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Computational Methods and Their Application in Catalysis

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

Deadline for manuscript submissions: closed (15 May 2017) | Viewed by 56308

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Special Issue Editor

Dr. José R. B. Gomes

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Guest Editor

Department of Chemistry, CICECO–Aveiro Institute of Materials, University of Aveiro, Campus Universitário de Santiago, 3810-193 Aveiro, Portugal
Interests: molecular structure; gas-phase thermochemistry; gas-phase reaction profiles; adsorption (chemisorption and physisorption); surface reactions; heterogeneous catalysis
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Special Issue Information

Dear Colleagues,

Computational catalysis is a rapidly developing field because of the impressive advancements in the quantum-mechanical techniques and in the speed and power of computers, which enable the elucidation and rationalization of how chemical processes are accelerated by the presence of a catalyst, with unprecedented accuracy. It is not only possible to calculate the structural parameters of important species interacting with a catalyst, e.g. reactants, products and intermediates, but also to determine the energetic profiles for each elementary step in a complex reaction, as well as reaction rates. Such information, using increasingly more realistic structural models and well-defined conditions, is crucial to understand the most favorable reaction paths and catalytic sites for aiding in the design of catalysts with improved characteristics for a given reaction, thus avoiding the formation of undesired side-products.

This Special Issue focuses on recent advances in the application of state-of-the-art computational approaches to better understand enzymes and homogeneous or heterogeneous catalysts, and on challenges that still need to be resolved for the ultimate goal of designing novel and/or more efficient catalysts entirely by a computer. Full papers, communications, perspectives, and mini-reviews are most welcome.

Dr. José R. B. Gomes
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All submissions that pass pre-check are peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Catalysts is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

adsorption
biocatalysts
cascade reactions
computational screening
doping effects
electrocatalysis
enzymes
organocatalysis
photocatalysis
reaction mechanisms

Published Papers (7 papers)

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Research

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1340 KiB

Open AccessArticle

A Theoretical Insight into Enhanced Catalytic Activity of Au by Multiple Twin Nanoparticles

by Kyoichi Sawabe, Taiki Koketsu, Junya Ohyama and Atsushi Satsuma

Catalysts 2017, 7(6), 191; https://doi.org/10.3390/catal7060191 - 19 Jun 2017

Cited by 5 | Viewed by 4255

Abstract

Recently, it has been reported that the morphology of Au nanoparticles (NPs) affects the catalytic activity of CO oxidation; twin crystal NPs show higher activity for CO oxidation than single-crystal NPs. In this study, density functional calculations have been carried out to investigate the morphology effect of Au NPs using CO as a probe molecule. In the case of Au NPs with a size of more than 2 nm, CO adsorption energy on the Au NPs is mainly determined by a coordination number (CN) of adsorption sites. CO binding to a multiple twin NP with a size of about 1 nm is stronger than that on a single-crystal NP with the same size. A simple CN explanation cannot be applied to the enhancement of CO binding to the small multiple twin NP. This enhancement is related to a deformation of the NP structure before and after CO adsorption. It is suggested that the multiple twin NP with a size of less than 1 nm, which shows the deformation upon CO adsorption, contributes to the higher activity for CO oxidation. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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2047 KiB

Open AccessArticle

Quantitative Structure-Thermostability Relationship of Late Transition Metal Catalysts in Ethylene Oligo/Polymerization

by Wenhong Yang, Zhifeng Ma, Jun Yi and Wen-Hua Sun

Catalysts 2017, 7(4), 120; https://doi.org/10.3390/catal7040120 - 18 Apr 2017

Cited by 10 | Viewed by 4277

Abstract

Quantitative structure–thermostability relationship was carried out for four series of bis(imino)pyridine iron (cobalt) complexes and α-diimine nickel complexes systems in ethylene oligo/polymerization. Three structural parameters were correlated with thermal stability, including bond order of metal-nitrogen (B), minimum distance (D) between central metal and ortho-carbon atoms on the aryl moiety and dihedral angle (α) of a central five-membered ring. The variation degree of catalytic activities between optimum and room temperatures (A_T) was calculated to describe the thermal stability of the complex. By multiple linear regression analysis (MLRA), the thermal stability presents good correlation with three structural parameters with the correlation coefficients (R²) over 0.95. Furthermore, the contributions of each parameter were evaluated. Through this work, it is expected to help the design of a late transition metal complex with thermal stability at the molecular level. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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13138 KiB

