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...     

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.     

On the Correlation between the Blue Shift of Hydrogen Bonding and the Proton Donor-Proton Acceptor Distance

It is demonstrated that in all types of hydrogen bonds (X—H…Y) there is a balance between the long-range attractive orbital interactions and short-range Pauli/nucleus repulsions. When the proton acceptor approaches the proton donor from distance, the hydrogen bonding energy becomes more negative at relatively large distance, goes through a minimum, and then starts to become less negative when the short-range repulsive forces come into effect.Meanwhile, the X--H bond length increases at relatively large distances, goes through a maximum and starts to shorten when the short-range repulsive forces come into effect. Whether the hydrogen bond is red or blue shifted is dictated by the energy minimum position. If at the energy minimum position the X—H bond length is shorter than that for the free monomer, the hydrogen bond is blue shifted and vice versa. Further studies demonstrate that the recent report about the correlation of C—H bond lengths with proton donor-acceptor distance in F3C—H…OH2 and F3C—H…Cl^- is not fully correct because the authors conducted an inappropriate comparison. Furthermore, it is shown for the first time that the Pauli/nucleus repulsion theory is applicable to the blue-shifted hydrogen bonds in the X—H…π complexes and the blue-shifted lithium bonds in the X—Li…Y complexes.     

A DFT Study on Intramolecular Hydrogen Bond in Substituted Catechols and Their Radicals

Density functional theory(DFT)at B3LYP/6-31G(d,p) level was employed to calculate intramolecular hydrogen bond enthalpies (H1HB),O-H charge differencces,O-H bond lengths and bond orders for various substituted catechols and their radicals generated after H-abstraction.It was found that although the charge difference between hydrogen-bonded H and O played a role in determining H1HB,H1HB was mainly governed by the hydrogen bond length.As the oxygen-centedred radiocal has great tendency to form a chemical bond with the H atom,hydrogen bond lengths in catechloic radicals are systematically shorter than those in catechlos,hence,the H1HB for the former are higher than those for the latter.     

A Supramolecular Polymer of Nitroxide Radicals via Hydrogen Bonding

Summary: 2,2,6,6-Tetramethylpiperidinyl-N-oxy (TEMPO) is a robust nitroxide radical molecule under ambient conditions. We found that the TEMPO derivatives act as a proton acceptor to form an intermolecular hydrogen-bonding complex with many kinds of phenol or urea derivatives. ORTEP analysis of the crystals of TEMPO with the phenol derivatives indicated that hydrogen bonding could be formed between the oxygen of the nitroxide and the phenolic proton and the N O bond of the hydrogen-bonded TEMPO was lengthened in comparison to that of the free N O bond. The formation constant of the hydrogen-bonding complex of TEMPO with the phenol or urea derivatives in a chloroform solution was spectroscopically determined by IR to be 10–100 M⁻¹. Hydrogen bonding of the thelechelic bis-TEMPO derivatives with thelechelic bis-phenol or bis-urea derivatives provided a supramolecular structure. The estimated molecular weights of the supramolecules in the chloroform solution, based on DOSY-NMR spectroscopy, were 3000–4000. The potential of the nitroxide radical's supramolecule as a new functional material is also described.     

Halogen Bonding versus Hydrogen Bonding: A Molecular Orbital Perspective

We have carried out extensive computational analyses of the structure and bonding mechanism in trihalides DX⋅⋅⋅A⁻ and the analogous hydrogen-bonded complexes DH⋅⋅⋅A⁻ (D, X, A=F, Cl, Br, I) using relativistic density functional theory (DFT) at zeroth-order regular approximation ZORA-BP86/TZ2P. One purpose was to obtain a set of consistent data from which reliable trends in structure and stability can be inferred over a large range of systems. The main objective was to achieve a detailed understanding of the nature of halogen bonds, how they resemble, and also how they differ from, the better understood hydrogen bonds. Thus, we present an accurate physical model of the halogen bond based on quantitative Kohn–Sham molecular orbital (MO) theory, energy decomposition analyses (EDA) and Voronoi deformation density (VDD) analyses of the charge distribution. It appears that the halogen bond in DX⋅⋅⋅A⁻ arises not only from classical electrostatic attraction but also receives substantial stabilization from HOMO–LUMO interactions between the lone pair of A⁻ and the σ* orbital of D–X.     

