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.     

准确快速计算含多肽酰胺和核酸碱基的氢键复合物的氢键强度和氢键作用势能曲线

N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用是蛋白质a-螺旋结构、b-折叠结构和DNA双螺旋结构形成的主要因素,在生物分子识别、蛋白质复制以及遗传信息传递等过程中起重要作用。准确快速计算生物体系中存在的N-H···O=C、C-H···O=C、N-H···N和C-H···N等氢键作用强度以及氢键强度随分子几何结构(距离和角度)变化的势能曲线对正确模拟(从而正确认识和理解)蛋白质折叠机制和DNA双螺旋结构形成机制等生物过程意义重大,对设计合成具有特殊功能的生物分子材料有重要指导价值。本文主要介绍了近年来建立的偶极-偶极氢键作用模型及其在快速预测多肽-多肽分子间和核酸碱基-多肽分子间氢键作用强度和氢键作用势能曲线方面的应用。     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要. 在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型, B3LYP方法得到了三种构型(复合物I, II和III), 而MP2方法只能得到一种构型(复合物II). 在复合物I和III中, HSO单元中的1H原子作为质子供体, 与O3分子中的端基O原子作为质子受体相互作用, 形成红移氢键复合物; 而在复合物II中, 虽与复合物I和III中具有相同的质子供体和质子受体, 却形成了蓝移氢键复合物. B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重叠误差(BSSE)和零点振动能(ZPVE)校正, 其值在-3.37到-4.55 kJ·mol-1之间. 采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查, 并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

气相中O3与HSO自由基间的氢键复合物

气相中O3与HSO自由基之间的相互作用及其反应在大气化学中非常重要.在DFT-B3LYP/6-311++G**和MP2/6-311++G**水平上求得O3+HSO复合物势能面上的稳定构型,B3LYP方法得到了三种构型(复合物Ⅰ,Ⅱ和Ⅲ),而MP2方法只能得到一种构犁(复合物Ⅱ).在复合物Ⅰ和Ⅲ中,HSO单元中的1H原子作为质子供体.与O3分子中的端基O原子作为质子受体相互作用,形成红移氢键复合物;而在复合物Ⅱ中,虽与复合物Ⅰ和Ⅲ中具有相间的质子供体和质子受体,却形成了蓝移氢键复合物.B3LYP/6-311++G**水平上计算的单体间相互作用能的计算考虑了基组重甍误差(BSSE)和零点振动能(ZPVE)校正,其值在-3.37到-4.55 kJ·mol-1之间.采用自然键轨道理论(NBO)对单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了三种复合物中氢键的电子密度拓扑性质.     

N2O…HOCl复合物结构和性质的理论研究

分别在DFT-B3LYP和MP2/6-311++G**水平上求得HOCl + N2O复合物势能面上的六种(S1, S2, S3, S4, S5和S6)和四种(S1, S2, S4和S5)构型. 频率分析表明,其中的S1和S3为过渡态,其它为稳定构型. 在复合物S3, S5 和S6中,HOCl 单体的σ*(5O-6H)作为质子供体,与N2O单体中作为质子受体的3O原子相互作用,形成氢键结构,而在氢键复合物S2中, 质子受体为N2O单体中的端1N原子;复合物S1中,HOCl分子的σ*(5O-4Cl)作为质子供体与N2O分子中的端1N原子(质子受体)相互作用,形成卤键结构,而复合物S4中的卤键结构的质子受体为N2O分子中的端3O原子. 经B3LYP/6-311++G**水平上的计算,考虑了基组重叠误差(BSSE)校正的单体间相互作用能在-1.56 ~ -8.73 kJ·mol-1之间. 采用自然键轨道理论(NBO)对两种单体间相互作用的本质进行了考查,并通过分子中原子理论(AIM)分析了复合物中氢键和卤键键鞍点处的电子密度拓扑性质.     

氢键的协同作用驱动水中苯甲醛的合成

以环氧氯丙烷作为交联溶剂合成和表征了纤维素功能化的β-环糊精,考察了这种超分子聚合物作为一种多相催化剂用于苯甲醛的合成的催化性能. 结果表明,该催化剂在温和的反应条件下具有较高的催化活性和选择性,容易恢复和重新利用,且活性没有大的损失. 进一步研究指出,β-环糊精聚合物中的b-环糊精能通过非极性共价键与肉桂醛形成主客包结物,此外,β-环糊精和纤维素的功能基团能与肉桂醛通过O-H…O的氢键形成多重氢键的相互作用,这种氢键的协同作用明显提高了催化剂的性能.     

取代基对N-H…O=C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N—H…O=C氢键强度, 探讨了氢键受体分子中不同取代基对N—H…O=C氢键强度的影响. 研究表明, 不同取代基对氢键三聚体中N—H…O=C氢键强度的影响是不同的: 取代基为供电子基团, 氢键键长r(H…O)缩短, 氢键强度增强; 取代基为吸电子基团, 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, N—H…O=C氢键强度越强, 氢键中氢原子的正电荷越多, 氧原子的负电荷越多, 质子供体和受体分子间的电荷转移越多. 供电子基团使N—H…O=C氢键中氧原子的孤对电子n(O)对N—H的反键轨道滓*(N—H)的二阶相互作用稳定化能增加, 吸电子基团使这种二阶相互作用稳定化能减小. 取代基对与其相近的N—H…O=C氢键影响更大.     

