与蛋白质调控DNA空穴迁移相关的具有负离解能特征的亚稳态氢键（英文）

利用密度泛函理论方法研究了作为空穴迁移载体的蛋白质复合的DNA三聚体(Protonated arginine…guanine…cytosine,Arg H+-GC)的氢键性质.结果表明,空穴迁移通过该载体单元时此类氢键表现为亚稳态,且具有明显的负离解能.正常情况下Arg H+基团在大小沟均能与GC碱对形成氢键,且具有正的离解能.然而,当空穴转移至此将削弱氢键至亚稳态,使之具有一定的离解势垒和负的离解能.这种势垒抑制的负离解能现象意味着由于空穴俘获导致此三聚体结构单元在它的Arg H+…N7/O6键区储存了一定的能量(约108.78 k J/mol).该氢键离解通道受控于此键区两个相关组分之间的静电排斥和氢键吸引之间的平衡以及这两个相反作用随氢键距离不同的衰减速率.基于电子密度分布的拓扑性质以及键临界点的Laplacian数值分析澄清了此类特殊的能量现象主要源自通过高能氢键(Arg H+…N7/O6)连接的授受体间的静电排斥.进一步空穴俘获诱导的G→C质子转移可扩展负离解能区至Arg H+…N7/O6和Watson-Crick(WC)氢键区.另外,Arg H+结合到GC的大小沟增加其电离势,因此削弱其空穴传导能力,削弱程度取决于Arg H+与GC的距离.推而广之,在protonated lysine-GC和protonated histidine-GC体系也可观察到类似的现象.显然,此类性质可调的亚稳态氢键可调控DNA空穴迁移机理.此工作为理解蛋白质调控的DNA空穴迁移机理提供了重要的能量学信息.     

腺嘌呤的氨基修饰增强DNA导电性的理论研究

利用密度泛函理论并结合非平衡态格林函数方法, 研究了腺嘌呤A的碳2位氨基修饰对DNA导电性的影响. 结果表明, 形成的双氨基嘌呤D可以与胸腺嘧啶T通过3个氢键进行配对, 由于氨基修饰形成了新的氢键, 使配对碱基D和T之间的结合比AT更紧密. 修饰后体系的能隙和电离能大大降低, 紫外吸收光谱在一定程度上会发生红移, 并增加了一些电荷转移跃迁. 计算的沿氢键方向的横向电荷输运和沿DNA链方向的纵向电荷输运性质, 证明了氨基的取代修饰可以很好地提高DNA的电荷输运性质. 揭示了DNA导电性增强是由于修饰调整了碱基对DT的最高占据轨道(HOMO)能级, 使之较天然碱基对AT更靠近GC的HOMO, 从而降低了空穴在DNA中迁移的势垒.     

取代基效应对褐煤模型化合物离解焓影响的理论研究

为了探究褐煤热解过程中氧桥键C-O均裂这一重要反应, 选取α-O-4和β-O-4类结构单元作为褐煤模型化合物, 运用不同密度泛函计算了部分模型化合物中C-O的离解焓, 并以CBS-QB3作为理论基准值进行比较, 最后选取M05-2X进行离解焓计算. 结果显示, 对于选定的α-O-4和β-O-4类模型化合物, 其平均离解焓分别为51.0 kcal/mol和66.1 kcal/mol. 周围取代环境能显著影响C-O离解焓, 芳环上存在给电子基团(OH, OCH₃和CH₃)能降低C-O离解焓, 而吸电子基团COOH则能增加其离解焓. 然后深层次分析了取代基效应对C-O离解焓的影响. 此外, 分子内氢键的形成对离解焓也有很大的影响. C-O的离解焓与其键长没有特定的相关性, 不能简单的通过C-O键长来预测其离解焓.     

