Computational Chemistry

Kekulé: OCR-Optical Chemical Recognition

A seminal 1992 system for Optical Chemical Structure Recognition (OCSR) using neural networks and heuristic graph …

Computational Chemistry
Carbon monoxide molecule adsorbed on Pt(100) FCC surface in hollow site configuration

Kinetic Oscillations on Pt(100): Theory

Theoretical model using coupled differential equations to explain CO oxidation oscillations via surface phase …

Computational Chemistry
Iridium fcc(001) surface with adatom

MD Study of Self-Diffusion on Metal Surfaces

Molecular dynamics simulation of Iridium surface diffusion confirming atomic exchange mechanisms using EAM and many-body …

Computational Chemistry

OCSR Methods: A Taxonomy of Approaches

Overview of optical chemical structure recognition methods organized by approach, from deep learning to rule-based …

Computational Chemistry
Early optical recognition system converts scanned chemical diagrams to connection tables

Optical Recognition of Chemical Graphics

A 1993 prototype system for converting scanned chemical diagrams into connection tables using vectorization and …

Computational Chemistry
Replication of Figure 7 showing stable oscillations in CO oxidation on Pt(110)

Oscillatory CO Oxidation on Pt(110)

A seminal kinetic model using coupled ODEs to explain temporal self-organization and mixed-mode oscillations on platinum …

Computational Chemistry
Chemical structure diagram for optical recognition

OSRA: Open Source Optical Structure Recognition

The first open-source optical structure recognition (OSR) utility for converting chemical images into SMILES/SD formats.

Computational Chemistry
Carbon monoxide molecule adsorbed on Pt(100) FCC surface in hollow site configuration

Oxidation/Reduction Oscillations on Pt/SiO2

In situ XRD validation of the oxide model driving kinetic rate oscillations in high-pressure CO oxidation on supported …

Computational Chemistry
Five-stage pipeline for reconstructing chemical molecules from raster images

Reconstruction of Chemical Molecules from Images

A 5-module system converting raster images of chemical structures into machine-readable SDF files with custom …

Computational Chemistry
Visualization of the Stillinger-Weber potential showing the two-body radial term and three-body angular penalty

Stillinger-Weber Potential for Silicon

The 1985 paper introducing the Stillinger-Weber potential, a 3-body interaction model for molecular dynamics of …

Computational Chemistry
Graph of the Lennard-Jones 12-6 potential showing the characteristic attractive and repulsive forces

Thermal Conductivity of the Lennard-Jones Fluid

A 1986 validation of the Evans NEMD method for simulating heat flow, identifying long-time tail anomalies near the …

Computational Chemistry
Delayed convolution approximation for distinct Van Hove function showing comparison between simulated data and theoretical model

Correlations in Motion of Atoms in Liquid Argon

Rahman's foundational 1964 MD simulation of 864 argon atoms revealing the cage effect and validating classical molecular …