Diels-Alder Reactivity of a Chiral Anthracene Template with Symmetrical and Unsymmetrical Dienophiles: A DFT Study

In this work, we used Density Functional Theory calculations to assess the factors that control the reactivity of a chiral anthracene template with three sets of dienophiles including maleic anhydrides, maleimides and acetoxy lactones in the context of Diels-Alder cycloadditions. The results obtained here (at the M06-2X/6-311++G(d,p) level of theory) suggest that the activation energies for maleic anhydrides and acetoxy lactones are dependent on the nature of the substituent in the dienophile. Among all studied substituents, only −CN reduces the energy barrier of the cycloaddition. For maleimides, the activation energies are independent of the heteroatom of the dienophile and the R group attached to it. The analysis of frontier molecular orbitals, charge transfer and the activation strain model (at the M06-2X/TZVP level based on M06-2X/6-311++G(d,p) geometries) suggest that the activation energies in maleic anhydrides are mainly controlled by the amount of charge transfer from the diene to the dienophile during cycloaddition. For maleimides, there is a dual control of interaction and strain energies on the activation energies, whereas for the acetoxy lactones the activation energies seem to be controlled by the degree of template distortion at the transition state. Finally, calculations show that considering a catalyst on the studied cycloadditions changes the reaction mechanism from concerted to stepwise and proceed with much lower activation energies.     

A comparison of the behavior of functional/basis set combinations for hydrogen-bonding in the water dimer with emphasis on basis set superposition error

We evaluate the performance of ten functionals (B3LYP, M05, M05-2X, M06, M06-2X, B2PLYP, B2PLYPD, X3LYP, B97D, and MPWB1K) in combination with 16 basis sets ranging in complexity from 6-31G(d) to aug-cc-pV5Z for the calculation of the H-bonded water dimer with the goal of defining which combinations of functionals and basis sets provide a combination of economy and accuracy for H-bonded systems. We have compared the results to the best non-density functional theory (non-DFT) molecular orbital (MO) calculations and to experimental results. Several of the smaller basis sets lead to qualitatively incorrect geometries when optimized on a normal potential energy surface (PES). This problem disappears when the optimization is performed on a counterpoise (CP) corrected PES. The calculated interaction energies (ΔEs) with the largest basis sets vary from -4.42 (B97D) to -5.19 (B2PLYPD) kcal/mol for the different functionals. Small basis sets generally predict stronger interactions than the large ones. We found that, because of error compensation, the smaller basis sets gave the best results (in comparison to experimental and high-level non-DFT MO calculations) when combined with a functional that predicts a weak interaction with the largest basis set. As many applications are complex systems and require economical calculations, we suggest the following functional/basis set combinations in order of increasing complexity and cost: (1) D95(d,p) with B3LYP, B97D, M06, or MPWB1k; (2) 6-311G(d,p) with B3LYP; (3) D95++(d,p) with B3LYP, B97D, or MPWB1K; (4) 6-311++G(d,p) with B3LYP or B97D; and (5) aug-cc-pVDZ with M05-2X, M06-2X, or X3LYP.     

Theoretical Studies on the Aminolysis of Ester: Effects of the Catalysis and Substituent to the Reaction of Methyl Indole-3-acetate with Ammonia

A comprehensive exploration of the aminolysis mechanism for methyl indole-3-acetate with ammonia is carried out by employing the B3 LYP/6-311++G(d,p), M06-2 X/6-311++G(d,p) and MP2/6-311++G(d,p)//M06-2 X/6-311++G(d,p) levels. Two alterative reaction channels of the concerted and addition/elimination stepwise processes including the uncatalyzed, base-catalyzed reactions are taken into consideration. Subsequently, the substituent effects and solvent effects in methanol are also evaluated at the M06-2 X/6-311++G(d,p) level. The calculated results indicate that the calculated values of M06-2 X level are quite close to those of MP2, the stepwise pathway has more advantages to the concerted one for all of the reaction processes and the catalyst facilitates the proton migration and decreases the energy barriers as well. It is shown that the most preferred mechanism is the based-catalyzed stepwise process, the substituent of NH2 group slightly accelerates all the aminolysis reaction processes, and the solvent effect does not remarkably change the mechanism of the reaction.     

