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class="c15 doc-content"><div><p class="c2"><span class="c11 c17"></span></p></div><p class="c16"><span class="c11 c5">Advances in Chemistry with Artificial Intelligence (AI)</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">This project explores how AI models are now driving modern chemistry in directions that range from molecular design and retrosynthesis to protein folding and reaction prediction. The integration of AI into chemistry makes the leap from conventional trial-and-error experimentation toward data-driven chemical discovery.</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">I'll give an overview of how AI models have evolved, how they work, and how specialized large language models (LLMs) like ChemDFM are changing the game with respect to chemical synthesis and molecular understanding. This presentation would demonstrate practical applications of AI in retrosynthesis planning, protein modeling by examples such as AlphaFold, and automated decision systems for chemical design.</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c5 c11"> Key Research Questions</span></p><ol class="c14 lst-kix_5vfje3qqc5q2-0 start" start="1"><li class="c0 li-bullet-0"><span class="c3">What is an AI model, and what types of models are used in chemistry today?</span></li><li class="c0 li-bullet-0"><span class="c3">How have AI models evolved, and what does the general term “AI” mean in modern chemistry?</span></li><li class="c0 li-bullet-0"><span class="c3">What is a system prompt, and how is it used in large language models for chemical reasoning?</span></li><li class="c0 li-bullet-0"><span class="c3">How do LLM-augmented synthesis design programs help automate and optimize reaction planning?</span></li><li class="c0 li-bullet-0"><span class="c3">What makes ChemDFM a breakthrough compared to earlier models like AlphaFold?</span></li><li class="c0 li-bullet-0"><span class="c3">What is retrosynthesis, and how can AI enhance it through atom-level reasoning?</span></li></ol><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3"> </span></p><p class="c2"><span class="c3"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c2"><span class="c11 c5"></span></p><p class="c4"><span class="c11 c5">Starting Sources</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">1. LLM-Augmented Chemical Synthesis and Design Decision Programs (arXiv: 2505.07027) – focus on pp. 16–18 (System Prompts).</span></p><p class="c4"><span class="c3">2. Developing ChemDFM as a Large Language Foundation Model for Chemistry (arXiv: 2401.14818) and ChemDFM on HuggingFace: [https://huggingface.co/OpenDFM/ChemDFM-v1.0-13B](https://huggingface.co/OpenDFM/ChemDFM-v1.0-13B)</span></p><p class="c4"><span class="c3">3. Deep Learning of Proteins with Local and Global Regions of Disorder (arXiv: 2502.11326) – compares protein understanding to AlphaFold.</span></p><p class="c4"><span class="c3">4. Atom-Anchored LLMs Speak Chemistry: A Retrosynthesis Demonstration (arXiv: 2510.16590).</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3"> </span></p><p class="c4"><span class="c5">Presentation Format</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">Format: Interactive Webpage (AI-style simulation).</span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">The presentation will mimic Google’s Gemini interface called “Chemini”, it will be an application permanently published on the web. When opened, the webpage begins an auto-running presentation as if the AI itself were explaining the research interactively. Viewers can type questions, and an AI version of me will explain it. I will also run the LLM that was trained on everything related to Chemistry, ChemDFM. </span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3">Visual and interactive elements:</span></p><ul class="c14 lst-kix_jy3mt9lo5o76-0 start"><li class="c0 li-bullet-0"><span class="c3">Background animation resembling a live AI terminal. AI generated me. </span></li><li class="c0 li-bullet-0"><span class="c3">Sections presented in a “chat-like” format for immersion. </span></li><li class="c0 li-bullet-0"><span class="c3">Embedded code blocks and molecule visualizations (if possible).</span></li><li class="c0 li-bullet-0"><span class="c3">Summaries narrated in real-time text.</span></li></ul><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3"> </span></p><p class="c2"><span class="c3"></span></p><p class="c2"><span class="c3"></span></p><p class="c2"><span class="c3"></span></p><p class="c2"><span class="c3"></span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c11 c5">Chemistry Units Linked</span></p><ul class="c14 lst-kix_51t1u0dcdjhi-0 start"><li class="c0 li-bullet-0"><span class="c3">Structures and Bonding: Chemical structure prediction via neural networks.</span></li><li class="c0 li-bullet-0"><span class="c3">Rates of Reaction: AI-assisted reaction kinetics simulations.</span></li><li class="c0 li-bullet-0"><span class="c3">Organic Chemistry: Retrosynthesis and molecular pathway prediction.</span></li><li class="c0 li-bullet-0"><span class="c3">Equilibrium: LLMs predicting stable reaction states.</span></li></ul><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3"> </span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c11 c5">Timeline</span></p><ul class="c14 lst-kix_r9t2nz3x04m3-0 start"><li class="c0 li-bullet-0"><span class="c3">Nov 7: Proposal and rubric submission.</span></li><li class="c0 li-bullet-0"><span class="c3">Nov 8–30: Build application layout, integrate research.</span></li><li class="c0 li-bullet-0"><span class="c3">Dec 1–15: Script interactive flow and design elements.</span></li><li class="c0 li-bullet-0"><span class="c3">Dec 18: Submit final interactive webpage.</span></li></ul><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c3"> </span></p><p class="c2"><span class="c3"></span></p><p class="c4"><span class="c5">RUBRIC </span><span class="c3">(Total: 30 Marks)</span></p><p class="c2"><span class="c10"></span></p><table class="c13"><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Criteria</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Level 1 (1-5)</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Level 2 (6-10)</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Level 3 (11-15)</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Level 4 (16-20)</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c9"><span class="c8">Marks</span></p></td></tr><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c8">Research Depth</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Minimal sources, unclear focus.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Basic understanding of AI in chemistry.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Clear explanations and integration of examples.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Deep, accurate research with strong source use.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">/10</span></p></td></tr><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c8">Chemistry Connection</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Weak chemistry relevance.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Links to one unit vaguely.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Connects clearly to multiple units.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Thorough explanation linking several units coherently.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">/6</span></p></td></tr><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c8">Creativity and Presentation</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Plain or non-interactive design.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Some interactivity.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Strong visuals and structure.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Highly creative, engaging AI-style simulation.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">/6</span></p></td></tr><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c8">Clarity and Organization</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Unclear or incomplete sections.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Some logical flow.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Well-organized content and transitions.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Seamless flow and polished presentation.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">/4</span></p></td></tr><tr class="c12"><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c8">Technical and Aesthetic Quality</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Low-quality visuals or bugs.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Basic webpage with errors.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">Stable and functional.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">High-quality layout resembling Gemini’s UI.</span></p></td><td class="c1" colspan="1" rowspan="1"><p class="c6"><span class="c7">/4</span></p></td></tr></table><p class="c2"><span class="c10"></span></p></body></html>