CN112466406A - Method for predicting reactivity and carcinogenicity of cyclic organic compounds by quantum chemical calculation - Google Patents
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- 206010007269 Carcinogenicity Diseases 0.000 title claims abstract description 32
- 230000007670 carcinogenicity Effects 0.000 title claims abstract description 32
- 231100000260 carcinogenicity Toxicity 0.000 title claims abstract description 32
- 238000000034 method Methods 0.000 title claims abstract description 27
- 230000009257 reactivity Effects 0.000 title claims abstract description 19
- -1 cyclic organic compounds Chemical class 0.000 title claims abstract description 14
- 238000003077 quantum chemistry computational method Methods 0.000 title claims abstract description 8
- 230000005428 wave function Effects 0.000 claims abstract description 14
- 239000000126 substance Substances 0.000 claims abstract description 13
- 238000003775 Density Functional Theory Methods 0.000 claims abstract description 8
- 150000001923 cyclic compounds Chemical class 0.000 claims description 18
- 238000004364 calculation method Methods 0.000 claims description 13
- 238000004057 DFT-B3LYP calculation Methods 0.000 claims description 8
- 241000283283 Orcinus orca Species 0.000 claims description 8
- 238000007350 electrophilic reaction Methods 0.000 claims description 7
- 230000000269 nucleophilic effect Effects 0.000 claims description 7
- 238000007344 nucleophilic reaction Methods 0.000 claims description 7
- 125000004122 cyclic group Chemical group 0.000 claims description 5
- 230000009977 dual effect Effects 0.000 claims description 4
- 238000004519 manufacturing process Methods 0.000 claims description 4
- 238000007348 radical reaction Methods 0.000 claims description 4
- 238000000324 molecular mechanic Methods 0.000 claims description 3
- 230000007935 neutral effect Effects 0.000 claims description 3
- 238000005457 optimization Methods 0.000 claims description 3
- 231100000820 toxicity test Toxicity 0.000 claims description 3
- 238000001311 chemical methods and process Methods 0.000 claims description 2
- 238000002474 experimental method Methods 0.000 claims description 2
- 150000003254 radicals Chemical class 0.000 claims description 2
- 230000006870 function Effects 0.000 abstract description 18
- 230000001988 toxicity Effects 0.000 abstract description 5
- 231100000419 toxicity Toxicity 0.000 abstract description 5
- 238000004458 analytical method Methods 0.000 abstract description 4
- 150000002894 organic compounds Chemical class 0.000 abstract description 4
- 150000001875 compounds Chemical class 0.000 abstract 2
- 231100000206 health hazard Toxicity 0.000 abstract 1
- RYYVLZVUVIJVGH-UHFFFAOYSA-N caffeine Chemical compound CN1C(=O)N(C)C(=O)C2=C1N=CN2C RYYVLZVUVIJVGH-UHFFFAOYSA-N 0.000 description 4
- 239000005416 organic matter Substances 0.000 description 3
- FMMWHPNWAFZXNH-UHFFFAOYSA-N Benz[a]pyrene Chemical compound C1=C2C3=CC=CC=C3C=C(C=C3)C2=C2C3=CC=CC2=C1 FMMWHPNWAFZXNH-UHFFFAOYSA-N 0.000 description 2
- LPHGQDQBBGAPDZ-UHFFFAOYSA-N Isocaffeine Natural products CN1C(=O)N(C)C(=O)C2=C1N(C)C=N2 LPHGQDQBBGAPDZ-UHFFFAOYSA-N 0.000 description 2
- 238000007259 addition reaction Methods 0.000 description 2
- HJJPJSXJAXAIPN-UHFFFAOYSA-N arecoline Chemical compound COC(=O)C1=CCCN(C)C1 HJJPJSXJAXAIPN-UHFFFAOYSA-N 0.000 description 2
- 230000009286 beneficial effect Effects 0.000 description 2
- HFACYLZERDEVSX-UHFFFAOYSA-N benzidine Chemical compound C1=CC(N)=CC=C1C1=CC=C(N)C=C1 HFACYLZERDEVSX-UHFFFAOYSA-N 0.000 description 2
- 229960001948 caffeine Drugs 0.000 description 2
- VJEONQKOZGKCAK-UHFFFAOYSA-N caffeine Natural products CN1C(=O)N(C)C(=O)C2=C1C=CN2C VJEONQKOZGKCAK-UHFFFAOYSA-N 0.000 description 2
- 230000000711 cancerogenic effect Effects 0.000 description 2
