分子间相互作用对核酸碱基中17O屏蔽张量与四极耦合常数影响的理论计算研究

doi:10.11938/cjmr20160303

波谱学杂志 ›› 2016, Vol. 33 ›› Issue (3): 378-394.doi: 10.11938/cjmr20160303

分子间相互作用对核酸碱基中¹⁷O屏蔽张量与四极耦合常数影响的理论计算研究

宋本腾^1,2, 褚月英², 王吉清¹, 郑安民², 邓风²

1. 湖南工业大学, 绿色包装与生物纳米技术应用省重点实验室, 湖南株洲 412008;
2. 波谱与原子分子国家重点实验室(中国科学院武汉物理与数学研究所), 湖北武汉 430071

收稿日期:2015-09-22 修回日期:2016-07-12 出版日期:2016-09-05 发布日期:2016-09-05
通讯作者: 王吉清,E-mail:wjqwh2006@163.com;郑安民,电话:027-87197127,E-mail:zhenganm@wipm.ac.cn. E-mail:wjqwh2006@163.com;zhenganm@wipm.ac.cn
作者简介:宋本腾(1990-),男,山东鄄城县人,硕士研究生,分析化学专业.
基金资助:
国家自然科学基金资助项目（21522310，21173255），湖南省教育厅重点资助项目（14A040）.

Influences of Intermolecular Interactions on the ¹⁷O Nuclear Magnetic Parameters in Nucleic Acid Bases: A Theoretical Investigation

SONG Ben-teng^1,2, CHU Yue-ying², WANG Ji-qing¹, ZHENG An-min², DENG Feng²

1. Hunan Key Laboratory of Green-Packaging and Application of Biological Nanotechnology, Hunan University of Technology, Zhuzhou 412008, China;
2. State Key Laboratory of Magnetic Resonance and Atomic and Molecular Physics (Wuhan Institute of Physics and Mathematics, Chinese Academy of Sciences), Wuhan 430071, China

Received:2015-09-22 Revised:2016-07-12 Online:2016-09-05 Published:2016-09-05

摘要/Abstract

摘要：

通过高精度量子化学理论计算的方法研究了分子间弱的非键相互作用对胸腺嘧啶、尿嘧啶、胞嘧啶和鸟嘌呤四种核酸碱基中¹⁷O核的屏蔽张量（σ_O）和四极耦合常数（Q_CC）的影响．计算结果表明分子间强的氢键作用以及弱的范德华（vdW）相互作用都对¹⁷O核的化学位移（d_O）具有较大的影响．随着分子间氢键作用的逐渐增强，d_O逐渐减小，当采用包含所有弱相互作用的周期性模型进行计算时，理论结果与实验值吻合．进一步的电荷分析显示，¹⁷O核化学位移的减小主要是由于分子间氢键作用强度增加导致¹⁷O原子的负电荷密度逐渐增加．此外，计算结果表明碱基中分子间氢键网络和弱的范德华作用对碱基¹⁷O Q_CC也具有显著的影响．周期性模型下，碱基上氧原子的局域结构环境得到平衡，¹⁷O Q_CC达到最小值，与实验结果最为接近．以核酸碱基为例，说明了分子间的氢键网络以及分子间弱的相互作用对于准确计算生物样品的核磁共振（NMR）参数非常重要，以小的团簇模型来计算生物体系的核磁参数将会产生较大的偏差．

关键词: 核磁共振(NMR), 屏蔽张量, 量子化学计算, 核酸碱基, 四极耦合常数

Abstract:

The influence of hydrogen bonding on the shielding tensors and quadrupole coupling constant (Q_CC) of oxygen atoms in [¹⁷O-2] thymine, [¹⁷O-4] thymine, [¹⁷O-2] uracil, [¹⁷O-4] uracil, [¹⁷O-2] cytosine, and [¹⁷O-6] guanine monohydrate has been studied by high quality quantum chemical calculations with different cluster models. The results showed that both hydrogen bonding and van der Waals (vdW) interactions are crucial for accurate prediction of isotropic ¹⁷O chemical shifts (d_O). In addition, experimentally measured ¹⁷O chemical shifts in these bases decrease with the increase of intermolecular hydrogen bonding interactions, and such interactions need to be accounted for in the theoretical models in order to obtain satisfactory calculated results. Relative to that of d_O, the calculation of ¹⁷O shielding tensors (d₁₁, d₂₂ and d₃₃) are even more model-dependent. NMR parameters calculated by periodic structure models taking all hydrogen bonding interactions and non-bonding vdW interactions into account were found to be in good agreement with the experimental results. Further analysis revealed that intermolecular hydrogen bonding-induced decrease of d_O is mainly due to the increaseof ¹⁷O negative charge density coming from the carboxyl (C=O) carbon. Furthermore, it was found that hydrogen bonding and weak interaction have remarkable effects on calculated ¹⁷O quadrupole coupling constant (Q_CC)as well. In conclusion, it is essential to take intermolecular hydrogen bonding and weak interactions into accounts in theoretical calculations in order to predict NMR parameters of biological samples correctly.

