Diels-Alder反应中的次级轨道效应

利用概念密度泛函理论下的局域软度和广义局域软度,结合局域硬软酸碱(HSAB)原理,研究环戊二烯与CH2=CHCOCnH2n+1之间的Diels-Alder反应的立体选择性,其中活性因子均是由ABEEMσπ模型获得.与以往不同的是,除了将主要参与反应的4个原子作为反应中心之外,还将产生次级轨道效应(SOI)的2个原子也作为参与反应的一部分.得到的结果表明,所有反应的立体选择性均与实验结果取得了很好的一致性,由此提出了一种定量快速处理包含次级轨道效应的Diels-Alder反应的立体选择性的方法.     

Valence state parameters of all transition metal atoms in metalloproteins—development of ABEEMσπ fluctuating charge force field

To promote accuracy of the atom‐bond electronegativity equalization method (ABEEMσπ) fluctuating charge polarizable force fields, and extend it to include all transition metal atoms, a new parameter, the reference charge is set up in the expression of the total energy potential function. We select over 700 model molecules most of which model metalloprotein molecules that come from Protein Data Bank. We set reference charges for different apparent valence states of transition metals and calibrate the parameters of reference charges, valence state electronegativities, and valence state hardnesses for ABEEMσπ through linear regression and least square method. These parameters can be used to calculate charge distributions of metalloproteins containing transition metal atoms (Sc‐Zn, Y‐Cd, and Lu‐Hg). Compared the results of ABEEMσπ charge distributions with those obtained by ab initio method, the quite good linear correlations of the two kinds of charge distributions are shown. The reason why the STO‐3G basis set in Mulliken population analysis for the parameter calibration is specially explained in detail. Furthermore, ABEEMσπ method can also quickly and quite accurately calculate dipole moments of molecules. Molecular dynamics optimizations of five metalloproteins as the examples show that their structures obtained by ABEEMσπ fluctuating charge polarizable force field are very close to the structures optimized by the ab initio MP2/6–311G method. This means that the ABEEMσπ/MM can now be applied to molecular dynamics simulations of systems that contain metalloproteins with good accuracy. © 2014 Wiley Periodicals, Inc.     

Molecular electronegativity in density functional theory(VIII) Charge polarization modes in a closed system

Based on the density functional theory and the atom-bond electronegativity equalization model (ABEEM), a method is proposed to construct the softness matrix and to obtain the electron population normal modes (PNMs) for a closed system. Using this method the information about the bond charge polarization in a molecule can be obtained easily. The test calculation shows that the PNM obtained by this method includes all the modes about the bond charge polarization explicitly. And the bond charge polarization mode characterized by the biggest eigenvalue, which is the softest one of all modes related with chemical bonds, can describe the charge polarization process in a molecule as exquisitely as the correspondingab initio method.     

Theoretical study on the hydration of hydrogen peroxide in terms of ab initio method and atom-bond electronegativity equalization method fused into molecular mechanics

In this paper, the interaction between hydrogen peroxide (HP) and water were systemically studied by atom-bond electronegativity equalization method fused into molecular mechanics (ABEEM/MM) and ab initio method. The results show that the optimized geometries, interaction energies and dipole moments of hydrated HP clusters HP(H₂O) _n (n = 1–6) calculated by ABEEM/MM model are fairly consistent with the MP2/aug-cc-pVTZ//MP2/aug-cc-pVDZ results. The ABEEM/MM results indicate that n = 4 is the transition state structure from 2D planar structure to 3D network structure. The variations of the average hydrogen bond length with the increasing number of water molecules given by ABEEM/MM model agree well with those of ab initio studies. Moreover, the radial distribution functions (RDFs) of water molecule around HP in HP aqueous solution have been analyzed in detail. It can be confirmed that HP is a good proton donor and poor proton acceptor in aqueous solution by analysis of the RDFs.     

Molecular electronegativity in density functional theory(VIII)

Based on the density functional theory and the atom-bond electronegativity equalization model (ABEEM), a method is proposed to construct the softness matrix and to obtain the electron population normal modes (PNMs) for a closed system. Using this method the information about the bond charge polarization in a molecule can be obtained easily. The test calculation shows that the PNM obtained by this method includes all the modes about the bond charge polarization explicitly. And the bond charge polarization mode characterized by the biggest eigenvalue, which is the softest one of all modes related with chemical bonds, can describe the charge polarization process in a molecule as exquisitely as the correspondingab initio method.     

