scholarly journals On the stacking disorder of DL-norleucine

2017 ◽  
Vol 73 (6) ◽  
pp. 1075-1084 ◽  
Author(s):  
Christian Czech ◽  
Jürgen Glinnemann ◽  
Kristoffer E. Johansson ◽  
Michael Bolte ◽  
Martin U. Schmidt
Keyword(s):  
Density Functional ◽  
Layer Structure ◽  
Lattice Energy ◽  
Double Layers ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Β Phase ◽  
Diffraction Patterns ◽  
Model Structures ◽  
Stacking Disorder

DL-Norleucine (2-aminohexanoic acid, C6H13NO2) forms a double-layer structure in all known phases (α, β, γ). The crystal structure of the β-phase was redetermined at 173 K. Diffraction patterns of the α- and β-phases frequently show diffuse streaks parallel to c*, which indicates a stacking disorder of the layers. A symmetry analysis was carried out to derive possible stacking sequences. Lattice-energy minimizations by force fields and by dispersion-corrected density functional theory (DFT-D) were performed on a set of ordered model structures with Z = 4, 8 and 16 with different stacking sequences. The calculated energies depend not only on the arrangement of neighbouring double layers, but also of next-neighbouring double layers. Stacking probabilities were calculated from the DFT-D energies. According to the calculated stacking probabilities large models containing 100 double layers were constructed. Their simulated diffraction patterns show sharp reflections for h + k = 2n and diffuse streaks parallel to c* through all reflections with h + k = 2n + 1. Experimental single-crystal X-ray diffraction revealed that at 173 K norleucine exists in the β-phase with stacking disorder. After reheating to room temperature, the investigated crystal showed a diffraction pattern with strong diffuse scattering parallel to c* through all reflections with h + k = 2n + 1, which is in good agreement with the simulated disordered structure.

scholarly journals Explanation of the stacking disorder in the β-phase of Pigment Red 170

2014 ◽  
Vol 70 (2) ◽  
pp. 296-305 ◽  
Author(s):  
Jaroslav L. Teteruk ◽  
Jürgen Glinnemann ◽  
Tatiana E. Gorelik ◽  
Anthony Linden ◽  
Martin U. Schmidt
Keyword(s):  
Layer Structure ◽  
Lattice Energy ◽  
Large Set ◽  
Electron Diffraction Investigation ◽  
Industrial Sample ◽  
Local Structures ◽  
Β Phase ◽  
Diffraction Patterns ◽  
Stacking Disorder ◽  
Good Agreement

The β-phase of Pigment Red 170, C26H22N4O4, which is used industrially for the colouration of plastics, crystallizes in a layer structure with stacking disorder. The disorder is characterized by a lateral translational shift between the layers with a componenttyof either +0.421 or −0.421. Order–disorder (OD) theory is used to derive the possible stacking sequences. Extensive lattice-energy minimizations were carried out on a large set of structural models with different stacking sequences, containing up to 2688 atoms. These calculations were used to determine the actual local structures and to derive the stacking probabilities. It is shown that local structures and energies depend not only on the arrangement of neighbouring layers, but also next-neighbouring layers. Large models with 100 layers were constructed according to the derived stacking probabilities. The diffraction patterns simulated from those models are in good agreement with the experimental single-crystal and powder diffraction patterns. Electron diffraction investigation on a nanocrystalline industrial sample revealed the same disorder. Hence the lattice-energy minimizations are able to explain the disorder and the diffuse scattering.

Local structure and stacking disorder of chloro(phthalocyaninato)aluminium

2017 ◽  
Vol 73 (4) ◽  
pp. 744-755 ◽  
Author(s):  
Christian Czech ◽  
Lena Kalinowsky ◽  
Martin U. Schmidt
Keyword(s):  
Density Functional ◽  
Layer Structure ◽  
Double Layers ◽  
Molecular Compound ◽  
Crystal Data ◽  
Functional Theory ◽  
Experimental Structure ◽  
Symmetry Operations ◽  
Packing Effects ◽  
Stacking Disorder

Chloro(phthalocyaninato)aluminium [(C32H16N8)AlCl, Pigment Blue 79] is a molecular compound which crystallizes in a layer structure with stacking disorder. Order–disorder theory was applied to analyse and explain the stacking disorder and to determine the symmetry operations, which generate subsequent layers from a given one. Corresponding ordered structural models were constructed and optimized by force field and dispersion-corrected density functional theory methods. The superposition of the four lowest-energy stackings lead to a structure in which every second double layer looks to be ordered; in the other double layers the molecules occupy one of two lateral positions. This calculated superposition structure agrees excellently with an (incomplete) experimental structure determined from single-crystal data. From the optimized ordered models, the stacking probabilities and the preferred local arrangements were derived. Packing effects such as the distortion of the molecules depending on the arrangement of neighbouring molecules could also be determined.

