Double- and triple-decker lanthanide phthalocyaninates exhibit unique physical-chemical properties, particularly single-molecule magnetism. Among other factors, the magnetic properties of these sandwiches depend on their conformational state, which is determined via the skew angle of the phthalocyanine ligands. Thus, in the present work we report the comprehensive conformational study of substituted terbium(III) and yttrium(III) trisphthalocyaninates in solution depending on the substituents at the periphery of molecules, redox-states and nature of solvents. Conjunction of UV-vis-NIR spectroscopy and quantum-chemical calculations within simplified time-dependent DFT in Tamm-Dancoff approximation provided the spectroscopic signatures of staggered and gauche conformations of trisphthalocyaninates. Altogether, it allowed us to demonstrate that the butoxy-substituted complex behaves as a molecular switcher with controllable conformational state, while the crown-substituted triple-decker complex maintains a staggered conformation regardless of external factors. The analysis of noncovalent interactions within the reduced density gradient approach allowed to shed light on the nature of factors stabilizing certain conformers.
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http://dx.doi.org/10.3390/molecules27196498 | DOI Listing |
Proc Natl Acad Sci U S A
January 2025
Laboratory for Protein Crystallography, Institute for Protein Research, Osaka University, Suita, Osaka 565-0871, Japan.
[FeFe]-hydrogenases catalyze the reversible two-electron reduction of two protons to molecular hydrogen. Although these enzymes are among the most efficient H-converting biocatalysts in nature, their catalytic cofactor (termed H-cluster) is irreversibly destroyed upon contact with dioxygen. The [FeFe]-hydrogenase CbA5H from has a unique mechanism to protect the H-cluster from oxygen-induced degradation.
View Article and Find Full Text PDFJ Am Chem Soc
January 2025
Warshel Institute for Computational Biology, School of Life and Health Sciences, School of Medicine, The Chinese University of Hong Kong (Shenzhen), Shenzhen 518172, China.
The parathyroid hormone type 1 receptor (PTH1R) plays a crucial role in modulating various physiological functions and is considered an effective therapeutic target for osteoporosis. However, a lack of detailed molecular and energetic information about PTH1R limits our comprehensive understanding of its activation process. In this study, we performed computational simulations to explore key events in the activation process, such as conformational changes in PTH1R, Gs protein coupling, and the release of guanosine diphosphate (GDP).
View Article and Find Full Text PDFJ Phys Chem B
January 2025
Institute of Quantitative Biology, College of Life Sciences, and School of Physics, Zhejiang University, Hangzhou, Zhejiang 310058, China.
The emergence of nanopores in two-dimensional (2D) nanomaterials offers an attractive solid-state platform for high-throughput and low-cost DNA sequencing. However, several challenges remain to be addressed before their wide application, including the too-fast DNA translocation speed (compared to state-of-the-art single nucleoside detection techniques) and too large noise/signal ratios due to DNA fluctuations inside the nanopores. Here, we use molecular dynamics (MD) simulations to demonstrate the feasibility of utilizing RNA-DNA interactions in modulating DNA translocations in 2D MoS nanopores.
View Article and Find Full Text PDFJ Chem Theory Comput
January 2025
Computational Chemistry and Molecular Biophysics Section, Molecular Targets and Medications Discovery Branch, National Institute on Drug Abuse - Intramural Research Program, National Institutes of Health, Baltimore, Maryland 21224, United States.
We have developed a method that uses energy landscapes of unbound and bound ligands to compute reorganization free energies for end-point binding free-energy calculations. The method is applied to our previous simulations of fentanyl derivatives bound to the μ opioid receptor in different orientations. Whereas the mean interaction energy provides an ambiguous ranking of binding poses, interaction entropy and ligand reorganization strongly penalize geometric decoys such that native poses observed in CryoEM structures are best ranked.
View Article and Find Full Text PDFGenome organization recapitulates function, yet ciliates like possess highly-specialized germline genomes, which are largely transcriptionally silent. During post-zygotic development, 's germline undergoes large-scale genome editing, rearranging precursor genome elements into a transcriptionally-active genome with thousands of gene-sized nanochromosomes. Transgenerationally-inherited RNAs, derived from the parental somatic genome, program the retention and reordering of germline fragments.
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