ABEEM模型下铁卟啉分子的电荷分布
摘要
铁卟啉分子在生物体内起着十分重要的作用。人们熟知的进行氧传递作用的血红蛋白、氧活化和电子传递的细胞色素C和细胞色素P-450都是金属铁卟啉系列。由于分子中的电荷分布与分子的性质息息相关，计算铁卟啉化合物的电荷分布就显得非常重要。 由于传统的从头计算方法所需要的计算量太大，很难应用到大的分子体系。因此，发展准确的、计算上易于实行的方法用于探讨大分子的性质是现在理论化学的重要任务。我们以密度泛函理论[1-4]和电负性均衡原理[5-9]为基础，应用和开发了原子-键电负性均衡模型（ABEEM）。利用最小二乘法拟合确定了一些分子的各种类型原子及化学键区域的参数。运用这些参数，计算了有关铁卟啉分子的电荷分布以及分子的总能量，其得到的结果可以和从头计算相媲美,并且计算所需要的时间与从头计算相比非常短。
The calculation of charge distribution in iron porphyrins
Iron porphyrins play an important role in organism. People are familiar with iron porphyrins including hemoglobin of transferring oxygen, cytochrome C and cytochrom P-450. Since molecular charge distribution is closely related to molecular properties, it is important to calculate charge distribution of iron porphyrin compound. Conventional ab initio methods are hard to apply to the large molecular systems, so developing an accurate and economic method to probe the relationship between structures and properties of large molecules is a promising research area in nowadays theoretical chemistry. We have proposed an atom-bond electronegativity equalization model(ABEEM) on the basis of density functional theory and electronegativity equalization principle. Using separated program, through regression and least-squares optimization, the parameters of atoms and bonds in molecules are determined. By these parameters, the charge distributions and the energy of iron porphyrins are calculated. The time of calculation is short and the results are good.
The calculation of charge distribution in iron porphyrins
Iron porphyrins play an important role in organism. People are familiar with iron porphyrins including hemoglobin of transferring oxygen, cytochrome C and cytochrom P-450. Since molecular charge distribution is closely related to molecular properties, it is important to calculate charge distribution of iron porphyrin compound. Conventional ab initio methods are hard to apply to the large molecular systems, so developing an accurate and economic method to probe the relationship between structures and properties of large molecules is a promising research area in nowadays theoretical chemistry. We have proposed an atom-bond electronegativity equalization model(ABEEM) on the basis of density functional theory and electronegativity equalization principle. Using separated program, through regression and least-squares optimization, the parameters of atoms and bonds in molecules are determined. By these parameters, the charge distributions and the energy of iron porphyrins are calculated. The time of calculation is short and the results are good.
引文
[1] Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys. Rev. B, 1964, 136:864.
[2] Kohn W, Sham L. Self-consistent equations including exchange and correlation effects. Phys. Rev. A , 1965, 140:1133
[3] Levy M, Perdew J. In Density-Functional Methods in Physics, edited by Dreizler R H and J da Providencia. Plenum, New York, 1985.
[4] Parr R G, Yang W. Density-Functional Theory of Atoms and Molecules. Oxford University, New York, 1989.
[5] Parr R G, Donnelly R A, Levy R A, Palke W E. Electronegativity: the density functional viewpoint. J. Chem. Phys. 1978, 68:3801.
[6] Fukui K, Yonezawa T, Nagata C. and Shingu H. A molecular orbital theory of reactivity in aromatic hydrocarbons. J. Chem. Phys, 1952, 20:722.
[7] Parr R G, Yang W. Density functional approach to the frontier electron theory of chemical reactivity. J. Am. Chem. Soc, 1984, 106:4049.
[8] Lee C, Yang W, and Parr R G. Local softness and chemical reactivity in the molecules CO, SCN－and H3CO3. J. Mol. Struct (Theochem), 1988, 163:305.
[9] Sen K D, Jorgensen C K. Electronegativity in Structure and Bonding New York, Heidelberg: Springer-Verlag, 1987, 66:1-25, 125-143.
[10] Bader R.F.W., Atoms in Molecules: A quantum Theory (Clarendon, Oxford,1994).
[11] Hohenberg P., Kohn W., Phys. Rev. B 1964,136:864.
[12] Kohn W., Sham L., Phys. Rev. A 1965,140:1133.
