Na-呋喃荷移络合物弱相互作用的密度泛函理论研究

在B3LYP/6-311+C*水平上,对Na-呋喃体系可能存在的弱相互作用复合物进行了全自由度能量梯度优化,发现了Na-呋喃体系存在两个能量极小结构A、B,其中,结构A是Na原子的3s1电子直接和呋喃杂环体系中的所有重原子的共轭大π体系相互偶合,形成一个具有C8对称性的金属有机复合物;而结构B为Na原子的3s1电子主要通过杂原子O和杂环上原有的五中心六电子大π体系形成一个新的平面六中心七电子大π体系,具有C2v对称性.结构B较结构A稳定3.40kJ/mol.结构A中的Na-O键长为0.38 nm,∠COC为106.9°,由于金属Na对呋喃杂环的作用使整个分子平面变形,C1、C2、C3、C4在同一个平面内,而O5则稍微翘离平面且O5原子距离由Cl、C2、C3、C4组成的平面的垂直距离约为0.035 nm.结构B中Na-O键长为0.26 nm,∠COC为106.8°,金属Na原子和杂环中所有的原子在同一个平面内.并在MP2和B3LYP水平下,用6-311+G*基组精确计算了最稳定结构B的结合能为ΔE=4.5～5.1 kJ/mol.     

Experimental and theoretical electronic absorption spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and its derivatives: Solvatochromic effect and time dependent density functional theory approach

Electronic spectra of 2,4‐diphenyl‐1,5‐benzothiazepine and some of its derivatives in 1,2‐dichloromethane and ethanol are investigated experimentally and theoretically using the time dependent density functional theory (TD‐DFT) method at the B3LYP/6‐311G** level of the theory. The origin of the spectrum of the parent compound is found to be an additive one. The observed ultra violet (UV) spectra in both solvents show two bands S1 in the range between 312–334 nm and S2 in the range between 248–272 nm. The solvent effect is investigated experimentally and theoretically and a blue shift is observed, which is explained in terms of a hydrogen bond model between the solvent and the most negative site of the solute (N atom). This theoretical model is robust in reproducing the experimental blue shift and calculating the hydrogen bond energy and hydrogen bond length. The extent of delocalization and charge transfer processes of the studied compounds is estimated and discussed in terms of natural bond orbital (NBO) analysis and second order perturbation interactions (E²) between donors and acceptors. The effect of substituents of the studied compounds in both solvents shows a noticeable red shift attributed to hyperconjugation effects of the π electron systems of the different moieties.     

DFT investigation of sites of protonation of antitumor of 2‐(4‐aminophenyl)benzazoles in the gas phase and in solution

The proton affinity on each of the possible sites in the antitumor 2‐(4‐aminophenyl)benzazoles has been calculated at the B3LYP/6‐311G** level of theory in the gas phase and in solution. The N₃‐site of protonation is found to be strongly favored over the NH₂‐site for the studied compounds both in gas phase and in solution. The stability of N₃‐protonated species is explained by the resonance interaction of the NH₂‐group with the heterocyclic ring. The potential energy surface (PES) for the protonation process was studied at the density functional theory (DFT)/B3LYP/6‐311++G** level of theory. Solvent effects on the PES were also examined using two models: Onsager self‐consistent field and polarizable continuum model (PCM). © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Density functional theory and RRKM calculations of the gas‐phase unimolecular rearrangements of methylfuran and pyran ions before fragmentations