Quantum Study on the Hydrogen Bonding Interaction of Luteolin-（CH_3OH）_n

The optimized geometries and vibration frequencies of luteolin,methanol and luteolin-(CH3OH)n complexes have been investigated by density functional theory using B3LYP method.Four stable luteolin-CH3OH complexes,six stable luteolin-(CH3OH)2 complexes and four stable luteolin-(CH3OH)3 complexes have been obtained.The theories of atoms in molecules(AIM) and natural bond orbital(NBO) have been used to analyze the hydrogen bonds of these compounds,and their interaction energies corrected by basis set superposition error are between-8.046 and-76.124 kJ/mol.The calculation results indicate strong hydrogen bonding interactions in the luteolin-(CH3OH)n complexes.Then the nuclear magnetic resonance(NMR) and electronic absorption spectrum of luteolin have been calculated,and the results are in agreement with the experimental data.     

Phenylacetylene: A Hydrogen Bonding Chameleon

Molecules with multiple hydrogen bonding sites offer the opportunity to investigate competitive hydrogen bonding. Such an investigation can become quite interesting, particularly when the molecule of interest has neither lone‐pair electrons nor strongly acidic/basic groups. Phenylacetylene is one such molecule with three hydrogen bonding sites that cannot be ranked into any known hierarchical pattern. Herein we review the structures of several binary complexes of phenylacetylene investigated using infrared optical double‐resonance spectroscopy in combination with high‐level ab initio methods. The diversity of intermolecular structures formed by phenylacetylene with various reagents is remarkable. The nature of intermolecular interaction with various reagents is the result of a subtle balance between various configurations and competition between the electrostatic and dispersion energy terms, while trying to maximize the total interaction strength.     

Kinetic Modeling of Hydrogen Abstractions Involving Sulfur Radicals

One of the requisites for the development of detailed reaction networks is the availability of accurate kinetic data. Group additivity based models linking the Arrhenius parameters to structural characteristics of the transition state have proven to be a valuable tool to obtain those data. In this work, group additivity values are presented to allow a broad range of C H and S H hydrogen abstraction reactions by S radicals to be modeled. Rate coefficients in the temperature range from 300 to 1500 K are obtained by using the CBS-QB3 method in the high-pressure limit and are corrected for tunneling and anharmonicity of rotation about the transitional bond. A total of 149 reactions are studied. From these reactions, a total of 52 group additivity values and 35 resonance corrections are derived. The general applicability of the group additivity method is demonstrated for a test set containing 25 reactions. At 300 K, rate coefficients are on average reproduced within a factor of 2.8. The mean absolute deviations on the Arrhenius parameters are 2 kJ mol⁻¹ for the activation energy and 0.38 for log A in which A is the pre-exponential factor.     

A Comparative Study of Hydrogen Bonding Using Density Functional Theory

The hydrogen‐bond energies of water dimer and water‐formaldehyde complexes have been studied using density functional theory (DFT). Basis sets up to aug‐cc‐pVXZ (X=D, T, Q) were used. It was found that counterpoise corrected binding energies using the aug‐cc‐pVDZ basis set are very close to those predicted with the aug‐cc‐pVQZ set. Comparative studies using various DFT functionals on these two systems show that results from B3LYP, mPW1PW91 and PW91PW91 functionals are in better agreements with those predicted using high‐level ab initio methods. These functionals were applied to the study of hydrogen bonding between guanine (G) and cytosine (C), and between adenine (A) and thy mine (T) base pairs. With the aug‐cc‐pVDZ basis set, the predicted binding energies of base pairs are in good agreement with the most elaborate ab initio results.     

