HF分子与惰性气体二聚体的分子形貌的理论研究

采用Gaussian-03程序中的MP2/6-311++G(2d,2p)方法,优化了FH- Rg(Rg=He,Ne,Ar)二聚体的结构.使用MELD精密从头计算中的CISD方法,结合我们自编的程序,计算了这些二聚体的单电子作用势(PAEM),并绘出了它们的分子形貌图象.分子形貌所提供的形貌特征、前沿电子密度的特征等,可以直观地揭示He,Ne和Ar等原子与HF分子相互作用时2种相互作用的差别,即共价相互作用与非共价相互作用区分的直观形象的表征.从二聚体的内禀特征信息可以看出,F,H和Rg原子都发生了不同程度的变形,HF分子对惰性气体原子有一定影响,而惰性气体原子对HF分子的影响较小.     

Theoretical study on intermolecular interaction of epoxyethane dimer

Ab initio calculations at Hartree–Fock and fourth‐order Mø ller–Plesset (MP4) correlation correction levels with 6‐31G* basis set have been performed on the epoxyethane dimer. Dimer binding energies have been corrected for the basis set superposition error (BSSE) and the zero‐point energy. The greatest corrected dimer binding energy is −8.36 kJ/mol at the MP4/6‐31G*//HF/6‐31G* level. The natural bond orbital analysis has been performed to trace the origin of the weak interactions that stabilize dimer. © 2000 John Wiley & Sons, Inc. Int J Quant Chem 78: 94–98, 2000     

Contraction of supramolecular double-threaded dimer formed by alpha-cyclodextrin with a long alkyl chain

A double-threaded dimer bearing a long substituent part and a large stopper group has been prepared and showed a conformational change with increased solvent polarity. [structure: see text]     

Theoretical study on Pd dimer and trimer interaction with the hydrogen molecule

The H₂ interaction with the Pd dimer and trimer were studied using multiconfigurational self-consistent field (MC-SCF) calculations with the relativistic effective core potential (RECP); the correlation energy correction was included in the extended multireference configuration interaction (MRCI), variational and perturbative to second order. Here, we considered the Pd₂ first six states: ³Σ⁺_u, ¹Σ⁺_g, ³Π_g, ³Δ_xy, ¹Σ⁺_u, and ³Σ⁺_g. For them, the four geometrical approaches included were the side-on H₂ toward Pd₂, for the hydrogen molecule in and out the Pd dimer plane; the perpendicular end-on H₂ toward Pd₂; and the perpendicular end-on Pd₂ to H₂. The Pd₂ ground state is ³Σ⁺_u, which only captures H₂ in the C_2v end-on approach, softly relaxing the H(SINGLE BOND)H bond. The closed-shell ¹Σ⁺_g captures the H₂ molecule in all the approaches considered: The side-on approach of this state presents deep wells and relaxes the H(SINGLE BOND)H bond, and the end-on approach captures H₂ with a relatively longer H(SINGLE BOND)H distance and also a deep well. The ³Π_g state was the only one which did not capture H₂. For the triangular Pd₃ clusters, H₂ was approached in the C_2v symmetry in and out of the Pd₃ plane. In the triangular case, H₂ was absorbed in both spin states, with deep wells and relaxing the H(SINGLE BOND)H distance. The linear Pd₃ singlet and triplet states capture outside of the Pd₃ and break the H(SINGLE BOND)H bond. © 1997 John Wiley & Sons, Inc.     

Theoretical study of helical structure caused by chirality of cysteine dimer

In this work we report a theoretical study of the helix structure and chiral discrimination on the interactions between the chiral cysteine–cysteine. Two reasonable geometries on the potential energy hypersurface of the cysteine–cysteine system are considered with the global minimum. Accurate geometric structures, relative stabilities, harmonic vibrational frequencies, and infrared (IR) intensities were investigated. To take into account the water solvation effect, the Onsager model within the self‐consistent reaction field (SCRF) method and the polarized continuum (PCM) method were used to evaluate the interaction energy, ΔG_solv at the same level employed in the gas phase. The results indicate that the polarity of the solvent plays an important role in the structures and relative stabilities of different isomers. Computational results indicate that the global minimum should be conformer I regardless of whether in the gas phase or in aqueous solution, which differs from previous theoretical reports. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of chiral discrimination in the hydrogen bonding complexes of the hydrazine dimer

In this work, the discrimination of different chiral forms of the hydrazine dimer were investigated using Density Functional Theory (DFT) and second‐order Moller–Plesset Perturbation (MP2) theory at basis set levels from 6‐31g to 6‐31++g(d,p). Four chiral structures were studied. The optimized geometric parameters, interaction energies, and chirodiastatic energy for various isomers at different levels were estimated. Finally, the solvent effects on the geometries of the hydrazine dimers were also investigated using self‐consistent reaction‐field (SCRF) calculations at the B3LYP/6‐31++g(d,p) level. The results indicate that the polarity of the solvent has played an important role in the structures and relative stabilities of different isomers. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Theoretical study of hydrogen and deuterium bond in glutaric acid crystal dimer

