哈尔满碱分子光谱的密度泛函理论研究

采用密度泛函理论(Density Functional Theory,DFT),在M062X/6-31g(d)水平上,对哈尔满碱分子结构进行结构优化,计算其振动频率,获得该分子的红外光谱,利用势能函数分布(Potential energy distribution,PED)结合VEDA4软件对哈尔满碱分子的红外光谱简正振动模式进行了指认.采用含时密度泛函理论(Time-dependent density functional theory,TDDFT)计算了该分子在不同溶剂条件下的吸收光谱和激发态.将理论计算的红外光谱和紫外光谱与实验值进行对比分析,对哈尔满碱分子的激发态进行了分析计算,讨论了哈尔满碱分子的前线分子轨道和分子静电势.为哈尔满碱分子的光谱检测技术及电子结构分析提供参考.     

磺胺甲恶唑的振动光谱和密度泛函理论研究

磺胺甲恶唑(Sulfamethoxazole, SMX)是一种磺胺类广谱抗生素.基于密度泛函理论(DFT)的B3LYP方法,在B3LYP/6-311++G (d, p)基组水平上对SMX初始构型进行结构优化,得出该分子最稳定结构构型.同时,给出了SMX的键长、键角和二面角等空间结构参数值,确定该分子空间构型为非平面结构.相同基组水平下进行频率计算,通过频率校正因子0.9630修正并绘制了SMX分子的红外光谱和拉曼光谱图.发现光谱谱段主要分布在3600-2800 cm^-1和1700-300 cm^-1频率段,并且理论计算值和实验测定值有较好吻合,表明DFT计算方法是可取和可信的.借助GaussView 6.0软件和计算得到的势能分布结果对频率范围内每一个振动模式进行了指认归属.此外,采用Multiwfn和VMD程序计算并分析SMX分子的静电势和前线分子轨道,预测了该分子的反应活性位点.该结果为SMX分子的振动光谱检测提供基础数据,为其结构鉴定提供技术参考.     

3,5-二甲氧基苯甲醇振动光谱的研究

实验测量了3,5-二甲氧基苯甲醇(L₁OH)分子的拉曼和红外光谱,运用密度泛函理论(DFT)采用B3LYP混合泛函和6-311G(d, p)基函数组,计算了该分子的平衡构型和振动频率。结果表明：理论计算出的振动频率值和实验观测值吻合得较好。同时采用简正振动分析方法得到了各振动频率的势能分布(PED),从而对L₁OH分子的振动频率归属做出了全面指认。已有文献中还未见有对L₁OH分子振动光谱研究的报道。     

氨分子的激发特征和电子态与振动态相互作用

采用密度泛函(DFT)B3P86方法优化得到了氨分子的基态稳定构型、红外光谱和拉曼光谱,利用对称匹配耦合簇-组态相互作用(SAC/SAC-CI)方法在D95++基组水平上,研究了氨分子基态的激发特征。结果表明,氨分子基态的红外光谱频率和拉曼光谱频率移位是完全相符的,振动的红外光谱和拉曼光谱都是活性的,这与理论分析一致。二维垂直振动ν3,5的红外强度为0.206km/mol,接近于零,这与氨分子的激发特征有关。基态氨分子是C3V群,激发态则变为D3h群,基态转变成激发态引起对称性增加和能量升高,这种变化不是Jahn-Teller效应,而是电子态与振动态相互作用的结果。从理论上分析了这种电子态与振动态相互作用,理论分析与计算结果一致。     

激发态下甘氨酸与水分子间氢键性质研究

在生物体中氨基酸通常以水作为溶剂,是形成细胞的重要成分.在该环境下,分子间氢键的产生会对氨基酸分子与水分子的结构和性质产生影响.为了研究其在基态和激发态下的性质,本文利用密度泛函理论(DFT)和含时密度泛函理论(TD-DFT)对甘氨酸分子和H₂O分子在基态和激发态下的分子间氢键的静电势、键长、自然键轨道(NBO)电荷、分子中的原子理论(AIM)分析、Wiberg键级b、红外(IR)光谱、空穴-电子轨道和基态与激发态之间的电子转移进行了理论研究.结果表明：分子间氢键的形成会导致分子结构的改变和红外光谱振动频率的移动.在激发态下,分子间氢键有不同程度的增强或减弱.该计算结果为氢键的形成和激发态下分子间氢键的研究提供理论依据.     

