氢键识别超分子聚合物的新进展

近年来,由于氢键作用对聚合物的热力学性质、微观自组装、结晶及液晶行为的重要影响,氢键识别在超分子聚合物的分子设计与结构控制方面的应用受到广泛关注。本文系统介绍了氢键识别体系的类型与性质,以及分子结构、分子内氢键对氢键识别强度的影响,讨论了羧酸与吡啶间氢键识别体系、与核苷相关的氢键识别体系以及四重氢键识别体系在超分子聚合物中的最新应用,主要介绍了氢键识别超分子聚合物的合成、结构、性质及功能。     

环双(对-蒽基-对草快)的分子识别与谱学性质

环双(对-蒽基-对草快)是一种新型的缺电子大环仿生主体, 分子识别是其最重要的应用之一. 考察主体对一系列客体分子如水、氨、醇及杂环等的识别能力, 用密度泛函理论(DFT)中的B3LYP/3-21G基组对主客体复合物的结构进行优化. 在B3LYP/6-31G(d)水平上进行单点能计算, 校正后得到复合物的结合能. 用B3LYP/3-21G方法计算13C和3He化学位移. 结果表明, 主体对客体分子的识别主要靠客体上的杂原子与主体上的氢原子之间的氢键进行. 复合物的稳定化能受氢键的数目和距离影响. 氢键的形成导致部分复合物LUMO与HOMO能隙增大, 同时导致与氢键相连的C—H键上C原子的化学位移向低场移动. 复合物的芳香性与其结合能的大小及结合方式有关. 主体的芳香性因其与客体之间的弱相互作用而提高, 但太强的相互作用及客体在主体空腔内都将影响主体的环电流, 从而削弱其芳香性.     

双铂核药物与DNA作用的理论研究

利用分子力学和量子化学方法研究了双铂核药物［{trans-PtCl(NH₃)₂}₂(μ-NH₂(CH₂)_nNH₂)］²⁺与寡聚DNA片段d(ATATG*TACATAT)·d(ATGTG*TACATAT)复合物的几何构型和电子结构. 计算结果表明,Pt配合物与DNA中碱基G的N7原子形成了较强的配位键,并与O6原子之间存在较强的静电作用,使药物与DNA产生稳定作用,药物中的烃链的伸缩性使得DNA在键合药物后其构型并未发生大的变化. 同时,铂配合物中配体NH₃上的H与其邻近的鸟嘌呤的O6,DNA中磷酸根上的O以及与其邻近的碱基T上的O或N等电负性较大的原子间形成的氢键及弱氢键也是影响Pt配合物与DNA键合及其几何结构变化的重要因素. 这些化学键和氢键是药物分子能够对DNA进行识别的重要基础. 因此,可以认为药物结合后所引起DNA的变形较小可能是药物与顺铂产生不同的抗癌机理的主要原因.     

聚合物多层膜的表面分子工程

概述了作者及其研究群体发展的基于氢键、配位键和共价键的聚合物交替沉积组装方法.在此基础上,重点讨论将溶液中的超分子组装与界面交替沉积相结合的非常规界面交替沉积组装方法.通过结构构筑与功能组装的结合,实现了不同表面物理化学性质的可控调节,包括仿生矿化、超疏水涂层、可控组装与释放、表面分子印迹等.这些研究结果对发展基于聚合物多层膜的表面分子工程具有重要意义.     

DNA小沟结合二脒:水分子的识别作用

采用分子动力学模拟了DB921-DNA复合物, 通过7 ns的模拟研究表明: DB921一端的氨基氮原子与一个水分子形成氢键, 同时, 水分子又与DNA的5位A碱基的氮原子形成一个氢键. 水分子在DB921与DNA小沟结合中起了桥连的作用, 使得直线型的芳香二脒化合物DB921通过水桥与DNA小沟结合, 水分子诱导DB921分子与DNA的小沟域构型相适应, 与DNA小沟域的AATTC碱基有较强的结合作用. 在分子水平上提供了DB921与双螺旋DNA相互作用的结构及复合物的动态变化情况, 指出水分子在DNA小沟结合二脒化合物中的识别作用, 为设计出更高生物活性的DNA小沟结合剂提供一定的理论依据.     

