Life Scientist's guide to chemistry - @ a glance

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This guide is a quick reference to the important chemical concepts of relevance to the life science researcher. The information is not intended to be an exhaustive list, but to provide assistance to those researches who are new to this field. This guide includes the following chemical topics:

 

Chemical Bonds and Orbitals

Structural Drawings

Synthesis

Acid, Base and Salt Compounds

Isomerism

Moles (n) and Molecular Weight (Mw)

 

Chemical Bonds and Orbitals

There are two basic types of bond; ionic and covalent.

Ionic:

Result from the electrostatic interaction between a negatively charged anion and a positively charged cation. This type of bonding is generally seen between a metal and a non-metal where there is a large difference in the electronegativity of the atoms.

Covalent:

This bond occurs when one atom is able to donate electrons to another atom. For example a hydrogen atom has 1 electron in its outer shell but needs 2 to have a full, stable configuration, therefore when 2 H atoms bond each H donates its 1 electron into the bond so that the 2 atoms can share the 2 electrons and become stable as H2.

In reality most bonds exist between the two extremes of the ideal ionic and covalent bond structure.

Orbitals:

Electrons are arranged in specific energy levels at different distances from the nucleus (1 being the closest and so on). Within each energy level there are ‘orbitals’, an orbital is a region in which it is most likely to find an electron. There are different orbitals represented by the letters s, p, d, f and g. Orbitals are filled with electrons in a specific order to ensure that the lowest overall energy is obtained.

Molecular orbital theory
Molecular orbital theory describes how atomic orbitals are combined to form bonding orbitals between two elements. When two atomic orbitals are in phase (opposite electron spin states) they can either overlap end on, creating σ-bonding orbitals, or they can overlap side on which creates a π-bonding orbital. If the atomic orbitals are out of phase then it creates an anti-bonding orbital (figure 1A). Hybridized orbitals arise when two or more orbitals merge together; this increases stability by eliminating an unoccupied orbital. In alkenes two hybrid orbitals overlap end on forming the σ-bond and the p-orbitals overlap, side on, around the sigma bond to form the π-bond (figure 1B).

 

 

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 Structural Drawings

Generally σ bonds are represented by lines between atoms and π bonds are shown by double lines. For example a structural drawing of ethane (i) and ethene (ii) shows each carbon and hydrogen atom and how they are bonded to one another. (figure 2).

Ethane and ethene


Usually hydrogen and carbon atoms are removed for simplicity; as shown in the below example of propan-1-ol. Each ‘apex’ in the skeletal structure represents a carbon atom. As carbon forms 4 bonds to be stable it is assumed that any bond not shown is occupied by hydrogen. (figure 3)

Skeletal structural drawing

Stereochemistry

Drawings give a 2D representation of the compounds 3D structure. Stereochemistry is often included in structural drawings to give a better representation of the 3D structure.

  • Stereochemical drawing of Dihyrokainic acidStraight line = a bond in the plane of the page
  • Dashed wedge = a bond that is 'going into the page'
  • Solid wedge = a bond 'coming out of the page'

This is shown in the example of Dihydrokainic acid. (figure 4)

 

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Synthesis

This process involves the complete chemical synthesis of complex organic molecules from simpler, more readily available precursors. A synthesis is carried out in stages:

  • Choose a reaction route 
  • Determine the safety of the synthesis
  • Calculate the molar quantities of each reactant needed to produce the desired amount of product
  • Set out the appropriate conditions and carrying out the reaction
  • Separate the product formed in the reaction mixture from any by-product that may occur
  • Purify the product to an acceptable purity. (>98% in the majority of Abcam Biochemicals products)
  • Measure the yield and performing QC on the product to ensure its integrity

Routes can vary from the most simple to highly complex with numerous steps. For more complex syntheses each of the above steps is likely to be carried out for each stage of the route.

 

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Acid, Base and Salt Compounds

Acids and bases

  • Commonly used chemical compounds.
  • Readily ionize or dissociate in water depending on the strength of the original acid or base compound.
  • An acid is a substance that donates an H+ ion to another species.
  • A base is a substance that accepts an H+ ion and therefore acts inversely to an acid.

Hydrogen ion molarity ([H+]) is used to measure the H+ concentration in solution. This can be used to work out the pH of the solution.
pH=-log[H+]; [H+]=10-pH

pH scale

 (figure 5, Scale used to identify the pH of a compound based on the colour of the pH paper after contact.)

