用密度泛函理论研究一种新型有机硅化合物异构体的振动光谱

在B3LYP/6-31＋G(d)的水平上, 对两种含有手性Si原子的新型有机硅单体Si₂(CH₃)₂H₂N₂(C₂H₅)₄和Si₄(CH₃)₄H₄N₂(C₆H₅)₂的几种异构体进行了研究, 在全参量几何构型优化的基础上, 进行了简谐振动频率计算, 同时对所研究的体系进行了热力学性质和低能激发态的含时密度泛函理论(TDDFT)计算. 理论计算表明, 构象异构体之间的红外光谱差异不大, 热力学和低能激发态性质也相似; 顺/反结构相似的异构体之间红外光谱差异不大, 但热力学和低能激发态性质却呈现差异; 旋光异构体或顺/反结构相差较大的异构体之间, 红外光谱和热力学及低能激发态性质有明显的差异. 从理论上解释了实验红外光谱中Si—H振动峰的裂分是由异构体的存在所致, 并找到裂分峰所对应的异构结构. Si—H键振动频率与其键长相关.     

The use of the hybrid density functional theory (DFT) approach for calculation of vibrational spectra: nitromethane

The molecular geometry of nitromethane was optimized and its force field and vibrational spectrum were calculated by the BECKE3LYP method. The accuracy of optimization of the geometry of MeNO₂ obtained by this method using the 6–311G(d,p) and 6–311++G(d,p) basis sets is not poorer than that obtained at the second-order Møller-Plesset level of perturbation theory (MP2). The vibrational frequencies of nitromethane and its d₁, d₂, and d₃ isotopomers obtained by the BECKE3LYP method are in much better agreement with the experimental data than those calculated at the MP2 level using the same basis set. The average absolute error of calculations performed without the use of any scaling factors is ～2% for frequencies; the maximum deviation is ～4%.     

Theory Study on Structures and Vibrational Frequencies of Pyruvic acid

Anumberoftheoreticalstudiesexistforpyruvicacid.IthasbeenstudiedatthesemiempiricalINDOandAMIlevell'2.AttheahinitiolevelstudiesofpyruvicacidrangefromthecalculationofenergiesattheSTO-3Glevel'tocalculationsofenergiesusingtheHF/3-2iG',HF/4-21G',HF/6-3iG*andMP2/4-21Gmethods.ExceptforthestudyofMurtoetal.,allthestudieshavefocussedontheenergiesandgeometriesofpyruvicacid.Moreoveralltheexistingtheoreticalstudieshavefocusedtheirattentionontheorientationofthecarboxylhydrogenextensively.Theorienta…     

Theoretical study of molecular and electronic structure of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid

A theoretical study of 2‐Se‐(2‐methyl‐2‐propenyl)‐1‐benzoic acid was carried out to investigate the molecular and electronic structure of this molecule, using the B3LYP density functional theory (DFT) method with the 6‐311+G** basis set. The optimized geometry of the molecule was obtained for the ortho, meta, and para isomers of the complex. In addition, the theoretical vibrational spectrum is presented, and thermal corrections in the limit of 100–1,000 K are discussed using the Shomate thermodynamic equations. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

阿魏酸分子结构和振动光谱的理论研究

阿魏酸是一种有效的天然油脂抗氧化剂.采用密度泛函理论(DFT) B3LYP方法和从头算HF两种方法,在6-311++G**基组水平上对阿魏酸分子的几何结构进行全优化,得到其几何结构参数,进一步计算得到阿魏酸的红外和拉曼振动光谱.计算结果表明,采用B3LYP和HF 2种方法优化得到的几何结构及频率值是一致的,对在B3LYP方法下计算得到的红外和拉曼振动频率进行合理的理论归属并与SDBS数据库实验数据进行比较,发现计算得到的红外和拉曼振动频率与实验测定结果符合较好.阿魏酸分子结构和振动光谱的研究,为研究阿魏酸及其衍生物的化学结构与生理活性之间的构效关系提供依据.     

