密度泛函研究细梗胡枝子提取物中新型抗氧化剂的分子结构和活性氧清除机理

The molecular structure and radical scavenging activity of three novel antioxidants from Lespedeza Virgata, lespedezavirgatol, lespedezavirgatal, and lespedezacoumestan, have been studied using density functional theory with the B3LYP and BhandHLYP methods. The optimized geometries of neutral, radical cation, radical and anion forms were obtained at the B3LYP/6-31G(d) level, in which it was found that all the most stable conformations contain intramolecular hydrogen bonds. The same results were obtained from the MP2 method. The homolytic O-H bond dissociation enthalpy and the adiabatic ionization potential of neutral and anion forms for the three new antioxidants and adiabatic electron affinity and H-atom affinity for hydroxyl radical, superoxide anion radical, and hydrogen peroxide radical were determined both in gas phase and in aqueous solution using IEF-PCM and CPCM model with UAHF or Bondi cavity. The antioxidant activities and reactive oxygen species scavenging mechanisms were then discussed, and the results obtained from different methods are consistent. Furthermore, the antioxidant activities are consistent with the experimental findings of the compounds under investigation.     

Molecular structure and antioxidant properties of delphinidin

Density functional theory calculations were performed to evaluate the antioxidant activity of delphinidin, taking into account its acid/base equilibrium. The conformational behavior of both the isolated and the aqueous solvation species (simulated with the polarizable continuum model) were analyzed at the B3LYP/6-31++G(d,p) level, considering the cationic, neutral, and anionic forms, the latter two forms consisting of diverse tautomers. The analysis of their electron density distributions, using the quantum theory of atoms in molecules, reveals several facts that are not in line with their usual Lewis structures. The prototropic preferences observed in the gas phase and in solution are similar. Thus, in both phases, most stable tautomer of neutral delphinidin is obtained by deprotonating the hydroxyl at C4', and the most stable tautomer of the anion is obtained by deprotonating the hydroxyls at C4' and C5. All the planar conformers obtained display an intramolecular hydrogen bond (IHB) between O3 and H6'. Furthermore, the most stable tautomers of the neutral and anionic forms display two IHBs between O4' and H3' and H5'. To obtain ionization potentials (IPs) and homolytic O-H bond dissociation enthalpies (BDEs), the corresponding radical species were optimized at the UB3LYP level. Heterolytic O-H bond dissociation enthalpies (proton dissociation enthalpies, PDEs) were also computed. The expected important antioxidant activity can be justified from these results. IP, O-H BDE, and O-H PDE values suggest that one-step H atom transfer rather than sequential proton loss-electron transfer or electron transfer-proton transfer would be the most favored mechanisms for explaining the antioxidant activity of delphinidin in nonpolar solvents as well as in aqueous solution.     

Theoretical studies on the effects of methods and parameterization on the calculated free energy of hydration for small molecules

Free energies of hydration (FEH) have been computed for 13 neutral and nine ionic species as a difference of theoretically calculated Gibbs free energies in solution and in the gas phase. In‐solution calculations have been performed using both SCIPCM and PCM polarizable continuum models at the density functional theory (DFT)/B3LYP and ab initio Hartree–Fock levels with two basis sets (6‐31G* and 6‐311++G**). Good linear correlation has been obtained for calculated and experimental gas‐phase dipole moments, with an increase by ～30% upon solvation due to solute polarization. The geometry distortion in solution turns out to be small, whereas solute polarization energies are up to 3 kcal/mol for neutral molecules. Calculation of free energies of hydration with PCM provides a balanced set of values with 6‐31G* and 6‐311++G** basis sets for neutral molecules and ionic species, respectively. Explicit solvent calculations within Monte Carlo simulations applying free energy perturbation methods have been considered for 12 neutral molecules. Four different partial atomic charge sets have been studied, obtained by a fit to the gas‐phase and in‐solution molecular electrostatic potentials at in‐solution optimized geometries. Calculated FEH values depend on the charge set and the atom model used. Results indicate a preference for the all‐atom model and partial charges obtained by a fit to the molecular electrostatic potential of the solute computed at the SCIPCM/B3LYP/6‐31G* level. © 2004 Wiley Periodicals, Inc. Int J Quantum Chem, 2004     

Neutral and Oxidized Triisopropylsilyl End‐Capped Oligothienoacenes: A Combined Electrochemical,Spectroscopic, and Theoretical Study

