A method for predicting chemical reactions using orbital coefficient vector projection

Abstract

The present application relates to the theoretical and computational chemistry technical field, specifically relates to a kind of method for predicting chemical reaction using orbital coefficient vector projection.The present application obtains different site, different direction atomic vector reaction index and other activity index by the valence orbital coefficient vector projection method developed, the coefficient vector projection in the multiple possible valence orbital overlap direction in molecule is calculated, so that different site, different direction atomic vector reaction index is obtained.By comparing the atomic vector reaction index of different sites, the activity of site can be predicted, i.e.the possibility of atom participating in chemical reaction at the site.By calculating the atomic vector reaction index of different sites, directional charge density and corresponding reaction energy barrier, the possibility of multiple potential reaction sites in molecule to occur chemical reaction can be quantitatively and directionally predicted, which will have potential application value for solving the problems such as activity prediction and chemical selectivity control of reaction in precise synthesis.

Description

Technical Field

[0001] This invention relates to the fields of theoretical and computational chemistry, and more specifically to a method for predicting chemical reactions using orbital coefficient vector projection. Background Technology

[0002] Under conditions such as light, heat, and the addition of catalysts, chemical reactions can generally be divided into two stages: substrate activation and product transformation. In the substrate activation stage, inert substrates can be activated into highly reactive species; subsequently, in the product transformation stage, the substrate is converted into a product through coupling or addition. Theoretical calculations can explore new activation mechanisms in the substrate activation stage, and can also explain or even predict the stereoselectivity, chemoselectivity, and regioselectivity of the reaction in the product transformation stage.

[0003] Chemical reactions are directional; therefore, accurate prediction of reactivity must consider the possible directions of orbital interactions. An ideal reactivity prediction method should include the direction of electron transfer, as described in chemical reaction mechanisms, and be able to determine possible orbital overlap directions. In fact, the type of molecular orbital and the direction and pattern of orbital overlap are closely related to the orbital type; for example, π orbitals typically exhibit a side-by-side overlap pattern perpendicular to the bond axis.

[0004] However, commonly used methods for calculating activity indices typically do not distinguish between the direction and mode of orbital interactions. While this simplifies the calculation, it may be inaccurate when predicting the activity of atoms in molecules with multiple orbital overlap directions. Summary of the Invention

[0005] To address the problems existing in the prior art, this invention provides a method for predicting the direction of chemical reactions using orbital coefficient vector projection. The method provided by this invention can predict the activity of atoms in a molecule with multiple overlapping orbital directions, thereby predicting the likelihood of a chemical reaction.

[0006] To achieve the above-mentioned objectives, the present invention provides the following technical solution:

[0007] This invention provides a method for predicting the direction of a chemical reaction using orbital coefficient vector projection, comprising the following steps:

[0008] Based on the results of calculating the time-independent Schrödinger equation from the output of the Gaussian quantization program, the molecular orbitals were obtained.

[0009] Based on molecular orbitals, a linear combination of valence shell 2px, 2py, and 2pz atomic orbitals was obtained;

[0010] The projection direction of main group atoms is defined using the valence shell atomic orbital coefficient vector projection method;

[0011] Based on the linear combination of valence shell 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection onto the surface yields the projection vectors of the main group atoms in the molecule along the projection direction. And atomic vector reaction indicators at different sites and in different directions;

[0012] Based on the main group atoms in the projection direction By projecting the vector onto the vector and applying equations 4-7, we obtain the vector activity index.

[0013] Based on vector activity index The maximum vector activity index is obtained by iteratively solving using the gradient descent method. Predicting the likelihood of atoms participating in chemical reactions at relevant sites;

[0014] The time-independent Schrödinger equation is shown in Equation 1; HΨ n =E n Ψ n n = 1, 2... Equation 1;

[0015] The expression for the molecular orbital is shown in Equation 2; Ψ n =∑C i,n ψ i n = 1, 2... Equation 2;

[0016] The linear combination of the valence shell 2px, 2py, and 2pz atomic orbitals is shown in Equation 3;

[0017]

[0018] In equations 4 to 7, M′ is the density matrix corresponding to the changed coefficient matrix. AB The constrained Mayer bond order of atom A and all its neighboring atoms; P′ is the vector activity index of atom A; AB Let A be the order of the bounded π bonds between atom A and all its neighboring atoms.

