Computational Chemistry
Visualization of Gabor wavelets and Kohonen networks for chemical image classification

Chemical Machine Vision

This 2003 paper introduces a machine vision approach for extracting chemical metadata from raster images. By using Gabor wavelets for feature extraction and Kohonen networks for classification, it distinguishes between chemical and non-chemical images, as well as ring and non-ring systems, without requiring high-resolution inputs.

Computational Chemistry
Overview of the ChemReader pipeline for extracting chemical structures from raster images using Hough transform and OCR

ChemReader: Automated Structure Extraction

This paper presents ChemReader, a fully automated optical structure recognition tool that converts raster images of chemical diagrams into machine-readable formats. It introduces a modified Hough transform for bond detection and a chemical spell checker that improves OCR accuracy from 66% to 87%.

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

Dynamical Corrections to TST for Surface Diffusion

This paper bridges Molecular Dynamics and Transition State Theory by applying a dynamical corrections formalism to surface diffusion, identifying a low-temperature bounce-back mechanism causing non-Arrhenius behavior.

Computational Chemistry
Embedding energy and effective charge functions for Ni and Pd from the original EAM paper

Embedded-Atom Method User Guide: Voter's 1994 Chapter

This 1994 handbook chapter serves as a practical user guide for the Embedded-Atom Method (EAM). It details the theoretical derivation from density-functional theory, synthesizes related methods like the Glue Model, and provides a complete tutorial on fitting potentials, illustrated with a specific implementation for the Ni-Al-B system.

Computational Chemistry
Embedding energy and effective charge functions for Ni and Pd from the original EAM paper

Embedded-Atom Method: Theory and Applications Review

This 1993 review systematizes the Embedded-Atom Method (EAM) as a practical semi-empirical approach for metallic systems. It synthesizes theory, applications, and connections to related methods while addressing the limitations of pair potentials.

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

Evans 1986: Thermal Conductivity of Lennard-Jones Fluid

This paper validates the homogeneous Evans method for calculating thermal conductivity against experimental Argon data. It demonstrates broad agreement across the phase diagram but identifies significant non-monotonic behavior and enhanced long-time tails near the critical point.

Computational Chemistry
Early OCR pipeline for converting chemical structure images into connectivity tables using sweeping algorithms and feature extraction

Graph Perception for Chemical Structure OCR

This 1990 paper presents an early OCR pipeline for converting hand-drawn or printed chemical structures into connectivity tables. It introduces novel sweeping algorithms for graph perception and a matrix-based feature extraction method for character recognition.

Computational Chemistry

Hand-Drawn Chemical Diagram Recognition (AAAI 2007)

An early method paper (AAAI ‘07) proposing a multi-stage sketch recognition pipeline. It introduces a domain verification step that uses chemical rules to refine ink parsing, achieving a 27% error reduction over geometric-only baselines.

Computational Chemistry
Optical chemical structure recognition example

IMG2SMI: Translating Molecular Structure Images to SMILES

A 2021 image-to-text approach treating OCSR as an image captioning task. It uses Transformers with SELFIES representation to convert molecular structure diagrams into SMILES strings, enabling extraction of visual chemical knowledge from scientific literature.

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

In Situ XRD of Oxidation-Reduction Oscillations on Pt/SiO2

This study provides the first direct experimental proof that rate oscillations in catalytic CO oxidation on supported Pt are driven by a periodic oxidation and reduction of the catalyst surface. By monitoring Bragg peak intensities in situ, the authors confirm the ‘oxide model’ over competing reconstruction or carbon models.

Computational Chemistry

Kekulé: OCR-Optical Chemical Recognition

This 1992 paper introduces Kekulé, one of the first complete Optical Chemical Structure Recognition (OCSR) systems. It details a pipeline integrating raster-to-vector conversion, neural network-based OCR, and rule-based logic to convert printed chemical diagrams into connection tables.

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

Kinetic Oscillations in CO Oxidation on Pt(100): Theory

Imbihl et al. establish the first detailed microscopic model for CO oxidation oscillations on Pt(100), identifying the adsorbate-induced hex to 1x1 phase transition as the driving force. The study combines linear stability analysis with numerical reaction-diffusion simulations.