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The structure of organic compounds - Organic Chemistry Tutor

The way in which component atoms of an organic substance are bound between them and influence each other, defines the chemical structure. This fundamental idea has been developed within "Theory of organic compounds' structure" of A.M.Butlerov (1861). Being enriched with new remarkable theoretical gains such as stereochemical theory, electronic theory in organic chemistry and others, the theory of structure of the organic compounds allowed scientific systematization of the wide experimental material of organic chemistry, correct explanation of the already known phenomenons and getting to discover new ones. On the foundation offered by this theory, through the tireless work of thousands of scientists, the modern organic chemistry has been created and developed.

Chemical structure notion

The chemical structure of a molecule represents its most characteristic and unique aspect because it determines its general properties (mechanic, physical, chemical and biochemical); any interference brought to the chemical structure determine corollary changes of its properties.

In case of little structural changes brought to one molecule, there are registered little modification of its properties (usually the physical ones are affected); if the molecule suffers profound structural changes, its properties (especially the chemical ones) are deeply modified.

For example, alfa-aminopropionic acid (alfa-alanine) has the next indicated structure: CH3-CH(NH2)-COOH in which we can observe: presence of certain atomic classes (C, H, O, N), of a certain number of atoms belonging each class, that are bound in a certain order; all these structural aspects will determine a number of properties for alfa-alanine such as: solid aggregation status, boiling point at 295°C, water solubility, characteristics of aminoacids , optical activity, etc.

Transferring the aminic group to the other C atom (which is a minimal structural change) corresponds to beta-alanine: NH2-CH2-CH2-COOH whose general chemical properties are still the ones of an aminoacid but has a boiling point at 200°C and doesn't present an optical activity anymore. If the two O atoms from this molecule are connected by the N atom (a profound structural change), the substance will become a nitroderivative, 1-nitro-propane: CH3-CH2-CH2-NO2 its physical and chemical properties being totally different from the ones of an aminoacid. 1-nitro-propane is an yellow fluid, with boiling point at 131°C, water insoluble and can be reduced to n-propilamine. Moving the nitro- group to the neighbouring C atom (a minimal structural change): CH3-CH(NO2)-CH3 doesn't modify the chemical essence of this compound (2-nitro-propane is still an aliphatic nitroderivative), but changes little of its physical properties (boiling point at 115°C). The interrelation structure-properties allows describing general properties of a substance with a known structure and, by contraries, allows finding the chemical structure of a substance by knowing its general properties.

General principles of determining the structure of organic compounds

In the essence of determining the structure of an organic compound, there lie the next principles which undercome from the connection between structure and properties:
a) an organic substance, in analytical purity state, has the same composition regardless the source from which is obtained;
b) an organic substance, in analytical purity state, has constant physical and chemical properties;
c) an organic substance with constant composition and properties has an unique structure and only one.

The meaning of these principles can be easier comprehended by understanding the schedule in the figure bellow:

Relation between composition-properties-structure

Where the dotted arrows represent the correlation between the composition of a substance and its properties meaning that for a constant composition correspond constant properties and vice versa. From this schedule it results that determining chemical structure is possible only through properties and composition. Ignoring the relationship structure-properties there will be discovered that, due to the isomeric phenomenon, proportionally with the substance's complexity, there are a number of chemical structures representing still as many different chemical compounds that correspond to a certain composition.

If, by contraries, we ignore the relation composition- structure, there can be observed that the chemical structure notion loses its sense completely, based on the fact that a chemical structure can be organized in the limits of a certain reestablished composition only.

These are the reasons why determining the structure of an organic compound is made step by step, essentially going through a certain order, a serie of specific work stages which are:

a) the purification of the substance until it reaches analytical purity, observed through invariableness of constant physical parameters(boiling point, refraction index, density, etc);

b) establishing its composition using the quality and quantity study and determining the percent that each atomic group participates with, in order to obtain that certain composition. This is how the percentual formula of the analyzed substance is created, formula that can be used in order to calculate its gross formula. Then, there is determined - using the physical or chemical path - the molecular mass that simultaneously expresses the qualitative (the atomic groups) and quantitative composition (the number of atoms coming from each group) of the studied substance. This is why the molecular formula of an organic compound will always appear as a sequence of chemical symbols (belonging to the organogenic elements placed in order of their importance) followed by, from case to case, correspondent numeric indexes, as shown below: C5H10; C7H6O; C8H9N; C4H10O2N2; C5H10NCl; C10H7O4N2Br. Meanwhile, not every sequence of symbols and numeric indexes represents an existing molecular formula. The verification criteria of the validity of a molecular formula is represented by the sum of all the covalences of the composing elements which always has to be an even number.

