Advancing the use of Voronoi–Dirichlet polyhedra to describe interactions in organic molecular crystal structures by the example of galunisertib polymorphs

CrystEngComm ◽  
2021 ◽  
Author(s):  
Viktor N. Serezhkin ◽  
Anton V. Savchenkov
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Noncovalent Interactions ◽  
Organic Molecular Crystal ◽  
Universal Approach ◽  
Structure Properties

The universal approach for studying structure/properties relationships shows that every polymorph of galunisertib is characterized with unique noncovalent interactions.

A novel characterization of organic molecular crystal structures for the purpose of crystal engineering

2015 ◽  
Vol 71 (4) ◽  
pp. 463-477 ◽  
Author(s):  
Noel W. Thomas
Keyword(s):  
Crystal Structures ◽  
Crystal Engineering ◽  
Molecular Crystal ◽  
Dimensional Space ◽  
Three Dimensional ◽  
Close Packing ◽  
Organic Molecular Crystal ◽  
Reference Axis ◽  
Three Dimensional Space

A novel analytical approach is proposed for the characterization of organic molecular crystal structures where close packing is an important factor. It requires the identification of a unique reference axis within the crystal, along which three-dimensional space is divided into close-packed blocks (CPB) and junction zones (JZ). The degree of close packing along the reference axis is quantified by a two-dimensional packing function, φ2D, of symmetry determined by the space group. Values of φ2Dreflect the degree of area-filling in planes perpendicular to this axis. The requirement of close packing within CPB allows the planar structures perpendicular to the reference axis to be analysed as tessellations of area-filling molecular-based cells (MBC), which are generally hexagonal. The form of these cells reflects the molecular shape in the cross-section, since their vertices are given by the centres of the voids between molecules. There are two basic types of MBC, Type 1, of glide or pseudo-glide symmetry, and Type 2, which is formed by lattice translations alone and generally requires a short unit-cell axis. MBC at layers of special symmetry are used to characterize the structures in terms of equivalent ellipses with parametersaell,belland χell. The ratioaell/bellallows the established α, β, γ classification to be integrated into the current framework. The values of parametersaellandbellarising from all the structures considered, polynuclear aromatic hydrocarbons (PAH), substituted anthracenes and anthraquinones (SAA) and 2-benzyl-5-benzylidene (BBCP) are mapped onto a universal curve. The division of three-dimensional space into CPB and JZ is fundamentally useful for crystal engineering, since the structural perturbations brought about by substitution at hydrogen positions located within JZ are minimal. A contribution is also made to ongoing debate concerning the adoption of polar space groups, isomorphism and polymorphism.

scholarly journals Crystal-to-Crystal Transformation from K2[Co(C2O4)2(H2O)2]·4H2O to K2[Co(μ-C2O4)(C2O4)]

2021 ◽  
Vol 7 (6) ◽  
pp. 77
Author(s):  
Bin Zhang ◽  
Yan Zhang ◽  
Guangcai Chang ◽  
Zheming Wang ◽  
Daoben Zhu
Keyword(s):  
Hydrogen Bond ◽  
Physical Properties ◽  
Crystal Structures ◽  
Molecular Crystal ◽  
Trigonal Prism ◽  
Space Group ◽  
Cell Parameters ◽  
Oxalate Anion ◽  
Crystal Transformation ◽  
Antiferromagnetic Ordering

Crystal-to-crystal transformation is a path to obtain crystals with different crystal structures and physical properties. K2[Co(C2O4)2(H2O)2]·4H2O (1) is obtained from K2C2O4·2H2O, CoCl2·6H2O in H2O with a yield of 60%. It is crystallized in the triclinic with space group P1 and cell parameters: a = 7.684(1) Å, b = 9.011(1) Å, c = 10.874(1) Å, α = 72.151(2)°, β = 70.278(2)°, γ = 80.430(2)°, V = 670.0(1) Å3, Z = 2 at 100 K. 1 is composed of K+, mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. Co2+ is coordinated by two bidentated oxalate anion and two H2O in an octahedron environment. There is a hydrogen bond between mononuclear anion [Co(C2O4)2(H2O)22−] and H2O. K2[Co(μ-C2O4)(C2O4)] (2) is obtained from 1 by dehydration. The cell parameters of 2 are a = 8.460(5) Å, b = 6.906 (4) Å, c = 14.657(8) Å, β = 93.11(1)°, V = 855.0(8) Å3 at 100 K, with space group in P2/c. It is composed of K+ and zigzag [Co(μ-C2O4)(C2O42−]n chain. Co2+ is coordinated by two bisbendentate oxalate and one bidentated oxalate anion in trigonal-prism. 1 is an antiferromagnetic molecular crystal. The antiferromagnetic ordering at 8.2 K is observed in 2.

scholarly journals Validation of molecular crystal structures from powder diffraction data with dispersion-corrected density functional theory (DFT-D)

2014 ◽  
Vol 70 (6) ◽  
pp. 1020-1032 ◽  
Author(s):  
Jacco van de Streek ◽  
Marcus A. Neumann
Keyword(s):  
Density Functional Theory ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Energy Minimization ◽  
Molecular Crystal ◽  
Density Functional ◽  
Powder Diffraction Data ◽  
High Quality ◽  
Functional Theory ◽  
Atomic Coordinates

