全部 标题 作者
关键词 摘要

OALib Journal期刊
ISSN: 2333-9721
费用:99美元

查看量下载量

相关文章

更多...
科学通报  2012 

偶极子势模拟水溶液对酪氨酸电子结构的影响

DOI: 10.1360/972011-1442, PP. 1646-1656

Keywords: 酪氨酸,电子结构,,等效势,团簇埋入自洽计算

Full-Text   Cite this paper   Add to My Lib

Abstract:

为了更可靠地得到水溶液中蛋白质分子的电子结构,有必要构建水溶液对蛋白质分子电子结构的等效势,这个等效势必须简单、易用.通过第一性原理、全电子、从头计算,构造了水溶液对酪氨酸(Tyr)电子结构的等效势.工作分为三步(1)用“自由团簇计算法”计算一个含酪氨酸和水分子的系统的能量最低时的空间结构;(2)基于第一步的空间结构,用“团簇埋入自洽计算法”计算酪氨酸在以水分子为外势条件下的电子结构;(3)用“团簇埋入自洽计算法”计算酪氨酸在用偶极子势代替水分子势条件下的电子结构.结果显示,由于水溶液的存在,酪氨酸电子结构的两个能级平均降低了约0.0158Ry,其他6个能级平均上升约0.0302Ry;水溶液对酪氨酸电子结构的影响可以很好地被偶极子势模拟.

