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.

Formation and dissociation of protonated cytosine–cytosine base pairs in i-motifs by ab initio quantum chemical calculations

Formation and dissociation mechanisms of C-C＋ base pairs in acidic and alkaline environments are investigated, employing ab initio quantum chemical calculations. Our calculations suggest that, in an acidic environment, a cytosine monomer is first protonated and then dimerized with an unprotonated cytosine monomer to form a C-C＋ base pair; in an alkaline environment, a protonated cytosine dimer is first unprotonated and then dissociated into two cytosine monomers. In addition, the force for detaching a C-C＋ base pair was found to be inversely proportional to the distance between the two cytosine monomers. These results provide a microscopic mechanism to qualitatively explain the experimentally observed reversible formation and dissociation of i-motifs.

Pt(Ⅱ), Pd(Ⅱ) and Ni(Ⅱ) Complexes Binding to the N(7) Position of Guanine: Influence on the Guanine and Watson-crick GC Base Pair

Comprehensive ab initio calculations were performed on the coordination of Pt(II), Pd(II) and Ni(II) adducts to the N(7) of guanine and guanine-cytosine (GC) base pair at the DFT level. The fully optimized geometries of the metal complexes were obtained and the stabilization energies of the interaction between metal adducts and nucleobase were calculated with B3LYP method by using 6-31* basis set for the light atom. While the effective core potential (ECP) is used for metal cation. The results show that both cispalladium and cisnickel cause similar geometric changes of the base pair as cisplatin. For the coordination of metal adducts to guanine, platinum adduct possesses the highest stabilization energy; but the interaction between metal-guanine and cytosine for nickel is larger than that for platinum and palladium. It is worthy to note that hydrolysis effect can also cause significant changes in H-bonds.

Cis Watson-Crick/Watson-Crick Base Pairs in DNA： A Density Functional Theory(DFT) Study

The four nucleic acid DNA bases（adenine, thymine, guanine, cytosine） and ten cis Watson-Crick/Watson-Crick（cis WC/WC） DNA base pairs were investigated by density functional theory（DFT） quantum chemical calculations. Geometry optimizations were carried out on the four bases and ten base pairs at the B3LYP level with 6-31G^（＊＊） basis set. All the optimizations were performed within Cs symmetry. The optimum structures for the four bases and seven cis WC/WC base pairs were obtained, and Natural Bond Orbital analysis（NBO） was based on these structures. The possibilities of matches between any two of the four bases through their Watson-Crick（WC） edges were discussed. The structures of seven cis WC/WC base pairs change to a certain extent relative to these of the four bases due to the formation of hydrogen bonds. These base pairs existing in DNA have an important influence on the structural stability of the double helix. The analysis of the electronic structures and molecular orbitals for seven cis WC/WC base pairs can provide significant information about the relationship between charge transfer along the hydrogen bond and the Frontier orbitals of these base pairs.

DFT Calculations on the Effect of Solvation on the Tautomeric Reactions for Wobble Gua-Thy and Canonical Gua-Cyt Base-Pairs

To elucidate the reaction mechanism from wobble Guanine-Thymine (wG-T) to tautomeric G-T base-pairs, we investigate its transition state (TS) by density functional theory (DFT) calculations, in vacuum and in water approximated by continuum solvation model. From the comparison of these results, we attempt to elucidate the effect of solvation on the tautomeric reaction for wG-T. In addition, the same DFT calculations are performed for the canonical G-C base-pair, in order to reveal the difference in the activation energy for the reactions involving wG-T and G-C. The obtained TS structures between wG-T and G*-T/G-T* (asterisk is an enol-form of base) are almost the same in vacuum and in water. However, the activation energy is 16.6 and 19.1 kcal/mol in vacuum and in water, respectively, indicating that the effect of solvation enlarges the energy barrier for the reactions from wG-T to G-T*/G*-T. The activation energy for the tautomeric reaction from G-C to G*-C* is also evaluated to be 15.8 and 12.9 kcal/mol in vacuum and in water, respectively. Therefore, it is expected that the tautomeric reaction from wG-T to G*-T/G-T* can occur in vacuum with a similar probability as that from G-C to G*-C*. We furthermore investigate the TS structure for wG-BrU to reveal the effect of the BrU introduction into wG-T. The activation energy is 14.5 and 16.7 kcal/mol in vacuum and in water, respectively. Accordingly, the BrU introduction is found to increase the probability of the tautomeric reaction producing the enol-form G* and T* bases. Because G* prefers to bind to T rather than to C, and T* to G not A, our calculated results reveal that the spontaneous mutation from C to T or from A to G bases is accelerated by the introduction of wG-BrU base-pair.

