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Phosphotyrosine residues are essential functional switches in health and disease. Thus, phosphotyrosine biomimetics are crucial for the development of chemical tools and drug molecules. We report here the discovery and investigation of pentafluorophosphato amino acids as novel phosphotyrosine biomimetics. A mild acidic pentafluorination protocol was developed and two PF5-amino acids were prepared and employed in peptide synthesis. Their structures, reactivities, and fluorine-specific interactions were studied by NMR and IR spectroscopy, X-ray diffraction, and in bioactivity assays. The mono-anionic PF5 motif displayed an amphiphilic character binding to hydrophobic surfaces, to water molecules, and to protein-binding sites, exploiting charge and H−F-bonding interactions. The novel motifs bind 25- to 30-fold stronger to the phosphotyrosine binding site of the protein tyrosine phosphatase PTP1B than the best current biomimetics, as rationalized by computational methods, including molecular dynamics simulations.
In the pursuit of discovering materials with desirable properties, extending the available material libraries is crucial. High-throughput simulations have become an integral part in designing new materials in the past decades. However, there is no straightforward way of distinguishing synthesizable materials from all the proposed candidates. This project focuses on employing AI-driven methods to estimate synthesizability of materials.
Up to now, material scientists and engineers have relied on domain knowledge as well as empirical heuristics to guess the stability and synthesizability of molecules and crystals. The famous Pauling rules of crystal stability are an example of such heuristics. However, after the accelerating material discovery in all the years since Pauling, these rules now fail to account for the stability of most known crystals. A new predictive set of heuristics for crystal stability/synthesizability is unlikely to be uncovered by human perception, given the magnitude and dimensionality of crystallographic data. Hence, a data-driven approach should be proposed to find a predictive model or set of heuristics which differentiate synthesizable crystal structures from the rest. The main challenge of this research problem is the lack of a negative set for classification. Here, there are two classes of data: the positive class which contains synthesizable materials and the negative class which contains materials which are not synthesizable. While the data from the positive class is simply the data of crystals which have been experimentally synthesized, we do not have access to data points which are certainly unsynthesizable. Strictly speaking, if an attempt of synthesizing a crystal fails, it does not necessarily follow that the crystal is not synthesizable. Also, there is no database available which contains the intended crystal structures of unsuccessful synthesis attempts.
This project proposes a semi-supervised learning scheme to predict crystal synthesizability. The ML model is trained on experimental and theoretical crystal data. The initial featurization focuses on local environments which is inspired by the Pauling Rules. The experimental data points are downloaded through the Pymatgen API from the Materials Project database which contains relaxed structures recorded in Inorganic Crystal Structure Database – ICSD. The theoretical data is queried from select databases accessible through the Optimade project’s API.
Highly anharmonic thermal vibrations may serve as a source of structural instabilities resulting in phase transitions, chemical reactions and even the mechanical disintegration of a material. Ab initio calculations model thermal motion within a harmonic or sometimes quasi-harmonic approximation and must be complimented by experimental data on temperature-dependent vibrational frequencies. Here multi-temperature atomic displacement parameters (ADPs), derived from a single-crystal synchrotron diffraction experiment, are used to characterize low-frequency lattice vibrations in the alpha-FOX-7 layered structure. It is shown that despite the limited quality of the data, the extracted frequencies are reasonably close to those derived from inelastic scattering, Raman measurements and density functional theory (DFT) calculations. Vibrational anharmonicity is parameterized by the Grüneisen parameters, which are found to be very different for in-layer and out-of-layer vibrations.
A recent approach to measure electron radiation doses in the kGy range is the use of phosphors with an irradiation dose-dependent luminescence decay time. However, the applicability of the previously investigated material NaYF4:Yb3+,Er3+ is limited as it shows pronounced fading. Therefore, in this work, a modified SrF2 synthesis is presented that results in SrF2 nanoparticles codoped with Yb and either Er, Hm, or Tm. To assess their suitability as dosimeter material, dose response, as well as its degree of fading over 50 up to 140 days after irradiation were measured. Fading rates as small as 5% in SrF2:Er,Yb and 4% in SrF2:Ho,Yb were derived, which are comparable to established dosimeter materials. A combination of spectroscopy, diffraction and DFT calculations was used to elucidate the effect of irradiation, pointing towards the formation of a secondary phase of Yb2+ that we predict could be Yb2OF2. This irreversible formation of a secondary phase is considered to be the explanation for the low fading behavior in SrF2-based phosphors compared to NaYF4:Yb, Er, a highly attractive feature for electron beam dosimetry.
Using solid catalysts in disulfide-based dynamic combinatorial solution- and mechano-chemistry
(2022)
We here show for the first time that solid amines can act as catalysts for disulfide-based dynamic combinatorial chemistry by ball mill grinding. The mechanochemical Equilibrium for the two disulfide reactions studied is reached within one to three hours using ten different amine catalysts. This contrasts with the weeks to months to achieve solution equilibrium for most solid amine catalysts at 2%M at 2mM concentration in a suitable solvent. The final mechanochemical equilibrium is independent of the catalyst used, but varies with other ball mill grinding factors such as the presence of traces of solvent. The different efficiencies of the amines tested are discussed.
