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1.
IUCrJ ; 6(Pt 5): 884-894, 2019 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-31576221

RESUMO

The present work reports on the charge and spin density modelling of YTiO3 in its ferromagnetic state (T C = 27 K). Accurate polarized neutron diffraction and high-resolution X-ray diffraction (XRD) experiments were carried out on a single crystal at the ORPHÉE reactor (LLB) and SPRING8 synchrotron source. The experimental data are modelled by the spin resolved pseudo-atomic multipolar model (Deutsch et al., 2012 ▸). The refinement strategy is discussed and the result of this electron density modelling is compared with that from XRD measured at 100 K and with density functional theory calculations. The results show that the spin and charge densities around the Ti atom have lobes directed away from the O atoms, confirming the filling of the t 2g orbitals of the Ti atom. The d xy orbital is less populated than d xz and d yz , which is a sign of a partial lift of degeneracy of the t 2g orbitals. This study confirms the orbital ordering at low temperature (20 K), which is already present in the paramagnetic state above the ferromagnetic transition (100 K).

2.
Phys Chem Chem Phys ; 20(37): 24192-24200, 2018 Oct 07.
Artigo em Inglês | MEDLINE | ID: mdl-30209451

RESUMO

In an effort to describe π-hole interactions, we undertook accurate high-resolution X-ray diffraction analyses of single crystals of 1,4-dinitrobenzene, a co-crystal of cis-tartaric acid and bis-pyridine N-oxide and the hydrochloride of B-4-pyridinylboronic acid. We selected these three compounds owing to the π-hole accessibility features that the sp2 hybridized B, C and N atoms provide, thus allowing us to compare the fundamental characteristics of π-hole interactions using Bader's Atom in Molecules (AIM) theory. This particular study required extremely accurate experimental diffraction data, because the interaction of interest is weak. As shown by the experimental charge density maps of the -YO2 (Y = B, C, N) units, we assign the depletion of electron-density present in the central boron, carbon and nitrogen atoms (electrophilic π-holes) as the main origin for the establishment of intermolecular Lewis acid-Lewis base attractive interaction with complementary electron-rich regions. Unexpectedly, the Bader's analyses of both experimentally and theoretically calculated charge distribution maps for the solid involving the - BO2H2 group do not show the presence of bond paths, neither of the bond critical points, between the interacting electron rich sites and the boron or carbon atoms featuring the electron hole. In contrast, these topological descriptors of chemical interactions for the AIM theory were easily located in the solid-state structures of the compounds involving the carboxylic and the nitro groups.

3.
IUCrJ ; 5(Pt 5): 647-653, 2018 Sep 01.
Artigo em Inglês | MEDLINE | ID: mdl-30224967

RESUMO

In this study, the nature and characteristics of a short Br⋯π interaction observed in an ebselen derivative, 2-(2-bromophenyl)benzo[d][1,2]selenazol-3(2H)-one, has been explored. The electronic nature of this Br⋯π interaction was investigated via high-resolution X-ray diffraction and periodic density functional theory calculations using atoms-in-molecules (AIM) analysis. This study unravels the simultaneous presence of σ-hole and π-hole bonding characteristics in the same interaction. The dual characteristics of this unique Br⋯π interaction are further established via molecular electrostatic potentials (MESPs) and natural bond orbitals (NBOs).

4.
J Chem Phys ; 148(16): 164106, 2018 Apr 28.
Artigo em Inglês | MEDLINE | ID: mdl-29716230

RESUMO

In this paper, we propose a simple cluster model with limited basis sets to reproduce the unpaired electron distributions in a YTiO3 ferromagnetic crystal. The spin-resolved one-electron-reduced density matrix is reconstructed simultaneously from theoretical magnetic structure factors and directional magnetic Compton profiles using our joint refinement algorithm. This algorithm is guided by the rescaling of basis functions and the adjustment of the spin population matrix. The resulting spin electron density in both position and momentum spaces from the joint refinement model is in agreement with theoretical and experimental results. Benefits brought from magnetic Compton profiles to the entire spin density matrix are illustrated. We studied the magnetic properties of the YTiO3 crystal along the Ti-O1-Ti bonding. We found that the basis functions are mostly rescaled by means of magnetic Compton profiles, while the molecular occupation numbers are mainly modified by the magnetic structure factors.

