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.     

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.     

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

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。     

儿茶素与脱氧腺苷相互作用的理论研究

本文采用密度泛函理论的M05方法,在6-311+G**基组水平上对建模的儿茶素-脱氧腺苷复合物进行几何结构的优化,得到了13个稳定的儿茶素-脱氧腺苷复合物.应用了自然键轨道(NBO)理论和分子中的原子理论(AIM)进行研究,氢键临界点电荷密度,拉普拉斯值,糖基扭转角!,假扭转角P等数据进行辅助研究,对这13种复合物中氢键的特征与性质进行了分析,还考虑了溶剂化效应对儿茶素与脱氧腺苷相互作用的影响.计算结果表明氢键对于复合物的稳定性起着非常重要的作用,而氢键的类型以及键级的大小共同影响着复合物的稳定性.所有的复合物进行基组重叠误差(BSSE)校正,相互作用能主要来自氢键贡献.通过计算结果分析比较,进而在理论上为儿茶素类药物的设计、修饰﹑合成和筛选提供有价值的信息.     

1,1,3,3-四甲基脲—溶剂氢键复合物的理论研究

采用密度泛函理论在B3LYP/6-311++G(d,p)水平上对水、苯胺、氯仿与1,1,3,3-四甲基脲分子形成的1:1气相氢键复合物进行计算研究.结果表明,三种物质与1,1,3,3-四甲基脲形成的复合物存在氢键,表现为羰基氧原子的孤对电子与H—X(X=O,N,C)反键轨道的相互作用.氢键的形成使C=O和H—X的伸缩振动频率红移.在标准压力和298.15 K下,氢键复合物的形成是一个放热的非自发过程.     

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.     

荧光法研究木犀草素与人血清白蛋白的相互作用

用荧光光谱、同步荧光光谱和紫外吸收光谱方法,研究了木犀草素与人血清白蛋白（HSA）的相互作用。研究表明木犀草素对HSA有较强的荧光猝灭作用,根据不同温度下木犀草素对HSA的荧光猝灭作用,利用Stern-Volmer方程处理实验数据,表明木犀草素对HSA的荧光猝灭作用属于静态猝灭。根据Fōrster非辐射能量转移理论计算了木犀草素与HSA间的结合常数和结合位点数,求得了木犀草素与HSA间的结合距离r。热力学数据表明二者主要靠疏水作用力结合。同时用同步荧光光谱探讨了木犀草素对HSA构象的影响。     

分子间相互作用对核酸碱基中17O屏蔽张量与四极耦合常数影响的理论计算研究

通过高精度量子化学理论计算的方法研究了分子间弱的非键相互作用对胸腺嘧啶、尿嘧啶、胞嘧啶和鸟嘌呤四种核酸碱基中~(17)O核的屏蔽张量(σO)和四极耦合常数(QCC)的影响.计算结果表明分子间强的氢键作用以及弱的范德华(vd W)相互作用都对~(17)O核的化学位移(δO)具有较大的影响.随着分子间氢键作用的逐渐增强,δO逐渐减小,当采用包含所有弱相互作用的周期性模型进行计算时,理论结果与实验值吻合.进一步的电荷分析显示,~(17)O核化学位移的减小主要是由于分子间氢键作用强度增加导致~(17)O原子的负电荷密度逐渐增加.此外,计算结果表明碱基中分子间氢键网络和弱的范德华作用对碱基~(17)O QCC也具有显著的影响.周期性模型下,碱基上氧原子的局域结构环境得到平衡,~(17)O QCC达到最小值,与实验结果最为接近.以核酸碱基为例,说明了分子间的氢键网络以及分子间弱的相互作用对于准确计算生物样品的核磁共振(NMR)参数非常重要,以小的团簇模型来计算生物体系的核磁参数将会产生较大的偏差.     

光谱法比较木犀草素及槲皮素与牛血清白蛋白相互作用

在模拟生理pH条件下,采用荧光光谱、紫外-可见吸收光谱、同步荧光光谱和圆二色谱法研究木犀草素及槲皮素与牛血清白蛋白（BSA）的相互作用的异同.结果确定木犀草素及槲皮素对BSA的荧光猝灭是以静态猝灭为主,同时伴随非辐射能量转移猝灭.木犀草素结合BSA的位点与荧光发射基团的距离比槲皮素的小.结合常数Ka表明二者与BSA的结合都属于强的非共价键结合,且结合位点数都约为1.二者均主要通过氢键和范德华力与BSA作用.二者都能影响BSA的酪氨酸残基附近环境的极性,且高浓度下能够引起BSA构象轻微地改变.结果表明黄酮C环上3位羟基的引入会降低其对BSA的亲和力.     

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.     

2,2,6,6-四甲基哌啶氮氧自由基与卤仿形成卤键或氢键的理论研究

利用理论计算化学研究了2,2,6,6-四甲基哌啶-N-氧自由基与卤仿形成卤键和氢键络合物的可能性. 从分子静电势、络合物分子的结构参数、络合物的作用能以及自然键轨道理论的角度着手研究. 结果表明,卤键与氢键络合物的键合能均遵循氯化物<溴化物<碘化物,氢键络合物作用强度大于相应的卤键络合物. 因此,卤仿与2,2,6,6-四甲基哌啶-N-氧自由基之间作用模式氢键为主. 需要注意的是,碘仿形成卤键的作用强度与氢键相当,因此在碘仿中,卤键与氢键两种模式应该竞争性的存在.     

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.     