The potential energy profiles for the mutual conversion of the isomeric molecular ions [C₅H₆O]^+? of 2‐methylfuran, 3‐methylfuran and 4H‐pyran and the fragmentations that lead to [C₅H₅O]⁺ ions were obtained from calculations at the B3LYP/6‐311G + + (3df,3pd)//B3LYP/6‐31G(d,p) level of theory. The various competing unimolecular processes were characterized by their RRKM microcanonical rate coefficients, k(E), using the sets of reactant and transition state frequencies and the kinetic barriers obtained from the density functional method. In either a high‐ or a low‐energy regime, the pyrylium ion [C₅H₅O]⁺ is generated directly from the 4H‐pyran molecular ion by a simple cleavage. In contrast, in the metastable kinetic window, the molecular ions of methylfurans irreversibly isomerize to a mixture of interconverting structures before dissociation, which includes the 2H‐ and 3H‐pyran ions. The hydrogen atoms attached to saturated carbons of the pyran rings are very stabilizing at the position 2, but they are very labile at position 3 and can be shifted to adjacent positions. Once 4H‐pyran ion has been formed, the C? H bond cleavage begins before any hydrogen shift occurs. According to our calculation, there would not be complete H scrambling preceding the dissociation of the molecular ions [C₅H₆O]^+?. On the other hand, as the internal energy of the 2‐methylfuran molecular ion increases, H^? loss can become more important. These results agree with the available experimental data. Copyright © 2009 John Wiley & Sons, Ltd.     

Theoretical investigation of the proton affinities of benzazoles in the gas phase and in solution

The ground‐state equilibrium geometries of benzothiazole, benzoxazole, and benzimidazole were optimized at the density functional theory (DFT)/6‐31G** level of theory. Proton affinities on each of the possible sites in the studied series of compounds have been calculated at the DFT/6‐31G**/6‐311++G** level. The results indicate clearly that N‐site protonation is strongly favored over X‐site protonation (X = NH, O, S) for the series studied. Correlation of the computed proton affinities to the energy (E_HOMO) of the highest occupied MO in the gas phase and in solution has been explored and discussed. A comprehensive investigation of the effect of solvent on the process of protonation of the studied compounds has been performed. Different dielectric continuum models (i.e., Onsager, PCM, and IPCM) have been tested; their performance and range of applicability are reported and discussed. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

DFT conformational studies of alpha-maltotriose

Recent DFT optimization studies on alpha-maltose improved our understanding of the preferred conformations of alpha-maltose. The present study extends these studies to alpha-maltotriose with three alpha-D-glucopyranose residues linked by two alpha-[1-->4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (phi(H) and psi(H)) move from the region of conformational space of (-, -), relative to (0 degrees , 0 degrees), to a new position defined by (+, +). Further, it was found previously that the relative energies of alpha-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the alpha-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here.     

不饱和类碳烯H2C(=)CLiBr的DFT研究

采用量子化学计算方法，在B3LYP／6－311G^*水平上全优化得到了不饱和类碳烯H2C＝CLiBr的平衡结构，结果表明，不饱和类碳烯H2C＝CLiBr只有两种平衡结构，对这两种平衡结构之间相互转化的过渡态进行计算，求得了转化势垒，根据计算得到的微观性质，采用统计热力学方法，研究了两种平衡结构之间相互转化的热力学性质，进而讨论了两种平衡结构在不同温度下的稳定性问题，在计算得到振动频率及强度的基础上，模拟了稳定平衡结构的红外光谱图。     

Local analysis and comparative study of the hydrogen bonds in the linear (HCN)n and (HNC)n clusters

B3LYP/6-311+G(2d,p), the density functional theory method of 98 package, is applied to study the hydrogen bonding of a series of linear (HCN)_n and (HNC)_n molecular clusters (for n=1–10). By the localization analysis methods we developed, pair-wised σ type H-bond orders and bond energies are calculated for each pair of the two near-by molecules in both (HCN)_n and (HNC)_n clusters. The calculated results are checked well with the shortening of N–H or C–H distance, the elongation of CH or NH bond distance, and the red shift of stretching frequencies of CH or NH. All pieces of evidence show that the central pair of the two molecules forms the strongest H bond when n of (HCN)_n or (HNC)_n is even, and the two middle pairs form the two strongest H bonds when n is odd. Two terminal pairs of HCN or HNC molecules always form the two weakest H-bonds in each molecular cluster. When comparing molecular cluster energies between (HCN)_n and (HNC)_n for various values of n, the well-known (HCN)_n is found more stable than the related (HNC)_n from energy calculation. However, if outcomes of H-bond local analysis are contrasted, our analysis significantly shows that inter-molecular H-bonds inside of (HNC)_n clusters are much stronger than the corresponding H-bonds in (HCN)_n with the same n. In comparing energy differences between these related clusters per monomer, [E_(HNC)n−E_(HCN)n]/n is found decreasing monotonically as n increases. All pieces of evidence from this theoretical prediction indicate that (HNC)_n with large n is probably constructed by its relative strong H-bonds.     

