Experimental Charge Density Research Articles

The Elusive Structural Origin of Plastic Bending in Dimethyl Sulfone Crystals with Quasi-isotropic Crystal Packing.

Bending in molecular crystals is typically associated with the anisotropy of intermolecular interactions. The intriguing observation is reported of plastic bending in dimethyl sulfone, which exhibits nearly isotropic crystal packing and interaction topology, defying the known structural models of bending crystals. The origin of the bending phenomenon has been explored in terms of intermolecular interaction energies, experimental X-ray charge density analysis, and variable temperature neutron diffraction studies. H⋅⋅⋅H dihydrogen interactions and differences in electrostatic complementarity between molecular layers are found to facilitate the bending behavior.

Is Hexachloro-cyclo-triphosphazene Aromatic? Evidence from Experimental Charge Density Analysis.

Experimental charge density studies of hexachloro-cyclo-triphosphazene (1) and the boat conformation of octachloro-cyclo-tetraphosphazene (2 a) were performed to unambiguously describe the origin of the electron delocalization in the P3 N3 ring in 1. The obtained results were compared to DFT studies in the solid state and the gas phase. Electron density analysis revealed a highly polarized nature of the P-N bonds and a modular structure of the P3 N3 and P4 N4 rings, which can be separated into independent Cl2 PN units with a perfect transferability between the compounds. Further analysis of the source function experimentally proves the presence of negative hyperconjugation involving both out-of-plane and in-plane nitrogen electrons as well as electrons of the chlorine atoms. Finally, these results discard the presence of pseudoaromatic delocalization in the nearly planar P3 N3 ring.

Charge-Assisted Halogen Bonds in Halogen-Substituted Pyridinium Salts: Experimental Electron Density

Favorable electrostatic interactions dominate the packing of three halogen-substituted pyridinium salts with chloride or tetrachloridometallate counteranions. The electron density in these solids was determined based on high resolution X-ray diffraction experiments. Residues carrying opposite charges subtend short interhalogen contacts X···X in which the anionic chlorides act as electron donors and the cationic halogen substituents of the pyridinium cations act as acceptors. The X···X interactions coexist and in part compete with classical N–H···Cl hydrogen bonds. Properties derived from the experimental charge density such as the position of the bond critical point, electron density, Laplacian and energy densities help to establish the relevance of the competing interactions. Multipole-derived charge densities allow classification of short contacts more reliably than exclusively geometry-based analyses and simple promolecule densities.

Ab initio calculation of the potential bubble nucleus Si34

The possibility that an unconventional depletion in the center of the charge density distribution of certain nuclei occurs due to a purely quantum mechanical effect has attracted theoretical and experimental attention in recent years. We report on ab initio self-consistent Green's function calculations of one of such candidates, $^{34}$Si, together with its Z+2 neighbour $^{36}$S. Binding energies, rms radii and density distributions of the two nuclei as well as low-lying spectroscopy of $^{35}$Si, $^{37}$S, $^{33}$Al and $^{35}$P are discussed. The interpretation of one-nucleon removal and addition spectra in terms of the evolution of the underlying shell structure is also provided. The study is repeated using several chiral effective field theory Hamiltonians as a way to test the robustness of the results with respect to input inter-nucleon interactions. The prediction regarding the (non-)existence of the bubble structure in $^{34}$Si varies significantly with the nuclear Hamiltonian used. However, demanding that the experimental charge density distribution and the root mean square radius of $^{36}$S are well reproduced, along with $^{34}$Si and $^{36}$S binding energies, only leaves the NNLO$_{\text{sat}}$ Hamiltonian as a serious candidate to perform this prediction. In this context, a bubble structure, whose fingerprint should be visible in an electron scattering experiment of $^{34}$Si, is predicted. Furthermore, a clear correlation is established between the occurrence of the bubble structure and the weakening of the 1/2$^-$-3/2$^-$ splitting in the spectrum of $^{35}$Si as compared to $^{37}$S.