5.
Acta Crystallogr A Found Adv ; 74(Pt 3): 170-183, 2018 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-29724964

RESUMO

Estimating uncertainties of property values derived from a charge-density model is not straightforward. A methodology, based on calculation of sample standard deviations (SSD) of properties using randomly deviating charge-density models, is proposed with the MoPro software. The parameter shifts applied in the deviating models are generated in order to respect the variance-covariance matrix issued from the least-squares refinement. This `SSD methodology' procedure can be applied to estimate uncertainties of any property related to a charge-density model obtained by least-squares fitting. This includes topological properties such as critical point coordinates, electron density, Laplacian and ellipticity at critical points and charges integrated over atomic basins. Errors on electrostatic potentials and interaction energies are also available now through this procedure. The method is exemplified with the charge density of compound (E)-5-phenylpent-1-enylboronic acid, refined at 0.45 Šresolution. The procedure is implemented in the freely available MoPro program dedicated to charge-density refinement and modelling.

6.
Acta Crystallogr B Struct Sci Cryst Eng Mater ; 73(Pt 4): 544-549, 2017 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-28762966

RESUMO

Joint refinement of X-ray and polarized neutron diffraction data has been carried out in order to determine charge and spin density distributions simultaneously in the nitronyl nitroxide (NN) free radical Nit(SMe)Ph. For comparison purposes, density functional theory (DFT) and complete active-space self-consistent field (CASSCF) theoretical calculations were also performed. Experimentally derived charge and spin densities show significant differences between the two NO groups of the NN function that are not observed from DFT theoretical calculations. On the contrary, CASSCF calculations exhibit the same fine details as observed in spin-resolved joint refinement and a clear asymmetry between the two NO groups.

7.
Acta Crystallogr B Struct Sci Cryst Eng Mater ; 73(Pt 4): 610-625, 2017 Aug 01.
Artigo em Inglês | MEDLINE | ID: mdl-28762971

RESUMO

A database describing the electron density of common chemical groups using combinations of real and virtual spherical atoms is proposed, as an alternative to the multipolar atom modelling of the molecular charge density. Theoretical structure factors were computed from periodic density functional theory calculations on 38 crystal structures of small molecules and the charge density was subsequently refined using a density model based on real spherical atoms and additional dummy charges on the covalent bonds and on electron lone-pair sites. The electron-density parameters of real and dummy atoms present in a similar chemical environment were averaged on all the molecules studied to build a database of transferable spherical atoms. Compared with the now-popular databases of transferable multipolar parameters, the spherical charge modelling needs fewer parameters to describe the molecular electron density and can be more easily incorporated in molecular modelling software for the computation of electrostatic properties. The construction method of the database is described. In order to analyse to what extent this modelling method can be used to derive meaningful molecular properties, it has been applied to the urea molecule and to biotin/streptavidin, a protein/ligand complex.

8.
Artigo em Inglês | MEDLINE | ID: mdl-26830798

RESUMO

The experimental and theoretical charge densities of 1,4-bis(5-hexyl-2-thienyl)butane-1,4-dione, a precursor in the synthesis of thiophene-based semiconductors and organic solar cells, are presented. A dummy bond charges spherical atom model is applied besides the multipolar atom model. The results show that the dummy bond charges model is accurate enough to calculate electrostatic-derived properties which are comparable with those obtained by the multipolar atom model. The refinement statistics and the residual electron density values are found to be intermediate between the independent atom and the multipolar formalisms.