双酚A和双酚A二缩水甘油醚振动谱的理论和实验比较分析

利用基于密度泛函理论的第一性原理计算,本文研究双酚A(BPA)和双酚A二缩水甘油醚(EDGEBA)分子的结构和振动性质,分析了两种分子红外活性和拉曼活性特征振动的频率和对称性。计算结果表明,BPA分子的拉曼散射峰基本归属于对位取代苯的骨架振动,500~1600cm-1红外强度较强;对于DGEBA分子环氧基团指纹区的特征振动频率为860,930,1123,1260cm-1,其红外光谱强度较大,可用于DGEBA类树脂固化反应过程监控;1260cm1附近的振动模,其拉曼散射强度较高,可成为拉曼光谱研究固化反应过程的特征振动。而1160cm-1附近的振动属于芳香环的特征振动,强度基本不变。     

基于溶剂化效应的BDE-15分子振动光谱增强特征振动研究

利用密度泛函与自洽反应场理论在B3LYP/6-31+G(d)水平下分别计算气态及24种不同极性溶剂中4,4’-二溴二苯醚(4,4’-dibrominated diphenyl ethers, BDE-15)的分子振动光谱(红外光谱、拉曼光谱),以气态分子振动光谱为基准,筛选出对溶剂极性敏感的特征振动作为指标构建溶剂对BDE-15振动光谱溶剂化效应指标体系,探究溶剂对BDE-15分子振动频率、红外/拉曼峰强溶剂化效应及综合效应,并寻求显著增强BDE-15分子特征振动频移/强度的溶剂。研究表明：从分子振动频率角度,溶剂极性敏感的(频移>1 cm-1)分子特征振动均为伸缩振和面外弯曲振,但24种溶剂对BDE-15分子振动频率溶剂化效应并不显著;从分子振动峰强角度,24种溶剂对BDE-15分子振动光谱峰强的增强效应主要发生在红外光谱的中低频区及拉曼光谱的高频区,其中起显著增强(红外/拉曼效应指标值分别大于6与5)的溶剂为醇类、乙腈、二甲亚砜、硝基苯;不同极性溶剂对BDE-15拉曼峰强溶剂化效应及综合效应指标值均表现出随溶剂介电常数增长由线性到对数的增长趋势,而红外峰强只保留低介电常数溶剂时的线性关系。利用上述BDE-15分子振动光谱峰强增强方法对BDE-153,BDE-154和BDE-209进行验证,醇类、乙腈、二甲亚砜、硝基苯对三者的振动光谱红外/拉曼峰强的效应指标值分别大于6与5,且最大峰强增倍数皆大于33,说明所建BDE-15分子振动光谱增强特征振动方法有助于进一步开展基于分子振动光谱的PBDEs同系物间辨识研究。     

外电场下4-氯-2-三氟甲基噻吩并[3,2-D]嘧啶分子的结构和光谱

4-氯-2-三氟甲基噻吩并[3,2-D]嘧啶(4-chloro-2-(trifluoromethyl)thieno[3,2-d] pyrimidine, CTTP)分子具有很高的生物和医学活性,是重要的医药中间体,因此了解外电场下对其结构和光谱的影响具有重要意义。采用密度泛函理论B3LYP方法和def2-tzvp基组,优化计算了CTTP分子在不同外电场作用下的稳定结构;然后从外电场对其结构、原子电荷分布、前线轨道、静电势、红外和拉曼光谱等方面的影响进行了分析。结果显示：随着外电场强度增加,分子结构和原子电荷分布发生改变,分子极性增强,能隙降低,化学反应活性增强,静电势分布极值点发生了明显改变,红外和拉曼在不同区域内发生振动斯塔克效应,既有蓝移又有红移,峰的强度也出现了复杂的变化。     

三硝基芳香族炸药的表面静电势、活化能与感度理论研究

运用密度泛函DFT-BHand HLYP/6-311G**方法,对八种三硝基芳香族炸药分子进行全优化、能量频率计算,研究其各自的活化能、表面静电势等几种统计量.建立起这八种化合物实验撞击感度h50与分子表面静电势及统计量之间的定量关系,结果发现其相关系数很大(0.91+).随后引入活化能影响因子,在撞击感度与分子活化能、分子表面静电势及其统计量之间建立关系模型,结果表明撞击感度与活化能、表面静电势及其他统计量之间存在很好的相关关系(0.95+).这对预估炸药分子的撞击感度值有一定意义.     