The electronic spectra of the sandwich stacked PFBT: a theoretical study

Stacked models that include 9,9'-bis(6'-N,N,N-trimethylammonium)hexyl]fluorene-co-alt-4,7-(2,1,3-benzothiadiazole)dibromide (F(BT)F) monomer sandwiched between two stacked 2,1,3-benzothiadiazole (BT) units were explored using theoretical approaches. Molecular structures and the optical characteristics of the investigated species were investigated at the M06-2X/6-311G(d,p)//TD-M06-2X/6-311G(d,p) level of theory. In all models, the electronic excitation to the lowest singlet ππ* excited state (S1(ππ*)) is governed by the highest occupied molecular orbital to lowest unoccupied molecular orbital (HOMO → LUMO) transitions. The obtained results suggest that stacking interaction might have only minor effects on the transition energy for both absorption and emission processes. Instead, the reduction in the excitation energy of the stacked complexes should be attributed to the dipole-dipole interaction. The larger the interaction energy of the stacked models, the bigger the observed differences between absorption-emission energies. The presence of the solvation medium with small dielectric constant may increase the absorption-emission energy differences. It is expected that the largest absorption-emission shift can be observed in the benzene solution.     

黄嘌呤异构体质子转移异构化反应机理的理论研究

采用量子化学密度泛函B3LYP/6-31G(d,p)和M06-2X/6-311++G(d,p)方法对黄嘌呤两种酮式异构体X(1,3,7)与X(1,3,9)间质子转移引起的互变异构反应机理进行了计算研究,获得了异构化反应过程的反应焓﹑活化吉布斯自由能和质子转移反应的速率常数等参数。水相计算采用极化连续(PCM)模型。结果表明,由于可能的氢迁移顺序差异,分子内由X(1,3,7)向X(1,3,9)异构化可能共有16条反应通道,涉及11个中间体和20个过渡态,其主反应通道速控步骤的活化吉布斯自由能为183.10k J/mol,速率常数为5.17×10-20s-1,其余各通道速控步骤活化吉布斯自由能均较高,而且整体水溶剂效应不利于质子转移的发生。     

氢分子与超氧阴离子自由基反应的微观机理

为了认识氢气生物学效应的分子机制,采用量子化学的M06-2X/6-311+G(d,p)和CCSD(t)/aug-cc-pVTZ方法模拟了人体条件(310K、液相)下氢分子与超氧阴离子自由基的反应机理。研究表明,反应的吉布斯自由能变化值为117.2kJ·mol~(-1),活化自由能垒为156.2kJ·mol~(-1),从热力学及动力学角度该反应都不容易进行。然后从电子结构和轨道作用层面对反应的微观机制进行了探讨,发现从反应物变为过渡态过程中,复合物轨道的组成和轨道能级发生显著变化(尤其是第8号轨道能级升高最多,达到2.73eV),O~-_2片段向H_2片段的电子转移数增加了0.1760个,并且转移的电子主要集居于第8号轨道,这削弱了H_2片段两个H原子间的化学键,也是反应活化能的主要来源。     

Density functional study of organocatalytic mannich‐type reactions: Insight into reverse diastereoselectivities arising from catalysts with different scaffolds

Density functional study have been carried out to investigate the stereoselectivities in the Mannich‐type reactions promoted by five typical amino acid catalysts with different scaffolds. The reverse diastereoselectivities in the cyclic and acyclic α‐ and β‐amino acids‐promoted Mannich reactions have been satisfactorily explained by the density functional theory (DFT) methods at the SMD/M06‐2X/6‐31G** computational level. The activation strain analysis has been used to account for the selectivity‐switching for these selected bifunctional catalysts. © 2015 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     

Structures and energetics of darunavir and active site amino acids of native and mutant HIV–1 protease: a computational study

Structural Chemistry - Quantum chemical calculations have been performed at the M06–2X/6–31G(d,p) level of theory to investigate the strength and nature of interactions between the...     