This work presents an analysis of the structural, electrochemical, and optical properties of a family of triisopropylsilyl end‐capped oligothienoacenes (TIPS‐ Tn ‐TIPS, n=4–8) by combining cyclic voltammetry, spectroscopic techniques, and quantum‐chemical calculations. TIPS‐ Tn ‐TIPS compounds form stable radical cations, and dications are only obtained for the longest oligomers (n=7 and 8). Oxidation leads to the quinoidization of the conjugated backbone, from which electrons are mainly extracted. The absorption and fluorescence spectra show partially resolved vibronic structures even at room temperature, due to the rigid molecular geometry. Two well‐resolved vibronic progressions are observed at low temperatures due to the vibronic coupling, with normal modes showing wavenumbers of ≈1525 and ≈480 cm^?1. Optical absorption bands display remarkable bathochromic dispersion with the oligomer length, indicative of the extent of π conjugation. The optical properties of the oxidized compounds are characterized by in situ UV/Vis/NIR spectroelectrochemistry. The radical cation species show two intense absorption bands emerging at energies lower than in the neutral compounds. The formation of the dication is only detected for the heptamer and the octamer, and shows a new band at intermediate energies. Optical data are interpreted with the help of density functional theory calculations performed at the B3LYP/6‐31G** level, both for the neutral and the oxidized compounds.     

DFT and QTAIM based investigation on the structure and antioxidant behavior of lichen substances Atranorin,Evernic acid and Diffractaic acid

In this study, the structural and antioxidant behavior of the three lichen-derived natural compounds such as atranorin (AT), evernic acid (EV) and diffractaic acid (DF) has been investigated in the gas and water phase using both B3LYP and M06-2X functional level of density functional theory (DFT) with two different basis sets 6-31+G (d, p) and 6-311++G (d, p). The intramolecular H–bonds (IHB) strength, aromaticity and noncovalent interactions (NCI) have been computed with the help of the quantum theory of atoms in molecules (QTAIM). This calculation gives major structural characteristics that indirectly influence the antioxidant behavior of the investigated compounds. The spin density (SD) delocalization of the unpaired electron is found to be the main stabilizing factor of neutral and cationic radical species. The main mechanisms, recommended in the literature, for the antioxidant action of polyphenols as radical scavengers such as hydrogen atom transfer (HAT), single electron transfer followed by proton transfer (SET-PT), and sequential proton loss electron transfer (SPLET), were examined. The result shows that the HAT and SPLET mechanism are the most conceivable one for the antioxidant action of this class of compounds in gas and water phase respectively. Preference of SPLET over HAT in water phase is due to the significantly lower value of proton affinity (PA) compared to the bond dissociation enthalpy (BDE) value. This study reveals that O₂-H₃, O₉-H₂₆ and O₄-H₄₅ respectively are the most favored site of AT, EV and DF for homolytic as well as heterolytic OH bond breaking.     

The HCSHSC and HCS+HSC+ systems: molecular properties, isomerization, and energetics

The isomer pair HCSHSC and related cations have been studied by means of a highly accurate level of theory. For all the species investigated the near-equilibrium potential energy surface has been calculated using the coupled cluster method in conjunction with correlation consistent basis sets ranging in size from quadruple to sextuple zeta. After extrapolation to the complete basis set limit, additional corrections due to core-valence correlation and scalar relativistic effects have also been included. Consequently, the molecular and spectroscopic properties as well as the ionization potentials and dissociation energies have been predicted to high accuracy. Isomerization path and energy for both radical and cationic species have also been investigated. Finally, the anharmonic vibrational frequencies have been employed in order to obtain zero-point corrections to ionization potentials, dissociation energies, and isomerization barriers: IP0(HCS) = 7.57(4) eV and IP0(HSC) = 9.00(5) eV; D0(C-H) = 49.29(55) kcal/mol and D0(S-H) = 9.99(37) kcal/mol; deltaE0(HCSHSC) = 39.29(49) kcal/mol, and deltaE0(HCS+HSC+) = 72.24(75) kcal/mol.     