氮分子固体中配位环境对其分子振动的影响

研究了孤立氮分子与处于氮分子固体中氮分子之间的振动频率差异.基于α-N_2晶体结构建立了5种不同氮分子数的氮分子固体团簇模型,采用密度泛函理论计算了孤立自由氮分子及各固体模型中氮分子的振动频率,并对它们的频率进行了比较和讨论.比较发现:受集体效应的影响,处于分子固体模型中的所有氮分子的键长较孤立自由氮分子的键长更短,振动频率更高;就固体模型本身而言,分子数越多,平均振动频率越大,而且,内部氮分子的振动频率总是大于表面氮分子的振动频率,整体来说,频率大小关系为v_(内部)v_(表面)v_(孤立).讨论分析认为这种频率差异主要是由于孤立自由氮分子、固体表面和内部分子的配位关系不同引起的;表面分子存在大量配位缺陷,与其相互作用的分子相对较少,氮分子键力较弱,从而频率更低.     

光谱法结合分子模拟技术研究左氧氟沙星与胃蛋白酶的相互作用机理

在模拟生理条件下,采用荧光光谱法结合分子对接技术研究了左氧氟沙星与胃蛋白酶的相互作用。不同温度下的Stern-Volmer曲线结果表明,左氧氟沙星主要以静态猝灭的方式使胃蛋白酶的荧光产生猝灭。由热力学数据确定了两者之间存在的作用力主要为静电作用力。三维荧光光谱实验结果表明,在左氧氟沙星与胃蛋白酶发生作用过程中引起了胃蛋白酶中酪氨酸和色氨酸残基构象的变化,从而导致胃蛋白酶发生了猝灭作用。为了进一步探讨左氧氟沙星与胃蛋白酶相互作用的分子机理,利用分子对接技术对两者的相互作用进行模拟。结果表明两者发生作用的区域位于胃蛋白酶的催化活性中心,左氧氟沙星的进入导致酶催化中心氨基酸残基的微环境发生改变,从而对胃蛋白酶的活性造成影响,这可能也是左氧氟沙星引起消化不良的主要原因。     

1.06μm区域的Cs2分子吸收光谱

用ＲＫＲ（Ｒｙｄｂｅｒｇ－Ｋｌｅｉｎｎ－Ｒｅｅｓ）方法计算了Ｃｓ２分子的Ｘ＾１∑ｇ和Ａ＾１∑ｕ的势能曲线，求解了Ｃｓ２分子核运动的径向薛定谔方程，获得Ｘ态与Ａ态间跃迁的Ｆｒａｎｃｋ－Ｃｏｎｄｏｎ因子和１．０６μｍ附近区域的吸收光谱，并与实验测得的吸收光谱作了比较，两者相当符合。     

五种典型硝基苯胺类炸药的静电势与撞击感度的关系研究

利用HONDO程序包,采用从头算法对硝基苯胺类炸药的分子结构和电偶极矩等性质以及 C-NO2键中点静电势等进行计算,讨论了硝基苯胺类炸药C-NO2键中点静电势最大值Vmidmax与其实验撞击感度之间的关系.研究表明:对于硝基苯胺类炸药,不宜单独用C-NO2键中点静电势最大值Vmidmax来表征撞击感度的变化,但可以用静电势最大值Vmidmax与电偶极矩的积来确定其撞击感度的变化趋势,讨论了硝基和胺基的相对位置以及硝基和胺基的数目对这类炸药感度的影响.     

硝基甲苯类炸药C-NO2键中点的静电势

利用HONDO程序包,采用从头计算法对硝基甲苯类炸药的分子结构及其C-NO2键中点的静电势进行了计算,讨论了硝基甲苯类炸药C-NO2键中点的静电势最大值Vmidmax与其实验撞击感度之间的关系.研究表明:对于硝基甲苯类炸药,可用其分子C-NO2键中点的静电势最大值Vmidmax来确定其撞击感度的变化趋势.以静电势为判据,讨论了硝基和甲基数目以及硝基和甲基的相对位置对这类炸药撞击感度的影响.     

Understanding the molecular interaction and relaxation findings in amphiphilics on solution state using TDR

The dielectric behavior of stearic acid in 1,4-dioxane medium at various temperature 303 K–288 K and frequency regime (10 MHz–30 GHz) determined from the complex dielectric permittivity spectra obtained by Time Domain Reflectometry(TDR). In this frequency range, the dielectric study gives the electrostatic interaction as well as orientational polarizability of complex mixtures of long chain molecules significantly. Dielectric parameters were calculated from the complex spectra of the binary mixture by non linear least square fit method. The excess permittivity (ε^E), correlation factors were calculated for the binary system. Thermal parameters(ΔH-enthalpy, ΔS-entropy and ΔG-Gibbs free energy) were calculated and the direction of reaction is determined. The FTIR spectrum of the binary system recorded and the assignments are discussed. The FTIR spectral assignments confirm the molecular interactions.     