[0019] Preferably, the linear combination is a coefficient vector. The expansion of the product form with the corresponding atomic orbital matrix.

[0020] Preferably, for planar unsaturated main group atoms, the defined projection directions maintain equal angles, i.e., the angle around the bond is ≥90°.

[0021] Preferably, for carbene-type unsaturated main group atoms, the defined projection direction is the projection direction distributed within the semi-circular region.

[0022] Preferably, for linear unsaturated main group atoms, the defined projection direction is the projection direction that covers the circular region.

[0023] This invention utilizes a developed valence shell orbital coefficient vector projection method to calculate the coefficient vector projections along the overlapping directions of multiple possible valence shell orbitals in a molecule, thereby obtaining activity indicators such as atomic vector reaction indices at different sites and in different directions. By comparing the atomic vector reaction indices at different sites, the activity of a site can be predicted, i.e., the probability of an atom participating in a chemical reaction at that site. By calculating the atomic vector reaction indices, directional charge density, and corresponding reaction energy barriers at different sites, the probability of chemical reactions occurring at multiple potential reaction sites in a molecule can be quantitatively and directionally predicted. This has potential application value in solving problems such as reaction activity prediction and chemoselectivity control in precise synthesis. Attached Figure Description

[0024] Figure 1 A flowchart of the valence layer orbit coefficient vector projection method provided by this invention;

[0025] Figure 2 To use projection vectors and Calculate the π bond order (P' AB (b) is for use by Calculate the bound Mayer bond order (M′) AB );

[0026] Figure 3 To determine the (a) bond lengths of different conformations obtained at the B3LYP / 6-31G(d,p) level by rotating the dihedral angle Ф (C2-C3-C12-C14) of the biphenyl molecule. (b) π bond order and Mayer bond order calculated by valence shell orbital coefficient vector projection method and (c) atomic vector reaction index;

[0027] Figure 4 Predicting the maximum vector activity index using the valence layer orbit coefficient vector projection method And atomic vector reaction index. Detailed Implementation

[0028] This invention provides a method for predicting the direction of a chemical reaction using orbital coefficient vector projection, comprising the following steps:

[0029] Based on the results of calculating the time-independent Schrödinger equation from the output of the Gaussian quantization program, the molecular orbitals were obtained.

[0030] Based on molecular orbitals, a linear combination of valence shell 2px, 2py, and 2pz atomic orbitals was obtained;

[0031] The projection direction of main group atoms is defined using the valence shell atomic orbital coefficient vector projection method;

[0032] Based on the linear combination of valence shell 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection onto the surface yields the projection vectors of the main group atoms in the molecule along the projection direction. And atomic vector reaction indicators at different sites and in different directions;

[0033] Based on the main group atoms in the projection direction By projecting the vector onto the vector and applying equations 4-7, we obtain the vector activity index.

[0034] Based on vector activity index The maximum vector activity index is obtained by iteratively solving using the gradient descent method. Predict the likelihood of atoms participating in chemical reactions at relevant sites.

[0035] This invention obtains molecular orbitals based on the results of calculating the time-independent Schrödinger equation from the output of the Gaussian isoquantization calculation program.

[0036] The time-independent Schrödinger equation is shown in Equation 1; HΨ n =E n Ψ n n = 1, 2... Equation 1;

[0037] The expression for the molecular orbital is shown in Equation 2; Ψ n =∑C i,n ψ i n = 1, 2... Equation 2;

[0038] Based on molecular orbitals, this invention obtains a linear combination of valence shell 2px, 2py, and 2pz atomic orbitals.

