基于元素和化学键的快速计算分子体积和表面积的方法
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摘要
为了快速准确的计算分子的体积和表面积参数,将构成分子的元素和化学键作为贡献单元,基于分子的体积和表面积由相应的元素和化学键的体积和表面积加和得到的思想,提出了估算化合物分子体积和表面积的元素和化学键贡献法。元素视作球体,其体积和表面积由van der Waals半径计算得到,在1412种有机物分子体积和表面积数据的基础上,回归得到化学键对分子体积和表面积的贡献值。结果表明,元素和化学键贡献法计算的分子体积和表面积的平均相对误差分别为2.02%、2.84%,不同化合物类型的平均相对误差均小于5%。与其它分子体积和表面积方法相比较,本方法更简单、快速、准确,应用范围更广。
In order to calculate molecular volume and surface rapidly and accurately,a new method was proposed.Elements and chemical bonds of the molecule were considered contribution unit,the volume and surface of the molecule was obtained by summing the volume and surface of the corresponding elements and chemical bonds.The elements was treated as sphere,its volume and surface was calculated by the van der Waals radii.On the basis of 1412 kinds of credible data,the contributions chemical bonds to the molecular volume and surface were obtained by regression.The result shows that the average relative error of molecular volume and surface are 2.02%,2.84%.The average relative error for different types of compounds are less than 5%.Compared with the other methods for calculating molecular volume and surface,the new method based on elements and chemical bonds is simpler,faster,accurater and the range of application is larger.
In order to calculate molecular volume and surface rapidly and accurately,a new method was proposed.Elements and chemical bonds of the molecule were considered contribution unit,the volume and surface of the molecule was obtained by summing the volume and surface of the corresponding elements and chemical bonds.The elements was treated as sphere,its volume and surface was calculated by the van der Waals radii.On the basis of 1412 kinds of credible data,the contributions chemical bonds to the molecular volume and surface were obtained by regression.The result shows that the average relative error of molecular volume and surface are 2.02%,2.84%.The average relative error for different types of compounds are less than 5%.Compared with the other methods for calculating molecular volume and surface,the new method based on elements and chemical bonds is simpler,faster,accurater and the range of application is larger.
引文
1 Hu Can,Wang Zhenzhen,Xu Wenbin,Xu Huiying.QSPR studies on vapor pressure of poly-and perfluorinated chemicals.Chemical Research and Application,2013,25(1):43-46.
2 Zevatskii Y E,Vlasov E A.Dependence of the protonation constants of organic compounds on their molecular volume. Russian Journal of General Chemistry,2007,77(2):234-240.
3 Zevatskii Y E,Lysova S S.Empirical procedure for the calculation of ionization constants of organic compounds in water from their molecular volume.Russian Journal of General Chemistry,2009, 45(6):825-834.
4 Liu Fufeng,Ji Luo,Dong Xiaoyan.Effects of molecular volume and fractional polar surface area of osmolytes on the thermal stability of chymotrypsin inhibitor 2.Acta Physico-Chimica Sinica, 2010,26(10):2813-2820.
5 Abrams D S,Prausnitz J M.Statistical Thermodynamics of Liquid Mixtures:A new expression for the excess Gibbs energy of partly or completely miscible systems.AIChEJ,1975,21:116-128.
6 Bondi A.van der Waals volumes and radii.J Phys Chem,1964, 68(3):441-451.
7 Pealman R S.Physical Chemical Properties of Drugs.New York: Marcel Dekker,1980:321-347.
8 Stouch T R,Jurs P C.A simple method for the representation, quantification,and comparison of the volumes and shapes of chemical compounds.J Chem Inf Comput Sci,1986,26(1):4-12.
9 Wong M W,Wiberg K B,Frisch M J.Ab initio calculation of molar volumes:Comparison with experiment and use in solvation models.J Comp Chem,1995,16:385-391.
10 Felipe A,Bulat Alejandro Toro-Labbe,Tore Brinck,Jane S. Murray,Peter P.Quantitative analysis of molecular surfaces:areas, volumes,electrostatic potentials and average local ionization energies.Journal of Molecular Modeling,2010,16(11):1679- 1691.
11 Zhao Feng,Du Yukou,Xu Jingkun,Liu Shufeng.Determination of surfactant molecular volume by atomic force microscopy. Colloid Journal,2006,68(6):784-787.
12 Tran D,Hunt J P,Wherland S.In Org Chem,1992,31:2460-2464.
13 Xia Li,Li Zhongjie,Xiang Shuguang.A new method based on elements and chemical bonds for estimating normal boiling point of organic compounds.Chemical Industry and Engineering Progress,2007,26(1):138-144.
14 Jing Yujie,Xiang Shuguang.New method for estimating critical pressure of organic compounds-elements and chemical bonds contribution method.Petrochemical Technology,2004,33(7):636- 641.
