Molecular dynamics method for simulating hydrogen bond network structure of fluid interface surfactant

Abstract

The invention discloses a molecular dynamics method for simulating a hydrogen bond network structure of a fluid interface surfactant. According to the method, a molecular model of the surfactant on the gas-liquid interface is constructed, a molecular dynamics simulation technology is utilized, and microscopic behaviors of the surfactant on the gas-liquid interface are simulated, including key parameters such as the degree of extension, the inclination angle, the rising height, the hydrogen bond and the radial distribution function. The method comprises the following specific steps: constructing an air / surfactant / water three-phase system model; utilizing molecular dynamics simulation software to obtain dynamic behavior data of surfactant molecules on the interface; the stretching degree, the inclination angle and the rising height are analyzed, and arrangement and orientation characteristics of molecules on an interface are revealed; and representing the molecular interface network structure of the surfactant through hydrogen bond analysis and radial distribution function calculation. The invention provides a new perspective for understanding the regulation and control mechanism of the hydrogen bond on the interface self-assembly behavior of the surfactant, and can provide an important theoretical basis for research and development of a novel biomass-based surfactant.

Description

Technical Field

[0001] The invention belongs to the technical field of colloid interfaces, and in particular relates to a molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface. Background Art

[0002] Petroleum is a core energy resource for human society. As conventional oil resources gradually deplete, tertiary oil recovery (TER) technologies, represented by chemical flooding, have become crucial for stabilizing oilfield production and increasing efficiency. Surfactant flooding systems play a key role in reducing oil-water interfacial tension and altering reservoir wettability. However, traditional petroleum-based surfactants face technical bottlenecks such as non-renewable raw materials, high environmental accumulation risks, and a single molecular structure. Their sustainable application faces significant challenges, particularly driven by carbon reduction policies.

[0003] Currently, the development of new surfactants based on biomass resources has become an important trend. Their multi-hydroxyl and multi-functional group characteristics manifest as various hydrogen bonds within molecules, between molecules, and with water, providing a natural structural basis for optimizing interfacial behavior. However, the evolution of molecular conformation and the mechanism of interfacial hydrogen bonding at the microscale are still unclear, which restricts the targeted design of high-performance products. Therefore, revealing the structure-activity relationship between molecular configuration, hydrogen bonding, and interfacial performance through molecular dynamics simulation technology is of great significance for promoting the scientific design and efficient application of biomass-based surfactants in the field of enhanced oil recovery. Summary of the Invention

[0004] To address these technical issues, the present invention aims to provide a molecular dynamics method for simulating the hydrogen-bonding network structure of surfactants at fluid interfaces. This method reveals, at the microscopic scale, how hydrogen-bonding networks regulate the self-assembly behavior of air / water interfaces, elucidating the synergistic mechanism of polyhydroxyl functional groups. This method provides theoretical guidance for the design of biomass-based surfactants with high interfacial activity, temperature resistance, and salt tolerance, ultimately serving the needs of enhanced oil recovery from chemical flooding in complex reservoirs.

[0005] The purpose of the present invention is achieved through the following technical solutions.

[0006] The present invention discloses a molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface, which specifically comprises the following steps:

[0007] (1) Construct a single-molecule structure model of the surfactant molecule, optimize the initial topological structure of the surfactant, calculate the charge parameters of the all-atom structure, and generate the corresponding force field parameters from the Amber molecular force field;

[0008] (2) Constructing an air / surfactant / water three-phase system model for simulation calculations;

[0009] (3) performing energy minimization on the air / surfactant / water three-phase system model to eliminate unreasonable contacts generated by model construction and obtain an energy-minimized structure file;

[0010] (4) performing molecular dynamics simulation on the energy-minimized structure file as input file, determining the air / surfactant / water three-phase system model in a stable state, collecting molecular trajectory files and three-dimensional coordinate files, and exporting files in .xtc and .gro formats;

[0011] (5) Analyze the obtained molecular trajectory file and three-dimensional coordinate file to study the system density, interface arrangement and interaction, and obtain the research results of the interface behavior of the surfactant molecules in the system.

