儿茶素-胞嘧啶分子间相互作用的密度泛函研究

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-胞嘧啶分子间相互作用机制,得到稳定的儿茶素-胞嘧啶复合物11个.计算结果表明氢键对于复合物的稳定性起着重要的作用,并且当复合物形成2个或更多的氢键时,氢键的类型及强度共同决定着复合物的稳定性.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11种复合物中氢键的性质和特征进行了分析.通过研究发现,所有的氢键复合物进行基组重叠误差(BSSE)校正后的相互作用能为-17.35～-43.27kJ/mol,相互作用能主要由氢键所贡献.振动分析显示,氢键的形成使相对应键的对称伸缩振动频率减小,说明这些复合物中形成的氢键都是正常的红移型氢键,与实验结果相一致.     

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.     

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...     

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.     

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     

肾上腺素与二甲亚砜氢键作用的理论研究

The hydrogen bond is one of the most important intermolecular interactions playing an important role in intermolecular recognition processes essential to most biological systems. Adrenaline is an important catecholamine neurotransmitter in the mammalian central nervous system. Dimethyl sulphoxide can carry with it drugs across membranes. The geometries of adrenaline and six stable 1 : 1 complexes formed between adrenaline and dimethyl sulphoxide were optimized by Berny method at PM3 level and thus were optimized by density functional theory（B3LYP method）at the 6-31G,6-31G*,and 6-31+G* level respectively to obtain accurate structures. Single-point energies of all optimized molecular geometries were calculated to discuss the energies and structural parameters between reactants and products. All the binding energies have been corrected by the zero point vibrational energies（ZPVE）at varied basis set levels from 6-31G to 6-31 + G*. The results indicated that stronger hydrogen-bonded complexes were formed by molecular interaction between adrenaline and dimethyl sulphoxide. The calculation results can be better used to explain some experimental phenomena.     

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 .     

十二烷基苯磺酸钠和无机阳离子之间相互作用的密度泛函理论研究

研究阴离子表面活性剂和阳离子之间的相互作用对于理解阴离子表面活性剂的沉淀和溶解现象具有十分重要的理论和实际意义,但关于两者相互作用的相关理论模型鲜有报道。本文采用密度泛函理论(DFT)方法研究了十二烷基苯磺酸根阴离子(DBS^-)与阳离子(Na⁺, Mg²⁺和Ca²⁺)在溶液内及气/液界面处的相互作用。在溶液内,在两种不同溶液环境中(水相和正十二烷)构建DBS^-/阳离子相互作用模型,并对其进行优化。结果表明, DBS^-能够与阳离子以双齿结构稳定结合。DBS^-与阳离子的结合能不仅取决于参与的无机盐离子种类,还与溶剂的性质有关。在气/液界面处, DBS^-与六个水分子相互作用形成的水合物DBS^-·6H₂O最为稳定。但是,无机盐离子的引入会严重破坏DBS^-·6H₂O水合物的水化层结构。本文定义无量纲参量def用来对水化层结构的变化程度进行评价。无机盐离子对DBS^-·6H₂O水化层结构破坏程度的顺序为:Ca²⁺ > Mg²⁺ >Na⁺。电荷分析结果表明水化层在十二烷基苯磺酸钠(SDBS)头基与阳离子的相互作用中起了重要作用。     

杯[4]二吡咯与卤素阴离子相互作用的密度泛函理论研究

采用密度泛函B3LYP方法, 在6\|31G*/LANL2DZ水平上对杯[4]二吡咯主体分子及其与卤素阴离子形成的复合物进行研究.  结果表明, 杯[4]二吡咯可与卤素阴离子相互作用形成具有较高对称性的复合物, 其8个吡咯NH基团上的H原子均可以和卤素阴离子形成氢键; 杯[4]二吡咯与卤素阴离子结合能力大小的顺序为F- >Cl- >Br- > I-.  振动光谱、 电荷分布以及前线轨道计算结果表明, 杯[4]二吡咯与卤素阴离子相互作用的本质为氢键, 经BSSE校正的结合能与电荷转移程度、 N-H键键长和N-H伸缩振动频率变化呈线性关系.      

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 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。     

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.     

Density functional theory studies on the dissociation energies of metallic salts: relationship between lattice and dissociation energies

The formation and physicochemical properties of polymer electrolytes strongly depend on the lattice energy of metal salts. An indirect but efficient way to estimate the lattice energy through the relationship between the heterolytic bond dissociation and lattice energies is proposed in this work. The heterolytic bond dissociation energies for alkali metal compounds were calculated theoretically using the Density Functional Theory (DFT) of B3LYP level with 6‐311+G(d,p) and 6‐311+G(2df,p) basis sets. For transition metal compounds, the same method was employed except for using the effective core potential (ECP) of LANL2DZ and SDD on transition metals for 6‐311+G(d,p) and 6‐311+G(2df,p) calculations, respectively. The dissociation energies calculated by 6‐311+G(2df,p) basis set combined with SDD basis set were better correlated with the experimental values with average error of ca. ±1.0% than those by 6‐311+G* combined with the LANL2DZ basis set. The relationship between dissociation and lattice energies was found to be fairly linear (r>0.98). Thus, this method can be used to estimate the lattice energy of an unknown ionic compound with reasonably high accuracy. We also found that the dissociation energies of transition metal salts were relatively larger than those of alkaline metal salts for comparable ionic radii. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 827–834, 2001     

Study of the formamide–methanol dimer with ab initio and density functional theory methods

For the first time, the structures and energies for the hydrogen bonding of a 1:1 complex formed between formamide and methanol molecules have been computed with various pure and hybrid density functional theory (DFT) and ab initio methods at varied basis set levels from 6‐31g to 6‐31+g(d,p). Five reasonable geometries on the potential energy surface of methanol and formamide system are considered and their relative stability is discussed. The infrared (IR) spectrum frequencies, IR intensities, and vibrational frequency shifts are reported. From the systematic studies, it is found that all the DFT methods selected here correctly compute the dimerization energies and geometries, with the B3P86 method predicting the hydrogen bond lengths relatively shorter and BPW91 yielding the interaction energies relatively lower. Finally, the solvent effects on the geometries of the formamide–methanol complexes have also been investigated using self‐consistent reaction field (SCRF) calculations with five different DFT methods at the 6‐31+g(d,p) basis set level. The results indicate that the polarity of the solvent has played an important role on the structures and relative stabilities of different isomers. Moreover, the basis set superposition error correction is critical to the interaction energies in the polar solvents. © 2003 Wiley Periodicals, Inc. Int J Quantum Chem, 2004