A method for discriminating between molecular layering packing modes

Abstract

The present application relates to a kind of method of identifying molecular lamellar packing mode.The method of the present application is directed to designed molecule, by quantitatively characterizing molecular shape, all planar molecules can be screened, specifically for planar molecules, draw its molecular surface electrostatic potential, observe whether there is area and positive electrostatic potential value larger π-hole region near nitro group, that is, whether the target has lamellar crystal packing structure can be judged.The method provided by the present application can help lamellar compound molecular structure design.

Description

Technical Field

[0001] The present invention relates to a method for identifying whether a molecule has a layered stacking pattern, which is suitable for judging whether the compound has a layered crystal stacking structure at the molecular level. Background Art

[0002] Constructing layered crystal structures is considered a structural design approach that could improve the safety performance of energetic materials. Currently, methods such as crystal structure prediction and machine learning classification can be used to determine the packing pattern of planar molecules and determine whether a compound can form a layered crystal structure. However, because crystal structure prediction is computationally expensive and has limited accuracy, and classification models constructed using machine learning lack key descriptors, resulting in low precision, these methods struggle to accurately determine the packing pattern of planar molecules during high-throughput molecular structure design. Summary of the Invention

[0003] In view of the defects or shortcomings of the prior art, the present invention provides a method for identifying molecular lamellar stacking patterns.

[0004] To this end, the method for identifying the molecular lamellar stacking pattern provided by the present invention comprises:

[0005] a. Optimizing the molecular structure of the compound to be identified using quantum chemical calculation methods to determine whether the optimized molecular structure is a planar molecule. If it is a planar molecule, step b is performed. If not, the corresponding compound cannot form a layered crystal structure. The compound to be identified is selected from an energetic compound containing two "NH2-CC-NO2" intramolecular fragments and NH2 ... NO2 intermolecular interactions within the molecule.

[0006] b. Observe the surface electrostatic potential distribution of the optimized molecular structure. Based on the surface electrostatic potential distribution, determine whether there is a large π-hole region with a high positive electrostatic potential value near the -NO2 bond. If so, it is considered that the corresponding compound cannot form a layered stacking pattern.

[0007] Furthermore, the area of ​​the region near the -NO2 bond is larger than When the positive electrostatic potential value is greater than 33 kcal / mol in the π-hole region, it is considered that the corresponding compound cannot form a layered crystal structure.

[0008] Furthermore, the surface electrostatic potential distribution of the optimized molecular structure is: the electrostatic potential distribution on the 0.002 au equal electron density surface of the optimized molecular structure.

[0009] Furthermore, the quantum chemical calculation method adopts M06-2X / 6-311+g(d,p).

[0010] Furthermore, in step a, it is determined whether the optimized molecular structure is a planar molecule based on the molecular shape parameter SI or the best fitting plane PBF.

[0011] Furthermore, when the value of SI is less than 0.01, it is a planar molecule.

[0012] Furthermore, the observation of the surface electrostatic potential distribution of the optimized molecular structure in step b includes: calculating the electrostatic potential value on the 0.002 au electron density surface of the optimized molecular structure, and then plotting the surface electrostatic potential value distribution to obtain an electrostatic potential value distribution map, and using the map to observe the surface electrostatic potential distribution of the optimized molecular structure.

[0013] The present invention can realize the rapid identification of whether a planar molecule has a layered stacking pattern; and the method of the present invention is simple, rapid, accurate and efficient, and has important reference significance for the high-throughput design of layered compounds. BRIEF DESCRIPTION OF THE DRAWINGS

[0014] Figure 1 Schematic diagram of the molecular structure of layered compounds and their molecular surface electrostatic potential;

[0015] Figure 2 The molecular and crystal structures identified in Example 1;

[0016] Figure 3 This is a numerical distribution diagram of the electrostatic potential of the molecular structure after optimization in Example 1;

[0017] Figure 4 The molecular and crystal structures identified in Example 2;

[0018] Figure 5 This is the numerical distribution diagram of the electrostatic potential of the molecular structure after optimization in Example 2. DETAILED DESCRIPTION

[0019] Unless otherwise specified, the terms and methods herein are understood by ordinary technicians in the relevant fields or implemented using existing methods.

