Computational Chemistry Research Notes

This section collects research notes on computational chemistry. The bulk of the notes cover optical chemical structure recognition (OCSR), the problem of extracting structured chemical information from images of molecular diagrams. The remaining notes span molecular dynamics simulations, molecular representations, chemical language models that learn from molecular string notations, LLMs for chemistry covering multimodal and reasoning models adapted for chemical tasks, molecular modeling, curated datasets, and a small set of classic papers in the field.

LLMs for Chemistry

An archive of notes covering large language models and multimodal models adapted for chemistry tasks. Unlike chemical language models that learn directly from molecular string representations (SMILES, SELFIES), these models build on general-purpose LLM or VLM backbones and are fine-tuned for chemical reasoning, multimodal molecular understanding, or scientific document processing.

Molecular Modeling

Notes on 3D molecular representations, conformer generation, and neural network potentials. Covers geometric deep learning approaches for molecules.

Chemical Language Models

An archive of notes covering models that learn representations directly from molecular string notations. Topics include encoder-only transformers for property prediction (ChemBERTa, MoLFormer), sequence-to-sequence models for reaction prediction and molecular generation (Chemformer, GP-MoLFormer), and structure-to-name translation (STOUT).

Benchmark Problems

Standard test problems and datasets for evaluating computational chemistry methods, covering energy surfaces, optimization, and modeling benchmarks.

Foundational Computational Chemistry Papers

Explore the landmark papers that shaped computational chemistry, covering breakthroughs in molecular dynamics, quantum chemistry, and statistical mechanics.

Molecular Databases & Datasets

A curated collection of molecular databases and datasets used in computational chemistry. These dataset cards provide overviews of molecular enumeration databases, conformer generation datasets, and reaction modeling resources.

Molecular Dynamics

A collection of notes on classical molecular dynamics literature from the 1980s and 1990s. The focus is on interatomic potential models (embedded atom method, Stillinger-Weber), adatom diffusion and self-diffusion on metal surfaces, and oscillatory reactions on platinum surfaces.

Molecular Representations

Notes on SMILES, InChI, SELFIES, and other molecular string formats. Covers encoding schemes, their properties, and applications in cheminformatics.

Optical Chemical Structure Recognition

Notes on recognizing molecular structures from images, covering 35 years of methods: from rule-based vectorization to vision-language models.