I15-1-X-ray Pair Distribution Function (XPDF)
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Maximillian G.
Stanzione
,
Oxana V.
Magdysyuk
,
Daniel J. M.
Irving
,
Chinnasamy
Murugesan
,
Nicole L.
Kelly
,
Yingling
Liao
,
Pech
Thongkam
,
Heitor S.
Seleghini
,
Paul S.
Wheatley
,
David B.
Cordes
,
Simon J.
Coles
,
Daniel N.
Rainer
,
Aamod V.
Desai
,
Sharon E.
Ashbrook
,
Julia L.
Payne
,
Russell E.
Morris
,
A. Robert
Armstrong
Diamond Proposal Number(s):
[36333]
Open Access
Abstract: Organic anode materials for sodium-ion batteries are attracting a great deal of interest due to their sustainability and design flexibility. However, the Na+ insertion mechanism is poorly understood, especially for disordered organic anode materials. A lack of understanding restricts optimization efforts and potential commercialization. Herein, we apply a range of characterization techniques, such as three-dimensional electron diffraction, powder X-ray diffraction, Raman spectroscopy, electron paramagnetic resonance spectroscopy, and pair distribution function (PDF) analysis to a model system, sodium naphthalene-2,6-dicarboxylate, to elucidate the Na+ storage mechanism. A combined ab initio random structure search and PDF study was conducted to postulate a structure of sodiated Na2+xNDC (s-NDC). Our work reveals an expansion in the Na+–O storage layer to allow for the accommodation of inserted Na+. Meanwhile, the naphthalene units exist as radical species, promoting a reorientation to accommodate the inserted Na+, as well as facilitating a stabilizing π interaction. Ultimately, our results illustrate the efficacy of using a multi-technique approach to study the sodiation mechanism of an organic anode material and offer insight into the sodiated structure. This approach can inform the strategic molecular design of future organic anode materials.
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Mar 2026
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I15-1-X-ray Pair Distribution Function (XPDF)
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Maximillian G.
Stanzione
,
Oxana V.
Magdysyuk
,
Daniel J. M.
Irving
,
Chinnasamy
Murugesan
,
Nicole L.
Kelly
,
Yingling
Liao
,
Pech
Thongkam
,
Heitor S.
Seleghini
,
Paul S.
Wheatley
,
David B.
Cordes
,
Simon J.
Coles
,
Daniel N.
Rainer
,
Aamod V.
Desai
,
Sharon E.
Ashbrook
,
Julia L.
Payne
,
Russell E.
Morris
,
A. Robert
Armstrong
Diamond Proposal Number(s):
[36333]
Open Access
Abstract: Organic anode materials for sodium-ion batteries are attracting a great deal of interest due to their sustainability and design flexibility. However, the Na+ insertion mechanism is poorly understood, especially for disordered organic anode materials. A lack of understanding restricts optimization efforts and potential commercialization. Herein, we apply a range of characterization techniques, such as three-dimensional electron diffraction (3D ED), powder X-ray diffraction (PXRD), Raman spectroscopy, electron paramagnetic resonance spectroscopy (EPR), and pair distribution function (PDF) analysis to a model system, sodium naphthalene-2,6-dicarboxylate (Na2NDC) to elucidate the Na+ storage mechanism. A combined Ab initio Random Structure Search (AIRSS) and PDF study was conducted to postulate a structure of sodiated Na2+xNDC (s-NDC). Our work reveals an expansion in the Na+-O storage layer, to allow for accommodation of inserted Na+. Meanwhile, the naphthalene units exist as radical species, promoting a re-orientation to accommodate the inserted Na+, and facilitating a stabilizing π interaction. Ultimately, our results illustrate the efficacy of using a multitechnique approach to study the sodiation mechanism of organic electrodes and offer insight into the sodiated structure. This approach can inform the strategic molecular design of future organic anode materials.
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Feb 2026
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I19-Small Molecule Single Crystal Diffraction
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Amy V.
Hall
,
Alice C.
Taylor
,
Natalie E.
Pridmore
,
Aurora J.
Cruz-Cabeza
,
David K.
Smith
,
Niccolò
Cosottini
,
Mark A.
Fox
,
Amrita
Chattopadhyay
,
Stefanos
Konstantinopoulos
,
Daniel N.
Rainer
,
Simon J.
Coles
,
Nicholas
Blagden
,
Qi
Zhang
,
Leon
Bowen
,
Toby J.
