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Pd-catalyzed hydroaminocarbonylation (HAC) of alkenes with CO and NH4Cl enables atom-economic and regiodivergent synthesis of primary amides, but the origin of regioselectivity was incorrectly interpreted in previous computational studies. A density functional theory study was performed herein to investigate the mechanism. Different from the previous proposals, both alkene insertion and aminolysis were found to be potential regioselectivity-determining stages. In the alkene insertion stage, 2,1-insertion is generally faster than 1,2-insertion irrespective of neutral or cationic pathways for both P(tBu)3 and xantphos. Such selectivity results from the unconventional proton-like hydrogen of the Pd-H bond in alkene insertion transition states. For less bulky alkenes, aminolysis with P(tBu)3 shows low selectivity, while linear selectivity dominates in this stage with xantphos due to a stronger repulsion between xantphos and branched acyl ligands. It was further revealed that the less-mentioned CO concentration and solvents also influence the regioselectivity by adjusting the relative feasibilities of CO-involved steps and NH3 release from ammonium chloride, respectively. The presented double-regiodetermining-stages mechanistic model associated with the effects of ligands, CO concentration, and solvents well reproduced the experimental selectivity to prove its validity and illuminated new perspectives for the regioselectivity control of HAC reactions.

For C-H alkenylation of aryl-substituted diarylisoxazoles, one mode is N-directed C-H alkenylation and the other is C-H alkenylation in the isoxazole ring. In this study, selective C-H alkenylations of 3,5-diarylisoxazoles have been investigated theoretically with the aid of density functional theory (DFT) calculations. With Cp*RhIII as the catalyst, the N-directed C-H alkenylation is preferred as a result of the stronger interaction energy caused by the nitrogen-directing effect. With Pd(OAc)2 as the catalyst and Ag2CO3 as the cocatalyst, their combination switches the regioselectivity to the C-H alkenylation in the isoxazole ring. The strong structural distortion involved in the competing N-directed olefin insertion transition state was found to suppress N-directed C-H alkenylation. With Pd(OAc)2 as the catalyst and Cu(OTf)2 as the cocatalyst, the N-directed C-H alkenylation becomes preferred due to the strong coordination of the nitrogen atom to the copper center. In particular, the structural and mechanistic information involved in the above two heterodimetallic Pd/Ag and Pd/Cu catalytic systems will help toward understanding and designing novel relevant heterodimetallic-catalyzed reactions.

Iridium-catalyzed oxidative o-alkenylation of benzylamines with acrylates was enabled by the directing group pentafluorobenzoyl (PFB). Density functional theory calculations were performed to explore the detailed reaction mechanism. The calculated results reveal that N-deprotonation prior to C–H activation is favored over direct C–H activation. Moreover, C–H activation is reversible and not the rate-determining step, which has been supported by the experimental observation. The regio- and stereoselectivity of ethyl acrylate insertion are controlled by the steric effect and the carbon atom with a larger orbital coefficient of the π* antibonding orbital in the nucleophilic attack, respectively. The migratory insertion of ethyl acrylate is computationally found to be rate-determining for the whole catalytic cycle. Finally, the seven-membered ring intermediate IM11 undergoes a sequential N-protonation and β-H elimination with the assistance of AcOH, rather than β-H elimination and reductive elimination proposed experimentally, to afford the o-alkenylated product. IM11 is unable to directly cyclize through C–N reductive elimination because both sp3-hybridized N and C atoms are unfavorable for N–C reductive elimination. The origin of the directing group PFB preventing the product and intermediates undergoing aza-Michael addition has been explained.

The graphitic carbon nitride (g-C3N4) nanodots (CN-dots) exhibit properties different from those of g-C3N4 crystal. However, the electronic structure of g-C3N4 nanodots, which determines their properties intrinsically, has not been explored comprehensively. Herein, the many-body Green’s function theory is used to analyze the electronic and optical properties of CN-dots; and the effects of size, shape, and functional group on properties were systematically investigated. The large size and the nonlinear shape are effective means to decrease electronic band gap. The increase in the functional group –CHO can make the complex composed of 1D g-C3N4 and 2D g-C3N4 change from type I to type II heterojunction. Different functional groups are related to the absorption edge of CN-dots, while have little effect on the electron–hole recombination rate. These results can provide theoretical support for modifying the properties of CN-dots and further designing CN-dots-based functional materials.

The Ni(0)-catalyzed coupling of benzimidazole with 1,1-disubstituted allenes represents a new strategy for achieving controllable C–H allylations, alkenylations and dienylations. To understand the detailed mechanisms and origins of the switchable selectivities, density functional theory (DFT) calculations were conducted. The results using a tBu-substituted allene demonstrate that the formation of the allylated product involves a Ni-catalyzed C–H activation mechanism through ligand-to-ligand-hydrogen transfer (LLHT) under base-free conditions. In contrast, a Ni/NaOtBu co-promoted C–H activation mechanism is newly proposed in the presence of NaOtBu, which is remarkably different from the previously reported literature. The novel mechanism emphasizes that NaOtBu abstracts the Ni-activated heterocyclic (ipso-C)H atom followed by turnover limiting Ni slippage, and subsequently the allylated product is generated after alkene insertion and protonation. The strong electrostatic attraction between Ni and heterocyclic ipso-C in the Ni slippage pre-intermediate is critical for facilitating the Ni slippage. Once formed, the allylated product, assisted by NaOtBu, further evolves into a more stable alkenylated isomer. Employing a (tert-butyldimethylsilyl)-ether substituted allene as the substrate, the NaOtBu-induced chemoselectivity for dienylation vs. alkenylation was also probed and it was found that the O(tBu)–H⋯O(Si) hydrogen bonding interaction in the C–O(Si) cleavage pre-intermediate remarkably weakens the adjacent C–O(Si) σ-bond, thereby resulting in an exclusive C–O(Si) cleaved dienylation product. Further theoretical predictions suggest that the chemoselectivity might be reversed by replacing tBu in NaOtBu by the withdrawing C(CF3)3 group.

