Comment on "Exploring nature and predicting strength of hydrogen bonds: A correlation analysis between atoms-in-molecules descriptors, binding energies, and energy components of symmetry-adapted perturbation theory"

Alkoxy-Bridged Dicopper(II) Cores Meet Tetracyanonickelate Linkers: Structural, Magnetic, and Theoretical Investigation of Cu/Ni Coordination Polymers

Two heterometallic Cu(II)/Ni(II) coordination polymers, [Cu2(Hbdea)2Ni(CN)4]n (1) and [Cu2(dmea)2Ni(CN)4]n·nH2O (2), were successfully self-assembled in water by reacting Cu(II) nitrate with H2bdea (N-butyldiethanolamine) and Hdmea (N,N-dimethylethanolamine) in the presence of sodium hydroxide and [Ni(CN)4]2-. These new coordination polymers were investigated by single-crystal and powder X-ray diffraction and fully characterized by FT-IR spectroscopy, thermogravimetry, elemental analysis, variable-temperature magnetic susceptibility measurements, and theoretical DFT and CASSCF calculations. Despite differences in crystal systems, in both compounds, each dinuclear building block [Cu2(μ-aminopolyalcoholate)2]2+ is bridged by diamagnetic [Ni(CN)4]2- linkers, resulting in 1D (1) or 2D (2) metal-organic architectures. Experimental magnetic studies show that both compounds display strong antiferromagnetic coupling (J = -602.1 cm-1 for 1 and -151 cm-1 for 2) between Cu(II) ions within the dimers mediated by the μ-O-alkoxo bridges. These results are corroborated by the broken symmetry DFT studies, which also provide further insight into the electronic structures of copper dimeric units. By reporting a facile self-assembly synthetic protocol, this study can be a model to widen a still limited family of heterometallic Cu/Ni coordination polymer materials with different functional properties.

Mechanistic Insights into S-Depalmitolyse Activity of Cln5 Protein Linked to Neurodegeneration and Batten Disease: A QM/MM Study

Ceroid lipofuscinosis neuronal protein 5 (Cln5) is encoded by the CLN5 gene. The genetic variants of this gene are associated with the CLN5 form of Batten disease. Recently, the first crystal structure of Cln5 was reported. Cln5 shows cysteine palmitoyl thioesterase S-depalmitoylation activity, which was explored via fluorescent emission spectroscopy utilizing the fluorescent probe DDP-5. In this work, the mechanism of the reaction between Cln5 and DDP-5 was studied computationally by applying a QM/MM methodology at the ωB97X-D/6-31G(d,p):AMBER level. The results of our study clearly demonstrate the critical role of the catalytic triad Cys280-His166-Glu183 in S-depalmitoylation activity. This is evidenced through a comparison of the pathways catalyzed by the Cys280-His166-Glu183 triad and those with only Cys280 involved. The computed reaction barriers are in agreement with the catalytic efficiency. The calculated Gibb's free-energy profile suggests that S-depalmitoylation is a rate-limiting step compared to the preceding S-palmitoylation, with barriers of 26.1 and 25.3 kcal/mol, respectively. The energetics were complemented by monitoring the fluctuations in the electron density distribution through NBO charges and bond strength alterations via local mode stretching force constants during the catalytic pathways. This comprehensive protocol led to a more holistic picture of the reaction mechanism at the atomic level. It forms the foundation for future studies on the effects of gene mutations on both the S-palmitoylation and S-depalmitoylation steps, providing valuable data for the further development of enzyme replacement therapy, which is currently the only FDA-approved therapy for childhood neurodegenerative diseases, including Batten disease.

Iridium-Catalyzed Regioselective Borylation through C-H Activation and the Origin of Ligand-Dependent Regioselectivity Switching

Research efforts in catalytic regioselective borylation using C-H bond activation of arenes have gained considerable recent attention. The ligand-enabled regiocontrol, such as in the borylation of benzaldehyde, the selectivity could be switched from the ortho to meta position, under identical conditions, by just changing the external ligand (L) from 8-aminoquinoline (8-AQ) to tetramethylphenanthroline (TMP). The DFT(B3LYP-D3) computations helped us learn that the energetically preferred catalytic pathway includes the formation of an Ir-π-complex between the active catalyst [Ir(L)(Bpin)₃] and benzaldimine, a C-H bond oxidative addition (OA) to form an Ir(V)aryl-hydride intermediate, and a reductive elimination to furnish the borylated benzaldehyde as the final product. The lowest energetic span (δE_ortho = 26 kcal/mol with 8-AQ) is noted in the ortho borylation pathway, with the OA transition state (TS) as the turnover-determining TS. The change in regiochemical preference to the meta borylation (δE_meta = 26) with TMP is identified. A hemilabile mode of 8-AQ participation is found to exhibit a δE_ortho of 24 kcal/mol for the ortho borylation, relative to that in the chelate mode (δE_ortho = 26 kcal/mol). The predicted regioselectivity switching is in good agreement with the earlier experimental observations.