A chemical bonding analysis method based on electron localization

Abstract

The present invention relates to a chemical bonding analysis method based on electron localization, comprising: (1) constructing and optimizing a molecular structure; (2) molecular orbital (MO) and natural bond orbital (NBO) analysis: deducting the contribution of the inner core orbitals that are useless for bonding to the density matrix, as preparation files MO.log and NBO.log for subsequent AdNDP analysis; (3) obtaining the number of basis functions of atoms in the molecule: obtaining the number of all atomic basis functions in the molecule and the number of basis functions occupied by each atom by querying the basis function and Eigenvalues ​​in the MO.log file; (4) performing bonding analysis on the molecule: analyzing the electronic bonding of the molecule: analyzing the chemical bonds and the number of valence electrons present in the molecule; deducting 1c-2e and 2c-2e; and deducting the remaining nc-2e. The present invention can simultaneously deduct all m-centered 2-electron chemical bonds, without having to classify the chemical bonds for deduction, and can simultaneously exclude the influence of the surrounding atomic environment and analyze a specific chemical bond in a targeted manner.

Description

Technical Field

[0001] The present invention relates to a chemical bonding analysis method, in particular to a chemical bonding analysis method based on electron localization. Background Art

[0002] In quantum chemistry, chemical bond analysis is a method used to study and understand the properties of molecular chemical bonds and chemical reactions. It plays a crucial role in molecular design, chemical reaction mechanism research, and the development of new materials. It can reveal the electronic structure, bond strength, and properties of molecules. By plotting images of molecular orbitals, electron density distribution, and charge distribution, it can intuitively observe and analyze the position, direction, and properties of chemical bonds. For finite systems such as molecules and clusters, established methods exist for electronic structure and multi-center bond analysis, such as molecular orbital (MO) theory, natural bond orbital (NBO) theory, and the adaptive natural density partitioning (AdNDP) method. The AdNDP method, based on NBO results, offers a more flexible analysis and is a powerful tool for studying multi-center bonds. In 2012, Schmidt et al. (J. Chem. Theory Comput., 2012, 8, 1902-1911.) developed an NBO method for periodic systems (solids and two-dimensional materials) and developed a patch for the VASP software package to obtain NBO results for periodic systems. Then, in 2013, Boldyrev et al. (Phys. Chem. Chem. Phys. 2013, 15, 5022-5029.) developed the AdNDP method for solid-state systems (SSAdNDP software package) based on the NBO method for periodic systems. This method can perform bond analysis on solids and provide visual results.

[0003] However, the AdNDP software package currently has several functional limitations and bugs. Large systems may experience buffer overflows, and there are also several bottlenecks in search capabilities:

[0004] 1) The influence of the surrounding atomic environment cannot be eliminated, making it impossible to analyze a specific chemical bond in a targeted manner;

[0005] 2) It can only give the overall occupation number of a chemical bond, but cannot give the sub-occupancy number of each atom.

[0006] Therefore, it is necessary to study a new chemical bonding analysis method that can perform very beautiful chemical bonding analysis on molecules and cluster systems. Summary of the Invention

[0007] The technical problem to be solved by the present invention is how to achieve targeted analysis of a specific chemical bond and provide the sub-occupancy number of each atom in the analysis result.

[0008] The present invention solves the above technical problems by the following technical means: a chemical bonding analysis method based on electron localization, comprising the following steps:

[0009] (1) Build and optimize the molecular structure;

[0010] (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: deduct the contribution of the core orbitals that are not useful for bonding to the density matrix, and use them as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis;

[0011] (3) Obtain the number of basis functions of atoms in the molecule: obtain the number of basis functions of all atoms in the molecule and the number of basis functions occupied by each atom by querying the basis function and Eigenvalues ​​in the MO.log file;

[0012] (4) Bond analysis of molecules, including:

[0013] 1) Analyze the electronic bonding of molecules: Analyze the chemical bonds and the number of valence electrons in the molecules;

[0014] 2) Subtract one-center two-electron (1c-2e) and two-center two-electron 2c-2e: Obtain the density matrix information of the system from the MO.log and NBO.log files, take out the diagonal blocks of the density matrix corresponding to the atoms of 1c-2e and 2c-2e in turn, and obtain the output file AdNDP_Resid.log after deducting 1c-2e and 2c-2e, the orbital visualization file mo.log, and the occupancy number and residual electron density file NDP_nbo.log. Further check NDP_nbo.log to obtain the AdNDP orbital and the remaining electron density after deducting 1c-2e and 2c-2e. If the remaining electron density is greater than or equal to the preset value, it is necessary to further analyze the bonding situation of the remaining electrons. If it is less than the preset value, it proves that the bonding analysis is complete;

[0015] 3) Subtract the remaining nc-2e: where n represents the number of central atoms, n>2 and less than or equal to the total number of atoms in the system k. After subtracting 1c-2e and 2c-2e, based on the output files AdNDP_Resid.log and mo.log in step 2), obtain the remaining density matrix information from the AdNDP_Resid.log and mo.log files. Sequentially extract the diagonal blocks of the density matrix corresponding to the atoms in the nc-2e group. Obtain the output file AdNDP_Resid.log after subtracting nc-2e, the orbital visualization file mo_FR.log, and the occupancy number and residual electron density file NDP_nbo.log. By viewing NDP_nbo.log, you can obtain the AdNDP orbitals and the remaining electron density after subtracting nc-2e. If the remaining electron density is less than the preset value, the bonding analysis is complete. If it is greater than or equal to the preset value, repeat step 3) based on the output files AdNDP_Resid.log and mo_FR.log after subtracting nc-2e in step 3) until the remaining electron density is close to less than the preset value.

