Qinghua Liao, Mariana A B Morais, Carme Rovira, Alba Nin-Hill
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We apply three metadynamics approaches standard, well-tempered, and parallel bias using Cremer-Pople polar coordinates and ring dihedral angles as collective variables. Consistent conformational stability trends are observed across methods and environments. In both gas and aqueous phases, the free energy landscape (FEL) identifies the <sup>4</sup> <i>C</i> <sub>1</sub> chair as the global minimum, followed by equatorial conformers and the inverted <sup>1</sup> <i>C</i> <sub>4</sub> chair, which is less stable in solution than in the gas phase. In the gas phase, the most stable distorted conformers (in the <sup>2</sup> <i>S</i> <sub>O</sub> -<i>B</i> <sub>3,O</sub> - <sup>1</sup> <i>S</i> <sub>3</sub> region) exhibit structural and electronic features characteristic of an oxocarbenium ion, including a high C1-O1/C1-O5 bond length ratio, a pronounced anomeric effect, and negative charge accumulation at O1 and O5. 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引用次数: 0
摘要
β-葡萄糖的构象灵活性对于纤维素和淀粉等碳水化合物的酶分解至关重要。对其环构象的详细了解有助于合理设计治疗剂和功能分子,包括基于葡萄糖苷酶活性的探针。尽管量子力学方法已被用于研究β-葡萄糖构象,但对cremer - people构象空间的全面分析,特别是考虑溶剂效应,仍然不完整。利用密度泛函理论(DFT),我们系统地表征了β-葡萄糖在气相和水相中的构象。我们采用三种元动力学方法标准,良好调节,平行偏差使用克雷默-波普尔极坐标和环二面角作为集体变量。在不同的方法和环境中观察到一致的构象稳定性趋势。在气相和水相中,自由能图(FEL)表明4c1椅是整体最小的构象,其次是赤道构象和倒置的1c4椅,其在溶液中的稳定性低于气相。在气相中,最稳定的畸变构象(在2s O - b3,O - 1s 3区)表现出氧羰基离子的结构和电子特征,包括高C1-O1/C1-O5键长比,明显的头形效应,以及在O1和O5处的负电荷积累。这些特征在水溶液中明显减弱,这表明气相FEL更好地反映了糖苷酶-底物复合物中-1亚位糖的构象偏好。这些发现为研究糖类构象,建立β-葡萄糖作为计算和方法基准的模型系统提供了有价值的框架。
Conformational Free Energy Landscape of β‑Glucose in the Gas Phase and Aqueous Solution: Energetic, Structural, and Electronic Changes.
The conformational flexibility of β-glucose is critical for the enzymatic breakdown of carbohydrates such as cellulose and starch. Detailed knowledge of its ring conformations supports the rational design of therapeutic agents and functional molecules, including glucosidase activity-based probes. Although quantum mechanical methods have been employed to study β-glucose conformations, a comprehensive analysis of the Cremer-Pople conformational space, particularly accounting for solvent effects, remains incomplete. Using density functional theory (DFT), we systematically characterize β-glucose conformations in both gas and aqueous phases. We apply three metadynamics approaches standard, well-tempered, and parallel bias using Cremer-Pople polar coordinates and ring dihedral angles as collective variables. Consistent conformational stability trends are observed across methods and environments. In both gas and aqueous phases, the free energy landscape (FEL) identifies the 4C1 chair as the global minimum, followed by equatorial conformers and the inverted 1C4 chair, which is less stable in solution than in the gas phase. In the gas phase, the most stable distorted conformers (in the 2SO -B3,O - 1S3 region) exhibit structural and electronic features characteristic of an oxocarbenium ion, including a high C1-O1/C1-O5 bond length ratio, a pronounced anomeric effect, and negative charge accumulation at O1 and O5. These features are significantly diminished in aqueous solution, suggesting that the gas-phase FEL better reflects the conformational preferences of the saccharide at the -1 subsite in enzyme-substrate complexes of glucosidases. These findings provide a valuable framework for investigating saccharide conformations, establishing β-glucose as a model system for computational and methodological benchmarking.
ACS OmegaChemical Engineering-General Chemical Engineering
CiteScore
6.60
自引率
4.90%
发文量
3945
审稿时长
2.4 months
期刊介绍:
ACS Omega is an open-access global publication for scientific articles that describe new findings in chemistry and interfacing areas of science, without any perceived evaluation of immediate impact.