Stability of Ordered B2-βO and Disordered BCC-β Phases in Tial - A First Principles Study

2021 ◽  
Vol 1016 ◽  
pp. 1159-1165
Author(s):  
Florian Pyczak ◽  
Victoria Kononikhina ◽  
Andreas Stark
Keyword(s):  
First Principles ◽  
Density Functional ◽  
High Energy ◽  
First Principles Calculations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Tial Alloys ◽  
Β Phase ◽  
Phase Ordering ◽  
Strength And Ductility

Either at higher temperatures or when a certain alloying element content is exceeded, γ-TiAl alloys contain the β phase (bcc) or its ordered derivate βo (B2). The relatively soft β phase can facilitate hot deformation, but βo is detrimental for creep strength and ductility. Thus, knowledge about βo→β phase transformation is desirable. Surprisingly, even for the binary Ti-Al system it is under discussion whether the ordered βo phase exists. Also, the effect of alloying elements on the β phase ordering is still unclear. In the present work the ordering of the β phase in binary Ti-(39,42,45)Al and ternary Ti-42Al-2X alloys (X=Fe, Cr, Nb, Ta, Mo) which was experimentally investigated by neutron and high energy X-ray diffraction is compared with the results of first principles calculations using density functional theory. Except for Cr the experimentally determined and the predicted behavior correspond.

Powder X-ray diffraction of pazopanib hydrochloride Form 1, C21H24N7O2SCl

2021 ◽  
pp. 1-3
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Lattice Energy ◽  
Powder Diffraction Data ◽  
X Ray Diffraction ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
X Ray

The crystal structure of pazopanib hydrochloride Form 1 has been refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pazopanib hydrochloride crystallizes in space group P-1 (#2) with a = 8.45008(6), b = 8.71310(12), c = 16.05489(35) Å, α = 79.5996(9), β = 86.4784(5), γ = 87.3764(3)°, V = 1159.724(9) Å3, and Z = 2. The crystal structure is essentially identical to that of CSD Refcode CEVYEK. There are four strong N–H⋯Cl hydrogen bonds to the chloride anion. Several additional weaker N–H⋯Cl and C–H⋯Cl hydrogen bonds are also present. A variety of C–H⋯O, C–H⋯N, and N–H⋯S hydrogen bonds also contribute to the lattice energy. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™.

Inverse bilayer structure of mononuclear CoII and NiII complexes of the type M(H2O)3(SO4)(4-CNpy)2

2009 ◽  
Vol 65 (4) ◽  
pp. 467-473 ◽  
Author(s):  
Birinchi K. Das ◽  
Sanchay J. Bora ◽  
Manjit K. Bhattacharyya ◽  
Rama K. Barman
Keyword(s):  
Density Functional ◽  
Similarity Index ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Metal Compounds ◽  
X Ray ◽  
Π Interactions ◽  
Hartree Fock ◽  
Non Covalent Interactions ◽  
Diffraction Patterns

Two new metal compounds of the formula [M(H2O)3(SO4)(4-CNpy)2]·H2O [M = Ni (1) and Co (2), 4-CNpy = 4-cyanopyridine] have been prepared and studied by X-ray diffraction. In both of these compounds the 4-CNpy ligands are coordinated via pyridyl-N atoms to the metal ions in a cis fashion. The neutral complexes along with the uncoordinated H2O molecules are glued together preferentially into inverse bilayers by non-covalent interactions, including unique interlayer π–π interactions between antiparallel nitrile groups. Hartree–Fock and density-functional theory (DFT) calculations indicate that the π–π interactions are energetically significant. The unit-cell similarity index (Π) of 0.0046 for the compounds suggests their isostructurality, which is also supported by their X-ray powder diffraction patterns that can be almost superimposed.

