Accurately extracting the signature of intermolecular interactions present in the NCI plot of the reduced density gradient versus electron density

Abstract

An electron density (ED)-based methodology is developed for the automatic identification of intermolecular interactions using pro-molecular density. The expression of the ED gradient in terms of atomic components furnishes the basis for the Independent Gradient Model (IGM). This model leads to a density reference for non interacting atoms/fragments where the atomic densities are added whilst their interaction turns off. Founded on this ED reference function that features an exponential decay also in interference regions, IGM model provides a way to identify and quantify the net ED gradient attenuation due to interactions. Using an intra/inter uncoupling scheme, a descriptor (δg) is then derived that uniquely defines intermolecular interaction regions. An attractive feature of the IGM methodology is to provide a workflow that automatically generates data composed solely of intermolecular interactions for drawing the corresponding 3D isosurface representations.

Nature of halogen‐centered intermolecular interactions in crystal growth and design: Fluorine‐centered interactions in dimers in crystalline hexafluoropropylene as a prototype

“…While the axial sites on the halogens in CF 4 and CH 3 Cl had previously been shown to be entirely negative or neutral, which means they cannot halogen bond, this is contrary to our recent findings . Some of us, and others, have argued that such a suggestion is perversely counterintuitive since H 3 CCl and CF 4 can halogen bond, as the halogen in both of them features weakly positive σ‐holes. The discrepancy between these views and those expressed in other studies arises primarily from the choice of the low‐level computational method.…”

“…to enable the detection of NCI as isosurfaces of the RDG s , which covers large regions of space containing interacting atoms. Although there are several drawbacks of this theory, it has been shown on several occasions that this approach can present a more intuitive picture of van der Waals interactions, hydrogen bonds, and steric repulsions than might be obtained by other approaches such as QTAIM, or electron localization function (ELF). One of the main differences between RDG and QTAIM methods is that the former predicts the nonlocal nature of charge density distributions between atomic basins, whereas the latter concentrates locally on the critical points of ρ (r) but not on the nonlocal nature of the surrounding regions.…”

A Noncovalent Fluorescence Turn‐on Strategy for Hypoxia Imaging

“…We observed the intermolecular correlations between benzene protons of Rho123 and phenolic protons of CAC4A, and also correlations between xanthene protons of Rho123 and substituted benzoic acid protons of CAC4A. [22]). Thebenzene part of Rho123 locates at the centre of the cavity and xanthene part is at upper rim (Figure 2a), which is in good agreement with the NMR results.T he optimized structure of CAC4A-Rho123 displays three evident intermolecular hydrogen bonds:t wo NÀH···O (1.71 and 1.73 )b etween carboxyl groups of CAC4A and amino groups of Rho123 and one CÀH···O (2.24 )b etween an aromatic hydrogen of CAC4A and the carbonyl oxygen of Rho123.…”

Modulation of Conformational Preferences of Heteroaromatic Ethers and Amides through Protonation and Ionization: Charge Effect

“…To provide a more unambiguous physical image on the origin of conformational preferences and switching, the interfragment interactions between the substituent and heteroaromatic ring were investigated by performing IGM analysis. The IGM proposed by Lefebvre et al ., is a very useful methodology to study interfragment and intrafragment interactions by using pro‐molecular density. Briefly, only some essential idea of this method is outlined in the most general forms.…”

“…The exchange repulsion and delocalization (Here, the delocalization effect (ΔE deloc ) includes p‐π* conjugation (ΔE p‐π* ) and σ‐σ* hyperconjugation (ΔE Hyper ) nearby the OCH 3 group are calculated by using the stand‐alone NBO 5.0 program . The Independent Gradient Model (IGM) is employed to visually explore the interfragment interactions, which is performed by using Multiwfn package and the Visual Molecular Dynamics (VMD) program …”