鸟嘌呤四链体中Na~+的移动

Na+-G-四链体复合物是一个明显的极化体系,其形成或解离过程中,Na+的移动路线目前还不十分明确.σπ水平的原子-键电负性均衡方法融合进分子力学(ABEEMσπ/MM)模型除原子位点外,还明确地定义了孤对电子、σ键和π键的位置,并且各位点电荷随分子环境改变而浮动,因此能更好地反映该体系的极化现象.本文应用ABEEMσπ/MM方法研究了Na+-G-四平面复合物的性质,包括它的几何构型、电荷分布和结合能等,并在MP2/6-31G(d,p)水平上做了相应的从头算,两种结果十分吻合.Na+的存在改变了G-tetrad的氢键方式.通过比较Na+各条移动路线中体系的结合能,预测G-四链体中三个Na+最有可能沿α方向依次移出.以上研究为进一步应用ABEEMσπ/MM模型进行G-四链体中离子交换通道的动力学模拟打下坚实的基础.     

鸟嘌呤四链体中K＋移动路径的预测

结合鸟嘌呤四链体(G4)的结构特点, 取G4中的一个K^＋与一片g-tetrad (g-tetrad-K^＋)为研究对象, 和一个K^＋与两片g-tetrad (1,2-g-tetrads-K^＋和2,3-g-tetrads-K^＋)为研究对象. 为g-tetrad-K^＋, 1,2-g-tetrads-K^＋和2,3-g-tetrads-K^＋三体系中的K^＋设计了几种移动路径, 来探讨G4中K^＋与g-tetrad的作用. 首先分别应用从头计算MP2/6-31G(d,p)和ABEEMσπ/MM(σπ水平的原子键电负性均衡原理融入到分子力学)方法, 对g-tetrad-K^＋中K^＋移动过程中体系的结构和能量变化进行了详细研究. 结果表明ABEEMσπ/MM方法能够准确地描述g-tetrad-K^＋体系的结构、结合能等性质. 为了更接近实际体系, 进而用ABEEMσπ/MM方法预测了更大的体系: 一个K^＋和两片g-tetrad. 由于体系较大, MP2方法无法计算其结合能. ABEEMσπ/MM方法对g-tetrad-K^＋, 1,2-g-tetrads-K^＋和2,3-g-tetrads-K^＋体系中K^＋移动而产生的结合能变化表明: 如果吸收足够的能量, G4中K^＋最容易沿α方向移出.     

鸟嘌呤四链体中Na+的移动

Na+-G-四链体复合物是一个明显的极化体系, 其形成或解离过程中, Na+的移动路线目前还不十分明确. σπ水平的原子-键电负性均衡方法融合进分子力学(ABEEMσπ/MM)模型除原子位点外, 还明确地定义了孤对电子、σ键和π键的位置, 并且各位点电荷随分子环境改变而浮动, 因此能更好地反映该体系的极化现象. 本文应用ABEEMσπ/MM方法研究了Na+-G-四平面复合物的性质, 包括它的几何构型、电荷分布和结合能等, 并在MP2/6-31G(d,p)水平上做了相应的从头算, 两种结果十分吻合. Na+的存在改变了G-tetrad的氢键方式. 通过比较Na+各条移动路线中体系的结合能, 预测G-四链体中三个Na+最有可能沿α方向依次移出. 以上研究为进一步应用ABEEMσπ/MM模型进行G-四链体中离子交换通道的动力学模拟打下坚实的基础.     

水合氢离子团簇从头算和ABEEM/MM的理论研究

应用高水平的从头计算方法和ABEEM/MM模型, 研究了水合氢离子团簇H3O＋(H2O)n (n＝1～6), 优化得到了低能构象, 探讨了其结合能和稳定性, 显示出H3O＋(H2O)3局域结构的优势存在．对H3O＋(H2O)6VIa团簇的ABEEM电荷分布进行分析, 表明第一水合层水分子与水合氢离子之间的氢键相互作用要明显强于与第二水层水分子的氢键相互作用. 研究结果表明, ABEEM/MM方法计算的结果和从头算得到的结果存在很好的一致性.     

