A method, medium and device for simulating the dissolution process of nanocrystals

Abstract

The present invention discloses a method, medium and device for simulating the dissolution process of nanocrystals, and relates to the field of molecular dynamics technology, including: constructing nanocrystal and water molecule models; determining simulation parameters and potential functions; optimizing the nanocrystal and water molecule models by a conjugate gradient method, and relaxing and performing controlled molecular dynamics simulation on atoms in the optimized model according to the simulation parameters and potential functions to obtain atomic trajectory information; and obtaining the microscopic motion state of ions at different times and the distribution of water molecules around them according to the atomic trajectory information. The present invention is based on controlled molecular dynamics simulation, and by constructing a solution model, atoms are displaced in a fixed direction, and the forces on atoms at different positions and the distribution of water molecules around them are obtained, so as to understand the state of individual ions and water molecules and their role in the dissolution process at the molecular level.

Description

Technical Field

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

[0002] The salt-water interface is one of the most important and common interfaces on the earth, and plays an important role in disciplines such as atmospheric science, biology, physical chemistry, and materials science. The key point is the dissolution process involving the destruction of the crystal structure of salts (such as NaCl). Techniques such as infrared spectroscopy measurement, atomic force microscopy (AFM), scanning force microscopy (SFM), and scanning polarization force microscopy (SPFM) can obtain dynamic auxiliary information on a larger scale during the dissolution process. However, the above methods lack clear images at the atomic / molecular scale and the kinetic properties of the detailed changes in the crystal structure during the dissolution process, and it is difficult to reveal the basic reaction steps and microscopic mechanisms.

[0003] Currently, there are still controversies about the changes in the physicochemical properties and the microscopic interaction mechanism during the dissolution process. For example, in the dissolution process of NaCl crystals, the sequence of sodium ions and chloride ions detaching from the crystal, and the distribution and evolution characteristics of water molecules during the ion dissolution process. With the continuous development of computer capabilities and algorithms, molecular simulation techniques help 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, in the prior art, the molecular dynamics simulation research using the micro-solvation method lacks the analysis of the stability of the hydrated ion cluster structure due to the lack of consideration of the number of surface adsorbed water molecules and the trend of energy change, so 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 for simulating the dissolution process of nanocrystals to solve the problem in the prior art that it is difficult to explore the ion dissolution process and the distribution and evolution characteristics of water molecules at the microscopic level. Summary of the Invention

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

[0006] According to the state of the nanocrystal during dissolution in water, a nanocrystal and water molecule model are constructed. 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 with a fixed density.

[0007] According to the intermolecular and intramolecular potential functions, the conjugate gradient method is used to optimize the nanocrystal and water molecule models. The atoms in the optimized models are relaxed and subjected to constrained molecular dynamics simulations to obtain atomic trajectory information. Among them, 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 Coulomb potentials is used to represent the interaction of all point charges between molecules. The OH bond vibration is frozen using the SHAKE algorithm.

[0008] Based on the atomic trajectory information, the atomic trajectory information is visualized, and combined with the forces on the atoms at different positions and the radial distribution function images, the microscopic motion states of the ions at different times and the distribution of the surrounding water molecules are obtained.

[0009] Optionally, the method further includes:

[0010] Export the nanocrystal and water molecule models as a molecular dynamics geometry model data file, and determine the atomic charges and structural information.

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

[0012] Optionally, the step of using the conjugate gradient method to optimize the nanocrystal and water molecule models, relaxing the atoms in the optimized models, and performing constrained molecular dynamics simulations to obtain atomic trajectory information specifically includes:

[0013] Use the conjugate gradient method to optimize the model to obtain a stable configuration with the minimum energy.

[0014] Use the Velocity-Verlet method to solve the atomic motion equations to obtain atomic information and thermodynamic parameters during the simulation.

[0015] Perform a fixed-direction displacement on the atoms and fix the central atom of the model to obtain atomic trajectory information.

[0016] Optionally, the step of using the Velocity-Verlet method to solve the atomic motion equations to obtain atomic information and thermodynamic parameters during the simulation specifically includes:

[0017] Use the following calculation formulas to obtain atomic information and thermodynamic parameters during the simulation:

[0018]

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

[0020] The present invention provides a computer-readable storage medium, which stores a computer program. When the computer program is executed by a processor, the above-mentioned method for simulating the nanocrystal dissolution process is realized.

[0021] The present invention provides a computer device, including a memory, a processor, and a computer program stored on the memory and executable on the processor. When the processor executes the program, the above-mentioned method for simulating the nanocrystal dissolution process is realized.

[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 nanocrystal dissolution process. By constructing a solution model, the atoms are displaced in a fixed direction, the forces on the atoms at different positions and the distribution of the surrounding water molecules are obtained, the binding state of a single ion and water molecules and the role of water molecules in the dissolution process are obtained, and the dissolution process of the crystal and the synergistic effect of water molecules and ions during dissolution can be explored from the overall structure. Description of the Drawings

[0023] The drawings here are incorporated into the specification and form a part of this specification, showing embodiments consistent with the present invention and used together with the specification to explain the principles of the present invention.

