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Instruments / Technical Area	Publication Details	Published
I07-Surface & interface diffraction	Structure of langmuir monolayers of perfluorinated fatty acids: Evidence of a new 2D smectic C phase Philippe Fontaine , Eduardo J. M. Filipe , Marie-claude Fauré , Tomas Rego , Stephanie Tassler , Ana Carolina Alves , Gonçalo M. C. Silva , Pedro Morgado , Michel Goldmann Molecules 24 DOI: 10.3390/molecules24193590 Diamond Proposal Number(s): [17042] Open Access Show Abstract ▼ Abstract: Due to the characteristic chain rigidity and weak intermolecular interactions of perfluorinated substances, the phase diagram of Langmuir monolayer formed by perfluorinated molecules has been interpreted so far as displaying only two phases, a 2D gas (G) and a liquid condensed (LC). However, in this work, we presented Grazing Incidence X-ray Diffraction measurements, which exhibit two diffraction peaks on the transition plateau: One is the signature of the hexagonal structure of the LC phase, the second one is associated to the low-density fluid phase and is thus more ordered than expected for a 2D gas or a typical fluid phase. Atomistic molecular dynamics simulations, performed on the transition plateau, revealed the existence of clusters in which domains of vertical molecules organized in a hexagonal lattice coexist with domains of parallel lines formed by tilted molecules, a new structure that could be described as a “2D smectic C” phase. Moreover, the diffraction spectrum calculated from the simulation trajectories compared favorably with the experimental spectra, fully validating the simulations and the proposed interpretation. The results were also in agreement with the thermodynamic analysis of the fluid phase and X-ray Reflectivity experiments performed before and after the transition between these two phases.	Oct 2019
I19-Small Molecule Single Crystal Diffraction	Linear, non-conjugated cyclic and conjugated cyclic paraphenylene under pressure Miriam Peña-álvarez , Samuele Fanetti , Naomi Falsini , Giulia Novelli , Juan Casado , Valentín G. Baonza , Mercedes Taravillo , Simon Parsons , Roberto Bini , Margherita Citroni Molecules 24 DOI: 10.3390/molecules24193496 Diamond Proposal Number(s): [16139] Open Access Show Abstract ▼ Abstract: The n-paraphenylene family comprises chains of phenylene units linked together by C-C bonds that are between single- and double-bonded, and where n corresponds to the number of phenylene units. In this work, we compare the response of the optical properties of different phenylene arrangements. We study linear chains (LPP), cyclic systems (CPPs), and non-conjugated cyclic systems with two hydrogenated phenylenes (H4[n]CPP). Particularly, the systems of interest in this work are [6]LPP, [12]- and [6]CPP and H4[6]CPP. This work combines Raman and infrared spectroscopies with absorption and fluorescence (one- and two-photon excitations) measured as a function of pressure up to maximum of about 25 GPa. Unprecedented crystallographic pressure-dependent results are shown on H4[n]CPP, revealing intramolecular π-π interactions upon compression. These intramolecular interactions justify the H4[n]CPP singular optical properties with increasing fluorescence lifetime as a function of pressure.	Oct 2019
I19-Small Molecule Single Crystal Diffraction	High Pressure Crystal Structure and Electrical Properties of a Single Component Molecular Crystal [Ni(dddt)2] (dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate) Hengbo Cui , Takao Tsumuraya , Hamish H.-m. Yeung , Chloe S. Coates , Mark R. Warren , Reizo Kato Molecules 24 DOI: 10.3390/molecules24101843 Diamond Proposal Number(s): [15000] Open Access Show Abstract ▼ Abstract: Single-component molecular conductors form an important class of materials showing exotic quantum phenomena, owing to the range of behavior they exhibit under physical stimuli. We report the effect of high pressure on the electrical properties and crystal structure of the single-component crystal [Ni(dddt)2] (where dddt = 5,6-dihydro-1,4-dithiin-2,3-dithiolate). The system is isoelectronic and isostructural with [Pd(dddt)2], which is the first example of a single-component molecular crystal that exhibits nodal line semimetallic behavior under high pressure. Systematic high pressure four-probe electrical resistivity measurements were performed up to 21.6 GPa, using a Diamond Anvil Cell (DAC), and high pressure single crystal synchrotron X-ray diffraction was performed up to 11.2 GPa. We found that [Ni(dddt)2] initially exhibits a decrease of resistivity upon increasing pressure but, unlike [Pd(dddt)2], it shows pressure-independent semiconductivity above 9.5 GPa. This correlates with decreasing changes in the unit cell parameters and intermolecular interactions, most notably the π-π stacking distance within chains of [Ni(dddt)2] molecules. Using first-principles density functional theory (DFT) calculations, based on the experimentally-determined crystal structures, we confirm that the band gap decreases with increasing pressure. Thus, we have been able to rationalize the electrical behavior of [Ni(dddt)2] in the pressure-dependent regime, and suggest possible explanations for its pressure-independent behavior at higher pressures.	May 2019
