溶液中Zn2+与腺嘌呤异构体间相互作用的理论研究

用B3LYP/6-311++G**方法和PCM及Onsager模型研究了Zn2+与腺嘌呤异构体在溶液中的11种较为稳定配合物. 结果显示, 这些配合物在溶液中的稳定性顺序与气相中明显不同, 其结合位点表现出如下的规律性, 在亚氨基类配合物中, Zn2+与腺嘌呤的N7、N6位结合比与N1、N6位结合形成的配合物更稳定; 氨基类配合物中, Zn2+以"双齿"形式与腺嘌呤异构体上的氮结合时的优先顺序为(N3和N9)>(N7和N6)>(N1和N6). 研究表明, 不论气相还是溶液相, 孤立的腺嘌呤分子内的质子转移较困难, 结合Zn2+后也不能明显降低关键步骤的活化能; 结合Cu2+却能明显地降低气相中关键步骤的活化能, 但溶剂效应却不利于Cu2+引发腺嘌呤分子内的质子转移.     

碱基腺嘌呤与多肽酰胺间氢键作用的最佳位点

正确理解核酸碱基和蛋白质多肽间的作用机制有助于人们利用这些生物分子有效地进行分子设计,进而制备具有特殊纳米结构和功能的生物分子材料.本文优化得到了碱基腺嘌呤与N-甲基乙酰胺、甘氨酸二肽、丙氨酸二肽形成的20个氢键复合物的结构并计算了结合能,探讨了腺嘌呤与多肽酰胺间氢键作用的最佳位点.研究发现:腺嘌呤可以使用两个不同位点(A1位点和A2位点)与N-甲基乙酰胺形成N―H…N型或者N―H…O=C型氢键复合物,腺嘌呤使用A1位点与N-甲基乙酰胺形成的N―H…N型氢键复合物更稳定;二肽分子可以使用主链上两个不同位点(丙氨酸的Ala7位点和Ala5位点或者甘氨酸的Gly7位点和Gly5位点)与腺嘌呤形成含有N―H…N和N―H…O=C两条氢键的复合物,二肽分子使用Ala7或Gly7位点与腺嘌呤形成的氢键复合物更稳定;腺嘌呤与多肽间的氢键作用强于其与N-甲基乙酰胺的作用.基于分子中的原子理论与自然键轨道计算结果分析了氢键作用的本质.     

腺嘌呤激发态失活通道的动力学模拟

采用半经典动力学方法模拟了1nπ*态9H-腺嘌呤的无辐射失活过程,模拟发现了一条新的失活通道,即N7-C8断键,释放的键能转化为分子动能.C8-H的强烈振动会导致无辐射跃迁,从而使分子返回基态.     

还原型辅酶烟酰胺腺嘌呤二核苷酸与人血清白蛋白相互作用的研究

运用荧光光谱、紫外光谱和计算机模拟分子对接等技术,研究了在模拟生理条件下还原型辅酶烟酰胺腺嘌呤二核苷酸(NADH)与人血清白蛋白(HSA)的作用方式及热力学特征。结果表明,NADH与人血清白蛋白的荧光猝灭机理属于静态猝灭;NADH与HSA在温度283K和310K时的结合常数和结合位点数分别为1.972×104 L.mol-1、0.9657和1.468×104 L.mol-1、0.9105,通过热力学计算得到反应的热力学参数;同步荧光光谱表明NADH使色氨酸残基的微环境亲水性增强;分子模型研究表明,二者通过疏水力、静电力和氢键共同作用结合。     

羟基自由基与N6,N6-二甲基腺嘌呤反应机理研究

N^6,N^6-二甲基腺嘌呤(DMAP)是生物分子的组成部分,在决定生物分子的活性和构型性能方面起到了重要作用。羟基自由基(·OH)可与DMAP反应,改变其结构,从而影响它的生物功能。因此有必要了解DMAP与·OH反应的具体过程。本文运用量子化学方法从理论上研究了·OH与DMAP的反应机理。根据反应的能垒及产物的稳定性,DMAP与·OH最可能的反应是·OH夺取DMAP的N(6)甲基H、N(9)H以及·OH加成到DMAP的C(8)位。N(6)位的甲基化提高了腺嘌呤的反应活性,也影响了其与·OH的反应机理。     

儿茶素结构和振动光谱的密度泛函理论研究

本文利用密度泛函理论方法B3LYP在6-311 G(d,p)水平上研究了儿茶素及其异构体表儿茶素分子的几何构型,计算结果与实验所得结构参数一致.计算了儿茶素分子平衡构型下的力常数,使用Wilson的GF矩阵方法计算了振动基频以及相应的势能分布,据此结合理论计算的光谱强度,对儿茶素分子的振动基频进行了完善合理的理论归属.     

