We report a computational study on the mechanism of the reaction of ethyl acetoacetate (1) with two sulfur reagents: Martin's sulfurane (Ra) and a mixture of diphenyl sulfide and triflic anhydride (Rb). These reagents are able to provide a sulfonium ion [Ph₂S-OX]⁺ and an anionic nucleophile ^–OX as active species [X = C(CF₃)₂Ph for Ra and X = SO₂CF₃ for Rb] in the reaction. Experimentally, the reaction of Ra with carbonyl compounds provides an S-ylide as the only product whereas a low yield of S-ylide is obtained in the case of Rb. To elucidate the mechanism of these reactions with prototype substrate 1, different plausible pathways have been investigated using density functional theory (DFT), mostly at the B3LYP-D/6-31+G** level. According to DFT calculations, initial deprotonation of 1 may furnish either an enolate (with Ra) or an O-sulfenylated enolate (with Rb). Subsequent nucleophilic addition of the enolate to the sulfonium ion provides the simplest route to S-ylide product, which is favored when using reagent Ra. In the case of reagent Rb, the preferentially formed O-sulfenylated enolate may undergo either a series of nucleophilic displacements or a [1,3] sigmatropic shift or a [3,3] sigmatropic rearrangement, all followed by a final deprotonation to yield the product. These conversions are highly exothermic and involve thermodynamically stable products. The [3,3] sigmatropic rearrangement that directly produces an arylated carbonyl compound is computed to be the kinetically most facile reaction with Rb. Overall, the computational results unveil detailed mechanistic scenarios detailing possible transformations and providing qualitative explanations for some of the experimental findings.

We explore the influence of two solvents, namely water and the ionic liquid 1-ethyl-3-methylimidazolium acetate (EmimAc), on the conformations of two cellulose models (cellobiose and a chain of 40 glucose units) and the solvent impact on glycosidic bond cleavage by acid hydrolysis by using molecular dynamics and metadynamics simulations. We investigate the rotation around the glycosidic bond and ring puckering, as well as the anomeric effect and hydrogen bonds, in order to gauge the effect on the hydrolysis mechanism. We find that EmimAc eases hydrolysis through stronger solvent–cellulose interactions, which break structural and electronic barriers to hydrolysis. Our results indicate that hydrolysis in cellulose chains should start from the ends and not in the centre of the chain, which is less accessible to solvent.

We report the first X-ray structure of a spiroaminal hydrochloride. The chiral spiroaminal crystallizes as a racemic hydrochloride in the monoclinic space group P2₁/n and adopts the thermodynamically most stable conformation. Density functional calculations on several spiroaminals were used to establish correlations between trends in conformational energies, steric repulsions, and anomeric effects and to reveal the mechanism of the ring-opening tautomerization reaction. In the unsubstituted and backbone-substituted spiroaminals, the aminal tautomer is thermodynamically preferred. N-Substituted spiroaminals favor the amine/imine form for steric reasons, except for those with bridging N,N′ groups. The tautomerization from the aminal to the amine/imine is endergonic and kinetically hindered in the neutral species but quite facile after protonation. Anomeric effects lower the barriers but are less important than steric factors for relative energies.

Fluorescence emission of wild-type green fluorescent protein (GFP) is lost in the S65T mutant, but partly recovered in the S65T/H148D double mutant. These experimental findings are rationalized by a combined quantum mechanics/molecular mechanics (QM/MM) study at the QM(CASPT2//CASSCF)/AMBER level. A barrierless excited-state proton transfer, which is exclusively driven by the Asp148 residue introduced in the double mutant, is responsible for the ultrafast formation of the anionic fluorescent state, which can be deactivated through a concerted asynchronous hula-twist photoisomerization. This causes the lower fluorescence quantum yield in S65T/H148D compared to wild-type GFP. Hydrogen out-of-plane motion plays an important role in the deactivation of the S65T/H148D fluorescent state.

A joint experimental and computational study on the glucose–fructose conversion in water is reported. The reactivity of different metal catalysts (CrCl₃, AlCl₃, CuCl₂, FeCl₃, and MgCl₂) was analyzed. Experimentally, CrCl₃ and AlCl₃ achieved the best glucose conversion rates, CuCl₂ and FeCl₃ were only mediocre catalysts, and MgCl₂ was inactive. To explain these differences in reactivity, DFT calculations were performed for various metal complexes. The computed mechanism consists of two proton transfers and a hydrogen-atom transfer; the latter was the rate-determining step for all catalysts. The computational results were consistent with the experimental findings and rationalized the observed differences in the behavior of the metal catalysts. To be an efficient catalyst, a metal complex should satisfy the following criteria: moderate Brønsted and Lewis acidity (pK_a=4–6), coordination with either water or weaker σ donors, energetically low-lying unoccupied orbitals, compact transition-state structures, and the ability for complexation of glucose. Thus, the reactivity of the metal catalysts in water is governed by many factors, not just the Lewis acidity.