[0016] As a further optimized technical solution, the step (1) of building the molecular structure specifically includes:

[0017] First, GaussView was used to build the initial structure of the molecule, and the total number of atoms in the system was determined to be k. The atoms were labeled with numbers 1-k to obtain their initial molecular coordinates. The b3lyp / 6-31G* method basis set was then used to optimize the initial structure of the molecule, which served as the basic unit for subsequent steps.

[0018] As a further optimized technical solution, the molecular orbital MO and natural bond orbital NBO analysis in step (2) specifically includes:

[0019] The molecular coordinates of the optimized molecular structure in step (1) are extracted, and MO and NBO analyses are performed on the molecular structure based on the Hatree-Fock equation. The contribution of the core orbitals that are useless for bonding to the density matrix is ​​deducted and used as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis.

[0020] As a further optimized technical solution, in the step (4) of performing bonding analysis on the molecule, in the deduction of 1c-2e and 2c-2e, first prepare the input file AdNDP.in: the number of atoms k, the number of all atomic basis functions queried in the above step (3), and the number of basis functions occupied by each atom are input into the file AdNDP.in, and then run the AdNDP.exe program, which obtains the density matrix information of the system from the MO.log and NBO.log files;

[0021] In the step (4) of performing bonding analysis on the molecule, in the step 2) of subtracting the remaining nc-2e, an input file AdNDP.FR.in for subtracting the remaining nc-2e is prepared, the number of fragments to be subtracted, i.e., the number of nc-2e to be subtracted and the atomic numbers of all the atomic numbers to be subtracted for connecting nc-2e are input, and the AdNDP_FR.exe program is run. The program obtains the remaining density matrix information from the AdNDP_Resid.log and mo.log files.

[0022] As a further optimized technical solution, the step (4) of performing bonding analysis on the molecules further includes:

[0023] 4) Orbital visualization: Use the unix2dos command to convert all orbital visualization files from Unix to DOS format, and open them based on the Molekel.exe software to obtain orbital visualization diagrams. If a specific chemical bond is viewed separately, this chemical bond can be deducted separately.

[0024] The advantages of the present invention are:

[0025] The present invention can simultaneously deduct all m-centered 2-electron (mc-2e) chemical bonds, without having to classify them separately, where m represents the number of central atoms and is less than or equal to the total number of atoms in the system. For example, in B2H6, both 3c-2e bonds can be directly deducted, while other methods can only deduct one 3c-2e bond at a time.

[0026] The present invention can also eliminate the influence of the surrounding atomic environment and analyze a specific chemical bond in a targeted manner, for example, for naphthalene molecules (C 10 H8) We can directly deduct all four 6c-2e and conduct a detailed analysis, while other methods can only deduct one 6c-2e at a time and cannot exclude the influence of other 6c-2e.

[0027] In addition to providing the overall occupancy number of a chemical bond, the present invention can also provide the sub-occupancy number of each atom. BRIEF DESCRIPTION OF THE DRAWINGS

[0028] Figure 1 This is the initial structure of the benzene molecule in the embodiment of the present invention.

[0029] Figure 2 This is a visualization diagram of the orbitals of the benzene molecule minus 2c-2e in the example of the present invention.

[0030] Figure 3 This is a visualization diagram of the orbitals of the benzene molecule minus 6c-2e in the example of the present invention.

[0031] Figure 4 This is the initial structure of the B2H6 molecule in the embodiment of the present invention.

[0032] Figure 5 This is a visualization diagram of the orbitals of the B2H6 molecule minus 2c-2e in the example of the present invention.

[0033] Figure 6 This is a visualization diagram of the orbitals of the B2H6 molecule after deducting 3c-2e in the example of the present invention.

[0034] Figure 7 This is the initial structure of the naphthalene molecule in the embodiment of the present invention.

[0035] Figure 8 This is a visualization diagram of the orbitals of the naphthalene molecule minus 2c-2e in the example of the present invention.

[0036] Figure 9 This is a visualization diagram of the orbitals of the naphthalene molecule minus 6c-2e in the example of the present invention.

[0037] Figure 10 This is a visualization diagram of the orbitals of the naphthalene molecule minus 10c-2e in the example of the present invention. DETAILED DESCRIPTION

[0038] To make the objectives, technical solutions, and advantages of the embodiments of the present invention more clear, the technical solutions in the embodiments of the present invention will be clearly and completely described below in conjunction with the embodiments of the present invention. Obviously, the described embodiments are only part of the embodiments of the present invention, not all of the embodiments. All other embodiments obtained by ordinary technicians in this field based on the embodiments of the present invention without making any creative efforts shall fall within the scope of protection of the present invention.

