A molecular simulation method for ionic hydrogen-bonded cross-linked supramolecular networks

Abstract

The present invention provides a molecular simulation method for an ionic hydrogen bond cross-linked supramolecular network. On the initial structure of the polymer chain, a new protonated initial structure model is established according to the proton transfer law between ionic hydrogen bond groups. A suitable force field is selected, and the RESP atomic charge of the polymer chain is calculated using the fragment segmentation method; a suitable number of polymer chains are determined and randomly arranged in a simulation box, and a series of equilibrium simulation processes are added to realize the non-reactive force field molecular dynamics simulation of the supramolecular network based on ionic hydrogen bond cross-linking under simple conditions. The present invention adopts the fragment segmentation method to calculate the atomic charge of the macromolecular chain, which provides an idea for the calculation of the atomic charge of a single polymer chain with a large molecular weight; the idea of ​​rationally using the protonation model is proposed, which is helpful to solve the molecular dynamics simulation problem involving ionic hydrogen bonding.

Description

Technical Field

[0001] The invention belongs to the field of computational simulation of polymer materials, and in particular relates to a molecular simulation method of an ionic hydrogen bond cross-linked supramolecular network. Background Art

[0002] In the past decade, polymer materials cross-linked by non-covalent interactions, especially hydrogen bonding, have become one of the hot topics of research. When the strength of hydrogen bonding is strong enough, the supramolecular polymer network constructed solely by it has good mechanical properties; when it works synergistically with other non-covalent bonds, it can dissipate energy as a sacrificial bond to improve the toughness of the material and bring better self-healing ability. Ionic hydrogen bonding is a special type of hydrogen bonding, which has stronger interactions. The supramolecular network formed by it has both good mechanical properties and self-healing ability, and has great application potential. However, our understanding of the mechanism of ionic hydrogen bonding in polymer cross-linked networks is still insufficient. In most cases, researchers use indirect experimental tests to explain the internal mechanism of the material. After years of development, molecular dynamics simulation has become an important technical means to study the microstructure of matter. In the simulation, we can easily obtain the type and quantity information of hydrogen bonds, and observe their changes and their impact on the internal structure of the material. Since general molecular dynamics simulations use force fields that do not involve chemical reactions, the proton transfer effect between groups is ignored to a certain extent when simulating systems containing ionic hydrogen bonds, resulting in deviations in the results. Currently, there are few studies on the simulation of supramolecular materials based on ionic hydrogen bond crosslinking. How to reflect this non-covalent effect in the simulation in a more accurate way is of great significance for molecular simulation research in this field. Summary of the invention

[0003] The present invention aims to solve at least one of the technical problems existing in the above-mentioned prior art. To this end, the present invention proposes a molecular simulation method of ionic hydrogen bond cross-linked supramolecular network.

[0004] In some embodiments of the present invention, the molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network comprises the following steps:

[0005] S1: Establish the atomic structure model of the polymer chain and obtain the initial coordinate file of the polymer chain;

[0006] S2: According to the proton transfer rule, modify the groups that can form ionic hydrogen bonds in the polymer chain atomic structure model described in S1 to obtain a protonated polymer chain structure model;

[0007] S3: setting a full-atom force field for the protonated polymer chain structure model described in S2, so that the system potential energy is the sum of bond stretching energy, dihedral angle distortion energy, van der Waals non-bonding potential energy and Coulomb electrostatic potential energy;

[0008] S4: selecting atomic charges, segmenting the polymer chain into fragments, and calculating atomic charges of different fragments respectively;

[0009] S5: Determine the number of molecular chains, establish a simulation box, randomly fill the molecular chains, and obtain a low-density system that can be used for simulation;

[0010] S6: Performing an equilibrium simulation process on the low-density system described in S5 to calculate the radial distribution function between the ionic hydrogen bonding groups.

[0011] In the present invention, without using a reaction force field with a larger computational effort, a good simulation effect of an ionic hydrogen-bonded cross-linked supramolecular network can be achieved by establishing a protonation model of ionic hydrogen-bonded groups in a polymer chain and applying reasonable atomic charges and simulation procedures.

[0012] In some preferred embodiments of the present invention, the Moltemplate program is used to construct the polymer chain atomic structure model.

[0013] In some preferred embodiments of the present invention, the initial structure file of the polymer chain is processed using the pdb2gmx applet of the gromacs software to obtain a protonated polymer chain structure model and a corresponding topological relationship file.

[0014] In some preferred embodiments of the present invention, the main chain of the polymer chain in S1 is selected from any one of a polysiloxane molecular chain, a polyethylene chain, and a polyether chain.