DNA G-四链体的结构完整性对催化性质的影响

DNA酶中的G-四链体-血红素(G4-hemin)DNA酶结构具有较高的设计性和化学稳定性,因此格外受研究者关注.G-平面作为辅酶因子hemin的结合位点,不仅提供大π平面与hemin结合,而且其平面上的G碱基还可以充当近端配位基团与hemin进行配位.因此,研究G-平面完整性在G4-DNA酶体系中的作用具有重要意义....     

鸟嘌呤四链体在生化分析中的应用进展

鸟嘌呤四链体(G-四链体)是一种特殊的核酸二级结构,它可与高铁血红素结合,形成具有过氧化物酶活性的核酶;也可增强特殊结构染料的荧光强度。G-四链体作为功能核酸中的一种,具有性质稳定、特异性好、功能多样等特点,被广泛应用于各种生化分析中。本文对近年来G-四链体在生化分析中的研究和应用进展进行了评述,对其应用前景进行了展望。     

人体端粒中(3+1)混合结构G-四链体稳定性的分子动力学模拟

利用分子动力学模拟方法, 考察了人体端粒中(3+1)混合结构G-四链体的结构及稳定性问题. 讨论了配位K+离子、药物分子(端粒抑素)和溶剂水分子对G-四链体的Hoogsteen氢键结构、π-π堆积作用的影响. 研究表明, K+离子与鸟嘌呤碱基上O6原子的配位作用减弱了对角鸟嘌呤间O6-O6的静电排斥作用, 使得相邻的四个鸟嘌呤能够以Hoogsteen氢键结合的方式形成具有近平面结构的稳定G-四平面. 另一方面, G-四平面间、G-四平面与药物分子间的π-π堆积作用降低了G-四链体复合物的总能, 有利于其稳定存在. 此外, 溶剂水分子主要分布在G-四链体的TTA环、骨架和糖环的周围, 使其位移涨落增大; 然而, 在3 ns动力学模拟中, 由于水分子没有进入到G-四链体的空腔中, 溶剂水对G-四平面的结构影响不明显.     

实验与理论研究G-四链体中鸟嘌呤自由基阳离子脱质子反应

G-四链体传输空穴的特殊性质使其有望应用于发展分子电子器件.由于鸟嘌呤自由基阳离子（G^·+）脱质子反应会中断空穴传递,影响传递效率,我们对G-四链体AG₃（T₂AG₃）₃中G^·+脱质子过程展开了理论与实验的研究.根据瞬态紫外可见吸收光谱,确定了脱质子产物是G（N（2）-H）^·;通过测量不同温度下G^·+脱N（2）-H质子的速率常数,得到脱质子活化能为20.0±1.0 kJ/mol.进而,采用显性水和连续溶剂化模型相结合的方法模拟G-四链体中G^·+脱质子环境,在M062X/6-31G（d）水平上得到了脱质子势垒（26.4 kJ/mol）.结合实验值,理论计算的势能面描述了G-四链体中G^·+脱N2-H的过程.这些结果为G-四链体在电子器件方面的应用提供了重要依据和指导.     

钾离子浓度依赖的铅离子稳定G-四链体构型转化

已有研究普遍认为铅离子(Pb²⁺)诱导富G适体链形成的G-四链体(Pb²⁺-G4)比钾离子(K⁺)诱导富G适体链形成的G-四链体(K⁺-G4)更为稳定,因而Pb²⁺可以置换K⁺-G4中的K⁺,而且K⁺的存在不影响Pb²⁺-G4的稳定性。有趣的是本研究发现K⁺ (20 μmol∙L⁻¹–1 mmol∙L⁻¹)不仅可以诱导10 µmol∙L⁻¹ Pb²⁺稳定的T2TT(Pb²⁺-T2TT,杂合G4结构)发生构型转换,甚至还可取代Pb²⁺-T2TT中的Pb²⁺,形成K⁺稳定的T2TT (K⁺-T2TT,平行G4结构),最终转化形成的K⁺-G4结构与单独K⁺诱导富G适体链形成K⁺-G4的构型基本一致。随后,进一步考察了另外7条富G适体链,发现这一转化过程具有一定的普适性。该研究结果为理解G4构型转化以及内嵌离子交换提供了新的视角,也为拓展G4在生化分析和生物领域的应用提供了新的理论基础。     