[0024] Figure 1 It is a schematic flowchart provided by an embodiment of the present invention;

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

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

[0027] Figure 4 It is an intuitive diagram of the molecular dynamics model of Cl atoms at different moments after displacement provided by an embodiment of the present invention;

[0028] Figure 5 It is a force image of Cl atoms provided by an embodiment of the present invention;

[0029] Figure 6 It is a Cl-O radial distribution function provided by an embodiment of the present invention for describing the distribution of oxygen atoms around a displaced Cl atom at different distances;

[0030] Figure 7Schematic diagram of the computer device provided by the embodiment of the present invention.

[0031] Through the above-mentioned drawings, specific embodiments of the present invention have been shown, and more detailed descriptions will be given later. These drawings and textual descriptions are not intended to limit the scope of the inventive concept in any way, but to illustrate the concept of the present invention to those skilled in the art by referring to specific embodiments. Detailed implementation manners

[0032] To make the objectives, technical solutions and advantages of the present invention clearer, the technical solutions in the present invention will be clearly and completely described below with reference to the drawings in the present invention. Apparently, the described embodiments are some but not all of the embodiments of the present invention. All other embodiments obtained by those of ordinary skill in the art based on the embodiments in the present invention without creative efforts shall fall within the protection scope of the present invention.

[0033] First, the terms related to the present invention are explained:

[0034] Molecular Dynamics (MD) simulation: It is a computational method for analyzing the dynamic behavior of the structure of substances that has emerged in recent years with the rapid development of computer technology. Based on classical mechanics and statistical mechanics, it numerically solves the equations of motion of a molecular system with the aid of a computer, simulates and studies the interactions between atoms within the structure of a substance and its dynamic properties, and the obtained results can give the details of the motion trajectory of an object under specific conditions.

[0035] Steered Molecular Dynamics (SMD): It refers to introducing specific control conditions such as applying a pulling force to an atom, specific velocity control, temperature increase / decrease, etc. during molecular dynamics simulation to study specific structural transformation phenomena. Furthermore, it can simulate the specific behavior of molecules under controlled conditions, such as stretching molecules, studying intermolecular interactions, exploring the mechanical properties of materials, and studying phenomena such as phase transitions of substances.

[0036] Relaxation: It is a process of gradually returning to an equilibrium state in a gradual physical process. In high-energy physics, after the atomic nucleus undergoes nuclear magnetic resonance and reaches a stable high-energy state under the action of an externally applied radio-frequency pulse RF (B1), the process from the moment the externally applied radio-frequency disappears until it returns to the magnetic moment state before nuclear magnetic resonance occurs, that 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 needs to utilize the first derivative information, but overcomes the drawback of the slow convergence of the Steepest Descent Method and avoids the drawbacks of the Newton Method that require storing and calculating the Hesse matrix and finding its inverse. The basic idea of the conjugate gradient method is to construct a set of conjugate directions using the gradients at known points and search along these directions to find the minimum point of the objective function.

[0038] Currently, techniques such as infrared spectroscopy measurement and atomic force microscopy (AFM) can be used to obtain dynamic auxiliary information at a larger scale during the dissolution process, but the kinetic properties of the crystal structure details changes at the atomic / molecular scale during the dissolution process are lacking.

[0039] Regarding the above problem of lacking the kinetic properties of the crystal structure details changes at the atomic / molecular scale during the dissolution process, the general solution of the existing technology is: adopting the micro-solvation method to simulate and study molecular dynamics, simulating the interaction and kinetic properties between atoms inside the substance structure, but not considering the number of surface adsorbed water molecules and the energy change trend, lacking the stability analysis of the hydrated ion cluster structure. Therefore, it is difficult to explore the dissolution process of the crystal and the synergistic effect of water molecules and ions during dissolution from the overall structure.

[0040] Regarding 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 the 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 played by water molecules during the dissolution process, so as to be able to explore the dissolution process of crystals in liquid water and the evolution characteristics of the water molecule distribution from the microscopic level.

[0041] The following will specifically describe the technical solution of the present invention and how the technical solution of the present invention solves the above technical problems with specific embodiments. These specific embodiments below 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 with reference to the accompanying drawings.

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

[0043] S1: Construct a nanocrystal and water molecule model.

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

[0045] Specifically, it includes the following steps:

[0046] S101: Use the Material Studio software to build a model, import the topological structures of NaCl crystal and water molecules, and create a new empty box of the specified size.

