New refinement strategies for a pseudoatom databank – toward rapid electrostatic interaction energy estimations
Pseudoatom databanks, collections of parameters from the multipole model of electron densities for various atom types, are used to replace the Independent Atom Model with the more accurate Transferable Aspherical Atom Model (TAAM) in crystal structure refinements. The databanks are also employed to reconstruct the electron density of a molecule, crystal or biomacromolecular complex in a fast yet accurate way and compute various properties such as the energy of electrostatic interactions, for example. A even faster but similarly accurate model for estimations of electrostatic energy exists called aug-PROmol [Bojarowski, Kum...
Source: Acta Crystallographica Section B - November 1, 2022 Category: Chemistry Authors: Bojarowski, S.A. Gruza, B. Trzybi ń ski, D. Kami ń ski, R. Hoser, A.A. Kumar, P. Wo ź niak, K. Dominiak, P.M. Tags: quantum crystallography TAAM refinement multipole model refinement charge density electrostatic interaction energy research papers Source Type: research
Zr3Mn3Sn4Ga: a new hexagonal Ti6Sn5-type quaternary intermetallic
The discovery of a new quaternary intermetallic compound of composition Zr3Mn3Sn4Ga during a survey of the Zr – Mn – Sn – Ga phase diagram is reported. Single-crystal X-ray diffraction reveals that the new compound crystallizes in a hexagonal lattice (space group P63/mmc, No. 194). The analysis of single-crystal X-ray diffraction data indicates that the atomic arrangement is an ordered variant of the high-temperature hexagonal Ti6Sn5 crystal structure. From a simple geometry point of view, the unit cell consists of GaZr3 octahedra chains and Mn chains growing along the sixfold symmetry axis c. The Mn chains are stack...
Source: Acta Crystallographica Section B - October 30, 2022 Category: Chemistry Authors: Clausse, T. Diop, L.V.B. Martin, N.P. Sibille, R. Mazet, T. Tags: intermetallic X-rays diffraction kagome neutron diffraction research papers Source Type: research
X-ray diffraction and M ö ssbauer spectroscopy study of oxoborate azoproite (Mg,Fe2+)2(Fe3+,Ti,Mg,Al)O2(BO3): an in situ temperature-dependent investigation (5 ≤ T ≤ 1650 K)
This work is devoted to an investigation of elemental composition, crystal structure and thermal expansion of natural oxoborate azoproite from the Tazheran massif (Siberia, Russia) in the temperature range 5 – 1650 K. Elemental composition was determined by energy-dispersive X-ray spectroscopy (EDX). Its empirical formula based on five oxygen atoms is (Mg1.81Fe2+0.19) ∑ 2.00(Fe3+0.36Ti0.26Mg0.26Al0.12) ∑ 1.00O2(BO3). Local environment, oxidation states and ratio of Fe atoms are determined using M ö ssbauer spectroscopy and compared with EDX and single-crystal X-ray diffraction (SCXRD) data. A refinement of the c...
Source: Acta Crystallographica Section B - October 29, 2022 Category: Chemistry Authors: Biryukov, Y.P. Zinnatullin, A.L. Levashova, I.O. Shablinskii, A.P. Cherosov, M.A. Bubnova, R.S. Vagizov, F.G. Krzhizhanovskaya, M.G. Filatov, S.K. Shilovskikh, V.V. Pekov, I.V. Tags: oxoborate azoproite ludwigite group crystal structure oxidation thermal expansion research papers Source Type: research
Learning from approximate periodic symmetry in organic P1 structures
(Source: Acta Crystallographica Section B)
Source: Acta Crystallographica Section B - September 29, 2022 Category: Chemistry Authors: Young, V.G. Tags: approximate symmetry pseudosymmetry P1 structures inversion mimics layered crystals scientific commentaries Source Type: research
Structures of Ca5(VO4)3Cl and Ca4.78(1)Na0.22(PO4)3Cl0.78: positions of channel anions and repulsion on the anion in apatite-type compounds
Single crystal specimens of apatite-type compounds Ca5(VO4)3Cl and Ca4.78 (1)Na0.22(PO4)3Cl0.78 were prepared with a flux-growth technique and their structures were examined with single-crystal X-ray diffraction. The anion channel is defined by a face-sharing array of nearly regular Ca octahedra, which run along c, together with flat O3 trigonal antiprisms that are concentric with the Ca octahedra and highly oblate in [001]. The position of the channel anion in Ca5(VO4)3Cl is split into two at [0, 0, ± 0.1691 (6)] with half occupancies. Dynamic disorder among these two positions is suggested from a saddle-shaped e...