Open AccessArticle

The Distribution and Strength of Brönsted Acid Sites on the Multi-Aluminum Model of FER Zeolite: A Theoretical Study

by Miao He, Jie Zhang, Rui Liu, Xiuliang Sun and Biaohua Chen

Catalysts 2017, 7(1), 11; https://doi.org/10.3390/catal7010011 - 01 Jan 2017

Cited by 9 | Viewed by 7679

Abstract

One of the fundamental issues in catalysis is to identify the catalytic active site. Due to its prominent pore topology and acidity, ferrierite (FER) zeolite has attracted extensive interest in various catalytic reactions such as isomerization of butenes. However knowledge on the active Brönsted acid site is still absent. In the present study, we perform extensive density functional theory calculations to explore the distribution and strength of the Brönsted acid sites and their potential catalytic activity for the double-bond isomerization of 1-butene to 2-butene. We employ a two-layered ONIOM scheme (our Own N-layered Integrated molecular Orbital + molecular Mechanics) to describe the structure and energetic properties of FER zeolite. We find that the hydrogen bond could improve the stability of Brönsted acid sites effectively, and, as a result, Al4-O6-Si2 and Al4-O-(SiO)₂-Al4 are the most stable sites for 1-Al substitution and 2-Al substitution, respectively. We further find that the Brönsted acid strength tends to decrease with the increase of Al contents and increase when the distance between the Al atoms is increased in 2-Al substitution. Finally it is demonstrated that the strength of acid sites determines the catalytic activity for the double bond isomerization of 1-butene to 2-butene. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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Review

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1376 KiB

Open AccessReview

In Silico Studies of Small Molecule Interactions with Enzymes Reveal Aspects of Catalytic Function

by Rajni Verma and Katie Mitchell-Koch

Catalysts 2017, 7(7), 212; https://doi.org/10.3390/catal7070212 - 14 Jul 2017

Cited by 18 | Viewed by 8370

Abstract

Small molecules, such as solvent, substrate, and cofactor molecules, are key players in enzyme catalysis. Computational methods are powerful tools for exploring the dynamics and thermodynamics of these small molecules as they participate in or contribute to enzymatic processes. In-depth knowledge of how small molecule interactions and dynamics influence protein conformational dynamics and function is critical for progress in the field of enzyme catalysis. Although numerous computational studies have focused on enzyme–substrate complexes to gain insight into catalytic mechanisms, transition states and reaction rates, the dynamics of solvents, substrates, and cofactors are generally less well studied. Also, solvent dynamics within the biomolecular solvation layer play an important part in enzyme catalysis, but a full understanding of its role is hampered by its complexity. Moreover, passive substrate transport has been identified in certain enzymes, and the underlying principles of molecular recognition are an area of active investigation. Enzymes are highly dynamic entities that undergo different conformational changes, which range from side chain rearrangement of a residue to larger-scale conformational dynamics involving domains. These events may happen nearby or far away from the catalytic site, and may occur on different time scales, yet many are related to biological and catalytic function. Computational studies, primarily molecular dynamics (MD) simulations, provide atomistic-level insight and site-specific information on small molecule interactions, and their role in conformational pre-reorganization and dynamics in enzyme catalysis. The review is focused on MD simulation studies of small molecule interactions and dynamics to characterize and comprehend protein dynamics and function in catalyzed reactions. Experimental and theoretical methods available to complement and expand insight from MD simulations are discussed briefly. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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5936 KiB

Open AccessFeature PaperReview

Process Simulation for the Design and Scale Up of Heterogeneous Catalytic Process: Kinetic Modelling Issues

by Antonio Tripodi, Matteo Compagnoni, Rocco Martinazzo, Gianguido Ramis and Ilenia Rossetti