[0039] The present invention proposes a chemical bonding analysis method based on electron localization, comprising the following steps:

[0040] (1) Building molecular structure: First, GaussView is used to build the initial structure of the molecule, and the total number of atoms in the system is determined to be k. The atoms are marked with numbers 1-k to obtain their initial molecular coordinates; then the b3lyp / 6-31G* method basis set is used to optimize the initial structure of the molecule to obtain the lowest energy and most stable optimized molecular structure, which serves as the basic unit for subsequent steps. GaussView is a graphical user interface program developed specifically for Gaussian users to help create input files and view output results;

[0041] (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: Extract the molecular coordinates of the optimized molecular structure in step (1), perform MO and NBO analysis on the molecular structure based on the Hatree-Fock equation, and deduct the contribution of the core orbitals that are not useful for bonding to the density matrix as preparation files for subsequent AdNDP analysis (MO.log, NBO.log files);

[0042] (3) Obtain the number of basis functions of atoms in the molecule: obtain the number of basis functions of all atoms in the molecule and the number of basis functions occupied by each atom by querying the basis function and Eigenvalues ​​values ​​in the MO.log file;

[0043] (4) Bond analysis of molecules:

[0044] 1) Analyze the electronic bonding of molecules: Analyze the chemical bonds and the number of valence electrons in the molecules;

[0045] 2) Deduction of 1c-2e and 2c-2e: First prepare the input file (AdNDP.in): input the number of atoms k, the number of all atomic basis functions queried in step (3) above, and the number of basis functions occupied by each atom into the file AdNDP.in; then run the AdNDP.exe program. Specifically, the program reads the data from MO.log and NBO.log

[0046] The density matrix information of the system is obtained from the file. The diagonal blocks of the density matrix corresponding to the atoms of 1c-2e and 2c-2e are taken out in sequence to obtain the output file AdNDP_Resid.log after deducting 1c-2e and 2c-2e, the orbital visualization file mo.log, and the file NDP_nbo.log for viewing the occupancy number and residual electron density.

[0047] NDP_nbo.log obtains the AdNDP orbital and the remaining electron density after deducting 1c-2e and 2c-2e. If the remaining electron density is greater than or equal to 2, further analysis of the bonding of the remaining electrons is required. If it is less than 2, the bonding analysis is complete.

[0048] 3) Subtract the remaining nc-2e: where n represents the number of central atoms, n>2 and less than or equal to the total number of atoms in the system, k. After subtracting 1c-2e and 2c-2e, prepare the input file (AdNDP.FR.in) for subtracting the remaining nc-2e based on the output files AdNDP_Resid.log and mo.log in 2). Enter the number of fragments to be subtracted (i.e., the number of nc-2e to be subtracted) and the atomic numbers of all atoms to be subtracted from the connected nc-2e. Run the AdNDP_FR.exe program. Specifically, the program extracts the remaining density matrix information from the AdNDP_Resid.log and mo.log files, sequentially extracts the diagonal blocks of the density matrix corresponding to the atoms in the nc-2e group, and generates the output file AdNDP_Resid.log after subtracting nc-2e, the orbital visualization file mo_FR.log, and the file NDP_nbo.log for viewing the occupancy numbers and the remaining electron density. By checking NDP_nbo.log, we can obtain the AdNDP orbital and the remaining electron density after deducting nc-2e. If the remaining electron density is less than 2, the bonding analysis is complete. If it is greater than or equal to 2, we need to repeat the 3) operation based on the output files AdNDP_Resid.log and mo_FR.log after deducting nc-2e in step 3) until the remaining electron density is close to less than 2.

[0049] 4) Orbital visualization: All orbital visualization files were converted from Unix to DOS format using the unix2dos command and opened using the Molekel.exe software to obtain orbital visualizations. In this invention, if a specific chemical bond is to be isolated, it can be deducted independently of the surrounding atoms.

[0050] The above calculation process can be performed in Linux system.

[0051] The present invention can simultaneously deduct all m-centered 2-electron chemical bonds without having to classify the chemical bonds. For example, in B2H6, both 3c-2e can be directly deducted, while other methods can only deduct one 3c-2e at a time. At the same time, it can eliminate the influence of the surrounding atomic environment and analyze a specific chemical bond in a targeted manner. For example, for the naphthalene molecule (C 10 H8), all four 6c-2e can be directly deducted for specific analysis, while other methods can only deduct one 6c-2e at a time and cannot rule out the influence of other 6c-2e. In addition to giving the overall occupation number of a chemical bond, it can also give the sub-occupancy number of each atom.

[0052] Example 1:

[0053] Taking the bonding analysis of benzene molecule C6H6 as an example, the specific implementation steps are:

[0054] (1) Build the benzene molecular structure: First, use GaussView to build the initial structure of the benzene molecule, and determine that the total number of atoms in the benzene molecule is 12 and mark the atoms with numbers 1-12, such as Figure 1 As shown, the initial molecular coordinates are obtained; then the b3lyp / 6-31G* method basis set is used to optimize the initial molecular structure to obtain the lowest energy and most stable benzene molecular structure, which is used as the basic unit for subsequent steps.