Blundell
Diamond Proposal Number(s):
[35994]
Open Access
Abstract: The ability to understand crystallization and predict the resulting solid form of a system is not always easily achieved, but it is critical, particularly in the field of materials science. Intriguing (and previously unreported) crystallization behavior is observed with terephthalic dihydrazide (TeDi) as it rapidly forms two concomitant crystalline polymorphs upon cooling in solution. The crystal morphology of Form I (FI) has not been seen before in organic systems and involves impressive, accordion-like stacks, composed of numerous twin domains and remains stable in solution for years. Form II (FII) exists as large needles that disappear in solution after 20 h. All experimental methods employed reveal that FI is the most stable polymorph. Conversely, all computational methods utilized (conformational analyses, lattice energy calculations, and crystal structure prediction) suggest that FII is the most stable polymorph. Isolation of FII was achieved by the crystallization of TeDi powder with a supramolecular mimetic gelator, as the gel fibers act as a template for the preferential crystallization of FII, due to the comparable crystal packing of FII and the gelator. This work highlights the impact of crystallization behavior in a real laboratory and the defects, disorder, and twinning that lead to remarkable crystal morphologies that may not be accounted for with idealized calculations, and also explores approaches for controlling and directing crystallization outcomes.
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Jan 2026
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[30280]
Open Access
Abstract: A new metal–organic framework (MOF) comprising copper and 2,3-dihydroxyterephthalate (2,3-dhtp) has been prepared using solvothermal synthesis. The solid (chemical formula of the as-made material): Cu12(dhtp)4(H2dhtp)3(CH3CO2)2 2DMF·10H2O is flexible in that its pore size adapts to match the size of guest molecules that are adsorbed. Carboxylate-containing molecules of different sizes (acetate, benzoic acid and ibuprofen) can be accommodated within the pores of the material and are coordinated to a dimeric copper unit. The localisation of the adsorbate guest molecule, the mode of binding and relatively low symmetry of the MOF allows the system to be used as a crystalline sponge. The crystal structure determination of the as-synthesised acetate-bound MOF was accomplished using single-crystal X-ray diffraction using a synchrotron source, while the benzoate- and ibuprofen-bound structures were solved using electron diffraction. A more practical adsorbent can be formulated by growing the MOF on a cotton fabric substrate, and this is shown to adsorb ibuprofen in a similar manner to the powdered MOF.
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Nov 2025
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I19-Small Molecule Single Crystal Diffraction
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Martin A.
Screen
,
James F.
Mccabe
,
Sean
Askin
,
Jamie L.
Guest
,
Paul
Hodgkinson
,
Aurora J.
Cruz-Cabeza
,
Toby J.
Blundell
,
Daniel N.
Rainer
,
Simon J.
Coles
,
Alexandra
Longcake
,
Michael R.
Probert
,
Clare S.
Mahon
,
Mark R.
Wilson
,
Jonathan W.
Steed
Diamond Proposal Number(s):
[30280]
Open Access
Abstract: PROTACs are new drug molecules in the beyond Rule of Five (bRo5) chemical space with extremely poor aqueous solubility and intrinsically poor crystallizability due to their structure, which comprises two distinct ligands covalently linked by a flexible linker. This makes PROTACs particularly challenging to understand from a solid-state preformulation perspective. While several X-ray structures have been reported of PROTACs in ternary complexes, to date no structures have been published of single component densely packed PROTACs, from which an understanding of PROTACs’ intermolecular interactions, and therefore physical properties, can be developed. An extensive crystallization protocol was applied to grow single crystals of a cereblon-recruiting PROTAC “AZ1” resulting in structures of an anhydrous form and a nonstoichiometric p-xylene solvate using 3D electron diffraction and synchrotron X-ray crystallography, respectively. The lattice energies are dominated by dispersive interactions between AZ1 molecules despite the presence of multiple hydrogen-bond donors and acceptors and planar aromatic groups, and both structures are built on similar intermolecular interactions. Thermal and spectral characterization revealed another solvate form containing dichloromethane. Amorphous solids produced by mechanochemical grinding of anhydrous AZ1 crystals also differed in dissolution characteristics from an amorphous solid produced by desolvating the dichloromethane solvate crystals, indicating that AZ1 may demonstrate pseudo-polyamorphism. This study paves the way for solid form screening and understanding in pharmaceutical systems that are far bRo5.
