scholarly journals High Pressure Crystal Structure and Electrical Properties of a Single Component Molecular Crystal [Ni(dddt)2] (dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate)

Molecules ◽  
2019 ◽  
Vol 24 (10) ◽  
pp. 1843
Author(s):  
Hengbo Cui ◽  
Takao Tsumuraya ◽  
Hamish H.-M. Yeung ◽  
Chloe S. Coates ◽  
Mark R. Warren ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Electrical Properties ◽  
Molecular Crystal ◽  
Density Functional ◽  
Nodal Line ◽  
Single Component ◽  
Molecular Conductors ◽  
Cell Parameters ◽  
Pressure Independent

Single-component molecular conductors form an important class of materials showing exotic quantum phenomena, owing to the range of behavior they exhibit under physical stimuli. We report the effect of high pressure on the electrical properties and crystal structure of the single-component crystal [Ni(dddt)2] (where dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate). The system is isoelectronic and isostructural with [Pd(dddt)2], which is the first example of a single-component molecular crystal that exhibits nodal line semimetallic behavior under high pressure. Systematic high pressure four-probe electrical resistivity measurements were performed up to 21.6 GPa, using a Diamond Anvil Cell (DAC), and high pressure single crystal synchrotron X-ray diffraction was performed up to 11.2 GPa. We found that [Ni(dddt)2] initially exhibits a decrease of resistivity upon increasing pressure but, unlike [Pd(dddt)2], it shows pressure-independent semiconductivity above 9.5 GPa. This correlates with decreasing changes in the unit cell parameters and intermolecular interactions, most notably the π-π stacking distance within chains of [Ni(dddt)2] molecules. Using first-principles density functional theory (DFT) calculations, based on the experimentally-determined crystal structures, we confirm that the band gap decreases with increasing pressure. Thus, we have been able to rationalize the electrical behavior of [Ni(dddt)2] in the pressure-dependent regime, and suggest possible explanations for its pressure-independent behavior at higher pressures.

scholarly journals Synthesis, Crystal Structure, DFT studies, Docking Studies and Fluorescent Properties of 2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile

2018 ◽  
Author(s):  
Jacques Joubert
Keyword(s):  
Crystal Structure ◽  
Binding Affinity ◽  
Active Site ◽  
Density Functional ◽  
Protein Crystal ◽  
Frontier Molecular Orbital ◽  
Biological Interactions ◽  
Fluorescent Properties ◽  
Orthorhombic Space Group ◽  
Cell Parameters

2-(Adamantan-1-yl)-2H-isoindole-1-carbonitrile (1) has been identified as a neurobiological fluorescent ligand that may be used to develop receptor and enzyme binding affinity assays. Compound 1 was synthesised using an optimised microwave irradiation reaction and crystallised from ethanol. Crystallization occurred in the orthorhombic space group P212121 with unit cell parameters: a = 6.4487(12) Å, b = 13.648(3) Å, c = 16.571(3) Å, V = 1458(5) Å3, Z = 4. Density functional theory (DFT) (B3LYP/6-311++G (d,p)) calculations of 1 were carried out. Results showed that the optimised geometry is similar to the crystal structure parameters with a root-mean-squared deviation of 0.143 Å. Frontier molecular orbital energies and net atomic charges are discussed with a focus on potential biological interactions. Docking experiments within the active site of the neuronal nitric oxide synthase (nNOS) protein crystal structure were carried out and analysed. Important binding interactions between the DFT optimised structure and amino acids within the nNOS active site were identified that explain the strong NOS binding affinity reported. Fluorescent properties of 1 were studied using aprotic solvents of different polarities. Compound 1 showed the highest fluorescence intensity in polar solvents with excitation and emission values of 336 nm and 380 nm, respectively.

Microporous crystal structure of labuntsovite-Fe and high-pressure behavior up to 23 GPa

2018 ◽  
Vol 74 (1) ◽  
pp. 1-11 ◽  
Author(s):  
Sergey M. Aksenov ◽  
Elena A. Bykova ◽  
Ramiza K. Rastsvetaeva ◽  
Nikita V. Chukanov ◽  
Irina P. Makarova ◽  
...  
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
Single Crystal ◽  
Cross Section ◽  
Structure Refinement ◽  
Alkaline Complex ◽  
X Ray ◽  
Cell Parameters ◽  
Diamond Anvil ◽  
The Stability