The molecular understanding of the chemistry of 1,4-β-glucans is essential for designing new approaches to the conversion of cellulose into platform chemicals and biofuels. In this endeavor, much attention has been paid to the role of hydrogen bonding occurring in the cellulose structure. So far, however, there has been little discussion about the implications of the electronic nature of the 1,4-β-glycosidic bond and its chemical environment for the activation of 1,4-β-glucans toward acid-catalyzed hydrolysis. This report sheds light on these central issues and addresses their influence on the acid hydrolysis of cellobiose and, by analogy, cellulose. The electronic structure of cellobiose was explored by DFT at the BB1 K/6-31++G(d,p) level. Natural bond orbital (NBO) analysis was performed to grasp the key bonding concepts. Conformations, protonation sites, and hydrolysis mechanisms were examined. The results for cellobiose indicate that cellulose is protected against hydrolysis not only by its supramolecular structure, as currently accepted, but also by its electronic structure, in which the anomeric effect plays a key role.

The light-induced processes of two flavin mononucleotide derivatives (1- and 5-deaza flavin mononucleotide, 1DFMN and 5DFMN), incorporated into the LOV domain of YtvA protein from Bacillus subtilis, were studied by a combination of experimental and computational methods. Quantum mechanics/molecular mechanics (QM/MM) calculations were carried out in which the QM part was treated by density functional theory (DFT) using the B3LYP functional for geometry optimizations and the DFT/MRCI method for spectroscopic properties, whereas the MM part was described by the CHARMM force field. 1DFMN is incorporated into the protein binding site, yielding a red-shifted absorption band (λ_max=530 nm compared to YtvA wild-type λ_max=445 nm), but does not undergo any LOV-typical photoreactions such as triplet and photoadduct formation. QM/MM computations confirmed the absence of a channel for triplet formation and located a radiation-free channel (through an S₁/S₀ conical intersection) along a hydrogen transfer path that might allow for fast deactivation. By contrast, 5DFMN-YtvA-LOV shows a blue-shifted absorption (λ_max=410 nm) and undergoes similar photochemical processes to FMN in the wild-type protein, both with regard to the photophysics and the formation of a photoadduct with a flavin-cysteinyl covalent bond. The QM/MM calculations predict a mechanism that involves hydrogen transfer in the T₁ state, followed by intersystem crossing and adduct formation in the S₀ state for the forward reaction. Experimentally, in contrast to wild-type YtvA, dark-state recovery in 5DFMN-YtvA-LOV is not thermally driven but can only be accomplished after absorption of a second photon by the photoadduct, again via the triplet state. The QM/MM calculations suggest a photochemical mechanism for dark-state recovery that is accessible only for the adduct with a C4aS bond but not for alternative adducts with a C5S bond.

We report computational investigations on the mechanism and the selectivity of Pd-catalyzed allylic alkylation of γ-valerolactone. Density functional calculations using the B3LYP functional are performed on the selectivity-determining nucleophilic addition step of this reaction. The B3LYP results of commonly assumed pathways fail to reproduce the observed selectivity of the reaction. Therefore, alternative pathways are considered for the nucleophilic addition step, to explain the experimentally established role of the additives LiCl and lithium diisopropyl amide (LDA) in the Pd-catalyzed reaction. These pathways involve different approaches of the enolate toward the η³-allylpalladium complex that are mainly guided by stabilizing Cl^δ−⋅⋅⋅Li^δ+⋅⋅⋅O(enolate) interactions in the transition state. In the calculations, the experimentally observed trans-product selectivity for the prototypical reaction with (S)-BINAP ligands is found only when assuming the addition of a “mixed” Li-enolate/LiCl adduct to the η³-allylpalladium complex. This mechanism provides a reasonable explanation for the experimental results and sheds light on the role of LiCl in the reaction. The analysis of the different transition-state models allows us to identify steric and electronic factors that stabilize or destabilize the relevant diastereomeric transition states. Calculations for different combinations of substrates (γ-valerolactone and δ-caprolactone) and catalysts (with (R)- and (S)-BINAP ligands) reproduce the experimentally observed selectivities well and thus provide further support for the proposed mechanism.