儿茶素-胸腺嘧啶分子间相互作用模式的密度泛函研究

采用密度泛函理论的B3LYP方法,在6-31+G*基组水平上研究了儿茶素-胸腺嘧啶分子间相互作用机制,得到稳定的儿茶素-胸腺嘧啶复合物13个,并且复合物形成了2个或更多的氢键. 另外,在相同机组水平上进行了振动分析,结果表明儿茶素-胸腺嘧啶复合物间存在N-H…O、C-H…O、O-H…O三种类型氢键,氢键对于复合物的稳定性起着重要的作用. 应用了分子中的原子理论和自然键轨道理论对这13种复合物中氢键的性质和特征进行了分析. 发现所有的氢键复合物进行基组重叠误差校正后的相互作用能为-18.15～-32.99     

紫草素与胞嘧啶相互作用的理论研究北大核心CSCD

采用密度泛函理论的M06方法在6-311++G**基组水平下对紫草素-胞嘧啶复合物进行了结构优化,得到了14个稳定的紫草素-胞嘧啶复合物.我们还应用了分子中的原子(AIM)理论和自然键轨道(NBO)理论对这14个复合物中的氢键的性质和特征进行了分析.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,二阶稳定化能的计算和分析,发现复合物1的结构是最稳定的.     

紫草素与胞嘧啶相互作用的理论研究

采用密度泛函理论的M06方法在6-311++G**基组水平下对紫草素-胞嘧啶复合物进行了结构优化,得到了14个稳定的紫草素-胞嘧啶复合物。我们还应用了分子中的原子(AIM)理论和自然键轨道(NBO)理论对这14个复合物中的氢键的性质和特征进行了分析。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、二阶稳定化能的计算和分析,发现复合物1的结构是最稳定的。     

木犀草素和鸟嘌呤间相互作用的理论研究

采用密度泛函理论中的B3LYP方法对木犀草素和鸟嘌呤之间的相互作用和机理进行研究,分别找到了十八种木犀草素和鸟嘌呤复合物. 结果表明这些复合物是通过氢键相互作用而稳定存在的. 利用分子中的原子理论(AIM)和自然键轨道理论(NBO)对体系中的氢键进行研究. 通过基组重叠误差校正的复合物间的相互作用能为6.04～56.94 kJ/mol,计算结果表明在木犀草素-鸟嘌呤复合物中有很强的氢键相互作用. 比较了木犀草素和四个DNA碱基间的相互作 用,发现木犀草素-胸腺嘧啶是最强的,木犀草素-腺嘌呤是最弱的.     

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.     

硝酸羟胺-(H_2O)_n复合物氢键相互作用的密度泛函研究

为研究硝酸羟胺-(H_2O)_n复合物的氢键作用,采用密度泛函B3LYP方法在6-311++G(d, p)基组水平上对硝酸羟胺-(H_2O)_n复合物的结构进行优化,采用MP2/6-311++G(d, p)方法,经基组叠加误差和零点能校正计算得到复合物的相互作用能.利用自然键轨道分析方法研究复合物氢键作用的本质,并对复合物中水分子的振动光谱进行分析.计算结果表明,硝酸羟胺-(H_2O)_n复合物存在着6个硝酸羟胺-H_2O稳定构型和8个硝酸羟胺-(H_2O)_2稳定构型,且最稳定构型的相互作用能分别为52.821 kJ·mol~(-1)和73.349 kJ·mol~(-1).在硝酸羟胺-(H_2O)_n复合物中,水中H-O伸缩振动频率明显红移,且红移增大的程度与复合物稳定化能的变化趋势基本一致.     

5-氟尿嘧啶与一氧化碳复合物的结构与性质

采用量子化学密度泛函理论在B3LYP/6-311++G**水平上对5-氟尿嘧啶(5-FU)与CO形成的复合物体系进行了理论计算. 计算共获得了稳定的5-FU异构体12个,双酮式结构5-FU0为其最稳定的构型. 优化获得了稳定复合物44个,其结合方式是CO中的C或O原子与5-FU 的H8或H12键形成氢键;CO分子的C 与5-FU结合具有更大的优势,形成复合物的结合能大,更稳定. 研究还发现,复合物的稳定性与其单体稳定性和C13对氢键相邻单键的二阶稳定化能有关,5-FU0-A为最稳定复合物.     

5-氟尿嘧啶与一氧化碳复合物的结构与性质

采用量子化学密度泛函理论在B3LYP/6-311++G**水平上对5-氟尿嘧啶(5-FU)与CO形成的复合物体系进行了理论计算. 计算共获得了稳定的5-FU异构体12个,双酮式结构5-FU0为其最稳定的构型. 优化获得了稳定复合物44个,其结合方式是CO中的C或O原子与5-FU 的H8或H12键形成氢键;CO分子的C 与5-FU结合具有更大的优势,形成复合物的结合能大,更稳定. 研究还发现,复合物的稳定性与其单体稳定性和C13对氢键相邻单键的二阶稳定化能有关,5-FU0-A为最稳定复合物.     

