Holographic methods in X-ray crystallography. III. First numerical results

Author(s):  
G. J. Maalouf ◽  
J. C. Hoch ◽  
A. S. Stern ◽  
H. Szöke ◽  
A. Szöke

The holographic method for the completion of crystal structures, described in paper II [Szöke (1993). Acta Cryst. A49, 853–866], is implemented numerically. The purpose of these modest calculations is to show that the holographic method can handle real crystallographic data in easy problems and to test various algorithms for its implementation. Both synthetic and experimental data are used and sources of error are systematically introduced. The numerical experiments support the theory presented in paper II and show that the holographic method may be a potentially viable alternative to conventional methods for the completion of crystal structures.

Biomolecules ◽  
2021 ◽  
Vol 11 (12) ◽  
pp. 1837
Author(s):  
Anna Sandner ◽  
Khang Ngo ◽  
Christoph P. Sager ◽  
Frithjof Scheer ◽  
Michael Daude ◽  
...  

The transient specificity pocket of aldose reductase only opens in response to specific ligands. This pocket may offer an advantage for the development of novel, more selective ligands for proteins with similar topology that lack such an adaptive pocket. Our aim was to elucidate which properties allow an inhibitor to bind in the specificity pocket. A series of inhibitors that share the same parent scaffold but differ in their attached aromatic substituents were screened using ITC and X-ray crystallography for their ability to occupy the pocket. Additionally, we investigated the electrostatic potentials and charge distribution across the attached terminal aromatic groups with respect to their potential to bind to the transient pocket of the enzyme using ESP calculations. These methods allowed us to confirm the previously established hypothesis that an electron-deficient aromatic group is an important prerequisite for opening and occupying the specificity pocket. We also demonstrated from our crystal structures that a pH shift between 5 and 8 does not affect the binding position of the ligand in the specificity pocket. This allows for a comparison between thermodynamic and crystallographic data collected at different pH values.


Author(s):  
Jakub Pedziwiatr ◽  
Ion Ghiviriga ◽  
Khalil A. Abboud ◽  
Adam S. Veige

This report describes a synthetic protocols and the crystal structures involving a novel pincer-type H3[NNN] ligand, namely di-μ-bromido-μ-{2-(2,2-dimethylpropanimidoyl)-N-[2-(2,2-dimethylpropanimidoyl)-4-methylphenyl]-4-methylaniline}-bis[(diethyl ether)lithium], [Li2Br2(C24H33N3)(C4H10O)2] (1) and a dinuclear metal complex, namely di-μ-bromido-2:3κ4Br:Br-bis{2-(2,2-dimethylpropanimidoyl)-N-[2-(2,2-dimethylpropanimidoyl)-4-methylphenyl]-4-methylaniline}-1κ3N,N′,N′′;4κ3N,N′,N′′-tetra-μ-isopropanolato-1:2κ4O:O;3:4κ4O:O-diisopropanolato-1κO,4κO-2,3-dilithium-1,4-dititanium, [Li2Ti2Br2(C24H32N3)2(C3H7O)6] or {[NHNNH]Ti(OiPr)3(LiBr)2}2(2). Complex1, which sits on a twofold rotation axis, is a rare example of a pincer-type ligand which bears ketimine side arms. A unique feature of complex1is that the ketimine N atoms have an LiBr(Et2O) fragment bonded to them, with the Li atom adopting a distorted tetrahedral geometry. This particular fragment creates an LiBr bridge between the two ketimine sidearms, which leads to a cage-type appearance of the ligand. Complex2consists of the previously described ligand and a TiIVmetal atom in an octahedral environment, and is located on an inversion center. Complex2crystallizes as a dinuclear species with the metal atoms being bridged by an LiBr entity [the Br atoms are disordered and refined in two positions with their site occupation factors refining to 0.674 (12)/0.372 (12)], and the Li cation being bonded to the isopropoxide O atoms (Li having a tetrahedral coordination as in1). The organic ligand of compound2exhibits disorder in its periphery groups; isopropyl andtert-butyl groups (occupation factors fixed at 0.6/0.4). The novel [NNN]H3pincer-type ligand was characterized by multinuclear and multidimensional NMR, HRMS and X-ray crystallography. The dinuclear metal complex2was characterized by X-ray crystallography. Although each structure exhibits donor N—H groups, no hydrogen bonding is found in either one, perhaps due to the bulky groups around them. One of the ethyl groups of the ether ligand of1is disordered and refined in two parts with site-occupation factors of 0.812 (8) and 0.188 (8). One and a half toluene solvent molecules are also present in the asymmetric unit of2. The toluene molecules were significantly disordered and could not be modeled properly, thusSQUEEZE[Spek (2015).Acta Cryst.C71, 9–18] was used to remove their contributions to the overall intensity data.