[0020] The planarity of the molecule is a basic condition for the formation of a layered crystal structure. The present invention first constructs an initial molecular structure model, that is, optimizes the molecular structure based on quantum chemical calculation methods, obtains the molecular structure at the local minimum point on the potential energy surface, and ensures the rationality of the molecular conformation through frequency analysis. Then, based on the reasonable molecular structure, the molecular shape index (SI) or the best fit plane PBF is calculated to determine whether the optimized molecular structure is a planar molecule to preliminarily identify the layered stacking mode of the compound, where the SI value of the planar molecule is less than 0.01 and tends to 0.

[0021] In layered crystal structures, the electrostatic interaction between molecules is the dominant factor. The physical meaning of the molecular electrostatic potential is the work done to move a positive charge from infinity to a certain point in the space around the molecule. In other words, the molecular electrostatic potential is basically one of the sources of electrostatic interaction and can be used to predict molecular self-assembly behavior and detect local chemical reaction trends. Moreover, since the electrostatic interaction force of molecules is the main long-range intermolecular interaction, the electrostatic potential plays a unique role in the identification of molecules and intermolecular reaction sites. The inventors have found that the molecular structure of layered crystal compounds does not have an electrostatic potential distribution on the 0.002au isoelectronic value surface that simultaneously satisfies the requirement of "a large area (at least larger than the area of ​​the area) near the -NO2 bond of the planar molecule". ) and a π-hole region with a high positive electrostatic potential value (at least greater than 33 kcal / mol). Figure 1 The figure shows the molecular structure of a layered compound and a schematic diagram of its surface electrostatic potential. Although π-hole regions can be observed in this type of molecular structure, the size of the region and the magnitude of the positive electrostatic potential do not simultaneously meet the aforementioned threshold conditions. Therefore, it can be considered that the π-hole region in this type of molecule is not prone to interaction with the electron-rich NO2 group. Figure 1 The acquisition method is:

[0022] a. Optimize the molecular structure and calculate the molecular shape index SI by the M06-2X / 6-311+g(d,p) method. When the SI value is less than 0.01, it is a planar molecule, such as Figure 2 As shown;

[0023] b. Use Multiwfn software to extract the electron orbital function files of each optimized analysis structure and calculate the electrostatic potential value on its 0.002au isoelectronic value surface, and use VMD software to draw a schematic diagram of the electrostatic potential value distribution of each optimized molecular structure. Figure 1 .

[0024] Based on this, the present invention further identifies the layered stacking mode of the compound to be identified by examining the electrostatic potential distribution of the molecular structure after optimization on the 0.002 au isoelectronic value surface. Specifically, when there is a large positively charged area (i.e., π-hole) near the -NO2 bond, it is easy for the electron-rich -NO2 groups to interact, and the unique directionality of the π-hole leads to the construction of a non-layered crystal structure. Therefore, the layered stacking mode can be identified according to the size of the π-hole area and the value of its positive electrostatic potential.

[0025] In the specific plan, the surface electrostatic potential distribution of the optimized molecular structure can be observed with the help of relevant software. For example, the electrostatic potential value on the electron density surface of 0.002au of the optimized molecular structure is calculated using Multiwfn, Gaussview, Spartan and other software. Then, its distribution is plotted using VMD, Gaussview, Spartan and other software to obtain an electrostatic potential value distribution map, which is used to observe the surface electrostatic potential distribution of the optimized molecular structure.

[0026] Example 1:

[0027] This embodiment screens multiple compounds containing only C, H, O, and N elements in the CSD database as research examples, wherein the structures of such compounds must contain two "NH2-CC-NO2" intramolecular fragments and contain NH2...NO2 intermolecular interactions.

