Reaction of hypochlorous acid with imidazole: formation of 2-chloro- and 2-oxoimidazoles

Reaction of hypochlorous acid (HOCl) with imidazole (Im) taken as a model for the 5-membered ring of guanine, leading to the products 2-chloro- and 2-oxo-imidazoles was investigated at the B3LYP/6-31+G* and B3LYP/AUG-cc-pVDZ levels of density functional theory. For all cases, single point energy calculations were performed at the MP2/AUG-cc-pVDZ level of theory using the geometries optimised at the B3LYP/AUG-cc-pVDZ level. Intrinsic reaction coordinate calculations were performed to ensure genuineness of all the calculated transition states. Effect of aqueous media was investigated by solvating all the species involved in the reactions using the polarizable continuum model. It is found that 2-chloroimidazole (2-ClIm) can be formed following three different reaction schemes while 2-oxoimidazole (2-oxoIm) can be formed following two different reaction schemes. The calculated barrier energies show that formation of 2-oxoIm would be less favored than that of 2-ClIm, which explains the experimental observations on relative yields of 8-chlorodeoxyguanosine and 8-oxodeoxyguanosine.     

Computational study of the transamination reaction in vinylogous acyls: Paving the way to design vitrimers with controlled exchange kinetics

One of the key points in the design of vitrimers is controlling the associative exchange kinetics. One common chemistry used in vitrimers is based on the dynamic amine exchange reaction of vinylogous acyl compounds in presence of free amine. Understanding the reaction mechanism is essential to assist the optimization of the reaction conditions as well as the molecular structure of the reactant compounds in the pursuit of new materials. In this work, a computational study has been performed to explore different reaction mechanisms in neutral, acidic and in basic conditions or in the presence of Lewis acids, as well as the effect of chemical modifications in the exchange reaction. The results reveal that the formation of hydrogen bonds are a key feature and that the vinylogous urea improves the transamination compared to vinylogous urethane. The esteric hindrance of the amino group in the vinylogous compound also plays an important role. Finally, the nature of the free amine can improve the reactivity by equilibrating two contrary effects: the basicity favors the nucleophilic attack and the conjugated acidity favors the protonation. The findings of this theoretical work shed light in the design of new vitrimers with controlled exchange kinetics by chemical modifications.     

Computational and Experimental Study of Turbo-Organomagnesium Amide Reagents: Cubane Aggregates as Reactive Intermediates in Pummerer Coupling

The dynamic equilibria of organomagnesium reagents are known to be very complex, and the relative reactivity of their components is poorly understood. Herein, a combination of DFT calculations and kinetic experiments is employed to investigate the detailed reaction mechanism of the Pummerer coupling between sulfoxides and turbo-organomagnesium amides. Among the various aggregates studied, unprecedented heterometallic open cubane structures are demonstrated to yield favorable barriers through a concerted anion-anion coupling/ S−O cleavage step. Beyond a structural curiosity, these results introduce open cubane organometallics as key reactive intermediates in turbo-organomagnesium amide mixtures.     

Design of dinuclear copper species with carboranylcarboxylate ligands: study of their steric and electronic effects

A series of new mononuclear and carboranylcarboxylate‐bridged dinuclear copper(II) compounds containing the 1‐CH₃‐2‐CO₂H‐1,2‐closo‐C₂B₁₀H₁₀ carborane ligand ( L H) has been synthesized. Reaction of different copper salts with L H at room temperature leads to dinuclear compounds of the general formula [Cu₂(μ‐ L )₄( L_t )₂] ( L_t =thf ( 1 ), L_t =H₂O ( 1′ )). The reaction of 1 and 1′ with different terminal pyridyl (py) ligands leads to the formation of a series of structurally analogous complexes by substitution of the terminal ligand thf or H₂O ( L_t =py ( 2 ), p‐CF₃‐py ( 3 ), p‐CH₃‐py ( 4 ), pz ( 6 ), and 4,4′‐bpy ( 7 )), which maintain the structural Cu₂(μ‐O₂CR)₄ core in the majority of the cases except for o‐(CH₃)₂‐py, where a mononuclear compound ( 5 ) is exclusively obtained. These compounds have been characterized through analytical, spectroscopic (NMR, IR, UV‐visible, ESI‐MS) and magnetic techniques. X‐ray structural analysis revealed a paddle‐wheel structure for the dinuclear compounds, with a square‐pyramidal geometry around each copper ion and the carboranylcarboxylate ions bridging two copper atoms in syn–syn mode. The mononuclear complex obtained with the o‐(CH₃)₂‐py ligand presents a square‐planar structure, in which the carboranylcarboxylate ligand adopts a monodentate coordination mode. The magnetic properties of the dinuclear compounds 1 , 3 , 4 , and 6 show a strong antiferromagnetic coupling in all cases (J=?261 ( 1 ), ?255 ( 3 ), ?241 ( 4 ), ?249 cm^?1 ( 6 )). Computational studies based on hybrid density functional methods have been used to study the magnetic properties of the complexes and also to evaluate their relative stability on the basis of the strength of the bond between each Cu^II and the terminal ligand.     

