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.     

有机分子识别和聚集体组装中的非共价键协同作用

综述了近年来不同的非共价键作用力包括分子间氢键、供体-受体相互作用、π-π堆积作用、静电作用、疏溶剂作用和金属-配体配位作用等的协同作用在有机分子识别和有序聚集体组装研究中的应用.     

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.     

水溶液中几种芳香族氨基酸π-π自堆叠作用

利用精密的流动混合微量热法测定了298.15 K时D/L-色氨酸、L-色氨酸、L-组氨酸和L-苯丙氨酸四种天然芳香族氨基酸水溶液的稀释焓, 根据所建立的拟等步自堆叠作用的化学模型对实验数据进行了处理, 计算得到模型参数K△Hm. 该化学作用参数与McMillan-Mayer理论模型中的焓对作用系数具有高度一致性, 即hxx=K△Hm. 结合文献报道的结果, 认为芳核π-π自堆叠作用在本质上是一种特殊的疏水-疏水作用, 一般表现为吸热效应; 取代基空间位阻、芳核以外部分的静电、氢键和手性选择性作用等对芳核π-π自堆叠作用有显著影响; 组合参数K△Hm实际上描述了芳核π-π自堆叠作用平衡及焓变的综合效应.     

金属卟啉对杂环及DNA分子识别研究进展

介绍了近几年国内外关于组装金属卟啉对杂环分子、DNA碱基以及RNA的分子识别的研究进展, 并简述了本课题组对金属卟啉与杂环及药物分子复合物的理论研究工作. 金属卟啉广泛存在于自然界和生物体中, 此识别过程对研究和模拟生命体中各种细胞之间的相互作用具有重要意义. 组装后的金属卟啉可通过轴向配位、氢键及π-π堆积作用等识别杂环分子. 金属卟啉对DNA的识别主要有四种作用方式, 而金属卟啉对DNA以及RNA分子的识别主要靠疏水作用力、静电力以及自堆叠作用. 卟啉阳离子与DNA的结合位点受主体侧链取代基的空间结构影响. 金属卟啉对药物分子的识别靠配位键和氢键进行, 以配位键结合的复合物通常具有更高的结合能.     

分子间作用力对咪唑盐介晶相性质的影响

通过对咪唑环1位(N1)取代烷基、3位(N3)取代基及阴离子的修饰合成了一系列具有近晶A (SmA)相的咪唑类离子液晶. 利用差示扫描量热法、单晶衍射、小角度X射线衍射等手段研究了咪唑盐的介晶相温度范围、介晶态的结构, 并测量了部分咪唑盐的各向异性导电率. 结果表明, 咪唑环N1取代烷基、N3取代基及咪唑盐的阴离子会改变分子间范德华力和氢键, 从而对咪唑盐的介晶相性质产生影响. 此外, 当乙烯基引入到咪唑环N3位置时, 咪唑盐相邻的层结构之间形成π-π堆积作用, 不仅有利于介晶态的形成, 同时使氟硼酸类离子液晶具有最大的层间距和最小的各向异性导电率. 这一结果表明, 调控离子液晶的性质时必须综合考虑各种分子间作用力的影响.     

喜树碱合成中间体的光学异构体分离及分离机理研究

首次在CHI-DMB及(R,R)-DNB-DPEDA手性柱上对喜树碱合成中间体--2-[N-对甲苯磺酰基-(R)-脯氨酰氧基]-2-[6-氰基-(1,1-亚乙二氧基)-5-酮-1,2,3,9-四氢中氮茚-7-基]-丁酸乙酯进行了光学异构体分离. 考察了流动相中极性醇类添加剂对手性分离种类及浓度对分离的影响, 并比较了溶质在这两种手性柱上的手性识别机理, 结果发现在这两种手性固定相上, 溶质与手性固定相之间的吸引作用都是产生手性识别的关键. 从溶质与固定相的空间结构看, 在CHI-DMB手性柱上, π-π堆积作用及偶极偶极作用起了关键作用; 而在(R,R)-DNB-DPEDA手性柱上, π-π堆积作用, 偶极偶极作用及氢键作用对分离起了重要作用. 此外, 空间位阻在喜树碱中间体的光学异构体分离中也起了一定的作用. 根据溶质和固定相的空间结构, 推导出的两个光学异构体的流出顺序, 并通过相应的光学异构体得到验证.     