Probing the influence of non-covalent contact networks identified by charge density analysis on the oxidoreductase BacC.

Bacillus subtilis BacC is an oxidoreductase involved in the biosynthesis of the potent antibiotic bacilysin. The crystal structure of BacC was determined at 1.19 Å resolution. An experimental charge density approach was used to calculate non-covalent interactions within the monomer and across the dimeric interface of BacC. This interaction network, in turn, enabled an analysis of non-covalently connected paths that span the protein structure. One of the pathways of non-covalent interactions was examined by mutational analysis. Biochemical analysis of BacC mutants with potential disruptions in non-covalent interactions along this path revealed that residues that form nodes in pathways of non-covalent interactions influence catalytic activity more than others in a similar chemical environment. Furthermore, we note that nodes in the non-covalent interaction networks are co-localized with compensatory mutation sites identified by multiple sequence alignment of proteins with low sequence similarity to BacC. Put together, this analysis supports the hypothesis that non-covalent nodes represent conserved structural features that can impact the catalytic activity of an enzyme.

Spatial distribution of electrons near the Fermi level in the metallic LaB6 through accurate X-ray charge density study

Charge densities of iso-structural metal hexaborides, a transparent metal LaB6 and a semiconductor BaB6, have been determined using the d > 0.22 Å ultra-high resolution synchrotron radiation X-ray diffraction data by a multipole refinement and a maximum entropy method (MEM). The quality of the experimental charge densities was evaluated by comparison with theoretical charge densities. The strong inter-octahedral and relatively weak intra-octahedral boron-boron bonds were observed in the charge densities. A difference of valence charge densities between LaB6 and BaB6 was calculated to reveal a small difference between isostructural metal and semiconductor. The weak electron lobes distributed around the inter B6 octahedral bond were observed in the difference density. We found the electron lobes are the conductive π-electrons in LaB6 from the comparison with the theoretical valence charge density. We successfully observed a spatial distribution of electrons near the Fermi level from the X-ray charge density study of the series of iso-structural solids.

Copper atom representation in charge density analysis of (5-chlorosalicylate)-(2,9-dimethylphenanthroline)-(aqua) copper complex: Experimental and theoretical study

The crystal structure of (5-chlorosalicylate)-(2,9-dimethylphenanthroline)-(aqua) copper complex (1) was determined at 100 K. In order to explore the electronic structure of the studied compound in the solid state, an experimental charge density analysis has been performed from high-resolution X-ray data. Moreover, three different approaches for the treatment of copper atom within the multipolar refinement were used to model the experimental charge density of the studied compound. Appropriateness of the individual copper atom representations were critically compared to each other and to BLYP/6-311G** theoretical calculations by means of refinement statistics, error analysis, negative Laplacian or deformation density plots as well as Bader's Atoms In Molecule (AIM) analysis and d-populations analysis. The electrostatic potential was calculated to evaluate the reactivity of (1).

Charge density analysis of metformin chloride, a biguanide anti-hyperglycemic agent

The experimental charge density analysis of the anti-hyperglycemic agent metformin chloride with high-resolution X-ray diffraction data at low temperature (100 K) has been performed and these experimental results were compared with that derived from the corresponding periodic theoretical calculations at the B3LYP/6-31G** level of theory. The experimental and theoretical multipolar charge-density analyses of metformin chloride have been accomplished in order to understand its structural and electronic properties. The C and N atoms of the molecular backbone adopt a near trigonal geometry due to the occurrence of extensive delocalization/resonance of C—N bonds, as confirmed by topological analysis and also found by Natural Resonance Theory calculations performed in the isolated metformin cation. The molecule contains six C—N bonds and the topological bond order analysis shows that four bonds have bond orders close to 4/3 and two bonds can be considered as single. The analysis of numerical parameters of the valence shell charge concentration reports that the N3 atom, which forms two bonds with C atoms, possesses one non-bonding valence-shell charge concentration (VSCC) in the direction of the electron lone pair. Among the intermolecular interactions of the chloride atom with the H—C and H—N atoms, eight have been found to be shorter than the sum of van der Waals radii. The analysis of contacts on the Hirshfeld surface reveals that the H—N...Cl hydrogen bonds are enriched (over-represented) and act as the driving force in the crystal packing formation. The metformin cations form favorable electrostatic interactions with the chloride anions which have globally a stronger energy than the unfavorable cation/cation interactions.