[0039] In one implementation, the linear combination is a coefficient vector. The expansion of the product form with the corresponding atomic orbital matrix is ​​Equation 3;

[0040]

[0041] The projection direction of unsaturated main group atoms is defined using the valence shell atomic orbital coefficient vector projection method.

[0042] As one implementation method, such as Figure 1As shown in b, for planar unsaturated main group atoms, the defined projection directions maintain equal angles, i.e., the angle around the bond is ≥90°; for carbene unsaturated main group atoms, the defined projection directions are those distributed within a semi-circular region; and for linear unsaturated main group atoms, the defined projection directions are those distributed throughout a circular region.

[0043] Based on the linear combination of valence shell 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection onto the surface yields the projection vectors of the main group atoms in the molecule along the projection direction. And atomic vector reaction indicators at different sites and in different directions;

[0044] As one implementation method, the main group atom (denoted as A) In the projection direction New vector projected upwards Represented by Equation 8;

[0045]

[0046] Based on the main group atoms in the projection direction By projecting the vector onto the vector and applying equations 4-7, we obtain the vector activity index.

[0047]

[0048] In equations 4 to 7, M′ is the density matrix corresponding to the changed coefficient matrix. AB The constrained Mayer bond order of atom A and all its neighboring atoms; P′ is the vector activity index of atom A; AB Let A be the order of the bounded π bonds between atom A and all its neighboring atoms.

[0049] Based on vector activity index The maximum vector activity index is obtained by iteratively solving using the gradient descent method. Predict the likelihood of atoms participating in chemical reactions at relevant sites.

[0050] When calculating At that time, the maximum bond order of a carbon atom in a single direction is defined as 3.

[0051] when The iteration stops when the maximum value is reached or the condition is no longer met, at which point the final vector is obtained. It is worth noting that the projection direction There are three initial guesses, corresponding to Figure 1There are three types of atoms in b. When atom A has three adjacent atoms (i.e., B1, B2, B3), the initial projection direction is... It is the normal vector of the plane formed by these three adjacent atoms; when atom A has two adjacent atoms (B1, B2) and they are on the same straight line, the initial projection direction is... It is any direction perpendicular to this line, where is a random unit vector; when atom A has two adjacent atoms (B1, B2) but not on the same straight line, the initial projection direction is... It is the sum of two vectors from atom A to (B1, B2).

[0052] In this invention, the coefficient vector projection of multiple possible valence orbitals in the molecule can be calculated by using the valence orbital coefficient vector projection method, thereby obtaining activity indicators such as atomic vector reaction indicators at different sites and in different directions.

[0053] In this invention, the accuracy of the prediction is also verified by calculating the energy barrier of the reaction. If the predicted active site is indeed the site where the reaction occurs, the corresponding reaction energy barrier is low and the reaction rate is high; conversely, if the predicted site is not an active site, the corresponding reaction energy barrier is high and the reaction rate is slow.

[0054] This invention also includes the development of corresponding wavefunction analysis and visualization programs. Using Python to write these programs can effectively improve the efficiency of extracting orbital information from output files of quantum chemistry calculation software (such as Gaussian), calculating vector activity indices such as vector reaction indices using the valence layer orbital coefficient vector projection method, and reduce the risk of errors.

[0055] In addition, this invention will use Python to further write and optimize programs to achieve the visualization and processing of characteristic orbitals, electronic structure information, and directional activity indicators, providing convenience and support for the subsequent construction of large molecular activity databases.

[0056] This invention also includes building a database of activity indicators for functional molecules such as carbene and axially chiral pyridoxines. In addition to constructing a large number of molecular structures for carbene and axially chiral pyridoxines, this invention can also integrate published organic molecule datasets such as QM9 to expand the diversity and practicality of the database. The database will include not only properties such as π-electron distribution and activity indicators, but also information on the chemical structure and physicochemical properties of molecules to provide a more comprehensive description of molecular characteristics.

[0057] In summary, this invention establishes a novel strategy for predicting chemical reactions based on orbital overlap direction by calculating atomic vector reaction indices, directional charge densities, and corresponding reaction energy barriers at different sites. Using the valence shell orbital coefficient vector projection method, a corresponding wavefunction analysis, calculation, and visualization program is developed to achieve accurate prediction of different types of chemical reactions of atoms in molecules.