Fukui函数和局域软度应用于亲电加成反应的区位选择性的研究

Fukui函数、局域软度、广义Fukui函数以及广义软度通常被称为反应描述符。使用它们研究和探讨了HCl与不对称烯烃以及溴苯硒与不对称苯乙烯的亲电加成反应的区位选择性。在MP2/6-311++G(d, p)理论水平下,采用有限差分方法计算这些反应描述符,同时也使用ABEEMσπ方法进行了计算。ABEEMσπ模型下的局域软度和广义局域软度,分别结合局域硬-软酸碱(HSAB)原理,得出亲电试剂氯化氢与溴苯硒,更容易进攻不对称乙烯和苯乙烯中的马氏碳原子,符合马氏规则。而有限差分方法不能完全地解释该系列反应的区位选择性。此外,主要产物所对应的马氏碳原子的广义局域软度值,就能够预测出此类反应的活性序列,所得结果与速率常数有很好的关联。     

Local HSAB principle in the conjugate addition of p‐substituted thiophenols to cyclohexenone

In the formation of new bonds through the Michel‐type addition of thiolates to a α,β‐conjugate system, it is observed that the reaction takes place faster if the thio donor compound contains an electron‐rich group or the enone acceptor is highly electron deficient. In contrast, the hard–soft acid–base (HSAB) principle predicts that this reaction is favored when a soft–soft interaction between the reactants takes place. Taking into account that softness is related to a barely electronegative atom of high polarizability, we consider it of interest to analyze the effect of charge transfer of a p‐substituent on the softness of sulfur in thiophenols, as well as its impact in the conjugate addition to 2‐cyclohexen‐1‐one. Experiments‐in‐competition, net charge of X‐groups at the p‐position of the aromatic ring, the global and local softness at sulfur, and the electrophilicity, obtained by density functional theory (DFT), led to the observation that the reaction is faster for electron attractor thiophenols. The softness at sulfur increases by delocalization of charge through the aromatic ring. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Insight into Markovnikov regioselectivity rule via molecular face and ABEEM‐σπ theory

Electrophilic additions of HCl to a series of asymmetric alkenes in the gas phase are investigated by the Molecular Face (MF) theory and ABEEM‐σπ model. The interesting features of regioselectivity for these reactions are characterized by the electron density (ED) encoded on the MF of alkenes and charge distribution of alkenes obtained via the ABEEM‐σπ model, respectively. It is then demonstrated that for a series of alkenes, the Hammett constant σ_p (substituent constant) has a good linear correlation with K_ED, where K_ED is character of the ED at the π region in the initial state of alkenes. Comparison between investigations using MF, ABEEM‐σπ, molecular electrostatic potential, and DFT theories, in essence, give similar conclusions for explaining the regioselectivity of the electrophilic additions to alkenes, although from different points of view. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011     

Increasing the time step with mass scaling in Born‐Oppenheimer ab initio QM/MM molecular dynamics simulations

Born‐Oppenheimer ab initio QM/MM molecular dynamics simulation with umbrella sampling is a state‐of‐the‐art approach to calculate free energy profiles of chemical reactions in complex systems. To further improve its computational efficiency, a mass‐scaling method with the increased time step in MD simulations has been explored and tested. It is found that by increasing the hydrogen mass to 10 amu, a time step of 3 fs can be employed in ab initio QM/MM MD simulations. In all our three test cases, including two solution reactions and one enzyme reaction, the resulted reaction free energy profiles with 3 fs time step and mass scaling are found to be in excellent agreement with the corresponding simulation results using 1 fs time step and the normal mass. These results indicate that for Born‐Oppenheimer ab initio QM/MM molecular dynamics simulations with umbrella sampling, the mass‐scaling method can significantly reduce its computational cost while has little effect on the calculated free energy profiles. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

Multiobjective evolutionary algorithm with many tables for purely ab initio protein structure prediction

