Nanocrystal dissolution process simulation method, medium and equipment

Abstract

The invention discloses a nanocrystal dissolution process simulation method, medium and equipment, and relates to the technical field of molecular dynamics, and the method comprises the following steps: constructing a nanocrystal and water molecule model; determining simulation parameters and potential functions; a conjugate gradient method is adopted to optimize a nanocrystal and water molecule model, relaxation and controlled molecular dynamics simulation are carried out on atoms in the optimized model according to simulation parameters and potential functions, and atom trajectory information is obtained; and according to the atomic trajectory information, obtaining the microcosmic motion states of ions at different moments and the distribution of surrounding water molecules. According to the invention, on the basis of controlled molecular dynamics simulation, by constructing a solution model, atoms are displaced in a fixed direction, so that the stress of the atoms at different positions and the distribution of surrounding water molecules are obtained, and the states of single ions and water molecules and the effects of the single ions and water molecules in the dissolution process are known on the molecular level.

Description

Technical Field

[0001] The invention relates to the technical field of molecular dynamics, and in particular to a method, medium and equipment for simulating the dissolution process of nanocrystals. Background Art

[0002] The saltwater interface is one of the most important and common interfaces on Earth, playing an important role in atmospheric science, biology, physical chemistry, materials science and other disciplines. The key point is the dissolution process involving the destruction of the crystal structure of salt (such as NaCl). Dynamic auxiliary information on a larger scale of the dissolution process can be obtained using techniques such as infrared spectroscopy, atomic force microscopy (AFM), scanning force microscopy (SFM) and scanning polarization force microscopy (SPFM), but the above methods still lack clear images at the atomic / molecular scale and the kinetic properties of the detailed changes in the crystal structure during the dissolution process, making it difficult to reveal the basic reaction steps and microscopic mechanisms.

[0003] At present, the process of changes in the physicochemical properties of the dissolution process and the mechanism of microscopic interactions are still controversial, such as the order in which sodium ions and chloride ions leave the crystal during the dissolution of NaCl crystals, and the distribution evolution characteristics of water molecules during ion dissolution. With the continuous development of computer capabilities and algorithms, molecular simulation technology helps to deepen the microscopic understanding of the dissolution process of salt crystals at the atomic / molecular level, and provide theoretical support for experimental research and related industrial technology fields. However, the existing technology uses microsolvation methods for molecular dynamics simulation research. Since it does not take into account the number of surface adsorbed water molecules and the trend of energy changes, it lacks stability analysis of the structure of hydrated ion clusters. Therefore, it is difficult to explore the dissolution process of crystals and the synergistic effect of water molecules and ions during dissolution from the overall structure.

[0004] Therefore, it is necessary to propose a method to simulate the dissolution process of nanocrystals to solve the problem that it is difficult to explore the ion dissolution process and the evolution characteristics of water molecule distribution at the microscopic level in the existing technology. Summary of the invention

[0005] The present invention provides a method, medium and device for simulating the dissolution process of nanocrystals, which are used to solve the above-mentioned problem existing in the prior art, that is, the problem that it is difficult to explore the dissolution process of substances at the microscopic level in the prior art. The method comprises:

[0006] According to the state of the nanocrystal when it is dissolved in water, a model of the nanocrystal and water molecules is constructed, wherein the nanocrystal is composed of NaCl ion pairs arranged in a face-centered cubic crystal structure, and the water molecules are wrapped around the nanocrystal at a fixed density;

[0007] According to the potential functions between molecules and within molecules, the conjugate gradient method is used to optimize the nanocrystal and water molecule models, and the atoms in the optimized model are relaxed and subjected to controlled molecular dynamics simulation to obtain atomic trajectory information; wherein, in the potential function, the CVFF potential function is used to simulate the interaction between NaCl crystals, and the TIP3P model is used to simulate the interaction between water molecules; the Lennard-Jones potential is used to describe the interaction between O atoms, and the sum of the Coulomb potential is used to represent the interaction between all point charges between molecules, and the OH bond vibration is frozen using the SHAKE algorithm;

[0008] According to the atomic trajectory information, the atomic trajectory information is visualized, and combined with the force and radial distribution function images of atoms at different positions, the microscopic motion state of ions at different times and the distribution of water molecules around them are obtained.