Acyl Group Migration in Pyranosides as Studied by Experimental and Computational Methods

Acyl group migration affects the synthesis, isolation, manipulation and purification of all acylated organic compounds containing free hydroxyl groups, in particular carbohydrates. While several isolated studies on the migration phenomenon in different buffers have been reported, comprehensive insights into the overall migration process in different monosaccharides under similar conditions have been lacking. Here, we have studied the acyl migration in different monosaccharides using five different acyl groups by a combination of experimental, kinetic and theoretical tools. The results show that the anomeric configuration in the monosaccharide has a major influence on the migration rate, together with the relative configurations of the other hydroxyl groups and the nature of the migrating acyl group. Full mechanistic model, based on computations, demonstrates that the acyl migration proceeds through an anionic stepwise mechanism with linear dependence on the [OH⁻] and the pK_a of the hydroxyl group toward which the acyl group is migrating.     

A highly reactive and magnetic recyclable catalyst based on silver nanoparticles supported on ferrite for N‐monoalkylation of amines with alcohols

Fe₃O₄@SiO₂‐Ag catalyst was found to be highly active and selective in the N ‐alkylation of amines with a variety of aromatic and linear alcohols. The heterogeneous nature of the Fe₃O₄@SiO₂‐Ag catalyst allows easy recovery and regeneration by applying an external magnet for six subsequent reaction cycles. The prepared catalyst was characterized using electron microscopy techniques, X‐ray diffraction, vibrating sample magnetometry and atomic absorption spectroscopy.     

Mild and eco‐friendly chemoselective acylation of amines in aqueous medium using a green,superparamagnetic, recoverable nanocatalyst

Copper‐grafted guanidine acetic acid‐modified magnetite nanoparticles (Fe₃O₄@GAA‐Cu(II)) as a green, superparamagnetic and recoverable nanocatalyst is found to promote quantitative N ‐acylation of various amines in a very short time with an equimolar amount of thioacetic acid in water at room temperature. This method is found to be highly selective for amines and not sensitive to other functional groups. Mild reaction condition, high selectivity, efficiency, simple workup and excellent yields are some of the major advantages of the procedure.     

Mechanisms of oxidation of K4Fe(CN)6 by hypochlorous acid and catalytic activation by azide, bromide, and iodide

Summary HOCl reacts with Fe(CN) ₆ ^4– to generate an intermediate, presumably FeCl(CN) ₆ ^3– , which exhibits a weak absorption around 282 nm and decays simultaneously with the formation of Fe(CN) ₆ ^3– . When decreasing the HOCl/Fe(CN) ₆ ^4– concentration ratio fromR>1 toR<1, a drastic change in the kinetics of the oxidation is observed. Depending onR, the intermediate obviously oxidizes either Fe(CN) ₆ ^4– or HOCl. AtR1, a further intermediate appears which also precedes the oxidation and absorbs strongly around 360 nm. The intermediates detected may represent reactive high oxidation states of iron (Fe(IV) and Fe(VI)). HOCl induced oxidation of Fe(CN) ₆ ^4– is activated catalytically by Br^–, I^–, and N ₃ ^– , obviously due to generation of stronger oxidants (HOBr, HOI, and ClN₃), but oxidation is efficiently inhibited by CN^– and NCS^–.

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Mechanismen der Oxidation von K₄Fe(CN)₆ durch Hypochlorsäure und katalytische Aktivierung durch Azid, Bromid und Iodid

Zusammenfassung HOCl reagiert mit Fe(CN) ₆ ^4– unter Bildung eines Intermediats, vermutlich FeCl(CN) ₆ ^3– , das bei 282 nm eine schwache Absorption aufweist und parallel zum Erscheinen von Fe(CN) ₆ ^3– verschwindet. Man beobachtet eine drastische Änderung in der Oxidationskinetik, wenn das HOCl/Fe(CN) ₆ ^4– Konzentrationsverhältnis vonR>1 zuR<1 verändert wird. In Abhängigkeit vonR wird offenbar entweder Fe(CN) ₆ ^4– oder HOCl durch das Intermediat oxidiert. FürR1 erscheint ein weiteres Intermediat mit einer starken Absorptionsbande bei 360 nm, das ebenfalls der Oxidation vorangeht. Bei den beobachteten Intermediaten handelt es sich vermutlich um reaktive höhere Oxidationsstufen des Eisens (Fe(IV) und Fe(VI)). Die HOCl-induzierte Oxidation von Fe(CN) ₆ ^4– wird einerseits durch Br^–, I^– und N ₃ ^– katalytish aktiviert (offenbar infolge der Bildung stärkerer Oxidantien wie HOBr, HOI und ClN₃), andererseits durch CN^– und NCS^– effektiv inhibiert.

