Photodetachment of Deprotonated R-Mandelic Acid: The Role of Proton Delocalization on the Radical Stability

The photodetachment and stability of R-Mandelate, the deprotonated form of the R-Mandelic acid, was investigated by observing the neutral species issued from either simple photodetachment or dissociative photodetachment in a cold anions set-up. R-Mandalate has the possibility to form an intramolecular ionic hydrogen-bond between adjacent hydroxyl and carboxylate groups. The potential energy surface along the proton transfer (PT) coordinate between both groups (O⁻…H⁺…⁻OCO) features a single local minima, with the proton localized on the O⁻ group (OH…⁻OCO). However, the structure with the proton localized on the ⁻OCO group (O⁻…HOCO) is also observed because it falls within the extremity of the vibrational wavefunction of the OH…⁻OCO isomer along the PT coordinate. The stability of the corresponding radicals, produced upon photodetachment, is strongly dependent on the position of the proton in the anion: the radicals produced from the OH…⁻OCO isomer decarboxylate without barrier, while the radicals produced from the O⁻…HOCO isomer are stable.     

Criegee中间体CH3CHOO与H2O反应机理及酸催化效应

采用CCSD（T）//B3LYP/6-311+G（d,p）方法研究了H₂O及甲酸等6种有机酸对CH₃CHOO与H₂O加成反应的催化作用。结果表明,非催化反应存在双质子迁移和加成反应2条通道,其中加成反应为优势通道。其加成机理为H₂O中OH加到CH₃CHOO的α-C上,同时H₂O中另一个H迁移到CH₃CHOO的端O上。催化剂H₂O及有机酸以氢键复合物的形式参与反应促进了H质子转移,可降低基元反应能垒和表观活化能,且催化效应与有机酸的强度成正比。例如,当分别用H₂O（pK_a=15.7）、甲酸（pK_a=3.75）和草酸（pK_a=1.23）催化时,生成syn-HAHP的基元反应能垒由非催化的69.12 kJ·mol^-1分别降至40.78、18.88和10.61 kJ·mol^-1。非催化反应具有正的表观活化能,而所有催化反应则均具有负的表观活化能。     

Radical Chemistry and Reaction Mechanisms of Propane Oxidative Dehydrogenation over Hexagonal Boron Nitride Catalysts

Although hexagonal boron nitride (h‐BN) has recently been identified as a highly efficient catalyst for the oxidative dehydrogenation of propane (ODHP) reaction, the reaction mechanisms, especially regarding radical chemistry of this system, remain elusive. Now, the first direct experimental evidence of gas‐phase methyl radicals (CH₃^.) in the ODHP reaction over boron‐based catalysts is achieved by using online synchrotron vacuum ultraviolet photoionization mass spectroscopy (SVUV‐PIMS), which uncovers the existence of gas‐phase radical pathways. Combined with density functional theory (DFT) calculations, the results demonstrate that propene is mainly generated on the catalyst surface from the C?H activation of propane, while C₂ and C₁ products can be formed via both surface‐mediated and gas‐phase pathways. These observations provide new insights towards understanding the ODHP reaction mechanisms over boron‐based catalysts.     

脂肪酰胺水解酶催化三联体膦酰化失活的机理：一个模型体系的理论研究

甲基花生四烯基氟代膦酸酯(MAFP)是脂肪酰胺水解酶(FAAH)的一个抑制剂. FAAH的丝氨酸241(Ser241)-丝氨酸217(Ser217)-赖氨酸142(Lys142)催化三联体被MAFP膦酰化后将导致FAAH失活. 本文采用B3LYP/6-311G(d,p)和MP2/6-311G(d,p)方法及一个简化的计算模型体系对这个膦酰化抑制反应进行理论研究. 考虑了两种反应途径. Path A涉及FAAH的催化三联体的所有残基, 是一个分步的加成-消除过程, 形成两性离子的三角双锥中间体, 其中第一步反应是决速步骤. 在这个反应途径中, Ser217和Lys142对亲核试剂Ser241起到碱催化活化的作用, 而Ser217充作Lys142和Ser241之间的桥梁. 此外, 溶剂中的一个水分子作为Lys142和MAFP间的“氢桥”具有关键的作用, 通过给出和接收质子促进了长距离的质子转移. Path B是催化三联体中的残基Lys142被突变为丙氨酸以后的膦酰化反应, 也是一个分步过程. 水的本体溶剂效应通过极化连续介质模型(PCM)估算. 计算结果显示膦酰化反应的Path A是优势途径, 在水溶液中其决速步骤的活化能垒为64.9 kJ·mol-1. FAAH催化三联体中残基Lys142的变异会降低膦酰化反应的速率, 这与实验结果相一致.     