[0058] Figure 1 The flowchart of the valence layer orbit coefficient vector projection method provided by the present invention is shown.

[0059] Figure 2 (a) is to use the projection vector and Calculate the π bond order (P' AB (b) is for use by Calculate the bound Mayer bond order (M′) AB ), where vector and They are vectors. and In their respective projection directions (such as the projection onto the plane normal vector direction, which is always perpendicular to the existing bond).

[0060] Figure 3 To determine the (a) bond lengths of different conformations obtained at the B3LYP / 6-31G(d,p) level by rotating the dihedral angle Ф (C2-C3-C12-C14) of the biphenyl molecule. (b) π-bond order and Mayer bond order calculated by the valence layer orbital coefficient vector projection method. Scan Figure 4 The atomic vector reaction index is predicted by the valence shell orbital coefficient vector projection method, and the maximum vector activity index is obtained by comparison.

[0061] The technical solutions provided by the present invention will be described in detail below with reference to the embodiments, but they should not be construed as limiting the scope of protection of the present invention.

[0062] Example 1

[0063] like Figure 3 As shown, the three-dimensional structure of the biphenyl molecule was first selected and constructed. Then, 36 structures were obtained by rigidly scanning at 10° intervals of dihedral angle C2-C3-C12-C14. For each structure, the time-independent Schrödinger equation (Equations 1-3) output by the Gaussian isoquantization calculation program was used to calculate the molecular orbitals composed of linear combinations of the corresponding valence shell 2px, 2py, and 2pz atomic orbitals.

[0064] The time-independent Schrödinger equation is shown in Equation 1; HΨ n =En Ψ n n = 1, 2... Equation 1;

[0065] The expression for the molecular orbital is shown in Equation 2; Ψ n =∑C i,n ψ i n = 1, 2... Equation 2;

[0066] The linear combination of the valence shell 2px, 2py, and 2pz atomic orbitals is shown in Equation 3;

[0067]

[0068] according to Figure 1 The atom types in b and the orbital coefficient vector selected in Formula 8 are used to calculate the orbital coefficient vector. In the projection direction Projection vector on

[0069]

[0070] Subsequently, based on the replacement of the original coefficient C 2px C 2py C 2pz For the new coefficient C′ 2px ,C′ 2py ,C′ 2pz This leads to the new coefficient matrix C′, and the density matrix is ​​calculated using Equation 4. Finally, the corresponding π bond order is calculated according to Formula 5, and a π bond order change diagram is plotted. Figure 3 .

[0071] The Mayer bond order can be calculated by substituting the original coefficient matrix C into the density matrix and Mayer bond order calculation formula, which are of the same form as those in Equations 4 and 5.

[0072]

[0073] Depend on Figure 3 As shown in b, the π-bond order curve calculated by this method is smoother and exhibits comparable stability to the Mayer bond order. Furthermore, the absolute value of the π-bond order for C3-C12 is significantly more reasonable than the Mayer bond order of C3-C12 minus 1 (resulting in a negative value). It is worth noting that molecular orbitals change continuously with dihedral scanning, so the bond order should also change continuously. The orbital projection method can capture the π-electron component in molecular orbitals, and its changes are continuous and smooth. Traditional π-orbital selection methods cannot handle the σ-π orbital splitting of non-planar molecules; therefore, the orbital projection method is more reasonable than the π-orbital selection method.

[0074] Example 2

[0075] like Figure 4 As shown, the three-dimensional structure of the active intermediate is first selected and constructed. Based on the results of the time-independent Schrödinger equation (Equations 1-3) output by the Gaussian isoquantization calculation program, the molecular orbitals composed of linear combinations of the corresponding valence layer 2px, 2py, and 2pz atomic orbitals are obtained.