On the stability of metal–aminoacid complexes in water based on water–ligand exchange reactions and electronic properties: Detailed study on iron–glycine hexacoordinated complexes

Thermodynamic stability of metal–aminoacid complexes in water is discussed in terms of the Gibbs free energy of water–ligand exchange processes, and the electronic stabilizing factors thoroughly investigated by means of 1‐electron and 2‐electron density properties. Hexacoordinated complexes formed between iron cations and glycine molecules acting as monodentate or bidentate ligands have been chosen as targets for the current study. Results agree with experimental findings, and complexes formed with bidentate ligands are found to be more stable than those formed with monodentate ones. The larger the number of the coordinated glycine molecules the more stable is the complex. Fe(III) complexes are more stable than Fe(II) ones, but differences are small and the Fe³⁺/Fe²⁺ exchange process appears to be energetically feasible for these complexes. Formation of the second glycine–iron interaction involving the amino nitrogen in the bidentate ligands is enthalpycally unfavorable but takes place due to the large entropy rise of the process. The larger stability of Fe(III) complexes is due however to the balance between energetic and solvation terms, which is favorable to these complexes. Electron density properties account satisfactorily for the electronic energy changes along the complex formation in terms of ligand–metal electron transfer and covalent bond orders. © 2010 Wiley Periodicals, Inc. J Comput Chem 2010     

Vibrational spectra of trinitromethane derivatives

Spectroscopic parameters of trinitromethane derivatives RC(NO₂)₃ (R = F, Cl, Br, I, NC, NF₂, N₃) were determined. Vibrational frequencies and modes were calculated and the assignment of experimental spectra was performed. Spectral features due to the mutual influence of the C(NO₂)₃ group and other atomic groups and particular atoms were revealed.     

Structure and vibrational spectra of dicyclopentadienylzinc. A DFT study

The quantum-chemical DFT calculations of the Cp₂Zn structure confirm the conclusion made earlier from the vibrational spectra that the sandwich structure (⁵-C₅H₅)₂Zn (A) is not energetically favorable and more favorable are the close in energy -structure (⁵-C₅H₅)(¹-C₅H₅)Zn (B) and -structure (¹-C₅H₅)₂Zn (C). The vibrational spectra of structures B and C with the DFT-derived force fields were calculated. A comparison of the calculated spectra of the isolated Cp₂Zn molecules with the experimental data gives no way of deciding between the B and C structures. It is most likely that the molecule is nonrigid and experiences a strong influence from the nearest environment in solution or in the crystalline state.     

DFT and experimental studies of the structure and vibrational spectra of curcumin

The potential energy surface of curcumin [1,7‐bis(4‐hydroxy‐3‐methoxyphenyl)‐1,6‐heptadiene‐3,5‐dione] was explored with the DFT correlation functional B3LYP method using 6‐311G* basis. The single‐point calculations were performed at levels up to B3LYP/6‐311++G**//B3LYP/6‐311G*. All isomers were located and relative energies determined. According to the calculation the planar enol form is more stable than the nonplanar diketo form. The results of the optimized molecular structure are presented and compared with the experimental X‐ray diffraction. In addition, harmonic vibrational frequencies of the molecule were evaluated theoretically using B3LYP density functional methods. The computed vibrational frequencies were used to determine the types of molecular motions associated with each of the experimental bands observed. Our vibrational data show that in both the solid state and in all studied solutions curcumin exists in the enol form. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Thermochemistry of aqueous solutions of nucleic acid bases and their alkylated derivatives

Enthalpy of solution, ΔH _sol ^o , enthalpy of sublimation, ΔH _subl ^o , apparent partial molar volume and heat capacities,V ₂ ^o andC _p,2 ^o were determined for aqueous solutions of thirty alkylated derivatives of uracyl and adenine, eight derivatives of cytosine and guanine. Calculated accessible surface areas and molar volumes are presented, too. The values of enthalpy of solution, enthalpy of sublimation can be useful in the studies on the nature of interaction between these compounds and water molecules. Apparent partial molar volume and heat capacity give a new aspect on hydrophob properties of the examined nucleic acid base derivatives.     

Self‐Assembly Structures of 1H‐Indazoles in the Solution and Solid Phases: A Vibrational (IR,FIR, Raman,and VCD) Spectroscopy and Computational Study

1H‐indazoles are good candidates for studying the phenomena of molecular association and spontaneous resolution of chiral compounds. Thus, because the 1H‐indazoles can crystallize as dimers, trimers, or catemers, depending on their structure and the phase that they are in, the difficulty in the experimental analysis of the structure of the family of 1H‐indazoles becomes clear. This difficulty leads us to contemplate several questions: How can we determine the presence of different structures of a given molecular species if they change according to the phase? Could these different structures be present in the same phase simultaneously? How can they be determined? To shed light on these questions, we outline a very complete strategy by using various vibrational spectroscopic techniques that are sensitive (VCD) and insensitive (IR, FIR, and Raman) towards the chirality, together with quantum chemical calculations.     