On the Limited Stability of BDPA Radicals

1,3-Bis(diphenylene)-2-phenylallyl (BDPA)-based radicals are of interest as polarizing agents for dynamic nuclear polarization (DNP). For this purpose, a BDPA-nitroxide biradical, employing a phosphodiester linkage, was synthesized. Contrary to what is commonly assumed, BDPA-derived radicals were observed to have limited stability. Hence, the effects of various factors on the stability of BDPA radicals were investigated. Solvent polarity was found to play a significant role on degradation; a polar BDPA radical was observed to degrade faster in a non-polar solvent, whereas non-polar radicals were more unstable in polar solvents. The rate of decomposition was found to increase non-linearly with increasing radical concentration; a 2-fold increase in concentration led to a 3-fold increase in the rate of degradation. Collectively, these results indicate that the dimerization is a significant degradation pathway for BDPA radicals and indeed, a dimer of one BDPA radical was detected by mass spectrometry.     

Functionalized Hydroperoxide Formation from the Reaction of Methacrolein-Oxide,an Isoprene-Derived Criegee Intermediate,with Formic Acid: Experiment and Theory

Methacrolein oxide (MACR-oxide) is a four-carbon, resonance-stabilized Criegee intermediate produced from isoprene ozonolysis, yet its reactivity is not well understood. This study identifies the functionalized hydroperoxide species, 1-hydroperoxy-2-methylallyl formate (HPMAF), generated from the reaction of MACR-oxide with formic acid using multiplexed photoionization mass spectrometry (MPIMS, 298 K = 25 °C, 10 torr = 13.3 hPa). Electronic structure calculations indicate the reaction proceeds via an energetically favorable 1,4-addition mechanism. The formation of HPMAF is observed by the rapid appearance of a fragment ion at m/z 99, consistent with the proposed mechanism and characteristic loss of HO₂ upon photoionization of functional hydroperoxides. The identification of HPMAF is confirmed by comparison of the appearance energy of the fragment ion with theoretical predictions of its photoionization threshold. The results are compared to analogous studies on the reaction of formic acid with methyl vinyl ketone oxide (MVK-oxide), the other four-carbon Criegee intermediate in isoprene ozonolysis.     

The Catalytic Mechanism of the Marine‐Derived Macrocyclase PatGmac

Cyclic peptides are a class of compounds with high therapeutic potential, possessing bioactivities including antitumor and antiviral (including anti‐HIV). Despite their desirability, efficient design and production of these compounds has not been achieved to date. The catalytic mechanism of patellamide macrocyclization by the PatG macrocyclase domain has been computationally investigated by using quantum mechanics/molecular mechanics methodology, specifically ONIOM(M06/6‐311++G(2d,2p):ff94//B3LYP/6‐31G(d):ff94). The mechanism proposed herein begins with a proton transfer from Ser783 to His 618 and from the latter to Asp548. Nucleophilic attack of Ser783 on the substrate leads to the formation of an acyl–enzyme covalent complex. The leaving group Ala‐Tyr‐Asp‐Gly (AYDG) of the substrate is protonated by the substrate's N terminus, leading to the breakage of the P1?P1′ bond. Finally, the substrate's N terminus attacks the P1 residue, decomposing the acyl–enzyme complex forming the macrocycle. The formation and decomposition of the acyl–enzyme complex have the highest activation free energies (21.1 kcal mol^?1 and 19.8 kcal mol^?1 respectively), typical of serine proteases. Understanding the mechanism behind the macrocyclization of patellamides will be important to the application of the enzymes in the pharmaceutical and biotechnological industries.     

