WinXPRO, 3DPlot and TrajPlot computer software: new options for orbital-free quantum crystallography studies

Сташ, А. И.; Tsirelson, Vladimir G.

doi:10.1107/s1600576722002321

Cited by 10 publications

(18 citation statements)

References 36 publications

(33 reference statements)

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“…However, while the kinetic force F k ( r ) = F P ( r ) + F W ( r ) is always directed away from the closest atomic nucleus at any point within the system, both von Weizsäcker F W ( r ) and Pauli F P ( r ) forces have their direction governed by the local ED features as the valence shell charge concentrations (VSCCs) and ED depletions as well as the shared and lone electron pairs. Features of F W -field within VSCC regions were considered earlier ,, and generally appear in smaller volumes and closer to the nucleus, which may complicate the visual inspection of the 3D arrow representation of the vector field. In contrast, the F P -field behaves differently.…”

Section: Resultsmentioning

confidence: 99%

“…The static EDs and related functions were restored from the multipole models and further analyzed by means of the WinXPRO, 3DPlot, and TrajPlot software packages for quantum crystallography. , For each compound, all calculations were performed within a finite spherical electroneutral cluster with a radius of more than 15 Å to simulate the crystalline environment, which is critically important for φ es ( r ) and the derived functions.…”

Section: Experimental and Computational Methodsmentioning

confidence: 99%

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Electronic and Crystal Packing Effects in Terms of Static and Kinetic Force Field Features: Picolinic Acid N-Oxide and Methimazole

Kartashov

Shteingolts

Stash

et al. 2023

Crystal Growth & Design

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Herein, we experimentally obtained and studied the inner-crystal scalar potential fields and the associated vector force fields of static and kinetic nature in picolinic acid N-oxide (PANO) and methimazole. The “through-bond” and “through-space” electronic effects were defined and distinguished via the vector fields and concurred with the penetration of the electron contributor’s electrostatic and kinetic force field pseudoatoms (φes- and φ k -basins) into the occupier’s chemical atom (ρ-basin). A special focus was given to the dipolar N+–O– bond as well as to the thioamide N–CS and carboxylic OC–OH fragments. An unusual way of interatomic charge transfer was revealed between two nonbonded hydrogen atoms [COO−]H···H[−C] in the PANO crystal. The experimental electric and kinetic force fields in the molecular crystals were compared to the theoretical ones for the free molecules and hydrogen-bonded associates, which helped figure out the natural consequences of the crystal packing effect. As expected, the appearance of neighboring attractors in a dense crystal packing requires zero-flux surfaces (ZFSs) emerging in the vector fields and the compression of the outer force field pseudoatoms of a molecule. We proposed to consider a ZFS in the kinetic force field to be a turning surface for electrons in the sense that an electron passed through the boundary is immediately affected by the redirected force attributed to another attractor. The strengthening and noticeable increase observed in the covalency of the intramolecular hydrogen bond O–H···O in the PANO crystal is a direct consequence of such compression of the hydrogen atom and pseudoatoms by the inner-crystal environment. The Pauli and fermionic scalar and vector fields were applied to locate electron lone pairs and describe their involvement in noncovalent interactions within the donor–acceptor mechanism.

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Section: Resultsmentioning

confidence: 99%

Section: Experimental and Computational Methodsmentioning

confidence: 99%

Electronic and Crystal Packing Effects in Terms of Static and Kinetic Force Field Features: Picolinic Acid N-Oxide and Methimazole

Kartashov

Shteingolts

Stash

et al. 2023

Crystal Growth & Design

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“…Experimental static ED distributions were restored via multipole models for crystalline oxalic acid dihydrate (COOH) 2 ×2H 2 O, sodium chloride (NaCl), [20] high‐temperature superconductor magnesium diboride (MgB 2 ), [73] and 1‐{2‐[2‐(methoxycarbonylmethylsulfonyl)ethoxy]ethyl}‐3,5‐dimethylisocyanurate ( ica ; see Scheme S1) [64] . Analysis of multipole‐modeled ED and scalar fields was performed using the WinXPRO software [74] according to the published procedures [15,75] . The orbital‐free local density approximation of

ϕ_{x} (boldr)

by von Barth and Hedin was used [76] .…”

