A Review on Computational Chemistry

There is no doubt we are in the age of the computer. Everywhere you look computers are being used: laptops, desktops, mobile phones, tablets and even watches. Businesses are now sending emails instead of letters; schools are using projectors to teach and people are shopping online. In fact, if you’re reading this article then you must be on a computer!

For most of us computers are part of our daily lives, which is incredible when you realise that in the 1950s only a third of UK houses owned a television. Yet, recent numbers show that nearly 90 % of houses in the UK own a computer.

Computers have also become very important in science, especially in chemistry. Normally, mention chemistry and many instantly picture laboratories filled with colourful liquids, furiously bubbling in glass containers of different shapes; weird looking instruments whirring away and dusty bookcases filled with very large complicated books.

Amongst it all usually stands a figure dressed in a faded white lab coat stained with splodges and wearing goggles and gloves (safety is important!). These often mad people enjoy nothing better than pouring liquids into other liquids and then another liquid before it finally fizzes up and a shriek of joy greets some new discovery.

This wonderful image is great for fantasy stories, but sadly not how the average chemist works (although some do try to be like this). In fact, many chemists do not wear white lab coats or even spend their days working in a lab. Instead, they are using computers to discover new and exciting science. Unsurprisingly, these people are called computational chemists and spend their time showing off all the fantastic things that can be done with computers from an office and not a lab.

One of these is the different way to look at molecules or atoms – a process called visualisation. This can be a very simple and boring picture of how the individual atoms are joined together and what shape it adopts. Things become much more exciting when we look at how all the molecules move around.

We can see the funny dances individual molecules make – what we refer to as vibrations – or we can look at how hundreds and thousands of particles (which could be atoms or molecules) move over time and arrange to form all kinds of funky shapes.

Using computers we can then predict how these change when we change the temperature or put them in a smaller box where there is less room (decrease the volume). The image below shows a series of water molecules moving around.

Usually we view all this through a computer screen, giving us a flat two-dimensional picture. And although we can point and click on the screen to move things around, it would be great to able to see everything in 3D, as if we could hold it in our hands or walk around it like a museum exhibit. Currently, there are research groups working on being able to view molecules through virtual reality (VR) technology. This not only allows us to view molecules in 3D, but also to grab them, twist them or move them using controllers. To see VR in action, check out this video from Dr David Glowacki from the University of Bristol, https://www.youtube.com/watch?v=vJ10_sltxfc. VR technology is also being used for teaching chemistry in Universities (https://phys.org/news/2018-07-virtual-reality-chemistry-d.html) and will no doubt eventually be found in schools. Talking of schools…

Distance learning – when you can take part in a lesson without actually having to go to a school or university yourself – is only going to get more common in the future.

Amongst all the subjects taught at school, maths is most like marmite – people either love it or hate it, and yet we cannot escape using it some way every day. Luckily, the calculator is able to quickly give us the right answer to any difficult multiplication or division problem we have. The best thing about this miniature computer is the speed at which we can get an answer. For example, multiplying two very large numbers together can be worked using only pen and paper, but this is a very slow process. Why bother doing this though when we can easily pick up a calculator? Similarly, computers can be used to give answers to lots of difficult maths problems in a short amount of time. This is the beauty of using them.

Throughout science, complex maths problems are being solved using computers. This has enabled us to predict the weather, send rockets into space and find the tiny building blocks of the universe. A recent image of a black hole was a staggering one petabyte (a million gigabytes (GB)) large and needed to be sent to supercomputers all over the world to analyse. In chemistry, such calculations are important for seeing how molecules react, how much energy they need to do so and how their shape changes. We are able to predict what atoms will do because they obey a series of rules that can be described by mathematical equations.

Any fans of Sci-Fi or the US sitcom ‘The Big Bang Theory’ will have heard of phrases such as ‘Quantum Mechanics’ or the ‘Schrodinger Equation’. This describes how the very small things in our Universe like molecules and atoms work. It is a weird world where the normal rules do not apply. It also involves lots of very difficult maths –a perfect job for a computer. Computational chemists often use computers to solve quantum mechanics problems. This can include what happens when we shine light onto things, which can explain why things glow in the dark, how our eye sight works (see molecule of the month: retinal) and photosynthesis in plants that allows them to make food and grow. By using computers for quantum mechanics, we are able to get very accurate answers that help in explaining how and why things work.

Unfortunately, sometimes the maths gets too long and difficult even for a computer. This stops us using quantum mechanics for large systems such as materials or biological molecules like proteins. Despite this, there are still different ways to explore how these work using different types of maths, but for which computers are still vital. By doing this, lots of different shapes and sizes can be designed and tested to see which ones work best. The computational chemists can then inform those in the lab which is best to make and which may end up being used in your home. There is currently lots of work being done on designing cage like structures to trap nasty gases such as nitrogen oxides or carbon dioxide. This is very important as these molecules are responsible for global warming and climate change. There are efforts around the world to try and reduce how much of this gas is made and drifting up into the atmosphere. Chemists are vital for helping to do this.

Please don’t feed the molecules – they cause climate change!

Building and testing lots of molecules is also vital in drug discovery. If you have ever been ill or in pain, you have probably been given medicine to help. Creating medicine for humans is quite complicated. It needs to be safe to use (obviously), but also needs to be able to move through the body and reach its target without any problems. But even then, once the medicine has reached the right place in your body it needs to do its job properly and be very good at it.

Testing lots of different molecules on people takes a long time and is expensive. Quite often the molecules do not have their intended effects! This is where computational chemists can help. With the knowledge that atoms and molecules obey mathematic rules, albeit complex ones, we can write algorithms that are put together as a collection we called software.  These software programs accelerate the progress in testing the activity of drug molecules, enabling us to predict the activity of hundreds of molecules. From thousands of molecules we can filter out a much smaller sample that are most likely to be successful in combating the targeted illness or condition.

The area of computational chemistry is growing and becoming ever more popular. By working together, chemists on computers and in labs are tackling the major issues in the world today. The future for computers in chemistry and science in general is set to become more exciting through the rise in machine learning. Here the computer becomes more than just a calculator and is able to learn from existing data. If it could learn all the rules and knowledge of chemistry then it could potentially completely change the way people do research. This could lead to the computer, without any human input, making new, exciting and probably surprising discoveries. However, there is still a long way to go for this to become widely used in chemistry research.

Finally, returning to Dr Glowacki, he and his group are transforming chemistry and computers into art. A very cool video showing some of the dazzling and colourful displays can be viewed here: https://www.youtube.com/watch?v=w8BrJBX6yhg

The traditional view of a white coated chemist working in a lab is unlikely to disappear. However, the desk bound chemist clicking away at their keyboard is a very common sight and now more than ever computers are a valuable tool in science research. Computer models and programs are leading the way in research and the growing use of VR and machine learning makes the future look very promising indeed. As Alan Turing, the father of the computer, once said,

“Those who can imagine anything, can create the impossible”. 

Alan Turing

Just imagine then what once impossible things might be created with the help of the computer.    

This article was written by Marcus Taylor as a guest author article.
The author wishes to thank Rupert Ting and Phil Jemmett for their input and suggestions.  

Graphics by Phil Jemmett.

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