1,2,3-三氮杂苯-水簇复合物氢键结构与性质的理论研究

在B3LYP/6-31 G**水平上对1,2,3-三氮杂苯和水形成1∶1,1∶2和1∶3复合物的基态氢键结构进行几何优化和性质计算,结果表明复合物之间存在较强的氢键作用。氢键的形成使水分子中H-O键振动频率减小(红移)。NBO分析表明,最稳定的1∶1,1∶2和1∶3复合物发生分子间电荷转移总量分别为0.0222e,0.0261e和0.0273e。     

The infrared spectra of polycyclic aromatic hydrocarbons containing a five-membered ring: symmetry breaking and the B3LYP functional

The infrared spectra of six molecules, each of which contains a five-membered ring, and their cations are determined using density functional theory; both the B3LYP and BP86 functionals are used. The computed results are compared with the experimental spectra. For the neutral molecules, both methods are in good agreement with experiment. Even the Hartree–Fock (HF) approach is qualitatively correct for the neutral species. For the cations, the HF approach fails, as found for other organic ring systems. The B3LYP and BP86 approaches are in good mutual agreement for five of the six cation spectra, and are in good agreement with experiment for four of the five cations where the experimental spectra are available. It is only for the fluoranthene cation where the BP86 and B3LYP functionals yield different results; the BP86 approach yields the expected C _{2 v} symmetry, while the B3LYP approach breaks symmetry. The experimental spectra support the BP86 spectra over the B3LYP spectra, but the quality of the experimental spectra does not allow a critical evaluation of the accuracy of the BP86 approach for this difficult system. Received: 9 February 1999 / Accepted: 31 March 1999 / Published online: 14 July 1999     

Adsorption and dissociation of methanol on Au(1 1 1) surface: A first-principles periodic density functional study

The adsorption and dissociation of methanol on Au(111) surface were studied using the first-principles calculations based on density functional theory (DFT) with the generalized gradient approximation (GGA). Adsorption energies, geometric structures, Mulliken charges population, and vibrational frequencies of the various intermediates were computed from full-geometry optimization with a three-layer slab model. The most stable adsorption modes of the species, i.e. CH₃OH, CH₃O, and HCHO were considered in calculation. The possible decomposition pathways were investigated with transition state search methods. The results indicate that methoxyl radical is likely the decomposition intermediate.     

First-principles study of structural and vibrational properties of crystalline silver azide under high pressure

A detailed first-principles study of the structural and vibrational properties of crystalline silver azide under hydrostatic pressure of 0–500 GPa has been performed with density functional theory in the generalized gradient approximation. The crystal structure is relaxed to allow ionic configurations, cell shape, and volume to change without any symmetry constraints. It is found that the silver azide crystal remains orthorhombic structure with Ibam space group for pressures up to 7 GPa, where there is a transition to an I4/mcm tetragonal symmetry. The lattice parameter and electronic structure are investigated as functions of pressure. The calculated vibrational frequencies at ambient pressure are in agreement with available experimental data. We also discuss the pressure-induced frequency shifts for the internal and lattice modes of silver azide crystal upon compression.     

Experimental and quantum chemical study of pyrrole self-association through N-H?π hydrogen bonding

An FT-IR study of pyrrole self-association in CCl₄ solutions was carried out. According to the IR measurements, pyrrole forms self-associated dimeric species via N-H?π hydrogen bonding. This was also confirmed by quantum chemical calculations for pyrrole monomer and dimer at B3LYP/6-31++G(d,p) level of theory. A T-shaped minimum was located on B3LYP/6-31++G(d,p) PES of pyrrole dimer characterized with a hydrogen bond of an N-H?π type, with centers-of-mass separation of monomeric units of 4.520 Å, H?π distance of 2.475 Å, the interplanar angle between the two monomeric units being 72.9°. The anharmonic vibrational frequency shift upon dimer formation calculated on the basis of 1D DFT vibrational potentials is in excellent agreement with the experimental data (84 vs. 87 cm⁻¹). Harmonic vibrational analysis predicts somewhat smaller shift (68 cm⁻¹). On the basis of NIR spectroscopic data, anharmonicity constants for the 2ν(N-H) and 2ν(N-H?π) vibrational transitions were calculated. The orientational dynamics of monomeric and self-associated pyrrole species was studied within the framework of the transition dipole moment time correlation function formalism. The period of essentially free rotation in the condensed phase reduces from 0.05 ps for the monomeric pyrrole to 0.02 ps for the proton-donor molecule within the dimer.     

