Chemistry ​

Alexander Shulgin and David E. Nichols are amazing.

Links ​

• Periodic Table
• A crash course in organic chemistry | Jakob Magolan
• The 2018 Löwdin Lectures - Markus Reiher
• The 2019 Nobel Prize in Chemistry - Lithium Ion Batteries
• Quantum Chemistry - Introduction
• Marie Curie's PhD thesis (2020)
• Organic Chemistry Portal
• The Vespiary - Virtual encyclopedia of drug synthesis, precursor synthesis and drug pharmacology with many links.
• What gear/glassware should I need for some easy beginner synths and what should my budget be? (2020)
• What should a beginner do to get started synthesizing? (2020)
• Chemify - Project dedicated to making chemical synthesis accessible to everyone, regardless of training. (Code)
• The Nobel Prize in Chemistry 2020: Genetic Scissors (HN)
• Zhang Lab - Studies biological diversity to discover systems and processes that may be harnessed for the improvement of human health.
• Machine Learning in Chemistry 101 course
• Highly Opinionated List of Open Source Cheminformatics Resources
• Beginners Guide to Understanding Chemistry (2021)
• Reddit Recommended Chemistry Books
• Chemistry Resources Collection
• Chemical space is really big (2014) (HN)
• Chemistry Development Kit - Open Source modular Java libraries for Cheminformatics. (Code)
• vabene - Python library for automatically making valid molecular graphs.
• stk - Python library which allows construction and manipulation of complex molecules, as well as automatic molecular design and the creation of molecular databases.
• stk-vis - Cross-platform application for visualization of molecular databases.
• moldoc - Sphinx extension for making better chemistry documentation.
• Reaktoro - Unified framework for modeling chemically reactive systems. (Docs)
• Chemistry Book Recommendations
• exmol - Explainer for black box models that predict molecule properties.
• Whitelab - Using Simulation and Machine Learning to Understand Chemistry and Design Materials. (GitHub)
• MatDeepLearn - Package for graph neural networks in materials chemistry.
• Graph neural network for predicting NMR chemical shifts
• Awesome Python Chemistry
• Awesome Cheminformatics
• Illustrated Glossary of Organic Chemistry (Common names)
• Solugen - Make chemicals from sugar, not petroleum. Carbon negative chemicals. (Twitter) (Tweet)
• 3D Periodic Table (Code)
• The Nobel Prize in Chemistry 2021 (HN)
• OpenChem - Deep learning toolkit for Computational Chemistry with PyTorch backend. (Docs)
• How to grow sodium chloride crystals at home (HN)
• Structure of benzene is fascinating
• Compositional Thermostatics (2021) (Tweet)
• The Effect of Noise on the Performance of Variational Algorithms for Quantum Chemistry (2021)
• AiZynthFinder - Tool for retrosynthetic planning. (Docs)
• Surge - Fast Open-Source Chemical Graph Generator.
• Quantum Chemistry Done Wrong: One-Electron Systems
• Directional Message Passing on Molecular Graphs via Synthetic Coordinates (Code)
• NequIP - Code for building E(3)-equivariant interatomic potentials.
• Pushing the frontiers of density functionals by solving the fractional electron problem (2021) (Tweet)
• pyscf - Python module for quantum chemistry.
• Matthew Carey Lea and the Origins of Mechanochemistry (2021)
• Fermi - Quantum chemistry program written in (nearly) pure Julia.
• Chemical Computing with Clojure (Code)
• Penny Codes (2022)
• Chemfiles - Library for reading and writing chemistry files. (Web)
• Hamilton Morris interviews a chromium carbene chemist (2022)
• Phenethylamines I have feared and loathed (2020) (HN)
• Shulgin's lab in 3D (Reddit)
• Ketcher - Web-based molecule sketcher.
• AI is changing chemical discovery (2022) (HN)
• Materials Informatics Resources
• ChemiScripts - Translate ASCII chemical formulas into Unicode. (Code)
• These are real compounds (2022) (HN)
• cmlkit - Tools for machine learning in condensed matter physics and quantum chemistry.
• DiffiQult - Open source autodifferentiable quantum chemistry package.
• ChemPy - Package useful for chemistry written in Python.
• RDKit - Collection of cheminformatics and machine-learning software written in C++ and Python.
• Open Babel - Chemical toolbox designed to speak the many languages of chemical data.
• Practical Cheminformatics Tutorials
• Call for a Public Open Database of All Chemical Reactions (2022)
• openmoltools - Tools for Small Molecules, Antechamber, OpenMM, and More.
• autodE - Automated reaction profile generation.
• molfunc - Python tool for functionalization of 3D molecules.
• Morfeus - Python package for calculating molecular features.
• C++ Programming Tutorial in Chemistry
• NWChem - Open Source High-Performance Computational Chemistry.
• Psi4 - Open-Source Quantum Chemistry – an electronic structure package in C++ driven by Python.
• xtb - Semiempirical Extended Tight-Binding Program Package.
• PENSA - Protein Ensemble Analysis.
• Torsional Diffusion for Molecular Conformer Generation (2022) (Code)
• Recreating one of the weirdest reactions
• cclib - Python library that provides parsers for output files of computational chemistry packages.
• overreact - Create and analyze chemical microkinetic models built from computational chemistry data.
• ccinput - Computational Chemistry Input Generator.
• CalcUS - Quantum Chemistry Web Platform.
• Legault Research Group - Investigating hypervalent iodine chemistry and organometallic catalysis to develop new synthetic methodologies with lower environmental impact. (Twitter)
• Time Machine - High-performance differentiable molecular dynamics, docking and optimization engine.
• Chemiscope - Interactive structure/property explorer for materials and molecules. (Web)
• rxnutils - Utilities for working with datasets of chemical reactions, reaction templates and template extraction.
• ChemPlot - Python package for chemical space visualization.
• chem_interp - Use interpretable machine learning to explain complicated chemical reactions.
• Faked Crystallography (2022) (HN)
• Scientific Computing for Chemists with Python
• Introductory tutorials on deep learning for chemistry
• Mofdscribe - Ecosystem for digital reticular chemistry.
• Nobel Prize in Chemistry Awarded to Bertozzi, Meldal, and Sharpless (2022) (HN)
• Electron states, light, and mitochondria (2022)
• Water: the liquid of life (2021)
• libcint - General GTO integrals for quantum chemistry.
• BAGEL - Brilliantly Advanced General Electronic-structure Library.
• gauche - Library for Gaussian Processes in Chemistry.
• Awesome Chemistry Datasets
• Pura - Clean chemical and reaction data.
• MolSkill - Learning chemical intuition from humans in the loop.
• ChemMatData - Overview over chemical datasets and where to find them.
• Chemicals - Chemical database of Chemical Engineering Design Library.
• OpenFF Interchange - Storing, manipulating, and converting molecular mechanics data.
• ORDerly - Chemical reaction data & benchmarks. Extraction and cleaning of data from Open Reaction Database (ORD).
• biotransfer - Machine learning-driven antibody design.