Up to six different techniques are utilized to estimate the equilibrium structures (r(e)) of a series of mostly unsaturated, N-containing heterocycles. Accurate Born-Oppenheimer (r(e)(BO)) and, if allowed, semiexperimental (r(e)(SE)), as well as empirical (r(m)-type) estimates of the equilibrium structures of three-membered (1H- and 2H-azirine, aziridine), four-membered (azete), five-membered (pyrrole, pyrazole, imidazole), six-membered (pyridine, pyrimidine, uracil), and seven-membered (1H-azepine) rings, containing usually one but in some cases two N atoms, are determined. The agreement among the structural results of the different techniques is very satisfactory. It is shown that it is possible to use the CCSD(T) electronic structure method with the relatively small wCVTZ basis set, with all electrons correlated, and the effect of further basis set enlargement, wCVTZ → wCVQZ, computed at the MP2 level, to obtain reliable equilibrium structures for the semirigid molecules investigated. Extension to larger basis sets does not significantly improve the accuracy of the computed results. Although all molecules investigated are oblate, and their principal axis system is subject to large rotations upon isotopic substitution, the semiexperimental method, when applicable, provides accurate results, though in the difficult cases it must be augmented with the mixed regression method. Finally, it is noteworthy that the empirical mass-dependent (r(m)) method also delivers surprisingly accurate structures for this class of compounds.
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Angew Chem Int Ed Engl
January 2025
TU Dortmund University, Faculty for Chemistry and Chemical Biology, Otto-Hahn-Str. 6, 44227, Dortmund, GERMANY.
Precise control over the catenation process in interlocked supramolecular systems remains a significant challenge. Here, we report a system in which a lantern-shaped Pd2L4 cage can dimerize to form two distinct Pd4L8 catenanes with different interlocking degree: a previously described quadruply interlocked double cage motif of D4 symmetry and an unprecedented triply interlocked structure of C2h symmetry. While the former structure features a linear arrangement of four Pd(II) centers, separated by three mechanically linked pockets, the new motif has a staggered shape.
View Article and Find Full Text PDFMol Pharm
January 2025
Department of Industrial and Molecular Pharmaceutics, College of Pharmacy, Purdue University, 575 Stadium Mall Drive, West Lafayette, Indiana 47907, United States.
Lumefantrine (LMF) is a low-solubility antimalarial drug that cures acute, uncomplicated malaria. It exerts its pharmacological effects against erythrocytic stages of spp. and prevents malaria pathogens from producing nucleic acid and protein, thereby eliminating the parasites.
View Article and Find Full Text PDFJ Chem Inf Model
January 2025
Institute of Biophysics of the Czech Academy of Sciences, Kralovopolska 135, 612 00 Brno, Czech Republic.
RNA recognition motifs (RRMs) are a key class of proteins that primarily bind single-stranded RNAs. In this study, we applied standard atomistic molecular dynamics simulations to obtain insights into the intricate binding dynamics between uridine-rich RNAs and TbRGG2 RRM using the recently developed OL3-Stafix AMBER force field, which improves the description of single-stranded RNA molecules. Complementing structural experiments that unveil a primary binding mode with a single uridine bound, our simulations uncover two supplementary binding modes in which adjacent nucleotides encroach upon the binding pocket.
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View Article and Find Full Text PDFComput Struct Biotechnol J
December 2024
Department of Physics, University of Exeter, Stocker Rd., Exeter EX4 4QL, UK.
Magnetoreception, the ability to sense magnetic fields, is widespread in animals but remains poorly understood. The leading model links this ability in migratory birds to the photo-activation of the protein cryptochrome. Magnetic information is thought to induce structural changes in cryptochrome via a transient radical pair intermediate.
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