Hydrogen Bonding versus Halogen Bonding: Spectroscopic Investigation of Gas-Phase Complexes Involving Bromide and Chloromethanes

Hydrogen bonding and halogen bonding are important non-covalent interactions that are known to occur in large molecular systems, such as in proteins and crystal structures. Although these interactions are important on a large scale, studying hydrogen and halogen bonding in small, gas-phase chemical species allows for the binding strengths to be determined and compared at a fundamental level. In this study, anion photoelectron spectra are presented for the gas-phase complexes involving bromide and the four chloromethanes, CH₃Cl, CH₂Cl₂, CHCl₃, and CCl₄. The stabilisation energy and electron binding energy associated with each complex are determined experimentally, and the spectra are rationalised by high-level CCSD(T) calculations to determine the non-covalent interactions binding the complexes. These calculations involve nucleophilic bromide and electrophilic bromine interactions with chloromethanes, where the binding motifs, dissociation energies and vertical detachment energies are compared in terms of hydrogen bonding and halogen bonding.     

Tetrel Bonding Interactions

Tetrel (Tr) bonding is first placed into perspective as a σ‐hole bonding interaction with atoms of the Tr family. An sp³ R₄Tr unit has four σ‐holes with which a Lewis base can form a complex. We then highlight some inspiring crystal structures where Tr bonding is obvious, followed by an account of our own work. We have shown that Tr bonding is ubiquitous in the solid state and we have highlighted that Tr bonding with carbon is possible when C is placed in the appropriate chemical context. We hope that this account serves as an initial guide and source of inspiration for others wishing to exploit this vastly underexplored interaction.     

The hydroperoxy radical as a hydrogen bond acceptor. HOO-HCl complexes--Ab initio study

Protonacceptor properties of the HOO radical were investigated previously by means of ab initio as well as topological Atoms in Molecules (AIM) and Electron Localization Function (ELF) methods. It was pointed out that in the radical there are three nonequivalent positions most susceptible to protonation, and on this basis three structures of possible hydrogen bonded complexes were proposed. Results reported in the present article concern all possible 1:1 complexes formed by HCl and HOO molecules, and fully confirm suppositions given on the basis of the above-mentioned investigations. There are three various complexes referring to the local minima, and the transition structure predicted by topological methods has been found as well. The cyclic structure appeared to be the most stable one, which confirms conclusions given in the experimental article. Apart from structure optimization, harmonic as well as anharmonic spectra of the complexes have been simulated. Anharmonicity of H-Cl stretching vibration was of special interest, as the frequency of this vibration characterizes the Cl-H...O hydrogen bond in these complexes. To obtain values of these frequencies the one-dimensional Hamiltonian has been diagonalized numerically. The potential for this Hamiltonian has been taken from a set of single-point scanning of the part of the Potential Energy Surface (PES) connected with this vibration. The potential calculated on the MP2 level leads to the result close to the experimental value, whereas the B3LYP method is inappropriate for the purpose of PES investigation of these complexes.     

1,2,4-三氮杂苯-(H2O)n复合物氢键相互作用的密度泛函理论研究

用密度泛函理论方法在B3LYP/6-31++G**水平上对1,2,4-三氮杂苯-(H₂O)_n (n＝1, 2, 3)氢键复合物的基态进行了结构优化和能量计算, 结果表明复合物之间存在较强的氢键作用, 所有稳定复合物结构中形成一个N…H—O氢键并终止于弱O…H—C氢键的氢键水链的构型最稳定. 同时, 用含时密度泛函理论方法(TD-DFT)在TD-B3LYP/6-31++G**水平上计算了1,2,4-三氮杂苯单体及其氢键复合物的单重态第一¹(n, π^*)垂直激发能.     

On the Mechanism of Hydrogen Activation by Frustrated Lewis Pairs

We report herein a comprehensive theoretical study of the thermodynamics and kinetics of molecular hydrogen activation by frustrated Lewis pairs (FLPs). A series of intermolecularly combined boranes (Lewis acids) and phosphines (Lewis bases), with experimentally established different reactivities towards H₂, have been subjected to DFT and (SCS‐)MP2 calculations, and analyzed in terms of their structural properties, the energetics of association of the FLPs, and the kinetics of their interactions with H₂ and hydrogenation to the ion‐pair products. The analysis included the following steps: 1) assessment of the ability/inability of the Lewis species to preorganize into FLPs with an optimum arrangement of the acid and base sites for preconditioning the reaction with H₂, 2) comprehension of the different thermodynamics of hydrogenation of the selected FLPs by comparing the Gibbs energies of the overall reactions, and 3) estimation of the mechanism of the activation of H₂ by identifying the reaction steps and the associated kinetic barriers. The results of our studies correlate well with experimental findings and have clarified the reasons for the observed different reactivities of the investigated systems, ranging from reversible or nonreversible activation to no reaction with H₂. The derived predictions could assist the future design of Lewis acid–base systems with desired properties and applicability as metal‐free hydrogenation catalysts.     