Source: Acta Crystallographica Section B - September 10, 2022 Category: Chemistry Authors: Matsuura, M. Okudera, H. Tags: apatite ionic conductor site splitting channel topology Ca5(VO4)3Cl research papers Source Type: research
The potential of dispersion-corrected density functional theory calculations for distinguishing between salts and cocrystals
Validation of a method for distinguishing between salts and cocrystals based on dispersion-corrected density functional theory is presented. Existing related works (van de Streek& Neumann, 2010; LeBlanc et al., 2018) indicate that this approach is problematic and leads to incorrect results in multiple situations. The method suggested here is based on the geometry optimization of an artificially constructed wrong structure (hydrogen atom placed in salt position near the potential acceptor for cocrystals and vice versa cocrystal position with hydrogen atom placed near the potential donor of the salts). The verification of th...
Source: Acta Crystallographica Section B - September 9, 2022 Category: Chemistry Authors: Hu š á k, M. Š ajbanov á , S. Klime š , J. Jegorov, A. Tags: DFT salt cocrystal research papers Source Type: research
Lattice defects in quinacridone
Various lattice defects in the α I-phase of quinacridone (C20H12N2O2) were simulated using lattice-energy minimizations. α I-Quinacridone forms a chain structure in P1, Z = 1. The molecules are connected by hydrogen bonds along [010], by π -stacking along [100] and by weak van der Waals interactions along [001]. α I-Quinacridone is inherently nanocrystalline. Lattice defects were calculated in correspondingly large supercells with up to 4464 atoms, using a previously evaluated force field. Vacancies, vacancy aggregates and interstitial molecules are energetically very unfavourable. A misorientation of a single molecule...
Source: Acta Crystallographica Section B - September 9, 2022 Category: Chemistry Authors: Brey, D. Scherer, B. Schmidt, M.U. Tags: lattice defects crystal modelling orientation fault twinning organic semiconductor commensurate misfit-layer structure research papers Source Type: research
The effect of hydrostatic compression on the crystal structure of glycinium phosphite
The crystal structure of glycinium phosphite (GPI) was studied in the pressure range from ambient to 6.5 GPa at 293 K using single-crystal X-ray diffraction. The changes in the unit-cell volume and parameters were continuous and anisotropic. The major compression was observed normal to the direction of the spontaneous polarization that occurs in this structure during a ferroelectric phase transition on cooling, whereas the structural compression along the b axis coinciding with the 21 axis was almost zero. The effect of pressure on the hydrogen bonds linking the H2PO3 tetrahedra into zigzag chains along the c axis ...
Source: Acta Crystallographica Section B - September 1, 2022 Category: Chemistry Authors: Bogdanov, N.E. Korabel'nikov, D.V. Fedorov, I.A. Zakharov, B.A. Boldyreva, E.V. Tags: glycinium phosphite ferroelectrics high pressure X-ray diffraction DFT hydrogen bonds research papers Source Type: research
Heterocyclic 1,3-diazepine-based thiones and selones as versatile halogen-bond acceptors
Utilizing the N-heterocyclic chalcogenones hexahydro-1,3-bis(2,4,6-trimethylphenyl)-2H-1,3-diazepine-2-thione (SDiazMesS) and hexahydro-1,3-bis(2,4,6-trimethylphenyl)-2H-1,3-diazepine-2-selone (SDiazMesSe) as halogen-bond acceptors, a total of 24 new cocrystals were prepared. The solid-state structures of the parent molecules were also determined, along with those of their acetonitrile solvates. Through the reaction of the chalcogen atom with molecular diiodine, a variety of S — I — I and Se — I — I fragments were formed, spanning a wide range of I — I bond orders. With acetone as a reaction solvent, molecular di...
Source: Acta Crystallographica Section B - August 31, 2022 Category: Chemistry Authors: Ragusa, A.C. Peloquin, A.J. Shahani, M.M. Dowling, K.N. Golen, J.A. McMillen, C.D. Rabinovich, D. Pennington, W.T. Tags: halogen bonding thione selone organoiodine cocrystal diiodine research papers Source Type: research
Evolution of microstructure and crystallographic texture throughout the rolling process of AA3104
The metallic components are manufactured through several thermomechanical processes. Each selected procedure has multiple targets. The first target is to obtain the required dimensional criteria and second, to achieve the ideal mechanical response toward the application. This is currently accomplished through years of knowhow combined with an academic background of materials science and engineering. Since metals are polycrystalline materials, the several rotations of the crystals, the preferred orientation also known as texture, and their interactions, are crucial characteristics that are directly correlated to the final r...
