Molecular dynamics simulation method for constructing hierarchical pore carbon molecular model

Abstract

The invention relates to a molecular dynamics simulation method for constructing a hierarchical pore carbon molecular model, which comprises the following steps of: constructing mesopores and microporous carbon tubes with different pore diameters by using VMD software, digging out microporous pores conforming to the pore diameters of the microporous carbon tubes on the mesopore walls, and then splicing the microporous carbon tubes and the microporous pores on the mesopore walls by using a pack tool to obtain the hierarchical pore carbon molecular model. After optimization, parameters are set, a topological file is generated by using a Sobtop script, and after geometric optimization, hierarchical pore carbon molecular system model boxes with different topological structures are finally obtained. The method realizes the construction of hierarchical pore carbon molecular model systems with different topological structures, accurately constructs the complex hierarchical pore structures on the nanoscale, can be applied to a simulation system for adsorbing various substances, can quickly judge the adsorption effect of an adsorbent, reduces the experiment research and development time, remarkably reduces the experiment cost, and is suitable for large-scale popularization and application. And important theoretical support is provided for design and structure optimization of the hierarchical porous carbon material.

Description

Technical Field

[0001] The invention relates to the fields of nano material technology, adsorption material development and molecular dynamics simulation, and in particular to a molecular dynamics simulation method for constructing a multi-level porous carbon molecular model. Background Art

[0002] Hierarchical carbon has a porous structure composed of interconnected pores of different sizes from micropores, mesopores to macropores, combining the advantages of pores of different sizes while providing a large specific surface area and low mass transfer resistance. These characteristics make it an ideal choice for a variety of applications, including adsorption, separation, catalysis, electrode manufacturing and energy storage, especially in the field of adsorption, it has excellent adsorption capacity and fast removal rate. And the hierarchical pore structure helps guest molecules enter the micropores and transfer mass, thereby enhancing the adsorption performance.

[0003] Molecular dynamics simulation is a powerful computational tool that has become increasingly popular in the past few decades. Compared with experimental methods, molecular dynamics simulation can provide insights into microstructural mechanisms and dynamic behaviors at the molecular or atomic level, making up for the inability of existing experimental techniques to describe the structural characteristics of hierarchical porous carbon materials at the molecular level. Recently, molecular dynamics simulation has been widely used to elucidate the underlying mechanisms of adsorption behavior. Molecular dynamics simulation can study the migration and adsorption behavior of guest molecules in hierarchical nanopores. By observing the molecular trajectories, adsorption kinetics, sites and affinities during the simulation process, the intragranular diffusion-adsorption synergistic mechanism of hierarchical nanopores can be explored, providing important theoretical support for the design and structural optimization of hierarchical porous carbon materials.

[0004] Based on this, this case is brought forward. Summary of the invention

[0005] The purpose of the present invention is to provide a molecular dynamics simulation method for constructing a multi-level porous carbon molecular model, which can be applied to a simulation system for adsorbing multiple substances and studying its adsorption characteristics. It has strong flexibility and adaptability. In addition, the adsorption effect of the adsorbent can be quickly judged. The molecular weight of the multi-level porous carbon spliced ​​by single-layer carbon tubes is smaller than that of the traditional multi-layer carbon adsorbent model, which reduces the experimental research and development time, significantly reduces the experimental cost, and provides important theoretical support for the design and structural optimization of multi-level porous carbon materials.

[0006] In order to achieve the above object, the technical solution of the present invention is as follows:

[0007] A molecular dynamics simulation method for constructing a multi-level porous carbon molecular model comprises the following steps:

[0008] S10. Use the Nanotube Builder module in VMD software to build mesoporous and microporous carbon tube models with different pore sizes, then select the Selected Atoms module on VMD software to dig microporous holes of the composite microporous carbon tube pore size on the mesoporous carbon tube wall, and save the microporous carbon tube and the mesoporous carbon tube after digging micropores in pdb format;

[0009] S20. Use the packmal tool to splice the microporous holes on the walls of microporous carbon tubes and mesoporous carbon tubes to obtain a multi-level porous carbon molecular model, and use Materials Studio software to optimize the interface, then export the multi-level porous carbon molecular model as a mol2 file, and then import the multi-level porous carbon molecular model mol2 file into the Sobtop script to generate a topology file;

[0010] S30. Set the molecular dynamics simulation parameter file, and use Materials Studio software to geometrically optimize the structure of the obtained multi-level porous carbon molecular model, add the box size in the structure file, and finally obtain the multi-level porous carbon molecular system model box with different topological structures.

