecular formula C₅H₁₃N  (17 isomers)

• Some of these numbers of these isomers (highlighted in blue) have been worked out using a computer program i.e. an algorithm is used to compute possible numbers of molecules of a given general formula given a set of rules based on valencies.

• As the number of carbon atoms increases the number of possible arrangement of the atoms increases dramatically even for molecules just containing carbon and hydrogen.

• Once you substitute a hydrogen atom for another element or group of atoms, there is a bewildering number of possible molecular structures.

• The fact that life, as far as we know it, is based on carbon chemistry, and we do not know of another element from which the same huge variety of stable molecules can be me made.

  • Even unstable organic molecules can be synthesised and manipulated in the laboratory and biochemistry is based on the thousands of molecules that exist in living systems e.g. sugars, proteins (tissue, enzymes etc.), RNA, DNA, fats like lipids etc. etc. etc.!!!.

    • In one of the simplest living cells like an E coli cell, there may be 5000 different compounds, most of them organic molecules! (e.g. as many as 3000 proteins and 1000 nucleic acids i.e. RNA/DNA molecules)

• The compounds in each family have a similar chemical structure and a similar chemical formula and each family of organic compounds forms what is called a homologous series.

  • As pointed out, different families arise because carbon atoms readily join together in chains (catenation) and strongly bond with other atoms such as hydrogen, oxygen and nitrogen.

  • The result is a huge variety of 'organic compounds' which can be classified into groups of similar compounds i.e. these different homologous series.

• A homologous series is a family of compounds which have a general formula and have similar physical and chemical properties because they have the same functional group of atoms i.e. a significant similarity in molecular structure, but with an increasing number of carbon atoms (usually in a chain).

  • e.g. C=C alkene, C-OH alcohol or -COOH carboxylic acid etc.

  • Usually, the addition of a -CH₂- group gives the next member in the homologous series.

  • A functional group is an atom or combination of atoms which gives an organic molecule its particular chemistry - a characteristic set of reactions..

    • In effect a functional group is an atom or group of atoms, when part of different molecules, gives those molecules similar and distinctive chemical properties.

    • This applies to all homologous series except alkanes which do not have a defined functional group.

  • The term 'functional' group is linked to the concept of a homologous series.

  • A homologous series is a group of molecules with the same general formula and the same functional group.

    • All homologous series have a functional group apart from alkanes.

  • They have similar physical and chemical properties such as similar characteristic chemical reactions, appearance, melting/boiling points, solubility etc. albeit with trends in physical properties e.g. increasing boiling point with increasing carbon chain length i.e. increase in molecular mass due to increasing intermolecular attractive forces.

    • The terms higher/lower refer to a larger/smaller or longer/shorter carbon chains e.g.. the higher or lower number of CH₂ groups in the carbon chain.

    • You should notice as you move from one member of a homologous series to the next, you add on an extra -CH₂- unit.

• The molecular formula represents a summary of all the atoms in the molecule e.g. butane is C₄H₁₀ and can be derived from a general formula - which is explained more in section 9.1.1 onwards.

0.3 Bonding theory and examples of ways bonds surround a carbon might be represented

An advanced introduction to organic chemistry - BONDING THEORY

You might not have encountered all the types of molecular/ionic bonding situations mentioned here, but that shouldn't matter too much if you have started studying molecules with different functional groups.

Reminder of s and p orbitals

 From the quantum level rules, carbon's electron configuration is 1s²2s²2p²

In terms of the separate orbitals you can express it as 1s², 2s², 2p_x¹, 2p_y¹, 2p_z⁰

This can be further expressed as an electron box diagram: 1s2s2p with two unpaired electrons.

However, as you should know by now, carbon usually forms four bonds (valency of 4) rather than two.

This is because it is energetically favourable to promote one electron from the 2s orbital into the third empty 2p_z orbital, the energy required for this 'promotion' is far less than that released when the carbon atom forms four bonds rather than two..

This gives a theoretical electron configuration of 1s², 2s¹, 2p_x¹, 2p_y¹, 2p_z¹  or  1s2s2p

This gives four unpaired electrons, all of which can pair up with an electron from another atom to form four covalent bonds, but they may be of two varieties if a double or triple bond is involved in the carbon based molecule - read on ...

Reminders (if needed): The diagrams below show the bonding situation in alkenes, that conveniently involve two of the most important types of covalent bond between atoms, including carbon.

        Sigma and pi covalent bonds in alkenes

A single bond (sigma bond, σ bond) is formed by the overlap of two orbitals which can be either an s orbital or a p orbital (illustrated above).

Two electrons (an electron pair) are mutually attracted to the positive nuclei on either side.

A molecular orbital is formed and the axis of the bond lies on a central line between the two nuclei.

