Abstract
AbstractThe surface area of atoms and molecules plays a crucial role in shaping many physiochemical properties of materials. Despite its fundamental importance, precisely defining atomic and molecular surfaces has long been a puzzle. Among the available definitions, a straightforward and elegant approach by Bader describes a molecular surface as an iso-density surface beyond which the electron density drops below a certain cut-off. However, so far neither this theory nor a decisive value for the density cut-off have been amenable to experimental verification due to the limitations of conventional experimental methods. In the present study, we employ a state-of-the-art experimental method based on the recently developed concept of thermodynamically effective (TE) surfaces to tackle this longstanding problem. By studying a set of 104 molecules, a close to perfect agreement between quantum chemical evaluations of iso-density surfaces contoured at a cut-off density of 0.0016 a.u. and experimental results obtained via thermodynamic phase change data is demonstrated, with a mean unsigned percentage deviation of 1.6% and a correlation coefficient of 0.995. Accordingly, we suggest the iso-density surface contoured at an electron density value of 0.0016 a.u. as a representation of the surface of atoms and molecules.
Funder
Deutsche Forschungsgemeinschaft
Publisher
Springer Science and Business Media LLC
Reference50 articles.
1. Alibakhshi, A. & Hartke, B. Implicitly perturbed Hamiltonian as a class of versatile and general-purpose molecular representations for machine learning. Nat. Commun. 13, 1245 (2022).
2. Herbert, J. M. Dielectric continuum methods for quantum chemistry. WIREs Comput. Mol. Sci. 11, e1519 (2021).
3. Alibakhshi, A. & Hartke, B. Improved prediction of solvation free energies by machine-learning polarizable continuum solvation model. Nat. Commun. 12, 3584 (2021).
4. Hu, X., Lenz-Himmer, M.-O. & Baldauf, C. Better force fields start with better data: A data set of cation dipeptide interactions. Sci. Data 9, 327 (2022).
5. Visscher, K. M. & Geerke, D. P. Deriving a polarizable force field for biomolecular building blocks with minimal empirical calibration. J. Phys. Chem. B 124, 1628–1636 (2020).
Cited by
1 articles.
订阅此论文施引文献
订阅此论文施引文献,注册后可以免费订阅5篇论文的施引文献,订阅后可以查看论文全部施引文献