[0055] (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: The molecular coordinates of the benzene molecular structure optimized in step 1 were extracted, as shown in Table 1. MO and NBO analyses were performed on the benzene molecular structure based on the Hatree-Fock equation. The contribution of the inner core orbitals that were not useful for bonding to the density matrix was deducted and used as preparation files for the subsequent AdNDP analysis (MO.log, NBO.log files).

[0056] (3) Obtain the number of atomic basis functions in the benzene molecule: By querying the basis function and Eigenvalues ​​in the MO.log file, it is obtained that the number of basis functions of all atoms in the benzene molecule is 102, the number of basis functions occupied by each C atom is 15, and the number of basis functions occupied by each H atom is 2.

[0057] (4) Bond analysis of benzene molecules:

[0058] 1) Analyze the electronic bonding of the benzene molecule: The benzene molecule has 12 C—C bonds and σ bonds (2c-2e) between C—H bonds; 3 large π bonds (6c-2e), with a total of 30 valence electrons.

[0059] 2) Subtract σ bonds (2c-2e) between carbon and carbon and between carbon and hydrogen: First, prepare the input file (AdNDP.in): Enter the number of atoms (12), the number of all atomic basis functions (102) queried in step (3), and the number of basis functions occupied by each atom (C: 15, H: 2) into the file. Run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, and subtract all σ bonds between carbon and carbon and between carbon and hydrogen. Output the output file AdNDP_Resid.log after subtracting σ bonds, the orbital visualization file mo.log, and the file NDP_nbo.log for viewing the occupancy number and residual electron density. Viewing NDP_nbo.log, we can see 12 AdNDP orbitals with an occupancy number of approximately 2 (1.985-1.987) and a residual electron density of 6.168 after subtracting the 12 2c-2e σ bonds.

[0060] 3) Subtract the large π bonds (6c-2e) on the benzene ring: Prepare the input file (AdNDP.FR.in), enter the atomic numbers (1, 2; 3, 4; 5, 6) between the large π bonds to be deducted, and the number of fragments to be deducted (3). Run the AdNDP_FR.exe program to deduct the large π bonds on the benzene ring, and output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files. Reviewing NDP_nbo_FR.log, we can see that there are three AdNDP orbitals with an occupation number of 2.00 and that the remaining electron density after deducting the three large 6c-2e π bonds is approximately 0, confirming that all bonding in the benzene molecule has been analyzed.

[0061] 4) Orbit visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them based on the Molekel.exe software to obtain the orbit visualization diagram as shown below: Figure 2 , as shown in 3. The initial and optimized results of the C6H6 molecular structure are shown in Table 1. The occupancy numbers of each atom in C6H6 are shown in Table 2. While other methods can only fully deduct 2c-2e, this method can directly deduct all mc-2e simultaneously.

[0062] Table 1: Optimized C6H6 coordinates

[0063] x y z C -0.000000 -1.394331 -0.000000 C 1.207526 -0.697166 -0.000000 C 1.207526 0.697166 -0.000000 C -0.000000 1.394331 0.000000 C -1.207526 0.697166 0.000000 C -1.207526 -0.697166 -0.000000 H -0.000000 -2.478538 -0.000000 H 2.146477 -1.239269 -0.000000 H 2.146477 1.239269 -0.000000 H -0.000000 -2.478538 -0.000000 H -2.146477 1.239269 0.000000 H -2.146477 1.239269 0.000000

[0064] Table 2: Occupancy number of each atom in C6H6

[0065]

[0066]

[0067] Example 2

[0068] Taking the bonding analysis of diborane (B2H6) as an example, the specific implementation steps are:

[0069] (1) Build the molecular structure of diborane (B2H6): First, use GaussView to build the initial structure of the benzene molecule, and determine that the total number of atoms in the B2H6 molecule is 8 and mark the atoms with numbers 1-8, such as Figure 5 As shown, the initial molecular coordinates are obtained; then the b3lyp / 6-31G* method basis set is used to optimize the initial molecular structure to obtain the lowest energy and most stable B2H6 molecular structure, which is used as the basic unit for subsequent steps.

[0070] (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: The molecular coordinates of the B2H6 molecular structure optimized in step (1) are extracted as shown in Table 2. MO and NBO analyses are performed on the B2H6 molecular structure based on the Hatree-Fock equation. The contribution of the inner core orbitals that are not useful for bonding to the density matrix is ​​deducted and used as preparation files for subsequent AdNDP analysis (MO.log, NBO.log files).

[0071] (3) Obtain the number of basis functions of atoms in the B2H6 molecule: By querying the basis function and Eigenvalues ​​in the MO.log file, it is obtained that the number of basis functions of all atoms in the benzene molecule is 42, the number of basis functions occupied by each B atom is 15, and the number of basis functions occupied by each H atom is 2.

