Fapy-G对碱基氢键复合物影响的理论研究

应用量子化学方法对2,6-二氨基-4-羟基-5-甲酰胺嘧啶(Fapy-G)与正常碱基作用形成的20种氧化碱基对的多种性质进行了理论分析,碱基G的C8位被氧化后N7和N9位分别增加一个H原子,使其由氢键受体变成氢键供体,N7,N9及O6原子所带的电荷变负,同时O6作为氢键受体的能力增强.与碱基单体相比,碱基对中形成氢键的受体原子所带的电荷平均减小0.05 e;供体H原子所带的电荷平均增大0.02 e.Fapy-G分子中六元环上受体N原子参与形成氢键时,环的呼吸振动模式和N与对位C的振动模式的振动频率蓝移;与氢键相关的振动频率红移.所有氧化碱基对中,NH…N比NH…O氢键作用更强,且在NH…N氢键中,在六元环上的供体N原子形成的氢键比在氨基或开环上的供体N原子形成的氢键强.Fapy-G与碱基A作用结合能区域顺序为1>2>4>3,与碱基T(R)作用区域顺序为3=4>1>2;水溶液使Fapy-G与碱基C作用的结合能减弱程度最大,结合能达到41.84~58.58 k J/mol,且使碱基对结合能力次序发生改变.     

氨基酸侧链与氧化鸟嘌呤碱基对体系的氢键作用

应用量子化学方法,分别在气相和水溶液中对氨基酸侧链与氧化鸟嘌呤碱基对(8-oxo-G∶C)形成的三体复合物的氢键键能、几何结构、电荷分布及二阶稳定化能进行了研究.结果表明,水溶液的存在削弱了复合物中的氢键强度,电荷分布变化明显,水溶液中形成氢键位点的电荷变化量约为气相中的10倍,而几何结构变化不明显、对于酶与DNA之间的相互作用的研究需在水溶液中进行.水溶液对带电三体复合物中8-oxo-G∶C与氨基酸侧链间的氢键有较大影响,键能平均减小了69.23 k J/mol,不带电复合物仅减小了3.60k J/mol.水溶液中三体复合物中8-oxo-G∶C间的氢键受侧链的影响不大,且与侧链带电与否无关,带电复合物和不带电复合物的氢键强度分别减小了24.57和30.05 k J/mol,且二阶稳定化能越大,其对应的氢键键长越短.     

Synthesis and Crystal Structures of Hydrogen Monofluorophosphates with N‐containing Organic Cations. The Influence of Fluorine on their Hydrogen Bond Systems

The synthesis and crystal structures of guanidinium monofluorophosphate and hydrogen monofluorophosphates with the following cations: piperazinium, di‐ and triethylammonium, guanidinium, and dimethyluronium, are described and discussed. The structures of the acid salts consist of hydrogen‐bonded HPO₃F tetrahedra, which form infinite chains or cyclic dimers. The organic cations link these units together. All of the hydrogen bond systems observed consist of short O—H···O and longer N—H···O bonds. No O—H···F or N—H···F bonds were found. The F atom avoids hydrogen acceptor positions in the structures. The thermal behavior of [NHEt₃]HPO₃F was also studied.     

电场极化对碱基对质子转移和电子传递的影响

在B3LYP/6-31+G**//HF/6-31+G**水平上研究了在不同电场极化环境下碱基对A-T的几何构型和电子结构. 通过碱基对的氢键和结合能的变化讨论了碱基对间的质子转移, 进一步利用密度泛函理论结合非平衡态格林函数方法研究了通过碱基对的电子输运行为. 结果表明, 在0.6～2.0 V的偏压下, 由T向A方向的电子传递更易进行, 表现了微弱的整流行为.     

Artificial Nucleotide-containing Aptamers Used in Tumor Therapy

The high pharmaceutical cost and multi-drug resistance in tumor therapeutic agents hinder the further application of chemotherapy in tumor therapy.Artificial modified nucleic acid aptamers have the advantages of high binding affinity,programmability,and easy synthesis.Thus,the rational design of artificial modified aptamers is expected to provide a versatile platform for the optimization of chemotherapy agents.In this review,we summarize the modification strategies and the application of the artificial modified nucleotide-containing aptamers,aiming to provide a promising step toward aptamer-related chemotherapeutic agents.     

Asymmetric Hydrogenation of Ketones and Enones with Chiral Lewis Base Derived Frustrated Lewis Pairs

The concept of frustrated Lewis pairs (FLPs) has been widely applied in various research areas, and metal‐free hydrogenation undoubtedly belongs to the most significant and successful ones. In the past decade, great efforts have been devoted to the synthesis of chiral boron Lewis acids. In a sharp contrast, chiral Lewis base derived FLPs have rarely been disclosed for the asymmetric hydrogenation. In this work, a novel type of chiral FLP was developed by simple combination of chiral oxazoline Lewis bases with achiral boron Lewis acids, thus providing a promising new direction for the development of chiral FLPs in the future. These chiral FLPs proved to be highly effective for the asymmetric hydrogenation of ketones, enones, and chromones, giving the corresponding products in high yields with up to 95 % ee. Mechanistic studies suggest that the hydrogen transfer to simple ketones likely proceeds in a concerted manner.     