[13] Levy M., Perdew H., in Density-Functional Method in Physics, edited by R. H. Dreizler and J. da Providencia (Plenum, New York, 1985)
[14] Parr R.G., Yang W., Density-Functional Theory of Atoms and Molecules (Oxford University, New York,1989)
[15] Pauling L., The Nature of the Chemical bond, 3rd (edn.m Cornell University Press, Ithaca, NY, 1960.)
[16] Parr R.G., Donnelly R.A., Levy N., Palke W.E., J.Chem.Phys. 1978,68: 3801.
[17]
[18]Iczkowski,R.P. and Margrave,J.L. J.Am.Chem.Soc. 1961,83:3547.
[19] Parr,R.G. and Pearson,R.G. J.Am.Chem.Soc. 1983,105:7512.
[20] Pearson,R.G. Inorg.Chem. 1988,27:734.
[21] Hohenberg,P. and Kohn,W. Phys.Rev.B 1964,136:864
[22] Pauling L,. The Nature of Chemical Bond, 3rd Ed.,Cornell University Press, Ithaca, NY, 1960.
[23] Pauling L ,. Die Natur der Chemischen Binding, Verlag Chemie, Weinheim, 1973.
[24] Sanderson R.T., Science 1951,114:670; Chemical Bonds and Bond Energy (Academic, New York, 1976).
[25] Parr R.G., Donnelly R.A., Levy M., and Palke W.E. Atom-bond electronegativity method, II. Lone-pair electron model. J.Chem.Phys. 1978,68:3801
[26] Donnelly R.A., Parr R.G. Elementary properties of an energy functional of the first-order reduced density matrix. J.Chem.Phys. 1978,69:4431
[27] Mortier W.J., Ghosh S.K., Shankar S. Electronegativity equalization method for the calculation of atomic charges in molecules. J.Am.Chem.Soc. 1986,108:4315
[28] Mortier W.J., Genechten K.V., Gasteriger J., Elementary properties of an energy functional of the first-order reduced density matrix. J.Am.Chem.Soc.1985,1027:829
[29] Baekelandt B.G., Mortier W.J., Lievens J.L., Schoonheydt R. J.Am.Chem.Soc. 1991,113:6730;
[30] Baekelandt B.G., Mortier,W.J., Schoonheydt R.A. Structure and Bonding, 1993,80:187.
[31] Baekelandt B.G., Janssens G.O.A., Toufar H., Mortier W.J., and Schoonheydt R.A. J.Phys.Chem. 1995,99:9784
[32] Nalewajski R.F., J. Am. Chem. Soc. 1984,106:944.
[33] Nalewajski R.F., J. Phys. Chem. 1985,89:2831.
[34] Nalewajski.R.F., Int.J.Quant.Chem. 1991,40:265.
[35] J.Korchowiec , R.F. Nalewajski., ibid ,1992,44:1027
[36] Darrin M. Y, Yang W, A chemical potential equalization method for molecularsimulations J.Chem.Phys. 1996,104(1):159-172.
[37] Toufar H., Baeklandt B.G., Janssens G.O.A., Mortier W.J., Schoonheydt R.A. J. Phys. Chem. 1995,99:13876.
[38] 沈尔忠,杨忠志. 由电负性均衡原理直接计算分子中的原子电荷.中国科学B辑 1995,25:126.
[39] 沈尔忠,杨忠志. 分子总能量的直接计算 化学学报 1996,54:152.
[40] Yang Z.Z, and Shen E.Z. Direct calculation of group electronegativity and the atomic charges in a group. Science in China(Series B) 1996,39:20.
[41] Yang Z.Z., Shen E.Z. J.Mol.Struct(Theochem) 1996,312:167.
[42] Yang Z. Z., Wang C. S. Atom-bond electronegativity method, I. Calculation of the charge distribution in large molecules. J. Phys. Chem. 1997, A101, 6315.
[43] Wang C. S., Li S. M., Yang Z. Z. Calculation of molecular energies by atom-bond electronegativity equalization method.J. Mol. Struct. (Theochem). 1998, 430: 191.
[44] Yang Z. Z., Wang, C. S., Tang, A. Q. Molecular electronegativity in the density functional theory atom-bond electonegativity equalization model. Science in China (Series B). 1998, 41:331.
[45] Wang, C. S., Yang, Z. Z. Atom-bond electronegativity method, II. Lone-pair electron model. J. Chem. Phys. 1999, 110(13):6189.