- 231100000315 carcinogenic Toxicity 0.000 description 2
- 238000010586 diagram Methods 0.000 description 2
- 238000009826 distribution Methods 0.000 description 2
- ZMMJGEGLRURXTF-UHFFFAOYSA-N ethidium bromide Chemical compound [Br-].C12=CC(N)=CC=C2C2=CC=C(N)C=C2[N+](CC)=C1C1=CC=CC=C1 ZMMJGEGLRURXTF-UHFFFAOYSA-N 0.000 description 2
- 229960005542 ethidium bromide Drugs 0.000 description 2
- 238000011156 evaluation Methods 0.000 description 2
- 238000011160 research Methods 0.000 description 2
- 238000012502 risk assessment Methods 0.000 description 2
- ZRCMNWRTDNPVFL-UHFFFAOYSA-N 8-hydroxy-9-methoxy-6-nitronaphtho[2,1-g][1,3]benzodioxole-5-carboxylic acid Chemical compound C1=C2OCOC2=C2C3=CC=C(OC)C(O)=C3C=C([N+]([O-])=O)C2=C1C(O)=O ZRCMNWRTDNPVFL-UHFFFAOYSA-N 0.000 description 1
- 208000005623 Carcinogenesis Diseases 0.000 description 1
- 206010064571 Gene mutation Diseases 0.000 description 1
- 206010028980 Neoplasm Diseases 0.000 description 1
- BBFQZRXNYIEMAW-UHFFFAOYSA-N aristolochic acid I Chemical compound C1=C([N+]([O-])=O)C2=C(C(O)=O)C=C3OCOC3=C2C2=C1C(OC)=CC=C2 BBFQZRXNYIEMAW-UHFFFAOYSA-N 0.000 description 1
- 201000011510 cancer Diseases 0.000 description 1
- 230000036952 cancer formation Effects 0.000 description 1
- 231100000504 carcinogenesis Toxicity 0.000 description 1
- 238000012512 characterization method Methods 0.000 description 1
- 238000006243 chemical reaction Methods 0.000 description 1
- 238000011161 development Methods 0.000 description 1
- 231100000673 dose–response relationship Toxicity 0.000 description 1
- 239000003651 drinking water Substances 0.000 description 1
- 235000020188 drinking water Nutrition 0.000 description 1
- 230000000694 effects Effects 0.000 description 1
- 230000007613 environmental effect Effects 0.000 description 1
- 231100000727 exposure assessment Toxicity 0.000 description 1
- 231100001267 hazard identification Toxicity 0.000 description 1
- 238000011835 investigation Methods 0.000 description 1
- 125000005575 polycyclic aromatic hydrocarbon group Chemical group 0.000 description 1
- 125000003367 polycyclic group Chemical group 0.000 description 1
- 238000011002 quantification Methods 0.000 description 1
- 231100000048 toxicity data Toxicity 0.000 description 1
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Abstract
The invention discloses a method for predicting the reactivity and carcinogenicity of a cyclic organic compound by quantum chemical calculation, which comprises the steps of firstly optimizing the energy and structure of various structures according to the molecular structures of several organic compounds in an IARC database, calculating the energy and wave functions of different electronic states on the basis, and establishing the quantitative index prediction of the reactivity and the carcinogenicity prediction of the cyclic organic compound by comparing the obtained parameters. The method is based on wave function analysis of a Concept Density Functional Theory (CDFT), and 5 optimal descriptors are screened out by calculating quantum chemical parameters such as a global index, a real space function, an atomic index and the like of a compound as prediction descriptors and combining an IARC database for classification. The model has definite application domain and good robustness and prediction capability. The prediction method can accurately and efficiently predict the toxicity and carcinogenicity of the compound, and provides an effective method for evaluating the health hazard of the organic compound.
Description
Technical Field
The invention relates to a method for predicting cyclic organic compounds, in particular to a method for predicting reactivity and carcinogenicity of cyclic organic compounds by quantum chemistry calculation.
