氨分子对纤维素Iβ性能影响的分子动力学模拟

以纤维素Iβ为研究对象,通过分子模拟的方法,分别对其在有氨环境和无氨环境下的性能变化进行了仿真分析,主要包括对纤维素末端距、氨分子的扩散运动及氨分子与纤维素的氢键作用的研究.结果表明:氨分子的加入使得纤维素链的末端距增大,改善了纤维素链的柔顺性,合理的解释了"液氨整理可以用来改善棉麻纤维的柔顺性"的普遍共识;氨分子在纤维素中的均方位移和扩散系数随着温度的提高而变大,温度从298 K升高到398 K,氨分子的扩散系数增大87.8%,所以液氨整理过程中相应升高温度可以减少浸泡时间,提高生产效率;氨分子与纤维素形成的氢键,使得系统内的氢键总数增加,纤维素链内氢键数基本不变,但削弱了纤维素链间的氢键作用,加剧了纤维素链的运动,体现出良好的溶胀性能.     

超临界水的分子动力学模拟

采用分子动力学(MD)模拟的方法对超临界条件下水的结构及扩散性质进行了研究.模拟结果表明超临界条件下水分子之间的氢键作用明显减弱,分子极性大大降低.扩散性质与常温下相比,其大小约上升了两个数量级.     

水蒸气在高分子膜中吸附和传递行为的研究进展

水蒸气作为一种可凝聚性气体,导致它在高分子膜中的渗透行为比其它非凝聚性气体复杂。简要综述了水蒸气分子在高分子膜中的溶解和扩散行为,在不同的水蒸气活度下,考察了水蒸气在高分子膜中的溶解系数、扩散系数和渗透系数。分析了水分子与膜之间的相互作用,及水分子的成簇机理。     

水化镁基蒙脱石的分子动力学模拟

利用分子动力学(MD)模拟了300 K时镁基蒙脱石(粘土)层间水和镁离子的结构和动力学性质.模拟结果显示水在粘土层间分为二层,只有一小部分水被粘土表面吸附,与粘土结构中的羟基形成氢键,不同分布位置的水处于动态平衡.层间水分子氢键配位数比普通水少24%左右,水在粘土中自扩散系数D＝5.355×10^-10 m²·s^-1,约为主体相水的1/4.镁离子在粘土层间形成一层,其与水分子配位数约为6.进一步讨论了温度对粘土层中水的结构和动力学性质的影响.随着温度升高,水层的局部密度ρ(z)降低,水在XY方向的扩散系数不断增大.当温度达到600 K后,层间水分子间的氢键断裂,与超临界状态下水的结构相似,层间水的扩散系数达最大值,温度进一步升至700 K时,其值基本无变化.     

碱/脲水溶液体系中纤维素包合物构型及纤维素与溶剂分子间相互作用力的分子动力学模拟

采用分子动力学模拟方法研究了纤维素分子在碱/脲水溶液体系中形成的包合物结构,研究了纤维素包合物的空间构型、氢键网格结构、纤维素分子与溶剂分子的相互作用以及碱金属阳离子对包合物稳定性的影响.在纤维素包合物结构中,碱金属阳离子和OH-主要吸附在纤维素分子链羟基的附近,与纤维素上的羟基氧直接接触形成稳定的吸附构型;尿素分子更倾向于在纤维素糖环面结构上聚集,可以与纤维素上的羟基氧和醚键氧相互作用形成氢键.通过对纤维素与溶剂分子间非键相互作用的研究发现,在纤维素羟基附近,羟基与金属阳离子之间的相互作用能最大,其次为与尿素分子、氢氧根离子的相互作用,最小的为与水分子的相互作用;在纤维素糖环面结构上,Na~+、OH~-、尿素、水与纤维素醚键氧的相互作用远小于与纤维素羟基的相互作用,纤维素上的醚键氧与尿素分子相互作用能最大.比较KOH/尿素和NaOH/尿素2种溶剂体系中碱金属阳离子与纤维素羟基形成的吸附构型的结合能,发现Na~+对纤维素分子内和分子间的氢键具有更强的破坏作用,NaOH/尿素溶剂体系中的分子与纤维素分子形成的包合物构型更稳定.     