[0009] Optionally, the method further includes:

[0010] Export the nanocrystal and water molecule models as molecular dynamics geometry model data files, and determine the atomic charge and structure information;

[0011] Determine the simulation boundary conditions, simulation step size, cutoff radius and initial temperature of the system for the nanocrystal dissolution process.

[0012] Optionally, the method of optimizing the nanocrystal and water molecule model by using the conjugate gradient method, performing relaxation and controlled molecular dynamics simulation on the atoms in the optimized model to obtain atomic trajectory information specifically includes:

[0013] The conjugate gradient method was used to optimize the model and obtain the stable configuration with minimum energy;

[0014] The Velocity-Verlet method is used to solve the atomic motion equations to obtain the atomic information and thermodynamic parameters during the simulation process;

[0015] The atoms are displaced in a fixed direction and the central atom of the model is fixed to obtain the atomic trajectory information.

[0016] Optionally, the Velocity-Verlet method is used to solve the atomic motion equations to obtain atomic information and thermodynamic parameters during the simulation process, specifically including:

[0017] The atomic information and thermodynamic parameters in the simulation process are obtained using the following calculation formula:

[0018]

[0019] Among them, v(t) and v(t+δt) represent the atomic velocities at the current moment and the next moment respectively, r(t) and r(t+δt) represent the atomic coordinates at the current moment and the next moment respectively, δt represents the time interval, and a(t) and a(t+δt) represent the atomic accelerations at the current moment and the next moment respectively.

[0020] The present invention provides a computer-readable storage medium, wherein the storage medium stores a computer program, and when the computer program is executed by a processor, the above-mentioned method for simulating the dissolution process of nanocrystals is implemented.

[0021] The present invention provides a computer device, comprising a memory, a processor and a computer program stored in the memory and executable on the processor, wherein the processor implements the above-mentioned method for simulating the dissolution process of nanocrystals when executing the program.

[0022] Compared with the prior art, the beneficial effects of the present invention are as follows: The present invention provides a method for simulating the dissolution process of nanocrystals. The method constructs a solution model to displace atoms in a fixed direction, obtains the forces on atoms at different positions and the distribution of water molecules around them, obtains the binding state of single ions and water molecules and the role of water molecules in the dissolution process, and can explore the dissolution process of crystals and the synergistic effect of water molecules and ions during dissolution from the overall structure. BRIEF DESCRIPTION OF THE DRAWINGS

[0023] The accompanying drawings, which are incorporated in and constitute a part of this specification, illustrate embodiments consistent with the invention and, together with the description, serve to explain the principles of the invention.

[0024] Figure 1 A schematic diagram of a process flow provided by an embodiment of the present invention;

[0025] Figure 2 A diagram of the initial solution structure provided by an embodiment of the present invention;

[0026] Figure 3 A geometric model data file provided by an embodiment of the present invention;

[0027] Figure 4 A visual diagram of the molecular dynamics model of the Cl atom at different times after displacement provided by an embodiment of the present invention;

[0028] Figure 5 The force image of Cl atoms provided by the embodiment of the present invention;

[0029] Figure 6 A Cl-O radial distribution function for describing the distribution of surrounding oxygen atoms at different distances of the displaced Cl atom provided in an embodiment of the present invention;

[0030] Figure 7A schematic diagram of the structure of a computer device provided in an embodiment of the present invention.

[0031] The above drawings have shown clear embodiments of the present invention, which will be described in more detail below. These drawings and text descriptions are not intended to limit the scope of the present invention in any way, but to illustrate the concept of the present invention for those skilled in the art by referring to specific embodiments. DETAILED DESCRIPTION

[0032] In order to make the purpose, technical solution and advantages of the present invention clearer, the technical solution of the present invention will be clearly and completely described below in conjunction with the drawings of the present invention. Obviously, the described embodiments are part of the embodiments of the present invention, not all of the embodiments. Based on the embodiments of the present invention, all other embodiments obtained by ordinary technicians in this field without creative work are within the scope of protection of the present invention.

