Simulation method for regulating L-isoleucine physical vapor deposition self-assembly structure

Abstract

The invention discloses a simulation method for regulating and controlling an L-isoleucine physical vapor deposition self-assembly structure. The method comprises the following steps: constructing a gold Au (111) substrate and L-isoleucine molecular structure model; selecting a force field of an Au (111) substrate and L-isoleucine; dynamic balance parameters are set, and energy minimization and NVT relaxation are carried out on the system; sequentially carrying out deposition and molecular dynamics simulation on the L-isoleucine molecules; the relaxation time is iteratively updated until the amino acid structure is stable, the self-assembly structure is arranged, and morphology and interaction energy parameters are output; and analyzing data to obtain conditions suitable for self-assembly. The invention provides an effective molecular dynamics simulation method for regulating and controlling the self-assembly structure of the L-isoleucine, L-isoleucine molecules are obtained from an atomic level, the method has the structural evolution characteristic of physical vapor deposition self-assembly in a vacuum environment, and an important basis is provided for preparation of L-isoleucine crystals.

Description

Technical Field

[0001] The present invention belongs to the field of simulation technology, and further relates to a simulation method for regulating the self-assembly structure of L-isoleucine by physical vapor deposition in the field of molecular dynamics simulation technology. The present invention simulates the self-assembly structure of L-isoleucine by physical vapor deposition on an Au (111) surface by means of a molecular dynamics simulation method, and can be widely used to guide the self-assembly of amino acid molecules on an Au (111) substrate in a vacuum. Background Art

[0002] Amino acids are the basic units that make up proteins (biological functional macromolecules). Their structure has a clear α-amino acid formula (containing amino groups, carboxyl groups, and R groups), and they are easy to functionalize through chemical modification. In the field of interface engineering, the ordered modification techniques of amino acid molecules mainly include two categories: (1) self-assembly methods, such as slow evaporation solution method, which spontaneously form two-dimensional ordered structures through intermolecular hydrogen bonds, π-π interactions, etc.; (2) physical vapor deposition (PVD), which forces the molecules to be deposited in a directional manner through physical means such as vacuum evaporation. The PVD method uses vapor flow or surface energy to guide the molecular arrangement to form an apparently directional stacking structure. Its vacuum environment and low-temperature deposition conditions (usually lower than the boiling point of the solvent in the solution method) can reduce thermal damage and solvent molecule incorporation. In theory, it can prepare ordered layers with fewer defects than solution self-assembly (especially under high-temperature evaporation conditions). However, the non-specific deposition mechanism of PVD limits its precise control of molecular orientation and interaction. To reveal the molecular mechanism of the self-assembly process, molecular dynamics simulation can quantitatively analyze the energy changes, molecular orientation dynamics, and final structural stability of the self-assembly process by calculating atomic trajectories.

[0003] Fuzhou University disclosed a simulation method for regulating the self-assembly structure of tyrosine dipeptide in its patent application, "A Simulation Method for Regulating the Self-Assembly Structure of Tyrosine Dipeptide" (application number 202210277805.5, application publication number CN 114611314 A). This method can explore the effects of density and temperature on self-assembly by regulating the self-assembly environment parameters. By analyzing the structural evolution of the dipeptide self-assembly process under different environmental parameters, the optimal density and temperature for tyrosine dipeptide self-assembly are determined, and the corresponding zero-dimensional or one-dimensional structure is obtained, providing a reference for the experimental preparation of tyrosine dipeptide nanostructures. However, the method still has the disadvantage that the invention explores the self-assembly of tyrosine dipeptide in solution and does not involve the self-assembly of amino acids and their derivatives in a vacuum environment.

