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)!
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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) |
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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) |
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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) |
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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) |
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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) |
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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) |
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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) |
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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) |
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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) |
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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) |