Labuntsovite-Fe, an Fe-dominant member of the labuntsovite subgroup, was first discovered in the Khibiny alkaline massif on Mt Kukisvumchorr [Khomyakov et al. (2001). Zap. Vseross. Mineral. Oba, 130, 36–45]. However, no data are published about the crystal structure of this mineral. Labuntsovite-Fe from a peralkaline pegmatite located on Mt Nyorkpakhk, in the Khibiny alkaline complex, Kola Peninsula, Russia, has been investigated by means of electron microprobe analyses, single-crystal X-ray structure refinement, and IR and Raman spectroscopies. Monoclinic unit-cell parameters of labuntsovite-Fe are: a = 14.2584 (4), b = 13.7541 (6), c = 7.7770 (2) Å, β = 116.893 (3)°; V = 1360.22 (9) Å3; space group C2/m. The structure was refined to final R 1 = 0.0467, wR 2 = 0.0715 for 3202 reflections [I > 3σ(I)]. The refined crystal chemical formula is (Z = 2): Na2K2Ba0.7[(Fe0.5Ti0.1Mg0.05)(H2O)1.3]{[Ti2(Ti1.9Nb0.1)(O,OH)4][Si4O12]2}·4H2O. The high-pressure in situ single-crystal X-ray diffraction study of the labuntsovite-Fe has been carried out in a diamond anvil cell. The labuntsovite-type structure is stable up to 23 GPa and phase transitions are not observed. Calculations using the BM3 equation of state resulted in the bulk modulus K = 72 (2) GPa, K′0 = 3.7 (2) and V 0 = 1363 (2) Å3. Compressing of the heteropolyhedral zeolite-like framework leads to the deformation of main structural units. Octahedral rods show the gradual increase of distortion and the wave-like character of rods becomes more distinct. Rod deformations result in the distortion of the silicon–oxygen ring which is not equal in different directions. Structural channels are characterized by a different ellipticity–pressure relationship: the cross-section of the largest channel I and channel II demonstrates the stability of the geometrical characteristics which practically do not depend on pressure: ∊channel I ≃ 0.85 (4) (cross-section is rather regular) and ∊channel II ≃ 0.52 (2) within the whole pressure range. However, channel III is characterized by the increasing of ellipticity with pressure (∊ = 0.40 → 0.10).

scholarly journals Synthesis, Characterization, and Crystal Structure Determination of a New Lithium Zinc Iodate Polymorph LiZn(IO3)3

Crystals ◽  
2019 ◽  
Vol 9 (9) ◽  
pp. 464 ◽  
Author(s):  
Hebboul ◽  
Galez ◽  
Benbertal ◽  
Beauquis ◽  
Mugnier ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Density Functional Theory ◽  
Density Functional ◽  
Second Harmonic ◽  
Infrared Absorption Spectrum ◽  
Density Functional Theory Calculations ◽  
Functional Theory ◽  
Space Group ◽  
X Ray ◽  
Cell Parameters

Synthesis and characterization of anhydrous LiZn(IO3)3 powders prepared from an aqueous solution are reported. Morphological and compositional analyses were carried out by using scanning electron microscopy and energy-dispersive X-ray measurements. The synthesized powders exhibited a needle-like morphology after annealing at 400 °C. A crystal structure for the synthesized compound was proposed from powder X-ray diffraction and density-functional theory calculations. Rietveld refinements led to a monoclinic structure, which can be described with space group P21, number 4, and unit-cell parameters a = 21.874(9) Å, b = 5.171(2) Å, c = 5.433(2) Å, and  = 120.93(4)°. Density-functional theory calculations supported the same crystal structure. Infrared spectra were also collected, and the vibrations associated with the different modes were discussed. The non-centrosymmetric space group determined for this new polymorph of LiZn(IO3)3, the characteristics of its infrared absorption spectrum, and the observed second-harmonic generation suggest it is a promising infrared non-linear optical material.

scholarly journals High-Pressure Structural Behavior and Equation of State of Kagome Staircase Compound, Ni3V2O8

Crystals ◽  
2020 ◽  
Vol 10 (10) ◽  
pp. 910
Author(s):  
Daniel Diaz-Anichtchenko ◽  
Robin Turnbull ◽  
Enrico Bandiello ◽  
Simone Anzellini ◽  
Daniel Errandonea
Keyword(s):  
High Pressure ◽  
Equation Of State ◽  
Density Functional ◽  
Room Temperature ◽  
Ambient Pressure ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Cell Parameters ◽  
A Chain

We report on high-pressure synchrotron X-ray diffraction measurements on Ni3V2O8 at room-temperature up to 23 GPa. According to this study, the ambient-pressure orthorhombic structure remains stable up to the highest pressure reached in the experiments. We have also obtained the pressure dependence of the unit-cell parameters, which reveals an anisotropic compression behavior. In addition, a room-temperature pressure–volume third-order Birch–Murnaghan equation of state has been obtained with parameters: V0 = 555.7(2) Å3, K0 = 139(3) GPa, and K0′ = 4.4(3). According to this result, Ni3V2O8 is the least compressible kagome-type vanadate. The changes of the crystal structure under compression have been related to the presence of a chain of edge-sharing NiO6 octahedral units forming kagome staircases interconnected by VO4 rigid tetrahedral units. The reported results are discussed in comparison with high-pressure X-ray diffraction results from isostructural Zn3V2O8 and density-functional theory calculations on several isostructural vanadates.

scholarly journals Persistence of the stereochemical activity of the Bi3+ lone electron pair in Bi2Ga4O9 up to 50 GPa and crystal structure of the high-pressure phase