[0072] (4) Bond analysis of B2H6 molecules:

[0073] 1) Analyze the bonding of the B2H6 molecule. The B2H6 molecule has four σ bonds (2 centers, 2 electrons) between BHs and a 3-center, 2-electron bond between two BHBs. There are a total of 12 valence electrons.

[0074] 2) Subtract 2c-2e; First, prepare the input file (AdNDP.in): Enter the number of atoms (8), the number of all atomic basis functions (42) queried in step (3), and the number of basis functions occupied by each atom (B: 15, H: 2) into the file. Run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, and subtract all 2c-2e between BH. Output the output file AdNDP_Resid.log after subtracting 2c-2e, the orbital visualization file mo.log, and the file NDP_nbo.log for viewing the occupancy number and residual electron density. Viewing NDP_nbo.log, we can obtain four AdNDP orbitals with an occupancy number of approximately 2.00 (1.993) and a residual electron density of 4.028 after subtracting the four 2c-2e σ bonds.

[0075] 3) Subtract 3c-2e; prepare the input file (AdNDP.FR.in), enter the atomic numbers (1, 8, 4; 1, 8, 7) between the 3c-2e and the desired subtraction fragments (2). Run the AdNDP_FR.exe program to subtract all 3c-2e on B2H6, and output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files. Reviewing NDP_nbo_FR.log, we find two AdNDP orbitals with occupancy numbers approximately 2.00 (1.969-1.999) and a residual electron density of approximately 0 after subtracting the two 3c-2e, confirming that all bonding in the B2H6 molecule has been analyzed.

[0076] 4) Orbit visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them based on the Molekel.exe software to obtain the orbit visualization diagram as shown below: Figure 5 , as shown in 6. The initial and optimized results of the B2H6 molecular structure are shown in Table 3. The occupancy numbers of each atom in B2H6 are shown in Table 4. This method can directly deduct the two 3c-2e between BHB at the same time, while other methods can only deduct them in two steps.

[0077] Table 3: Optimized B2H6 coordinates

[0078] x y z B 0.00000000 0.00000000 -0.71676529 H 0.00000000 0.76886384 -1.59983934 H 0.00000000 -0.76886384 -1.59983934 B 0.00000000 0.00000000 0.71676529 H -0.00000000 -0.76886384 1.59983934 H 0.00000000 0.76886384 1.59983934 H -1.10952273 0.00000000 -0.00000000 H 1.10952273 0.00000000 -0.00000000

[0079] Table 4: Occupancy number of each atom in B2H6

[0080]

[0081]

[0082] Example 3

[0083] Naphthalene (C 10 H8) Bond analysis is taken as an example, and the specific implementation steps are as follows:

[0084] (1) Construction of naphthalene (C 10 H8) Molecular structure: First, use GaussView to build the initial structure of the benzene molecule and determine the C 10 The total number of atoms in the H8 molecule is 18 and the atoms are numbered from 1 to 18, such as Figure 7 As shown, the initial molecular coordinates were obtained; then the b3lyp / 6-31G* method basis set was used to optimize the initial molecular structure to obtain the lowest energy and most stable C 10 The H8 molecular structure serves as the basic unit for subsequent steps.

[0085] (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: For the C optimized in step (1), 10 The molecular coordinates of H8 molecular structure are shown in Table 5. Based on the Hatree-Fock equation, the molecular coordinates of C 10 The H8 molecular structure was subjected to MO and NBO analysis, and the contribution of the inner core orbitals that were not useful for bonding to the density matrix was deducted as preparation files for subsequent AdNDP analysis (MO.log, NBO.log files).

[0086] (3) Get C 10 The number of atomic basis functions in the H8 molecule: By querying the basis function and Eigenvalues ​​in the MO.log file, it is found that the number of all atomic basis functions in the benzene molecule is 166, the number of basis functions occupied by each C atom is 15, and the number of basis functions occupied by each H atom is 2.

[0087] (4) To C 10 Bonding analysis of H8 molecules:

[0088] 1) Analysis of C 10 Bonding of H8 molecules; C 10 The H8 molecule has 19 σ bonds (2c-2e) between CC and CH; 5 large π bonds, namely 4 6c-2e and 1 10c-2e; a total of 48 valence electrons.

[0089] 2) Subtract 2c-2e; First, prepare the input file (AdNDP.in): Input the number of atoms (18), the number of all atomic basis functions (166) queried in step (3), and the number of basis functions occupied by each atom (C: 15, H: 2) into the file. Run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, and subtract all 2c-2e between CC and CH. Output the output file AdNDP_Resid.log after subtracting 2c-2e, the orbital visualization file mo.log, and the file NDP_nbo.log for viewing the occupation number and residual electron density. Viewing NDP_nbo.log, we can find 19 AdNDP orbitals with occupation numbers (1.976-1.988) approximately 2.00, and the residual electron density after subtracting the 19 2c-2e σ bonds is 10.298.

