CN116343931B - Method for calculating bonding energy between crystal faces of NTO (non-thermal-mechanical) crystal - Google Patents
Method for calculating bonding energy between crystal faces of NTO (non-thermal-mechanical) crystal Download PDFInfo
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- 239000013078 crystal Substances 0.000 title claims abstract description 138
- 238000000034 method Methods 0.000 title claims abstract description 22
- 238000000329 molecular dynamics simulation Methods 0.000 claims abstract description 33
- 238000004364 calculation method Methods 0.000 claims abstract description 19
- 238000004220 aggregation Methods 0.000 claims abstract description 16
- 230000002776 aggregation Effects 0.000 claims abstract description 16
- 230000012010 growth Effects 0.000 claims abstract description 8
- 238000005457 optimization Methods 0.000 claims abstract description 6
- 230000010261 cell growth Effects 0.000 claims abstract description 5
- 238000012163 sequencing technique Methods 0.000 claims description 4
- 238000004088 simulation Methods 0.000 claims description 4
- 239000000126 substance Substances 0.000 claims description 4
- 239000013589 supplement Substances 0.000 abstract description 3
- QJTIRVUEVSKJTK-UHFFFAOYSA-N 5-nitro-1,2-dihydro-1,2,4-triazol-3-one Chemical compound [O-][N+](=O)C1=NC(=O)NN1 QJTIRVUEVSKJTK-UHFFFAOYSA-N 0.000 description 42
- 210000004027 cell Anatomy 0.000 description 27
- 238000010586 diagram Methods 0.000 description 3
- 239000002360 explosive Substances 0.000 description 3
- 210000002858 crystal cell Anatomy 0.000 description 2
- 230000000694 effects Effects 0.000 description 2
- 230000009286 beneficial effect Effects 0.000 description 1
- 238000005094 computer simulation Methods 0.000 description 1
- 238000010276 construction Methods 0.000 description 1
- 230000007547 defect Effects 0.000 description 1
- 229910052739 hydrogen Inorganic materials 0.000 description 1
- 239000001257 hydrogen Substances 0.000 description 1
- 239000000463 material Substances 0.000 description 1
- 238000002360 preparation method Methods 0.000 description 1
- 239000000047 product Substances 0.000 description 1
- 230000000750 progressive effect Effects 0.000 description 1
- 238000003860 storage Methods 0.000 description 1
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C10/00—Computational theoretical chemistry, i.e. ICT specially adapted for theoretical aspects of quantum chemistry, molecular mechanics, molecular dynamics or the like
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- G—PHYSICS
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- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/30—Prediction of properties of chemical compounds, compositions or mixtures
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- G—PHYSICS
- G16—INFORMATION AND COMMUNICATION TECHNOLOGY [ICT] SPECIALLY ADAPTED FOR SPECIFIC APPLICATION FIELDS
- G16C—COMPUTATIONAL CHEMISTRY; CHEMOINFORMATICS; COMPUTATIONAL MATERIALS SCIENCE
- G16C20/00—Chemoinformatics, i.e. ICT specially adapted for the handling of physicochemical or structural data of chemical particles, elements, compounds or mixtures
- G16C20/50—Molecular design, e.g. of drugs
Abstract
The invention provides a method for calculating the binding energy among NTO crystal faces, which relates to the technical field of binding energy calculation and comprises the following steps: adjusting NTO atoms of the obtained alpha type NTO unit cell to obtain an NTO unit cell to be calculated, and performing growth prediction to obtain 5 main crystal faces of the NTO unit cell to be calculated and a percentage value of the main crystal faces to the total area; carrying out section and cell expansion on each main crystal face to obtain a crystal face model of each main crystal face; performing approximate matching of lattice parameters on any two crystal face models to obtain an action model; c, adjusting the parameter c of the action model; sequentially performing geometric optimization and molecular dynamics simulation on the adjusted action model to obtain a molecular dynamics result; and (3) carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result. The invention supplements microscopic level information of NTO crystals, reveals the action essence of different crystal faces in crystal aggregation, and can determine main crystal faces causing NTO aggregation in specific embodiments.
Description
Technical Field
The invention relates to the technical field of binding energy calculation, in particular to a method for calculating the binding energy among NTO crystal faces.