固态锂电池中正极/电解质界面的密度泛函计算研究

锂离子电池的广泛应用对储能器件的能量密度、安全性和充放电速度提出了新的要求. 全固态锂电池与传统锂离子电池相比具有更少的副反应和更高的安全性,已成为下一代储能器件的首选. 构建匹配的电极/电解质界面是在全固态锂电池中获得优异综合性能的关键. 本文采用第一性原理计算研究了固态电池中电解质表面及正极/电解质界面的局域结构和锂离子输运性质. 选取β-Li₃PS₄ (010)/LiCoO₂ (104)和 Li₄GeS₄ (010)/LiCoO₂ (104)体系计算了界面处的成键情况及锂离子的迁移势垒. 部分脱锂态的正极/电解质界面上由于Co-S成键的加强削弱了P/Ge-S键的强度,降低了对Li⁺的束缚,从而导致了更低的锂离子迁移势垒. 理解界面局域结构及其对Li+输运性质的影响将有助于我们在固态电池中构建性能优异的电极/电解质界面.     

硫酸钾水溶液亚稳区性质的研究(Ⅳ)——杂质Li+对结晶过程的影响

本文根据实际生产的需要,详细地研究了杂质Li⁺对K₂SO₄结晶过程的影响,并结合理论分析。计算了杂质Li⁺对K₂SO₄结晶过程中成核特征的影响.结果表明,Li⁺改变了体系的比表面自由能δ₁₂、成核势垒△G(r^*),使亚稳区宽度增加.     

BaFCI:Tb晶体的热释发光和光激励发光

BaFCl:Tb晶体的光激励发光和热释发光过程为:在X射线辐照下,晶体中产生F色心,同时掺杂的Tb³⁺离子俘获空穴形成Tb⁴⁺离子。X线辐照后的晶体在可见光或热激励下,F色心中释放出的电子与Tb⁴⁺复合成Tb³⁺并处于激发态,随后发出Tb³⁺)子的跃迁辐射。     

利用原位变温EPR研究富勒烯双体笼间的弱C―C键

本文研究了(C₆₀)₂-[P(O)(OCH₃)]₂富勒烯双体内的笼间C―C键的热力学性质(该双体的结构详见文献, Chem. Commun. 2011, 47, 6111)。原位、变温电子顺磁共振波谱实验结果表明,该C―C键的键离解能(BDE)为72.4 kJ·mol^-1 (17.3 kcal·mol^-1),仅约为常见氢键的两倍,或约为常见有机C―C键的五分之一。因此,该二聚体于较高温度时容易发生均裂反应,形成单体自由基;降温时又容易发生自由基聚合反应。基于该笼间C―C键所具有的这些热力学特性,我们对其可被用于制备有序的富勒烯分子元器件等材料作展开讨论。     

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.     

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.     

过渡金属和硅烯配体相互作用的理论研究(Ⅰ)——MSiH2+的从头算研究

以HF/6-311+G^*基组研究了过渡金属硅烯离子MSiH₂⁺(M从Sc至Cu)的构型、成键特征以及M-Si键解离能.具有共平面构型的MSiH₂⁺,其M=Si键带有明显的双键特征,M=Si键解离能从Sc至Cu呈现周期性变化,与M的金属离子激发能有近似的线性关系.     

Marked variations of dissociation energy and H-bond character of the guanine-cytosine base pair induced by one-electron oxidation and Li+ cation coupling

The variation of dissociation energy and H-bond character of the G-C cation and the Li-GC cation have been investigated by employing density functional theory (B3LYP) with the 6-31+G* basis set. The one-electron oxidation and the coupling of Li(+) to the guanine-cytosine base pair can strengthen the interaction between guanine and cytosine. The interaction of the cation Li(+) with guanine is attractive and is attributed to the polarization of the H-bonds between G-C that enhances G-C interaction. The cooperativity of the three H-bonds in the GC and Li-GC cations is different from that in the neutral GC base pair. The proton-transfer process between N(1) of the guanine and N(3) of the cytosine can occur in the GC cation and the Li-GC cation. The geometries of the transition state are out of plane, especially for the transition state of the Li-GC cation. The analysis of the activation energy for the proton-transfer process shows that the GC(+) before and after proton transfer can exist simultaneously in the gas phase, but for the Li-GC(+) system, the Li-GC(+) without proton transfer is the dominating species in the gas phase.     