折叠型双银配合物电子结构与相关性质

在密度泛函B3LYP/LanL2DZ的水平上,对具有π-π弱相互作用调控的折叠型银配合物Ag₂(MPTQ)₂²⁺进行计算研究。探讨该配合物的电子结构、成键特征、π-π弱相互作用机理、电荷布居及其相关性质。计算结果表明,Ag…Ag之间存在弱的直接相互作用,HOMO主要布居在配体中芳香环的σ-p轨道、S的σ-p轨道及与S相连的C12的S轨道上,LUMO主要布居在配体中芳香环的π^*-p轨道上,基态电子光谱主要是配体中的n→π^*跃迁产生的电荷转移光谱。论文还讨论了分子间π-π弱相互作用的本质及活性部位等。计算结果能较好地解释实验现象与规律。     

聚噻吩/多壁碳纳米管复合材料的导电性能

通过共混多壁碳纳米管(MWNTs)和聚噻吩(PTh), 制备了PTh/MWNTs复合材料, 复合材料表现出良好的导电性能(电导率达16.1 S/m). 通过Raman, TG, XPS, UV-Vis等对复合材料进行了分析, 结果表明, MWNTs和 PTh之间存在强的相互作用, MWNTs上的离域电子与噻吩共轭主链上的π电子之间形成π-π共轭, 电子从MWNTs转移到聚噻吩, 增加了噻吩主链的有效共轭长度, 提高了复合材料的导电性能. FESEM分析表明, MWNTs和它周围被掺杂的聚噻吩通过π-π共轭作用结合在一起, 形成相对独立的导电单元, 在复合材料的导电体系中起到主要作用.     

分子间作用力构筑的具有柔性结构的醋氯芬酸多聚物: 晶体结构, 热稳定性, 溶解度和DFT计算

非甾体类抗炎药物醋氯芬酸(ACF)的水溶性差, 导致其生物利用度较低. 本文制备了三种多聚物, 分别是醋氯芬酸与4,4'-联吡啶(BIPY)共晶(1), 与3-氨基苯甲酸(3-ABA)盐(2)和与二甲基亚砜(DMSO)的溶剂化物(3), 利用红外光谱、粉末X射线衍射和单晶X射线衍射对它们的结构进行了表征. 结果表明, 化合物1-3的超分子结构是通过氢键、C―H…π和π…π堆积作用构筑而成, 三个多聚物具有良好的热稳定性. 从热力学角度分析和密度泛函理论(DFT)计算说明ACF在化合物3中的构象比其在化合物1和2中更稳定. 此外, ACF形成共晶、盐和溶剂化物后有效提高了其溶解度.     

On the stability of single- and double-stranded DNA helices: The application of the PPT-MCF method on large fragments of DNA

The pseudo-polarization tensor mutually consistent field (PPT -MCF ) method recently introduced [1] has been applied to study the stacking interactions between the nucleotide bases in large periodic B-DNA fragments. The effects on the global and local binding properties caused by replacing one base in the periodic sequence by another base are investigated. The increase in the stability for comparable fragments owing to this base substitution is further enforced in the case of periodic alternating helices. The most important results are that the stacking interaction between two bases is slowly converging with the interbase distance and that the average contribution per base to the binding energy is repulsive. Furthermore, the energetical properties of double helix models in B- and Z-DNA configurations, respectively, consisting of up to five base pairs have been compared. It turns out that the G C G C sequence in Z-DNA is significantly more stable than either in periodic or periodic alternating B-DNA. In these cases the average energy contribution of a single Watson–Crick-type base pair is predicted also to be positive. From the calculations it follows that the double helix is not stabilized owing to the hydrogen bonding between the bases belonging to both strands, in contradiction to most other investigations.     

Understanding the role of base stacking in nucleic acids. MD and QM analysis of tandem GA base pairs in RNA duplexes

Preceding NMR experiments show that the conformation of tandem GA base pairs, an important recurrent non-canonical building block in RNA duplexes, is context dependent. The GA base pairs adopt "sheared" N3(G)-N6(A), N2(G)-N7(A) geometry in the r(CGAG)(2) and r(iGGAiC)(2) contexts while switching to "imino" N1(G)-N1(A), O6(G)-N6(A) geometry in the r(GGAC)(2) and r(iCGAiG)(2) contexts (iC and iG stand for isocytosine and isoguanine, respectively). As base stacking is likely to be one of the key sources of the context dependence of the conformation of GA base pairs, we calculated base stacking energies in duplexes containing such base pairs, to see if this dependence can be predicted by stacking energy calculations. When investigating the context dependence of the GA geometry two different conformations of the same duplex were compared (imino vs. sheared). The geometries were generated via explicit solvent MD simulations of the respective RNA duplexes, while the subsequent QM energy calculations focused on base stacking interactions of the four internal base pairs. Geometrical relaxation of nucleobase atoms prior to the stacking energy computations has a non-negligible effect on the results. The stacking energies were derived at the DFT-D/6-311++G(3df,3pd) level. We show a rather good correspondence between the intrinsic gas-phase stacking energies and the NMR-determined GA geometries. The conformation with more favorable gas-phase stacking is in most cases the one observed in experiments. This correlation is not improved when including solvent effects via the COSMO method. On the other side, the stacking calculations do not predict the relative thermodynamic stability of duplex formation for different sequences.     

