scholarly journals Graded IR Filters: Distinguishing Between Single and Multipoint NO2···I Halogen Bonded Supramolecular Synthons (P, Q, and R Synthons)

2014 ◽  
Vol 67 (12) ◽  
pp. 1840 ◽  
Author(s):  
Subhankar Saha ◽  
Somnath Ganguly ◽  
Gautam R. Desiraju
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Supramolecular Synthon ◽  
High Throughput Analysis ◽  
Disordered Structures ◽  
Recognition Pattern ◽  
The Individual ◽  
Ir Spectroscopic

The NO2···I supramolecular synthon is a halogen bonded recognition pattern that is present in the crystal structures of many compounds that contain these functional groups. These synthons have been previously distinguished as P, Q, and R types using topological and geometrical criteria. A five step IR spectroscopic sequence is proposed here to distinguish between these synthon types in solid samples. Sets of known compounds that contain the P, Q, and R synthons are first taken to develop IR spectroscopic identifiers for them. The identifiers are then used to create graded IR filters that sieve the synthons. These filters contain signatures of the individual NO2···I synthons and may be applied to distinguish between P, Q, and R synthon varieties. They are also useful to identify synthons that are of a borderline character, synthons in disordered structures wherein the crystal structure in itself is not sufficient to distinguish synthon types, and in the identification of the NO2···I synthons in compounds with unknown crystal structures. This study establishes clear differences for the three different geometries P, Q, and R and in the chemical differences in the intermolecular interactions contained in the synthons. Our IR method can be conveniently employed when single crystals are not readily available also in high throughput analysis. It is possible that such identification may also be adopted as an input for crystal structure prediction analysis of compounds with unknown crystal structures.

scholarly journals Crystal structures of two furazidin polymorphs revealed by a joint effort of crystal structure prediction and NMR crystallography

2020 ◽  
Vol 76 (3) ◽  
pp. 322-335 ◽  
Author(s):  
Marta K. Dudek ◽  
Piotr Paluch ◽  
Edyta Pindelska
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Determination ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Determination ◽  
Crystal Structure Prediction ◽  
Crystal Forms ◽  
Space Groups ◽  
Nmr Crystallography

This work presents the crystal structure determination of two elusive polymorphs of furazidin, an antibacterial agent, employing a combination of crystal structure prediction (CSP) calculations and an NMR crystallography approach. Two previously uncharacterized neat crystal forms, one of which has two symmetry-independent molecules (form I), whereas the other one is a Z′ = 1 polymorph (form II), crystallize in P21/c and P 1 space groups, respectively, and both are built by different conformers, displaying different intermolecular interactions. It is demonstrated that the usage of either CSP or NMR crystallography alone is insufficient to successfully elucidate the above-mentioned crystal structures, especially in the case of the Z′ = 2 polymorph. In addition, cases of serendipitous agreement in terms of 1H or 13C NMR data obtained for the CSP-generated crystal structures different from the ones observed in the laboratory (false-positive matches) are analyzed and described. While for the majority of analyzed crystal structures the obtained agreement with the NMR experiment is indicative of some structural features in common with the experimental structure, the mentioned serendipity observed in exceptional cases points to the necessity of caution when using an NMR crystallography approach in crystal structure determination.

Crystal Structure Prediction of Aminols:  Advantages of a Supramolecular Synthon Approach with Experimental Structures

2005 ◽  
Vol 127 (30) ◽  
pp. 10545-10559 ◽  
Author(s):  
Archan Dey ◽  
Michael T. Kirchner ◽  
Venu R. Vangala ◽  
Gautam R. Desiraju ◽  
Raju Mondal ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Supramolecular Synthon

scholarly journals Powder diffraction and crystal structure prediction identify four new coumarin polymorphs