[0090] 3) Subtract 6c-2e; prepare the input file (AdNDP.FR.in), input the atomic numbers (1, 2, 3, 4, 5, 6; 2, 3, 7, 8, 9, 10) between 6c-2e and the number of fragments (4) to be subtracted. Run the AdNDP_FR.exe program to subtract C 10Output files AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log for all 6c-2e on H8. Reviewing NDP_nbo_FR.log reveals four AdNDP orbitals with an occupation number of 2.00 and a residual electron density of 2.298 after deducting the four 6c-2e.

[0091] 4) Subtract 10c-2e; prepare the input file (AdNDP.FR.in), input the atomic number (1, 2, 3, 4, 5, 6, 7, 8, 9, 10) between 10c-2e and the number of fragments (1) to be subtracted. Then run the AdNDP_FR.exe program to subtract C 10 Output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files for all 10c-2e on H8. Check NDP_nbo_FR.log to get an AdNDP orbital with an occupation number of 2.00 and the residual electron density is approximately 0 after deducting one 10c-2e. Determine C 10 All bonding of the H8 molecule has been analyzed.

[0092] 5) Orbit visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them with the Molekel.exe software to obtain the orbit visualization diagram. Figure 8 , 9, 10. C 10 The initial and optimized results of H8 molecular structure are shown in Table 5. 10 The occupancy numbers of each atom in H8 are shown in Table 6. This method can directly deduct the four 6c-2e atoms from the two benzene rings in naphthalene simultaneously for analysis, while other methods can only deduct one 6c-2e atom from each benzene ring at a time, and the adjacent benzene rings will affect it.

[0093] Table 5: Optimized C 10 H8 coordinates

[0094]

[0095]

[0096] Table 6: Occupancy number of each atom in B2H6

[0097]

[0098]

[0099] The present invention can simultaneously deduct m-centered 2-electron chemical bonds, eliminating the need to distinguish between different types of chemical bonds. For example, when deducting 3c-2e, other methods can only deduct one 3c-2e first and then another 3c-2e, while the method proposed by the present invention can deduct all 3c-2e simultaneously.

[0100] The above embodiments are only used to illustrate the technical solutions of the present invention, rather than to limit the same. Although the present invention has been described in detail with reference to the aforementioned embodiments, those skilled in the art should understand that they can still modify the technical solutions described in the aforementioned embodiments, or make equivalent replacements for some of the technical features therein. However, these modifications or replacements do not deviate the essence of the corresponding technical solutions from the spirit and scope of the technical solutions of the various embodiments of the present invention.

Claims

1. A chemical bonding analysis method based on electron localization, characterized by: The steps include: (1) Build and optimize the molecular structure; (2) Molecular orbital (MO) and natural bond orbital (NBO) analysis: deduct the contribution of the core orbitals that are not useful for bonding to the density matrix, and use them as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis; (3) Obtain the number of basis functions of atoms in the molecule: obtain the number of basis functions of all atoms in the molecule and the number of basis functions occupied by each atom by querying the basis function and Eigenvalues ​​in the MO.log file; (4) Bond analysis of molecules, including: 1) Analyze the electronic bonding of molecules: Analyze the chemical bonds and the number of valence electrons in the molecules; 2) Subtract 1c-2e and 2c-2e: Obtain the density matrix information of the system from the MO.log and NBO.log files, take out the diagonal blocks of the density matrix corresponding to the atoms of 1c-2e and 2c-2e in turn, and obtain the output file AdNDP_Resid.log after subtracting 1c-2e and 2c-2e, the orbital visualization file mo.log, and the occupancy number and residual electron density file NDP_nbo.log. Further check NDP_nbo.log to obtain the AdNDP orbital and the remaining electron density after subtracting 1c-2e and 2c-2e. If the remaining electron density is greater than or equal to the preset value, it is necessary to further analyze the bonding of the remaining electrons. If it is less than the preset value, it proves that the bonding analysis is complete. 3) Subtract the remaining nc-2e: where n represents the number of central atoms, n>2 and less than or equal to the total number of atoms in the system k. After subtracting 1c-2e and 2c-2e, based on the output files AdNDP_Resid.log and mo.log in step 2), obtain the remaining density matrix information from the AdNDP_Resid.log and mo.log files. Sequentially extract the diagonal blocks of the density matrix corresponding to the atoms in the nc-2e group. Obtain the output file AdNDP_Resid.log after subtracting nc-2e, the orbital visualization file mo_FR.log, and the occupancy number and residual electron density file NDP_nbo.log. By viewing NDP_nbo.log, you can obtain the AdNDP orbitals and the remaining electron density after subtracting nc-2e. If the remaining electron density is less than the preset value, the bonding analysis is complete. If it is greater than or equal to the preset value, repeat step 3) based on the output files AdNDP_Resid.log and mo_FR.log after subtracting nc-2e in step 3) until the remaining electron density is close to less than the preset value.

2. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: The step (1) of building the molecular structure specifically includes: First, GaussView was used to build the initial structure of the molecule, and the total number of atoms in the system was determined to be k. The atoms were labeled with numbers 1-k to obtain their initial molecular coordinates. The b3lyp / 6-31G* method basis set was then used to optimize the initial structure of the molecule, which served as the basic unit for subsequent steps.

3. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: The molecular orbital MO and natural bond orbital NBO analysis in step (2) specifically includes: The molecular coordinates of the optimized molecular structure in step (1) are extracted, and MO and NBO analyses are performed on the molecular structure based on the Hatree-Fock equation. The contribution of the core orbitals that are useless for bonding to the density matrix is ​​deducted and used as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis.

4. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: In the step (4) of performing bonding analysis on the molecule, in the deduction of 1c-2e and 2c-2e, first prepare the input file AdNDP.in: the number of atoms k, the number of all atomic basis functions queried in the above step (3), and the number of basis functions occupied by each atom are input into the file AdNDP.in, and then run the AdNDP.exe program, which obtains the density matrix information of the system from the MO.log and NBO.log files; In the step (4) of performing bonding analysis on the molecule, in the step 2) of subtracting the remaining nc-2e, an input file AdNDP.FR.in for subtracting the remaining nc-2e is prepared, the number of fragments to be subtracted, i.e., the number of nc-2e to be subtracted and the atomic numbers of all the atomic numbers to be subtracted for connecting nc-2e are input, and the AdNDP_FR.exe program is run. The program obtains the remaining density matrix information from the AdNDP_Resid.log and mo.log files.

5. The method for chemical bonding analysis based on electron localization according to any one of claims 1 to 4, characterized in that: The step (4) of performing bonding analysis on the molecules further comprises: 4) Orbital visualization: Use the unix2dos command to convert all orbital visualization files from Unix to DOS format, and open them based on the Molekel.exe software to obtain orbital visualization diagrams. If a specific chemical bond is viewed separately, this chemical bond can be deducted separately.

6. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: For the bonding analysis of benzene molecules C6H6, the specific implementation steps are: (1) First, GaussView was used to build the initial structure of the benzene molecule. The total number of atoms in the benzene molecule was determined to be 12, and the atoms were labeled with numbers 1-12 to obtain their initial molecular coordinates. The b3lyp / 6-31G* method basis set was then used to optimize the initial molecular structure. (2) Extract the molecular coordinates of the benzene molecular structure optimized in step 1, perform MO and NBO analysis on the benzene molecular structure based on the Hatree-Fock equation, and deduct the contribution of the core orbitals that are not useful for bonding to the density matrix. These files are used as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis. (3) By querying the basis function and Eigenvalues ​​in the MO.log file, we can find that the number of all atomic basis functions in the benzene molecule is 102, the number of basis functions occupied by each C atom is 15, and the number of basis functions occupied by each H atom is 2; (4) Bond analysis of benzene molecules: 1) Analyze the electronic bonding of the benzene molecule: The benzene molecule has 12 C—C bonds and σ bonds 2c-2e between C—H bonds; 3 large π bonds 6c-2e, and a total of 30 valence electrons; 2) Subtract the σ bonds 2c-2e between carbon and carbon and between carbon and hydrogen: First, prepare the input file AdNDP.in: input the number of atoms 12, the number of all atomic basis functions 102 queried in the above step (3), and the number of basis functions occupied by each atom C: 15, H: 2 into the file, run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, subtract all σ bonds between all carbon and carbon and between carbon and hydrogen, output the output file AdNDP_Resid.log after subtracting the σ bonds, the orbital visualization file mo.log, and the file NDP_nbo.log for viewing the occupation number and residual electron density. Viewing NDP_nbo.log, we can obtain 12 AdNDP orbitals with an occupation number of approximately 2 and a residual electron density of 6.168 after subtracting the 12 2c-2e σ bonds; 3) Subtract the large π bond 6c-2e on the benzene ring: Prepare the input file AdNDP.FR.in, enter the atomic numbers 1, 2; 3, 4; 5, 6 between the large π bonds to be deducted, and the number of fragments to be deducted 3, and run the AdNDP_FR.exe program to deduct the large π bonds on the benzene ring. Output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files. Check NDP_nbo_FR.log to obtain three AdNDP orbitals with an occupation number of 2.00 and a residual electron density of approximately 0 after deducting the three large 6c-2e π bonds, confirming that all bonding of the benzene molecule has been analyzed; 4) Orbital visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them based on the Molekel.exe software to obtain the orbital visualization diagram.

7. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: For the bonding analysis of diborane B2H6, the specific implementation steps are: (1) First, GaussView was used to build the initial structure of the benzene molecule. The total number of atoms in the B2H6 molecule was determined to be 8, and the atoms were labeled with numbers 1-8 to obtain their initial molecular coordinates. The b3lyp / 6-31G* method basis set was then used to optimize the initial molecular structure. (2) Extract the molecular coordinates of the B2H6 molecular structure optimized in step (1), perform MO and NBO analysis on the B2H6 molecular structure based on the Hatree-Fock equation, and deduct the contribution of the core orbitals that are useless for bonding to the density matrix. These files are used as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis. (3) By querying the basis function and Eigenvalues ​​in the MO.log file, we can find that the number of all atomic basis functions in the benzene molecule is 42, the number of basis functions occupied by each B atom is 15, and the number of basis functions occupied by each H atom is 2; (4) Bond analysis of B2H6 molecules: 1) Analyze the bonding of the B2H6 molecule. The B2H6 molecule has 4 BH σ bonds with 2 centers and 2 electrons; 2 BHBs with 3 centers and 2 electrons; and a total of 12 valence electrons. 2) Subtract 2c-2e; First, prepare the input file AdNDP.in: input the number of atoms 8, the number of all atomic basis functions queried in step (3) above 42, and the number of basis functions occupied by each atom B: 15, H: 2 into the file, run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, subtract all 2c-2e between BH, output the output file AdNDP_Resid.log after subtracting 2c-2e, the orbital visualization file mo.log, and check the occupation number and residual electron density file NDP_nbo.log. Check NDP_nbo.log to obtain 4 AdNDP orbitals with an occupation number of approximately 2.00 and a residual electron density of 4.028 after subtracting the 4 2c-2e σ bonds; 3) Subtract 3c-2e; prepare the input file AdNDP.FR.in, enter the atomic numbers 1, 8, 4; 1, 8, 7 between the 3c-2e to be subtracted, and the number of fragments to be subtracted 2, and run the AdNDP_FR.exe program to subtract all 3c-2e on B2H6. Output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files. Check NDP_nbo_FR.log to obtain two AdNDP orbitals with an occupation number of approximately 2.00 and a residual electron density of approximately 0 after subtracting the two 3c-2e, confirming that all bonding of the B2H6 molecule has been analyzed; 4) Orbital visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them based on the Molekel.exe software to obtain the orbital visualization diagram.

8. The method for chemical bonding analysis based on electron localization according to claim 1, wherein: For naphthalene C 10 H8 bonding analysis, the specific implementation steps are: (1) First, GaussView was used to build the initial structure of the benzene molecule and determine the C 10 The total number of atoms in the H8 molecule is 18, and the atoms are labeled from 1 to 18 to obtain its initial molecular coordinates. The initial molecular structure is then optimized using the b3lyp / 6-31G* method basis set. (2) For the C optimized in step (1) 10 The molecular coordinates of H8 molecular structure were extracted and the C 10 Perform MO and NBO analysis on the H8 molecular structure, deduct the contribution of the inner core orbitals that are not useful for bonding to the density matrix, and use them as the preparation files MO.log and NBO.log for the subsequent AdNDP analysis; (3) By querying the basis function and Eigenvalues ​​in the MO.log file, we can find that the number of all atomic basis functions in the benzene molecule is 166, the number of basis functions occupied by each C atom is 15, and the number of basis functions occupied by each H atom is 2; (4) To C 10 Bonding analysis of H8 molecules: 1) Analysis of C 10 Bonding of H8 molecules; C 10 The H8 molecule has 19 σ bonds 2c-2e between C—C and C—H; 5 large π bonds, 4 6c-2e and 1 10c-2e; a total of 48 valence electrons; 2) Subtract 2c-2e; First, prepare the input file AdNDP.in: input the number of atoms 18, the number of all atomic basis functions 166 queried in the above step (3), and the number of basis functions occupied by each atom C: 15, H: 2 into the file, run the AdNDP.exe program, take out the diagonal blocks corresponding to each atom of the density matrix in turn, subtract all 2c-2e between CC and CH, output the output file AdNDP_Resid.log after subtracting 2c-2e, the orbital visualization file mo.log, and check the occupation number and residual electron density file NDP_nbo.log. Check NDP_nbo.log to obtain 19 AdNDP orbitals with an occupation number of approximately 2.00 and a residual electron density of 10.298 after subtracting 19 2c-2e σ bonds; 3) Subtract 6c-2e; prepare the input file AdNDP.FR.in, enter the atomic numbers 1, 2, 3, 4, 5, 6; 2, 3, 7, 8, 9, 10 between 6c-2e and the number of fragments to be subtracted 4, and run the AdNDP_FR.exe program to subtract C 10 For all 6c-2e on H8, output AdNDP_Resid_FR.log, mo_FR.log and NDP_nbo_FR.log files. Check NDP_nbo_FR.log to get 4 AdNDP orbitals with occupation number of 2.00 and the residual electron density of 2.298 after deducting 4 6c-2e. 4) Subtract 10c-2e; prepare the input file AdNDP.FR.in, enter the atomic numbers 1, 2, 3, 4, 5, 6, 7, 8, 9, 10 between 10c-2e and the number of fragments to be subtracted, and run the AdNDP_FR.exe program to subtract C 10 Output the AdNDP_Resid_FR.log, mo_FR.log, and NDP_nbo_FR.log files for all 10c-2e on H8. Check NDP_nbo_FR.log to get an AdNDP orbital with an occupation number of 2.00 and a residual electron density of approximately 0 after deducting one 10c-2e. Determine C 10 All bonding of the H8 molecule has been analyzed; 5) Orbital visualization: Use the unix2dos command to convert the mo.log and mo_FR.log files from Unix to DOS format, and open them based on the Molekel.exe software to obtain the orbital visualization diagram.

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