Charge-assisted intramolecular hydrogen bonds in disubstituted cyclohexane derivatives

In this paper, the N(+)-H···N, N(+)-H···O, and O-H···O(-) charge-assisted intramolecular hydrogen bonds (CAHBs) are investigated using different theoretical approaches. Monocharged cyclohexyldiamines (CHDA), aminocyclohexanols (ACHO), and cyclohexanediols (CHDO) are used as model compounds. Geometry optimizations at the MP2/aug-cc-pVDZ level are used to find the equilibrium structures for all possible H-bonded conformers. CAHBs are characterized geometrically and spectroscopically, and their energy is evaluated by means of homodesmic reactions. By comparison with the neutral forms, the presence of the charge is found to have a deep influence on the geometric and energetic H-bond parameters. In addition, these parameters are strongly dependent on the type of the groups involved as well as on their relative position in the cyclohexyl ring. For the systems under study, the H-bond energies vary from -23 to -113 kJ mol(-1), being classified from moderate to strong H-bonds. These H-bonds are also characterized by the application of the NBO and AIM theories. NBO analysis reveals that the energy corresponding to the charge transfer between the lone-pairs of the electron donor group and the antibonding orbitals of the acceptor group represents an important contribution in the H-bond stabilization. From the application of the AIM theory it is possible to see that these H-bonds possess some covalence which varies according to the type and relative position of the intervenient groups.     

The models of proton assisted and the unassisted formation of CGC base triplets

The triple helix is formed by combining a double and a single strand DNAs in low pH and dissociates in high pH. Under such conditions, protonation of cytosine in the single strand is necessary for triplex formation where cytosine-guanine-cytosine (CGC+) base triplet stabilizes the triple helix. The mechanism of CGC+ triplet formation from guanine-cytosine (GC) and a protonated cytosine (C+) shows the importance of N3 proton. Similarly in the case of CGC (unprotonated) triplet, the donor acceptor H-bond at N3 hydrogen of the cytosine analog (C) initiates the interaction with GC. The correspondence between the two models of triplets, CGC+ and CGC, unambiguously assigned that protonation at N3 cytosine in low pH to be the first step in triplet formation, but a donor acceptor triplet (CGC) can be designed without involving a proton in the Hoogsteen H-bond. Further, the bases of cytosine analogue also show the capability of forming Watson Crick (WC) H-bonds with guanine.     

Density functional and multiphoton ionization studies of N,N-dimethylformamide–(methanol)n clusters

The multiphoton ionization of the hydrogen-bonded clusters N,N-dimethylformamide–(methanol)_n (DMF–(CH₃OH)_n) was studied using a time-of-flight mass spectrometer at the wavelengths of 355 and 532 nm. At both wavelengths, a series of protonated DMF–(CH₃OH)_nH⁺ ions was obtained. The clusters were also investigated by density functional theory B3LYP method in conjunction with basis sets 6-31+G(d,p) and 6-311+G(2d,p). Equilibrium geometries of both neutral and ionic DMF–CH₃OH clusters, and dissociation channels and dissociation energies of the ionic clusters are presented. The results show that when DMF–CH₃OH is vertically ionized and dissociated, DMFH⁺ and CH₃O are the dominant products via proton transfer reaction. A high energy barrier makes another channel corresponding to the production of DMFH⁺ and CH₂OH disfavored. In the DMF–(CH₃OH)H⁺ ion, the proton prefers to link with the O atom of DMF molecule. Variation of atomic charges during proton transfer in hydrogen bond of the protonated cluster DMF–(CH₃OH)H⁺ ion is also discussed.     

