M-Uracil复合物(M=Ca2+和Mg2＋)特征振动的密度泛函理论分析

采用密度函数理论的B3LYP交换关联能泛函在6-311 G(2df,2p)基组水平上,对Ca2 、Mg2 与尿嘧啶(简称U)三种各互变异构体(简称U1、U2和U3)形成的复合物进行了优化计算,获得稳定复合物的构形,并对这些稳定复合物进行振动频率计算.分析计算结果发现由于离子的参与,单体分子振动的力常数和折合质量均会发生变化,导致红外振动谱线发生不同程度移动;进一步分析发现C-H和O-H键的氢原子作弯曲振动和伸缩振动的谱线移动不确定,直接与离子作用的氧原子参与的振动谱线会发生红移,不直接与离子作用的氧原子参与的振动谱线会发生蓝移.     

复合物Ca+-RNA碱基的结构与稳定性

用密度泛函理论(DFT)中的杂化密度泛函B3LYP方法,在6311+G(2df,2p)基组水平上,确定了RNA碱基与Ca+的气相金属离子亲和能和复合物的优化结构.通过考虑Ca+作用于RNA碱基互变异构体的不同位置,获得了所有稳定的复合物.对于胞核嘧啶,最稳定的复合物起源于最稳定的分子互变异构体;对于胸腺嘧啶,最稳定的分子互变异构体形成的复合物的键能最小,而最不稳定的互变异构体形成的复合物键能最强;尿嘧啶的情形与胸腺嘧啶相似.在互变异构体复合物中,键能是依赖于金属离子成键的位置,而总能量取决于全部的原子和它们之间的相对位置,这可能是造成几种互变异构体复合物键能和总能量变化趋势并不一致的原因.     

碱土金属Be 、Mg 、Ca掺杂磷团簇结构演变规律与光谱性质研究

采用第一性原理在B3LYP\6-311G水平上对MnPm（n=1～2, m=1～10）（M=Be 、Mg 、Ca）团簇进行几何构型优化和频率分析,得到团簇各个尺寸的基态结构,结果表明,在m+n=5～6时锥体结构居多,相应的稳定性要高于同尺寸其他构型,m+n>6时,基态结构中出现四元环和五元环。裂化能和二阶能量差分计算结果表明,MPm（m=1～10）团簇在m=2时同时获得局域的最大值, Be2Pm（m=1～10）团簇幻数结构呈现规则的奇偶振荡。Be掺杂P团簇稳定性高于同尺寸的Mg 、Ca掺杂,与Mg 、Ca相比Be原子更易于与P原子结合。稳定结构团簇红外和拉曼光谱显示,高频段MP2团簇红外和拉曼活性较强,Mg2P2, Ca2P2团簇红外谱主峰在高频段出现,与拉曼活性谱主峰相反。     

木犀草素与腺嘌呤相互作用的理论研究

本文采用密度泛函理论中的B3LYP方法,在6-31+G~*基组水平上对木犀草素—腺嘌呤复合物进行结构优化和振动频率分析,得到了16种稳定的木犀草素—腺嘌呤复合物.应用分子中的原子理论(AIM)分析、自然键轨道(NBO)理论分析得到复合物氢键性质和特征.通过基组重叠误差(BSSE)校正后的相互作用能、成键临界点电荷密度、二阶稳定化能综合分析,得出三氢键复合物C-11结构是最稳定的.综合比较DNA的四个碱基与木犀草素间的相互作用,木犀草素与胸腺嘧啶的相互作用最强,木犀草素-腺嘌呤相互作用最弱,DNA的四个碱基与木犀草素间的相互作用能均比木犀草素与水间相互作用能大,这说明木犀草素作为抗癌药物能有效的发挥作用.     

内嵌富勒烯[M@C70] (M=Li, Na, K, Be, Mg, Ca)与[Mg(H2O)6]2+相互作用的密度泛函理论研究

使用密度泛函理论方法, 对内嵌多种碱金属及碱土金属原子(M=Li, Na, K, Be, Mg, Ca)的富勒烯C70与水合Mg(II)离子之间的相互作用进行了理论研究. 首先对各原子(M=Li, Na, K, Be, Mg, Ca)嵌入C70后的形成能进行了讨论, 之后计算了[M@C70]各体系与[Mg(H2O)6]2+的相互作用能, 并采用自然键轨道理论(NBO)研究了电荷转移的情况, 最后进行了电子密度拓扑分析. 结果表明, 内嵌原子半径越大, [M@C70]各体系的热力学稳定性就越高, 转移至[Mg(H2O)6]2+的电荷也随之增加, 二者之间的相互作用属于闭壳层相互作用及共价作用.     