Crystal chemistry, X-ray diffraction reference patterns, and bandgap studies for (BaxSr1–x)2CoWO6 (x = 0.1, 0.2, 0.3, 0.5, 0.7, and 0.9)

2020 ◽  
Vol 35 (3) ◽  
pp. 197-205
Author(s):  
W. Wong-Ng ◽  
G. Y. Liu ◽  
D. D. Shi ◽  
Y. Q. Yang ◽  
R. Derbeshi ◽  
...  
Keyword(s):  
Density Functional ◽  
Alkaline Earth ◽  
Double Perovskite ◽  
Density Functional Theory Calculations ◽  
X Ray Diffraction ◽  
Functional Theory ◽  
Rietveld Refinements ◽  
X Ray ◽  
Diffraction Patterns ◽  
End Members

X-ray reference powder patterns and structures have been determined for a series of cobalt- and tungsten-containing cubic alkaline-earth perovskites, (BaxSr1–x)2CoWO6 (x = 0.1, 0.2, 0.3, 0.5, 0.7, and 0.9). The structure of the end members of the series, Sr2CoWO6 and Ba2CoWO6, were tetragonal and cubic, respectively, agreeing with the literature data. From Rietveld refinements, it was found that when x = 0.1 and 0.2, the structure was tetragonal I4/m (a = 5.60481(6) and 5.62305(11) Å and c = 7.97989(12) and 7.9847(2) Å, respectively; Z = 2). When x > 0.2, the structure was cubic (Fm$\bar{3}$m, No. 225; Z = 4) (from x = 0.3 to 0.9, a increases from 7.98399(13) to 8.08871(10) Å). This tetragonal series of compounds exhibit the characteristics of a distorted double-perovskite structure. The bond valence sum values for the alkaline-earth (Ba, Sr) sites in all (BaxSr1−x)2CoWO6 members are greater than the ideal value of 2.0, indicating over-bonding situation, whereas for the W sites, as x increases, a change from under-bonding to slightly over-bonding situation was observed. Density functional theory calculations revealed that while Sr2CoWO6 is a semiconductor, Ba2CoWO6 and SrBaCoWO6 are half-metals. Powder X-ray diffraction patterns of this series of compounds (BaxSr1−x)2CoWO6, with x = 0.1, 0.2, 0.3, 0.5, 0.7, and 0.9, have been submitted to be included in the Powder Diffraction File.

scholarly journals Моделирование фазовых переходов графитов в алмазоподобные фазы

2018 ◽  
Vol 60 (7) ◽  
pp. 1290
Author(s):  
Е.А. Беленков ◽  
В.А. Грешняков
Keyword(s):  
Density Functional ◽  
Local Density ◽  
X Ray Diffraction ◽  
Generalized Gradient ◽  
Functional Theory ◽  
X Ray ◽  
Graphene Layers ◽  
Generalized Gradient Approximation ◽  
The Density Functional Theory ◽  
Diffraction Patterns

AbstractThe method of the density functional theory is used to study structural transformations between graphites and diamond-like phases. The calculations have been carried out in two approximations: a local density approximation and a generalized gradient approximation. It is found that the phase transitions of hexagonal graphene layers to a cubic diamond and diamond-like phases must occur at uniaxial compressions of ~57–71 GPa, whereas some diamond-like phases can be obtained from tetragonal graphene layers at significantly lower pressures of 32–52 GPa. The X-ray diffraction patterns have been calculated for the phase transition of graphite I 4_1/ amd to tetragonal LA 10 phase that takes place at the minimum pressure that can be used for experimental identification of these compounds.

scholarly journals Exo⇔Endo Isomerism, MEP/DFT, XRD/HSA-Interactions of 2,5-Dimethoxybenzaldehyde: Thermal, 1BNA-Docking, Optical, and TD-DFT Studies

Molecules ◽  
2020 ◽  
Vol 25 (24) ◽  
pp. 5970
Author(s):  
Nabil Al-Zaqri ◽  
Mohammed Suleiman ◽  
Anas Al-Ali ◽  
Khaled Alkanad ◽  
Karthik Kumara ◽  
...  
Keyword(s):  
Density Functional ◽  
Energy Gap ◽  
Structural Parameters ◽  
Population Analysis ◽  
Xrd Analysis ◽  
X Ray Diffraction ◽  
Optical Energy Gap ◽  
Functional Theory ◽  
Reactivity Descriptors ◽  
Td Dft

