CN112992279B - Method for simulating hydrogenated graphene nano-box based on molecular dynamics - Google Patents

Method for simulating hydrogenated graphene nano-box based on molecular dynamics Download PDF

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CN112992279B
CN112992279B CN202110230413.9A CN202110230413A CN112992279B CN 112992279 B CN112992279 B CN 112992279B CN 202110230413 A CN202110230413 A CN 202110230413A CN 112992279 B CN112992279 B CN 112992279B
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张扬
雷祖祥
罗帅
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Abstract

The invention discloses a method for simulating a hydrogenated graphene nano box based on molecular dynamics, which comprises the steps of hydrogenating on a double-cross single-layer graphene model, selecting a potential function capable of reflecting interaction force between atoms in a hydrogenated graphene system, setting parameters of system relaxation and molecular dynamics simulation in molecular modeling software, calculating the charge amount contained in each atom in the hydrogenated graphene nano box through the molecular dynamics simulation software, controlling the hydrogenated graphene nano box to be unfolded and closed through an electric field, and carrying out C 60 And C 180 Simple absorption and graded release of molecules, visual analysis is conducted by introducing visual software, and information in the structure is obtained through section analysis. According to the invention, the microstructure change of the hydrogenated graphene nano-box under the action of an electric field can be simulated by adopting molecular dynamics, and the process of the structure change can be visually observed, so that a feasible scheme is provided for the controllable absorption and release of micro-scale molecules.