[0033] First, the nouns involved in the present invention are explained:

[0034] Molecular dynamics (MD) simulation: It is a computational method for analyzing the dynamic behavior of material structure that has developed rapidly in recent years with the rapid development of computer technology. It is based on classical mechanics and statistical mechanics, uses computers to numerically solve the motion equations of molecular systems, simulates the interaction between atoms and dynamic properties within the material structure, and the results obtained can give the details of the motion trajectory of an object under specific conditions.

[0035] Steered Molecular Dynamics (SMD): refers to the introduction of specific control conditions such as applying tension to atoms, specific speed control, temperature increase / decrease, etc. during molecular dynamics simulation in order to study specific structural transformation phenomena. It can then simulate specific behaviors of molecules under controlled conditions, such as stretching molecules, studying intermolecular interactions, exploring mechanical properties of materials, studying phase transitions of materials, and other phenomena.

[0036] Relaxation: is the process of gradually recovering from a certain state to the equilibrium state in a gradual physical process. In high-energy physics, under the action of an external radio frequency pulse RF (B1), after the atomic nucleus undergoes magnetic resonance and reaches a stable high-energy state, the process from the disappearance of the external radio frequency to the recovery to the magnetic moment state before the magnetic resonance occurs is the process of physical state recovery.

[0037] Conjugate gradient method: It is an optimization algorithm between the steepest descent method and the Newton method. It only uses the first-order derivative information, but overcomes the disadvantage of the slow convergence of the steepest descent method, and avoids the disadvantage of the Newton method that it needs to store and calculate the Hesse matrix and inverse it. The basic idea of ​​the conjugate gradient method is to use the gradient at a known point to construct a set of conjugate directions, and search along this set of directions to find the minimum point of the objective function.

[0038] Currently, dynamic auxiliary information on a larger scale of the dissolution process can be obtained through infrared spectroscopy measurement, atomic force microscopy (AFM) and other technologies, but the dynamic properties of the detailed changes in the crystal structure of the dissolution process at the atomic / molecular scale are lacking.

[0039] In response to the above-mentioned problem of lack of detailed dynamic properties of changes in crystal structure during dissolution process at atomic / molecular scale, the general solution of the prior art is to use microsolvation method to simulate molecular dynamics, simulate the interaction and dynamic properties between atoms within the material structure, but do not consider the number of water molecules adsorbed on the surface and the trend of energy changes, lack of stability analysis of the hydrated ion cluster structure, therefore, it is difficult to explore the dissolution process of crystals and the synergistic effect of water molecules and ions during dissolution from the overall structure.

[0040] In response to the above problems, the present invention provides a method for simulating the dissolution process of nanocrystals. This method constructs a solution model to displace atoms in a fixed direction, obtains the forces on atoms at different positions and the distribution of water molecules around them, and then obtains the binding state of single ions and water molecules and the role of water molecules in the dissolution process, thereby exploring the dissolution process of crystals in liquid water and the evolution characteristics of water molecule distribution from a microscopic level.

[0041] The technical solution of the present invention and how the technical solution of the present invention solves the above-mentioned technical problems are described in detail below with specific embodiments. The following specific embodiments can be combined with each other, and the same or similar concepts or processes may not be repeated in some embodiments. The embodiments of the present invention will be described below in conjunction with the accompanying drawings.

[0042] Figure 1 It is a schematic diagram of a flow chart provided by an embodiment of the present invention, such as Figure 1 As shown, the method for simulating the dissolution process of nanocrystals shown in this embodiment includes:

[0043] S1: Construct nanocrystal and water molecule models.

