肾上腺素与胞嘧啶相互作用的密度泛函理论研究

采用密度泛函理论（DFT）B3LYP方法和6-311＋G（d,p）基组对肾上腺素-胞嘧啶复合物进行结构优化和频率计算,得到15种稳定的复合物.研究发现,所有的复合物进行基组重叠误差（BSSE）校正后的相互作用能为-11.43^-48.96kJ/mol,符合氢键能量范围,相互作用能主要由氢键所贡献.结构和振动频率分析显示,氢键的形成使相应O（N）—H键的键长变长,对称伸缩振动频率减小,说明复合物中形成的氢键都是正常的红移型氢键.应用自然键轨道（NBO）理论和分子中的原子（AIM）理论对15种复合物的氢键性质和特征进行分析,发现氢键对于复合物的稳定性起着重要作用,当复合物形成2个或更多的氢键时,氢键的数目、类型及强度共同决定着复合物的稳定性,复合物基本符合三氢键〉二氢键〉单氢键的稳定顺序,三氢键复合物4是最稳定的,复合物3存在单氢键O—H…O,比部分二氢键复合物要稳定.     

密度泛函方法研究气相胞嘧啶的互变异构化

By comparing the ready experimental results with the calculated results obtained at 7 basis sets and 3 theoretical levels, respectively, for the tautomeric form Cyt1 of cytosine, the relatively accurate B3LYP/6-311+G** theoretical method to study the tautomerism of cytosine was chosen. The ground-state structures of 8 tautomers of cytosine were fully optimized at B3LYP/6-311+G** level, and the tautomerism of 6 relatively stable tautomers of cytosine was studied. The frequency analysis was performed on all the optimized structures. For the ground state geometries, all the calculated frequencies are real; for the transition-state geometries, there is only one imaginary frequency for each structure. Detailed Intrinsic Reaction Coordination calculations were carried out to guarantee the optimized transition-state structures being connected to the related tautomers. All the energies given include the zero-point energy corrections. The theoretical results can give a reasonable interpretation for the experimental results.     

羟基自由基和鸟嘌呤-胞嘧啶碱基对反应的密度泛函理论研究

为了解决年龄衰老、基因突变和癌症等问题, 理解DNA的氧化损伤机理非常重要. 本文利用密度泛函方法和极化连续介质模型在液相条件下研究了羟基自由基夺取鸟嘌呤-胞嘧啶(GC)碱基对上5 个氢原子的反应机理. 研究结果表明, 所有的脱氢反应路径都是放热过程, 热力学上五个脱氢反应路径形成自由基的稳定性顺序是(H2b-GC)^·>(GC-H4b)^·>(GC-H6)^·>(GC-H5)^·~(H8-GC)^·, 其中H2b反应路径的能量变化最大, 说明该反应平衡时的转化率最高. 动力学上, 相对于反应复合物的局部反应能垒大小顺序是H2b     

木犀草素与胞嘧啶相互作用的理论研究

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、胞嘧啶、木犀草素-胞嘧啶复合物进行结构优化和振动频率分析,得到了12种稳定复合物.并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...     

儿茶素结构和振动光谱的密度泛函理论研究

本文利用密度泛函理论方法B3LYP在6-311 G(d,p)水平上研究了儿茶素及其异构体表儿茶素分子的几何构型,计算结果与实验所得结构参数一致.计算了儿茶素分子平衡构型下的力常数,使用Wilson的GF矩阵方法计算了振动基频以及相应的势能分布,据此结合理论计算的光谱强度,对儿茶素分子的振动基频进行了完善合理的理论归属.     

5-氟胞嘧啶互变异构的密度泛函理论计算

采用BH-HLYP/6-311＋G**方法对10种气相和水相中可能存在的5-氟胞嘧啶互变异构体进行了几何全优化, 并计算出它们的总能量和吉布斯自由能. Onsager反应场溶剂模型用于水相的计算. 计算结果表明, 5-氟胞嘧啶在气相中主要以烯醇式-氨基式形式存在, 在水相中主要以酮式-氨基式形式存在. 溶剂化自由能与异构体的气相偶极矩存在相关性．进一步求得互变异构化以及构象异构化和顺反异构化的过渡态, 探讨异构化过程中的几何结构和能量的变化.     