In the spirit of the work of Blaise et al. [J Chem Phys, 2005, 122, 64306], we have extended their quantum theoretical approach by accounting for the intrinsic anharmonicity of the slow frequency mode, which is described by a Morse potential to reproduce the polarized infrared line shapes of glutaric acid dimer and its deuterium derivative at different temperatures. In this approach, the adiabatic approximation is performed for each separate H‐bond bridge of the dimer, and a strong nonadiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. Working within the strong anharmonic coupling theory, according to which the high‐frequency mode is anharmonically coupled to the H‐bond bridge, this approach incorporated the Davydov coupling between the excited states of the two moieties, the quantum direct and indirect dampings and the intrinsic anharmonicity of the H‐bond bridge. The spectral density was obtained within the linear response theory by Fourier transform of the damped autocorrelation functions. The numerical results show that the theoretical line shapes of the glutaric acid dimer are in fairly good agreement with the experimental ones. Using a minimum number of independent parameters, this theoretical approach fits correctly the experimental line shapes of the glutaric acid dimer. The effects of deuteration and temperature have been successfully reproduced by our calculations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical study of O--O single bond formation in the oxidation of water by the ruthenium blue dimer

The first key step in the oxidation of water to O(2) by the oxidized species [(bpy)(2)(O)Ru(V)ORu(V)(O)(bpy)(2)](4+) of the Ru blue dimer is studied using density functional theory (DFT) and an explicit solvent treatment. In the model reaction system [L(2)(O)Ru(V)ORu(V)(O)L(2)](4+)·(H(2)O)(4)·W(76), the surrounding water solvent molecules W are described classically while the inner core reaction system is described quantum mechanically using smaller model ligands (L). The reaction path found for the O--O single bond formation involves a proton relay chain: direct participation of two water molecules in two proton transfers to yield the product [L(2)(HOO)Ru(IV)ORu(IV)(OH)L(2)](4+)·(H(2)O)(3)·W(76). The calculated ～3 kcal/mol reaction free energy and ～15 kcal/mol activation free energy barrier at 298 K are consistent with experiment. Structural changes and charge flow along the intrinsic reaction coordinate, the solvent's role in the reaction barrier, and their significance for water oxidation catalysis are examined in detail.     

Hartree-Fock and density functional theory study of alpha-cyclodextrin conformers

Herein, we report the geometry optimization of four conformers of alpha-cyclodextrin (alpha-CD) by means of PM3, HF/STO-3G, HF/3-21G, HF/6-31G(d), B3LYP/6-31G(d), and X3LYP/6-31G(d) calculations. The analysis of several geometrical parameters indicates that all conformers possess bond lengths, angles, and dihedrals that agree fairly well with the crystalline structure of alpha-CD. However, only three of them (1-3) resemble the polar character of CDs and show intramolecular hydrogen-bonding patterns that agree with experimental NMR data. Among them, conformer 3 appears to be the most stable species both in the gas phase and in solution; therefore, it is expected to be the most suitable representative structure for alpha-CD conformation. The purpose of selecting such a species is to identify an appropriate structure to be employed as a starting point for reliable computational studies on complexation phenomena. Our results indicate that the choice of a particular alpha-CD conformer should affect the results of ab initio computational studies on the inclusion complexation with this cyclodextrin since both the direction and the magnitude of the dipole moment depend strongly on the conformation of alpha-CD.     

Theoretical and experimental vibrational spectrum study of 4-hydroxybenzoic acid as monomer and dimer

Theoretical calculations on the molecular geometry and the vibrational spectrum of 4-hydroxybenzoic acid were carried out by the Density Functional Theory (DFT/B3LYP) method. In addition, IR and Raman spectra of the 4-hydroxybenzoic acid in solid phase were newly recorded using them in conjunction the experimental and theoretical data (including SQM calculations), a vibrational analysis of this molecular specie was accomplished and a reassignment of the normal modes corresponding to some spectral bands was proposed. The geometries of monomers and dimers in gas phase were optimized using the DFT B3LYP method with the 6-31G*, D95** and 6-311++G** basis sets. Also, both the vibrational spectra recorded and the results of the theoretical calculations show the presence of one stable conformer for the 4-hydroxybenzoic acid cyclic dimer. The B3LYP/6-31G* method was used to study the structure for cyclic dimer of 4-hydroxybenzoic acid and for a complete assignment our results were compared with results of the cyclic dimer of benzoic acid. A scaled quantum mechanical analysis was carried out to yield the best set of harmonic force constants. The formation of the hydrogen bond was investigated in terms of the charge density by the AIM program and by the NBO calculations.     

