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1. Gas Phase Preparation of the Elusive Monobridged Ge( μ ‐H)GeH Molecule through Nonadiabatic Reaction Dynamics

   https://doi.org/10.1002/chem.202103999  

   Yang, Zhenghai; Sun, Bing‐Jian; He, Chao; Fatimah, Siti; Chang, Agnes_H_H; Kaiser, Ralf_I (January 2022, Chemistry – A European Journal)

   Abstract The hitherto elusive monobridged Ge(μ‐H)GeH (X¹A′) molecule was prepared in the gas phase by bimolecular reaction of atomic germanium with germane (GeH₄). Electronic structure calculations revealed that this reaction commenced on the triplet surface with the formation of a van der Waals complex, followed by insertion of germanium into a germanium‐hydrogen bond over a submerged barrier to form the triplet digermanylidene intermediate (HGeGeH₃); the latter underwent intersystem crossing from the triplet to the singlet surface. On the singlet surface, HGeGeH₃predominantly isomerized through two successive hydrogen shifts prior to unimolecular decomposition to Ge(μ‐H)GeH isomer, which is in equilibrium with the vinylidene‐type (H₂GeGe) and dibridged (Ge(μ‐H₂)Ge) isomers. This reaction leads to the formation of cyclic dinuclear germanium molecules, which do not exist on the isovalent C₂H₂surface, thus deepening our understanding of the role of nonadiabatic reaction dynamics in preparing nonclassical, hydrogen‐bridged isomers carrying main group XIV elements. 

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2. Structural analysis of wild-type and Val120Thr mutant Candida boidinii formate dehydrogenase by X-ray crystallography

   https://doi.org/10.1107/s2059798323008070  

   Gul, Mehmet; Yuksel, Busra; Bulut, Huri; DeMirci, Hasan (November 2023, Acta Crystallographica Section D Structural Biology)

   Candida boidiniiNAD⁺-dependent formate dehydrogenase (CbFDH) has gained significant attention for its potential application in the production of biofuels and various industrial chemicals from inorganic carbon dioxide. The present study reports the atomic X-ray crystal structures of wild-typeCbFDH at cryogenic and ambient temperatures, as well as that of the Val120Thr mutant at cryogenic temperature, determined at the Turkish Light Source `Turkish DeLight'. The structures reveal new hydrogen bonds between Thr120 and water molecules in the active site of the mutantCbFDH, suggesting increased stability of the active site and more efficient electron transfer during the reaction. Further experimental data is needed to test these hypotheses. Collectively, these findings provide invaluable insights into future protein-engineering efforts that could potentially enhance the efficiency and effectiveness ofCbFDH. 

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3. Helical twists and β‐turns in structures at serine–proline sequences: Stabilization of cis ‐proline and type VI β‐turns via C–H/O interactions

   https://doi.org/10.1002/prot.26701  

   Oven, Harrison_C; Yap, Glenn_P_A; Zondlo, Neal_J (May 2024, Proteins: Structure, Function, and Bioinformatics)

