tutorials

One of the most common ways in which we can think about improving on a given molecule, whether it is an inorganic catalyst or even an organic drug, is to explore small functionalizations of the basic structure – adding small new groups or replacing existing ones while keeping the core intact.

In this follow up to our first tutorial , we are going to describe how to use molSimplify to control the placement of molecules, atoms and complexes on surfaces. We’ll assume you have followed the last tutorial and have a file containing the xyz coordinates of your surface (you might want to relax the surface geometry in a quantum chemistry code first, depending on your usecase).

We have recently implemented an artificial neural network (ANN) in molSimplify – you can read all about it in our recent Chemical Science paper here, but the basic principle is easy to understand.

In this tutorial, we’ll show how to use molSimplify to perform chemical database screening, leveraging on calls to OpenBabel together with useful preprocessing and postprocessing tools for seamless integration with the rest of the molSimplify package.

In this tutorial, we’ll show how to use molSimplify’s custom core functionalization feature. This feature allows new functional groups (FGs) or ligands to be attached to user-specified positions in existing structures, and is most useful for studying the effects of ligand functionalization on transition metal complexes.

In this tutorial, we are going to introduce the latest molSimplify feature – a tool that allows the construction of periodic geometries and facilitates adsorbing any type of molecule supported by the basic molSimplify onto a slab in various ways.

In our first tutorial, we’ll briefly discuss how to use molSimplify to generate simple coordination complexes. Our example today is a cobalt porphyrin with an imidazole axial ligand and an empty 6th coordination site.

molSimplify is an open source Python code that enables high-throughput screening in inorganic chemistry. It generates high-quality geometries of transition metal complexes for use as input in electronic structure calculations.

In this tutorial, we’ll briefly review how to set up fixed atom or boundary condition molecular dynamics calculations in TeraChem. In a fixed atom molecular dynamics calculation, specified atoms are fixed at their initial positions, without physical movements.

Today I’ll briefly review how to set up a steered molecular dynamics calculation in TeraChem. In these steered molecular dynamics calculations, specific atoms (attachment points, APs) are pulled at constant force towards pulling points (PPs) that are some distance in space.