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Jul 2025
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I19-Small Molecule Single Crystal Diffraction
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Emily
Howarth
,
Jordan
Lopez
,
Joseph O.
Ogar
,
Toby J.
Blundell
,
Hiroki
Akutsu
,
Yasuhiro
Nakazawa
,
Shusaku
Imajo
,
Yoshihiko
Ihara
,
Simon J.
Coles
,
Peter N.
Horton
,
Jeppe
Christensen
,
Lee
Martin
Open Access
Abstract: This paper reports the synthesis, crystal structures and conducting properties of the first BEDT-TTF radical-cation salts with D3 symmetry tris-coordinated racemic lanthanide(III) anions. It is also the first crystallographic determination of the nine-coordinate tris(chelidonato)terbate and tris(chelidonato)dysprosate anions (chelidonic acid = clo = 4-oxo-4H-pyran-2,6-dicarboxylic acid). Salt α-(BEDT-TTF)5M(chelidonato)3·EtOH·2H2O is semimetallic for M = Tb, and semiconducting for M = Dy. These conducting properties are consistent with the band structure for both salts.
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Jan 2025
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I24-Microfocus Macromolecular Crystallography
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Rachel
Bolton
,
Moritz M.
Machelett
,
Jack
Stubbs
,
Danny
Axford
,
Nicolas
Caramello
,
Lucrezia
Catapano
,
Martin
Maly
,
Matthew J.
Rodrigues
,
Charlotte
Cordery
,
Graham J.
Tizzard
,
Fraser
Macmillan
,
Sylvain
Engilberge
,
David
Von Stetten
,
Takehiko
Tosha
,
Hiroshi
Sugimoto
,
Jonathan A. R.
Worrall
,
Jeremy S.
Webb
,
Mike
Zubkov
,
Simon
Coles
,
Eric
Mathieu
,
Roberto A.
Steiner
,
Garib
Murshudov
,
Tobias E.
Schrader
,
Allen M.
Orville
,
Antoine
Royant
,
Gwyndaf
Evans
,
Michael A.
Hough
,
Robin L.
Owen
,
Ivo
Tews
Diamond Proposal Number(s):
[15722, 14493, 23570]
Open Access
Abstract: The marine cyanobacterium Prochlorococcus is a main contributor to global photosynthesis, whilst being limited by iron availability. Cyanobacterial genomes generally encode two different types of FutA iron-binding proteins: periplasmic FutA2 ABC transporter subunits bind Fe(III), while cytosolic FutA1 binds Fe(II). Owing to their small size and their economized genome Prochlorococcus ecotypes typically possess a single futA gene. How the encoded FutA protein might bind different Fe oxidation states was previously unknown. Here, we use structural biology techniques at room temperature to probe the dynamic behavior of FutA. Neutron diffraction confirmed four negatively charged tyrosinates, that together with a neutral water molecule coordinate iron in trigonal bipyramidal geometry. Positioning of the positively charged Arg103 side chain in the second coordination shell yields an overall charge-neutral Fe(III) binding state in structures determined by neutron diffraction and serial femtosecond crystallography. Conventional rotation X-ray crystallography using a home source revealed X-ray-induced photoreduction of the iron center with observation of the Fe(II) binding state; here, an additional positioning of the Arg203 side chain in the second coordination shell maintained an overall charge neutral Fe(II) binding site. Dose series using serial synchrotron crystallography and an XFEL X-ray pump–probe approach capture the transition between Fe(III) and Fe(II) states, revealing how Arg203 operates as a switch to accommodate the different iron oxidation states. This switching ability of the Prochlorococcus FutA protein may reflect ecological adaptation by genome streamlining and loss of specialized FutA proteins.
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Mar 2024
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I19-Small Molecule Single Crystal Diffraction
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Jogirdas
Vainauskas
,
Tristan H.
Borchers
,
Mihails
Arhangelskis
,
Laura J.
Mccormick Mcpherson
,
Toni S.
Spilfogel
,
Ehsan
Hamzehpoor
,
Filip
Topić
,
Simon J.
Coles
,
Dmytro F.
Perepichka
,
Christopher J.
