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An accurate quantum mechanical description of the vibrational dynamics and IR spectra of molecules is illustrated here for the formic acid dimer, (HCOOH)2 and its isotopologues (DCOOH)2 and (DCOOD)2 in full dimensionality. The calculations make use of recent full-dimensional ab initio potential energy and dipole moment surfaces and are done with the code MULTIMODE. IR spectra are reported for the three dimers and also compared to available experimental spectra. In addition, standard classical and "semiclassically prepared" quasiclassical molecular dynamics calculations of the IR spectra of these complexes are reported and compared to the quantum spectra and also experiment. These comparisons indicate good accuracy of the MD spectra for sharp bands but not for the complex O-H stretch band, where the complex molecular dynamics band is upshifted from experiments by roughly 300 cm-1. For the fully deuterated dimer (DCOOD)2, the quantum spectral band for the O-D stretch sharpens relative to the O-H spectral bands in (HCOOH)2 and (DCOOH)2; however, the molecular dynamics OD stretch band does not exhibit this sharpening.
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http://dx.doi.org/10.1039/c8fd00077h | DOI Listing |
Biochem J
September 2025
Department of Biological Sciences, Indian Institute of Science Education and Research Kolkata, Mohanpur Campus, Mohanpur, 741246 Nadia, West Bengal, India.
Transcription initiation factor TFIID subunit 1 (TAF1) is a pivotal component of the TFIID complex, critical for RNA polymerase II-mediated transcription initiation. However, the molecular basis by which TAF1 recognizes and associates with chromatin remains incompletely understood. Here, we report that the tandem bromodomain module of TAF1 engages nucleosomal DNA through a distinct positively charged surface patch on the first bromodomain (BD1).
View Article and Find Full Text PDFVet Res Commun
September 2025
College of Veterinary Medicine, Vietnam National University of Agriculture, 100000, Hanoi, Vietnam.
African swine fever (ASF) is a contagious viral disease that affects domestic pigs and Eurasian wild boars, causing significant economic losses to the global pig industry. Since its first outbreak in February 2019, ASF has had a profound impact on the Vietnamese pig sector. This review presents a comprehensive analysis of ASF outbreaks in Vietnam from 2019 to 2024, focusing on outbreak dynamics, control strategies, economic impact, and key lessons learned.
View Article and Find Full Text PDFMol Divers
September 2025
Department of Pharmacognosy, College of Pharmacy, Prince Sattam Bin Abdulaziz University, 11942, Al Kharj, Saudi Arabia.
Cyclin-dependent kinase 20 (CDK20), also known as cell cycle-related kinase (CCRK), plays a pivotal role in hepatocellular carcinoma (HCC) progression by regulating β-catenin signaling and promoting uncontrolled proliferation. Despite its emerging significance, selective small-molecule inhibitors of CDK20 remain unexplored. In this study, a known CDK20 inhibitor, ISM042-2-048, was employed as a reference to retrieve structurally similar compounds from the PubChem database using an 85% similarity threshold.
View Article and Find Full Text PDFMol Divers
September 2025
State Key Laboratory Basis of Xinjiang Indigenous Medicinal Plants Resource Utilization, Xinjiang Technical Institute of Physics and Chemistry, Chinese Academy of Sciences, Urumqi, 830011, Xinjiang, China.
Aurora kinases are a group of serine/threonine kinases essential for cell mitosis, comprising Aurora A, B, and C. However, the Aurora B is overexpressed in multiple tumors and the aurone has been proved to exhibit potent inhibitory activity against Aurora B kinase by our group. The indolinone was considered as an aurone scaffold hopping analog, and the indolinone-based Aurora B inhibitor library (3577 molecules) was constructed by FBDD strategy.
View Article and Find Full Text PDFJ Math Biol
September 2025
Department of Mathematics, University of Illinois Urbana-Champaign, Urbana, USA.
A fundamental question in the field of molecular computation is what computational tasks a biochemical system can carry out. In this work, we focus on the problem of finding the maximum likelihood estimate (MLE) for log-affine models. We revisit a construction due to Gopalkrishnan of a mass-action system with the MLE as its unique positive steady state, which is based on choosing a basis for the kernel of the design matrix of the model.
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