scholarly journals Development of polarizable force field for the prediction of molecular crystal structures

2008 ◽  
Vol 64 (a1) ◽  
pp. C207-C207
Author(s):  
N. Nakayama ◽  
S. Obata ◽  
K. Ohta ◽  
H. Goto
Keyword(s):  
Force Field ◽  
Crystal Structures ◽  
Molecular Crystal ◽  
Polarizable Force Field

scholarly journals Crystal structure prediction of indomethacin

2014 ◽  
Vol 70 (a1) ◽  
pp. C1540-C1540
Author(s):  
Xiaozhou Li ◽  
Kristoffer Johansson ◽  
Andrew Bond ◽  
Jacco van de Streek
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Molecular Crystal ◽  
Density Functional ◽  
Computational Cost ◽  
Stable Form ◽  
Crystal Structure Prediction ◽  
Blind Test

Indomethacin is a non-steroidal anti-inflammatory and antipyretic agent. Because different packing arrangements of the same drug can greatly affect drug properties such as colours, solubility, stability, melting point, dissolution rate and so forth, it is important to predict its polymorphs. The computational prediction of the stable form will reduce undesirable risks in both clinical trials and manufacturing. Reported polymorphs of indomethacin include α, β, γ, δ, ε, η and ζ [1], of which only the thermodynamically stable form γ and the metastable form α are determined. Density functional theory with dispersion-correction (DFT-D) has been used extensively to study molecular crystal structures[2]. It gives better results with a compromise between the computational cost and accuracy towards the reproduction of molecular crystal structures. In the fourth blind test of crystal structure prediction in 2007, the DFT-D method gave a very successful result that predicted all four structures correctly. Rather than using transferable force fields, a dedicated tailor-made force field (TMFF) parameterised by DFT-D calculations[3] is used for every chemical compound. The force field is used to generate a set of crystal structures and delimit a candidate window for energy ranking. The powder diffraction patterns of predicted polymorphs are calculated to compare with experimental data.

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.

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.

Parametrizing a polarizable force field from ab initio data. I. The fluctuating point charge model

1999 ◽  
Vol 110 (2) ◽  
pp. 741-754 ◽  
Author(s):  
Jay L. Banks ◽  
George A. Kaminski ◽  
Ruhong Zhou ◽  
Daniel T. Mainz ◽  
B. J. Berne ◽  
...  
Keyword(s):  
Force Field ◽  
Ab Initio ◽  
Point Charge ◽  
Point Charge Model ◽  
Polarizable Force Field ◽  
Charge Model

Molecular Dynamics Study of Hydration in Ethanol−Water Mixtures Using a Polarizable Force Field†

2005 ◽  
Vol 109 (14) ◽  
pp. 6705-6713 ◽  
Author(s):  
Sergei Yu. Noskov ◽  
Guillaume Lamoureux ◽  
Benoît Roux
Keyword(s):  
Molecular Dynamics ◽  
Force Field ◽  
Polarizable Force Field

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.

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