Background
With the increasing progress of global development and the production and application of a large amount of chemicals, the kinds and amounts of chemicals discharged to the environment and food and drinking water are increasing, and safety evaluation and environmental evaluation of chemicals are becoming more and more important. Among them, the most important having the greatest impact on life and health are cyclic compounds and easily formed oxidized or nitrated polycyclic aromatic hydrocarbon derivatives, which tend to have greater toxicity and carcinogenicity. Therefore, the method has important theoretical and practical significance for risk assessment, management and control, life application and the like of dangerous substances by acquiring dangerous properties of cyclic organic substances and derivatives thereof, such as toxicity, DNA base binding, carcinogenicity and the like. The traditional toxicity risk assessment comprises the following four steps: hazard identification, dose-response assessment, exposure assessment, and risk characterization. However, in actual research analysis, these data are acquired experimentally, and the workload is enormous in the face of the large number of organic compounds that are already present and are about to be put into use. This results in inadequate measured toxicity data and inconsistent toxicity test receptors, which are not effective in evaluating toxicity and carcinogenicity.
Disclosure of Invention
The invention aims to provide a method for predicting the reactivity and the carcinogenicity of a cyclic organic compound by quantum chemical calculation, which determines the optimal prediction index parameters of the reactivity and the carcinogenicity of the cyclic compound by quantum chemical calculation and wave function analysis. The problems set forth in the background art described above can be solved by quantitative structure-reactivity-related studies of cyclic compounds and predicting their carcinogenicity.
In order to achieve the purpose, the invention provides the following technical scheme:
the method for predicting the reactivity and carcinogenicity of the cyclic organic compounds by quantum chemistry calculation comprises the following steps:
step 1: obtaining the data that the carcinogenicity of 6 cyclic organic matters is negative or positive through related toxicity tests or the existing database and literature;
step 2: constructing the molecular structure of the cyclic compound by using ChemDraw chemical software, and performing structure optimization on the cyclic compound by using a B3LYP method of not less than DFT and 6-311G basis group by using quantum chemical software Gaussian or ORCA;
and step 3: taking the optimized structure file, respectively manufacturing quantitative software Gaussian or ORCA input files corresponding to different charged states for neutral N, molecules with 1 electron N +1 and 3 states of losing one electron N-1;
and 4, step 4: calculating single-point energy of molecules at a calculation level not lower than B3LYP/6-311G to obtain quantum chemical parameters and corresponding wfn file containing wave function information;
and 5: by utilizing a CDFT module of wave function analysis software Multiwfn, various CDFT indexes are obtained by reading energy information and wave function information in wfn files and calculating Hirshfeld charges;
step 6: further calculating the FOWEL function isosurface of molecules in different charged states by a Fukui function calculation module of Multiwfn, and deriving corresponding isosurface maps of electrophilic reaction, nucleophilic reaction, free radical reaction and double descriptors;
and 7: through investigating the correlation between different carcinogenicity values and CDFT indexes and different descriptors, the optimal prediction index parameters of the reactivity and the carcinogenicity of the cyclic compound are determined and used for predicting the related reactivity and the carcinogenicity of the same type of organic matters which are not determined through experiments.
Further, in the step 2, a molecular mechanics method is adopted, the established geometric configuration is preliminarily optimized under an MM2 force field, or the structure is directly optimized through a semi-empirical PM6 quantum chemistry method, so that a stable configuration with the lowest energy is obtained.
Further, step 3, an optimized molecular structure is taken, an input file of quantum chemical software Gaussian or ORCA is constructed, and the structure of the cyclic compound is optimized by a B3LYP method not lower than DFT and 6-311G-base group, so that quantum chemical parameters and check point files are obtained.
Further, the CDFT index in step 5 includes a global index, a real space function, an atomic index, a fujing function, a dual descriptor, a relative electrophilic index, and a relative nucleophilic index.
Compared with the prior art, the invention has the beneficial effects that:
1) the method realizes the prediction of two aspects of reactivity and carcinogenicity of the cyclic compound, is also applicable to other organic compounds, and is more beneficial to popularization and application.