Density functional theory and RRKM calculations of decompositions of the metastable E‐2,4‐pentadienal molecular ions

The potential energy profiles for the fragmentations that lead to [C₅H₅O]⁺ and [C₄H₆]^+? ions from the molecular ions [C₅H₆O]^+? of E‐2,4‐pentadienal were obtained from calculations at the UB3LYP/6‐311G + + (3df,3pd)//UB3LYP/6‐31G(d,p) level of theory. Kinetic barriers and harmonic frequencies obtained by the density functional method were then employed in Rice–Ramsperger–Kassel–Marcus calculations of individual rate coefficients for a large number of reaction steps. The pre‐equilibrium and rate‐controlling step approximations were applied to different regions of the complex potential energy surface, allowing the overall rate of decomposition to be calculated and discriminated between three rival pathways: C? H bond cleavage, decarbonylation and cyclization. These processes should have to compete for an equilibrated mixture of four conformers of the E‐2,4‐pentadienal ions. The direct dissociation, however, can only become important in the high‐energy regime. In contrast, loss of CO and cyclization are observable processes in the metastable kinetic window. The former involves a slow 1,2‐hydrogen shift from the carbonyl group that is immediately followed by the formation of an ion‐neutral complex which, in turn, decomposes rapidly to the s‐trans‐1,3‐butadiene ion [C₄H₆]^+?. The predominating metastable channel is the second one, that is, a multi‐step ring closure which starts with a rate‐limiting cis—trans isomerization. This process yields a mixture of interconverting pyran ions that dissociates to the pyrylium ions [C₅H₅O]⁺. These results can be used to rationalize the CID mass spectrum of E‐2,4‐pentadienal in a low‐energy regime. Copyright © 2010 John Wiley & Sons, Ltd.     

CH3SOCH3与XO(X=Cl,Br)自由基反应的理论研究

采用密度泛函理论B3LYP方法,在6-311 G(d,p)基组水平上研究了二甲亚砜(DMSO)与XO(X=Cl,Br)自由基反应的微观动力学机理,并利用经过wigner校正的传统过渡态理论计算了标题反应在200~2000 K温度范围内的反应速率常数。研究结果表明,DMSO与XO(X=Cl,Br)自由基反应主要有氧转移和抽氢两种反应机理,氧转移反应的能垒显著低于抽氢反应,且前者为放热反应后者为吸热反应;低温时氧转移反应占绝对优势,298 K时DMSO与XO(X=Cl,Br)两个反应体系的总速率常数分别为2.09×10-15和1.75×10-14cm3.molecu le-1.s-1,氧转移反应分支比均为100%。高温时抽氢反应上升为主通道。2000 K时其总速率常数分别为6.32×10-12和8.41×10-12cm3.molecule-1.s-1,抽氢反应分支比分别为91.8%和79.4%。     

Structural Relevance of Intramolecular H-Bonding in Ortho-Hydroxyaryl Schiff Bases: The Case of 3-(5-bromo-2-hydroxybenzylideneamino) Phenol

A new Schiff base compound, 3-(5-bromo-2-hydroxybenzylideneamino)phenol (abbreviated as BHAP) was synthesized and characterized by ¹H- and ¹³C- nuclear magnetic resonance and infrared spectroscopies. DFT/B3LYP/6-311++G(d,p) calculations were undertaken in order to explore the conformational space of both the E- and Z- geometrical isomers of the enol-imine and keto-amine tautomers of the compound. Optimized geometries and relative energies were obtained, and it was shown that the most stable species is the E-enol-imine form, which may exist in four low-energy intramolecularly hydrogen-bonded forms (I, II, V, and VI) that are almost isoenergetic. These conformers were concluded to exist in the gas phase equilibrium with nearly equal populations. On the other hand, the infrared spectra of the compound isolated in a cryogenic argon matrix (10 K) are compatible with the presence in the matrix of only two of these conformers (conformers II and V), while conformers I and VI convert to these ones by quantum mechanical tunneling through the barrier associated with the rotation of the OH phenolic group around the C–O bond. The matrix isolation infrared spectrum was then assigned and interpreted with help of the DFT(B3LYP)/6-311++G(d,p) calculated infrared spectra for conformers II and V. In addition, natural bond orbital (NBO) analysis was performed on the most stable conformer of the experimentally relevant isomeric form (E-enol-imino conformer V) to shed light on details of its electronic structure. This investigation stresses the fundamental structural relevance of the O–H···N intramolecular H-bond in o-hydroxyaryl Schiff base compounds.     