[0015] In some preferred embodiments of the present invention, the group capable of forming an ionic hydrogen bond in S2 is selected from an amino group and an unsaturated carboxyl group.

[0016] In some preferred embodiments of the present invention, the modification treatment in S2 does not include the situation where the repeating unit structure of the ionic hydrogen bonding group remains unchanged, the organic acid group removes the hydrogen atom and the organic base group obtains one hydrogen atom.

[0017] In some preferred embodiments of the present invention, the all-atom force field in S3 is selected from COMPASS force field, OPLS-AA force field, DREIDING force field, GAFF force field, and AMBER force field; preferably, OPLS-AA force field.

[0018] In some preferred embodiments of the present invention, S4 is specifically: selecting RESP atomic charges, optimizing the geometry of the fragments using the B97-3c method in the ORCA program, and then calculating the RESP charges of the optimized different fragments under the basis set of the B3LYP-D3 / def2-TZVP level; when calculating the charges, both ends of the repeating structural unit in the middle of the fragment are closed with hydrogen atoms, and the two chain end groups are combined into a complete molecule; wherein, the total charge constraint of the fragment not containing an ionic hydrogen bonding group is specified to be 0, the total charge constraint of the fragment with an organic acid group is specified to be -1, and the total charge constraint of the fragment with an organic base group is specified to be +1.

[0019] In some preferred embodiments of the present invention, the number of the molecular chains in S5 ranges from 40 to 60.

[0020] In some preferred embodiments of the present invention, the establishment of the simulation box and the random filling of the molecular chains in S5 are performed by the Packmol program.

[0021] In some preferred embodiments of the present invention, the simulation box in S5 is a cube with a size of 10 nm to 15 nm.

[0022] In some preferred embodiments of the present invention, the interatomic distances between the different molecular chains in S5 are ≥0.2 nm.

[0023] In some preferred embodiments of the present invention, the equilibrium simulation process described in S6 is energy minimization, system compression, high temperature relaxation, cooling, and NPT equilibrium under isothermal and isobaric conditions.

[0024] In some preferred embodiments of the present invention, the equilibrium simulation in S6 is performed using gromacs software; wherein the energy minimization uses the steep method, which can adjust the unreasonable structure in the system and effectively prevent the collapse of the initial molecular dynamics simulation.

[0025] In some preferred embodiments of the present invention, in S6, after the system compression is completed, the NVT ensemble is used to allow the simulation system to fully relax at 600K, and the simulation uses LINCS to constrain all chemical bonds with hydrogen atoms participating in the connection, with a step size of 2fs, and the total simulation time of the process is 200ns; after the relaxation process is completed, linear cooling is performed from 600K to 300K, and the bond constraints are released at the same time, the step size is changed to 1fs, and the time is 10ns; the final equilibrium simulation uses the NPT ensemble, and a 100ns simulation is performed at 300K and 1.0bar (close to one atmosphere); the temperature control of all equilibrium simulations uses the V-rescale method with a coupling time constant of 0.2ps, and the pressure control uses the Berendsen method with a coupling time constant of 0.5ps.

[0026] In some preferred embodiments of the present invention, density and total potential energy are used as criteria for determining the equilibrium state of the system.

[0027] In some preferred embodiments of the present invention, the criterion for determining the equilibrium state in the equilibrium simulation is that the density and potential energy changes of the system are less than 5%.

[0028] The beneficial effects of the present invention are:

[0029] (1) The present invention helps to solve the molecular dynamics simulation problem involving ionic hydrogen bonding. Reasonable use of the protonated initial structure model can better reflect the strong interaction of ionic hydrogen bonding in the simulation.

[0030] (2) The present invention adopts the fragment segmentation method to calculate the atomic charge of the macromolecular chain, which ensures accuracy while greatly reducing the computing resources, and provides a method for calculating the atomic charge of a single chain of a large molecular weight polymer. BRIEF DESCRIPTION OF THE DRAWINGS

[0031] The present invention will be further described below with reference to the accompanying drawings and embodiments, wherein:

[0032] Figure 1 is the chemical structural formula of the amino-grafted polysiloxane and the unsaturated carboxyl-grafted polysiloxane in Example 1 of the present invention.

[0033] Figure 2 The radial distribution function diagram between the amino group and the unsaturated carboxyl group in the protonated model of the present invention and the non-protonated model of the prior art. DETAILED DESCRIPTION

[0034] The following will be combined with the embodiments to clearly and completely describe the concept of the present invention and the technical effects produced, so as to fully understand the purpose, characteristics and effects of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of them. Based on the embodiments of the present invention, other embodiments obtained by those skilled in the art without creative work are all within the scope of protection of the present invention.