1997 ◽  
Vol 53 (5) ◽  
pp. 812-821 ◽  
Author(s):  
J. C. Cole ◽  
J. M. Cole ◽  
G. H. Cross ◽  
M. Farsari ◽  
J. A. K. Howard ◽  
...  

The crystal structures of {4-[bis(diethylamino)methylium]phenyl}dicyanomethanide (I), {4-[cyano(4-methylpiperidyl)methylium]phenyl } dicyanomethanide (II), {4-[cyano(1-pyrrolidinyl)methylium]phenyl}dicyanomethanide (IV) and (Z)-{4-[1,3-dicyano-3-(diethylamino)-2-propenylium]phenyl} dicyanomethanide have been determined by X-ray crystallography. Together with (Z)-{4-[1-cyano-3-(diethylamino)-2-propenylium]phenyl}dicyanomethanide [(III): Cole, J. C., Howard, J. A. K., Cross, G. H. & Szablewski, M. (1995). Acta Cryst. C51, 715–718], these compounds exhibit varying degrees of quinoidal characteristics and yet have predominantly zwitterionic ground state character. The presence of high dipole moments in the crystal can thus be inferred and are substantiated by measurements of high solution-state dipole moments. Negative solvatochromism (hypsochromism on increasing solvent polarity) confirms the zwitterionic character in at least two of the series.


2021 ◽  
Author(s):  
Stéphane Baeriswyl ◽  
Hippolyte Personne ◽  
Ivan Di Bonaventura ◽  
Thilo Köhler ◽  
Christian van Delden ◽  
...  

We report the first X-ray crystal structures of mixed chirality α-helices comprising only natural residues as the example of bicyclic and linear membrane disruptive amphiphilic antimicrobial peptides containing seven l- and four d-residues.


2001 ◽  
Vol 79 (3) ◽  
pp. 263-271
Author(s):  
Paul K Baker ◽  
Michael GB Drew ◽  
Deborah S Evans

Reaction of [WI2(CO)3(NCMe)2] with two equivalents of 1-phenyl-1-propyne (MeC2Ph) in CH2Cl2, and in the absence of light, gave the bis(1-phenyl-1-propyne) complex [WI2(CO)(NCMe)(η2-MeC2Ph)2] (1) in 77% yield. Treatment of equimolar quantities of 1 and NCR (R = Et, i-Pr, t-Bu, Ph) in CH2Cl2 afforded the nitrile-exchanged products, [WI2(CO)(NCR)(η2-MeC2Ph)2] (2-5) (R = Et (2), i-Pr (3), t-Bu (4), Ph (5)). Complexes 1, 2, and 5 were structurally characterized by X-ray crystallography. All three structures have the same pseudo-octahedral geometry, with the equatorial sites being occupied by cis and parallel alkyne groups, which are trans to the cis-iodo groups. The trans carbon monoxide and acetonitrile ligands occupy the axial sites. In structures 1 and 2, the methyl and phenyl substituents of the 1-phenyl-1-propyne ligands are cis to each other, whereas for the bulkier NCPh complex (5), the methyl and phenyl groups are trans to one another. This is the first time that this arrangement has been observed in the solid state in bis(alkyne) complexes of this type.Key words: bis(1-phenyl-1-propyne), carbonyl, nitrile, diiodo, tungsten(II), crystal structures.


