叔丁氧基自由基引发氢迁移过程的理论研究

采用多种密度泛函理论方法(如CAM-B3LYP, M062x和wB97x方法), 并辅以极化连续介质模型对叔丁氧基自由基(^tBuO·)与一系列胺类、 烷烃、 醇类和醚类反应物之间氢迁移反应的反应机理进行研究. 计算结果表明, 这类氢迁移反应主要受熵的控制. 通过对液相平动熵和气相平动熵得到的活化自由能数据进行对比, 可以看出, 使用气相平动熵得出的活化自由能明显偏高于实验测量值, 而以液相平动熵计算的反应活化自由能垒与实际结果相近, 3种方法对胺类和烷烃类反应物体系得出的结果更可靠, 对醇类和醚类反应物体系自由能垒则略低.     

Facial Synthesis of o‐Carborane‐Substituted Alkenes and Allenes by a Regioselective Ene Reaction of 1,3‐Dehydro‐o‐carborane

1,3‐Dehydro‐o‐carborane is a useful synthon for selective cage boron functionalization of o‐carboranes. It reacts readily with alkenes or alkynes to give a variety of cage B(3)‐alkenyl/allenyl o‐carboranes by ene reactions in very high yields and excellent regioselectivity. This can be ascribed to the highly polarized cage C?B multiple bond, which lowers the activation barriers of the ene reaction.     

Depolymerization of Free‐Radical Polymers with Spin Migrations

The mechanism of depolymerization is one of the most essential issues in chemical engineering and materials science. In this work, we investigate the depolymerization reactions of three typical free‐radical poly(alpha‐methylstyrene) tetramers by using first‐principles density functional theory. The calculated results show that these reactions all need to overcome the energy barriers in the range of 0.58 to 0.77 eV, and that breaking the C?C bond at the chain end leads to the dissociation of alpha‐methylstyrene monomers from the polymers. Electronic‐structure analysis indicates that the reactions occur easily at the CR₃ unsaturated end, and that the frontier molecular orbitals that participate in the reactions are mainly localized at the unsaturated ends. Meanwhile, spin population analysis presents the unique net spin‐transfer process in free‐radical depolymerization reactions. We hope the current findings can contribute to understanding the free‐radical depolymerization mechanism and help guide future experiments.     

Associative Versus Dissociative Mechanisms of Phosphate Monoester Hydrolysis: On the Interpretation of Activation Entropies

Phosphate monoester and anhydride hydrolysis is ubiquitous in biology, being involved in, amongst other things, signal transduction, energy production, and the regulation of protein function. Therefore, this reaction has understandably been the focus of intensive research. Nevertheless, the precise mechanism by which phosphate monoester hydrolysis proceeds remains controversial. Traditionally, it has been assumed and frequently implied that a near‐zero activation entropy is indicative of a dissociative pathway. Herein, we examine free‐energy surfaces for the hydrolysis of the methyl phosphate dianion and the methyl pyrophosphate trianion in aqueous solution. In both cases, the reaction can proceed through either compact or expansive concerted (A_ND_N) transition states, with fairly similar barriers. We have evaluated the activation entropies for each transition state and demonstrate that both associative and dissociative transition states have near‐zero entropies of activation that are in good agreement with experimental values. Therefore, we believe that the activation entropy alone is not a useful diagnostic tool, as it depends not only on bond orders at the transition state, but also on other issues that include (but are not limited to) steric factors determining the configurational volumes available to reactants during the reaction, solvation and desolvation effects that may be associated with charge redistribution upon approaching the transition state and entropy changes associated with intramolecular degrees of freedom as the transition state is approached.     

Calculations of solute and solvent entropies from molecular dynamics simulations

The translational, rotational and conformational (vibrational) entropy contributions to ligand-receptor binding free energies are analyzed within the standard formulation of statistical thermodynamics. It is shown that the partitioning of the binding entropy into different components is to some extent arbitrary, but an appropriate method to calculate both translational and rotational entropy contributions to noncovalent association is by estimating the configurational volumes of the ligand in the bound and free states. Different approaches to calculating solute entropies using free energy perturbation calculations, configurational volumes based on root-mean-square fluctuations and covariance matrix based quasiharmonic analysis are illustrated for some simple molecular systems. Numerical examples for the different contributions demonstrate that theoretically derived results are well reproduced by the approximations. Calculation of solvent entropies, either using total potential energy averages or van't Hoff plots, are carried out for the case of ion solvation in water. Although convergence problems will persist for large and complex simulation systems, good agreement with experiment is obtained here for relative and absolute ion hydration entropies. We also outline how solvent and solute entropic contributions are taken into account in empirical binding free energy calculations using the linear interaction energy method. In particular it is shown that empirical scaling of the nonpolar intermolecular ligand interaction energy effectively takes into account size dependent contributions to the binding free energy.     