The mechanism of ruthenium-catalyzed [4 + 1] annulation of benzamide and propargyl alcohol has been investigated by density functional theory calculations. The reaction undergoes N–H and C–H deprotonations by a concerted metalation-deprotonation mechanism to afford a 5-membered ruthenacyclic species, which then undergoes ring expansion by alkyne insertion to deliver a 7-membered ring intermediate. Our study focused on how the successive hydrogen migrations take place that remains unclear. The 1,2-proton migration and 1,3-proton transfer from O to C are successively finished by using acetate anion as a shuttle (a stepwise process). In contrast to the experimental proposal that the reaction experiences a Ru(II)–Ru(0)–Ru(II) transformation, our study unveiled a Ru(II)–Ru(IV)–Ru(II) transformation in the reaction. In addition, our calculations suggested that the EtO–N bond cleavage rather than the C–H activation is likely to be the rate-determining step for the entire reaction, which is not in contradiction w...

The combination of carbon monoxide with palladium chemistry has been demonstrated to be a promising tool for the synthesis of carbonyl compounds, and relative mechanistic studies are desirable to take this field one step further. In this manuscript, density functional theory calculations were performed to investigate the mechanism and origin of stereoselectivity of Pd-catalyzed cascade annulation of aryl iodide, alkene, and carbon monoxide to access the core of cephanolides B and C. It was found that the favorable mechanism proceeds via oxidative addition of Ar-I bond, migratory insertion of the C═C bond, CO insertion into the Pd-(sp3) bond, Ar-H activation, and C(sp2)-C(sp2) reductive elimination. The Ar-H activation is the rate-determining step and goes through an I-assisted outer-sphere concerted metalation-deprotonation mechanism. The C═C bond insertion is irreversible and controls the stereoselectivity. In contrast, other two pathways involving the direct Ar-H activation after the C═C bond insertion is less favored because of the following difficult CO insertion on the palladacycle intermediate. Further calculations well reproduced the experimental results, which supports the rationality of our computation. Meanwhile, the influence of the steric effect of three substitution sites on the stereoselectivity was disclosed, which should be helpful to the further experimental design in the synthesis of analogues.

The gold(iii)-catalyzed annulations of alkynes with anthranils were evaluated using DFT calculations. A unified rationale for the Br-migration on α-imino gold(iii)-carbene was proposed, from which an unprecedented "N-donation/abstraction substitution" mechanism was established using the substituted anthranils, while direct C-H nucleophilic attack was involved with the unsubstituted anthranils. The controlling factors guiding the site-selectivity were uncovered. These computational studies provide insight for developing new α-imino gold(iii)-carbene mediated reactions.

Polycyclic compounds having biological activities can be modified by employing different substituents. Substituent-dependent generation of tricyclic frameworks by the rhodium-catalyzed cycloisomerization of homopropargyl allene-alkynes was investigated by using density functional theory calculations. A mechanistic study revealed that all the three reactions, A (Z = Me, X = tBu), B (Z = Me, X = Me), and C (Z = H, X = Me), underwent initial oxidative cyclization, from which the divergent cycloisomerization was triggered when different substituents were employed. It was found from our calculations that reactions A and B underwent alkyne insertion into the Rh-C(sp2) bond and resulted in a key metal carbenoid intermediate. From the metal carbenoid species, reaction A bearing a more hindered tert-butyl group prefers 1,2-hydrogen migration to produce a 6/5/4 tricyclic product, while reaction B bearing a less hindered methyl group prefers 1,2-carbon migration leading to ring expansion and producing a 6/5/5 tricyclic product. The origins of the distinct selectivity were disclosed, which are beneficial for the development of novel related reactions. For reaction C (Z=H, Z=H or Z=H, Z=Me), the β-hydrogen elimination was found to be favored over the alkyne insertion into the Rh-C(sp2) bond and thus the monocyclic product is delivered. The E/Z effects involved in the above two cases were also discussed.

Pd-catalyzed alkoxycarbonylation of alkynes provided a redox-neutral method to selectively access branched/linear α,β-unsaturated monoesters and 1,4-dicarboxylic acid diesters. Herein, a systematic computational study was performed to elucidate the mechanism and origin of ligand-controlled chemo- and regioselectivities. It is found that the catalytic cycle, including hydrometallation, carbon monoxide insertion, and methanolysis, is more likely than that involving palladium alkoxycarbonyl intermediates. Both hydrometallation and methanolysis stages are important to determine the chemo- and regioselectivities. Hydrometallation proceeds via anti-Markovnikov-selective migratory insertion or Markovnikov-selective ligand-participated electrophilic addition. A flexible bidentate phosphine ligand slows down migratory insertion due to the stronger trans effect of the CO ligand but accelerates the ligand-participated electrophilic addition by adopting better orbital orientations. On the other hand, a ligand-participated mechanism and an unrevealed mechanism involving ketene intermediates can promote methanolysis, whereas ligands with large bite angles or bulky substituents are detrimental to methanolysis. On the basis of these mechanistic foundations, the influence of the flexibility, basicity, bite angle, and steric hindrance of ligands on chemo- and regioselectivities was clarified. The present study provided more universal and deeper mechanistic insights into Pd-catalyzed alkoxycarbonylation reactions and shed light on the superior regulation performance of the bifunctional pyridyl-containing phosphine ligands.

Cu-catalyzed aerobic C(CO)–CH3 activation of (hetero)aryl methyl ketones provides a rare tool for aldehyde formation from ketones through oxidative processes. To elucidate the detailed reaction mec...

Density functional theory (DFT) calculations have been performed to unravel the detailed mechanism of the CpRe(CO)3-catalyzed coupling reaction of CO2 with chloromethyloxirane (R). The mechanisms proposed in previous literature have been examined. However, the computed results seem not to completely rationalize the experimental findings. Alternatively, by performing an exhaustive search on the potential energy surface, we presented a novel CO-assisted mechanism, which provides an effective access to the catalytic coupling. The newly established mechanism involves the C O bond cleavage of R from the less hindered side, release of one CO ligand, CO2 insertion, re-coordination of the dissociated CO ligand, another CO ligand shift, reductive elimination with simultaneous migration of carbonyl substituent, resulting in P and regeneration of CpRe(CO)2. Two CO ligands attached to CpRe(CO)2 play significant roles in lowering the key CO2 insertion and reductive elimination: (i) One CO ligand dissociation prior to CO2 insertion contributes to reduce the electron density on the Re metal, facilitating the CO2 O atom nucleophilic attack. (ii) After performing the migration, another initially inactive CO ligand serves as a carbonyl substituent, which lowers the energy penalty for later reductive elimination through the resultant extra π-interaction and the smaller ring tension energy involved in TS. The theoretical results provide insight into the mechanism of the important coupling reaction and rationalize well the experimental observations.

