Theoretically derived thermodynamic properties can be improved by the refinement of low-frequency modes against X-ray diffraction data

2021 ◽  
Author(s):  
Anna Agnieszka Hoser ◽  
Marcin Sztylko ◽  
Damian Trzybiński ◽  
Anders Østergaard Madsen
Keyword(s):  
Thermodynamic Properties ◽  
Dft Calculations ◽  
Diffraction Data ◽  
Molecular Crystals ◽  
Low Frequency ◽  
X Ray Diffraction ◽  
X Ray ◽  
Efficient Approach

A framework for estimation of thermodynamic properties for molecular crystals via refinement of frequencies from DFT calculations against X-ray diffraction data is presented. The framework provides an efficient approach to...

scholarly journals X-ray diffraction data as a source of the vibrational free-energy contribution in polymorphic systems

IUCrJ ◽  
2019 ◽  
Vol 6 (4) ◽  
pp. 558-571 ◽  
Author(s):  
Phillip Miguel Kofoed ◽  
Anna A. Hoser ◽  
Frederik Diness ◽  
Silvia C. Capelli ◽  
Anders Østergaard Madsen
Keyword(s):  
Thermodynamic Properties ◽  
Normal Mode ◽  
Diffraction Data ◽  
High Frequency ◽  
Low Frequency ◽  
General Question ◽  
Vibrational Entropy ◽  
X Ray Diffraction ◽  
X Ray ◽  
High Frequency Modes

In this contribution we attempt to answer a general question: can X-ray diffraction data combined with theoretical computations be a source of information about the thermodynamic properties of a given system? Newly collected sets of high-quality multi-temperature single-crystal X-ray diffraction data and complementary periodic DFT calculations of vibrational frequencies and normal mode vectors at the Γ point on the yellow and white polymorphs of dimethyl 3,6-dichloro-2,5-dihydroxyterephthalate are combined using two different approaches, aiming to obtain thermodynamic properties for the two compounds. The first approach uses low-frequency normal modes extracted from multi-temperature X-ray diffraction data (normal coordinate analysis), while the other uses DFT-calculated low-frequency normal mode in the refinement of the same data (normal mode refinement). Thermodynamic data from the literature [Yang et al. (1989), Acta Cryst. B45, 312–323] and new periodic ab initio DFT supercell calculations are used as a reference point. Both approaches tested in this work capture the most essential features of the systems: the polymorphs are enantiotropically related, with the yellow form being the thermodynamically stable system at low temperature, and the white form at higher temperatures. However, the inferred phase transition temperature varies between different approaches. Thanks to the application of unconventional methods of X-ray data refinement and analysis, it was additionally found that, in the case of the yellow polymorph, anharmonicity is an important issue. By discussing contributions from low- and high-frequency modes to the vibrational entropy and enthalpy, the importance of high-frequency modes is highlighted. The analysis shows that larger anisotropic displacement parameters are not always related to the polymorph with the higher vibrational entropy contribution.

A combined model of electron density and lattice dynamics refined against elastic diffraction data. Thermodynamic properties of crystalline L-alanine

2020 ◽  
Vol 76 (1) ◽  
pp. 32-44 ◽  
Author(s):  
Ioana Sovago ◽  
Anna A. Hoser ◽  
Anders Ø. Madsen
Keyword(s):  
Dft Calculations ◽  
Electron Density ◽  
Normal Mode ◽  
Diffraction Data ◽  
Lattice Dynamics ◽  
Phonon Dispersion ◽  
Form Factors ◽  
X Ray Diffraction ◽  
Crystalline Materials ◽  
X Ray