6-N,N-二甲基腺嘌呤激发态结构动力学的共振拉曼光谱

采用共振拉曼光谱技术和密度泛函理论方法研究了6-N,N-二甲基腺嘌呤(DMA)的A带和B带电子激发和Franck-Condon 区域结构动力学. π_H→π_L^*跃迁是A带吸收的主体, 其振子强度约占整个A带吸收的79%.由弥散轨道参与的n→Ryd 和π_H→Ryd 跃迁在B带跃迁中扮演重要角色, 其振子强度约占B带吸收的62%,而在A带吸收中占主导的π_H→π_L^*跃迁的振子强度在B带吸收中仅占33%. 嘌呤环变形伸缩+C8H/N9H面内弯曲振动ν₂₃和五元环变形伸缩+C8H弯曲振动ν₁₃的基频、泛频和合频占据了A带共振拉曼光谱强度的绝大部分, 说明¹π_Hπ_L^*激发态结构动力学主要沿嘌呤环的变形伸缩振动, N9H/C8H/C2H弯曲振动等反应坐标展开, 而ν₁₀, ν₂₉, ν₂₁, ν₂₆和ν₄₀的基频、泛频和合频占据了B带共振拉曼光谱强度的主体部分, 它们决定了B带激发态的结构动力学. A带共振拉曼光谱中ν₂₆和ν₁₂被认为与1nπ*/1ππ*势能面锥型交叉有关. B带共振拉曼光谱中ν₂₁的激活与¹ππ^*/¹πσ_N9H^*势能面锥型交叉相关.     

十二烷基吗啉选择性吸附氯化钠的分子模拟

采用分子模拟方法研究氯化钠-光卤石反浮选体系中捕收剂十二烷基吗啉(DMP)选择性吸附氯化钠的机理. 用Material Studio 4.0软件和COMPASS分子力场方法建立了DMP在氯化钠和光卤石两种矿物表面的吸附模型, 并进行动力学模拟和能量优化, 确立了DMP在两种矿物表面的最佳吸附构型. 结果表明, DMP分子通过其官能团中的O、N原子与氯化钠界面水结构中的H原子之间的氢键作用吸附在氯化钠表面, 吸附作用能为-119.49 kJ·mol-1, 而光卤石界面水结构不能保持稳定排列, 致使DMP直接作用在光卤石表面, 吸附能为-37.97 kJ·mol-1, 在两种矿物共存体系中, 这种吸附能差异导致了DMP在氯化钠表面的选择性吸附.     

腺嘌呤与富马酸共晶体的太赫兹光谱分析

利用太赫兹时域光谱(THz-TDS)技术在室温下对腺嘌呤、富马酸及两者的共晶体进行测量, 实验结果显示腺嘌呤与富马酸共晶体在0.92、1.24、1.52 THz处有明显的吸收峰, 与腺嘌呤和富马酸不同, 表明共晶体物相结构不同于原料. 根据腺嘌呤分子氢键供体与受体的结构特点, 使用密度泛函理论(DFT)对腺嘌呤与富马酸三种可能的共晶体结构进行模拟. 结果显示其中一种可能的共晶体结构在0.89、1.16、1.41 THz处存在特征吸收峰, 与实验结果较好吻合. 由此判断腺嘌呤与富马酸共晶体氢键形成位置为腺嘌呤的氨基与富马酸其中一个羧酸的碳氧双键形成氢键, 而此羧酸的羟基与腺嘌呤六元环上的邻位氮原子形成第二处氢键. 本文还结合理论模拟的结果对腺嘌呤与富马酸共晶体的特征吸收峰对应的相关振动模式进行了归属.     

