Tutorials

This page contains some tutorials that I started while a postdoc at Stanford University. We'd also like to bring you some new tutorials about how to run TeraChem shortly. In the meantime, I'll be posting some elective slides that cover the basics of force fields and electronic structure (density functional theory, wave function theory....). Please let us know what you think (the 'fun' link in the menubar above)!

molSimplify changelog
Thursday, November 9, 2017
This is a placeholder document for updates, small and large, that get committed to Github. New features will eventually get their own tutorials and will be linked from here. 11/17/2017, TG: Tetradentate ligand alignment now attempts to minimize RMSD between the connecting atoms and the template.... (read more)
molSimplify Tutorial 7: Easy ligand functionalization in molSimplify
Monday, October 2, 2017
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.... (read more)
molSimplify Tutorial 6: Placing structures on slabs
Friday, March 10, 2017
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... (read more)
molSimplify Tutorial 5: Using machine learning to build better structures
Monday, February 27, 2017
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. We first collected information from 2700 transition metal complexes that we optimized using DFT, and... (read more)
molSimplify Tutorial 3: Custom Core Functionalization
Sunday, December 25, 2016
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... (read more)
molSimplify Tutorial 4: Database Searching
Sunday, December 25, 2016
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. Today, we will demonstrate how to search a... (read more)
Guide to Charge Shift Analysis and Fukui Shift Analysis
Tuesday, December 13, 2016
Here, we outline the procedure for our recently developed CSA and FSA methods, which provide systematic methods for determining QM region in QM/MM simulation. 1. In charge shift analysis, we introduce the idea that rigidly removing core active site residues and computing the electronic... (read more)
molSimplify Tutorial 2: Slab Builder
Friday, December 2, 2016
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. This tool is under development and is only... (read more)
Installing molSimplify
Monday, October 31, 2016
System requirements: The code should work on any recent OS supporting Python 2.7. These include Windows 7 to 10, OS X 10.10 to 10.13 and Ubuntu 14.14. There are no specific memory or processor requirements, but we recommend disabling the force field (-ffoption B) or switching to UFF from the... (read more)
molSimplify Tutorial 1: Structure Generation
Saturday, June 18, 2016
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. Graphical User Interface Firstly, we'll show how to use the graphical user... (read more)

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About Us

The Kulik group focuses on the development and application of new electronic structure methods and atomistic simulations tools in the broad area of catalysis.

Our Interests

We are interested in transition metal chemistry, with applications from biological systems (i.e. enzymes) to nonbiological applications in surface science and molecular catalysis.

Our Focus

A key focus of our group is to understand mechanistic features of complex catalysts and to facilitate and develop tools for computationally driven design.

Contact Us

Questions or comments? Let us know! Contact Dr. Kulik: