This is another part of my blog series on molecular modelling. I use GAMESS for the QM calculations, and Avogadro and wxMacMolPlt as the GUI.

This post is going to be about basis sets, mainly about their usage in GAMESS, with a little bit of theory at the beginning. Skip the first three points if you don’t want that.

Orbital Approximation

In QM calculations, we attempt to solve the Schrödinger Equation for chemical systems (molecules, ions etc). If we could solve it exactly, then we would have the wavefunction for the system, which would give use all the properties (including energy) of the system. Unfortunately, it is not possible to have analytic solutions for systems larger than a hydrogen atom, so a lot of approximations are used to get something that can be solved. And guess what! …

This is another part of the series of blogs about molecular modelling, mainly about the actual usage of the software, rather than the detailed theory. The QM calculations are done with GAMESS, and visualisation with wxMacMolPlt.

One of the main uses of quantum chemistry is to calculate the Gibbs free energy of activation(ΔG‡) of reactions. This is basically the difference in free energy between the reactant and transition state.

This is important because we can measure the reaction rates in a lab, and then we can relate the rate to the free energy of activation by a simple mathematical relation: the Eyring-Polanyi equation. …

This is a part of the series of blogs on the basics of molecular modelling. The QM program GAMESS is used for the calculations. This post follows part 4, where the optimization of a transition state(TS) is described. In this part, we will perform an intrinsic reaction coordinate (IRC) calculation on that TS.

IRC is basically a method that we can use to confirm if we actually have the transition state that we wanted. The TS from the calculation represents a geometry where the energy w.r.t. one vibrational mode is the maximum, and for all other vibrational modes, the energy is minimum: a saddle point. What IRC does is that it takes the TS, and then slowly moves along the vibrational mode that has the imaginary frequency, while allowing other coordinates to relax. This means that we effectively follow the minimum energy path going down on either side from the TS. The IRC stops when on the energy path becomes flat i.e. …

This is part of the ongoing series of blogs where I write about the how-to of the molecular modelling. This is mainly focused on the software side of it (GAMESS).

Modelling transition states(TS) is important in studying chemistry. Not only can it give data about the Gibbs free energy of activation (which can be used to calculate rates), it can also help in understanding the possible mechanistic pathways, and how different functional groups may alter the reaction rate.

Getting the TS guess structure

To optimize the TS structure, we need a good guess of the TS structure. This is often very difficult, and it requires a good knowledge of chemistry. The QM programs all operate on a garbage-in-garbage-out manner, so if the guess structure is wrong, even if the program detects a transition state, it would not be the right one. …

This is part of an ongoing series of blogs giving a non-technical introduction to molecular modelling.

This post is in a slightly different topic than the usual. In chemistry, visualisation is often the key part of explaining something, and 3D molecular structure like this are indispensable:

There are lots of softwares available, both free and otherwise that can generate 3D molecular structures. One tool that’s very useful in creating that 3D perspective is POV-ray, a free open-source software that can generate really beautiful images by ray-tracing. …

This is the part 2 of the ongoing series of blogs, where I write about the how-to of the molecular modelling. These are focused mainly on its software side (GAMESS) instead of the theory.

Optimization is a process is that is routine in molecular modelling. It is generally used to find stationary points where the gradient of the energy is zero. These stationary points are energy minima, maxima which you would call reactants, products, transition states etc. (Usually optimization means finding the minima, but transition state search works on the same principle)

How does optimization work?

We can represent a molecule by the 3D cartesian coordinates of its atoms. If the QM program has a set of cartesian coordinates and atoms, it can approximate to the solution of the Schrödinger’s equation, which would give the total energy of that system. When any of the atoms are moved, that energy will change. Each atom can be moved in 3 directions (x,y,z) so we can express the energy of the system as a function of the cartesian coordinates of each of its atoms…

Computational modelling has now become a routine procedure in all branches of chemistry. From modelling crystals to organic reaction mechanisms, it is being used to predict data,understand it, or to explain it.

However, the learning curve for this field is quite steep. Very few softwares are user-friendly, and most do not have a graphical interface. Efficient softwares like Gaussian and Spartan exist, but they are both commercial. When I first started to learn this, I found this very problematic, as I wanted to try it before I committed to it. …