[0011] Furthermore, the step S10 includes the following process:

[0012] Open the Nanotube Builder module in VMD and set the diameter to Length is The microporous carbon tubes with a diameter of Length is and diameter Length is Two types of mesoporous carbon tubes, each type of carbon tube is saved as a pdb file;

[0013] Lead-in diameter is In the Selected Atoms module, select the specified range using the basic syntax of the VMD software range selection statement. Enter "resname CNT and((x-25.03)^2+(z-16.184)^2>9.45^2)" in the Selected Atoms module, select to delete and save the remaining carbon atoms, and in the y-axis direction, two atoms with a radius of The microporous holes are dug, and other microporous holes are obtained by analogy. The mesoporous carbon tubes after the microporous holes are dug are saved as pdb files.

[0014] Furthermore, the step S20 includes the following process:

[0015] In a virtual machine with the GROMACS software package and the packmol tool installed, import the microporous carbon nanotubes and mesoporous carbon nanotubes with holes dug in step S10, create a packmol file, write the packmol file, define the placement rules of the carbon nanotubes through the packmol file, and input "packmol < packmol.inp" in the terminal to run the packmol tool. The microporous carbon nanotubes and mesoporous carbon nanotubes will be arranged according to the placement rules defined in the packmol file, and a pdb file of the hierarchical porous carbon molecular model will be generated;

[0016] Import the pdb file of the hierarchical porous carbon molecular model into Materials Studio software, use the bonding tool to connect the carbon atoms at the splicing points, and adjust the bonding relationship. Save the hierarchical porous carbon molecular model with optimized interfaces as a mol2 file;

[0017] Import the mol2 file of the hierarchical porous carbon molecular model into the Sobtop script, and sequentially select to generate the GROMACS topology file, manually set the atomic type, select all atoms, set them to the ca atomic type, use the preset force field parameters, and generate the topology file of the hierarchical porous carbon molecule.

[0018] Furthermore, step S30 includes the following process:

[0019] Set the molecular dynamics simulation parameter file, set the hierarchical porous carbon molecular model as a periodic molecule, use periodicity in the x / y / z directions, add the box size in the structure file, obtain the hierarchical porous carbon molecular system model box with different topological structures, and place it under the classical force field by Materials Studio software to perform geometric optimization on its structure;

[0020] Perform kinetic calculations on the hierarchical porous carbon molecular model box. First, in order to pursue system convergence and cancel any significant repulsive forces, the steepest descent algorithm in the energy minimization stage is configured with a maximum step size of 0.01 nm. Once the maximum force threshold drops below 100 Kcal / mol, convergence is considered to have occurred; then use the Berendsen barostat combined with the V-rescale thermostat to perform a 100 ps simulation to enable the system to relax to a stable temperature of 298 K and a constant pressure of 1 bar, thereby eliminating any structural irregularities and reaching an equilibrium and stable state; subsequently, use the Parrinello-Rahman barostat combined with the V-rescale thermostat to perform a 15 ns simulation.

[0021] The advantages of the present invention are:

[0022] 1. The construction of a molecular model system of multi-level porous carbon with different topological structures has been realized. These complex multi-level porous structures are accurately constructed at the nanoscale, and the size and morphology of the multi-level pores and their influence on the selectivity and adsorption capacity of adsorbed substances can be analyzed at the atomic level;

[0023] 2. The multi-level porous carbon molecular model constructed by molecular dynamics simulation proposed in the present invention can better demonstrate the microstructure and dynamic trajectory behavior of the guest molecules in the multi-level nanopores, and further reveal its synergistic mechanism;

[0024] 3. The method of the present invention can be applied to simulated systems for adsorbing a variety of substances and study their adsorption characteristics, and has strong flexibility and adaptability;

[0025] 4. The method of the present invention can quickly determine the adsorption effect of the adsorbent. The molecular weight of the multi-level porous carbon molecular model spliced ​​by single-layer carbon tubes is smaller than that of the traditional multi-layer carbon adsorbent model, which reduces the experimental research and development time, significantly reduces the experimental cost, and provides important theoretical support for the design and structural optimization of multi-level porous carbon materials. BRIEF DESCRIPTION OF THE DRAWINGS