槲皮素分子结构和振动光谱的理论研究

本文采用密度泛函理论(DFT)方法研究了槲皮素分子的平衡几何构型和振动光谱。在B3LYP水平上,以6-311++G**为基组计算了其平衡构型下的谐振动力场﹑振动频率和振动强度。使用Wilson的GF矩阵方法对其进行了简正坐标分析,依据所得的势能分布(PEDs)对槲皮素分子的振动基频进行了合理的理论归属。     

The electronic spectrum of protonated adenine: theory and experiment

In this work we present the results of a combined experimental and theoretical study concerned with the question how a proton changes the electronic spectrum and dynamics of adenine. In the experimental part, isolated adenine ions have been formed by electro-spray ionisation, stored, mass-selected and cooled in a Paul trap and dissociated by resonant photoexcitation with ns UV laser pulses. The S(0)-S1 spectrum of protonated adenine recorded by fragment ion detection lies in a similar energy range as the first pipi* transition of neutral 9H-adenine. It shows a flat onset with a broad substructure, indicating a large S(0)-S1 geometry shift and an ultra-short lifetime. In the theoretical part, relative energies of the ground and the excited states of the most important tautomers have been calculated by means of a combined density functional theory and multi-reference configuration interaction approach. Protonation at the nitrogen in position 1 of the neutral 9H-adenine tautomer yields the most stable protonated adenine species, 1H-9H-A+. The 3H-7H-A+ and the 3H-9H-A+ tautomers, formed by protonation of 7H- and 9H-adenine in 3-position, are higher in energy by 162 cm(-1) and 688 cm(-1), respectively. Other tautomers lie at considerably higher energies. Calculated vertical absorption spectra are reported for all investigated tautomers whereas geometry optimisations of excited states have been carried out only for the most interesting ones. The S1 state energies and geometries are found to depend on the protonation site. The theoretical data match best with the experimental onset of the spectrum for the 1H-9H-A+ tautomer although we cannot definitely exclude contributions to the experimental spectrum from the 3H-7H-A+ tautomer at higher energies. The vertical S(0)--> S1 excitation energy is similar to the one in neutral 9H-adenine. As for the neutral adenine, we find a conical intersection of the S1 of protonated adenine with the ground state in an out-of-plane coordinate but at lower energies and accessible without barrier.     

DFT energy surfaces for aminopurine homodimers and their conjugate acid ions

Dimers of free nucleobases with their conjugate acid ions can be assigned to either of two categories: protonated dimers or proton-bound dimers. In the former, the extra proton attaches to a lone pair of a neutral dimer. In the latter, the extra proton is situated between two lone pairs and participates in a proton bridge. In general, proton-bound dimers are found to be more tightly held together than protonated dimers. While neutral adenine and its isomer 8-aminopurine (C(5)H(5)N(5)) are substantially more stable than their 7H tautomers, their conjugate acid ions and those of their respective 7H tautomers have nearly the same heats of formation. Correspondingly, the most stable (C(5)H(5)N(5))2H+ structures contain 7H tautomers as the neutral partner. Proton transit from one partner to the other within the most stable protonated dimer of 8-aminopurine has a low barrier (6 kJ mol(-1)). The potential energy curve for the NH stretch in that case is better fitted as a double minimum rather than as a harmonic potential. Purine-purine mismatches have been observed in nucleic acids, to which calculated (C(5)H(5)N(5))2H+ dimer geometries appear nearly isosteric.     

Electronic spectra of adenine and 2-aminopurine: an ab initio study of energy level diagrams of different tautomers in gas phase and aqueous solution

Ground and lowest two singlet excited state geometries of four tautomeric forms (N9H, N7H, N3H and N1H) of each of adenine and 2-aminopurine (2AP) were optimized using an ab initio approach employing a mixed basis set (6-311 + G* on the nitrogen atom of the amino group and 4-31G basis set on the other atoms). Excited states were generated employing configuration interaction involving single electron excitations (CIS). Subsequently, the different species were solvated in water employing the self-consistent reaction field (SCRF) approach along with the corresponding gas phase optimized geometries. Thus the observed absorption and fluorescence spectra of adenine and 2AP have been explained successfully. It is concluded that both the N9H and N7H forms of 2AP would contribute to absorption and fluorescence spectra. Further, the fluorescence of 2AP would be absorbed by its cation in which both the N9 and N7 atoms are protonated, the fluorescence of which can have an anti-Stokes component. Among the different tautomers of adenine, the N9H form would be present dominantly in the ground state in aqueous solutions but the N7H form would be produced by energy transfer and subsequent fluorescence. The N3H form of adenine appears to be responsible for the observed absorption near 300 nm by its solutions intermittently exposed to ultraviolet radiation. The rings of the different species related to 2AP and adenine remain almost planar in the pi-pi* and n-pi* singlet excited states as in the ground state. The pyramidal character of the amino group is usually less in the pi-pi* excited states than that in the corresponding ground or n-pi* excited states. Molecular electrostatic potential (MEP) maps of the molecules provide useful clues regarding phototautomerism.     