Background
Traditional explosives have potential safety hazards in the process of storage and transportation, and the importance of high-energy insensitive explosives in modern wars is increasingly prominent. 3-nitro-1, 2, 4-triazol-5-one (NTO) has been widely studied as a novel insensitive explosive. However, NTO molecules have stronger polarity, and intermolecular hydrogen bonds are easy to form between crystal faces, so that crystals are easy to aggregate in the preparation process, the granularity of the obtained product is large, and the practical application requirement is not met.
The development of the molecular dynamics calculation method is mature, and the method can be used for calculating the binding energy of a system under a microscopic scale. Although the calculation method of the binding energy exists, the calculation of the binding energy among different crystal faces of the same molecule is unprecedented, and the difficulty is in the establishment of a model. The duplication of the crystal face structure can cause large difference of lattice data of two crystal faces, and the two crystal faces cannot be matched, so that a difficult problem is set for building a model. At present, a method for calculating the binding energy between NTO crystals and crystals through crystal planes from a microscopic angle is lacking. The specific details are as follows:
(1) Lack of a computational model of the bonding energy between crystal faces and a construction method;
(2) There is a lack of a set of computational schemes to characterize the interplanar binding energy.
Disclosure of Invention
In order to overcome the defects of the prior art, the invention aims to provide a method for calculating the bonding energy between crystal faces of NTO crystals.
In order to achieve the above object, the present invention provides the following solutions:
a method for calculating the binding energy between the crystal faces of an NTO crystal, comprising:
adjusting NTO atoms of the obtained alpha-type NTO unit cell to obtain an NTO unit cell to be calculated;
performing growth prediction on the NTO unit cell to be calculated to obtain 5 main crystal faces of the NTO unit cell to be calculated and a percentage value of the main crystal faces to the total area;
carrying out section and cell expansion on each main crystal face to obtain a crystal face model of each main crystal face;
performing approximate matching of lattice parameters on any two crystal face models to obtain an action model; the crystal orientation in the action model is based on the crystal face with the largest percentage value;
c parameters of the action model are adjusted to add a vacuum layer for molecular dynamics calculation;
sequentially performing geometric optimization and molecular dynamics simulation on the adjusted action model to obtain a molecular dynamics result;
and (3) carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result.
Preferably, the adjustment of the ntu atoms of the obtained α -type ntu unit cell results in an ntu unit cell to be calculated, comprising:
acquiring the alpha-type NTO unit cells from a crystal data center database;
and adjusting the force field of each atom according to the bonding mode and chemical environment of each atom of the alpha-type NTO unit cell to obtain the NTO unit cell to be calculated.
Preferably, the performing the approximate matching of lattice parameters on any two crystal face models to obtain an action model includes:
taking the a, b and gamma parameters of the unit cells of the two crystal face models as new unit cell parameters of an action model respectively, so that the action model accommodates the supercell structures of the two crystal faces to obtain the action model.
Preferably, the vacuum layer has a thickness of 20 a.
Preferably, the simulation parameters of the molecular dynamics simulation specifically include: at 298k, the number of steps is 100000, and one frame is output every 50 steps.
Preferably, the energy analysis is performed on the molecular dynamics result, and the binding energy is calculated according to the analysis result, including:
sequencing the analysis results, and respectively carrying out system total energy E by selecting three frames corresponding to the lowest energy step in 50000 steps tot And two crystal plane supercell energy E l1 、E l2 Is calculated;
according to formula E int =E tot -E l1 -E l2 Calculating to obtain the combination energy of three frames respectively, and taking the average value of the combination energy corresponding to the three frames as a final result; wherein E is int Is the binding energy.
Preferably, after energy analysis is performed on the molecular dynamics result, and binding energy is calculated according to the analysis result, the method further comprises:
and comparing the calculated results of the binding energy of each action model to determine the main crystal face which causes the NTO aggregation phenomenon.
Preferably, the main crystal plane that induces the NTO aggregation phenomenon is (0 0.1).