Barrett
,
Tomislav
Friscic
Diamond Proposal Number(s):
[26802]
Open Access
Abstract: Carbon, although the central element in organic chemistry, has been traditionally neglected as a target for directional supramolecular interactions. The design of supramolecular structures involving carbon-rich molecules, such as arene hydrocarbons, has been limited almost exclusively to non-directional π-stacking, or derivatisation with heteroatoms to introduce molecular assembly recognition sites. As a result, the predictable assembly of non-derivatised, carbon-only π-systems using directional non-covalent interactions remains an unsolved fundamental challenge of solid-state supramolecular chemistry. Here, we propose and validate a different paradigm for the reliable assembly of carbon-only aromatic systems into predictable supramolecular architectures: not through non-directional π-stacking, but via specific and directional halogen bonding. We present a systematic experimental, theoretical and database study of halogen bonds to carbon-only π-systems (C–I⋯πC bonds), focusing on the synthesis and structural analysis of cocrystals with diversely-sized and -shaped non-derivatised arenes, from one-ring (benzene) to 15-ring (dicoronylene) polycyclic atomatic hydrocarbons (PAHs), and fullerene C60, along with theoretical calculations and a systematic analysis of the Cambridge Structural Database. This study establishes C–I⋯πC bonds as directional interactions to arrange planar and curved carbon-only aromatic systems into predictable supramolecular motifs. In >90% of herein presented structures, the C–I⋯πC bonds to PAHs lead to a general ladder motif, in which the arenes act as the rungs and halogen bond donors as the rails, establishing a unique example of a supramolecular synthon based on carbon-only molecules. Besides fundamental importance in the solid-state and supramolecular chemistry of arenes, this synthon enables access to materials with exciting properties based on simple, non-derivatised aromatic systems, as seen from large red and blue shifts in solid-state luminescence and room-temperature phosphorescence upon cocrystallisation.
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Nov 2023
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[31778]
Open Access
Abstract: The synthesis and characterisation of eleven different 2-(thienyl)quinoxaline species that incorporate different points of functionality, including at the thiophene or quinoxaline rings, are described. These species display variable fluorescence properties in the visible region (λem = 401–491 nm) depending upon the molecular structures and extent of conjugation. The series of 2-(thienyl)quinoxaline species were then investigated as cyclometalating agents for Ir(III) to yield [Ir(C^N)2(bipy)]PF6 (where C^N = the cyclometalated ligand; bipy = 2,2′-bipyridine). Eight complexes were successfully isolated and fully characterised by an array of spectroscopic and analytical techniques. Two Ir(III) examples were structurally characterised in the solid state using single crystal X-ray diffraction; both structures confirmed the proposed formulations and coordination spheres in each case showing that the thiophene coordinates via a Ir–C bond. The photophysical properties of the complexes revealed that each complex is luminescent under ambient conditions with a range of emission wavelengths observed (665–751 nm) indicating that electronic tuning can be achieved via both the thienyl and quinoxaline moieties.
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Oct 2023
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I19-Small Molecule Single Crystal Diffraction
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Diamond Proposal Number(s):
[20876]
Open Access
Abstract: Cyclic porphyrin oligomers have been studied as models for photosynthetic light-harvesting antenna complexes and as potential receptors for supramolecular chemistry. Here, we report the synthesis of unprecedented β,β-directly linked cyclic zinc porphyrin oligomers, the trimer (CP3) and tetramer (CP4), by Yamamoto coupling of a 2,3-dibromoporphyrin precursor. Their three-dimensional structures were confirmed by nuclear magnetic resonance (NMR) spectroscopy, mass spectrometry, and single-crystal X-ray diffraction analyses. The minimum-energy geometries of CP3 and CP4 have propeller and saddle shapes, respectively, as calculated using density functional theory. Their different geometries result in distinct photophysical and electrochemical properties. The smaller dihedral angles between the porphyrin units in CP3, compared with CP4, result in stronger π-conjugation, splitting the ultraviolet–vis absorption bands and shifting them to longer wavelengths. Analysis of the crystallographic bond lengths indicates that the central benzene ring of the CP3 is partially aromatic [harmonic oscillator model of aromaticity (HOMA) 0.52], whereas the central cyclooctatetraene ring of the CP4 is non-aromatic (HOMA –0.02). The saddle-shaped structure of CP4 makes it a ditopic receptor for fullerenes, with affinity constants of (1.1 ± 0.4) × 105 M–1 for C70 and (2.2 ± 0.1) × 104 M–1 for C60, respectively, in toluene solution at 298 K. The formation of a 1:2 complex with C60 is confirmed by NMR titration and single-crystal X-ray diffraction.
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May 2023
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