取代基对腺嘌呤与胸腺嘧啶氢键复合物体系结合能的影响简

优化得到了17个取代胸腺嘧啶与腺嘌呤形成的氢键复合物的结构,并计算了这些复合物的结合能,探讨了胸腺嘧啶上不同取代基对结合能的影响. 结果表明,CF3取代的胸腺嘧啶与腺嘌呤间的结合能大于胸腺嘧啶与腺嘌呤间的结合能,这可能是屈氟尿苷具有阻止病毒及肿瘤扩散功能的原因所在. SO3H,CN和NO2取代的胸腺嘧啶与腺嘌呤间具有更大的结合能,表明这3个基团取代的胸腺嘧啶也可能具有潜在的抗肿瘤作用. 分子中原子理论与自然键轨道分析表明,在所有体系中,氢键N—H…N最强,N—H…O=C次之,C—H…O=C最弱,轨道作用在氢键作用中占有重要地位.     

核酸碱基与甘氨酸二肽间氢键作用的最佳位点

优化得到了碱基腺嘌呤、胸腺嘧啶、尿嘧啶、鸟嘌呤及胞嘧啶与甘氨酸二肽分子形成的28个氢键复合物的稳定结构并计算了结合能, 探讨了五种碱基与甘氨酸二肽分子间氢键作用的最佳位点. 本文研究发现: 每种碱基均可以通过不同位点与二肽分子形成氢键复合物, 腺嘌呤、胸腺嘧啶、尿嘧啶、鸟嘌呤及胞嘧啶分别最倾向使用A3、T1、U1、G3及C1位点与甘氨酸二肽分子形成氢键复合物; 碱基分子某位点的质子化反应焓变越负所形成的氢键复合物越稳定, 去质子化反应焓变越小所形成的氢键复合物越稳定; 由氢键复合物的结合能计算得到的稳定性次序与由碱基分子质子化和去质子化反应焓变推得的稳定性次序一致.     

带电组氨酸侧链与DNA碱基间非键作用强度的理论研究

采用MP2方法和6-31+G(d,p)基组优化得到了带有一个正电荷的组氨酸侧链与4个DNA碱基间形成的18个氢键复合物的气相稳定结构, 从文献中获取了组氨酸侧链与DNA碱基间形成的12个堆积和T型复合物的气相稳定结构, 使用包含基组重叠误差(BSSE)校正的MP2方法和aug-cc-pVTZ基组及密度泛函理论M06-2X-D3方法和aug-cc-pVDZ基组计算了这些复合物的结合能. 研究结果表明, 包含BSSE校正的M06-2X-D3方法和aug-cc-pVDZ基组能够给出较准确的结合能; 气相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用明显强于堆积作用和T型作用, 组氨酸侧链最易通过离子氢键与胞嘧啶C和鸟嘌呤G作用形成氢键复合物, 组氨酸与胞嘧啶C和鸟嘌呤G间的T型作用强于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用; 水相条件下, 组氨酸侧链与同种DNA碱基间的离子氢键作用仍明显强于堆积作用和T型作用, 组氨酸侧链更易与胞嘧啶C和鸟嘌呤G相互作用形成氢键复合物, 但是最强的组氨酸侧链与胞嘧啶C间的T型作用明显弱于与腺嘌呤A和胸腺嘧啶T间的离子氢键作用, 说明水相条件下组氨酸侧链与DNA碱基间主要通过离子氢键作用形成氢键复合物.     

槲皮素与尿嘧啶和胸腺嘧啶氢键的结合位点

深入理解药物分子和核酸碱基间的相互作用机制对合理设计研发新型高效药物有重要意义. 本文运用密度泛函理论B3LYP方法对核酸碱基尿嘧啶和胸腺嘧啶与药物分子槲皮素间的氢键相互作用位点进行了研究. 使用B3LYP/6-31G(d)方法优化得到了30个稳定的氢键复合物结构, 使用B3LYP/6-311++G(3df,2p)方法计算了这些复合物的结合能. 研究结果表明, 槲皮素可以使用5个不同的结合位点与尿嘧啶或胸腺嘧啶形成氢键复合物, 尿嘧啶或胸腺嘧啶可以使用3个不同的结合位点与槲皮素形成氢键复合物. 当槲皮素的结合位点固定时, 槲皮素与尿嘧啶的位点u1或胸腺嘧啶的位点t1形成的氢键作用最强, 与位点u2或位点t2形成的氢键强度最弱; 当尿嘧啶或胸腺嘧啶的作用位点固定时, 二者与槲皮素的位点qu1 形成的氢键作用最强, 与位点qu5 作用强度次之, 与位点qu3的作用强度最弱. 分子中原子(AIM)和自然键轨道(NBO)分析计算结果表明, 轨道作用在氢键中起重要作用.     