错配核酸的研究进展

本文通过介绍多种错配核酸的结构及其热力学性质，详细地描述了非Watson-Crick配对核酸的最新进展。这方面的研究有利于阐明生物体内错配核酸的识别修复机理及核酸二级结构的预测，并为合理设计新的人工核酸修复酶提供了理论基础。     

A-T碱基对单羟基自由基加成产物的单电子氧化还原性质

采用密度泛函理论在B3LYP/DZP++//B3LYP/6-31 ++G(d,p)水平上研究A-T碱基对的单羟基加成产物的氧化还原性质.计算表明,所有8种加成复合物都表现出显著的氧化性,但其还原性却很弱.加成复合物AC2-T、AC4-T、AC5-T的俘获电子诱发T碱基N3位上的H原子向A碱基的N1位迁移,产生这种氢迁移的根源在于A碱基俘获电子后电子密度较大,有利于在A碱基上形成新的N-H键.     

Artificial Genetic Sets Composed of Size‐Expanded Base Pairs

We describe in this Minireview the synthesis, properties, and applications of artificial genetic sets built from base pairs that are larger than the natural Watson–Crick architecture. Such designed systems are being explored by several research groups to investigate basic chemical questions regarding the functions of the genetic information storage systems and thus of the origin and evolution of life. For example, is the terrestrial DNA structure the only viable one, or can other architectures function as well? Working outside the constraints of purine–pyrimidine geometry provides more chemical flexibility in design, and the added size confers useful properties such as high binding affinity and helix stability as well as fluorescence. These features are useful for the investigation of fundamental biochemical questions as well as in the development of new biotechnological, biomedical, and nanostructural tools and methods.     

铂配合物与DNA碱基对间相互作用的理论研究

用量子化学方法研究一系列Pt(II)配合物作用于嘌呤碱基N7位点后对Watson-Crick碱基对AT、GC的影响. 计算结果显示铂配体与碱基对AT、GC的作用以静电作用为主，同时极化作用也是影响GC碱基对的重要因素. 静电作用极大地增强了铂化嘌呤碱基与嘧啶碱基间的相互作用，而嘌呤碱基与嘧啶碱基间作用与未铂化碱基对作用相近. Pd(II) 和 Ni(II)的相关研究得到类似的结果. 碱基对间氢键作用“二阶微扰能”分析结果与氢键强弱变化一致.     

50 Years of Hydrogen Bond Theory

The “hydrogen bond” or “hydrogen bridge” concept has proved to be one of the most useful structural concepts in modern science. The properties of substances containing hydrogen bonds depend on the strength, symmetry, and polarity of these bonds. These characteristics, in turn, are related to the effective electronegativities of the bridgehead atoms, the distance between these atoms, and the degree of coupling with other hydrogen bonds. Symmetrical hydrogen bonds exist in the FHF^? and H₅O ions and in some acidic compounds. Coupled hydrogen bond systems exist, for example, in ice, liquid water, hydroquinone clathrates, starch, cellulose, polypeptides, nucleic acids, KH₂PO₄, and silicate hydrates. It is suggested that systems of coupled, nearly symmetrical, hydrogen bonds should be interesting subjects of further research.     

One-Step Manufacturing of Supramolecular Liquid-Crystal Elastomers by Stress-Induced Alignment and Hydrogen Bond Exchange

Liquid-crystal elastomers (LCEs) capable of performing large and reversible deformation in response to an external stimulus are an important class of soft actuators. However, their manufacturing process typically involves a multistep approach that requires harsh conditions. For the very first time, LCEs with customized geometries that can be manufactured by a rapid one-step approach at room temperature are developed. The LCEs are hydrogen bond (H-bond) crosslinked main chain polymers comprising flexible short side chains. Applying a stretching/shear force to the LCE can simultaneously induce mesogen alignment and H-bond exchange, allowing for the formation of well-aligned LCE networks stabilized by H-bonds. Based on this working principle, soft actuators in fibers and 2D/3D objects can be manufactured by mechanical stretching or melt extrusion within a short time (e.g. <1 min). These actuators can perform reversible macroscopic motions with large, controlled deformations up to 38 %. The dynamic nature of H-bonds also provides the actuators with reprocessability and reprogrammability. Thus, this work opens the way for the one-step and custom manufacturing of soft actuators.     