Assuntos
Butanonas/análise , Butanonas/química , Tionas/análise , Tionas/química , Tiofenos/química , Cristalografia por Raios X/métodos , Estrutura Molecular , Teoria Quântica , Difração de Raios X/métodos
9.
IUCrJ ; 2(Pt 4): 441-51, 2015 Jul 01.
Artigo em Inglês | MEDLINE | ID: mdl-26175903

RESUMO

Electron density is a fundamental quantity that enables understanding of the chemical bonding in a molecule or in a solid and the chemical/physical property of a material. Because electrons have a charge and a spin, two kinds of electron densities are available. Moreover, because electron distribution can be described in momentum or in position space, charge and spin density have two definitions and they can be observed through Bragg (for the position space) or Compton (for the momentum space) diffraction experiments, using X-rays (charge density) or polarized neutrons (spin density). In recent years, we have witnessed many advances in this field, stimulated by the increased power of experimental techniques. However, an accurate modelling is still necessary to determine the desired functions from the acquired data. The improved accuracy of measurements and the possibility to combine information from different experimental techniques require even more flexibility of the models. In this short review, we analyse some of the most important topics that have emerged in the recent literature, especially the most thought-provoking at the recent IUCr general meeting in Montreal.

10.
IUCrJ ; 2(Pt 2): 161-3, 2015 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-25866651

RESUMO

Professor Dunitz questions the usefulness of ascribing crystalline structural stability to individual atom-atom intermolecular interactions viewed as bonding (hence stabilizing) whenever linked by a bond path. An alternative view is expressed in the present essay that articulates the validity and usefulness of the bond path concept in a crystallographic and crystal engineering context.

11.
Artigo em Inglês | MEDLINE | ID: mdl-25449620

RESUMO

High-resolution crystal structure determination and spherical and multipolar refinement enabled an organic solid solution of 1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole-5-carbonitrile and 5-bromo-1-(4'-chlorophenyl)-2-methyl-4-nitro-1H-imidazole to be found, which would not normally be revealed using only standard resolution data (ca 0.8 Å), as the disordered part is only visible at high resolution. Therefore, this new structure would have been reported as just another polymorphic form, even more reasonably as isostructural with other derivatives. To the best of our knowledge this is the first example of organic solid solution modelled via charge density Hansen-Coppens formalism and analysed by means of quantum theory of atoms in molecules (QTAIM) theory.

12.
Artigo em Inglês | MEDLINE | ID: mdl-25274511

RESUMO

The new generation of X-ray detectors, the hybrid pixel area detectors or `pixel detectors', is based on direct detection and single-photon counting processes. A large linearity range, high dynamic and extremely low noise leading to an unprecedented high signal-to-noise ratio, fast readout time (high frame rates) and an electronic shutter are among their intrinsic characteristics which render them very attractive. First used on synchrotron beamlines, these detectors are also promising in the laboratory, in particular for pump-probe or quasi-static experiments and accurate electron density measurements, as explained in this paper. An original laboratory diffractometer made from a Nonius Mach3 goniometer equipped with an Incoatec Mo microsource and an XPAD pixel area detector has been developed at the CRM2 laboratory. Mo Kα accurate charge density quality data up to 1.21 Å(-1) resolution have been collected on a sodium nitroprusside crystal using this home-made diffractometer. Data quality for charge density analysis based on multipolar modelling are discussed in this paper. Deformation electron densities are compared to those already published (based on data collected with CCD APEXII and CAD4 diffractometers).

13.
Artigo em Inglês | MEDLINE | ID: mdl-25274525

RESUMO

The stacked two-dimensional supramolecular compound catena-{Co(amp)3Cr(ox)3·6H2O} (amp = 2-picolylamine, ox = oxalate) has been synthesized from the bimolecular approach using hydrogen bonds. It is built from layers in which both Co(amp)(3+) (D) and Cr(ox)(3-) (A) ions are bonded in a repeating DADADA… pattern along the a and c axes by multiple hydrogen bonds. These layers host a well resolved R12 dodecameric discrete ring of water clusters built by six independent molecules located around the 2c centrosymmetric Wyckoff positions of the P21/n space group in which the compound crystallizes. These clusters are ranged along the [001] direction, occupy 733.5 Å(3) (22.0%) of the unit cell and have a chair conformation via 12 hydrogen bonds. The water molecules of the cluster are linked with stronger hydrogen bonds than those between the cluster and its host, which explains the single continuous step of the dehydration process of the compound.