15 Jing Yujie,Xiang Shuguang.A new method based on elements and chemical bonds for estimating critical volume of organic compounds.Journal of Qingdao University of Science and Technology,2004,25(5):397-401.
16 Yaws C L.The Yaws Handbook of Thermodynamic Properties for Hydrocarbons and Chemicals.New York,1980:656-665.
1胡灿,王珍珍,徐文斌,许惠英.一些全氟(及多氟)有机化合物蒸汽压的QSPR研究[J].化学研究与应用,2013,25(1):43-46.
4刘夫锋,纪络,董晓燕.渗透剂的分子体积和极性表面积分率对胰凝乳蛋白酶抑制剂2热稳定性的影响[J].物理化学学报, 2010.26(10):2813-2820.
13夏力,李忠杰,项曙光.估算有机物正常沸点的元素和化学键贡献法[J].化工进展,2007,26(1):138-144.
14荆玉杰.项曙光.估算有机物临界压力的元素和化学键贡献法[J].石油化工,2004,33(7):636-641.
15荆玉杰,项曙光.基于元素和化学键的临界体积估算新方法[J].青岛科技大学学报,2004,25(5):397-401.
2 Zevatskii Y E,Vlasov E A.Dependence of the protonation constants of organic compounds on their molecular volume. Russian Journal of General Chemistry,2007,77(2):234-240.
3 Zevatskii Y E,Lysova S S.Empirical procedure for the calculation of ionization constants of organic compounds in water from their molecular volume.Russian Journal of General Chemistry,2009, 45(6):825-834.
4 Liu Fufeng,Ji Luo,Dong Xiaoyan.Effects of molecular volume and fractional polar surface area of osmolytes on the thermal stability of chymotrypsin inhibitor 2.Acta Physico-Chimica Sinica, 2010,26(10):2813-2820.
5 Abrams D S,Prausnitz J M.Statistical Thermodynamics of Liquid Mixtures:A new expression for the excess Gibbs energy of partly or completely miscible systems.AIChEJ,1975,21:116-128.
6 Bondi A.van der Waals volumes and radii.J Phys Chem,1964, 68(3):441-451.
7 Pealman R S.Physical Chemical Properties of Drugs.New York: Marcel Dekker,1980:321-347.
8 Stouch T R,Jurs P C.A simple method for the representation, quantification,and comparison of the volumes and shapes of chemical compounds.J Chem Inf Comput Sci,1986,26(1):4-12.
9 Wong M W,Wiberg K B,Frisch M J.Ab initio calculation of molar volumes:Comparison with experiment and use in solvation models.J Comp Chem,1995,16:385-391.
10 Felipe A,Bulat Alejandro Toro-Labbe,Tore Brinck,Jane S. Murray,Peter P.Quantitative analysis of molecular surfaces:areas, volumes,electrostatic potentials and average local ionization energies.Journal of Molecular Modeling,2010,16(11):1679- 1691.
11 Zhao Feng,Du Yukou,Xu Jingkun,Liu Shufeng.Determination of surfactant molecular volume by atomic force microscopy. Colloid Journal,2006,68(6):784-787.
12 Tran D,Hunt J P,Wherland S.In Org Chem,1992,31:2460-2464.
13 Xia Li,Li Zhongjie,Xiang Shuguang.A new method based on elements and chemical bonds for estimating normal boiling point of organic compounds.Chemical Industry and Engineering Progress,2007,26(1):138-144.
14 Jing Yujie,Xiang Shuguang.New method for estimating critical pressure of organic compounds-elements and chemical bonds contribution method.Petrochemical Technology,2004,33(7):636- 641.
15 Jing Yujie,Xiang Shuguang.A new method based on elements and chemical bonds for estimating critical volume of organic compounds.Journal of Qingdao University of Science and Technology,2004,25(5):397-401.
16 Yaws C L.The Yaws Handbook of Thermodynamic Properties for Hydrocarbons and Chemicals.New York,1980:656-665.
1胡灿,王珍珍,徐文斌,许惠英.一些全氟(及多氟)有机化合物蒸汽压的QSPR研究[J].化学研究与应用,2013,25(1):43-46.
4刘夫锋,纪络,董晓燕.渗透剂的分子体积和极性表面积分率对胰凝乳蛋白酶抑制剂2热稳定性的影响[J].物理化学学报, 2010.26(10):2813-2820.
13夏力,李忠杰,项曙光.估算有机物正常沸点的元素和化学键贡献法[J].化工进展,2007,26(1):138-144.
14荆玉杰.项曙光.估算有机物临界压力的元素和化学键贡献法[J].石油化工,2004,33(7):636-641.
15荆玉杰,项曙光.基于元素和化学键的临界体积估算新方法[J].青岛科技大学学报,2004,25(5):397-401.