The fundamental ties that bind also confuse the world’s chemists

In the last decade or so, scientists around the globe have been questioning one of the foundations of chemistry, namely the existence and nature of a chemical bond. The chemical bond is one of the very first concepts taught to students: atoms, attracted towards each other, form bonds and eventually molecules. It is considered simple enough to not even warrant an exam question. But, at the same time, it is also one of the largest head-scratchers of 21st century chemistry.

The problem actually started with computers, and their use in modelling chemical systems. Chemists use them to support experimental results, predict the outcomes of experiments and investigate chemical thinking on a theoretical level. Doing so requires using quantum mechanics — the branch of physics dealing with the (sometimes strange) universe at an atomic scale. Modelling chemical systems is by no means an easy feat, because the quantum mechanical description of a chemical system is extremely complex and generally unsolvable without some hand-waving. 

For instance, calculating the properties of paracetamol (the active ingredient in Panado), a simple compound consisting of only 17 atoms, can take anything from 20 minutes to a few weeks, depending on the accuracy required. That would be even when you’re using the full capacity of the BlueGene cluster of the South African Centre for High Performance Computing, which has about 2 000 times more processing capacity than the average household computer.

By comparison, the average human cell contains about 100-trillion atoms. So while a complete computational description of every-day chemical and biological systems lies far in the future, we can already investigate many chemical hypotheses at a molecular and theoretical level using computer modelling. In fact, many academic chemistry journals require researchers to validate their results through computational methods, and the winners of the 2013 Nobel prize in Chemistry were three computational chemists. 

However, the strongest computer in the world is useless if the theory and its models are inaccurate, a problem commonly known as “garbage in, garbage out”. This leads us to a conundrum: if a quantum mechanical model predicts results that differ from what is interpreted in experiments, how does a chemist know whether it is the theory or their interpretation of experimental data that is wrong? 

The same problem applies to the chemical bond. Centuries of accumulated chemical intuition, built on classical interpretations of experimental data, have led to experienced chemists being able to say, intuitively, which atoms tend to form bonds and which do not. But the same powerful intuition can also induce a strong bias, creating popular but not necessarily true ideas about the chemical bond.

 “Chemical intuition” is not just hand-waving. It is scientific in origin, but due to the lack of 21st century technology in the previous centuries, concepts which are not necessarily correct or accurate have evolved to explain experimental results. These concepts have been built-on instead of rethought. Early chemists had very primitive ideas of atoms, molecules and bonds, but were still able to synthesise new compounds successfully, leading to self-validation of their theories. Unfortunately, when new results poked holes in old theories, chemical theory was adjusted with situational rules, rather than an overhaul of archaic ideas.

A breakthrough in the field came in the 1980s with the late Richard Bader, a Canadian researcher whose fame for scientific reasoning was only trumped by his infamous temper. He ignored the research trend in his time (the nuances of quantum mechanics) and instead decided to focus on the “glue” which binds atoms together: the electrons. 

Electrons are small, negatively charged particles present in large clouds around a positively charged nucleus. When two atoms approach each other, electrons are shared between the atoms. This increases the overall favourable attraction between the atoms and leads to them being “glued” or bonded to each other. Atoms bonded in this way are called a molecule. In even the smallest molecule, it is generally difficult to determine which electrons originate from which atom, making a description of bonding difficult. 

However, Bader studied the distribution of electrons in many molecules and found a consistent pattern: the probability of finding an electron is highest in a direct line connecting two atoms, called a “bond path”, which experimentalists believed to be bonded to each other. The result was phenomenal. Not only was Bader’s model of a molecule easy to calculate, while still derived from the fundamentals of quantum theory, but it recovered every instance where an experimental chemist would intuitively place a chemical bond. The theoreticians and experimentalists agreed — a remarkable feat — and his theory was adopted as a general description of chemical bonding. 

But every now and then, a scientist would discover a bond path predicted by Bader’s theory where a classical chemist would not expect to see a bond, usually between hydrogen atoms that were already bonded to another atom. Any organic chemist will tell you this is not possible. As a result, these anomalies were written off as computational caveats, bugs or inaccuracies, and were largely ignored because Bader’s theory worked so well everywhere else.

In the early 2000s, as Bader’s theory was still in vogue and being used more often, serious attention was called to these anomalies. The debate centred on what is incorrect: the theory which correlates in every case (except for the anomalies) or our understanding of chemical bonds? Many scientists started questioning their own basic ideas of chemical bonding.

The confusion surrounding Bader’s theory was eventually distilled into these questions: “What is a bond?” “How can we quantify it?” and “Does a chemical bond even exist?” Although these questions sound irrelevant to everyday life, our industry and science on Earth depend on its answers. They dictate geological formations, the catalysis reactions in the petroleum and energy industries, the synthesis of new drugs and their interactions with plants and animals, and the subtle bonds of our DNA. One of the foundations of science, the chemical bond, continues to be fundamentally misunderstood.

Jurgens de Lange is a PhD candidate at the University of Pretoria.

Subscribe to the M&G

These are unprecedented times, and the role of media to tell and record the story of South Africa as it develops is more important than ever.

The Mail & Guardian is a proud news publisher with roots stretching back 35 years, and we’ve survived right from day one thanks to the support of readers who value fiercely independent journalism that is beholden to no-one. To help us continue for another 35 future years with the same proud values, please consider taking out a subscription.

Guest Author

Related stories

‘Plebs’ finally get to understand a bit of ‘lab-coat lingo’

Writing about their research in last year's Science Voices supplement has been beneficial to the 28 young scientists involved. Participate this year!

Making plant fibres flame-retardant might make them fly.

There is renewed interest in natural materials, as recyclability and environmental safety become more important in manufacturing and consumables.

Satellites can help save the environment

In 10 years, Thohoyandou in Limpopo has become unrecognisable.

The climate behind human evolution

Investigating past climate change and its human impact.

Unique local genetic problem needs a unique local solution

Spinal muscular atrophy (SMA), a muscle-wasting disease that causes paralysis, is one of the most common genetic causes of infant death in the world.

Astrophysical jets in distant galaxy could teach us physics

At present, technology can only aid us to see so much, but that could change soon.

Subscribers only

Toxic power struggle hits public works

With infighting and allegations of corruption and poor planning, the department’s top management looks like a scene from ‘Survivor’

Free State branches gun for Ace

Parts of the provincial ANC will target their former premier, Magashule, and the Free State PEC in a rolling mass action campaign

More top stories

Why anti-corruption campaigns are bad for democracy

Such campaigns can draw attention to the widespread presence of the very behaviour they are trying to stamp out — and subconsciously encourage people to view it as appropriate

Tax, wage bill, debt, pandemic: Mboweni’s tightrope budget policy statement

The finance minister has to close the jaws of the hippo and he’s likely to do this by tightening the country’s belt, again.

SA justice delays extradition of paedophile to UK

Efforts to bring Lee Nigel Tucker to justice have spanned 16 years and his alleged victims have waited for 30 years

Former state security minister Bongo back in court

Bongo and his co-accused will appear in the Nelspruit magistrate’s court in Mpumalanga over charges of fraud, corruption and theft

press releases

Loading latest Press Releases…

The best local and international journalism

handpicked and in your inbox every weekday