The effects of nonlocal gradient corrections in density functional calculations of hydrocarbon radical hyperfine structures

Ground-state equilibrium geometries and hyperfine structures of a number of organic neutral and charged radical compounds are computed using the linear combination of Gaussian-type orbitals–density functional theory method. In addition to the local spin-density approximation, we also use two different nonlocal (gradient corrected) schemes for the calculations of the exchange and correlation potentials. The different functional forms are found to generate slightly different total and unpaired spin-density distributions in the molecules, and as a result, the computed isotropic hyperfine coupling constants vary markedly. The smallest variations are found for the hydrogens, where the results are generally in satisfactory agreement with experiment. For the carbon atoms, however, large differences in isotropic coupling constants are observed. The anisotropic hyperfine structures are generally very well described at all levels of theory. © John Wiley & Sons, Inc.     

A DFT and direct MO dynamics study on the structures and electronic states of phenyl-capped terthiophene

The structures and electronic states of phenyl-capped terthiophene (denoted by P3T) and the ionic species of P3T have been investigated by means of density functional theory (DFT) and direct MO dynamics calculations. P3T is one of the high-performance molecular devices, which has been utilized as a semi-conductor. The calculations indicated that the neutral P3T has a non-planar structure whose the phenyl rings in both ends of thiophene chain are largely deviated from the molecular plane. The cation and anion radicals, dication and dianion were considered as its ionic states. The structure for cation radical of P3T is close to more planar than that of neutral P3T. The structures for anion radical, dication and dianion take a pure planar structure. The first excitation energy of neutral P3T is calculated to be 2.90 eV at the TD-B3LYP/6-31G(d)//B3LYP/6-311+G(d) level, while the P3T cation and anion radicals have lower excitation energies (1.22 and 1.10 eV, respectively). The direct MO dynamics calculation showed that neutral, cation and anion hold near planar structure at 300 K. On the other hand, oligothiophene (n = 5) and its ionic species are strongly deformed from the planar structure, and thiophene rings in both ends of chain rotate rapidly by thermal activation. The mechanism of the electron conductivity in P3T was discussed on the basis of theoretical results.     

Characterization of the oxidation products of styryl-substituted terthiophenes and sexithiophenes using electronic absorption spectroscopy and time-dependent DFT

The electronic absorption spectra of a series of alkoxy-styryl substituted terthiophenes, their corresponding sexithiophenes, and the oxidation products of both have been measured. The terthiophenes studied sigma-dimerize to sexithiophenes during the oxidation process and there is clear evidence of sexithiophene radical cations, dications, and pi-dimers in the electronic absorption spectra. The oxidation of concentrated solutions produces predominantly pi-dimer bands, as expected. The absorption spectrum of the styryl-functionalized sexithiophene dication without alkoxy substitution closely resembles that of unsubstituted sexithiophene, while alkoxy substitution induces changes in the wavelength of the dication band maximum and the overall band shape. Time-dependent density functional theory (TDDFT) calculations have shown that styryl-based molecular orbitals are important in the transitions of the neutral molecules as well as the charged species, the dication in particular. Kinetics analyses confirm the stabilization effect induced by the alkoxy substituents. The presence of a reversible pi-dimer equilibrium was verified by cyclic voltammetry. It is clear from the experimental observations and the theoretical calculations that both the styryl and alkoxy groups are influencing the electronic properties of this class of molecules.     

Theoretical study of Pu and Am tetracarbide molecules

The electronic structure and ground‐state molecular properties of Pu and Am tetracarbides have been investigated by relativistic multireference calculations using CASSCF/CASPT2 theory as well as by density functional theory in conjunction with relativistic pseudopotentials. The CASSCF/CASPT2 treatment has been extended by spin–orbit coupling effects for selected species using the CAS state‐interaction method. The five atoms can form various structural isomers, from which 12 ones have been identified in our study. The electronic ground state in both molecules corresponds to a planar fan‐type structure of C_2v symmetry, in which the actinide atom is connected to a bent C₄ moiety. The other structures are much higher in energy, the ones computed in this study appear between 250 and 1050 kJ/mol. The bonding characteristics in the most relevant structures have been analyzed on the basis of the valence molecular orbitals and natural bond orbital analysis. The most stable structures have been characterized by their spectroscopic (vibrational and electron) properties. © 2014 Wiley Periodicals, Inc.     