Theoretical study of modes of adsorption of water dimer on H-ZSM-5 and H-Faujasite zeolites

Modes of adsorption of water dimer on H-ZSM-5 and H-Faujasite (H-FAU) zeolites have been investigated by a quantum embedded cluster approach, using the hybrid B3LYP density functional theory. The results indicate that there are two possible adsorption pathways, namely the stepwise process where only one water binds strongly to the (-O)3-Al-O(H) tetrahedral unit while the other weakly binds to the zeolite framework and the concerted process where both water molecules form a large ring of hydrogen-bonding network with the Br?nsted proton and an oxygen framework. With inclusion of the effects of the Madelung potential from the extended zeolite framework, for adsorption on H-ZSM-5 zeolite, both the neutral and ion-pair complexes exist with adsorption energies of -15.13 and -14.73 kcal/mol, respectively. For adsorption on the H-FAU, only the ion-pair complex exists with the adsorption energy of -14.63 kcal/mol. Our results indicate that adsorption properties depend not only on the acidity of the Br?nsted acidic site but also on the topology of the zeolite framework, such as on the spatial confinement effects which lead to very different adsorption structures for the ion-pair complexes in H-ZSM-5 and H-FAU, even though their adsorption energies are quite similar. Our calculated vibrational spectra for these ion-pair complexes support previous experimental IR interpretations.     

Fe/Fe_2和NO反应的密度泛函理论研究

利用密度泛函理论(Density Functional Theory)中的B3LYP方法在6-311+G(d,p)的计算水平上研究了Fe/Fe_2与NO反应的相关微观机理.全参数优化了Fe+NO和Fe_2+NO反应体系在不同重态反应势能面上各驻点的几何结构,并用频率分析法以及内禀反应坐标(Intrinsic Reaction Coordinate)方法对过渡态进行了验证,得到了相对应的反应的微观反应路径.用"两态反应"分析反应机理,计算结果表明2个体系的优先选择路径均为低自旋态进入和高自旋态离开反应.通过对2个体系反应活化能的比较,Fe_2+NO体系更易进行.     

Theoretical calculations of the molecular properties of maleimide and its dimer

B3LYP theoretical calculations with 6-31++G(d,p) basis set have been performed to study the infrared spectrum of maleimide and its dimer. Our calculations have shown that the dimer formation leads to a binding energy of 44.0kJmol(-1) involving two intermolecular hydrogen bonds between the amide hydrogen and a carbonyl group of two neighboring maleimides. This value is essentially due to the electrostatic interaction term. Our calculations have also revealed the vibrational changes, in terms of frequencies and IR intensities, after dimer formation. The most affected modes are associated with the NH stretching and in-plane bending bands. This behavior can be adequately interpreted by the hydrogen atomic charge and NH charge-flux based on the modified charge-charge flux-overlap model for infrared intensities. The B3LYP frequency shifts are in very good agreement with the experimental ones.     

A computational study of the LiH dimer

A theoretical study of the properties of the linear LiH dimer was undertaken. In this dimer, an unusual type of hydrogen bonding (termed "inverse" hydrogen bonding by some authors), which involves the hydrogen bonded molecule acting as an electron donor (rather than as a proton donor), is exhibited. The optimized geometry, dipole moment, interaction energy, atomic charges, harmonic vibrational frequencies, and frequency shifts for the dimer are computed at the SCF, MP2, and QCISD levels of theory using mainly a 6-31++G(d,p) basis set. We also examined the relative stability of the mono-deuterated isotopomers of linear (LiH)(2), i.e., Li-H...Li-D and Li-D...Li-H. Analysis of the normal vibrational modes, changes in the partial atomic charges, and changes in the vibrational frequencies of LiH on complexation were used to gain insight into the bonding and properties of the linear LiH dimer and its isotopomers.     

Theoretical interpretation of the line shape of the gaseous acetic acid cyclic dimer

A general quantum theoretical approach of the nu(X-H) IR line shape of cyclic dimers of weakly H-bonded species in the gas phase is proposed. In this model, the adiabatic approximation (allowing to separate the high frequency motion from the slow one of the H-bond bridge), is performed for each separate H-bond bridge of the dimer and a strong nonadiabatic correction is introduced into the model via the resonant exchange between the fast mode excited states of the two moieties. The present model reduces satisfactorily to many models in the literature dealing with more special situations. It has been applied to the cyclic dimers (CD(3)CO(2)H)(2) and (CD(3)CO(2)D)(2) in the gas phase. It correctly fits the experimental line shape of the hydrogenated compound and predict satisfactorily the evolution in the line shapes, to the deuterated one by reducing simply the angular frequency of the H-bond bridge and the anharmonic coupling parameter by the factor 1/ square root of 2.     