2017 ◽  
Vol 8 (7) ◽  
pp. 4926-4940 ◽  
Author(s):  
Alexander G. Shtukenberg ◽  
Qiang Zhu ◽  
Damien J. Carter ◽  
Leslie Vogt ◽  
Johannes Hoja ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Powder Diffraction ◽  
Structure Prediction ◽  
Prediction Method ◽  
Crystal Structure Prediction ◽  
Free Energies ◽  
Structure Prediction Method

Crystal structures of four new coumarin polymorphs were solved by crystal structure prediction method and their lattice and free energies were calculated by advanced techniques.

scholarly journals Nicotinamide: Seven New Polymorphic Structures Revealed by Melt Crystallization and Crystal Structure Prediction

2020 ◽  
Author(s):  
Xizhen Li ◽  
Xiao Ou ◽  
Bingquan Wang ◽  
Haowei Rong ◽  
Bing Wang ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Melt Crystallization ◽  
Efficient Tool ◽  
Single Crystal Structures ◽  
Solution Crystallization

<p>Here, we reported nicotinamide (NIC), a long-known vitamin, was revealed in fact to be a highly polymorphic compound with nine solved single-crystal structures by performing melt crystallization. A CSP calculation successfully identified all six Z’ = 1 and 2 experimental structures. Melt crystallization has turned out to be an efficient tool for exploring polymorphic landscape, especially in regions inaccessbile by solution crystallization.</p>

COMPACK: a program for identifying crystal structure similarity using distances

2005 ◽  
Vol 38 (1) ◽  
pp. 228-231 ◽  
Author(s):  
James Alexander Chisholm ◽  
Sam Motherwell
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Structural Features ◽  
Crystal Structure Prediction ◽  
Blind Test ◽  
Interatomic Distances ◽  
Structure Similarity ◽  
Measure Of Similarity ◽  
Orientation Of Molecules

A method is presented for comparing crystal structures to identify similarity in molecular packing environments. The relative position and orientation of molecules is captured using interatomic distances, which provide a representation of structure that avoids the use of space-group and cell information. The method can be used to determine whether two crystal structures are the same to within specified tolerances and can also provide a measure of similarity for structures that do not match exactly, but have structural features in common. Example applications are presented that include the identification of an experimentally observed crystal structure from a list of predicted structures and the process of clustering a list of predicted structures to remove duplicates. Examples are also presented to demonstrate partial matching. Such searches were performed to analyse the results of the third blind test for crystal structure prediction, to identify the frequency of occurrence of a characteristic layer and a characteristic hydrogen-bonded chain.

Modelling the crystal structure of the 2-hydronitronylnitroxide radical (HNN): observed and computer-generated polymorphs

1999 ◽  
Vol 55 (4) ◽  
pp. 543-553 ◽  
Author(s):  
G. Filippini ◽  
A. Gavezzotti ◽  
J. J. Novoa
Keyword(s):  
Crystal Structure ◽  
Force Field ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
X Ray ◽  
Narrow Energy Range ◽  
Coulomb Type ◽  
Atomic Coordinates ◽  
Hydrogen Bonded

The crystal structures of two polymorphs of 4,4,5,5-tetramethyl-4,5-dihydro-1H-imidazol-1-oxyl 3-oxide (the 2-hydronitronylnitroxide radical, HNN) are analyzed by packing energy criteria. Other unobserved polymorphic crystal structures are generated using a polymorph predictor package and three different force fields, one of which is without explicit Coulomb-type terms. The relative importance of several structural motifs (hydrogen-bonded dimers, shape-interlocking dimers or extended hydrogen-bonded chains) is discussed. As usual, many crystal structures within a narrow energy range are generated by the polymorph predictor, confirming that ab initio crystal-structure prediction is still problematic. Comparisons of powder patterns generated from the atomic coordinates of the X-ray structure and from computational crystal structures confirm that although the energy ranking depends on the force field used, the X-ray structure of the \alpha polymorph was found to be among the most stable ones produced by the polymorph predictor, even using the chargeless force field.

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