[0035] Example 1

[0036] This embodiment takes amino-grafted polysiloxane and unsaturated carboxyl-grafted polysiloxane as examples to implement a molecular simulation method of an ionic hydrogen-bonded cross-linked supramolecular network. The specific process is as follows:

[0037] (1) Establish the full atomic structure model of two polymer chains: amino-grafted polysiloxane and unsaturated carboxyl-grafted polysiloxane. Their chemical structures are as follows: Figure 1As shown, the polymerization degree of both is 160, the grafting rate is 5%, and the amino groups and unsaturated carboxyl groups are randomly grafted on the main chain of polysiloxane;

[0038] (2) According to the proton transfer rules, the groups that can form ionic hydrogen bonds are modified. In this simulation system, there is proton transfer between the amino group and the unsaturated carboxyl group during the formation of ionic hydrogen bonds. The unsaturated carboxyl group loses a hydrogen atom and becomes deprotonated, while the amino group gains a hydrogen atom and becomes protonated. The full atomic structure model obtained in (1) is modified accordingly.

[0039] (3) The OPLS-AA force field is selected for the non-covalent cross-linking system of amino-grafted polysiloxane and unsaturated carboxyl-grafted polysiloxane. This force field has a wide range of applications, a large number of atomic types, and corresponding force field parameters for some complex organic structures. The total potential energy of this force field is the sum of bond stretching energy, bond angle bending energy, dihedral angle distortion energy, van der Waals non-bonding potential energy, and Coulomb electrostatic potential energy. According to the literature, the non-bonding van der Waals interaction parameters σ and ε of Si are set to 0.4nm and 0.4184kJ / mol, respectively, and the dihedral angle distortion term parameter centered on Si is set to 0.

[0040] (4) RESP atomic charges were selected for the simulation of the system. In order to reduce the amount of calculation, the amino-grafted polysiloxane and the unsaturated carboxyl-grafted polysiloxane were divided into the following fragments: dimethylsiloxane unit, amino-grafted unit, unsaturated carboxyl-grafted unit and the first and tail end groups. The repeating unit in the middle was closed with hydrogen atoms, and the first and tail end groups were combined together, and then the atomic charge calculations were performed separately. The above fragments were all geometrically optimized in the ORCA program using the B97-3c method, and then the RESP charges of the optimized fragments were calculated under the basis set of the B3LYP-D3 / def2-TZVP level; the necessary constraints were set in the charge calculation, among which the total charge of the dimethylsiloxane fragment was constrained to 0, while the total charge of the fragment with a protonated amino group was constrained to +1, and the deprotonated carboxyl part was constrained to -1.

[0041] (5) The number of amino-grafted polysiloxane chains and unsaturated carboxyl-grafted polysiloxane chains in the simulation system was set to 20, so that the validity of the simulation results could be ensured without consuming too many computing resources. The Packmol program was used to complete the tasks of establishing the simulation box and filling the molecular chains. These 40 polymer chains were randomly stacked in a large simulation box, forming a low-density system that could be used for simulation, that is, a protonated initial structure model was established.

[0042] (6)On the basis of establishing a good protonation initial structure model, adding a suitable simulation process can obtain better simulation results. The simulation was completed using gromacs software, in which the equilibrium simulation process mainly consists of system energy minimization, system compression, high temperature relaxation, cooling, and NPT equilibrium at room temperature and pressure; the energy minimization uses the steep method, which can adjust the unreasonable structure in the system and effectively prevent the collapse of the initial molecular dynamics simulation. After completing the system compression, the NVT ensemble is used to allow the simulation system to fully relax at 600K. The simulation uses LINCS to constrain all chemical bonds involving hydrogen atoms, with a step size of 2fs. The total simulation time of this process is 200ns; after the relaxation process, the system will experience a linear cooling stage, with the temperature dropping from 600K to 300K, and the bond constraints are released at the same time, the step size is changed to 1fs, and the time is 10ns. The final equilibrium simulation uses the NPT ensemble and is simulated for 100 ns at 300 K and 1.0 bar (close to one atmosphere); the temperature control and pressure control of all equilibrium simulations use the V-rescale method and the Berendsen method, respectively, with coupling time constants of 0.2 ps and 0.5 ps, respectively. Density and total potential energy are used as the criteria for determining the equilibrium state of the system. When the fluctuation value is within the range of 5%, the system is considered to be basically in equilibrium.

