胞嘧啶-巴比妥酸分子间相互作用的密度泛函理论研究

用密度泛函理论研究了胞嘧啶(Cyt)-巴比妥酸(BA)分子间相互作用,以期从理论上预测巴比妥酸类物质对核酸可能产生的影响.在B3LYP/6-311G* *理论水平上优化复合物构型,得到5个Cyt-BA1,8个Cyt-BA2和9个Cyt-BA3稳定复合物,经基组重叠误差和零点振动能校正后,发现在3个系列中最稳定的复合物分别是Cyt-BA1-Ⅳ,Cyt-BA2-Ⅲ和Cyt-BA3-ⅤⅢ,其结合能各自为53.98,96.48和92.50 kJ/mol,相互作用能主要由氢键贡献.cyt与BA2-Ⅲ、BA3-Ⅸ以三氢键,其余均以二氢键形成复合物,其稳定性与氢键强度关系非常密切.分析自然键轨道而揭示相互作用的本质.用统计热力学求出常温下从单体形成复合物的热力学性质的变化,发现除Cyt-BA3-Ⅰ、Ⅱ、Ⅵ外,Cyt与BA均可在常温下形成复合物.     

1-吡啶-3-[4-(苯基偶氮)苯基]-三氮烯异构体基态和激发态电子结构和光谱性质理论研究

采用B3LYP/6-310*方法,对1-吡啶-3-[4-(苯基偶氮)苯基]-三氮烯(PYPAPT)各异构体进行优化,同时用ab initio HF单激发组态相互作用(CIS)法在6-31G*基组上优化各异构体最低激发单重态几何结构,并探讨了其分子结构与能量的关系,计算结果表明:(1)所有基态异构体基本保持Cs对称性,各原子基本处在同一平面中,而激发态各异构体分子的共轭性不如基态分子,在激发态分子中与偶氮相连的另一苯环与三氮烯及与其相连的苯和吡啶环都不在一个平面;(2)无论在气相中还是在二氯甲烷(DCM,ε=8.93),乙醇(EtOH,ε=24.55)和乙腈(ACN,ε=36.64)溶剂中,基态时PYPAPT主要以M11存在,激发态时为J11较稳定。运用含时密度泛函理论(TD-DFT)计算了PYPAPT基态和激发态各异构体在溶剂中的吸收与发射光谱,研究了溶剂模型对理论光谱的影响。计算结果表明,PYPAPT各异构体基态和激发态的HOMO和LUMO都是离域π键,随着溶剂极性的增强,HOMO和LUMO轨道能量都逐渐下降。理论电子光谱证实,PYPAPT各异构体的吸收光谱随溶剂极性的增强略微红移,吸收强度也有微弱升高;最...     

2,6-二硫代黄嘌呤互变异构体的密度泛函理论研究

在密度泛函B3LYP/6-311G~(**)水平下,对14种气相和水相中可能存在的2,6-二硫代黄嘌呤异构体进行了几何构型全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能。Onsager反应场溶剂模型用于水相的计算,计算结果表明,2,6-二硫代黄嘌呤在气相和水相中主要以双硫酮形式存在。在气相和水相中,硫酮-N(7)(H)均比硫酮-N(9)(H)稳定,计算结果同已有实验结果一致。2,6-二硫代黄嘌呤互变异构的熵效应小,对互变异构平衡没有显著影响,而焓变对互变异构产生了主要影响。较详细地讨论了水溶剂化作用对异构体的能量、几何结构、电荷分布和偶极矩的影响。溶剂化自由能与异构体的偶极矩存在相关性。并且以在水相中最稳定的两种异构体为对象,采用超分子模型探讨了它们与水分子之间氢键作用的情况。     