A novel boron ester-catalyzed amidation reaction of carboxylic acids and amines with unprecedented functional group tolerance was recently reported. To gain deeper insights into this reaction, a computational study with density functional theory methods was performed in this manuscript. Calculations indicate that the amidation starts with the condensation of carboxylic acids with the boron ester catalyst. The resulting monoacyloxylated boron species further undergoes the carboxylic acid-assisted nucleophilic addition with amines to generate the amide product and a monohydroxyboron species. The condensation of the carboxylic acid with the monohydroxyboron species with the assistance of an amine regenerates monoacyloxylated boron species to finish the catalytic cycle. The rate-determining step is catalyst regeneration and the amine-coordinated monohydroxyboron species is the resting state in the catalytic cycle. The present results are consistent with the previous NMR study and the observed reaction orders of catalyst and substrates; it is expected to benefit further reaction optimization.

Pd-catalyzed C(sp3)–H activation/alkylation of 2-tert-butylaryl halides with alkyl halides and CH2Br2 represents an advantageous strategy for the C–H functionalization with halogens as traceless directing groups. Several possible mechanisms were proposed for the reactions, but no further evidence was available to judge their relative feasibilities. Herein, a mechanistic study was performed with the aid of density functional theory (DFT) methods. Calculations indicate that the coupling of aryl bromides with alkyl chlorides is likely to generate alkylated benzocyclobutenes via aryl–Br oxidative addition on Pd(0) catalysts, C(sp3)–H activation, alkyl–Cl oxidative addition, aryl–alkyl reductive elimination, aryl–H activation, and aryl–C(sp3) reductive elimination. The coupling of aryl iodides with CH2Br2 is likely to generate indane derivatives via aryl–I oxidative addition, C(sp3)–H activation, alkyl–Br oxidative addition, aryl–CH2Br reductive elimination, alkyl–Br oxidative addition, C(sp3)–alkyl reductive ...

Acyl transfer of in situ-generated mixed anhydrides is an important method for amide bond formation from short linkages with the easily removed byproduct CO2. To improve our understanding of the inherently difficult acyl transfer hindered by the large ring strain, a density functional theory study was performed. The calculations indicate that the amidation of activated α-aminoesters and N-protected amino acids is more likely to proceed via the self-catalytic nucleophilic substitution of the two substrates and the subsequent 1,3-acyl transfer. By comparison, the mechanism involving 1,5-acyl transfer is less kinetically favored because of the slow homocoupling of activated α-aminoesters. Furthermore, we found that the detailed mechanism of 1,3-acyl transfer on the mixed carboxylic–carbamic anhydrides depends on the catalysts. Strong acidic catalysts and bifunctional catalysts both lead to stepwise pathways, but their elementary steps are different. Basic catalysts cause a concerted C–N bond formation/decarb...

Reactions of thiocarboxylic acids and dithiocarbamate-terminal amines provide a linker-traceless method for amide bond formation under mild conditions, whereas the reaction mechanism is not clear. A systematic study was performed herein with density functional theory (DFT) calculations to elucidate the detailed mechanism, the substitution effect on the proposed CS2-releasing 1,3-acyl transfer and the differences between CS2- and CO2-releasing 1,3-acyl transfer. Relevant results indicate that this type of reaction proceeds via the nucleophilic addition of an in situ generated dithiocarbamic acid on thiocarboxylic acid, H2S elimination, rate-determining 1,3-acyl transfer and CS2 release. For the generation of secondary amides via the 1,3-acyl transfer, a thiocarboxylic acid- or dithiocarbamic acid-assisted pathway, in which both the carbonyl group and amide nitrogen are activated, is the most favored. For the generation of tertiary amides, MeOH-assisted carbonyl-activation is the most favorable pathway. N,N-Dialkyl substitution of the mixed anhydride intermediate promotes the 1,3-acyl transfer by the steric effect. In contrast, N-phenyl substitution and using thiobenzoic acid as a substrate slow down 1,3-acyl transfer by both the conjugation effect and steric effect. Furthermore, CS2-releasing 1,3-acyl transfer was found to be favored over CO2-releasing 1,3-acyl transfer in the aspects of both kinetics and thermodynamics mainly because the S–COR bond is weaker than the O–COR bond.

Density functional theory (DFT) calculations have been conducted to unravel the mechanisms and chemoselectivities of Au-catalyzed diazo-based couplings with phenyl unsaturated aliphatic alcohols: the propargyl alcohol Ba resulting in the [4 + 1]-cycloaddition product P4a and the allyl alcohol Db giving the [2,3]-σ rearrangement species P5b. P4a formation involves a catalyst interaction with phenyldiazoacetate, N2 release, a hydroxyl O nucleophilic attack of Ba, a [1,4]-H shift, coordination isomerization, 5-endo-dig cyclization, a [4,1]-H shift and a H2O-assisted [1,3]-H shift. After the [4,1]-H shift, the slightly less favorable five-membered ring-opening possibly follows to afford trace P5a ([2,3]-σ rearrangement product), which would be kept in solution due to subsequent irreversible evolution. In addition, the Ba-involved chemoselectivity was probed and explained as follows: (i) both large H(hydroxyl)⋯C(carbene) electrostatic repulsion and strong three-membered ring strain involved in the TS make the formation of the O–H insertion product P1a difficult and (ii) the nucleophilic attack from the C2 atom of Ba brings about a structural twisting and thus increases the energy penalty forming the cyclopropenation product P2a. On the other hand, compared with the sp-C2 atom of Ba, the sp2-C2 atom of Db greatly facilitates the five-membered ring-opening step because of the presence of an extra pπ–pπ orbital overlap and eventually provides P5b exclusively.

The Cl-initiated degradation mechanism of methylallyl alcohol (MA) has been investigated by performing quantum chemical calculations. The reactants, transition states, intermediates and products are optimized at the MP2/6-311G(d,p) level. A detailed degradation mechanism is presented and discussed in this paper. The possible reactions of MA include two Cl-addition channels and eight H-abstraction reactions. Present results show that Cl-addition reactions are more favorable than H-abstraction processes, and the most energetically favorable pathway is the Cl-addition to the terminal carbon C1 atom. Main products detected in experiments and obtained in our study have been determined. The rate constants of dominant paths over a temperature range of 180–380 K are estimated. The total rate coefficients show a negative temperature dependence, and the Arrhenius equation is fitted as ktotal = (1.81 × 10−11)exp(511.21/T). At 298 K, the atmospheric lifetime of MA with respect to Cl is estimated to be 1.11 days.

