Cryptate Binding Energies Towards High Throughput Chelator Design: Metadynamics Ensembles with Cluster-Continuum Solvation

IF 2.9 3区化学 Q3 CHEMISTRY, PHYSICAL

Physical Chemistry Chemical Physics Pub Date : 2024-10-08 DOI:10.1039/d4cp03129f

Sean Nations, Lauren Burrows, Scott Crawford, Wissam Saidi

引用次数: 0

Abstract

A tiered forcefield/semiempirical/meta-GGA pipeline together with a thermodynamic scheme designed with error cancellation in mind was developed to calculate binding energies of [2.2.2] cryptate complexes of mono- and divalent cations. Stable complexes of Na, K, Rb, Ca, Zn and Pb were generated, revealing consistent cation-N lengths but highly variable cation-O lengths and an amine stacking mechanism potentially augmenting the cation size selectivity. Metadynamics, used for searching the high-dimensional potential energy surface, together with a cluster-continuum model for affordable - yet accurate - solvation modeling, enabled the discovery of more stable geometries than those previously reported. Similar solvation energy curve shapes for lone vs. coordinated ions enabled rapid solvation convergence via the cancellation of errors stemming from finite cluster sizes. An R2 of 0.850 vs. experimental aqueous binding energies was obtained, validating this scheme as the backbone of a high-throughput workflow for chelator design.

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实现高通量螯合剂设计的隐子结合能：具有簇连续求解的元动力学集合

我们开发了一个分层力场/半经验/meta-GGA 管道以及一个考虑到误差消除的热力学方案，用于计算一价和二价阳离子的 [2.2.2] 隐酸盐络合物的结合能。结果表明，Na、K、Rb、Ca、Zn 和 Pb 的稳定配合物具有一致的阳离子-N 长度，但阳离子-O 长度变化很大，而且胺堆积机制可能会增强阳离子的大小选择性。用于搜索高维势能面的元动力学以及用于建立经济而精确的溶解模型的簇连续模型，使我们发现了比以前报告的更稳定的几何结构。孤离子与配位离子的溶解能曲线形状相似，通过消除有限簇大小产生的误差，实现了快速溶解收敛。与实验水结合能的 R2 值为 0.850，从而验证了该方案可作为螯合剂设计高通量工作流程的骨干。

本文章由计算机程序翻译，如有差异，请以英文原文为准。

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来源期刊

Physical Chemistry Chemical Physics 化学-物理：原子、分子和化学物理

CiteScore

5.50

自引率

9.10%

发文量

2675

审稿时长

2.0 months

期刊介绍： Physical Chemistry Chemical Physics (PCCP) is an international journal co-owned by 19 physical chemistry and physics societies from around the world. This journal publishes original, cutting-edge research in physical chemistry, chemical physics and biophysical chemistry. To be suitable for publication in PCCP, articles must include significant innovation and/or insight into physical chemistry; this is the most important criterion that reviewers and Editors will judge against when evaluating submissions. The journal has a broad scope and welcomes contributions spanning experiment, theory, computation and data science. Topical coverage includes spectroscopy, dynamics, kinetics, statistical mechanics, thermodynamics, electrochemistry, catalysis, surface science, quantum mechanics, quantum computing and machine learning. Interdisciplinary research areas such as polymers and soft matter, materials, nanoscience, energy, surfaces/interfaces, and biophysical chemistry are welcomed if they demonstrate significant innovation and/or insight into physical chemistry. Joined experimental/theoretical studies are particularly appreciated when complementary and based on up-to-date approaches.