内嵌富勒烯[M@C_(70)](M=Li,Na,K,Be,Mg,Ca)与[Mg(H_2O)_6]~(2+)相互作用的密度泛函理论研究

使用密度泛函理论方法,对内嵌多种碱金属及碱土金属原子(M=Li,Na,K,Be,Mg,Ca)的富勒烯C70与水合Mg(II)离子之间的相互作用进行了理论研究.首先对各原子(M=Li,Na,K,Be,Mg,Ca)嵌入C70后的形成能进行了讨论,之后计算了[M@C70]各体系与[Mg(H_2O)6]2~+的相互作用能,并采用自然键轨道理论(NBO)研究了电荷转移的情况,最后进行了电子密度拓扑分析.结果表明,内嵌原子半径越大,[M@C70]各体系的热力学稳定性就越高,转移至[Mg(H_2O)6]2~+的电荷也随之增加,二者之间的相互作用属于闭壳层相互作用及共价作用.     

硅烯饱和吸附碱金属原子的第一性原理研究

基于密度泛函理论的第一性原理计算, 研究了硅烯饱和吸附碱金属元素原子的稳定性、微观几何结构和电子性质, 并与纯硅烯及其饱和氢化结构进行了对比分析. 研究发现复合物SiX(X=Li, Na, K, Rb)的形成能都是负的, 相对于纯硅烯来说可以稳定存在. Bader电荷分析表明, 电荷从碱金属原子转移至硅原子. 从成键方式来看, 硅烯与氢原子形成共价键, 而与碱金属原子之间形成的键主要是离子性成键, 但还存在部分共价关联成分. 能带计算表明, 锂原子饱和吸附在硅烯形成的复合物SiLi是直接带隙的半导体, 带隙大小为0.34 eV. 其他碱金属饱和吸附在硅烯上形成的复合物都表现为金属性.     

青碧与青玉的红外光谱特征及意义

青碧为碧玉系列中外观类似青玉的称呼。二者虽外观相似,但青碧价格高很多,故市场上出现了以青玉充青碧售卖的现象。此外,一些出土玉文物中也出现了这类外观的玉石材质,但无法准确判别其类型。这使得快速准确鉴别二者有十分重要的意义。采用紫外-可见光谱、傅里叶变换红外光谱和电子探针分析方法,给出了青碧和青玉样品的谱学特征和矿物的化学组成等特征,并进行了对比分析。二者在紫外-可见反射光谱上没有明显差异,然而,二者的红外光谱特征存在可识别的差异。为了探讨出更有效的鉴别特征,采用了反射和透射两种方法来获取红外光谱。二者的红外光谱总体上一致,有以下可区分差异特征：青碧的红外反射光谱中出现了青玉光谱中未出现的1 050和1 018 cm-1附近吸收峰、肩峰及411 cm-1附近宽肩峰;青玉的红外透射光谱中出现了青碧光谱中未出现的453 cm-1附近肩峰和401 cm-1附近吸收峰。以上可作为快速鉴别青碧和青玉的谱学特征标志。红外透射光谱经朗伯-比尔定律(A=log(1/T))转换后,在3 674,3 661和3 643 cm-1附近处的OH伸缩振动谱带的强度与M1,M3位的Mg及Fe2+含量有很好的相关性。利用以上二者关系计算的Mg(M1+M3)#(在M1和M3位的Mg/(Mg+Fe2+))值可用于鉴别青碧和青玉。青碧的Mg(M1+M3)#值为0.871～0.892,小于青玉0.927～0.949。另外,电子探针分析结果显示青碧和青玉的化学成分存在一定差异：青碧Mg含量(a.p.f.u)为4.45～4.53,比青玉的4.66～4.78小;青碧Fe2+含量为0.28～0.49,大于青玉的0.10～0.23。但部分青碧和青玉间的Mg和Fe2+含量差异不大,说明红外光谱差异除了与成分有一定的关联性外,可能还与结晶时的物理化学条件有关(青碧和青玉的成因类型分别为超基性岩型和白云质大理岩型)。以上红外光谱识别特征不仅在鉴别青碧和青玉上具有重要的宝石学意义,还在古代玉制品源区的判别、产状分析等方面具有潜在的应用价值。     

