Organic Compounds

Organic Compounds:
“Those compounds which contain carbon and hydrogen elements and their derivatives. An organic compound is any member of a large class of gaseous, liquid, or solid chemical compounds whose molecules contain carbon.”
Carboxylic acid
Amino acids etc.

“A contaminant is a substance that is where it shouldn’t be and is at high enough levels to have a negative effect on our health or on the health of animals or plants. A contaminant is any potentially undesirable substance (physical, chemical or biological).”
Environmental contaminants:
The term environmental contaminants  refers to harmful chemicals present in soil, air and water. These compounds may come directly from human sources such as industrial manufacturing, agricultural run-off and wastewater discharge – or they may originate from natural sources, such as the taste and odor-causing chemicals in water generated by algae and bacteria blooms.

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List of Environmental Contaminants:
Pesticides and herbicides
Fuels and fuel additives (e.g. MTBE and BTEX)
VOCs (e.g. PCE and TCE)
Endocrine disruptor chemicals (EDCs)
Analytical techniques:
“An analytical technique is a method that is used to determine the concentration of a chemical compound or chemical element.”
There are a wide variety of techniques used for analysis, from simple weighing (gravimetric analysis) to titrations (titrimetric) to very advanced techniques using highly specialized instrumentation.

Any analytical techniques can be used for the purpose of identification, though their potentialities are not the same.

Gas chromatography (GC)
Gas Chromatography-Mass Spectrometry (GC-MS Analysis)
Gel Permeation Chromatography (GPC Analysis)
Fourier Transform Infrared Analysis (FTIR)
NMR (Nuclear Magnetic Resonance) Spectroscopy
High Performance Liquid Chromatography (HPLC)
These techniques are described as follows:
Gas chromatography (GC)
Gas Chromatography (GC) provides a quantitative analysis of volatile and semi-volatile organic compounds found in a variety of matrices (gases, liquids and solids) in foods, medical materials, plastics, environmental samples and occupational monitoring samples.

Flame-ionization detectors (FID), Flame photometric detectors (FPD) and thermal conductivity detectors (TCD) are useful for determining the concentration of specific compounds.

Rapid, quantitative, cost effective and compound specific.

Can be performed with minimal sample preparation or clean up.

Quantification of bulk gases methane, carbon dioxide, carbon monoxide, N2, O2, Ethane, Propane, Acetylene, Ethylene and helium.

Quantification of hydrogen sulphide, mercaptans, DMS and carbon disulphide.

Characterization and quantification of oils and fuels and phthalates.

Quantification of bulk gases in landfill gas and biogas.

Quantification of sulphurous compounds in landfill gas and biogas.

Determination of carbon monoxide for landfill underground fires.

Determination of TPH content of wastes.

Determination of phthalate content in children’s toys and packaging for medical devices.

Typical Industries using Gas Chromatography
Medical devices
Waste water treatment plants
Landfill operators
Waste treatment plants
Manufacturers of children’s toys.

Gas Chromatography-Mass Spectrometry (GC-MS Analysis)
Gas Chromatography-Mass Spectrometry provides a quantitative analysis of volatile and semi-volatile organic compounds found in a variety of matrices (gases, liquids and solids) in foods, medical materials, plastics, environmental samples and occupational monitoring samples.

Mass spectrometers are useful for determining the concentration of known compounds and providing identifications of unknown compounds.

Analysis is sensitive and specific
Can quantify 2 or more co-eluting peaks of different chemical structures
Can provide qualitative data as well as quantitative data
Good starting position for the identification of unknown compounds, odors or initial tests of unknown material contaminants
Can be used for a much wider range of compounds types than an FID, TCD or FPD as long as the compound can be volatilised below 340°C.

Quantification of Trace Volatile organic gases in landfill gas and biogas
Residual solvent analysis in pharmaceuticals and medical materials
Identification of some unknown odour sources
Identification of unknown contaminants
Identification and quantification of siloxanes in landfill gas and biogas.

Typical Industries using Gas Chromatography
Medical devices and materials
Waste water treatment plants
Landfill operators
Waste treatment plants
Manufacturers of children’s toys.