Key words: NMR, shielding tensor, quantum chemical calculation, nucleic acid bases, quadrupole coupling constant

中图分类号:

O482.53

宋本腾, 褚月英, 王吉清, 郑安民, 邓风. 分子间相互作用对核酸碱基中¹⁷O屏蔽张量与四极耦合常数影响的理论计算研究[J]. 波谱学杂志, 2016, 33(3): 378-394.

SONG Ben-teng, CHU Yue-ying, WANG Ji-qing, ZHENG An-min, DENG Feng. Influences of Intermolecular Interactions on the ¹⁷O Nuclear Magnetic Parameters in Nucleic Acid Bases: A Theoretical Investigation[J]. Chinese Journal of Magnetic Resonance, 2016, 33(3): 378-394.

参考文献

[1] Bedi D, Gillespie J W, Petrenko V A, et al. Targeted delivery of siRNA into breast cancer cells via phage fusion proteins[J]. Mol Pharm, 2013, 10(2): 551-559.

[2] Khandelwal G, Jayaram B. DNA-water interactions distinguish messenger RNA genes from transfer RNA genes[J]. J Am Chem Soc, 2012, 134(21): 8 814-8 816.

[3] Kierzek E, Pasternak A, Pasternak K, et al. Contributions of stacking, preorganization, and hydrogen bonding to the thermodynamic stability of duplexes between RNA and 2′-O-Methyl RNA with locked nucleic acids[J]. Biochemistry, 2009, 48(20): 4 377-4 387.

[4] Shaw N N, Arya D P. Recognition of the unique structure of DNA: RNA hybrids[J]. Biochimie, 2008, 90(7): 1 026-1 039.

[5] Sardo M, Siegel R, Santos S M, et al. Combining multinuclear high-resolution solid-state MAS NMR and computational methods for resonance assignment of glutathione tripeptide[J]. J Phys Chem A, 2012, 116(25): 6 711-6 719.

[6] Yao L, Grishaev A, Cornilescu G, et al. The impact of hydrogen bonding on amide ¹H chemical shift anisotropy studied by cross-correlated relaxation and liquid crystal NMR spectroscopy[J]. J Am Chem Soc, 2010, 132(31): 10 866-10 875.

[7] Nozad A G, Meftah S, Ghasemi M H, et al. Investigation of intermolecular hydrogen bond interactions in crystalline l-Cysteine by DFT calculations of the oxygen-17, nitrogen-14, and hydrogen-2 EFG tensors and AIM analysis[J]. Biophys Chem, 2009, 141(1): 49-58.

[8] Morrissey J H, Tajkhorshid E, Sligar S G, et al. Tissue factor/factor VIIa complex: role of the membrane surface[J]. Thromb Res, 2012, 129(S2): S8-S10.

[9] Bechinger B, Resende J M, Aisenbrey C. The structural and topological analysis of membrane-associated polypeptides by oriented solid-state NMR spectroscopy: Established concepts and novel developments[J]. Biophys Chem, 2011, 153(2, 3): 115-125.

[10] Dai Chen-ye(戴晨晔), Liu Mai-li(刘买利), Li Cong-gang(李从刚). Salt content-dependent conformational changes of α-Synuclein studied by ¹⁹F NMR(低盐和高盐环境下α-Synuclein构象的¹⁹F NMN研究)[J]. Chinese J Magn Reson(波谱学杂志), 2015, 32(1): 33-40.

[11] Yu Gui-yun(郁桂云), Peng Lu-ming(彭路明). Solid-state NMR studies of layered double hydroxides: a review(固体核磁共振谱学研究层状双氢氧化物)[J]. Chinese J Magn Reson(波谱学杂志), 2015, 32(2): 228-247.

[12] Pike K J, Lemaitre V, Kukol A, et al. Solid-state ¹⁷O NMR of amino acids[J]. J Phys Chem B, 2004, 108(26): 9 256-9 263.