Comprehensive Analysis of DNA Strand Breaks at the Guanosine Site Induced by Low‐Energy Electron Attachment

To elucidate the role of guanosine in DNA strand breaks caused by low‐energy electrons (LEEs), theoretical investigations of the LEE attachment‐induced C? O σ‐bonds and N‐glycosidic bond breaking of 2′‐deoxyguanosine‐3′,5′‐diphosphate (3′,5′‐dGMP) were performed using the B3LYP/DZP++ approach. The results reveal possible reaction pathways in the gas phase and in aqueous solutions. In the gas phase LEEs could attach to the phosphate group adjacent to the guanosine to form a radical anion. However, the small vertical detachment energy (VDE) of the radical anion of guanosine 3′,5′‐diphosphate in the gas phase excludes either C? O bond cleavage or N‐glycosidic bond breaking. In the presence of the polarizable surroundings, the solvent effects dramatically increase the electron affinities of the 3′,5′‐dGDP and the VDE of 3′,5′‐dGDP^?. Furthermore, the solvent–solute interactions greatly reduce the activation barriers of the C? O bond cleavage to 1.06–3.56 kcal mol^?1. These low‐energy barriers ensure that either C_5′? O_5′ or C_3′? O_3′ bond rupture takes place at the guanosine site in DNA single strands. On the other hand, the comparatively high energy barrier of the N‐glycosidic bond rupture implies that this reaction pathway is inferior to C? O bond cleavage. Qualitative agreement was found between the theoretical sequence of the bond breaking reaction pathways in the PCM model and the ratio for the corresponding bond breaks observed in the experiment of LEE‐induced damage in oligonucleotide tetramer CGTA. This concord suggests that the influence of the surroundings in the thin solid film on the LEE‐induced DNA damage resembles that of the solvent.     

The Effect of Solvation on the Radiation Damage Rate Constants for Adenine

It is well known that water plays an important part in almost all biological systems and that inclusion of solvation effects might therefore be of utmost importance in studies of radiation damage to DNA. In the present investigation, we have studied the effect of different solvation models in calculations of Gibbs free energies and reaction rates for the reaction between the OH radical and the DNA nucleobase adenine by conducting density functional theory calculations at the ωB97X‐D/6‐311++G(2df,2pd) level with the Eckart tunnelling correction. The solvent, water, was included through either the implicit polarizable continuum model (PCM) or through explicit modelling of micro‐solvation by a single water molecule at the site of reaction as well as by the combination of both. Scrutiny of the thermodynamics and kinetics of the individual sub‐reactions suggests that the qualitative differences introduced by the solvation models do not significantly alter the conclusions made based solely on simple gas‐phase calculations. Abstraction of the amine hydrogen atoms H₆₁ and H₆₂ and addition onto C₈ remain the most likely reaction pathways.     

Lewis碱稳定的硼代苯与亲二烯体的Diels-Alder反应的理论研究

采用密度泛函理论方法在B3LYP/6-31G(d)水平上研究了Lewis碱稳定的硼代苯与一些亲二烯体的两种可能的Diels-Alder反应的微观机理和势能剖面, 并研究了反应的溶剂效应和取代基效应. 计算结果表明, 一部分反应以直接的近同步的协同方式进行, 而在另一部分反应中, 两个反应物分子先形成分子间复合物, 然后再经过协同的过渡态生成产物. 与气相中相比, 二氯甲烷溶剂使所研究的大部分反应的活化能垒有所增加. 在乙炔或乙烯分子中分别引入吸电子基团CO2Me或CN能显著降低反应的活化能垒. 形成一个C—B键的杂Diels-Alder反应都比相应的Diels-Alder反应在热力学和动力学上容易进行, 这与实验结果一致.     