In this case. the pi bond (π bond) is formed by the overlap of two p orbitals, but, due to repulsion with the bonded pairs of the sigma bond electrons, they cannot form another sigma bond molecular orbital along the same central axis.

Instead, a pi orbital (containing one electron), is formed above and below the planar arrangement of the bonds linking the two carbon, and other atoms together (>C=C< planar bond arrangement).

Incidentally, the presence of the pi orbitals inhibits rotation around the double bond in unsaturated alkenes, because it requires a lot of energy to twist the orbitals around and break the pi bond. However, in alkanes everything is free to rotate around the sigma bonds of the C-C bonds in saturated alkane molecules.

Note 1. to 7. apply to the above diagram.

1. Four single bonds (four sigma bonds σ): You find this tetrahedral bonding arrangement around the carbon atom in methane (CH₄) or methanol (CH₃OH). See VSEPR theory - predicting molecule/ion shapes

2. Two single bonds and one double bond (three sigma bonds σ and one pi bond π): You find this trigonal planar bonding situation in alkenes like ethene (H₂C=CH₂) or propene and also in ketones like propanone (CH₃)₂C=O).

3. One single bond and one triple bond (two sigma bonds σ and two pi bonds π): You find this linear triple/single bonding arrangement in alkyne hydrocarbons like ethyne H–C≡C–H. See VSEPR theory - predicting molecule/ion shapes

4. Three single bonds (three sigma bonds σ): The unpaired electron means this is a free radical fragment of a molecule e.g. the ethyl free radical CH₃CH₂^.. The trigonal pyramidal arrangement of the bonds arises from there being four groups of electrons around the carbon atom highlighted. See VSEPR theory - predicting molecule/ion shapes

5. Three single bonds (three sigma bonds σ): You find this trigonal planar arrangement of bonds in carbocations e.g. the ethyl carbocation would be written as [CH₃CH₂]⁺. There are three groups of electrons around the carbon atom (highlighted) carrying the positive charge, hence the trigonal planar arrangement of the bonds. See predicting molecule shapes

6. One single bond and a double bond (two sigma bonds σ and one pi bond π): You might not come across one of these, but its called an acylium cation, a positive ions based on an acyl group e.g. [CH₃C=O]⁺, the positive ion based on the ethanoyl group. There are two groups of electrons around the carbon atom (highlighted) carrying the positive charge, hence the linear arrangement of the bonds.

7. Three single bonds (three sigma bonds σ): The lone pair of electrons means that this carbon species is a negative ion, known as a carbanion e.g. the ethyl carbanion is [CH₃CH₂:]^–. There are four groups of electrons around the carbon atom (highlighted) carrying the negative charge, hence the trigonal pyramidal arrangement of the bonds

8. 8 You can also have, but not shown in the diagram above, another version of two sigma bonds and two pi bonds about a carbon atom, but this time involving two double bonds

   • e.g.   O=C=O in carbon dioxide   and   H₂C=C=CH₂ in propa-1,2-diene.

9. Notice for 4., 5. and 7., I've deliberately used structures based on the ethyl (CH₃CH₂) group to highlight their essential differences.

TOP OF PAGE - INDEX

0.4 Representation of organic molecular formulae and structures and definitions

A molecular formula e.g. C₃H₆O₂, gives a summary of all the atoms in the molecule, but gives no information on structure.

e.g. the above molecular formula three atoms of carbon combined with six atoms of hydrogen and two atoms of oxygen.

However, there may be more than one structure with that molecular formula and you can't tell which is which from the molecular formula.

You have no idea about the arrangement of atoms i.e. their structural arrangement, positions of bonds and atoms and not a clue about what its shape may be!

An empirical formula is the simplest whole number ratio of the atoms in a compound as found by experiment i.e. chemical analysis.

It gives no structural information and may or may not be the same as the molecular formula e.g. CH₄ is both the empirical formula and the molecular formula of methane. You can't simplify CH₄ into a simple integer ratio formula.

However, the molecular formula of the butane molecule is C₄H₁₀ but its empirical formula is C₂H₅  (≡ C₄H₁₀ ÷ 2)

The molecular formula of a glucose sugar molecule is C₆H₁₂O₆ but its empirical formula is only CH₂O  (≡ C₆H₁₂O₆  ÷ 6)

The molecular formula will be a simple integer multiple of the empirical formula ... (atomic masses H = 1, C = 12, O =16)

e.g. 2 x C₂H₅ gives C₄H₁₀  (since molecular mass of butane is 58 and the empirical formula mass is 29)

and  6 x CH₂O gives C₆H₁₂O₆  (since molecular mass of the sugar is 180 and the empirical formula mass is 30)

In order to decide what the real molecular formula is, you need more information - need to know the relative molecular mass.