The exo⇔endo isomerization of 2,5-dimethoxybenzaldehyde was theoretically studied by density functional theory (DFT) to examine its favored conformers via sp2–sp2 single rotation. Both isomers were docked against 1BNA DNA to elucidate their binding ability, and the DFT-computed structural parameters results were matched with the X-ray diffraction (XRD) crystallographic parameters. XRD analysis showed that the exo-isomer was structurally favored and was also considered as the kinetically preferred isomer, while several hydrogen-bonding interactions detected in the crystal lattice by XRD were in good agreement with the Hirshfeld surface analysis calculations. The molecular electrostatic potential, Mulliken and natural population analysis charges, frontier molecular orbitals (HOMO/LUMO), and global reactivity descriptors quantum parameters were also determined at the B3LYP/6-311G(d,p) level of theory. The computed electronic calculations, i.e., TD-SCF/DFT, B3LYP-IR, NMR-DB, and GIAO-NMR, were compared to the experimental UV–Vis., optical energy gap, FTIR, and 1H-NMR, respectively. The thermal behavior of 2,5-dimethoxybenzaldehyde was also evaluated in an open atmosphere by a thermogravimetric–derivative thermogravimetric analysis, indicating its stability up to 95 °C.

Site preference and atomic ordering in the ternary Rh5Ga2As: first-principles calculations

2021 ◽  
Vol 0 (0) ◽  
Author(s):  
Nilanjan Roy ◽  
Sucharita Giri ◽  
Harshit ◽  
Partha P. Jana
Keyword(s):  
Total Energy ◽  
First Principles ◽  
Density Functional ◽  
Structure Type ◽  
Site Preference ◽  
X Ray Diffraction ◽  
Atomic Ordering ◽  
Functional Theory ◽  
The Stability ◽  
Bonding Characteristics

Abstract The site preference and atomic ordering of the ternary Rh5Ga2As have been investigated using first-principles density functional theory (DFT). An interesting atomic ordering of two neighboring elements Ga and As reported in the structure of Rh5Ga2As by X-ray diffraction data only is confirmed by first-principles total-energy calculations. The previously reported experimental model with Ga/As ordering is indeed the most stable in the structure of Rh5Ga2As. The calculation detected that there is an obvious trend concerning the influence of the heteroatomic Rh–Ga/As contacts on the calculated total energy. Interestingly, the orderly distribution of As and Ga that is found in the binary GaAs (Zinc-blende structure type), retained to ternary Rh5Ga2As. The density of states (DOS) and Crystal Orbital Hamiltonian Population (COHP) are calculated to enlighten the stability and bonding characteristics in the structure of Rh5Ga2As. The bonding analysis also confirms that Rh–Ga/As short contacts are the major driving force towards the overall stability of the compound.

Crystal structure of pomalidomide Form I, C13H11N3O4

2021 ◽  
pp. 1-6
Author(s):  
James A. Kaduk ◽  
Amy M. Gindhart ◽  
Thomas N. Blanton
Keyword(s):  
Crystal Structure ◽  
Hydrogen Bonds ◽  
Powder Diffraction ◽  
Density Functional ◽  
Double Layers ◽  
Carbonyl Groups ◽  
Hydrogen Atoms ◽  
Powder Diffraction File ◽  
Functional Theory ◽  
Amine Hydrogen

The crystal structure of pomalidomide Form I has been solved and refined using synchrotron X-ray powder diffraction data and optimized using density functional theory techniques. Pomalidomide Form I crystallizes in the space group P-1 (#2) with a = 7.04742(9), b = 7.89103(27), c = 11.3106(6) Å, α = 73.2499(13), β = 80.9198(9), γ = 88.5969(6)°, V = 594.618(8) Å3, and Z = 2. The crystal structure is characterized by the parallel stacking of planes parallel to the bc-plane. Hydrogen bonds link the molecules into double layers also parallel to the bc-plane. Each of the amine hydrogen atoms acts as a donor to a carbonyl group in an N–H⋯O hydrogen bond, but only two of the four carbonyl groups act as acceptors in such hydrogen bonds. Other carbonyl groups participate in C–H⋯O hydrogen bonds. The powder pattern has been submitted to ICDD® for inclusion in the Powder Diffraction File™ (PDF®).

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