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2025
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| Online Access: | https://doi.org/10.5281/zenodo.17934589 |
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| author | Yui, Toshifumi |
| author_facet | Yui, Toshifumi |
| contents | <p><span lang="EN-US">We report </span><span lang="EN-US">a</span><span lang="EN-US"> molecular dynamics </span><span lang="EN-US">(MD) </span><span lang="EN-US">simulation study of the process of peeling off a single molecular chain from cellulose Iβ crystal models. This study serves as a model for crystal surface decrystallization. We combined two </span><span lang="EN-US">types of </span><span lang="EN-US">extended ensemble MD simulation methods: adaptive steered MD to define the chain peeling-off trajectory along the reaction coordinate and umbrella sampling MD to calculate the potential of mean force and free energy change along the chosen reaction coordinate. </span><span lang="EN-US">The </span><span lang="EN-US">crystal models </span><span lang="EN-US">were solvated with </span><span lang="EN-US">water, benzene, a 10 wt% aqueous solution of NaOH, <em>N</em>,<em>N</em>-dimethylacetamide with 1 wt% LiCl, <em>N</em>-methylpyrrolidone with 1 wt% LiCl, or 1-allyl-3-methylimidazolium chloride (AMIMCl). Endothermic free energy changes were required the chain to peel off in all of the solvents. However, extremely low free energy values were observed in the AMIMCl solvent over the entire chain peeling-off range. This suggests that surface decrystallization is the dominant factor in the initial stage of </span><span lang="EN-US">real </span><span lang="EN-US">crystal dissolution in AMIMCl. In water, the free energy change required for the chain to peel off from the reducing end was slightly lower than that required for it to peel off from the nonreducing end. This is consistent with the</span><span lang="EN-US"> </span><span lang="EN-US">direction of the chain peel off observed in physical and enzymatic decrystallization at the crystal surface. Other umbrella sampling simulations that allowed for spatial motion of the peeled-off chain segment revealed that after linearly increasing, the potential of mean force values leveled off for all of the solvent systems, except </span><span lang="EN-US">for the </span><span lang="EN-US">AMIMCl</span><span lang="EN-US"> system</span><span lang="EN-US">.</span></p> |
| format | Recurso digital |
| id | zenodo_https___doi_org_10_5281_zenodo_17934589 |
| institution | Zenodo |
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| publishDate | 2025 |
| publisher | Zenodo |
| record_format | zenodo |
| spellingShingle | Free energy changes of a single molecular chain peeling off from the surface of the native cellulose crystal model in various solvents Yui, Toshifumi <p><span lang="EN-US">We report </span><span lang="EN-US">a</span><span lang="EN-US"> molecular dynamics </span><span lang="EN-US">(MD) </span><span lang="EN-US">simulation study of the process of peeling off a single molecular chain from cellulose Iβ crystal models. This study serves as a model for crystal surface decrystallization. We combined two </span><span lang="EN-US">types of </span><span lang="EN-US">extended ensemble MD simulation methods: adaptive steered MD to define the chain peeling-off trajectory along the reaction coordinate and umbrella sampling MD to calculate the potential of mean force and free energy change along the chosen reaction coordinate. </span><span lang="EN-US">The </span><span lang="EN-US">crystal models </span><span lang="EN-US">were solvated with </span><span lang="EN-US">water, benzene, a 10 wt% aqueous solution of NaOH, <em>N</em>,<em>N</em>-dimethylacetamide with 1 wt% LiCl, <em>N</em>-methylpyrrolidone with 1 wt% LiCl, or 1-allyl-3-methylimidazolium chloride (AMIMCl). Endothermic free energy changes were required the chain to peel off in all of the solvents. However, extremely low free energy values were observed in the AMIMCl solvent over the entire chain peeling-off range. This suggests that surface decrystallization is the dominant factor in the initial stage of </span><span lang="EN-US">real </span><span lang="EN-US">crystal dissolution in AMIMCl. In water, the free energy change required for the chain to peel off from the reducing end was slightly lower than that required for it to peel off from the nonreducing end. This is consistent with the</span><span lang="EN-US"> </span><span lang="EN-US">direction of the chain peel off observed in physical and enzymatic decrystallization at the crystal surface. Other umbrella sampling simulations that allowed for spatial motion of the peeled-off chain segment revealed that after linearly increasing, the potential of mean force values leveled off for all of the solvent systems, except </span><span lang="EN-US">for the </span><span lang="EN-US">AMIMCl</span><span lang="EN-US"> system</span><span lang="EN-US">.</span></p> |
| title | Free energy changes of a single molecular chain peeling off from the surface of the native cellulose crystal model in various solvents |
| url | https://doi.org/10.5281/zenodo.17934589 |