含氮杂冠醚和核酸碱基双亲聚合物的合成及性能

设计合成了含氮杂冠醚和胸腺嘧啶的双亲聚合物聚[N,N-二乙氧基-1,10-二氮杂-18冠-6-5-甲基-胸腺嘧啶-异酞酸酯](PCTSE). 用SEM观测到其在水溶液中自发聚集成直径为150~220 nm的纳米球; 用动态光散射测得PCTSE纳米球水溶液的粒径分布主要集中在130~240 nm, 用FTIR研究了PCTSE/腺嘌呤中胸腺嘧啶与底物腺嘌呤的分子识别作用, 结果表明, 聚合物中胸腺嘧啶环上C₄=O伸缩振动峰从1670 cm^-1位移至1664 cm^-1, 表明胸腺嘧啶与腺嘌呤间形成了氢键. 变温红外光谱表明, 该峰又随温度的升高逐渐向高波数位移, 最后位移到识别前的1670 cm^-1处, 表明所形成的氢键断裂.     

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计,进而制备具有特殊纳米结构和功能的生物分子材料.本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20个氢键复合物的结构并计算了结合能,探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点.研究发现:腺嘌呤可以使用两个不同位点(A1位点和A2位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物,腺嘌呤使用A1位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定;二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物,二肽分子使用Ala7或Gly7位点与腺嘌呤形成的氢键复合物更稳定;腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用.基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.     

槲皮素与腺嘌呤氢键作用的最佳位点

本文优化得到了16个由槲皮素与腺嘌呤形成的氢键复合物的稳定结构,并计算了它们的结合能.研究发现,在气相和水相中,槲皮素均通过qu1位点与腺嘌呤作用形成稳定的氢键复合物.比较了腺嘌呤与槲皮素形成的氢键复合物、腺嘌呤与胸腺嘧啶形成的Watson-Crick碱基对的相对稳定性.在气相条件下Watson-Crick碱基对更稳定,在水相条件下腺嘌呤与槲皮素形成的氢键复合物更稳定,说明水相条件下腺嘌呤与槲皮素之间的相互作用强于与胸腺嘧啶之间的相互作用.基于标准反应Gibbs自由能变的计算结果估算了水相条件下腺嘌呤与槲皮素形成的氢键复合物和Watson-Crick碱基对的相对平衡浓度.     

精氨酸侧链和核酸碱基间离子氢键作用强度分析

采用MP2/6-31+G(d,p)方法优化得到了22个由精氨酸侧链与碱基尿嘧啶、 胸腺嘧啶、 胞嘧啶、 鸟嘌呤及腺嘌呤形成的氢键复合物的气相稳定结构, 使用包含BSSE校正的MP2/aug-cc-pVTZ方法计算得到了复合物的气相结合能, 通过MP2/6-31+G(d,p)方法和PCM模型优化得到了复合物的水相稳定结构, 采用MP2/aug-cc-pVTZ方法和PCM模型计算得到了复合物的水相结合能. 研究发现, 精氨酸侧链与碱基间的离子氢键作用强度与单体间电荷转移量、 氢键临界点电子密度及二阶作用稳定化能密切相关. 与中性氢键相比, 离子氢键作用具有更显著的共价作用成分. 研究还发现, 精氨酸侧链和碱基间形成的氢键复合物的稳定性次序可以通过氢键受体碱基分子上氧原子和氮原子的质子化反应焓变进行预测, 质子化反应焓变越负, 形成的氢键复合物越稳定.     