1H, 13C NMR and ESI–MS studies of 1:1 complexes of some sulfenyl carbon acids with 1,5,7-triazabicyclo[4.4.0]dec-5-ene in solution

The carbon acids activated by two thiobenzyl groups have been synthesized and the products of the proton transfer reaction between 1,5,7-triazabicyclo[4.4.0]dec-5-ene (TBD) and studied compounds in solution were defined by electrospray ionization mass spectrometry method. The ionization of carbon acids and derivative fragmentary carbanions at various cone voltages are compared. The fragmentation pathways of the carbanions of studied carbon acids are proposed and the differences in fragmentation of these ions are mentioned. Substituent effect on the fragmentation of molecular anions has been discussed. The electron densities of the studied carbanions were determined using experimental 13C chemical shifts and compared with those obtained for sulfonyl carbon acids, cyano and nitroalkanes. The relationship between changes in 13C shifts after ionization and experimental charge density have been discussed.

Topological characterization of electron density, electrostatic potential and intermolecular interactions of 2-nitroimidazole: an experimental and theoretical study.

An experimental charge density distribution of 2-nitroimidazole was determined from high-resolution X-ray diffraction and the Hansen-Coppens multipole model. The 2-nitroimidazole compound was crystallized and a high-angle X-ray diffraction intensity data set has been collected at low temperature (110 K). The structure was solved and further, an aspherical multipole model refinement was performed up to octapole level; the results were used to determine the structure, bond topological and electrostatic properties of the molecule. In the crystal, the molecule exhibits a planar structure and forms weak and strong intermolecular hydrogen-bonding interactions with the neighbouring molecules. The Hirshfeld surface of the molecule was plotted, which explores different types of intermolecular interactions and their strength. The topological analysis of electron density at the bond critical points (b.c.p.) of the molecule was performed, from that the electron density ρbcp(r) and the Laplacian of electron density ∇2ρbcp(r) at the b.c.p.s of the molecule have been determined; these parameters show the charge concentration/depletion of the nitroimidazole bonds in the crystal. The electrostatic parameters like atomic charges and the dipole moment of the molecule were calculated. The electrostatic potential surface of the molecule has been plotted, and it displays a large electronegative region around the nitro group. All the experimental results were compared with the corresponding theoretical calculations performed using CRYSTAL09.

Analysis of an unusual hetero-halogen bonded trimer using charge density analysis: A case of concerted type I Br⋯Br and type II Br⋯Cl interactions

The crystal structure of 4−bromo−2−chlorobenzoic acid generates an unusual triangular motif consisting of a hitherto uncharacterized Type I Br⋯Br contact along with two Type II Br⋯Cl interactions as edges of the triangle. The nature of such bonding is analyzed based on both experimental and theoretical charge density followed by topological analysis. An unusual triangular motif consisting of a hitherto uncharacterized Type I Br⋯×Br contact along with two Type II Br⋯Cl interactions as edges of the triangle is seen in the crystal structure of 4−bromo−2−chlorobenzoic acid. The nature of such bonding is analyzed based on both experimental and theoretical charge density followed by topological analysis.

