This chapter demonstrates the practical application of prompt engineering methodologies to design a comprehensive net zero refinery. The design process follows industrial project phases from problem definition through conceptual design, system architecture, detailed design, and implementation planning. Using systematic prompt engineering techniques including context-rich framing, multi perspective analysis, tree of thoughts, and chain of thought reasoning, a Large Language Model helps to develop a viable refinery concept that processes diverse alternative feedstocks through integrated conversion technologies powered by renewable energy. The resulting design demonstrates potential for carbon negative performance while addressing the technical, economic, and implementation challenges inherent in such a transformation. This chapter provides concrete examples of how Large Language Models can contribute to complex industrial innovation when properly supervised and directed through structured prompting methodologies, with particular attention to realistic system sizing and practical implementation considerations.