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Theoretical Investigations of C–O Activation in Biomass
Stockholm University, Faculty of Science, Department of Organic Chemistry. (Joseph Samec)
2019 (English)Doctoral thesis, comprehensive summary (Other academic)
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.

Place, publisher, year, edition, pages
Stockholm: Department of Organic Chemistry, Stockholm University , 2019. , p. 77
Keywords [en]
DFT calculations, global minima hopping, reactive force field, lignin, palladium, nucleophilic substitution
National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
URN: urn:nbn:se:su:diva-167592ISBN: 978-91-7797-709-4 (print)ISBN: 978-91-7797-710-0 (electronic)OAI: oai:DiVA.org:su-167592DiVA, id: diva2:1301188
Public defence
2019-05-22, Magnélisalen, Kemiska övningslaboratoriet, Svante Arrhenius väg 16 B, Stockholm, 10:00 (English)
Opponent
Supervisors
Note

At the time of the doctoral defense, the following paper was unpublished and had a status as follows: Paper 2: Manuscript.

Available from: 2019-04-25 Created: 2019-04-01 Last updated: 2019-04-10Bibliographically approved
List of papers
1. Detecting Important Intermediates in Pd Catalyzed Depolymerization of a Lignin Model Compound by a Combination of DFT Calculations and Constrained Minima Hopping
Open this publication in new window or tab >>Detecting Important Intermediates in Pd Catalyzed Depolymerization of a Lignin Model Compound by a Combination of DFT Calculations and Constrained Minima Hopping
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2016 (English)In: The Journal of Physical Chemistry C, ISSN 1932-7447, E-ISSN 1932-7455, Vol. 120, no 41, p. 23469-23479Article in journal (Refereed) Published
Abstract [en]

Density functional theory (DFT) calculations, combined with a constrained minima hopping algorithm (global minimum search while preserving the molecular identity), have been performed to investigate important reaction intermediates for the heterogeneously catalyzed beta-O-4' bond cleavage in lignin derivatives. More specifically, we have studied the adsorption properties of a keto tautomer (1-methoxypropan-2-one) and its enol form on a catalytically active Pd(111) surface. In agreement with experiments, we find that for the gas phase molecules the keto tautomer is the most stable. Interestingly, the enol tautomer has a higher affinity to the Pd catalyst than the keto form, and becomes the most stable molecular form when adsorbed on the catalyst surface. The global minimum complex found on the metal surface corresponds to an enolate structure formed when the enol tautomer chemisorbs onto the surface and donates its pi-electrons from the C=C region to two adjacent palladium atoms. The actual formation of a chemical bond to the surface in the case of the enol molecule could be the key to understanding why the enol derivative is needed for an efficient beta-O-4' bond cleavage.

Place, publisher, year, edition, pages
American Chemical Society (ACS), 2016
National Category
Chemical Sciences Nano Technology Materials Engineering
Identifiers
urn:nbn:se:su:diva-136052 (URN)10.1021/acs.jpcc.6b05622 (DOI)000386107600018 ()
Funder
Swedish Research Council
Available from: 2016-12-21 Created: 2016-11-29 Last updated: 2019-04-01Bibliographically approved
2. Lignin Intermediates on the Palladium Surface: Factors for Structural and Energetic Changes
Open this publication in new window or tab >>Lignin Intermediates on the Palladium Surface: Factors for Structural and Energetic Changes
(English)Manuscript (preprint) (Other academic)
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.

National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-167712 (URN)
Available from: 2019-04-01 Created: 2019-04-01 Last updated: 2019-04-02Bibliographically approved
3. ReaxFF Simulations of Lignin Fragmentation on a Palladium-Based Heterogeneous Catalyst in Methanol-Water Solution
Open this publication in new window or tab >>ReaxFF Simulations of Lignin Fragmentation on a Palladium-Based Heterogeneous Catalyst in Methanol-Water Solution
2018 (English)In: Journal of Physical Chemistry Letters, ISSN 1948-7185, E-ISSN 1948-7185, Vol. 9, no 18, p. 5233-5239Article in journal (Refereed) Published
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.

