scholarly journals Extracting Extremely Localized Molecular Orbitals from X-ray Diffraction Data

2014 ◽  
Vol 70 (a1) ◽  
pp. C284-C284 ◽  
Author(s):  
Alessandro Genoni

The accurate determination of electron densities in crystals from high-resolution X-ray diffraction data has become more and more important over the years. The existing techniques to accomplish this task can be subdivided into two great families: the multipole models and the wave function-based strategies. The former, which are the most widely used, are essentially linear scaling and allow an easy chemical interpretation of the obtained molecular charge densities, but they are also characterized by some drawbacks, such as the possible presence of unphysical negative regions in the resulting electron distributions. On the contrary, the latter always provide quantum mechanically rigorous electron densities, but they are more computationally expensive and, above all, the ease of chemical interpretation is almost completely lost. In this context, in order to combine the easy chemical interpretability of the multipole models with the quantum mechanical rigor of the wave-function based methods, we have recently extended the X-ray constrained wave function approach proposed by Jayatilaka in the framework of a quantum chemistry technique for the a priori determination of Extremely Localized Molecular Orbitals (ELMOs), namely we have developed a new strategy that allows to extract from X-ray diffraction data a single Slater determinant built up wit Molecular Orbitals strictly localized on small molecular fragments (e.g., atoms, bonds or functional groups). Preliminary tests have shown that the determination of X-ray constrained ELMOs is really straightforward. Furthermore, given the reliable transferability of the obtained Molecular Orbitals, we are constructing new ELMOs databases that can be used as alternative to the existing pseudo-atoms libraries for refining crystallographic structures and electron distributions of large systems. A detailed comparison between the new technique and the multipole models is also currently under investigation.

2014 ◽  
Vol 70 (6) ◽  
pp. 532-551 ◽  
Author(s):  
Leonardo H. R. Dos Santos ◽  
Alessandro Genoni ◽  
Piero Macchi

The recently developed X-ray constrained extremely localized molecular orbital (XC-ELMO) technique is a potentially useful tool for the determination and analysis of experimental electron densities. Molecular orbitals strictly localized on atoms, bonds or functional groups allow one to combine the quantum-mechanical rigour of the wavefunction-based approaches with the easy chemical interpretability typical of the traditional multipole models. In this paper, using very high quality X-ray diffraction data for the glycylglycine crystal, a detailed assessment of the capabilities and limitations of this new method is given. In particular, the effects of constraining the ELMO wavefunctions to experimental X-ray structure-factor amplitudes and the ability of the method to reproduce benchmark electron distributions have been accurately investigated. Topological analysis of the XC-ELMO electron densities and of the zero-flux surface-integrated charges and dipole moments shows that the new strategy is already reliable, provided that sufficiently flexible basis sets are used. These analyses also raise new questions and call for further improvements of the method.


2005 ◽  
Vol 38 (1) ◽  
pp. 232-236 ◽  
Author(s):  
Riccardo Bianchi ◽  
Alessandra Forni

VALTOPOis a program for the multipole refinement of accurate X-ray diffraction data and for the determination of electrostatic properties. It is a new version ofVALRAY, including the quantum theory of atoms in molecules analysis as implemented in theTOPOND98program. Two test structures, L-alanine and the complex of (E)-1,2-bis(4-pyridyl)ethylene with 1,4-diiodotetrafluorobenzene, have been analysed in order to illustrate some of the potentialities of the program.


1999 ◽  
Vol 55 (11) ◽  
pp. 1914-1916 ◽  
Author(s):  
F. A. V. Seixas ◽  
W. F. de Azevedo ◽  
M. F. Colombo

In this work, initial crystallographic studies of human haemoglobin (Hb) crystallized in isoionic and oxygen-free PEG solution are presented. Under these conditions, functional measurements of the O2-linked binding of water molecules and release of protons have evidenced that Hb assumes an unforeseen new allosteric conformation. The determination of the high-resolution structure of the crystal of human deoxy-Hb fully stripped of anions may provide a structural explanation for the role of anions in the allosteric properties of Hb and, particularly, for the influence of chloride on the Bohr effect, the mechanism by which Hb oxygen affinity is regulated by pH. X-ray diffraction data were collected to 1.87 Å resolution using a synchrotron-radiation source. Crystals belong to the space group P21212 and preliminary analysis revealed the presence of one tetramer in the asymmetric unit. The structure is currently being refined using maximum-likelihood protocols.


