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True molecular conformation and structure determination of remarkable polycyclic aromatic hydrocarbons
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ECM33 BOOK OF ABSTRACTS
279
MS39 Crystallography at the nanoscale
MS39-03
True molecular conformation and structure determination of remarkable polycyclic aromatic hydrocarbons
I. Andrusenko 1, E. Mugnaioli 2, M. Gemmi 1, W. Schmidt 3
1Istituto Italiano di Tecnologia, Center for Materials Interfaces, Electron Crystallography - Pontedera (Italy),
2Università di Pisa, Dipartimento di Scienze della Terra - Pisa (Italy), 3PAH Research - Igling-Holzhausen
(Germany)
Abstract
The true molecular conformation and the crystal structure of four large (30 – 46 C atoms) polycyclic aromatic
hydrocarbons (PAHs)1,2 were determined by direct methods from 3D electron diffraction (3D ED)3 data, a result
that could not be achieved by single crystal X-ray diffraction (XRD) due to limited crystal size and the thin leaflet
morphology of the samples. Additionally, three of such compounds were isolated as by-products in the synthesis
of similar materials and, therefore, were available only in very limited amount.
The main strength of 3D ED is the ability to perform single crystal diffraction on sub-micrometric areas. Therefore,
this technique can be used for structure determination when crystal size is the limiting factor for single crystal
XRD. Remarkably, this analytical protocol can be performed even on extremely small sample batches, which
cannot be conveniently prepared for conventional powder XRD.
Moreover, the molecular conformation of two compounds could not be determined via classical spectroscopic
methods due to the large size of the molecules and the occurrence of multiple and reciprocally connected
aromatic rings. On the other hand, 3D ED data provided not only ab-initio structure solution, but also the
unbiased determination of the internal molecular conformation. It is noteworthy that ab-initio crystal structure
determination does not require information about the molecular conformation, but only a rough estimation of the
atomic content of the unit cell.
The other two compounds were synthesised more than 50 years ago, but have hitherto remained structurally
unsolved. All molecules have a considerable interest due to their optoelectronic properties, which led to the
creation of a number of functionalised materials based on PAH backbones. Detailed synthetic routes,
spectroscopic analyses and promising properties are also discussed.
References
1. Hall, C. L., Andrusenko, I., Potticary, J., Gao, S., Liu, X., Schmidt, W., Marom, N., Mugnaioli, E., Gemmi, M.
& Hall, S. R. (2021) 3D Electron Diffraction Structure Determination of Terrylene, a Promising Candidate for
Intermolecular Singlet Fission. ChemPhysChem 22(15), 1631-1637.
2. Andrusenko, I., Hall, C. L., Mugnaioli, E., Potticary, J., Schmidt, W., Gao, S., Marom, N., Hall, S. R. & Gemmi,
M. (2022) True Molecular Conformation and Structure Determination by 3D Electron Diffraction of PAH By-
Products Potentially Useful for Electronic Applications, in preparation.
3. Gemmi, M., Mugnaioli, E., Gorelik, T. E., Kolb, U., Palatinus, L., Boullay, P., Hovmöller, S. & Abrahams, J. P.
(2019) 3D Electron Diffraction: The Nanoctystallography Revolution. ACS Cent. Sci. 5, 1315-1329
Nanostructures and microinfrared behavior of black opal from Gracias, Honduras
No full textThis paper reports nanostructural and microinfrared data of a black opal from Gracias, Honduras. The opal is hosted in
a volcanoclastic rock, as the cement among glass shards and as the fi lling material of steam vesicles (100–400 μm in diameter). It
is amorphous (opal-A), inclusions-free and consist of silica spheres, 450 nm in diameter, arranged in ordered close-packed fcc lattice,
producing intense play of color effects. The observation of thin sections under the polarizing light microscope reveals that the
Honduran opal is characterized by pleochroism and sharp birefringence, together with striae, "twins" and zoning.
Electron microscopy revealed that all these features are due to sphere packing mistakes. "Twins" and striae are due to changes
in the close-packed planes stacking, whereas zoning is related to a preferential concentration of point defects (i.e., vacant silica
spheres) at the opal/glass boundary.