Modeling competitive reaction mechanisms of peroxynitrite oxidation of guanine

5-Guanidino-4-nitroimidazole is a stable product from the peroxynitrite induced one-electron oxidation of guanine. Reaction mechanisms to form the 5-guanidino-4-nitroimidazole as well as 8-nitroguanine, through the combination of the guanine radical cation and nitrogen dioxide radical and through the combination of the deprotonated neutral guanine radical and nitrogen dioxide radical, have been investigated by the use of the B3LYP method of density functional theory. Our calculations suggest that the guanine radical cation mechanism is preferred over the neutral guanine radical mechanism and that a water molecule is involved in the reaction as a catalyst or as a reactant.     

Collision-induced fragmentation of deprotonated methoxylated flavonoids, obtained by electrospray ionization mass spectrometry

Electrospray operated in the negative mode was used to analyse methoxylated flavonoids. They were found to produce radical anions by collision-induced fragmentation of the aglycones. Loss of a methyl group from the deprotonated molecule corresponding to [M - H - 15]-* ions, as well as [M - H - 15-28]-* and [M - H - 15-29]- fragment ions, were found to constitute the characteristic fragmentation for the monomethoxylated species, whereas [M - H - 15]-*, [M - H - 30]- and [M - H - 30-28]- were predominant for the polymethoxylated species. Obtained under similar conditions, the product-ion spectra of isomeric compounds were characteristically different. It is therefore possible to distinguish between methoxylated flavonoids with identical molecular mass, e.g. when screening plant extracts for flavonoid composition. However, comparison with standard compounds is necessary for the identification of unknown flavonoid aglycones.     

A profound density functional theory study to unravel the spectroscopic and molecular properties of two Flavanols differing in α-pyrone ring position

A comprehensive theoretical model was designed for two new flavanols that have been reported from Glycosmis pentaphylla, differing in the placement of α-pyrone ring. The density functional theory (DFT) approach was utilized for computing different properties of these compounds to validate the experimental findings and stereochemical assignments. Electronic properties, geometric parameters, frontier molecular orbitals (FMOs), molecular electrostatic potential (MESP), and natural bond orbital analysis were performed for the first time at the PBE0-D3BJ/def2-TZVP level of theory for the compounds under study. The simulated vibrational frequencies for compounds 1 and 2 were computed and compared with the experimental results. nuclear magnetic resonance (NMR) (¹H and ¹³C) chemical shift values were computed at the PBE0-D3BJ/def2-TZVP/SMD_DMSO level of theory and showed a very good agreement with the experimental results for both the compounds. The electronic circular dichroism (ECD) and ultraviolet–visible (UV) spectra for both the compounds were obtained using time-dependent DFT in methanol, whose results exhibited excellent correlation with experimental data. The intermolecular interaction effect on geometric parameters, vibrational frequencies, and electronic properties were studied for the first time.     

A novel quantum mechanical/molecular mechanical approach to the free energy calculation for isomerization of glycine in aqueous solution

The free energy change associated with the isomerization reaction of glycine in water solution has been studied by a hybrid quantum mechanical/molecular mechanical (QM/MM) approach combined with the theory of energy representation (QM/MM-ER) recently developed. The solvation free energies for both neutral and zwitterionic form of glycine have been determined by means of the QM/MM-ER simulation. The contributions of the electronic polarization and the fluctuation of the QM solute to the solvation free energy have been investigated. It has been found that the contribution of the density fluctuation of the zwitterionic solute is estimated as -4.2 kcal/mol in the total solvation free energy of -46.1 kcal/mol, while that of the neutral form is computed as -3.0 kcal/mol in the solvation free energy of -15.6 kcal/mol. The resultant free energy change associated with the isomerization of glycine in water has been obtained as -7.8 kcal/mol, in excellent agreement with the experimental data of -7.3 or -7.7 kcal/mol, implying the accuracy of the QM/MM-ER approach. The results have also been compared with those computed by other methodologies such as the polarizable continuum model and the classical molecular simulation. The efficiency and advantage of the QM/MM-ER method has been discussed.     