     

Mechanism,kinetics, and environmental assessment of OH-initiated transformation of CTDE in the atmosphere

The transformation mechanism and kinetics of 2-chloro-1,1,2-trifluoroethyl-difluoromethyl-ether (CTDE, CHF₂OCF₂CHFCl) triggered by OH radicals are studied by density-functional theory methods and canonical variational transition state theory. The computational rate constant including small-curvature tunneling correction is found to be in commendable agreement with the experimental data. Two hydrogen abstraction channels to form the alkyl radicals of C·F₂OCF₂CHFCl and CHF₂OCF₂C·FCl are observed, and the formation of CHF₂OCF₂C·FCl is found to be more favorable than C·F₂OCF₂CHFCl kinetically and thermodynamically. Subsequent evolution of CHF₂OCF₂C·FCl in the presence of NO and O₂ indicates that the organic nitrate (CHF₂OCF₂CONO₂FCl) is the stable product. The dechlorinate of alkoxy radical (CHF₂OCF₂C(O·)FCl) is the most favorable degradation channel, and the estimated ozone depletion potential for CTDE relative to chlorofluorocarbon-11 is 0.0204, which could lead to ozone depletion as a consequence. The computed atmospheric lifetime for CTDE is found to be 3.69 years by considering the combined contributions from OH radicals and Cl atoms. The total radiative forcing and global warming potential of CTDE are, respectively, 0.547 W m⁻² ppbv and 628.58 (100 years) at 298 K, suggesting that the contribution of CTDE to the greenhouse effect is moderate.     

2,6-Dimethyl-4-quinolinecarboxylic acid N-hydroxysuccinimide ester: a fluorogenic hydrophilic derivatizing reagent for liquid chromatographic analysis of aliphatic amines

The use of a fluorogenic, hydrophilic, and amine-reactive reagent, 2,6-dimethyl-4-quinolinecarboxylic acid N-hydroxysuccinimide ester (DMQC-OSu) has been investigated in the procolumn derivatization for the LC separation of aliphatic amines. In pH 8.0 aqueous medium, DMQC-OSu reacted with amines at 50 degrees C within 20 min to form highly fluorescent carboxamides and the excess reagent hydrolyzed to the corresponding carboxylic acid. The separation of representative amine derivatives with DMQC-OSu has been performed using a C18 column with the fluorescence detection at 326/409 nm. The detection limits reached nanomolar level. The proposed method has been applied to the analysis of real samples with recoveries of 94-108%. Compared with other succinimidyl esters used in the derivatization of amino compounds, DMQC-OSu and its hydrolysate had negligible fluorescence (phi(fl) = 0.09 and 0.02, respectively), which implied that small peaks appeared in chromatograms and slight interference was introduced to the determination.     

Density functional theory study of mechanism of epoxy‐carboxylic acid curing reaction

A comprehensive picture on the mechanism of the epoxy‐carboxylic acid curing reactions is presented using the density functional theory B3LYP/6‐31G(d,p) and simplified physical molecular models to examine all possible reaction pathways. Carboxylic acid can act as its own promoter by using the OH group of an additional acid molecule to stabilize the transition states, and thus lower the rate‐limiting barriers by 45 kJ/mol. For comparison, in the uncatalyzed reaction, an epoxy ring is opened by a phenol with an apparent barrier of about 107 kJ/mol. In catalyzed reaction, catalysts facilitate the epoxy ring opening prior to curing that lowers the apparent barriers by 35 kJ/mol. However, this can be competed in highly basic catalysts such as amine‐based catalysts, where catalysts can enhance the nucleophilicity of the acid by forming hydrogen‐bonded complex with it. Our theoretical results predict the activation energy in the range of 71 to 94 kJ/mol, which agrees well with the reported experimental range for catalyzed reactions. © 2017 Wiley Periodicals, Inc.     