Molecular mechanism of base pairing infidelity during DNA duplication upon one-electron oxidation

The guanine radical cation(G?+)is formed by one-electron oxidation from its parent guanine(G).G?+is rapidly deprotonated in the aqueous phase resulting in the formation of the neutral guanine radical[G(-H)?].The loss of proton occurs at the N1 nitrogen,which is involved in the classical Watson-Crick base pairing with cytosine(C).Employing the density functional theory(DFT),it has been observed that a new shifted base pairing configuration is formed between G(-H)?and C constituting only two hydrogen bonds after deprotonation occurs.Using the DFT method,G(-H)?was paired with thymine(T),adenine(A)and G revealing substantial binding energies comparable to those of classical G-C and A-T base pairs.Hence,G(-H)?does not display any particular specificity for C compared to the other bases.Taking into account the long lifetime of the G(-H)?radical in the DNA helix(5 s)and the rapid duplication rate of DNA during mitosis/meiosis(5-500 bases per s),G(-H)?can pair promiscuously leading to errors in the duplication process.This scenario constitutes a new mechanism which explains how one-electron oxidation of the DNA double helix can lead to mutations.

DFT Study on Reaction Mechanism of DNA Base Pair with Hydroxyl Radical

In order to elucidate the indirect effect by radiation on DNA base pairs, we investigate the mechanism for the attacking reaction of a hydroxyl radical (·OH-radical) to the G-C and A-T base pairs, by the density functional theory (DFT) calculations. The effect of solvation on the mechanism is also revealed by performing the same DFT calculations under the continuum solvation approximation. We find the stable structures for the dehydrogenated G-C and A-T base pairs, in which the hydrogen atom of NH2 group of G or A base is abstracted by the ·OH-radical. The solvation around the base pairs stabilizes the dehydrogenated structures significantly, indicating the acceleration of the attacking reaction by ·OH-radical to the base pairs in water. Therefore, we conclude that the hydrogen atom of the NH2 group of G or A base in the G-C and A-T base pairs is the most preferably abstracted by the ·OH-radical in living cells.

Spin fluctuations and unconventional superconducting pairing in iron-based superconductors

In this article, we review the recent theoretical works on the spin fluctuations and superconductivity in iron-based superconductors. Using the fluctuation exchange approximation and multi-orbital tight-binding models, we study the char- acteristics of the spin fluctuations and the symmetries of the superconducting gaps for different iron-based superconductors. We explore the systems with both electron-like and hole-like Fermi surfaces （FS） and the systems with only the electron-like FS. We argue that the spin-fluctuation theories are successful in explaining at least the essential part of the problems, indicating that the spin fluctuation is the common origin of superconductivity in iron-based superconductors.

Selective conformer detection of short-lived base pair tautomers: A computational study of the unusual guanine-cytosine pairs using ultrafast resonance Raman spectroscopy

Base pair mismatch has been regarded as the main source of DNA point mutations, where minor shortlived tautomers were usually involved. However, the detection and characterization of these unnatural species pose challenges to existing techniques. Here, by using systematic structural and ultrafast resonance Raman(RR) spectral analysis for the four possible conformers of guanine-cytosine base pairs, the prominent marker Raman bands were identified. We found that the hydrogen bonding vibrational region from 2300 cm^(-1) to 3700 cm^(-1) is ideal for the identification of these short live species. The marker bands provide direct evidence for the existence of the tautomer species, thus offering an effective strategy to detect the short-lived minor species. Ultrafast resonance Raman spectroscopy would be a powerful tool to provide direct evidence of critical dynamical details of complex systems involving protonation or tautomerization.