2010 ◽  
Vol 66 (3) ◽  
pp. 323-337 ◽  
Author(s):  
Alexandra Friedrich ◽  
Erick A. Juarez-Arellano ◽  
Eiken Haussühl ◽  
Reinhard Boehler ◽  
Björn Winkler ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
High Pressure ◽  
Density Functional ◽  
Lone Electron Pair ◽  
Electron Pair ◽  
High Pressure Phase ◽  
Functional Theory ◽  
Pressure Phase ◽  
Stereochemical Activity

The crystal structure of the high-pressure phase of bismuth gallium oxide, Bi2Ga4O9, was determined up to 30.5 (5) GPa from in situ single-crystal in-house and synchrotron X-ray diffraction. Structures were refined at ambient conditions and at pressures of 3.3 (2), 6.2 (3), 8.9 (1) and 14.9 (3) GPa for the low-pressure phase, and at 21.4 (5) and 30.5 (5) GPa for the high-pressure phase. The mode-Grüneisen parameters for the Raman modes of the low-pressure structure and the changes of the modes induced by the phase transition were obtained from Raman spectroscopic measurements. Complementary quantum-mechanical calculations based on density-functional theory were performed between 0 and 50 GPa. The phase transition is driven by a large spontaneous displacement of one O atom from a fully constrained position. The density-functional theory (DFT) model confirmed the persistence of the stereochemical activity of the lone electron pair up to at least 50 GPa in accordance with the crystal structure of the high-pressure phase. While the stereochemcial activity of the lone electron pair of Bi^{3+} is reduced at increasing pressure, a symmetrization of the bismuth coordination was not observed in this pressure range. This shows an unexpected stability of the localization of the lone electron pair and of its stereochemical activity at high pressure.

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 High Pressure Hydrocarbons Revisited: From van der Waals Compounds to Diamond

Geosciences ◽  
2019 ◽  
Vol 9 (5) ◽  
pp. 227 ◽  
Author(s):  
Lewis J. Conway ◽  
Andreas Hermann
Keyword(s):  
Crystal Structure ◽  
Phase Diagram ◽  
High Pressure ◽  
Density Functional ◽  
Elevated Temperatures ◽  
Van Der Waals ◽  
Density Functional Theory Calculations ◽  
Temperature Phase ◽  
Decomposition Reactions ◽  
Complete Study

Methane and other hydrocarbons are major components of the mantle regions of icy planets. Several recent computational studies have investigated the high-pressure behaviour of specific hydrocarbons. To develop a global picture of hydrocarbon stability, to identify relevant decomposition reactions, and probe eventual formation of diamond, a complete study of all hydrocarbons is needed. Using density functional theory calculations we survey here all known C-H crystal structures augmented by targeted crystal structure searches to build hydrocarbon phase diagrams in the ground state and at elevated temperatures. We find that an updated pressure-temperature phase diagram for methane is dominated at intermediate pressures by CH 4 :H 2 van der Waals inclusion compounds. We discuss the P-T phase diagram for CH and CH 2 (i.e., polystyrene and polyethylene) to illustrate that diamond formation conditions are strongly composition dependent. Finally, crystal structure searches uncover a new CH 4 (H 2 ) 2 van der Waals compound, the most hydrogen-rich hydrocarbon, stable between 170 and 220 GPa.

Intermolecular interactions, thermodynamic properties, crystal structure, and detonation performance of CL-20/TEX cocrystal explosive

2015 ◽  
Vol 93 (6) ◽  
pp. 632-638 ◽  
Author(s):  
Peng-Yuan Chen ◽  
Lin Zhang ◽  
Shun-Guan Zhu ◽  
Guang-Bin Cheng
Keyword(s):  
Crystal Structure ◽  
Thermodynamic Properties ◽  
Intermolecular Interactions ◽  
Density Functional ◽  
High Energy ◽  
High Energy Density ◽  
Detonation Performance ◽  
Dispersion Force ◽  
Cell Parameters ◽  
Crystal Density

Density functional theory calculation was performed to investigate the intermolecular interactions, thermodynamic properties, crystal structure, and detonation performance of CL-20 (2,4,6,8,10,12-hexanitrohexaazaisowurtzitane)/TEX (4,10-dinitro-2,6,8,12-tetraoxa-4,10-diaza-tetracyclododecane) cocrystal explosive. The results of natural bond orbital (NBO) and atoms in molecules analysis show that unconventional CH···O type hydrogen bonds and dispersion force are the main driving forces for the cocrystal formation. Monte Carlo simulation was employed to predict the crystal structure of the CL-20/TEX cocrystal. The cocrystal is most likely to crystallize in a monoclinic system (space group C2/C), with cell parameters a = 40.62 Å, b = 7.35 Å, c = 41.36 Å, and β = 157.38°. Based on crystal density, chemical energy, and heat of formations, detonation performance was calculated using Kamlet–Jacobs formulas. Detonation velocity and pressure of the CL-20/TEX cocrystal are higher than those of TEX but a litter lower than those of CL-20. Bond dissociation energy analysis shows that the cocrystal is thermal stable and meets the requirement of high energy density materials.

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