A theoretical study of the structure and vibrations of 2,4,6-trinitrotolune

Theoretical calculations of the structure, internal rotations and vibrations of 2,4,6-trinitrotolune, TNT, in the gas phase were performed at the B3LYP/6-31G* and B3LYP/6-311+G** levels of theory. Two genuine energy minimum structures were found. In both structures the 4-nitro group is planar to the phenyl ring, while the 2,6-nitro groups are slightly out of plane with the phenyl ring due to steric interaction with the methyl group. The two structures are related by internal rotations of the methyl and 2, or 6-nitro group. The lowest energy route for interconversion between them is a concerted motion of the methyl group and 2 or 6 nitro group in a ‘cog wheel’ type of mechanism. The geometry of the low energy structure A is closest to that observed in the crystal structures of TNT, where all three nitro groups are out of plane with the phenyl ring. FTIR and Raman spectra of solid TNT and ¹³C, ¹⁵N enriched TNT are presented and assigned with the help of the B3LYP/6-311+G** calculations on A. The lower level B3LYP/6-31G* calculation fails to predict the correct vibrational coupling between the nitro and phenyl groups. The B3LYP/6-311+G** calculation gives a good prediction of the nitro vibrations and the isotopic shifts observed for TNT isotopomers.     

Statistical theory for a hydrogen bonding fluid system of A a D d type (IV): Depletion potential between colloid particles

The depletion potential between two colloid particles immersed in a hydrogen bonding fluid has been investigated by density functional theory. The study is motivated by the wide applications of hydrogen bonding fluids in the field of colloid science, and the effects of relevant factors on the depletion potential and depletion force between colloid particles have been studied. These factors include the size ratio of the colloid particle to the fluid molecule, the bulk density of the fluid, the functionality (the number of proton acceptors a and proton donors d) and hydrogen bonding strength as well as the colloid-fluid interaction energy. By comparing the depletion potential calculated under various conditions, it is shown that the effects of these factors on the depletion potential are very significant, and in particular in regulating the depletion force and its range.     

The electrostatic potential at atomic sites as a reactivity index in the hydrogen bond formation

The paper reviews results from computational studies by molecular orbital and density functional theories on several series of hydrogen bonded complexes. These studies aim at quantifying the reactivity of molecules for the complexation process. Excellent linear relationships are found between the electrostatic potential values at the sites of the electron donor and electron accepting atoms and the energy of hydrogen bond formation (ΔE). The series studied are: (a) complexes of R–CHO and R–CN molecules with hydrogen fluoride; (b) complexes of mono-substituted acetylene derivatives with ammonia; (c) (HCN)_n hydrogen bonded cluster for n=2–7. All 22 studied complexes of carbonyl and nitrile compounds with hydrogen fluoride fall in the same dependence between the energy of hydrogen bond formation and the electrostatic potential at the atomic site of the carbonyl oxygen and nitrile nitrogen atoms, with linear regression correlation coefficient r=0.979. In the case of complexes of mono-substituted acetylene and diacetylene derivatives with NH₃, the correlation coefficient for the dependence between the electrostatic potential at the acidic hydrogen atom and ΔE equals 0.996. For the series of hydrogen bonded (HCN)_n clusters, the correlation coefficient for the relationship between the electrostatic potential at the end nitrogen atom and ΔE is r=0.9996. Similarly, the analogous relationship with the electrostatic potential at the end hydrogen atom has a regression coefficient equal to 0.9994. The dependencies found are theoretically substantiated by applying the Morokuma energy decomposition scheme. The results show that the molecular electrostatic potential at atomic sites can be successfully used to predict the ability of molecules to form hydrogen bonds.     