SO_4~(2-)微观水合结构DFT研究

运用密度泛函理论(DFT)计算方法系统研究硫酸根阴离子水合团簇,[SO_4(H_2O)_n]~(2-)(n=1-18),微观水合结构。理论计算采用ωB97XD泛函和6-311++G(d,p)基组。每个尺寸团簇结构,尽可能考虑所有合理初始结构,以此进行结构优化和频率分析等。结果表明,气相和液相条件下SO_4~(2-)与H_2O之间的相互作用能和溶剂稳定化能均与团簇尺寸n成线性关系,因此优化得到稳定结构均是合理构型。在[SO_4(H_2O)_n]~(2-)水合团簇稳定结构中,氢键的形式有两种,即溶质-溶剂(SO_4~(2-)…HOH)之间形成的对称双氢键,以及溶剂-溶剂(H_2O... HOH)之间形成的氢键。当SO_4(H_2O)_n]~(2-)水合团簇的尺寸为5个水分子时,由于水分子内氢键的形成,出现氢键环状结构,且团簇结构中出现水分子内氢键时,结构较为稳定。随着n增加,氢键结构逐渐变为网状直至稳定的笼状。通过能量参数和键参数分析可知,当团簇尺寸n≥18时,SO_4~(2-)第一水合层水分子数≥9,而第二水合层还有待进一步研究。同时随着浓度降低SO_4~(2-)与H_2O分子之间总相互作用能增加,溶液中溶剂-溶质相互作用增强。     

Cr(CO)_n(n=1-5)与C_6 H_6相互作用的密度泛函研究

用密度泛函理论在B3LYP/LANL2DZ基组水平上对(η~x-C_6H_6)Cr(CO)_n(x=1-6;n=1-5)复合物体系的可能构型进行了自由优化及相互作用能的计算,研究了不同羰基数对复合物稳定性、苯和羰基铬相互作用的影响,并对苯和羰基铬相互作用进行了NBO分析。得到以下结论:(1)当n≤3时,苯与Cr(CO)_n以η~6配位;当n≥4时,苯与Cr(CO)_n以η~2配位;(2)最稳定复合物中随羰基数的增加Cr-C_(benzene)平均键长增长,最大二面角H-C-C-H偏离碳环的角度随复合物对称性降低而逐渐增大;(3)当n为奇数时,复合物相互作用主要表现为苯C-C键的π轨道和Cr-CO键的σ反键轨道;当n为偶数时,复合物相互作用主要表现为苯C-C键的π轨道或π~*轨道与Cr的孤对电子轨道;(4)复合物羰基数越多,最稳定复合物的相互作用能数值越大,稳定性越小。     

理论计算5-氟尿嘧啶三水复合物质子转移的异构化

为了研究5-氯尿嘧啶三水复合物异构体的相对稳定性和异构体之间的转变机理,以至于了解药理性质,对实验进行指导,故本文采用密度泛函B3LYP/6-311+G(d,p)法,研究计算5一氟尿嘧啶6种三水复合物的稳定性及质子转移而引起的双酮式-双醇式或酮醇式互变异构的反应机理,获得零点能、总能量及质子转移过程的反应焓、活化能、活化吉布斯自由能和速率常数等参数.IPCM反应场溶剂模型用于计算水相.本文与文献[9]的区别在于重点研究3个水分子存在下及三水复合物在整体溶剂中的质子专移规律,而文献[9]仅讨论了分子内和-水催化时的规律.本文证明在三水复合物中,双酮式Fu1a-3w最稳定,与已有实验结果相符.由双酮式三水复合物通过双质子转移向双醇式或酮醇式异构化中,找到3条反应通道(P1,P2,P3),其速控步骤活化吉布斯自由能分别为71.6、74.3和83.6kJ·mol-1,是文献报道分子内质子转移所需活化能垒的近三分之一,却均比文献报道-水催化所需活化能垒高.还表明,整体溶剂效应使三水复合物(FU6-3w除外)的偶极矩均增大且质子转移所需活化能垒也相应增大,质子转移反应反而更困难.     

3-卤代吲唑水助质子转移反应机理的理论研究(英文)

在密度泛函B3LYP/6-311G**理论水平上,对气相和水相中3-卤代吲唑瓦变异构体进行几何构型伞自由度优化,获得它们在气相和水相中的几何结构和电子结构,PCM反应场溶剂模型用于水相计算.结果显示在气相和水相中,3.卤代吲唑的N1-H形式比N2-H形式稳定.探讨了不同的3-取代基团和溶剂化效应对互变异构体的几何结构,能量,电荷分布以及互变异构反应活化能的影响等.进一步研究了3-卤代吲唑水催化质子迁移的反应机理,提出了平面五元环的过渡态结构.     