三核金配合物分子间Au-Au相互作用及其发光性质的含时密度泛函理论研究

使用混合密度泛函方法(MPW1PW91交换相关势), 对Au₃(HOC＝NH)₃分子进行了几何构型全优化, 在此基础上构建了Au₃(HOC＝NH)₃二聚体和三聚体模型, 采用含时密度泛函方法研究了单体和低聚体模型的分子间Au-Au相互作用与其发光性质的关系. 计算结果表明: 此d¹⁰亚金化合物低能激发态的主要成分是反键或非键的Au(5d)电子轨道到前线附近Au(6p)空轨道的跃迁, 并且这种激发大大加强了分子间Au-Au相互作用, 从而形成激发多聚体, 导致这类化合物溶液或固体发射谱红移.     

4-羟甲基吡啶－水红移氢键的密度泛函理论研究

使用密度泛函理论B3LYP方法和6-311++G**基函数对4-羟甲基吡啶与水形成的1:1和1:2（摩尔比）氢键复合物进行了理论计算研究,分别得到稳定的4-羟甲基吡啶－H₂O和4-羟甲基吡啶－(H₂O)₂氢键复合物3个和8个。经基组重叠误差和零点振动能校正后,最稳定的1:1和1:2氢键复合物的相互作用能分别为-20.536和-44.246 kJ/mol。振动分析显示O-H···N(O)氢键的形成使复合物中O-H键对称伸缩振动频率红移(减小)。自然键轨道分析表明,4-羟甲基吡啶与水形成最稳定的1:1和1:2氢键复合物时,分子间电荷转移分别为0.02642 e 和0.03813 e 。含时密度泛函理论TD-B3LYP/ 6-311++G**计算显示,相对于4-羟甲基吡啶单体分子,氢键H-OH···N和H-OH···OH的形成分别使最大吸收光谱波长兰移8~16纳米和红移4~11纳米。     

嘧啶及其异构体的密度泛函理论研究

胞嘧啶、尿嘧啶和胸腺嘧啶都有酮式和烯醇式互变异构。有人认为DNA的错配频率,与酮,烯醇或氨,亚氨的互变异构平衡有关。迄今,在相同理论水平上同时对三种嘧啶互变异构体进行理论计算研究的文献较少,     

阳离子-π体系相互作用的理论研究——Ⅰ.铵离子-苯复合物构型及相互作用的密度泛函研究

运用密度泛函B3LYP/6 31G 方法对铵离子 苯复合物的 6种可能构型进行了计算研究 ,发现铵离子的 2个氢指向苯环且不具对称性的结构为能量优势结构 .根据计算得到的复合物结构特点 ,分子间作用方式及热力学参数 ,得出铵离子和苯之间的作用是氢键相互作用的结论 .     

Density functional theory study on the interaction of catechin and cytosine

The interacting patterns and mechanism of the catechin and cytosine have been investigated using the density functional theory B3LYP method with 6-31+G* basis set.Eleven stable structures of the catechin-cytosine complexes have been found respectively.The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions.Theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been utilized to investigate the hydrogen bonds involved in all the systems.The interactio...     

Density functional theory study of the interaction between formamide and uracil

The hydrogen bonding of complexes formed between the formamide and uracil molecule has been fully investigated in the present study using the density functional theory (DFT) method at varied basis set levels from 6‐31G to 6‐311++G(d,p). Eight stable cyclic structures with two hydrogen bonds involved in the interaction are found on the potential energy surface (PES). The four structures are seven‐membered rings; the others are eight‐membered rings. The eight‐membered ring is preferred over the seven‐membered one by analyzing the hydrogen bond lengths and the interaction energies. The infrared (IR) spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

Density Functional Theory Study of the Interaction between Guanine and Catechin

The interacting patterns and mechanism of the catechin and guanine have been investigated with the density functional theory B3LYP method by 6‐31G* basis set. Fourteen stable structures for the catechin‐guanine complexes have been found which form two hydrogen bonds at least. The results indicate that the complexes are mainly stabilized by the hydrogen bonding interactions. At the same time, the number and strength of hydrogen bond play a co‐determinant parts in the stability of the complexes which can form two or more hydrogen bonds. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been adopted to investigate the hydrogen bonds involved in all systems. The interaction energies of all complexes have been corrected for basis set superposition error (BSSE), ranging from ?38.86 to ?14.56 kJ/mol. The results showed that the hydrogen bonding contributes to the interaction energies dominantly. The corresponding bonds stretching motions in all complexes are red‐shifted relative to that of the monomer, which is in agreement with experimental results.     