In 2010 we energy-minimized 225 high-quality single-crystal (SX) structures with dispersion-corrected density functional theory (DFT-D) to establish a quantitative benchmark. For the current paper, 215 organic crystal structures determined from X-ray powder diffraction (XRPD) data and published in an IUCr journal were energy-minimized with DFT-D and compared to the SX benchmark. The on average slightly less accurate atomic coordinates of XRPD structures do lead to systematically higher root mean square Cartesian displacement (RMSCD) values upon energy minimization than for SX structures, but the RMSCD value is still a good indicator for the detection of structures that deserve a closer look. The upper RMSCD limit for a correct structure must be increased from 0.25 Å for SX structures to 0.35 Å for XRPD structures; the grey area must be extended from 0.30 to 0.40 Å. Based on the energy minimizations, three structures are re-refined to give more precise atomic coordinates. For six structures our calculations provide the missing positions for the H atoms, for five structures they provide corrected positions for some H atoms. Seven crystal structures showed a minor error for a non-H atom. For five structures the energy minimizations suggest a higher space-group symmetry. For the 225 SX structures, the only deviations observed upon energy minimization were three minor H-atom related issues. Preferred orientation is the most important cause of problems. A preferred-orientation correction is the only correction where the experimental data are modified to fit the model. We conclude that molecular crystal structures determined from powder diffraction data that are published in IUCr journals are of high quality, with less than 4% containing an error in a non-H atom.

Drastic photoluminescence modulation of an organic molecular crystal with high pressure

2019 ◽  
Vol 3 (8) ◽  
pp. 1510-1517 ◽  
Author(s):  
Junjie Guan ◽  
Chunfang Zhang ◽  
Dexiang Gao ◽  
Xingyu Tang ◽  
Xiao Dong ◽  
...  
Keyword(s):  
Phase Transition ◽  
High Pressure ◽  
Molecular Crystal ◽  
Near Infrared ◽  
Infrared Region ◽  
Photoluminescence Spectra ◽  
Organic Molecular Crystal ◽  
Greenish Yellow ◽  
Near Infrared Region

The pressure-induced phase transition of diphenylfluorenone leads to a drastic redshift of the photoluminescence spectra from greenish-yellow to the near-infrared region.

Halogen bonds and other noncovalent interactions in the crystal structures of trans-1,2-diiodo alkenes: an ab initio and QTAIM study

2020 ◽  
Vol 26 (11) ◽  
Author(s):  
Yongna Yuan ◽  
Matthew J. L. Mills ◽  
Fuyang Li ◽  
Yuhong Du ◽  
Jiaxuan Wei ◽  
...  
Keyword(s):  
Ab Initio ◽  
Crystal Structures ◽  
Noncovalent Interactions ◽  
Halogen Bonds

scholarly journals Stable rotation of fullerenes in molecular crystal structures

2020 ◽  
Vol 1537 ◽  
pp. 012006
Author(s):  
A M Bubenchikov ◽  
M A Bubenchikov ◽  
D V Mamontov
Keyword(s):  
Crystal Structures ◽  
Molecular Crystal ◽  
Stable Rotation

scholarly journals Noncovalent Interactions between 1,3,5-Trifluoro-2,4,6-triiodobenzene and a Series of 1,10-Phenanthroline Derivatives: A Combined Theoretical and Experimental Study

Crystals ◽  
2019 ◽  
Vol 9 (3) ◽  
pp. 140 ◽  
Author(s):  
Yu Zhang ◽  
Jian-Ge Wang ◽  
Weizhou Wang
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Quantum Chemical ◽  
Halogen Bond ◽  
Noncovalent Interactions ◽  
Stacking Interactions ◽  
Halogen Bonds ◽  
Π Stacking ◽  
Π Stacking Interaction ◽  
Structural Competition

How many strong C−I⋯N halogen bonds can one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule form in a crystal structure? To answer this question, we investigated in detail the noncovalent interactions between 1,3,5-trifluoro-2,4,6-triiodobenzene and a series of 1,10-phenanthroline derivatives by employing a combined theoretical and experimental method. The results of the quantum chemical calculations and crystallographic experiments clearly show that there is a structural competition between a C−I⋯N halogen bond and π⋯π stacking interaction. For example, when there are much stronger π⋯π stacking interactions between two 1,10-phenanthroline derivative molecules or between two 1,3,5-trifluoro-2,4,6-triiodobenzene molecules in the crystal structures, then one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule forms only one C−I⋯N halogen bond with one 1,10-phenanthroline derivative molecule. Another example is when π⋯π stacking interactions in the crystal structures are not much stronger, one 1,3,5-trifluoro-2,4,6-triiodobenzene molecule can form two C−I⋯N halogen bonds with two 1,10-phenanthroline derivative molecules.

scholarly journals Furosemide's one little hydrogen atom: NMR crystallography structure verification of powdered molecular organics

2016 ◽  
Vol 52 (40) ◽  
pp. 6685-6688 ◽  
Author(s):  
Cory M. Widdifield ◽  
Harry Robson ◽  
Paul Hodgkinson
Keyword(s):  
Hydrogen Atom ◽  
Crystal Structures ◽  
Molecular Crystal ◽  
Structural Databases ◽  
Nmr Crystallography

The potential of NMR crystallography to verify molecular crystal structures deposited in structural databases is evaluated, with two structures of the pharmaceutical furosemide serving as examples.

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