[0076] The time-independent Schrödinger equation is shown in Equation 1; HΨ n =E n Ψ n n = 1, 2... Equation 1;

[0077] The expression for the molecular orbital is shown in Equation 2; Ψ n =∑C i,n ψ i n = 1, 2... Equation 2;

[0078] The linear combination of the valence shell 2px, 2py, and 2pz atomic orbitals is shown in Equation 3;

[0079]

[0080] according to Figure 1 The atom types in b and the orbital coefficient vector selected in Formula 8 are used to calculate the orbital coefficient vector. In the projection direction Projection vector on

[0081]

[0082] Subsequently, based on the replacement of the original coefficient C 2px C 2py C 2pz For the new coefficient C′ 2px ,C′ 2py ,C′ 2pz This yields a new coefficient matrix C′, which is then used to calculate the density matrix using Equation 4. Finally, the corresponding bond order M′ is calculated according to formula 6-7. AB and vector response index in the selected projection direction Finally, as Figure 4 Comparison of vector reaction indices of carbon atoms at three active sites in different directions The maximum vector activity index can be obtained. Figure 4 The three possible reaction sites of the active intermediate (i.e., C(α) / C(β) / C(γ)) were calculated. After comparison, it was found that the maximum reactivity vector was 1.27 at the C(α) site. Therefore, the most likely reaction site was predicted to be the C(α) site.

[0083] To verify the above argument, the energy barriers for α-addition and γ-addition reactions were further calculated. The energy barrier for α-addition (14.8 kcal / mol) was lower than that for γ-addition (19.9 kcal / mol), further confirming that the likely reaction site is the C(α) site. Furthermore, the calculated results are consistent with experimental observations, demonstrating the reliability of this method in predicting the chemoselectivity of the reaction.

[0084]

[0085] Although the above embodiments have provided a detailed description of the present invention, they are only some embodiments of the present invention, and not all embodiments. Other embodiments can be obtained based on these embodiments without creative effort, and these embodiments all fall within the protection scope of the present invention.

Claims

1. A method for predicting the direction of a chemical reaction using orbital coefficient vector projection, characterized by, The method comprises the following steps: According to the results of the calculation of the time-independent Schrödinger equation output by the Gaussian quantification calculation program, molecular orbitals are obtained; According to the molecular orbitals, linear combinations of valence layer 2px, 2py and 2pz atomic orbitals are obtained; The projection direction of the main group atom is defined by using the valence layer atomic orbital coefficient vector projection method; Based on the linear combination of valence shell 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection onto the surface yields the projection vectors of the main group atoms in the molecule along the projection direction. And atomic vector reaction indicators at different sites and in different directions; According to the projection vector of the main group atom on the projection direction and equations 4-7, the vector activity index is obtained According to the vector activity index The maximum vector activity index is obtained by iterative solution using gradient descent method Predict the possibility of atoms at relevant sites participating in chemical reactions; The time-independent Schrödinger equation is seen in equation 1; HΨ n = E n Ψ n n = 1, 2... equation 1; The expression of the molecular orbital is seen in equation 2; Ψ n =∑C i，n ψ i n=1,2... Equation 2; The linear combinations of the valence layer 2px, 2py and 2pz atomic orbitals are shown in formula 3. In formulas 4-7, M' is the density matrix corresponding to the modified coefficient matrix; M AB is the constrained Mayer bond order of atom A with all its neighboring atoms; P' is the vectorial activity index of atom A; AB is the constrained π-bond order of atom A with all its neighboring atoms.

2. The method of claim 1, wherein, The linear combination is a coefficient vector (C 2px , C 2py , C 2pz ) and the expansion is in the form of a product of the respective atomic orbital matrices.

3. The method of claim 1, wherein, For a planar unsaturated main group atom, the defined projection direction maintains an equal angle, i.e. the angle around the bond is ≥ 90°.

4. The method of claim 1, wherein, For a carbene-type unsaturated main group atom, the defined projection direction is a projection direction distributed in a semicircular region.

5. The method of claim 1, wherein, For a linear unsaturated main group atom, the defined projection direction is a projection direction distributed in a circular region.

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