A multinuclear magnetic resonance study of intramolecular hydrogen bonding in some Schiff and Schiff-Mannich bases in solution and in the solid state

Two Schiff bases; N, N′-bis(5-bromosalicylidene)-1,2-diaminoethane, BS, and 7-[(1-{5-bromo-2-hydroxyphenyl} methylidene)amino]-4-methylcoumarin, Sc, and two appropriate Schiff–Mannich bases, N, N′-bis{5-bromo-3-[(diethylamino)methyl]salicylidene}-1,2-diaminoethane, BSM, and 7-[(1-{5-bromo-3-[(diethylamino)methyl]-2-hydroxyphenyl} methylidene)amino]-4-methylcoumarin, SMc, capable of intramolecular hydrogen bonding have been investigated by multinuclear magnetic resonance methods in both solid and liquid phases. In all of the compounds under investigation tautomeric equilibrium involving an intramolecular hydrogen bond has been found. The Schiff–Mannich bases, which can form two different kinds of H bonds at room temperature, form relatively weak H bonds with the imino nitrogen atoms. At low temperatures the tautomeric proton exchange becomes slow on the NMR time scale and both hydrogen-bonded forms can be observed by ¹H, ¹³C, and ¹⁵N NMR methods. In the solid state the tautomeric process is frozen and only one H-bonded form is present. On the basis of 13C and ¹⁵N CPMAS NMR spectra this is identified as the form with hydrogen bonds involving the imino groups. This conclusion is in good agreement with previous results obtained by X-ray diffraction methods.

The investigated Schiff bases (BS and Sc) form relatively weak H bonds. The proton position in the hydrogen bridge, estimated from ¹⁵N and ¹³C chemical shifts, is very similar in both the solution and solid phases. In chloroform solution the observed tautomeric equilibria are almost insensitive to a temperature change within the range 223 to 303 K.     

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．     

On difference of properties between organic fluorine hydrogen bond C–H···F–C and conventional hydrogen bond

The existence of C–H···F–C hydrogen bonds in the complexes of trifluoromethane and cyclic molecule (oxirane, cyclobutanone, dioxane, and pyridine) has been experimentally proven by Caminati and co-workers. This study presents a theoretical investigation on these C–H···F–C hydrogen bonds at B97D/6-311++G^** and MP2/6-311++G^** levels, in terms of C–H vibrational frequency shifts, atoms in molecules characteristics, and the bonding feature of C–H···F–C hydrogen bonds. It is found that in three important aspects, there are significant differences in properties between C–H···F–C and conventional hydrogen bonds. The C–H···F–C hydrogen bonds show a blueshift in the C–H vibrational frequencies, instead of the X–H normal redshift in X–H···Y conventional hydrogen bonds. The natural bond orbital (NBO) analyses show that σ and p types of lone pair orbitals of the F atom to an antibonding σ^*_H–C orbital form a dual C–H···F–C hydrogen bond. Such a dual hydrogen bonding leads to the proton acceptor directionality of the C–H···F–C hydrogen bond softer. Our studies also show that the Laplacian of the electron density (▽²ρ_BCP) is not always a good criterion for hydrogen bonds. Therefore, we should not recommend the use of the Laplacian of the electron density as a criterion for C–H···F–C hydrogen bonds.     

Symmetric bifurcated halogen bonds: substituent and cooperative effects

ABSTRACT

The aim of this study is to investigate the geometries, interaction energies and bonding properties of the symmetrical bifurcated halogen bond interactions (BXBs) by means of ab initio calculations. For this purpose, the NCX (X = Cl, Br) molecule is paired with a series of N-formyl formamide (NFF) derivatives (NFF-Z, Z = H, CN, CCH, OH, CH₃ and Li), and the properties of the resulting complexes are studied by molecular electrostatic potential, quantum theory of atoms in molecules, noncovalent interaction index and natural bond orbital analyses. For a fixed NCX molecule, interaction energies increase in the order of Z = Li > CH₃ > H > OH > CCH > CN. We found a strong correlation between the interaction energies of NCX:NFF-Z complexes and molecular electrostatic potential minimum values associated with NFF-Z monomers. Moreover, cooperative effects between BXB and X???N halogen bond interactions are studied in the ternary NCX:NCX:NFF-Z systems. Our results indicate that the strength of BXB interactions in the ternary complexes is enhanced by the presence of X???N bonds. Besides, cooperativity effects tend to increase the covalency of BXBs in these systems.     

Effect of hydrogen bond formation on the NMR properties of microhydrated ortho-aminobenzoic acid

The in?uence of the hydrogen bond formation on the nuclear magnetic resonance parameters has been investigated in the case of microhydrated ortho-aminobenzoic acid (o-Abz) in the gas-phase. DFT-B3LYP/aug-cc-pVDZ predicted ¹H and ¹³C isotropic chemical shifts with respect to TMS of the isolated o-Abz are in reasonable agreement with available experimental data. The isotropic and anisotropic chemical shifts for all atoms of o-Abz within the o-Abz?···?(H₂O)_1-3 complexes have been calculated at the Hartree–Fock, and density functional (B3LYP) theoretical levels using the 6-31++G(2d,2p) and aug-cc-pVDZ basis sets and considering the counterpoise corrections for the basis set superposition errors. The chemical shift values of the carboxyl group atoms of microhydrated o-Abz relative to isolated o-abz do not show significant basis set dependence. Both the hydrogen and carbon atoms constituting the carboxyl group of o-Abz suffer downfield shift due to formation of hydrogen bond with water. The length of hydrogen bond formed between o-Abz and water is found to vary with the number of water molecules present around o-Abz. A direct correlation between the hydrogen bond length and isotropic chemical shift of the bridging hydrogen is observed for both C?=?O?···?H-O and O-H?···?O interactions.