Combined analysis of chemical bonding in a CuIIdimer using QTAIM, Voronoi tessellation and Hirshfeld surface approaches

2015 ◽  
Vol 71 (5) ◽  
pp. 543-554 ◽  
Author(s):  
Anna V. Vologzhanina ◽  
Svitlana V. Kats ◽  
Larisa V. Penkova ◽  
Vadim A. Pavlenko ◽  
Nikolay N. Efimov ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Voronoi Tessellation ◽  
Quantitative Description ◽  
Hirshfeld Surface ◽  
Epr Spectra ◽  
Antiferromagnetic Coupling ◽  
X Ray Diffraction ◽  
Spin Distribution ◽  
X Ray

Interaction of 1-(1H-pyrazol-5-yl)ethanone oxime (H2PzOx) with copper(II) chloride in the presence of pyridine afforded a binuclear discrete [Cu2(HPzOx)2Cl2py2] complex, which was characterized by Fourier transform–IR and electron paramagnetic resonance (EPR) spectra, magnetochemistry and high-resolution X-ray diffraction experiments. Multipole refinement of X-ray diffraction data and density-functional theory (DFT) calculations of an isolated molecule allowed charge and spin distributions to be obtained for this compound. Magnetochemistry data, EPR spectra and DFT calculations of an isolated molecule show antiferromagnetic coupling between copper(II) ions. The spin distribution suggests an exchange pathwayviathe bridging pyrazole ring in the equatorial plane of the CuN4Cl coordination polyhedron, thus providing support for the classical superexchange mechanism; the calculated value of the magnetic coupling constant −2Jis equal to 220 cm−1, which compares well with the experimental value of 203 ± 2 cm−1. Chemical connectivity was derived by Bader's `quantum theory of atoms in molecules' and compared with Voronoi tessellation and Hirshfeld surface representations of crystal space. All methodologies gave a similar qualitative and semi-quantitative description of intra- and intermolecular connectivity.

scholarly journals Synthesis, Crystal Structure, Thermal Analysis, and DFT Calculations of Molecular Copper(II) Chloride Complexes with Bitopic Ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane

Crystals ◽  
2019 ◽  
Vol 9 (4) ◽  
pp. 222
Author(s):  
Lider ◽  
Sukhikh ◽  
Smolentsev ◽  
Semitut ◽  
Filatov ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Coordination Compounds ◽  
Density Functional ◽  
Water Molecules ◽  
X Ray Diffraction ◽  
Chloride Complexes ◽  
Functional Theory ◽  
X Ray ◽  
Lattice Water ◽  
Ir Bands

Two binuclear coordination compounds of Cu(II) chloride with the bitopic ligand 1,1,2,2-tetrakis(pyrazol-1-yl)ethane (Pz4) of the composition [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O and [Cu2(µ2Pz4)(DMSO)2Cl4]∙2DMSO were prepared and characterized by elemental analysis, IR spectroscopy, thermogravimetric analysis, single-crystal X-ray diffraction, and powder diffraction analysis. It was shown that in contrast to silver(I) and copper(II) nitrates, copper(II) chloride forms discrete complexes instead of coordination polymers. The supramolecular structure of the complex [Cu2(µ2Pz4)(DMSO)2Cl4]·4H2O with lattice water molecules is formed by OH···Cl and OH···O hydrogen bonds. Density functional theory (DFT) calculations of vibrational frequencies of the ligand and its copper(II) complex allowed for assigning IR bands to specific vibrations.

scholarly journals Interplay of weak noncovalent interactions in alkoxybenzylidene derivatives of benzohydrazide and acetohydrazide: a combined experimental and theoretical investigation and lipoxygenase inhibition (LOX) studies

CrystEngComm ◽  
2021 ◽  
Author(s):  
Muhammad Naeem Ahmed ◽  
Muneeba Arif ◽  
Hina Andleeb ◽  
Syed Wadood Ali Shah ◽  
Ifzan Arshad ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Surface Analysis ◽  
Schiff Bases ◽  
Theoretical Investigation ◽  
Noncovalent Interactions ◽  
Hirshfeld Surface ◽  
X Ray Diffraction ◽  
X Ray ◽  
Lipoxygenase Inhibition ◽  
Derivatives Of

Three hydrazide-based Schiff bases have been synthesized and characterized by IR, UV-vis and X-ray diffraction methods. A detail analysis of intermolecular interactions has been performed by Hirshfeld surface analysis and DFT calculations.

