Editorial

2 pages, 148 KiB

Open AccessEditorial

Computational Catalysis—Trends and Outlook

by Christoffer Heath Turner

Catalysts 2021, 11(4), 479; https://doi.org/10.3390/catal11040479 - 08 Apr 2021

Viewed by 1214

Computational catalysis has been one of the most dynamic research fields over the last decade, and it now represents a critical tool for the analysis of chemical mechanisms and active sites [...] Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

Research

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16 pages, 5041 KiB

Open AccessArticle

Mechanistic Insights into Selective Hydrogenation of C=C Bonds Catalyzed by CCC Cobalt Pincer Complexes: A DFT Study

by Zheng Zuo and Xinzheng Yang

Catalysts 2021, 11(2), 168; https://doi.org/10.3390/catal11020168 - 26 Jan 2021

Cited by 4 | Viewed by 2502

Abstract

The mechanistic insights into hydrogenations of hex-5-en-2-one, isoprene, and 4-vinylcyclohex-1-ene catalyzed by pincer (^MesCCC)Co (Mes = bis(mesityl-benzimidazol-2-ylidene)phenyl) complexes are computationally investigated by using the density functional theory. Different from a previously proposed mechanism with a cobalt dihydrogen complex (^MesCCC)Co-H [...] Read more.

The mechanistic insights into hydrogenations of hex-5-en-2-one, isoprene, and 4-vinylcyclohex-1-ene catalyzed by pincer (^MesCCC)Co (Mes = bis(mesityl-benzimidazol-2-ylidene)phenyl) complexes are computationally investigated by using the density functional theory. Different from a previously proposed mechanism with a cobalt dihydrogen complex (^MesCCC)Co-H₂ as the catalyst, we found that its less stable dihydride isomer, (^MesCCC)Co(H)₂, is the real catalyst in those catalytic cycles. The generations of final products with H₂ cleavages for the formations of C−H bonds are the turnover-limiting steps in all three hydrogenation reactions. We found that the hydrogenation selectivity of different C=C bonds in the same compound is dominated by the steric effects, while the hydrogenation selectivity of C=C and C=O bonds in the same compound could be primarily influenced by the electronic effects. In addition, the observed inhabition of the hydrogenation reactions by excessive addition of PPh₃ could be explained by a 15.8 kcal/mol free energy barrier for the dissociation of PPh₃ from the precatalyst. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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17 pages, 2274 KiB

Open AccessArticle

Sustainable Option for Hydrogen Production: Mechanistic Study of the Interaction between Cobalt Pincer Complexes and Ammonia Borane

by Yan Li, Chi-Wing Tsang, Eve Man Hin Chan, Eugene Yin Cheung Wong, Danny Chi Kuen Ho, Xiao-Ying Lu and Changhai Liang

Catalysts 2020, 10(7), 723; https://doi.org/10.3390/catal10070723 - 28 Jun 2020

Cited by 2 | Viewed by 2481

Abstract

The mechanism of the solvolysis/hydrolysis of ammonia borane by iridium (Ir), cobalt (Co), iron (Fe) and ruthenium (Ru) complexes with various PNP ligands has been revisited using density functional theory (DFT). The approach of ammonia borane (NH₃BH₃) to the [...] Read more.

The mechanism of the solvolysis/hydrolysis of ammonia borane by iridium (Ir), cobalt (Co), iron (Fe) and ruthenium (Ru) complexes with various PNP ligands has been revisited using density functional theory (DFT). The approach of ammonia borane (NH₃BH₃) to the metal center has been tested on three different possible mechanisms, namely, the stepwise, concerted and proton transfer mechanism. It was found that the theoretical analyses correlate with the experimental results very well, with the activities of the iridium complexes with different PNP ligands following the order: (tBu)₂P > (iPr)₂P > (Ph)₂P through the concerted mechanism. The reaction barriers of the rate-determining steps for the dehydrogenation of ammonia borane catalyzed by the active species [(^tBu)₂PNP-IrH] (Complex I-8), are found to be 19.3 kcal/mol (stepwise), 15.2 kcal/mol (concerted) and 26.8 kcal/mol (proton transfer), respectively. Thus, the concerted mechanism is the more kinetically favorable pathway. It is interesting to find that stable (^tBu)₂PNP Co-H₂O and (^tBu)₂PNP Co-NH₃ chelation products exist, which could stabilize the active I-8 species during the hydrolysis reaction cycle. The use of more sterically hindered and electron-donating PNP ligands such as (adamantyl)₂P- provides similar activity as the t-butyl analogue. This research provides insights into the design of efficient cobalt catalysts instead of using precious and noble metal, which could benefit the development of a more sustainable hydrogen economy. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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32 pages, 3997 KiB