Catalysts 2017, 7(5), 159; https://doi.org/10.3390/catal7050159 - 18 May 2017

Cited by 23 | Viewed by 12419

Abstract

Process simulation represents an important tool for plant design and optimization, either applied to well established or to newly developed processes. Suitable thermodynamic packages should be selected in order to properly describe the behavior of reactors and unit operations and to precisely define phase equilibria. Moreover, a detailed and representative kinetic scheme should be available to predict correctly the dependence of the process on its main variables. This review points out some models and methods for kinetic analysis specifically applied to the simulation of catalytic processes, as a basis for process design and optimization. Attention is paid also to microkinetic modelling and to the methods based on first principles, to elucidate mechanisms and independently calculate thermodynamic and kinetic parameters. Different case studies support the discussion. At first, we have selected two basic examples from the industrial chemistry practice, e.g., ammonia and methanol synthesis, which may be described through a relatively simple reaction pathway and the relative available kinetic scheme. Then, a more complex reaction network is deeply discussed to define the conversion of bioethanol into syngas/hydrogen or into building blocks, such as ethylene. In this case, lumped kinetic schemes completely fail the description of process behavior. Thus, in this case, more detailed—e.g., microkinetic—schemes should be available to implement into the simulator. However, the correct definition of all the kinetic data when complex microkinetic mechanisms are used, often leads to unreliable, highly correlated parameters. In such cases, greater effort to independently estimate some relevant kinetic/thermodynamic data through Density Functional Theory (DFT)/ab initio methods may be helpful to improve process description. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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7649 KiB

Open AccessReview

Functional and Biochemical Analysis of Glucose-6-Phosphate Dehydrogenase (G6PD) Variants: Elucidating the Molecular Basis of G6PD Deficiency

by Saúl Gómez-Manzo, Jaime Marcial-Quino, Daniel Ortega-Cuellar, Hugo Serrano-Posada, Abigail González-Valdez, America Vanoye-Carlo, Beatriz Hernández-Ochoa, Edgar Sierra-Palacios, Adriana Castillo-Villanueva and Horacio Reyes-Vivas

Catalysts 2017, 7(5), 135; https://doi.org/10.3390/catal7050135 - 02 May 2017

Cited by 24 | Viewed by 10641

Abstract

G6PD deficiency is the most common enzymopathy, leading to alterations in the first step of the pentose phosphate pathway, which interferes with the protection of the erythrocyte against oxidative stress and causes a wide range of clinical symptoms of which hemolysis is one of the most severe. The G6PD deficiency causes several abnormalities that range from asymptomatic individuals to more severe manifestations that can lead to death. Nowadays, only 9.2% of all recognized variants have been related to clinical manifestations. It is important to understand the molecular basis of G6PD deficiency to understand how gene mutations can impact structure, stability, and enzymatic function. In this work, we reviewed and compared the functional and structural data generated through the characterization of 20 G6PD variants using different approaches. These studies showed that severe clinical manifestations of G6PD deficiency were related to mutations that affected the catalytic and structural nicotinamide adenine dinucleotide phosphate (NADPH) binding sites, and suggests that the misfolding or instability of the 3D structure of the protein could compromise the half-life of the protein in the erythrocyte and its activity. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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490 KiB

Open AccessFeature PaperReview

Strengths, Weaknesses, Opportunities and Threats: Computational Studies of Mn- and Fe-Catalyzed Epoxidations

by Filipe Teixeira and M. Natália D. S. Cordeiro

Catalysts 2017, 7(1), 2; https://doi.org/10.3390/catal7010002 - 23 Dec 2016

Cited by 12 | Viewed by 7355

Abstract

The importance of epoxides as synthetic intermediates in a number of highly added-value chemicals, as well as the search for novel and more sustainable chemical processes have brought considerable attention to the catalytic activity of manganese and iron complexes towards the epoxidation of alkenes using non-toxic terminal oxidants. Particular attention has been given to Mn(salen) and Fe(porphyrin) catalysts. While the former attain remarkable enantioselectivity towards the epoxidation of cis-alkenes, the latter also serve as an important model for the behavior of cytochrome P450, thus allowing the exploration of complex biological processes. In this review, a systematic survey of the bibliographical data for the theoretical studies on Mn- and Fe-catalyzed epoxidations is presented. The most interesting patterns and trends are reported and finally analyzed using an evaluation framework similar to the SWOT (Strengths, Weaknesses, Opportunities and Threats) analysis performed in enterprise media, with the ultimate aim to provide an overview of current trends and areas for future exploration. Full article

(This article belongs to the Special Issue Computational Methods and Their Application in Catalysis)

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