胸腺嘧啶单体及环丁烷型胸腺嘧啶二聚体的表面增强拉曼散射

采用DFT-B3LYP方法,6-311G(d,p)(C,H,O原子)和lanl2dz（Ag原子）基组计算了胸腺嘧啶单体（Th）和DNA光损伤产物—环丁烷型胸腺嘧啶二聚体（Th2）吸附在Ag纳米粒子上形成复合物的结构和表面增强拉曼散射（SERS）。结果显示, Ag纳米粒子在胸腺嘧啶单体（Th）和环丁烷型胸腺嘧啶二聚体中最有利的吸附位点是O7位,相比于单个分子,复合物Th-Ag,Th2-Ag的结构和光谱发生了变化。对胸腺嘧啶单体分子,其SERS的增强因子为10,主要由N-H伸缩振动引起;复合物Th2-Ag中, SERS增强了大约18倍,主要由C2=O的伸缩振动引起,此增强机理属于极化率变化产生的静化学增强。     

三苯基咔咯金属配合物的振动光谱和DFT计算

对三苯基咔咯金属配合物(MTPC, M=Ni, Cu, Co, Mn)的拉曼和红外光谱进行了实验研究. 用DFT方法计算了其基态几何结构以及红外和拉曼光谱,并基于计算结果对测量到的振动谱带进行了局域坐标归属. 研究发现,由于对称性降低,咔咯金属配合物的振动光谱比卟啉金属配合物更为复杂,若干咔咯骨架振动与苯取代基强烈耦合.考察了拉曼和红外谱带频率变化与咔咯环结构的关系,发现随着环内核尺寸的减小,与C^I_αC^I_α键伸缩振动和C?Cm键伸缩振动相关的拉曼谱带频率增加,其中C^I_αC^I_α伸缩振动的拉曼谱带对环内核尺寸的变化更为敏感且呈良好的线性关系,可以作为反映金属咔咯骨架结构变化的特征谱带.     

Hydrogen bonding in different pyrimidine–methanol clusters probed by polarized Raman spectroscopy and DFT calculations

We report on the hydrogen bonding between pyrimidine (Pd) and methanol (M) as H‐donor in this study. Hydrogen bonds between pyrimidine and methanol molecules as well as those between different methanol molecules significantly influence the spectral features at high dilution. The ring‐breathing mode ν₁ of the reference system Pd was chosen as a marker band to probe the degree of hydrogen bonding. Polarized Raman spectra in the region 970–1020 cm⁻¹ for binary mixtures of (pyrimidine + methanol) at 28 different mole fractions were recorded. A Raman line shape analysis of the isotropic Raman line profiles at all concentrations revealed three distinct spectral components at mole fractions of Pd below 0.75. The three components are attributed to three distinct groups of species: ‘free Pd’ (pd), ‘Pd with low methanol content’ (pd1) and ‘Pd with high‐methanol content’ (pd2). The two latter species differ considerably in the pattern and the strengths of the hydrogen bonds. The results of density functional theory calculations on structures and vibrational spectra of neat Pd and eight Pd/M complexes with varying methanol content support our interpretations of the experimental results. A nice spectra–structure correlation for the different cluster subgroups was obtained, similar to earlier results obtained for Pd and water. Apart from N···H and O···H hydrogen bonds between pyrimidine and methanol, O···H hydrogen bonds formed among the methanol molecules in the cluster at high methanol content also play a crucial role in the interpretation of the experimental results. Copyright © 2010 John Wiley & Sons, Ltd.     

Structural analysis of base mispairing in DNA containing oxidative guanine lesion

Classical molecular dynamics methods were used to analyze the importance of 8-oxoguanine (8-oxoG) pairing with other DNA bases in order to determine the impact of oxidative guanine lesions on DNA structure. Six lesioned molecules, each containing 8-oxoG mispaired with one of the four normal bases on the the opposite strand at the center of 40-mer DNA, and one non-damaged DNA molecule, were simulated for 2 nanoseconds of real time. The 8-oxoG lesioned bases were found to incorporate opposite all normal bases. There are observed conformational and energetical differences among these parings. 8-oxoG in anti-form creates firm hydrogen bonds with cytosine and this bonding has a strong attractive electrostatic interaction energy similar to that of a native base pair-guanine to cytosine. Meanwhile, it does not form a stable base pair with purine bases (adenine and guanine) nor with the pyrimidine base thymine. On the other hand, the 8-oxoG in syn-form was found to pair with adenine.      

