On the Relative Preference of Enamine/Iminium Pathways in an Organocatalytic Michael Addition Reaction

The right path : The mechanism of organocatalyzed Michael addition between propanal and methyl vinyl ketone is investigated using the density functional and ab intio methods. The kinetic preference for the formation of key intermediates is established in an effort to identify the competing pathways associated with the reaction. The effect of co‐catalyst/protic solvent on the energetics of the reaction is also studied

     

Novel Bonding Character of the Cyclic AlS2 and GaS2 Systems

The geometries, the harmonic vibrational frequencies and the bonding properties have been predicted for cyclic AlS2 and GaS₂ species at the density functional theory (DFT), MPn (n = 2, 3, 4), QCISD(T) and CCSD(T) levels with 6‐311 + G (2df) basis set. The novel bonding character was discussed.     

The Apparently Unreactive Substrate Facilitates the Electron Transfer for Dioxygen Activation in Rieske Dioxygenases

Rieske dioxygenases belong to the non-heme iron family of oxygenases and catalyze important cis-dihydroxylation as well as O-/N-dealkylation and oxidative cyclization reactions for a wide range of substrates. The lack of substrate coordination at the non-heme ferrous iron center, however, makes it particularly challenging to delineate the role of the substrate for productive activation. Here, we studied the role of the substrate in the key elementary reaction leading to activation from a theoretical perspective by systematically considering (i) the 6-coordinate to 5-coordinate conversion of the non-heme Fe^II upon abstraction of a water ligand, (ii) binding of , and (iii) transfer of an electron from the Rieske cluster. We systematically evaluated the spin-state-dependent reaction energies and structural effects at the active site for all combinations of the three elementary processes in the presence and absence of substrate using naphthalene dioxygenase as a prototypical Rieske dioxygenase. We find that reaction energies for the generation of a coordination vacancy at the non-heme Fe center through thermoneutral H₂O reorientation and exothermic binding prior to Rieske cluster oxidation are largely insensitive to the presence of naphthalene and do not lead to formation of any of the known reactive Fe-oxygen species. By contrast, the role of the substrate becomes evident after Rieske cluster oxidation and exclusively for the 6-coordinate non-heme Fe sites in that the additional electron is found at the substrate instead of at the iron and oxygen atoms. Our results imply an allosteric control of the substrate on Rieske dioxygenase reactivity to happen prior to changes at the non-heme Fe in agreement with a strategy that avoids unproductive activation.     

Electronic Structure of the Low-Lying States of the Triatomic MoS2 Molecule: The Building Block of 2D MoS2

Molybdenum disulfide (MoS₂) is the building component of 1D-monolayer, 2D-layered nanosheets and nanotubes having many applications in industry, and it is detected in various molecular systems observed in nature. Here, the electronic structure and the chemical bonding of sixteen low-lying states of the triatomic MoS₂ molecule are investigated, while the connection of the chemical bonding of the isolated MoS₂ molecule to the relevant 2D-MoS₂, is emphasized. The MoS₂ molecule is studied via DFT and multireference methodologies, i. e., MRCISD(+Q)/aug-cc-pVQZ(−PP)_Mo. The ground state, ³B₁, is bent (Mo−S=2.133 Å and ϕ(SMoS)=115.9°) with a dissociation energy to atomic products of 194.7 kcal/mol at MRCISD+Q. In the ground and in the first excited state a double bond is formed between Mo and each S atom, i. e., . These two states differ in which d electrons of Mo are unpaired. The Mo−S bond distances of the calculated states range from 2.108 to 2.505 Å, the SMoS angles range from 104.1 to 180.0°, and the Mo−S bonds are single or double. Potential energy curves and surfaces have been plotted for the ³B₁, ⁵A₁ and ⁵B₁ states. Finally, the low-lying septet states of the triatomic molecule are involved in the material as a building block, explaining the variety of its morphologies.     

On the Origin of the Enhanced Acidity of Chalcocyclopentadienes (Cyclopentadiene Chalcogenols) in the Gas Phase

The intrinsic acidity of chalcocyclopentadienes (CpXH; X=O, S, Se, Te) is investigated by high‐level G3B3 and G2 ab initio as well as B3LYP DFT calculations, which show that, independent of the nature of the heteroatom, all chalcocyclopentadienes are stronger acids in the gas phase than cyclopentadiene. However the acidity does not increase regularly down the group, and the acidity enhancement for Te derivatives is five times larger than for O derivatives, but only twice that of S‐containing compounds. The most favorable deprotonation process corresponds to loss of the proton attached to the heteroatom, with the sole exception of the 5‐substituted 1,3‐cyclopentadienes, for which the O and S derivatives are predicted to behave as carbon acids. No matter the nature of the heteroatom, the 1‐substituted 1,3‐cyclopentadienes are the strongest acids. The intrinsic acidity of all isomers, namely, 1‐substituted, 2‐substituted, and 5‐substituted 1,3‐cyclopentadienes, increases with increasing aromaticity of the anion formed on deprotonation, and therefore the Te compound is the strongest acid for the three series. However, the intrinsic acidity of chalcocyclopentadienes is not dictated by aromaticity, so that, in general, the most stable deprotonated species do not coincide with the most aromatic ones.     