A systematic investigation over the formation mechanism of the subphthalocyanine, SubPc(Cl), with phthalonitrile as the initial reagent mediated by boron trichloride in the solvent of p-xylene has been carried out on the basis of density functional theory, revealing truly a long reaction pathway containing twenty-three elementary reactions. The calculation results well reproduce and rationalize the experimental findings including the selection of high boiling point reaction media of p-xylene, employment of excessive amount of BCl3 reagent, and liberation of Cl2 during the reaction process. In particular, the crucial catalytic nature of BCl3 has been clearly disclosed: in addition to activating the cyano groups, boron trichloride also works as chloride-transfer shuttle to prompt the reactions occurring and proceeding. The present result will put forwards the exploration over the formation mechanisms of phthalocyanines and porphyrins.

The mechanisms and chemo- and regioselectivities of divergent (Ni(cod)2/PCy3)-mediated/-catalyzed C(sp3)–F bond activation of 2-trifluoromethyl-1-alkenes (1) with alkynes (2) were investigated by density functional theory (DFT) calculations. The nickel-mediated/-catalyzed reaction involves sequential ligand exchange, alkene coordination, oxidative cyclization (1 + Ni(0) + 2), and first β-F(C(sp3)) elimination to give a common and requisite alkenylnickel(II) species, which bifurcates into either stoichiometric defluorinative [3 + 2] cycloaddition product 3 or catalytic defluorinative coupling products (nonmethylated 5, monomethylated 8, or trimethylated 9) depending on the absence and presence of additional reagents (Et3SiH, ZnMe2, and AlMe3). The Et3SiH-induced formation of 5 is found to be a result of facile metathesis relative to the 5-endo insertion leading to 3. Because of the presence of an F→Zn/Al interaction, ZnMe2/AlMe3 brings the methyl into defluorinative coupling products. In the stoichiometric...

Benzene ring functionalization provides useful alternatives to access indole derivatives and has received much attention in recent years. In this work, the mechanism of Pt(II)-catalyzed cyclization/alkynylation of benziodoxole with pyrrole homopropargylic ethers to generate C5-alkenylated indole derivatives has been studied with the aid of density functional theory (DFT) calculations. We found that five-membered-ring cyclization/six-membered-ring cyclization is competitive in the formation of an indole skeleton. The following aromatization stage prefers the reaction sequence bicarbonate-assisted deprotonation at the C3a position, H2CO3-promoted methoxy elimination at the C7 position, and bicarbonate-assisted deprotonation at the C6 position. In the last alkynylation stage, the oxidative substitution mechanism assisted by H2CO3 is found to be favored over the previously proposed 1,2-iodo shift and oxidative addition. The overall rate-determining step is oxidative substitution. Additionally, an interesting ...

An enamide-based 9-fluorenylmethoxycarbonyl (Fmoc) solid-phase peptide synthesis (SPPS) method was recently disclosed for the synthesis of peptide thioesters. In this manuscript, density functional theory (DFT) calculations were performed to provide deeper mechanistic insights into this reaction. The calculation results clarified the detailed mechanisms of the relevant N-to-S acyl transfer and hydrolysis, the overall rate-determining step, the role of trifluoroacetic acid (TFA), as well as the influence of the stereo-configuration of amide bond and C C bond on reaction rate.

Density functional theory (DFT) calculations have been performed to unravel the mechanism of Lewis-acid-induced Ni(cod)2-catalyzed selective coupling reactions of one diketene and two alkynes. Complex mixtures (unsymmetrical phenylacetic acid P1, symmetrical phenylacetic acid P2 and (3E)-4-ethyl-5-methylene-3-heptenoic acid P3) were obtained in the absence of Et2Al(OEt). P1 formation involves C(sp2)-O oxidative addition of diketene, twice alkyne insertion, intramolecular C═C insertion, acidolysis, and β-H elimination. For P2/P3 formation, the common key issue related to the C═C double bond cleavage of the substrate diketene was explored and found that it was accomplished via a four-membered-ring-closure/four-membered-ring-opening process. And then, P2 was produced via the second alkyne insertion while P3 was accessed by a stoichiometric reaction with HCl. The Et2Al(OEt)-induced chemoselectivity was also probed. It is found that the Ni–O (from Al reagent) bonding facilitates the second alkyne insertion, an...

Lungs are easily damaged by the inflammatory responses induced after extensive burns. The aim here was to investigate the protective role of epigallocatechin gallate (EGCG) in mitochondrial DNA (mtDNA)-mediated inflammatory responses and acute respiratory distress syndrome (ARDS) in a rat model of thermal injury. Male Sprague-Dawley rats were randomly assigned to five groups. In the first experiment, a full-thickness thermal injury or control procedure, covering 30% of the TBSA, was inflicted on three groups designated as the thermal injury, EGCG, and sham control groups. In the second experiment, another two groups were established by transfusion with either mtDNA (mtDNA group) or phosphate-buffered saline (phosphate-buffered saline group). Blood samples and lung tissue from all five groups were collected and the plasma concentrations of mtDNA and inflammatory mediators were measured. Bronchoalveolar lavage fluid was collected and histological analysis of the lung tissue was performed to evaluate the severity of ARDS. Significant increases in mtDNA and inflammatory mediator plasma concentrations were seen in the thermal injury and EGCG groups when compared with controls (P < .05). The plasma concentrations of mtDNA and inflammatory mediators were significantly decreased after the administration of EGCG (P < .05). EGCG also significantly reduced the severity of acute lung injury (P < .05). Intravenous administration of mtDNA significantly increased concentrations of inflammatory mediators and caused severe ARDS (P < .05). Our results suggest that mtDNA is important for thermal injury-induced inflammation and associated ARDS. EGCG possesses anti-inflammatory and lung-protective properties, and might act by limiting mtDNA release after thermal injury.