Theoretical Study on the Stable Structures and Aromaticities for Pnictogen Dianionic Sb42-, Bi42-, and (SbBi)22- Clusters

运用密度泛函方法(B3LYP)和后Hartree-Fock (post-HF：MP2、CCSD(T)),对三个新的磷属二价阴离子团簇Sb42-、Bi42-和(SbBi)22-的几个可能的同分异构体进行结构优化、振动频率和原子化能的理论计算．计算结果表明Sb42-和Bi42-团簇有三种稳定的结构：正方形(D4h)、屋顶型(roof,C2v-1)和C2v-2结构,其中正方形结构是基态．由异原子组成的(SbBi)22-团簇也有三种稳定结构：菱形(D4h)、屋顶型(roof,C1)和C2v结构,其中菱形结构是基态．计算显示Sb42-、Bi42-和(SbBi)22-团簇的所有屋顶型(roof)结构的核独立化学位移(NICS)全部为负值,从而说明这些屋顶型结构拥有芳香性;平面环结构(正方形或菱形)的核独立化学位移值全部为正值,说明这三种平面环结构具有反芳香性．用分子轨道分析对这两类屋顶型和平面环结构的芳香性和反芳香性作了解释和讨论．     

带-NH2的嘧啶环对钌配合物与DNA相互作用的瞬态发光特性的影响

采用时间分辨的发光光谱技术,分别测量了两种新合成的钌配合物[Ru(bpy)2 (dpbpd(NH2)2)]2 和[Ru(phen)2(dpbpd(NH2)2)]2 与小牛胸腺脱氧核糖核酸(ctDNA)相互作用时的瞬态发光动力学过程,并与以往对[Ru(phen)2dppz]2 等的研究结果进行对比,从而研究带-NH2的嘧啶环对配合物与DNA作用动力学过程的影响.结果表明:这两种含有带-NH2的嘧啶环的钌配合物与DNA相互作用时的发光按双指数规律衰减,发光寿命为几十纳秒,比dppz类钌配合物与DNA作用时的发光衰变寿命(几百纳秒)小一个数量级.归因于嘧啶环上的N和-NH2可能与水分子、DNA的碱基对或磷酸骨架形成氢键,从而加快激发态的无辐射弛豫,削弱发射光强,缩短发光寿命.该结论为进一步研究配合物分子与DNA的相互作用的机理提供了一定的依据.     

第一性原理比较研究MnPm(M=Al,Ga,In,2≤n+m≤3)团簇

利用密度泛函理论对MnPm (M=Al,Ga,and In,2≤n+m≤3)团簇的几何和电子结构性质及稳定性进行了研究.结果表明,三原子的MnPm团簇是二重态,而单体则是三重态.富P的MP2团簇是具有C2V对称性的等腰三角形结构,而富M的M2P团簇则是具有Cs对称性的三角形结构.在三原子磷化物团簇中,MP2团簇比M2P团簇稳定,而后者中M-P键的强度比前者强.对于这些小的磷化物团簇,电离势高于裂解能,表明裂解比电离占优势.Ga2P比Al2P和In2P的HOMO-LUMO能隙和电离势都高,归咎于在富金属的M2P团簇中,相对较强的Ga-P键.     

Theoretical study of B3O radical isomers and their interconversion pathways

Despite the fact that B₃O is the second simplest B _n O radical after BO, a controversy recently emerged concerning the molecular structure of its global minimum. Two recent theoretical groups predicted the linear quartet BBBO to be the ground isomer. By contrast, another recent theoretical group reported that B₃O has a doublet B₃-ring ground structure. Moreover, larger B _n O clusters usually have low-lying B₃-ring isomers. In order to determine the accurate energetic competition between linear and cyclic structures in both the doublet and quartet, and to understand the detailed isomerism between various isomers, which is vital for understanding the formation mechanism of B₃O, we report the first potential energy surface (PES) study of B₃O at various computational levels, including CCSD(T)/6-311+G(2df), CCSD(T)/aug-cc-pVTZ, CCSD(T)/aug-cc-pVQZ and G3B3 for the single-point energy, as well as B3LYP/6-311+G(d) and QCISD/6-311+G(d) for geometrical optimisation. It is shown that the isomers in the quartet state are all thermodynamically more stable than the corresponding doublet ones, and on both the quartet and doublet PESs, the linear form has the lowest energy. Therefore, our study on both linear and cyclic isomers shows that the linear quartet BBBO ⁴ 01 is definitively the ground isomer. Although being much less stable than the quartet linear BBBO global minimum by >20 kcal mol^?1, five cyclic isomers exist as local minima, with the bi-cyclic structure ⁴ 02 possessing the smallest barrier of around 15 kcal mol^?1. The dissociation energies for direct combination processes B₃ + O, B₂ + BO and B + B₂O are discussed. The present work may be helpful in obtaining a deep understanding of the doping and oxidation process of pure B _n clusters.     