Open AccessFeature PaperEditor’s ChoiceArticle

Exploring the Mechanism of Catalysis with the Unified Reaction Valley Approach (URVA)—A Review

by Elfi Kraka, Wenli Zou, Yunwen Tao and Marek Freindorf

Catalysts 2020, 10(6), 691; https://doi.org/10.3390/catal10060691 - 19 Jun 2020

Cited by 16 | Viewed by 4120

Abstract

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far [...] Read more.

The unified reaction valley approach (URVA) differs from mainstream mechanistic studies, as it describes a chemical reaction via the reaction path and the surrounding reaction valley on the potential energy surface from the van der Waals region to the transition state and far out into the exit channel, where the products are located. The key feature of URVA is the focus on the curving of the reaction path. Moving along the reaction path, any electronic structure change of the reacting molecules is registered by a change in their normal vibrational modes and their coupling with the path, which recovers the curvature of the reaction path. This leads to a unique curvature profile for each chemical reaction with curvature minima reflecting minimal change and curvature maxima, the location of important chemical events such as bond breaking/forming, charge polarization and transfer, rehybridization, etc. A unique decomposition of the path curvature into internal coordinate components provides comprehensive insights into the origins of the chemical changes taking place. After presenting the theoretical background of URVA, we discuss its application to four diverse catalytic processes: (i) the Rh catalyzed methanol carbonylation—the Monsanto process; (ii) the Sharpless epoxidation of allylic alcohols—transition to heterogenous catalysis; (iii) Au(I) assisted [3,3]-sigmatropic rearrangement of allyl acetate; and (iv) the Bacillus subtilis chorismate mutase catalyzed Claisen rearrangement—and show how URVA leads to a new protocol for fine-tuning of existing catalysts and the design of new efficient and eco-friendly catalysts. At the end of this article the pURVA software is introduced. The overall goal of this article is to introduce to the chemical community a new protocol for fine-tuning existing catalytic reactions while aiding in the design of modern and environmentally friendly catalysts. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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8 pages, 1357 KiB

Open AccessArticle

Quantum-Based Modeling of Dephosphorylation in the Catalytic Site of Serine/Threonine Protein Phosphatase-5 (PPP5C)

by E. Alan Salter, Andrzej Wierzbicki and Richard E. Honkanen

Catalysts 2020, 10(6), 674; https://doi.org/10.3390/catal10060674 - 16 Jun 2020

Cited by 3 | Viewed by 2020

Abstract

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M₁/M₂), an associated bridge hydroxide (W¹(OH⁻)), an M₁-bound water/hydroxide (W [...] Read more.