[46] Yang Z.Z., Wang C.S. Atom-bond electronegativity method, I. Calculation of the charge distribution in large molecules. J. Phys. Chem. A, 1997, 101: 6315.
[47] Tapan k.Ghanty., Swapan K. Ghosh Electornegativity and Covalent Binding in Homonuclear Diatomic Molecules J.Phys.Chem.1991,95:6512-6514.
[48] Swapan K. Ghosh Electronegativity, Hardness, and a Semiempirical Density Functional Theory of Chemical Binging Int.J.Quantum Chem. 1994,49:239-251.
[49] 李早英. 金属卟啉化学研究进展. 金属有机化学与催化, 化学工业出版社,1997，842.
[50] (a) Ghadiri Reza M., Granja Juan R., Buehier Lukas K. Aritificial transmembrane ion channerl from self-assembling peptide nanotubes Nature 1994,369:301-304. (b) JamesP. Lewis, Norma H. Pawley, Otto F. Sankey Theoretical investigation of the cyclic peptide systeem cyclo[(D-ala-Glu-D-Ala-Gln)m=1-4] J.Phys.Chem.B 1997, 101:10576-10583. (c)Hanna Rapaport, Hui Sun Kim, Krstian Kjaer, Paul g. Howes, Sidney Cohen, jens Als-Nielsen, M. Reza Ghadiri, Leslie Leiserowitz, and Meir Lahav J.Am.Chem.Soc. 1999,121:1186.
[51] 王长生,孙仁安,杨忠志.高等学校化学学报, 1997,18:1353.
[52] Parr.R.G., Yang,W. J.Am.Chem.Soc. 1984,106:4049.
[53] 唐有祺，张惠珠，吴相钰，顾孝诚，林性玉，章有章. 生物化学. 北京大学出版社，1990，32-33.
[54] 朱寿珩，王宏康. 金属与代谢. 科学普及出版社.1983，153-156.
[55] A.J. Gow, J.S. Stamler. Nature（London）,1998,391:169.
[56] J.S. Stamler,G. Meissner. Physiol. Rev.2001,81:209
[57] L.E. Otterbein, A.M.K Choi. Am.J.Physiol. Lung Cell. Molec. Physiol. 2000,279:L1029.
[58] B.G. Bentz, R.L. Simmons, G.K. Haines, J.A Radosevich. Head Neck—J. 2000,22:71.
[59] C.K. Mathews, K.E. Van Holde. Biochemistry, 2ed ed.,Benjamin/Cummings, Menlo Park, CA,1996.
[60] C.D. Klaassen, M.O. Amdur, O.Doull(Eds.), Casarett and Doull's Toxicology:The Basic Science of Poisons 5th ed., Macmillian, New York, 1996.
[61] Sakir Erkoc,Figen Erkoc. J.Mol.Struct.(Theochem), 2001,546:175-176.
[62] (a)D.F.Lewis, J.M.Pratt. Drug Metab.Rev. 1998,30,739. (b) T. L. Poulos, Curr. Opin. Struct. Biol. 1995,5,767.
[63] Ortiz de Montellane, P.R. Cytochrome P-450:Structure,Mecanism and Biochemistry, Plenum Press:New York,1995.
[64] F.P.Guengerich, T.L.MacDonald. FASEB J. 1990,4,2453.
[65] J.H.Dawson, M.Sono. Chem.Rev. 1987,87,1255.
[66] H.M.Marques, O.Q.Munro, N.E.Grimmer, D.O.Levendis, F.Marsicano, G.Pattrick,T.Markoulides. J. Chem. Soc., Faraday Trans. 1995,91,1741.
[67] Damian A.Scherlis, Cora B,Cymeryang, Dario A.Estrin, Nitric Oxide Binding to Ferric Cytochrome P450:A Computational Study. Inorg. Chem. 2000,39,2352.
[68] 朱寿珩，王宏康. 金属与代谢. 科学普及出版社.1983,163.
[2] Kohn W, Sham L. Self-consistent equations including exchange and correlation effects. Phys. Rev. A , 1965, 140:1133
[3] Levy M, Perdew J. In Density-Functional Methods in Physics, edited by Dreizler R H and J da Providencia. Plenum, New York, 1985.
[4] Parr R G, Yang W. Density-Functional Theory of Atoms and Molecules. Oxford University, New York, 1989.
