硝酸正丙酯和硝酸异丙酯的密度泛函理论研究

用密度泛函理论(DFT)中的B3LYP、B3PW91、B3P86方法研究硝酸正丙酯(n-propyl nitrate,NPN)和硝酸异丙醣(isopro- pyl nitrate,IPN)的平衡分子构型、前线轨道能(E_(HOMO)、E_(LUMO))、能差(△E=E_(LUMO)-E_(HOMO))和O-NO_2键的裂解能(BDE)。分析了两种硝酸酯分子和对应自由基的热稳定性。NPN和IPN中的O-NO_2键的裂解能用B3P86方法计算出最接近实验值。由O- NO_2键的裂解能符合文献中对应物质的表观活化能,推知两种物质的热分解反应只是单分子O-NO_2键的均裂反应。     

Molecular dynamics and density functional theory studies of substrate binding and catalysis of human brain aspartoacylase

The active-site dynamics of human brain aspartoacylase (hASPA) complexed with its substrate (N-acetyl-l-aspartate) has been studied using a hybrid quantum mechanical/molecular mechanical (QM/MM) approach based on the self-consistent charge-density functional tight-binding (SCC-DFTB) model. The Michaelis complex, which is constructed from a recent X-ray structure of the human brain aspartoacylase with a stable tetrahedral intermediate analogue, is reproduced in 1 ns molecular dynamics simulations at 300 K. The simulation shows that the substrate is tightly held in the active site by a hydrogen bond network and the putative nucleophilic water molecule is reasonably close to the nucleophilic center. The catalysis is further modeled with the density functional theory (DFT) in a truncated active-site model at the B3LYP/6-31G(d) level of theory. The DFT calculations indicate the reaction proceeds via a water promoted pathway with Glu178 serving as the general base and general acid. Transition state stabilization for nucleophilic addition is achieved by formations of the weak coordination bond between the substrate carbonyl oxygen atom and the zinc ion as well as of the strong hydrogen bonds between the substrate carbonyl oxygen atom and Arg63.     

Parallel implementation of time-dependent density functional theory

We present a massively parallel implementation of time-dependent density functional theory in real space, aimed at computing optical absorption spectra of realistic systems with hundreds of atoms from first principles. We provide details of the formalism and discuss its implementation, optimization, and efficient parallelization, as well as remaining limitations, in detail. The capabilities of the code are illustrated by calculations of optical properties of hydrogenated silicon quantum dots.     

Structures and spectroscopic properties of nonperipherally and peripherally substituted metal-free phthalocyanines: a substitution effect study based on density functional theory calculations

The molecular structures, molecular orbitals, atomic charges, electronic absorption spectra, and infrared (IR) and Raman spectra of a series of substituted metal-free phthalocyanine compounds with four (1, 3, 5, 7) or eight (2, 4, 6, 8) methoxyl (1, 2, 5, 6) or methylthio groups (3, 4, 7, 8) on the nonperipheral (1-4) or peripheral positions (5-8) of the phthalocyanine ring are studied by density functional theory (DFT) and time-dependent DFT (TD-DFT) calculations. The calculated structural parameters and simulated electronic absorption and IR spectra are compared with the X-ray crystallography structures and the experimentally observed electronic absorption and IR spectra of the similar molecules, and good agreement between the calculated and experimental results is found. The substitution of the methoxyl or methylthio groups at the nonperipheral positions of the phthalocyanine ring has obvious effects on the molecular structure and spectroscopic properties of the metal-free phthalocyanine. Nonperipheral substitution has a more significant influence than peripheral substitution. The substitution effect increases with an increase in the number of substituents. The methylthio group shows more significant influence than the methoxyl group, despite the stronger electron-donating property of the methoxyl group than the methylthio group. The octa-methylthio-substituted metal-free phthalocyanine compounds have nonplanar structures whose low-lying occupied molecular orbitals and electronic absorption spectra are significantly changed by the substituents. The present systematical study will be helpful for understanding the relationship between structures and properties in phthalocyanine compounds and designing phthalocyanines with typical properties.     

