Grand Canonical Adaptive Resolution Simulation for Molecules with Electrons: A Theoretical Framework based on Physical Consistency

A theoretical scheme for the treatment of an open molecular system with electrons and nuclei is proposed. The idea is based on the Grand Canonical description of a quantum region embedded in a classical reservoir of molecules. Electronic properties of the quantum region are calculated at constant electronic chemical potential equal to that of the corresponding (large) bulk system treated at full quantum level. Instead, the exchange of molecules between the quantum region and the classical environment occurs at the chemical potential of the macroscopic thermodynamic conditions. T he Grand Canonical Adaptive Resolution Scheme is proposed for the treatment of the classical environment; such an approach can treat the exchange of molecules according to first principles of statistical mechanics and thermodynamic. The overall scheme is build on the basis of physical consistency, with the corresponding definition of numerical criteria of control of the approximations implied by the coupling. Given the wide range of expertise required, this work has the intention of providing guiding principles for the construction of a well founded computational protocol for actual multiscale simulations from the electronic to the mesoscopic scale.Comment: Computer Physics Communications (2017), in pres

Mechanistic Study of Chemoselectivity in Ni-Catalyzed Coupling Reactions between Azoles and Aryl Carboxylates

Itami et al. recently reported the C–O electrophile-controlled chemoselectivity of Ni-catalyzed coupling reactions between azoles and esters: the decarbonylative C–H coupling product was generated with the aryl ester substrates, while C–H/C–O coupling product was generated with the phenol derivative substrates (such as phenyl pivalate). With the aid of DFT calculations (M06L/6-311+G­(2d,p)-SDD//B3LYP/6-31G­(d)-LANL2DZ), the present study systematically investigated the mechanism of the aforementioned chemoselective reactions. The decarbonylative C–H coupling mechanism involves oxidative addition of C­(acyl)–O bond, base-promoted C–H activation of azole, CO migration, and reductive elimination steps (C–H/Decar mechanism). This mechanism is partially different from Itami’s previous proposal (Decar/C–H mechanism) because the C–H activation step is unlikely to occur after the CO migration step. Meanwhile, C–H/C–O coupling reaction proceeds through oxidative addition of C­(phenyl)–O bond, base-promoted C–H activation, and reductive elimination steps. It was found that the C–O electrophile significantly influences the overall energy demand of the decarbonylative C–H coupling mechanism, because the rate-determining step (i.e., CO migration) is sensitive to the steric effect of the acyl substituent. In contrast, in the C–H/C–O coupling mechanism, the release of the carboxylates occurs before the rate-determining step (i.e., base-promoted C–H activation), and thus the overall energy demand is almost independent of the acyl substituent. Accordingly, the decarbonylative C–H coupling product is favored for less-bulky group substituted C–O electrophiles (such as aryl ester), while C–H/C–O coupling product is predominant for bulky group substituted C–O electrophiles (such as phenyl pivalate)

Photoredox/Brønsted Acid Co-Catalysis Enabling Decarboxylative Coupling of Amino Acid and Peptide Redox-Active Esters with N‑Heteroarenes

An iridium photoredox catalyst in combination with a phosphoric acid catalyzes the decarboxylative α-aminoalkylation of natural and unnatural α-amino acid-derived redox-active esters (<i>N</i>-hydroxyphthalimide esters) with a broad substrate scope of N-heteroarenes at room temperature under irradiation. Dipeptide- and tripeptide-derived redox-active esters are also amenable substrates to achieve decarboxylative insertion of a N-heterocycle at the C-terminal of peptides, yielding molecules that have potential medicinal applications. The key factors for the success of this reaction are the following: use of a photoredox catalyst of suitable redox potential to controllably generate α-aminoalkyl radicals, without overoxidation, and an acid cocatalyst to increase the electron deficiency of N-heteroarenes

Irradiation-Induced Palladium-Catalyzed Decarboxylative Heck Reaction of Aliphatic <i>N</i>‑(Acyloxy)­phthalimides at Room Temperature

It is reported that Pd­(PPh₃)₂Cl₂ in combination with 4,5-bis­(diphenyl­phosphino)-9,9-dimethyl­xanthene (Xantphos) under irradiation of blue LEDs efficiently catalyzes a decarboxylative Heck reaction of vinyl arenes and vinyl heteroarenes with aliphatic <i>N</i>-(acyloxy)­phthalimides at room temperature. A broad scope of secondary, tertiary, and quaternary carboxylates, including α-amino acid derived esters, can be applied as amenable substrates with high stereoselectivity. The experimental observation was explained by excitation-state reactivity of the palladium complex under irradiation to induce single-electron transfer to activate <i>N</i>-(acyloxy)­phthalimides, and to suppress undesired β-hydride elimination of alkyl palladium intermediates

Integrated Production of Aromatic Amines and N‑Doped Carbon from Lignin via <i>ex Situ</i> Catalytic Fast Pyrolysis in the Presence of Ammonia over Zeolites