Cu2+对腺嘧啶-胸腺嘧啶碱基对阴离子质子转移的影响

采用B3LYP/DZP++方法研究了腺嘌呤-胸腺嘧啶(A-T)碱基对阴离子(AT)-的单质子转移机理以及金属离子Cu2+对(AT)-碱基对质子转移的影响.(AT)-碱基对的单质子转移路径是由胸腺嘧啶N25位上的质子H26沿分子间的氢键N25-H26…N10转移到腺嘌呤的N10位.金属Cu2+可通过络合作用分别吸附在(AT)-碱基对O24、O28、N4、N13上,从而影响(AT)-碱基对中质子转移过程.Cu2+络合作用在胸腺嘧啶(T)的O24、O28上时,发生了从胸腺嘧啶到腺嘌呤方向上的单质子转移反应;而作用在腺嘌呤(A)的N4、N13上时,得到了双质子转移的稳定产物.     

B3N3H6…CO复合物中弱相互作用竞争的理论研究

本文在MP2/aug-cc-pVTZ水平下对一氧化碳(CO)和环硼氮烷(B₃N₃H₆)之间的弱相互作用进行理论研究，得到6种稳定的B₃N₃H₆…CO复合物结构。B₃N₃H₆…CO复合物中存在N—H…C/O氢键以及π…π、lp…π相互作用，其中含N—H…C氢键复合物的相互作用能(ΔE)最大，为-1.42 kcal·mol^-1。系统的理论计算结果表明π…π相互作用和N—H…C/O氢键可以成功地与lp…π相互作用竞争。取代基效应结果显示，B₃N₃X₃H₃(X=-NH₂)…CO、B₃N₃H₆…CO、B₃N₃X₃H₃(X...     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,氢键键长r(H…O)伸长,氢键强度减弱.自然键轨道(NBO)分析表明,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子n(O)对N-H的反键轨道σ~*(N-H)的二阶相互作用稳定化能增加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

Molecular orbital theory of the hydrogen bond : XXXII. The effect of H and Li association on the A---T and G---C pairs

Ab initio molecular orbital calculations have been performed to determine the structures and stabilization energies of the A---T and G---C base pairs and their complexes with H⁺ and Li⁺, H⁺ and Li⁺ association stabilizes the A---T pair except for Li⁺ association at O₄ in thymine. Protonation of thymine stabilizes the A---T pair to a greater extent than protonation of adenine. The association of H⁺ and Li⁺ with guanine stabilizes the G---C pair, but protonation of cytosine destabilizes G---C. Changes in the structures of the hydrogen bonds in the A---T and G---C pairs reflect changes in hydrogen bond strengths.     

Density Functional Theory Study on Interaction between Catechin and Thymine

The interacting patterns and mechanism of the catechin and thymine have been investigated with the density functional theory Becke's three-parameter nonlocal exchange functional and the Lee, Yang, and Parr nonlocal correlation functional (B3LYP) method by 6-31+G*basis set. Thirteen stable structures for the catechin-thymine complexes have been found which form two hydrogen bonds at least. The vibrational frequencies are also studied at the same level to analyze these complexes. The results indicated that catechin interactedwith thymine by three different hydrogen bonds as N-H…O、C-H…O、O-H…O and the complexes are mainly stabilized by the hydrogen bonding interactions. Theories of atoms in molecules and natural bond orbital have been adopted to investigate the hydrogen bondsinvolved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error, which are from -18.15 kJ/mol to -32.99 kJ/mol. The results showed that the hydrogen bonding contribute to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red-shifted relative to that of the monomer, which is in agreement with experimental results.     

A comparative study of open‐close and related rotamers methods to evaluate the intramolecular hydrogen bond energies in 3‐imino‐propen‐1‐ol and its derivatives

MP2 study of O? H…N intramolecular hydrogen bond (IMHB) in 3‐imino‐propen‐1‐ol and its derivatives were performed and their IMHB energies were obtained using the related rotamers and open‐close methods. Also the topological properties of electron density distribution and charge transfer energy associated with IMHB were gained by quantum theory of atoms in molecules and natural bond orbital theory, respectively. The computational results reveal that the related rotamers method energies are well correlates with geometrical parameters, topological parameters at hydrogen bond and ring critical points, integrated properties, proton transfer barrier and charge transfer energy of O? H…N unit. Surprisingly, it was found that the open‐close hydrogen bond energies cannot represent good linear correlations with these parameters. Consequently, we extrapolate a number of equations that can be used in estimation of O? H…N IMHB energy in complex biological systems. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