小分子肽缀合异核苷的合成与性质研究

设计合成可识别RNA的特定结构(包括二级、三级结构)的分子是以RNA为靶的药物设计的一个重要方面,这些分子可以调节基因表达,作为诊断或者分子生物学探针.同蛋白质一样,RNA具有非常丰富的折叠结构,为产生特异性的分子识别提供了许多靶点.相比DNA而言,由于RNA和RNA-蛋白复合物的结构信息较少,所以对于RNA分子识别的研究相对滞后.RNA的三级结构作为分子相互作用的识别位点对RNA的生物功能的实现具有决定作用[1～3].     

基于偏苯三甲酸与对羟基吡啶复合物的超分子水凝胶

基于偏苯三甲酸和对羟基吡啶合成了一种具有支化结构的凝胶因子,采用氢核磁、红外光谱及元素分析确认其结构.该凝胶因子熔体在冷却时可拉出数厘米的长丝,表明分子间形成了强相互作用.将凝胶因子的水溶液分别在25℃和0℃下自然冷却、以及在25℃的超声作用下冷却,凝胶因子自组装成纤维状网络结构并使水凝胶化,纤维网络的密度及凝胶的稳定性均按上述凝胶形成条件顺序增加.通过干凝胶能谱面扫描分析发现氮元素主要处于纤维内部,表明两亲性凝胶因子对分子自组装的影响.通过分析邻苯二甲酸与对羟基吡啶复合物、偏苯三甲酸的单晶结构表明,凝胶因子基于多种氢键识别作用组装成纤维结构.干凝胶的粉末X射线衍射分析表明在凝胶化过程中凝胶因子沿着特定方向进行组装.     

铂类抗肿瘤药物ZD0473与双链及单链DNA作用差异的理论研究

用分子力学与量子化学相结合的MM/uff//HF/lanl2dz方法及单独的密度泛函方法探讨了新型铂类抗肿瘤药物(ZD0473)与碱基序列相同的双链及单链DNA片段几何结构、相互作用及电子结构方面的异同.结果表明,虽然药物分子都能与单、双链DNA形成稳定的复合物,但双链复合物与DNA形成的配位键比单链复合物稍强,氨中的氢与O6G₈间形成的氢键更强,甲基吡啶所造成的位阻效应更高,使得肿瘤细胞对药物的抗药性进一步降低.     

芳杂环类多重氢键分子钳人工受体研究新进展

氢键是分子识别的重要推动力之一.综述了芳杂环类多重氢键分子钳人工受体研究进展.     

氢键复合物自组装性质的研究

超分子复合物体系因近年来发展较快及应用范围广而颇具吸引力。作为形成超分子复合物的主要手段,氢键自组装对于高分子聚合材料以及生命科学等领域有着重要的意义。本文根据氢键的多重性及不同氢键的缔合方式对氢键复合物进行分类,并对氢键自组装复合物的性质和研究状况作了综述,同时介绍了本研究组在此方面的理论研究工作。     

Molecular Engineering of Free‐Base Porphyrins as Ligands—The N−H⋅⋅⋅X Binding Motif in Tetrapyrroles

The core N?H units of planar porphyrins are often inaccessible to forming hydrogen‐bonding complexes with acceptor molecules. This is due to the fact that the amine moieties are “shielded” by the macrocyclic system, impeding the formation of intermolecular H‐bonds. However, methods exist to modulate the tetrapyrrole conformations and to reshape the vector of N?H orientation outwards, thus increasing their availability and reactivity. Strategies include the use of porpho(di)methenes and phlorins (calixphyrins), as well as saddle‐distorted porphyrins. The former form cavities due to interruption of the aromatic system. The latter are highly basic systems and capable of binding anions and neutral molecules via N?H???X‐type H‐bonds. This Review discusses the role of porphyrin(oid) ligands in various coordination‐type complexes, means to access the core for hydrogen bonding, the concept of conformational control, and emerging applications, such as organocatalysis and sensors.     