This article focuses on the development of an approach for ab initio protein structure prediction (PSP) without using any earlier knowledge from similar protein structures, as fragment‐based statistics or inference of secondary structures. Such an approach is called purely ab initio prediction. The article shows that well‐designed multiobjective evolutionary algorithms can predict relevant protein structures in a purely ab initio way. One challenge for purely ab initio PSP is the prediction of structures with β‐sheets. To work with such proteins, this research has also developed procedures to efficiently estimate hydrogen bond and solvation contribution energies. Considering van der Waals, electrostatic, hydrogen bond, and solvation contribution energies, the PSP is a problem with four energetic terms to be minimized. Each interaction energy term can be considered an objective of an optimization method. Combinatorial problems with four objectives have been considered too complex for the available multiobjective optimization (MOO) methods. The proposed approach, called “Multiobjective evolutionary algorithms with many tables” (MEAMT), can efficiently deal with four objectives through the combination thereof, performing a more adequate sampling of the objective space. Therefore, this method can better map the promising regions in this space, predicting structures in a purely ab initio way. In other words, MEAMT is an efficient optimization method for MOO, which explores simultaneously the search space as well as the objective space. MEAMT can predict structures with one or two domains with RMSDs comparable to values obtained by recently developed ab initio methods (GAPF_CG, I‐PAES, and Quark) that use different levels of earlier knowledge. © 2013 Wiley Periodicals, Inc.     

Chemical Reactivity of Oxo‐ and Aza‐γ‐lactam Rings

Different mechanisms for the alkaline hydrolysis of oxo and aza‐γ‐lactam rings have been studied by ab initio calculations at the MP2/6‐31+G*//MP2/6‐31+G* and B3LYP/6‐31+G*//B3LYP/6‐31+G* levels. The tetrahedral intermediate can undergo two different reactions, the cleavage of the C₂−N₂ bond (the classical mechanism) and the cleavage of the C₂−X₆ bond (X=O, N). Both compounds present similar energy barriers for the classical fragmentation, and show considerably lower barriers for the alternative mechanism. Because of this reactivity, the compounds studied are expected to be β‐lactamase inhibitors.     

致癌性胺离子反应过程中电荷和化学位移的计算

应用原子-键电负性均衡方法中的σπ模型(ABEEMσπ)计算了由致癌性胺离子所参与的反应过程中的电荷分布,所计算出的电荷分布可以和从头算很好的相关联,并且所需要的时间也大大的缩短;同时应用从头计算程序计算致癌性胺离子反应过程中的NMR化学位移.结果表明,在反应过程中电荷的变化和NMR化学位移的变化有很好的对应关系.     

Dealkenylative Alkenylation: Formal σ‐Bond Metathesis of Olefins

The dealkenylative alkenylation of alkene C(sp³)?C(sp²) bonds has been an unexplored area for C?C bond formation. Herein 64 examples of β‐alkylated styrene derivatives, synthesized through the reactions of readily accessible feedstock olefins with β‐nitrostyrenes by ozone/Fe^II‐mediated radical substitutions, are reported. These reactions proceed with good efficiencies and high stereoselectivities under mild reaction conditions and tolerate an array of functional groups. Also demonstrated is the applicability of the strategy through several synthetic transformations of the products, as well as the syntheses of the natural product iso‐moracin and the drug (E)‐metanicotine.     

Peptide models XXXI. Conformational properties of hydrophobic residues shaping the core of proteins. An ab initio study of N‐formyl‐L‐valinamide and N‐formyl‐L‐phenylalaninamide

Employing introductory (3‐21G RHF) and medium‐size (6‐311++G** B3LYP) ab initio calculations, complete conformational libraries, containing as many as 27 conformers, have been determined for diamide model systems incorporating the amino acids valine (Val) and phenylalanine (Phe). Conformational and energetic properties of these libraries were analyzed. For example, significant correlation was found between relative energies from 6‐311++G** B3LYP and single‐point B3LYP/6‐311++G**//RHF/3‐21G calculations. Comparison of populations of molecular conformations of hydrophobic aromatic and nonaromatic residues, based on their ab initiorelative energies, with their natural abundance indicates that, at least for the hydrophobic core of proteins, the conformations of Val (Ile, Leu) and Phe (Tyr, Trp) are controlled by the local energetic preferences of the respective amino acids. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 732–751, 2001     

Theoretical investigation of the stereoselectivity of some Diels＇Alder reactions involving cyclopentadiene

The stereoselectivity of some Diels-Alder reactions was investigated by means of ABEEM-oTr model. Combined with local hard-soft and acid-base （HSAB） principle, we made reasonable explanation by calculating local softness of atom and bond regions for the stereoselectivity of four Diels-Alder reactions involving cyclopentadiene.     