References

[1]  1 Yang W T. Direct calculation of electron density in density-functional theory. Phys Rev Lett, 1991, 66: 1438-1441??
[2]  2 Cortona P. Self-consistently determined properties of solids without band structure calculations. Phys Rev B, 1991, 44: 8454-8458??
[3]  4 Mauri F, Galli G, Car R. Orbital formulation for electronic-structure calculations with linear system-size scaling. Phys Rev B, 1993, 47:9973-9976??
[4]  5 Li X P, Nunes R W, Vanderbilt D. Density-matrix electronic-structure method with linear system-size scaling. Phys Rev B, 1993, 47:10891-10894??
[5]  6 Ordejon P, Drabold D A, Martin R M, et al. Linear system-size scaling methods for electronic-structure calculations. Phys Rev B, 1995, 51:1456-1476??
[6]  7 Yang W T, Lee T S. A density-matrix divide-and-conquer approach for electronic structure calculations of large molecules. Chem Phys, 1995,103: 5674-5678
[7]  9 Ordejón P, Artacho P E, Soler J M. Self-consistent order-N density-functional calculations for very large systems. Phys Rev B, 1996, 53:10441-10444??
[8]  10 Baer R, Gordon M H. Sparsity of the density matrix in Kohn-Sham density functional theory and an assessment of linear system-size scaling methods. Phys Rev Lett, 1997, 79: 3962-3965??
[9]  13 Wesolowski T A, Warshel A. Frozen density fucntional approach for ab initio calculations of solvated molecules. J Phys Chem, 1993, 97:8050-8053??
[10]  15 Govind N, Wang Y A, da Silva A J R, et al. Accurate ab initio energetics of extended systems via explicit correlation embedded in a density functional environment. Chem Phys Lett, 1998, 295: 129-134??
[11]  19 Zheng H, Rao B K, Khanna S N, et al. Electronic structure and binding energies of hydrogen-decorated vacancies in Ni. Phys Rev B, 1997, 55:4174-4181??
[12]  20 Zheng H, Wang Y, Ma G. Electronic structure of LaNi5 and its hydride LaNi5H7. Eur Phys J B, 2002, 29: 61-69??
[13]  21 何军, 郑浩平. GaN 及其Ga 空位的电子结构. 物理学报, 2002, 51: 2580-2588
[14]  22 林少杰, 郑浩平. LaNi5 晶体表面态的计算研究. 物理学报, 2005, 54: 4680-4687
[15]  23 Zhen H, Lin S. First-principles calculation of LaNi5 surface. J Phys Conf Ser, 2006, 29: 129-140??
[16]  24 Zheng H. Electronic structure of trypsin inhibitor from squash seeds in aqueous solution. Phys Rev E, 2000, 62: 5500-5508??
[17]  25 郑浩平. 蛋白质分子电子结构的第一性原理从头计算. 物理学进展, 2000, 20: 291-300
[18]  26 Zheng H. Ab initio calculations of the electronic structures and biological functions of protein molecules. Mod Phys Lett B, 2002, 16:1151-1162??
[19]  27 Zheng H. Electronic structures of Ascaris trypsin inhibitor in solution. Phys Rev E, 2003, 68: 051908??
[20]  28 Sato F, Yoshihiro T, Era M, et al. Calculation of all-electron wavefunction of hemoprotein cytochrome c by density functional theory. Chem Phys Lett, 2001, 341: 645-651??
[21]  29 Yoshihiro T, Sato F, Kashiwagi H. Distributed parallel processing by using the object-oriented technology in ProteinDF program for all-electron calculations on proteins. Chem Phys Lett, 2001, 346: 313-321??
[22]  30 Lazaridis T, Karplus M. Effective energy function for proteins in solution. Proteins, 1999, 35: 133-152??
[23]  31 Lazaridis T, Karplus M. Discrimination of the native from misfolded protein models with an energy function including implicit solvation. J Mol Biol, 1998, 288: 477-487
[24]  32 Onsager L. Electric moment of molecules in liquids. J Am Chem Soc, 1936, 58: 1486-1493??
[25]  38 Wang X, Zheng H, Li C. The equivalent potential of water molecules for electronic structure of cysteine. Eur Phys J B, 2006, 52: 255-263??
[26]  42 闫述, 郑浩平, 张甜. 水溶液势对丙氨酸电子结构影响的模拟. 科学通报, 2008, 53: 758-768
[27]  43 Zhang T, Zheng H, Yan S. Equivalent potential of water molecules for electronic structure of aspartic acid. J Comput Chem, 2008, 29:1780-1787??
[28]  44 Wang X, Zheng H. Simulation of water potential for the electronic structure of serine. Chin Phys B, 2009, 18: 1968-1978??
[29]  45 Shen X, Gao Y, Zheng H. The equivalent dipole potential of water for the electronic structure of threonine. Mol Phys, 2009, 107: 1393-1405??
[30]  47 Min P, Zheng H. Equivalent potential of water for electronic structure of glycine. J Mol Model, 2010, 17: 111-124
[31]  48 Hohenberg P, Kohn W. Inhomogeneous electron gas. Phys Rev B, 1964, 136: 864-871??
[32]  49 Kohn W, Sham L. Self-consistent equations including exchange and correlation effects. J Phys Rev A, 1965, 140: 1133-1138
[33]  52 van Duijneveldt F B. Gaussian basis sets for the atoms HNe for use in molecular calculations. IBM J Res Dev, 1971, 945: 16437
[34]  53 Lie G C, Clementi E. Study of the electronic structure of molecules XXI. Correlation energy corrections as a functional of the Hartree-Fock density and its application to the hydrides of the second row atoms. J Chem Phys, 1974, 60: 1275-1287??
[35]  54 Poirier R A, Daudel R, Mezey P G, et al. Ab initio calculations on sulfur-containing compounds I. Uniform quality basis sets for sulfur: Total energies and geometries of H2S. Int J Quant Chem, 1982, 21: 799-811
[36]  61 徐万宏, 郑浩平. 不同大小的Co 和Ni 团簇性质的理论计算. 同济大学学报, 2003, 31: 374-378