A cyanide-bridged FeIII–MnII heterobimetallic one-dimensional coordination polymer: synthesis, crystal structure, experimental and theoretical magnetism investigation

2019 ◽  
Vol 75 (11) ◽  
pp. 1475-1481 ◽  
Author(s):  
Wenlong Lan ◽  
Zhen Zhou ◽  
Jie Li ◽  
Yong Dou ◽  
Xiaoyun Hao ◽  
...  
Keyword(s):  
Coordination Polymer ◽  
Single Crystal ◽  
Density Functional ◽  
Linear Chain ◽  
Coupling Constants ◽  
Antiferromagnetic Coupling ◽  
Chain Model ◽  
X Ray Diffraction ◽  
One Dimensional ◽  
X Ray

A new cyanide-bridged FeIII–MnII heterobimetallic coordination polymer (CP), namely catena-poly[[[N,N′-(1,2-phenylene)bis(pyridine-2-carboxamidato)-κ4 N,N′,N′′,N′′′]iron(III)]-μ-cyanido-κ2 C:N-[bis(4,4′-bipyridine-κN)bis(methanol-κO)manganese(II)]-μ-cyanido-κ2 N:C], {[FeMn(C18H12N4O2)(CN)2(C10H8N2)2(CH3OH)2]ClO4} n , (1), was prepared by the self-assembly of the trans-dicyanidoiron(III)-containing building block [Fe(bpb)(CN)2]− [bpb2− = N,N′-(1,2-phenylene)bis(pyridine-2-carboxamidate)], [Mn(ClO4)2]·6H2O and 4,4′-bipyridine, and was structurally characterized by elemental analysis, IR spectroscopy, single-crystal X-ray crystallography and powder X-ray diffraction (PXRD). Single-crystal X-ray diffraction analysis shows that CP 1 possesses a cationic linear chain structure consisting of alternating cyanide-bridged Fe–Mn units, with free perchlorate as the charge-balancing anion, which can be further extended into a two-dimensional supramolecular sheet structure via inter-chain π–π interactions between the 4,4′-bipyridine ligands. Within the chain, each MnII ion is six-coordinated by an N6 unit and is involved in a slightly distorted octahedral coordination geometry. Investigation of the magnetic properties of 1 reveals an antiferromagnetic coupling between the cyanide-bridged FeIII and MnII ions. A best fit of the magnetic susceptibility based on the one-dimensional alternating chain model leads to the magnetic coupling constants J 1 = −1.35 and J 2 = −1.05 cm−1, and the antiferromagnetic coupling was further confirmed by spin Hamiltonian-based density functional theoretical (DFT) calculations.

Configurations and conformations of glycosyl sulfoxides

2010 ◽  
Vol 88 (11) ◽  
pp. 1154-1174 ◽  
Author(s):  
Hong Liang ◽  
Micheline MacKay ◽  
T. Bruce Grindley ◽  
Katherine N. Robertson ◽  
T. Stanley Cameron
Keyword(s):  
Solid State ◽  
Dft Calculations ◽  
Gas Phase ◽  
Density Functional ◽  
Lone Pair ◽  
Azido Group ◽  
X Ray Diffraction ◽  
X Ray ◽  
Comparison Of The Results ◽  
P Type

X-ray crystallographic studies of two axial glycosyl sulfoxides having RS configurations (derivatives of phenyl 2-azido-2-deoxy-1-thio-α-d-galactopyranoside S-oxide) show that they adopt anti conformations in the solid state, in contrast to previous observations and assumptions. Density functional theory (DFT) calculations at the B3lYP6–311G+(d,p)/6–31G(d) level confirm that anti conformations of both phenyl and methyl RS glycosyl sulfoxides of 2-azido-2-deoxy-α-d-pyranosides are more stable than exo-anomeric conformations in the gas phase. 1D NOE measurements indicate that the more polar exo-anomeric conformers are only populated to a slight extent in solution. The anti conformations are distorted so that the glycosyl substituents are closer to being eclipsed with H1. This distortion allows S n → σ* overlap if the sulfur lone pair is a p-type lone pair. Evidence for this overlap comes from short C1–S bond distances, as short as the comparable bond distances in the X-ray crystal structure and in the results from DFT calculations for the SS glycoside, which does adopt the expected exo-anomeric conformation, both in the solid state and in solution, and has normal n → σ* overlap. For 2-deoxy derivatives not bearing a 2-azido group, gas-phase DFT calculations at the same level indicate that the anti- and exo-anomeric conformers have comparable stabilities. Comparison of the results of the two series shows that electronegative substituents in equatorial orientations at C2 destabilize conformations with parallel S–O arrangements, the conformation favored by having an endocyclic C–O dipole antiparallel to the S–O dipole, by about 2.5 kcal mol–1 (1 cal = 4.184 J). An equatorial glycosyl sulfoxide, (SS) phenyl 3,4,6-tri-O-acetyl-2-deoxy-2-phthalimido-1-thio-β-d-glucopyranoside S-oxide, also adopts an anti conformation in the solid state as shown by X-ray diffraction. It also adopts this conformation in solution, in contrast to studies of other equatorial glycosyl sulfoxides.