The condensation of carboxylic acids and amines mediated by silane derivatives provided a straightforward and sustainable method for amide bond formation with minimal waste. However, the detailed mechanism and structure-activity relationship of substrates, the topics that are of interest for both academic and industrial applications, were not clear. Herein, a systematic computational study was conducted to solve the two questions. We found that the two previously proposed mechanisms involving intramolecular acyl transfer or silanolate were less likely because the associated silanone intermediate and zwitterion adducts were too unstable with higher overall energy barriers. By comparison, the mechanism involving deprotonation of carboxylic acids, addition of carboxylates on silane reagents, dihydrogen formation to afford an acyloxysilane intermediate, carboxylic-acid-assisted addition of amines, and concerted proton transfer/amide formation, was found to be more favorable with overall energy barriers varying between 24 and 28 kcal mol-1 for the different calculated cases. Meanwhile, the dihydrogen formation and amide formation processes are both potential rate-determining steps. Energy composition, atomic charge, and distortion-interaction analyses indicated that the steric effect of silane reagents was more important than the electronic effect, making less bulky silane reagents more reactive. On the other hand, the dihydrogen formation process was mainly controlled by the electronic effect of the substituents of carboxylic acids and amines while the amide formation process was mainly influenced by their steric effect. As a result, less bulky, less acidic alkyl carboxylic acids are more reactive than unsaturated carboxylic acids, and less bulky, medium basic primary alkyl amines are more reactive than secondary alkyl amines and primary aryl amines. The related results provided deeper mechanistic insights into the amide bond formation mediated by silane derivatives and can act as a reference for further experimental design.

The Rh(III)-catalyzed oxidative coupling of oxime ether (S1) and cyclopropanol (S2) with Cu(II) as the oxidant features the combination of C-H activation and strained ring opening. The sequential order of C-H activation versus ring opening was investigated with the aid of density functional theory calculations. Prior ring opening due to the release of ring strain is found to be favored over the prior C-H activation. For the prior ring-opening mechanisms, the outer-sphere concerted metalation-deprotonation (CMD) mechanism in C-H bond activation is energetically favored. The outer-sphere CMD mechanism proposed in this work favors solvent effects and affords the N→Rh binding that allows a directing role of the Schiff base group. In conclusion, the reaction was suggested to undergo prior ring opening followed by C-H activation via the outer-sphere CMD mechanism.

A computational study is carried out to understand the mechanism and excellent regioselectivity in metal-free heteroarylation of amides reported by Zhu’s group. The heteroarylation reaction started with the initial generation of key nitrogen-centered radicals via ligand exchange between reactant 1a and initiator PIFA under visible-light irradiation. Following, this reaction undergoes four-stages: 1,5-hydrogen atom transfer, C C coupling, single electron transfer and proton transfer. The C C coupling step is identified as the selectivity-determining step in which the carbon-centered radical (C) selectively only attacks the carbon atom adjacent to nitrogen of lepidine (2a). And the radical C more easily attacks the protonated 2a, compared with unprotonated 2a, due to significantly lowered SOMO/LUMO energy difference between them to promote this nucleophilic radical addition. From the calculated result, we can see that the positive effect of the acidity of the reaction substrates on the nucleophilic addition to heteroarenes. Fukui functions of different types of heteroarene substrates are calculated to predict the favorable nucleophilic sites. The calculated most favorable reactive sites of heteroarene substrates are well consistent with the experimental observed ones. This theoretical research provides deeper understandings for the underlying mechanism and the origin of exclusive regioselectivity of the heteroarylation of amides.

Gold-catalyzed cyclization of 2-alkynyl-N-propargylanilines provides a step-economic method for the construction of three-dimensional indolines. In this article, the M06 functional of density functional theory was employed to gain deeper insights into the reaction mechanism and the associated intriguing experimental observations. The reaction was found to first undergo Au(I)-induced cyclization to form an indole intermediate, 1,3-propargyl migration, and substitution with the substrate 2-alkynyl-N-propargylaniline (R1) to generate the intermediate product P1, an allene species. Subsequently, Au(I)-catalyzed conversion of P1 into the final product P2, an indoline compound, occurs first through direct cyclization rather than via the previously proposed four-membered carbocycle intermediate. Thereafter, water-assisted oxygen heterocycle formation and proton transfer generate the final product. The calculated activation free energies indicate that P1 formation is 5.9 times slower than P2 formation, in accordance with the fact that P1 formation is rate-limiting. Futhermore, the intriguing experimental phenomenon that P2 can be accessed only after almost all the substrate R1 converts to P1 although P1 formation is rate-limiting was rationalized by employing an energetic span model. We found the initial facile cyclization to form a highly stable indole intermediate in the formation of P1 is the key to the intriguing experimental phenomenon.

The reaction mechanisms of the (NHC)Ni(0)-catalyzed aldehyde–alkyne reductive couplings with silanes as reducing agent have been theoretically investigated with the aid of DFT calculations. The impacts of N-heterocyclic carbene (NHC) ligands and silanes on the reversal of regioselectivity and the rate-limiting step alteration were rationalized. It is found that the steric effects play a dominant role. The reversal of the regioselectivity is found to be related to the switching of the steric effect, from the aldehyde phenyl hindrance with the adjacent alkyne substituent to the NHC ligand hindrance with the adjacent alkyne substituent, when the NHC ligand employed is changed from small to large. The rate-limiting step alteration caused by using bulkier silanes is due to the generated strong steric effect, which makes the σ-bond metathesis transition state relatively high in enthalpic energy, thus with the entropy penalty making the metathesis step rate-limiting instead of the oxidative cyclization step.

Malonyl-CoA decarboxylase (MCD) can control the level of malonyl-CoA in cell through the decarboxylation of malonyl-CoA to acetyl-CoA, and plays an essential role in regulating fatty acid metabolism, thus it is a potential target for drug discovery. However, the interactions of MCD with CoA derivatives are not well understood owing to unavailable crystal structure with a complete occupancy in the active site. To identify the active site of MCD, molecular docking and molecular dynamics simulations were performed to explore the interactions of human mitochondrial MCD (HmMCD) and CoA derivatives. The findings reveal that the active site of HmMCD indeed resides in the prominent groove which resembles that of CurA. However, the binding modes are slightly different from the one observed in CurA due to the occupancy of the side chain of Lys183 from the N-terminal helical domain instead of the adenine ring of CoA. The residues 300 - 305 play an essential role in maintaining the stability of complex mainly through hydrogen bond interactions with the pyrophosphate moiety of acetyl-CoA. Principle component analysis elucidates the conformational distribution and dominant concerted motions of HmMCD. MM_PBSA calculations present the crucial residues and the major driving force responsible for the binding of acetyl-CoA. These results provide useful information for understanding the interactions of HmMCD with CoA derivatives. Proteins 2016; 84:792-802. © 2016 Wiley Periodicals, Inc.