Due to the irregular polymeric structure and carbon based inactive property, lignin valorization is very difficult. In this study we proposed a new route for lignin valorization by which aromatic amines can be directly produced from lignin by <i>ex situ</i> catalytic fast pyrolysis with ammonia over zeolite catalysts. Meanwhile, the obtained pyrolytic biochar can be activated to produce high surface area N-doped carbon for electrochemical application. Wheat straw lignin served as feed to optimize the pyrolysis conditions. MCM-41, β-zeolite, HZSM-5, HY, ZnO/HZSM-5, and ZnO/HY were screened, and ZnO/HZSM-5 (2 wt % Zn, Si/Al = 50) showed the optimal reactivity for producing aromatic amines due to the desired pore structure and acidity. Temperature, residence time, and ammonia content in the carrier gas displayed significant effects on the product distribution. The maximum yield of aromatic amines was obtained at moderate temperatures around 600 °C, 0.57 s, and 75% ammonia in the carrier gas. Under the optimized conditions, the total carbon yields of pyrolytic bio-oil and aromatic amines were 9.8% and 5.6%, respectively. The selectivity of aniline in the aromatic amines was up to 87.3%. Moreover, the pyrolysis byproduct, biochar, was further activated by KOH at 800 °C under ammonia atmosphere for producing N-doped carbon with high surface area. The pyrolytic biochar and N-doped carbon were characterized by elemental analysis, SEM, XRD, nitrogen adsorption–desorption, and XPS. Cyclic voltammetry (CV) and galvanostatic charge–discharge were employed to investigate the electrochemical performance of pyrolytic biochar and N-doped carbon. The specific capacitance of N-doped carbon reached about 128.4 F g^–1

Theoretical Study of Ir-Catalyzed Chemoselective C1–O Reduction of Glucose with Silane

Density functional theory (DFT) calculations have been performed to study the mechanism of Ir­(III) pincer complex (POCOP)­Ir­(H)­(acetone)⁺ (POCOP = 2,6-bis­(dibutylphosphinito)­phenyl) catalyzed chemoselective C1–O hydrosilylative reduction of glucose. The mechanisms for reduction of the external and internal C1–O (i.e., C1–O^ext and C1–O^int) on the C1-MeO-substituted glucose (i.e., <b>1</b>_<b>Me</b>) and C1–Me₂EtSiO-substituted glucose (i.e., <b>1</b>_<b>Si</b>) have been investigated. The calculation results show that both mechanisms proceed with the first concerted silyl transfer and the subsequent C1–O^ext or C1–O^int bond cleavage and hydride transfer steps. In the hydride transfer step, the Ir-H moiety acts as the hydride source. The C1–O cleavage is the rate-determining step of the overall mechanism. The C1–O^ext reduction is more favorable than C1–O^int reduction for the substrate <b>1</b>_<b>Me</b>, while the C1–O^int reduction is more favorable for <b>1</b>_<b>Si</b>. These results are consistent with the recent experimental outcomes. Analyzing the origin of chemoselectivity for the C1–O^ext or C1–O^int cleavage, we found that the more stable precursor of C1–O^ext cleavage and retention of the six-membered-ring structure result in the selective C1–O^ext reduction of <b>1</b>_<b>Me</b>. Meanwhile, the higher basicity of the alkyl ether O^int atom (in comparison to the silyl ether O^ext atom) and greater steric hindrance in the precursor favor the C1–O^int bond weakening. Therefore, the C1–O^int reduction occurs selectively for <b>1</b>_<b>Si</b>

Theoretical Study on Homogeneous Hydrogen Activation Catalyzed by Cationic Ag(I) Complex

Recently, the Li group reported the first Ag-catalyzed hydrogenation of aldehydes in water, demonstrating the utility of Ag complexes in homogeneous catalytic transformations through hydrogen activation. In the present study, density functional theory methods have been used to study the mechanism of Ag-catalyzed hydrogen activation. Three possible pathways, including base-assisted hydrogen activation, ligand-assisted hydrogen activation, and oxidative addition were investigated. The ligand-assisted hydrogen activation is disfavored because the neutral biaryl phosphine ligand XPhos is not a competent proton acceptor and results in the destruction of the aromaticity of an aryl group. Oxidative addition of H₂ on Ag^I complexes was also found to be unlikely. The resulting Ag^III hydride complexes are highly unstable and can undergo spontaneous reduction due to the weakly electron-donating ligand and the relatively low electronegativity of hydrogen. By contrast, the base-assisted hydrogen activation mechanism is more favored. This mechanism mainly includes three steps: base-assisted heterolytic H–H bond cleavage, hydride transfer, and protonation. Hydride transfer is the rate-determining step of the whole catalytic cycle. In addition, the ligand XPhos was found to coordinate with the Ag center by both the phosphine and the isopropyl-substituted phenyl groups, and this coordination mode is able to facilitate hydrogen activation

Mechanistic Study of Palladium-Catalyzed Chemoselective C(sp³)–H Activation of Carbamoyl Chloride