I03-Macromolecular Crystallography I04-1-Macromolecular Crystallography (fixed wavelength) I24-Microfocus Macromolecular Crystallography	Structural comparison of enterococcus faecalis and human thymidylate synthase complexes with the substrate dUMP and its analogue FdUMP provides hints about enzyme conformational variabilities Cecilia Pozzi , Stefania Ferrari , Rosaria Luciani , Giusy Tassone , Maria Costi , Stefano Mangani Molecules 24 DOI: 10.3390/molecules24071257 Diamond Proposal Number(s): [1358] Open Access Show Abstract ▼ Abstract: Thymidylate synthase (TS) is an enzyme of paramount importance as it provides the only de novo source of deoxy-thymidine monophosphate (dTMP). dTMP, essential for DNA synthesis, is produced by the TS-catalyzed reductive methylation of 2′-deoxyuridine-5′-monophosphate (dUMP) using N5,N10-methylenetetrahydrofolate (mTHF) as a cofactor. TS is ubiquitous and a validated drug target. TS enzymes from different organisms differ in sequence and structure, but are all obligate homodimers. The structural and mechanistic differences between the human and bacterial enzymes are exploitable to obtain selective inhibitors of bacterial TSs that can enrich the currently available therapeutic tools against bacterial infections. Enterococcus faecalis is a pathogen fully dependent on TS for dTMP synthesis. In this study, we present four new crystal structures of Enterococcus faecalis and human TSs in complex with either the substrate dUMP or the inhibitor FdUMP. The results provide new clues about the half-site reactivity of Enterococcus faecalis TS and the mechanisms underlying the conformational changes occurring in the two enzymes. We also identify relevant differences in cofactor and inhibitor binding between Enterococcus faecalis and human TS that can guide the design of selective inhibitors against bacterial TSs.	Mar 2019
I19-Small Molecule Single Crystal Diffraction	A pseudouridine isoxazolidinyl nucleoside analogue structural analysis: a morphological approach Giuseppe Floresta , Venerando Pistarà , Kirsten E. Christensen , Emanuele Amata , Agostino Marrazzo , Davide Gentile , Antonio Rescifina , Francesco Punzo Molecules 23 DOI: 10.3390/molecules23123381 Open Access Show Abstract ▼ Abstract: An in silico study has been conducted upon (3′RS,5′SR)-5-[2′-benzyl-5′-hydroxymethyl-1′,2′-isoxazolidin-3′-yl]uracil through a molecular dynamics/docking approach that highlights its potential inhibitory activity upon the wild-type pseudouridine 5′-monophosphate glycosidase. The crystal structure of this compound has been solved by means of X-ray single crystal diffraction and the data inferred were used to predict its crystal morphology. These data were compared with optical microscopy images and confirmed the validity of the computed models. This robust approach, already used for several other different compounds, provides a fast and reliable tool to standardize a crystallization method in order to get similar and good quality crystals. As different crystal shapes could be associated with different polymorphic forms, this method could be considered a fast and cheap screening to choose among different and coexistent polymorphic forms. Furthermore, a match with the original crystal structure of pseudouridine 5′-monophosphate is provided.	Dec 2018
B23-Circular Dichroism	UV-denaturation assay to assess protein photostability and ligand-binding interactions using the high photon flux of Diamond B23 beamline for SRCD Rohanah Hussain , Edoardo Longo , Giuliano Siligardi Molecules 23 DOI: 10.3390/molecules23081906 Diamond Proposal Number(s): [9786, 11563, 10484] Open Access Show Abstract ▼ Abstract: Light irradiation with high photon flux in the vacuum and far-UV region is known to denature the conformation of biopolymers. Measures are in place at Diamond Light Source B23 beamline for Synchrotron Radiation Circular Dichroism (SRCD) to control and make this effect negligible. However, UV denaturation of proteins can also be exploited as a novel method for assessing biopolymer photostability as well as ligand-binding interactions. Usually, host⁻ligand binding interactions can be assessed monitoring CD changes of the host biopolymer upon ligand addition. The novel method of identifying ligand binding monitoring the change of relative rate of UV denaturation using SRCD is especially important when there are very little or insignificant secondary structure changes of the host protein upon ligand binding. The temperature study, another method used to determine molecular interactions, can often be inconclusive when the thermal effect associated with the displacement of the bound solvent molecules by the ligand is also small, making the determination of the binding interaction inconclusive. Herein we present a review on the UV-denaturation assay as a novel method to determine the relative photostability of protein formulations as well as the screening of ligand-binding interactions using the high photon flux Diamond B23 beamline for SRCD.	Jul 2018
