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Structure and stretching dynamics of water molecules around an amphiphilic amide from FPMD simulations: A case study of N,N-dimethylformamide
Journal of Molecular Liquids ( IF 6 ) Pub Date : 2020-01-17 , DOI: 10.1016/j.molliq.2020.112524
Aritri Biswas , Bhabani S. Mallik

N,N-Dimethylformamide (DMF) is a unique tertiary amphiphilic amide, where the presence of a hydrophilic aldehyde group favors hydrogen bond acceptance, but two hydrophobic methyl substituents inhibit interaction with water molecules. As a result, the water molecules encounter two different environments in the vicinity of DMF molecule: around the hydrophobic nitrogen site; and near the hydrophilic carbonyl oxygen. We employ first principles molecular dynamics methods to simulate an aqueous solution of DMF using PBE functional with Grimme's D3 dispersion correction at 330 K. Investigations on the liquid structure to understand inter-atomic interactions in amides attract much attention. We calculated various structural and dynamical properties along with vibrational stretching frequency of water molecules to understand heterogeneously affected water molecules by an amphiphilic amide molecule. In solvated DMF, the first peak minimum of the N-OW and OC-OW radial distribution functions (‘w’ subscript denotes atoms of water) are located at 5.72 and 3.16 Å, respectively. These distance cutoffs decide the boundary of the solvation shell. At OC-HW distance 2.45 Å, the deep peak minimum indicates stable OC … HW hydrogen bond. Previous Monte Carlo simulations reported the presence of hydrogen bonds between the oxygen site of DMF and hydrogen of water. The time-series wavelet method was used to compute the time-dependent frequencies of the hydroxyl groups of water. The average frequency of the OH modes inside the CO solvation shell (~3364 cm−1) in DMF is higher than bulk (~3337 cm−1), and the trend matches with an aqueous solution of acetone. In nitrogen hydration shell, the intense band resembles the bulk frequency distribution, and a narrow distinctive peak at the high-frequency side (range ~3650–3750 cm−1) represents the non‑hydrogen bonded or dangling OH groups. Raman spectroscopy in hydrophobic TBA and air/water interface displayed dangling OH stretch peak at ~3660 cm−1 and ~3710 cm−1, respectively. Our calculation of the frequency distribution, frequency-frequency correlation function, and hydrogen bond dynamics show the water molecules at bulk behave as in pure water. Inside the solvation shell of aminic nitrogen, non‑hydrogen bonded OH modes with a dangling lifetime ~0.38 ps dominates over the water-water hydrogen bonds. The time-dependent decay of the frequency correlation inside CO solvation shell has three decay components, a rapid decay, then, an intermediate component (~1.52 ps) corresponding to the lifetime of the carbonyl-water hydrogen bond, and the longer timescale ~11.97 ps representing the residence time of water molecules in the vicinity of carbonyl oxygen. We find that the carbonyl-water hydrogen bond (OC … HW) is stronger than the water-water hydrogen bond. The methyl substituents on the nitrogen of DMF impose weak hydrophobic interaction, and the hydrophilic carbonyl oxygen forms a strong hydrogen bond with the neighboring water resulting in localized dynamics.



中文翻译:

FPMD模拟中两亲酰胺周围水分子的结构和拉伸动力学:以NN-二甲基甲酰胺为例

ññ-二甲基甲酰胺(DMF)是独特的叔两亲酰胺,其中亲水性醛基的存在有利于氢键的接受,但是两个疏水性甲基取代基抑制了与水分子的相互作用。结果,水分子在DMF分子附近遇到两个不同的环境:疏水氮位点附近;并且靠近亲水性羰基氧。我们采用分子动力学方法的第一原理来模拟PMF的DBE水溶液,并在330 K上使用Grimme的D3色散校正。研究液体结构以了解酰胺中的原子间相互作用引起了人们的广泛关注。我们计算了水分子的各种结构和动力学特性以及振动拉伸频率,以了解两亲酰胺分子对异质性水分子的影响。在溶剂化DMF中,NO的第一个峰值最小值W和O C -O W径向分布函数(“ w”下标表示水原子)分别位于5.72和3.16Å。这些距离界限决定了溶剂化壳的边界。在O C -H W距离2.45Å,最小的深峰表示稳定的O C …H W氢键。先前的蒙特卡洛模拟报告了DMF的氧位与水的氢之间存在氢键。时间序列小波方法用于计算水的羟基随时间变化的频率。C O溶剂化壳内部OH模式的平均频率(〜3364 cmDMF中的-1)高于体积(〜3337 cm -1),并且该趋势与丙酮水溶液匹配。在氮水合壳中,强频带类似于整体频率分布,并且在高频侧(〜3650-3750 cm -1的范围内)狭窄的独特峰表示非氢键或悬挂的OH基团。在疏水性TBA和空气/水界面的拉曼光谱显示的〜3660厘米悬空OH拉伸峰-1和〜3710厘米-1, 分别。我们对频率分布,频率-频率相关函数和氢键动力学的计算表明,散装的水分子的行为与纯净水中的行为相同。在胺态氮的溶剂化壳内部,悬垂寿命约为0.38 ps的非氢键OH模式在水-水氢键中占主导地位。C O溶剂化壳内部频率相关性随时间的衰减具有三个衰减分量,一个是快速衰减,然后是一个对应于羰基-水氢键寿命的中间分量(〜1.52 ps),并且时标较长。 11.97 ps代表水分子在羰基氧附近的停留时间。我们发现羰基-水氢键(O C …H W)比水-水氢键强 DMF氮上的甲基取代基具有弱的疏水作用,而亲水的羰基氧与周围的水形成很强的氢键,从而导致局部动力学。

更新日期:2020-01-21
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