Computational comparison of the stacking interactions between the aromatic amino acids and the natural or (cationic) methylated nucleobases

The strongest gas-phase MP2/6-31G*(0.25) stacking energies between the aromatic amino acids and the natural or methylated nucleobases were considered. The potential energy surfaces of dimers were searched as a function of the vertical separation, angle of rotation and horizontal displacement between monomers stacked according to their centers of mass. Our calculations reveal that the stacking interactions of adducts for a given nucleobase are dependent on the methylation site (by up to 20 kJ mol(-1)), where the relative magnitudes of the interactions are determined by the dipole moments of the adducts and the proton affinities of nucleobase methylation sites. Nevertheless, the differences in the (gas-phase) stacking of methylated adducts are small compared with the differences between the stacking of the corresponding natural and methylated nucleobases. Indeed, methylation increases the stacking energy by up to 40 kJ mol(-1) (or 135%). Although immersing the dimers in different solvents decreases the gas-phase stacking energies with an increase in the polarity of the environment, base methylation still has a significant effect on the nucleobase stacking ability in solvents with large dipole moments, and, perhaps more importantly, environments that mimic enzyme active sites. Our results shed light on the workings of DNA repairs enzymes that selectively remove a wide variety of alkylated nucleobases over the natural bases.     

Effect of loop distortion on the stability and structural dynamics of DNA hairpin and dumbbell conjugates

The thermal stability and conformational dynamics of DNA hairpin and dumbbell conjugates having short A-tract base pair domains connected by tri- or hexa(ethylene glycol) linkers is reported. The formation of stable base-paired A-tract hairpins having oligo(ethylene glycol) linkers requires a minimum of four or five A-T base pairs. The formation of base-paired dumbbells having oligo(ethylene glycol) linkers by means of chemical ligation of nicked dumbbells requires a minimum of two A-T base pairs on either side of the nick. Molecular modeling indicates that the hexa(ethylene glycol) linker is sufficiently long to permit formation of strain-free loop regions and B-DNA base pair domains. In contrast, the tri(ethylene glycol) is too short to permit Watson-Crick base pairing between the bases attached to the linker. The shorter linker distorts the duplex, resulting in fluxional behavior in which the base pairs adjacent to the linker and at the open end of the hairpin dissociate on the nanosecond time scale. The loss of interstrand binding energy caused by these fluctuations leads to a difference of approximately 5 degrees C in melting temperature between EG3 and EG6 hairpins. An analysis of the fluxional behavior of the EG3 adjacent base-pair has been used to study the pathways for base flipping and base stacking, including the identification of rotated base (partially flipped) intermediates that have not been described previously for A-T base pairs.     

米托蒽醌与B-DNA相互作用的分子模拟

针对嵌插型抗癌药物米托蒽醌(mitoxantrone,MTX)同B-DNA间作用模式的争议,采用分子模拟方法研究了米托蒽醌分子与B-DNA分子的相互作用.结果表明:米托蒽醌分子插入到B-DNA中有大小沟选择性及碱基对特异性,更倾向从小沟方向插入到DNA分子中;对5'-CG碱基对有特异性识别.通过详细能量项的分析,揭示了米托蒽醌插入DNA分子的驱动力及对碱基的特异性识别作用主要是空间相互作用特别是静电相互作用.在最佳作用位点复合物的构象分析则表明蒽醌环只有一部分插入碱基对中,侧链在小沟中延磷酸基骨架以3'-5'方向伸展,并通过静电作用进一步增强米托蒽醌与B-DNA的结合.     

Electronic structure of xDNA

xDNA is an artificial duplex made of natural and benzo-homologated bases. The latter can be seen as a fusion between benzene and a natural base. We have used two different ab initio techniques, one based on B3LYP and a Gaussian expansion of the wave functions, and the other on GGA and plane-waves, to investigate the electronic properties of an xDNA duplex and a natural one with an analogous sequence. The calculations were performed in dry conditions, i.e., H atoms were used to neutralize the charge. It is found that the HOMO-LUMO gap of xDNA is about 0.5 eV smaller than that of B-DNA, independent of the technique used. The pi-pi* gap of xDNA is 1.3 or 1.0 eV smaller than that of B-DNA, depending on whether one uses B3LYP/6-31G or GGA/plane-waves, respectively. An analysis of how saturation changes the electronic properties of the nucleotide pairs that make up these duplexes suggests that different saturation schemes significantly affect the HOMO-LUMO gap value of xDNA and B-DNA. The same is not true for the pi-pi* gap. That xDNA has a smaller pi-pi* gap than B-DNA suggests that xDNA could be a plausible candidate for molecular-wire applications.     