介质和力场协同作用对纳米纤维素形貌结构的调控

纤维素是一种由直链多聚糖通过糖苷键连接而成的巨型线性高分子,纤维素分子链通过氢键紧密排列形成纤维素晶体.由于纤维素晶体具有优良的化学可修饰性和机械性能等优点,纳米化加工的纤维素可广泛应用于日常生活和工业生产的各个领域.本文主要介绍了本课题组在机械剪切力作用下,实现纤维素纳米化并同时进行亲水或疏水改性的研究进展,重点介绍了介质极性对纤维素分子链之间相互作用的影响,并通过改变分子链之间的相互作用来调控纳米化纤维素的形貌和亲、疏水性.提出机械外力和环境极性协同作用下,晶面导向剥离纤维素的理论.     

水和盐分子在反渗透膜内扩散过程的分子模拟

采用分子动力学模拟方法研究了水和盐分子(NaCl, MgCl2, CaSO4, K2SO4)在8种反渗透复合膜中的扩散状态及扩散系数. 并对膜材料的结构单体与水和盐分子在膜内扩散系数相关性进行了分析与讨论. 在所模拟的8种膜内, 随着膜种类的不同, 水分子在其中的扩散系数有明显的变化, 且扩散系数的变化规律与实验所得到的膜的水通量一一对应. NaCl分子中的Na+和Cl-在膜内的扩散速率不一致, 其扩散系数值在同种膜中相差较大, 且当盐分子单独存在时, 制约其在膜内扩散过程的离子只与膜种类有关, 与盐分子本身无关. 在同种膜中, 水分子的扩散过程不受体系中盐分子类型的影响.     

CMC/PNIPAAm半互穿网络水凝胶的溶胀动力学研究

以羧甲基纤维素钠(CMC)和N-异丙基丙烯酰胺(NIPAAm)为原料,制备了具有温度和pH敏感性的半互穿网络(CMC／PNIPAAmsemi-IPN)水凝胶,并研究了水凝胶在不同温度和pH值条件下的溶胀行为。结果表明：在弱碱性(pH-7．4)条件下,凝胶的溶胀速率和溶胀度都随着凝胶中CMC含量的增加而增大;而在酸性(pH-1．O)条件下则相反。在弱碱性条件下,水分子在凝胶中的扩散行为都可用non-Fickian扩散来描述,水分子在凝胶中的扩散系数D随着凝胶溶胀速率的增大而增大;在酸性条件下,20℃时凝胶的溶胀过程符合non-Fickian扩散规律,而37℃时凝胶的溶胀过程符合Fickian扩散规律,但水分子的扩散系数D相差不大。     

金纳米颗粒周围水的结构和动力学性质的分子动力学模拟

采用经典的分子动力学模拟方法系统地研究了在常温条件下金纳米颗粒周围水的结构与动力学性质. 结果表明, 水分子在纳米颗粒附近形成了明显的多层结构. 同时随着径向距离的减小, 水分子的空间取向也从无序排列趋向于有序排列. 通过分析界面处不同水层中的均方位移及停留时间分布, 发现紧贴颗粒表面的第一和第二水层中的水分子表现出很低的扩散系数, 而第三和第四水层中的水分子则能够轻易地离开界面区域而进入主体相区域. 此外, 在界面处的每个水分子的氢键平均数要高于在主体相的平均值.     

海藻糖和氨基酸之间相互作用的分子动力学模拟

虽然海藻糖已经广泛用于蛋白质稳定性研究,但海藻糖稳定蛋白质的作用机理尚不清晰. 本文利用全原子分子动力学模拟研究了20种常见氨基酸和海藻糖之间的分子机理. 结果表明,所有氨基酸,尤其是极性和带电氨基酸,均优先与水分子结合. 相反,仅有疏水性氨基酸与海藻糖发生相互作用,尤其是芳香族和疏水性氨基酸的侧链更易于和海藻糖接触. 所有氨基酸的主链与水分子接触的趋势一致. 虽然氨基酸和海藻糖与水之间均形成氢键,但氨基酸和海藻糖之间的氢键相互作用要弱于氨基酸和水之间的氢键相互作用. 上述分子模拟的结果对于海藻糖稳定蛋白质作用机理的解析及高效蛋白质稳定剂的理性设计具有非常重要的理论指导意义.     

