Papers for

chemical software developers

Papers whose findings have a practical use for this group, as judged from the abstract. Open a paper to read what it means in practice.

Chemxrg makes 3d chemistry animations from reaction programs

Constrained Program Generation for 3D Reaction Animation with a 0.8B Model

Abstract: Visualizing a chemical reaction requires making its molecular changes visible while keeping the animation faithful to the stated chemistry. Equations, structural diagrams and molecular viewers provide complementary descriptions, but assembling an interactive three-dimensional explanation still requires specifying the changes and checking their consistency. We present ChemXRG, a domain-specific language (DSL) framework that addresses this gap by representing a reaction animation as an executable program. Persistent atom identifiers and explicit bond, charge and grouping operations connect the symbolic reaction to the displayed transformation. This shared representation lets generation, verification and rendering operate on the same account of what changes. Given known, atom-mapped reactant and product structures, reaction-grounded constraints fix input-determined facts and restrict action choices; execution checks validate the resulting transformation before geometry and frames are constructed. We implement this paradigm with a reaction-program corpus and ChemQwen, a trained 0.8B DSL generator. Paired and component evaluations show improved compiler acceptance and normalized full-program agreement under input-conditioned constraints, while identifying remaining failures that require execution checks. A public browser application demonstrates the connection from symbolic reaction descriptions to inspectable programs and interactive 3D animations.

Mon 21 SeptGraphics
The gist
Showing chemical reactions as animations can be tricky because the changes at the atomic level must match the chemistry exactly. The authors created ChemXRG, a special programming language that treats these animations like computer programs, making sure every change in the molecules is clear and correct. They also made a smart system called ChemQwen that uses this language to automatically generate these programs for 3D animations. This approach helps connect chemical equations and structures directly to interactive visualizations that can be checked for accuracy.
Open 2609.24457v1