The CHARMM force field for DMPC lipids was modified in order to improve agreement with experiment for a number of important properties of hydrated lipid bilayer. The modification consists in introduction of a scaling factor 0.83 for 1-4 electrostatic interactions (between atoms separated by three covalent bonds), which provides correct transgauche ratio in the alkane tails, and recalculation of the headgroup charges on the basis of HF/6-311(d,p) ab-initio computations. Both rigid TIP3P and flexible SPC water models were used with the new lipid model, showing similar results. The new model in a 75 ns simulation has shown a correct value of the area per lipid at zero surface tension, as well as good agreement with the experiment for the electron density, structure factor, and order parameters, including those in the headgroup part of lipids.
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http://dx.doi.org/10.1002/jcc.20974 | DOI Listing |
Polymers (Basel)
December 2024
Department of Chemistry and Biochemistry, University of South Carolina, Columbia, SC 29208, USA.
The mechanical properties of lignin, an aromatic heteropolymer constituting 20-30% plant biomass, are important to the fabrication and processing of lignin-based sustainable polymeric materials. In this study, atomistic simulations are performed to provide microscopic insights into the mechanics of lignin. Representative samples of miscanthus, spruce, and birch lignin are studied.
View Article and Find Full Text PDFJ Phys Condens Matter
January 2025
Departamento de Física, Universidade Federal de Santa Maria, 97105-900 Santa Maria, Brazil.
The study of emerging contaminants (ECs) in water resources has garnered significant attention due to their potential risks to human health and the environment. This review examines the contribution from computational approaches, focusing on the application of machine learning (ML) and molecular dynamics (MD) simulations to understand and optimize experimental applications of ECs adsorption on carbon-based nanomaterials. Condensed matter physics plays a crucial role in this research by investigating the fundamental properties of materials at the atomic and molecular levels, enabling the design and engineering of materials optimized for contaminant removal.
View Article and Find Full Text PDFJ Chem Phys
December 2024
Department of Chemistry, University of Chicago, Chicago, Illinois 60637, USA.
Peptoids (N-substituted glycines) are a class of sequence-defined synthetic peptidomimetic polymers with applications including drug delivery, catalysis, and biomimicry. Classical molecular simulations have been used to predict and understand the conformational dynamics of single chains and their self-assembly into morphologies including sheets, tubes, spheres, and fibrils. The CGenFF-NTOID model based on the CHARMM General Force Field has demonstrated success in accurate all-atom molecular modeling of peptoid structure and thermodynamics.
View Article and Find Full Text PDFbioRxiv
December 2024
Department of Biochemistry and Molecular Biology, Indiana University School of Medicine, Indianapolis, IN 46202, USA.
RNA-binding proteins shape biology through their widespread functions in RNA biochemistry. Their function requires the recognition of specific RNA motifs for targeted binding. These RNA binding elements can be composed of both unmodified and chemically modified RNAs, of which over 170 chemical modifications have been identified in biology.
View Article and Find Full Text PDFJ Comput Chem
January 2025
Laboratoire d'Optique et Biosciences (CNRS UMR7645, INSERM U1182), Ecole Polytechnique, Institut polytechnique de Paris, Palaiseau, France.
Folates comprise a crucial class of biologically active compounds related to folic acid, playing a vital role in numerous enzymatic reactions. One-carbon metabolism, facilitated by the folate cofactor, supports numerous physiological processes, including biosynthesis, amino acid homeostasis, epigenetic maintenance, and redox defense. Folates share a common pterin heterocyclic ring structure capable of undergoing redox reactions and existing in various protonation states.
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