scholarly journals Further Validation of Quantum Crystallography Approaches

Molecules ◽  
2021 ◽  
Vol 26 (12) ◽  
pp. 3730
Author(s):  
Monika Wanat ◽  
Maura Malinska ◽  
Anna A. Hoser ◽  
Krzysztof Woźniak
Keyword(s):  
Charge Density ◽  
Theoretical Calculations ◽  
Geometrical Parameters ◽  
X Ray Diffraction ◽  
Low Resolution ◽  
Hydrogen Atoms ◽  
Model Compounds ◽  
X Ray ◽  
Density Distributions ◽  
Quantum Crystallography

Quantum crystallography is a fast-developing multidisciplinary area of crystallography. In this work, we analyse the influence of different charge density models (i.e., the multipole model (MM), Hirshfeld atom refinement (HAR), and the transferable aspherical atom model (TAAM)), modelling of the thermal motion of hydrogen atoms (anisotropic, isotropic, and with the aid of SHADE or NoMoRe), and the type of radiation used (Mo Kα and Cu Kα) on the final results. To achieve this aim, we performed a series of refinements against X-ray diffraction data for three model compounds and compared their final structures, geometries, shapes of ADPs, and charge density distributions. Our results were also supported by theoretical calculations that enabled comparisons of the lattice energies of these structures. It appears that geometrical parameters are better described (closer to the neutron values) when HAR is used; however, bonds to H atoms more closely match neutron values after MM or TAAM refinement. Our analysis shows the superiority of the NoMoRe method in the description of H-atom ADPs. Moreover, the shapes of the ADPs of H atoms, as well as their electron density distributions, were better described with low-resolution Cu Kα data in comparison to low-resolution Mo Kα data.

scholarly journals An analysis of the experimental and theoretical charge density distributions of the piroxicam–saccharin co-crystal and its constituents

RSC Advances ◽  
2016 ◽  
Vol 6 (85) ◽  
pp. 81578-81590 ◽  
Author(s):  
Jonathan J. Du ◽  
Linda Váradi ◽  
Peter A. Williams ◽  
Paul W. Groundwater ◽  
Jacob Overgaard ◽  
...  
Keyword(s):  
High Resolution ◽  
Dft Calculations ◽  
Charge Density ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Distributions ◽  
Multipole Refinement

Experimental and theoretical charge density of piroxicam, saccharin and their 1 : 1 co-crystal have been determined using high-resolution X-ray diffraction, multipole refinement and DFT calculations

Experimental charge density study on FLPs and a FLP reaction product

2018 ◽  
Vol 233 (9-10) ◽  
pp. 723-731
Author(s):  
Christian Joseph Schürmann ◽  
Regine Herbst-Irmer ◽  
Thorsten Lennart Teuteberg ◽  
Daniel Kratzert ◽  
Gerhard Erker ◽  
...  
Keyword(s):  
Charge Transfer ◽  
Charge Density ◽  
Theoretical Calculations ◽  
X Ray Diffraction ◽  
Charge Density Distribution ◽  
X Ray ◽  
Charge Densities ◽  
A Charge ◽  
Density Study ◽  
Experimental Charge Density

Abstract The charge density distribution of the intramolecular frustrated Lewis pair (FLP) Mes2PCH2CH2B(C6F5)2 (1), the phosphinimine HNPMes2CH2CH2B(C6F5)2 (2), as well as a FLP homologue with nitrogen NEt2CHPhCH2B(C6F5)2 (3) were investigated with Bader’s quantum theory of atoms in molecules (QTAIM). The charge densities were derived from both experimental high-resolution X-ray diffraction data (2, 3) and theoretical calculations (1, 3). The QTAIM analysis for the FLPs 1 and 3 showed the prominent B-pnictogen interaction to be weak dative bonds without significant charge-transfer. This holds also true for the B–N–bond of 2. The nitrogen atom is negatively charged, due to a charge transfer from phosphorous and shows features of a sp2-hybridization. The bond is therefore best described as a non-hypervalent Pδ+–Nδ− moiety.

Maximum Entropy Method Charge Density Distributions of Novel Thermoelectric Clathrates

1999 ◽  
Vol 590 ◽  
Author(s):  
B. Iversen ◽  
A. Bentien ◽  
A. Palmqvist ◽  
D. Bryan ◽  
S. Latturner ◽  
...  
Keyword(s):  
Thermal Conductivity ◽  
Charge Density ◽  
Maximum Entropy ◽  
Maximum Entropy Method ◽  
Mixed Valence ◽  
Entropy Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Distributions ◽  
Positively Charged

ABSTRACTRecently materials with promising thermoelectric properties were discovered among the clathrates. Transport data has indicated that these materials have some of the characteristics of a good thermoelectric, namely a low thermal conductivity and a high electrical conductivity. Based on synchrotron powder and conventional single crystal x-ray diffraction data we have determined the charge density distribution in Sr8Ga16Ge3O using the Maximum Entropy Method. The MEM density shows clear evidence of guest atom rattling, and this contributes to the reduction of the thermal conductivity. Analysis of the charge distribution reveals that Sr8Ga16Ge30 contains mixed valence alkaline earth guest atoms. The Sr atoms in the small cavities are, as expected, doubly positively charged, whereas the Sr atoms in the large cavities appear negatively charged. The MEM density furthermore suggests that the Ga and Ge atoms may not be randomly disordered on the framework sites as found in the conventional leastsquares refinements.