Quantum-chemical study of the silver trifluoroacetate dimer

The results of quantum-chemical calculations of the formation energy, equilibrium structure, and potential surface sections along the nonrigid degrees of freedom of the silver trifluoroacetate dimer are presented. Calculations were performed by the B3LYP method with the cc-pVTZ correlation-coherent basis for C, O, and F atoms using the basis and relativistic effective core potentials Stuttgart 1997 RSC for Ag atoms, and, for comparison, by the HF method in the 6-31G(d) basis and MP2 method in the 6-311G(df) basis for C, O, and F atoms using the basis and relativistic effective core potentials SBKJC for Ag atoms. The eight-membered ring is a rigid planar fragment with a bond order of 0.2 between the silver nuclei. The nearly free internal rotation of the CF₃ group affects the geometrical parameters of the ring. It was substantiated that in electron diffraction experiments, the difficulties of interpretation could be explained not only by the presence of decomposition products in the sample, but also by possible oligomerization of silver trifluoroacetate.     

β-1型木质素二聚体高温蒸汽气化机理的理论研究

以β-1型木质素二聚体为研究对象,采用以密度泛函理论B3LYP/6-31G(d,p)为基础的Gaussian工具包对该木质素二聚体的高温纯蒸汽气化反应过程进行了分子动力学模拟研究。结果表明,在木质素二聚体高温蒸汽气化的初反应中,R4和R5的反应焓变较小分别为243.9和323.2 kJ/mol,Cα-Cβ键和Cβ-C1键较易断裂。通过计算次反应路径的势垒,发现R4-1和R5-1反应的势垒较小分别为4.4和24.0 kJ/mol,因此,在该气化过程中会优先选择R4-1和R5-1路径。该反应路径最后得到的产物有甲醇、乙醇、苯酚、对羟基甲苯和对羟基苯甲醛,与实验产物吻合。     

Theoretical study of the polarized infrared spectra of the hydrogen bond in 2‐furoic acid crystal dimer

This work presents a theoretical simulation of ν_{O? H} and ν_{O? D} band shapes in the polarized infrared spectra of 2‐furoic acid dimer crystals measured at liquid‐nitrogen temperature. The line shapes are studied theoretically within the framework of the anharmonic couplings between low‐frequency hydrogen‐bond vibrations and degenerate excited states of high‐frequency hydrogen vibrations in hydrogen‐bonded dimers and the anharmonic coupling between the first excited state of the fast mode and the harmonics or band combinations of some low‐frequency bending modes, which lead to Fermi resonances.This approach takes into account the adiabatic approximation, the intrinsic anharmonicity of the low‐frequency mode through a Morse potential, Davydov coupling triggered by resonance exchange between the excited states of the fast modes of the two hydrogen bonds involved in the cyclic dimer, and the direct and indirect damping of the fast‐stretching modes of the hydrogen bonds and of the bending modes. The infrared spectral density was calculated within the linear response theory by Fourier transform of the autocorrelation function of the transition dipole moment operator of the fast mode. Numerical results show that mixing of all these effects allows satisfactory reproduction of the main features of the experimental IR line shapes of crystalline H‐ and D‐bonded 2‐furoic acid at liquid‐nitrogen temperature and for different polarizations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

Theoretical studies on the properties of uracil and its dimer upon thioketo substitution

The influences of thioketo substitution on the properties of uracil monomer and dimer and their interactions with Zn²⁺ have been systematically investigated at the B3LYP/6-311+G^*level of theory. Those properties include the structural characteristics, acidities, ionization potentials, and singlet–triplet energy gaps of SU monomers and their dimers, where SU=2-thiouracil, 4-thiouracil, and 2,4-dithiouracil, respectively. Computational results suggest that thioketo substitution leads to an increase in the acidities of the N-H groups for both uracil and its dimer, where the N₁–H group is still the most acidic site relative to that of N₃–H group. However, the opposite behaviors are true for the ionization potentials and the singlet–triplet energy gaps of uracil monomer and its dimer, suggesting that thiouracils are more susceptible to radiation damage relative to the unsubstituted uracil. For uracil and 2-thiouracil, the corresponding triplet excited-state geometries are predicted to be highly nonplanar compared with the planar geometries of the ground state as well as 4-thiouracil and 2,4-dithiouracil upon triplet excitation. As a rule, the intermolecular H-bonds involving the sulfur atom directly have been influenced more significant than those the oxygen atom directly involved for U::U and SU::SU base pairs upon ionization and excitation. Additionally, Zn²⁺ binding is expected to lead to an increase in the stability of U::U and SU::SU base pairs.