Competitive hydrogen bonding of cyclopropenium ions: Implications of an anion switch

This work demonstrates how modulating hydrogen bonding between intermolecular, bifurcated, and intramolecular interactions can be used to tune the structural, electronic, and photophysical properties of cyclopropenium ions and their respective fluorophores. The basis of this switchability was examined using X-ray diffraction analysis, ¹H NMR spectroscopy, DFT calculations, and fluorescence spectroscopy.     

First-principles study of hydrogen adsorption on Mo(1 1 0)

First-principles calculations based on density functional theory-generalized gradient approximation method have been performed for hydrogen (H) adsorption on Mo(1 1 0) surface. For various coverages, the hollow (hol) site was found to be the most stable binding site. The adsorption energy of this site was slightly increased as the increasing of hydrogen coverage. Subsurface (sub) occupation at low and medium coverages was ruled out while it became to be stable at the coverage of 1 ML. This is also supported by the potential energy surface (PES) study for hydrogen diffusing from hol to sub site. It’s interesting to find a surface reconstruction at the coverage of 1 ML, which is characterized by the lateral shift of the topmost layer for the sub adsorption. At higher coverage, the local density of states (LDOS) analysis showed that a new peak was clearly visible which was ascribed to a surface state induced by hydrogen adsorption. This surface state was mostly localized on the hydrogen atom and the first Mo layer, implying the hybridization of the hydrogen 1s states and the Mo metal states.     

Computational modeling of green hydrogen generation from photocatalytic H2S splitting: Overview and perspectives

Hydrogen plays an important role in developing a clean and sustainable future energy scenario. Substantial efforts to produce green hydrogen from water splitting, biomass and hydrogen sulfide (H₂S) have been made in recent years. H₂S, naturally occurring or generated in fuel gas processing and industrial wastewater treatment, can be split into hydrogen and sulfur via photocatalysis. Although it is not as widely used as water splitting for green hydrogen production, this process is considered to be an appropriate and sustainable way to meet the future energy demands, adding value to H₂S. Therefore, it is essential to understand how to improve the solar light utilization and splitting efficiency of H₂S based on the existing technology and materials. Along with that effort, molecular modeling and theoretical calculations are indispensable tools to provide guidance to effectively design photocatalysts for improving hydrogen generation efficiency. In this review, we summarize the published work on H₂S photocatalysis modeling and illustrate the use of different computational methods to gain more in-depth insight into the reaction mechanisms and processes. Moreover, an overview of quantum mechanical and molecular simulation approaches combined with other modeling techniques, relevant to material science and catalysis design and applicable to H₂S splitting is also presented. Challenges and future directions for developing H₂S splitting photocatalysts are highlighted in this contribution, which is intended to inspire further simulation developments and experiments for H₂S splitting, tailoring photocatalysts design towards highly efficient hydrogen production.     

Computational study of the process of hydrogen bond breaking: the case of the formamide-formic acid complex

MP2/6-311++G(d,p) and B3LYP/6-311++G(d,p) quantum calculations are used to study the formamide-formic acid complex (FFAC), a system bound by two hydrogen bonds, N--H...O and O--H...O, that forms a bond ring at equilibrium. When the intermolecular separation between monomers R increases, this ring opens at a distance for which the weaker N--H...O bond breaks remaining the stronger O--H...O bond. The computational study characterizes that process addressing changes of interaction energy DeltaE, structure and properties of the electron density rho(r) as well as spatial distributions of rho(r), the electrostatic potential U(r), and the electron localization function eta(r). It is shown that the spatial derivatives of DeltaE, the topology of rho(r), and qualitative changes noticed in U(r) = 0 isocontours allow to identify a precise distance R for which one can say the N--H...O hydrogen bond has broken. Both levels of theory predict essentially the same changes of structure and electron properties associated to the process of breaking and virtually identical distances at which it takes place.     