C6H5—H…X分子间氢键的理论计算

利用密度泛函理论B3LYP方法, 在6-311+G(3df,2p)水平上对C6H5—H…X型分子间氢键进行了几何构型优化、氢键相互作用能、电子密度分布等计算. 其中C6H6为质子供体, HCOH、H2O、NH3、CH2NH和HCN为质子受体. 从电荷布居分析、自然键轨道等角度详细地讨论了C6H5—H…X 体系中, 共轭π键、O和N的不同键型结构对氢键形成的影响以及孤电子对与C—H 反键轨道之间的相互作用(n→σ*)等.     

The explicit interactions of five-membered saturated heterocyclics containing one and two heteroatoms with single water molecule

In this article, the hydrogen bonding interaction between saturated five-membered heterocyclic molecules and water has been investigated. Molecular orbital and density functional theory methods have been used to evaluate the stabilization energies associated with the adduct formation between heterocyclic molecules and water. The hydrogen bond acceptor ability of O, S, Se, and N as members of five-membered ring has been analyzed. The effect of the presence of second heteroatom N in the ring on the hydrogen bond interaction has also been evaluated. Atoms in molecules theory calculations were carried out to characterize the hydrogen bond through the changes in electron density and Laplacian of electron density. A natural energy decomposition analysis and natural bond orbital analysis is also performed to understand the nature of hydrogen bonding interaction in monohydrated five-membered heterocyclic adducts.     

Theoretical investigation of gas phase ethanol–(water)n (n = 1–5) clusters and comparison with gas phase pure water clusters (water)n (n = 2–6)

Various properties (such as optimal structures, structural parameters, hydrogen bonds, natural bond orbital charge distributions, binding energies, electron densities at hydrogen bond critical points, cooperative effects, and so on) of gas phase ethanol–(water)_n (n = 1–5) clusters with the change in the number of water molecules have been systematically explored at the MP2/aug‐cc‐pVTZ//MP2/6‐311++G(d,p) computational level. The study of optimal structures shows that the most stable ethanol‐water heterodimer is the one where exists one primary hydrogen bond (O? H…O) and one secondary hydrogen bond (C? H …O) simultaneously. The cyclic geometric pattern formed by the primary hydrogen bonds, where all the molecules are proton acceptor and proton donor simultaneously, is the most stable configuration for ethanol–(water)_n (n = 2–4) clusters, and a transition from two‐dimensional cyclic to three‐dimensional structures occurs at n = 5. At the same time, the cluster stability seems to correlate with the number of primary hydrogen bonds, because the secondary hydrogen bond was extremely weaker than the primary hydrogen bond. Furthermore, the comparison of cooperative effects between ethanol–water clusters and gas phase pure water clusters has been analyzed from two aspects. First of all, for the cyclic structure, the cooperative effect in the former is slightly stronger than that of the latter with the increasing of water molecules. Second, for the ethanol–(water)₅ and (water)₆ structure, the cooperative effect in the former is also correspondingly stronger than that of the latter except for the ethanol–(water)₅ book structure. © 2012 Wiley Periodicals, Inc.     

Theoretical study of the red‐ and blue‐shifted hydrogen bonds of nitroxyl and acetylene dimers

Ab initio molecular orbital and density functional theory (DFT) in conjunction with different basis sets calculations were performed to study the C? H…O red‐shifted and N? H…π blue‐shifted hydrogen bonds in HNO? C₂H₂ dimers. The geometric structures, vibrational frequencies and interaction energies were calculated by both standard and counterpoise (CP)‐corrected methods. In addition, the G3B3 method was employed to calculate the interaction energies. The topological and natural bond orbital (NBO) analysis were investigated the origin of N? H…π blue‐shifted hydrogen bond. From the NBO analysis, the electron density decrease in the σ* (N? H) is due to the significant electron density redistribution effect. The blue shifts of the N? H stretching frequency are attributed to a cooperative effect between the rehybridization and electron density redistribution. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006