Li Xiao-Tian, Mi Sixuan, Xu Yuzhi, Li Bo-Wen, Zhu Tong, Zhang John Z H
Faculty of Synthetic Biology, Shenzhen University of Advanced Technology, Shenzhen 518055, China.
Shanghai Engineering Research Center of Molecular Therapeutics and New Drug Development, School of Chemistry and Molecular Engineering, East China Normal University, Shanghai 200062, China.
JACS Au. 2024 Nov 18;4(12):4757-4768. doi: 10.1021/jacsau.4c00685. eCollection 2024 Dec 23.
The origin of life on Earth remains one of the most perplexing challenges in biochemistry. While numerous bottom-up experiments under prebiotic conditions have provided valuable insights into the spontaneous chemical genesis of life, there remains a significant gap in the theoretical understanding of the complex reaction processes involved. In this study, we propose a novel approach using a roto-translationally invariant potential (RTIP) formulated with pristine Cartesian coordinates to facilitate the simulation of chemical reactions. By employing RTIP pathway sampling to explore the reactivity of primitive molecules, we identified several low-energy reaction mechanisms, such as two-hydrogen-transfer hydrogenation and HCOOH-catalyzed hydration and amination. This led to the construction of a comprehensive reaction network, illustrating the synthesis pathways for glycine, serine, and alanine. Further thermodynamic analysis highlights the pivotal role of formaldimine as a key precursor in amino acid synthesis, owing to its more favorable reactivity in coupling reactions compared to the traditionally recognized hydrogen cyanide. Our study demonstrates that the RTIP methodology, coupled with a divide-and-conquer strategy, provides new insights into the simulation of complex reaction processes, offering promising applications for advancing organic design and synthesis.
地球上生命的起源仍然是生物化学领域最令人困惑的挑战之一。虽然在益生元条件下进行的大量自下而上的实验为生命的自发化学起源提供了宝贵的见解，但在对所涉及的复杂反应过程的理论理解方面仍存在重大差距。在这项研究中，我们提出了一种新方法，使用基于原始笛卡尔坐标制定的旋转平移不变势（RTIP）来促进化学反应的模拟。通过采用RTIP路径采样来探索原始分子的反应性，我们确定了几种低能反应机制，如双氢转移氢化以及HCOOH催化的水合和胺化反应。这导致构建了一个全面的反应网络，阐明了甘氨酸、丝氨酸和丙氨酸的合成途径。进一步的热力学分析突出了亚胺甲醛作为氨基酸合成中关键前体的关键作用，这是因为与传统认可的氰化氢相比，它在偶联反应中具有更有利的反应性。我们的研究表明，RTIP方法与分而治之策略相结合，为复杂反应过程的模拟提供了新的见解，为推进有机设计和合成提供了有前景的应用。
