Tag: Water

Sep 24 2025

Quantifying water hydrogen bonding from the surface electrostatic potential at varying iso-density contours

Authors: Goedele Roos, Danny E.P. Vanpoucke, Ralf Blossey, Marc F. Lensink, and Jane S. Murray
Journal: J. Chem. Phys. 163, 114112 (2025)
doi: 10.1063/5.0268712
IF(2023): 3.1
export: bibtex
pdf: <JChemPhys_163>

 

Graphical abstract for Quantifying water hydrogen bonding from the surface electrostatic potential at varying iso-density contours. The figure shows the ESP of interacting water molecules, and water molecules interacting with protein fractions.
Graphical Abstract: The Electrostatic Potential of water in different situations. On the left two interacting water molecules are shown, while on the right a water molecule interacting with a protein model representation is shown.

Abstract

The electrostatic potential plotted on varying contours (VS) of the electron density guides us in the
understanding of how water interactions exactly take place. Water—H2O—is extremely well balanced, having a hydrogen VS,max and an oxygen VS,min of similar magnitude. As such, it has the capacity to donate and accept hydrogen bonds equally well. This has implications for the interactions that water molecules form, which are reviewed here, first in water–small molecule models and then in complex sites as lactose and its crystals and in protein–protein interfaces. Favorable and unfavorable interactions are evaluated from the electrostatic potential plotted on varying contours of the electronic density, allowing these interactions to be readily visualized. As such, with one calculation, all interactions can be analyzed by gradually looking deeper into the electron density envelope and finding the nearly touching contour. Its relation with interaction strength has the electrostatic potential to be used in scoring functions. When properly implemented, we expect this approach to be valuable in modeling and structure validation, avoiding tedious interaction strength calculations. Here, applied to water interactions in a variety of systems, we conclude that all water interactions take the same general form, with water behaving as a “neutral” agent, allowing its interaction partner to determine if it donates or accepts a hydrogen bond, or both, as determined by the highest possible interaction strength(s).

Permanent link to this article: https://dannyvanpoucke.be/2025-paper-wateresp-roos-en/

Feb 14 2025

No boundaries and naturally-defined boundaries obtained via the electrostatic potential

Authors: Goedele Roos, Danny E.P. Vanpoucke, and Jane S. Murray
Journal: ChemPhysChem 26(7), e202401065 (2025)
doi: 10.1002/cphc.202401065
IF(2023): 2.3
export: bibtex
pdf: <ChemPhysChem_26>

 

Graphical Abstract: Schematic representation of the electrostatic potential within a water molecule along the lines between the atoms. The color background shows the electrostatic potential on the 0.001 a.u. contour of the density. The Vs,min and Vs,max points on the surface are indicated.

Abstract

This paper discusses the use of the electrostatic potential in both recent and older literature, with an emphasis upon a 2022 Molecular Physics article by Politzer and Murray entitled “Atoms do exist in molecules: analysis using electrostatic potentials at nuclei“. We discuss electrostatic potentials at nuclei and how they easily lead to atoms in molecules, without physically separating the individual atoms. We further summarize the work by the Politzer group on definitions of atomic radii by means of the electrostatic potential. The earlier studies began in the 1970’s and continued through the 1990’s. Unfortunately, access to these older publications is often limited, cfr. digital libraries often limit the authorized access until a certain publication year, and these papers are often not cited in current publications. Although still being highly interesting and relevant, this older literature is in danger of being lost. Digging into this older literature thus opens up new views. Our feeling is that Peter passed ‘on’ a vision that boundaries do not exist between atoms in molecules, but that some useful and meaningful radii can be obtained using the electrostatic potential between atoms in molecules.

Permanent link to this article: https://dannyvanpoucke.be/2025-paper-esp-politzer-rev-en/