[5] Parr R G, Donnelly R A, Levy R A, Palke W E. Electronegativity: the density functional viewpoint. J. Chem. Phys. 1978, 68:3801.
[6] Fukui K, Yonezawa T, Nagata C. and Shingu H. A molecular orbital theory of reactivity in aromatic hydrocarbons. J. Chem. Phys, 1952, 20:722.
[7] Parr R G, Yang W. Density functional approach to the frontier electron theory of chemical reactivity. J. Am. Chem. Soc, 1984, 106:4049.
[8] Lee C, Yang W, and Parr R G. Local softness and chemical reactivity in the molecules CO, SCN－and H3CO3. J. Mol. Struct (Theochem), 1988, 163:305.
[9] Sen K D, Jorgensen C K. Electronegativity in Structure and Bonding New York, Heidelberg: Springer-Verlag, 1987, 66:1-25, 125-143.
[10] Bader R.F.W., Atoms in Molecules: A quantum Theory (Clarendon, Oxford,1994).
[11] Hohenberg P., Kohn W., Phys. Rev. B 1964,136:864.
[12] Kohn W., Sham L., Phys. Rev. A 1965,140:1133.
[13] Levy M., Perdew H., in Density-Functional Method in Physics, edited by R. H. Dreizler and J. da Providencia (Plenum, New York, 1985)
[14] Parr R.G., Yang W., Density-Functional Theory of Atoms and Molecules (Oxford University, New York,1989)
[15] Pauling L., The Nature of the Chemical bond, 3rd (edn.m Cornell University Press, Ithaca, NY, 1960.)
[16] Parr R.G., Donnelly R.A., Levy N., Palke W.E., J.Chem.Phys. 1978,68: 3801.
[17]
[18]
[19] Parr,R.G. and Pearson,R.G. J.Am.Chem.Soc. 1983,105:7512.
[20] Pearson,R.G. Inorg.Chem. 1988,27:734.
[21] Hohenberg,P. and Kohn,W. Phys.Rev.B 1964,136:864
[22] Pauling L,. The Nature of Chemical Bond, 3rd Ed.,Cornell University Press, Ithaca, NY, 1960.
[23] Pauling L ,. Die Natur der Chemischen Binding, Verlag Chemie, Weinheim, 1973.
[24] Sanderson R.T., Science 1951,114:670; Chemical Bonds and Bond Energy (Academic, New York, 1976).
[25] Parr R.G., Donnelly R.A., Levy M., and Palke W.E. Atom-bond electronegativity method, II. Lone-pair electron model. J.Chem.Phys. 1978,68:3801
[26] Donnelly R.A., Parr R.G. Elementary properties of an energy functional of the first-order reduced density matrix. J.Chem.Phys. 1978,69:4431
[27] Mortier W.J., Ghosh S.K., Shankar S. Electronegativity equalization method for the calculation of atomic charges in molecules. J.Am.Chem.Soc. 1986,108:4315
[28] Mortier W.J., Genechten K.V., Gasteriger J., Elementary properties of an energy functional of the first-order reduced density matrix. J.Am.Chem.Soc.1985,1027:829
[29] Baekelandt B.G., Mortier W.J., Lievens J.L., Schoonheydt R. J.Am.Chem.Soc. 1991,113:6730;
[30] Baekelandt B.G., Mortier,W.J., Schoonheydt R.A. Structure and Bonding, 1993,80:187.
[31] Baekelandt B.G., Janssens G.O.A., Toufar H., Mortier W.J., and Schoonheydt R.A. J.Phys.Chem. 1995,99:9784
[32] Nalewajski R.F., J. Am. Chem. Soc. 1984,106:944.
[33] Nalewajski R.F., J. Phys. Chem. 1985,89:2831.
[34] Nalewajski.R.F., Int.J.Quant.Chem. 1991,40:265.
[35] J.Korchowiec , R.F. Nalewajski., ibid ,1992,44:1027
[36] Darrin M. Y, Yang W, A chemical potential equalization method for molecular
[37] Toufar H., Baeklandt B.G., Janssens G.O.A., Mortier W.J., Schoonheydt R.A. J. Phys. Chem. 1995,99:13876.
[38] 沈尔忠,杨忠志. 由电负性均衡原理直接计算分子中的原子电荷.中国科学B辑 1995,25:126.
[39] 沈尔忠,杨忠志. 分子总能量的直接计算 化学学报 1996,54:152.