Model studies of the optical rotation,and theoretical determination of its sign for β‐pinene and trans‐pinane

We have carried out extensive studies on the basis set dependence of the calculated specific optical rotation (OR) in molecules at the level of the time–dependent Hartree–Fock and density functional approximations. To reach the limits of the basis set saturation, we have devised an artificial model, the asymmetrically deformed (chiral) methane (CM) molecule. This small system permits to use basis sets which are prohibitively large for real chiral molecules and yet shows all the important features of the basis set dependence of the OR values. The convergence of the OR has been studied with n‐aug‐cc‐pVXZ basis sets of Dunning up to the 6–ζ. In a parallel series of calculations, we have used the recently developed large polarized (LPolX) basis sets. The relatively small LPolX sets have been shown to be competitive to very large n‐aug‐cc‐pVXZ basis sets. The conclusions reached in calculations of OR in CM concerning the usefulness of LPolX basis sets have been further tested on (S)‐methyloxirane and (S)‐fluoro‐oxirane. The smallest set of the LPolX family (LPol–ds) has been found to yield OR values of similar quality as those obtained with much larger Dunning's aug‐cc‐pVQZ basis set. These results have encouraged us to carry out the OR calculations with LPol–ds basis sets for systems as large as β‐pinene and trans‐pinane. In both cases, our calculations have lead to the correct sign of the OR value in these molecules. This makes the relatively small LPol–ds basis sets likely to be useful in OR calculations for large molecules. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

Theoretical Study on the Structures and Properties of Hydrogen Bonding Complexes between Diazines and Water

Density functional theory B3LYP method and second-order Moller-Plesset perturbation theory MP2 method were employed to obtain the optimized geometries of the ground state and interaction energy for diazines and water complexes. The results show that the ground state complexes have strong hydrogen bonding interaction with -20.99, -16.73 and -15.31 kJ/mol after basis set superposition error and zero-point vibration energy correction for pyridazine-water, pyrimidine-water and pyrazine-water, respectively, and large red-shift for the symmetric H-O stretching vibration frequencies due to the formation of N…H-O hydrogen bond in the diazine-water complexes. The NBO analysis indicates that intermolecular charge transfer are 0.0316, 0.0255 and 0.0265 e respectively. In addition, the first singlet （n,n＊） vertical excitation energy of the monomer and the hydrogen bonding complexes between diazines and water was investigated by time-dependent density functional theory.     

CH_3SH和CH_3SLi分子间的锂键和氢键共存型相互作用

在CH3SLi+CH3SH势能面上求得锂键和氢键共存型复合物的两种稳定构型.频率分析表明,与单体相比复合物中S(5)—Li(6)键伸缩振动频率发生红移,而C(8)—H(10)键伸缩振动频率发生蓝移.经B3LYP/6-311++G**,MP2/6-311++G**及MP2/AUG-CC-PVDZ水平计算的含基组重叠误差(BSSE)校正的复合物Ⅰ中相互作用能分别为-58.99,-57.87和-62.89kJ·mol-1.采用自然键轨道(NBO)理论,分析了复合物中单体轨道间的电荷转移,电子密度重排及其与相关键键长变化的本质等.采用分子中的原子(AIM)理论分析了复合物中氢键和锂键的电子密度拓扑性质.在极化连续模型(PCM)下,考察了溶剂化效应.结果表明,所考察的水、二甲亚砜、乙醇和乙醚等四种溶剂均使单体间的相互作用能增大,且溶剂对复合物中的锂键结构及其振动频率具有显著的影响,而对复合物中的氢键的振动频率影响不大.