Pandey Poonam, Mallajosyula Sairam S
Department of Chemistry, Indian Institute of Technology Gandhinagar , Simkheda, Gandhinagar, Gujarat 382355, India.
J Phys Chem B. 2016 Jul 14;120(27):6621-33. doi: 10.1021/acs.jpcb.6b05546. Epub 2016 Jun 23.
Carbohydrates are known to closely modulate their surrounding solvent structures and influence solvation dynamics. Spectroscopic investigations studying far-IR regions (below 1000 cm(-1)) have observed spectral shifts in the libration band (around 600 cm(-1)) of water in the presence of monosaccharides and polysaccharides. In this paper, we use molecular dynamics simulations to gain atomistic insight into carbohydrate-water interactions and to specifically highlight the differences between additive (nonpolarizable) and polarizable simulations. A total of six monosaccharide systems, α and β anomers of glucose, galactose, and mannose, were studied using additive and polarizable Chemistry at HARvard Macromolecular Mechanics (CHARMM) carbohydrate force fields. Solvents were modeled using three additive water models TIP3P, TIP4P, and TIP5P in additive simulations and polarizable water model SWM4 in polarizable simulations. The presence of carbohydrate has a significant effect on the microscopic water structure, with the effects being pronounced for proximal water molecules. Notably, disruption of the tetrahedral arrangement of proximal water molecules was observed due to the formation of strong carbohydrate-water hydrogen bonds in both additive and polarizable simulations. However, the inclusion of polarization resulted in significant water-bridge occupancies, improved ordered water structures (tetrahedral order parameter), and longer carbohydrate-water H-bond correlations as compared to those for additive simulations. Additionally, polarizable simulations also allowed the calculation of power spectra from the dipole-dipole autocorrelation function, which corresponds to the IR spectra. From the power spectra, we could identify spectral signatures differentiating the proximal and bulk water structures, which could not be captured from additive simulations.
已知碳水化合物能紧密调节其周围的溶剂结构并影响溶剂化动力学。研究远红外区域(低于1000 cm⁻¹)的光谱研究观察到,在单糖和多糖存在的情况下,水的摇摆带(约600 cm⁻¹)出现了光谱位移。在本文中,我们使用分子动力学模拟来深入了解碳水化合物与水的相互作用,并特别强调加和性(非极化)模拟与极化模拟之间的差异。使用加和性和极化性的哈佛大分子力学(CHARMM)碳水化合物力场,研究了总共六个单糖体系,即葡萄糖、半乳糖和甘露糖的α和β异头物。在加和性模拟中,使用三种加和性水模型TIP3P、TIP4P和TIP5P对溶剂进行建模;在极化性模拟中,使用极化性水模型SWM4。碳水化合物的存在对微观水结构有显著影响,对近端水分子的影响尤为明显。值得注意的是,在加和性和极化性模拟中,由于形成了强的碳水化合物 - 水氢键,观察到近端水分子的四面体排列受到破坏。然而,与加和性模拟相比,纳入极化作用导致了显著的水桥占有率、改善的有序水结构(四面体序参量)以及更长的碳水化合物 - 水氢键相关性。此外,极化性模拟还允许从偶极 - 偶极自相关函数计算功率谱,这与红外光谱相对应。从功率谱中,我们可以识别区分近端和本体水结构的光谱特征,而这些特征无法从加和性模拟中获得。