This study explores the entanglement potential in a graphyne (GM) system embedded with lithium ions, employing time-dependent density functional theory (TD-DFT) calculations. A finite, non-periodic GM structure was optimized using the B3LYP functional and the 6-311G(d,p) basis set. Lithium ions were strategically positioned at various distances from the GM to investigate their interactions, focusing on charge transfer transitions to the unoccupied 2s orbitals of the lithium ions. Successful electronic transitions were identified and validated, emphasizing the role of contemporary atomic manipulation technologies such as optical tweezers. This research enhances the understanding of entanglement mechanisms in quantum systems and proposes potential applications in secure quantum communication and advanced quantum computing. The practical feasibility of precise atomic manipulation, enabled by cutting-edge technologies, underscores the applicability of the proposed configurations.