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Molecular dynamics (MD) simulations of cellulose Iβ are essential for understanding its structural properties and enhancing its usability. However, MD models often deviate in reproducing experimental structural properties. This study aimed to 1) improve OPLS-AA force field in stabilizing the crystalline integrity of cellulose Iβ, and 2) overcome limitations in modeling surface-functionalized forms. To achieve this, we combined the CM5 charge model with the carbohydrate OPLS-AA force field, creating the CM5-OPLS model. Significantly improving upon the extreme instability of the original OPLS-AA model, the OPLS-CM5 model retained 90 % of tg conformations of primary alcohol groups, 90 % of intra-chain, and 64 % of inter-chain hydrogen bond populations along the simulation time. Accordingly, the OPLS-CM5 model reproduced the unit cell parameters with <1.5 % error compared to experimental data, outperforming other common carbohydrate force fields, such as CHARMM36 and GLYCAM06. Moreover, the OPLS-CM5 model also captured the thermal and mechanical properties of cellulose Iβs, and enabled successful modeling of surface-functionalized cellulose Iβ, previously limited in most models. Overall, the CM5-OPLS model proved itself as a rigorous candidate for studying cellulose Iβ, and modeling its surface-functionalized forms, advancing understanding of its properties and facilitating its modification for broader applications.
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http://dx.doi.org/10.1016/j.carbpol.2025.123572 | DOI Listing |
Interdiscip Sci
August 2025
School of Chemistry and Chemical Engineering, Liaoning Normal University, Dalian, 116029, China.
Magnesium is an essential element involved in diverse life activities. The strong polarization and significant charge transfer effects pose challenges to the traditional fixed charge force fields. Here we establish the ABEEM/MM magnesium force field for proteins and aqueous solutions.
View Article and Find Full Text PDFJ Phys Chem B
August 2025
CNRS UMR 8516 - LASIRe - Laboratoire Avancé de Spectroscopie pour les Interactions la Réactivité et l'environnement, University of Lille, Lille 59000, France.
Curcumin (CUR), a bioactive compound with known polymorphism, exhibits distinct conformational and thermophysical properties across its three crystalline forms. In this study, we employ molecular dynamics simulations to investigate the thermal behavior, local structural organization, and polymorph-specific stability of CUR in the bulk phase. We first evaluate four widely used classical force fields (OPLS-AA, CGENFF, GAFF2, and GROMOS) against experimental melting points, densities, and conformational preferences, identifying OPLS-AA as the most suitable one.
View Article and Find Full Text PDFJ Chem Phys
July 2025
Center for Computational Physics, Moscow Institute of Physics and Technology (National Research University), Institutskiy Pereulok 9, Dolgoprudny 141701, Moscow Oblast, Russia.
Molecular dynamics methods have proven their applicability for the reproduction and prediction of molecular conformations during the past decades. However, most of works considered dilute solutions and relatively short trajectories that limit insights into conformational dynamics. In this study, we investigate the conformational dynamics of sucrose in aqueous solution using microsecond-scale molecular dynamics simulations.
View Article and Find Full Text PDFPhys Chem Chem Phys
July 2025
Centro de Química Estrutural, Institute of Molecular Sciences, Departamento de Química e Bioquímica, Faculdade de Ciências, Universidade de Lisboa, Campo Grande, 1749-016 Lisboa, Portugal.
An all-atom force field for MD simulations on crystalline Active Pharmaceutical Ingredients (API) containing sulfur and halogens was developed and tested. Validation was performed by comparing the MD results with enthalpies of sublimation experimentally determined by Calvet microcalorimetry and reported single crystal X-ray diffraction data. The test set consisted of sulfanilamide, sulfapyridine, chlorzoxazone, clioquinol, and triclosan.
View Article and Find Full Text PDFPhys Chem Chem Phys
July 2025
Polymer Electrolytes and Materials Group (PEMG), Department of Physics, Indian Institute of Technology Jodhpur, Rajasthan, 342030, India.
Single-stranded DNA (ssDNA) in ionic liquids (ILs) represents an unexplored class of polymer electrolytes with significant potential for rechargeable battery applications. This study investigates ssDNA + [BMIM][PF] systems using all-atom molecular dynamics simulations with OL15/OL3 force fields for DNA/RNA and an optimized OPLS-AA force field for [BMIM][PF]. Density profile analysis reveals that ssDNA + IL systems maintain an isotropic distribution of ions.
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