[37]  62 林少杰, 郑浩平. 新型氧分子O4 的理论计算研究. 同济大学学报, 2004, 32: 551-555
[38]  67 Guillot B. A reappraisal of what we have learnt during three decades of computer simulations on water. J Mol Liquids, 2002, 101: 219-260??
[39]  68 Rick S W. Simulations of ice and liquid water over a range of temperatures using the fluctuating charge model. J Chem Phys, 2001, 114:2276-2283??
[40]  3 Galli G, Parrinello M. Large scale electronic structure calculations. Phys Rev Lett 1992, 69: 3547-3550
[41]  8 Kohn W. Density functional and density matrix method scaling linearly with the number of atoms. Phys Rev Lett, 1996, 76: 3168-3171??
[42]  11 Klessinger M, Mcweeny R. Self-consistent group calculations on polyatomic molecules. J Chem Phys, 1965, 42: 3343-3354??
[43]  12 Li J B, McWeeny R. VB2000: Pushing valence bond theory to new limits. Int J Quant Chem, 2002, 89: 208-216??
[44]  14 Wesolowski T A. One-electron equations for embedded electron density: Challenge for theory and practical payoffs in multi-level modeling of soft condensed matter. In: Leszczynski J, ed. Computational Chemistry: Reviews of Current Trends. Singapore: World Scientific, 2006. 1-82
[45]  16 Zheng H. One-electron approach and the theory of the self-consistent cluster-embedding calculation method. Phys Lett A, 1997, 226: 223-230??
[46]  17 Zheng H. Self-consistent cluster-embedding calculation method and the calculated electronic structure of NiO. Phys Rev B, 1993, 48:14868-14883??
[47]  18 Zheng H. Electronic structure of CoO. Physica B, 1995, 212: 125-138??
[48]  33 Klamt A, Schuurmann G. COSMO: A new approach to dielectric screening in solvents with explicit expressions for the screening energy and its gradient. J Chem Soc Perkin Trans, 1993, 2: 799-803
[49]  34 Guo H, Karplus M. Solvent influence on the stability of the peptide hydrogen bond: A supramolecular cooperative effect. J Phys Chem, 1994,98: 7104-7105??
[50]  35 Schaefer M, Karplus M. A comprehensive analytical treatment of continuum electrostatics. J Phys Chem, 1996, 100: 1578-1599??
[51]  36 Eckert F, Klamt A. Fast solvent screening via quantum chemistry: COSMO-RS approach. AIChE J, 2002, 48: 369-385??
[52]  37 Foresman J B, Keith T A, Wiberg K B. Solvent effects. 5. Influence of cavity shape, truncation of electrostatics, and electron correlation on ab initio reaction field calculations. J Phys Chem, 1996, 100: 16098-16104
[53]  39 Li C, Zheng H, Wang X. The equivalent potential of water molecules for electronic structure of lysine. Sci China Ser G: Phys Mech Astron,2007, 50: 15-30??
[54]  40 Li C, Zheng H, Wang X. The equivalent potential of water molecules for the electronic structure of histidine. J Phys Cond Matt, 2007, 19:116102??
[55]  41 Zhang T, Zheng H, Yan S. Equivalent potential of water molecules for electronic structure of glutamic acid. J Comput Chem, 2007, 28:1848-1857??
[56]  46 Gao Y, Shen X, Zheng H. Equivalent potential of water for electronic structure of asparagines. Int J Quant Chem, 2010, 110: 925-938
[57]  50 Von Barth U, Hedin L. A local exchange-correlation potential for the spin polarized case I. J Phys C, 1972, 5: 1629-1637??
[58]  51 Rajagopal A K. Theory of inhomogeneous electron systems: Spin-density-functional formalism. In: Prigogine G I, Rice S A, eds. Advance in Chemical Physics. New York: Wiley, 2007. 59-193
[59]  55 Huzinaga S. Gaussian-type functions for polyatomic systems I. J Chem Phys, 1965, 42: 1293-1302??
[60]  56 Poirier R, Kari R, Csizmadia I G. Handbook of Gaussian Basis Sets. Amsterdam: Elsevier, 1985
[61]  57 Chen H. Electronic structure of clusters: Applications to high-Tc superconductors. Doctoral Dissertation. Baton Rouge, LA: Louisiana State University, 1988??
[62]  58 Chen H, Callaway J, Misra P K. Electronic structure of Cu-O chains in the high-Tc superconductor YBa2Cu3O7. Phys Rev B, 1988, 38: 195-203??
[63]  59 Chen H, Callaway J. Local electronic structure and magnetism of 3d transition-metal impurities (Cr, Mn, Fe, Co, and Ni) in La2-xSrxCuO4. Phys Rev B, 1991, 44: 2289-2296
[64]  60 郑浩平, 何军. 传统单电子近似计算法的局限性. 同济大学学报, 2001, 29: 593-597
[65]  63 郝静安, 郑浩平. Ga6N6 团簇结构性质的理论计算研究. 物理学报, 2004, 53: 1044-1049
[66]  64 Zheng H, Hao J. Ab initio study of the electronic properties of the planar Ga5N5 cluster. Chin Phys, 2005, 14: 529-532??
[67]  65 Zheng H. Self-consistent cluster-embedding calculation method and the electronic structure of NiO and CoO. Doctoral Dissertation. Baton Rouge, LA: Louisiana State University, 1993
[68]  66 Sample H, Felton R H. A new computational approach to Slater’s SCF-Xα equation. J Chem Phys, 1975, 62: 1122-1126??
[69]  69 Berendsen H J C, Postma J P M, van Gunsteren W F, et al. Intermolecular Forces. Dordrecht: Reidel, 1981. 331
[70]  70 Robinson G W, Zhu S B, Singh S, et al. Water in Biology, Chemistry and Physics: Experimental Overviews and Computational Methodologies. Singapore: World Scientific, 1996. 11-213??

Full-Text

Contact Us

service@oalib.com

QQ:3279437679

WhatsApp +8615387084133