Structure and properties of some chiralanes and chirolanes

The molecular structures, spectra and properties of six chiralanes and chirolanes (approximately spheroidal, saturated, cage hydrocarbons) have been determined by density functional theory (DFT) quantum chemistry calculations. The main features determined are: molecular geometry, partial atomic charges, standard enthalpy of formation, IR, nuclear magnetic resonance (NMR) and circular dichroism (CD) spectra. On the basis of the calculated standard enthalpies of formation and highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gaps, we suggest that chiralanes/chirolanes are potential synthetic targets. We have calculated the anomalously large downfield ¹³C-NMR shifts for endohedral carbons in the spectra of [5.5] and [5.7]chiralanes.     

Predicting XAFS scattering path cumulants and XAFS spectra for metals (Cu,Ni, Fe,Ti, Au) using molecular dynamics simulations

The ability of molecular dynamics (MD) simulations to support the analysis of X‐ray absorption fine‐structure (XAFS) data for metals is evaluated. The low‐order cumulants (ΔR, σ², C₃) for XAFS scattering paths are calculated for the metals Cu, Ni, Fe, Ti and Au at 300 K using 28 interatomic potentials of the embedded‐atom method type. The MD cumulant predictions were evaluated within a cumulant expansion XAFS fitting model, using global (path‐independent) scaling factors. Direct simulations of the corresponding XAFS spectra, χ(R), are also performed using MD configurational data in combination with the FEFFab initio code. The cumulant scaling parameters compensate for differences between the real and effective scattering path distributions, and for any errors that might exist in the MD predictions and in the experimental data. The fitted value of ΔR is susceptible to experimental errors and inadvertent lattice thermal expansion in the simulation crystallites. The unadjusted predictions of σ² vary in accuracy, but do not show a consistent bias for any metal except Au, for which all potentials overestimate σ². The unadjusted C₃ predictions produced by different potentials display only order‐of‐magnitude consistency. The accuracy of direct simulations of χ(R) for a given metal varies among the different potentials. For each of the metals Cu, Ni, Fe and Ti, one or more of the tested potentials was found to provide a reasonable simulation of χ(R). However, none of the potentials tested for Au was sufficiently accurate for this purpose.     

FTIR and FT‐Raman spectra and density functional computations of the vibrational spectra,molecular geometry and atomic charges of the biomolecule: 5‐bromouracil

FTIR and FT‐Raman spectra of 5‐bromouracil in the powder form were recorded in the region 400–4000 cm⁻¹ and 50–4000 cm⁻¹, respectively. The observed wavenumbers were analysed and assigned to different normal modes of vibration of the molecule. Quantum chemical calculations were performed to support the assignments of the observed wavenumbers. The performance of the B3LYP hybrid density functional (DFT) method was compared with other methods. With the 6–31 G** and 6–311 + G(2d,p) basis sets, the calculated geometry, dipole moments and harmonic vibrations were determined. A comparison with the uracil molecule was made, and specific scale factors were deduced and employed in the predicted wavenumbers of 5‐bromouracil. The total atomic charges and thermodynamic parameters were calculated, and are discussed briefly. Structure and harmonic vibrations of 5‐bromouracil were also calculated in the presence of water within a simple model with one molecule. It is observed that the bromine atom at position 5 exhibits smaller inductive effects than the fluorine atom, producing a small distortion of the electrostatic potential around the ring and a reduction of the molecular dipole moment. Copyright © 2007 John Wiley & Sons, Ltd.     

Novel electrostatic trap for cold polar molecules

We propose a novel scheme in which cold polar molecules are trapped by an electrostatic field generated by the combination of a pair of parallel transparent electrodes (i.e., two infinite transparent plates) and a ring electrode (i.e., a ring wire). The spatial distributions of the electrostatic fields from the above charged wire and the charged plates and the corresponding Stark potentials for cold CO molecules are calculated; the dependences of the trap centre position on the geometric parameters of the electrode are analysed. We also discuss the loading process of cold molecules from a cold molecular beam into our trap. This study shows that the proposed scheme is not only simple and convenient to trap, manipulate and control cold polar molecules in weak-field-seeking states, but also provides an opportunity to study cold collisions and collective quantum effects in a variety of cold molecular systems, etc.