The behavior of cellulose molecules in aqueous environments

Molecular motions of cellulose chains in aqueous environments were investigated by comparison with those in non-aqueous environments using molecular simulation techniques. The cellulose chains under non-aqueous conditions approached each other closely and then made tight aggregates that were formed by direct hydrogen bonding. Those in aqueous environments, such as in a bio-system, were separated from each other by water molecules and did not have direct hydrogen bonding between the cellulose chain molecules. Folded-chain structures were not found in either aqueous or non-aqueous environments that were somewhat crowded. In the aqueous system, the water molecules around the cellulose chains restricted their molecular motions and interrupted formation of direct, interchain hydrogen bonds. In the non-aqueous system, the cellulose chains approached each other closely and then made a tight cluster before the chain molecules could wind and bend. It was concluded that a very dilute solution of cellulose molecules in appropriate solvents is necessary to create folded-chain or random-coiled structures. We also confirmed that the driving force for making tight clusters of cellulose molecules in highly concentrated solutions is the energy of the hydrogen bonding created directly between the hydroxyl groups of the cellulose chains. These results strongly suggest that hydrogen bonding plays a very important role in the characteristics of cellulose molecules.     

Molecular dynamics simulation of cellulose-coated oil-in-water emulsions

The behaviors of cellulose chains and cellulose mini-crystal in oil-in-water emulsions were studied by molecular dynamics simulations to investigate the coating states and the structural features of cellulose in these emulsions. In oil-in-water emulsion, dispersed cellulose chains gradually assemble during the progress of the simulation, eventually surrounding the octane droplet. In case of a cellulose mini-crystal, the cellulose chain at the corner of the crystal first contacts with the octane droplet through its hydrophobic surface. The other cellulose chains along the crystal plane then gradually move toward the octane molecules. In both emulsions, the cellulose was found to interact with both water and octane surfaces with specific conformations that allow the CH groups of the glucose rings to contact with octane molecules, while the OH groups of these rings contact with water molecules to form hydrogen bonds. The cellulose chains on the octane droplet also contact with each other through lateral hydrogen bonding between chains. These interactions stabilize the emulsion formed by cellulose molecules as surfactants.     

Binding strength of sodium ions in cellulose for different water contents

The interaction strength of sodium ions (Na(+)) with cellulose is investigated from first principles for varying degrees of water content. We find that the interaction of water molecules and Na(+) can be studied independently at the various OH groups in cellulose which we categorize as two different types. In the absence of water, Na(+) forms strong ionic bonds with the OH groups of cellulose. When water molecules are anchored to the OH groups via hydrogen bonds, Na(+) can eventually no longer bind to the OH groups, but will instead interact with the oxygen atoms of the water molecules. Due to the rather weak attachment of the latter to the OH groups, Na(+) becomes effectively more mobile in the fully hydrated cellulose framework. The present study thus represents a significant step toward a first-principles understanding of the experimentally observed dependence of ionic conductivity on the level of hydration in cellulose network.     

Solvents effects on the mechanism of cellulose hydrolysis: A QM/MM study

This article reports a combined quantum mechanics/molecular mechanics (QM/MM) investigation on the acid hydrolysis of cellulose in water using two different models, cellobiose and a 40‐unit cellulose chain. The explicitly treated solvent molecules strongly influence the conformations, intramolecular hydrogen bonds, and exoanomeric effects in these models. As these features are largely responsible for the barrier to cellulose hydrolysis, the present QM/MM results for the pathways and reaction intermediates in water are expected to be more realistic than those from a former density functional theory (DFT) study with implicit solvent (CPCM). However, in a qualitative sense, there is reasonable agreement between the DFT/CPCM and QM/MM predictions for the reaction mechanism. Differences arise mainly from specific solute–solvent hydrogen bonds that are only captured by QM/MM and not by DFT/CPCM. © 2015 Wiley Periodicals, Inc.     

Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

Local heterogeneous dynamics of water around lysozyme: a computer simulation study

Water present near the surface of a protein exhibits dynamic properties different from that of water in the pure bulk state. In this work, we have carried out atomistic molecular dynamics simulation of an aqueous solution of hen egg-white lysozyme. Attempts have been made to explore the correlation between the local heterogeneous mobility of water around the protein segments and the rigidity of the hydration layers with the microscopic dynamics of hydrogen bonds formed by water molecules with the protein residues. The kinetics of breaking and reformation of hydrogen bonds involving the surface water molecules have been calculated. It is found that the reformations of broken hydrogen bonds are more frequent for the hydration layers of those segments of the protein that are more rigid. The calculation of the low-frequency vibrational modes of hydration layer water molecules reveals that the protein influences the transverse and longitudinal degrees of freedom of water around it in a differential manner. These findings can be verified by appropriate experimental studies.     

Investigation of water diffusion process in ethyl cellulose-based films by attenuated total reflectance Fourier transform infrared spectroscopy and two-dimensional correlation analysis

Two-dimensional correlation spectroscopy (2Dcos) analysis on the time-resolved attenuated total reflectance Fourier transform infrared spectroscopy has been employed to investigate the diffusion behavior of water in ethyl cellulose/triethyl citrate (EC/TEC) films with varied TEC content. The diffusion coefficients of water in the EC-based films are calculated from the diffusion curves according to the Fickian Diffusion Model. And they are observed to increase with TEC content, possibly caused by the increased free volume in the film matrix. In the 2Dcos analysis, the broad O–H stretching vibration region is split into at least four bands, which can be assigned to four different states of water molecules, that is, bulk water, cluster water, relatively free water and free water. Moreover, it is found that as water molecules disperse into the EC-based films, cluster water with moderate hydrogen bonds diffuses faster than bulk water with strong hydrogen bonds. The relatively free water and free water are formed during the diffusion process due to their interactions with the films matrix, which makes water molecules confined and restricted in limited space.     

Properties of a water layer on hydrophilic and hydrophobic self-assembled monolayer surfaces: A molecular dynamics study

The microscopic behaviors of a water layer on different hydrophilic and hydrophobic surfaces of well ordered self-assembled monolayers (SAMs) are studied by molecular dynamics simulations. The SAMs consist of 18-carbon alkyl chains bound to a silicon(111) substrate, and the characteristic of its surface is tuned from hydrophobic to hydrophilic by using different terminal functional groups ( CH 3 , COOH). In the simulation, the properties of water membranes adjacent to the surfaces of SAMs were reported by comparing pure water in mobility, structure, and orientational ordering of water molecules. The results suggest that the mobility of water molecules adjacent to hydrophilic surface becomes weaker and the molecules have a better ordering. The distribution of hydrogen bonds indicates that the number of water-water hydrogen bonds per water molecule tends to be lower. However, the mobility of water molecules and distribution of hydrogen bonds of a water membrane in hydropho- bic system are nearly the same as those in pure water system. In addition, hydrogen bonds are mainly formed between the hydroxyl of the COOH group and water molecules in a hydrophilic system, which is helpful in understanding the structure of interfacial water.     

Hydrogen Bonding of Carboxylic Acids in Aqueous Solutions—UV Spectroscopy, Viscosity, and Molecular Simulation of Acetic Acid

The UV spectra of aqueous acetic acid solutions up to 2M were investigated. At these wavelengths, the carboxylic acids exhibit an absorption peak, attributed to the C=O group, which shifts when hydrogen bonds are formed.. The measured spectra were best fitted to several bands, either of Gaussian or Lorentzian shape, which can be explained as several types of structural units formed by hydrogen bonds established between acetic acid and water molecules and between acetic acid molecules themselves. Molecular dynamics simulation of these mixtures was also performed, confirming the occurrence of several types of hydrogen bonds and showing the presence of dimers at higher concentrations. The viscosity and density of these solutions were also measured at different concentrations and temperatures. These results give a more complete picture of the hydrogen bond network of the system.