Computation of large systems with an economic basis set: structures and reactivity indices of nucleic acid base pairs from density functional theory

We show here that an economic basis set can describe nucleic acid base pairs involving the hydrogen bond interactions in density functional calculations. The economic basis set in which the polarization function is added only to oxygen and nitrogen atoms of strong electronegativity can predict reliable geometric structures and dipole moment of nucleic acid base pairs, comparable to those obtained from the basis set of 6-31G* in B3LYP calculations. Combining single point calculations with the standard basis set on the geometric structures optimized by the economic basis set, the present approach has predicted accurate natural bond orbital charge, binding energy, electronegativity, hardness, softness, and electrophilicity index. The principle for basis selection presented in this study can be regarded as a general guideline in the computation of large biological systems with considerably high accuracy and low computational expense.     

Electron‐pair density decomposition for core–valence separable systems

The electron pair density of a core‐valence separable system can be decomposed into three parts: core‐core, core‐valence, and valence‐valence. The core‐core part has a Hartree‐Fock like structure. The core‐valence part can be written as Γ_cv (1,2) = γ_c (1,1)γ_v (2,2) ? γ_c (1,2)γ_v (2,1) + γ_c (2,2)γ_v (1,1) ? γ_c (2,1)γ_v (1,2), where only the 1‐matrices from the core and valence orbitals contribute. The valence‐valence part is left to be determined from the reduced frozen‐core type wave function, which often contains the essential information on the electron correlation and the chemical bond. We demonstrate the analysis to the ground state of negative ion Li^? and 2¹Σ_u⁺ excited state of the Li₂ molecule. © 2012 Wiley Periodicals, Inc.     

Vibrational frequencies of hydrazoic acid and methyl azide: density functional theory study

Harmonic vibrational frequencies of HN3 and CH3N3 molecules and their several isotopomers are calculated using HF, MP2 and five popular density functional theory (DFT) methods. On the basis of the comparison between calculated and experimental results, assignments of fundamental vibrational modes arc examined. HF and MP2 results are in bad agreement with experimental values. Of the five DFT methods, BLYP reproduces the observed fundamental frequencies the most satisfactorily. Two hybrid DFT methods are found to yield frequencies generally higher than the observed fundamental frequencies. The results indicate that BLYP calculation is a very promising approach for understanding the observed spectral features.     

Spin–Spin Artificial DNA Intercalated with Silver Cations: Theoretical Prediction

The indirect nuclear spin–spin coupling constants of Ag⁺ cation intercalated between imidazole rings in DNA chains are calculated by means of DFT with relativistic effects taken into account by the use of the zeroth‐order regular approximation Hamiltonian (DFT‐ZORA). The calculations model how the ¹J(¹⁵N,¹⁰⁹Ag) coupling constant is affected by different types of geometry deformations and by the presence of water, which is simulated by means of the polarizable continuum model and explicitly present water molecules. Calculations for systems containing two and three imidazole pairs are also carried out to model the influence of stacking interactions. The computed ¹J(¹⁵N,¹⁰⁹Ag) spin–spin coupling constant is in the range of 85–105 Hz (depending on the computational model) and is in good agreement with the experimental value (ca. 92 Hz). This coupling constant is very little affected by the presence of solvent, stacking interactions, and geometry deformations. Such behavior is explained by visualization of the coupling path by means of coupling energy density (CED). Bigger models allow the coupling constant between two adjacent silver ions to be computed, and give a value of approximately 1 Hz, which is probably too small to be of practical interest. The ²J(¹⁵N,¹⁵N) value is calculated to be about 2.5 Hz, and is therefore of measurable magnitude.     

Theoretical determination of electron affinity and ionization potential of DNA and RNA bases

The ionization potentials and electron affinities of thymine, cytosine, adenine, guanine, and uracil were determined at density functional level using different exchange‐correlation functionals and basis sets. Results showed that the computed ionization potentials are very close to the experimental counterparts. The sign of adiabatic electron affinities of adenine, thymine, and uracil is unaffected by the used level of theory while that for guanine and cytosine depends on both the used potential and basis set. Vertical electron affinities are always negative in agreement with the experimental indications. © 2000 John Wiley & Sons, Inc. J Comput Chem 21: 1243–1250, 2000