Study of the oxidative half‐reaction catalyzed by a non‐heme ferrous catalytic center by means of structural and computational methodologies

Deacetoxycephalosporin C synthase (DAOCS) is a mononuclear ferrous enzyme that catalyzes the expansion of the five‐membered thiazolidine ring of the penicillin nucleus into the six‐membered dihydrothiazine ring of the cephalosporins. In the first half‐reaction with dioxygen and 2‐oxoglutarate, a reactive iron–oxygen species is produced that can subsequently react with the penicillin substrate to yield the cephalosporin. We describe quantum mechanical calculations of the first part of the reaction based on the high‐resolution structures of the active site of DAOCS and its complexes with ligands. These studies are aimed at understanding how the reactive species can be produced and contained in the active site of the enzyme. The results demonstrate the priming of the active site by the co‐substrate for oxygen binding and hint to the presence of a stable iron–peroxo intermediate in equilibrium with a more reactive ferryl species and the formation of CO₂ as a leaving group by decarboxylation of 2‐oxoglutarate. A conclusion from these studies is that substitution of CO₂ by the penicillin substrate triggers the oxidation reaction in a booby‐trap‐like mechanism. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007     

The Catalytic Mechanism of Fluoroacetate Dehalogenase: A Computational Exploration of Biological Dehalogenation

The biological dehalogenation of fluoroacetate carried out by fluoroacetate dehalogenase is discussed by using quantum mechanical/molecular mechanical (QM/MM) calculations for a whole‐enzyme model of 10 800 atoms. Substrate fluoroacetate is anchored by a hydrogen‐bonding network with water molecules and the surrounding amino acid residues of Arg105, Arg108, His149, Trp150, and Tyr212 in the active site in a similar way to haloalkane dehalogenase. Asp104 is likely to act as a nucleophile to attack the α‐carbon of fluoroacetate, resulting in the formation of an ester intermediate, which is subsequently hydrolyzed by the nucleophilic attack of a water molecule to the carbonyl carbon atom. The cleavage of the strong C? F bond is greatly facilitated by the hydrogen‐bonding interactions between the leaving fluorine atom and the three amino acid residues of His149, Trp150, and Tyr212. The hydrolysis of the ester intermediate is initiated by a proton transfer from the water molecule to His271 and by the simultaneous nucleophilic attack of the water molecule. The transition state and produced tetrahedral intermediate are stabilized by Asp128 and the oxyanion hole composed of Phe34 and Arg105.     

DFT Methods to Study the Reaction Mechanism of Iridium‐Catalyzed Hydrogenation of Olefins: Which Functional Should be Chosen?

To enable the selection of more accurate computational methods for the future theoretical exploration of the reaction mechanism of Ir‐catalyzed olefin hydrogenation, we compared high‐level ab initio coupled cluster and DFT calculations with a simplified model of Pfaltz's Ir/P,N‐type catalyst for all four previously proposed Ir^I/Ir^III and Ir^III/Ir^V mechanisms. Through the systematic assessment of the DFT performances, the DFT empirical dispersion correction (DFT‐D3) is found to be indispensable for improving the accuracy of relative energies between the Ir^I/Ir^III and Ir^III/Ir^V mechanisms. After including the DFT‐D3 correction, the three best performing density functionals (DFs) are B2‐PLYP, BP86, and TPSSh. In these recommended DFs, the computationally more expensive double‐hybrid functional B2‐PLYP‐D3 has a balanced and outstanding performance for calculations of the reaction barriers, reaction energies, and energy gaps between different mechanisms, whereas the less costly BP86‐D3 and TPSSh‐D3 methods have outstanding, but relatively less uniform performances.     

Accurate pKa Calculation of the Conjugate Acids of Alkanolamines,Alkaloids and Nucleotide Bases by Quantum Chemical Methods

The pK_a of the conjugate acids of alkanolamines, neurotransmitters, alkaloid drugs and nucleotide bases are calculated with density functional methods (B3LYP, M08‐HX and M11‐L) and ab initio methods (SCS‐MP2, G3). Implicit solvent effects are included with a conductor‐like polarizable continuum model (CPCM) and universal solvation models (SMD, SM8). G3, SCS‐MP2 and M11‐L methods coupled with SMD and SM8 solvation models perform well for alkanolamines with mean unsigned errors below 0.20 pK_a units, in all cases. Extending this method to the pK_a calculation of 35 nitrogen‐containing compounds spanning 12 pK_a units showed an excellent correlation between experimental and computational pK_a values of these 35 amines with the computationally low‐cost SM8/M11‐L density functional approach.     

CHF_2CF_2CH_2OCHF_2与OH自由基反应机理的理论研究

采用从头算和密度泛函方法研究了多通道反应CHF2CF2CH2OCHF2+OH→产物的反应机理.首先在BMK/6-311+G(d,p)水平下优化了稳定点的几何构型并计算了振动频率;然后在BMC-CCSD水平下,对势能面进行高水平能量校正.结果表明,此反应存在提氢和取代两类反应通道,但是无论从动力学还是从热力学分析,提氢反应通道才是主要的反应通道,且从-CH2-基团上提取氢原子的提氢通道是主要的反应通道.