Author(s):  
Robert E. Dinnebier ◽  
Hanne Nuss ◽  
Martin Jansen

AbstractThe crystal structures of solvent-free lithium, sodium, rubidium, and cesium squarates have been determined from high resolution synchrotron and X-ray laboratory powder patterns. Crystallographic data at room temperature of Li


Author(s):  
Н.Л. Лунина ◽  
N.L. Lunina

Advances in the methodology of the X-ray diffraction experiments leads to a possibility to register the rays scattered by large isolated biological particles (viruses and individual cells) but not only by crystalline samples. The experiment with an isolated particle provides researchers with the intensities of the scattered rays for the continuous spectrum of scattering vectors. Such experiment gives much more experimental data than an experiment with a crystalline sample where the information is limited to a set of Bragg reflections. This opens up additional opportunities in solving underlying problem of X-ray crystallography, namely, calculating phase values for the scattered waves needed to restore the structure of the object under study. In practice, the original continuous diffraction pattern is sampled, reduced to the values at grid points in the space of scattering vectors (in the reciprocal space). The sampling step determines the amount of the information involved in solving the phase problem and the complexity of the necessary calculations. In this paper, we investigate the effect of the sampling step on the accuracy of the phase problem solution obtained by the method proposed earlier by the authors. It is shown that an expected improvement of the accuracy of the solution with the reducing the sampling step continues even after crossing the Nyquist limit defined as the inverse of the double size of the object under study.


Author(s):  
Marcin Rojkiewicz ◽  
Piotr Kuś ◽  
Maria Książek ◽  
Joachim Kusz

Cathinones belong to a group of compounds of great interest in the new psychoactive substances (NPS) market. Constant changes to the chemical structure made by the producers of these compounds require a quick reaction from analytical laboratories in ascertaining their characteristics. In this article, three cathinone derivatives were characterized by X-ray crystallography. The investigated compounds were confirmed as: 1-[1-(4-methylphenyl)-1-oxohexan-2-yl]pyrrolidin-1-ium chloride (1, C17H26NO+·Cl−, the hydrochloride of 4-MPHP), 1-(4-methyl-1-oxo-1-phenylpentan-2-yl)pyrrolidin-1-ium chloride (2; C16H24NO+·Cl−, the hydrochloride of α-PiHP) and methyl[1-(4-methylphenyl)-1-oxopentan-2-yl]azanium chloride (3; C13H20NO+·Cl−, the hydrochloride of 4-MPD). All the salts crystallize in a monoclinic space group: 1 and 2 in P21/c, and 3 in P21/n. To the best of our knowledge, this study provides the first detailed and comprehensive crystallographic data on salts 1–3.


2019 ◽  
Vol 6 (6) ◽  
pp. 780-790 ◽  
Author(s):  
Maciej Barłóg ◽  
Ihor Kulai ◽  
Xiaozhou Ji ◽  
Nattamai Bhuvanesh ◽  
Somnath Dey ◽  
...  

A series of 11 novel fluorinated and non-fluorinated di(thiazolyl)benzenes have been synthesized via microwave assisted Stille coupling and characterized using X-ray crystallography.


2016 ◽  
Vol 71 (3) ◽  
pp. 231-239 ◽  
Author(s):  
Roumaissa Belguedj ◽  
Sofiane Bouacida ◽  
Hocine Merazig ◽  
Ali Belfaitah ◽  
Aissa Chibani ◽  
...  

AbstractThree benzoindolizine derivatives, 1, 2, and 3, were obtained via 1,3-dipolar cycloaddition. The reaction of 1-(2′-benzimidazolylmethyl)isoquinolinium ylides with dimethyl acetylenedicarboxylate gave a mixture of pyrrolo[2,1-a]isoquinoline-1,2-dicarboxylate (1) and 1,10b-dihydropyrrolo[2,1-a]isoquinoline-1,2-dicarboxylate (2) derivatives containing a benzimidazole moiety. The reaction of this isoquinolinium N-ylide with dimethyl maleate gave an unexpected 2,3-dihydropyrrolo[2,1-a]isoquinoline-1,2-dicarboxylate (3). The structures of all reported compounds have been examined by X-ray crystallography, mass spectrometry, and NMR spectroscopy.


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