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DFT Applications in Molecular Biology and Biophysics

A special issue of International Journal of Molecular Sciences (ISSN 1422-0067). This special issue belongs to the section "Molecular Biophysics".

Deadline for manuscript submissions: closed (20 February 2025) | Viewed by 3585

Special Issue Editor

Special Issue Information

Dear Colleagues,

Density functional theory (DFT), in its various forms, is a computational quantum method that has become an invaluable tool for many researchers across a range of disciplines. DFT methods have emerged during the past several decades as a powerful methodology for the simulation of chemical systems, and they have become an important research tool for chemists, physicists and molecular biologists. DFT methods provide the best combination of accuracy and efficiency, and they are extensively used today in the prediction of the biomolecular structure and electronic properties of many systems, in computer-aided drug design, in catalysis and chemical reactivity, in surfaces and periodic solids, in transport, optical and magnetic properties, etc. The combination of DFT calculations with molecular dynamics promises to provide an efficient way to study structures and reactions in molecules and extended systems. They are less computationally demanding than other computational methods, and have a similar accuracy.

This Special Issue aims to collect papers related to any aspect of DFT Applications in Molecular Biology and Biophysics, including molecular simulations, structure predictions, and inter-molecular interactions, in computer-aided drug design and in all biomolecules more generally.

Dr. Mauricio Alcolea Palafox
Guest Editor

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Keywords

  • biophysics
  • molecular biology
  • molecular systems and processes
  • biomolecular interactions
  • docking calculations
  • DFT applications

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Published Papers (2 papers)

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Research

25 pages, 6627 KiB  
Article
Theoretical Insight into Antioxidant Mechanism of Caffeic Acid Against Hydroperoxyl Radicals in Aqueous Medium at Different pH-Thermodynamic and Kinetic Aspects
by Agnieszka Kowalska-Baron
Int. J. Mol. Sci. 2024, 25(23), 12753; https://doi.org/10.3390/ijms252312753 - 27 Nov 2024
Cited by 1 | Viewed by 969
Abstract
In this study, the DFT/M062X/PCM method was applied to investigate thermodynamic and kinetic aspects of reactions involved in possible mechanisms of antioxidant activity of caffeic acid against HOO radicals in aqueous medium at different pH values. Kinetic parameters of the reactions involved [...] Read more.
In this study, the DFT/M062X/PCM method was applied to investigate thermodynamic and kinetic aspects of reactions involved in possible mechanisms of antioxidant activity of caffeic acid against HOO radicals in aqueous medium at different pH values. Kinetic parameters of the reactions involved in HAT (Hydrogen Atom Transfer), RAF (Radical Adduct Formation), and SET (Single Electron Transfer) mechanisms, including reaction energy barriers and bimolecular rate constants, were determined, and identification and characterization of stationary points along the reaction pathways within HAT and RAF mechanisms were performed. Inspection of geometrical parameters and spin densities of the radical products formed within HAT and RAF mechanisms revealed that they are stabilized by hydrogen bonding interactions and the odd electron originated through the reaction with the HOO radical is spread over the entire molecule, resulting in significant radical stabilization. Thermodynamic and kinetic data collected in this study indicated that increasing pH of the medium boosts the antioxidant activity of caffeic acid by reducing the energy required to generate radicals within the RAF and/or HAT mechanism and, at extremely high pH, where the trianionic form of caffeic acid is a dominant species, by the occurrence of an additional fast, diffusion-limited electron-related channel. Full article
(This article belongs to the Special Issue DFT Applications in Molecular Biology and Biophysics)
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18 pages, 1760 KiB  
Article
Quantum Mechanical Study of Oxygen Ligands Protonation for the Stable States of the Laccase Active Site
by Sergei Gavryushov, Nikolay N. Kuzmich and Konstantin M. Polyakov
Int. J. Mol. Sci. 2023, 24(3), 2990; https://doi.org/10.3390/ijms24032990 - 3 Feb 2023
Cited by 3 | Viewed by 1857
Abstract
Laccases are enzymes catalyzing the oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Recently, oxygen reduction by laccases has been studied by single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution. There [...] Read more.
Laccases are enzymes catalyzing the oxidation of a wide range of organic and inorganic substrates accompanied by molecular oxygen reduction to water. Recently, oxygen reduction by laccases has been studied by single-crystal serial X-ray crystallography with increasing absorption doses at subatomic resolution. There were two determined structures corresponding to the reduced and oxidized stable states of the laccase active site. However, the protonation of the oxygen ligands involved cannot be determined even at subatomic resolution. In the present work, the protonation of oxygen ligands in the active site of laccase for the two stable states determined in the X-ray study was explored using quantum mechanical and continuum-electrostatics calculations. This is important for understanding the reaction of the oxygen reduction mechanism in laccases. The high precision of X-ray data at subatomic resolutions allowed us to optimize the quantum mechanical calculations. Full article
(This article belongs to the Special Issue DFT Applications in Molecular Biology and Biophysics)
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