Journal of Molecular Modeling最新文献

Context: Recent outbreaks of the Zika virus (ZIKV) worldwide have underscored its growing epidemiological significance, leading to its recognition as an international health concern. The steady annual rise in ZIKV cases has transformed it into a major challenge for global public health systems. Despite ongoing efforts, the development of effective therapeutic agents against the virus remains difficult. Among the promising avenues for treatment are natural products, particularly those derived from medicinal and aromatic plants.

Methods: These substances act as reservoirs of beneficial chemical compounds that can contribute to developing effective therapies. This work used computer methods to examine 26 bioactive molecules derived from plants as potential Zika inhibitors. Baicalin, epicatechin gallate, epigallocatechin gallate, isoquercetin, and sophoroflavenone are plant-derived bioactive molecules that have demonstrated significant stability at the active site of the receptor examined (PDB code: 5TFR). They provided intense binding energies and were also stabilized at the active site of the target receptor by standard hydrogen bonds. These results were validated by molecular dynamics simulation at 500 ns. The molecules chosen to meet essential therapeutic criteria, such as those of Lipinski, have good ADMET characteristics and are not toxic. As a result, they have excellent pharmacokinetic properties and appreciable bioavailability. The findings of this research strongly suggest that these five molecules could be potential inhibitors of anti-Zika action in the future.

Context: Chirality-induced spin selectivity (CISS) represents a remarkable quantum phenomenon whereby electron transmission through chiral molecules, such as DNA, becomes intrinsically spin-polarized even in the absence of magnetic fields. Despite extensive experimental verification of static CISS effects, achieving dynamic control over spin polarization remains an open challenge. Terahertz (THz) radiation offers a promising route to externally modulate molecular electronic structure on sub-picosecond timescales. In this study, we develop a theoretical model that unifies THz-driven Floquet dynamics with the spin-orbit coupling inherent to chiral DNA, thereby introducing the concept of Floquet-CISS, a light-induced regime of topologically controlled spin transport in biological helices.

Method: An effective low-energy Hamiltonian incorporating kinetic motion along the DNA helix, spin-orbit coupling, and the interaction with circularly polarized THz fields was formulated and solved using Floquet theory. The resulting quasi-energy spectra, Berry curvature, and spin polarization were numerically evaluated using plane-wave expansion and LAPACK-based diagonalization. The simulations reveal that THz fields dynamically reshape the Berry curvature, induce tunable spin-split Floquet bands, and produce helicity-dependent spin polarization exceeding 60%. These effects arise entirely from light-matter coupling without magnetic components, establishing DNA as a bio-topological spin filter capable of ultrafast, reversible spin control. The Floquet-CISS mechanism provides a theoretical blueprint for THz-programmable molecular spintronics and paves the way toward optically reconfigurable bio-quantum devices.

A modified attachment energy model combined with classical molecular dynamics simulations is employed to study the solvent-dependent crystal growth of α-CL-20 in six solvent systems commonly used for the preparation of CL-20: maleic acid, pentaerythritol, glycine, citric acid, polyvinyl alcohol, and butyl carbamate. Surface roughness is quantified via the ratio of solvent-accessible area to geometric cross-sectional area, and electrostatic potential maps and radial distribution functions are used to characterize the polarity and non-bonded interactions at the interfaces. The results show that the interactions between α-CL-20 and solvent are dominated by hydrogen bonding, with some contributions from van der Waals contacts. The calculation results based on modified attachment energy theory show that in all six solvent systems, the growth of the (021) face is substantially inhibited, while the (020), (102), (111), and (002) faces tend to remain as persistent, moderately growing facets. The predicted morphologies in solutions evolve from the prismatic vacuum habit toward nearly polyhedral, spheroidal crystals, which suggest that strong, face-selective hydrogen bonding on rough, polar faces can serve as an effective microscopic mechanism for solvent-based morphology engineering of CL-20.

The Materials Studio software was used to calculate crystal growth, electrostatic potential, and radial distribution functions of α-CL-20. The VISTA software was used to predict morphologies of α-CL-20 in six solutions.