14.
IUCrJ ; 1(Pt 2): 110-8, 2014 Mar 01.
Artigo em Inglês | MEDLINE | ID: mdl-25075327

RESUMO

The harmonic model of atomic nuclear motions is usually enough for multipole modelling of high-resolution X-ray diffraction data; however, in some molecular crystals, such as 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole [Paul, Kubicki, Jelsch et al. (2011 ▶). Acta Cryst. B67, 365-378], it may not be sufficient for a correct description of the charge-density distribution. Multipole refinement using harmonic atom vibrations does not lead to the best electron density model in this case and the so-called 'shashlik-like' pattern of positive and negative residual electron density peaks is observed in the vicinity of some atoms. This slight disorder, which cannot be modelled by split atoms, was solved using third-order anharmonic nuclear motion (ANM) parameters. Multipole refinement of the experimental high-resolution X-ray diffraction data of 1-(2'-aminophenyl)-2-methyl-4-nitro-1H-imidazole at three different temperatures (10, 35 and 70 K) and a series of powder diffraction experiments (20 ≤ T ≤ 300 K) were performed to relate this anharmonicity observed for several light atoms (N atoms of amino and nitro groups, and O atoms of nitro groups) to an isomorphic phase transition reflected by a change in the b cell parameter around 65 K. The observed disorder may result from the coexistence of domains of two phases over a large temperature range, as shown by low-temperature powder diffraction.

15.
IUCrJ ; 1(Pt 3): 194-9, 2014 May 01.
Artigo em Inglês | MEDLINE | ID: mdl-25075338

RESUMO

Since the 1980s it has been possible to probe crystallized matter, thanks to X-ray or neutron scattering techniques, to obtain an accurate charge density or spin distribution at the atomic scale. Despite the description of the same physical quantity (electron density) and tremendous development of sources, detectors, data treatment software etc., these different techniques evolved separately with one model per experiment. However, a breakthrough was recently made by the development of a common model in order to combine information coming from all these different experiments. Here we report the first experimental determination of spin-resolved electron density obtained by a combined treatment of X-ray, neutron and polarized neutron diffraction data. These experimental spin up and spin down densities compare very well with density functional theory (DFT) calculations and also confirm a theoretical prediction made in 1985 which claims that majority spin electrons should have a more contracted distribution around the nucleus than minority spin electrons. Topological analysis of the resulting experimental spin-resolved electron density is also briefly discussed.

16.
Artigo em Inglês | MEDLINE | ID: mdl-24675589

RESUMO

The experimental charge-density distribution in 2-methyl-1,3-cyclopentanedione in the crystal state was analyzed by synchrotron X-ray diffraction data collection at 0.33 Šresolution. The molecule in the crystal is in the enol form. The experimental electron density was refined using the Hansen-Coppens multipolar model and an alternative modeling, based on spherical atoms and additional charges on the covalent bonds and electron lone-pair sites. The crystallographic refinements, charge-density distributions, molecular electrostatic potentials, dipole moments and intermolecular interaction energies obtained from the different charge-density models were compared. The experimental results are also compared with the theoretical charge densities using theoretical structure factors obtained from periodic quantum calculations at the B3LYP/6-31G** level. A strong intermolecular O-H···O hydrogen bond connects molecules along the [001] direction. The deformation density maps show the resonance within the O=C-C=C-OH fragment and merged lone pair lobes on the hydroxyl O atom. This resonance is further confirmed by the analysis of charges and topology of the electron density.

17.
Acta Crystallogr C Struct Chem ; 70(Pt 1): 12-5, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-24399217

RESUMO

The title compound, [KCr(C2O2)2(C6H8N2)]n, was obtained from aqueous solution and analyzed with single-crystal X-ray diffraction at 100 K. It crystallizes in the monoclinic space group C2/c and displays a three-dimensional polymeric architecture built up by bimetallic oxalate-bridged Cr(III)-K helical chains linked through centrosymmetric K2O2 units to yield a sheet-like alternating P/M arrangement which looks like that of the previously described two-dimensional [NaCr(ox)2(pyim)(H2O)]·2H2O [pyim is 2-(pyridin-2-yl)imidazole; Lei et al. (2006). Inorg. Chem. Commun. 9, 486-488]. The Cr(III) ions in each helix have the same chirality. The infinite neutral sheets are eclipsed with respect to each other and are held together by a hydrogen-bonding network involving 2-(aminomethyl)pyridine H atoms and oxalate O atoms. Each sheet gives rise to channels of Cr4K4 octanuclear rings and each resultant hole is occupied by a pair of 2-(aminomethyl)pyridine ligands with partial overlap. The shortest Cr...Cr distance [5.593 (4) Å] is shorter than usually observed in the K-M(III)-oxalate family.