苯与羰基钼相互作用的密度泛函研究

用密度泛函理论在B3LYP/LANL2DZ基组水平上自由优化(η~x-C_6H_6)Mo(CO)_n(x=1-6;n=1-5)复合物体系的可能构型及计算相互作用能,探索不同羰基数对复合物稳定性、苯和羰基钼相互作用的影响,并分析苯和羰基钼相互作用的NBO。结论(1)苯以η~6与Mo(CO)_n(n=1-3)配位形成的复合物比较稳定,但η~6配位复合物CO的个数越多,则越不稳定;(2)复合物1、2、3和10中,Mo(CO)_n与苯的相互作用拉动电荷由苯的π键电子向Mo(CO)_n的σ_(Mo-CO)~*键转移,而在复合物7中,苯的π键电子向Mo(CO)_n中Mo的孤对电子轨道d转移。     

用密度泛函研究(ηx-C6H6)Mo(CO)n复合物单态和三重态相互作用

用密度泛函理论在B3LYP/LANL2DZ基组水平上计算(ηx-C6H6)Mo(CO)n(x=1-6;n=1-5)的可能构型的自由优化及相互作用能,研究不同羰基数对复合物稳定性、苯和羰基钼相互作用的影响,并NBO分析苯和羰基钼的相互作用.结论(1)苯以η6与Mo(CO)n(n=1-5)配位所形成的复合物很稳定,且η6配...     

卤素取代基对二氯-4,5-二氮芴-9-酮合钯(Ⅱ)的能带影响

二氯-4,5-二氮芴-9-酮作为1,10-邻二氮杂菲的衍生物,能与Pd(Ⅱ)等金属离子形成配合物,研究表明,其具有丰富的二维或三维的空间结构特点,在共轭环间的π-π堆积下其有序的堆积结构可能产生具半导体性质,但对它及它的取代衍生物的导电性研究还未有相关报道.采用Materials Studio4.0软件中的CASTEP软件的LDA/CA-PZ法,计算二氯-4,5-二氮芴-9-酮合钯(Ⅱ)及其卤素取代衍生物的晶体优化构型、能带结构和态密度,结果表明,卤素原子较趋于取代分子γ位的氢原子.PddafoCl2及其卤素取代衍生物晶体的禁带宽度在(1.1691～1.5221)eV间,显示该系列物质均具有半导体属性.引入卤素取代基显然降低了体系的禁带宽度,同时提高了态密度,增强导电性质.其中以碘原子α取代衍生物的禁带最窄,态密度最大.引入不同的卤索取代基,配合物呈现不同的导电性,导电性的改变对于非线形光学材料及磁性材料方面等有很重要的研究意义,二氯-4.5-二氨芴-9-酮合钯(Ⅱ)及它的卤素取代衍生物将在不同的领域获得广泛的应用.     

Solvent effect on hydrogen bonded ammonia-hydrogen halide complexes: continuum medium versus cluster models

The influence of water and dinitrogen environment on the structures of hydrogen bonded XH-NH3 (X = F, Cl, and Br) complexes has been investigated using the self-consistent isodensity polarizable continuum solvent model (SCI-PCM) with two values of dielectric constants, 1.5 and 78.0, respectively. The geometrical parameters, along with the interaction energies as well as harmonic frequencies were calculated at the B3M-LYP/6-311 + + G(d,p) level of theory. The results from dielectric continuum model were compared with those obtained by traditional supermolecule approach. In order to model the proton transfer in XH-NH3 systems by supermolecular approach, one should add from two to four explicit water or dinitrogen molecules to the calculations. The dielectric continuum model provides similar effect using less effort. As our results shown, the SCI-PCM model, where a solvent is treated as a continuum medium, reproduces quite accurately the molecular properties of investigated medium strong hydrogen bonded systems both with dinitrogen and water environment. In order to represent solvent effects on hydrogen-bonded complexes with less acidic HX subunit it is necessary to take explicit solvent molecules into account.     

