Biphenyl is a prototype molecule, the study of which is important for a proper understanding of stereo-electronic effects. In the gas phase it has an equilibrium central torsion angle of ~ 45° and shows both a planar (0°) and a perpendicular (90°) torsional energy barrier. The latter is analysed for the first time. We use the newly proposed REG method, which is an procedure that ranks atomic energy contributions according to their importance in explaining the energy profile of a total system. Here, the REG method operates on energy contributions computed by the interacting quantum atoms method. This method is minimal in architecture and provides a crisp picture of well-defined and well-separated electrostatic, steric and exchange (covalent) energies at atomistic level. It is shown that the bond critical point occurring between the -hydrogens in the planar geometry has been wrongly interpreted as a sign of repulsive interaction. A convenient metaphor of analysing football matches is introduced to clarify the role of a REG analysis.
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http://dx.doi.org/10.1007/s00214-018-2383-0 | DOI Listing |
J Chem Phys
January 2025
Department of Chemistry, New York University, New York, New York 10003, USA.
The water trimer, as the smallest water cluster in which the three-body interactions can manifest, is arguably the most important hydrogen-bonded trimer. Accurate, fully coupled quantum treatment of its excited intermolecular vibrations has long been an elusive goal. Here, we present the methodology that for the first time allows rigorous twelve-dimensional (12D) quantum calculation of the intermolecular vibration-tunneling eigenstates of the water trimer, with the monomers treated as rigid.
View Article and Find Full Text PDFChem Sci
December 2024
ByteDance Research Bellevue Washington 98004 USA
A force field is a critical component in molecular dynamics simulations for computational drug discovery. It must achieve high accuracy within the constraints of molecular mechanics' (MM) limited functional forms, which offers high computational efficiency. With the rapid expansion of synthetically accessible chemical space, traditional look-up table approaches face significant challenges.
View Article and Find Full Text PDFJOR Spine
March 2025
Beijing Key Laboratory for Design and Evaluation Technology of Advanced Implantable & Interventional Medical Devices, Beijing Advanced Innovation Center for Biomedical Engineering, School of Biological Science and Medical Engineering Beihang University Beijing China.
Background: Growth rods are the gold standard for treating early-onset scoliosis (EOS). However, current treatments with growth rods do not optimize spinal growth in EOS patients, and frequent distraction surgeries significantly increase complications, imposing considerable economic and psychological burdens on patients. An improved growth rod is urgently required to address the need for dynamic growth and external regulation.
View Article and Find Full Text PDFSensors (Basel)
December 2024
Institute of Fundamental Technological Research, Polish Academy of Sciences, ul. Pawińskiego 5B, 02-106 Warsaw, Poland.
In this paper, we demonstrate that torsional surface elastic waves can propagate along the curved surface of a metamaterial elastic rod (cylinder) embedded in a conventional elastic medium. The crucial parameter of the metamaterial rod is its elastic compliance s44(1)ω, which varies as a function of frequency ω analogously to the dielectric function εω in Drude's model of metals. As a consequence, the elastic compliance s44(1)ω can take negative values s44(1)ω<0 as a function of frequency ω.
View Article and Find Full Text PDFProteins
January 2025
Department of Biotechnology, Maulana Abul Kalam Azad University of Technology, Haringhata, India.
The structural plasticity of proteins at the molecular level is largely dictated by backbone torsion angles, which play a critical role in ligand recognition and binding. To establish the anion-induced cooperative arrangement of the main-chain (mc) torsion, herein, we analyzed a set of naturally occurring CαNN motifs as "static models" for their anion-binding competence through docking and molecular dynamics simulations and decoded its torsion angle influenced mc-driven anion recognition potential. By comparing a pool of 20 distinct sets of CαNN motif with identical sequences in their "anion bound/present, aP" and "anion free/absent, aA" versions, we could discern that there exists a positive correlation between the "difference of anion residence time (ΔR)" and "difference among the main-chain torsion angle" of the aP and aA population.
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