The phonon modes of molecular crystals in the terahertz frequency region often feature delicately coupled inter- and intra-molecular vibrations. Recent advances in density functional theory such as DFT-D(*) have enabled accurate frequency calculation. However, the nature of normal modes has not been quantitatively discussed against experimental criteria such as isotope shift (IS) and correlation field splitting (CFS). Here, we report an analytical mode-decoupling method that allows for the decomposition of a normal mode of interest into intermolecular translation, libration, and intramolecular vibrational motions. We show an application of this method using the crystalline anthracene system as an example. The relationship between the experimentally obtained IS and the IS obtained by PBE-D(*) simulation indicates that two distinctive regions exist. Region I is associated with a pure intermolecular translation, whereas region II features coupled intramolecular vibrations that are further coupled by a weak intermolecular translation. We find that the PBE-D(*) data show excellent agreement with the experimental data in terms of IS and CFS in region II; however, PBE-D(*) produces significant deviations in IS in region I where strong coupling between inter- and intra-molecular vibrations contributes to normal modes. The result of this analysis is expected to facilitate future improvement of DFT-D(*).
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http://dx.doi.org/10.1063/1.4873421 | DOI Listing |
J Am Chem Soc
January 2025
Department of Chemistry, The Hong Kong Branch of Chinese National Engineering Research Center for Tissue Restoration and Reconstruction, Division of Life Science, State Key Laboratory of Molecular Neuroscience, and Department of Chemical & Biological Engineering, The Hong Kong University of Science and Technology, Clear Water Bay, Kowloon, Hong Kong 999077, China.
The two contradictory entities in nature often follow the principle of unity of opposites, leading to optimal overall performance. Particularly, aggregation-induced emission luminogens (AIEgens) with donor-acceptor (D-A) structures exhibit tunable optical properties and versatile functionalities, offering significant potential to revolutionize cancer treatment. However, trapped by low molar absorptivity (ε) owing to the distorted configurations, the ceilings of their photon-harvesting capability and the corresponding phototheranostic performance still fall short.
View Article and Find Full Text PDFInt J Mol Sci
December 2024
Department of Medicine, Division of Clinical Immunology, Ribeirão Preto Medical School, University of São Paulo, Ribeirão Preto 14049-900, SP, Brazil.
Citrullination, a post-translational modification (PTM), plays a critical role in rheumatoid arthritis (RA) by triggering immune responses to citrullinated self-antigens. Some HLA-DRB1 genes encode molecules with the shared epitope (QKRAA/QRRAA) sequence in the peptide-binding groove which preferentially presents citrulline-modified peptides, like vimentin, that intensifies the immune response in RA. In this study, we used computational approaches to evaluate intermolecular interactions between vimentin peptide-ligands (with/without PTM) and HLA-DRB1 alleles associated with a significantly increased risk for RA development.
View Article and Find Full Text PDFPhys Chem Chem Phys
January 2025
Department of Chemical Engineering, National Institute of Technology, Nara College, Yamatokoriyama, Nara 639-1080, Japan.
This study focuses on two types of phosphonium cation-based ionic liquids (P-ILs) with different alkyl chains: triethylalkylphosphonium (P222R) and tributylalkylphosphonium (P444R) cations. Broadband dielectric spectroscopy showed that the translational motion of the ions accelerated with an increasing number of alkyl chains by coupling with their rotational motion in both P-ILs. Raman spectroscopy revealed that P222R cations, despite dielectric similarities to P444R cations, can form all-trans conformations and cation-rich nanodomains because they have a relatively polar, short alkyl chain moiety with a central P atom and less-polar alkyl chains than those of P444R cations.
View Article and Find Full Text PDFInt J Biol Macromol
January 2025
State Key Laboratory of Heavy Oil Processing and Centre for Bioengineering and Biotechnology, China University of Petroleum (East China), Qingdao, Shandong, People's Republic of China. Electronic address:
Combining polymer and surfactant in one agent namely polymeric surfactants with both high viscosity and surface activity has become a viable alternative for the traditional enhanced oil recovery (EOR) processes. With the purpose of developing new polymeric surfactants, the biopolymer flooding agent sphingan WL gum was modified by octenyl succinic anhydride (OSA) through the esterification reaction. The effects of molecular weight (MW) of WL and the OSA: WL ratio on the properties of the products were investigated.
View Article and Find Full Text PDFTrends Biochem Sci
December 2024
Walter and Eliza Hall Institute of Medical Research, 1G Royal Parade, Parkville, VIC 3052, Australia; Department of Medical Biology, University of Melbourne, Parkville, VIC 3052, Australia; Drug Discovery Biology, Monash Institute of Pharmaceutical Sciences, Monash University, Parkville, VIC 3052, Australia. Electronic address:
Necroptosis is a mode of programmed cell death executed by the mixed lineage kinase domain-like (MLKL) pseudokinase following its activation by the upstream receptor-interacting protein kinase-3 (RIPK3), subsequent to activation of death, Toll-like, and pathogen receptors. The pathway originates in innate immunity, although interest has surged in therapeutically targeting necroptosis owing to its dysregulation in inflammatory diseases. Here, we explore how protein conformation and higher order assembly of the pathway effectors - Z-DNA-binding protein-1 (ZBP1), RIPK1, RIPK3, and MLKL - can be modulated by post-translational modifications, such as phosphorylation, ubiquitylation, and lipidation, and intermolecular interactions to tune activities and modulate necroptotic signaling flux.
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