吡咯两类加聚物的密度泛函计算及结构与热化学性质关系

采用B3LYP/6-31G~*方法对吡咯分子的两类加聚物体系(C_4H_4N)_n(n=1～4)进行了全优化计算,频率分析可知构型皆为稳定构型,在优化构型上计算了这两种加聚物总能量(E_T),零点能(ZPE),热容(C_p~0)和熵(S°),分析了两类加聚物的几何结构和成键特征,通过线性拟合得到了吡咯加聚物的热力学性质与聚合度n的关系,并计算了两类加聚物的反应焓变。计算表明吡咯加聚物具有稳定的链式构象,其中交错式加聚物具有更稳定的结构,吡咯加聚反应主要为交错加聚过程,可为同类化合物结构与性能关系的研究以及加成聚合反应机理研究提供方法和理论依据。     

卟吩结构的HARTREE-FORCK和密度泛函研究比较

采用传统的Hartree-Fock(HF)从头算和密度泛函中的B3LYP和B3PW91方法,选择了不同基组水平(STO-3G,3-21G和6-31G~*)对卟吩结构进行了全几何优化,并对得到的结果相互进行了比较,同时与实验数据进行了对照。结果表明,对于H_2P以及具有类似结构的卟啉衍生物,传统的HF方法得到的几何构型以及相关性质(核磁共振谱,NMR)并不可靠。这种体系中电子相关能是不可忽略的。在B3LYP水平上选用较小的基组3-21G得到的结果与中等基组6-31G~*差别不大,但是最小基组STO-3G得到的优化构型却是一个鞍点结构。     

乙炔基双二茂铁丙烷衍生物的密度泛函理论研究

为揭示取代基对金属有机化合物乙炔基双二茂铁丙烷电子结构的影响,采用密度泛函理论方法模拟计算了乙炔基双二茂铁丙烷及其2个衍生物苯炔基双二茂铁丙烷及二茂铁炔基双二茂铁丙烷的电子结构、前线轨道、电离能(IP)以及电子亲和势(EA),并讨论了取代基对化合物能级和能隙的影响。计算结果表明,电子在基态与激发态间的跃迁,主要是发生在双二茂铁丙烷和乙炔基苯或乙炔基二茂铁之间。取代基为苯基时化合物最高占据轨道(HOMO)能级降低量小于最低空轨道(LUMO)能级降低量,因此二者之间的能隙总体降低。取代基为二茂铁基时化合物HOMO能级增加,LUMO能级降低,从而使HOMO-LUMO能隙降低。结合化合物6-苯炔基双二茂铁丙烷电子亲和势最大以及化合物6-二茂铁炔基双二茂铁丙烷电离能最小,可见苯基取代使炔基双二茂铁丙烷类化合物电子传输能力增强,而二茂铁基取代则可以使该类化合物的空穴传输能力增强,这使炔基双二茂铁丙烷类化合物在功能导电材料方面具有较好的应用前景。     

密度泛函方法研究辣椒碱分子的结构和性质

辣椒碱(Capsaicin)在医药、农业和反恐装备方面具有广泛的应用前景.本文用密度泛函理论DFT/B3LYP方法,在6-31+G(d,p)基组水平上对其进行了计算.密度泛函理论方法既考虑了电子相关,又较其他组态相互作用或微扰方法节省机时,其计算结果可靠,被广泛应用于研究各类化合物结构性质.本文获得了辣椒碱分子稳定的几何构象和电荷分布,确定O(12)、N(16)、O(19)、C(37)和C(38)原子,可以作为氢键受体;C(18)与O(19)原子形成一对偶极,它们均是关键药效团的活性部位.通过进行分子轨道特征分析,确定苯环区是参加化学反应时的活性部位.进行的自然键轨道分析结果与分子轨道特征分析结论一致.在振动分析的基础上获得分子的振动频率、IR光谱与实验结论一致;在振动分析的基础上,同时获得不同温度下的热力学性质以及温度对热力学性能影响的关系式,其中,当T＞2 542 K时,热容Cp,mθ会随温度的升高而减小,各表达式和热力学量对深入研究辣椒碱分子的其它热力学性质有帮助.探讨了辣椒碱热分解机理,获得该分子热分解时C-N键的断裂能为306.6 kJ·mol-1.本文为研究辣椒碱类化合物的定量构效关系研究提供理论依据.     