According to the specific embodiment provided by the invention, the invention discloses the following technical effects:
the invention provides a method for calculating the bonding energy between crystal faces of NTO crystals, which comprises the following steps: adjusting NTO atoms of the obtained alpha-type NTO unit cell to obtain an NTO unit cell to be calculated; performing growth prediction on the NTO unit cell to be calculated to obtain 5 main crystal faces of the NTO unit cell to be calculated and a percentage value of the main crystal faces to the total area; carrying out section and cell expansion on each main crystal face to obtain a crystal face model of each main crystal face; performing approximate matching of lattice parameters on any two crystal face models to obtain an action model; the crystal orientation in the action model is based on the crystal face with the largest percentage value; c parameters of the action model are adjusted to add a vacuum layer for molecular dynamics calculation; sequentially performing geometric optimization and molecular dynamics simulation on the adjusted action model to obtain a molecular dynamics result; and (3) carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result. The invention supplements microscopic level information of NTO crystals, reveals the action essence of different crystal faces in crystal aggregation, and can determine main crystal faces causing NTO aggregation in specific embodiments.
Drawings
In order to more clearly illustrate the embodiments of the present invention or the technical solutions of the prior art, the drawings that are needed in the embodiments will be briefly described below, it being obvious that the drawings in the following description are only some embodiments of the present invention, and that other drawings may be obtained according to these drawings without inventive effort for a person skilled in the art.
FIG. 1 is a flow chart of a method according to an embodiment of the present invention;
FIG. 2 is a schematic diagram of a calculation flow provided in an embodiment of the present invention;
FIG. 3 is a schematic diagram of a supercell model with 5 crystal planes according to an embodiment of the present invention;
fig. 4 is a schematic diagram of bonding energy between crystal planes according to an embodiment of the present invention.
Description of the embodiments
The following description of the embodiments of the present invention will be made clearly and completely with reference to the accompanying drawings, in which it is apparent that the embodiments described are only some embodiments of the present invention, but not all embodiments. All other embodiments, which can be made by those skilled in the art based on the embodiments of the invention without making any inventive effort, are intended to be within the scope of the invention.
The invention aims to provide a calculation method of the bonding energy among NTO crystal faces, which can supplement microscopic level information of the NTO crystal, reveal the action essence of different crystal faces in crystal aggregation and determine main crystal faces causing the NTO aggregation.
In order that the above-recited objects, features and advantages of the present invention will become more readily apparent, a more particular description of the invention will be rendered by reference to the appended drawings and appended detailed description.
Fig. 1 is a flow chart of a method provided by an embodiment of the present invention, and as shown in fig. 1, the present invention provides a method for calculating an inter-crystal plane bonding energy of an ntu crystal, including:
step 100: adjusting NTO atoms of the obtained alpha-type NTO unit cell to obtain an NTO unit cell to be calculated;
step 200: performing growth prediction on the NTO unit cell to be calculated to obtain 5 main crystal faces of the NTO unit cell to be calculated and a percentage value of the main crystal faces to the total area;
step 300: carrying out section and cell expansion on each main crystal face to obtain a crystal face model of each main crystal face;
step 400: performing approximate matching of lattice parameters on any two crystal face models to obtain an action model; the crystal orientation in the action model is based on the crystal face with the largest percentage value;
step 500: c parameters of the action model are adjusted to add a vacuum layer for molecular dynamics calculation;
step 600: sequentially performing geometric optimization and molecular dynamics simulation on the adjusted action model to obtain a molecular dynamics result;
step 700: and (3) carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result.
Preferably, step 100 comprises:
acquiring the alpha-type NTO unit cells from a crystal data center database;
and adjusting the force field of each atom according to the bonding mode and chemical environment of each atom of the alpha-type NTO unit cell to obtain the NTO unit cell to be calculated.
As shown in fig. 2, in this example, first, an α -type ntu unit cell (α is a stable crystal form of ntu at normal temperature, which is more suitable for the general conditions for studying the aggregation of ntu) was obtained from a Cambridge Crystal Data Center (CCDC) database, opened with a Material Studio, and Force field adjustment of the ntu atom was performed to obtain an ntu unit cell for calculation. The Force field adjustment belongs to the prior art and is not described in detail here. In this embodiment, the molecular structure is closer to the actual situation by adjusting the force field of each atom according to the bonding mode and chemical environment of each atom, so as to increase the accuracy of the subsequent simulation calculation.
Further, growth prediction was performed on the ntu unit cells in this example. Morphology, calculation is selected in Modules, task is Growth morphology, quality is Fine, the force field in Energy tab is COMPASS II, and run is clicked to obtain 5 main crystal planes and area ratios of NTO as shown in Table 1.