Microinfrared spectrometry indicates that the Honduran opal is closely associated with minor CO2, possibly infi ltrating among
silica spheres
Fermi surface study of LaRu2Si2 and of heavy-fermion CeRu2Si2 above the Kondo temperature
No full textThe Two-dimensional (2D) angular correlation of the positron annihilation radiation of the heavy-fermion system (formula presented) was measured above the Kondo temperature (formula presented) and compared to that of the reference isostructural non-(formula presented)-electron system (formula presented) The (formula presented)-space densities of the two compounds, obtained via the Lock-Crisp-West folding of the 3D-reconstructed electron-positron momentum densities, were very similar. These results are in reasonable agreement with the band structure calculated for (formula presented) using the local-density approximation (LDA). Conversely, in the case of (formula presented) a clear discrepancy between the LDA calculation and the experiment appears unless the Fermi level (formula presented) is raised by (formula presented) After the (formula presented) adjustment the calculated Fermi surfaces are rather similar and in agreement with both experiments. The implications of this similarity on the physics of the heavy fermions are discussed. © 2002 The American Physical Society
3D electron diffraction applied to complex nanoparticles and nanominerals
No full text3D electron diffraction applied to complex nanoparticles and nanominerals
Enrico Mugnaioli (1), Mauro Gemmi (2)
(1) Dipartimento di Scienze della Terra, Università di Pisa, Pisa, Italy. (2) Center for Materials Interfaces, Electron Crystallography, Istituto Italiano di Tecnologia, Pontedera (PI), Italy.
Electron diffraction has been long regarded as a purely quantitative method, due to poor accuracy and dynamical effects. Yet, in the late 2000’s the first attempts to collect single-crystal electron diffraction data and to use them for ab-initio structure determination revealed unexpectedly successful [1]. In the following ten years, the method has attracted the attention of mineralists, chemists, material scientists and structural biologists, because it has proved able to cover the missing gap between the smallest crystals tractable with X-rays (1-50 μm) and the smallest crystalline seeds (10-100 nm) [2].
The so-called 3D electron diffraction method is very efficient with organic compounds and macromolecules despite their beam sensitivity, but is especially powerful for inorganic materials. In fact, it is possible to collect reliable structural data from particles and areas as small as few tens of nanometers. Here we will show the recent characterization of a series of sub-micrometric crystalline phases found in corundum grains from Luobusa ophiolite, Tibet, China [3-4] (Figure 1). A rich collection of unexpected new minerals was discovered inside a handful of FIB lamellae. Moreover, we will display that 3D electron diffraction can be used for the structural characterization of complex synthetic nanoparticle systems [5-6], possibly besting more established crystallographic methods like powder X-ray diffraction and high-resolution (S)TEM imaging
Disorder and modulation in first aragonite precipitates from Obstanser Eishöle (Austria)
No full textAragonite is thermodynamically metastable at near-surface conditions, and still it is relatively widespread
in marine and terrestrial sediments. In this contribution we propose the detailed chemical and crystallographic
analysis of fresh aragonitic precipitates. Wet samples, collected from a dolomitic cold cave in the East Alpine
range, were directly taken from underground dripping water and from the surface of aragonite speleothems.
Calcium carbonate nano- and microcrystals are always found in association with magnesite and hydromagnesite
and incorporate variable amounts of magnesium and possibly hydroxyl groups.
The typical size of the analyzed precipitates ranges from some tens of nanometers to few microns. Advanced
electron crystallographic tools were therefore necessary for a proper structural characterization. Indeed, in the
last ten years electron diffraction (ED) turned into a robust protocol for phase identification and ab-initio
structure determination. Such evolution was mostly propelled by the development of semi-automatic routines
for 3D data collection (Mugnaioli & Gemmi, 2018). The concept at the basis of 3D ED is the same as for
single-crystal X-ray diffraction, but electrons allow sampling single crystals 10 to 1000 times smaller, despite
the presence of surrounding crystals of other mineralogical phases.