A theoretical study has been carried out on the palladium-catalyzed C­(sp³)–H activation/amidation reaction of carbamoyl chloride precursors (Takemoto, Y. Angew. Chem. Int. Ed. 2012, 51, 2763 ). In Takemoto’s reaction, although the C­(sp²)–H bond of naphthalene was present in the substrate, the benzylic C­(sp³)–H bond was activated exclusively. Mechanistic calculations have been performed on the two possible pathways: the C­(sp³)–H activation/amidation pathway (Path-sp³) and the C­(sp²)–H activation/amidation pathway (Path-sp²). Calculation results show that both paths include three steps: oxidative addition (via the mono-phosphine mechanism), C–H activation involving the PivNHO^– anion (via the CMD mechanism), and final reductive elimination. The calculations indicate that the Path-sp³ mechanism is kinetically favored, and the C­(sp³)–H amidated product is predicted to be the main product. This conclusion is consistent with Takemoto’s experimental observations. The rate-determining step of Path-sp³ is the oxidative addition step, and the C­(sp³)–H bond activation step determines the selectivity. Further examination on the origin of the selective C­(sp³)–H activation shows that the higher acidity of the benzylic C­(sp³)–H (in comparison to the naphthalene C­(sp²)–H in this system) is the main reason for the chemoselectivity. The additive might promote the reaction by forming a more soluble organic base (PivNHOCs) via reaction with Cs₂CO₃

Mechanistic Study of Borylation of Nitriles Catalyzed by Rh–B and Ir–B Complexes via C–CN Bond Activation

Recently the Chatani group reported the Rh­(I)-catalyzed borylation of nitriles, which provided an efficient protocol for transformation of the C–CN bond to the C–B bond (<i>J. Am. Chem. Soc.</i> <b>2012</b>, <i>134</i>, 115). Although an unconventional β-carbon elimination mechanism was proposed in their study, the other previously proposed mechanisms, i.e., oxidative addition, deinsertion, and initial C–H bond activation, cannot be excluded. To clarify the dominant mechanism of this reaction, a density functional theory study on borylation of PhCN and BnCN catalyzed by [Rh­(XantPhos)­(B­(nep))] (nep = neopentylglycolate, XantPhos = 4,5-Bis­(diphenylphosphino)-9,9-dimethylxanthene) was conducted. The computational results indicated that the deinsertion mechanism (2,1-insertion of the Rh–B bond into the CN bond occurs first, followed by the insertion of the metal center into C–CN bond) is favored over oxidative addition, β-carbon elimination, and the initial C–H bond activation mechanism within all the investigated reactions. The activation of the C–CN bond is a facile step in the deinsertion mechanism, and the oxidative addition of the diboron reagent is the rate-determining step. On this basis, the mechanism of borylation of PhCN catalyzed by a similar Ir–B complex ([Ir­(XantPhos)­(B­(nep))]) was also examined. The deinsertion mechanism was found to be the most favorable. The overall energy barrier of the Ir–B complex-catalyzed borylation of benzonitriles was slightly higher than that of the same Rh–B complex-catalyzed reaction (by 1.1 kcal/mol), indicating that [Ir­(XantPhos)­(B­(nep))] could act as an alternative catalyst for borylation of nitriles

Mechanism of Vanadium-Catalyzed Deoxydehydration of Vicinal Diols: Spin-Crossover-Involved Processes

Vanadium-catalyzed deoxydehydration (DODH) reactions provide a cost-effective approach for the conversion of vicinal diols to olefin and polycyclic aromatic hydrocarbons. In this paper, density functional theory (DFT) calculations employing M06 and M06-L methods were conducted to clarify the mechanism of V-catalyzed DODH. Three types of mechanisms generally proposed for transition-metal-catalyzed DODH, associated with the previously omitted spin crossover processes, were considered herein. As a result, a different catalytic cycle including a new olefin-formation mechanism was located, which is in contrast to the findings of a recent study. We found that the favorable mechanism involves the condensation of diols to form vanadium­(V) diolate, reduction of the vanadium­(V) diolate by PPh₃, and spin-crossover steps to form a triplet vanadium­(III) diolate. Thereafter, single C–O bond cleavage occurs followed by another spin crossover to form a singlet alkylvanadium­(V) intermediate. The final concerted V–O/C–O bond cleavage generates an olefin and finishes the catalytic cycle. The reduction of vanadium­(V) diolate by PPh₃ and the extrusion of olefin have close overall free energy barriers of 34.3 and 33.7 kcal/mol, respectively. These results suggest that both steps influence the reaction rate. On the other hand, the two mechanisms starting by the reduction of the oxovanadium­(V) catalyst with either PPh₃ or a secondary alcohol were excluded due to their higher energy demands in the reduction and the olefin-formation stages. The good consistency between the experimental observations and the calculation results verified the proposed mechanism and also enabled us to clarify the reason for the efficiency of different reductants