scholarly journals Crystal structure determination of karibibite, an Fe3+ arsenite, using electron diffraction tomography

2017 ◽  
Vol 81 (5) ◽  
pp. 1191-1202 ◽  
Author(s):  
Fernando Colombo ◽  
Enrico Mugnaioli ◽  
Oriol Vallcorba ◽  
Alberto García ◽  
Alejandro R. Goñi ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Electron Diffraction ◽  
Dft Calculations ◽  
Density Functional ◽  
Weak Interactions ◽  
Diffraction Tomography ◽  
X Ray Diffraction ◽  
Orthorhombic Space Group ◽  
X Ray ◽  
Cell Parameters

AbstractThe crystal structure of karibibite, Fe33+(As3+O2)4(As23+O5)(OH), from the Urucum mine (Minas Gerais, Brazil), was solved and refined from electron diffraction tomography data [R1 = 18.8% for F > 4σ(F)] and further confirmed by synchrotron X-ray diffraction and density functional theory (DFT) calculations. The mineral is orthorhombic, space group Pnma and unit-cell parameters (synchrotron X-ray diffraction) are a = 7.2558(3), b = 27.992(1), c = 6.5243 (3) Å, V = 1325.10(8) Å3, Z = 4. The crystal structure of karibibbite consists of bands of Fe3+O6 octahedra running along a framed by two chains of AsO3 trigonal pyramids at each side, and along c by As2O5 dimers above and below. Each band is composed of ribbons of three edge-sharing Fe3+O6 octahedra, apex-connected with other ribbons in order to form a kinked band running along a. The atoms As(2) and As(3), each showing trigonal pyramidal coordination by O, share the O(4) atom to form a dimer. In turn, dimers are connected by the O(3) atoms, defining a zig-zag chain of overall (As3+O2)n-n stoichiometry. Each ribbon of (Fe3+O6) octahedra is flanked on both edges by the (As3+O2)n-n chains. The simultaneous presence of arsenite chains and dimers is previously unknown in compounds with As3+. The lone-electron pairs (4s2) of the As(2) and As(3) atoms project into the interlayer located at y = 0 and y = ½, yielding probable weak interactions with the O atoms of the facing (AsO2) chain.The DFT calculations show that the Fe atoms have maximum spin polarization, consistent with the Fe3+ state.

scholarly journals Pressure-dependent X-ray diffraction of the multiferroics RMn2O5

2019 ◽  
Vol 75 (4) ◽  
pp. 687-696 ◽  
Author(s):  
Wei Peng ◽  
Victor Balédent ◽  
Marie-Bernadette Lepetit ◽  
Antoine Vaunat ◽  
Elisa Rebolini ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Room Temperature ◽  
Exchange Interactions ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
X Ray ◽  
X Ray Scattering ◽  
Pressure Evolution ◽  
Good Agreement

The room-temperature structural properties of the RMn2O5 multiferroics have been investigated under pressure, using powder X-ray scattering and density functional theory (DFT) calculations. It was possible to determine the lattice parameters and the main atomic positions as a function of pressure. Good agreement was observed between the X-ray and DFT results for most of the determined crystallographic data. From the DFT calculations, it was possible to infer the pressure evolution of the exchange interactions, and this analysis led to the conclusion that the onset of the q = (½, 0, ½) magnetic structure under pressure is related to the increase in the J 1 super-exchange terms (due to the reduction in the Mn—O distances) compared with the Mn—R exchange interactions. In addition, the 1D antiferromagnetic character of the compounds should be reinforced under pressure.

scholarly journals Theoretical and experimental studies of compression and shear deformation behavior of Osmium to 280 GPa

2021 ◽  
Author(s):  
Chia Min Lin ◽  
Kaleb C Burrage ◽  
Chris Perreault ◽  
Wei-Chih Chen ◽  
Cheng-Chien Chen ◽  
...  
Keyword(s):  
Shear Stress ◽  
Shear Strength ◽  
Dft Calculations ◽  
Density Functional ◽  
Theoretical Calculations ◽  
Experimental Studies ◽  
Axial Ratio ◽  
Shear Direction ◽  
X Ray Diffraction ◽  
X Ray