卤素、 氰基及N原子修饰对四硫富瓦烯衍生物载流子传输性质影响的理论研究

基于密度泛函理论结合跳跃模型和能带理论研究了氟、 氯、 氰基和N原子的引入对四硫富瓦烯(TTF)衍生物载流子传输性质的影响. 计算结果表明, 嵌N修饰会降低分子重组能, 特别是当N原子靠近TTF主体环时作用更明显. 与引入卤素修饰相比, 引入氰基修饰的分子具有更小的电子和空穴重组能及更低的前线分子轨道(FMO)能级. 同时迁移率的计算结果显示, 分子6具有1.15 cm²·V^-1·s^-1的高电子迁移率, 考虑其较低的LUMO能级, 推测其有望成为潜在的优异电子传输材料, 而相似的电子和空穴迁移率使分子2有望成为潜在的双极性传输材料. 同时还考察了S和N原子之间的弱相互作用, 当S或N原子对分子HOMO(或LUMO)有贡献时, 其相应的空穴(或电子)传输能力会有所提高.     

Outline of a transition-state hydrogen-bond theory

Though the H-bond is well characterized as a D–H:A three-center-four-electron interaction, the formulation of a general H-bond theory has turned out to be a rather formidable problem because of the extreme variability of the bonds formed (for instance, O–HO energies range from 0.1 to 31 kcal mol⁻¹). This paper surveys our previous contributions to the problem, including: (a) the H-bond chemical leitmotifs (CLs), showing that there are only four classes of strong H-bonds and one of moderately strong ones; (b) the PA/pK_a equalization principle, showing that the four CLs forming strong H-bonds are actually molecular devices apt to equalize the acid–base properties (PA or pK_a) of the H-bond donor and acceptor groups; (c) the driving variable of the H-bond strength, which remains so identified as the difference ΔpK_a=pK_AH(D–H)−pK_BH(A–H⁺) or, alternatively, ΔPA=PA(D⁻)−PA(A); and, in particular, (d) the transition-state H-bond theory (TSHBT), which interprets the H-bond as a stationary point along the complete proton transfer pathway going from D–HA to DH–A via the DHA transition state. TSHBT is verified in connection with a series of seven 1-(X-phenylazo)-2-naphthols, a class of compounds forming a strong intramolecular resonance-assisted H-bond (RAHB), which is switched from N–HO to NH–O by the decreasing electron-withdrawing properties of the substituent X. The system is studied in terms of: (i) variable-temperature X-ray crystallography; (ii) DFT emulation of stationary points and full PT pathways; (iii) Marcus rate-equilibrium analysis correlated with substituent LFER Hammett parameters.     

Nature of one-dimensional short hydrogen bonding: bond distances, bond energies, and solvent effects

On the basis of recently synthesized calix[4]hydroquinone (CHQ) nanotubes which were self-assembled with infinitely long one-dimensional (1-D) short hydrogen bonds (SHB), we have investigated the nature of 1-D SHB using first-principles calculations for all the systems including the solvent water. The H-bonds relay (i.e., contiguous H-bonds) effect in CHQs shortens the H...O bond distances significantly (by more than 0.2 A) and increases the bond dissociation energy to a large extent (by more than approximately 4 kcal/mol) due to the highly enhanced polarization effect along the H-bond relay chain. The H-bonds relay effect shows a large increase in the chemical shift associated with the SHB. The average binding energies for the infinite 1-D H-bond arrays of dioles and dions increase by approximately 4 and approximately 9 kcal/mol per H-bond, respectively. The solvent effect (due to nonbridging water molecules) has been studied by explicitly adding water molecules in the CHQ tube crystals. This effect is found to be small with slight weakening of the SHB strength; the H...O bond distance increases only by 0.02 A, and the average binding energy decreases by approximately 1 kcal/mol per H-bond. All these results based on the first-principles calculations are the first detailed analysis of energy gain by SHB and energy loss by solvent effect, based on a partitioning scheme of the interaction energy components. These reliable results elucidate not only the self-assembly phenomena based on the H-bond relay but also the solvent effect on the SHB strength.     