For example, for the formula C10H7O4N2Br it is observed the following: the 10 C atoms participate with a sum of 40 covalences (10*4), the 7 H atoms with 7 covalences, the 4 O atoms with 8 covalences, the 2 N atoms with 6 and brome with one covalence, a total of 62 covalences, that is an even number of covalences, which confirms the validity of this composition. The rule will be the same for all cases and will not be considered, and of course they will not be written, the molecular formulas that don't respect this criteria.

Through the molecular formula, we can calculate a theoretical parameter called equivalent unsaturation or the unsaturation number, which indicates global unsaturation produced in the molecule by the presence of multiple links (heterogeneous or homogenous) or by the presence of certain cycles.

For a general situation of a molecular formula such as CaHbOcNdXe, the equivalent unsaturation will be determined using the next formula: E.U. = (2a+2) - (b-d+e) / 2

There will be observed that: O (and any other bicovalent element) doesn't interphere in this calculation no matter the number of atoms it participates with; the factor (2a+2) represents the total number of H atoms in the alkane molecule which has the same number of C atoms.

E.U. values can be only integer and positive numbers (including 0), this condition represents the second verification criteria of the validity of a molecular formula which can, possibly, respect the parity of covalences criteria, but not be a real substance. For example, in the compound with the molecular formula C5H12NBr3 the elements participate with 20 + 12 + 3 + 3 = 38, 38 is an even number the formula should be real, but E.U. = (5x2+2) - (12-1+3) / 2 = -1. The equivalent unsaturation has a negative value which shows that it doesn't exist a substance which such a composition.

Based on the N.E. numbers there can be made certain assessment on the global structure regarding that substance's molecule, namely:
- degrees of N.E. equal to 0, 1, 2, 3 belong to aliphatic compounds with linear or cyclic structure
- degrees of N.E. equal to 4, 5, 6 belong to mononucleus aromatic structural compounds
- degrees of N.E. higher than 7 belong to polinucleus aromatic structural compounds

In the following, in order to determine the structure of an organic compound it is proceeded to new stages of work such as:

c) determining the properties by using several chemical and physical methods

d) creating a structural pattern represented by appropriate means (regular formulas, special formulas, structural models etc.)

e) examining the structural model trough synthesis of the investigated substance starting from compounds with a pre-known structure which react via pre-known mechanisms as well

If exact determining of an organic substance's composition became nowadays a routine practice, examining and establishing its properties continues to be a source of various problems, which, in order to be solved, determine the scientists to put a great effort in. Generally, in studying the properties and the chemical structure of an organic substance, there are used chemical and physical methods and even combined techniques using the two types of methods.

If using chemical methods, the analyzed substance undergoes a number of chemical transformations corresponding to its chemical nature being identified and, in some cases, being dosed the obtained compounds; the nature (and quantity) of this elements helps deducing certain conclusions about the initial compounds structure. The main chemical processes used in this sense are: oxidation, reduction and hydrolysis.

Oxidation is used for some classes of hydrocarbons, alcohols, aldehydes, ketones etc.; as reactive products result ketones or carboxylic acids with the same number of C atoms or, as a result of breaking some of the chemical bounds in the molecule, compounds with an inferior number of C atoms.

Reduction and hydrogenation (usually catalytic) are used for unsaturated compounds which are transformed in correspondent saturated compounds.

Hydrolysis is a reaction used for halogenated derivatives substances, policondensed products obtained trough water disposal (polyzaharides, polyamides, polyesters etc.) or functional derivatives (esters, amides, nitriles). As a result of hydrolysis there are obtained certain mixes of different components that are being separated and identified individually.

In the chemical methods group used to determine the organic compound's structure there are included the functional analysis, which can be qualitative or quantitative and that sets, trough specific reactions, the nature and number of the functional groups in an organic molecule.

The chemical methods that are used to determine the structure have several disadvantages, amidst which the most significant are: the long period of time needed, total used of a large quantity of substance, limited structural information, unable automation of some of the steps etc. Most of this disadvantages are solved today by using physical methods.

The physical methods that help determining the structure have occurred during the last few decades and have widely extended as a result of their undeniable advantages: are very quick, need very little substance (10-2 - 10-4 g) that is in the end fully regained, they offer a great deal of structural information. Usually by the instrumentality of the physical methods it is studied the way organic molecules react towards different physical agents: electromagnetic radiations, beams of elementary particles, magnetic fields, polarized light, heat etc. and from the obtained data, we can deduct the conclusions regarding the studied compound's structure.


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