基于2,4-二丙稀酰胺嘧啶的氢键复合物的稳定性和光谱

氢键对含有以嘧啶为基的衍生物的生命体具有重要作用。用AM1 和 DFT 方法对2,4-二丙稀酰胺嘧啶(2,4-BAAP) 衍生物与1-取代的脲嘧啶形成的氢键复合物电子结构进行理论研究。用INDO/SCI 和 B3LYP/6-31G(d)方法分别计算了复合物的UV和NMR光谱。结果表明,由于结合能为负值,两单体能通过三重氢键形成复合物,取代基存在时结合能变小。这种削弱效应取决于电子效应和空间效应的协同作用。当2,4-BAAP上哌啶基存在时,由于异构复合物的形成,复合物的结合能变小。供电基存在时复合物的能隙变小。共轭体系的扩展使复合物易于注入电子和空穴。复合物电子光谱的第一吸收峰与母体相比发生红移由于其具有较小的LUMO-HOMO能隙。在13C NMR谱中,复合物C=O键上的C原子的化学位移向低场移动。     

水溶液中氨基酸侧链对G∶C碱基对间氢键影响的理论研究

利用量子化学方法研究了气相和水溶液下,氨基酸侧链与鸟嘌呤和胞嘧啶间的氢键作用.应用B3LYP/6-31+G(d,p)方法优化复合物几何结构,使用MP2/aug-cc-p VDZ方法进行复合物能量、自然键轨道(NBO)电荷和二阶稳定化能的计算.结果表明,水溶液可使氨基酸侧链与碱基或碱基对之间氢键键能显著减小;带电复合物气相和水溶液氢键键能之差范围为50.63~146.48 k J/mol,中性为0.17~24.94 k J/mol;电荷的转移量与氢键键能成正比,电荷转移量越多,复合物越稳定;二阶稳定化能与氢键键长成反比,与电荷转移量成正比,且气相与水溶液氢键二阶稳定化能之比约为两相的电荷转移量之比.水溶液对该类体系中氢键作用具有明显影响.     

精氨酸侧链和核酸碱基间离子氢键作用强度分析

采用MP2/6-31+G(d,p)方法优化得到了22个由精氨酸侧链与碱基尿嘧啶、 胸腺嘧啶、 胞嘧啶、 鸟嘌呤及腺嘌呤形成的氢键复合物的气相稳定结构, 使用包含BSSE校正的MP2/aug-cc-pVTZ方法计算得到了复合物的气相结合能, 通过MP2/6-31+G(d,p)方法和PCM模型优化得到了复合物的水相稳定结构, 采用MP2/aug-cc-pVTZ方法和PCM模型计算得到了复合物的水相结合能. 研究发现, 精氨酸侧链与碱基间的离子氢键作用强度与单体间电荷转移量、 氢键临界点电子密度及二阶作用稳定化能密切相关. 与中性氢键相比, 离子氢键作用具有更显著的共价作用成分. 研究还发现, 精氨酸侧链和碱基间形成的氢键复合物的稳定性次序可以通过氢键受体碱基分子上氧原子和氮原子的质子化反应焓变进行预测, 质子化反应焓变越负, 形成的氢键复合物越稳定.     

计算机分子模拟辅助设计分子印迹聚合物及其机理研究

对三聚氰胺(MEL)为模板,丙烯酰胺(AM)为功能单体,乙二醇二甲基丙烯酸酯(EGDMA)为交联剂的分子印迹组装体系分子模拟分析,辅助设计了三聚氰胺分子印迹聚合物,分析其印迹机理。结果表明:组装体系中发生相互作用的基团主要为MEL分子的三个氨基氢和三嗪环上的三个氮,AM中的氨基氢和羰基氧,EGDMA中羰基氧。AM的羰基氧比EGDMA对质子的亲和力强,易于形成氢键。AM中两个氨基氢靠近羰基的氨基质子形成氢键能力强。AM与EGDMA形成复合物的AVG△E均高于对应模板复合物体系,EGDMA比模板更有利于竞争单体。MEL与AM、EGDMA相互作用主要形成MEL-AM-EGDMA复合物,其次为MEL-3AM。最终MIPs中对MEL具有特异性识别的作用位点为AM的氨基氢和羰基氧和EGDMA中的羰基氧。选定c(MEL)∶c(AM)∶c(EGDMA)=1∶1∶10,即浓度分别为:c(MEL)=4 mmol/L,c(AM)=4 mmol/L,c(EGDMA)=40 mmol/L作为最优MEL-MIPs制备基础浓度。     