[0004] In his paper “Side-chain effects on the co-existence of emergent nanopatterns in amino acid adlayers on graphene” (Nanoscale volume 12, pages 13662-13673 (2020)), Joel B. Awuah provides a molecular dynamics simulation method to explore the influence of amino acid side chain properties on the types of ordered nanostructures spontaneously formed in amino acid adlayers adsorbed on vacuum graphene interfaces. Using three different forms of amino acids: neutral, zwitterionic, and neutral zwitterionic, this method found that spontaneous nanopatterning was only observed in adlayers containing zwitterions, with no evidence of ordered motifs in neutral adlayers. In collaboration with experiments, these findings provide a rational, knowledge-based guide for producing programmable, surface-induced nanostructures. However, a drawback of this method is that the paper only explores the self-assembly properties of amino acid molecules on graphene surfaces and does not address the self-assembly properties of amino acid molecules on metal surfaces. Summary of the Invention

[0005] The purpose of the present invention is to address the deficiencies in the above-mentioned prior art and to provide a simulation method for regulating the physical vapor deposition self-assembly structure of L-isoleucine, aiming to solve the problem in the prior art that it is difficult to observe and predict the physical vapor deposition self-assembly structure of L-isoleucine molecules on Au (111) from a microscopic level.

[0006] The technical idea for achieving the purpose of the present invention is that the simulation method of the present invention is based on molecular dynamics simulation to regulate the parameter conditions of the self-assembly of L-isoleucine on the Au (111) surface, which is used to simulate the method of preparing the self-assembly structure of L-isoleucine by physical vapor deposition in the experiment, so as to understand and verify the preparation method. This solves the problem that the existing technology is difficult to understand the self-assembly mechanism of L-isoleucine molecules on the Au (111) surface at the atomic level. The present invention explores the effect of temperature on self-assembly by regulating the self-assembly parameters, and by analyzing the structural evolution of the L-isoleucine self-assembly process under different parameters, determines the optimal temperature for L-isoleucine self-assembly, and obtains the corresponding structure, which has important guiding significance for the preparation of L-isoleucine crystals.

[0007] The specific method for achieving the purpose of the present invention is as follows:

[0008] Step 1, constructing the Au (111) substrate and L-isoleucine molecular structure model;

[0009] Step 2: Select the force field of Au(111) substrate and L-isoleucine; set the dynamic equilibrium parameters, and perform energy minimization and NVT relaxation on the system;

[0010] Step 3, performing deposition and molecular dynamics simulation on the L-isoleucine molecule in sequence;

[0011] Step 4: determine whether the amino acid structure is stable. If so, proceed to step 5. Otherwise, increase the relaxation time and re-execute step 3.

[0012] Step 5: Arrange the self-assembled structure and output the morphology and interaction energy parameters;

[0013] Step 6: Data analysis to obtain conditions suitable for self-assembly.

[0014] Furthermore, the gold Au (111) substrate refers to an Au unit cell that is cut into (111) surfaces and then expanded, with the vacuum layer in the z direction set to 300 Å, and the substrate size parameters in the x, y and z directions being 99.9 Å x 100.93 Å x 321.48 Å.

[0015] Furthermore, the L-isoleucine molecular structure is obtained from an L-isoleucine unit cell.

[0016] Furthermore, the force field of the Au (111) substrate and L-isoleucine is selected, the Morse force field is used between Au atoms and between Au and S atoms, the OPLS-AA force field is used between the L-isoleucine molecule, and the universal force field UFF is used between Au and L-isoleucine molecules.

[0017] Furthermore, the dynamic equilibrium parameters are set as follows: the system adopts periodic boundary conditions in the x and y directions and fixed boundary conditions in the z direction; the velocity-Verlet algorithm is used to integrate the motion equation, and the time step is set to 1 fs.

[0018] Furthermore, the system was subjected to energy minimization and NVT relaxation using the Lorentz-Berthelot mixing rule; only short-range electrostatic interactions were considered, the cutoff radius of non-bonded interactions was set to 1.1 nm, and the conjugate gradient method was selected for energy minimization. Then, under the canonical ensemble NVT, the system was relaxed for 0.5 ns at 400 K, 500 K, 600 K, and 700 K, respectively.

[0019] Furthermore, the L-isoleucine molecules were deposited, and the initial velocities of the L-isoleucine molecules in the x, y and z directions were set to 0, 0 and 5 Å / fs, respectively. The temperatures of the kinetic equilibrium parameters were maintained at 400 K, 500 K, 600 K and 700 K, respectively. One L-isoleucine molecule was deposited every 0.25 ns, for a total of 160 molecules. After that, relaxation was continued for 225 ns without changing the kinetic parameters.