Theoretical Study on the Reaction Mechanism of Ketene CH2CO with Isocyanate NCO Radical

The bimolecular single collision reaction potential energy surface of an isocyanate NCO radical with a ketene CH2CO molecule was investigated by means of B3LYP and QCISD（T） methods. The computed results indicate that two possible reaction channels exist on the surface. One is an addition-elimination reaction process, in which the CH2CO molecule is attacked by the nitrogen atom at its methylene carbon atom to lead to the formation of the intermediate OCNCH2CO followed by a C-C rupture channel to the products CH2NCO＋CO. The other is a direct hydrogen abstraction channel from CHzCO by the NCO radical to afford the products HCCO＋HNCO. Because of a higher barrier in the hydrogen abstraction reaction than in the addition-elimination reaction, the direct hydrogen abstraction pathway can only be considered as a secondary reaction channel in the reaction kinetics of NCO＋ CH2CO. The predicted results are in good agreement with previous experimental and theoretical investigations.     

Coupling Interactions between Sulfurous Acid and the Hydroperoxyl Radical

Radical–molecule complexes associated with the hydroperoxyl radical (HOO) play an important role in atmospheric chemistry. Herein, the nature of the coupling interactions between sulfurous acid (H₂SO₃) and the HOO radical is systematically investigated at the B3LYP/6‐311++G(3df,3pd) level of theory in combination with the atoms in molecules (AIM) theory, the natural bond orbital (NBO) method, and energy decomposition analyses (EDA). Eight stable stationary points possessing double H‐bonding features were located on the H₂SO₃???HOO potential energy surface. The largest binding energies of ?12.27 and ?11.72 kcal mol^?1 are observed for the two most stable complexes, where both of them possess strong double intermolecular H‐bonds of partially covalence. Moreover, the characteristics of the IR spectra for the two most stable complexes are discussed to provide some help for their possible experimental identification.     

On the mechanism of intramolecular nitrogen‐atom hopping in the carbon chain of C6N radical: A Plausible 3c−4e crossover Long‐Bond

Linear isomers of C₆N radical differ in the position of the nitrogen atom in the carbon chain of C₆N. Reaction routes, involving intramolecular nitrogen atom insertion at varying position in the carbon chain of C₆N, are analyzed for the isomerisation between linear isomers of C₆N. Through an automated and systematic search performed with global reaction route mapping of the potential energy surface, thermal isomerisation pathways for C₆N radical are proposed based on the computations carried out at CASSCF/aug‐cc‐pVTZ, and CCSD(T)/6‐311++G(d,p)//B3LYP/6‐311++G(d,p) levels of the theory. Notably, a high lying linear isomer, centrosymmetric with respect to the nitrogen atom, is observed to be stabilized by a unique crossover three center‐four electron π long bond between the carbon atoms that are spatially separated by a nitrogen atom in a natural bond orbital. This long bond is concluded to be responsible for the predicted thermal isomerisation to be more feasible than the dissociation during the isomerisation pathway of a linear isomer of C₆N. © 2014 Wiley Periodicals, Inc.     

A Stable and Crystalline Triarylgermyl Radical: Structure and EPR Spectra

A radical thing : After being obtained unexpectedly in low yields, the synthesis of the first stable triarylgermyl radical ^.Ge[3,5‐tBu₂‐2,6‐(EtO)₂C₆H]₃ ( 1 ; C gray, O blue) was considerably optimized, and the product was investigated by X‐ray analysis and EPR spectroscopy. The results were compared with DFT‐MO studies for the model compound ^.Ge[2,6‐(MeO)₂C₆H₃].

     

Time‐Resolved Crystallography of the Reaction Intermediate of Nitrile Hydratase: Revealing a Role for the Cysteinesulfenic Acid Ligand as a Catalytic Nucleophile

The reaction mechanism of nitrile hydratase (NHase) was investigated using time‐resolved crystallography of the mutant NHase, in which βArg56, strictly conserved and hydrogen bonded to the two post‐translationally oxidized cysteine ligands, was replaced by lysine, and pivalonitrile was the substrate. The crystal structures of the reaction intermediates were determined at high resolution (1.2–1.3 Å). In combination with FTIR analyses of NHase following hydration in H₂¹⁸O, we propose that the metal‐coordinated substrate is nucleophilically attacked by the O(SO^?) atom of αCys114‐SO^?, followed by nucleophilic attack of the S(SO^?) atom by a βArg56‐activated water molecule to release the product amide and regenerate αCys114‐SO^?.