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1. Structurally Diverse Divalent Metal Adamantanedicarboxylate Coordination Polymers with Hydrogen‐bonding Capable Dipyridyl Pillaring Ligands

   https://doi.org/10.1002/zaac.201700388  

   Travis, Jamelah Z. ; Martinez, Brianna L. ; LaDuca, Robert L. ( November 2017 , Zeitschrift für anorganische und allgemeine Chemie)

   Five new divalent metal coordination polymers containing either 1,3‐adamantanedicarboxylate (adc) or 1,3‐adamantanediacetate (ada) and pillaring dipyridyl ligands were prepared and structurally characterized by single‐crystal X‐ray diffraction. Using the V‐shaped linker 4,4′‐dipyridylamine (dpa), three new phases were isolated. {[Zn₂(ada)₂(dpa)₂]·4.5H₂O}_n(1) shows a (4,4) grid topology with embedded octameric water clusters. {[Co(ada)(dpa)(H₂O)]·H₂O}_n(2) also manifests a 2D dimensionality, but with an intriguing novel (4)(12)(4.12⁵) looped topology. {[Cd(adc)(H₂O)₂]·H₂O}_n(3) did not incorporate dpa ligands during self‐assembly, but exhibits an uncommon 3‐connected 8³etbnetwork topology. [Co(ada)(ebin)]_n(4) [ebin = ethanediaminebis(nicotinamide)] possesses a (3,6) triangular net based on {Co₂(OCO)₂} dimeric units. {[Cd(adc)(ebin)]·2H₂O}_n(5) also shows dimeric units, although linked into a decorated (4,4) grid topology. Magnetic susceptibility studies of compound4revealed a decrease inχ_mTproduct upon cooling, ascribed to antiferromagnetic coupling concomitant with single‐ion effects [g= 2.39(2) withD= 40(3) cm^–1andJ= –3.55(4) cm^–1]. Compounds1and5undergo blue‐violet fluorescence upon ultraviolet irradiation; the zinc derivative1shows potential as a sensor for the solution‐phase detection of nitrobenzene andm‐nitrophenol. Thermal decomposition behavior of the five new phases is also discussed.

    

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2. Reactivity of Thiol-Rich Zn Sites in Diacylglycerol-Sensing PKC C1 Domain Probed by NMR Spectroscopy

   https://doi.org/10.3389/fmolb.2021.728711  

   Cole, Taylor R. ; Igumenova, Tatyana I. ( August 2021 , Frontiers in Molecular Biosciences)

   null (Ed.)

   Conserved homology 1 (C1) domains are peripheral zinc finger domains that are responsible for recruiting their host signaling proteins, including Protein Kinase C (PKC) isoenzymes, to diacylglycerol-containing lipid membranes. In this work, we investigated the reactivity of the C1 structural zinc sites, using the cysteine-rich C1B regulatory region of the PKCα isoform as a paradigm. The choice of Cd 2+ as a probe was prompted by previous findings that xenobiotic metal ions modulate PKC activity. Using solution NMR and UV-vis spectroscopy, we found that Cd 2+ spontaneously replaced Zn 2+ in both structural sites of the C1B domain, with the formation of all-Cd and mixed Zn/Cd protein species. The Cd 2+ substitution for Zn 2+ preserved the C1B fold and function, as probed by its ability to interact with a potent tumor-promoting agent. Both Cys 3 His metal-ion sites of C1B have higher affinity to Cd 2+ than Zn 2+ , but are thermodynamically and kinetically inequivalent with respect to the metal ion replacement, despite the identical coordination spheres. We find that even in the presence of the oxygen-rich sites presented by the neighboring peripheral membrane-binding C2 domain, the thiol-rich sites can successfully compete for the available Cd 2+ . Our results indicate that Cd 2+ can target the entire membrane-binding regulatory region of PKCs, and that the competition between the thiol- and oxygen-rich sites will likely determine the activation pattern of PKCs. 

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3. Probing the Ni 2+ ‐selective Response of Fluorescent Probe NiSensor‐1 with the NiCast Photocaged Complex † ‡

   https://doi.org/10.1111/php.13567  

   Hickey, Erin E. ; Kennedy, Daniel P. ; Gwizdala, Celina ; Basa, Prem N. ; Müller, Peter ; MacDonald, John ; Burdette, Shawn C. ( December 2021 , Photochemistry and Photobiology)