[0020] Furthermore, the molecular dynamics simulation refers to collecting dynamic trajectories and information every 0.25 ns, outputting a total of 1060 sets of data; visualizing the trajectory information, analyzing the motion trajectory of the L-isoleucine molecule, organizing the evolutionary morphology of the self-assembled structure of the L-isoleucine molecule, and analyzing the morphology, root mean square deviation (RMSD), interaction energy, hydrogen bond, and dipole moment parameters of the structure.

[0021] Furthermore, whether the amino acid structure is stable refers to whether the interatomic interaction energy and RMSD are simultaneously stable.

[0022] The root mean square deviation RMSD is obtained by the following formula:

[0023] RMSD=

[0024] Among them, N atoms represents the total number of atoms constituting 160 L-isoleucine molecules during the molecular dynamics simulation, x i and x i ',y i and y i ', z i and z i 'represent the x, y and z coordinate values ​​of the ith atom of the same molecule at different times during the molecular dynamics simulation.

[0025] Compared with the prior art, the present invention has the following advantages:

[0026] First, the simulation method of the present invention uses molecular dynamics simulation to control the parameters of the self-assembly of L-isoleucine on the Au (111) surface, which is used to simulate the corresponding physical vapor deposition method for preparing the self-assembled structure of L-isoleucine in the experiment, so as to understand and verify the preparation method. This method makes up for the defect of the existing technology that it is difficult to understand the self-assembly mechanism of L-isoleucine molecules on the Au (111) surface at the atomic level, so that the present invention can obtain L-isoleucine molecules at the atomic level, which have the structural evolution characteristics of physical vapor deposition self-assembly in a vacuum environment.

[0027] Second, the present invention addresses the problem that existing technologies make it difficult to observe and predict self-assembly structures at a microscopic level. By regulating self-assembly parameters, the present invention explores the effect of temperature on self-assembly. By analyzing the structural and energy changes in the L-isoleucine self-assembly process under different parameters, the optimal temperature for L-isoleucine self-assembly is determined to be 600 K, and the corresponding self-assembly structure is obtained. Therefore, the present invention provides an effective method for molecular dynamics simulation of regulating the self-assembly structure of L-isoleucine, providing an important basis for the preparation of L-isoleucine crystals. BRIEF DESCRIPTION OF THE DRAWINGS

[0028] Figure 1 A flowchart of the steps for implementing an embodiment of the present invention;

[0029] Figure 2 Schematic diagram of the Au (111) substrate model according to an embodiment of the present invention;

[0030] Figure 3 Schematic diagram of the structure of the L-isoleucine molecule of the present invention;

[0031] Figure 4 Schematic diagram of the structure of the present invention when all L-isoleucine molecules are deposited at different temperatures;

[0032] Figure 5 Schematic diagram of the final structure obtained by self-assembly of L-isoleucine molecules at different temperatures of the present invention;

[0033] Figure 6 RMSD diagram of the self-assembly process of L-isoleucine molecules at different temperatures of the present invention;

[0034] Figure 7 Graph showing the evolution of interaction energy between L-isoleucine molecules at different temperatures according to the present invention;

[0035] Figure 8 The hydrogen bond distribution diagram of the self-assembled structure of L-isoleucine molecules at different temperatures of the present invention;

[0036] Figure 9 This is a graph showing the change in the number of hydrogen bonds in the self-assembled structure of L-isoleucine at different deposition temperatures during a relaxation period of 225 ns;

[0037] Figure 10 Schematic diagram of the dipole moment when all L-isoleucine molecules are deposited at different temperatures of the present invention;

[0038] Figure 11 Schematic diagram of the dipole moment of the final structure obtained by self-assembly of L-isoleucine molecules at different temperatures in the present invention. DETAILED DESCRIPTION

[0039] The present invention will be further described in detail below with reference to the accompanying drawings and specific embodiments.