The shape of gaseous n-butylbenzene: assessment of computational methods and comparison with experiments

Conformational landscape of neutral and ionized n-butylbenzene has been examined. Geometries have been optimized at the B3LYP/6-31G(d), B3LYP/6-31+G(d,p), B3LYP-D/6-31+G(d,p), B2PLYP/6-31+G(d,p), B2PLYP-D/6-31+G(d,p), B97-D/6-31+G(d,p), and M06-2X/6-31+G(d,p) levels. This study is complemented by energy computations using 6-311++G(3df,2p) basis set and CBS-QB3 and G3MP2B3 composite methods to obtain accurate relative enthalpies. Five distinguishable conformers have been identified for both the neutral and ionized systems. Comparison with experimentally determined rotational constants shows that the best geometrical parameters are provided by B3LYP-D and M06-2X functionals, which include an explicit treatment of dispersion effects. Composite G3MP2B3 and CBS-QB3 methods, and B2PLYP-D, B3LYP-D, B97-D, and M06-2X functionals, provide comparable relative energies for the two sets of neutral and ionized conformers of butyl benzene. An exception is noted however for conformer V(+) the stability of which being overestimated by the B3LYP-D and B97-D functionals. The better stability of neutral conformers I, III, and IV, and of cation I(+) , demonstrated by our computations, is in perfect agreement with conclusions based on micro wave, fluorescence, and multiphoton ionization experiments.     

Analysis of the Electron Density Laplacian of Lithium Complexes of Polycyclic Aromatic Hydrocarbons

Russian Journal of Organic Chemistry - According to DFT/M06-2X/6-311G(d,p) calculations, the binding energy of the lithium cation with benzene and polycyclic aromatic hydrocarbons of the general...     

Intramolecular proton transfer in the isomerization of hydroxyacetone: Characterization based on reaction force analysis and the bond fragility spectrum

The mechanism of isomerization of hydroxyacetone to 2-hydroxypropanal is studied within the framework of reaction force analysis at the M06-2X/6-311++G(d,p) level of theory. Three unique pathways are considered: (a) a step-wise mechanism that proceeds through the formation of the Z-isomer of their shared enediol intermediate, (b) a step-wise mechanism that forms the E-isomer of the enediol, and (c) a concerted pathway that bypasses the enediol intermediate. Energy calculations show that the concerted pathway has the lowest activation energy barrier at 45.7 kcal mol⁻¹. The reaction force, chemical potential, and reaction electronic flux are calculated for each reaction to characterize electronic changes throughout the mechanism. The reaction force constant is calculated in order to investigate the synchronous/asynchronous nature of the concerted intramolecular proton transfers involved. Additional characterization of synchronicity is provided by calculating the bond fragility spectrum for each mechanism.     

Theoretical study of hydrogen bonding in homodimers and heterodimers of amide, boronic acid, and carboxylic acid, free and in encapsulation complexes

The homodimers and the heterodimers of two amides, two boronic acids, and two carboxylic acids have been calculated in the gas phase and in N,N-dimethylformamide (DMF) and CCl(4) solvents using the DFT (M06-2X and M06-L) and the MP2 methods in conjunction with the 6-31G(d,p) and 6-311+G(d,p) basis sets. Furthermore, their pairwise coencapsulation was studied to examine its effect on the calculated properties of the hydrogen bonds at the ONIOM[M06-2X/6-31G(d,p);PM6], ONIOM[MP2/6-31G(d,p); PM6], and M06-2X/6-31G(d,p) levels of theory. The present work is directed toward the theoretical rationalization and interpretation of recent experimental results on hydrogen bonding in encaptulation complexes [D. Ajami et al. J. Am. Chem. Soc. 2011, 133, 9689-9691]. The calculated dimerization energy (ΔE) values range from 0.74 to 0.35 eV for the different dimers in the gas phase, with the ordering carboxylic homodimers > amide-carboxylic dimers > amide homodimers > boronic-carboxylic dimers > amide-boronic dimers > boronic homodimers. In solvents, generally smaller ΔE values are calculated with only small variations in the ordering. In the capsule, the ΔE values range between 0.67 and 0.33 eV with practically the same ordering as in the gas phase. The calculated % distributions of the encapsulated dimers, taking into account statistical factors, are in agreement with the experimental distribution, where the occurrence of boronic homodimer dominates, even though it is calculated to have the smallest ΔE.     