Thermodynamic stability is an essential property of crystalline materials, and its accurate calculation requires a reliable description of the thermal motion – phonons – in the crystal. Such information can be obtained from periodic density functional theory (DFT) calculations, but these are costly and in some cases insufficiently accurate for molecular crystals. This deficiency is addressed here by refining a lattice-dynamics model, derived from DFT calculations, against accurate high-resolution X-ray diffraction data. For the first time, a normal-mode refinement is combined with the refinement of aspherical atomic form factors, allowing a comprehensive description and physically meaningful deconvolution of thermal motion and static charge density in the crystal. The small and well diffracting L-alanine system was used. Different lattice-dynamics models, with or without phonon dispersion, and derived from different levels of theory, were tested, and models using spherical and aspherical form factors were compared. The refinements indicate that the vibrational information content in the 23 K data is too small to study lattice dynamics, whereas the 123 K data appear to hold information on the acoustic and lowest-frequency optical phonons. These normal-mode models show slightly larger refinement residuals than their counterparts using atomic displacement parameters, and these features are not removed by considering phonon dispersion in the model. The models refined against the 123 K data, regardless of their sophistication, give calculated heat capacities for L-alanine within less than 1 cal mol−1 K−1 of the calorimetric measurements, in the temperature range 10–300 K. The findings show that the normal-mode refinement method can be combined with an elaborate description of the electron density. It appears to be a promising technique for free-energy determination for crystalline materials at the expense of performing a single-crystal elastic X-ray diffraction determination combined with periodic DFT calculations.

scholarly journals Spatially Resolving Anharmonic Lattice Dynamics in Molecular Crystals With X-Ray Diffraction and Terahertz Spectroscopy

2019 ◽  
Author(s):  
Martin Hutereau ◽  
Peter Banks ◽  
Ben Slater ◽  
J. Axel Zeitler ◽  
Andrew Bond ◽  
...  
Keyword(s):  
Terahertz Spectroscopy ◽  
Molecular Crystals ◽  
Low Frequency ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Terahertz Time Domain Spectroscopy ◽  
X Ray ◽  
Anharmonic Lattice ◽  
Thermal Displacements ◽  
The Relationship

<div><div><div><div><p>The combination of X-ray diffraction and low-frequency vibrational spectroscopy has proven to be a powerful method for understanding the relationship between molecular and crystalline structures, dynamics, and the properties of materials. In this work, we show how information obtained from terahertz time-domain spectroscopy (THz-TDS) measurements, coupled with first-principles simulations including anharmonic effects, is able to reconcile specific vibrational motions to the experimentally observed large- amplitude thermal displacements in a pair of isomeric molecular crystals. In particular, we show that a single terahertz mode is responsible for the observed structural data, and provide a framework for predicting and interpreting the origins of related phenomena.</p></div></div></div></div>

Application of the Volterra filter in experimental diffraction data processing

Open Physics ◽  
2003 ◽  
Vol 1 (3) ◽  
Author(s):  
Stanislav Jurečka ◽  
Mária Jurečková
Keyword(s):  
Diffraction Data ◽  
High Frequency ◽  
Digital Filters ◽  
Low Frequency ◽  
Frequency Noise ◽  
X Ray Diffraction ◽  
Volterra Type ◽  
X Ray ◽  
Effective Signal

AbstractThe effective signal in x-ray diffraction analysis of material properties often contains high frequency (noise) and low frequency (trend) components as additive parts. It is necessary to extract the effective signal from the noise to ensure high quality of signal processing. Digital filters of Volterra type are proposed for filtering purposes and a comparison of Volterra filtration implemented on x-ray diffraction data versus results from a set of other digital filters is given.

Dipole Moment Enhancement in Molecular Crystals from X-ray Diffraction Data

ChemPhysChem ◽  
2007 ◽  
Vol 8 (14) ◽  
pp. 2051-2063 ◽  
Author(s):  
Mark A. Spackman ◽  
Parthapratim Munshi ◽  
Birger Dittrich
Keyword(s):  
Dipole Moment ◽  
Diffraction Data ◽  
Molecular Crystals ◽  
X Ray Diffraction ◽  
X Ray

scholarly journals Resolving Anharmonic Lattice Dynamics in Molecular Crystals With X-Ray Diffraction and Terahertz Spectroscopy