Abstract The compression behavior of osmium metal was investigated up to 280 GPa (volume compression V/Vo =0.725) under nonhydrostatic conditions at ambient temperature using angle dispersive axial x-ray diffraction (A-XRD) with a diamond anvil cell (DAC). In addition, shear strength of osmium was measured to 170 GPa using radial x-ray diffraction (R-XRD) technique in DAC. Both diffraction techniques in DAC employed platinum as an internal pressure standard. Density functional theory (DFT) calculations were also performed, and the computed lattice parameters and volumes under compression are in good agreement with the experiments. DFT predicts a monotonous increase in axial ratio (c/a) with pressure and the structural anomalies of less than 1 % in (c/a) ratio below 150 GPa were not reproduced in theoretical calculations and hydrostatic measurements. The measured value of shear strength of osmium (τ) approaches a limiting value of 6 GPa above a pressure of 50 GPa in contrast to theoretical predictions of 24 GPa and is likely due to imperfections in polycrystalline samples. DFT calculations also enable the studies of shear and tensile deformations. The theoretical ideal shear stress is found along the (001)[1-10] shear direction with the maximal shear stress ~24 GPa at critical strain ~0.13.

Pressure-induced polymorphism in nanostructured SnSe

2016 ◽  
Vol 49 (1) ◽  
pp. 213-221 ◽  
Author(s):  
Sergio Michielon de Souza ◽  
Hidembergue Ordozgoith da Frota ◽  
Daniela Menegon Trichês ◽  
Angsula Ghosh ◽  
Puspitapallab Chaudhuri ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Density Functional ◽  
Rietveld Method ◽  
X Ray Diffraction ◽  
Synchrotron Source ◽  
X Ray ◽  
Cell Parameters ◽  
Theoretical Approaches ◽  
Diffraction Patterns ◽  
Murnaghan Equation

The pressure-induced phase transitions in nanostructured SnSe were investigated using angle-dispersive X-ray diffraction in a synchrotron source along with first-principles density functional theory (DFT) calculations. The variation of the cell parameters along with enthalpy calculations for pressures up to 18 GPa have been considered. Both the experimental and the theoretical approaches demonstrate a phase transition at around 4 GPa. Below 8.2 GPa the X-ray diffraction patterns were fitted using the Rietveld method with space groupPnma(No. 62). The lattice parameters and atomic positions for the above-mentioned symmetry were used in DFT calculations of thermodynamic parameters. The enthalpy calculations with the computationally optimized structure and the proposedPnmastructure of SnSe were compatible. The variations of the cell volume for the high-pressure phases are described by a third-order Birch–Murnaghan equation of state.

scholarly journals Intramolecular sp2-sp3 Disequalization of Chemically Identical Sulfonamide Nitrogen Atoms: Single Crystal X-Ray Diffraction Characterization, Hirshfeld Surface Analysis and DFT Calculations of N-Substituted Hexahydro-1,3,5-Triazines

Crystals ◽  
2020 ◽  
Vol 10 (5) ◽  
pp. 369 ◽  
Author(s):  
Alexey V. Kletskov ◽  
Diego M. Gil ◽  
Antonio Frontera ◽  
Vladimir P. Zaytsev ◽  
Natalia L. Merkulova ◽  
...  
Keyword(s):  
Dft Calculations ◽  
Single Crystal ◽  
Surface Analysis ◽  
Noncovalent Interactions ◽  
Xrd Analysis ◽  
Hirshfeld Surface ◽  
Hirshfeld Surface Analysis ◽  
X Ray Diffraction ◽  
X Ray

In this manuscript, the synthesis and single crystal X-ray diffraction characterization of four N-substituted 1,3,5-triazinanes are reported along with a detailed analysis of the noncovalent interactions observed in the solid state architecture to these compounds, focusing on C–H···π and C–H···O H-bonding interactions. These noncovalent contacts have been characterized energetically by using DFT calculations and also by Hirshfeld surface analysis. In addition, the supramolecular assemblies have been characterized using the quantum theory of “atoms-in-molecules” (QTAIM) and molecular electrostatic potential (MEP) calculations. The XRD analysis revealed a never before observed feature of the crystalline structure of some molecules: symmetrically substituted 1,3,5-triazacyclohexanes possess two chemically identical sulfonamide nitrogen atoms in different sp2 and sp3-hybridizations.

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