IUCrData ◽  
2019 ◽  
Vol 4 (11) ◽  
Author(s):  
Artem V. Malin ◽  
Sergei I. Ivlev ◽  
Roman V. Ostvald ◽  
Florian Kraus

Single crystals of rubidium tetrafluoridobromate(III), RbBrF4, were grown by melting and recrystallizing RbBrF4 from its melt. This is the first determination of the crystal structure of RbBrF4 using single-crystal X-ray diffraction data. We confirmed that the structure contains square-planar [BrF4]− anions and rubidium cations that are coordinated by F atoms in a square-antiprismatic manner. The compound crystallizes in the KBrF4 structure type. Atomic coordinates and bond lengths and angles were determined with higher precision than in a previous report based on powder X-ray diffraction data [Ivlev et al. (2015). Z. Anorg. Allg. Chem. 641, 2593–2598].


2020 ◽  
Vol 105 (3) ◽  
pp. 353-362
Author(s):  
Katarzyna Luberda-Durnaś ◽  
Marek Szczerba ◽  
Małgorzata Lempart ◽  
Zuzanna Ciesielska ◽  
Arkadiusz Derkowski

Abstract The primary aim of this study was the accurate determination of unit-cell parameters and description of disorder in chlorites with semi-random stacking using common X-ray diffraction (XRD) data for bulk powder samples. In the case of ordered chlorite structures, comprehensive crystallographic information can be obtained based on powder XRD data. Problems arise for samples with semi-random stacking, where due to strong broadening of hkl peaks with k ≠ 3n, the determination of unit-cell parameters is demanding. In this study a complete set of information about the stacking sequences in chlorite structures was determined based on XRD pattern simulation, which included determining a fraction of layers shifted by ±1/3b, interstratification with different polytypes and 2:1 layer rotations. A carefully selected series of pure Mg-Fe tri-trioctahedral chlorites with iron content in the range from 0.1 to 3.9 atoms per half formula unit cell was used in the study. In addition, powder XRD patterns were carefully investigated for the broadening of the odd-number basal reflections to determine interstratification of 14 and 7 Å layers. These type of interstratifications were finally not found in any of the samples. This result was also confirmed by the XRD pattern simulations, assuming interstratification with R0 ordering. Based on h0l XRD reflections, all the studied chlorites were found to be the IIbb polytype with a monoclinic-shaped unit cell (β ≈ 97°). For three samples, the hkl reflections with k ≠ 3n were partially resolvable; therefore, a conventional indexing procedure was applied. Two of the chlorites were found to have a monoclinic cell (with α, γ = 90°). Nevertheless, among all the samples, the more general triclinic (pseudomonoclinic) crystal system with symmetry C1 was assumed, to calculate unit-cell parameters using Le Bail fitting. A detailed study of semi-random stacking sequences shows that simple consideration of the proportion of IIb-2 and IIb-4/6 polytypes, assuming equal content of IIb-4 and IIb-6, is not sufficient to fully model the stacking structure in chlorites. Several, more general, possible models were therefore considered. In the first approach, a parameter describing a shift into one of the ±1/3b directions (thus, the proportion of IIb-4 and IIb-6 polytypes) was refined. In the second approach, for samples with slightly distinguishable hkl reflections with k ≠ 3n, some kind of segregation of individual polytypes (IIb-2/4/6) was considered. In the third approach, a model with rotations of 2:1 layers about 0°, 120°, 240° was shown to have the lowest number of parameters to be optimized and therefore give the most reliable fits. In all of the studied samples, interstratification of different polytypes was revealed with the fraction of polytypes being different than IIbb ranging from 5 to 19%, as confirmed by fitting of h0l XRD reflections.


2009 ◽  
Vol 98 (6) ◽  
pp. 2113-2121 ◽  
Author(s):  
Minakshi Asnani ◽  
K. Vyas ◽  
Apurba Bhattacharya ◽  
Surya Devarakonda ◽  
Santu Chakraborty ◽  
...  

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