Method for predicting chemical reaction by using orbital coefficient vector projection

Abstract

The invention relates to the technical field of theoretical and computational chemistry, in particular to a method for predicting a chemical reaction by using orbital coefficient vector projection. Through the developed valence layer orbit coefficient vector projection method, coefficient vector projections in the overlapping direction of a plurality of possible valence layer orbits in molecules are calculated, so that activity indexes such as atom vector reaction indexes in different sites and different directions are obtained. By comparing the atom vector reaction indexes of different sites, the activity of the sites can be predicted, namely the possibility that atoms participate in the chemical reaction on the sites. By calculating atom vector reaction indexes, directional charge density and corresponding reaction energy barriers of different sites, the possibility of chemical reaction of a plurality of potential reaction sites in molecules can be quantitatively and directionally predicted, which has potential application value for solving the problems of reaction activity prediction, chemical selectivity control and the like in precise synthesis.

Description

Technical Field

[0001] The invention relates to the technical field of theoretical and computational chemistry, and in particular to a method for predicting chemical reactions by using orbital coefficient vector projection. Background Art

[0002] Under conditions such as light, heating, and the addition of catalysts, chemical reactions can generally be divided into two stages: substrate activation and product conversion. In the substrate activation stage, inert substrates can be activated into highly active species; then, in the product conversion stage, they are converted into products 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, chemical selectivity, and regioselectivity of the reaction in the product conversion stage.

[0003] Chemical reactions are directional, so accurate prediction of reactivity must take into account possible orbital action directions. An ideal activity prediction method should include the electron transfer direction as described in the chemical reaction mechanism, and be able to determine the possible orbital overlap direction. In fact, the type of molecular orbital is closely related to the orbital overlap direction and pattern, for example, π orbitals are usually shoulder-to-shoulder overlap patterns perpendicular to the bond axis.

[0004] However, currently commonly used activity index calculation methods usually do not distinguish between the direction and mode of orbital interaction. Although this can simplify the calculation, it may not be accurate when predicting the activity of atoms in molecules with multiple orbital overlapping directions. Summary of the invention

[0005] In order to solve the problems existing in the prior art, the present invention provides a method for predicting the direction of chemical reactions by using orbital coefficient vector projection. The method provided by the present invention can predict the activity of atoms in molecules with multiple orbital overlapping directions, and further predict the possibility of chemical reactions.

[0006] In order to achieve the above-mentioned object of the invention, the present invention provides the following technical solutions:

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

[0008] The molecular orbitals are obtained based on the results of the time-independent Schrödinger equation output by a quantitative computing program such as Gaussian;

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

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

[0011] According to the linear combination of the valence layer 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection vector of the main group atom in the molecule in the projection direction is obtained by and atomic vector reaction indicators at different sites and directions;

[0012] According to the main group atoms in the projection direction The projection vector on and equations 4 to 7 give the vector activity index

[0013] According to the vector activity index The gradient descent method is used to iteratively solve and obtain the maximum vector activity index Predict 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…Formula 1;

[0015] The molecular orbital expression is shown in Formula 2; Ψ n =∑C i,n ψ i n=1,2…Formula 2;

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

[0017]

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

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

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

[0021] Preferably, for the carbene-type unsaturated main group atoms, the defined projection directions are projection directions distributed within a semicircular region.

[0022] Preferably, for linear unsaturated main group atoms, the defined projection direction is the projection direction covering the circular area.

[0023] The present invention uses the developed valence orbital coefficient vector projection method to calculate the coefficient vector projections of multiple possible valence orbital overlapping directions in the molecule, thereby obtaining activity indicators such as atomic vector reaction indicators at different sites and in different directions. By comparing the atomic vector reaction indicators at different sites, the activity of the site can be predicted, that is, the possibility of an atom participating in a chemical reaction at the site. By calculating the atomic vector reaction indicators, directional charge density, and corresponding reaction energy barriers at different sites, the possibility of chemical reactions at multiple potential reaction sites in a molecule can be quantitatively and directionally predicted, which will have potential application value in solving problems such as reaction activity prediction and chemical selectivity control in precision synthesis. BRIEF DESCRIPTION OF THE DRAWINGS

[0024] Figure 1 A flow chart of the valence orbital coefficient vector projection method provided by the present invention;

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

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

[0027] Figure 4 Prediction of the maximum vector activity index for the valence orbital coefficient vector projection method and atomic vector reaction indicators. DETAILED DESCRIPTION

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

[0029] The molecular orbitals are obtained from the results of the time-independent Schrödinger equation output from a quantitative computing program such as Gaussian;

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

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

[0032] According to the linear combination of the valence layer 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection vector of the main group atom in the molecule in the projection direction is obtained by and atomic vector reaction indicators at different sites and directions;

[0033] According to the main group atoms in the projection direction The projection vector on and equations 4 to 7 give the vector activity index

[0034] According to the vector activity index The gradient descent method is used to iteratively solve and obtain the maximum vector activity index Predict the probability of an atom participating in a chemical reaction at a relevant site.