DFT和热力学研究氢键协同效应及对关联1H NMR的影响

用DFT方法在B3LYP/6-311＋＋G (d,p)水平下研究了甲醇线性和环状分子簇. 对于不同大小的分子簇之间定义了协同因子. 计算得到的协同因子可以验证氢键的强协同效应, 环状分子簇之间的协同效应远远大于线性分子簇. 做为理论验证和比较, 热力学模型分别采用含氢键缔合的格子流体状态方程(LFHB), 以及含氢键协同效应的LFHB, 关联醇-惰性体系的¹H核磁共振化学位移. 考虑协同效应的关联结果优于原始的LFHB. 比较量子化学计算的和热力学模型中采用的协同因子, 认为甲醇和乙醇在溶液中更可能大部分以线性缔合形式存在.     

取代基对N—H…O＝C氢键三聚体中氢键强度的影响

使用MP2方法研究了氢键三聚体中N-H…O=C氢键强度,探讨了氢键受体分子中不同取代基对N-H…O=C氢键强度的影响.研究表明,不同取代基对氢键三聚体中N-H…O=C氢键强度的影响是不同的:取代基为供电子基团,氢键键长r(H…O)缩短,氢键强度增强;取代基为吸电子基团,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,N-H…O=C氢键强度越强,氢键中氢原子的正电荷越多,氧原子的负电荷越多,质子供体和受体分子间的电荷转移越多.供电子基团使N-H…O=C氢键中氧原子的孤对电子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加,吸电子基团使这种二阶相互作用稳定化能减小.取代基对与其相近的N-H…O=C氢键影响更大.     

乙炔与H2O分子之间的氢键结构与性质

采用B3LYP方法,在6-311++G水平上优化得到了H2O…C2H2氢键复合物的σ-n和H-π型两种稳定构型,并进行频率分析,讨论了相关自然键红外振动光谱的红移现象.采用NBO理论对σ-n和H-π氢键复合物形成过程中的电荷转移的类型进行了分析讨论.分子间的氢键相互作用能结果表明,σ-n型比H-π型氢键复合物更稳定.     

对羧基苯甲醛缩-2-噻吩甲酰腙合成、结构及量子化学计算

以2-噻吩甲酸乙酯、水合肼和对醛基苯甲酸为原料合成了对羧基苯甲醛缩-2-噻吩甲酰腙。通过元素分析、IR、UV和X射线单晶衍射对化合物结构进行了表征。晶体中化合物分子间由弱的N—H…O、O-H…O氢键作用形成三维网状结构。分子中噻吩环平面和苯环平面之间的夹角为14.9°。发光性质显示,化合物在396 nm处有强的紫外发射峰(激发波长为286 nm)。热分析表明,化合物在298℃下比较稳定。依据晶体结构数据使用Gaussian 03W程序对化合物进行了量子化学计算,分析了化合物分子轨道能量、原子净电荷布居和成键特征,分析了化合物分子反应活性、选择性和稳定性。计算的分子键长、键角与X射线衍射晶体结构数据基本符合,其差值证实晶体中分子间存在氢键,化合物中的羰基是主要的活性中心。     

A DFT-based study of the hydrogen-bonding interactions between epicatechin and methanol/water

Tea polyphenols are essential components that give tea its medicinal properties. Methanol and water are frequently used as solvents in the extraction of polyphenols. Hydrogen-bonding interactions are significant in the extraction reaction. Density functional theory (DFT) techniques were used to conduct a theoretical investigation on the hydrogen-bonding interactions between methanol or water and epicatechin, an abundant polyphenol found in tea. After first analyzing the epicatechin monomer's molecular geometry and charge characteristics, nine stable epicatechin (EC) H₂O/CH₂OH complex geometries were discovered. The presence of hydrogen bonding in these improved structures has been proven. The calculated hydrogen bond structures are very stable, among which the hydrogen bond bonded with a hydroxyl group has higher stability. The nine complex structures’ hydrogen bonds were thought to represent closed-shell-type interactions. The interaction energy with 30O-31H on the epicatechin benzene ring is the strongest in the hydrogen bond structure. While the other hydrogen bonds were weak in strength and mostly had an electrostatic nature, the hydrogen bonds between the oxygen atoms in H₂O or CH₂OH and the hydrogen atoms of the hydroxyl groups in epicatechin were of moderate strength and had a covalent character. Comparing the changes in the hydrogen bond structure vibration peak, the main change in concentration peak is the hydrogen bond vibration peak in the complex. Improved the study on the hydrogen bond properties of CH₂OH and H₂O of EC.     