Authenticated Privacy Preserving Pairing-Based Scheme for Remote Health Monitoring Systems

The digitization of patient health information has brought many benefits and challenges for both the patients and physicians. However, security and privacy preservation have remained important challenges for remote health monitoring systems. Since a patient’s health information is sensitive and the communication channel (i.e. the Internet) is insecure, it is important to protect them against unauthorized entities. Otherwise, failure to do so will not only lead to compromise of a patient’s privacy, but will also put his/her life at risk. How to provide for confidentiality, patient anonymity and un-traceability, access control to a patient’s health information and even key exchange between a patient and her physician are critical issues that need to be addressed if a wider adoption of remote health monitoring systems is to be realized. This paper proposes an authenticated privacy preserving pairing-based scheme for remote health monitoring systems. The scheme is based on the concepts of bilinear paring, identity-based cryptography and non-interactive identity-based key agreement protocol. The scheme also incorporates an efficient batch signature verification scheme to reduce computation cost during multiple simultaneous signature verifications.

Construction and Implementation of a Privacy-Preserving Identity-Based Encryption Architecture

A recent proposal by Adams integrates the digital credentials (DC) technology of Brands with the identity-based encryption (IBE) technology of Boneh and Franklin to create an IBE scheme that demonstrably enhances privacy for users. We refer to this scheme as a privacy-preserving identity-based encryption (PP-IBE) construction. In this paper, we discuss the concrete implementation considerations for PP-IBE and provide a detailed instantiation (based on q-torsion groups in supersingular elliptic curves) that may be useful both for proof-of-concept purposes and for pedagogical purposes.

基于身份的R-ate对聚合签名方案

聚合签名是一种密码学技术,其核心思想在于将多个签名者的签名结果聚合成一个新的签名,让多方签署者以群体的形式生成数字签名,以提高签名及签名验证的效率。通过改进Gentry和Ramzan等人的方案,提出了两种基于身份的R-ate对聚合签名方案,分别适用于对相同消息和不同消息的签名值生成、聚合和验证。新的聚合签名方案签名值长度适中,签名值生成及验证过程时间合理,其中签名过程主要涉及两次点乘运算,验证过程主要涉及3次R-ate配对运算。

激发态DNA碱基对分子间相互作用的理论研究

[目的]利用本课题组发展的定量分析方法研究激发态DNA碱基对分子间相互作用的本质,以及不同类型的电子跃迁对DNA碱基对分子间相互作用的影响.[方法]采用广义Kohn-Sham能量分解分析方法(generalized Kohn-Sham based energy decomposition analysis,GKS-EDA),对两种Waston-Crick构型和两种stacked构型的DNA碱基对分子间相互作用本质进行理论研究.[结果]对于Waston-Crick构型的碱基对,n→π^(*)跃迁削弱了轨道极化作用但加强了电子相关作用,激发态分子间相互作用由电子相关作用主导,而π→π^(*)跃迁对分子间氢键影响较小;对于stacked构型的碱基对,π→π^(*)跃迁削弱了静电相互作用但增强了电子相关作用.[结论]Waston-Crick构型碱基对分子间相互作用本质受电子激发跃迁影响较大,而电子激发跃迁基本不改变stacked构型碱基对分子间相互作用本质.

超支化高分子水基钻井液仿生润滑机理

随着定向钻井技术的发展,水基钻井液润滑性逐渐成为确保定向井钻进的关键指标,设计新型钻井液润滑材料已成为油田化学领域的研究热点和重点。为探究超支化高分子水基钻井液仿生润滑机理,首先采用发散法合成了第1.5代超支化聚丙烯酸乙二胺基丙烯酸十八酯G1.5 P(EDA—MA—OA),然后进行了合成产物结构、微观形貌与热稳定性检测及其强化水基钻井液润滑性能评价,最后系统分析了超支化高分子与膨润土粒子的吸附行为。研究结果表明:①G1.5 P是粒径分布在几十纳米的分散性粒子,具有良好的热稳定性,热解温度集中在214℃;②以G1.5 P为润滑添加剂,构建的水基钻井液润滑系数为0.068,具有良好降摩减磨性;③G1.5 P呈“分子刷”状吸附于亲水材料表面,不仅改变了表面润湿性,而且还可促进膨润土粒子聚结形成致密、韧性的泥饼;④基于超支化高分子强化水基钻井液润滑的构效关系,提出了一种水基钻井液边界—固体润滑新模型,即超支化高分子促进在钻具与井壁摩擦副间形成低剪切强度泥饼,以泥饼结构内摩擦代替钻具刚性外摩擦,实现钻井液降摩减磨功能。结论认为,该认识完善了水基钻井液润滑添加剂的设计思路,为新型高性能润滑处理剂设计及超滑水基钻井液的开发提供了理论与技术支撑。

基于文本和图像门控融合机制的多模态方面级情感分析

多模态方面级情感分析是多模态情感分析领域的一项新兴任务,旨在对给定的方面实体在文本和图像中所体现的情感进行识别。尽管多模态方面级情感分析研究近年来取得了突破性的进展,但是现有的模型在多模态特征融合阶段大都仅采用简单的拼接方法,而没有考虑图像中是否存在与文本语义不相关的信息,这在一定程度上可能会为模型引入额外的噪声。为了解决上述问题,提出了一种基于文本和图像门控融合机制的多模态方面级情感分析模型(TIGFM)。该模型在文本和图像进行交互的同时引入了从数据集图像中提取的形容词-名词对(ANPs),并将其中形容词的加权作为图像辅助信息;此外,在特征融合阶段,通过构建一种动态控制图像和图像辅助信息输入的门控机制实现多模态特征融合。实验结果表明,TIGFM模型在两个基于Twitter的数据集上取得了具有竞争力的结果,进而验证了所提方法的有效性。

融合单残基信息的U-RF算法识别SO_(4)^(2-)和PO_(4)^(3-)配体结合位点

SO_(4)^(2-)和PO_(4)^(3-)配体与蛋白质相结合在生命活动中起着重要的作用,因此,准确预测蛋白质-酸根离子配体结合残基具有重要意义。前人对酸根离子配体结合位点的研究多数是在片段水平上进行的,而极少考虑单残基水平,这可能导致信息的缺失。因此,在片段和单残基水平两个方面提取特征,可以避免信息丢失。在片段水平上使用前人对氨基酸、二级结构、相对溶剂可及性和亲疏水提取的组分信息和位点保守信息作为基础特征,在此基础上引入了单残基水平上的氨基酸、氨基酸的酸碱极性、能量及亲疏水的倾向性因子;结合残基左右残基对信息和9个正交因子为新的特征,使用欠采样和随机森林相融合的算法(U-RF)进行五交叉检验和独立检验,得到了好于前人的预测结果。

Dtrie-allpair:高效的集合T-覆盖连接算法

传统的T-覆盖连接算法会因生成的候选集庞大而导致系统性能降低,为此,文中提出了一种基于trie的动态索引结构——DTI结构,并构建了基于该结构的相似度连接算法——Dtrie-allpair算法.通过该算法可以直接得到allpair连接的结果,不产生任何候选集,有效解决了高候选集产生的问题,克服了传统算法因生成并验证候选集而带来的开销.文中还研究了数据库中记录的顺序及记录中元素顺序对Dtrie-allpair算法性能的影响,并在msweb、msnbc两个数据集下对Dtrie-allpair算法与All-pair、PPJoin算法进行对比.结果表明:Dtrie-allpair算法具有明显的优势,覆盖阈值较小时优势更明显;对msweb数据集,阈值为2时,Dtrie-allpair算法的效率相对于All-pair、PPJoin算法提高近两个数量级;通过对数据集进行频率降序和长度升序组合预处理可大幅降低Dtrie-allpair算法访问的trie结点数量,从而显著提升性能.