Gel Permeation Chromatography (GPC Analysis)
GPC (Gel Permeation Chromatography), also called Size Exclusion Chromatography (SEC), provides molecular weight data of polymers by separating analytes according to size.

A type of liquid chromatography, samples is typically dissolved in an organic solvent before filtering the solution and injecting it into a chromatography column.  A molecular weight sensitive detector then monitors the concentration by weight of polymer in the eluting solvent.

Gel Permeation Chromatography offers:
Identification of molecular weight distribution
Separation of different molecular weight polymers
Little chance of analyte loss occurring.

Characterization of polymers (e.g. viscosity, strength)
Understanding of polymer performance
Analysis of polymer wearing and degradation
Development of new products (understanding how polymers behave)
QA / QC during polymer production.

Typical Industries using GPC:
Polymer manufacturers / processors
Medical device manufacturers who use polymers (e.g. in catheters)
Bone cement manufacturers
Consumer health
Packaging manufacturers.

Fourier Transform Infrared Analysis (FTIR)

“FTIR Spectroscopy is a technique based on the determination of the interaction between an IR radiation and a sample that can be solid, liquid or gaseous.”
It measures the frequencies at which the sample absorbs, and also the intensities of these absorptions.
The frequencies are helpful for the identification of the sample’s chemical make-up due to the fact that chemical functional groups are responsible for the absorption of radiation at different frequencies.

The concentration of component can be determined based on the intensity of the absorption. The spectrum is a two-dimensional plot in which the axes are represented by intensity and frequency of sample absorption. Because all compounds show characteristic absorption/emission in the IR spectral region and based on this property they can be analyzed both quantitatively and qualitatively using FT-IR spectroscopy.
In case of environmental studies FTIR Spectroscopy is used to analyze relevant amount of compositional and structural information concerning environmental samples (Grube et al., 2008). The analysis can be performed also to determine the nature of pollutants, but also to determine the bonding mechanism in case of pollutants removal by sorption processes. Techniques for measuring gas pollutants such as continuous air pollutants analyzer (SO2, NO2, O3, NH3), on-line gas chromatography (GC) used simple real-time instruments to quantify gas pollutants. They need to use several sensors in order to analyze multiple gas pollutants simultaneously.

FTIR provides detailed information on the bond structures within compounds. FTIR depends upon the absorption of infrared radiation arising from the vibrational and rotational characteristics of dipolar chemical compounds. The arrangement and strength of chemical bonds within a molecule have a direct effect on the characteristic modes of vibration and vibrational bond frequencies of a molecule, resulting in the formation of a series of characteristic mid-infrared absorption bands (4000-400 cm-1) which can be used to characterise and quantify individual compounds.

To ensure that the highest quality of data is obtained several alternative FTIR sample presentation techniques including FTIR microscopy are available covering an extensive range of applications.

Identification of solid or liquid organic and inorganic compounds.

Multi-component mixture analysis of solids liquids and gels using spectral subtraction and data mining.

Identification of polymers, polymer blends, rubbers and filled rubbers, adhesives, coatings, promoters and hardening agents.

Confirmation of consistency of raw and finished manufacturing materials.

Surface modification and sample weathering studies.

Multi-component quantitative analysis of complex mixtures by Partial Least Squares (PLS) analysis.

Solvent extraction and identification of manufacturing impurities, metabolites and contaminants.

Analysis of unknown solvents, cleaning agents and detergents.

FTIR microscopy for examination of microstructures and manufacturing defects.

Mapping the consistency of raw and finished products and investigation of product irregularities.

Mapping coating thickness and cross sectional imaging of cut sections.

NMR (Nuclear Magnetic Resonance) Spectroscopy
“NMR (Nuclear Magnetic Resonance) Spectroscopy provides physical, chemical, electronic and structural information from organic compounds in liquid or solid form”.

Samples are typically dissolved in a deuterium-labelled solvent to form, a clear solution before being transferred to a thin, transparent glass NMR tube.  The sample is then placed into a very strong magnetic field whereby the nuclei of the atoms absorb and then re-emit electromagnetic radiation at a particular resonance frequency.  This information provides structural and electronic information which translates into an extremely powerful analytical technique.