[0047] S102: Use the supercell function of the software to expand the NaCl crystal cell to obtain a cubic crystal with 500 NaCl ion pairs, and each direction is approximately

[0048] S103: Copy the expanded crystal cell into the empty box, calculate the centroid of the crystal, and adjust the centroid 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 create an equipotential surface to wrap the crystal and prevent water molecules from entering the interior of the crystal during placement, resulting in structural chaos.

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

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

[0052] As Figure 3 shown, the first fifteen lines in the data file can contain information on the number and type of atoms, bonds, angles, dihedral angles, and out-of-plane, and can also contain the coordinate range of the simulation region. The first column of Masses is the atomic type number. In this example, there are 4 atomic types, and the second column represents the corresponding mass of each atomic type. Atoms contains the ID number, coordinates, and charge information of each atom.

[0053] S3: Determine the simulation parameters.

[0054] Among them, the simulation parameters can include, for example, simulation boundary conditions, simulation step size, and cutoff radius;

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

[0056] S4: Select the potential function.

[0057] Among them, the potential function is a mathematical model used to describe the intramolecular and intermolecular interactions.

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

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

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

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

[0062] U angel (θ) = k θ (θ - θ 0 ) 2

[0063]

[0064] Calculate ε ij and σ ij in the LJ potential energy 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 the angle, θ is the angle, θ 0 is the equilibrium angle; U(r ij) is the Lennard-Jones potential energy, where ε and σ are potential energy parameters used to describe non-bonded interactions and vary depending on the atomic species. ε ij and σ ij are the non-bonded interaction potential energy parameters for atoms i and j. U elec is the Coulomb interaction potential energy, e is the elementary charge, q i and q j are the charges of atoms i and j respectively, and 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 irrationalities, and relaxation and molecular dynamics calculations are to assign initial velocities to atoms and perform simulations to enable the atoms to reach an equilibrium state.

[0069] The specific process is as follows:

[0070] The Velocity-Verlet method is used to solve the atomic motion equations, and atomic information and thermodynamic parameters during the statistical simulation are calculated. The calculation formulas include:

[0071]

[0072] In the above formulas, 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, so that a stable configuration with the minimum energy can be obtained. The model can be equilibrated for 500 ps in the NVT ensemble at a temperature of 300 K, and the Nose-Hover thermostat 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 atomic trajectory information.

[0075] Specifically, in LAMMPS, the atomic displacement command uses "fix 3corner move linear 000.00001". Fix is a command to apply constraints to atoms, and 3 is the sequence number of the fix command; there are multiple fix commands in the in file of LAMMPS; the displaced atoms are named corner, and the linear displacement command is move linear. The three parameters in the format represent the displacement velocities in the X, Y, and Z directions respectively; the displaced Cl atoms are located at the corners of the model, such as Figure 2The red particles shown, with serial number 982, are displaced upward along the Z-axis, and the displacement simulation time is 1 ns, and the distance is Fix the central atom of the model to prevent excessive rotation and offset 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 trajectory and combine the atomic forces processed by the origin software. The obtained force directions can reflect the moving direction trends of ions at different positions, and the force magnitudes can judge the difficulty of ions detaching from the crystal structure. Furthermore, the binding state of single ions with surrounding water molecules and the role of water molecules in the dissolution process can be obtained.

[0078] Figure 6 is the radial distribution function image along the Z direction. The black curve represents the initial distribution of water molecules around the ions, and the red, blue, and brown curves respectively represent Figure 5 the radial distribution functions at the three peak moments of the force along the Z-axis direction corresponding to 150 ps, 350 ps, and 700 ps. The purple dots represent the experimental values of the chloride ion hydration state, Figure 6 The results shown represent the evolution characteristics of the water molecule concentration around the ions when the chloride ions are displaced to different positions. By comparing with the experimental values, it can be judged when the ions completely enter the solution and are in a solvated state.

[0079] The simulation method for the dissolution process of nanocrystals provided in this embodiment constructs a NaCl crystal solution model wrapped with a solvent of a specific density, and through the selected simulation parameters and potential functions, makes a single ion offset in a fixed direction to simulate the dissolution path of the ion leaving the crystal, so as to obtain the forces on the ions at different positions and the distribution of surrounding water molecules, and further be able to explore the dissolution process of the crystal in liquid water and the evolution characteristics of the water molecule distribution from a microscopic level.

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

[0081] The present invention also provides Figure 7 the structural schematic diagram of the computer device shown, as 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. Of course, it may also include other 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 nano-crystal dissolution process simulation method, medium, and device provided in the above embodiments.

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

[0083] The technical features of the above embodiments can be combined arbitrarily. For the sake of brevity of description, 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, it should be considered as the scope recorded in the present invention.

Claims

1. A method for simulating the dissolution process of nanocrystals, 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; 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 atomic trajectory information; 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, 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, 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.

4. A computer-readable storage medium, 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 3 is implemented.

5. A computer device, 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 as claimed in any one of claims 1 to 3 is implemented.

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