Serine/threonine protein phosphatase-5 (PP5; PPP5C) is a member of the phosphoprotein phosphatase (PPP) gene family. The PPP catalytic domains feature a bimetal system (M₁/M₂), an associated bridge hydroxide (W¹(OH⁻)), an M₁-bound water/hydroxide (W²), and a highly conserved core sequence. The PPPs are presumed to share a common mechanism: The seryl/threonyl phosphoryl group of the phosphoprotein coordinates the metal ions, W¹(OH⁻) attacks the central phosphorous atom, rupturing the antipodal phosphoester bond and releasing the phosphate-free protein. Also, a histidine/aspartate tandem is responsible for protonating the exiting seryl/threonyl alkoxide. Here, we employed quantum-based computations on a large section of the PP5 catalytic site. A 33-residue, ONIOM(UB3LYP/6-31G(d):UPM7) model was built to perform computations using methylphosphate dianion as a stand-in substrate for phosphoserine/phosphothreonine. We present a concerted transition state (TS) in which W¹(OH⁻) attacks the phosphate center at the same time that the exiting seryl/threonyl alkoxide is protonated directly by the His³⁰⁴/Asp²⁷⁴ tandem, with W² assigned as a water molecule: W²(H₂O). Arg²⁷⁵, proximal to M₁, stabilizes the substrate and TS by binding both the ester oxygen (O^γ) and a phosphoryl oxygen (O¹) in a bidentate fashion; in the product state, Tyr⁴⁵¹ aids in decoupling Arg²⁷⁵ from O¹ of the product phosphate ion. The reaction is exothermic (ΔH = −2.0 kcal/mol), occurs in a single step, and has a low activation barrier (ΔH^‡ = +10.0 kcal/mol). Our work is an improvement over an earlier computational study that also found bond rupture and alkoxide protonation to be concerted, but concluded that Arg²⁷⁵ is deprotonated during the reactant and TS stages of the pathway. In that earlier study, the critical electron-withdrawal role that Arg²⁷⁵ plays during the hydroxide attack was not correctly accounted for. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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10 pages, 3465 KiB

Open AccessArticle

Dispersion of Defects in TiO₂ Semiconductor: Oxygen Vacancies in the Bulk and Surface of Rutile and Anatase

by Mohammadreza Elahifard, Mohammad Reza Sadrian, Amir Mirzanejad, Reza Behjatmanesh-Ardakani and Seyedsaeid Ahmadvand

Catalysts 2020, 10(4), 397; https://doi.org/10.3390/catal10040397 - 03 Apr 2020

Cited by 45 | Viewed by 5108

Abstract

Oxygen deficiency (O-vacancy) contributes to the photoefficiency of TiO₂ semiconductors by generating electron rich active sites. In this paper, the dispersion of O-vacancies in both bulk and surface of anatase and rutile phases was computationally investigated. The results showed that the O-vacancies [...] Read more.

Oxygen deficiency (O-vacancy) contributes to the photoefficiency of TiO₂ semiconductors by generating electron rich active sites. In this paper, the dispersion of O-vacancies in both bulk and surface of anatase and rutile phases was computationally investigated. The results showed that the O-vacancies dispersed in single- and double-cluster forms in the anatase and rutile phases, respectively, in both bulk and surface. The distribution of the O-vacancies was (roughly) homogeneous in anatase, and heterogenous in rutile bulk. The O-vacancy formation energy, width of defect band, and charge distribution indicated the overlap of the defect states in the rutile phase and thus eased the formation of clusters. Removal of the first and the second oxygen atoms from the rutile surface took less energy than the anatase one, which resulted in a higher deficiency concentration on the rutile surface. However, these deficiencies formed one active site per unit cell of rutile. On the other hand, the first O-vacancy formed on the surface and the second one formed in the subsurface of anatase (per unit cell). Supported by previous studies, we argue that this distribution of O-vacancies in anatase (surface and subsurface) could potentially create more active sites on its surface. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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13 pages, 4090 KiB

Open AccessArticle

Bioinspired Design and Computational Prediction of SCS Nickel Pincer Complexes for Hydrogenation of Carbon Dioxide

by Xiaoyun Liu, Bing Qiu and Xinzheng Yang

Catalysts 2020, 10(3), 319; https://doi.org/10.3390/catal10030319 - 11 Mar 2020

Cited by 6 | Viewed by 3099

Abstract

Inspired by the structures of the active site of lactate racemase and H₂ activation mechanism of mono-iron hydrogenase, we proposed a series of sulphur–carbon–sulphur (SCS) nickel complexes and computationally predicted their potentials for catalytic hydrogenation of CO₂. Density functional theory [...] Read more.