Section: Resultsmentioning

confidence: 99%

Real‐Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields**

Shteingolts

Сташ

Tsirelson

et al. 2022

Chemistry A European J

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Intricate behaviour of one‐electron potentials from the Euler equation for electron density and corresponding gradient force fields in crystals was studied. Channels of locally enhanced kinetic potential and corresponding saddle Lagrange points were found between chemically bonded atoms. Superposition of electrostatic ϕesboldr and kinetic ϕkboldr potentials and electron density ρboldr allowed partitioning any molecules and crystals into atomic ρ ‐ and potential‐based ϕ ‐basins; ϕk ‐basins explicitly account for the electron exchange effect, which is missed for ϕes ‐ones. Phenomena of interatomic charge transfer and related electron exchange were explained in terms of space gaps between zero‐flux surfaces of ρ ‐ and ϕ ‐basins. The gap between ϕes ‐ and ρ ‐basins represents the charge transfer, while the gap between ϕk ‐ and ρ ‐basins is a real‐space manifestation of sharing the transferred electrons caused by the static exchange and kinetic effects as a response against the electron transfer. The regularity describing relative positions of ρ ‐, ϕes ‐, and ϕk ‐ basin boundaries between interacting atoms was proposed. The position of ϕk ‐boundary between ϕes ‐ and ρ ‐ones within an electron occupier atom determines the extent of transferred electron sharing. The stronger an H⋅⋅⋅O hydrogen bond is, the deeper hydrogen atom's ϕk ‐basin penetrates oxygen atom's ρ ‐basin, while for covalent bonds a ϕk ‐boundary closely approaches a ϕes ‐one indicating almost complete sharing of the transferred electrons. In the case of ionic bonds, the same region corresponds to electron pairing within the ρ ‐basin of an electron occupier atom.

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“…The experimental data for Appel’s salt were taken from the recent work . All calculations and further analysis were performed using WinXPRO, 3DPlot, and TrajPlot software , according to the known procedures. , For the crystal, the calculations were performed within a finite spherical electroneutral cluster with a radius of 18.2 Å. When calculating trajectory maps, the out-of-plane distance was set up to 0.8 Å.…”

Section: Methodsmentioning

confidence: 99%

“…It is worth noting that the FAEM scriptF ( r ) and Ehrenfest force density frakturH ( r ) exhibit similar behavior, topology, and physical meaning, , but scriptF ( r ) , as well as the other abovementioned force fields F i ( r ), is accessible from experimental ED distributions in crystals applying the ideas of the orbital-free density functional theory (OF DFT). , In particular, the behavior of FAEM scriptF ( r ) and kinetic force F k ( r ) in crystals obtained from experimental data has recently been described in detail on the several examples. − ,,, The behavior of frakturH ( r ) in calculated systems has also been the subject of fruitful research. − …”

Section: Introductionmentioning

confidence: 99%

Unified Picture of Interatomic Interactions, Structures, and Chemical Reactions by Means of Electrostatic and Kinetic Force Density Fields: Appel’s Salt and Its Ion Pairs

Saifina

Kartashov

Stash

et al. 2023

Crystal Growth & Design

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This paper presents a binding approach based on the electrostatic and kinetic force density fields and proposed to elucidate interatomic interactions, structures, and chemical reactions. Among other elements, it consists in the understanding of (i) the arrangement of pseudoatomic zero-flux surfaces (ZFSs), (ii) the mutual compression of force-field pseudoatoms of the same type, (iii) the penetration of a bonded atom into neighboring forcefield pseudoatoms, (iv) the distortion of the force fields, and (v) the occurrence of a binding path connecting two force-field attractors as the inherent consequences of the emergence and existence of any many-electron multinuclear system. Herein, the interatomic charge transfer and the reciprocal quantum-chemical response accompanying the covalent and noncovalent bond formation were studied using the abovementioned penetration, exemplified by Appel's salt. Such consideration gave rise to the concept of force-induced "push−pull" assembling of interacting (pseudo)atoms. In this regard, various halogen, chalcogen, and tetrel noncovalent interactions, as well as polar covalent bonds, were examined. Furthermore, the notion of the force-based binding structure was proposed instead of the bonding one, which defines the mutual connectivity of force-field pseudoatoms of the same type via binding paths. The thus-defined chemical structure proved to be more sensitive to variations in the configuration space of nuclear coordinates. It was found that the three-center chalcogen bonding Cl − •••S−S and tetrel bonding Cl − •••C•••Cl − in the crystal studied resemble the initial and transition states of bimolecular nucleophilic substitution reactions, respectively. Their central atoms act as electron contributors with a different degree of the transferred electron density sharing. Being extracted from the crystal structure, the corresponding ion pairs undergo chemical rearrangement: Forming the covalent bonds Cl−S and Cl−C leads to the collapse of the pseudoatomic ZFSs and the alignment of the bond and binding paths in the internuclear regions.

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WinXPRO, 3DPlot and TrajPlot computer software: new options for orbital-free quantum crystallography studies

Cited by 10 publications

References 36 publications

Electronic and Crystal Packing Effects in Terms of Static and Kinetic Force Field Features: Picolinic Acid N-Oxide and Methimazole

Electronic and Crystal Packing Effects in Terms of Static and Kinetic Force Field Features: Picolinic Acid N-Oxide and Methimazole

Real‐Space Interpretation of Interatomic Charge Transfer and Electron Exchange Effects by Combining Static and Kinetic Potentials and Associated Vector Fields**

Unified Picture of Interatomic Interactions, Structures, and Chemical Reactions by Means of Electrostatic and Kinetic Force Density Fields: Appel’s Salt and Its Ion Pairs

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