Helium cryostat synchrotron charge densities determined using a large CCD detector – the upgraded beamline D3 at DESY

Morgenroth, Wolfgang; Overgaard, Jacob; Clausen, Henrik F.; Svendsen, Helle; Jørgensen, Mads Ry Vogel; Larsen, Finn; Iversen, Bo B.

doi:10.1107/s0021889808024643

Cited by 23 publications

(25 citation statements)

References 43 publications

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“…In general, the ADPs serve as a bin for uncorrected systematic errors in the experiments, and hence inaccurate data tend to show higher deviation between X‐ray and neutron ADPs 66. Comparing the ADPs of the 33 heavy atoms in 1 by using the program UIJXN leads to a mean deviation ${\left\langle {\Delta U} \right\rangle }$ of 0.00058 Å 2 ,67 which, for such a large system, is an excellent correspondence compared with other X/N studies 68. The hydrogen nuclear positions and ADPs, which are important in accurate ED modeling of hydrogen‐bonded systems such as 1 ,69 were therefore expected to be of excellent quality.…”

Section: Methodssupporting

confidence: 57%

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Clausen

Jørgensen

Cenedese

et al. 2014

Chemistry A European J

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X-ray/neutron (X/N) diffraction data measured at very low temperature (15 K) in conjunction with ab initio theoretical calculations were used to model the crystal charge density (CD) of the host-guest complex of hydroquinone (HQ) and acetonitrile. Due to pseudosymmetry, information about the ordering of the acetonitrile molecules within the HQ cavities is present only in almost extinct, very weak diffraction data, which cannot be measured with sufficient accuracy even by using the brightest X-ray and neutron sources available, and the CD model of the guest molecule was ultimately based on theoretical calculations. On the other hand, the CD of the HQ host structure is well determined by the experimental data. The neutron diffraction data provide hydrogen anisotropic thermal parameters and positions, which are important to obtain a reliable CD for this light-atom-only crystal. Atomic displacement parameters obtained independently from the X-ray and neutron diffraction data show excellent agreement with a |ΔU| value of 0.00058 Å(2) indicating outstanding data quality. The CD and especially the derived electrostatic properties clearly reveal increased polarization of the HQ molecules in the host-guest complex compared with the HQ molecules in the empty HQ apohost crystal structure. It was found that the origin of the increased polarization is inclusion of the acetonitrile molecule, whereas the change in geometry of the HQ host structure following inclusion of the guest has very little effect on the electrostatic potential. The fact that guest inclusion has a profound effect on the electrostatic potential suggests that nonpolarizable force fields may be unsuitable for molecular dynamics simulations of host-guest interaction (e.g., in protein-drug complexes), at least for polar molecules.

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Section: Methodssupporting

confidence: 57%

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Clausen

Jørgensen

Cenedese

et al. 2014

Chemistry A European J

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“…To our knowledge, Iversen et al (1996) were the first to demonstrate explicitly that, if low research papers 362 Silvia C. Capelli et al Hirshfeld atom refinement temperatures are used and if one is careful with the data analysis, then quantitative agreement between X-ray and neutron diffraction ADPs can be achieved for non-H atoms. In a recent update of this work similar conclusions were reached (Morgenroth et al, 2008).…”

Section: Introductionsupporting

confidence: 65%

“…Moreover, several of the values listed by Morgenroth et al (2008) are based on studies in which H-atom positions and ADPs were fixed to values derived from neutron experiments. By contrast, in this study all parameters are derived from the X-ray data only and without constraints to the neutron experiment.…”

mentioning

confidence: 99%

Hirshfeld Atom Refinement

Grabowsky

Woinska

Jayatilaka

2016

Journal of the Crystallographic Society of Japan

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Hirshfeld atom refinement (HAR) is a method which determines structural parameters from single-crystal X-ray diffraction data by using an aspherical atom partitioning of tailor-made ab initio quantum mechanical molecular electron densities without any further approximation. Here the original HAR method is extended by implementing an iterative procedure of successive cycles of electron density calculations, Hirshfeld atom scattering factor calculations and structural least-squares refinements, repeated until convergence. The importance of this iterative procedure is illustrated via the example of crystalline ammonia. The new HAR method is then applied to X-ray diffraction data of the dipeptide Gly-l-Ala measured at 12, 50, 100, 150, 220 and 295 K, using HartreeFock and BLYP density functional theory electron densities and three different basis sets. All positions and anisotropic displacement parameters (ADPs) are freely refined without constraints or restraints -even those for hydrogen atoms. The results are systematically compared with those from neutron diffraction experiments at the temperatures 12, 50, 150 and 295 K. Although non-hydrogenatom ADPs differ by up to three combined standard uncertainties (csu's), all other structural parameters agree within less than 2 csu's. Using our best calculations (BLYP/cc-pVTZ, recommended for organic molecules), the accuracy of determining bond lengths involving hydrogen atoms from HAR is better than 0.009 Å for temperatures of 150 K or below; for hydrogen-atom ADPs it is better than 0.006 Å 2 as judged from the mean absolute X-ray minus neutron differences. These results are among the best ever obtained. Remarkably, the precision of determining bond lengths and ADPs for the hydrogen atoms from the HAR procedure is comparable with that from the neutron measurements -an outcome which is obtained with a routinely achievable resolution of the X-ray data of 0.65 Å .

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“…certainly larger than for standard charge density models, though not unusual for synchrotron data collections (see Morgenroth et al, 2008). On the other hand, analysis of the residual electron densities is quite promising.…”

Section: Resultsmentioning

confidence: 94%

“…For this reason, it is expected that the precision of the measurements is significantly lower than in standard charge density data collections. In addition, for synchrotron data collections, it is rather normal to obtain larger R int values (see, for example, Morgenroth et al, 2008), due to beam instabilities and other effects that may compromise a perfect reproducibility. This suggests that a large redundancy is a must in order to mediate all the effects.…”

Section: Resultsmentioning

confidence: 99%

Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling

Casati

Genoni

Meyer

et al. 2017

Acta Crystallogr B Struct Sci Cryst Eng Mater

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The possibility to determine electron-density distribution in crystals has been an enormous breakthrough, stimulated by a favourable combination of equipment for X-ray and neutron diffraction at low temperature, by the development of simplified, though accurate, electron-density models refined from the experimental data and by the progress in charge density analysis often in combination with theoretical work. Many years after the first successful charge density determination and analysis, scientists face new challenges, for example: (i) determination of the finer details of the electron-density distribution in the atomic cores, (ii) simultaneous refinement of electron charge and spin density or (iii) measuring crystals under perturbation. In this context, the possibility of obtaining experimental charge density at high pressure has recently been demonstrated [Casati et al. (2016). Nat. Commun. 7, 10901]. This paper reports on the necessities and pitfalls of this new challenge, focusing on the species syn-1,6:8,13-biscarbonyl[14]annulene. The experimental requirements, the expected data quality and data corrections are discussed in detail, including warnings about possible shortcomings. At the same time, new modelling techniques are proposed, which could enable specific information to be extracted, from the limited and less accurate observations, like the degree of localization of double bonds, which is fundamental to the scientific case under examination.

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Helium cryostat synchrotron charge densities determined using a large CCD detector – the upgraded beamline D3 at DESY

Cited by 23 publications

References 43 publications

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Host Perturbation in a β‐Hydroquinone Clathrate Studied by Combined X‐ray/Neutron Charge‐Density Analysis: Implications for Molecular Inclusion in Supramolecular Entities

Hirshfeld Atom Refinement

Exploring charge density analysis in crystals at high pressure: data collection, data analysis and advanced modelling

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