Inspired by the structures of the active site of lactate racemase and H₂ activation mechanism of mono-iron hydrogenase, we proposed a series of sulphur–carbon–sulphur (SCS) nickel complexes and computationally predicted their potentials for catalytic hydrogenation of CO₂. Density functional theory calculations reveal a metal–ligand cooperated mechanism with the participation of a sulfur atom in the SCS pincer ligand as a proton receiver for the heterolytic cleavage of H₂. For all newly proposed complexes containing functional groups with different electron-donating and withdrawing abilities in the SCS ligand, the predicted free energy barriers for the hydrogenation of CO₂ to formic acid are in a range of 22.2–25.5 kcal/mol in water. Such a small difference in energy barriers indicates limited contributions of those functional groups to the charge density of the metal center. We further explored the catalytic mechanism of the simplest model complex for hydrogenation of formic acid to formaldehyde and obtained a total free energy barrier of 34.6 kcal/mol for the hydrogenation of CO₂ to methanol. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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13 pages, 2791 KiB

Open AccessArticle

Oxygen Reduction Reaction Catalyzed by Pt₃M (M = 3d Transition Metals) Supported on O-doped Graphene

by Chaonan Cui, Mengnan Sun, Xinli Zhu, Jinyu Han, Hua Wang and Qingfeng Ge

Catalysts 2020, 10(2), 156; https://doi.org/10.3390/catal10020156 - 01 Feb 2020

Cited by 7 | Viewed by 3706

Abstract

Pt₃M (M = 3d transition metals) supported on oxygen-doped graphene as an electrocatalyst for oxygen reduction was investigated using the periodic density functional theory-based computational method. The results show that oxygen prefers to adsorb on supported Pt₃M in a [...] Read more.

Pt₃M (M = 3d transition metals) supported on oxygen-doped graphene as an electrocatalyst for oxygen reduction was investigated using the periodic density functional theory-based computational method. The results show that oxygen prefers to adsorb on supported Pt₃M in a bridging di-oxygen configuration. Upon reduction, the O–O bond breaks spontaneously and the oxygen adatom next to the metal–graphene interface is hydrogenated, resulting in co-adsorbed O* and OH* species. Water formation was found to be the potential-limiting step on all catalysts. The activity for the oxygen reduction reaction was evaluated against the difference of the oxygen adsorption energy on the Pt site and the M site of Pt₃M and the results indicate that the oxygen adsorption energy difference offers an improved prediction of the oxygen reduction activity on these catalysts. Based on the analysis, Pt₃Ni supported on oxygen-doped graphene exhibits an enhanced catalytic performance for oxygen reduction over Pt₄. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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Review

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22 pages, 5099 KiB

Open AccessReview

Trends and Outlook of Computational Chemistry and Microkinetic Modeling for Catalytic Synthesis of Methanol and DME

by Jongmin Park, Hyo Seok Kim, Won Bo Lee and Myung-June Park

Catalysts 2020, 10(6), 655; https://doi.org/10.3390/catal10060655 - 11 Jun 2020

Cited by 16 | Viewed by 4632

Abstract

The first-principle modeling of heterogeneous catalysts is a revolutionarily approach, as the electronic structure of a catalyst is closely related to its reactivity on the surface with reactant molecules. In the past, detailed reaction mechanisms could not be understood, however, computational chemistry has [...] Read more.

The first-principle modeling of heterogeneous catalysts is a revolutionarily approach, as the electronic structure of a catalyst is closely related to its reactivity on the surface with reactant molecules. In the past, detailed reaction mechanisms could not be understood, however, computational chemistry has made it possible to analyze a specific elementary reaction of a reaction system. Microkinetic modeling is a powerful tool for investigating elementary reactions and reaction mechanisms for kinetics. Using a microkinetic model, the dominant pathways and rate-determining steps can be elucidated among the competitive reactions, and the effects of operating conditions on the reaction mechanisms can be determined. Therefore, the combination of computational chemistry and microkinetic modeling can significantly improve computational catalysis research. In this study, we reviewed the trends and outlook of this combination technique as applied to the catalytic synthesis of methanol (MeOH) and dimethyl ether (DME), whose detailed mechanisms are still controversial. Although the scope is limited to the catalytic synthesis of limited species, this study is expected to provide a foundation for future works in the field of catalysis research based on computational catalysis. Full article

(This article belongs to the Special Issue Feature Papers to Celebrate "Computational Catalysis"—Trends and Outlook)

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