Theoretical comparison of ketene dimerization in the gas and liquid phase

We present the first theoretical comparison between ketene dimerization in gas phase and ketene dimerization in solution. Density functional theory (DFT) calculations on the ketene dimerization were carried out considering the following product dimers: diketene (d-I), 1,3-cyclobutanedione (d-II), 2,4-dimethylene-1,3-dioxetane (d-III), and 2-methyleneoxetan-3-one (d-IV). All structures were optimized at the PW86x+PBEc/DZP level of theory. Based on these geometries, a total of 58 meta and hybrid functionals were used to evaluate the heat of dimerization. The MPW1K functional was found to fit the experimental data best and subsequently used in the final analyses for all energy calculations. It was found on both kinetic and thermodynamic grounds that only d-I and d-II are formed during ketene dimerization in gas phase and solution. In gas phase, d-I is favored over d-II by 2 kcal/mol. However, the dimerization barrier for d-I is 1 kcal/mol higher than for d-II. Solvation makes dimerization more favorable. On the enthalpic surface this is due to a favorable interaction between the dimer dipole moment and solvent molecules. The dimer is stabilized further on the Gibbs energy surface by an increase of the dimerization entropy in solution compared to gas phase. The species d-I remains the most stable dimer in solution by 1 kcal/mol. Kinetically, the dimerization barriers for the relevant species d-I and d-II are cut in half by solvation, due to both favorable dimer-dipole/solvent interactions (DeltaH++, DeltaG++) and an increase in the activation entropies (DeltaS++). While the dimerization barrier for d-II is lowest for the gas phase and toluene, the barrier for d-I formation becomes lowest for the more polar solvent acetone by 1 kcal/mol as d-I dimerization has the most polar transition state.     

Solvent effects on methyl transfer reactions. 2. The reaction of amines with trimethylsulfonium salts.

The reaction of ammonia and pyridine with trimethylsulfonium ion has been studied in gas phase and solution. Density functional theory at the B3LYP/6-31+G level was used to describe the energy changes along the reaction coordinate in the gas phase, and the self-consistent isodensity polarizable continuum model (SCI-PCM) was used to calculate the effect of cyclohexane and dimethyl sulfoxide as the solvent on the energy changes. The effect of water as the solvent was studied using the Monte Carlo free energy perturbation method. The reaction with both ammonia and pyridine follows a similar rather convoluted path in gas phase, with the formation of several reaction complexes before and after the formation of the transition state. All the species found in gas phase persist in cyclohexane, yielding a reaction path very similar to that in gas phase but with significant differences in the relative energy of the critical points. In DMSO, the energy profile is greatly simplified by the disappearance of several of the species found in gas phase and in cyclohexane. The activation free energy increases with the polarity of the solvent in both reactions. Increasing the polarity of the solvent also increases the exothermicity of the reaction of trimethylsulfonium ion with ammonia and reduces it in the reaction with pyridine. In water, the free energy profile follows the same trend as found for DMSO, and free energy of activation is calculated to be larger by about 2-3 kcal/mol. This is in good agreement with an experimental measurement of the effect of solvent on the rate of reaction.     

Alder-ene reaction: aromaticity and activation-strain analysis

We have computationally explored the trend in reactivity of the Alder-ene reactions between propene and a series of seven enophiles using density functional theory at M06-2X/def2-TZVPP. The reaction barrier decreases along the enophiles in the order H₂CCH₂ > HCCH > H₂CNH > H₂CCH(COOCH₃) > H₂CO > H₂CPH > H₂CS. Thus, barriers drop in particular, if third-period atoms become involved in the double bond of the enophile. Activation-strain analyses show that this trend in reactivity correlates with the activation strain associated with deforming reactants from their equilibrium structure to the geometry they adopt in the transition state. We discuss the origin of this trend and its relationship with the extent of synchronicity between H transfer from ene to enophile and the formation of the new C C bond. © 2011 Wiley Periodicals, Inc. J Comput Chem, 2011     

