Computational Data Archive in Support of the Ping-Pong Mechanism for Peptide Bond Formation and Hydrolysis

In search for the goldilocks zone in the chemical space for amino acid oligomerization that is relevant to the emergence of protein-based metabolism, we identified a significant gap in our understanding about how peptide bond is formed and hydrolyzed under ambient aqueous conditions. We identified a six-step mechanism that reproduces the experimentally known experimental barriers. By careful evaluation of a comprehensive set of levels of theory, modelling of solvation effect, and calculation of thermochemical parameters, we established a robust computational model to expand the bulk water focus to interfacial phenomena of atmospheric/hydrospheric and litospheric/hydrospheric boundaries. 

While we cannot travel back in time billions of years to witness the "birth" of the first macromolecule with pre-biotic relevance, we present the dataset and the corresponding publication in RSC Organic and Biomolecular Chemistry (July 26, 2023 issue) our attempt to establish an unbiased computational platform where we can evaluate experiments and generate experimentally testable ideas.

为探寻与蛋白质基代谢起源相关的氨基酸低聚化（amino acid oligomerization）化学空间中的适宜区间，我们发现当前学界对常温水环境下肽键（peptide bond）的形成与水解机制的认知存在显著空白。我们提出了一套六步反应机理，其可重现实验中观测到的反应能垒。通过系统评估多套理论计算水平、构建溶剂化效应（solvation effect）模型并计算热化学参数（thermochemical parameters），我们建立了一套稳健的计算模型，将研究范畴从体相水（bulk water）拓展至大气-水圈界面与岩石圈-水圈界面的界面现象。

尽管我们无法回溯数十亿年以观测与前生物（pre-biotic）过程相关的首个大分子的诞生，但本数据集及对应发表于英国皇家化学学会《有机与生物分子化学》（RSC Organic and Biomolecular Chemistry，2023年7月26日刊）的论文，正是我们为构建一个无偏倚计算平台所做的尝试——该平台可用于评估实验结果并生成可实验验证的研究构想。