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1. Search for Osme Bonds with π Systems as Electron Donors

   https://doi.org/10.3390/molecules29010079  

   Wang, Xin; Li, Qingzhong; Scheiner, Steve (January 2024, Molecules)

   The Osme bond is defined as pairing a Group 8 metal atom as an electron acceptor in a noncovalent interaction with a nucleophile. DFT calculations with the ωB97XD functional consider MO4 (M = Ru, Os) as the Lewis acid, paired with a series of π electron donors C2H2, C2H4, C6H6, C4H5N, C4H4O, and C4H4S. The calculations establish interaction energies in the range between 9.5 and 26.4 kJ/mol. Os engages in stronger interactions than does Ru, and those involving more extensive π-systems within the aromatic rings form stronger bonds than do the smaller ethylene and acetylene. Extensive analysis questions the existence of a true Osme bond, as the bonding chiefly involves interactions with the three O atoms of MO4 that lie closest to the π-system, via π(C-C)→σ*(M-O) transfers. These interactions are supplemented by back donation from M-O bonds to the π*(CC) antibonding orbitals of the π-systems. Dispersion makes a large contribution to these interactions, higher than electrostatics and much greater than induction. 

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2. Participation of transition metal atoms in noncovalent bonds

   https://doi.org/10.1039/D4CP03716B  

   Scheiner, Steve (November 2024, Physical Chemistry Chemical Physics)

   All metals of the d-block are capable of forming σ and π-hole bonds to a nucleophile. Some of these bonds are typical of noncovalent bonds, but others are strong enough to be characterized as a covalent coordinate bond. 

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3. Non‐classical Non‐covalent σ‐Hole Interactions in Protein Structure and Function: Concepts for Potential Protein Engineering Applications

   https://doi.org/10.1002/asia.202300026  

   Walker, Margaret G.; Mendez, C. Gustavo; Ho, P. Shing (April 2023, Chemistry – An Asian Journal)

   Abstract The structures and associated functions of biological molecules are driven by noncovalent interactions, which have classically been dominated by the hydrogen bond (H‐bond). Introduction of the σ‐hole concept to describe the anisotropic distribution of electrostatic potential of covalently bonded elements from across the periodic table has opened a broad range of nonclassical noncovalent ( nc NC) interactions for applications in chemistry and biochemistry. Here, we review how halogen bonds, chalcogen bonds and tetrel bonds, as they are found naturally or introduced synthetically, affect the structures, assemblies, and potential functions of peptides and proteins. This review intentionally focuses on examples that introduce or support principles of stability, assembly and catalysis that can potentially guide the design of new functional proteins. These three types of nc NC interactions have energies that are comparable to the H‐bond and, therefore, are now significant concepts in molecular recognition and design. However, the recently described H‐bond enhanced X‐bond shows how synergism among nc NC interactions can be exploited as potential means to broaden the range of their applications to affect protein structures and functions. 

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4. Engineering Colossal Anisotropic Thermal Expansion into Organic Materials through Dimensionality Control

   https://doi.org/10.1021/acs.chemmater.3c01677  

   Juneja, Navkiran; Unruh, Daniel K.; Hutchins, Kristin M. (September 2023, Chemistry of Materials)

   Thermal expansion (TE) behavior in solid-state materials is influenced by both molecular and supramolecular structure. For solid-state materials assembled through covalent bonds, such as carbon allotropes, solids with higher dimensionality (i.e., diamond) exhibit less TE than solids with lower dimensionality (e.g., fullerene, graphite). Thus, as the dimensionality of the solid increases, the TE decreases. However, an analogous and systematic variation of the dimensionality in solid-state materials assembled through noncovalent bonds with a correlation to TE has not been studied. Here, we designed a series of solids based on dimensional hierarchy to afford materials with zero-dimensional (0D), 1D, and 2D hydrogen-bonded structures. The 2D materials are structural analogues of graphite and covalent-organic frameworks, and we demonstrate that these 2D solids exhibit unique biaxial zero TE with anisotropic and colossal TE along the π-stacked direction (α ∼ 200 MK–1). The overall behavior in the 2D hydrogen-bonded solids is similar to 2D covalent-bonded solids; however, the coefficient of TE along the π-stacked direction for these hydrogen-bonded solids is an order of magnitude higher than in 2D graphite or phosphorus allotropes. The hierarchal materials design strategy and correlation to TE properties described herein can be broadly applied to the design and synthesis of new solid-state materials sustained by covalent or noncovalent bonds with control over solid-state behaviors. 

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5. An Inherent Difference between Serine and Threonine Phosphorylation: Phosphothreonine Strongly Prefers a Highly Ordered, Compact, Cyclic Conformation

   https://doi.org/10.1021/acschembio.3c00068  

   Pandey, Anil K.; Ganguly, Himal K.; Sinha, Sudipta Kumar; Daniels, Kelly E.; Yap, Glenn P.; Patel, Sandeep; Zondlo, Neal J. (September 2023, ACS Chemical Biology)

   Phosphorylation and dephosphorylation of proteins by kinases and phosphatases are central to cellular responses and function. The structural effects of serine and threonine phosphorylation were examined in peptides and in proteins, by circular dichroism, NMR spectroscopy, bioinformatics analysis of the PDB, small-molecule X-ray crystallography, and computational investigations. Phosphorylation of both serine and threonine residues induces substantial conformational restriction in their physiologically more important dianionic forms. Threonine exhibits a particularly strong disorder-to-order transition upon phosphorylation, with dianionic phosphothreonine preferentially adopting a cyclic conformation with restricted φ (φ ~ –60 ̊) stabilized by three noncovalent interactions: a strong intraresidue phosphate-amide hydrogen bond, an n→π* interaction between consecutive carbonyls, and an n→σ* interaction between the phosphate Oγ lone pair and the antibonding orbital of C–Hβ that restricts the χ2 side chain conformation. Proline is unique among the canonical amino acids for its covalent cyclization on the backbone. Phosphothreonine can mimic proline's backbone cyclization via noncovalent interactions. The preferred torsions of dianionic phosphothreonine are φ,ψ = polyproline II helix > α-helix (φ ~ –60 ̊); χ1 = g–; χ2 ~ +115 ̊ (eclipsed C–H/O–P bonds). This structural signature is observed in diverse proteins, including in the activation loops of protein kinases and in protein-protein interactions. In total, these results suggest a structural basis for the differential use and evolution of threonine versus serine phosphorylation sites in proteins, with serine phosphorylation typically inducing smaller, rheostat-like changes, versus threonine phosphorylation promoting larger, step function-like switches, in proteins. 

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