Reaction pathways of propene pyrolysis

The gas‐phase reaction pathways in preparing pyrolytic carbon with propene pyrolysis have been investigated in detail with a total number of 110 transition states and 50 intermediates. The structure of the species was determined with density functional theory at B3PW91/6‐311G(d,p) level. The transition states and their linked intermediates were confirmed with frequency and the intrinsic reaction coordinates analyses. The elementary reactions were explored in the pathways of both direct and the radical attacking decompositions. The energy barriers and the reaction energies were determined with accurate model chemistry method at G3(MP2) level after an examination of the nondynamic electronic correlations. The heat capacities and entropies were obtained with statistical thermodynamics. The Gibbs free energies at 298.15 K for all the reaction steps were reported. Those at any temperature can be developed with classical thermodynamics by using the fitted (as a function of temperature) heat capacities. It was found that the most favorable paths are mainly in the radical attacking chain reactions. The chain was proposed with 26 reaction steps including two steps of the initialization of the chain to produce H and CH₃ radicals. For a typical temperature (1200 K) adopted in the experiments, the highest energy barriers were found in the production of C₃ to be 203.4 and 193.7 kJ/mol. The highest energy barriers for the production of C₂ and C were found 174.1 and 181.4 kJ/mol, respectively. These results are comparable with the most recent experimental observation of the apparent activation energy 201.9 ± 0.6 or 137 ± 25 kJ/mol. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

Assessment of ab initio MP2 and density functionals for characterizing the potential energy profiles of the SN2 reactions at N center

The potential energy profiles of five selected bimolecular nucleophilic substitution (S_N2) reactions at nitrogen (N) center have been reinvestigated with the CCSD(T), G3[MP2,CCSD(T)], MP2, and some density functional methods. The basis sets of 6‐31+G(d,p) and 6‐311+G(3d,2p) are used for the MP2 and density functional calculations. Taking the relative energies at the CCSD(T)/CBS level of theory as benchmarks, we recommend the MP2, B97‐K, B2K‐PLYP, BMK, ωB97X‐D, M06‐2X, M05‐2X, CAM‐B3LYP, M08‐SO, and ωB97X methods to generally characterize the potential energy profiles for the S_N2 reactions at N center. Furthermore, these recommended methods with the relatively small 6‐31+G(d,p) basis set may also be used to perform direct classical trajectory simulations to uncover the dynamic behaviors of the S_N2 reactions at N center. © 2012 Wiley Periodicals, Inc.     

A DFT study on a mutipathways,one product reaction: Initially divergent radical reactions reconverge to form a single product

The mechanism for initially divergent radical reactions reconverging to form a single product is studied using density functional theory calculations. The calculation results suggest that there are six possible pathways from reactants to products. The free energy barriers of the rate‐determining steps of each pathway are almost equal. Thus, different from usual reaction, the selectivity of this reaction is determined by the relative value of free energy barriers of the two competitive reactions, that is, cyclization and bimolecular trapping, rather than that of rate‐determining steps. In all reaction pathways, cyclization reaction is more competitive than bimolecular trapping reaction due to its low free energy barrier. In addition, the free energy barriers of bimolecular trapping reaction between Bu₃SnH and reactants are all lower than that of NC? C₆H₁₁. However, Bu₃SnH is not always suitable due to its large steric repulsion. © 2014 Wiley Periodicals, Inc.     

A determination of antioxidant efficiencies using ESR and computational methods

Using Transition-State Theory, experimental rate constants, determined over a range of temperatures, for reactions of Vitamin E type antioxidants are analysed in terms of their enthalpies and entropies of activation. It is further shown that computational methods may be employed to calculate enthalpies and entropies, and hence Gibbs free energies, for the overall reactions. Within the linear free energy relationship (LFER) assumption, that the Gibbs free energy of activation is proportional to the overall Gibbs free energy change for the reaction, it is possible to rationalise, and even to predict, the relative contributions of enthalpy and entropy for reactions of interest, involving potential antioxidants. A method is devised, involving a competitive reaction between *CH3 radicals and both the spin-trap PBN and the antioxidant, which enables the relatively rapid determination of a relative ordering of activities for a series of potential antioxidant compounds, and also of their rate constants for scavenging *CH3 radicals (relative to the rate constant for addition of *CH3 to PBN).     

