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Thermodynamics and the solvent role in the acceleration of the Diels–Alder reaction between cyclopentadiene (CPD) and methyl vinyl ketone (MVK) have been revisited. In this work we use an ab initio hybrid QM/MM-MD scheme combined with multiple steered molecular dynamics to extract the free energy pofile in water and methanol using the bidirectional Minh–Adib estimator. We obtain 18.7 kcal mol–1 and 20.8 kcal mol–1 free energy barrier for the reaction in water and methanol, respectively. This methodology reproduces experimental values with an absolute error of about 0.8 kcal mol–1. The experimental difference between the activation free-energy barriers of water and methanol is also reproduced with an absolute error of about 0.1 kcal mol–1. We explore the charge transfer evolution along reaction coordinates to characterize the electronic behavior for this reaction. It is shown that the solvent molecules around the reaction system produce a global polarization along the reaction coordinate which is consistent with the solvent polarity. The results highlight the role of hydrogen bonding formed in the transition state to stabilize the system charge reorganization in the reaction process., Peer Reviewed, Postprint (author's final draft)

Fundamental characteristics of bioactive platforms based on biocomposites of poly(3,4-ethylenedioxythiophene) (PEDOT) and collagen, named P(EDOT:CLG), have been examined using an experimental–computational approach. The protein affects both the morphology and electrochemical activity of PEDOT. Specifically, P(EDOT:CLG) shows spherical-like nodules that have been attributed to the collagen rod aggregates organized in phases separated from that of PEDOT. This phase separation results in a reduction of the ability to exchange charge reversibly, even though collagen stabilizes the PEDOT matrix from electrochemical degradation. On the other hand, viability assays indicate that the bioactivity of P(EDOT:CLG) is significantly higher than that of PEDOT in terms of cellular adhesion and proliferation. Thus, the biocomposite promotes the formation of 3D biostructures formed by the superposition of cellular monolayers, mimicking the growth of biological tissues. In order to gain microscopic information about the formation of specific interactions between PEDOT and collagen molecules in the biocomposite, quantum mechanical calculations on complexes formed by their building blocks have been performed in different environments (i.e. vacuum, chloroform and aqueous solution). Results evidence the important role played by non-conventional C–HO hydrogen bonds, which is consistent with previous findings on complexes involving DNA and dopamine. The environment affects considerably the binding energy, which decreases with increasing polarity of the environment. However, in all environments the repeating units of PEDOT form stronger interactions with L-hydroxyproline than with L-proline. On the other hand, intermolecular interaction patterns predicted using implicit and explicit solvation models present a remarkable agreement and have been identified by visualizing the reduced electron density gradient., Peer Reviewed, Postprint (published version)

[EN] The thermal and Lewis acid (LA) catalyzed cyclizations of quinone 1 involved in the synthesis of Colombiasin A and Elipsaterosin B have been theoretically studied using DFT methods at the B3LYP/6-311G(d,p) computational level. B3LYP calculations suggest that the formal endo [4 + 2] cycloadduct allowing the synthesis of Colombiasin A is preferentially formed under thermal conditions, while in the presence of the BF3 LA catalyst the formal [5 + 2] cycloadduct is seen, allowing the synthesis of Elipsaterosin B. The BF3 LA catalyst not only accelerates the nucleophilic attack on the C2 carbon of the quinone framework through a more polar C-C bond formation, but also provokes a different electron density rearrangement along the nucleophilic attack favoring the subsequent C-C bond formation at the C4 carbon with the formation of the formal [5 + 2] cycloadduct. ELF bonding analysis along these cyclizations indicates that the C-C single bond formation takes place in the range of 1.91-2.1 angstrom by C-to-C coupling of two pseudoradical centers. Along the formation of the first C2-C9 single bond, these pseudoradical centers appear at one of the most electrophilic and at one of the most nucleophilic centers of quinone 1, C2 and C9 carbons, respectively. Analysis of the Parr functions suggests that although the most favorable electrophilic/nucleophilic interaction is that involving the C2 carbon of quinone and the C12 carbon of the butadiene framework, the intramolecular nature of the cyclization prevents the corresponding reactive channel.