Natural bond orbital analysis and vibrational spectroscopic studies of H-bonded N,N′-diphenylguanidinium nitrate

NIR-FT Raman and FT-IR spectra of the crystallized biologically active molecule N,N′-diphenylguanidinium nitrate (DGN) have been recorded and analyzed using quantum chemical computations based on density functional theory. The extraordinary basicity and strong stability of this novel bioactive compound has been discussed as the consequence of resonance stabilization leading to Y-aromaticity and hydrogen bonding. This peculiar Y-delocalization character of DGN is well reflected in the optimized geometry and bond order (BO) calculations. The observance of the equality of C–N bond lengths in the protonated species indicates delocalization of the π-electron system. The spectroscopic and natural bonds orbital (NBO) analysis confirms the occurrence of strong network of inter molecular hydrogen bonds. The changes in electron density in the global minimum and in the energy of hyperconjugative interactions of DGN calculated by second order perturbation theory have been studied extensively in comparison with the values of the neutral species. The observed characteristic ring vibrations are well fit with the theoretical values calculated at B3LYP/6-31G* level.     

Theoretical Study on the Optical Properties for 2,7- and 3,6-Linked Carbazole Trimers by Time-dependent Density Functional Theory

Electronic properties, such as HOMO and LUMO energies, band gaps, ionization potential (IP) and electron affinity (EA) of 2,7- and 3,6-linked carbazole trimers, two conjugated oligomers with different linkages of carbazole, were studied by the density functional theory with Becke-Lee-Young-Parr composite exchange correlation functional (B3LYP). The absorption spectra of these compounds were also investigated by time-dependent density functional theory (TD-DFT) with 6-31G* basis set. The calculated results indicated that the HOMO and LUMO of the 2,7- and 3,6-linked carbazole trimers are both slightly destabilized on going from methyl substitution to sec-butyl substitution. Both IP and EA exhibit their good hole-transporting but poor electron- accepting ability. The presence of alkyl groups on the nitrogen atoms does not affect the intra-chain electronic delocalization along the molecular frame. Thus no significant effect on the band gap and absorption spectra of compounds has been found.     

HO3、HO+3、HO-3光谱和结构的MP2和DFT理论研究

用B3LYP和MP2量子化学理论,详细地计算了HO3、HO+3、HO-3可能的平衡构型、能量和光谱参数,分析了它们可能的解离通道和稳定性.还分析了HO3的电离势(IE)及电子亲和势(Ea),讨论了HO3、HO3-自由基的光电子能谱的特征,及用光电子能谱去探测HO3的可能性.     

Topological analysis of the electron density distribution in perturbed systems. I. Effect of charge on the bond properties of hydrogen fluoride

Within the framework of the molecular orbital (MO) theory, the addition of one electron to the 4sigma antibonding orbital of the neutral (F...H) system or the removal of one electron from its pi nonbonding orbitals, leading to (F...H)- and to (F...H)+, has permitted the investigation of these charge perturbations on the bond properties of the hydrogen fluoride molecule by using the topological analysis of rho(r). For (F...H), (F...H)-, and (F...H)+, the topological and energetic properties calculated at the F...H bond critical point (BCP) have been related to the 3sigma bonding molecular orbital (BMO) distribution, as this orbital is the main contributor to rho(r) at the interatomic surface. The analysis has been carried out at several F...H internuclear distances, ranging from 0.8 to 3.0 A. As far as the BMO distribution results from its interaction with the average Coulomb and exchange potential generated by the charge filling the other MOs, and in particular by the pi and 4sigma electrons, the comparison between the BCP properties calculated for the charged systems and those corresponding to the neutral one permits the interpretation of the differences in terms of the charge perturbation on BMO. Along with the BCP properties of (F...H), (F...H)-, and (F...H)+, the interaction energy magnitudes of these systems have been also calculated within the same range of internuclear distances, indicating that the applied perturbations do not break the F-H bond but soften it, giving rise to the stable species (F-H)- and (F-H)+. Comparing the three systems at their equilibrium geometries, the most stable configuration, which corresponds to the unperturbed (F...H) system, shows the highest quantity and the most locally concentrated charge density distribution, along with the largest total electron energy density magnitude, at the interatomic surface as a consequence of the BMO contraction toward the fluorine nucleus in (F...H)+ and of the BMO expansion toward both nuclei in (F...H)-. On the other hand, if the comparison is carried out at the equilibrium distance of (F...H) (d(eq)0), this one exhibits both the smallest total energy density magnitude and the largest quantity of bonding charge at the interatomic surface. Hence, being the signature of the most stable configuration, the characteristic magnitudes of the neutral system rho(d(eq)0), inverted triangle2 rho(d(eq)0), and H(d(eq)0) appear as boundary conditions at the interatomic surface of its unperturbed and relaxed electron distribution.