Pd催化甲醇裂解制氢的反应机理

基于密度泛函理论(DFT), 研究了甲醇在Pd(111)面上首先发生O—H键断裂的反应历程(CH3OH(s)→CH3O(s)+H(s)→CH2O(s)+2H(s)→CHO(s)+3H(s)→CO(s)+4H(s)). 优化了裂解过程中各反应物、中间体、过渡态和产物的几何构型, 获得了反应路径上各物种的吸附能及各基元反应的活化能数据. 另外, 对甲醇发生C—O键断裂生成CH3(s)和OH(s)的分解过程也进行了模拟计算. 计算结果表明, O—H键的断裂(活化能为103.1 kJ·mol-1)比C—O键的断裂(活化能为249.3 kJ·mol-1)更容易; 甲醇在Pd(111)面上裂解的主要反应历程是: 甲醇首先发生O—H键的断裂, 生成甲氧基中间体(CH3O(s)), 然后甲氧基中间体再逐步脱氢生成CO(s)和H(s). 甲醇发生O—H键断裂的活化能为103.1 kJ·mol-1, 甲氧基上脱氢的活化能为106.7 kJ·mol-1, 两者均有可能是整个裂解反应的速控步骤.     

Probing Protonation Sites of Isolated Flavins Using IR Spectroscopy: From Lumichrome to the Cofactor Flavin Mononucleotide

Infrared spectra of the isolated protonated flavin molecules lumichrome, lumiflavin, riboflavin (vitamin B₂), and the biologically important cofactor flavin mononucleotide are measured in the fingerprint region (600–1850 cm^?1) by means of IR multiple‐photon dissociation (IRMPD) spectroscopy. Using density functional theory calculations, the geometries, relative energies, and linear IR absorption spectra of several low‐energy isomers are calculated. Comparison of the calculated IR spectra with the measured IRMPD spectra reveals that the N10 substituent on the isoalloxazine ring influences the protonation site of the flavin. Lumichrome, with a hydrogen substituent, is only stable as the N1‐protonated tautomer and protonates at N5 of the pyrazine ring. The presence of the ribityl unit in riboflavin leads to protonation at N1 of the pyrimidinedione moiety, and methyl substitution in lumiflavin stabilizes the tautomer that is protonated at O2. In contrast, flavin mononucleotide exists as both the O2‐ and N1‐protonated tautomers. The frequencies and relative intensities of the two C?O stretch vibrations in protonated flavins serve as reliable indicators for their protonation site.     

Are Conical Intersections Responsible for the Ultrafast Processes of Adenine,Protonated Adenine,and the Corresponding Nucleosides?

Excited-state potential energy surfaces of adenine, protonated adenine, and their N9-methylated analogs are explored by means of a complete active space (CAS) and time-dependent density functional theory (TD-DFT) study to understand the dynamics associated with internal conversion. After photoexcitation of the ground-state molecules to the S(1) state, the nuclear motions that are responsible for taking the wavepacket out of the Franck-Condon region are either an H--N9/C--N9 stretch or a ring-puckering motion that leads to pyramidalization. These motions lead to accessible conical intersections with the ground-state surface. The results are used to successfully interpret previous measurements on the photodissociation of adenosine 5'-monophosphate nucleotide anions and cations, where the latter react in a highly nonstatistical manner.     

Investigation of proton transport tautomerism in clusters of protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia by high-pressure mass spectrometry and ab initio calculations

The energetics of the ion-molecule interactions and structures of the clusters formed between protonated nucleic acid bases (cytosine, uracil, thymine, and adenine) and ammonia have been studied by pulsed ionization high-pressure mass spectrometry (HPMS) and ab initio calculations. For protonated cytosine, uracil, thymine, and adenine with ammonia, the measured enthalpies of association with ammonia are -21.7, -27.9, -22.1, and -17.5 kcal mol-1, respectively. Different isomers of the neutral and protonated nucleic acid bases as well as their clusters with ammonia have been investigated at the B3LYP/6-31+G(d,p) level of theory, and the corresponding binding energetics have also been obtained. The potential energy surfaces for proton transfer and interconversion of the clusters of protonated thymine and uracil with ammonia have been constructed. For cytosine, the experimental binding energy is in agreement with the computed binding energy for the most stable isomer, CN01-01, which is derived from the enol form of protonated cytosine, CH01, and ammonia. Although adenine has a proton affinity similar to that of cytosine, the binding energy of protonated adenine to ammonia is much lower than that for protonated cytosine. This is shown to be due to the differing types of hydrogen bonds being formed. Similarly, although uracil and thymine have similar structures and proton affinities, the binding energies between the protonated species and ammonia are different. Strikingly, the addition of a single methyl group, in going from uracil to thymine, results in a significant structural change for the most stable isomers, UN01-01 and TN03-01, respectively. This then leads to the difference in their measured binding energies with ammonia. Because thymine is found only in DNA while uracil is found in RNA, this provides some potential insight into the difference between uracil and thymine, especially their interactions with other molecules.     