[0044] Among them, the nanocrystals can be composed of NaCl ion pairs arranged in a face-centered cubic crystal structure, and water molecules are wrapped around the nanocrystals at a fixed density.

[0045] The specific steps include:

[0046] S101: Use Material Studio software to build a model, import the NaCl crystal and water molecule topology, and create a new Empty boxes of different sizes.

[0047] S102: Using the software supercell function, the NaCl crystal is expanded to obtain a cubic crystal with 500 NaCl ion pairs, with approximately

[0048] S103: Copy the expanded crystal into an empty box, calculate the crystal center of mass, and adjust the center of mass coordinates to the center of the box. At this time, the entire NaCl crystal is located in the center of the empty box.

[0049] S104: Use the constraints function to fix the atomic coordinates in the crystal. The Atom Volumes & Surfaces tool in the Tools toolbar can establish equipotential surfaces to wrap the crystal to prevent water molecules from entering the crystal during the placement process and causing structural chaos.

[0050] S105: In the Amorphous Cell Calculation module, select Packing mode in the task bar and adjust the density parameter to 1g / cm 3 , select Pack in isosurface enclosed volume in the more tab. After the calculation is completed, 3382 water molecules are placed in the box except for the area enclosed by the equipotential surface, such as Figure 2 shown.

[0051] S2: Check the geometry model data file.

[0052] like Figure 3 As shown in the figure, the first fifteen lines in the data file can contain the number and type information of atoms, bonds, angles, dihedrals and off-planes, and can also contain the coordinate range of the simulation area. The first column of Masses is the atomic type number, which contains 4 atomic types in this example. The second column indicates the corresponding mass of each atomic type. Atoms contains the ID number of each atom as well as the coordinate and charge information.

[0053] S3: Determine simulation parameters.

[0054] The simulation parameters may include, for example, simulation boundary conditions, simulation step length and cutoff radius;

[0055] Generally, the crystal is not fixed during the simulation process, and it will move out of the boundary due to force, resulting in atomic loss and crystal defects. Therefore, set the X, Y, and Z directions as periodic boundaries, the step size is 1fs, and the truncation radius is The initial temperature of the system is set to 300K to prevent the crystal from moving out of the boundary due to force and causing the loss of atoms.

[0056] S4: Select the potential function.

[0057] Among them, potential functions are used to describe the mathematical models of intramolecular interactions and intermolecular interactions.

[0058] Specifically, the CVFF potential function is selected to describe the interaction between NaCl crystals, and the interaction between water molecules is described using the TIP3P model, which uses the Lennard-Jones potential to describe the interaction between O atoms and the sum of the Coulomb potential to represent the interaction between all point charges in molecules; the OH bond vibration is frozen using the SHAKE algorithm.

[0059] Among them, the potential functions used include:

[0060] U(r)=U bond (r)+U angel (θ)+U(r ij )+U elec (r ij )

[0061] U bond (r) = k r (rr 0 ) 2

[0062] U angel (θ) = k θ (θ-θ 0 ) 2

[0063]

[0064] Calculating ε in the LJ potential ij , σ ij Using the geometric mixing rule, the formula is:

[0065]

[0066] In the above formula, U(r) is the total potential energy, U bond is the bond length stretching potential energy, U angel is the bond angle bending potential energy; k r is the elastic coefficient of the bond, r is the bond length, r 0 is the equilibrium bond length; k θ is the elastic coefficient of angle, θ is the angle, θ 0 is the equilibrium angle; U(r ij) is the Lennard-Jones potential energy, ε and σ are potential energy parameters used to describe non-bonded interactions and vary depending on the type of atoms. ij and σ ij is the potential energy parameter of the non-bonded interaction between atoms i and j. elec is the Coulomb potential energy, e is the elementary charge, q i ,q j are the charges of atoms i and j, r ij is the distance between atoms i and j.

[0067] S5: Energy minimization, relaxation and molecular dynamics calculations.

[0068] Among them, the role of energy minimization is to eliminate local irrationality, and relaxation and molecular dynamics calculations are to give atoms initial velocities and perform simulations so that the atoms reach a state of equilibrium.