Nuclear Magnetic Resonance Spectroscopy offers:
Identification of molecular chemical environments and structures
Physical and chemical properties at the atomic and molecular level
Well resolved, highly sensitive, analytically tractable and highly predictable analysis.

Structural determination of molecules including bio macromolecules.

Determination of molecular motion and interaction profiles.

The study of proteins including enzyme active sites.

Compound identification
Purity analysis
Stability studies.

Typical Industries using NMR Spectroscopy:
Pharmaceutical industry
Agrochemical industry
Chemical industry
Polymer industry
Medical device industry
Nuclear industry
Consumer health
Packaging manufacturers
Petrochemical and oil.

High performance liquid chromatography is basically a highly improved form of column chromatography. Instead of a solvent being allowed to drip through a column under gravity, it is forced through under high pressures of up to 400 atmospheres. That makes it much faster.

It also allows you to use a very much smaller particle size for the column packing material which gives a much greater surface area for interactions between the stationary phase and the molecules flowing past it. This allows a much better separation of the components of the mixture.

The other major improvement over column chromatography concerns the detection methods which can be used. These methods are highly automated and extremely sensitive.

The column and the solvent
Confusingly, there are two variants in use in HPLC depending on the relative polarity of the solvent and the stationary phase.

Normal phase HPLC
This is essentially just the same as you will already have read about in thin layer chromatography or column chromatography. Although it is described as “normal”, it isn’t the most commonly used form of HPLC.

The column is filled with tiny silica particles, and the solvent is non-polar – hexane, for example. A typical column has an internal diameter of 4.6 mm (and may be less than that), and a length of 150 to 250 mm.

Polar compounds in the mixture being passed through the column will stick longer to the polar silica than non-polar compounds will. The non-polar ones will therefore pass more quickly through the column.

Reversed phase HPLC
In this case, the column size is the same, but the silica is modified to make it non-polar by attaching long hydrocarbon chains to its surface – typically with either 8 or 18 carbon atoms in them. A polar solvent is used – for example, a mixture of water and an alcohol such as methanol.

In this case, there will be a strong attraction between the polar solvent and polar molecules in the mixture being passed through the column. There won’t be as much attraction between the hydrocarbon chains attached to the silica (the stationary phase) and the polar molecules in the solution. Polar molecules in the mixture will therefore spend most of their time moving with the solvent.

Non-polar compounds in the mixture will tend to form attractions with the hydrocarbon groups because of van der Waals dispersion forces. They will also be less soluble in the solvent because of the need to break hydrogen bonds as they squeeze in between the water or methanol molecules, for example. They therefore spend less time in solution in the solvent and this will slow them down on their way through the column.

That means that now it is the polar molecules that will travel through the column more quickly.

Reversed phase HPLC is the most commonly used form of HPLC.

A flow scheme for HPLC

Injection of the sample
Injection of the sample is entirely automated, and you wouldn’t be expected to know how this is done at this introductory level. Because of the pressures involved, it is not the same as in gas chromatography (if you have already studied that).

Retention time
The time taken for a particular compound to travel through the column to the detector is known as its retention time. This time is measured from the time at which the sample is injected to the point at which the display shows a maximum peak height for that compound.

Different compounds have different retention times. For a particular compound, the retention time will vary depending on:
the pressure used (because that affects the flow rate of the solvent)
the nature of the stationary phase (not only what material it is made of, but also particle size)
the exact composition of the solvent
the temperature of the column
That means that conditions have to be carefully controlled if you are using retention times as a way of identifying compounds.

The detector
There are several ways of detecting when a substance has passed through the column. A common method which is easy to explain uses ultra-violet absorption.

Many organic compounds absorb UV light of various wavelengths. If you have a beam of UV light shining through the stream of liquid coming out of the column, and a UV detector on the opposite side of the stream, you can get a direct reading of how much of the light is absorbed.

The amount of light absorbed will depend on the amount of a particular compound that is passing through the beam at the time.