Hirshfeld Surfaces: A New Tool for Visualising and Exploring Molecular Crystals

McKinnon, Joshua J.; Mitchell, Anthony S.; Spackman, Mark A.

doi:10.1002/(sici)1521-3765(19981102)4:11<2136::aid-chem2136>3.0.co;2-g

Cited by 737 publications

(332 citation statements)

References 18 publications

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“…In order to gain a deeper appreciation of the supramolecular association in the polymorphs 1 and 2, an analysis of the Hirshfeld surfaces was conducted [49]. The variation in the crystal packing interactions due to the different dispositions of the terminal pyridyl rings around the eight-membered oxalamide chromophore in polymorphs 1 and 2 can be conveniently discerned from the views of Hirshfeld surfaces.…”

Section: Hirshfeld Surfacesmentioning

confidence: 99%

Structural, Hirshfeld surface and theoretical analysis of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide

Jotani¹,

Zukerman-Schpector

Madureira

et al. 2016

Zeitschrift Für Kristallographie - Crystalline Materials

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Section: Hirshfeld Surfacesmentioning

confidence: 99%

Structural, Hirshfeld surface and theoretical analysis of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide

Jotani¹,

Zukerman-Schpector

Madureira

et al. 2016

Zeitschrift Für Kristallographie - Crystalline Materials

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“…These include the originally proposed hexagonal and orthorhombic models [18][19][20] . None of these fit well, so we went directly to test the carbonate ordered superstructure model (P6 5 22) 11 shown as the best fit of synchrotron x-ray powder data for a synthetic sample 21 . They had tested 5 other structural models, P6 3 /mmc, P3 2 21, Pnma, Ama2 20 , C2/c; however, for those the Rietveld fits were not as good.…”

Section: Resultsmentioning

confidence: 99%

“…If one examines the Hirshfeld surfaces 22 of the carbonates groups in vaterite, calcite and aragonite generated using CrystalExplorer 23 , a picture emerges that emphasizes the interactions between the carbonate groups as a contributor to the stability of each of the calcium carbonate polymorphs (Fig. 6).…”

Section: Discussionmentioning

confidence: 99%

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Empirically Testing Vaterite Structural Models Using Neutron Diffraction and Thermal Analysis

Chakoumakos

Pracheil

Koenigs

et al. 2016

Geological Society of America Abstracts With Programs

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Otoliths, calcium carbonate (CaCO 3 ) ear bones, are among the most commonly used age and growth structures of fishes. Most fish otoliths are comprised of the most dense CaCO 3 polymorph, aragonite. Sturgeon otoliths, in contrast, have been characterized as the rare and structurally enigmatic polymorph, vaterite-a metastable polymorph of CaCO 3 . Vaterite is an important material ranging from biomedical to personal care applications although its crystal structure is highly debated. We characterized the structure of Lake Sturgeon otoliths using thermal analysis and neutron powder diffraction, which is used non-destructively. We confirmed that while Lake Sturgeon otoliths are primarily composed of vaterite, they also contain the denser CaCO 3 polymorph, calcite. For the vaterite fraction, neutron diffraction data provide enhanced discrimination of the carbonate group compared to x-ray diffraction data, owing to the different relative neutron scattering lengths, and thus offer the opportunity to uniquely test the more than one dozen crystal structural models that have been proposed for vaterite. Of those, space group P6 5 22 model, a = 7.1443(4)Å, c = 25.350(4)Å, V = 1121.5(2) Å 3 provides the best fit to the neutron powder diffraction data, and allows for a structure refinement using rigid carbonate groups.Vaterite, a metastable polymorph of calcium carbonate (CaCO 3 ) 1 is of substantial interest as a naturally occurring biomaterial, and for its use as an additive in various consumer products ranging from paper and coatings to plastic and elastomer reinforcement to food supplements, oral hygiene aids, and cosmetics 2 . For instance, vaterite's greater ability to dissolve in body fluids compared to other polymorphs of CaCO 3 makes it desirable for manufacturing nanocapsules for delivering drugs at the cellular level 3 . Despite the realized and potential importance of vaterite to humans, some of the most basic facts about this compound such as its crystalline structure have challenged researchers. Currently, more than a dozen crystal structure models have been proposed with little weight favoring one over the others 1 . Many basic properties of vaterite are unresolved due in part to the rarity of naturally occurring vaterite. Naturally occurring vaterite structures include human gallstones and portions of fish ear bones, or otoliths, from primitive fishes such as sturgeons 4 or sporadically from more modern fishes such as salmon and trout, and are potentially formed in response to physiological stress, especially thermal stress 5 and captive rearing 6,7 . In fact, only a few reliable sources of biogenic vaterite exist for study including sea squirt spicules 8,9 and otoliths of sturgeons, but only rarely those of other fish or animals. The ability of making biogenic vaterite has apparently been retained through evolution in some fish such as salmonids because these fishes sometimes have vaterite patches in their otoliths 4,10 , but sturgeons are really the sole reliable source of vaterite from fish otoliths. Unlike...

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“…The vibrational frequencies were calculated at the same theoretical level to confirm that all optimized ground configurations had no imaginary frequencies and the groundstate minima were on potential energy surfaces. The 19F NMR chemical shifts were obtained using the Gauge-Including surface [13][14][15], which is constructed from points with fixed ratio (usually 0.5) between the contribution to the electron density from a molecule and the contribution from electron density from the whole crystal. Particularly instructive is to colour-code the surface by the distance to the nearest atom within the surface or external to it.…”

Section: Methodsmentioning

confidence: 99%

Synthesis, Characterization and Crystal Structure of 1,4,5,8-Tetrakis(Perfluoropyridin4-yloxy) Naphthalene

Beyki¹,

Kaminsky²,

Heydari³

et al. 2017

Struct Chem Crystallogr Commun

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1,4,5,8-tetrakis(perfluoropyridin-4-yloxy)naphthalene (tetra-PPN) was synthesized via a one-pot pseudo-five-component reaction of pentafluoropyridine and 5,8-dihydroxy-1,4-tetralindione under basic conditions in DMF. The asymmetric unit contains one half-mol ecule of tetra-PPN and data reveals that half of the molecule being related to the other via inversion symmetry. A detailed analysis of the intermolecular interactions of the compound has been performed using Hirshfeld surfaces. The optimized geometrical parameters and calculated spectroscopic features obtained by quantum chemical calculations using density functional (DFT) methods. In addition, to support the experimental results, the 19F NMR values are obtained using B3LYP method. The obtained results are compared with experimental values show a very good agreement with the experimental data.

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Hirshfeld Surfaces: A New Tool for Visualising and Exploring Molecular Crystals

Cited by 737 publications

References 18 publications

Structural, Hirshfeld surface and theoretical analysis of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide

Structural, Hirshfeld surface and theoretical analysis of two conformational polymorphs of N,N′-bis(pyridin-3-ylmethyl)oxalamide

Empirically Testing Vaterite Structural Models Using Neutron Diffraction and Thermal Analysis

Synthesis, Characterization and Crystal Structure of 1,4,5,8-Tetrakis(Perfluoropyridin4-yloxy) Naphthalene

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