Acids can also be measured by their pKa value, defined as the pH at which 50% of the acid is dissociated into H+ ions and base. On the pKa scale the higher the number the weaker the acid.

Salts

A salt results when an acid and base react with one another. Both become neutral as the H+ and OH- ions combine forming the by-product, water. This is shown in the common example of the formation of the sodium chloride salt below;

 Sodium chloride salt formation


Organic small molecules can also form salts for example NBQX disodium or MPEP hydrochloride. Salts are generally water soluble so are preferred for bioactive molecules, however, the addition of a salt to a bioactive molecule often does not affect the biological activity. View our Just-Add-WaterTM range (products typically water-soluble to at least 10 mM and above)

 

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Isomerism

  • Isomers are compounds with the same molecular formulae but different connectivity.
  • Stereoisomers show a different arrangement in space.

Isomers are important as a different isomer of a compound could show very different effects and results to another. An example of this is thalidomide, whilst one isomer cured morning sickness; the other resulted in birth defects in the unborn child. This is often given the term SAR (structure-activity relationship) which describes how the altering of the molecular structure of a drug alters the interaction it has within the body with receptors and enzymes etc.

Isomerism - mirror image

Some Key Terms.

  • A non-superimposable mirror image: (see left) there is no way that the structure can be rotated to exactly match its mirror image.
  • Enantiomers: Structures that are not identical but are mirror images of each other.
  • Chiral Structures: A molecule that cannot be superimposed on it mirror image.
  • Achiral Structures: A molecule that can be superimposed on its mirror image.
  • Racemic Mixture: An equal proportioned mixture of two enantiomers.
  • Chiral Centre: A carbon that is bonded to 4 different functional groups 

 

 

There are many different types of isomerism that are categorised by the relation between the two isomers.

Constitutional isomerism:

Compounds with the same molecular formula but different bond arrangement.

Conformational isomerism:

A type of stereoisomerism where molecules form different shapes by rotation around one or more σ bond. 

Geometric isomerism (cis/trans, E/Z):

Different arrangements of the molecules around a bond at which no rotation can occur. In this case the two isomers are known as cis or (when two functional group are next to one another, in cis PDA) or trans or E (when the two groups are opposite each other as in trans-Retonic Acid)

Optical isomerism (R/S, +/-):

Chiral compounds (which have a non-superimposable mirror image) show this type of isomerism. The two isomers in this case are enantiomers of one another.  Enantiomers are labeled as either R or and these are assigned depending on the arrangement of the substituents around the compound's chiral centre. Enantiomers can also be classified by the direction in which they rotate the plane of polarized light, clockwise is labeled (+) and anticlockwise (-) these are also commonly termed d- and l- respectively. Optical isomerism is shown in Rolipram; (R)-(-)-Rolipram shows one enantiomer while (S)-(+)-Rolipram represents the other, (R,S)-Rolipram is a racemic mixture.

Enantiomers differ in the way they react with chiral receptors. For example one enantiomer of limonene smells like oranges while the other smells of lemons, this is because each enantiomer will react differently with the chiral receptors in your nose.

Diastereoisomerism:

Stereoisomers that are not enantiomers of each other. Commonly diastereoisomers result when there are one or more tetrahedral chiral centres in a molecule. This type of isomerism gives 2n stereoisomers, each diastereomeric pair are enantiomers of one another. (n = number of stereo centres)

 

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Moles (n) and Molecular Weight (Mw)

All Abcam Biochemicals products are sold by mass; however it is always important to consider the moles (a measure of the number of molecules) in each compound. 

The Mole is a relative measure given to each atom that takes into account differing molecular weights. The weights that you measure (in μg, mg, g etc) can be converted into the number of moles

Mole formula

m = mass 

Mw = molecular weight.


Biological activity will always be dependent on the number of moles rather than the mass of the compound used.

The atomic mass for each atom is shown on the periodic table.
(The larger of the two numbers shown)
1 mole is the amount of pure substance that contains the same chemical units as there are in 12g of Carbon 12.

Molecular weights of compounds can be calculated by simply adding together the molecular weights of each atom.

E.g. in Water O = 16, H = 1 so H2O = 18. If Mw is 18, then 1 mole = 18g (m = n x Mw; m = 1 x 18) So 18g of water contains the same number of atoms as 12g of Carbon 12.


When a compound is in solution, molarity (M) is the concentration of the solution, relative to the molar value. A 1M solution contains one mole of the substance per litre of solution.

Molarity formula


m = mass

Mw = molecular weight 

V = volume

For more solubility equations check out our product FAQ page.

 

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