Flupyradifurone (FLU) is a novel butenolide insecticide with partial agonist activity for insect nicotinic acetylcholine receptors. Its safety for non-target organisms has been questioned in the literature, despite initial claims of its harmlessness. Detailed understanding of its toxicity and related molecular mechanisms remain under discussion. Thus, in this work, an optimized set of CHARMM compatible parameters for FLU is presented. CHARMM General Force Field program was used as a starting point while the non-bonded and bonded parameters were adjusted and optimized to reproduce MP2/6-31G(d) accuracy level results. For the validity assessment of these parameters, infrared spectrum, water-octanol partition coefficient, and normal modes were computed and compared to experimental values found in the literature. Several MD simulations of FLU in water and FLU in complex with an acetylcholine-binding protein were performed to estimate the ability of the optimized parameters to correctly describe its torsional space and reproduce observed crystallographic trends respectively.
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http://dx.doi.org/10.1002/jcc.27245 | DOI Listing |
J 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 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.
View Article and Find Full Text PDFJ Chem Inf Model
December 2024
Biological Sciences Division, Pacific Northwest National Laboratory, Richland, Washington 99352, United States.
Noncanonical amino acids (ncAAs) provide numerous avenues for the introduction of novel functionality to peptides and proteins. ncAAs can be incorporated through solid-phase synthesis or genetic code expansion in conjugation with heterologous expression of the encoded protein modification. Due to the difficulty of synthesis or overexpression, wide chemical space, and lack of empirically resolved structures, modeling the effects of ncAA mutation is critical for rational protein design.
View Article and Find Full Text PDFNat Commun
September 2024
Department of Chemical and Biological Engineering, University of Colorado at Boulder, Boulder, CO, USA.
The simulation of chemical reactions and mechanical properties including failure from atoms to the micrometer scale remains a longstanding challenge in chemistry and materials science. Bottlenecks include computational feasibility, reliability, and cost. We introduce a method for reactive molecular dynamics simulations using a clean replacement of non-reactive classical harmonic bond potentials with reactive, energy-conserving Morse potentials, called the Reactive INTERFACE Force Field (IFF-R).
View Article and Find Full Text PDFNucleic Acids Res
July 2024
BioISI - Instituto de Biossistemas e Ciências Integrativas, Faculdade de Ciências, Universidade de Lisboa, 1749-016 Lisboa, Portugal.
When preparing biomolecular structures for molecular dynamics simulations, pKa calculations are required to provide at least a representative protonation state at a given pH value. Neglecting this step and adopting the reference protonation states of the amino acid residues in water, often leads to wrong electrostatics and nonphysical simulations. Fortunately, several methods have been developed to prepare structures considering the protonation preference of residues in their specific environments (pKa values), and some are even available for online usage.
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