2) By applying quantum chemical calculation and wave function analysis and by considering the quantum chemical parameters such as the global index, the wave function and the Fujing function as prediction descriptors, the optimal prediction index is established, the prediction accuracy is improved, and the prediction capability is improved.
3) By inspecting the size distribution of the Fullwell function of each atom in the cyclic organic matter, the corresponding reactivity is predicted, and the electrophilic reaction, the nucleophilic reaction and the nucleophilic radical reaction of the cyclic organic matter and DNA base are more intuitively and clearly predicted through the coverage degree of the isosurface of the Fullwell function.
4) According to the real space function defined by the density functional theory, the characteristic values of the double descriptors simultaneously display the electrophilic reaction sites and the nucleophilic reaction sites, and different welfare function characteristic values do not need to be considered respectively. By deriving and directly examining the isosurface map of the dual descriptors, the addition reaction of the circular organic matter and DNA base and the gene mutation carcinogenesis caused by the addition reaction can be correctly predicted.
Drawings
FIG. 1 is an iso-surface diagram of the active site of electrophilic or nucleophilic reactions upon covalent addition of 6 cyclic compounds (benzopyrene A-B, benzidine C-D, ethidium bromide E-F, arecolin G-H, aristolochic acid I-J, caffeine K-L) to DNA bases for use in the present invention;
FIG. 2 is a two-descriptor iso-surface diagram of the covalent addition of 6 cyclic compounds (benzopyrene A, benzidine B, ethidium bromide C, arecolin D, aristolochic acid E, caffeine F) used in the present invention to DNA bases.
Detailed Description
The technical solutions in the embodiments of the present invention will be clearly and completely described below with reference to the drawings in the embodiments of the present invention, and it is obvious that the described embodiments are only a part of the embodiments of the present invention, and not all of the embodiments. All other embodiments, which can be derived by a person skilled in the art from the embodiments given herein without making any creative effort, shall fall within the protection scope of the present invention.
The method for predicting the reactivity and carcinogenicity of the cyclic organic compounds by quantum chemistry calculation comprises the following steps:
step 1: selecting 6 cyclic compounds with different structures as investigation objects, and modeling various molecules through ChemDraw or online modeling software;
step 2: the established geometric configuration is preliminarily optimized under an MM2 force field by adopting a molecular mechanics method, or the structure is directly optimized by a semi-empirical PM6 quantum chemical method so as to obtain a stable configuration with the lowest energy;
and step 3: taking the optimized molecular structure, constructing an input file of quantum chemical software Gaussian or ORCA, and performing structural optimization on the cyclic compound by using a B3LYP method not lower than DFT and 6-311G basis group to obtain quantum chemical parameters and check point files;
and 4, step 4: taking the optimized structure file, and respectively manufacturing input files of quantization software Gaussian or ORCA (object oriented language) corresponding to different charged states aiming at neutral N, molecules with 1 electron N +1 and 3 states of losing one electron N-1;
and 5: calculating single-point energy of molecules in different charged states under the calculation level not lower than B3LYP/6-311G to obtain quantum chemical parameters and corresponding wfn file containing wave function information;
step 6: by utilizing a CDFT module of wave function analysis software Multiwfn, obtaining quantitative indexes such as a global index, a real space function, an atomic index, a welfare function, a double descriptor, a relative electrophilic index, a relative nucleophilic index and the like by reading energy information and wave function information in wfn files and calculating Hirshfeld charges;
and 7: further, by means of a Fukui function calculation module of Multiwfn, the well function isosurface of the molecules in different charged states is calculated, and corresponding electrophilic, nucleophilic, radical reaction and double-descriptor isosurface maps are derived.
The various output quantities of the CDFT of different cyclic organic compounds are compared with the carcinogenicity reported by the International agency for research on cancer (IARC), and the prediction results are scored. Due to the fact that the actual situation is complex, the score is adjusted according to the reasonable degree of the prediction result. Table 1 gives the partial CDFT parameters and the score for the predicted carcinogenicity for 6 cyclic compounds of different carcinogenic degrees. As can be seen from table 1, the CDFT parameters obtained by partial calculation have a large correlation with the carcinogenicity of the literature sources, especially the polycyclic compounds have the highest hardness and nucleophilic index scores and the moderate softness and electrophilic index scores, which indicates that the first two descriptors can be used as two indicators for predicting carcinogenicity.