Hydrogen Bonds in Coal -The Influence of Coal Rank and the Recognition of a New Hydrogen Bond in Coal

By means of in-situ diffuse reflectance FTIR.The IR spectra of 6 coals with different ranks were obtained from room temperature to 230℃.A new curve fitting method was used to recognize the different hydrogen bonds in the coals.and the influence of coal ranks on the distribution of hydrogen bonds(HBs) in the coals and their thermal stability were discussed.The results show that there is another new HB(around 2514cm^-1) between the-SH in mercaptans or thiophenols and the nitrogen in the pyridine-like compounds in the coals.and the evidence for that was provided.The controversial band of the HB between hydroxyl and the nitrogen of the pyridine-like compounds was determined in the range of 3028-2984cm^-1,and the result is comsistent with but more specific than that of Painter et al.It was ound that the stability of different HBs in the coals is influenced by both coal rank and temperature,For some HBs.the higher the coal rank,the higher the stability of them.Within the temperature range of our research,the stability of the HB between the hydroxyl and the π bond increases to some extent for some coals at temperatures higher than 110 or 140℃.     

Synthesis,Reactivity, and Structural Characterization of Dioxovanadium(V) Complexes with Tridentate Schiff Base Ligand: Vanadium Complexes in Supramolecular Networks

The synthesis, characterization and crystal structure analysis of the ammonium salt of the dioxovanadium(V) complex NH₄[VO₂(salhyph)] with the tridentate Schiff base ligand derived from salicylaldehyde and benzoic acid hydrazide (H₂salhyph) is reported. NH₄[VO₂(salhyph)] crystallizes in the monoclinic space group Pn with a = 708.8(2), b = 1444.3(3), c = 717.1(2) pm and β = 101.09(2)°. The vanadium atom of the dioxovanadium(V) moiety has a distorted square‐pyramidal coordination geometry. Extensive hydrogen bonding is observed between the ammonium cation and the oxygen atoms coordinated to the vanadium atom yielding to a two‐dimensional network, where the complex anions are arranged in a bilayer. Additional crystal packing within the bilayer appears to be controlled mostly by π stacking between the aromatic rings of the ligand. The reactions of NH₄[VO₂(salhyph)] with several proton acidic compounds including water, methanol, and proton acids lead to neutral monooxovanadium(V) and dioxovanadium(V) complexes ([VO₂(Hsalhyph)], [V₂O₃(salhyph)₂] and [VO(OMe)(salhyph)(HOMe)]).     

Electronic Structures and Spectra of the Bases and Base Pairs of Nucleic Acids

The present paper covers electronic structures and spectra of the bases and the base pairs of nucleic acids calculated by using the INDO/S method. For free bases we give the energy levels of ground states and transition energies of low-lying excited states and discuss the band characters. The results indicate that the calculated spectra are in good agreement with experimental values. On the other hand, our calculations for A-T and G-C pairs are very beneficial to understanding hydrogen bond properties of these pairs.     

Acceleration of Long‐Range Photoinduced Electron Transfer through DNA by Hydroxyquinolines as Artificial Base Pairs

The C‐nucleoside based on the hydroxyquinoline ligand (Hq) is complementary to itself and forms stable Hq–Hq pairs in double‐stranded DNA. These artificial Hq–Hq pairs may serve as artificial electron carriers for long‐range photoinduced electron transfer in DNA, as elucidated by a combination of gel electrophoretic analysis of irradiated samples and time‐resolved transient absorption spectroscopy. For this study, the Hq–Hq pair was combined with a DNA‐based donor–acceptor system consisting of 6‐N,N‐dimethylaminopyrene conjugated to 2′‐deoxyuridine as photoinducible electron donor, and methyl viologen attached to the 2′‐position of uridine as electron acceptor. The Hq radical anion was identified in the time‐resolved measurements and strand cleavage products support its role as an intermediate charge carrier. Hence, the Hq–Hq pair significantly enhances the electron hopping capability of DNA compared to natural DNA bases over long distances while keeping the self‐assembly properties as the most attractive feature of DNA as a supramolecular architecture.     

Theoretical study of hydrogen bonded clusters of water and cyanic acid: Hydrogen bonding in terms of the molecular structure

Ab initio and density functional calculations were used to analyze the interaction between a molecule of cyanic acid (HOCN) and up to 4 molecules of water at the B3LYP/6-311++G(d,p) and MP2/6-311++G(d,p) computational levels. The cooperative effect (CE) is increased with the increasing size of the studied clusters. Red shifts of the H–O stretching frequency for complexes involving HOCN as an H-donor were predicted. The strength of the hydrogen bonds in terms of molecular structures could be deduced from a comparison of HOCN–H₂O with HCNO–H₂O, HONC–H₂O and HNCO–H₂O HB clusters. The atom in molecules (AIM) method was used to analyze the cooperative effects on topological parameters.     

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的反键轨道滓*(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.     

氢键对水杨酸酸度影响的量子化学研究

分子内氢键的形成影响羧酸的酸性,实验测定表明,水杨酸的酸性大约比苯甲酸强18倍,而其异构体——对羟基苯甲酸的酸性仅为苯甲酸的一半,已有文献从氢键形成角度定性讨论这一问题,我们采用CNDO/2法对其影响实质给予进一步的探讨,从微观角度阐述了该过程的可能机理,得到了与实验一致的结果。