N—O键解离焓的密度泛函理论研究

在高精度计算方法G3和G3B3的基础上,比较了密度泛函理论(DFT)十几种方法对N—O键解离焓(BDE)相对于实验值的计算精度,发现用B3P86方法计算15种化合物N—O键的BDE,均方根误差最小,仅为6.36kJ·mol-1,计算值与实验值的线性相关系数为0.991.在此基础上,用该方法分别计算了非芳香化合物及芳香化合物的N—O键BDE.通过自然键轨道分析,发现部分N—O键的BDE与N—O键的键长、原子电荷密度及键级之间存在定量关系.此外,在B3P86方法的基础上预测了几种典型的杂环芳香化合物N—O键BDE值.     

Identification of hydrogen bonds using quantum electrodynamics

A method for the identification of hydrogen bonds was investigated from the viewpoint of the stress tensor density proposed by Tachibana and following other works in this field. Hydrogen bonds are known to exhibit common features with ionic and covalent bonds. In quantum electrodynamics, the covalent bond has been demonstrated to display a spindle structure of the stress tensor density. Importantly, this spindle structure is also seen in the hydrogen bond, although the covalency is considerably weaker than in a typical covalent bond. Distinguishing it from the ionic bond is most imperative for the identification of the hydrogen bond. In the present study, the directionality of the hydrogen bond is investigated as the ionic bond is nearly isotropic, while the hydrogen bond exhibits the directionality. It was demonstrated that the hydrogen bond can be distinguished from the ionic bond using the angle dependence of the largest eigenvalue of the stress tensor density.     

A simple method for the characterization of OHO-hydrogen bonds by H-solid state NMR spectroscopy

A set of OHO hydrogen bonded systems with known neutron diffraction structure has been studied by fast ¹H-MAS echo spectroscopy. It is shown that the application of a simple rotor synchronized echo sequence combined with fast MAS allows a faithful determination of the chemical shift of the proton in the hydrogen bond. Employing the empirical valence bond order model, the experimental ¹H chemical shifts of the hydrogen bonded protons are correlated to the hydrogen bond geometries. The resulting correlation between the proton chemical shift and the deviation of the proton from the center of the hydrogen bond covers a broad range of substances. Deviations from the correlation curve, which are observed in certain systems with strong hydrogen bonds, are explained in terms of proton tautomerism or delocalization in low-barrier hydrogen bonds. These deviations are a highly diagnostic tool to select potential candidates for further experimental and theoretical studies. Thus, the combination of the ¹H-MAS echo sequence with the correlation curve yields a simple and versatile tool for the structural analysis of OHO hydrogen bonds.     

Cover Feature: An Exploration of the Hydrogen Bond Donor Ability of Ammonia (ChemPhysChem 20/2023)

Ammonia is an important molecule due to its wide use in the fertiliser industry. It is also used in aminolysis reactions. Theoretical studies of the reaction mechanism predict that in reactive complexes and transition states, ammonia acts as a hydrogen bond donor forming N−H⋅⋅⋅O hydrogen bond. Experimental reports of N−H⋅⋅⋅O hydrogen bond, where ammonia acts as a hydrogen bond donor are scarce. Herein, the hydrogen bond donor ability of ammonia is investigated with three chalcogen atoms i. e. O, S, and Se using matrix isolation infrared spectroscopy and electronic structure calculations. In addition, the chalcogen bond acceptor ability of ammonia has also been investigated. The hydrogen bond acceptor molecules used here are O(CH₃)₂, S(CH₃)₂, and Se(CH₃)₂. The formation of the 1 : 1 complex has been monitored in the N−H symmetric and anti-symmetric stretching modes of ammonia. The nature of the complex has been delineated using Atoms in Molecules analysis, Natural Bond Orbital analysis, and Energy Decomposition Analysis. This work presents the first comparison of the hydrogen bond donor ability of ammonia with O, S, and Se.     

The structure, properties, and nature of HArF-HOX (X = F, Cl, Br) complex: an ab initio study and an unusual short hydrogen bond

The structure and properties (geometric, energetic, electronic, spectroscopic, and thermodynamic properties) of HArF‐HOX (X = F, Cl, Br) complex have been investigated at the MP2/aug‐cc‐pVTZ level. Three types of complexes are formed through a hydrogen bond or a halogen bond. The HArF‐HOX complex is the most stable, followed by the FArH‐OHX complex, and the HArF‐XOH complex is the most unstable. The binding distance in FArH‐OHX complex is very short (1.1–1.7 Å) and is smaller than that in HArF‐HOX complex. However, the interaction strength in the former is weaker than that in the latter. Thus, an unusual short hydrogen bond is present in FArH‐OHX complex. The associated H‐Ar bond exhibits a red shift, whereas the distant one gives a blue shift. A similar result is also found for the O? H and O? X bonds. The isotropic chemical shift is negative for the associated hydrogen atom but is positive for the associated halogen atom. However, a reverse result is found for the anisotropic chemical shift. The analyses of natural bond orbital and atoms in molecules have been performed for these complexes to understand the nature and properties of hydrogen and halogen bonds. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011