TABLE 1 comparison and scoring of CDFT quantification parameters and carcinogenicity prediction results for cyclic compounds of different carcinogenic degrees
The unit of the CDFT index is eV, except for softness.bThe scores (good, medium and bad) are adjusted according to the reasonable degree of the prediction result.
A more intuitive and convenient way to look at the higher scoring descriptors in (8) is to derive and observe their iso-surface maps. By means of a Fukui function calculation module of Multiwfn, the well function isosurface of molecules with different charge states is calculated, and corresponding electrophilic and nucleophilic reactions (figure 1) and isosurface maps of double descriptors (figure 2) are derived, wherein the green isosurface in figure 1 represents a high-activity reaction site, and consistent with the literature report, nucleophilic and electrophilic reaction sites are simultaneously displayed in a double-descriptor isosurface mode in figure 2 without the need of respectively inspecting the distribution states of 2 well functions, so that the method is more convenient. By calculating important concepts in the conceptual density functional theory framework, the well function and the dual descriptors, the sites where the circular organics react with DNA bases can be predicted.
The above description is only for the preferred embodiment of the present invention, but the scope of the present invention is not limited thereto, and any person skilled in the art should be able to cover the technical solutions and the inventive concepts of the present invention within the technical scope of the present invention.
Claims (4)
1. The method for predicting the reactivity and carcinogenicity of the cyclic organic compounds by quantum chemical calculation is characterized by comprising the following steps of:
step 1: obtaining the data that the carcinogenicity of 6 cyclic organic matters is negative or positive through related toxicity tests or the existing database and literature;
step 2: constructing the molecular structure of the cyclic compound by using ChemDraw chemical software, and performing structure optimization on the cyclic compound by using a B3LYP method of not less than DFT and 6-311G basis group by using quantum chemical software Gaussian or ORCA;
and step 3: taking the optimized structure file, respectively manufacturing quantitative software Gaussian or ORCA input files corresponding to different charged states for neutral N, molecules with 1 electron N +1 and 3 states of losing one electron N-1;
and 4, step 4: calculating single-point energy of molecules at a calculation level not lower than B3LYP/6-311G to obtain quantum chemical parameters and corresponding wfn file containing wave function information;
and 5: by utilizing a CDFT module of wave function analysis software Multiwfn, various CDFT indexes are obtained by reading energy information and wave function information in wfn files and calculating Hirshfeld charges;
step 6: further calculating the FOWEL function isosurface of molecules in different charged states by a Fukui function calculation module of Multiwfn, and deriving corresponding isosurface maps of electrophilic reaction, nucleophilic reaction, free radical reaction and double descriptors;
and 7: through investigating the correlation between different carcinogenicity values and CDFT indexes and different descriptors, the optimal prediction index parameters of the reactivity and the carcinogenicity of the cyclic compound are determined and used for predicting the related reactivity and the carcinogenicity of the same type of organic matters which are not determined through experiments.
2. The method for predicting the reactivity and carcinogenicity of cyclic organic compounds through quantum chemistry calculation as claimed in claim 1, wherein in the step 2, a molecular mechanics method is adopted, and the established geometric configuration is preliminarily optimized under an MM2 force field, or the structure is directly optimized through a semi-empirical PM6 quantum chemistry method, so that a stable configuration with the lowest energy is obtained.
3. The method for predicting the reactivity and carcinogenicity of cyclic organic compounds by quantum chemistry calculation according to claim 1, wherein the optimized molecular structure is taken in step 3, an input file of quantum chemistry software Gaussian or ORCA is constructed, and the cyclic compound is structurally optimized by a B3LYP method not lower than DFT and a 6-311G basis group to obtain quantum chemistry parameters and a check point file.
4. The method for predicting reactivity and carcinogenicity of cyclic organic compounds by quantum chemical calculation according to claim 1, wherein the CDFT index in step 5 comprises a global index, a real space function, an atomic index, a foell function, a dual descriptor, a relative electrophilic index and a relative nucleophilic index.
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| CN104995625A (en) * | 2012-12-18 | 2015-10-21 | 弗·哈夫曼-拉罗切有限公司 | Prediction of molecular bioactivation |
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