[0035] The present invention obtains the molecular orbital according to the result of calculating the time-independent Schrödinger equation output by a quantitative calculation program such as Gaussian.

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

[0037] The molecular orbital expression is shown in Formula 2; Ψ n =∑C i,n ψ i n=1,2…Formula 2;

[0038] The present invention obtains a linear combination of valence layer 2px, 2py, and 2pz atomic orbitals based on molecular orbitals.

[0039] As an implementation, the linear combination is a coefficient vector The expansion in the form of the product 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 an implementation method, Figure 1As shown in b, for planar unsaturated main group atoms, the defined projection direction maintains an equal angle, that is, the angle around the bond is ≥90°; for carbene-type unsaturated main group atoms, the defined projection direction is the projection direction distributed in the semicircular area; for linear unsaturated main group atoms, the defined projection direction is the projection direction distributed throughout the circular area.

[0043] According to the linear combination of the valence layer 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection vector of the main group atom in the molecule in the projection direction is obtained by and atomic vector reaction indicators at different sites and directions;

[0044] As an embodiment, the main group atom (denoted as A) In the projection direction The new vector projected onto It is expressed as formula 8;

[0045]

[0046] According to the main group atoms in the projection direction The projection vector on and equations 4 to 7 give the vector activity index

[0047]

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

[0049] According to the vector activity index The gradient descent method is used to iteratively solve and obtain the maximum vector activity index Predict the probability of an atom participating in a chemical reaction at a relevant site.

[0050] When calculating The maximum bond order of a carbon atom in a single direction is defined as 3.

[0051] when When the maximum value is reached or the condition is not met, the iteration stops and the final vector is obtained. It is worth noting that the projection direction There are three initial guesses, corresponding to Figure 1b. When atom A has three neighboring atoms (i.e. B1, B2, B3), the initial projection direction is the normal vector of the plane formed by these three adjacent atoms; when atom A has two adjacent atoms (B1, B2) and are on the same straight line, the initial projection direction is an arbitrary direction perpendicular to this line, where is a random unit vector; when atom A has two adjacent atoms (B1, B2) but are not on the same line, the initial projection direction is the sum of the two vectors from atom A to (B1,B2).

[0052] In the present invention, the present invention can also calculate the coefficient vector projections of multiple possible valence orbital overlapping directions in the molecule through the valence orbital coefficient vector projection method, thereby obtaining activity indicators such as atomic vector reaction indicators at different sites and directions.

[0053] In the present invention, the energy barrier of the reaction is calculated to verify whether the predicted result is correct. 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; if the predicted site is not the active site, the corresponding reaction energy barrier is high and the reaction rate is slow.

[0054] The present invention also includes writing corresponding wave function analysis and visualization programs. Using Python to write programs can effectively improve the efficiency of extracting orbital information from the output files of quantum chemical calculation software (such as Gaussian, etc.), using the valence orbital coefficient vector projection method to calculate vector activity indicators such as vector reaction indicators, and reduce the risk of errors.

[0055] In addition, the present invention will further write and optimize the program using Python language to realize the visualization of characteristic orbitals, graphical display and processing of electronic structure information and directional activity indicators, providing convenience and support for the subsequent construction of large-scale molecular activity databases.

[0056] In the present invention, it also includes building an activity index database of functional molecules such as carbenes and axial chiral pyridoxines. In addition to constructing a large number of molecular structures such as carbenes and axial chiral pyridoxines, the present invention can also integrate published organic molecule data sets such as QM9 to expand the diversity and practicality of the database. In the database, in addition to properties such as π electron distribution and activity indicators, it will also include chemical structure information, physicochemical properties, etc. of the molecule, so as to more comprehensively describe the characteristics of the molecule.

[0057] In summary, the present invention establishes a new strategy for chemical reaction prediction based on the direction of orbital overlap by calculating the atomic vector reaction index, directional charge density and corresponding reaction energy barrier at different sites, uses the valence orbital coefficient vector projection method, and develops the corresponding wave function analysis calculation and visualization program to achieve accurate prediction of different types of chemical reactions of atoms in molecules.

[0058] Figure 1 This is a flow chart of the valence orbital coefficient vector projection method provided by the present invention.

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

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

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

[0062] Example 1

[0063] like Figure 3 As shown, firstly, the three-dimensional structure of the biphenyl molecule is selected and constructed, and 36 structures are obtained by rigid scanning by rotating the dihedral angles C2-C3-C12-C14 every 10°. Then, for each structure, the result of the time-independent Schrödinger equation (Formulas 1 to 3) output by quantitative calculation programs such as Gaussian is used to obtain the molecular orbital composed of the linear combination of the corresponding valence layer 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…Formula 1;

[0065] The molecular orbital expression is shown in Formula 2; Ψ n =∑C i,n ψ i n=1,2…Formula 2;

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

[0067]

[0068] according to Figure 1 The atom type in b and formula 8 are used to calculate the orbital coefficient vector In the projection direction The projection vector on

[0069]

[0070] Then, according to replace the original coefficient C 2px ,C 2py ,C 2pz is the new coefficient C′ 2px ,C′ 2py ,C′ 2pz Then we get the new coefficient matrix C′, and calculate the density matrix by formula 4 Finally, the corresponding π bond order is calculated according to formula 5, and the π bond order change diagram is shown in Figure 5. Figure 3 .

