Special Issue "Catalysis Assisted by Calculations: From Organic and Metal Catalysts to Enzymes"

A special issue of Catalysts (ISSN 2073-4344). This special issue belongs to the section "Metal Catalysis".

Deadline for manuscript submissions: closed (31 October 2017)

Special Issue Editor

Guest Editor
Dr. Albert Poater

Institute of Computational Chemistry and Catalysis (IQCC), Universitat de Girona, Campus de Montilivi sn, 17071 Girona, Spain
Website | E-Mail
Phone: (+34) 972418358
Fax: (+34) 972418356
Interests: homogeneous catalysis; organometallic chemistry; DFT calculations; computational chemistry; coordination chemistry; NHC-metal complexes; ruthenium based olefin metathesis; gold chemistry; hydrogenation by iron catalysts

Special Issue Information

Dear Colleagues,

Catalysis can be defined as “the causing or accelerating of a chemical change by the addition of a catalyst” and ab initio static or molecular dynamics calculations can be the right tool to face new challenges in science, saving time and experiments. Calculations can generate in silico predictions that then can be tested experimentally. Thus, nowadays, calculations could be defined as one of the catalysts of science. Even though, when we hear about catalysts we automatically think about metal catalysts, organic catalysts that are able to fix CO2 or in silico enzymes that mimethize biological reactions are the present and future of catalysis as well.

This Special Issue aims is to gather the different approaches to catalysis assisted by calculations. Contributions dealing with catalyst development, synthesis, and applications in organic, inorganic and polymer chemistry, biological enzymes, and green processes are particularly welcome. All in all, mechanistic studies and theoretical investigations should demonstrate that they are not only a tool, but a solution to face new challenges in catalysis, with predictions before experiments. Research papers, as well as reviews or perspectives, are welcome.

Dr. Albert Poater
Guest Editor

Manuscript Submission Information

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Keywords

  • in silico enzymes
  • catalyst development
  • organic catalyst
  • organometallic chemistry
  • metal catalyst
  • calculations
  • DFT
  • mechanistic studies
  • theoretical investigations

Published Papers (5 papers)