[13] Lemaître V, de Planque M R R, Howes A P, et al. Solid-state ¹⁷O NMR as a probe for structural studies of proteins in biomembranes[J]. J Am Chem Soc, 2004, 126(47): 15 320-15 321.

[14] Wu G, Dong S. Two-dimensional ¹⁷O multiple quantum magic-angle spinning NMR of organic solids[J]. J Am Chem Soc, 2001, 123(37): 9 119-9 125.

[15] Profeta M, Mauri F, Pickard C J. Accurate first principles prediction of ¹⁷O NMR parameters in SiO₂: assignment of the zeolite ferrierite spectrum[J]. J Am Chem Soc, 2003, 125(2): 541-548.

[16] Yamada K, Dong S, Wu G. Solid-state ¹⁷O NMR investigation of the carbonyl oxygen electric-field-gradient tensor and chemical shielding tensor in amides[J]. J Am Chem Soc, 2000, 122(47): 11 602-11 609.

[17] Latosińska J N, Latosińska M, Tomczak M A, et al. Conformational stability and thermal pathways of relaxation in triclosan (Antibacterial/Excipient/Contaminant) in solid-state: Combined spectroscopic (¹H NMR) and computational (Periodic DFT) study[J]. J Phys Chem A, 2015, 119 (20): 4 864-4 874.

[18] Sutrisno Andre, Huang Yi-ning(黄忆宁). Multinuclear solid-state NMR and quantum chemical investigations of layered transition metal disulfides(应用多核固体核磁共振光谱与量子化学计算的方法研究层状的过渡金属硫化物)[J]. Chinese J Magn Reson(波谱学杂志), 2013, 30(4): 461-487.

[19] ?uczyńska K, Dru?bicki K, Lyczko K, et al. Experimental (X-ray, ¹³C CP/MAS NMR, IR, RS, INS, THz) and solid-state DFT study on (1:1) co-crystal of bromanilic acid and 2,6-dimethylpyrazine[J]. J Phys Chem B, 2015, 119(22): 6 852-6 872.

[20] Zheng A, Liu S B, Deng F. ¹⁹F Chemical shift of crystalline metal fluorides: Theoretical predictions based on periodic structure models[J]. J Phys Chem C, 2009, 113(33): 15 018-15 023.

[21] Gervais C, Dupree R, Pike K J, et al. Combined first-principles computational and experimental multinuclear solid-state NMR investigation of amino acids[J]. J Phys Chem A, 2005, 109(31): 6 960-6 969.

[22] Uldry A C, Griffin J M, Yates J R, et al. Quantifying weak hydrogen bonding in iracil and 4-cyano-4'-ethynylbiphenyl: A combined computational and experimental investigation of NMR chemical shifts in the solid state[J]. J Am Chem Soc, 2008, 130(3): 945-954.

[23] Esrafili M D, Elmi F, Hadipour N L. Density functional theory investigation of hydrogen bonding effects on the oxygen, nitrogen and hydrogen electric field gradient and chemical shielding tensors of anhydrous chitosan crystalline structure[J]. J Phys Chem A, 2007, 111(5): 963-970.

[24] Wu G, Dong S, Ida R, et al. A Solid-state¹⁷O nuclear magnetic resonance study of nucleic acid bases[J]. J Am Chem Soc, 2002, 124(8): 1 768-1 777.

[25] Ozeki K, Sakabe N, Tanaka J. The crystal structure of thymine[J]. Acta Cryst, Section B, 1969, 25(6): 1 038-1 045.

[26] Stewart R F, Jensen L H. Redetermination of the crystal structure of uracil[J]. Acta Cryst, 1967, 23(6): 1 102-1 105.

[27] Barker D L, Marsh R E. The crystal structure of cytosine[J]. Acta Cryst, 1964, 17(12): 1 581-1 587.

[28] Thewalt U, Bugg C E, Marsh R E. The crystal structure of guanine monohydrate[J]. Acta Cryst, Section B, 1971, 27(12): 2 358-2 363.

[29] Frisch M J, Trucks G W, Schlegel H B, et al. Gaussian 09, B.01[M]. Wallingford: Gaussian Inc, 2009.

[30] Chai J D, Head-Gordon M. Long-range corrected hybrid density functionals with damped atom-atom dispersion corrections[J]. Phys Chem Chem Phys, 2008, 10(44): 6 615-6 620.