Electrostatic Properties of N‐Heterocyclic Carbenes Obtained by Experimental Charge‐Density Analysis of Two Selenium Adducts

High‐resolution X‐ray diffraction data and Hansen–Coppens multipole formalism have been used to obtain the charge density distribution in two selenium adducts with the N‐heterocyclic carbenes 1,3‐dimesitylimidazolidin‐2‐ylidene (1) and 1,3‐dimesityl‐4,5‐dioxoimidazolidin‐2‐ylidene (2). Application of Bader's quantum theory of atoms in molecules and calculation of the atomic charges by integration of the experimental electron density over the atomic basins showed that the main electrostatic difference between the Se adducts is in the significantly different accumulation of electron density in their C(carbene)–Se fragments (–0.10 vs. +0.30 e in 1 and 2). Deformation electron density features along the C–Se bond and topological values at the bond critical point indicate that this bond has π character in both compounds but it is more pronounced in the case of 2. This is in agreement with stronger C–N bonds and a larger N–C–N angle in 1. The experimental charge density distribution also clearly indicates the important role of the N‐mesityl substituent as an electron‐donating group, which increases the electron density in the imidazole ring thus contributing to the electronic stabilization of the carbene C atom. Because the N‐mesityl substituents donate similar amounts of electron density in both molecules (0.75 and 0.64 e in 1 and 2), it was concluded that the decisively different electronic properties of the two NHCs have to be attributed to their different backbone structures.

X-ray derived experimental charge density distribution in GaF3 and VF3 solid systems

The electronic structure and bonding features of metal and transition metal fluorides in low oxidation states, GaF3 and VF3, have been studied from precise single crystal X-ray diffraction data using multipole and maximum entropy methods. The topology of the charge density is analyzed and the (3,−1) bond critical points are determined. Existences of ionic nature of bonding in low valent fluorine compounds are clearly evident. The spherical core of metal atom and aspherical or twisted core of transition metal atom reveal the fact that GaF3 is much more rigid than VF3. Aspherical cores of the polarized ligand atoms are also visible in the two-dimensional density distribution pictures. The true valence charge density surfaces with encapsulating the atomic basins maps are elucidated. An elongated saddle with mid-bond density of 0.6191e/Å3, observed in the compound VF3, shows that its lattice is less rigid and has more ionic character than GaF3.

Measurement of atomic electric fields and charge densities from average momentum transfers using scanning transmission electron microscopy

This study sheds light on the prerequisites, possibilities, limitations and interpretation of high-resolution differential phase contrast (DPC) imaging in scanning transmission electron microscopy (STEM). We draw particular attention to the well-established DPC technique based on segmented annular detectors and its relation to recent developments based on pixelated detectors. These employ the expectation value of the momentum transfer as a reliable measure of the angular deflection of the STEM beam induced by an electric field in the specimen. The influence of scattering and propagation of electrons within the specimen is initially discussed separately and then treated in terms of a two-state channeling theory.A detailed simulation study of GaN is presented as a function of specimen thickness and bonding. It is found that bonding effects are rather detectable implicitly, e.g., by characteristics of the momentum flux in areas between the atoms than by directly mapping electric fields and charge densities. For strontium titanate, experimental charge densities are compared with simulations and discussed with respect to experimental artifacts such as scan noise. Finally, we consider practical issues such as figures of merit for spatial and momentum resolution, minimum electron dose, and the mapping of larger-scale, built-in electric fields by virtue of data averaged over a crystal unit cell. We find that the latter is possible for crystals with an inversion center. Concerning the optimal detector design, this study indicates that a sampling of 5mrad per pixel is sufficient in typical applications, corresponding to approximately 10×10 available pixels.

Describing the heavy-ion above-barrier fusion using the bare potentials resulting from Migdal and M3Y double-folding approaches

Systematic calculations of the Coulomb barrier parameters for collisions of spherical nuclei are performed within the framework of the double folding approach. The value of the parameter (which estimates the Coulomb barrier height) varies in these calculations from 10 MeV up to 150 MeV. The nuclear densities came from the Hartree–Fock calculations which reproduce the experimental charge densities with good accuracy. For the nucleon-nucleon effective interaction two analytical approximations known in the literature are used: the M3Y and Migdal forces. The calculations show that Migdal interaction always results in the higher Coulomb barrier. Moreover, as BZ increases the difference between the M3Y and Migdal barrier heights systematically increases as well. As the result, the above barrier fusion cross sections calculated dynamically with the M3Y forces and surface friction are in agreement with the data. The cross sections calculated with the Migdal forces are always below the experimental data even without accounting for the dissipation.