National Category
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-161204 (URN)10.1021/acs.jpclett.8b02275 (DOI)000445713200006 ()30130109 (PubMedID)
Available from: 2018-10-26 Created: 2018-10-26 Last updated: 2019-04-01Bibliographically approved
4. Brønsted Acid-Catalyzed Intramolecular Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer
Open this publication in new window or tab >>Brønsted Acid-Catalyzed Intramolecular Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer
Show others...
2015 (English)In: Journal of the American Chemical Society, ISSN 0002-7863, E-ISSN 1520-5126, Vol. 137, no 14, p. 4646-4649Article in journal (Refereed) Published
Abstract [en]

The hydroxyl group of enantioenriched benzyl, propargyl, allyl, and alkyl alcohols has been intramolecularly displaced by uncharged O-, N-, and S-centered nucleophiles to yield enantioenriched tetrahydrofuran, pyrrolidine, and tetrahydrothiophene derivatives with phosphinic acid catalysis. The five-membered heterocyclic products are generated in good to excellent yields, with high degree of chirality transfer, and water as the only side-product. Racemization experiments show that phosphinic acid does not promote S(N)1 reactivity. Density functional theory calculations corroborate a reaction pathway where the phosphinic acid operates as a bifunctional catalyst in the intramolecular substitution reaction. In this mechanism, the acidic proton of the phosphinic acid protonates the hydroxyl group, enhancing the leaving group ability. Simultaneously, the oxo group of phosphinic acid operates as a base abstracting the nucleophilic proton and thus enhancing the nucleophilicity. This reaction will open up new atom efficient techniques that enable alcohols to be used as nucleofuges in substitution reactions in the future.

National Category
Organic Chemistry
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-117729 (URN)10.1021/jacs.5b02013 (DOI)000353177100014 ()
Funder
Swedish Research CouncilStiftelsen Olle Engkvist ByggmästareThe Wenner-Gren FoundationGöran Gustafsson Foundation for Research in Natural Sciences and MedicineKnut and Alice Wallenberg Foundation
Available from: 2015-06-09 Created: 2015-06-01 Last updated: 2019-04-01Bibliographically approved
5. Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer
Open this publication in new window or tab >>Nucleophilic Substitution of the Hydroxyl Group in Stereogenic Alcohols with Chirality Transfer
Show others...
2016 (English)In: Synlett: Accounts and Rapid Communications in Synthetic Organic Chemistry, ISSN 0936-5214, E-ISSN 1437-2096, Vol. 27, no 2, p. 173-176Article in journal (Refereed) Published
Abstract [en]

A brief overview of the development of direct substitution of the hydroxyl (OH) group of alcohols in our research group is presented. By applying a BrOnsted acid, an intramolecular substitution of the OH group in stereogenic alcohols with chirality transfer was achieved. Noteworthy, the intramolecular substitution has a wide scope in respect to both the nucleophile and also the nucleofuge. A mechanistic study by both experiments and DFT calculations revealed a unique reaction pathway in which the BrOnsted acid operates in a bifunctional manner to promote an S(N)2-type reaction mechanism.

Keywords
green chemistry, BrOnsted acid, base catalysis, chirality transfer, nucleophilic substitutions, asymmetric synthesis, mechanistic studies, DFT calculations
National Category
Chemical Sciences
Research subject
Organic Chemistry
Identifiers
urn:nbn:se:su:diva-126782 (URN)10.1055/s-0035-1560494 (DOI)000368131300004 ()
Funder
Swedish Research CouncilStiftelsen Olle Engkvist ByggmästareWenner-Gren FoundationsKnut and Alice Wallenberg Foundation
Available from: 2016-06-28 Created: 2016-02-15 Last updated: 2019-10-04Bibliographically approved

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