[40] Yang Z.Z, and Shen E.Z. Direct calculation of group electronegativity and the atomic charges in a group. Science in China(Series B) 1996,39:20.
[41] Yang Z.Z., Shen E.Z. J.Mol.Struct(Theochem) 1996,312:167.
[42] Yang Z. Z., Wang C. S. Atom-bond electronegativity method, I. Calculation of the charge distribution in large molecules. J. Phys. Chem. 1997, A101, 6315.
[43] Wang C. S., Li S. M., Yang Z. Z. Calculation of molecular energies by atom-bond electronegativity equalization method.J. Mol. Struct. (Theochem). 1998, 430: 191.
[44] Yang Z. Z., Wang, C. S., Tang, A. Q. Molecular electronegativity in the density functional theory atom-bond electonegativity equalization model. Science in China (Series B). 1998, 41:331.
[45] Wang, C. S., Yang, Z. Z. Atom-bond electronegativity method, II. Lone-pair electron model. J. Chem. Phys. 1999, 110(13):6189.
[46] Yang Z.Z., Wang C.S. Atom-bond electronegativity method, I. Calculation of the charge distribution in large molecules. J. Phys. Chem. A, 1997, 101: 6315.
[47] Tapan k.Ghanty., Swapan K. Ghosh Electornegativity and Covalent Binding in Homonuclear Diatomic Molecules J.Phys.Chem.1991,95:6512-6514.
[48] Swapan K. Ghosh Electronegativity, Hardness, and a Semiempirical Density Functional Theory of Chemical Binging Int.J.Quantum Chem. 1994,49:239-251.
[49] 李早英. 金属卟啉化学研究进展. 金属有机化学与催化, 化学工业出版社,1997，842.
[50] (a) Ghadiri Reza M., Granja Juan R., Buehier Lukas K. Aritificial transmembrane ion channerl from self-assembling peptide nanotubes Nature 1994,369:301-304. (b) James
[51] 王长生,孙仁安,杨忠志.高等学校化学学报, 1997,18:1353.
[52] Parr.R.G., Yang,W. J.Am.Chem.Soc. 1984,106:4049.
[53] 唐有祺，张惠珠，吴相钰，顾孝诚，林性玉，章有章. 生物化学. 北京大学出版社，1990，32-33.
[54] 朱寿珩，王宏康. 金属与代谢. 科学普及出版社.1983，153-156.
[55] A.J. Gow, J.S. Stamler. Nature（London）,1998,391:169.
[56] J.S. Stamler,G. Meissner. Physiol. Rev.2001,81:209
[57] L.E. Otterbein, A.M.K Choi. Am.J.Physiol. Lung Cell. Molec. Physiol. 2000,279:L1029.
[58] B.G. Bentz, R.L. Simmons, G.K. Haines, J.A Radosevich. Head Neck—J. 2000,22:71.
[59] C.K. Mathews, K.E. Van Holde. Biochemistry, 2ed ed.,Benjamin/Cummings, Menlo Park, CA,1996.
[60] C.D. Klaassen, M.O. Amdur, O.Doull(Eds.), Casarett and Doull's Toxicology:The Basic Science of Poisons 5th ed., Macmillian, New York, 1996.
[61] Sakir Erkoc,Figen Erkoc. J.Mol.Struct.(Theochem), 2001,546:175-176.
[62] (a)D.F.Lewis, J.M.Pratt. Drug Metab.Rev. 1998,30,739. (b) T. L. Poulos, Curr. Opin. Struct. Biol. 1995,5,767.
[63] Ortiz de Montellane, P.R. Cytochrome P-450:Structure,Mecanism and Biochemistry, Plenum Press:New York,1995.
[64] F.P.Guengerich, T.L.MacDonald. FASEB J. 1990,4,2453.
[65] J.H.Dawson, M.Sono. Chem.Rev. 1987,87,1255.
[66] H.M.Marques, O.Q.Munro, N.E.Grimmer, D.O.Levendis, F.Marsicano, G.Pattrick,
[67] Damian A.Scherlis, Cora B,Cymeryang, Dario A.Estrin, Nitric Oxide Binding to Ferric Cytochrome P450:A Computational Study. Inorg. Chem. 2000,39,2352.
[68] 朱寿珩，王宏康. 金属与代谢. 科学普及出版社.1983,163.