Defects in structure as the sources of the surface charges of kaolinite

The sign and magnitude of the surface charge govern the particle interactions and hence determine the physical properties of dispersions. The present work is to evaluate the distortions, isomorphic and broken surface bond as the sources of the permanent or variable surface charges of kaolinite. The theoretical permanent charge density (σcc) was calculated by XRF. The experimental permanent charge density (σp) and variable charge density (σv) were obtained by the method of potentiometric titration. The degree of broken bonds (Db, b) of Al–O–Al and Si–O–Si at the side of kaolinite structure were characterized by the numbers and strength of surface hydrogen in 1H MAS NMR, absorbance of Al–OH or Si–OH in FTIR and edge fractures in FESEM. The surface area was measured by N2 adsorption–desorption. The defects such as basal z corrugation (∆z), tetrahedral rotation angles (θ) and octahedral flattening angles (ψ) were obtained by the XRD rietveld refinement. The negative σcc or σp of three samples KA, KB and KC are 0.012, 0.007 and 0.009C·m−2 or 0.24, 0.19 and 0.22C·m−2, respectively. Db, b of three samples are Db, b-KA>Db, b-KC>Db, b-KB. The σv depend on the degree of the broken bonds at edges of kaolinite and can be affected by pH significantly. The negative variable charge density at alkaline condition decreased with the increase of the degree of broken bonds at the side of kaolinite structures. Surface charges of kaolinite come from the defects such as isomorphic substitutions and broken bonds Al–O–Al and Si–O–Si. The distortions in structure e.g. ∆z, θ and ψ may not directly create the surface charges.

Experimental and Theoretical Electron Density Analysis of Copper Pyrazine Nitrate Quasi-Low-Dimensional Quantum Magnets.

The accurate electron density distribution and magnetic properties of two metal-organic polymeric magnets, the quasi-one-dimensional (1D) Cu(pyz)(NO3)2 and the quasi-two-dimensional (2D) [Cu(pyz)2(NO3)]NO3·H2O, have been investigated by high-resolution single-crystal X-ray diffraction and density functional theory calculations on the whole periodic systems and on selected fragments. Topological analyses, based on quantum theory of atoms in molecules, enabled the characterization of possible magnetic exchange pathways and the establishment of relationships between the electron (charge and spin) densities and the exchange-coupling constants. In both compounds, the experimentally observed antiferromagnetic coupling can be quantitatively explained by the Cu-Cu superexchange pathway mediated by the pyrazine bridging ligands, via a σ-type interaction. From topological analyses of experimental charge-density data, we show for the first time that the pyrazine tilt angle does not play a role in determining the strength of the magnetic interaction. Taken in combination with molecular orbital analysis and spin density calculations, we find a synergistic relationship between spin delocalization and spin polarization mechanisms and that both determine the bulk magnetic behavior of these Cu(II)-pyz coordination polymers.

Equilibria Between Cell Membranes and Electrolyte Solution: Effect of Fatal Accidental Hypothermia.

Equilibria between the membranes of erythrocytes as well as thrombocytes and solution ions in fatal accidental hypothermia were analyzed using a theoretical four-equilibria model. The model was developed to determinate parameters characterizing cell membrane—surrounding ion interactions: the total surface concentrations of both acidic and basic groups CA, CB, and association constants KAH, KBOH. Knowledge of these parameters was necessary to calculate the theoretical values of surface charge density. The model was validated by curve-fitting the experimental data points to simulated data generated by the model. The experimental and theoretical surface charge density values agree at pH 2–8, at higher pH the deviation was observed.

Experimental and theoretical charge-density analysis of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione: applications of a virtual-atom model.

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.

An analysis of the experimental and theoretical charge density distributions of the piroxicam–saccharin co-crystal and its constituents

Experimental and theoretical charge density of piroxicam, saccharin and their 1 : 1 co-crystal have been determined using high-resolution X-ray diffraction, multipole refinement and DFT calculations