Description

Method for simulating hydrogenated graphene nano-box based on molecular dynamics
Technical Field
The invention belongs to the field of hydrogenated graphene folded paper materials, and particularly relates to a method for simulating a hydrogenated graphene nano box based on molecular dynamics.
Background
At present, a great deal of literature describes how to synthesize different graphene materials by using different synthesis methods, and with the discovery of the self-folding capability of graphene, a way of functionalizing graphene with atomic precision to control the structure of graphene is started, and therefore, the graphene paper folding technology also becomes one of the current research hotspots. Such components produced by unconventional nano-fabrication techniques typically have unique mechanical properties and excellent stability. The research on simulation research on the completion of hydrogenated graphene paper folding by utilizing molecular dynamics at the microscale is less, and the hydrogenated graphene paper folding technology provides a feasible scheme for controllable absorption and release of microscale molecules
The common graphene paper folding method is realized by applying high voltage to graphene 2 Hybridisation to sp 3 Hybrid transformation to form creases to induce graphene self-folding. This is to construct the graphene origami structure by the folding and pressing method of the conventional origami technology, but it is still a not small problem to precisely control the generation of creases by these methods.
In addition, the graphene paper folding box is a cross paper folding structure, and the structure can also enable single-layer graphene to be folded into the box by self, but the stability is low, the hydrogenation requirement is high, and an electric field cannot be stably applied to realize the controllable absorption and release of molecules.
Disclosure of Invention
The invention aims to provide a simulation method of a hydrogenated graphene nano-box based on molecular dynamics.
The technical scheme for realizing the purpose of the invention is as follows: a simulation method of hydrogenated graphene nano-boxes based on molecular dynamics comprises the following steps:
step 1, reading single-layer graphene data, shearing the single-layer graphene into double-cross graphene according to the atomic position of the graphene, and defining nine areas;
step 2, adding hydrogen atoms to form hydrogenated graphene according to the direction of graphene on each region boundary and the coordinates of carbon atoms;
step 3, selecting a potential function capable of describing interatomic interaction force in a hydrogenated graphene hydrocarbon system;
step 4, setting parameters of system relaxation and molecular dynamics simulation;
step 5, performing energy minimization calculation on the hydrogenated graphene sheet, determining an energy optimal structure of the hydrogenated graphene, and importing system potential energy information into Origin for data visualization processing to obtain a relation curve between time and potential energy;
step 6, calculating the polarization effect of the hydrogenated graphene model obtained in the step 5, outputting coordinates and electric charge quantity of each atom, and guiding the output model coordinates and electric charge files into visualization software Ovito for visualization analysis to obtain a hydrogenated graphene model with polarization characteristics;
step 7, adding an electric field with variable strength and C according to the polarization characteristic of the hydrogenated graphene model obtained in the step 6 60 And C 180 The molecular weight of the molecule(s),pair C for realizing hydrogenated graphene box 60 And C 180 Controlled absorption and release of molecules.
Preferably, each atom position of the double cross graphene is calculated by using a large-scale atom-molecule parallel simulator.
Preferably, hydrogen atoms are added to form hydrogenated graphene according to the graphene direction and the coordinates of carbon atoms on the boundaries of each region, specifically:
according to the direction of graphene on the boundary of each defined area, hydrogen atoms are added to the armchair-shaped graphene three-wire carbon atoms, and hydrogen atoms are added to the zigzag graphene two-wire carbon atoms.
Preferably, the hydrogen atom coordinates are set on the basis of carbon atom coordinates:
the hydrogen atom coordinate is kept consistent with the carbon atom coordinate in both the X and Y directions, and is increased in the Z direction
Figure BDA0002958936400000023
Wherein the content of the first and second substances,
Figure BDA0002958936400000024
in angstrom size units.
Preferably, the selected potential function is an aireibo potential function, and the energy formula is:
Figure BDA0002958936400000021
Figure BDA0002958936400000022
in the formula, E ij REBO Representing the energy formula of the potential function of REBO, b ij Denotes the bond order between two atoms i and j, D ij And σ ij Is a parameter of the Lennard-Jonesde potential function, D ij Depth of potential energy well, σ ij Is the distance, r, at which the potential energy of the interaction between two atoms is exactly zero ij Is the distance between atom i and atom j, r c Is to cut offA radius.
Preferably, the set parameters of system relaxation and molecular dynamics simulation include isothermal and isobaric ensemble temperature control conditions, energy minimization, neighborhood list and electric field direction.
Preferably, in step 6, polarization characteristics of the hydrogenated graphene cassette are calculated by using ReaxFF, and the reaction force field formula of the ReaxFF is as follows:
E system ＝E bond +E over +E under +E val +E pen +E tors +E conj +E vdWaals +E Coulomb
wherein E bond Corresponding bond energy, E over And E under Respectively representing an under-coordinated atomic energy and an over-coordinated atomic energy E val 、E pen 、E tors 、E conj 、E vdWaals And E coulomb Bond angle terms, loss terms, torsion angle energies, conjugation effects versus molecular energies, non-bonding van der waals interactions, and coulomb interactions, respectively.
Compared with the prior art, the invention has the following remarkable advantages:
(1) the invention can form a controllable and stable hydrogenated graphene box;
(2) the method overcomes the high dependence on hydrogenation technology, can stabilize the hydrogenated graphene into a box with the hydrogenation rate of more than 80 percent, and can be unfolded and closed under the action of an electric field;
(3) the hydrogenated graphene nano-box can realize controllable absorption and release of micro-scale molecules.
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In order to more clearly illustrate the embodiments of the present invention or the technical solutions in the prior art, the drawings used in the description of the embodiments or the prior art will be briefly described below, it is obvious that the drawings in the following description are only some embodiments described in the present invention, and for those skilled in the art, other drawings can be obtained according to the drawings without creative efforts.
FIG. 1 is a flow chart of the present invention.
Fig. 2 is a top view of a double cross-shaped hydrogenated graphene structure according to an exemplary embodiment of the present invention.
Fig. 3 is a structural diagram of an energy optimization process of a hydrogenated graphene structure according to an exemplary embodiment of the present invention.
Fig. 4 is a diagram illustrating energy variation of an energy optimization process of a hydrogenated graphene structure according to an exemplary embodiment of the present invention.
FIG. 5 is a graph showing the charge distribution of hydrogenated graphene nano-boxes according to an exemplary embodiment of the present invention