Display Omitted F1P and F6P can bind to the same active site with different binding mode.Ligands affect the conformational spaces and motions of GKRP.Electrostatic interaction provides a major driving force for the ligand binding.F6P makes loop2 of GKRP more protruding and strengthens its contacts with GK.The residues 179-184 play a critical role in the binding of phosphate group. Glucokinase (GK) plays a critical role in maintaining glucose homeostasis in the human liver and pancreas. In the liver, the activity of GK is modulated by the glucokinase regulatory protein (GKRP) which functions as a competitive inhibitor of glucose to bind to GK. Moreover, the inhibitory intensity of GKRP-GK is suppressed by fructose 1-phosphate (F1P), and reinforced by fructose 6-phosphate (F6P). Here, we employed a series of computational techniques to explore the interactions of fructose phosphates with GKRP. Calculation results reveal that F1P and F6P can bind to the same active site of GKRP with different binding modes, and electrostatic interaction provides a major driving force for the ligand binding. The presence of fructose phosphate severely influences the motions of protein and the conformational space, and the structural change of sugar phosphate influences its interactions with GKRP, leading to a large conformational rearrangement of loop2 in the SIS2 domain. In particular, the binding of F6P to GKRP facilitates the protruding loop2 contacting with GK to form the stable GK-GKRP complex. The conserved residues 179-184 of GKRP play a major role in the binding of phosphate group and maintaining the stability of GKRP. These results may provide deep insight into the regulatory mechanism of GKRP to the activity of GK.

With the aid of density functional theory (DFT) calculations, the Pd-catalyzed reactions of aryl iodide with unsymmetrical alkyne leading to two products containing C(sp 3 )−I bond ( P3 and P4 ) and one product containing a three-membered carbocyclic unit ( P5 ), have been studied theoretically. It is found that both the alkyne insertion and the subsequent C C bond insertion involved in the reaction are the major thermodynamic driving forces. The alkyne insertion instead of the C(sp 3 )−I reductive elimination is predicted to be rate-determinant. Similar barrier heights calculated for the two insertion modes of unsymmetrical internal alkyne ( TS 3-4 and TS 3′-4′ ) lead to the products P3 (47.2%) and P4 + P5 (48.8%) having similar product yields. The intriguing formation of the product containing a three-membered carbocyclic unit ( P5 ) was investigated in details. The second alkene insertion is found to be kinetically more favored than the C(sp 3 )−I reductive elimination, leading to product P5 (39.0%) more productive than P4 (9.8%). The remarkably thermodynamically favored β−H elimination is the key factor enabling formation of P5 . Why significant bulky phosphine ligand such as P(t-Bu) 3 instead of small one such as P(Me) 3 was employed experimentally have also been rationalized based on our calculation results.

Pd-catalyzed decarboxylative Heck-type coupling of 3-chlorobenzo[b]thiophene-2-carboxylic acids with styrenes have been developed as an efficient strategy for the construction of functionalized benzo[b]thiophenes. Theoretical analysis shows that AgCl generated during the reaction, instead of Pd, π-coordinates with the carboxyl O atom, making easy the rate-determining CO2 dissociation. The divergent reactivities of the Cl-substituted and H-substituted 3-benzo[b]thiophene-2-carboxylic acids are mainly due to the presence of the Cl substituent, which reduces the adjacent π-π interplay, thereby significantly contributing to decarboxylation. Therefore, the presence of both AgCl and the Cl substituent are of key importance in ensuring the occurrence of the reaction under the given conditions.

The reaction features combination of C H activation and ring opening of cyclopropanol was studied with the aid of DFT calculations. With the reaction of N-pyrimidylindoline and 1-benzylcyclopropanol as an example to accomplish the alkylation, we found the order of C H activation/ring opening is difficult to occur. Instead, the order of ring opening/C H activation is predicted to be more reasonable, which circumvents the N→Rh bond breaking. Two catalytic cycles were suggested. The first cycle relates to the catalytic oxidation of cyclopropanol by Cu(II) to generate an intermediate product, the vinyl ketone. The mechanism mainly involves prior ring opening of cyclopropanol and β-H elimination. The second cycle relates to the product formation from the resultant intermediate product, in which the C H activation of N-pyrimidylindoline, C C bond insertion of the intermediate product and protonation are included. The insights gained in this study are expected to be pertinent in other reaction systems involving combination of C H activation and ring opening.

The mechanism on the oxidative [3 + 2] annulation reaction of 2-acetyl-1-phenylhydrazine (S1) with N-phenylmaleimide (S2) leading to the tricyclic pyrrolo [3,4-b]indole (P) was elucidated detailedly with the aid of the density functional theory calculations. Two C-N coupling modes involved in this annulation reaction were explored in details. It was found that the carbonyl-containing group attached to the azene nitrogen atom, such as acetate and ester groups, was vital for C-N coupling. This finding was also supported by other experimental observations that the C-N coupling works with the group being an ester and does not with the group being a methyl group. We anticipate this study would provide further understanding for such reactions at the molecular level and beneficial to the design of novel relevant annulation reactions involving C-N coupling.

Density functional theory (DFT) calculations were used to explore the Au(I)-catalyzed selective [4 + 1] annulations of cyclopropyl- and H-substituted 1,4-diyn-3-ols with isoxazole. The results indicated that after the N-nucleophilic attack of isoxazole, instead of obtaining the α–hydroxy gold carbene intermediate proposed experimentally, a concerted three-step forward product by isoxazole O[sbnd]N cleavage, 1,2-phenylalkyne shift and the hydroxyl H shift was identified as the key intermediate, for the reaction proceeding either via an Au-assisted C[dbnd]C double-bond rotation to produce the Z-isomeric enone or via two different Au-assisted C[dbnd]C rotations to furnish the E-configured enone depending on the substituents used. Further theoretical investigations indicated that the chemoselective step is the nucleophilic cyclization but not the C[dbnd]C double-bond rotation. The chemoselective preference for the Z-configured product using the cyclopropyl substitutent was attributed to two factors: i) the additional O[tbnd]H[sbnd]N hydrogen bonding interaction stabilizes the rate-determining cyclization TS leading to the Z-product, and ii) further Z-E product-isomerization is blocked due to significant structural deformation being involved. In contrast, using the H substituent results in a reversed chemoselectivity with exclusive formation of the E-configured enone, which is closely related to the smaller entropy effects involved.