We demonstrate here using a disulfide system the first example of reversible, selective, and quantitative transformation between three crystalline polymorphs by ball mill grinding. This includes the discovery of a previously unknown polymorph. Each polymorph is reproducibly obtained under well-defined neat or liquid-assisted grinding conditions, revealing subtle control over the apparent thermodynamic stability. We discovered that the presence of a contaminant as low as 1.5% mol mol−1 acting as a template is required to enable all these three polymorph transformations. The relative stabilities of the polymorphs are determined by the sizes of the nanocrystals produced under different conditions and by surface interactions with small amounts of added solvent. For the first time, we show evidence that each of the three polymorphs is obtained with a unique and reproducible crystalline size. This mechanochemical approach gives access to bulk quantities of metastable polymorphs that are inaccessible through recrystallisation.
Next-generation thermal management requires the development of low lattice thermal conductivity materials, as observed in ionic conductors. For example, thermoelectric efficiency is increased when thermal conductivity is decreased. Detrimentally, high ionic conductivity leads to thermoelectric device degradation. Battery safety and design also require an understanding of thermal transport in ionic conductors. Ion mobility, structural complexity, and anharmonicity have been used to explain the thermal transport properties of ionic conductors. However, thermal and ionic transport are rarely discussed in direct comparison. Herein, the ionic conductivity of Ag+ argyrodites is found to change by orders of magnitude without altering the thermal conductivity. Thermal conductivity measurements and two-channel lattice dynamics modeling reveal that the majority of Ag+ vibrations have a non-propagating diffuson-like character, similar to amorphous materials. It is found that high ionic mobility is not a requirement for diffuson-mediated transport. Instead, the same bonding and structural traits that can lead to fast ionic conduction also lead to diffuson-mediated transport. Bridging the fields of solid-state ionics and thermal transport, it is proposed that a vibrational perspective can lead to new design strategies for functional ionic conducting materials. As a first step, the authors relate the so-called Meyer-Neldel behavior in ionic conductors to phonon occupations.
n situ monitoring of mechanochemical reactions between dicyandiamide (DCD) and CuX2 salts (X = Cl−, NO3−), for the preparation of compounds of agrochemical interest, showed the appearance of a number of phases. It is demonstrated that milling conditions, such as the amount of water added in wet grinding and/or the milling frequency, may affect the course of the mechanochemical reactions, and drive the reaction towards the formation of different products. It has been possible to discover by in situ monitored experiments two novel crystalline forms, namely the neutral complexes [Cu(DCD)2(OH2)2(NO3)2] (2) and [Cu(DCD)2(OH2)Cl2]·H2O (4), in addition to the previously known molecular salt [Cu(DCD)2(OH2)2][NO3]2·2H2O (1, DIVWAG) and neutral complex [Cu(DCD)2(OH2)Cl2] (3, AQCYCU), for which no synthesis conditions were available. Compounds 2 and 4 were fully characterized via a combination of solid-state techniques, including X-ray diffraction, Raman spectroscopy and TGA.
Flexible organic crystals (elastic and plastic) are important materials for optical waveguides, tunable optoelectronic devices, and photonic integrated circuits. Here, we present highly elastic organic crystals of a Schiff base, 1-((E)-(2,5-dichlorophenylimino)methyl)naphthalen-2-ol (1), and an azine molecule, 2,4-dibromo-6-((E)-((E)-(2,6-dichlorobenzylidene)hydrazono)methyl)phenol (2). These microcrystals are highly flexible under external mechanical force, both in the macroscopic and the microscopic regimes. The mechanical flexibility of these crystals arises as a result of weak and dispersive C−H⋅⋅⋅Cl, Cl⋅⋅⋅Cl, Br⋅⋅⋅Br, and π⋅⋅⋅π stacking interactions. Singly and doubly-bent geometries were achieved from their straight shape by a micromechanical approach using the AFM cantilever tip. Crystals of molecules 1 and 2 display a bright-green and red fluorescence (FL), respectively, and selective reabsorption of a part of their FL band. Crystals 1 and 2 exhibit optical-path-dependent low loss emissions at the termini of crystal in their straight and even in extremely bent geometries. Interestingly, the excitation position-dependent optical modes appear in both linear and bent waveguides of crystals 1 and 2, confirming their light-trapping ability.
X-ray absorption spectroscopy (XAS) provides a unique, atom-specific tool to probe the electronic structure of solids. By surmounting long-held limitations of powder-based XAS using a dynamically averaged powder in a Resonant Acoustic Mixer (RAM), we demonstrate how time-resolved in situ (TRIS) XAS provides unprecedented detail of mechanochemical synthesis. The use of a custom-designed dispersive XAS (DXAS) setup allows us to increase the time resolution over existing fluorescence measurements from ∼15 min to 2 s for a complete absorption spectrum. Hence, we here establish TRIS-XAS as a viable method for studying mechanochemical reactions and sampling reaction kinetics. The generality of our approach is demonstrated through RAM-induced (i) bottom-up Au nanoparticle mechanosynthesis and (ii) the synthesis of a prototypical metal organic framework, ZIF-8. Moreover, we demonstrate that our approach also works with the addition of a stainless steel milling ball, opening the door to using TRIS-DXAS for following conventional ball milling reactions. We expect that our TRIS-DXAS approach will become an essential part of the mechanochemical tool box.