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Research

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Open AccessArticle Exploring Basic Components Effect on the Catalytic Efficiency of Chevron-Phillips Catalyst in Ethylene Trimerization
Catalysts 2018, 8(6), 224; https://doi.org/10.3390/catal8060224
Received: 26 April 2018 / Revised: 17 May 2018 / Accepted: 18 May 2018 / Published: 24 May 2018
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Abstract
In the present work, the effect of basic components on the energy pathway of ethylene oligomerization using the landmark Chevron-Phillips catalyst has been explored in detail, using density functional theory (DFT). Studied factors were chosen considering the main components of the Chevron-Phillips catalyst,
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In the present work, the effect of basic components on the energy pathway of ethylene oligomerization using the landmark Chevron-Phillips catalyst has been explored in detail, using density functional theory (DFT). Studied factors were chosen considering the main components of the Chevron-Phillips catalyst, i.e., ligand, cocatalyst, and halocarbon compounds, comprising (i) the type of alkyl substituents in pyrrole ligand, i.e., methyl, iso-propyl, tert-butyl, and phenyl, as well as the simple hydrogen and the electron withdrawing fluoro and trifluoromethyl; (ii) the number of Cl atoms in Al compounds (as AlMe2Cl, AlMeCl2 and AlCl3), which indicate the halocarbon level, and (iii) cocatalyst type, i.e., alkylboron, alkylaluminium, or alkylgallium. Besides the main ingredients, the solvent effect (using toluene or methylcyclohexane) on the oligomerization pathway was also explored. In this regard, the full catalytic cycles for the main product (1-hexene) formation, as well as side reactions, i.e., 1-butene release and chromacyclononane formation, were calculated on the basis of the metallacycle-based mechanism. According to the obtained results, a modification on the Chevron-Phillips catalyst system, which demonstrates higher 1-hexene selectivity and activity, is suggested. Full article
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Open AccessFeature PaperArticle Understanding the Heteroatom Effect on the Ullmann Copper-Catalyzed Cross-Coupling of X-Arylation (X = NH, O, S) Mechanism
Catalysts 2017, 7(12), 388; https://doi.org/10.3390/catal7120388
Received: 14 November 2017 / Revised: 7 December 2017 / Accepted: 11 December 2017 / Published: 13 December 2017
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Abstract
Density Functional Theory (DFT) calculations have been carried out in order to unravel the governing reaction mechanism in copper-catalyzed cross-coupling Ullmann type reactions between iodobenzene (1, PhI) and aniline (2-NH, PhNH2), phenol (2-O, PhOH) and
[...] Read more.
Density Functional Theory (DFT) calculations have been carried out in order to unravel the governing reaction mechanism in copper-catalyzed cross-coupling Ullmann type reactions between iodobenzene (1, PhI) and aniline (2-NH, PhNH2), phenol (2-O, PhOH) and thiophenol (2-S, PhSH) with phenanthroline (phen) as the ancillary ligand. Four different pathways for the mechanism were considered namely Oxidative Addition–Reductive Elimination (OA-RE), σ-bond Metathesis (MET), Single Electron Transfer (SET), and Halogen Atom Transfer (HAT). Our results suggest that the OA-RE route, involving CuIII intermediates, is the energetically most favorable pathway for all the systems considered. Interestingly, the rate-determining step is the oxidative addition of the phenyl iodide to the metal center regardless of the nature of the heteroatom. The computed energy barriers in OA increase in the order O < S < NH. Using the Activation Strain Model (ASM) of chemical reactivity, it was found that the strain energy associated with the bending of the copper(I) complex controls the observed reactivity. Full article
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Open AccessArticle Racemization of Serine Residues Catalyzed by Dihydrogen Phosphate Ion: A Computational Study
Catalysts 2017, 7(12), 363; https://doi.org/10.3390/catal7120363
Received: 26 October 2017 / Revised: 16 November 2017 / Accepted: 22 November 2017 / Published: 27 November 2017
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Abstract
Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate
[...] Read more.
Spontaneous, nonenzymatic reactions in proteins are known to have relevance to aging and age-related diseases, such as cataract and Alzheimer’s disease. Among such reactions is the racemization of Ser residues, but its mechanism in vivo remains to be clarified. The most likely intermediate is an enol. Although being nonenzymatic, the enolization would need to be catalyzed to occur at a biologically relevant rate. In the present study, we computationally found plausible reaction pathways for the enolization of a Ser residue where a dihydrogen phosphate ion, H2PO4, acts as a catalyst. The H2PO4 ion mediates the proton transfer required for the enolization by acting simultaneously as both a general base and a general acid. Using the B3LYP density functional theory method, reaction pathways were located in the gas phase and hydration effects were evaluated by single-point calculations using the SM8 continuum model. The activation barriers calculated for the reaction pathways found were around 100 kJ mol−1, which is consistent with spontaneous reactions occurring at physiological temperature. Our results are also consistent with experimental observations that Ser residue racemization occurs more readily in flexible regions in proteins. Full article
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Open AccessArticle Mechanistic Insight into the 2° Alcohol Oxidation Mediated by an Efficient CuI/L-Proline-TEMPO Catalyst—A Density Functional Theory Study
Catalysts 2017, 7(9), 264; https://doi.org/10.3390/catal7090264
Received: 10 August 2017 / Revised: 31 August 2017 / Accepted: 31 August 2017 / Published: 5 September 2017
Cited by 1 | PDF Full-text (4929 KB) | HTML Full-text | XML Full-text | Supplementary Files
Abstract
Density functional theory (DFT) calculations have been performed to investigate the 2° alcohol oxidation to acetophenone catalyzed by the CuI/L-Proline-2,2,6,6- tetramethylpiperidinyloxy (TEMPO) catalyst system. Seven possible pathways (paths A→F) are presented. Our calculations show that two pathways (path A and path
[...] Read more.
Density functional theory (DFT) calculations have been performed to investigate the 2° alcohol oxidation to acetophenone catalyzed by the CuI/L-Proline-2,2,6,6- tetramethylpiperidinyloxy (TEMPO) catalyst system. Seven possible pathways (paths A→F) are presented. Our calculations show that two pathways (path A and path B) are the potential mechanisms. Furthermore, by comparing with experimental observation, it is found that path A—in which substrate alcohol provides the proton to OtBu to produce HOtBu followed by the oxidation of substrate directly to product acetophenone by O2—is favored in the absence of TEMPO. Correspondingly, path B is likely to be favored when TEMPO is involved. In path B, the O–O bond cleavage of CuI–OOH to CuII–OH species occurs, followed by acetophenone formation assisted by ligand (L)2ˉ. It is also found that the cooperation of ligand (L)2ˉ and TEMPO plays an important role in assisting the formation of the product acetophenone in path B. Full article
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Review

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Open AccessReview A SET Approach to the Interplay of Catalysts and Reactants
Catalysts 2018, 8(3), 97; https://doi.org/10.3390/catal8030097
Received: 29 October 2017 / Revised: 25 January 2018 / Accepted: 31 January 2018 / Published: 28 February 2018
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Abstract
Research within the area of selective energy transfer (SET) on how resonance develops between a specific vibration within a catalyst system and a corresponding vibration within a reacting system that resonates with it is discussed here. The catalyst system is assumed to donate
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Research within the area of selective energy transfer (SET) on how resonance develops between a specific vibration within a catalyst system and a corresponding vibration within a reacting system that resonates with it is discussed here. The catalyst system is assumed to donate one or more vibrational quanta to the reacting system. The term ‘specific vibration’ refers to vibration of a type involving bending or stretching that, when transferred resonantly to the reacting system, serves to drive the reactant molecules involved to assume the basic structure of the molecules of the catalyst system. Regardless of whether the catalyst is a pure metal surface or a complex polymolecular system (an enzyme), its role is seen to be that of transferring energy to corresponding vibrations of the reactant system. Examples are here presented of vibrators of various types that can act as catalysts. Full article
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