A Pd- and norbornene-catalyzed domino procedure has been developed to synthesize indoline compounds. This reaction provides efficient access to indolines by employing aryl iodides with aziridines as new electrophiles. The transformation is scalable and tolerates a range of functional groups.

A recent experimental study by Tobisu et al. (J. Am. Chem. Soc. 2012, 134, 115–118.) reported a new type of catalytic borylation reactions, the Rh-catalytic reaction of aryl cyanides with diboron to afford arylboronic acids. To better understand the borylation mechanism at the molecular level, this work provides a theoretical description for the elementary steps of the reaction of a typical aryl cyanide with diboron in the presence of a rhodium catalyst [RhCl(cod)] 2 with the aid of DFT calculations. It is found that i) the catalytically active species is the Rh–B complex rather than the Rh–Cl one, ii) the Rh–Ar intermediate is formed through the iminoacyl species rather than the iminylrhodium species previously proposed by Tobisu et al., and iii) the structures of iminoacyl and boryl isocyanide species are also disagreement with those experimental studied by Tobisu et al. Calculated results show a clear mechanistic picture of the catalytic borylation reaction of the aryl cyanide.

By carrying out density functional theoretical calculations, we have performed a detailed mechanistic study of the Au(I)-catalyzed cycloisomerization of 1,6-enylnyl ester in a dry and wet dichloromethane solvent corresponding to hydrogenation and hydrolysis processes, respectively. The hydrogenation and hydrolysis mechanisms proposed in the previous literature starting from an enol ketal intermediate without the involvement of an Au(I) catalyst are found to involve high barriers and thus contradict the observed experimental findings. Alternatively, based on the theoretical calculations, a novel hydrogenation mechanism (i.e., Au-induced H-shift followed by enol intermediate self-promoted H-shift) and a hydrolysis mechanism (i.e., Au-stabilized H-shift/C-O binding with subsequent H2O-assisted H-shift) from an Au-enol ketal adduct corroborate the experimental observations. The calculated results indicate that under unchanged wet conditions, the formation of a hydrolysis product is not involved in the intermediacy of the hydrogenation product. However, if the initial dry environment is provided, a hydrogenation product will be afforded. And then it will relentlessly evolve into a hydrolysis product in the subsequent wet conditions. The present theoretical results not only rationalize the experimental observations well but provide new insight into the mechanisms of the significant water-mediated cycloisomerization reaction.

In this study, the adsorption behavior of carbon monoxide (CO) gas molecules on anionic M@Bn− (M = Co, Ir, Rh, Ru, Ta, Nb, n = 8–10) clusters has been systematically investigated by employing density functional theory (DFT). It was found that CO adsorption on boron clusters proceeds spontaneously and easily, accompanied with a dramatic structural deformation for the corresponding M@Bn− clusters. Large adsorption energies ranging from −22.82 to −27.38 kcal mol−1 have been observed for CO on boron clusters. The kinetic stabilities of the formed complexes have been verified by ab initio molecular dynamics. The IR spectra and adiabatic detachment energy of the M@Bn− clusters have been discussed before and after CO adsorption. In addition, the adsorption behavior of the other small gas molecules, such as CO2, N2, CH4, H2O, and O2, have also been explored. The potential applications of these wheel boron M@Bn− clusters in the detection of CO gas have been proposed for the first time.

The couplings of carboxylic acids and amines promoted by dichlorosilane derivatives provide a promising tool for amide synthesis and peptide coupling, in which an unprecedented mechanism was proposed for the amide bond formation process. To investigate this mechanistic proposal and enrich the understanding of this novel reaction, a theoretical study was conducted herein. The formation and interconversion of silylamine and silyl ester intermediates were calculated to be kinetically feasible under the experiment conditions. However, the subsequent amidation via direct elimination on the AcO-Si(L)(L')-NHMe intermediate was found to involve a high energy barrier due to the formation of an unstable silanone. By contrast, the in situ generated salts can promote the amidation process by generating a silanol as the temporary product. Similarly, the anhydride formation mechanism can proceed via direct elimination or salt-assisted elimination on the AcO-Si(L)(L')-OAc intermediate but is less favorable. Finally, we found that the intermolecular nucleophilic addition on the AcO-Si(L)(L')-Cl intermediate is the most favorable mechanism among all the candidates considered. In this mechanism, carboxylic acids or bases can act as self-catalysts to promote the amide bond formation via hydrogen bonding, and the formation of the unstable silanone or anhydride is avoided.

The Pd-catalyzed cross-coupling of aryl iodide, benzoic anhydride and ethyl acrylate provided a useful alternative to synthesize alkenylated aryl ketones with good selectivity and functional-group tolerance. In this manuscript, density functional theory (DFT) calculations were performed to address the detailed reaction mechanism. Computational results support the experimentally proposed Pd(0)–Pd(II)–Pd(IV) catalytic cycle and further clarify that the rate-determining step is the oxidative addition of benzoic anhydride, the regioselectivity-determining step is the migratory insertion of ethyl acrylate and the following β-H elimination determines the stereoselectivity. The regioselectivity can be attributed to the steric and electronic effect of ethyl acrylate and the stereoselectivity can be explained by the steric repulsion between the toluene moiety and the CO2Et moiety. Furthermore, we found that norbornene not only acts as the removable scaffold in Catellani–Lautens-type reactions, but also plays the role of suppressing the competitive migratory insertion of ethyl acetate. Norbornene insertion and ethyl acetate insertion are found to have close free energy barriers, which shed light on the origin of using stoichiometric amounts of norbornene.

The reaction mechanism for the palladium(II)-catalyzed cross-coupling of N-tosyl hydrazone S1 with alkene S2 has been studied with the help of density functional calculations. The acetate present in the catalyst was found to directly participate in the reaction. The tBuO– group that was added in excess into the reaction system plays an important role in forming the new C═C double bond. In addition, we clarified how water plays an assisting role to promote the catalytic reaction studied.