[0069] The specific process is as follows:

[0070] The Velocity-Verlet method is used to solve the atomic motion equations, statistically analyze the atomic information and thermodynamic parameters during the simulation process, and the calculation formula includes:

[0071]

[0072] In the above formula, v(t) and v(t+δt) represent the atomic velocities at the current moment and the next moment respectively, r(t) and r(t+δt) represent the atomic coordinates at the current moment and the next moment respectively, δt represents the time interval, and a(t) and a(t+δt) represent the atomic accelerations at the current moment and the next moment respectively.

[0073] The conjugate gradient method is used to optimize the model to obtain a stable configuration with minimum energy. The model can be balanced in the NVT ensemble for 500 ps at a temperature of 300 K. The Nose-Hover heat bath method can be used to control the system temperature.

[0074] The atoms are displaced in a fixed direction and the central atom of the model is fixed to obtain the atomic trajectory information.

[0075] Specifically, the atomic displacement command in LAMMPS uses "fix 3corner move linear 000.00001", where fix is ​​a command to impose constraints on atoms and 3 is the fix command number. There are multiple fix commands in the in file of LAMMPS. The displaced atom is named corner, and the linear displacement command is move linear. The three parameters in the format represent the displacement speed in the X, Y, and Z directions respectively. The displaced Cl atom is located at the corner of the model, such as Figure 2The red particle shown is numbered 982. Displacement upward along the Z axis, the displacement simulation time is 1ns, and the distance is Fix the central atom of the model to prevent excessive rotation and deviation of the model.

[0076] S6: Post-processing of simulation results.

[0077] After the simulation is completed, all atomic trajectory information during the entire simulation time can be obtained, such as Figure 4 and Figure 5 As shown, the open source software OVITO can be used to visualize the atomic trajectories and combined with the atomic forces processed by the origin software. The resulting force direction can reflect the trend of the movement direction of ions at different positions. The magnitude of the force can determine the difficulty of the ions detaching from the crystal structure, and then the binding state of the single ion and the surrounding water molecules and the role of water molecules in the dissolution process can be obtained.

[0078] Figure 6 The radial distribution function image of Cl-O along the Z direction. The black curve represents the initial distribution of water molecules around the ions, and the red, blue, and brown curves represent Figure 5 The three peaks of the force in the Z-axis direction correspond to the radial distribution functions at 150ps, 350ps, and 700ps. The purple dots represent the experimental values ​​of the chloride ion hydration state. Figure 6 The results shown indicate the evolution of the concentration of water molecules around the chloride ions when they move to different positions. By comparing with the experimental values, it can be determined when the ions completely enter the solution and are in a solvated state.

[0079] The method for simulating the dissolution process of nanocrystals provided in this embodiment constructs a model of a NaCl crystal solution wrapped in a solvent of a specific density, and through the selected simulation parameters and potential functions, a single ion is displaced in a fixed direction to simulate the dissolution path of the ion leaving the crystal, thereby being able to obtain the forces exerted on the ion at different positions and the distribution of water molecules around it, and furthermore, being able to explore the dissolution process of the crystal in liquid water and the evolution characteristics of the distribution of water molecules from a microscopic level.

[0080] The present invention also provides a computer-readable storage medium, which stores a computer program. The computer program can be used to execute the nanocrystal dissolution process simulation method provided above.

[0081] The present invention also provides Figure 7 The structural diagram of the computer device shown in FIG. Figure 7As shown, at the hardware level, the computer device includes a processor, an internal bus, a network interface, a memory, and a non-volatile memory, and may also include hardware required for other services. The processor reads the corresponding computer program from the non-volatile memory into the memory and then runs it to implement the nanocrystal dissolution process simulation method, medium, and device provided in the above embodiments.