从头计算研究水溶液中有机化合物的pKa值

运用量子化学方法计算水溶液中一些含氮小分子化合物和醇、酚、羧酸的pKa值。采取从头计算的Hartree-Fock法和6- 31G(d,p)基组,以及aug-cc-pVDZ基组,密度泛函理论的B3LYP法6-31G(d,p)基组,分别优化分子和离子的气相几何结构,采用极化连续介质模型模拟溶质和溶剂分子间的相互作用,不同方法和基组计算结果差别不大,18个化合物的均方根误差均为1．03,预测值与实验值的相关系数均为0．98,一致性较好。证明HF／6-31G(d,p)法和模型计算或预测含有相同官能团的小分子的pKa数值很合理,能够为研究药物分子体系的构效关系提供精确的pKa参数。     

Sphingosine 1-phosphate pKa and binding constants: intramolecular and intermolecular influences

The dissociation constant for an ionizable ligand binding to a receptor is dependent on its charge and therefore on its environmentally-influenced pKa value. The pKa values of sphingosine 1-phosphate (S1P) were studied computationally in the context of the wild type S1P1 receptor and the following mutants: E3.29Q, E3.29A, and K5.38A. Calculated pKa values indicate that S1P binds to S1P1 and its site mutants with a total charge of -1, including a +1 charge on the ammonium group and a -2 charge on the phosphate group. The dissociation constant of S1P binding to these receptors was studied as well. The models of wild type and mutant proteins originated from an active receptor model that was developed previously. We used ab initio RHF/6-31+G(d) to optimize our models in aqueous solution, where the solvation energy derivatives are represented by conductor-like polarizable continuum model (C-PCM) and integral equation formalism polarizable continuum model (IEF-PCM). Calculation of the dissociation constant for each mutant was determined by reference to the experimental dissociation constant of the wild type receptor. The computed dissociation constants of the E3.29Q and E3.29A mutants are three to five orders of magnitude higher than those for the wild type receptor and K5.38A mutant, indicating vital contacts between the S1P phosphate group and the carboxylate group of E3.29. Computational dissociation constants for K5.38A, E3.29A, and E3.29Q mutants were compared with experimentally determined binding and activation data. No measurable binding of S1P to the E3.29A and E3.29Q mutants was observed, supporting the critical contacts observed computationally. These results validate the quantitative accuracy of the model.     

TDDFT和实验结合研究丹皮酚及其西佛碱的紫外光谱

采用五个密度泛函LSDA,B3LPY,B3PW91,MPW1PW91和PBE1PBE,选择不同基组计算了气相和乙醇为溶剂下的丹皮酚及其两个丹皮酚西佛碱的激发态。LSDA不能给出合理的结果,MPW1PW91和PBE1PBE的结果和实验值接近,而B3LYP能给出准确的垂直激发能。基组中加入弥散函数有利于激发能计算精度的提高。溶剂效应对激发态计算的准确度有明显影响,极化连续模型(PCM)能较好地模拟溶剂的影响,垂直激发能计算结果明显好于气相。     

白芷香豆素分子电子结构及光谱性质的理论研究

采用量子化学密度泛函理论在B3LYP/6-31+G**水平上对白芷中的5种香豆素类化合物分子几何构型进行全优化:用含时密度泛函理论在相同水平对上述化合物分子进行电子吸收光谱研究.为模拟真实条件,采用PCM模型,以甲醇为溶剂,计算其对分子电子结构和光谱性质的影响.计算结果表明:标题化合物分子母环发生共轭形成大π键,为刚性...     

Studies on the solution conformation and dynamics of a polysaccharide from Sinorhizobium fredii HH103 and its monosaccharide repeating unit

The conformational behavior of the homopolysaccharide isolated from Sinorhizobium fredii HH103 and its monosaccharide repeating unit (5-acetamido-3,5,7,9-tetradeoxy-7-(3-hydroxybutyramido)-L-glycero- L- manno-nonulosonic acid) was analyzed by nuclear magnetic resonance (NMR) spectroscopy and extensive molecular dynamics simulations (MD). The results indicate that the glycosidic linkages and lateral chains may adopt a variety of conformations. MD simulations using the generalized Born solvent-accessible surface area (GB/SA) continuum solvent model for water and the MM3* force field provide a population distribution of conformers that satisfactorily agrees with the experimental NMR data for the torsional degrees of freedom of the molecule.     

