Special Issue "Quantum Chemical Modelling of Enzymatic Reactions"

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

Deadline for manuscript submissions: 30 June 2019

Special Issue Editors

Guest Editor
Prof. Dr. Tiziana Marino

Department of Chemistry and Chemical Technologies, Bridge Pietro Bucci, Building 14C, I-87036, RENDE (CS)-ITALY
Website | E-Mail
Interests: biological macromolecular systems; DFT; metal ions of biological interest
Guest Editor
Prof. Dr. Nino Russo

Department of Chemistry and Chemical Technologies, Università della Calabria, Via P. Bucci, Ponte Bucci cubo 14c, 87036 Rende (CS), Italy
Website | E-Mail
Interests: theoretical and computational chemistry; density functional theory; antioxidant reaction mechanisms; computational enzymology; homogeneous catalysis; photodynamic therapy; bioinorganic chemistry; structure-activity relationships; excited states; molecular dynamics

Special Issue Information

Dear Colleagues,

Enzymes are sophisticated natural machines that are able to selectively and efficiently catalyze a huge number of reactions indispensable for vital processes in both the vegetal and animal kingdoms. For a long time, the enzymes’ functions were essentially concentrated on their ability to stabilize low energy transition states that allow explaining the catalytic power of natural enzymes. Very recently, other important effects, such as preorganization, energetic destabilization of reaction intermediates, dynamics and the role of product complexes in the catalytic turnover, have emerged as key factors to explain some of the behaviors of complex enzyme chemistry.

In the last few years, the proposal of new artificial enzymes has also received great attention since the opening of a new scientific frontier that, not only enlarges the knowledge base on the enzyme structure and functions, but also opens new interesting applications in many technological fields.

DFT studies of mechanisms for enzymes and metalloenzymes over the past 15 years have increased a great deal, becoming of equal importance compared to traditional spectroscopic studies.  Lately, the QM/MM approach also achieved a significant role in the field of theoretical methodologies devoted to the untangling of different aspects of enzymatic catalysis.

This Special Issue aims to cover recent progress and advances in elucidating the catalytic role of important members of enzymatic families, implicated in important biological processes, as well as of artificial enzymes that will be involved in technological and industrial applications.

Prof. Dr. Tiziana Marino
Prof. Dr. Nino Russo
Guest Editors

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 papers will be 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 1300 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

  • Catalytic mechanism
  • potential energy surface
  • rate determining step
  • molecular dynamics
  • quantum mechanics model
  • QM/MM model

Published Papers (1 paper)

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Review

Open AccessFeature PaperReview A Comparative Review on the Catalytic Mechanism of Nonheme Iron Hydroxylases and Halogenases
Catalysts 2018, 8(8), 314; https://doi.org/10.3390/catal8080314
Received: 17 July 2018 / Revised: 25 July 2018 / Accepted: 30 July 2018 / Published: 31 July 2018
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Abstract
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl/Br
[...] Read more.
Enzymatic halogenation and haloperoxidation are unusual processes in biology; however, a range of halogenases and haloperoxidases exist that are able to transfer an aliphatic or aromatic C–H bond into C–Cl/C–Br. Haloperoxidases utilize hydrogen peroxide, and in a reaction with halides (Cl/Br), they react to form hypohalides (OCl/OBr) that subsequently react with substrate by halide transfer. There are three types of haloperoxidases, namely the iron-heme, nonheme vanadium, and flavin-dependent haloperoxidases that are reviewed here. In addition, there are the nonheme iron halogenases that show structural and functional similarity to the nonheme iron hydroxylases and form an iron(IV)-oxo active species from a reaction of molecular oxygen with α-ketoglutarate on an iron(II) center. They subsequently transfer a halide (Cl/Br) to an aliphatic C–H bond. We review the mechanism and function of nonheme iron halogenases and hydroxylases and show recent computational modelling studies of our group on the hectochlorin biosynthesis enzyme and prolyl-4-hydroxylase as examples of nonheme iron halogenases and hydroxylases. These studies have established the catalytic mechanism of these enzymes and show the importance of substrate and oxidant positioning on the stereo-, chemo- and regioselectivity of the reaction that takes place. Full article
(This article belongs to the Special Issue Quantum Chemical Modelling of Enzymatic Reactions)
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