Stepwise evolution of the structure and electronic properties of DNA

The optical properties of a family of duplex DNA conjugates possessing from 1 to 11 A:T base pairs and covalently attached stilbene chromophores at both ends have been investigated. As few as from two to four base bairs are needed to establish base-pair absorption and circular dichroism spectra similar to those of longer oligomers. The stilbene chromophores exhibit exciton-coupled circular dichroism, which can be observed even with 11 intervening base pairs, a distance of ca. 40 A. The dependence of the sign and amplitude of these spectra reveals the ability of B-DNA to serve as a helical ruler.     

Solution structure of a DNA duplex containing a biphenyl pair

Hydrogen-bonding and stacking interactions between nucleobases are considered to be the major noncovalent interactions that stabilize the DNA and RNA double helices. In recent work we found that one or multiple biphenyl pairs, devoid of any potential for hydrogen bond formation, can be introduced into a DNA double helix without loss of duplex stability. We hypothesized that interstrand stacking interactions of the biphenyl residues maintain duplex stability. Here we present an NMR structure of the decamer duplex d(GTGACXGCAG) d(CTGCYGTCAC) that contains one such X/Y biaryl pair. X represents a 3',5'-dinitrobiphenyl- and Y a 3',4'-dimethoxybiphenyl C-nucleoside unit. The experimentally determined solution structure shows a B-DNA duplex with a slight kink at the site of modification. The biphenyl groups are intercalated side by side as a pair between the natural base pairs and are stacked head to tail in van der Waals contact with each other. The first phenyl rings of the biphenyl units each show tight intrastrand stacking to their natural base neighbors on the 3'-side, thus strongly favoring one of two possible interstrand intercalation structures. In order to accommodate the biphenyl units in the duplex the helical pitch is widened while the helical twist at the site of modification is reduced. Interestingly, the biphenyl rings are not static in the duplex but are in dynamic motion even at 294 K.     

How well can new-generation density functional methods describe stacking interactions in biological systems?

We compare the performance of four recently developed DFT methods (MPW1B95, MPWB1K, PW6B95, and PWB6K) and two previous, generally successful DFT methods (B3LYP and B97-1) for the calculation of stacking interactions in six nucleic acid bases complexes and five amino acid pairs and for the calculation of hydrogen bonding interactions in two Watson-Crick type base pairs. We found that the four newly developed DFT methods give reasonable results for the stacking interactions in the DNA base pairs and amino acid pairs, whereas the previous DFT methods fail to describe interactions in these stacked complexes. We conclude that the new generation of DFT methods have greatly improved performance for stacking interaction as compared to previously available methods. We recommend the PWB6K method for investigating large DNA or protein systems where stacking plays an important role.     

Stabilization energies of the hydrogen-bonded and stacked structures of nucleic acid base pairs in the crystal geometries of CG, AT, and AC DNA steps and in the NMR geometry of the 5'-d(GCGAAGC)-3' hairpin: Complete basis set calculations at the MP2 and CCSD(T) levels

Stabilization energies of the H-bonded and stacked structures of a DNA base pair were studied in the crystal structures of adenine-thymine, cytosine-guanine, and adenine-cytosine steps as well as in the 5'-d(GCGAAGC)-3' hairpin (utilizing the NMR geometry). Stabilization energies were determined as the sum of the complete basis set (CBS) limit of MP2 stabilization energies and the Delta E(CCSD(T)) - Delta E(MP2) correction term evaluated with the 6-31G*(0.25) basis set. The CBS limit was determined by a two-point extrapolation using the aug-cc-pVXZ basis sets for X = D and T. While the H-bonding energies are comparable to those of base pairs in a crystal and a vacuum, the stacking energies are considerably smaller in a crystal. Despite this, the stacking is still important and accounts for a significant part of the overall stabilization. It contributes equally to the stability of DNA as does H-bonding for AT-rich DNAs, while in the case of GC-rich DNAs it forms about one-third of the total stabilization. Interstrand stacking reaches surprisingly large values, well comparable to the intrastrand ones, and thus contributes significantly to the overall stabilization. The hairpin structure is characterized by significant stacking, and both guanine...cytosine pairs possess stacking energies larger than 11.5 kcal/mol. A high portion of stabilization in the studied hairpin comes from stacking (similar to that found for AT-rich DNAs) despite the fact that it contains two GC Watson-Crick pairs having very large H-bonding stabilization. The DFT/B3LYP/6-31G** method yields satisfactory values of interaction energies for H-bonded structures, while it fails completely for stacking.