[0012] Furthermore, the specific steps of step (1) are:

[0013] The geometric structure model of the surfactant molecule was constructed using GaussView software, and the initial configuration of the surfactant was optimized using the Gaussian09 software package at the B3LYP / 6-31+g(d) calculation level. The van der Waals parameters and bonding parameters of each atom were directly obtained from the Amber molecular force field using the General Amber Force Field (GAFF) of the AmberTools19 program, combined with the atomic charges of the restrained electrostatic potential (RESP) calculated using the B3LYP / 6-311+g(d) method.

[0014] The potential energy function used in the Amber molecular force field is:

[0015]

[0016] Where N is the distance between the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant. W ), is the total number of oxygen atoms in the water phase, r is the number of oxygen atoms in water (O W ) to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant, and g(r) is the radial distribution function of the oxygen atom to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant.

[0017] Furthermore, the biomass-based surfactant is a sorbitol-based surfactant (2R, 3R, 4R, 5S)-1,6-di(dodecylamino)hexane-2,3,4,5-tetraol (SAAS-C12).

[0018] The beneficial effects of the present invention are:

[0019] This invention provides a molecular dynamics method for simulating the hydrogen-bonding network structure of surfactants at fluid interfaces. This method explains the hydrogen-bonding synergy of polyhydroxyl functional groups and their directional arrangement at the gas-liquid interface at the microscopic molecular level, and clarifies the mechanisms by which molecular chain flexibility and polar group distribution influence interfacial film formation and stability. This method provides an important theoretical basis for the development of new, highly efficient, and environmentally friendly surfactants, and is of great significance for improving tertiary oil recovery and reducing production costs. BRIEF DESCRIPTION OF THE DRAWINGS

[0020] Figure 1 Schematic diagram of the structure of the biomass surfactant molecule (SAAS-C12) in an embodiment of the present invention;

[0021] Figure 2 is a simulation structural model of the air / surfactant / water system in an embodiment of the present invention;

[0022] Figure 3 is the density distribution curve of each component of the air / surfactant / water system along the z-axis in an embodiment of the present invention;

[0023] Figure 4 Schematic diagram of the definition of stretch and tilt angle of SAAS-C12 molecules in an embodiment of the present invention.

[0024] Figure 5 The stretching degrees and tilt angles of the N1-C1 chain, N2-C2 chain, and N1-N2 chain of the SAAS-C12 molecule at different concentrations in the embodiment of the present invention are shown.

[0025] Figure 6 : These are the rising heights of the N1-C1 chain, N2-C2 chain, and N1-N2 chain in the z-axis direction at different concentrations of SAAS-C12 molecules in the embodiment of the present invention.

[0026] Figure 7 Schematic diagram of the intramolecular and intermolecular hydrogen bonds and surfactant-water hydrogen bonds formed by SAAS-C12 molecules in an embodiment of the present invention, as well as the percentages of intramolecular, intermolecular, and surfactant-water hydrogen bonds at different concentrations.

[0027] Figure 8 It is the average number of hydrogen bonds formed by each polar atom of the hydrophilic head group when 30 SAAS-C12 molecules are placed in a monolayer in the embodiment of the present invention.

[0028] Figure 9 : This is the radial distribution function of the polar atoms of the hydrophilic head group and the O atoms in water when 30 SAAS-C12 molecules are placed in a monolayer in an embodiment of the present invention. DETAILED DESCRIPTION

[0029] Example

[0030] This experimental example involves characterizing the interfacial behavior of the sorbitol-based surfactant (2R,3R,4R,5S)-1,6-di(dodecylamino)hexane-2,3,4,5-tetraol (SAAS-C12) at the gas-liquid interface. The following steps are involved:

[0031] (1) The geometric structure model of the surfactant molecule was constructed using GaussView software and the initial configuration of the surfactant was optimized using the Gaussian 09 software package at the B3LYP / 6-31+g(d) calculation level. The force field parameters used in the simulation were derived from the General Amber Force Field (GAFF) of the AmberTools19 program

[32] , combined with the restrained electrostatic potential (RESP) atomic charges calculated using the B3LYP / 6-311+g(d) method. The surfactant molecule used the all-atom model, and the water molecule used the SPC / E three-point water model.