[0026] Figure 1 Build a flowchart for the model in the embodiment;

[0027] Figure 2a In the embodiment Diameter microporous carbon tubes and Schematic diagram of the molecular model of hierarchical porous carbon composed of mesoporous carbon tubes with different diameters;

[0028] Figure 2b In the embodiment Diameter microporous carbon tubes and Schematic diagram of the hierarchical porous carbon molecular model composed of mesoporous carbon tubes with different diameters. DETAILED DESCRIPTION

[0029] The present invention is further described in detail below in conjunction with the embodiments. It should be understood that the directions or positional relationships indicated by the terms "upper", "lower", "front", "back", "left", "right", "top", "bottom", "inside" and "outside" herein are based on the directions or positional relationships shown in the accompanying drawings, and are only for the convenience of describing the present invention and simplifying the description, rather than indicating or implying that the device or element referred to must have a specific direction, be constructed and operated in a specific direction, and therefore cannot be understood as limiting the present invention.

[0030] This embodiment proposes a molecular dynamics simulation method for constructing a multi-level porous carbon molecular model. Figure 1 , Figure 2a and Figure 2b As shown, the following process is included.

[0031] Step 1: Open the VMD software, select Extensions→Modeling→Nanotube Builder, and then set the generation of microporous carbon nanotubes with a diameter of and a length of , and generate two kinds of mesoporous carbon nanotubes with a diameter of and a length of , and a diameter of and a length of . Save each carbon nanotube as a pdb file. Import the mesoporous carbon nanotube with a diameter of . Select Graphics→Representations. In the Selected Atoms column of the Graphics Representations module, select the specified range through the basic syntax of the VMD software range selection statement. Enter "resname CNT and ((x - 25.03)^2+(z - 16.184)^2>9.45^2)" in the Selected Atoms column, select to delete and save the remaining carbon atoms. In the y-axis direction, two micropores with a radius of will be obtained on the mesoporous wall. And so on to obtain other micropores. After digging the micropores, save it as a pdb file.

[0032] Step 2: In the virtual machine with the GROMACS software package and the packmol tool installed, import the microporous carbon nanotubes and the mesoporous carbon nanotubes with dug holes saved in Step 1, create a packmol file, write the packmol file, define the placement rules of the carbon nanotubes through the packmol file. Enter packmol < packmol.inp in the terminal to run the packmol tool. The microporous carbon nanotubes and the mesoporous carbon nanotubes will be arranged according to the placement rules defined in the packmol file, and a pdb file of the hierarchical porous carbon molecular model will be generated. Import the pdb file of the hierarchical porous carbon molecular model into the Materials Studio software, use the bonding tool to connect the carbon atoms at the splicing points, and adjust the bonding relationship. Save the optimized hierarchical porous carbon molecular model at the interface as a mol2 file. Then import the mol2 file of the hierarchical porous carbon molecular model into the Sobtop script, select to generate the GROMACS topology file→manually set the atom type→select all atoms→set them as ca atom type→use the preset force field parameters→generate the topology file of the hierarchical porous carbon molecule.

[0033] Step 3: Set the molecular dynamics simulation parameter file, set the multi-level porous carbon molecular model as a periodic molecule, use periodicity in the x / y / z directions, add the box size in the structure file, and obtain the multi-level porous carbon molecular system model box with different topological structures. Use Materials Studio software to place it under the classical force field and perform geometric optimization on its structure.

[0034] Step 4: Perform kinetic calculations on the multi-level porous carbon molecular model system obtained in step 3. First, in order to pursue system convergence and offset any significant repulsive forces, the steepest descent algorithm in the energy minimization phase is configured with a maximum step size of 0.01nm. Once the maximum force threshold drops below 100Kcal / mol, convergence is considered to have occurred. Then, a 100ps simulation is performed using a Berendsen barostat combined with a V-rescale thermostat, allowing the system to relax to a stable temperature of 298K and a constant pressure of 1bar, thereby eliminating any structural irregularities and reaching a state of equilibrium stability. Subsequently, a 15ns simulation is performed using a Parrinello-Rahman barostat combined with a V-rescale thermostat. Throughout the entire stage, data is carefully collected to ensure a comprehensive data set for subsequent analysis.