Exploring molecular structures,orbital interactions,intramolecular proton-transfer reaction kinetics,electronic transitions and complexation of 3-hydroxycoumarin species using DFT methods

Optimal structures and electronic properties of various species of 3-hydroxycoumarin (3-HCou) have been explored using density functional theory (DFT) methods under polarizable continuum model (PCM) of solvation. Electron transfer from pyrone to benzene moieties is enhanced upon deprotonation. Anionic and radical species have similar orbital-interaction characteristics but the charges in the former are distributed more uniformly. The rate of intramolecular proton transfer for the neutral species increases many folds upon excitation. The HOMO–LUMO transition with π → π* character mainly accounts for the UV absorption of most 3-HCou species in solution. The wavelengths of maximal absorption predicted using TD-DFT method are in agreement with the previous experiment. For the charged species, calculations with the range-corrected functional yield better agreement with the previous experiment. Anionic 3-HCou species shows high degrees of complexation with chromium(III) and copper(II) compared with oxovanadium(IV) and zinc(II). Either oxovanadium(IV) or zinc(II) prefers forming two isomeric complexes with comparable degrees of formation.     

Quantum-chemical, NMR and X-ray diffraction studies on (+/-)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane

Time-averaged conformations of (±)-1-[3,4-(methylenedioxy)phenyl]-2-methylaminopropane hydrochloride (MDMA, “ecstasy”) in D₂O, and of its free base and trifluoroacetate in CDCl₃, were deduced from their ¹H NMR spectra and used to calculate their conformer distribution. Their rotational potential energy surface (PES) was calculated at the RHF/6-31G(d,p), B3LYP/6-31G(d,p), B3LYP/cc-pVDZ and AM1 levels. Solvent effects were evaluated using the polarizable continuum model. The NMR and theoretical studies showed that, in the free base, the N-methyl group and the ring are preferentially trans. This preference is stronger in the salts and corresponds to the X-ray structure of the hydrochloride. However, the energy barriers separating these forms are very low. The X-ray diffraction crystal structures of the anhydrous salt and its monohydrate differed mainly in the trans or cis relationship of the N-methyl group to the -methyl, although these two forms interconvert freely in solution.     

Density functional theory study of adsorption geometries and electronic structures of azo-dye-based molecules on anatase TiO2 surface for dye-sensitized solar cell applications

Structural and electronic properties of eight isolated azo dyes (ArNNAr′, where Ar and Ar′ denote the aryl groups containing benzene and naphthalene skeletons, respectively) were investigated by density functional theory (DFT) based on the B3LYP/6-31G(d,p) and TD-B3LYP/6-311G(d,p) methods The effect of methanol solvent on the structural and electronic properties of the azo dyes was elucidated by employing a polarizable continuum model (PCM). Then, the azo dyes adsorbed onto the anatase TiO₂ (101) slab surface through a carboxyl group. The geometries and electronic structures of the adsorption complexes were determined using periodic DFT based on the PWC/DNP method. The calculated adsorption energies indicate that the adsorbed dyes preferentially take configuration of the bidentate bridging rather than chelating or monodentate ester-type geometries. Furthermore, the azo compounds having two carboxyl groups are coordinated to the TiO₂ surface more preferentially through the carboxyl group connecting to the benzene skeleton than through that connecting to the naphthalene skeleton. The dihedral angles (Φ_B-N) between the benzene- and naphthalene-skeleton moieties are smaller than 10° for the adsorbed azo compounds containing one carboxyl group. In contrast, Φ_B-N > 30° are obtained for the adsorbed azo compounds containing two carboxyl groups. The almost planar conformations of the former appear to strengthen both π-electrons conjugation and electronic coupling between low-lying unoccupied molecular orbitals of the azo dyes and the conduction band of TiO₂. On the other hand, such coupling is very weak for the latter, leading to a shift of the Fermi level of TiO₂ in the lower-energy direction. The obtained results are useful to the design and synthesize novel azo-dye-based molecules that give rise to higher photovoltaic performances of the dye-sensitized solar cells.