For calculations of empirical formula and molecular formula from chemical analysis and molecular mass ...

see Using moles to calculate empirical formula and deduce molecular formula of a compound/molecule

A structural formula - may be minimal, abbreviated or shortened e.g. ethanol or cyclohexene, to give a 'limited' molecular structure view of a molecule but unambiguous if you know how to interpret the representation.

Therefore, however abbreviated, a structural formula shows the unique arrangement of atoms in a molecule, but does not show all the individual bonds.

Some individual bonds may be shown (in cyclohexene) or non at all (ethanol).

Whatever, you need to be able to translate the structural formula into the full displayed formula showing the position of every atom and bond e.g. ethanol (right diagram and below). Lots more on displayed formula in the next section.

Displayed formulae: The full graphical formula or full structural formula, usually described these days as the full displayed formula shows all the individual atoms and bonds.

e.g. ethanol above right and 1-bromo-1-chlorobutane, shown here on the right (but don't worry about the naming at the moment).

However, it can be acceptable to show some side-chain groups in an abbreviated form e.g. methylpropane (left), where the side-chain methyl group may be written in the abbreviated 'structural' form, but take care in exams, if unsure, clearly show ALL the atoms and bonds if the displayed formula is requested!

In displayed formula many bond angles look as if they are 90⁰, when they are actually 109^o or 120^o.

Therefore you can go one stage further and give a 3D representation of the molecule e.g. to show the tetrahedral arrangement of the bonds emanating from a carbon atom.

A structural displayed formula with full 3D spatial representation e.g. which shows the shape of the molecule methanol and implies bond angles (in this case all are 109^o). The 'dotted line' bond is behind the plane of the screen/paper/page and the 'wedge' bond is towards you. The other two thin line bonds are in the plane of the screen/paper/page etc. This gives a good impression of the real shape of the molecule in terms of the directional covalent bonds and all bond angles here are ~109^o. The dotted line bond is now usually shown as a wedge pointing down away from the carbon atom.

Footnote on bond representation in structural-displayed formulae

C-C represents a single bond between carbon atoms, C-O a single bond between a carbon and oxygen atom.

A single bond consists of a single sigma bond (σ).

C=C represents a double bond between carbon atoms, C=O a double bond between a carbon and oxygen atom.

A double bond consists of a sigma bond (σ) and a pi bond (π), more details in appropriate sections.

C≡C represents a triple bond between carbon atoms, C≡N a triple bond between a carbon and nitrogen atom.

A triple bond consists of a single sigma bond (σ) and a two pi bonds (π).

Skeletal formula - something a bit different than all the other molecular representations so far!

A skeletal formula e.g. is one in which, (in most cases), none of the H atoms bonded to carbon atoms are shown, and none of the carbon atoms of the chain either! 

This is actually 3-ethylpent-1-ene, CH₃CH₂CH(CH₂CH₃)CH=CH₂,

(don't worry about the name if you haven't done the nomenclature of alkenes).

Instead of some kind of structural or displayed formula, lines represent carbon-carbon bonds (single, double or triple), but other lines are needed to show bonds from the carbon chain to other atoms which are NOT carbon or hydrogen e.g. like C-Cl in chlorobenzene or 2-chloropropane and the C-OH in alcohols like propan-1-ol or butan-2-ol .

(its acceptable to show the hydroxy group as OH rather than O-H, but you should put O-H in displayed formulae and make sure the bond line goes to the O of the -OH and the C of the -Cl.

The bond lines should indicate the underlying shape of the molecule e.g. the zig-zag chain of carbon atoms.

As already pointed out, where hydrogen is part of a functional group involving non-carbon atoms attached to a carbon atom, then you will show the H atoms involved.

e.g. –OH in alcohols (above), –OH in carboxylic acids e.g. the -COOH in propanoic acid

and –NH₂ in amines (-NH₂ functional group in ethylamine)

and in acid amides e.g. the CONH₂ functional group in propanamide

To sum up molecular representations using ethanol in all its various guises!

Empirical formula C₂H₆O, molecular formula C₂H₆O but you can't distinguish it from the isomer methoxymethane CH₃-O-CH₃

Isomers are molecules with different molecular structures, but have the same molecular formula (see isomerism)

Structural formula , ,

All of which clearly distinguish ethanol from methoxymethane.

Displayed formula and a 3D version of the displayed formula

In the 3D version of the displayed formula the dots mean bonds to atoms behind the plane of the paper/screen, wedges towards you mean bonds coming out from the plane of the paper/screen and you can consider the atoms of the H-C-C-O-H sequence to be all in the plane of the paper/screen. You also get a good impression of the bond angles of the molecule, all of which are ~109^o and NOT 90^o! for H-C-H, H-C-C, C-C-H and C-O-H.

and finally the skeletal formula is .