s-四嗪-水簇复合物的理论研究

用量子化学B3LYP方法和6-31＋＋G**基函数研究了s-四嗪-水簇复合物基态分子间相互作用, 并进行了构型优化和频率计算, 分别得到无虚频稳定的s-四嗪-(水)₂复合物、s-四嗪-(水)₃复合物和s-四嗪-(水)₄复合物6个、9个和12个. 复合物存在较强的氢键作用, 复合物结构中形成一个N…H—O氢键并终止于O…H—C氢键的氢键水链构型最稳定. 经基组重叠误差和零点振动能校正后, 最稳定的1∶2, 1∶3和1∶4(摩尔比)复合物的结合能分别是41.35, 70.9和 94.61 kJ/mol. 振动分析显示氢键的形成使复合物中水分子H—O键对称伸缩振动频率减小(红移). 研究表明N…H键越短, N…H—O键角越接近直线, 稳定化能越大, 氢键作用越强. 同时, 用含时密度泛函理论方法在TD-B3LYP/6-31＋＋G**水平计算了s-四嗪单体及其氢键复合物的第一¹(n, p*)激发态的垂直激发能.     

氨基酸侧链与氧化鸟嘌呤碱基对体系的氢键作用

应用量子化学方法,分别在气相和水溶液中对氨基酸侧链与氧化鸟嘌呤碱基对(8-oxo-G∶C)形成的三体复合物的氢键键能、几何结构、电荷分布及二阶稳定化能进行了研究.结果表明,水溶液的存在削弱了复合物中的氢键强度,电荷分布变化明显,水溶液中形成氢键位点的电荷变化量约为气相中的10倍,而几何结构变化不明显、对于酶与DNA之间的相互作用的研究需在水溶液中进行.水溶液对带电三体复合物中8-oxo-G∶C与氨基酸侧链间的氢键有较大影响,键能平均减小了69.23 k J/mol,不带电复合物仅减小了3.60k J/mol.水溶液中三体复合物中8-oxo-G∶C间的氢键受侧链的影响不大,且与侧链带电与否无关,带电复合物和不带电复合物的氢键强度分别减小了24.57和30.05 k J/mol,且二阶稳定化能越大,其对应的氢键键长越短.     

取代基对1-甲基尿嘧啶与N-甲基乙酰胺氢键复合物中氢键强度的影响

使用密度泛函理论B3LYP方法和二阶微扰理论MP2方法对由1-甲基尿嘧啶与N-甲基乙酰胺所形成的氢键复合物中的氢键强度进行了理论研究, 探讨了不同取代基取代氢键受体分子1-甲基尿嘧啶中的氢原子对氢键强度的影响和氢键的协同性. 研究表明: 供电子取代基使N－H…O＝C氢键键长r(H…O)缩短, 氢键强度增强; 吸电子取代基使N－H…O＝C氢键键长r(H…O)伸长, 氢键强度减弱. 自然键轨道(NBO)分析表明: 供电子基团使参与形成氢键的氢原子的正电荷增加, 使氧原子的负电荷增加, 使质子供体和受体分子间的电荷转移量增多; 吸电子基团则相反. 供电子基团使N－H…O＝C氢键中氧原子的孤对电子轨道n(O)对N－H的反键轨道σ^*(N－H)的二阶相互作用稳定化能增强, 吸电子基团使这种二阶相互作用稳定化能减弱. 取代基对与其相近的N－H…O＝C氢键影响更大.     

三唑酮分子印迹预组装体系的分子模拟与吸附性能

以三唑酮为模板分子, 以丙烯酰胺(AM)、 丙烯酸(AA)、 甲基丙烯酸(MAA)和三氟甲基丙烯酸(TFMAA)为功能单体预组装了分子印迹聚合物体系, 采用半经验法和从头算法, 利用Hyperchem软件模拟了三唑酮与4种功能单体所组成的分子印迹预组装体系的构型、 能量、 反应配比及复合反应的结合能, 选择复合物结合能最高的功能单体用于分子印迹聚合物的合成. 采用密度泛函方法计算了模板与单体在不同致孔剂中的溶剂化能. 结果表明, 三唑酮与三氟甲基丙烯酸所形成复合物的作用力最强, 在非极性溶剂中溶剂化能最弱. 由预组装体系的差示紫外光谱法研究发现, 一分子三唑酮可与两分子三氟甲基丙烯酸在氯仿中形成氢键复合物, 与分子模拟的结果一致. 在最佳模拟条件下, 合成了三唑酮的印迹聚合物, 利用吸附等温线Langmuir和Freundlich模型研究了印迹聚合物的吸附行为及识别机理. 上述方法对于分子印迹体系的筛选及分子印迹聚合物性能的预测有重要的意义.     

邻二氮杂苯-水复合物的氢键结构与性质

用密度泛函理论B3LYP方法和MP2方法对邻二氮杂苯-水复合物基态的氢键结构与相互作用能进行了理论计算,结果表明复合物之间存在较强的氢键N…H－O.在复合物中,水的H－O对称伸缩振动频率明显红移.同时,使用含时密度泛函理论方法计算了邻二氮杂苯单体及复合物的低占据1(n,π*) 和1(π,π*) 态的垂直激发能,计算结果与实验值吻合较好.     

