Abstract
In sub nanometer carbon nanotubes, water exhibits unique dynamic characteristics, and in the high-frequency region of the infrared spectrum, where the stretching vibrations of the internal oxygen-hydrogen (O-H) bonds are closely related to the hydrogen bonds (H-bonds) network between water molecules. Therefore, it is crucial to analyze the relationship between these two aspects. In this paper, the infrared spectrum and motion characteristics of the stretching vibrations of the O-H bonds in one-dimensional confined water (1DCW) and bulk water (BW) in (6, 6) single-walled carbon nanotubes (SWNT) are studied by molecular dynamics simulations. The results show that the stretching vibrations of the two O-H bonds in 1DCW exhibit different frequencies in the infrared spectrum, while the O-H bonds in BW display two identical main frequency peaks. Further analysis using the spring oscillator model reveals that the difference in the stretching amplitude of the O-H bonds is the main factor causing the change in vibration frequency, where an increase in stretching amplitude leads to a decrease in spring stiffness and, consequently, a lower vibration frequency. A more in-depth study found that the interaction of H-bonds between water molecules is the fundamental cause of the increased stretching amplitude and decreased vibration frequency of the O-H bonds. Finally, by analyzing the motion trajectory of the H atoms, the dynamic differences between 1DCW and BW are clearly revealed. These findings provide a new perspective for understanding the behavior of water molecules at the nanoscale and are of significant importance in advancing the development of infrared spectroscopy detection technology.
Water is an indispensable substance in life, carrying out essential functions necessary for sustaining life activities
In nature, most water exists in the form of free state bulk water (BW). However, in biochemical reactions and macromolecular biological functions, water often exists in the form of confined water within inorganic pores and certain protein structures, playing a key role. For example, the water channel protein Aquaporin-1 in biological organisms has been proven to efficiently transport water molecules across membranes while preventing ions from passing through
In recent years, with the capabilities of high-performance computing and large-scale data processing, scientists have conducted more precise and complex simulations and calculations of the water structure inside SWNT, discovering novel behaviors not observed on a macroscopic scale. These findings have propelled SWNT into new application prospects, such as precise water molecule control
This paper utilizes the SPC/E water model based on the MD simulation method to study the infrared spectroscopy and motion characteristics of 1DCW in (6, 6) SWNT. The results indicate significant differences in the O-H bond stretching vibration infrared spectra between 1DCW and BW. Subsequent analysis of the O-H bond length stretching changes, H-bonds, and motion trajectory diagrams reveals the fundamental reasons for the spectral differences.
First, we establish a cubic simulation box with dimensions of 3.00 nm × 5.11 nm × 7.00 nm, as shown in
. | (1) |

Fig. 1 Schematic of the simulation system for one-dimensional confined water (1DCW) through a single-walled carbon nanotube (SWNT) water channel
图1 一维受限水(1DCW)通过单壁碳纳米管(SWNT)水通道的模拟系统示意图
The first term represents long-range electrostatic interactions, while the second term involves short-range Lennard-Jones (L-J) interactions. Here, represents the dielectric constant in vacuum; is the distance between atoms and ; is the charge on atom ; and the parameters and represent the values for L-J interactions. The force field parameters for our flexible SPC/E water model are detailed in
Parameter | Value |
---|---|
0.316 6 | |
) | 0.650 |
-0.848 | |
/e | 0.424 |
109.470 | |
0.100 0 |
In studying the infrared spectra of the O-H bond stretching vibrations in water molecules within SWNT, the required infrared spectra are calculated by performing a Fourier transform on the time autocorrelation function of the O-H bond lengths in water molecules. The mathematical expression for this calculation is as follows:
. | (2) |
In the above expression, represents the vibrational intensity, is the frequency, is the time variable, and is the length of the O-H bond in the water molecules.
Weak interaction analysis can reveal the non-covalent interactions among water molecules, such as electrostatic forces, H-bonds, and van der Waals forces. In this study, based on the initial configurations output from the MD simulations of infrared spectroscopy analysis, one water molecule is fixed while allowing other water molecules to move freely. A 1 ns MD simulation is conducted under the same conditions, yielding 1000 trajectory data frames. Utilizing these coordinate data, the average reduced density gradient (aRDG) among the water molecules is analyzed using the quantum chemical wave function analysis program Multiwfn
. | (3) |
Firstly, we calculated the time autocorrelation functions of the O-H bond lengths in 1DCW and BW using MD simulations, and then processed these autocorrelation functions with Fourier transform to obtain the infrared spectra of the stretching vibrations. As shown in

Fig. 2 Infrared spectra of O-H bond stretching vibrations in 1DCW and BW: (a),(b) represent the spectra of O-H bond stretching vibrations in 1DCW and BW; in both spectra, the infrared absorption peaks of the stretching vibrations appear in the frequency () range of 90-110 THz; the gray curve represents the stretching vibration spectrum between the H1 atom and the O atom in water molecules (O-H1), while the red curve represents the stretching vibration spectrum between the H2 atom and the O atom (O-H2)
图2 1DCW和BW中O-H键伸缩振动的红外光谱:(a),(b) 为1DCW和BW中O-H键拉伸振动谱; 在两个光谱中,拉伸振动的红外吸收峰出现在频率(f)为90~110 THz的范围内;灰色曲线为水分子中H1原子与O原子之间的拉伸振动谱(O-H1),红色曲线为H2原子与O原子之间的拉伸振动谱(O-H2)
Typically, the vibrational frequency of water molecules is closely related to the internal constraints, which we liken to a spring in simple harmonic motion for the O-H bond stretching, where the force applied determines the stiffness coefficient k