Computational Investigations of Heme Carbenes and Heme Carbene Transfer Reactions

Engineered heme proteins and biomimetic iron porphyrins have been found to possess excellent catalytic properties for numerous carbene transfer reactions. Computational studies, including the use of DFT calculations and molecular dynamics simulations, have been employed to help understand some important mechanistic aspects of heme carbene transfer reactions. This review summarizes advances in the computational results published in the following two areas: 1) the electronic and geometric structures of heme carbenes; spectroscopic properties; and effects of carbene substituent, porphyrin substituent, axial ligand, and spin state on heme carbene formation; and 2) mechanisms of heme carbenoid X−H (X=C, Si, B, N, S) insertions and cyclopropanation, including effects of heme carbene structural components and protein environment, as well as oxidation state and spin state. A brief outlook of future development is also addressed.     

Almost Enclosed Buckyball Joints: Synthesis,Complex Formation,and Computational Simulations of Pentypticene‐Extended Tribenzotriquinacene

We report the synthesis of a tribenzotriquinacene‐based (TBTQ) receptor ( 3 ) for C₆₀ fullerene, which is extended by pentiptycene moieties to provide an almost enclosed concave ball bearing. The system serves as a model for a self‐assembling molecular rotor with a flexible and adapting stator. Unexpectedly, nuclear magnetic resonance spectroscopic investigations reveal a surprisingly low complex stability constant of K₁=213±37 M ^?1 for [C₆₀? 3 ], seemingly inconsistent with the previously reported TBTQ systems. Molecular dynamics (MD) simulations have been conducted for three different [C₆₀?TBTQ] complexes to resolve this. Because of the dominating dispersive interactions, the binding energies increase with the contact area between guest and host, however, only for rigid host structures. By means of free‐energy calculations with an explicit solvent model it can be shown that the novel flexible TBTQ receptor 3 binds weakly because of hampering entropic contributions.     

计算化学在正丁醚制备实验教学中的应用*

正丁醚的制备是重要的大学有机化学实验,为提高学生对该实验所涉及的反应机理和关键操作要点的深入了解,采用Gaussian计算软件对正丁醇在酸催化下和无催化剂下的反应体系进行了研究,重点考察了酸催化下反应的主、副反应方向的反应机理。结果表明无催化剂下,正丁醇在常压液相下几乎不能发生反应;在酸催化下,正丁醇发生取代反应生成醚的反应路径是优势反应通道;酸催化下正丁醇的取代和消除反应速率常数均随温度增加而迅速增大,但消除反应的反应速率随温度增加更快,温度超过420 K消除反应将变得很明显,综合考虑,制备正丁醚的反应温度应控制在130~140 ℃之间较为合适。利用计算化学以图、表和动图等形式直观、动态、量化地解释了正丁醇成醚和成烯反应的竞争,该结果有助于更好地控制该反应体系,可用作实验教材的补充内容。     

Unclicking the Click: Metal-Assisted Mechanochemical Cycloreversion of Triazoles Is Possible

The mechanochemical cycloreversion of 1,2,3-triazole compounds, which serve as unusually stable building blocks in materials and biomolecular chemistry as a result of mild “click chemistry”, remains puzzling. We show that the hitherto discussed straight-forward retro-click mechanism of the 1,4-disubstituted isomer, even if Cu^I catalyzed, can be ruled out in view of more favorable activation free energies of destructive pathways. In stark contrast, the 1,5-regioiomer can undergo cycloreversion under rather mild mechanochemical conditions owing to its favorable response to the external force in conjunction with standard Ru^II catalysis.     

Room-temperature palladium-catalyzed Negishi-type coupling: a combined experimental and theoretical study

An air-stable, bulky electron-accepting phosphine ligand (phosphabarrelene) allows the easy reduction of a Pd(II) precursor to a Pd(0) complex, highly active in room-temperature Negishi-type cross-coupling. DFT calculations show that the use of the electron-accepting ligand favors both transmetalation (TM) and reductive-elimination (RE) processes (see scheme; OA = oxidative addition).     

First ionization potentials of amines and electronic effects in their radical cations

The possibility of application of linear free energy relationships for studying the effects of substituents on the first vertical ionization potentials of amines, I(n_N), was substantiated. The I(n_N) values depend on the inductive, resonance, and polarizability effects of substituents and are also affected by hyperconjugation. The _R ⁺ resonance parameters of substituents MR₃ (M = Si, Ge, Sn) and CH₂SiMe₃ bound to the N ^·+ radical cation center were calculated for the first time.     

水促进的三组分PBM反应合成三级胺

首次报道了甲醛衍生的胺缩醛和芳基硼酸在水的促进下,可以在没有催化剂的条件下高效的合成三级胺.在此基础上建立了一种利用多聚甲醛,二级胺和芳基或杂环硼酸合成三级胺的高效合成方法.此反应条件温和,操作简单,具有很好的底物适应性,目标产物的收率最高可达93%.