Kenneth Geisshirt

Blogging about science and technology - mostly

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7 October 2011

Free chemistry software - Introduction

by Kenneth Geisshirt

The year of 2011 has been declared the International Year of Chemistry by UNESCO (United Nations Educational, Scientific and Cultural Organization) and IUPAC (International Union of Pure and Applied Chemistry). The purpose of devoting a full year to chemistry is to spread the notion that chemistry is important for our daily life.

In this series of blog post I have examine the state of free software in chemistry. This first post is an outline of the usage of computers in chemistry.

It is hard to imagine modern life without the discoveries and developments done by chemists and chemical engineers over the last two or three centuries. Plastic, gasoline, and pharmaceuticals are products from the chemical industry. And forensic scientists use many chemical analysis in order to provide evidence for police investigations all over the world. But chemistry is more that an applied science. It also give us an insight to how our world works. In the recent decade, the modern cuisine has changed. For example, the cheif Heston Blumenthal has been using chemistry to create new dishes (this branch of chemistry is called molecular gastronomy).

As you can see, chemistry is a broad science and engineering discipline. Modern chemistry is divided into a number of branches. Traditionally, an academic education of chemistry consists of courses in general, organic, inorganic, physical and even analytical chemistry. Chemistry is a wet science, and as a student you spend a lot of time in laboratories. Amongst chemists, it is still discussed whether chemistry is a descriptive science (classification of observations) or an exact science (explaining observations).

Chemistry interfaces most other sciences, including physics, mathematics, statistics and biology. Quantum chemistry applies quantum mechanics to calculate properties of chemical substances. But as you might imagine, the three-body problem is a serious show-stopper for a chemist as very few molecules have only three nucleus and electrons.

Computers are heavily used in chemistry. One example is to perform quantum chemistry calculation as finding an analytical solution for a many-body problem is impossible. A rough break-down of the usage of computers in chemistry consists of three major areas. Firstly, you have the end-user applications used by every chemist. The applications are domain-specific applications - the domain is as broad as chemistry. The second area is chemoinformatics. It is a fairly young area (a decade or two only). Chemoinformatics applies techniques from informatics to transform chemical data to knowledge and thereby improving the decision making process. The usage of specialized databases and search algorithms is an integral part of chemoinformatics. Any non-trivial chemical compound can be represented in a number of ways. Even a small molecule like styrene can be named in different ways depending on how you look at it. Chemoinformaticians have introduced a string representation for all chemical compounds called the simplified molecular input line entry specification (SMILES). The SMILES code for styrene is C=CC1=CC=CC=C1. Image to find all compounds in your database with a certain substructure. You cannot use a regular expression or an SQL query. As molecules can be regarded as graphs (atoms are connected by chemical bonds), searching in chemical databases is a variant of find subgraphs. This is the core of chemoinformatics.
The third area where computers are used in chemistry is to perform calculations and it is often refered to as computational chemistry. It is an old area - calculation and simulation of properties of chemical compounds and reaction have been carried out as long as computers have been available to scientists. The calculations either use a classical-mechanical approach or a quantum mechanical approach. In the first approach, electrons is neglected and a force-field between the atoms are applied. This is possible to simulate large molecules using this approach. But if you need to predict the energy levels, thermodynamical properties, and charge distribution of a molecule, you have to use a quantum mechanical approach. This involves solving the time-independent Schrödinger equation (or at least an approximation to the equation called the Born-Oppenheimer approximation).

It is important to understand that most chemists are not educated as programmers. On the other hand, using computational techniques can save chemical industries huge fortunes. Today, most pharmaceutical companies have specialized departments for performing chemical calculations and supporting an informatics infrastructure. These departments are small in terms of man-power compared to the company as a whole. As the market is small and the potential benefits huge (time-to-market and saving expensive laboratory time), vendors often ask for very high license-fees. Vendors like Schrödinger, Wavefunction and Gaussian, and OpenEye offer software packages for chemists. Sadly, free software is a minor player in chemistry but you can find free chemistry software for most needs. tags: chemistry - free software - IYC