There are lots more examples on the pages (links further down) covering the individual classes of organic compounds.

A general formula sums up the formulae a series of compounds e.g. a homologous series of chemically similar compounds with closely related formulae e.g. the only difference may be more/less -CH₂- groups in the longest carbon chain of the molecule.

There are many examples quoted throughout the rest of this page in the style C_xH_yO_z etc. where x, y and z are integer variables like 1 (never shown), 2, 3 etc. which must be shown, but they are related for a particular homologous series e.g. for saturated non-cyclo alkanes by a general formula e.g.

C_nH_2n+2 for alkanes,

so that n = 1 generates the formula for methane CH₄ and n = 5 generates the formula for pentane C₅H₁₂ etc.

C_nH_2n+1COOH is the general formula for monocarboxylic acids,

so that n = 0 generates the formula for methanoic acid HCOOH, the first aliphatic carboxylic acid

 and n = 4 generates the formula for pentanoic acid CH₃CH₂CH₂CH₂COOH, the 5th acid in the series.

NOTE:  Do not assume n always indicates the total carbon atoms in a molecule!

However in all cases, the IUPAC systematic name is derived from the longest possible carbon chain in the molecule, so both meth... (for one carbon) and pent... (for five carbons) occur in the names of the examples above.

More examples and details of functional groups and homologous series

• A homologous series is a family of compounds which have the same general formula (*) and have a similar molecular structure and similar chemical properties because they have the same functional group of atoms (e.g. C=C alkene, C-OH alcohol or -COOH carboxylic acid).
  • Members of a  homologous series have similar physical properties such as appearance, melting/boiling points, solubility etc. BUT show trends in them e.g. steady increase in melting/boiling point with increase in carbon number or molecular mass.

  • The functional group is a group atoms common to all members of a particular homologous series that confer a particular set of characteristic chemical reactions on each member molecule of the series.

• From one member of a homologous series to the next, you add on an extra -CH₂- unit

• Some examples of general formula and the functional group for four homologous series of organic molecules
  • These examples are based on a linear chain of 2 to 8 carbons atoms, but the amply illustrate the four homologous series described.
  • Homologous series of alkanes C_nH_2n+2, where n = 1, 2, 3 etc. number of carbon atoms in the molecule
    • The diagram shows ethane, the 2nd in the series, n = 2.
    • Alkanes don't really have a functional group like most other homologous series.
    • CH₃CH₂CH₂CH₂CH₂CH₂CH₂CH₃ octane C₈H₁₈, n = 8 and is 8th in the homologous series of linear alkanes.
  • Homologous series of alkenes C_nH_2n, where n = 2, 3, 4 etc. number of carbon atoms in the molecule
    • Here the functional group is the carbon - carbon double bond, >C=C<
      • The diagram shows ethene, the 1st in the series, n = 2.
      • pent-1-ene C₅H₁₀, n = 5 and is 4th in the homologous series of linear 1-ene alkenes.
  • Homologous series of alcohols C_nH_2n+1OH, where n = 1, 2, 3 etc. number of carbon atoms in the molecule
    • Here the functional group is the hydroxy group attached to a carbon atom, C-O-H
      • The diagram shows ethanol, the 2nd in the series, n = 2.
      • pentan-1-ol C₅H₁₁OH, n = 5 and is 5th in this homologous series of linear 1-ol aliphatic alcohols.
  • Homologous series of carboxylic acids C_nH_2n+1COOH, where n = 0, 1, 2 etc. number of carbon atoms in the molecule minus 1
    • Here the functional group is, COOH, a combination of one carbon, two oxygen and one hydrogen atom.
      • The diagram shows ethanoic acid, the 2nd in the series, n = 2.
      • hexanoic acid C₅H₁₁COOH, n = 5 and is 6th in this homologous series of linear aliphatic carboxylic acids.

AND the usefulness of skeletal formulae!

Skeletal formula are particular useful for depicting large complicated 'biological' molecules e.g. fats or opiate molecules.

Triglyceride fats are pretty big molecules and best represented using skeletal formula

The molecular formula of three well known opiate molecules - can you see all the functional groups present? (clockwise)

morphine, C₁₇H₁₉NO₃, functional groups: secondary alcohol, ether, (benzene ring), phenol, tertiary amine, alkene

codeine, C₁₈H₂₁NO₃, functional groups: secondary alcohol, ether, (benzene ring), ether, tertiary amine, alkene

heroin, C₂₁H₂₃NO₅, functional groups: ester, ether, (benzene ring), ester, tertiary amine, alkene

(Let me know if haven't spotted another functional group, and they all described below.)

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