[0043] Comparative Example 1

[0044] The difference between this comparative example and Example 1 is that the model established in this comparative example is a non-protonated model, and the remaining steps are the same as those in Example 1. The specific process is: two polymer chain structure models of amino-grafted polysiloxane and unsaturated carboxyl-grafted polysiloxane with a degree of polymerization of 160 and a grafting rate of 5% are established; the RESP atomic charge is calculated by the fragment segmentation method, the total charge of each fragment is constrained to 0, and the basis set and process used in the calculation are consistent with those in Example 1; a simulation system consisting of 20 amino-grafted polysiloxanes and 20 unsaturated carboxyl-grafted polysiloxanes is constructed, and the equilibrium simulation uses the same OPLS-AA force field parameters, simulation process and parameters as in Example 1.

[0045] Test example

[0046] The radial distribution function and the number of hydrogen bonds between the amino group and the unsaturated carboxyl group in the equilibrium simulation were analyzed to characterize the effect of the protonated structure model in Example 1 and the non-protonated structure model in Comparative Example 1 on the description of the ionic hydrogen bonding in the simulation. Figure 2 As shown, the radial distribution functions between the amino and unsaturated carboxyl centers in the two structural models show obvious differences, and the peak of the protonated model is higher, indicating that the ionic hydrogen bonding groups therein are more aggregated with each other. Table 1 shows the average number of hydrogen bonds formed between the main groups in the two structural models in equilibrium.

[0047] Table 1 Average number of hydrogen bonds formed between the main groups in the two structural models in equilibrium

[0048]

[0049] It can be seen that there are more hydrogen bonds in the protonated structural model and the hydrogen bonds formed between the amino group and the unsaturated carboxyl group are dominant. From the comparison results, compared with the general non-protonated model, the modified protonated model of this application can better reflect the strong interaction of ionic hydrogen bonds in the simulation, which can provide guidance for the simulation of this type of system.

[0050] The above is a detailed description of the embodiments of the present invention, but the present invention is not limited to the above embodiments. Various changes can be made within the knowledge of ordinary technicians in the relevant technical field without departing from the purpose of the present invention, all of which belong to the scope of the present invention.

Claims

1. A molecular simulation method for ionic hydrogen-bonded cross-linked supramolecular networks, It is characterized in that The following steps are involved: S1: Establish the atomic structure model of the polymer chain and obtain the initial coordinate file of the polymer chain; S2: According to the proton transfer rule, modify the groups that can form ionic hydrogen bonds in the polymer chain atomic structure model described in S1 to obtain a protonated polymer chain structure model; S3: setting an all-atom force field for the protonated polymer chain structure model described in S2 so that the system potential energy is the sum of bond stretching energy, dihedral angle distortion energy, van der Waals non-bonding potential energy and Coulomb electrostatic potential energy; S4: Select RESP atomic charges, segment the polymer chain, optimize the geometry of the fragments in the ORCA program using the B97-3c method, and then calculate the RESP charges of the optimized different fragments under the basis set of B3LYP-D3 / def2-TZVP level; when calculating the charges, both ends of the repeating structural unit in the middle of the fragment are closed with hydrogen atoms, and the two chain end groups are combined into a complete molecule; wherein, the total charge constraint of the fragment not containing an ionic hydrogen bonding group is 0, the total charge constraint of the fragment with an organic acid group is -1, and the total charge constraint of the fragment with an organic base group is +1; S5: Determine the number of molecular chains, establish a simulation box, randomly fill the molecular chains, and obtain a low-density system that can be used for simulation; S6: Performing an equilibrium simulation process on the low-density system described in S5 to calculate the radial distribution function between the ionic hydrogen bonding groups.

2. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The main chain of the polymer chain in S1 is selected from any one of a polysiloxane chain, a polyethylene chain, and a polyether chain.

3. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The group capable of forming an ionic hydrogen bond in S2 is selected from an amino group and an unsaturated carboxyl group.

4. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The modification treatment described in S2 does not include the situation where the repeating unit structure of the ionic hydrogen bonding group remains unchanged, the organic acid group removes the hydrogen atom and the organic base group obtains a hydrogen atom.

5. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The atomic distance between the different molecular chains in S5 is ≥0.2 nm.

6. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The all-atom force field in S3 is selected from any one of COMPASS force field, OPLS-AA force field, DREIDING force field, GAFF force field, and AMBER force field.

7. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 6, It is characterized in that The all-atom force field described in S3 is the OPLS-AA force field.

8. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 1, It is characterized in that The equilibrium simulation process described in S6 is energy minimization, system compression, high temperature relaxation, cooling, and isothermal and isobaric simulation.

9. The molecular simulation method of the ionic hydrogen bond cross-linked supramolecular network according to claim 8, It is characterized in that In S6, the density and total potential energy of the system are used as the criteria for determining the equilibrium state of the system. When the density and the total potential energy of the system change by less than 5%, the system is considered to be in equilibrium.

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