胞嘧啶-BH3复合物构型与性质的量子化学研究

对胞嘧啶-BH3复合物分别用B3LYP/6-31G和MP2/6-31G进行理论计算以预测该复合物的构型及稳定化能, 得到了5种构型。对各构型进行了振动频率分析和自然键轨道分析。结果表明, B与N和O直接相连的构型比较稳定, 其稳定化能为137.4和120.0 kJ/mol (MP2/6-31G)。其余的构型靠π-p作用而形成, 其稳定性较前两者弱。各构型的稳定化能与电荷转移量有良好的相关性。复合物的形成, 使其红外光谱均有不同程度的红移, 幅度与复合物的稳定性相关。     

Hydrogen-bonded assembly and binding affinity of the multi-point acceptor and isophthalic acid

Supermolecular complexes formed by oligophenyleneethynylene derivatives and isophthalic acid were studied using AM1 method to obtain binding energy. Electronic spectra and IR spectra of the complexes were calculated by INDO/CIS and AM1 methods based on AM1 geometries. Results indicated that the dimer could be formed by the monomers via hydrogen bonding because of the negative binding energy. Binding energy of the complexes was affected by electronegativity and steric effects of the substituents. The first UV absorptions and IR frequencies of N-H bonds of the complexes were both red-shifted compared with those of the monomers. The complexes could bind small molecules via hydrogen bonds, resulting in the change in UV absorptions and an increase in IR frequencies of N-H bonds.     

Study on UV, IR and NMR Spectra of Double Hydrogen-bonded Complexes

1 INTRODUCTION Currently, the theoretical study on supermolecular system, especially on hydrogen-bonded complexes, has played an important role in the field of scientific research thanks to the development of computer te- chnique. Venkatraman[1] found that the theoretical parameters for the adduct of levulinic acid and me- lamine, predicted by HF and DFT methods, are in good agreement with the experimental data. Jür- gens[2] synthesized melem with melamine and perfor- med theoretical c…     

The structure and spectra of H-bonded complexes formed by 2-pyridone

The self-assembly complexes formed by 2-pyridone derivatives were theoretically studied by the AM1 and DFT methods to determine their binding energies. The UV, IR, and NMR spectra of the complexes were calculated using the INDO/CIS, AM1, and B3LYP/3-21G methods, respectively. It was shown that the complexes could be formed by two monomers via double hydrogen bonding thanks to the negative binding energy. The affinity for binding was increased by substituents in the monomers. But this stimulating effect depended on the simultaneous influence of the electronic and steric effects. The first absorption bands in the UV spectra of the complexes were blue-shifted relative to that of the monomer because of their larger LUMO-HOMO energy gaps. As hydrogen bonds were formed, the N-H stretching vibrations of the monomers were weakened in the IR spectra of the complexes. And the chemical shifts of the C=C and C≡C carbon atoms were shifted downfield in the ¹³C NMR spectra. The article is published in the original.     

Theoretical studies on the binding affinities of β-cyclodextrin to small molecules and monosaccharides

Equilibrium geometries and electronic structures of complexes between β-cyclodextrin (β-CD) and some small molecules as well as monosaccharides were investigated by Austin Model 1 (AM1) to obtain binding energy of the complexes. It was indicated that β-CD could bind the structurally similar solvent molecules and monosaccharides because of the negative binding energy of the complexes, and especially could show the chiral binding ability to monosaccharides with more hydroxyl groups, due to its chiral characteristics. The complexes were stabilized by the hydrogen bonding between β-CD and guests. Based on the AM1 optimized geometries, the IR spectra were calculated by AM1 method. Vibration frequencies of O-H bonds in the guests were red-shifted owing to the weakening of the O-H bonds with the formation of the complexes.     

苝二酸酐与嘧啶衍生物的氢键组装

Semi-empirical AM1 method was used to study 1:1 and 1:2 hydrogen bond complexes formed with perylene dianhydride and pyridine derivatives. The weak interaction energy become bigger as the number of hydrogen bonds increases. The donor groups on the host and electron-withdrawing groups on the guest molecules favor hydrogen bonding interactions, and the formation of hydrogen bonding leads to electron density flow from the host to the guest molecules. Electronic spectra of these complexes were computed using INDO/SCI method. Blue-shift of the electronic absorption spectra for the complexes, comparing that of the host,takes place, and the first peaks for different complexes changed slightly. These are in agreement with the experimental results. The cause of blue-shift was discussed, and the electronic transitions were assigned based on theoretical calculations. The potential curve of double proton transfer in the complex was calculated, and the transition state and activated energy relative to the N-H bond were obtained.     