Sensing and catalytic decomposition of hydrogen peroxide by silicon carbide nanotubes: A DFT study

In this study, by carrying out detailed density functional theory calculations, we investigate the adsorption and stepwise decomposition of hydrogen peroxide (H₂O₂) over (6,0) and (7,0) zigzag silicon carbide nanotubes (SiCNTs). The results indicate that the H₂O₂ can be adsorbed on the exterior surface of the SiCNTs with noticeable adsorption energies and charge transfers. To gain insight into the catalytic activity of the surface, the interaction between the H₂O₂ and SiCNT is analyzed by detailed electronic analysis such as adsorption energy, charge density difference and activation barrier. The decomposition of H₂O₂ into O₂ and H₂ species can be viewed as the kinetically preferred reaction pathway for dehydrogenation of hydrogen peroxide over SiCNTs. There is also a curvature effect on the dehydrogenation kinetics of hydrogen peroxide, that small diameter SiCNTs with large curvature would be beneficial for decomposition of H₂O₂. © 2015 Wiley Periodicals, Inc.     

Analysis of vibrational spectra of 2 and 3-methylpiperidine based on density functional theory calculations

The experimental and theoretical vibrational spectra of 2 and 3-methylpiperidine (abbreviated as 2-MP and 3-MP) were studied. The FT-Infrared spectra of 2-MP and 3-MP molecules were recorded in the liquid phase. The structural and spectroscopic analysis of the title molecules were made by using density functional harmonic calculations. For the title molecules, only one form was found most stable structure by using B3LYP level with the 6-311G (d,p) basis set. Selected experimental bands were assigned and characterized based on the scaled theoretical wave numbers by their total energy distribution (TED).     

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     

一种天然产物Wangzaozin A的细胞毒活性

从总序香茶菜Isodon racemosa (Hemsl) Hara植物中分离得到一个对人类肿瘤细胞Bel-7402和HD-8910具有毒活性的对映-贝壳衫烷型二萜Wangzaozin A化合物(1). 应用密度泛函理论(DFT)B3LYP方法, 对该分子的几何构型进行优化, 结果表明用B3LYP/6-31G(d)优化的几何参数与它的X射线衍射结构参数基本一致. 在优化的几何构型基础上, 采用规范不变原子轨道(GIAO)法, 在B3LYP理论水平分别用6-31G(d), 6-31G(d,p), 6-31+G(d,p)和6-31++G(d,p)基组进行核磁共振(NMR)化学位移值计算, 预测的1H和13CNMR化学位移值与实验值吻合; 统计误差分析表明, 用B3LYP/6-31G(d)优化的分子构型接近实际的分子构型. 因此, DFT方法适用这一类型化合物的构型和NMR参数进行预测. 在几何优化的基础上, 在B3LYP/6-31G(d)水平上, 对Wangzaozin A分子的静电位(MEP)进行理论计算. MEP三维图表明, 在Wangzaozin A分子中α-亚甲基环戊酮的羰基和羟基附近出现富电子区域(负电位), 起着供电子作用, 与受体的正电子区域结合. 这些结果从理论上支持了α-亚甲基环戊酮结构是一种抗肿瘤活性中心的看法.     

Catalytic hydrogenolysis of alkyl halides by sulfido-bridged molybdenum clusters: A density functional study

Density functional theory has been used to explore the mechanism of cleavage of H₂ at a sulfido-bridged molybdenum cluster, CpMo(μ-SH)(μ-S)(μ-S₂CH₂)MoCp. The addition occurs across a single Mo-S bond, and the disruption of the strong Mo-S π bonding in the ground state leads to a very high-lying transition state (+43 kcal mol⁻¹). Once formed, the adsorbed hydrogen migrates over the cluster via a series of hops from metal to sulphur, formally corresponding to a switch from hydridic to protic character. The low barrier (+15 kcal mol⁻¹) for migration leads to facile hydrogenolysis of coordinated substrates.     

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.