Multiresolution non-covalent interaction analysis for ligand–protein promolecular electron density distributions

Leherte, Laurence

doi:10.1007/s00214-020-02705-w

Cited by 3 publications

(8 citation statements)

References 39 publications

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“…In a previous work [25,26], we used the iterative Newton-Raphson algorithm to locate the CPs in a molecular EDD function expressed as a summation over atomic Gaussian functions according to:…”

Section: Cps and Reduced Density Gradient (Rdg)mentioning

confidence: 99%

“…The regions surrounding BCPs and RCPs are characterized by low but non-zero values of s(r) [18]. To search for the RDG-based NCIs, we adopted a flood-filling type algorithm that is described in a previous paper [25,26]. In the present work, RDG grids were built with a grid step of 0.1 Å and a spatial cutoff criteria chosen to select RDG holes located in the intermolecular interaction regions only, i.e.…”

Section: Cps and Reduced Density Gradient (Rdg)mentioning

confidence: 99%

“…Second, at t > 0, the parameter c cannot be neglected since the peaks of the EDD are not located on the atoms any longer [25]. To overcome the problem, equation ( 3) is considered to be a sum over five Gaussian terms, with a 5 = c and b 5 = 0.…”

Section: Smoothed CM Edds Functionsmentioning

confidence: 99%

“…In the present work, we limit our investigations to intermolecular regions of the EDDs. We use an already described approach suitable for the construction [24] and analysis of Gaussian type EDDs at various levels of smoothing [25,26]. Gaussian-based functions present the great advantage to allow fast and analytic ways to provide ED-derived properties such as similarity indices [24,27,28], convolution products [29,30], and topological quantities based on ED first and second derivatives.…”

Section: Introductionmentioning

confidence: 99%

“…Gaussian-based functions present the great advantage to allow fast and analytic ways to provide ED-derived properties such as similarity indices [24,27,28], convolution products [29,30], and topological quantities based on ED first and second derivatives. The method [25,26] is applied here to crystal structures of small molecules interacting through chalcogen bonds. Particularly, analytical promolecular EDD functions are built from the Cromer-Mann (CM) approximation of QM scattering factors.…”

Section: Introductionmentioning

confidence: 99%

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Description of non-covalent interactions in benzyl chalcocyanate crystals from smoothed Cromer–Mann electron density distribution functions

Leherte¹,

Bodart²,

Wouters³

et al. 2022

J. Phys.: Condens. Matter

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A well-known method to characterize non-covalent interactions consists in the topological analysis of electron density distribution (EDD) functions, complemented by the search for minima in the reduced gradient density (RDG) distributions. Here, we characterize intermolecular interactions occurring in crystals of benzyl chalcocyanate compounds through bond critical points (BCP) of the promolecular electron density (ED) built from the crystallographic Cromer-Mann parameters, at several smoothing levels t. The trajectories formed by the t-dependent BCP locations are interpreted in terms of the intermolecular interactions occurring within the crystal arrangements. Chalcogen…nitro BCPs are clearly present in the unsmoothed EDDs but are annihilated as t increases, while chalcogen…chalcogen BCPs appear and are among the only BCPs left at the highest smoothing level. The chalcogen bonds are differentiated from the other chalcogen interactions through the linear chalcogen…BCP…nitro geometry at low smoothing level and their more negative Laplacian values. The annihilation of CPs can be followed by the apparition of a RDG minimum, associated with a very weak interaction. Along the BCP trajectories, the Laplacian shows a progressive concentration of the ED in the intermolecular space within the crystals and adopts the most negative values at the shortest atom…atom separations. At the termination point of a BCP trajectory, the drastic increase of the ellipticity value illustrates the flattening of the EDD.

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Section: Cps and Reduced Density Gradient (Rdg)mentioning

confidence: 99%