Source: Acta Crystallographica Section B - August 18, 2022 Category: Chemistry Authors: Papadopoulou, S. Tsiolis, F. Gavalas, E. Papaefthymiou, S. Tags: crystallographic texture 3xxx Al alloy Euler space Miller indices rolling process research papers Source Type: research
One-dimensional diffuse scattering of 1,3-di(tert-butyl)cyclopentadienyl pentaphosphaferrocene modelled with closed-form expressions
1,3-di(tert-butyl)cyclopentadienyl pentaphosphaferrocene (Cp ′ ′ FeP5) crystallizes as polytypes, where adjacent layers are related by either a c- or an n-glide reflection. In the simplest possible polytypes only one kind of glide reflections is realized, leading to overall Pca21 or Pna21 symmetry respectively. Crystals isolated from the same crystallization experiment feature a varying degree of stacking disorder. One-dimensional diffuse scattering of a crystal with particularly strong disorder was modelled with closed-form expressions derived from a growth model. A range of interaction of s = 2 was necessary to satis...
Source: Acta Crystallographica Section B - August 18, 2022 Category: Chemistry Authors: St ö ger, B. Peresypkina, E. Virovets, A. Tags: polytypism 1,3-di(tert-butyl)cyclopentadienyl pentaphosphaferrocene disorder diffuse scattering research papers Source Type: research
Engineering the band gap and optical properties of a two-dimensional molybdenum carbon fluoride MXene
Using first-principles density functional theory, we investigated the electronic and optical properties of monolayer and multilayer nanosheets of molybdenum carbon fluoride (Mo2CF2), a two-dimensional (2D) transition-metal carbide MXene. The indirect band gap of the Mo2CF2 semiconductor can be engineered by controlling the number of layers where the band gap energy changes from 0.278 eV for the monolayer to 0.249 eV for the trilayer nanosheet. The decrease in band gap energy in the multilayer is due to interlayer coupling, which splits the bands according to the number of layers. Mo2CF2 behaves as a metal with an a...
Source: Acta Crystallographica Section B - August 18, 2022 Category: Chemistry Authors: Anh, D.T.K. Mui, L.V. Minh, P.H. Binh, N.T. Cadatal-Raduban, M. Tags: two-dimensional materials MXene monolayer multilayer band gap engineering electronic properties optical properties crystal structure research papers Source Type: research
Formation of contact and multiple cyclic cassiterite twins in SnO2-based ceramics co-doped with cobalt and niobium oxides
Contact and multiple cyclic twins of cassiterite commonly form in SnO2-based ceramics when SnO2 is sintered with small additions of cobalt and niobium oxides (dual doping). In this work, it is shown that the formation of twins is a two-stage process that starts with epitaxial growth of SnO2 on CoNb2O6 and Co4Nb2O9 seeds (twin nucleation stage) and continues with the fast growth of (101) twin contacts (twin growth stage). Both secondary phases form below the temperature of enhanced densification and SnO2 grain growth; CoNb2O6 forms at ∼ 700 ° C and Co4Nb2O9 at ∼ 900 ° C. They are structurally related to the rutile-typ...
Source: Acta Crystallographica Section B - July 27, 2022 Category: Chemistry Authors: Daneu, N. Dra ž i č , G. Mazaj, M. Barou, F. Padr ó n-Navarta, J.A. Tags: growth twinning contact twins cyclic twins nucleation twinning orientation relationship research papers Source Type: research
The tetrel bonding role in supramolecular aggregation of lead(II) acetate and a thiosemicarbazide derivative
A new PbII coordination complex [PbL(OAc)], which was readily synthesized from a mixture of Pb(OAc)2 · 3H2O and 1-(pyridin-2-yl)benzylidene-4-phenylthiosemicarbazide (HL) is reported. The crystal structure analysis of [PbL(OAc)] showed that the PbII cation is N,N ′ ,S-chelated by the tridentate pincer-type ligand L and by the oxygen atoms of the acetate anion. In addition, the metal centre forms Pb...O and Pb...S tetrel bonds with an adjacent complex molecule, yielding a 1D zigzag polymeric chain, which is reinforced by N — H...O hydrogen bonds and π ... π interactions. These chains are interlinked by C — H...py n...
Source: Acta Crystallographica Section B - July 22, 2022 Category: Chemistry Authors: Mahmoudi, G. Garc í a-Santos, I. Pittelkow, M. Kamounah, F.S. Zangrando, E. Babashkina, M.G. Frontera, A. Safin, D.A. Tags: tetrel bond lead(II) complex crystal structure calculations Hirshfeld surface analysis research papers Source Type: research
Framboids. By David Rickard. Oxford University Press, 2021. Hardcover, pp. xxv+334. Price GBP 64.00. ISBN ISBN 978019008 0112.
(Source: Acta Crystallographica Section B)
Source: Acta Crystallographica Section B - July 20, 2022 Category: Chemistry Authors: Nespolo, M. Tags: book review pyrite framboids book reviews Source Type: research