Electrospray ionization of nucleic acid aptamer/small molecule complexes for screening aptamer selectivity

Molecular recognition of small molecule ligands by the nucleic acid aptamers for tobramycin, ATP, and FMN has been examined using electrospray ionization mass spectrometry (ESI-MS). Mass spectrometric data for binding stoichiometry and relative binding affinity correlated well with solution data for tobramycin aptamer complexes, in which aptamer/ligand interactions are mediated by hydrogen bonds. For the ATP and FMN aptamers, where ligand interactions involve both hydrogen bonding and significant pi-stacking, the relative binding affinities determined by MS did not fully correlate with results obtained from solution experiments. Some high-affinity aptamer/ligand complexes appeared to be destabilized in the gas phase by internal Coulombic repulsion. In CAD experiments, complexes with a greater number of intermolecular hydrogen bonds exhibited greater gas-phase stability even in cases when solution binding affinities were equivalent. These results indicate that in at least some cases, mass spectrometric data on aptamer/ligand binding affinities should be used in conjunction with complementary techniques to fully assess aptamer molecular recognition properties.     

Formation and stability of rare earth metalloporphyrin monolayer films on amino-terminated silanized quartz surfaces studied by ultraviolet-visible and X-ray photoelectron spectroscopy

We investigated the fabrication of self-assembled monolayers of 5,10,15,20-tetra-(p-chlorophenyl)-porphyrin metal hydroxyl compounds (MOH; M=Gd, Tb, Er, Lu) on amino-terminated silanized quartz surfaces using ultraviolet-visible (UV-vis) and X-ray photoelectron spectroscopy (XPS). The orientation of MOH molecules in the films, the kinetics of the adsorption of MOH from a chloroform solution on an amino-terminated quartz substrate, and the stability of the metalloporphyrin films under natural light, UV light, and acidic and basic conditions were studied by UV-vis spectroscopy. The results indicate that the central metal is crucial in the formation of self-assembled porphyrin films and that the stability of the MOH SAMs also depends on the central metal. Under natural and UV light irradiation conditions, the stability of the MOH SAMs depends on the strength of the M-N bonds between the central metal and pyrrole nitrogens or between the central metal and the axial ligand. In the acidic conditions, the UV-vis spectra of the MOH SAMs show decreases in the absorbance and blue shifts. These spectral changes lead us to suggest that the four M-N bonds between the central metal and the pyrrole nitrogens of the porphyrins are cleaved and the resulted porphyrins are protonated under acidic conditions. Thus, it is likely that the protonated porphyrins and MOH form pi-pi complexes with a parallel stacking of the macrocycles through the electrostatic attractive interaction in the SAMs, resulting in the blue shifts of the Soret bands of the SAMs.     

Dynamic properties of water around a protein-DNA complex from molecular dynamics simulations

Formation of protein-DNA complex is an important step in regulation of genes in living organisms. One important issue in this problem is the role played by water in mediating the protein-DNA interactions. In this work, we have carried out atomistic molecular dynamics simulations to explore the heterogeneous dynamics of water molecules present in different regions around a complex formed between the DNA binding domain of human TRF1 protein and a telomeric DNA. It is demonstrated that such heterogeneous water motions around the complex are correlated with the relaxation time scales of hydrogen bonds formed by those water molecules with the protein and DNA. The calculations reveal the existence of a fraction of extraordinarily restricted water molecules forming a highly rigid thin layer in between the binding motifs of the protein and DNA. It is further proved that higher rigidity of water layers around the complex originates from more frequent reformations of broken water-water hydrogen bonds. Importantly, it is found that the formation of the complex affects the transverse and longitudinal degrees of freedom of surrounding water molecules in a nonuniform manner.     

Hydrogen-bonded assembly and binding affinity of the multi-point acceptor and isophthalic acid

Supermolecular complexes formed by oligophenyleneethynylene derivatives and isophthalic acid were studied using AM1 method to obtain binding energy. Electronic spectra and IR spectra of the complexes were calculated by INDO/CIS and AM1 methods based on AM1 geometries. Results indicated that the dimer could be formed by the monomers via hydrogen bonding because of the negative binding energy. Binding energy of the complexes was affected by electronegativity and steric effects of the substituents. The first UV absorptions and IR frequencies of N-H bonds of the complexes were both red-shifted compared with those of the monomers. The complexes could bind small molecules via hydrogen bonds, resulting in the change in UV absorptions and an increase in IR frequencies of N-H bonds.     

