molSimplify

This page contains some tutorials that review how to use our molSimplify software toolkit. Check back here frequently for updates as we add new features!

molSimplify Tutorial 10: Adding ligands to molSimplify
Wednesday, May 9, 2018
molSimpliy comes with about 160 built in common ligands and a nifty decoration manager to modify them. However, this cannot hope to address the scope of possible ligands, so we also support providing your own ligands as SMILES or in 3D molecule formats.  Let's make a triple bidentate complex with... (read more)
QM9 kernel models using molSimplify, RACs and R: Part 1
Tuesday, February 20, 2018
*/ In this two-part tutorial, we’ll show you how to use molSimplify to collect autocorrelation-based descriptors from molecular structures and use those to make predictions using a simple kernel ridge regression (KRR) model, as shown in our recent paper. In this first part, we will explain how to... (read more)
QM9 kernel models using molSimplify, RACs and R: Part 2
Tuesday, February 20, 2018
*/ In the second part of our tutorial, we will demonstrate how to use R to conduct kernel based prediction of atomization energies based on RACs. You’ll need QM9_descriptor_file.csv, which we prepared using molSimplify in the previous tutorial and also provide here. We’ll use R to conduct a simple... (read more)
molSimplify Tutorial 9: Bidentate Ligand Replacement
Thursday, December 21, 2017
In this tutorial, we will show how to replace multidentate ligands in a prebuilt complex. This feature, which facilitates screening of diverse catalyst scaffolds, was recently added to molSimplify. Today’s example involves the following Zn(II) intermediate in a model carbonic anhydrase catalytic... (read more)
molSimplify Tutorial 8: Higher Period Transition Metal Complexes
Wednesday, December 6, 2017
So far in our molSimplify tutorials, we have been focusing on generating structures for first row transition metal complexes. While the study of such complexes is certainly crucial for research areas such as catalysis and pharmacology, it is imperative that we also include heavy metal complexes in... (read more)
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)

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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: