scholarly journals Halogen bonds in some dihalogenated phenols: applications to crystal engineering

IUCrJ ◽  
2013 ◽  
Vol 1 (1) ◽  
pp. 49-60 ◽  
Author(s):  
Arijit Mukherjee ◽  
Gautam R. Desiraju
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Variable Temperature ◽  
Type I ◽  
Type Ii ◽  
Halogen Bonds ◽  
Space Groups ◽  
Starting Model

3,4-Dichlorophenol (1) crystallizes in the tetragonal space groupI41/awith a short axis of 3.7926 (9) Å. The structure is unique in that both type I and type II Cl...Cl interactions are present, these contact types being distinguished by the angle ranges of the respective C—Cl...Cl angles. The present study shows that these two types of contacts are utterly different. The crystal structures of 4-bromo-3-chlorophenol (2) and 3-bromo-4-chlorophenol (3) have been determined. The crystal structure of (2) is isomorphous to that of (1) with the Br atom in the 4-position participating in a type II interaction. However, the monoclinicP21/cpacking of compound (3) is different; while the structure still has O—H...O hydrogen bonds, the tetramer O—H...O synthon seen in (1) and (2) is not seen. Rather than a type I Br...Br interaction which would have been mandated if (3) were isomorphous to (1) and (2), Br forms a Br...O contact wherein its electrophilic character is clearly evident. Crystal structures of the related compounds 4-chloro-3-iodophenol (4) and 3,5-dibromophenol (5) were also determined. A computational survey of the structural landscape was undertaken for (1), (2) and (3), using a crystal structure prediction protocol in space groupsP21/candI41/awith the COMPASS26 force field. While both tetragonal and monoclinic structures are energetically reasonable for all compounds, the fact that (3) takes the latter structure indicates that Br prefers type II over type I contacts. In order to differentiate further between type I and type II halogen contacts, which being chemically distinct are expected to have different distance fall-off properties, a variable-temperature crystallography study was performed on compounds (1), (2) and (4). Length variations with temperature are greater for type II contacts compared with type I. The type II Br...Br interaction in (2) is stronger than the corresponding type II Cl...Cl interaction in (1), leading to elastic bending of the former upon application of mechanical stress, which contrasts with the plastic deformation of (1). The observation of elastic deformation in (2) is noteworthy; in that it finds an explanation based on the strengths of the respective halogen bonds, it could also be taken as a good starting model for future property design. Cl/Br isostructurality is studied with the Cambridge Structural Database and it is indicated that this isostructurality is based on shape and size similarity of Cl and Br, rather than arising from any chemical resemblance.

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.

Polymorphism of 7-dimethylaminocyclopenta[c]coumarin: packing analysis and generation of trial crystal structures

1996 ◽  
Vol 52 (1) ◽  
pp. 201-208 ◽  
Author(s):  
A. Gavezzotti
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
Acta Cryst ◽  
Structure Generation ◽  
Space Groups ◽  
Energy Hypersurface ◽  
Packing Analysis ◽  
Potential Energy Hypersurface

The crystal structures of two polymorphs of the title compound [Pbca and Pna21; Jasinski & Woudenberg (1995). Acta Cryst. C51, 107–109] were analysed. Packing energies and indices were compared. Molecules in the two forms show a slight conformational difference; both conformers were packed in some of the most frequent space groups for organic molecules (P21, P21/c, P212121 and Pna21) using a computer program for crystal structure generation and prediction (PROMET3). The results of such calculations are used to provide tentative explanations for the preference of the two conformers for centrosymmetric and non-centrosymmetric space groups. Several comments on general problems encountered in crystal structure prediction are also presented, concerning in particular the multi-minima structure of the potential energy hypersurface.

scholarly journals Contact map based crystal structure prediction using global optimization

CrystEngComm ◽  
2021 ◽  
Author(s):  
Jianjun Hu ◽  
Wenhui Yang ◽  
Rongzhi Dong ◽  
Yuxin Li ◽  
Xiang Li ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Global Optimization ◽  
Crystal Engineering ◽  
Structure Prediction ◽  
Crystal Structure Prediction ◽  
New Materials ◽  
Contact Map

Crystal structure prediction is now playing an increasingly important role in the discovery of new materials or crystal engineering.

scholarly journals Crystal structures of aconitase X enzymes from bacteria and archaea provide insights into the molecular evolution of the aconitase superfamily

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Seiya Watanabe ◽  
Yohsuke Murase ◽  
Yasunori Watanabe ◽  
Yasuhiro Sakurai ◽  
Kunihiko Tajima
Keyword(s):  
Molecular Evolution ◽  
Agrobacterium Tumefaciens ◽  
Crystal Structures ◽  
Epr Spectroscopy ◽  
Binding Sites ◽  
Active Sites ◽  
Type I ◽  
Type Ii ◽  
Thermococcus Kodakarensis ◽  
Evolutionary Scenario

AbstractAconitase superfamily members catalyze the homologous isomerization of specific substrates by sequential dehydration and hydration and contain a [4Fe-4S] cluster. However, monomeric and heterodimeric types of function unknown aconitase X (AcnX) have recently been characterized as a cis-3-hydroxy-L-proline dehydratase (AcnXType-I) and mevalonate 5-phosphate dehydratase (AcnXType-II), respectively. We herein elucidated the crystal structures of AcnXType-I from Agrobacterium tumefaciens (AtAcnX) and AcnXType-II from Thermococcus kodakarensis (TkAcnX) without a ligand and in complex with substrates. AtAcnX and TkAcnX contained the [2Fe-2S] and [3Fe-4S] clusters, respectively, conforming to UV and EPR spectroscopy analyses. The binding sites of the [Fe-S] cluster and substrate were clearlydifferent from those that were completely conserved in other aconitase enzymes; however, theoverall structural frameworks and locations of active sites were partially similar to each other.These results provide novel insights into the evolutionary scenario of the aconitase superfamilybased on the recruitment hypothesis.

Crystal structure of magnesium chromium vanadate Mg2CrV3O11, a member of the A2BV3O11 vanadate family

2007 ◽  
Vol 22 (3) ◽  
pp. 246-252 ◽  
Author(s):  
A. Worsztynowicz ◽  
S. M. Kaczmarek ◽  
W. Paszkowicz ◽  
R. Minikayev
Keyword(s):  
Crystal Structure ◽  
Rietveld Method ◽  
Ion Pairs ◽  
Exchange Constant ◽  
Type I ◽  
Type Ii ◽  
Paramagnetic Resonance ◽  
Interatomic Distances ◽  
Electron Paramagnetic ◽  
Full Occupancy

The crystal structure of recently discovered chromium (III) dimagnesium trivanadate (V) Mg2CrV3O11 was refined using the Rietveld method. The crystal system of Mg2CrV3O11 is triclinic with space group P1− (Mg1.7Zn0.3GaV3O11 type) and lattice parameters a=6.4057(1) Å, b=6.8111(1) Å, c=10.0640(2) Å, α=97.523(1)°, β=103.351(1)°, γ=101.750(1)°, and Z=2. The characteristic feature of compounds in the A2BV3O11 (A=Mg, Zn and B=Ga, Fe, Cr) family is a strong tendency to share the octahedral M(1) and M(2) sites by both divalent A and trivalent B atoms, and the bipyramidal M(3) sites occupied by divalent A ions. In the present refinement, the only constraint assuming full occupancy of the M(1), M(2), and M(3) sites leads to the following Cr/(Cr+Mg) ratios: 0.70(2) at M(1), 0.24(2) at M(2), and 0.03(2) at M(3). These occupancies are discussed and compared to those of isotypic compounds. The values of interatomic distances are found to be comparable with those reported by R. D. Shannon in 1976. Electron paramagnetic resonance has been also analyzed. Two absorption lines with g≈2.0 (type I) and g≈1.98 (type II) have been recorded in the EPR spectra, and attributed to V4+ ions and Cr3+–Cr3+ ion pairs, respectively. The exchange constant J between Cr3+ ions has been calculated.

scholarly journals Unusual co-crystal of isonicotinamide: the structural landscape in crystal engineering

2012 ◽  
Vol 370 (1969) ◽  
pp. 2900-2915 ◽  
Author(s):  
Srinu Tothadi ◽  
Gautam R. Desiraju
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Organic Molecule ◽  
Reference Molecule ◽  
Hydrogen Bonded

The idea of a structural landscape is based on the fact that a large number of crystal structures can be associated with a particular organic molecule. Taken together, all these structures constitute the landscape. The landscape includes polymorphs, pseudopolymorphs and solvates. Under certain circumstances, it may also include multi-component crystals (or co-crystals) that contain the reference molecule as one of the components. Under still other circumstances, the landscape may include the crystal structures of molecules that are closely related to the reference molecule. The idea of a landscape is to facilitate the understanding of the process of crystallization. It includes all minima that can, in principle, be accessed by the molecule in question as it traverses the path from solution to the crystal. Isonicotinamide is a molecule that is known to form many co-crystals. We report here a 2:1 co-crystal of this amide with 3,5-dinitrobenzoic acid, wherein an unusual N−H⋯N hydrogen-bonded pattern is observed. This crystal structure offers some hints about the recognition processes between molecules that might be implicated during crystallization. Also included is a review of other recent results that illustrate the concept of the structural landscape.

scholarly journals Quantum Mechanical-Based Stability Evaluation of Crystal Structures for HIV-Targeted Drug Cabotegravir

Molecules ◽  
2021 ◽  
Vol 26 (23) ◽  
pp. 7178
Author(s):  
Yanqiang Han ◽  
Hongyuan Luo ◽  
Qianqian Lu ◽  
Zeying Liu ◽  
Jinyun Liu ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Ab Initio ◽  
Crystal Structures ◽  
Structure Prediction ◽  
Hiv Infections ◽  
Integrase Inhibitor ◽  
Hiv Integrase ◽  
Stability Evaluation ◽  
The Stability ◽  
Long Acting

The long-acting parenteral formulation of the HIV integrase inhibitor cabotegravir (GSK744) is currently being developed to prevent HIV infections, benefiting from infrequent dosing and high efficacy. The crystal structure can affect the bioavailability and efficacy of cabotegravir. However, the stability determination of crystal structures of GSK744 have remained a challenge. Here, we introduced an ab initio protocol to determine the stability of the crystal structures of pharmaceutical molecules, which were obtained from crystal structure prediction process starting from the molecular diagram. Using GSK744 as a case study, the ab initio predicted that Gibbs free energy provides reliable further refinement of the predicted crystal structures and presents its capability for becoming a crystal stability determination approach in the future. The proposed work can assist in the comprehensive screening of pharmaceutical design and can provide structural predictions and stability evaluation for pharmaceutical crystals.

Supramolecular [Na(15-crown-5)]+ cations anchored to face sharing octahedral lead bromide chains featuring a rotor in a one-dimensional perovskite with a reversible isostructural phase transition near room temperature

CrystEngComm ◽  
2021 ◽  
Author(s):  
Guo-Jun Yuan ◽  
Hong Zhou ◽  
Li Li ◽  
Hong Chen ◽  
Xiaoming Ren
Keyword(s):  
Crystal Structure ◽  
Phase Transition ◽  
Crystal Structures ◽  
Crystal Engineering ◽  
Room Temperature ◽  
One Dimensional ◽  
Lead Bromide ◽  
Engineering Study ◽  
Isostructural Phase Transition

Crystal engineering study aims at a better understanding of the correlation between the components and crystal structures, so that the desired crystal structure and functionality will be acquired. In this...

Crystal structure of three diaza-crowns-18

1997 ◽  
Vol 212 (5) ◽  
Author(s):  
P. Dokurno ◽  
R. Trokowski ◽  
B. Kościuszko-Panek ◽  
T. Ossowski ◽  
A. Konitz ◽  
...  
Keyword(s):  
Crystal Structure ◽  
Crystal Structures ◽  
Unit Cell ◽  
Unit Cell Parameters ◽  
Space Groups ◽  
Cell Parameters

AbstractThe crystal structures of three diaza crowns-18, namely 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane (crown 1), 1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diacetonitrile (crown 2) and N,N′-(1,4,10,13-tetraoxa-7,16-diazacyclooctadecane-7,16-diyldi-2,1-ethanediyl)bis-[4-methyl-benzenesulfonamide] (crown 3) have the following space groups and unit cell parameters: crown 1(C

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