Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

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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“…The TLS+INV approach35 provides a generally applicable and convenient open‐source solution to estimate such H‐ADPs.…”

Section: Discussionmentioning

confidence: 99%

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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“…To display the ESP directly after crystallographic least-squares structure refinement, the program SHELXLE [61] can call the APD-Toolkit [58] that assigns charges and writes a pqr file. To display the ESP directly after crystallographic least-squares structure refinement, the program SHELXLE [61] can call the APD-Toolkit [58] that assigns charges and writes a pqr file.…”

Section: Ac Onvenient Procedures To Obtainmolecularespsmentioning

confidence: 99%

“…To obtain scattering factors, the UBDB relies on quantum-chemical DFT single-point energy computations for selected crystal structures, which provide electron densities that are projected onto the multipole model and averaged. Benefits include being able to continuously add scattering factors to the database without modifying earlier entries and the estimation of the anisotropic displacement parameters of hydrogen atoms, [58] all from the same model compounds. [69] We consider the established empirical rules for transferability by selecting model compounds and their geometry optimization (as used in the invariom database) more suitable for generating scattering factors and for averaging to obtain RESP charges alike.…”

Section: Point Charges From Invariom-database Model Compoundsmentioning

confidence: 99%

“…We provide tools that allow the ESP mapped on am olecular surface to be obtained within seconds, for example, from coordinates provided by ac onventional crystal-structure determination. To display the ESP directly after crystallographic least-squares structure refinement, the program SHELXLE [61] can call the APD-Toolkit [58] that assigns charges and writes a pqr file. The program ESP-MCQ then reads this pqr file and calculates the molecular ESP mapped on the van der Waals-like surface.…”

Section: Ac Onvenient Procedures To Obtainmolecularespsmentioning

confidence: 99%

“…[69] We consider the established empirical rules for transferability by selecting model compounds and their geometry optimization (as used in the invariom database) more suitable for generating scattering factors and for averaging to obtain RESP charges alike. Benefits include being able to continuously add scattering factors to the database without modifying earlier entries and the estimation of the anisotropic displacement parameters of hydrogen atoms, [58] all from the same model compounds. There are also experimental scattering-factor databases that rely on averaging, [70] but due to their experimental nature these are not further considered here.…”

Section: Point Charges From Invariom-database Model Compoundsmentioning

confidence: 99%

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Molecular Electrostatic Potentials from Invariom Point Charges

2016

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A set of look-up point charges for generating molecular electrostatic potentials is provided. The set relies on atom classification of the invariom database, which has already been applied to assign aspherical scattering factors in single-crystal X-ray diffraction. The focus of the investigation is on improving the accuracy of electrostatic potentials calculated by using tabulated point charges. In this respect, the performance of invariom point charges is compared with 1) those from a restrained fit to the electrostatic potential directly following quantum-chemical DFT computations, 2) semi-empirical AM1-bcc charges, and 3) conceptually similar TPACM4 look-up charges. Invariom classification gives charges that perform better than those from TPACM4, although tabulated charges remain inferior to those from molecule-specific computations. Point-charge electrostatic potentials also agree favorably with those from charge-density studies on the basis of X-ray experiments, without requiring the considerable effort of the latter.

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The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting

Grabowsky

Genoni

Thomas

et al. 2020

21st Century Challenges in Chemical Crystallography II

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X-ray diffraction experiments contain much more information than the information usually exploited for structure determination. In quantum crystallography, quantum mechanical wavefunctions are used to extract that information about bonding and properties from the measured X-ray structure factors. Here we show how quantum mechanically derived structure factors and atomic form factors are constructed to allow the improved description of the diffraction experiment. Subsequently, we discuss the basics and the applications of the advanced structure refinement method Hirshfeld Atom Refinement and of the X-ray constrained wavefunction fitting technique.

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Estimating temperature-dependent anisotropic hydrogen displacements with the invariom database and a new segmented rigid-body analysis program

Cited by 11 publications

References 56 publications

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

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

Molecular Electrostatic Potentials from Invariom Point Charges

The Advent of Quantum Crystallography: Form and Structure Factors from Quantum Mechanics for Advanced Structure Refinement and Wavefunction Fitting

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