[0082] Those skilled in the art can understand that all or part of the processes in the above-mentioned embodiment methods can be completed by instructing the relevant hardware through a computer program, and the computer program can be stored in a non-volatile computer-readable storage medium. When the computer program is executed, it can include the processes of the embodiments of the above-mentioned methods. Among them, any reference to memory, storage, database or other media used in the embodiments provided by the present invention can include at least one of non-volatile and volatile memory. Non-volatile memory can include read-only memory (ROM), magnetic tape, floppy disk, flash memory or optical memory, etc. Volatile memory can include random access memory (RAM) or external cache memory. As an illustration and not limitation, RAM can be in various forms, such as static random access memory (SRAM) or dynamic random access memory (DRAM).

[0083] The technical features of the above embodiments may be arbitrarily combined. To make the description concise, not all possible combinations of the technical features in the above embodiments are described. However, as long as there is no contradiction in the combination of these technical features, they should be considered to be within the scope of the present invention.

Claims

1. A method for simulating the dissolution process of nanocrystals, It is characterized in that include: According to the state of the nanocrystal when it is dissolved in water, a model of the nanocrystal and water molecules is constructed, wherein the nanocrystal is composed of NaCl ion pairs arranged in a face-centered cubic crystal structure, and the water molecules are wrapped around the nanocrystal at a fixed density; According to the potential functions between molecules and within molecules, the conjugate gradient method is used to optimize the nanocrystal and water molecule models, and the atoms in the optimized model are relaxed and subjected to controlled molecular dynamics simulation to obtain atomic trajectory information; wherein, in the potential function, the CVFF potential function is used to simulate the interaction between NaCl crystals, and the TIP3P model is used to simulate the interaction between water molecules; the Lennard-Jones potential is used to describe the interaction between O atoms, and the sum of the Coulomb potential is used to represent the interaction between all point charges between molecules, and the OH bond vibration is frozen using the SHAKE algorithm; According to the atomic trajectory information, the atomic trajectory information is visualized, and combined with the force and radial distribution function images of atoms at different positions, the microscopic motion state of ions at different times and the distribution of water molecules around them are obtained.

2. The method for simulating the dissolution process of nanocrystals as claimed in claim 1, It is characterized in that The method further comprises: Export the nanocrystal and water molecule models as molecular dynamics geometry model data files, and determine the atomic charge and structure information; Determine the simulation boundary conditions, simulation step size, cutoff radius and initial temperature of the system for the nanocrystal dissolution process.

3. The method for simulating the dissolution process of nanocrystals as claimed in claim 1, It is characterized in that The conjugate gradient method is used to optimize the nanocrystal and water molecule models, and the atoms in the optimized models are relaxed and subjected to controlled molecular dynamics simulation to obtain atomic trajectory information, specifically including: The conjugate gradient method was used to optimize the model and obtain the stable configuration with minimum energy; The Velocity-Verlet method is used to solve the atomic motion equations to obtain the atomic information and thermodynamic parameters during the simulation process; The atoms are displaced in a fixed direction and the central atom of the model is fixed to obtain the atomic trajectory information.

4. The method for simulating the dissolution process of nanocrystals as claimed in claim 3, It is characterized in that The Velocity-Verlet method is used to solve the atomic motion equations to obtain atomic information and thermodynamic parameters during the simulation process, specifically including: The atomic information and thermodynamic parameters in the simulation process are obtained using the following calculation formula: Among them, v(t) and v(t+δt) represent the atomic velocities at the current moment and the next moment respectively, r(t) and r(t+δt) represent the atomic coordinates at the current moment and the next moment respectively, δt represents the time interval, and a(t) and a(t+δt) represent the atomic accelerations at the current moment and the next moment respectively.

5. A computer-readable storage medium, It is characterized in that The storage medium stores a computer program, and when the computer program is executed by a processor, the method for simulating the dissolution process of nanocrystals according to any one of claims 1 to 4 is implemented.

6. A computer device, It is characterized in that The method comprises a memory, a processor and a computer program stored in the memory and executable on the processor, wherein when the processor executes the program, the method for simulating the dissolution process of nanocrystals according to any one of claims 1 to 4 is implemented.

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