SUBSTITUENT EFFECT IN [2+4] DIELS–ALDER CYCLOADDITION REACTIONS OF ANTHRACENE WITH C2X2 (X = H,F, Cl,Me): A COMPUTATIONAL INVESTIGATION

Journal of Structural Chemistry - In the present article, a DFT approach is used at the M06-2X/6-311G(d,p) level of theory to survey [2+4] Diels–Alder cycloaddition reactions of anthracene...     

Probing the bent bonds in cyclopropane systems for gas storage and separation process: A computational study

The hydrogen, carbon dioxide, and carbon monoxide gas adsorption and storage capacity of lithium-decorated cyclopropane ring systems were examined with quantum chemical calculations at density functional theory, DFT M06-2X functional using 6-31G(d) and cc-pVDZ basis sets. To examine the reliability of M06-2X DFT functional, a few representative systems are also examined with complete basis set CBS-QB3 method and CCSD-aug-cc-pVTZ level of theory. The cyclopropane systems can bind to one Li⁺ ion; however, the corresponding the methylated systems can bind with two Li⁺ ions. The cyclopropane systems can adsorb six hydrogen molecules with an average binding energy of 3.8 kcal/mol. The binding free energy (ΔG) values suggest that the hydrogen adsorption process is feasible at 273.15 K. The calculation of desorption energies indicates the recyclable property of gas adsorbed complexes. The same number of CO₂ and CO gas molecules can also be adsorbed with an average binding energy of −14.4 kcal/mol and −10.7 kcal/mol, respectively. The carbon dioxide showed ~3–4 kcal/mol better binding energy as compared to carbon monoxide and hence such designed systems can function as a potential candidate for the separation of these flue gas molecules. The nature of interactions in complexes was examined with atoms in molecules analysis revealed the electrostatic nature for the interaction of Li⁺ ion with cyclopropane rings. The chemical hardness and electrophilicity calculations showed that the gas adsorbed complexes are rigid and therefore robust as gas storage materials.     

A theoretical study of H?H σ bond activation catalyzed by VO2+ in gas phase

The mechanism of H? H σ bond activation catalyzed by VO(¹A₁/³A′) has been investigated by using density functional theory at the B3LYP/6‐311G(2d, p) level and the single‐point energy calculations were done at the CCSD/6‐311G (2d, p)//B3LYP/6‐311G(2d, p) level of theory using the geometries along the minimum energy pathway. According to our calculation results, the different reaction mechanisms were found for the singlet and triplet potential energy surfaces (PESs). Specially, the crossing points (CPs) between the different PESs have been located by means of the intrinsic reaction coordinate approach used by Yoshizawa et al, and corresponding minimum energy CPs that we obtained by the mathematical algorithm proposed by Harvey et al. has also been employed. In addition, the orbital interaction for ion‐molecule complexes ¹IM1 and ³IM1 have been examined by fragment molecular orbital analysis. Finally, the frontier molecular orbital interaction analysis about ³TS1 and ³TS2 were used to gain useful information about the H? H σ bond activation by VO. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012     

CF3CH2CF2CH3（HFC-365mfc）与Cl原子反应的微观机理及动力学性质

采用密度泛函理论方法 M06-2X结合6-31+G(d,p)基组研究了CF3CH2CF2CH3与Cl原子反应的反应机理.计算获得了CF3CH2CF2CH3的两种可区分的稳定几何构象RC1和RC2以及与它们相对应的8条氢提取反应通道和2条取代反应通道.运用改进的正则变分过渡态理论(ICVT)并结合小曲率隧道效应校正(SCT),在M06-2X/6-31+G(d,p)水平上计算了各氢提取通道的速率常数,并由Boltzmann配分函数得到总包反应的速率常数kT(cm3.molecule-1.s-1).计算结果表明,体系的总反应速率常数与已有实验值相吻合,进而给出了该反应在200～1000 K温度区间内反应速率常数kT的三参数表达式kT=1.88×10-22T3.76.exp(-1780.69/T),并讨论了两种构象RC1和RC2对总反应的贡献及各构象中氢提取发生在—CH3或—CH2—基团上的位置选择性.此外,由于缺少相关反应物及产物自由基标准生成焓ΔHf,298 K的数据,利用等化学键法估算了在上述物种的标准生成焓.     