[0028] Selected molecules and crystal structures such as Figure 2 As shown, the following method is used to identify Figure 2 The layered stacking patterns of the compounds shown are:

[0029] a. Optimize the molecular structure and calculate the molecular shape index SI by the M06-2X / 6-311+g(d,p) method. When the SI value is less than 0.01, it is a planar molecule. Figure 2 It can be seen that the SI value of the SEDTUQ03 molecule is large, that is, the molecule has a non-planar structure, and the crystal cannot form a layered stacking structure; therefore, the SEDTUQ03 crystal is no longer used as an example for study, and step b identification is performed on other compounds;

[0030] b. Use Multiwfn software to extract the electronic orbital function files of each optimized analysis structure and calculate the electrostatic potential value on its 0.002au isoelectronic value surface. Use VMD software to draw a schematic diagram of the electrostatic potential value distribution of each optimized molecular structure, as shown in the figure. Figure 1 and 3 As shown in the figures;

[0031] As indicated by the arrows in the figure, in the molecular structures of BEWYOR, DATNBZ01 and YEKQAG, there is a large region (at least larger than ), the region with a high positive electrostatic potential value (at least greater than 33 kcal / mol) is the π-hole region;

[0032] Furthermore, AIM analysis shows that the π-hole region is prone to non-bonding interactions between electron-rich -NO2 groups in adjacent molecules, namely π-hole interactions, which lead to the formation of non-layered crystal structures due to their unique directionality (see Figure 3However, this is not observed in layered compounds (e.g. Figure 1 shown).

[0033] Example 2:

[0034] This embodiment uses Figure 2 The method of the present invention was verified by two types of F-containing compounds with similar structures. Their molecular and crystal structures are shown in FIG. Figure 4 As shown, the compound VIYNUP has a layered crystal structure, and the compound BEWYOR has a non-layered crystal structure.

[0035] The numerical distribution diagram of the molecular surface electrostatic potential is obtained by the calculation method in Example 1, as shown in FIG. Figure 5 As shown in Figure 2, it is obvious that compared with the molecular surface electrostatic potential of compound VIYNUP, the π-hole region in the molecular structure of compound BEWYOR is more obvious, with an area of ​​at least The electrostatic potential value is at least 37.44 kcal / mol. This phenomenon verifies the reliability of the method of the present invention and also broadens the scope of application of the method of the present invention.

Claims

1. A method for identifying a molecular lamellar stacking pattern, characterized in that: Methods include: a. Optimizing the molecular structure of the compound to be identified using quantum chemical calculation methods to determine whether the optimized molecular structure is a planar molecule. If it is a planar molecule, step b is performed. If not, the corresponding compound cannot form a layered crystal structure. The compound to be identified is selected from an energetic compound containing two "NH2-CC-NO2" intramolecular fragments and NH2 ... NO2 intermolecular interactions. b. Observe the surface electrostatic potential distribution of the optimized molecular structure, and judge whether there is a large π-hole region with a high positive electrostatic potential value near the -NO2 bond according to the surface electrostatic potential distribution. If it exists, it is considered that the corresponding compound cannot form a layered stacking mode; if there is a region with an area larger than 1 near the -NO2 bond, When the positive electrostatic potential value is greater than 33 kcal / mol in the π-hole region, it is considered that the corresponding compound cannot form a layered crystal structure.

2. The method according to claim 1, wherein The surface electrostatic potential distribution of the optimized molecular structure is: the electrostatic potential distribution on the 0.002 au equal electron density surface of the optimized molecular structure.

3. The method according to claim 1, wherein The quantum chemical calculation method adopts M06-2X / 6-311+g(d,p).

4. The method according to claim 1, wherein In the step a, it is determined whether the optimized molecular structure is a planar molecule according to the molecular shape parameter SI or the best fitting plane PBF.

5. The method according to claim 4, wherein When the SI value is less than 0.01, it is a planar molecule.

6. The method according to claim 1, wherein The observation of the surface electrostatic potential distribution of the optimized molecular structure in step b includes: The electrostatic potential value on the 0.002au isoelectronic density surface of the optimized molecular structure is calculated, and then the surface electrostatic potential value distribution is plotted to obtain an electrostatic potential value distribution map, which is used to observe the surface electrostatic potential distribution of the optimized molecular structure.

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