   Abstract Structures at serine‐proline sites in proteins were analyzed using a combination of peptide synthesis with structural methods and bioinformatics analysis of the PDB. Dipeptides were synthesized with the proline derivative (2S,4S)‐(4‐iodophenyl)hydroxyproline [hyp(4‐I‐Ph)]. The crystal structure of Boc‐Ser‐hyp(4‐I‐Ph)‐OMe had two molecules in the unit cell. One molecule exhibitedcis‐proline and a type VIa2 β‐turn (BcisD). Thecis‐proline conformation was stabilized by a C–H/O interaction between Pro C–H_αand the Ser side‐chain oxygen. NMR data were consistent with stabilization ofcis‐proline by a C–H/O interaction in solution. The other crystallographically observed molecule hadtrans‐Pro and both residues in the PPII conformation. Two conformations were observed in the crystal structure of Ac‐Ser‐hyp(4‐I‐Ph)‐OMe, with Ser adopting PPII in one and the β conformation in the other, each with Pro in the δ conformation andtrans‐Pro. Structures at Ser‐Pro sequences were further examined via bioinformatics analysis of the PDB and via DFT calculations. Ser‐Pro versus Ala–Pro sequences were compared to identify bases for Ser stabilization of local structures. C–H/O interactions between the Ser side‐chain O_γand Pro C–H_αwere observed in 45% of structures with Ser‐cis‐Pro in the PDB, with nearly all Ser‐cis‐Pro structures adopting a type VI β‐turn. 53% of Ser‐trans‐Pro sequences exhibited main‐chain CO_i•••HN_i+3or CO_i•••HN_i+4hydrogen bonds, with Ser as theiresidue and Pro as thei + 1 residue. These structures were overwhelmingly either type I β‐turns or N‐terminal capping motifs on α‐helices or 3₁₀‐helices. These results indicate that Ser‐Pro sequences are particularly potent in favoring these structures. In each, Ser is in either the PPII or β conformation, with the Ser O_γcapable of engaging in a hydrogen bond with the amide N–H of thei + 2 (type I β‐turn or 3₁₀‐helix; Serχ₁t) ori + 3 (α‐helix; Serχ₁g⁺) residue. Non‐prolinecisamide bonds can also be stabilized by C–H/O interactions. 

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4. Understanding structural distortions in hybrid layered perovskites with the n = 1 Ruddlesden–Popper structure

   https://doi.org/10.1107/S2052252523003743  

   Liu, Tianyu; Holzapfel, Noah P.; Woodward, Patrick M. (July 2023, IUCrJ)

   A symmetry mode analysis yields 47 symmetrically distinct patterns of octahedral tilting in hybrid organic–inorganic layered perovskites that adopt then= 1 Ruddlesden–Popper (RP) structure. The crystal structures of compounds belonging to this family are compared with the predictions of the symmetry analysis. Approximately 88% of the 140 unique structures have symmetries that agree with those expected based on octahedral tilting alone, while the remaining compounds have additional structural features that further lower the symmetry, such as asymmetric packing of bulky organic cations, distortions of metal-centered octahedra or a shift of the inorganic layers that deviates from thea/2 +b/2 shift associated with the RP structure. The structures of real compounds are heterogeneously distributed amongst the various tilt systems, with only 9 of the 47 tilt systems represented. No examples of in-phase ψ-tilts about theaand/orbaxes of the undistorted parent structure were found, while at the other extreme ∼66% of the known structures possess a combination of out-of-phase ϕ-tilts about theaand/orbaxes and θ-tilts (rotations) about thecaxis. The latter combination leads to favorable hydrogen bonding interactions that accommodate the chemically inequivalent halide ions within the inorganic layers. In some compounds, primarily those that contain either Pb²⁺or Sn²⁺, favorable hydrogen bonding interactions can also be achieved by distortions of the octahedra in combination with θ-tilts. 

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5. Hydrogen migration in inner-shell ionized halogenated cyclic hydrocarbons

   https://doi.org/10.1038/s41598-023-28694-x  

   Abid, Abdul Rahman; Bhattacharyya, Surjendu; Venkatachalam, Anbu Selvam; Pathak, Shashank; Chen, Keyu; Lam, Huynh Van Sa; Borne, Kurtis; Mishra, Debadarshini; Bilodeau, René C.; Dumitriu, Ileana; et al (February 2023, Scientific Reports)

   Abstract We have studied the fragmentation of the brominated cyclic hydrocarbons bromocyclo-propane, bromocyclo-butane, and bromocyclo-pentane upon Br(3d) and C(1s) inner-shell ionization using coincidence ion momentum imaging. We observe a substantial yield of CH₃⁺fragments, whose formation requires intramolecular hydrogen (or proton) migration, that increases with molecular size, which contrasts with prior observations of hydrogen migration in linear hydrocarbon molecules. Furthermore, by inspecting the fragment ion momentum correlations of three-body fragmentation channels, we conclude that CH_x⁺fragments (withx = 0, …, 3) with an increasing number of hydrogens are more likely to be produced via sequential fragmentation pathways. Overall trends in the molecular-size-dependence of the experimentally observed kinetic energy releases and fragment kinetic energies are explained with the help of classical Coulomb explosion simulations. 

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