Assessment of density functionals and force field methods on anion–π interaction in heterocyclic calix complexes

The performance of ten density functionals and four force field methods in describing non-covalent interactions have been assessed by studying the interaction energies and structures of the four anion–π complexes involving tetraoxacalix[2]arene[2]triazine and various anions. Their structures are optimized at MP2/6-311++G(d,p) level, and interaction energies are obtained at DF-MP2-F12/aug-cc-pVDZ level. The result shows that the functional M06-2X predicts the most reliable interaction energy, followed by wB97XD and BHandH. B97D slightly overestimates the interaction energy. Other functionals and force field methods seriously overestimate the interaction energy. For the structures, three functionals M06-2X, wB97XD and BH and H predict the most reliable results, followed by B97D. The force field methods predict the largest deviations. The present work suggests that the functional M06-2X is a reliable method to describe energies and structural properties of the large molecules involving the anion–π interactions.     

Coordination of methanol clusters to benzene: a computational study

Benzene-methanol cluster structures were investigated with theoretical chemistry methods to describe the microsolvation of benzene and the benzene-methanol azeotrope. Benzene-methanol (MeOH) clusters containing up to six methanol molecules have been calculated by ab initio [MP2/6-311++G(d,p)//MP2/6-31+G(d,p) + BSSE correction] method. The BSSE was found quite large with this basis set, hence, different extrapolation schemes in combination with the aug-cc-pVxZ basis sets have been used to estimate the complete basis set limit of the MP2 interaction energy [ΔE(MP2/CBS)]. For smaller clusters, n ≤ 3, DFT procedures (DFTB+, MPWB1K, M06-2X) have also been applied. Geometries obtained for these clusters by M06-2X and MP2 calculations are quite similar. Based on the MP2/CBS results, the most stable C(6)H(6)(MeOH)(3) cluster is characterized by a hydrogen bonded MeOH trimer chain interacting with benzene via π···H-O and O···H-C(benzene) hydrogen bonds. Larger benzene-MeOH clusters with n ≥ 4 consist of cyclic (MeOH)(n) subclusters interacting with benzene by dispersive forces, to be denoted by C(6)H(6) + (MeOH)(n). Interaction energies and cooperativity effects are discussed in comparison with methanol clusters. Besides MP2/CBS calculations, for selected larger clusters the M06-2X/6-311++G(d,p)//M06-2X/6-31+G(d,p) procedure including the BSSE correction was also used. Interaction energies obtained thereby are usually close to the MP2/CBS limit. To model the benzene-MeOH azeotrope, several structures for (C(6)H(6))(2)(MeOH)(3) clusters have been calculated. The most stable structures contain a tilted T-shaped benzene dimer interacting by π···H-O and O···H-C (benzene) hydrogen bonds with a (MeOH)(3) chain. A slightly less negative interaction energy results for a parallel displaced benzene sandwich dimer with a (MeOH)(3) chain atop of one of the benzene molecules.     

Theoretical study of 1,3-dipolar cycloaddition reactions between 7–10-membered simple cycloalkynes and triazoles R–N3 (R = H, CH3, Ph)

The energy contents in alkynes may be increased further by bending the normally linear triple bond, as in the small cycloalkynes. The strain energy in the cycloalkynes increases as the size of the ring decreases. Cycloadditions of 1,3-dipoles with alkynes occur by concerted mechanisms. In this study, the reactivity and strain energy effect of the cycloalkynes with substituted 1,2,3-triazoles R–N₃ (R = H, CH₃, and Ph) by the use of B3LYP/6-31G** level method will be discussed. The investigation of the structured properties, theoretical thermodynamic and kinetic data, i.e., ΔrG, ΔG* and rate constants of the reactions in 298 K will be presented.