乳清酸的DFT和红外光谱研究

乳清酸是配位化学中的一种良好配体,它的酮式和烯醇式瓦变异构体,以及不对称结构,使其成为多用途的多齿有机配体,为允分理解其空间构型、异构化过程以及获得一些有用的参数,使用Gaussian 98程序包在B3LYP/6-311+G*基组水平上优化了乳清酸的结构,发现la是能量上最稳定的构型.计算结果显示,空间效应、氢键和共轭相应在维持其特定结构中发挥了重要作用.对质子转移过程的研究表明,质子转移的能垒相对较高,而顺反异构的能垒相对较高.IR光谱可以帮助我们区别不同乳清酸异构体,并识别光谱实验的谱图.     

2-氨基-3H-吩噁嗪-3-酮的溶剂热法合成、晶体结构及密度泛函理论研究

采用溶剂热法合成了2-氨基-3H-吩噁嗪-3-酮,并通过红外光谱、元素分析、x射线单晶衍射进行了结构表征。结构解析表明,该晶体属于单斜晶系,P2₁/c空间群,晶胞参数为a=1.29322（10）nm,b=0.50832（4）nm,c=1.47609（11）nm,β=99.323（1）°,V=957.52（13） A³,Z=4,Dc=1.472 Mg/m³,F（000）=440,μ=0.10 mm^-1,Mr=212.20,最终偏差因子（对I>2σ（I）的衍射点）R₁[F²>2σ（F²）]=0.037,wR₂（F²）=0.097（对全部衍射点）,权重方案w^-1=1/[σ²（Fo²）+（0.0402P）²+0.2667P],P=（Fo²+2Fc²）/3。该化合物分子由3个共轭环形成几乎共平面的结构。应用密度泛函理论DFT方法,结合6-31*基组优化了几何构型,通过同一水平的振荡分析和单点能分析得出热力学参数、净电荷分布和原子轨道对分子轨道的贡献。     

Generalised theory on asymptotic stability and boundedness of stochastic functional differential equations

Asymptotic stability and boundedness have been two of most popular topics in the study of stochastic functional differential equations (SFDEs) (see e.g. Appleby and Reynolds (2008), Appleby and Rodkina (2009), Basin and Rodkina (2008), Khasminskii (1980), Mao (1995), Mao (1997), Mao (2007), Rodkina and Basin (2007), Shu, Lam, and Xu (2009), Yang, Gao, Lam, and Shi (2009), Yuan and Lygeros (2005) and Yuan and Lygeros (2006)). In general, the existing results on asymptotic stability and boundedness of SFDEs require (i) the coefficients of the SFDEs obey the local Lipschitz condition and the linear growth condition; (ii) the diffusion operator of the SFDEs acting on a C^2,1-function be bounded by a polynomial with the same order as the C^2,1-function. However, there are many SFDEs which do not obey the linear growth condition. Moreover, for such highly nonlinear SFDEs, the diffusion operator acting on a C^2,1-function is generally bounded by a polynomial with a higher order than the C^2,1-function. Hence the existing criteria on stability and boundedness for SFDEs are not applicable and we see the necessity to develop new criteria. Our main aim in this paper is to establish new criteria where the linear growth condition is no longer needed while the up-bound for the diffusion operator may take a much more general form.     

8-羟基喹啉衍生物密度泛函理论的研究

运用量子化学中的密度泛函理论(TD-DFT)法,在B3LYP/6-31G(d,p)水平上,理论计算两种新型的8-羟基喹啉衍生物,5-[(4-E-苯乙烯基)-苯甲亚胺基]-8-羟基喹啉(1)和5-[(4-溴-2-氟)苯甲亚胺基]-8-羟基喹啉(2).探讨化合物(1)和(2)的几何构型、电子结构、前线分子轨道和电子光谱性质.结果表明由于引入取代基使体系的HOMO与LUMO之间的能隙降低,增强了与金属铝配位的能力;电子吸收光谱与实验数据基本吻合.     

多溴二苯并噻吩系列化合物的热力学性质及稳定性的密度泛函理论

本文在298.15 K和1.013×10~5Pa时,根据密度泛函理论(DFT),使用Gaussian 03程序,在B3LYP/6-31G(d)水平上计算117个多溴二苯噻吩系列化合物(PBDTs),得各分子的热力学性质。设计等键反应,计算PBDTs系列化合物的标准生成热Δ_fH~(?)和标准生成自由能Δ_fG~(?)。同时用程序Origin7.5将这些热力学参数与溴原子的取代位置及取代数目线性回归,求出相关方程,研究表明:热力学参数、标准生成热、标准生成自由能与溴原子的取代位置及取代数目之间关系极密切。根据标准生成自由能的相对大小,本文从理论上求得该化合物异构体的相对稳定性顺序。本文研究该化合物热力学性质及其稳定性,对于研究其生成、降解以及对环境的潜在威胁具有重要意义。     