I03-Macromolecular Crystallography	1,2,6-Thiadiazinones as Novel Narrow Spectrum Calcium/Calmodulin-Dependent Protein Kinase Kinase 2 (CaMKK2) Inhibitors Christopher Asquith , Paulo Godoi , Rafael M. Counago , Tuomo Laitinen , John W. Scott , Christopher Langendorf , Jonathan S. Oakhill , David Drewry , William Zuercher , Panayiotis Koutentis , Timothy Willson , Andreas Kalogirou Molecules 23 DOI: 10.3390/molecules23051221 Diamond Proposal Number(s): [14664] Open Access Show Abstract ▼ Abstract: We demonstrate for the first time that 4H-1,2,6-thiadiazin-4-one (TDZ) can function as a chemotype for the design of ATP-competitive kinase inhibitors. Using insights from a co-crystal structure of a 3,5-bis(arylamino)-4H-1,2,6-thiadiazin-4-one bound to calcium/calmodulin-dependent protein kinase kinase 2 (CaMKK2), several analogues were identified with micromolar activity through targeted displacement of bound water molecules in the active site. Since the TDZ analogues showed reduced promiscuity compared to their 2,4-dianilinopyrimidine counter parts, they represent starting points for development of highly selective kinase inhibitors.	May 2018
I04-Macromolecular Crystallography	Chroman-4-One Derivatives Targeting Pteridine Reductase 1 and Showing Anti-Parasitic Activity Flavio Di Pisa , Giacomo Landi , Lucia Dello Iacono , Cecilia Pozzi , Chiara Borsari , Stefania Ferrari , Matteo Santucci , Nuno Santarem , Anabela Cordeiro-da-silva , Carolina Moraes , Laura Alcantara , Vanessa Fontana , Lucio Freitas-junior , Sheraz Gul , Maria Kuzikov , Birte Behrens , Ina Pöhner , Rebecca Wade , Maria Costi , Stefano Mangani Molecules 22 DOI: 10.3390/molecules22030426 Diamond Proposal Number(s): [8574] Open Access Show Abstract ▼ Abstract: Flavonoids have previously been identified as antiparasitic agents and pteridine reductase 1 (PTR1) inhibitors. Herein, we focus our attention on the chroman-4-one scaffold. Three chroman-4-one analogues (1–3) of previously published chromen-4-one derivatives were synthesized and biologically evaluated against parasitic enzymes (Trypanosoma brucei PTR1–TbPTR1 and Leishmania major–LmPTR1) and parasites (Trypanosoma brucei and Leishmania infantum). A crystal structure of TbPTR1 in complex with compound 1 and the first crystal structures of LmPTR1-flavanone complexes (compounds 1 and 3) were solved. The inhibitory activity of the chroman-4-one and chromen-4-one derivatives was explained by comparison of observed and predicted binding modes of the compounds. Compound 1 showed activity both against the targeted enzymes and the parasites with a selectivity index greater than 7 and a low toxicity. Our results provide a basis for further scaffold optimization and structure-based drug design aimed at the identification of potent anti-trypanosomatidic compounds targeting multiple PTR1 variants.	Mar 2017
I24-Microfocus Macromolecular Crystallography	Crystallographic Studies Evidencing the High Energy Tolerance to Disrupting the Interface Disulfide Bond of Thioredoxin 1 from White Leg Shrimp Litopenaeus vannamei Adam Campos-acevedo , Enrique Rudiño-piñera Molecules 19 (12), 21113 - 21126 DOI: 10.3390/molecules191221113 PMID: 25517346 Open Access Show Abstract ▼ Abstract: Thioredoxin (Trx) is a small 12-kDa redox protein that catalyzes the reduction of disulfide bonds in proteins from different biological systems. A recent study of the crystal structure of white leg shrimp thioredoxin 1 from Litopenaeus vannamei (LvTrx) revealed a dimeric form of the protein mediated by a covalent link through a disulfide bond between Cys73 from each monomer. In the present study, X-ray-induced damage in the catalytic and the interface disulfide bond of LvTrx was studied at atomic resolution at different transmission energies of 8% and 27%, 12.8 keV at 100 K in the beamline I-24 at Diamond Light Source. We found that at an absorbed dose of 32 MGy, the X-ray induces the cleavage of the disulfide bond of each catalytic site; however, the interface disulfide bond was cleaved at an X-ray adsorbed dose of 85 MGy; despite being the most solvent-exposed disulfide bond in LvTrx (~50 Å2). This result clearly established that the interface disulfide bond is very stable and, therefore, less susceptible to being reduced by X-rays. In fact, these studies open the possibility of the existence in solution of a dimeric LvTrx.	Dec 2014
B23-Circular Dichroism	Directed Formation of DNA Nanoarrays through Orthogonal Self-Assembly Jon Burns , Jurgita Zekonyte , Guiliano Siligardi , Rohanah Hussain , Eugen Stulz Molecules 16 (6), 4912 - 4922 DOI: 10.3390/molecules16064912 PMID: 21677604 Show Abstract ▼ Abstract: We describe the synthesis of terpyridine modified DNA strands which selectively form DNA nanotubes through orthogonal hydrogen bonding and metal complexation interactions. The short DNA strands are designed to self-assemble into long duplexes through a sticky-end approach. Addition of weakly binding metals such as Zn(II) and Ni(II) induces the formation of tubular arrays consisting of DNA bundles which are 50-200 nm wide and 2-50 nm high. TEM shows additional long distance ordering of the terpy-DNA complexes into fibers.	Jun 2011

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