[0032] The potential energy function used in the Amber molecular force field is:

[0033]

[0034] where K r , K θ 、V n are the force constants for the bond, bond angle, and dihedral angle, respectively; r eq and θ eq are the equilibrium bond length and bond angle respectively; n is the multiple; is the phase angle; q is the atomic charge; ε0 is the vacuum dielectric constant; ε ij and σ ij is the Lennard-Jones parameter for the two-atom non-bonding term.

[0035] (2) Using Packmol software, introduce the coordinate file of the surfactant molecule obtained in step (1),

[0036] Parallel to the interface normal vector z, an initial periodic box of dimensions 5.0nm × 5.0nm × 40.0nm (in the x, y, and z directions, respectively) was established. Based on the actual density of pure water corresponding to the simulation conditions, a 5.0nm × 5.0nm × 8.0nm water box consisting of 6660 water molecules was placed in the middle of the box. One, 30, 35, and 40 surfactant molecules were placed at each end of the water box, respectively, with the hydrophilic head group chain side close to the water phase and the hydrophobic tail chain stretched in the air. The resulting double-layer interface model of air / surfactant / water / surfactant / air was saved in the .gro file format, as shown in the following example. Figure 2 shown.

[0037] (3) Using Gromacs 2018.1 software, the .gro file obtained in step (2) was imported and the steepest descent method was used to minimize its energy to eliminate unreasonable contacts in the system. The system energy was converged to less than 100 kJ / mol; the Verlet scheme was used for the truncation scheme; the particle mesh summation (PME) method was used to calculate long-range electrostatic interactions; the cutoff radius for non-bonded forces was set to 1.4 nm, and the truncation method was used to calculate van der Waals interactions.

[0038] (4) Using Gromacs2018.1 software, the structure file obtained by successfully converging the energy in step (3) to less than 100 kJ / mol was introduced as the input file for a 10 ns NVT ensemble simulation to ensure that the system reached equilibrium and obtain the NVT structure file. Based on the equilibrium of the system, a 5 ns NVT simulation was performed for subsequent dynamic calculations and analysis. Periodic boundary conditions were used in the three dimensions x / y / z. The LINCS algorithm was used to constrain the bonds connected to hydrogen. The simulation time step was set to 2 fs, and data was output every 500 steps. The temperature was controlled at 298.15 K using the V-rescale algorithm, and the coupling time constant was set to 0.1 ps. The Verlet scheme was used as the truncation scheme, and the particle mesh (PME) summation method was used to calculate the long-range electrostatic interaction, and the truncation radius of the non-bonded force was set to 1.4 nm.

[0039] (5) Analyze the dynamic trajectory obtained in the last 5 ns of step (4). The main analysis steps are as follows:

[0040] 1) Analyze the mass density distribution of the system. Use the gmx density command in Gromacs to obtain the distribution of water, surfactant, two hydrophobic tail chains and one hydrophilic chain in the surfactant, such as Figure 3 Observe whether the density of the aqueous phase is consistent with the density of water in the actual system to ensure that the simulated system reflects the actual system. Also, determine the relative positions of the components based on their density distribution. The hydrophilic portion is primarily distributed in the aqueous phase, while the hydrophobic tail chains are exposed to air.