Density functional theory study of the hydrogen bonding interaction of 1:1 complexes of serine with water

The hydrogen bonding of 1:1 complexes formed between serine and water molecules were completely investigated in the present study employing ab initio and Density Functional Theory (DFT) methods at varied basis set levels from 6‐31g to 6‐311++g (2d,2p). For comparison, we also used the second‐order Moller–Plesset Perturbation (MP2) method at the 6‐31+g(d) level. Twelve reasonable geometries on the potential energy hypersurface of serine and water system were considered with the global minimum, 10 of which are cyclic double‐hydrogen bonded structures and the other two are one‐hydrogen bonded structures. The optimized geometric parameters and interaction energies for various isomers at different levels were estimated. The infrared spectrum frequencies, IR intensities, and the vibrational frequency shifts are reported. Finally, the solvent effects on the geometries of the serine–water complexes were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐311++g(d,p) level. The results indicate that the polarity of the solvent played an important role in the structures and relative stabilities of different isomers. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional study of AgnPd and AgnPdH clusters

Small Ag_nPd (n = 5) clusters and their hydrides Ag_nPdH (n = 5) have been studied by density functional theory calculations. For bare clusters, the structures in which the Pd atom has a maximum number of neighboring Ag atoms tend to be energetically favorable. Hydrogen prefers binding to Ag? Pd bridge site of Ag_nPd clusters except for Ag₅Pd. The binding energy has a strong odd–even oscillation. The electron transfers are from Ag atoms to Pd in bare clusters and are from metal clusters to H in cluster hydrides. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

磷化镍晶体结构的密度泛函理论研究

运用密度泛函理论系统地研究了已知的磷化镍晶体如Ni3P、 Ni12P5、 Ni2P、 Ni5P4、 NiP、 NiP2 和 NiP3等的结构、成键以及相关的热力学稳定性,对于结构简易化合物（Ni2P和NiP3）的弹性行为进行了预测。这些数据有助于更好的理解磷化镍的催化活性。     

Density Functional Theory Study on Hydrogen Bonding Interaction of Catechin-(H2O)n

Density functional theory B3LYP method with 6‐31G* basis set has been used to optimize the geometries of the catechin, water and catechin‐(H₂O)_n complexes. The vibrational frequencies have been studied at the same level to analyze these complexes. Six and eleven stable structures for the catechin‐H₂O and catechin‐(H₂O)₂ have been found, respectively. Theories of atoms in molecules (AIM) and natural bond orbital (NBO) have been utilized to investigate the hydrogen bonds involved in all the systems. The interaction energies of all the complexes corrected by basis set superposition error, are from ?13.27 to ?83.56 kJ/mol. All calculations also indicate that there are strong hydrogen‐bonding interactions in catechin‐water complexes. The strong hydrogen‐bonding contributes to the interaction energies dominantly. The O–H stretching motions in all the complexes are red‐shifted relative to that of the monomer.     

白藜芦醇清除自由基活性的密度泛函理论研究

采用密度泛函理论(DFT)方法,从静态与动态两大方面分析了白藜芦醇分子酚羟基在不同溶剂中清除自由基活性的能力大小.通过白藜芦醇的结构参数、前线轨道理论、3种抽氢反应机制等方面分析了分子活性位与其性质的关系.探讨了白藜芦醇分子不同位置酚羟基清除·OH和·OOH的抗氧化机理,得到了该分子与·OOH发生抽氢反应时的过渡态结构.计算结果表明,在任何溶剂中白藜芦醇分子C(4')位上酚羟基活性最高,发生抽氢反应时反应热最小,是高活性位点.