[0040] Reference Figure 1 , the implementation steps of the embodiment of the present invention are further described in detail.

[0041] Step 1: construct a gold Au(111) substrate and L-isoleucine molecular structure model.

[0042] The embodiment of the present invention uses Materials Studio software to construct a structural model of the Au(111) substrate, such as Figure 2 As shown. Among them, Figure 2 (a) is the top view of the model. Figure 2 (b) is the main view, Figure 2 (c) is the left view, Figure 2 (d) is a perspective view. The size parameters of the Au(111) substrate are 99.9 Å x 100.93 Å x 321.48 Å, as shown in Figure 3 As shown, Figure 3 The vacuum layer thickness in the z direction is 300 Å. Figure 3 The L-isoleucine molecular structure in is derived from the L-isoleucine unit cell with space group P21. Figure 3 The pink balls represent hydrogen atoms, the blue balls represent nitrogen atoms, the red balls represent oxygen atoms, and the brown balls represent carbon atoms.

[0043] Step 2: Select the force field of Au(111) substrate and L-isoleucine.

[0044] Set up appropriate force fields according to the present invention to obtain the Au(111) substrate and L-isoleucine molecules in step 1. Morse force fields were used between Au(111) atoms and between Au and S atoms, OPLS-AA force fields were used for L-isoleucine molecules, and universal force fields (UFF) were used between Au atoms and L-isoleucine molecules.

[0045] Step 3: Set the dynamic equilibrium parameters.

[0046] In the embodiment of the present invention, the dynamic equilibrium parameters of the atoms are set as shown in Table 1. In Table 1, represents the depth of the potential well in the interatomic LJ potential function of the L-isoleucine molecule, σ represents the zero potential energy distance between particles, and D e represents the potential well depth in the Morse potential function between Au atoms, r e represents the equilibrium bond length and α represents the “steepness” parameter of the potential well.

[0047] Table 1 List of atomic dynamic equilibrium parameters

[0048]

[0049] Step 4: Perform energy minimization and NVT relaxation on the system.

[0050] In the embodiments of the present invention, the Lorentz-Berthelot mixing rule is used to calculate the energy and distance parameters of the UFF force field, and the cutoff distances of the Morse potential and the Lenard-Jones (LJ) potential are 8 Å and 10 Å, respectively. Since the embodiments of the present invention only consider short-range electrostatic interactions, the cutoff radius of non-bonded interactions is set to 1.1 nm. The system adopts periodic boundary conditions in the x and y directions and fixed boundary conditions in the z direction. The velocity-Verlet algorithm is used to integrate the equations of motion, and the time step is set to 1 fs.

[0051] In the embodiment of the present invention, the minimize command is used to minimize the energy of the system, and the interatomic energy converges to 1.0x10 -5 Below kcal / mol, the force converges to 1.0x10 -7 The conjugate gradient method was used for energy minimization with a maximum of 10,000 iterations and a minimum energy of 100 kcal / mol / Angstrom. The Au substrate was then relaxed for 0.5 ns at 400 K, 500 K, 600 K, and 700 K in the canonical ensemble (NVT).

[0052] Step 5, depositing L-isoleucine molecules.

[0053] In this embodiment of the present invention, the initial velocities in the x, y, and z directions were set to 0, 0, and 5 Å / fs, respectively. The canonical ensemble (NVT) was used, and the deposition temperatures for the kinetic equilibrium parameters were set to 400 K, 500 K, 600 K, and 700 K, respectively. Using the molecular dynamics simulation software LAMMPS, 160 L-isoleucine molecules were sequentially deposited every 0.25 ns (250,000 steps). The relaxation was then continued for 225 ns without changing the kinetic parameters. A data set was output every 0.25 ns, for a total of 1060 data sets. Specifically, the kinetic trajectory and information were collected every 0.25 ns, for a total of 1060 data sets.

[0054] The structures of the present invention at different temperatures when all L-isoleucine molecules are deposited are as follows Figure 4 As shown. Among them, Figure 4 (a) Figure 4 (b) Figure 4 (c) Figure 4 (d) Schematic diagram of the structure when all 160 L-isoleucine molecules are deposited at deposition temperatures of 400 K, 500 K, 600 K, and 700 K, respectively.