TABLE 1 Crystal face and area ratio
| Crystal plane | Percentage of total area |
| （0 0 1） | 54.29 |
| （1 0 0） | 14.72 |
| （0 1 -1） | 14.23 |
| （0 1 0） | 13.09 |
| （1 0 -2） | 3.66 |
Further, in this embodiment, the corresponding crystal planes are cut and expanded, so that the length of each crystal plane U, V is close to 20 a. A model of 5 crystal planes was obtained.
Preferably, the performing the approximate matching of lattice parameters on any two crystal face models to obtain an action model includes:
taking the a, b and gamma parameters of the unit cells of the two crystal face models as new unit cell parameters of an action model respectively, so that the action model accommodates the supercell structures of the two crystal faces to obtain the action model.
Specifically, in this embodiment, a Build Layers option is selected in Build, and two crystal planes to be built are sequentially selected in defined Layers, and "Build layer structure as a crystal" is selected. Because the orientations of the two crystal faces are different, in order to construct a reasonable and computationally available model, approximate Matching of lattice parameters is needed, average is checked in a Matching tab, and the a, b and gamma parameters of the two crystal cells are respectively averaged to be used as new crystal cell parameters of an action model Layer, so that the action model can better accommodate the supercell structure of the two crystal faces. The crystal orientation is based on the crystal planes which occupy a relatively large area in the model.
Further, on the aggregation microscopic level between crystals, the effect of the force between two crystal planes is realized, as shown in fig. 3, the binding energy calculation of any two crystal planes is performed on 5 main crystal planes of the ntu, for example, the binding energy calculation of 1-1,1-2,1-3,1-4,1-5,2-3, …,4-5,5-5 total 15 models is performed on 5 main crystal planes with the serial numbers of 1 to 5, wherein the same crystal plane models such as 1-1,2-2 correspond to the energy of the growth of the crystal planes.
Optionally, the c-parameters of the resulting Layer structure are then adjusted to add a vacuum Layer for molecular dynamics calculations. The vacuum layer thickness is 20 a. The operation is to open the Rebuild Crystal tab in the Build module Crystal option, increasing the c value by 20 in Lattice Parameters.
Preferably, the simulation parameters of the molecular dynamics simulation specifically include: at 298k, the number of steps is 100000, and one frame is output every 50 steps.
Specifically, in this embodiment, the geometric optimization of the structure in the force field of the COMPASS ii is performed first in the force module, and then the molecular dynamics simulation in the force field of the COMPASS ii is performed. NVT ensemble is selected, 298K, with a step number of 100000, outputting one frame every 50 steps.
Preferably, the energy analysis is performed on the molecular dynamics result, and the binding energy is calculated according to the analysis result, including:
sequencing the analysis results, and respectively carrying out system total energy E by selecting three frames corresponding to the lowest energy step in 50000 steps tot And two crystal plane supercell energy E l1 、E l2 Is calculated;
according to formula E int =E tot -E l1 -E l2 Calculating to obtain the combination energy of three frames respectively, and taking the average value of the combination energy corresponding to the three frames as a final result; wherein E is int Is the binding energy.
Preferably, after energy analysis is performed on the molecular dynamics result, and binding energy is calculated according to the analysis result, the method further comprises:
and comparing the calculated results of the binding energy of each action model to determine the main crystal face which causes the NTO aggregation phenomenon.
Preferably, the main crystal plane that induces the NTO aggregation phenomenon is (0 0.1).
Finally, in this example, the molecular dynamics results were energy analyzed and Total kinetic energy was selected from the format module Analysis option. Sequencing, and selecting three frames corresponding to the lowest energy step in 50000 steps to respectively carry out total energy E of the system tot And two crystal plane supercell energy (E l1 、E l2 ) Is calculated by the computer. The binding energy E is calculated by a formula int = E tot - E l1 - E l2 As shown in fig. 4 and table 2, it can be found from comparison of the binding energy results of 15 models that the (0 00 1) crystal plane is the main crystal plane accounting for 54.29% of the crystal plane area, and the higher binding energy level with other crystal planes is an important cause for causing the NTO aggregation phenomenon.
