in StemSocial2 months ago

Greetings dear users and lover of the scientific world, continuing with this area of knowledge, we will address this time the functioning of biological systems, specifically in which refers to the substitution reactions involved in them and will be a material that we will develop through the @Stemsocial community, where knowledge is driven daily in the face of science.

Image courtesy of: jdn2001cn0

In this sense, it is necessary to understand that this type of substitution reactions at the level of organic chemistry, has as its fundamental basis the development of molecular inversion proposed by Paul Walden in 1896, this German chemist, had the ability to determine that metal acids could be inter-converted into pure enantiomers, through a series of reactions or chemical processes of simple substitution.

Undoubtedly, this discovery represented great advances for science and represents one of the great discoveries of the time, since through observation and experimentation, if you want basic, great advances were achieved that are the basis of the chemistry we know today, where the technological process and scientific advances we have achieved, have been able to establish that Walden's process is nothing more than a nucleophilic substitution reaction, where each step during the process involves a system of substitutions of the nucleophile that participates in it and are reactions of great utility and versatility in the current field of organic chemistry.

So that starting from this discovery, we can establish that at the level of reactions or chemical processes we are accustomed to establish that a process is fast or slow, but we do not know for sure the exact speed at which this phenomenon occurs, however, through the process of nucleophilic substitution of the nucleophilic substitution of the nucleophile that participates in it, through the process of nucleophilic substitution, emphasis was made on the need to know the speed at which each of these reactions is executed, hence it has managed to establish the speed within a chemical process and determine that the reaction rates depend on factors such as the concentration of the reagents which allows to investigate the different mechanisms of reaction that falls on this process.

So that when it is possible to establish a correlation between reaction rates and reagent concentration in a certain way what we are evaluating is the chemical kinetics of the reaction, so we can establish that in linear reactions also known as second order reactions the concentration of the reactants is directly proportional to the speed of it.

A clear example of this process can be seen in the nucleophilic substitution kinetics that occurs in the reaction of bromomethane with the hydroxyl ion, which generates the formation of methyl alcohol and the bromide ion. If we analyze the process, we can realize that at a certain temperature and concentration of the reagents, the reaction takes place at a certain rate, however when these concentrations are doubled, it is obviously to be expected that the rate of the reaction also accelerates or doubles.

Another variant of the nucleophilic substitution reactions are the well known bimolecular type reactions, where in the first instance the reactions are carried out through a stereochemical inversion in the carbon atom and the kinetics of the reactions are directly proportional to the concentration of the reagents, at this point in the bimolecular type nucleophilic substitution reactions tend to involve two molecules where a nucleophile and a respective alkyl halide or exiting group will be present.

The particularity of the bimolecular nucleophilic substitution mechanism is that the reaction is carried out in one stage without intermediates that affect the speed of the reaction, so that when the nucleophile attacks the alkyl halide it does so in the opposite direction to the leaving group, so that it has the freedom to bond with the respective carbon but at this point a different stereochemical configuration is generated in the molecule, as we can see in the figure below.

Once we have a picture of how the attack of the nucleophilic group and the displacement of the leaving group occurs, we have to take into account that within the substitution reactions there are variables that affect the behavior of these, variables that we can associate with the type of substrate that is participating, since if during the reaction the substrate presents a steric or bulky effect, it is to be expected that its large volume will affect the approach and the formation of the respective bond with the carbon, so that the nucleophilic attack is slower, thus generating a less accelerated transition state and consequently the reaction, in terms of time, becomes longer.

Another effect that is present in the nucleophilic reactions is the nature of the attacking nucleophile and although the term nucleophilicity is not yet well defined, it is necessary to explain that this phenomenon is more or less parallel to the process of basicity of a molecule and that it usually increases as it goes down the groups in the periodic table, consequently nucleophiles with negative charges are more reactive than those with neutral charges and under this behavior the substitution reaction is carried out in basic conditions and not in neutral or acidic conditions.

Periodic table of the chemical elements: Daniel Madriz

We can also find the leaving group, which is another variable that can affect the bimolecular substitution reactions, so that a negative charge on this group tends to expel it with great force throughout the reaction, hence the need for there to be a great polarity of the electrons shared between the leaving group and the respective carbon, so that the best leaving groups are those that tend to better stabilize the charges there, that the best leaving groups tend to be those that form weak bases, on the other hand we can find the solvent that is immersed inside the reaction where the solvents of protic type, that is to say, that have hydroxyl groups and amino groups are those that obtain worse behavior in this type of reactions, so that the aprotic solvents that lack hydroxyl groups and amino groups are the best.

In this sense and having a broader view of the processes affecting substitution reactions we have to keep in mind that all chemistry in general, whether it is executed at the experimental level or through living organisms in their different cellular processes, follow the same specific rules. Consequently, the diversity of biological reactions that take place daily through the different mechanisms of either elimination, addition or substitution are recorded through an experimental process.

So to understand the phenomenon explained, let us assume the biological process of methylation, understood as the transfer of the methyl group from an electron giver to a nucleophile, this process that is executed in living beings can be followed with the same direction and order through a laboratory, where it would be enough to assume iodine methane as a reagent, and at the biological level this process can be exemplified through the biological synthesis of adrenaline from norepinephrine that takes place in the spinal cord.

Consequently, knowing the mechanism of action of the different chemical reactions at the experimental level, allows us to understand the functioning of different biological processes, since the reactions according to their type meet the same standard or operation in a laboratory or in the living system in general, the only observable variant is the different compounds involved but the type of reaction meets the same principle.

So that through science and chemical behavior in general, we can establish how life is formed and why it is established that as living beings we are ambulatory reactions and that at the moment in which these reactions are paralyzed we would be ending our time on this planet.



[2] Chang, R. (2010). Química. Decima edicion. McGraw-hill Interamericana editores. ISBN: 978-607-15-0307-7.

[3] Ralph, H. Petrucci, William S. Harwood, E. Geoffrey Herring. (2003). QUIMICA GENERAL. Octava edición. PEARSON EDUCACIÓN. S.A., Madrid.



1. The molecular models presented were designed by @madridbg using Chem3D and Chemdraw software.

2. For more information related to the areas of science, technology, engineering and mathematics, do not hesitate to visit #stemsocial and #stem-espanol, they are communities that promote scientific advances in these areas


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