吡啶与HCl和CHCl3形成分子间红移氢键和蓝移氢键的理论研究

采用量子化学从头算的MP2方法, 分别在6-31G(d,p), 6-311+G(d,p)和AUG-cc-pVDZ基组下, 研究了复合物C5H5N…HCl(1), C5H5N…HCCl3(2)和C5H5N…HCCl3(3)的分子间氢键. 计算结果表明, 在复合物1中, HCl中Cl—H键伸长, 形成Cl—H…N红移氢键; 在复合物2中, HCCl3中C—H键伸长, 形成C—H…N 红移氢键; 在复合物3中, HCCl3中C—H键收缩, 形成C—H…π蓝移氢键. 自然键轨道(NBO)分析表明, 影响氢键红移和氢键蓝移主要有3个因素: n(Y)→σ*(X—H)超共轭作用、X—H键轨道再杂化和质子供体电子密度重排. 其中, 超共轭作用属于键伸长效应, 电子密度重排和轨道再杂化属于键收缩效应. 在复合物1和2中, 由于键伸长效应处于优势地位导致形成红移氢键; 在复合物3中, 由于键收缩效应处于优势地位导致形成蓝移氢键.     

Theoretical Studies on Thermal Decomposition of Benzoyl Peroxide in Ground State

Systematic studies of the thermal decomposition mechanism of benzoyl peroxide(BPO) in ground state,leading to various intermediates, products and the potential energy surface(PES) of possible dissociation reactions were made computationally. The structures of the transition states and the activation energies for all the paths causing the formation of the reaction products mentioned above were calculated by the AM1 semiempirical method. This method is shown to to be one predict correctly the preferred pathway for the title reaction. It has been found that in ground state, the thermal decomposition of benzoyl peroxide has two kinds of paths. The first pathway PhC(O)O--OC(O)Ph→PhC(O)O→Ph CO2 produces finally phenyl radicals and carbon dioxide. And the second pathway PhC (O) OO--C (O) Ph→PhC (O) OO PhC (O)→PhC(O) O2→Ph CO O2, via which the reaction takes place only in two steps, produces oxygen and PhC(O) radicals, and the further thermal dissociation of PhC(O) is quite difficult because of the high activation energy in ground state. The calculated activation energies and reaction enthalpies are in good agreement with the experimental values. The research results also show that also the thermal dissociation process of the two bonds or the three bonds for the benzoyl peroxide doesn‘t take place in ground state.     

Thermal dissociation of the protein homodimer ecotin in the gas phase

The influence of charge on the thermal dissociation of gaseous, protonated, homodimeric, protein ecotin ions produced by nanoflow electrospray ionization (nanoES) was investigated using the blackbody infrared radiative dissociation technique. Dissociation of the protonated dimer, (E₂ + nH)ⁿ⁺ E₂ⁿ⁺ where n = 14–17, into pairs of monomer ions is the dominant reaction at temperatures from 126 to 175 °C. The monomer pair corresponding to the most symmetric charge distribution is preferred, although 50–60% of the monomer product ions correspond to an asymmetric partitioning of charge. The relative abundance of the different monomer ion pairs produced from E₂¹⁴⁺, E₂¹⁵⁺, and E₂¹⁶⁺ depends on reaction time, with the more symmetric charge distribution pair dominating at longer times. The relative yield of monomer ions observed late in the reaction is independent of temperature indicating that proton transfer between the monomers does not occur during dissociation and that the different monomer ion pairs are formed from dimer ions which differ in the distribution of charge between the monomers. For E₂¹⁷⁺, the yield of monomer ions is independent of reaction time but does exhibit slight temperature dependence, with higher temperatures favoring the monomers corresponding to most symmetric charge distribution. The charge distribution in the E₂¹⁵⁺ and E₂¹⁶⁺ dimer ions influences the dissociation kinetics, with the more asymmetric distribution resulting in greater reactivity. In contrast, the charge distribution has no measurable effect on the dissociation kinetics and energetics of the E₂¹⁷⁺ dimer.