Science and medical background. Laboratory glassware.

The Wonders and Beauty of Chemistry… And the BS – Part 1

In this four-part series, toxicologist and organic chemist dr. Gerhard Verdoorn takes us on a journey to illustrate some of the fundamentals of chemistry. In doing so, the widely misunderstood subject of what makes a product toxic as well as organic versus synthetic chemistry will be explained with the help of practical examples and within the context of a particular environment.

Part 1 In the beginning

There was nothing. No space. No time. No matter. No energy. No sound. Nothing. It was 13 billion years ago. Suddenly, a massive explosion erupted. The Big Bang gave birth to our Universe in which time, space, matter, sounds and energy were all conceived to grow into what we have today: a massive, mystical entity that is unfathomable for the minds of the normal mortals. Guess what: The Big Bang was the largest synthetic chemistry experiment in the existence of the Universe and perpetuates to this very day with chemicals being formed, chemicals disappearing into black holes and chemicals being transformed into energy according to Einstein’s amazing theories.

The entire Universe is a massive collection of chemicals consisting of elements, molecules, black matter and the wonderful living organisms we have on planet Earth and hopefully, somewhere else in this massive chemical factory called Universe, there are other life forms as well.

Inorganic and organic chemicals in the Universe

Speculation is rife about the nature and character of the so-called God Particle that scientists postulate as the origin of the Universe, but in the modern day and age we can at least be certain about two things: The Universe has inorganic matter and organic matter.

Inorganic matter is the bulk of the Universe’s physical matter and is made of elements ranging from the simple hydrogen atom through to heavy metals, noble metals like the much sought after gold, radioactive elements such as radium and up to synthetic elements like Moscovium, and of course, combinations of such elements to form molecules like the fantastic array of minerals we have on the Blue Planet.

Stars, planets, galaxies, nebulae, meteorites, comets and other celestial bodies all consist of inorganic matter either in solid, liquid or gaseous form. It is beyond fascinating that we live in and amongst all this chemistry that was born, transformed and wiped out in universal processes over the past 13 billion years.

But despite this enormous pot of scientific wonders of elements and inorganic molecules that make up the minerals, metals, gases and other matter of the physical part of the Universe, humankind is far more intrigued by the organic chemistry of the Universe probably because it is the chemistry of life.

The fundamental elements of life are carbon, hydrogen, oxygen and nitrogen with much support from phosphorus, sulphur and a few other elements. Organic molecules are built on carbon skeletons with an ensemble of hydrogen and some oxygen and nitrogen. Simple amino acids have nitrogen atoms in the carbon skeletons and when a few amino acids are cemented together they form peptides, and a few peptides combined by chemical bonds form proteins, and the rest is simple: life is possible!

There is of course big debate about the origins of life: was it a divine intervention or was it purely random events that could have formed organic molecules that over millennia were expanded into life? It is yours to decide but let us look at the scientific side and leave the philosophical part for another day.

Organic molecules

The simplest of organic molecules is formaldehyde (remember the lab and the preservation of lab specimens in formalin?): it has one carbon atom, two hydrogen atoms and one oxygen atom. It is a natural chemical produced by nature while a fairly well qualified synthetic organic chemist can synthesise it in the laboratory in no time at all. Methane or CH4 is also a very simple organic molecule that is flagged as greenhouse gas but is something that can act as a building block for much more complex molecules.

Nature also synthesises other organic molecules from small to very large, like the proteins and the code of life namely deoxyribonucleic acid or DNA. They are all organic chemical compounds with carbon, hydrogen, oxygen, nitrogen, phosphorus, sulphur and some other elements like iron (haemoglobin) and magnesium (chlorophyll).

To date, more than nine million organic molecules are known to science and a very large percentage of those are man-made substances. Synthetic organic chemists like Nobel Prize winner Prof Elias J Corey can synthesise virtually any standard molecule that nature produces, but they also synthesise analogues of natural organic molecules and organic molecules that have never been and will never be synthesised in nature. The link between natural organic molecules and synthetic organic molecules is very, very strong.

Scientists often find their inspiration for synthetic organic molecules by searching for biologically active natural organic molecules. A simple example is the amazing salicylic acid found in the willow tree; it is easily transformed into acetylsalicylic acid, one of the oldest pain killers and mildest of anti-inflammatory agents in the world.

The great natural versus synthetic controversy

Certain schools of thought want the world to believe that synthetic chemicals are bad and natural chemicals are good. It is a particularly important argument when discussing pesticides and medicines, however the idea that synthetic products are “chemicals” and the natural ones are organic is unfortunately flawed. All these molecules, bar a small percentage of inorganic compounds like magnesium sulphate for example, are organic molecules consisting of carbon skeletons with other elements attached to form the molecules.

There are also many who claim that their products are free of chemicals. Brothers and sisters of the Universe: your bodies are chemical factories producing billions of molecules annually. There is no synthetic laboratory to match the synthetic ability of a living organism’s body. Not even the awesome Elias J Corey is a match for his own body’s synthetic prowess. Yet, we make molecules just like Mother Nature and the only difference is that ours are man-made synthetic molecules while nature’s are natural synthetic molecules. Synthesis in chemical terms means to build a molecule; both scientists and nature do synthesis.

Nature though, has a huge advantage over us and that advantage lies in the enzymes that synthesise the natural synthetic molecules, while Professor Corey and company use reagents and clever reactions to synthesise our man-made synthetic molecules. Perhaps to clear the confusion we should use the terms bio-synthesise versus synthesise, the former being the natural process and the latter being the laboratory process.

To end the first part of this series, an illustration of the power or laboratory chemical synthesis is as follows: cane sugar or sucrose (alpha-D-glucopyranoside-beta-D-fructofuranoside) can be transformed by a series of chemical reactions using a range of chemical reagents to synthesise natural or man-made analogues of prostaglandin hormones. So, what Mother Nature bio-synthesises in our bodies very quickly using enzymes, we can synthesise in the laboratory with a lot of effort and at great cost, but it is possible.

In the next part of this series we will explore the question of whether natural is safer and better than made-man chemicals.

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