Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory

Hoser, Anna A.; Madsen, Anders Ø.

doi:10.1107/s2053273315024699

Cited by 30 publications

(34 citation statements)

References 61 publications

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“…[172,173] In this approach,t he amplitudes of the acoustic and lowest-frequency opticalp honons are refineda gainstt he diffraction intensities. However,t he atomicm otion gives rise to changes in the diffraction intensities, which are taken into account in the form of the Debye-Waller factor.T he temporala nd spatiala verage of the atomic fluctuations-mean square displacements-can therefore be retrieved from ad iffraction measurement, and in recent work this information has been combined with lattice-dynamical models derived from periodic DFT calculations.…”

Section: Dynamicquantum Crystallographymentioning

confidence: 99%

“…However,t he atomicm otion gives rise to changes in the diffraction intensities, which are taken into account in the form of the Debye-Waller factor.T he temporala nd spatiala verage of the atomic fluctuations-mean square displacements-can therefore be retrieved from ad iffraction measurement, and in recent work this information has been combined with lattice-dynamical models derived from periodic DFT calculations. [172,173] In this approach,t he amplitudes of the acoustic and lowest-frequency opticalp honons are refineda gainstt he diffraction intensities. In the simplest model,t hesep honon modes are approximated by the motion at the Gamma point of the Brillouin zone.…”

Section: Dynamicquantum Crystallographymentioning

confidence: 99%

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Quantum Crystallography: Current Developments and Future Perspectives

Genoni

Bučinský

Claiser

et al. 2018

Chemistry A European J

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119

114

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Crystallography and quantum mechanics have always been tightly connected because reliable quantum mechanical models are needed to determine crystal structures. Due to this natural synergy, nowadays accurate distributions of electrons in space can be obtained from diffraction and scattering experiments. In the original definition of quantum crystallography (QCr) given by Massa, Karle and Huang, direct extraction of wavefunctions or density matrices from measured intensities of reflections or, conversely, ad hoc quantum mechanical calculations to enhance the accuracy of the crystallographic refinement are implicated. Nevertheless, many other active and emerging research areas involving quantum mechanics and scattering experiments are not covered by the original definition although they enable to observe and explain quantum phenomena as accurately and successfully as the original strategies. Therefore, we give an overview over current research that is related to a broader notion of QCr, and discuss options how QCr can evolve to become a complete and independent domain of natural sciences. The goal of this paper is to initiate discussions around QCr, but not to find a final definition of the field.

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Section: Dynamicquantum Crystallographymentioning

confidence: 99%

Section: Dynamicquantum Crystallographymentioning

confidence: 99%

Quantum Crystallography: Current Developments and Future Perspectives

Genoni

Bučinský

Claiser

et al. 2018

Chemistry A European J

Self Cite

119

114

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“…Normal mode refinement. We used the NoMoRe Python program, which is described in the first paper of this series (Hoser & Madsen, 2016). For each data set, we specified the number of frequencies that should be refined along with the measurement temperature.…”

Section: Computational Detailsmentioning

confidence: 99%

“…Therefore, we checked the percentage contribution of a given normal mode frequency to the mean-square displacements. As explained in detail in the first paper in this series (Hoser & Madsen, 2016), the contribution of a given normal mode to the U eq can be judged by summing up the U eq values weighted by their atomic numbers and divided by the total sum for all modes. Table 1 Refinement statistics and indicators for all IAM (first column) and normal mode models for tested data sets.…”

Section: Which Modes Can Be Refined?mentioning

confidence: 99%

“…In a previous paper (Hoser & Madsen, 2016) we have introduced this new approach (Normal Mode Refinement, NoMoRe), which enables the calculation of thermodynamic properties. The frequencies used to calculate the thermodynamic properties are obtained from ab initio latticedynamical models, which are refined against elastic X-ray diffraction data.…”

Section: Introductionmentioning

confidence: 99%

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Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. II. Applications to L-alanine, naphthalene and xylitol

Hoser

Madsen

2017

Acta Cryst Sect A

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In the first paper of this series [Hoser & Madsen (2016). Acta Cryst. A72, 206-214], a new approach was introduced which enables the refinement of frequencies of normal modes obtained from ab initio periodic computations against single-crystal diffraction data. In this contribution, the performance of this approach is tested by refinement against data in the temperature range from 23 to 205 K on the molecular crystals of L-alanine, naphthalene and xylitol. The models, which are lattice-dynamical models derived at the Γ point of the Brillouin zone, are able to describe the atomic vibrations of L-alanine and naphthalene to a level where the residual densities are similar to those obtained from the independent atom model. For the more flexible molecule xylitol, larger deviations are found. Hydrogen ADPs (anisotropic displacement parameters) derived from the models are in similar or better agreement with neutron diffraction results than ADPs obtained by other procedures. The heat capacity calculated after normal mode refinement for naphthalene is in reasonable agreement with the heat capacity obtained from calorimetric measurements (to less than 1 cal mol K below 300 K), with deviations at higher temperatures indicating anharmonicity. Standard uncertainties and correlation of the refined parameters have been derived based on a Monte Carlo procedure. The uncertainties are quite small and probably underestimated.

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Accurate Bond Lengths to Hydrogen Atoms from Single‐Crystal X‐ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

Dittrich

Lübben

Mebs

et al. 2017

Chemistry A European J

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Amino acid structures are an ideal test set for method‐development studies in crystallography. High‐resolution X‐ray diffraction data for eight previously studied genetically encoding amino acids are provided, complemented by a non‐standard amino acid. Structures were re‐investigated to study a widely applicable treatment that permits accurate X−H bond lengths to hydrogen atoms to be obtained: this treatment combines refinement of positional hydrogen‐atom parameters with aspherical scattering factors with constrained “TLS+INV” estimated hydrogen anisotropic displacement parameters (H‐ADPs). Tabulated invariom scattering factors allow rapid modeling without further computations, and unconstrained Hirshfeld atom refinement provides a computationally demanding alternative when database entries are missing. Both should incorporate estimated H‐ADPs, as free refinement frequently leads to over‐parameterization and non‐positive definite H‐ADPs irrespective of the aspherical scattering model used. Using estimated H‐ADPs, both methods yield accurate and precise X−H distances in best quantitative agreement with neutron diffraction data (available for five of the test‐set molecules). This work thus solves the last remaining problem to obtain such results more frequently. Density functional theoretical QM/MM computations are able to play the role of an alternative benchmark to neutron diffraction.

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Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. I. Theory

Cited by 30 publications

References 61 publications

Quantum Crystallography: Current Developments and Future Perspectives

Quantum Crystallography: Current Developments and Future Perspectives

Dynamic quantum crystallography: lattice-dynamical models refined against diffraction data. II. Applications to L-alanine, naphthalene and xylitol

Accurate Bond Lengths to Hydrogen Atoms from Single‐Crystal X‐ray Diffraction by Including Estimated Hydrogen ADPs and Comparison to Neutron and QM/MM Benchmarks

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