Binding affinities and spectra of complexes formed by dehydrotetrapyrido[20]annulene and small molecules

Theoretical study on the binding affinities of dehydrotetrapyrido[20] annulene to the alkene and aromatic molecules was performed using the AM1 and DFT methods. It indicated that the host possesses the ability to bind the above molecules since the binding energies of the complexes were negative. The complexes were stabilized via the hydrogen bonding, static effect, and π — π stacking interaction between the host and guest molecules. Based on the B3LYP/3-21G optimized geometries, the electronic, IR, and NMR spectra were calculated using the INDO/CIS, AM1, and B3LYP/3-21G methods, respectively. Due to the hydrogen bonding, the first absorption maxima in the electronic spectra of studied complexes were blue-shifted, whereas the main IR frequencies for some of the complexes were red-shifted. At the same time, the chemical shifts of carbon atoms forming the bonds in the complexes were lower, compared to those of the host.     

A TD-DFT study on the hydrogen bonding of three esculetin complexes in electronically excited states: strengthening and weakening

Time-dependent density functional theory (TD-DFT) method was used to study the excited-state hydrogen bonding of three esculetin complexes formed with aprotic solvents. The geometric structures, molecular orbitals (MOs), electronic spectra and the infrared (IR) spectra of the three doubly hydrogen-bonded complexes formed by esculetin and aprotic solvents dimethylsulfoxide (DMSO), tetrahyrofuran (THF) and acetonitrile (ACN) in both ground state S(0) and the first singlet excited state S(1) were calculated by the combined DFT and TD-DFT methods with the COSMO solvation model. Two intermolecular hydrogen bonds can be formed between esculetin and the aprotic solvent in each hydrogen-bonded complex. Based on the calculated bond lengths of the hydrogen bonds and the groups involved in the formation of the intermolecular hydrogen bonds in different electronic states, it is demonstrated that one of the two hydrogen bonds formed in each hydrogen-bonded complex is strengthened while the other one is weakened upon photoexcitation. Furthermore, it is found that the strength of the intermolecular hydrogen bonds formed in the three complexes becomes weaker as the solvents change from DMSO, via THF, to ACN, which is suggested to be due to the decrease of the hydrogen bond accepting (HBA) ability of the solvents. The spectral shifts of the calculated IR spectra further confirm the strengthening and weakening of the intermolecular hydrogen bonds upon the electronic excitation. The variations of the intermolecular hydrogen bond strengths in both S(0) and S(1) states are proposed to be the main reasons for the gradual spectral shifts in the absorption and fluorescence spectra both theoretically and experimentally.     

Theoretical study on the bromomethane-water 1:2 complexes

Bromomethane-water 1:2 complexes have been theoretically studied to reveal the role of hydrogen bond and halogen bond in the formation of different aggregations. Four stable structures exist on the potential energy surface of the CH3Br(H2O)2 complex. The bromine atom acts mainly as proton acceptor in the four studied structures. It is also capable of participating in the formation of the halogen bond. The properties and characteristics of the hydrogen bond and the halogen bond are investigated employing several different quantum chemical analysis methods. Cooperative effects for the pure hydrogen bonds or the mixed hydrogen bonds with halogen bonds and the possibility of describing cooperative effects in terms of the topological analysis of the electronic density or the charge-transfer stabilization energy are discussed in detail. An atoms-in-molecules study of the hydrogen bond or the halogen bond in the bromomethane-water 1:2 complexes suggests that the electronic density topology of the hydrogen bond or the halogen bond is insensitive to the cooperative effect. The charge-transfer stabilization energy is proportional to the cooperative effect, which indicates the donor-acceptor electron density transfer to be mainly responsible for the trimer nonadditive effect.     

Cyclodextrin in Artificial Enzyme Model, Rotaxane, and Nano-material Fabrication

The methods of obtaining and physicochemical properties of inclusion complexes of amlodipine (AM) and felodipine (FL) with methyl-β-cyclodextrin (MCD) clathrates have been studied. Solid complexes were obtained by two methods: the kneading one and lyophilization with the drug and MCD at the molar ratio of 1:1. The identity of the obtained clathrates was confirmed by IR, ¹³C-NMR spectra and DSC measurements. The process of AM and FL complexation with MCD was shown to involve the aromatic ring, the carbonyl groups in the ester bonds and the carbon atoms of the DHP ring linked via the ester bonds. One of the aims of complexation was to improve the drug solubility, so the dissolution rate of the obtained clathrates was tested. As a result of the inclusion complexes formation of AM, obtained both by kneading and lyophilization, the solubility of this therapeutic drug increased 3 times. The inclusion complex formation with FL and MCD brought the most dramatic increase in FL solubility, which increased 16 times.