Fig. 3 Changes and distributions of O-H bond lengths over time in 1DCW and BW: (a),(b) represent the stretching changes of O-H1 and O-H2 bond lengths over time in 1DCW and BW, respectively. Insets: the left and right sides respectively represent the stretched states of the two O-H bonds in 1DCW and BW; (c),(d) respectively represent the statistical distribution graphs of O-H1 and O-H2 bond lengths in 1DCW and BW, respectively. Herein, where the gray curve represents the distribution of the O-H1 bond lengths in water molecules, and the red curve represents the distribution of O-H2 bond lengths
图3 1DCW和BW的O-H键长伸缩幅度随时间的变化和分布:(a),(b) 分别表示了1DCW和BW中O-H1和O-H2键长度随时间的拉伸变化,并附有插图:左、右分别表示1DCW和BW中两个O-H键的拉伸状态;(c),(d)分别为1DCW和BW中O-H1键长和O-H2键长统计分布图,其中灰色曲线为O-H1键长在水分子中的分布,红色曲线为O-H2键长分布
In infrared spectroscopy analysis, the high-frequency stretching vibration frequencies of the O-H bonds within water molecules exhibit a strong correlation with the H-bond network structure. To deeply understand the influence of the differences in O-H bond stretching amplitudes in 1DCW and BW on vibration frequencies, we analyzed the forces exerted by the H-bonds.

Fig. 4 The average reduced density gradient (aRDG) calculations of weak interactions in water molecules under different conditions: (a) depicts the chain-like H-bond network structure in 1DCW, where only one H atom in 1DCW is involved in H-bond formation; the light blue curve represents the semi-sectional structure of a carbon nanotube, and the dark blue discs represent H-bond interactions; (b) shows the tetrahedral H-bond network structure in BW, where two H atoms of a BW molecule can simultaneously form H-bond with adjacent water molecules
图4 平均约化密度函数(aRDG)计算不同环境下水分子的弱相互作用:(a)为1DCW中的链状氢键网络结构,其中1DCW中只有一个H原子参与氢键的形成;浅蓝色曲线代表碳纳米管的半截面结构,深蓝色圆盘代表氢键相互作用;(b)为BW中的四面体氢键网络结构,其中BW分子的两个氢原子可以同时与相邻的水分子形成氢键
Finally, we compared the motion trajectories of water molecules in different environments.

Fig. 5 Three-dimensional motion trajectories of H atoms in 1DCW and BW:(a),(b) respectively show the projections of the motion trajectories of H1 and H2 atoms in 1DCW on a two-dimensional plane; (c),(d) respectively represent the projections of the motion trajectories of H1 and H2 atoms in BW on a two-dimensional plane. These trajectories are distinguished by red, green, and blue curves, representing the motion paths of H atoms on the XY plane, XZ plane, and YZ plane respectively
图5 1DCW和BW的H原子三维运动轨迹图:(a),(b) 分别为1DCW中H1、H2原子运动轨迹在二维平面上的投影;(c),(d)分别表示BW中H1和H2原子的运动轨迹在二维平面上的投影。这些轨迹用红、绿、蓝三色曲线来区分,分别代表氢原子在XY平面、XZ平面和YZ平面上的运动轨迹
In summary, this paper based on molecular dynamics simulations, analyzes the infrared spectroscopic characteristics of the O-H bonds of water in two different environments: SWNT and bulk phase. The study reveals that in 1DCW, the stretching vibration frequency of the O-H1 bond involved in H-bond is lower than that of the O-H2 bond which does not participate in H-bond. Conversely, in BW, the main peak frequencies of both O-H bonds are nearly identical. Further analysis showed that the stretching amplitude of the O-H1 bond in 1DCW is significantly higher than that of the O-H2 bond, resulting in a lower vibration frequency for O-H1. In BW, both O-H bonds have consistent stretching amplitudes, displaying both long and short bonds, hence there are two main frequency absorption peaks. To understand more deeply the reasons for these differences in stretching amplitudes, we conducted a detailed analysis of the H-bond networks of the water molecules. In SWNT, water molecules form a one-dimensional chain structure, with only one H atom involved in H-bond, leading to differentiated stretching characteristics of the two O-H bonds. In contrast, the tetrahedral H-bond network structure in BW results in more uniform stretching amplitudes for both O-H bonds. Finally, by comparing the motion trajectories of water molecules in different environments, it was found that in 1DCW, the H1 atom shows constrained dynamic behavior due to its participation in H-bond, while H2, not involved in H-bond, exhibits greater freedom of movement. This dynamic difference indirectly reflects the vibrational modes of the water molecule's O-H bonds and forms specific characteristics in the infrared spectrum. However, in the tetrahedral H-bond network of BW, both H atoms are subject to similar constraints, thus their motion trajectories show no significant differences, but the state of motion continuously transitions between free and constrained, further displaying the dynamic equilibrium of H-bonds. These findings reveal the structure and dynamics of the H-bond networks of water molecules in different microenvironments and clarify how these characteristics influence the infrared spectrum of water molecules. This research deepens our understanding of the unique characteristics of molecules in diverse environments
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