Molecular dynamics (MD) simulations have been utilized to study peptide ion conformer establishment during the electrospray process. An explicit water model is used for nanodroplets containing a model peptide and hydronium ions. Simulations are conducted at 300 K for two different peptide ion charge configurations and for droplets containing varying numbers of hydronium ions. For all conditions, modeling has been performed until production of the gas-phase ions and the resultant conformers have been compared to proposed gas-phase structures. The latter species were obtained from previous studies in which in silico candidate structures were filtered according to ion mobility and hydrogen-deuterium exchange (HDX) reactivity matches. Results from the present study present three key findings namely (1) the evidence from ion production modeling supports previous structure refinement studies based on mobility and HDX reactivity matching, (2) the modeling of the electrospray process is significantly improved by utilizing initial droplets existing below but close to the calculated Rayleigh limit, and (3) peptide ions in the nanodroplets sample significantly different conformers than those in the bulk solution due to altered physicochemical properties of the solvent.

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分子动力学 (MD) 模拟已用于研究电喷雾过程中肽离子构象异构体的建立。显式水模型用于包含模型肽和水合氢离子的纳米液滴。在 300 K 下对两种不同的肽离子电荷配置和含有不同数量水合氢离子的液滴进行模拟。对于所有条件，都进行了建模，直到产生气相离子并将所得构象异构体与所提出的气相结构进行比较。后一种物质是从之前的研究中获得的，其中根据离子淌度和氢-氘交换（HDX）反应性匹配对计算机候选结构进行过滤。本研究的结果呈现出三个关键发现，即 (1) 离子产生模型的证据支持之前基于迁移率和 HDX 反应性匹配的结构细化研究，(2) 通过利用下面存在的初始液滴，显着改进了电喷雾过程的建模但接近计算的瑞利极限，并且 (3) 由于溶剂的物理化学性质改变，纳米液滴样品中的肽离子与本体溶液中的肽离子的构象异构体显着不同。

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