TABLE 2 data on binding energy between crystal planes
| Eint(kJ/mol) | (0 0 1) | (1 0 0) | (0 1 -1) | (0 1 0) | (1 0 -2) |
| (0 0 1) | -1056.58 | -873.65 | -854.3 | -874.26 | -899.88 |
| (1 0 0) | -873.65 | -902.02 | -762.14 | -721.12 | -772.66 |
| (0 1 -1) | -854.3 | -762.14 | -626.96 | -857.81 | -858.22 |
| (0 1 0) | -874.26 | -721.12 | -857.81 | -571.91 | -792.5 |
| (1 0 -2) | -899.88 | -772.66 | -858.22 | -792.5 | -770.88 |
The beneficial effects of the invention are as follows:
according to the invention, molecular dynamics calculation is performed on the constructed crystal face action model, so that the aggregation essence of NTO crystals is further revealed, and the (0 0 1) crystal face is found to be the crystal face with stronger bonding capability with other crystal faces.
In the present specification, each embodiment is described in a progressive manner, and each embodiment is mainly described in a different point from other embodiments, and identical and similar parts between the embodiments are all enough to refer to each other.
The principles and embodiments of the present invention have been described herein with reference to specific examples, the description of which is intended only to assist in understanding the methods of the present invention and the core ideas thereof; also, it is within the scope of the present invention to be modified by those of ordinary skill in the art in light of the present teachings. In view of the foregoing, this description should not be construed as limiting the invention.
Claims (6)
1. A method for calculating the binding energy between the crystal faces of an NTO crystal, comprising:
adjusting NTO atoms of the obtained alpha-type NTO unit cell to obtain an NTO unit cell to be calculated;
performing growth prediction on the NTO unit cell to be calculated to obtain 5 main crystal faces of the NTO unit cell to be calculated and a percentage value of the main crystal faces to the total area;
carrying out section and cell expansion on each main crystal face to obtain a crystal face model of each main crystal face;
performing approximate matching of lattice parameters on any two crystal face models to obtain an action model; the crystal orientation in the action model is based on the crystal face with the largest percentage value;
c parameters of the action model are adjusted to add a vacuum layer for molecular dynamics calculation;
sequentially performing geometric optimization and molecular dynamics simulation on the adjusted action model to obtain a molecular dynamics result;
carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result;
the simulation parameters of the molecular dynamics simulation specifically comprise: the temperature is 298k, the number of steps is 100000, and one frame is output every 50 steps;
carrying out energy analysis on the molecular dynamics result, and calculating the binding energy according to the analysis result, wherein the energy analysis comprises the following steps:
sequencing the analysis results, and respectively carrying out system total energy E by selecting three frames corresponding to the lowest energy step in 50000 steps tot And two crystal plane supercell energy E l1 、E l2 Is calculated;
according to formula E int =E tot -E l1 -E l2 Calculating to obtain the combination energy of three frames respectively, and taking the average value of the combination energy corresponding to the three frames as a final result; wherein E is int Is the binding energy.
2. The method for calculating the inter-crystal plane binding energy of an ntu crystal according to claim 1, wherein the adjustment of the ntu atoms of the obtained α -type ntu unit cell to obtain the to-be-calculated ntu unit cell includes:
acquiring the alpha-type NTO unit cells from a crystal data center database;
and adjusting the force field of each atom according to the bonding mode and chemical environment of each atom of the alpha-type NTO unit cell to obtain the NTO unit cell to be calculated.
3. The method for calculating the binding energy between the crystal faces of the NTO crystal according to claim 1, wherein the performing the approximate matching of the lattice parameters on any two crystal face models to obtain an action model comprises:
taking the a, b and gamma parameters of the unit cells of the two crystal face models as new unit cell parameters of an action model respectively, so that the action model accommodates the supercell structures of the two crystal faces to obtain the action model.
4. The method of claim 1, wherein the vacuum layer has a thickness of 20 a.
5. The method according to claim 1, further comprising, after energy analysis of the molecular dynamics results and calculation of binding energy based on the analysis results:
and comparing the calculated results of the binding energy of each action model to determine the main crystal face which causes the NTO aggregation phenomenon.
6. The method of claim 5, wherein the main crystal plane that induces the NTO aggregation is (0.1).
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