FIG. 6 shows an absorption and release of C by the hydrogenated graphene nano-box under the action of an external electric field in an exemplary embodiment of the present invention 60 Schematic representation of the molecule.
FIG. 7 shows that the hydrogenated graphene nano-box selectively releases C under the action of an external electric field in an exemplary embodiment of the present invention 60 Schematic representation of the molecule.
FIG. 8 is a structural diagram of the hydrogenated graphene with a hydrogenation rate of 80% after energy optimization
FIG. 9 is a schematic diagram of the opening and closing of the hydrogenated graphene box with a hydrogenation rate of 80% under the action of an electric field according to the present invention
Detailed Description
As shown in fig. 1, an embodiment of the present invention provides a method for simulating a hydrogenated graphene nano-cassette based on molecular dynamics, which includes:
step 1, reading single-layer graphene data, as shown in fig. 2, calculating each atomic position of the double-cross graphene by using a large-scale atomic molecule parallel simulator (Lammps), shearing the double-cross graphene into double-cross hydrogenated graphene, and dividing nine areas according to the structure.
Step 2, adding hydrogen atoms to form hydrogenated graphene according to the graphene direction and the coordinates of carbon atoms on the boundaries of each region, specifically:
according to the direction of graphene on the boundary of each defined area, hydrogen atoms are added to the armchair-shaped graphene three-wire carbon atoms, and hydrogen atoms are added to the zigzag graphene two-wire carbon atoms. The hydrogen atom coordinates are set based on these carbon atom coordinates:
the hydrogen atom coordinate remaining seated with the carbon atom in both the X and Y directionsNormalized, increased in the Z direction
Figure BDA0002958936400000044
Wherein the content of the first and second substances,
Figure BDA0002958936400000045
in angstrom size units.
And 3, selecting a potential function capable of describing interaction force among carbon atoms in a multilayer fullerene carbon-carbon system, wherein the potential function specifically comprises the following steps: an Adaptive molecular Reactive Empirical Bond Order (AIREBO) potential function is used that includes a Lennard-Jones potential function describing long range interaction forces and a Reactive Empirical Bond Order (REBO) potential function describing carbon-carbon bonding forces.
Further, the energy formula of the AIREBO potential function is:
Figure BDA0002958936400000041
Figure BDA0002958936400000042
in the formula, E ij REBO Representing the energy formula of the potential function of REBO, E ij REBO Is composed of a repulsive term and an attractive term, b ij Denotes the bond order between two atoms i and j, D ij And σ ij Is a parameter of the Lennard-Jonesde potential function, D ij Depth of potential energy well, σ ij Is the distance at which the potential energy of interaction between two atoms is exactly zero, and is specified at 0.1050 and 3.8510. r is ij Is the distance between atom i and atom j. r is c Is the cutoff radius, and when the interatomic distance exceeds the cutoff radius, its interaction is ignored and no potential function calculation is used.
Wherein the radius of truncation r c Is arranged as
Figure BDA0002958936400000043
And 4, setting parameters of system relaxation and molecular dynamics simulation, including isothermal isobaric ensemble temperature control conditions, energy minimization, neighborhood list setting and the like, selecting a micro-canonical ensemble to perform energy optimization on the hydrogenated graphene structure, selecting a canonical ensemble to perform balance constraint on the hydrogenated graphene structure simulation under the action of an electric field, wherein the boundary condition is a periodic boundary condition, and the Nose-Hoover constant temperature used in the temperature control condition is 300K. The direction of the electric field is fixed and is along the positive direction of the Z axis;
and 5, establishing an energy optimization simulation of the hydrogenated graphene structure by using Lammps. As shown in fig. 3, energy minimization calculation is performed on the hydrogenated graphene model in a static state, and then molecular dynamics simulation is performed under a micro-canonical ensemble to further optimize the structural potential. Wherein the energy minimization calculation is performed using a conjugate gradient method and a steepest descent method in succession until the energy is iterated until the total energy change divided by the energy magnitude is less than or equal to 10 -10 Or total force less than
Figure BDA0002958936400000051
Until now.
And (3) importing the system potential energy information into Origin to perform data visualization to obtain a relation curve of potential energy and time, as shown in figure 4.
And 6, calculating the polarization effect of the hydrogenated graphene structure by using ReaxFF in Lammps, and importing the output model coordinate and the charge file into visualization software Ovito for visual analysis, as shown in FIG. 5.
The polarization properties of the hydrogenated graphene boxes were calculated using a reactive force Field (reacxff). ReaxFF is a bond order dependent counter stress field that uses a geometry dependent charge calculation scheme to account for polarization effects.
The formula of the ReaxFF reverse stress field is as follows:
E system ＝E bond +E over +E under +E val +E pen +E tors +E conj +E vdWaals +E Coulomb
wherein E bond Corresponding bond energy, E over And E under Respectively represent the energy of an under-coordinated atom and the energy of an over-coordinated atom. Other items, e.g. E val 、E pen 、E tors 、E conj 、E vdWaals And E coulomb Bond angle terms, loss terms, torsion angle energies, conjugation effects versus molecular energies, non-bonding van der waals interactions, and coulomb interactions, respectively.
Step 7, studying the unfolding and closing characteristics of the hydrogenated graphene boxes under the action of the electric field by using Lammps, as shown in fig. 6 and 7, adding the electric field by using a fixefield command, and modifying the electric field intensity to complete the C pair of the hydrogenated graphene boxes 60 And C 180 Simple absorption and staged release of molecules.
Examples
In certain embodiments, a method for molecular dynamics-based simulation of hydrogenated graphene nano-boxes comprises the steps of:
the method comprises the following steps: writing a Lammps simulation control file, namely an in file code;
step two: reading a graphene model, shearing the graphene model into a double cross shape, and adding hydrogen atoms;
step three: simulating and calculating atomic coordinate information and potential energy information, and finally outputting the calculated atomic coordinate information and potential energy and simulation time relation curves;
step four: and calculating the polarization effect of the obtained hydrogenated graphene box model, and importing the obtained atomic coordinate and charge amount information into visual Ovito software for visual analysis.
Step five: adding an electric field by using a fix field command in Lammps to complete the hydrogenation of the graphene box pair C under the action of the electric field 60 And C 180 Simple absorption and staged release of molecules.
The method can provide certain calculation help for the application of the hydrogenated graphene paper folding technology.
The invention overcomes the high dependence on hydrogenation technology, can stabilize the hydrogenated graphene into a box with the hydrogenation rate of more than 80 percent, and can be unfolded and closed under the action of an electric field.
The hydrogenated graphene nano-box can realize controllable absorption and release of micro-scale molecules.