脂肪族氨基酸二肽与水团簇的理论研究

用ABEEMσπ/MM模型和MP2/6-31+G(d)//B3LYP/6-31G(d)方法研究水合效应对脂肪族氨基酸二肽的影响.从结构和能量两方面说明Leu残基在蛋白质中起成旋作用,Val和Ⅱe残基在蛋白质中起解旋作用.同时得出:水分子严重影响了二肽分子的骨架二面角;对于结合相同数目水分子的团簇倾向于形成含有环状氢键的结构,并且含有环状氢键团簇的结合能大于含有链状氢键团簇的结合能.     

Ab initio study of the reaction mechanism of water dissociation into the ionic species OH− and H3O+

A reaction mechanism of water dissociation is proposed where solvent effects are accounted for via a minimum stable model that considers the interaction of five water molecules. It is based on the fully self-consistent field (SCF) optimized structures of the reactant, product, and transition state, the calculations being at the Hartree–Fock and configuration interaction level [Møller–Plesset second-order perturbation (MP2) and coupled-cluster single and double excitations (CCSD)]. They were performed with four different basis sets that included polarized and diffuse orbitals. The dissociative mechanism leads to the ionic species OH⁻+H₃O⁺ as stable products and upon analysis of the energy hypersurface, a transition state is found which yields an activation barrier of 21.2 kcal/mol. This value is in good agreement with the experimentally determined enthalpy for the reaction. The contribution of the aggregation energy is emphasized. © 1998 John Wiley & Sons, Inc. Int J Quant Chem 68: 253–259, 1998     

The interaction of water with sulfonium ions and the effects of hydration on the energetics of methyl group transfer: An ab initio molecular orbital study of the hydration of (CH3)3S+ and (CH3)2S+CH2CO2 −

The interactions of the sulfonium ions (CH₃)₃S⁺, (CH₃)₂S⁺CH₂CO₂ ^–, and (CH₃)₂S⁺-CH₂CH₂CO₂ ^– with up to four water molecules have been studied by ab initio molecular orbital methods. Complexes of (CH₃)₃S⁺ with one to three water molecules involve strong electrostatic sulfur-oxygen interactions; in contrast, the sulfide (CH₃)₂S interacts with water molecules via weak S-H hydrogen bonds, suggesting that methyl-group transfer from (CH₃)₃S⁺ in aqueous solution involves a significant alteration of the hydration pattern around the sulfur atom. Two conformers of (CH₃)₂S⁺CH₂CO₂ ^– were found that display sulfur-oxygen distances which are approximately 0.3 å less than the sum of the sulfur and oxygen van der Waals radii, indicating a strong intramolecular electrostatic interaction. For the complexes (CH₃)₂S⁺CH₂CO₂ ^–·nH₂O(n =1–4), water interacts primarily with the carboxylate group via hydrogen bonds, rather than electrostatically with the sulfur atom, although in complexes with the three- and four-water complexes, the proximity of the positively charged sulfur atom to the carboxylate group significantly alters the hydration pattern compared to that in the corresponding of complexes CH₃SCH₂CO₂ ^–· Thus, methyl transfer from (CH₃)₂S⁺CH₂CO₂ ^– to an acceptor in aqueous solution also involves substantial changes in the hydration pattern around the carboxylate group.     

Charge transfer mechanism in N4+ + He and B3+ + He/H2 ion–atom/molecule collisions

Ab initio potential energy curves and coupling matrix elements of the molecular states involved in the collision of the N⁴⁺(2s)²S and B³⁺(1s²)¹S multicharged ions on the helium atom or molecular hydrogen have been determined by means of configuration interaction methods. The total and partial electron capture cross-sections have been evaluated in the frame of a semiclassic approach in the 1- to 100-keV laboratory energy range and compared to experimental data. A comparative study of both targets is performed in the case of the B³⁺ ion. © 2002 Wiley Periodicals, Inc. Int J Quantum Chem, 2002     

Gas-phase reactivity of the O=P(OCH3)2 + phosphonium ion towards alpha,beta-unsaturated esters in a quadrupole ion trap