采收期、生长年限和加工方法对黄花乌头不同部位中关附甲素含量的影响

目的:为规范黄花乌头的人工栽培,通过优化高效液相法,对不同采收时期、生长年限黄花乌头不同部位中关附甲素的含量进行测定,比较不同加工方法对关附甲素含量的影响,为制定黄花乌头合理的采收时间和加工方式提供依据。方法:采用反相离子对高效液相色谱法,测定黄花乌头中不同部位中关附甲素的含量;色谱柱为安捷伦Zorbax SB-C18柱(250 mm×4.6 mm,5μm),流动相A为2 mg/mL庚烷磺酸钠水溶液(含0.2%三乙胺并以H_(3)PO_(4)调pH值至3.0),流动相B为乙腈,采用梯度洗脱,流速为1.0 mL/min,检测波长为205 nm,柱温20℃。结果:关附甲素的质量浓度在0.0251~0.2513 mg/mL^(2)范围内线性关系良好(R^(2)=1),精密度、重复性、稳定性试验结果的RSD均≤1.0%;平均加样回收率为97.83%,RSD为3.5%。不同采收期黄花乌头不同部位中9月份采集的样品子根含量最高,说明9月份为最佳采收期。不同生产年限样品中,三年生和三年以上生黄花乌头母根含量相差不大,但均大于两年生母根,地上部分中所含关附甲素都明显小于根部。不同加工方法所得关白附中关附甲素的含量大小依次为:阴干>晒干>炕干,说明不同条件对含量的影响较大。结论:建立的含量测定方法专属性强、精密度、重复性和稳定性较好,结果可靠,黄花乌头的最佳采收期为9月份,生长期限为3年,本研究为黄花乌头科学的人工栽培采收提供了实验依据。

碰撞激活诱导的双势阱势能面可以实现9-甲基-8-氧鸟嘌呤-9-甲基腺嘌呤碱基对阳离子自由基的质子转移

8-氧鸟嘌呤(OG)是最常见的核碱基氧化损伤,它在复制过程中可以用Hoogsteen的模式与腺嘌呤(A)错误配对.0G.A碱基对不仅可以诱发G·C→T·A的颠换突变,而且由于OG的电离势和氧化电位低于天然DNA碱基更容易受到电离辐射和单电子氧化的影响,本文报道了[9MOG·9MA]^(·+)碱華对阳离子自由基的形成.和碰撞诱导解离,该碱基对利用9-甲基8-氧鸟嘌呤(9MOG)和9-甲基腺嘌呤(9MA)模拟相对应的核苷酸.实验通过电喷雾产生Cu(Ⅱ)碱基复合物继之以氧化分离产生[9MOG·9MA]^(·+),并使用导向离子束串级质谱仪检测[9MOG·9MA]^(·+)的碰撞诱导解离、通过测量在不同碰撞能量下的解离产物和反应截面,可以得出[9MOG-H]+[9MA+H]^(+)(主要解离通道)和9MOG^(·+)+9MA(次要通道)的0 K解离阈能分别为1.8和1.65 eV.使用密度泛函理论对[9MOG·9MA]^(·+)的结构计算发现其所有重要构象都发生了质子转移生成[9MOG-H]^(·)·[9MA+H]^(+).另一方面,9MOG^(·+)+9MA的解离通道却需要9MOG^(·+)9MA作为中间体.看似矛盾的结果可以用碰撞活化后反应势能面上出现的双重势阱和由此触发的激发态质子转移平衡([9MOG-H]^(·)·[9MA+H]^(+))^(*)→←(9MOG6(·+)·9MA)^(*)来解释.本文实验和理论研究揭示了这种生物学上重要的非规范碱基对如何在氧化和电离损伤时发生解离.

关于frustrated Lewis pair的中文名

frustrated Lewis pair(FLP)是一个最近出现的新名词,指分子内或混合体系中同时具有路易斯酸和路易斯碱两个位点,由于空间位阻较大而使得这两个位点不能结合形成路易斯酸碱加合物,从而具有独特的反应活性。建议译为"受阻路易斯酸碱对"。