Theoretical influence of third molecule on reaction channels of weakly bound complex CO2… HF systems

In this investigation, reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…H₂O and CO₂…HF…CH₃OH systems were established at the B3LYP/6‐311++G(3df,2pd) level, using the Gaussian 98 program. The conformers of syn‐fluoroformic acid or syn‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH) were found to be more stable than the conformers of the related anti‐fluoroformic acid or anti‐fluoroformic acid plus a third molecule (NH₃, H₂O, or CH₃OH). However, the weakly bound complexes were found to be more stable than either the related syn‐ and anti‐type fluoroformic acid or the acid plus third molecule (NH₃, H₂O, or CH₃OH) conformers. They decomposed into CO₂ + HF, CO₂ + NH₄F, CO₂ + H₃OF or CO₂ + (CH₃)OH₂F combined molecular systems. The weakly bound complexes have four reaction channels, each of which includes weakly bound complexes and related systems. Moreover, each reaction channel includes two transition state structures. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly larger than that of internal rotation (T₂₃) between the syn‐ and anti‐FCO₂H (or FCO₂H…NH₃, FCO₂H…H₂O, or FCO₂H…CH₃OH) structures. However, adding the third molecule NH₃, H₂O, or CH₃OH can significantly reduce the activation energy of T₁₃. The catalytic strengths of the third molecules are predicted to follow the order H₂O < NH₃ < CH₃OH. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006     

Theoretical study of reaction channels for the weakly bound complex systems created with HF,CO2, and various amines

This investigation conducted reaction channels of weakly bound complexes CO₂…HF, CO₂…HF…NH₃, CO₂…HF…NH₂CH₃, CO₂…HF…NH(CH₃)₂, and CO₂…HF…N(CH₃)₃ systems, using the Gaussian 98 package at the B3LYP/6‐311++G(3df,2pd) level. The syn‐fluoroformic acid or syn‐fluoroformic acid plus NH₃ or amine conformers are more stable than the related anti‐fluoroformic acid or anti‐fluoroformic acid plus NH₃ or amine conformers. However, the above‐mentioned weakly bound complexes are more stable than both the related syn‐ and anti‐type fluoroformic acid or acid plus NH₃ or amine conformers and their related decomposed into CO₂ + HF or CO₂ + NHR₃F (R?H, CH₃) combined molecular systems. Five reaction channels of the weakly bound complexes exist. Each channel includes weakly bound complexes and their related above‐mentioned systems. Moreover, each reaction channel contains two transition states. The transition state between the weakly bound complex and anti‐fluoroformic acid type structure (T₁₃) is significantly higher than that of internal rotation (T₂₃) between syn‐ and anti‐FCO₂H (or FCO₂H…NR₃) structures. However, the above‐mentioned T₁₃ can significantly decrease its energy by adding the third molecule NH₃ or NR₃ (R?H or CH₃). The more CH₃ that is substituted in NR₃ of the reaction channel, the lower the activation energy of the transition state in the system is affected. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Comparative analysis of a full-electron basis set and pseudopotential for the iodine atom in DFT quantum-chemical calculations of iodine-containing compounds

A systematic study was performed to examine the possibilities of the B3LYP DFT method in a dgdzvp full-electron basis and of the method including a pseudopotential for iodine compounds. The full-electron basis generally gives better agreement for X-I bond lengths and reaction enthalpies of iodination of organic compounds and equally good agreement in calculations of the IR vibrations of the X-I bond length compared with the studies using the pseudopotential. The full-electron basis also allows adequate calculations of the quadrupole coupling constants of iodine atoms and is generally characterized by smaller computing times.     