[0041] 2) Analyze the stretch and tilt angle of SAAS-C12 molecules at different concentrations. The two hydrophobic tail chains N1-C1 chain and N2-C2 chain are represented by the definition vectors from the N1 atom to the C1 atom at the end of the tail chain and from the N2 atom to the C2 atom at the end of the tail chain, respectively. The hydrophilic head group chain N1-N2 chain is represented by the definition vector from the N1 atom to the N2 atom, as shown in Figure 2. Figure 4 shown.

[0042] The stretch is defined as the ratio of the average distance of the definition vector in the last 5 ns trajectory to the length of the corresponding vector of the fully stretched surfactant in vacuum, where the average distance in the last 5 ns is calculated using the gmx distance command in Gromacs. The tilt angle is defined as the angle between the definition vectors of the N1-C1 chain, N2-C2 chain, and N1-N2 chain and the z-axis direction, and is calculated using the gmxgangle command in Gromacs. The stretch and tilt angle of the N1-C1 chain, N2-C2 chain, and N1-N2 chain at different concentrations were calculated, as shown in Figure 3. Figure 5 As the concentration increases, the hydrophobic tail chain becomes more stretched and the tilt angle gradually decreases.

[0043] 3) Analyze the rising height of each chain of SAAS-C12 molecules in the z-axis direction at different concentrations, set the N1 atom as the reference point, and calculate the distance between each carbon atom on different chains and the reference point in the z-direction using the gmx distance command in Gromacs, as follows: Figure 6 As the concentration increases, the hydrophobic tail chain becomes more upright and the hydrophilic chain presents a unique configuration.

[0044] 4) Analyze the proportion of various types of hydrogen bonds formed by SAAS-C12 molecules at different concentrations, including surfactant-surfactant hydrogen bonds (i.e., intermolecular hydrogen bonds formed between two surfactant molecules), intramolecular hydrogen bonds formed within a single surfactant molecule, and surfactant-water hydrogen bonds (i.e., hydrogen bonds formed between a surfactant molecule and a water molecule). The criteria for defining the existence of a hydrogen bond are that the distance between the donor (D) and the acceptor (A) is less than 0.35 nm and the angle HDA is less than 30°. This is calculated using the gmx hbond command in Gromacs, as shown in the following example: Figure 7 As the concentration increases, the number of hydrogen bonds within the surfactant molecules decreases, the number of hydrogen bonds between molecules increases, and the number of hydrogen bonds formed with water decreases. This indicates that at low concentrations, the number of hydrogen bonds within the molecules is dominant, while at high concentrations, the number of hydrogen bonds between molecules is dominant.

[0045] At the same time, the above command was used to analyze the average number of hydrogen bonds formed by each polar atom on the hydrophilic chain when 30 SAAS-C12 molecules were placed in a monolayer, as shown in Figure 2. Figure 8 It was found that the more hydrogen bonds each polar atom forms with water, the deeper the carbon atoms connected to it penetrate into the aqueous phase, indicating that the interfacial arrangement of surfactants is regulated by the number of intermolecular hydrogen bonds.

[0046] 5) Analyze the radial distribution function of each polar atom of the hydrophilic chain and the O atom in water when 30 SAAS-C12 molecules are placed in a monolayer. The results are calculated using the gmx rdf command in Gromacs. Figure 9 As shown. When the number of hydrogen bonds formed between the groups where the polar atoms are located and water increases, the corresponding polar atoms and OW The higher the peak of the radial distribution function of the atom, the higher the peak of the radial distribution function of the atom.

[0047] The expression of the radial distribution function is:

[0048]

[0049] Where N is the distance between the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant. W ), ρ is the number density of oxygen atoms in the water phase, and r is the number of oxygen atoms in water (O W ) to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant, and g(r) is the radial distribution function of the oxygen atom to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant.

[0050] The above description is only a preferred embodiment of the present invention and is not intended to limit the present invention. Any modifications, equivalent substitutions or improvements made within the spirit and principles of the present invention should be included in the scope of protection of the present invention.