Charge density study of the first mixed-valent tetraphosphete

2014 ◽  
Vol 70 (a1) ◽  
pp. C1345-C1345
Author(s):  
Verena Breuers ◽  
Christian Lehmann ◽  
Walter Frank
Keyword(s):  
Charge Density ◽  
Theoretical Calculations ◽  
X Ray Diffraction ◽  
Ring Plane ◽  
X Ray ◽  
Coordination Behavior ◽  
Rhombic Distortion ◽  
Electrostatic Contribution ◽  
Density Study ◽  
Experimental Charge Density

The first λ3,λ5-tetraphosphete contains a 4π-electron four-membered ring as the central structural unit of a dispirocyclic system and can thus be classified as an analogue to diphosphetes and cyclodiphosphazenes. According to its crystal structure the central P4unit exhibits not only P–P bonds which are of equal length (P1–P2 2,139(1) Å, P1–P2A 2,142(1) Å), but also rhombic distortion (P1–P2–P1A 79,4(1)0, P2–P1–P2A 100,6(1)0).[1] Therefore its electronic structure cannot be described as 'Phosphacyclobutadiene' but either as a bis(ylide) or as a system with delocalized double bonds. After various quantum chemical calculations and an extensive examination of its reaction and coordination behavior failed to answer this question, we addressed the problem via a detailed analysis of its charge density distribution. The experimental charge density based on high resolution X-ray diffraction data collected at low temperature is determined by multipole least squares refinement using the program packageXD2006.[2] In a first step, the static deformation density exhibits charge density which is located mainly outside of the P4ring plane at the λ3-phosphorus atoms but simultaneously redistributed into the P–P bond area. In addition to that, a study of its topological properties and an inspection of the Laplacian of the electron density according to Bader's `Quantum Theory of Atoms in Molecules' (QTAIM)[3] further highlight the bonding features. They reveal polar Si–N, Si–C and P–N bonds with a decreasing amount of electrostatic contribution as well as four valence shell charge concentrations (thus sp3hybridization) at each of the phosphorus atoms. Finally supported by theoretical calculations, the results illustrate the unique bonding situation in the P4unit combining a high ylidic character with unusual not exclusively sigma-like P–P bonds.

scholarly journals Charge density studies of nucleobase analogues - the case of DAP and isocytosine

2014 ◽  
Vol 70 (a1) ◽  
pp. C968-C968
Author(s):  
Urszula Budniak ◽  
Katarzyna Jarzembska ◽  
Paulina Dominiak
Keyword(s):  
Nucleic Acids ◽  
Charge Density ◽  
Gas Phase ◽  
Crystal Packing ◽  
Theoretical Calculations ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Analysis ◽  
Modified Nucleobases ◽  
Comprehensive Study

Nucleobases belong to purine and pyrimidine family and constitute a biologically crucial group of compounds thank to their relation to nucleic acids. Specific interactions between these moieties are responsible for maintaining a proper structure of DNA, namely: hydrogen bonding and π-π stacking interactions (between aromatic ring fragments). Furthermore, many modifications of natural nucleobases serve as drugs, but some could be extremely harmful. In view of the above, investigating the properties of analogues of nucleobases may contribute to our knowledge about nucleic acid properties in general and give an opportunity to find novel ligands binding to DNA, what is essential for drug design. Within this project two modified nucleobases were examined: 2,6-diaminopurine (DAP) and isocytosine (iC). DAP is a derivative of the adenine and iC is an isomer of cytosine. These compounds do not appear naturally in nucleic acids, however, can be used to compare Watson-Crick pairing in DNA and pairing of alternative bases. High resolution X-ray diffraction experiments were carried out to obtain appropriate data for charge density analysis. A comprehensive study of crystal packing and energetic features of the analysed systems was conducted. The nature of intermolecular interactions, structural motifs and crystal packing was analysed via Hirshfeld surface analysis [1], charge density distribution examination, QTAIM (Quantum Theory of Atoms in Molecules) [2] and theoretical calculations (gas phase dimers and periodic). Implications of the observed interactions for biological systems are discussed. This study was supported by the Polish Ministry of Science and Higher Education within the Diamond Grant No DI 2011012441.

Nuclear and charge density distributions in ferroelectric PbTiO3: maximum entropy method analysis of neutron and X-ray diffraction data

2013 ◽  
Vol 28 (4) ◽  
pp. 276-280 ◽  
Author(s):  
Jinlong Zhu ◽  
Wei Han ◽  
Jianzhong Zhang ◽  
Hongwu Xu ◽  
Sven C. Vogel ◽  
...  
Keyword(s):  
Charge Density ◽  
Maximum Entropy ◽  
Maximum Entropy Method ◽  
Rietveld Analysis ◽  
Entropy Method ◽  
X Ray Diffraction ◽  
X Ray ◽  
Density Distributions ◽  
Increasing Temperature ◽  
Ionic States

We conducted in-situ high-temperature neutron and X-ray diffraction studies on tetragonal PbTiO3. Using a combination of Rietveld analysis and Maximum Entropy Method, the nuclear and charge density distributions were determined as a function of temperature up to 460 °C. The ionic states obtained from charge density distributions reveal that the covalency of Pb–O2 bonds gradually weakens with increasing temperature. The spontaneous polarizations calculated from the contributions of ionic state, ionic displacement, and nuclear polarization, are in good agreement with the experimental measurements. This method provides an effective approach to determine spontaneous polarizations in multiferroics with high-current leakage and low resistance.

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