The structure of fosfomycin salts in solution and in the solid state by nuclear magnetic resonance spectroscopy and DFT calculations

Two samples of fosfomycin salts, the calcium and the disodium ones, were used to record their NMR spectra both in solution and in the solid state. The existence of fosfomycin in a neutral and two ionized structures (mono and dianion) was considered to interpret the spectra that were solved using the GIAO calculated chemical shifts of the minimum energy conformations. Although the starting materials were dianions, the spectra in solution show the presence of monoanions.     

Theoretical Study of Weakly Bound Dimers between Hydrogen Fluoride and Some Polar Molecules

Weakly bound linear and bent dimers, FH—X (where X = CO, OC, CNH, NCH, N₂O and ON₂), are investigated using the DFT B3LYP and ab initio MP2 methods with the same basis sets (6–311++G(3df,2pd)). The strengths of the H—C or H—N H‐bonds in dimers FH—CO, FH—CNH, and FH—N₂O are compared with those of the H—O or H—N H‐bonds in dimers FH—OC, FH—NCH, and FH—ON₂. The results obtained for the H‐bond distances, the elongation effect of the HF bond, the red shift of the HF stretching frequency, and the energy difference between the dimer and the charge transfer reveal that the H‐bonds of the first group of dimers are stronger than those of the second. The Gibbs energies calculated for the six dimer formations indicate that the weakly bound dimers are unstable at room temperature (T = 298 K) (FH—X's → FH + X's, ΔG < 0).     

DFT study on the role of methanol solvent in Morita–Baylis–Hillman reaction

B3LYP/6‐311++G** calculations have been carried out to study the role of methanol solvent in the trimethylamine‐catalyzed Morita‐Baylis‐Hillman reaction between acraldehyde and formaldehyde with CPCM solvent method and supramolecular model with one explicit CH₃OH solvent molecule, respectively. The optimized geometries and energies of the reactant complexes, intermediates, transition states, and products of the two reaction channels (corresponding to the scenarios of syn‐ and anti‐acraldehyde, respectively) were obtained, and the relative energy profiles were completed. The results reveal that CH₃OH solvent molecules can stabilize the zwitterionic intermediates and largely reduce the barrier of H transfer process by taking part in the formation of the transition state in this process. C? C bond formation step is the rate‐determining step of the whole reaction cycle. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009     

Site-selective formation of N-arylmethylimidazoles and C-arylimines in the reaction of 4,5-diamino-2,1,3-benzothiadiazole with aromatic aldehydes

Regioselective formation of N-arylmethylimidazoles and C-arylimines was found in the reaction of 4,5-diamino-2,1,3-benzothiadiazole with selected aromatic aldehydes. The regiochemistry of the reaction products was confirmed by single crystal X-ray analysis. Gibbs free energy calculation using DFT method at the B3LYP/6-31G(d) level supports the regio-selectivity observed. The 4-imine obtained in the reaction of 4,5-diamino-2,1,3-benzothiadiazole with pyrene-1-carboxaldehyde showed an unusually low magnetic field shift of the imine proton that was reproduced by molecular calculations.     

基于2,4-二丙稀酰胺嘧啶的氢键复合物的稳定性和光谱

氢键对含有以嘧啶为基的衍生物的生命体具有重要作用。用AM1 和 DFT 方法对2,4-二丙稀酰胺嘧啶(2,4-BAAP) 衍生物与1-取代的脲嘧啶形成的氢键复合物电子结构进行理论研究。用INDO/SCI 和 B3LYP/6-31G(d)方法分别计算了复合物的UV和NMR光谱。结果表明,由于结合能为负值,两单体能通过三重氢键形成复合物,取代基存在时结合能变小。这种削弱效应取决于电子效应和空间效应的协同作用。当2,4-BAAP上哌啶基存在时,由于异构复合物的形成,复合物的结合能变小。供电基存在时复合物的能隙变小。共轭体系的扩展使复合物易于注入电子和空穴。复合物电子光谱的第一吸收峰与母体相比发生红移由于其具有较小的LUMO-HOMO能隙。在13C NMR谱中,复合物C=O键上的C原子的化学位移向低场移动。