The ligand field molecular mechanics method has been extended to treat η(6)-arene ligands coordinated to a ruthenium(II) centre by employing a dummy atom located at the centroid of the arene ring and distributing the forces on the dummy to the arene carbon atoms. Angular overlap model parameters based on orbital energies derived from Kohn-Sham density functional theory (KS-DFT) calculations show that, relative to the Ru-dummy vector, the arene behaves as a very strong π donor and weak σ donor. Based on KS-DFT geometries, partial atomic charges and potential energy scans for a series of homoleptic and half sandwich complexes spanning arene, am(m)ine, imine, pyridyl, hydride and chloride ligands, a new LFMM force field has been developed which accurately reproduces the KS-DFT data. This FF was validated against 47 half-sandwich complexes obtained from the Cambridge Structural Database which, after minor corrections to account for the systematic errors between our chosen functional (BP86) and the experimental structures, yields a 'structurally tuned' FF where 93% of the Ru-L contacts are reproduced to 0.05 Å or better and all bar two bond lengths are within 0.1 Å of experiment. Over half the systems have non-hydrogen-atom rmsds of less than 0.5 Å. Larger differences are usually due to rotation of the arene moiety which is shown by ligand field molecular dynamics (LFMD) simulations to be an inherently low-energy process. Comparisons between LFMD and Car-Parrinello MD for [Ru(p-cymene)(ethylenediamine)Cl](+)show that LFMD is equally accurate but much faster enabling modelling of dynamic properties which occur on a timescale beyond the scope of CPMD.
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http://dx.doi.org/10.1039/c1dt10794a | DOI Listing |
Commun Chem
January 2025
Faculty of Engineering, Hokkaido University, Kita 13, Nishi 8, Kita-ku, Sapporo, Hokkaido, 060-8628, Japan.
Photoinduced metal-to-ligand (or ligand-to-metal) charge-transfer (CT) states in metal complexes have been extensively studied toward the development of luminescent materials. However, previous studies have mainly focused on CT transitions between d- and π-orbitals. Herein, we report the demonstration of CT emission from 4f- to π-orbitals using a trivalent europium (Eu(III)) complex, supported by both experimental and theoretical analyses.
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January 2025
Athinoula A. Martinos Center for Biomedical Imaging, Department of Radiology, Massachusetts General Hospital, Harvard Medical School, Boston, MA 02129, USA.
Although the pathophysiology of migraine involves a complex ensemble of peripheral and central nervous system changes that remain incompletely understood, the activation and sensitization of the trigeminovascular system is believed to play a major role. However, non-invasive, in vivo neuroimaging studies investigating the underlying neural mechanisms of trigeminal system abnormalities in human migraine patients are limited. Here, we studied 60 patients with migraine (55 females, mean age ± SD: 36.
View Article and Find Full Text PDFProtein Sci
February 2025
Yusuf Hamied Department of Chemistry, University of Cambridge, Cambridge, UK.
We have recently demonstrated a novel anaerobic NADH-dependent haem breakdown reaction, which is carried out by a range of haemoproteins. The Yersinia enterocolitica protein, HemS, is the focus of further research presented in the current paper. Using conventional experimental methods, bioinformatics, and energy landscape theory (ELT), we provide new insight into the mechanism of the novel breakdown process.
View Article and Find Full Text PDFNanoscale
January 2025
Lawrence Livermore National Laboratory, 7000 East Ave, Livermore, CA 94550, USA.
Quantum dots (QDs) are promising materials for optoelectronic applications, but their widespread adoption requires controllable, selective, and scalable deposition methods. While traditional methods like spin coating and drop casting are suitable for small-scale deposition onto flat substrates, and ink-jet printing offers precision for small areas, these methods struggle with conformal deposition onto non-planar, large area substrates or selective deposition onto large area chips. Electrophoretic deposition (EPD) is an efficient and versatile technique capable of achieving conformal and selective area deposition over large areas, but its application to QD films has been limited.
View Article and Find Full Text PDFCurr Top Dev Biol
January 2025
Development, Aging, and Regeneration Program, Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA, United States. Electronic address:
All-trans RA (ATRA) is a small molecule derived from retinol (vitamin A) that directly controls gene expression at the transcriptional level by serving as a ligand for nuclear ATRA receptors. ATRA is produced by ATRA-generating enzymes that convert retinol to retinaldehyde (retinol dehydrogenase; RDH10) followed by conversion of retinaldehyde to ATRA (retinaldehyde dehydrogenase; ALDH1A1, ALDH1A2, or ALDH1A3). Determining what ATRA normally does during vertebrate development has been challenging as studies employing ATRA gain-of-function (RA treatment) often do not agree with genetic loss-of-function studies that remove ATRA via knockouts of ATRA-generating enzymes.
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