   CTEA (N,N‐bis[2‐(carboxylmethyl)thioethyl]amine) is a mixed donor ligand that has been incorporated into multiple fluorescent sensors such as NiSensor‐1 that was reported to be selective for Ni²⁺. Other metal ions such as Zn²⁺do not produce an emission response in aqueous solution. To investigate the coordination chemistry and selectivity of this receptor, we prepared NiCast, a photocage containing the CTEA receptor. Cast photocages undergo a photoreaction that decreases electron density on a metal‐bound aniline nitrogen atom, which shifts the binding equilibrium toward unbound metal ion. The unique selectivity of CTEA was examined by measuring the binding affinity of NiCast and the CTEA receptor for Ni²⁺, Zn²⁺, Cd²⁺and Cu²⁺under different conditions. In aqueous solution, Ni²⁺binds more strongly to the aniline nitrogen atom than Cd²⁺; however, in CH₃CN, the change in affinity virtually disappears. The crystal structure of [Cu(CTEA)], which exhibits a Jahn–Teller–distorted square pyramidal structure, was also analyzed to gain more insight into the underlying coordination chemistry. These studies suggest that the fluorescence selectivity of NiSensor‐1 in aqueous solution is due to a stronger interaction between the aniline nitrogen atom and Ni²⁺compared to other divalent metal ions except Cu²⁺.

    

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4. Harnessing interpretable and unsupervised machine learning to address big data from modern X-ray diffraction

   https://doi.org/10.1073/pnas.2109665119  

   Venderley, Jordan ; Mallayya, Krishnanand ; Matty, Michael ; Krogstad, Matthew ; Ruff, Jacob ; Pleiss, Geoff ; Kishore, Varsha ; Mandrus, David ; Phelan, Daniel ; Poudel, Lekhanath ; et al ( June 2022 , Proceedings of the National Academy of Sciences)

   The information content of crystalline materials becomes astronomical when collective electronic behavior and their fluctuations are taken into account. In the past decade, improvements in source brightness and detector technology at modern X-ray facilities have allowed a dramatically increased fraction of this information to be captured. Now, the primary challenge is to understand and discover scientific principles from big datasets when a comprehensive analysis is beyond human reach. We report the development of an unsupervised machine learning approach, X-ray diffraction (XRD) temperature clustering (X-TEC), that can automatically extract charge density wave order parameters and detect intraunit cell ordering and its fluctuations from a series of high-volume X-ray diffraction measurements taken at multiple temperatures. We benchmark X-TEC with diffraction data on a quasi-skutterudite family of materials, (Ca x Sr 1 − x ) 3 Rh 4 Sn 13 , where a quantum critical point is observed as a function of Ca concentration. We apply X-TEC to XRD data on the pyrochlore metal, Cd 2 Re 2 O 7 , to investigate its two much-debated structural phase transitions and uncover the Goldstone mode accompanying them. We demonstrate how unprecedented atomic-scale knowledge can be gained when human researchers connect the X-TEC results to physical principles. Specifically, we extract from the X-TEC–revealed selection rules that the Cd and Re displacements are approximately equal in amplitude but out of phase. This discovery reveals a previously unknown involvement of 5 d 2 Re, supporting the idea of an electronic origin to the structural order. Our approach can radically transform XRD experiments by allowing in operando data analysis and enabling researchers to refine experiments by discovering interesting regions of phase space on the fly. 

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5. Plastic recognition and electrogenic uniport translocation of 1 st -, 2 nd -, and 3 rd -row transition and post-transition metals by primary-active transmembrane P 1B-2 -type ATPase pumps

   https://doi.org/10.1039/D3SC00347G  

   Abeyrathna, Sameera S. ; Abeyrathna, Nisansala S. ; Basak, Priyanka ; Irvine, Gordon W. ; Zhang, Limei ; Meloni, Gabriele ( May 2023 , Chemical Science)

   Transmembrane P 1B -type ATPase pumps catalyze the extrusion of transition metal ions across cellular lipid membranes to maintain essential cellular metal homeostasis and detoxify toxic metals. Zn( ii )-pumps of the P 1B-2 -type subclass, in addition to Zn 2+ , select diverse metals (Pb 2+ , Cd 2+ and Hg 2+ ) at their transmembrane binding site and feature promiscuous metal-dependent ATP hydrolysis in the presence of these metals. Yet, a comprehensive understanding of the transport of these metals, their relative translocation rates, and transport mechanism remain elusive. We developed a platform for the characterization of primary-active Zn( ii )-pumps in proteoliposomes to study metal selectivity, translocation events and transport mechanism in real-time, employing a “multi-probe” approach with fluorescent sensors responsive to diverse stimuli (metals, pH and membrane potential). Together with atomic-resolution investigation of cargo selection by X-ray absorption spectroscopy (XAS), we demonstrate that Zn( ii )-pumps are electrogenic uniporters that preserve the transport mechanism with 1 st -, 2 nd - and 3 rd -row transition metal substrates. Promiscuous coordination plasticity, guarantees diverse, yet defined, cargo selectivity coupled to their translocation. 

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