3D ED revealed that first calcium carbonate precipitates have a structure strictly related to conventional
aragonite. Still, diffuse scattering and satellite reflections appear along aragonite {110} and point to a reduction
of symmetry into the monoclinic system (Németh et al., 2018). Following the order-disorder description
of aragonite proposed by Makovicky (2012), such disorder can be associated with the same mechanism
responsible for the twinning in mature aragonite. The frequent (or systematic) inversion of the stacking vector
can be imposed by the incorporation of magnesium in the structure, whose atomic radius and coordination
significantly differ from those of calcium. In turn, the necessity to include magnesium and hydroxyl groups in
the lattice may be the very factor that favors the crystallization of aragonite in respect to calcite, which should
otherwise be the stable mineral phase at near-surface conditions. Such ‘monoclinic-aragonite’ seeds might
therefore represent the key step for the formation of large amount of metastable aragonite sediments
Low temperature SR-XRPD study of akermanite-gehlenite solid solution
No full textLow temperature thermal expansion coefficients of members of the solid solution gehlenite (ge)-åkermanite (åk) were measured by synchrotron radiation X-Ray powder diffraction. The linear thermal expansion coefficient is maximum for a composition with about 50 % content of åk. In åk-rich compositions an incommensurate modulated structure is present. The ge-åk solid solution shows a non-ideal behaviour, with negative excess volume near the ge end-member
3D electron diffraction of nanocrystalline MOFs obtained by nonconventional synthetic methods
No full textMOFs are being synthesized and investigated at a fast pace due to their potential for
numerous applications, most notably in relation to gas adsorption, energy conversion
and storage and even medicine. To increase the sustainability of the solvothermal
processes typically used for MOF synthesis, the development of more environmentally
friendly approaches is desirable. Moreover, exploring different synthetic conditions
allow to obtain products, polymorphs and topologies different from those obtained with
conventional methods. Alternative synthetic methods involving solventless- or liquidassisted mechanochemistry as well as the use of supercritical fluids are becoming
more and more popular and an object of research themselves.1
The products obtained by non-conventional methods are often polycrystalline and the
control and optimization of the crystal growth is not easy to achieve. Conventional
single-crystal XRD is therefore usually not applicable in such cases and also powder
methods are extremely challenging, especially in case of large unit cells, low
symmetry, severe peak broadening and, not least, because of the difficulty of obtaining
pure phases. Further complications can be induced by the grinding process or rapid
nucleation in non-equilibrium conditions. Eventually, a proper structural
characterization of these materials can only be addressed with single-crystal
crystallographic techniques capable of high spatial resolution.
3D electron diffraction has nowadays evolved to become the method of choice to solve
complex crystallographic puzzles at the nanoscale.
2
In this contribution we will show
examples of successful indexing and structure solution of new metal-organic materials
obtained via mechanochemistry or synthesis in supercritical CO2.
3,4 New structures
with different dimensionalities, porosity and properties have been determined,
overcoming their typical beam sensitivity
Thermal expansion and phase transitions in akermanite and gehlenite
No full textThermal expansion has been measured by
laboratory and synchrotron X-ray powder diffraction
for end-member akermanite (ak, Ca2MgSi2O7) and gehlenite
(ge, Ca2Al2SiO7) in the range 20–1,500 K. In ak
in the range 340–390 K, there is a negative linear thermal
expansion in [001] direction. This is related to the
phase transition from an incommensurate modulated
structure (IC) to a normal one (N). The volumetric mean
thermal expansion coefficients for ak and ge, obtained
with a linear fit of the experimental data in the temperature
range 298–1,400 K, are respectively 32.1·10-6
and 28.3·10-6 K-1 . The variation of the c/a ratio with
temperature, due to different thermal expansion along
the crystallographic axes, can be related to the different
behaviour of the tetrahedral layers in the N and IC
phases. Analysis of the variation of the superstructure
peaks intensity across the phase transition confirms the
tricritical behaviour of the IC/N transition in ak
The formation of impact coesite
No full textCoesite in impact rocks is traditionally considered a retrograde product formed during pressure release by the crystallisation of an amorphous phase (either silica melt or diaplectic glass). Recently, the detailed microscopic and crystallographic study of impact ejecta from Kamil crater and the Australasian tektite strewn field pointed in turn to a different coesite formation pathway, through subsolidus quartz-to-coesite transformation. We report here further evidence documenting the formation of coesite directly from quartz. In Kamil ejecta we found sub-micrometric single-coesite-crystals that represent the first crystallization seeds of coesite. Coesite in Australasian samples show instead well-developed subeuhedral crystals, growing at the expenses of hosting quartz and postdating PDF deformation. Coesite (010) plane is most often parallel to quartz {10–11} plane family, supporting the formation of coesite through a topotactic transformation. Such reaction is facilitated by the presence of pre-existing and shock-induced discontinuities in the target. Shock wave reverberations can provide pressure and time conditions for coesite nucleation and growth. Because discontinuities occur in both porous and non-porous rocks and the coesite formation mechanism appears similar for small and large impacts, we infer that the proposed subsolidus transformation model is valid for all types of quartz-bearing target rocks
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