Computational Chemistry

What’s your impression of chemists? People with a white lab coat? People working with test tubes? People mixing colourful solutions in the lab? How about chemists experimenting with computers?

While some chemists continue to work on the experimental aspect of chemistry with pipettes and chemicals, some chemists immerse themselves in programming codes and molecular simulations. The joint forces between both fields of chemists have brought great discoveries to chemistry! In fact, the emergence of various journals in the field has highlighted the growing importance of computational chemistry!

So, what is computational chemistry? Back to Chem101, molecules break down into atoms, and atoms consist of electrons and the nucleus. The electrons revolving around the nucleus are what make molecules so special and unique in how they look and behave. Therefore, simulating electron movements tell us much about how the molecules behave.

However, there are many electrons in a single molecule. A simple molecule, such as water, has already got 10 electrons! Getting to know how each electron behaves is an impossible task because it involves solving the fundamental equation from quantum mechanics, which is too complicated for problems in the molecular world!

To tackle such difficulty, scientists come up with reasonable approximations. Instead of solving for the exact answers from quantum mechanics, chemists utilised computational power to obtain a good-enough answer numerically. This is like making any reasonable guesses and comparing the results from those guesses. When the results from consecutive guesses have insignificant differences, the guess is considered as the answer.

Chemists view electrons as groups instead of treating them individually. One of the popular approaches is to treat electrons as electron density. This leads to the development of Density Functional Theory (DFT). The popularity of DFT is boosted by the announcement of the 1998 Nobel Prize in Chemistry where Walter Kohn and John Pople for their development of DFT and computational methods. Nowadays, DFT is one of the effective tools to describe the properties of atoms,
molecules and solids.

So how do chemists calculate the structure of a molecule? A typical DFT input consists of three building blocks. First, the basis sets are the parameters that describe electrons in atoms or molecules. Second, the functionals are the approximated rules that electrons obey in the system. Third, the initial guess of the structure of the target molecule. Chemists start with a good guess of the molecular structure and calculate its energy. Since molecules tend to stay in the position with minimum energy, a computational program is set to search for the minimum energy for the structure. When the structure corresponds to the minimal energy is found, the molecule is said to be optimized. Chemists then carry out further calculations for molecular properties based on this optimized structures.

While DFT generally makes good enough description for small molecules, it often gets too complicated when dealing with larger molecules like DNA and proteins. There comes molecular dynamics. Instead of looking into electrons, they speculate the molecules at an upper level. They use a set of equations to describe the forces between atoms in the molecule.

Perhaps you may think computational chemistry is too abstract for everyone to get involved. This is certainly not the case. Researchers have built an online game that invites everyone to solve the difficult computational problems in science research. For example, by inviting players to solve molecular puzzles, researchers get insight on how proteins fold.

With the advancement of artificial intelligence and machine learning, computational chemistry has entered another era. By developing a computational network, researchers have now built neural networks to search for molecules with specific properties and even make predictions. These neural networks allow a computer to teach itself without prior programming. This is now widely used in drug discovery research for pharmaceutical companies.

It is envisaged with continuous improvements in computational power and technology, chemistry will flourish as with other scientific fields. Let’s look forward to the new advances and discoveries brought by computational chemistry in the future!

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