18.
J Phys Chem A ; 117(51): 14267-75, 2013 Dec 27.
Artigo em Inglês | MEDLINE | ID: mdl-24286247

RESUMO

Bromoethyl sulfonium trifluoromethanesulfonate is a salt complex in which a sulfur atom makes three covalent bonds. This molecule has been proved to act as an efficient annulation reagent which results in formation of synthetically challenging and pharmaceutically important 4-, 5-, 6-, and 7-membered heterocycles in excellent yields. The charge density of the molecule was determined from both experimentally and theoretically derived diffraction data. The stereochemistry and electron density topology of the sulfonium group was analyzed. To understand the chemical reactivity of the molecule, the electrostatic potential difference between the two carbon atoms of the bromoethyl group was investigated. It has been considered that the hydrogen atoms on the carbon atom bound to sulfur are more acidic in character due to their vicinity with the triply covalently bonded positively charged sulfur atom. The electropositivity of the S-attached and Br-attached methylene groups are compared in the experimental and theoretical charge densities using topological atomic charges and electrostatic potential at the molecular surface.


Assuntos
Hidrocarbonetos Bromados/química , Mesilatos/química , Compostos de Sulfônio/química , Cristalografia por Raios X , Compostos Heterocíclicos de 4 ou mais Anéis/síntese química , Estrutura Molecular , Teoria Quântica , Eletricidade Estática , Termodinâmica
19.
BMC Res Notes ; 6: 308, 2013 Aug 02.
Artigo em Inglês | MEDLINE | ID: mdl-23915572

RESUMO

BACKGROUND: Hydrogen atoms represent about half of the total number of atoms in proteins and are often involved in substrate recognition and catalysis. Unfortunately, X-ray protein crystallography at usual resolution fails to access directly their positioning, mainly because light atoms display weak contributions to diffraction. However, sub-Ångstrom diffraction data, careful modeling and a proper refinement strategy can allow the positioning of a significant part of hydrogen atoms. RESULTS: A comprehensive study on the X-ray structure of the diisopropyl-fluorophosphatase (DFPase) was performed, and the hydrogen atoms were modeled, including those of solvent molecules. This model was compared to the available neutron structure of DFPase, and differences in the protein and the active site solvation were noticed. CONCLUSIONS: A further examination of the DFPase X-ray structure provides substantial evidence about the presence of an activated water molecule that may constitute an interesting piece of information as regard to the enzymatic hydrolysis mechanism.


Assuntos
Hidrogênio/análise , Hidrolases de Triester Fosfórico/química , Proteínas/química , Difração de Raios X/métodos , Domínio Catalítico , Modelos Moleculares , Conformação Proteica , Água/química
20.
Artigo em Inglês | MEDLINE | ID: mdl-24426991

RESUMO

In the title compound, [CaCs2(C2O4)2(H2O)4] n , the Ca(2+) ion, lying on a twofold rotation axis, is coordinated by four O atoms from two oxalate ligands and two bridging water mol-ecules in an octa-hedral geometry. The Cs(+) ion is coordinated by seven O atoms from six oxalate ligands, one bridging water and one terminal water mol-ecule. The oxalate ligand displays a scarce high denticity. The structure contains parallel chain units runnig along [10-1], formed by two edge-sharing Cs polyhedra connected by CsO9 polyhedra connected by a face-sharing CaO6 octahedron. These chains are further linked by the oxalate ligands to build up a three-dimensional framework. O-H⋯O hydrogen bonds involving the water mol-ecules and the carboxyl-ate O atoms enhance the extended structure.

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