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  • 1.
    Bunrit, Anon
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Srifa, Pemikar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Dahlstrand, Christian
    Huang, Genping
    Biswas, Srijit
    Himo, Fahmi
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Watile, Rahul
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    H3PO2-Catalyzed Intramolecular Stereospecific Substitution of the Hydroxyl Group in Stereogenic Secondary Alcohols by N-, O-, and S-centered Nucleophiles to Generate HeterocyclesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    The direct intramolecular stereospecific substitution of the hydroxyl group in stereogenic secondary alcohols was successfully accomplished by phosphinic acid catalysis. The hydroxyl group was displaced by O-, S-, and N-centered nucleophiles to provide enantioenriched five- and six-membered heterocycles in good to excellent yields and high enantiospecificity with water as the only by product. Mechanistic studies using both experiments and calculations have been performed. Rate order determination shows first-order dependences in catalyst, internal nucleophile, and electrophile concentrations, however, independence on external nucleophile and electrophile. Furthermore, phosphinic acid does not promote SN1 reactivity. Computational studies support a bifunctional role of the phosphinic acid in which activations of both nucleofuge and nucleophile occur in a bridging SN2-type transition state. 

  • 2. Monti, Susanna
    et al.
    Srifa, Pemikar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Kumaniaev, Ivan
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Samec, Joseph S. M.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    ReaxFF Simulations of Lignin Fragmentation on a Palladium-Based Heterogeneous Catalyst in Methanol-Water Solution2018Inngår i: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, nr 18, s. 5233-5239Artikkel i tidsskrift (Fagfellevurdert)
    Abstract [en]

    The interaction of fragments derived from lignin depolymerization with a heterogeneous palladium catalyst in methanol-water solution is studied by means of experimental and theoretical methodologies. Quantum chemistry calculations and molecular dynamics simulations based on the ReaxFF approach are combined effectively to obtain an atomic level characterization of the crucial steps of the adsorption of the molecules on the catalyst, their fragmentation, reactions, and desorption. The main products are identified, and the most important routes to obtain them are explained through extensive computational procedures. The simulation results are in excellent agreement with the experiments and suggest that the mechanisms comprise a fast chemisorption of identified fragments from lignin on the metal interface accompanied by bond breaking, release of some of their hydrogens and oxygens to the support, and eventual desorption depending on the local environment. The strongest connections are those involving the aromatic rings, as confirmed by the binding energies of selected representative structures, estimated at the quantum chemistry level. The satisfactory agreement with the literature, quantum chemistry data, and experiments confirms the reliability of the multilevel computational procedure to study complex reaction mixtures and its potential application in the design of high-performance catalytic devices.

  • 3.
    Srifa, Pemikar
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Theoretical Investigations of C–O Activation in Biomass2019Doktoravhandling, med artikler (Annet vitenskapelig)
    Abstract [en]

    This thesis focuses on using computational chemistry approaches to study how biobased molecules interact with both homo- and heterogeneous catalysts. The reaction mechanisms of such transformations have also been studied.

    The first section comprises studies of interactions between organic molecules and a heterogeneous catalyst in the palladium-catalyzed depolymerization of models of lignin derivatives. From experiments, it was proposed that a keto intermediate and its enol tautomer play a significant role in the β-O-4′ bond cleavage. The study in the first section of this thesis has been divided into three parts. First, simplified models of the keto intermediate and its enol tautomer were used to investigate the adsorption to a Pd(111) surface. By using a combination of periodic density functional theory (DFT) calculations and a constrained minima hopping method, the most stable adsorption which is the so-called global minimum, was found to be an enol adsorbed to the surface.

    In the second part, the study was expanded to cope with models of lignin which were used in experiments. In addition, we studied the effect of adsorbate coverage, where two different Pd(111) super cells were compared. The optimizations were performed via dispersion-corrected density functional theory (DFT-D3). The molecules were found to bind more strongly to the surface at low coverages. These results support the experimental data and show that the tautomerization has an important role during lignin depolymerization. 

    The third part relates to using a multilevel procedure to study the interaction of fragments derived from lignin depolymerisation with a palladium catalyst in a solvent mixture. Specifically, QM calculations and MD simulations based on the ReaxFF approach were combined to explore the reaction mechanisms occurring on Pd surfaces with lignin derivatives obtained from a solvolysis reaction. The strongest adsorptions were found to be between the aromatic rings and the Pd surfaces.

    The second section focuses on a Brønsted acid-catalyzed nucleophilic substitution of the hydroxyl group in alcohols. Experimentally, phosphinic acid (H3PO2) was found to be an excellent catalyst for the direct intramolecular substitution of non-derivatized alcohols proceeding with good to excellent chirality transfer. In this section, benzylic alcohols with internal O-, N-, and S-centered nucleophiles were used in the calculations. By using a hybrid functional method, we found a bicyclic transition state where the proton of the H3PO2 protonates the leaving hydroxyl group, and the oxo-group of the same catalyst partially deprotonates the nucleophile. The transition state energies for the reactions were determined computationally. The calculations support an SN2 mechanism, which corresponds to the experimental data where inversion of the stereogenic carbon was observed.

  • 4.
    Srifa, Pemikar
    et al.
    Stockholms universitet, Naturvetenskapliga fakulteten, Institutionen för organisk kemi.
    Broqvist, Peter
    Hermansson, Kersti
    Lignin Intermediates on the Palladium Surface: Factors for Structural and Energetic ChangesManuskript (preprint) (Annet vitenskapelig)
    Abstract [en]

    In this work, dispersion-corrected density functional theory (DFT-D3), has been used to investigate interactions between important intermediates in lignin depolymerization and a palladium catalyst. The keto structure 2-phenoxy-1-phenylethanone and its enol tautomer have been used to model reactive intermediates derived from lignin. To investigate how the adsorption energies are affected by adsorbate coverage, we have used two different Pd(111) super cells; one smaller p(6 × 4) and one larger p(6 × 6). In the gas phase, the staggered conformer of the keto tautomer is more stable than both the eclipsed form of the keto tautomer and as expected much more stable than the E-enol tautomer. However, in interaction with the palladium surface, the E-enol tautomer has a similar binding energy as the keto tautomer. Also, the eclipsed conformer of the keto tautomer is more stable than the staggered conformer of the keto tautomer when adsorbed to the palladium. We found that the coverage, that is concentration of molecules on the surface had a pronounced effect on the adsorption energies. At higher coverage, both the keto and enol models prefer to adsorb on an atop configuration to the surface. Furthermore, we found that both the keto and the enol tautomers bind strongly to the surface through their phenyl rings. Despite the strong binding of the phenyl groups, the enol adsorbs to the surface through a chemisorption by cleavage of the C═C bond, that leads to two types of di-sigma complexes depending on the position of the newly formed Pd–C sigma bonds. The generated complex is a key intermediate in the subsequent depolymerization through cleavage of a C–O bond. Our simulations show that there is an intermolecular repulsion between adsorbates on the surface, and consequently, the molecules were found to bind more strongly to the surface at low coverages (by 8-14 kcal/mol). These results are important for experimental design purposes; as previous experiments have shown that the enol form is key for an efficient β-O-4′ bond cleavage and implies that low concentration reactions are favored.

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