[0035] The above embodiments are only used to explain the concept of the present invention, rather than to limit the protection of the rights of the present invention. Any non-substantial changes to the present invention using this concept shall fall within the protection scope of the present invention.

Claims

1. A molecular dynamics simulation method for constructing a multi-level porous carbon molecular model, characterized in that: It includes the following steps: S10. Use the Nanotube Builder module in VMD software to construct mesoporous and microporous carbon tube models with different pore diameters. Then, select the Selected Atoms module on VMD software to dig out micropores with the same pore diameter as the composite microporous carbon tube on the mesoporous carbon tube wall, and save the microporous carbon tube and the mesoporous carbon tube with dug micropores in pdb format; S20. Use the packmal tool to splice the microporous carbon tube and the micropores on the mesoporous carbon tube wall to obtain a hierarchical pore carbon molecular model, and use Materials Studio software to optimize the interface. Then, export the hierarchical pore carbon molecular model as a mol2 file. Next, import the mol2 file of the hierarchical pore carbon molecular model into the Sobtop script and generate a topology file; S30. Set the molecular dynamics simulation parameter file, and use Materials Studio software to geometrically optimize the structure of the obtained hierarchical pore carbon molecular model, and add the box size to the structure file, finally obtaining a hierarchical pore carbon molecular system model box with different topological structures.

2. A molecular dynamics simulation method for constructing a multi-level porous carbon molecular model according to claim 1, characterized in that: The step S10 includes the following process: Open the Nanotube Builder module in VMD and set the diameter to Length is The microporous carbon tubes with a diameter of Length is and diameter Length is Two types of mesoporous carbon tubes, each type of carbon tube is saved as a pdb file; Lead-in diameter is In the Selected Atoms module, select the specified range using the basic syntax of the VMD software range selection statement. Enter "resname CNT and((x-25.03)^2+(z-16.184)^2>9.45^2)" in the Selected Atoms module, and select to delete and save the remaining carbon atoms. In the y-axis direction, two radii of The microporous holes are dug, and other microporous holes are obtained by analogy. The mesoporous carbon tubes after the microporous holes are dug are saved as pdb files.

3. A molecular dynamics simulation method for constructing a multi-level porous carbon molecular model according to claim 1, characterized in that: The step S20 includes the following process: In a virtual machine installed with the GROMACS software package and the packmol tool, import the microporous carbon tube and the mesoporous carbon tube with dug holes saved in step S10, create a packmol file, write the packmol file, define the placement rules of the carbon tubes through the packmol file, and input "packmol < packmol.inp" in the terminal to run the packmol tool. The microporous carbon tube and the mesoporous carbon tube will be arranged according to the placement rules defined in the packmol file, and a pdb file of the hierarchical pore carbon molecular model will be generated; Import the pdb file of the hierarchical pore carbon molecular model into Materials Studio software, use the bonding tool to connect the carbon atoms at the splicing point, and adjust the bonding relationship. Save the hierarchical pore carbon molecular model with optimized interface as a mol2 file; Import the mol2 file of the hierarchical pore carbon molecular model into the Sobtop script, and successively select to generate a GROMACS topology file, manually set the atomic type, select all atoms, set it to the ca atomic type, use the preset force field parameters, and generate a topology file of the hierarchical pore carbon molecule.

4. A molecular dynamics simulation method for constructing a multi-level porous carbon molecular model according to claim 1, characterized in that: The step S30 includes the following process: Set the molecular dynamics simulation parameter file, set the hierarchical pore carbon molecular model as a periodic molecule, use periodicity in the x / y / z directions, add the box size to the structure file, obtain a hierarchical pore carbon molecular system model box with different topological structures, and let Materials Studio software place it under the classical force field and geometrically optimize its structure; Dynamic calculations were performed on the multi-level porous carbon molecular model box. First, in order to pursue system convergence and offset any significant repulsive forces, the steepest descent algorithm in the energy minimization phase was configured with a maximum step size of 0.01nm. Once the maximum force threshold dropped below 100Kcal / mol, convergence was considered to have occurred. Then, a Berendsen barostat combined with a V-rescale thermostat was used to perform a 100ps simulation, allowing the system to relax to a stable temperature of 298K and a constant pressure of 1bar, thereby eliminating any structural irregularities and achieving a stable equilibrium state. The simulation was then performed for 15 ns using a Parrinello-Rahman barostat in combination with a V-rescale thermostat.

Images