Advances in Modeling of Chemical Reactions by QM/MM Calculations

Dear Colleagues,

In the last several decades, the hybrid methodology, quantum mechanics/molecular mechanics (QM/MM), has become one of the most used techniques to model molecules embedded in a complex environment. Currently, it is the state-of-the-art for computational studies of chemical reactions and electronic properties in biomolecular systems. Chemical reactions are ubiquitous in biology, controlling a wide variety of fundamental biological processes, such as photosynthesis, bioluminescence, etc. It is crucial to obtain a full understanding of chemical mechanisms, and to confirm or discard different mechanistic proposals when they cannot be elucidated from experimental data.

To date, QM/MM methods have been applied to gain insight into different issues, such as enzymatic reaction mechanisms, the calculation of transition state structures, intermediates, activation energies, spectroscopic properties, electronically excited states, pKa values, etc. The multiple strengths of QM/MM methods are that they balance the simulation cost and accuracy, and the fact that large molecules can be modelled explicitly including the entire studied system in the calculations. In contrast, the main limitation of QM/MM calculations is that there are many possible conformations that macromolecules can assume. However, the available crystallographic structures can substantially aid in the modeling setup and preparation.

This Issue aims to gather new ideas and methodologies on all aspects of QM/MM techniques, as well as research studies on biomolecular or complex systems. Contributions in the form of both original research and review articles are particularly welcome.

Prof. Demeter Tzeli
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 250 words) can be sent to the Editorial Office for assessment.

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. Molecules is an international peer-reviewed open access semimonthly 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.