Computational Chemistry

The Number of Isomeric Hydrocarbons of the Methane Series

Henze and Blair's 1931 JACS paper introducing the recursive method for counting alkane isomers, founding mathematical …...

Computational Chemistry
GEOM dataset example molecule: N-(4-pyrimidin-2-yloxyphenyl)acetamide

GEOM: Energy-Annotated Molecular Conformations

A dataset card for the GEOM dataset, a collection of energy-annotated molecular conformations for property prediction …

Computational Chemistry
GDB-11 molecule structure showing FC1C2OC1c3c(F)coc23

GDB-11: Chemical Universe Database (26.4M Molecules)

A dataset card for the Generated Database 11 (GDB-11), a database of 26.4 million small organic molecules for virtual …

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

Implementing the Müller-Brown Potential in PyTorch

Guide to implementing the Müller-Brown potential in PyTorch, comparing analytical vs automatic differentiation with …

Computational Chemistry

Müller-Brown Basin MA: Langevin Dynamics Simulation

Langevin dynamics simulation showing particle motion in the deep reactant minimum (Basin MA) of the Müller-Brown …

Computational Chemistry

Müller-Brown Basin MB: Langevin Dynamics Simulation

Langevin dynamics simulation showing particle motion in the product minimum (Basin MB) of the Müller-Brown potential …

Computational Chemistry
Müller-Brown Potential Energy Surface showing the three minima and two saddle points

Müller-Brown Potential in PyTorch

PyTorch implementation of the Müller-Brown potential with performance optimizations, MD simulations, and analytical vs …...

Computational Chemistry

Müller-Brown Transition: Langevin Dynamics Simulation

Extended Langevin dynamics simulation showing particle transitions between different basins of the Müller-Brown …

Computational Chemistry

DenoiseVAE: Learning Molecule-Adaptive Noise Distributions for Denoising-based 3D Molecular Pre-training

Liu et al.'s ICLR 2025 paper introducing DenoiseVAE, which learns adaptive, atom-specific noise for better molecular …...

Computational Chemistry

Beyond Atoms: Enhancing Molecular Pretrained Representations with 3D Space Modeling

Lu et al. introduce SpaceFormer, a Transformer that models entire 3D molecular space—not just atoms—for superior …...

Computational Chemistry

Efficient and Scalable Density Functional Theory Hamiltonian Prediction through Adaptive Sparsity

Luo et al. introduce SPHNet, using adaptive sparsity to dramatically improve SE(3)-equivariant Hamiltonian prediction …...

Computational Chemistry

Learning Smooth and Expressive Interatomic Potentials for Physical Property Prediction

Fu et al. propose energy conservation as a key MLIP diagnostic and introduce eSEN, bridging test accuracy and real …...