Theoretical Studies on the Structure and Spectrum of Imidazole-Chloranil Charge Transfer Complex

测定了咪唑-四氯苯醌电荷转移复合物在氯仿溶液中的紫外可见吸收光谱,运用Benesi-Hildebrand方程和Job连续变换法确定了咪唑-四氯苯醌电荷转移复合物的化学计量比为1:1. 采用密度泛函理论和多体微扰理论研究了咪唑-四氯苯醌电荷转移复合物的空间构型与结合能. 理论计算结果显示,咪唑-四氯苯醌电荷转移复合物共有四种可能的空间构型,分别为两种边(咪唑)-面(四氯苯醌)式结合构型(S1、S2)和两种边(咪唑)-边(四氯苯醌)式结合构型(S3、S4). 通过比较它们的结合能,发现边(咪唑)-面(四氯苯醌)式构型比边(咪唑)-边(四氯苯醌)式构型更稳定. 运用自然布居分析、电子密度拓扑分析与自然键轨道分析研究了四个构型的咪唑与四氯苯醌结合特征. 结果表明,边(咪唑)-面(四氯苯醌)式构型为电荷转移复合物,而边(咪唑)-边(四氯苯醌)式构型为分子间氢键复合物. 对于复合物最稳定构型S1,咪唑n(N15)孤电子对轨道和四氯苯醌∏* (C1=O7)反键轨道的电荷转移相互作用对咪唑-四氯苯醌复合物的稳定性起着决定性的作用,此外O7…H20氢键也起一定的作用. 采用含时密度泛函理论计算了复合物(S1)的电子激发能. 基于理论计算结果,分析了复合物的紫外-可见吸收光谱.     

HNO二聚体蓝移氢键的理论研究

利用分子轨道从头算理论和密度泛函理论结合不同理论基组对于N-H…O蓝移氢键进行了详细的研究.利用标准方法和均衡校正方法对二聚体进行了几何优化,振动频率和相互作用能的计算.拓扑学和自然键轨道理论对于蓝移氢键的本质进行分析.自然键轨道(NBO)分析表明,σ*(N-H)轨道上电子密度降低是电子密度重排效应的结果.分子内电子重排、轨道再杂化和电子受体内部结构重组共同作用结果导致了N-H的振动频率大幅蓝移现象的出现.     

A density functional theory and quantum theory of atoms in molecules study on hydrogen bonding interaction between paracetamol and water molecules

To consider the hydrogen bonding interactions between paracetamol and water molecules, probable complexes of paracetamol from three active sites (carbonyl oxygen atom, hydroxyl oxygen atom, and nitrogen atom) with H₂O molecule were formed. The optimized geometries and total energies have been obtained at the B3PW91/6-31+G(d, p) level of theory. Comparison of hydrogen bond lengths and the energies of complexes showed hydrogen bond that form between the oxygen atom of the carbonyl group and hydrogen atom is stronger than others. Moreover, an increase in the number of hydrogen bonds increases stability of paracetamol-water complexes. At the end, the QTAIM was applied to explain the nature of the hydrogen bonds and confirm the more stability by complexation.     

Hydrogen-bonding studies of amino acid side-chains with DNA base pairs

The interactions of the amino acid side-chains arginine (ARG), aspartic acid (ASP), asparagine (ASN), lysine (LYS) and serine (SER) with nucleic acid base pairs have been investigated using theoretical methods. The interaction energy of the short intermolecular N–H?···?N, N–H?···?O, O–H?···?O, O–H?···?N, C–H?···?O and C–H?···?N hydrogen bonds present in both isolated base pairs and complexes and its role in providing stability to the complexes have been explored. The homonuclear interactions are found to be stronger than the heteronuclear interactions. An improper hydrogen bond has been observed for some of the N–H?···?O and N–H?···?N hydrogen-bond interactions with the contraction of the N–H bond varying from 0.001 to 0.0260?Å and the corresponding blue shift of the stretching frequency by 4–291?cm^?1. Localized molecular orbital energy decomposition analysis (LMOEDA) reveals that the major contributions to the energetics are from the long-range polarization (PL) interaction, and the short-range attractive (ES, EX) and repulsive (REP) interactions. The Bader's atoms in molecules (AIM) theory shows good correlation for the electron density and its Laplacian at the bond critical points (BCP) with the N–H?···?N and N–H?···?O hydrogen-bond lengths in the complexes, and gives a proper explanation for the stability of the structure. The charge-transfer from the proton acceptor to the antibonding orbital of the X–H bond in the complexes was studied using natural bond orbital (NBO) analysis.     