Ion-molecule reactions between the O=P(OCH3)2 + phosphonium ions and eight alpha,beta-unsaturated esters (methyl acrylate, ethyl acrylate, methyl crotonate, ethyl crotonate, methyl 3,3-dimethylacrylate, ethyl 3,3-dimethylacrylate, methyl methacrylate and ethyl methacrylate) were performed in a quadrupole ion trap mass spectrometer. The O=P(OCH3)2 + phosphonium ions, formed by electron ionization from neutral trimethyl phosphite, were found to react with alpha,beta-unsaturated esters to give an adduct [RR'C=CR'COOR', O=P(OCH3)2]+, which lose spontaneously a molecule of trimethyl phosphate (R'=CH3) or dimethyl ethyl phosphate (R'=C2H5). An ion corresponding to a protonated trialkyl phosphate is also observed when substituent R'=H. To confirm the experimental results, and to elucidate the mechanism for the formation of the ionic species, a theoretical study using the density functional theory (DFT) approach was carried out. The potential energy surface obtained from B3LYP/6-31G(d,p) calculations for the reaction between O=P(OCH3)2 + and methyl acrylate is described.     

Gas-phase reactivity of the O=P(OCH3)2+ phosphonium ion with aliphatic esters in a quadrupole ion trap. Spontaneous elimination of ketenes

Ion-molecule reactions between the O=P(OCH(3))(2) (+) phosphonium ions and five aliphatic esters (methyl acetate, methyl propionate, methyl 2-methylpropionate, methyl butyrate and ethyl acetate) were performed in a quadrupole ion trap mass spectrometer. The O=P(OCH(3))(2) (+) phosphonium ions, formed by electron ionization from neutral trimethyl phosphite, were found to react with aliphatic esters to give an adduct ion [RR'CHCOOR", O=P(OCH(3))(2)](+), which loses spontaneously a molecule of ketene CH(2)=CO or substituted ketenes RR'C=CO. Isotope-labeled methyl acetate was used to elucidate fragmentation mechanisms. The potential energy surface obtained from B3LYP/6-31G(d,p) calculations for the reaction between O=P(OCH(3))(2) (+) and methyl acetate is described.     

A Theoretical Study of LiHe+ n , NaHe+ n , and MgHe+ n Complexes, with n=1, 2, 3, 4

The LiHe⁺ _n , the NaHe⁺ _n , and the MgHe⁺ _n complexes with n=1, 2, 3, 4 were studied using ab initio calculations with the MP2/6-311+G(3df, 3pd) method. The complexes are found to be stable. For the n=1 complexes, previous results were available and the calculations performed are in good agreement with those results. This lends credibility to the results obtained for the complexes with higher n.     

Theoretical calculation of the low laying electronic states of the molecular ion RbH+

Using an ab initio method, the potential energy has been calculated for the 29 lowest molecular states of symmetries ²Σ⁺, ²Π, ²Δ for the molecular ion RbH⁺. The calculation is based on nonempirical pseudopotentials and parameterized ?‐dependent polarization potentials. Gaussian basis sets have been used for both atoms. The spectroscopic constants for 18 electronic sates have been calculated by fitting the calculated energy values to a polynomial in terms of the internuclear distance R. Through the canonical functions approach the eigenvalue E_v, the abscissas of the corresponding turning points (R_min and R_max) and the rotational constants B_v have been calculated up to 24 vibrational levels for the considered bound states. The comparison of the present results with those available in literature shows a very good agreement. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010     

超价化合物M_(n+1)F_n(n=1,2;M=Na,K)体系的非线性光学性质的理论研究

采用UMP2/6-311+G(3df)方法研究了一系列化合物M_(n+1)F_n(n=1,2;M=Na,K)体系的几何构型及非线性光学性质(NLO).结果表明:这些体系均为超价化合物,均拥有较大的第一超极化率(β_0).尤其是Na_3F_2体系中结构2c的β_0值为29.16×10~(-49)C~3·m~3·J~(-2),是已知超价化合物Li_3F_2的2c结构的β_0值2.22×10~(-49)C~3·m~3·J~(-2)的13.1倍.