SeOx(x=1,2)的从头算势能曲线和光谱常数

采用从头算的多种方法和基组优化计算SeO_x(x=1,2)自由基的基态结构、谐振频率及离解能,优选出QCISD(T)/6-311+G(2df)、B3LYP/6-311G(3d2f)方法分别对SeO、SeO₂自由基进行计算,计算结果与实验结果吻合很好.对SeO自由基拟合出Murrell-Sorbie势能函数参数,计算出SeO自由基的光谱常数和力常数.计算出SeO₂自由基力常数,导出SeO₂自由基的多体展式势能函数,发现SeO₂自由基对称伸缩振动势能图中在对称的O+SeO→SeO₂反应通道上有一鞍点,其活化能约为48.24 kJ·mol^-1,O原子需要越过0.5 eV的能垒才能生成SeO₂的稳定结构.     

A single pulse shock tube study of pentene isomer pyrolysis

A single-pulse shock tube study of the four pentene isomers is carried out at 2 ± 0.16 bar and 900–1600 K. C₁ to C₆ species profiles were recorded using gas chromatography mass spectrometry analyses. The species are identified using mass spectrometry and quantified by flame ionization detection. High-pressure limiting and pressure-dependent rate constants for 2M1B, 2M2B and 3M1B + ? were calculated using RRKM theory with a Master Equation (ME) analysis using the Master Equation System Solver, MESS. A mechanism was formulated based on rate rules and theoretical calculations. Comparisons between experimental results and model simulations are provided for all of the five pentene isomers investigated with satisfactory agreement. Furthermore, an insight is provided into the influence of molecular structure on the reactivity of pyrolysis chemistry. Interestingly, it is found that the HACA mechanism is much less prominent for benzene formation compared to the role of cyclopentadienyl radical recombination with methyl radicals and also the recombination of propargyl radicals.     

二面角弯曲异构体：M2Pt20/-团簇的理论研究

本文采用密度泛函理论和波函数理论研究了M₂Pt₂^0/-团簇(M表示碱土金属元素)在气相中的几何结构和电子性质. 研究表明,拥有平面结构的D_2h异构体比拥有较小二面角及较短Pt-Pt键长的C_2v异构体更稳定. M(s,p)与Pt(5d)的相互作用和Pt-Pt共价键之间的相互竞争导致了这两种异构体在稳定性方面有所不同. M(s,p)与Pt(5d)的相互作用支持D_2h异构体的平面结构;Pt-Pt共价键作用导致了C_2v异构体的弯曲结构. Be₂Pt₂的单重态和三重态的势能曲线有两个不同的交点,但是Ra₂Pt₂和Ca₂Pt₂^-的不同多重度的势能曲线间只有一个交点,这可能是由于三重态Ra₂Pt₂和四重态Ca₂Pt₂^-较平坦的势能曲线造成的. 上述结果揭示了一个拥有最小原子数的二面角弯曲异构现象,并且为解释其他潜在的角度弯曲异构体提供了理论帮助.     

Theoretical study of the CH3 + NS and related reactions: mechanism of HCN formation

More than thirty equilibrium and transition structures on the [CH₃NS] potential energy surface have been located using the B3LYP/6-311 + + G(d,p) method. Thioformaldoxime (3) turns out to be the most stable isomer followed by thionitrone (2), a three-membered ring, thionitrosyl methane (1) and thiazyl methane. These isomers are connected to each other by 1,2H and 1,3H shifts and ring—chain rearrangement, but the associated energy barriers are rather high, making most of them stable with respect to unimolecular transformations. Starting from CH₃ + NS, a possible initial atmospheric reaction, HCN formation appears to be the most favoured process through a cascade involvement of 1, 2 and 3. The standard heats of formation, ΔH ⁰ _f,298 are calculated to be: 3, 149kJmol^?1; and 1, 218kJmol^?1; using the CCSD(T)/6-311+ +G(3df,2p) method, with an error of ±10kJ mol^?1.