新型高能量密度化合物3,6-双(3,5-二硝基-1,2,4-三唑-1)-1,2,4,5-四嗪-1,4-二氧化物的性能预估及合成路线设计

采用C++自编译程序及组合原理,设计并筛选出一种未见报道的新型富氮类高能量密度化合物-3,6-双(3,5.二硝基.1,2,4-三唑.1)-1,2,4,5-四嗪-1,4-二氧化物,用B3LYP法,在6-31G**基组水平上得到该化合物全优化构型;在振动分析的基础上求得体系的振动频率、IR谱;通过键级分析得到热解引发键的键离解能(BDE);采用Monte-Carlo 方法预估了密度;设计等键等电子反应计算了生成焓;运用Kamlet-Jacobs公式预测爆速、爆压和爆热;运用Keshavarz 等推导的预估撞击感度H50的公式预测了撞击感度性能;并利用逆合成分析法设计其合成路线.结果表明:该化合物存在8个强吸收峰,校正后的热解引发键的BDE为264KJ·mol-1,稳定性较优;密度1.955 g·cm-3、生成焓901.72 kJ·mol-1、爆速9191.48 m·s-1、爆压39.32 GPa、爆热6705.15 j·g-1;撞击感度H50为55.85cm,低于黑索金(RDX)和奥克托今(HMx);以上性能均达到了高能量密度化合物的标准,且该化合物设计合成路线步骤较少、原料易得,有望得到广泛应用.     

Raman spectroscopic study of the tautomeric composition of adenine in water

An experimental and theoretical study of the tautomeric composition of adenine (Ade) in water using Raman spectroscopy is reported. Experimental resonance Raman spectra of adenine at excitation wavelengths of 200, 218, and 266 nm were compared with quantum-mechanical calculations of N(9)H- and N(7)H-adenine tautomers and their cations. Both theoretical and experimental studies of nonresonance Raman spectra (457 nm excitation) of adenine were also performed for comparison. A satisfactory agreement of the calculated results with the experimental data was obtained. The Raman spectra are interpreted, and the basic regularities of the Raman intensity distribution are explained. On the basis of the analysis performed, the tautomeric composition of adenine in water is revealed. It is shown that the Ade-N(9),N(1)H(+) cation is the predominant form and that some neutral forms of Ade-N(9)H and Ade-N(7)H tautomers exist in water at pH 3.     

Unimolecular dissociation of anthracene and acridine cations: the importance of isomerization barriers for the C2H2 loss and HCN loss channels

The loss of C(2)H(2) is a low activation energy dissociation channel for anthracene (C(14)H(10)) and acridine (C(13)H(9)N) cations. For the latter ion another prominent fragmentation pathway is the loss of HCN. We have studied these two dissociation channels by collision induced dissociation experiments of 50 keV anthracene cations and protonated acridine, both produced by electrospray ionization, in collisions with a neutral xenon target. In addition, we have carried out density functional theory calculations on possible reaction pathways for the loss of C(2)H(2) and HCN. The mass spectra display features of multi-step processes, and for protonated acridine the dominant first step process is the loss of a hydrogen from the N site, which then leads to C(2)H(2)/HCN loss from the acridine cation. With our calculations we have identified three pathways for the loss of C(2)H(2) from the anthracene cation, with three different cationic products: 2-ethynylnaphthalene, biphenylene, and acenaphthylene. The third product is the one with the overall lowest dissociation energy barrier. For the acridine cation our calculated pathway for the loss of C(2)H(2) leads to the 3-ethynylquinoline cation, and the loss of HCN leads to the biphenylene cation. Isomerization plays an important role in the formation of the non-ethynyl containing products. All calculated fragmentation pathways should be accessible in the present experiment due to substantial energy deposition in the collisions.