Theoretical Study on Co^3＋ in Aqueous Solution in Terms of ABEEM/MM Model

A detailed theoretical investigation on Co^3＋ hydration in aqueous solution has been carded out by means of molecular dynamics （MD） simulations based on the atom-bond electronegativity equalization method fused into molecular mechanics （ABEEM/MM）. The effective Co^3＋ ion-water potential has been constructed by fitting to ab initio structures and binding energies for ionic clusters. And then the ion-water interaction potential was applied in combination with the ABEEM-7P water model to molecular dynamics simulations of single Co^3＋（aq.） solution, managing to reproduce many experimental structural and dynamical properties of the solution. Here, not only the common properties （radial distribution function, angular distribution function and solvation energy） obtained for Co^3＋ in ABEEM-7P water solution were in good agreement with those from the experimental methods and other molecular dynamics simulations but also very interesting properties of charge distributions, geometries of water molecules, hydrogen bond, diffusion coefficients, vibrational spectra are investigated by ABEEM/MM model.     

Theoretical investigation of the stereoselectivity of some Diels-Alder reactions involving cyclopentadiene

The stereoselectivity of some Diels-Alder reactions was investigated by means of ABEEM-oTr model.Combined with local hard-soft and acid-base(HSAB)principle,we made reasonable explanation by calculating local softness of atom and bond regions for the stereoselectivity of four Diels-Alder reactions involving cyclopentadiene.     

Theoretical study of “protonated pyruvate”: A methylhydroxycarbene—carbon dioxide complex—implications for the decarboxylation of pyruvic acid

Two conformers of protonated pyruvate, CH₃C⁺(OH)COO, with the OH group either trans or cis to the methyl group and the carboxylate group in the C? C? C plane have been studied using the ab initio SCF/3-21G method, as well as by some semiempirical AM1 calculations. Both ab initio SCF and AM1 curves for the potential energy as a function of the C? COO distance exhibit a minimum corresponding to a complex of methylhydroxycarbene, CH₃COH, associated with carbon dioxide, but only the AM1 curves predict an inner minimum corresponding to a covalently bonded protonated pyruvate molecule with a C? COO distance of 1.6–1.7 Å. The two models also disagree on the dissociation pathway for pyruvic acid, with the AM1 calculations predicting formation of acetyl and HOCO radicals while the ab initio method predicts dissociation into methylhydroxycarbene and carbon dioxide following an initial intramolecular proton transfer. The weakly bound complexes of methylhydroxycarbene and carbon dioxide have been studied in some detail using ab initio SCF and MP2 methods in conjunction with 6-311G** basis sets, obtaining equilibrium geometries and vibrational frequencies. In addition, the lactone-type isomer of protonated pyruvate, which contains a C? C? O ring, was also studied. The conclusions of these calculations are consistent with those from earlier work using the smaller 3-21G basis set. The most stable complex is predicted to occur between trans-methylhydroxycarbene and carbon dioxide where substantial stabilization is provided by an OH ? OC hydrogen bond. © 1993 John Wiley & Sons, Inc.     

Hydrogen Radical Additions to Unsaturated Hydrocarbons and the Reverse β‐Scission Reactions: Modeling of Activation Energies and Pre‐Exponential Factors

The group additivity method for Arrhenius parameters is applied to hydrogen addition to alkenes and alkynes and the reverse β‐scission reactions, an important family of reactions in thermal processes based on radical chemistry. A consistent set of group additive values for 33 groups is derived to calculate the activation energy and pre‐exponential factor for a broad range of hydrogen addition reactions. The group additive values are determined from CBS‐QB3 ab‐initio‐calculated rate coefficients. A mean factor of deviation of only two between CBS‐QB3 and experimental rate coefficients for seven reactions in the range 300–1000 K is found. Tunneling coefficients for these reactions were found to be significant below 400 K and a correlation accounting for tunneling is presented. Application of the obtained group additive values to predict the kinetics for a set of 11 additions and β‐scissions yields rate coefficients within a factor of 3.5 of the CBS‐QB3 results except for two β‐scissions with severe steric effects. The mean factor of deviation with respect to experimental rate coefficients of 2.0 shows that the group additive method with tunneling corrections can accurately predict the kinetics and is at least as accurate as the most commonly used density functional methods. The constructed group additive model can hence be applied to predict the kinetics of hydrogen radical additions for a broad range of unsaturated compounds.