2019 ◽  
Author(s):  
Martin Hutereau ◽  
Peter Banks ◽  
Ben Slater ◽  
J. Axel Zeitler ◽  
Andrew Bond ◽  
...  
Keyword(s):  
Terahertz Spectroscopy ◽  
Molecular Crystals ◽  
Low Frequency ◽  
Structural Data ◽  
X Ray Diffraction ◽  
Terahertz Time Domain Spectroscopy ◽  
X Ray ◽  
Anharmonic Lattice ◽  
Thermal Displacements ◽  
The Relationship

<div><div><div><div><p>The combination of X-ray diffraction and low-frequency vibrational spectroscopy has proven to be a powerful method for understanding the relationship between molecular and crystalline structures, dynamics, and the properties of materials. In this work, we show how information obtained from terahertz time-domain spectroscopy (THz-TDS) measurements, coupled with first-principles simulations including anharmonic effects, is able to reconcile specific vibrational motions to the experimentally observed large- amplitude thermal displacements in a pair of isomeric molecular crystals. In particular, we show that a single terahertz mode is responsible for the observed structural data, and provide a framework for predicting and interpreting the origins of related phenomena.</p></div></div></div></div>

scholarly journals High-pressure synthesis and crystal structure of the mixed-cation borate Ga4In4B15O33(OH)3

2019 ◽  
Vol 74 (4) ◽  
pp. 357-363
Author(s):  
Daniela Vitzthum ◽  
Hubert Huppertz
Keyword(s):  
Crystal Structure ◽  
High Pressure ◽  
High Temperature ◽  
Diffraction Data ◽  
X Ray Diffraction ◽  
Synthesis And Crystal Structure ◽  
X Ray ◽  
Mixed Cation ◽  
High Pressure High Temperature ◽  
Pressure Synthesis

AbstractThe mixed cation triel borate Ga4In4B15O33(OH)3 was synthesized in a Walker-type multianvil apparatus at high-pressure/high-temperature conditions of 12.5 GPa and 1300°C. Although the product could not be reproduced in further experiments, its crystal structure could be reliably determined via single-crystal X-ray diffraction data. Ga4In4B15O33(OH)3 crystallizes in the tetragonal space group I41/a (origin choice 2) with the lattice parameters a = 11.382(2), c = 15.244(2) Å, and V = 1974.9(4) Å3. The structure of the quaternary triel borate consists of a complex network of BO4 tetrahedra, edge-sharing InO6 octahedra in dinuclear units, and very dense edge-sharing GaO6 octahedra in tetranuclear units.

Crystallization and preliminary x-ray diffraction data of the cryptomonad biliprotein phycocyanin-645 from a Chroomonas spec.

1984 ◽  
Vol 140 (2-3) ◽  
pp. 202-205 ◽  
Author(s):  
Walter Morisset ◽  
Werner Wehrmeyer ◽  
Tilman Schirmer ◽  
Wolfram Bode
Keyword(s):  
Diffraction Data ◽  
X Ray Diffraction ◽  
X Ray

Single-crystal investigation of Ce5AgxGe4−x (x = 0.1−1.08) with Sm5Ge4 type

2020 ◽  
Vol 75 (8) ◽  
pp. 765-768
Author(s):  
Bohdana Belan ◽  
Dorota Kowalska ◽  
Mariya Dzevenko ◽  
Mykola Manyako ◽  
Roman Gladyshevskii
Keyword(s):  
Crystal Structure ◽  
Single Crystal ◽  
Diffraction Data ◽  
Binary Compound ◽  
Lattice Parameters ◽  
X Ray Diffraction ◽  
Space Group ◽  
X Ray

AbstractThe crystal structure of the phase Ce5AgxGe4−x (x = 0.1−1.08) has been determined using single-crystal X-ray diffraction data for Ce5Ag0.1Ge3.9. This phase is isotypic with Sm5Ge4: space group Pnma (No. 62), Pearson code oP36, Z = 4, a = 7.9632(2), b = 15.2693(5), c = 8.0803(2) Å; R1 = 0.0261, wR2 = 0.0460, 1428 F2 values and 48 variables. The two crystallographic positions 8d and 4c show Ge/Ag mixing, leading to a slight increase in the lattice parameters as compared to those of the pure binary compound Ce5Ge4.

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