With the help of density functional theory (DFT) calculations, we theoretically investigated and rationalized the controlled metathesis reactions of methylruthenium complex trans-[Ru(CH3)2(dmpe)2] [dmpe = 1,2-bis(dimethylphosphanyl)ethane] (A) with terminal acetylenes. On the basis of the mechanistic study, two important issues related to the generation of mono- and bis-acetylido Ru complexes have been addressed. One issue is why the formation of bis-acetylido complex C, trans-[Ru(C≡CPh)2] (dmpe)2, is more difficult than the formation of mono-acetylido complex B, trans-[Ru(C≡CPh)(CH3)(dmpe)2]. A strong dπ*(C≡C) interaction between Ru and the alkynyl in B is believed to weaken π back-donation of Ru to the phenylacetylene C–H σ* bond, and then makes the phenylacetylene C–H bond difficult to break. The second issue is what role methanol plays in promoting the ligand metathesis between the methyl group in B and one alkynyl moiety in 1,4-diethynylbenzene to give bis-acetylido species D, trans-[(PhC≡C)Ru(dmpe)2(C≡CC6H4C≡CH)]. The relatively strong proton-donating ability of methanol was found to be the major reason. The present study is indicative of the controllable synthesis of mono- and bis-acetylido, and even di- and trinuclear acetylide-bridged ruthenium(II) complexes.

The Pd-catalyzed reactions of α-diazocarbonyl compounds with allylic esters have been comprehensively studied with the aid of DFT calculations. The reaction can be divided into two catalytic processes. The first process is Pd-catalyzed allylic ester decarboxylation leading to formation of the intermediate product 1,4-enyne (P1). In this process, the ester oxidative addition proceeds via an ion-pair mechanism rather than a concerted mechanism. The decarboxylative step from the oxidative addition product (4) proceeds via an (η2-C≡C)→Pd-coordinated ion-pair intermediate (9). The rate-determining step for this catalytic process is found to be the 1,4-enyne reductive elimination step. The second process is the Pd-catalyzed reaction between 1,4-enyne (P1) and the diazo substrate, leading to the final product. In this process, the coupling between 1,4-enyne (P1) and the metal carbene generated from the reaction of PdL2 with the diazo substrate forms a four-membered metallacyclic intermediate, from which β-phenyl...

High crystallinity magnesium oxide (MgO) microrods with hierarchical porous structure (ranging from micropores to mesopores and macropores) and well-defined rod-like morphology have been successfully synthesized via a flux NaCl and surfactant nonyl phenol polyoxyethylene ether (NP-9) directed thermal decomposition of the hydrothermally derived magnesium oxalate dihydrate (MgC2O4·2H2O) microrods. The successive and synergistic effect of NaCl and NP-9 assisted the thermal conversion and promoted the final formation of the well-defined porous MgO microrods with a specific surface area of 50.2 m2 g−1 and well preserved rod-like morphology of the MgC2O4·2H2O precursor. The as-obtained porous MgO microrods were employed as efficient adsorbents for removal of heavy metal ions such as Pb(II) and Cr(VI) from aqueous solutions, and the removal efficiency of Pb(II) (original concentration: 50.0 mg L−1) and Cr(VI) (original concentration: 1.0 mg L−1) was up to 99.5% and 55.6%, respectively. Such well-defined MgO microrods with hierarchical porous structure can also serve as promising candidates for catalyst supports and even as a catalyst themselves in addition to their present waste water treatment applications in various fields.

The hydrocarboxylation and hydrosilylation processes proposed in the copper-catalyzed reaction among carbon dioxide, diphenylacetylene and HSi(OEt)(3) were comparatively studied with the aid of density functional theory calculations. Our study is to explore why the reaction preferred a hydrocarboxylation rather than a hydrosilylation process. It was found that the sigma bond metathesis between Cu-C and H-Si involved in the hydrosilylation process had a significantly high reaction barrier in the presence of CO2 (47.4 kcal/mol). Instead, CO2 insertion and the subsequent s bond metathesis between Cu-O and H-Si involved in the hydrocarboxylation process were confirmed kinetically feasible, consistent with the experimental facts. (C) 2013 Elsevier B. V. All rights reserved.

Detailed mechanisms for the formation of hydroxyl or alkoxyl radicals in the reactions between tetrachloro-p-benzoquinone (TCBQ) and organic hydroperoxides are crucial for better understanding the potential carcinogenicity of polyhalogenated quinones. Herein, the mechanism of the reaction between TCBQ and H2O2 has been systematically investigated at the B3LYP/6-311++G** level of theory in the presence of different numbers of water molecules. We report that the whole reaction can easily take place with the assistance of explicit water molecules. Namely, an initial intermediate is formed first. After that, a nucleophilic attack of H2O2 onto TCBQ occurs, which results in the formation of a second intermediate that contains an OOH group. Subsequently, this second intermediate decomposes homolytically through cleavage of the O-O bond to produce a hydroxyl radical. Energy analyses suggest that the nucleophilic attack is the rate-determining step in the whole reaction. The participation of explicit water molecules promotes the reaction significantly, which can be used to explain the experimental phenomena. In addition, the effects of F, Br, and CH3 substituents on this reaction have also been studied.

Acylborons, as a growing class of boron reagents, were successfully applied to amide ligation and showed potential in chemoselective bioconjugation reactions in recent years. In this manuscript, a density functional theory (DFT) study was performed to investigate the mechanism of the amide formation between monofluoroacylboronates and hydroxylamines. An updated pathway was clarified herein, including water-assisted hemiaminal formation, pyridine ligand dissociation, elimination via a six-membered-ring transition state, and water-assisted tautomerization. The proposed mechanism was further examined by applying it to investigate the activation barriers of other monofluoroacylboronates, and the related calculations well reproduced the experimentally reported relative reactivities. On the basis of these results, we found that the ortho substitution of the pyridine ligand destabilizes the acylboron substrates and the hemiaminal intermediates by steric effects and thus lowers the energy demand of the ligand dissociation and elimination steps. By contrast, the para substitution of the pyridine ligand with an electron-donating group enhances the coordination of the ligand by electronic effects, which is a disadvantage to the ligand dissociation and elimination steps. The ligand bearing a rigid linkage blocks the rotation of the pyridine ligand and makes ligand dissociation difficult.