A mass spectrometric investigation of non-covalent interactions between ruthenium complexes and DNA

Electrospray ionisation mass spectrometry was used to investigate reactions between six ruthenium compounds and three different non self-complementary duplex oligonucleotides containing 16 base pairs. Each of the compounds studied formed non-covalent complexes containing between one and five ruthenium molecules bound to DNA. Competition experiments involving duplex 16mers and pairs of ruthenium compounds were used to determine the order of relative binding affinities of the metal compounds. Other competition experiments involving ruthenium compounds, and the organic DNA binding agents daunomycin and distamycin, provided information about the sites and modes of DNA binding of the ruthenium compounds.     

Bis(phenylethynyl)arene Linkers in Tetracationic Bis-triarylborane Chromophores Control Fluorimetric and Raman Sensing of Various DNAs and RNAs

We report four new luminescent tetracationic bis-triarylborane DNA and RNA sensors that show high binding affinities, in several cases even in the nanomolar range. Three of the compounds contain substituted, highly emissive and structurally flexible bis(2,6-dimethylphenyl-4-ethynyl)arene linkers ( 3 : arene=5,5′-2,2′-bithiophene; 4 : arene=1,4-benzene; 5 : arene=9,10-anthracene) between the two boryl moieties and serve as efficient dual Raman and fluorescence chromophores. The shorter analogue 6 employs 9,10-anthracene as the linker and demonstrates the importance of an adequate linker length with a certain level of flexibility by exhibiting generally lower binding affinities than 3 – 5 . Pronounced aggregation–deaggregation processes are observed in fluorimetric titration experiments with DNA for compounds 3 and 5 . Molecular modelling of complexes of 5 with AT-DNA, suggest the minor groove as the dominant binding site for monomeric 5 , but demonstrate that dimers of 5 can also be accommodated. Strong SERS responses for 3 – 5 versus a very weak response for 6 , particularly the strong signals from anthracene itself observed for 5 but not for 6 , demonstrate the importance of triple bonds for strong Raman activity in molecules of this compound class. The energy of the characteristic stretching vibration of the C≡C bonds is significantly dependent on the aromatic moiety between the triple bonds. The insertion of aromatic moieties between two C≡C bonds thus offers an alternative design for dual Raman and fluorescence chromophores, applicable in multiplex biological Raman imaging.     

Theoretical binding affinities and spectra of complexes formed by a cyclic β-peptoid with amino acids

Binding affinities of a cyclic β-peptoid to amino acids were studied using the density functional theory (DFT) at the B3LYP/6-311G(d,p) level after the basis set superior error (BSSE). The host molecule possesses binding ability to amino acids since the binding energies of the complexes formed are negative. The complexes were stabilized via hydrogen bonds between the host and the guest molecules. Based on the B3LYP/6-31G(d) optimized geometries, electronic spectra of the complexes were calculated using the INDO/CIS method. ¹³C NMR spectra and nucleus-independent chemical shift (NICS) values of the complexes were computed at the B3LYP/6-31G(d) level. Carbon atoms in the carboxyl groups of the complexes are shifted downfield relative to those of the host. Some complexes exhibit aromaticity although the host shows anti-aromaticity. Formation of hydrogen bonds leads to cyclic current formation in these complexes.     

水溶性金属卟啉与DNA相互作用的微量热法研究

叶琳化合物以其对肿瘤组织的特殊亲和性和光动力学效应受到广泛的重视，国内外研究报导甚多·自D79年nel等人山证实水溶性四一K甲基毗陡基）叶咐及其金属配合物能嵌入＊＊A的碱基之间后，人们以这类水溶性叶琳为模型利用各种物理和化学手段研究它们与＊NA相互作用［2，3］．但用微量热法进行研究尚未见报导．我们曾报导用共振拉曼光谱研究图1所示的二个水溶性金属叶琳ru（＊A仰）」和卜i（N＊＊刊I同＊＊A的作用＊‘］，本文进一步报导用微量热法和紫外可见光谱研究的结果．1实验部分1．1试剂将小牛胸腺DN以华美生物工程公司产品）直接…