[0055] Step 6, obtaining the optimal parameters and structure for the self-assembly growth of L-isoleucine.

[0056] In the embodiments of the present invention, the trajectory information of the deposited L-isoleucine self-assembly is visualized based on the .lammpstrj and .dump files using the OVITO program, the motion trajectory of the L-isoleucine molecules is analyzed, the evolutionary morphology of the self-assembled structure of the isoleucine molecules is sorted out, and the morphology, root mean square deviation (RMSD), interaction energy, hydrogen bond, and dipole moment parameters of the structure are analyzed to obtain the optimal parameters and structure suitable for the self-assembly growth of L-isoleucine.

[0057] The RMSD calculation formula of the self-assembled structure is:

[0058] RMSD=

[0059] Among them, N atoms represents the total number of atoms constituting 160 L-isoleucine molecules during the molecular dynamics simulation, x i and x i ',y i and y i ', z i and z i 'represent the x, y and z coordinate values ​​of the ith atom of the same molecule at different times during the molecular dynamics simulation.

[0060] The final structures obtained by self-assembly of L-isoleucine molecules at different temperatures of the present invention are as follows: Figure 5 As shown. Among them, Figure 5 (a) Figure 5 (b) Figure 5 (c) Figure 5 (d) The final structure diagram of L-isoleucine molecules self-assembled when the deposition temperature is 400 K, 500 K, 600 K and 700 K, respectively, and the simulated system relaxes for 225 ns.

[0061] The RMSD of the self-assembly process of L-isoleucine molecules at different temperatures of the present invention is as follows: Figure 6 As shown. Among them, Figure 6is the RMSD of the self-assembled structure of L-isoleucine at deposition temperatures of 400 K, 500 K, 600 K, and 700 K during the relaxation period of 225 ns.

[0062] The evolution of the interaction energy between L-isoleucine molecules at different temperatures is as follows: Figure 7 As shown. Among them, Figure 7 (a) Figure 7 (b) Figure 7 (c) Figure 7 (d) Figure 7 (e) Figure 7 (f) Changes in potential energy, kinetic energy, molecular energy, pairing energy, van der Waals pairing energy, and Coulomb pairing energy of the L-isoleucine self-assembly structure at different deposition temperatures during the relaxation period of 225 ns.

[0063] The hydrogen bond distribution of the self-assembled structure of L-isoleucine molecules at different temperatures of the present invention is as follows Figure 8 shown. Figure 8 in Figure 8 (a) Figure 8 (b) Figure 8 (c) Figure 8 (d) Hydrogen bond distribution of the self-assembled structure of L-isoleucine at deposition temperatures of 400 K, 500 K, 600 K, and 700 K, respectively, when the simulated system is relaxed for 225 ns.

[0064] At different deposition temperatures, the number of hydrogen bonds in the L-isoleucine self-assembly structure changes during the relaxation period of 225 ns. Figure 9 shown.

[0065] The dipole moment distribution of the L-isoleucine molecules at different temperatures when all the deposition is completed is as follows: Figure 10 As shown; the size and direction of the arrows represent the size and direction of the dipole moment of a single amino acid molecule in the xy plane, respectively, and the color represents the direction of the dipole moment of a single amino acid molecule in the xy plane. Figure 10 (a) Figure 10 (b) Figure 10 (c) Figure 10 (d) Dipole moment distribution of the self-assembled structure when all 160 L-isoleucine molecules are deposited at deposition temperatures of 400 K, 500 K, 600 K, and 700 K, respectively.

[0066] The dipole moments of the final structures obtained by self-assembly of L-isoleucine molecules at different temperatures of the present invention are as follows: Figure 11 As shown. Among them, Figure 11 (a) Figure 11 (b) Figure 11(c) Figure 11 (d) Dipole moment distribution of the L-isoleucine self-assembled structure at deposition temperatures of 400 K, 500 K, 600 K, and 700 K, respectively, when the simulated system is relaxed for 225 ns.