[31] Perdew J P, Ernzerhof M, Burke K. Rationale for mixing exact exchange with density functional approximations[J]. J Chem Phys, 1996, 105(22): 9 982-9 985.

[32] Perdew J P, Burke K, Ernzerhof M. Generalized gradient approximation made simple[J]. Phys Rev Lett, 1996, 77(18): 3 865-3 868

[33] Perdew J P, Burke K, Ernzerhof M. Perdew, burke, and Ernzerhof reply[J]. Phys Rev Lett, 1998, 80(4): 891-891.

[34] Pickard C J, Mauri F. All-electron magnetic response with pseudopotentials: NMR chemical shifts[J]. Phys Rev B, 2001, 63(24): 245 101.

[35] Vaara J, Lounila J, Ruud K, et al. Rovibrational effects, temperature dependence, and isotope effects on the nuclear shielding tensors of water: A new ¹⁷O absolute shielding scale[J]. J Chem Phys, 1998, 109(19): 8 388-8 397.

[36] Wasylishen R E, Mooibroek S, Macdonald J B. A more reliable oxygen-17 absolute chemical shielding scale[J]. J Chem Phys, 1984, 81(3): 1 057-1 059.

[37] Pyykko P. Spectroscopic nuclear quadrupole moments[J]. Mol Phys, 2001, 99(19): 1 617-1 629.

[38] Johnson E R, Keinan S, Mori-Sánchez P, et al. Revealing noncovalent interactions[J]. J Am Chem Soc, 2010, 132(18): 6 498-6 506.

[39] Lu T, Chen F W. Multiwfn: A multifunctional wavefunction analyzer[J]. J Comp Chem, 2012, 33(5): 580-592.

[40] Chu Y, Zheng A, Deng F. Slight channel difference influences the reaction pathway of methanol-to-olefins conversion over acidic H-ZSM-22 and H-ZSM-12 zeolites[J]. Catal Sci Technol, 2015, 5(7): 3 507-3 517.

[41] Chu Y, Zheng A, Deng F. Strong or weak acid, which is more efficient for Beckmann rearrangement reaction over solid acid catalysts?[J]. Catal Sci Technol, 2015, 5(7): 3 675-3 681.

[42] Danelius E, Andersson H, Brath U, et al. Solution NMR investigations of weak interactions using peptidomimetic templates[C]. San Francisco: 248^th ACS National Meeting, 2014.

[43] Bogle X, Vazquez R, Greenbaum S, et al. Understanding Li⁺-solvent interaction in nonaqueous carbonate electrolytes with¹⁷O NMR[J]. J Phys Chem Lett, 2013, 4(10): 1 664-1 668.

[44] Ropp J, Lawrence C, Farrar T C, et al. Rotational motion in liquid water is anisotropic: A nuclear magnetic resonance and molecular dynamics simulation study[J]. J Am Chem Soc, 2001, 123(33): 8 047-8 052.

[45] Ida R, De Clerk M, Wu G. Influence of N-H…O and C-H…O Hydrogen bonds on the ¹⁷O NMR tensors in crystalline uracil: computational study[J]. J Phys Chem A, 2006, 110(3): 1 065-1 071.

[46] Hu J Z, Facelli J C, Alderman D W, et al. ¹⁵N Chemical shift tensors in nucleic acid bases[J]. J Am Chem Soc, 1998, 120(38): 9 863-9 869.

[47] Zheng A, Liu S B, Deng F. ¹³C shielding tensors of crystalline amino acids and peptides: Theoretical predictions based on periodic structure models[J]. J Comp Chem, 2009, 30(2): 222-235.

[48] Reed A E, Weinstock R B, Weinhold F. Natural population analysis[J]. J Chem Phys, 1985, 83(2): 735-746.

[49] Lu Tian(卢天), Chen Fei-wu(陈飞武). Comparison of computational methods for atomic charges(原子电荷计算方法的对比)[J]. Acta Phys-Chim Sin(物理化学学报), 2012, 28(1): 1-18.

[50] Gawinecki R, Kolehmainen E, Dobosz R, et al. Intramolecular interactions in nitroamines studied by ¹H, ¹³C, ¹⁵N and ¹⁷O NMR spectral and quantum chemical methods[J]. J Iran Chem Soc, 2014, 11(1): 17-25.

分子间相互作用对核酸碱基中¹⁷O屏蔽张量与四极耦合常数影响的理论计算研究

Influences of Intermolecular Interactions on the ¹⁷O Nuclear Magnetic Parameters in Nucleic Acid Bases: A Theoretical Investigation

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