新型咔唑衍生物密度泛函理论的研究

运用量子化学中的密度泛函和含时密度泛函理论法,计算1种新型咔唑衍生物,以探讨其几何构型、电子结构、前线分子轨道和电子光谱性质。计算结果表明当2-(4-吡啶基)乙烯基的反式构型与咔唑环作用时比顺式稳定,引入取代基后使化合物的HOMO和LUMO之间的能隙降低,吸收光谱红移。电子被激发时,电子从咔唑环向吡啶环转移,说明新型咔唑类化合物具有很好的光学性能,可以作为空穴传输材料。     

用密度泛函理论研究三价铁掺杂锐钛矿二氧化钛

采用密度泛函理论(DFT)的全势PLAPW方法,通过构造超晶胞模型,按GGA-PW91水平计算,研究Fe(Ⅲ)掺杂锐钛矿TiO_2的电子态密度、化学键性质。结果表明,Fe(Ⅲ)掺杂TiO_2后,Ti-O键长及重叠布居数发生了变化;在费米能级附近,Fe (Ⅲ)周围的O2p轨道发生分裂,并与Fe(Ⅲ)的3d轨道有较明显的重叠,导致Fe(Ⅲ)/TiO_2晶体禁带变窄。     

DFT法研究取代芳烃结构与毒性的定量关系

应用密度泛函方法(DFT)在B3LYP/6-311G~(**)水平上全优化计算38个取代芳烃的量子化学参数,结合辛醇/水分配系数研究取代芳烃化合物对发光菌毒性的定量构效关系(QSAR)。对训练集样本经逐步多元回归分析(SMR)后,所建QSAR方程的复关系数R~2及去一法交互检验复相关系数Q_(LOO)~2分别为0.920和0.896,用预测集样本预测外部,所得外部预测样本复相关系数R_(ext)~2和外部预测集交互检验Q_(ext)~2分别为0.870和0.849。模型结果显示:辛醇/水分配系数愈大,即分子疏水性愈强,化合物对发光菌的毒性愈大;取代基的吸电子能力愈强,化合物毒性愈大;前沿轨道能级差愈小,化合物毒性愈大。     

CO在贵金属Pt(111)表面吸附的密度泛函理论研究

采用密度泛函理论研究CO在Pt(111)表面的吸附位和活化机理。研究采用三维周期结构取代以往的团簇模型,消除金属表面结构选择对计算结果的影响。结果表明,CO在不同的表面活性位吸附后C-O键有不同程度的增长,即C-O键均不同程度地削弱,从而活化CO分子。经比较吸附能、化学键参数和CO重叠布居数,发现在顶位、桥位、hcp空穴位和fcc空穴位4个吸附位中,fcc空穴位是CO的最佳活性位。通过考察原子轨道电子变化,分析CO在Pt(111)表面的吸附活化机理,得到了CO分子在Pt(111)表面吸附的σ／π键作用机理。     

萘类衍生物荧光发射光谱的密度泛函理论研究

运用密度泛函（DFT）及含时密度泛函（TDDFT）方法对萘类衍生物的荧光发射光谱进行了探讨，发现荧光发射波数υ↑-emit与分子基态能隙△ε以及单电子第一激发能△E成线性关系，运用所得回归方程的预测结果与实验结果符合得较好。对训练样本以外的6种分子的预测结果表明，该回归模型可以用于对萘类衍生物的荧光发射波数υ↑-emit进行预测。     

Efficient computation of the coupling matrix in time-dependent density functional theory

We present an efficient implementation of the computation of the coupling matrix arising in time-dependent density functional theory. The two important aspects involved, solution of Poisson's equation and the assembly of the coupling matrix, are investigated in detail and proper approximations are used. Poisson's equation is solved in the reciprocal space and bounded support of the wave functions are exploited in the numerical integration. Experiments show the new implementation is more efficient by an order of magnitude when compared with a standard real-space code. The method is tested to compute optical spectra of realistic systems with hundreds of atoms from first principles. Details of the formalism and implementation are provided and comparisons with a standard real-space code are reported.