Comparison of hydrogen and halogen bonds between dimethyl sulfoxide and hypohalous acid: competition and cooperativity

A theoretical study of the complexes formed between dimethyl sulfoxide (DMSO) and hypohalous acid (HOX, X = Cl, Br, and I) has been carried out at the MP2/aug-cc-pVTZ level. For each HOX, four minima binary complexes were found, two mainly with an OH???O hydrogen bond and the other two with an OX???O halogen bond. The hydrogen-bonded complexes are more stable than the halogen-bonded analogues for HOCl and HOBr, while both types of complexes have similar stability in the iodine case. A red shift was found for the associated H–O and X–O bond stretch vibrations and a small blue shift for the distant bonds. As the oxygen of DMSO simultaneously binds with two HOCl molecules, the corresponding interactions are weakened with diminutive effect. This diminutive effect is the largest in the complexes with two OH???O hydrogen bonds but the smallest in those with two OCl???O halogen bonds.     

Cooperativity between the hydrogen bonding and halogen bonding in F3CX ··· NCH(CNH) ··· NCH(CNH) complexes (X=Cl,Br)

MP2 calculations with the cc-pVTZ basis set were used to analyse the intermolecular interactions in F₃CX?···?NCH(CNH)?···?NCH(CNH) triads (X=Cl, Br), which are connected via hydrogen and halogen bonds. Molecular geometries, binding energies, and infrared spectra of the dyads and triads were investigated at the MP2/cc-pVTZ computational level. Particular attention was given to parameters such as the cooperative energies, cooperative dipole moments, and many-body interaction energies. All studied complexes, with the simultaneous presence of a halogen bond and a hydrogen bond, show cooperativity with energy values ranging between ?1.32 and ?2.88?kJ?mol^?1. The electronic properties of the complexes were analysed using the Molecular Electrostatic Potential (MEP), electron density shift maps and the parameters derived from the Atoms in Molecules (AIM) methodology.     

HArF和HNO二聚体相互作用氢键的理论研究

用二阶微扰理论结合6-311+G**、6-311++G**和6-311++G(2d,2p)基组对氢键相互作用二聚体HNO···HArF进行研究．在MP2/6-311+G**、MP2/6-311++G**和MP2/6-311++G(2d,2p)水平上，利用标准方法和均衡校正方法对二聚体进行了几何优化、振动频率和相互作用能的计算．对于相互作用能采用G2MP2方法计算．计算结果表明存在两种稳定的二聚体HNO···HArF结构，在这两种结构中，Dimer I(H···F)比Dimer II(H···O)更加稳定．通过振动频率的计算表明，在Dimer I(H···F)中存在N-H···F蓝移氢键，在DimerII(H···O)中存在Ar-H···O红移氢键，并对蓝移氢键加以确认．利用电子密度拓扑学分析和自然键轨道分析对于氢键红移和蓝移进行了合理解释．     

The mutual relationship between H-bonding and π-stacking interactions: the estimation of individual binding energies in the phenylalanine:G ··· C ternary complex

The mutual relationship between stacked interaction and the individual hydrogen bonds in the phenylalanine:guanine?···?cytosine (Ph:G-C) and phenylalanine:cytosine?···?guanine (Ph:C-G) complexes have been studied at the MPWB1K/6-311++G** and M05-2X/cc-pVDZ levels of theory. The interplay of π-stacking and H-bonding results in the weakening of both interactions. The effect of π-stacking on the geometries and individual hydrogen bond (HB) energies of guanine–cytosine (G-C) base pair have been investigated using electron densities calculated by the atoms in molecules (AIM) method at the hydrogen bond critical points (BCP). The results of AIM analysis are in good agreement with the calculated individual hydrogen bond energies. The π-stacking interactions strengths the HB1 and weakens HB2 and HB3 in the Ph:G-C complexes, while the opposite is true in the Ph:C-G complex. With the increase in the distance between phenylalanine ring and the groups involved in H-bond interactions the change in the H-bond energy increases and the changes in the individual H-bond and π-stacking energies decrease in the ternary complexes.     

Thermal and dielectric studies of self-assembly systems formed by hydroquinone and alkyloxy benzoic acids

Self-assembly systems formed by hydroquinone and alkyloxy benzoic acids are isolated and characterized. Hydroquinone formed double hydrogen bonds with p-n-alkyloxy benzoic acids. Various hydrogen bonded complexes have been synthesized with hydroquinone and pentyloxy to dodecyloxy benzoic acid, respectively. FTIR studies confirm the hydrogen bond formation in the complex. Polarizing Optical Microscopic (POM) studies revealed the textural information while the transition and enthalpy values are experimentally deduced from Differential Scanning Calorimetry (DSC) studies. Phase diagram has been constructed from the POM and DSC data. The members of the present homologous complexes are characterized by POM, DSC, optical tilt angle and dielectric studies. Odd-even effect has been evinced in enthalpy values and transition temperatures corresponding to the isotropic to nematic phase transition. Optical tilt angle in Smectic C phase data has been fitted to a power law and it has been observed that the temperature variation of the tilt angle follows Mean Field theory prediction. Results of Fourier Transform Infrared Spectra (FTIR), POM, DSC, tilt angle and dielectric studies are discussed.