Electron density in the water molecule in α-oxalic and dihydrate and the nature of short hydrogen bonds

Stevens, Edwin D.; Coppens, Philip; Feld, R.; Lehmann, M. S.

doi:10.1016/0009-2614(79)85224-0

Cited by 10 publications

(6 citation statements)

References 6 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…In this work, three organic systems were selected for testing: urea, oxalic acid dihydrate and 9,10-bis-diphenylthio-phosphoranylanthraceneÁtoluene (SPAnPS). Urea and oxalic acid dihydrate have been used in many studies on accurate refinements with aspherical atom models, and for electron density distributions in crystals (Stevens et al, 1979;Stevens & Coppens, 1980;Zobel et al, 1993;Krijn et al, 1988;Swaminathan et al, 1984;Gatti et al, 1994;Birkedal et al, 2004;Jayatilaka & Dittrich, 2008;Pisani et al, 2011;Wall, 2016). Urea and oxalic acid are small polar organic molecules, which makes testing them relatively easy with, in general, computationally demanding methods such as GAR.…”

Section: Investigated Structuresmentioning

confidence: 99%

Hirshfeld atom like refinement with alternative electron density partitions

Chodkiewicz

Woińska

Woźniak

2020

IUCrJ

View full text Add to dashboard Cite

Hirshfeld atom refinement is one of the most successful methods for the accurate determination of structural parameters for hydrogen atoms from X-ray diffraction data. This work introduces a generalization of the method [generalized atom refinement (GAR)], consisting of the application of various methods of partitioning electron density into atomic contributions. These were tested on three organic structures using the following partitions: Hirshfeld, iterative Hirshfeld, iterative stockholder, minimal basis iterative stockholder and Becke. The effects of partition choice were also compared with those caused by other factors such as quantum chemical methodology, basis set, representation of the crystal field and a combination of these factors. The differences between the partitions were small in terms of R factor (e.g. much smaller than for refinements with different quantum chemistry methods, i.e. Hartree–Fock and coupled cluster) and therefore no single partition was clearly the best in terms of experimental data reconstruction. In the case of structural parameters the differences between the partitions are comparable to those related to the choice of other factors. We have observed the systematic effects of the partition choice on bond lengths and ADP values of polar hydrogen atoms. The bond lengths were also systematically influenced by the choice of electron density calculation methodology. This suggests that GAR-derived structural parameters could be systematically improved by selecting an optimal combination of the partition and quantum chemistry method. The results of the refinements were compared with those of neutron diffraction experiments. This allowed a selection of the most promising partition methods for further optimization of GAR settings, namely the Hirshfeld, iterative stockholder and minimal basis iterative stockholder.

show abstract

Section: Investigated Structuresmentioning

confidence: 99%

Hirshfeld atom like refinement with alternative electron density partitions

Chodkiewicz

Woińska

Woźniak

2020

IUCrJ

View full text Add to dashboard Cite

show abstract

“…The spherical atomic electron densities usually used in charge density work are the analytical Hartree-Fock limit functions from Clementi238 or the more recent compilation by Clementi and Roetti.239 Computation of (r2) using these functions is straightforward and the results have been tabulated, along with other radial expectation values, by Boyd.240 Using these quantities we can readily obtain second moments of the total molecular electron distribution; e.g. for pzz Mzz(Ptot) = + V3 X (1-2^spherical atom (32) atoms a…”

Section: In the Expressionmentioning

confidence: 99%

Molecular electric moments from x-ray diffraction data

Spackman¹

1992

Chem. Rev.

183

128

View full text Add to dashboard Cite

“…The choice of oxalic acid has many advantages including facile crystal growth and high suitability for charge density measurements. Oxalic acid crystals were studied using X-ray diffraction by Stevens et al (1979) and later by Coppens and many others groups (Stevens & Coppens, 1980;Dam et al, 1983;Coppens et al, 1984;Zobel et al, 1992). An interesting electron density study was reported by Martin & Pinkerton (1998) which was the first application of CCD detectors for experimental electron density studies.…”

Section: Introductionmentioning

confidence: 99%

On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

Sanjuan-Szklarz

Woińska

Domagała

et al. 2020

IUCrJ

View full text Add to dashboard Cite

X-ray diffraction is the main source of three-dimensional structural information. In total, more than 1.5 million crystal structures have been refined and deposited in structural databanks (PDB, CSD and ICSD) to date. Almost 99.7% of them were obtained by approximating atoms as spheres within the independent atom model (IAM) introduced over a century ago. In this study, X-ray datasets for single crystals of hydrated α-oxalic acid were refined using several alternative electron density models that abandon the crude spherical approximation: the multipole model (MM), the transferable aspherical atom model (TAAM) and the Hirshfeld atom refinement (HAR) model as a function of the resolution of X-ray data. The aspherical models (MM, TAAM, HAR) give far more accurate and precise single-crystal X-ray results than IAM, sometimes identical to results obtained from neutron diffraction and at low resolution. Hence, aspherical approaches open new routes for improving existing structural information collected over the last century.

show abstract

Electron density in the water molecule in α-oxalic and dihydrate and the nature of short hydrogen bonds

Cited by 10 publications

References 6 publications

Hirshfeld atom like refinement with alternative electron density partitions

Hirshfeld atom like refinement with alternative electron density partitions

Molecular electric moments from x-ray diffraction data

On the accuracy and precision of X-ray and neutron diffraction results as a function of resolution and the electron density model

Contact Info

Product

Resources

About