Claims

1. A molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface, characterized in that: The specific steps include: (1) Construct a single-molecule structure model of the surfactant molecule, optimize the initial topological structure of the surfactant, calculate the charge parameters of the all-atom structure, and generate the corresponding force field parameters from the Amber molecular force field; (2) Constructing an air / surfactant / water three-phase system model for simulation calculations; (3) performing energy minimization on the air / surfactant / water three-phase system model to eliminate unreasonable contacts generated by model construction and obtain an energy-minimized structure file; (4) performing molecular dynamics simulation on the energy-minimized structure file as input file, determining the air / surfactant / water three-phase system model in a stable state, collecting molecular trajectory files and three-dimensional coordinate files, and exporting files in .xtc and .gro formats; (5) Analyze the obtained molecular trajectory file and three-dimensional coordinate file to study the system density, interface arrangement and interaction, and obtain the research results of the interface behavior of the surfactant molecules in the system.

2. A molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The specific steps of step (1) are: The geometric structure model of the surfactant molecule was constructed using GaussView software, and the initial configuration of the surfactant was geometrically optimized using the Gaussian 09 software package at the B3LYP / 6-31+g(d) calculation level. Subsequently, the general Amber force field (GAFF) of the AmberTools19 program was used, combined with the restrained electrostatic potential (RESP) atomic charges calculated using the B3LYP / 6-311+g(d) method, to directly obtain the van der Waals parameters and bonding parameters of each atom from the Amber molecular force field; The potential energy function used in the Amber molecular force field is: where K r , K θ 、V n are the force constants for the bond, bond angle, and dihedral angle, respectively; r eq and θ eq are the equilibrium bond length and bond angle respectively; n is the multiple; is the phase angle; q is the atomic charge; ε0 is the vacuum dielectric constant; ε ij and σ ij is the Lennard-Jones parameter for the two-atom non-bonding term.

3. The molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The specific steps of step (2) are: Using Packmol software, the coordinate file of the surfactant molecules obtained in step (1) was introduced to construct a double-layer interface model of air / surfactant / water / surfactant / air and save it in .gro file format. In this model, 1, 30, 35, and 40 surfactant molecules were placed on both sides of the water phase, respectively. The hydrophilic side was close to the water phase, and the hydrophobic side was stretched in the air.

4. A molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The energy minimization in step (3) adopts the steepest descent method in Gromacs software; the convergence criterion of energy minimization is: the system energy converges to 100 kJ / mol.

5. The molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The molecular dynamics simulation process in step (4) includes: performing a 10 ns NVT ensemble simulation to ensure that the system reaches an equilibrium state and obtain a structure file; using the obtained structure file as an input file, continuing to perform a 5 ns NVT ensemble simulation for subsequent dynamic calculations and analysis.

6. A molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, wherein the system temperature is controlled by a V-rescale temperature control method, the system temperature is selected to be 298.15K, and the coupling time constant is set to 0.1ps.

7. The molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The parameters of interest in interface arrangement include tilt angle, stretching degree and rising height along the z-axis; the parameters of interest in interaction include radial distribution function and hydrogen bonding.

8. A molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 7, characterized in that: The geometric criteria for defining the presence of the hydrogen bond are that the distance between the donor (D) and the acceptor (A) is less than 0.35 nm and the angle HDA is less than 30°; The expression of the radial distribution function is: Where N is the distance between the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant. W ), is the total number of oxygen atoms in the water phase, r is the number of oxygen atoms in water (O W ) to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant, and g(r) is the radial distribution function of the oxygen atom to the nitrogen atom (N) and oxygen atom (O) on the polar head group of the surfactant.

9. The molecular dynamics method for simulating the hydrogen bond network structure of a surfactant at a fluid interface according to claim 1, characterized in that: The biomass-based surfactant is a sorbitol-based surfactant (2R, 3R, 4R, 5S)-1,6-di(dodecylamino)hexane-2,3,4,5-tetraol (SAAS-C12).

Images