Claims (5)

1. A simulation method of a hydrogenated graphene nano-box based on molecular dynamics is characterized by comprising the following steps:
step 1, reading single-layer graphene data, shearing the single-layer graphene into double-cross graphene according to the atomic position of the graphene, and defining nine areas, wherein each atomic position of the double-cross graphene is calculated by using a large-scale atomic molecule parallel simulator;
step 2, adding hydrogen atoms to form hydrogenated graphene according to the direction of graphene on each region boundary and the coordinates of carbon atoms;
and 3, selecting a potential function capable of describing the interaction force among atoms in the hydrogenated graphene carbon-hydrogen system, wherein the selected potential function is an AIREBO potential function, and the energy formula is as follows:
Figure FDA0003681550550000011
Figure FDA0003681550550000012
in the formula, E ij REBO Representing the energy formula of the potential function of REBO, b ij Denotes the bond order between two atoms i and j, D ij And σ ij Is a parameter of the Lennard-Jonesde potential function, D ij Depth of potential energy well, σ ij Is the distance, r, at which the potential energy of the interaction between two atoms is exactly zero ij Is the distance between atom i and atom j, r c Is the cutoff radius;
step 4, setting parameters of system relaxation and molecular dynamics simulation;
step 5, performing energy minimization calculation on the hydrogenated graphene sheet, determining an energy optimal structure of the hydrogenated graphene, and importing system potential energy information into Origin for data visualization processing to obtain a relation curve between time and potential energy;
step 6, calculating the polarization effect of the hydrogenated graphene model obtained in the step 5, outputting the coordinates and the electric charge quantity of each atom, and guiding the output model coordinates and the electric charge file into visualization software Ovito for visualization analysis to obtain the hydrogenated graphene model with the polarization characteristic;
step 7, adding an electric field with variable strength and C according to the polarization characteristic of the hydrogenated graphene model obtained in the step 6 60 And C 180 Molecule, pair C realizing hydrogenated graphene boxes 60 And C 180 Controlled absorption and release of molecules.
2. The method for simulating a hydrogenated graphene nano-box based on molecular dynamics as claimed in claim 1, wherein hydrogen atoms are added to form hydrogenated graphene according to the graphene direction and the carbon atom coordinates at each zone boundary, specifically:
according to the direction of graphene on the boundary of each defined area, hydrogen atoms are added to the armchair-shaped graphene three-wire carbon atoms, and hydrogen atoms are added to the zigzag graphene two-wire carbon atoms.
3. The molecular dynamics-based simulation method of hydrogenated graphene nano-boxes according to claim 2, wherein the hydrogen atom coordinates are set based on the carbon atom coordinates:
the hydrogen atom coordinate is kept consistent with the carbon atom coordinate in both the X and Y directions, and is increased in the Z direction
Figure FDA0003681550550000021
Wherein the content of the first and second substances,
Figure FDA0003681550550000022
in angstrom size units.
4. The method according to claim 1, wherein the parameters for the system relaxation and molecular dynamics simulation include isothermal and isobaric ensemble temperature control, energy minimization, neighborhood list, and electric field direction.
5. The method for simulating hydrogenated graphene nano-cassette based on molecular dynamics according to claim 1, wherein ReaxFF is used in step 6 to calculate the polarization characteristics of the hydrogenated graphene nano-cassette, and the ReaxFF reaction force field formula is as follows:
E system ＝E bond +E over +E under +E val +E pen +E tors +E conj +E vdWaals +E Coulomb
wherein E bond Corresponding bond energy, E over And E under Respectively representing an under-coordinated atomic energy and an over-coordinated atomic energy E val 、E pen 、E tors 、E conj 、E vdWaals And E coulomb Bond angle terms, loss terms, torsion angle energies, conjugation effects versus molecular energies, non-bonding van der waals interactions, and coulomb interactions, respectively.
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JP2013211006A (en) * 2012-02-29 2013-10-10 Toray Ind Inc Molecular dynamics simulation method and program
CN106934137A (en) * 2017-03-05 2017-07-07 北京工业大学 A kind of coarse Molecular Dynamics method for analyzing Graphene assembly
CN111724862A (en) * 2020-06-22 2020-09-29 宁波大学 LST-GDC nanocluster sintering simulation method based on molecular dynamics

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Publication number Priority date Publication date Assignee Title
JP2013211006A (en) * 2012-02-29 2013-10-10 Toray Ind Inc Molecular dynamics simulation method and program
CN106934137A (en) * 2017-03-05 2017-07-07 北京工业大学 A kind of coarse Molecular Dynamics method for analyzing Graphene assembly
CN111724862A (en) * 2020-06-22 2020-09-29 宁波大学 LST-GDC nanocluster sintering simulation method based on molecular dynamics

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