[0071] The calculation of Mayer bond order can be obtained by directly substituting the original coefficient matrix C into the density matrix and Mayer bond order calculation formula of the same form as Equations 4 and 5.

[0072]

[0073] Depend on Figure 3 b It can be seen that the change curve of the π bond order calculated by this method is smoother and has comparable stability to the Mayer bond order. In addition, the absolute value of the π bond order of C3-C12 is obviously more reasonable than the value of the Mayer bond order of C3-C12 minus 1 (negative value). It is worth mentioning that the molecular orbital changes continuously with the dihedral angle scanning, so the bond order should also change continuously. The orbital projection method can capture the π electron component in the molecular orbital, and its change is also continuous and smooth, while the traditional π orbital selection method cannot achieve 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, firstly, the three-dimensional structure of the active intermediate is selected and constructed, and based on the results of the time-independent Schrödinger equation output by quantitative calculation programs such as Gaussian (Formulas 1 to 3), the molecular orbitals composed of the linear combination 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…Formula 1;

[0077] The molecular orbital expression is shown in Formula 2; Ψ n =∑C i,n ψ i n=1,2…Formula 2;

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

[0079]

[0080] according to Figure 1 The atom type in b and formula 8 are used to calculate the orbital coefficient vector In the projection direction The projection vector on

[0081]

[0082] Then, according to replace the original coefficient C 2px ,C 2py ,C 2pz is the new coefficient C′ 2px ,C′ 2py ,C′ 2pz Then we get the new coefficient matrix C′, and use formula 4 to calculate the density matrix Finally, the corresponding bound bond order M′ is calculated according to formula 6-7 AB and vector reaction index in the selected projection direction Finally Figure 4 Comparison of the vectorial reactivity indices of the three active site carbon atoms 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 of the C(α) position, so the most likely reaction site predicted was the C(α) position.

[0083] In order to verify the above argument, the α-addition reaction barrier and the γ-addition reaction barrier were further calculated. The α-addition reaction barrier (14.8 kcal / mol) is lower than the γ-addition reaction barrier (19.9 kcal / mol), which also proves that the possible reaction site is C (α). In addition, the calculated results are consistent with experimental observations, indicating the reliability of this method in predicting the chemical selectivity of the reaction.

[0084]

[0085] Although the above embodiment describes the present invention in detail, it is only a part of the embodiments of the present invention, not all of the embodiments. Other embodiments can be obtained based on this embodiment without creativity, 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 in that: The following steps are involved: The molecular orbitals are obtained from the results of the time-independent Schrödinger equation output from a quantitative computing program such as Gaussian; Based on the molecular orbitals, the linear combination of the valence shell 2px, 2py, and 2pz atomic orbitals is obtained; The projection direction of the main group atoms is defined by the valence shell atomic orbital coefficient vector projection method; According to the linear combination of the valence layer 2px, 2py, and 2pz atomic orbitals, the orbital coefficient vector is calculated in the projection direction. The projection vector of the main group atom in the molecule in the projection direction is obtained by and atomic vector reaction indicators at different sites and directions; According to the main group atoms in the projection direction The projection vector on and equations 4 to 7 give the vector activity index According to the vector activity index The gradient descent method is used to iteratively solve and obtain the maximum vector activity index Predict the likelihood of atoms participating in chemical reactions at relevant sites; The time-independent Schrödinger equation is shown in equation 1; HΨ n =E n Ψ n =1,2...Formula 1; The molecular orbital expression is shown in Formula 2; Ψ n =∑C i，n ψ i n=1,2...Formula 2; The linear combination of the valence layer 2px, 2py, and 2pz atomic orbitals is shown in Formula 3; In formulas 4 to 7, is the density matrix corresponding to the changed coefficient matrix; M′ AB is the constrained Mayer bond order of atom A and all its neighboring atoms; is the vector activity index of atom A; P′ AB is the constrained π-bond order of atom A and all its neighboring atoms.

2. The method according to claim 1, characterized in that The linear combination is the coefficient vector (C 2px , C 2py , C 2pz ) is expanded in the form of the product of the corresponding atomic orbital matrix.

3. The method according to claim 1, characterized in that For planar unsaturated main group atoms, the projection directions are defined to maintain equal angles, i.e., angles ≥ 90° around the bond.

4. The method according to claim 1, characterized in that For carbene-type unsaturated main group atoms, the defined projection direction is the projection direction distributed within the semicircular area.

5. The method according to claim 1, characterized in that For linear unsaturated main group atoms, the projection direction is defined as the projection direction over the circular area.

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