Claims

1. A simulation method for regulating the self-assembly structure of L-isoleucine physical vapor deposition, characterized in that: Based on molecular dynamics simulation to regulate the parameters of L-isoleucine self-assembly on the Au (111) surface, the L-isoleucine self-assembly structure was prepared by physical vapor deposition for simulation; the steps of the simulation method are as follows: Step 1, constructing the Au (111) substrate and L-isoleucine molecular structure model; Step 2: Select the force field of Au(111) substrate and L-isoleucine; set the dynamic equilibrium parameters, and perform energy minimization and NVT relaxation on the system; Step 3, performing deposition and molecular dynamics simulation on the L-isoleucine molecule in sequence; Step 4: determine whether the amino acid structure is stable. If so, proceed to step 5. Otherwise, increase the relaxation time and re-execute step 3. Step 5: Arrange the self-assembled structure and output the morphology and interaction energy parameters; Step 6: Data analysis to obtain conditions suitable for self-assembly.

2. The simulation method according to claim 1, characterized in that: The gold Au (111) substrate described in step 1 refers to the Au unit cell cut into (111) surfaces and then expanded, with the vacuum layer in the z direction set to 300 Å, and the substrate size parameters in the x, y and z directions being 99.9 Å x 100.93 Å x 321.48 Å.

3. The simulation method according to claim 1, wherein: The L-isoleucine molecular structure described in step 1 is obtained from the L-isoleucine unit cell.

4. The simulation method according to claim 1, wherein: As described in step 2, the force field of Au (111) substrate and L-isoleucine was selected, the Morse force field was used between Au atoms and between Au and S atoms, the OPLS-AA force field was used for L-isoleucine molecules, and the universal force field UFF was used between Au and L-isoleucine molecules.

5. The simulation method according to claim 1, wherein: The dynamic equilibrium parameters described in step 2 are set as follows: the system adopts periodic boundary conditions in the x and y directions and fixed boundary conditions in the z direction; the velocity-Verlet algorithm is used to integrate the equations of motion, and the time step is set to 1 fs.

6. The simulation method according to claim 1, wherein: The energy minimization and NVT relaxation of the system described in step 2 refers to the use of the Lorentz-Berthelot mixing rule; only short-range electrostatic interactions are considered, the cutoff radius for nonbonded interactions is set to 1.1 nm, and the conjugate gradient method is selected for energy minimization. The system is then relaxed for 0.5 ns at 400 K, 500 K, 600 K, and 700 K under the canonical ensemble NVT.

7. The simulation method according to claim 1, wherein: The deposition of L-isoleucine molecules described in step 3 involves setting the initial velocities of the L-isoleucine molecules in the x, y, and z directions to 0, 0, and 5 Å / fs, respectively, maintaining the temperatures of the kinetic equilibrium parameters at 400 K, 500 K, 600 K, and 700 K, respectively, depositing one L-isoleucine molecule every 0.25 ns for a total of 160 molecules, and then continuing the relaxation for 225 ns without changing the kinetic parameters.

8. The simulation method according to claim 1, wherein: The molecular dynamics simulation described in step 3 refers to collecting dynamic trajectories and information every 0.25 ns, outputting a total of 1060 sets of data; visualizing the trajectory information, analyzing the motion trajectory of the L-isoleucine molecule, organizing the evolutionary morphology of the self-assembled structure of the L-isoleucine molecule, and analyzing the structural morphology, root mean square deviation (RMSD), interaction energy, hydrogen bond, and dipole moment parameters.

9. The simulation method according to claim 8, characterized in that Whether the amino acid structure is stable in step 4 refers to whether the interatomic interaction energy and RMSD are both stable.

10. The simulation method according to claim 8, characterized in that The root mean square deviation RMSD is obtained by the following formula: RMSD= ; Among them, N atoms represents the total number of atoms constituting 160 L-isoleucine molecules during the molecular dynamics simulation, x i and x i ',y i and y i ', z i and z i 'represent the x, y and z coordinate values ​​of the ith atom of the same molecule at different times during the molecular dynamics simulation.

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