Influence of the solvent representation on vibrational entropy calculations: Generalized born versus distance‐dependent dielectric model

The harmonic model is the most popular approximation for estimating the “configurational” entropy of a solute in molecular mechanics/Poisson‐Boltzmann solvent accessible surface area (MM/PBSA)‐type binding free energy calculations. Here, we investigate the influence of the solvent representation in the harmonic model by comparing estimates of changes in the vibrational entropies for 30 trypsin/ligand complexes on ligand binding. Second derivatives of Amber generalized Born (GB) solvation models are available in the nucleic acid builder code. They allow one to use these models for the calculation of vibrational entropies instead of using a simpler solvation model based on a distance‐dependent dielectric (DDD) constant. Estimates of changes in the vibrational entropies obtained with a DDD model are systematically and significantly larger, by on average, 6 kcal mol^?1 (at T = 300 K), than estimates obtained with a GB model and so are more favorable for complex formation. The difference becomes larger the more the vibrational entropy contribution disfavors complex formation, that is, the larger the ligand is (for the complexes considered here). A structural decomposition of the estimates into per‐residue contributions reveals polar interactions between the ligand and the surrounding protein, in particular involving charged nitrogens, as a main source of the differences. Snapshots minimized with the DDD model showed a structural deviation from snapshots minimized in explicit water that is larger by, on average, 0.5 Å RMSD compared to snapshots that were minimized with GB^HCT. As experimental vibrational entropies of biomacromolecules are elusive, there is no direct way to establish a solvent model's superiority. Thus, we can only recommend using the GB harmonic model for vibrational entropy calculations based on the reasoning that smaller structural deviations should point to the implicit solvent model that closer approximates the energy landscape of the solute in explicit solvent. © 2012 Wiley Periodicals, Inc.     

Assessment of density functionals with long‐range and/or empirical dispersion corrections for conformational energy calculations of peptides

Density functionals with long‐range and/or empirical dispersion corrections, including LC‐ωPBE, B97‐D, ωB97X‐D, M06‐2X, B2PLYP‐D, and mPW2PLYP‐D functionals, are assessed for their ability to describe the conformational preferences of Ac‐Ala‐NHMe (the alanine dipeptide) and Ac‐Pro‐NHMe (the proline dipeptide) in the gas phase and in water, which have been used as prototypes for amino acid residues of peptides. For both dipeptides, the mean absolute deviation (MAD) is estimated to be 0.22–0.40 kcal/mol in conformational energy and 2.0–3.2° in torsion angles ? and ψ using these functionals with the 6‐311++G(d,p) basis set against the reference values calculated at the MP2/aug‐cc‐pVTZ//MP2/aug‐cc‐pVDZ level of theory in the gas phase. The overall performance is obtained in the order B2PLYP‐D ≈ mPW2PLYP‐D > ωB97X‐D ≈ M06‐2X > MP2 > LC‐ωPBE > B3LYP with the 6–311++G(d,p) basis set. The SMD model at the M06‐2X/6‐31+G(d) level of theory well reproduced experimental hydration free energies of the model compounds for backbone and side chains of peptides with MADs of 0.47 and 4.3 kcal/mol for 20 neutral and 5 charged molecules, respectively. The B2PLYP‐D/6‐311++G(d,p)//SMD M06‐2X/6‐31+G(d) level of theory provides the populations of backbone and/or prolyl peptide bond for the alanine and proline dipeptides in water that are consistent with the observed values. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010     

C-甲基硝酮与硝基乙烯1,3-偶极环加成反应及其溶剂效应的理论研究

用密度泛函B3LYP方法研究了硝基乙烯与C-甲基硝酮的1,3-偶极环加成反应, 并利用自洽反应场方法(SCRF)计算了环已烷与乙腈这两种溶剂分别对反应所产生的 影响。该反应进行时反应物的接近有四种方式,对气相情况下和上述两种溶剂中的 反应物、四种可能产物及其相应过渡态和反应前期复合物构型分别进行了优化并计 算了振动频率。四个反应均为放热反应,且均具有很低的反应势垒,四种产物均容 易生成。但在气相反应和以环已烷为溶剂的情况下,生成的产物中endo-4型产物略 占优势;而在乙腈溶剂中得到endo-5型略占优势的产物。     

Computational estimates of thermochemistry and pKa values of cyclopropenyl imine superbases

The thermochemical properties of superbase species derived from cyclopropeneimine are estimated by computations on systems of isodesmic reactions. Proton affinities, gas phase basicities, and pK_a values are well represented by computations incorporating G4 and CBS‐QB3 schemes augmented for large systems by DFT calculations with functionals M06‐2X and ωB97DX in the cc‐pVTZ Dunning basis. Our calculations show that relative base strengths in gas are enhanced by alkyl substitution, either by methyl groups or larger species. For acetonitrile solution, alkyl substitution seems to weaken the base. © 2013 Wiley Periodicals, Inc.