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Biomolecules in Non-aqueous Media, from Small Molecules to Macromolecules

A special issue of Molecules (ISSN 1420-3049). This special issue belongs to the section "Green Chemistry".

Deadline for manuscript submissions: closed (28 February 2023) | Viewed by 9801

Special Issue Editors

Department of Chemistry and Biochemistry, SUNY Brockport, 228 Smith Hall, 350 New Campus Drive, Brockport, NY 14420, USA
Interests: ionic liquids (ILs); deep eutectic solvents (DESs); cosolvent solutions with ILs and DESs; supercritical fluid solvation; proteins; microheterogeneous media; molecular solvation dynamics; laser-based spectroscopy
Special Issues, Collections and Topics in MDPI journals
Center for Nanobiology and Structural Biology, Institute of Microbiology of the Czech Academy of Sciences, Faculty of Science, University of South Bohemia, České Budějovice, Czech Republic
Interests: molecular dynamics simulation; computational chemistry; environmental chemistry; biocatalysis; nanotechnology; biomolecular applications; deep eutectic solvents; DNA; ionic liquids

Special Issue Information

Dear Colleagues,

The aim of this special issue on “Biomolecules in Non-Aqueous Media, from Small Molecules to Macromolecules” is to bring new information on the applications of non-aqueous media, such as organic solvents, ionic liquids (ILs) and deep eutectic solvents (DES) in many areas of research and technology. Non-aqueous media can be a new applicable medium for many research and application areas, including material science, bio-separation science, food science biotechnology, nano-medicine, biocatalysis, new technologies for wastewater treatment and other energy-efficient bioprocessing.

Interest in ionic liquid solutions has increased in this research area, allowing it to soar past the point of being just a curiosity; there is now a collective extensive effort aimed at understanding these materials. As one example, there is a growing number of applications of ionic liquids in areas such as biomolecular extraction, synthesis, engineering, bio-separation, food applications and nano-based biocatalysis, protein engineering, protein crystallization, and many others. However, it is often the case that applications outpace the development of a complete and detailed understanding of molecular interactions. The importance of building a predictive capability becomes necessarily and progressively more important. Appropriately, much of the research published to date (both theoretical and experimental) has focused on neat ionic liquids. However, as the diversity of applications continues to expand, designer solvent systems, such as IL+ molecular co-solvents, DES+co-solvent, etc., are under investigation to enhance their utility further.

The goal of this Special Issue is to highlight new results from both computational and experimental research that discuss the properties and applications of biomolecules in modified aqueous and non-aqueous solutions, to advance a more complete understanding of these systems. This Special Issue is not limited to ionic liquids. We wish to establish a broad scope, to include the many interesting areas of active research that study non-aqueous biomolecular systems. The chemistry, physics, and engineering of non-aqueous biomolecular solutions require both experimental and theoretical approaches to achieve the desired understanding of the underpinnings of the biomolecular interactions that drive the widening array of applications. We cordially invite submissions that describe research in these areas.

Dr. Mark P. Heitz
Dr. Babak Minofar
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 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. 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.

Keywords

  • Biomolecule applications
  • Ionic liquids
  • Structure and dynamics
  • Molecular dynamics
  • Deep eutectic solvents
  • DNA in non-aqueous media
  • Proteins in non-aqueous media
  • Protein and DNA stability in non-aqueous media
  • Spectroscopy of biomolecules in non-aqueous media
  • CD spectroscopy of biomolecules
  • NMR spectroscopy of biomolecules
  • Solvatochromic properties of ionic liquids
  • Room temperature ionic liquids
  • Green solvents

Published Papers (3 papers)

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Research

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15 pages, 4259 KiB  
Article
Surface Interaction of Ionic Liquids: Stabilization of Polyethylene Terephthalate-Degrading Enzymes in Solution
by Zeenat Zara, Deepti Mishra, Saurabh Kumar Pandey, Eva Csefalvay, Fatemeh Fadaei, Babak Minofar and David Řeha
Molecules 2022, 27(1), 119; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27010119 - 26 Dec 2021
Cited by 2 | Viewed by 3107
Abstract
The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of [...] Read more.
The effect of aqueous solutions of selected ionic liquids solutions on Ideonella sakaiensis PETase with bis(2-hydroxyethyl) terephthalate (BHET) substrate were studied by means of molecular dynamics simulations in order to identify the possible effect of ionic liquids on the structure and dynamics of enzymatic Polyethylene terephthalate (PET) hydrolysis. The use of specific ionic liquids can potentially enhance the enzymatic hydrolyses of PET where these ionic liquids are known to partially dissolve PET. The aqueous solution of cholinium phosphate were found to have the smallest effect of the structure of PETase, and its interaction with (BHET) as substrate was comparable to that with the pure water. Thus, the cholinium phosphate was identified as possible candidate as ionic liquid co-solvent to study the enzymatic hydrolyses of PET. Full article
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20 pages, 3135 KiB  
Article
Interactions between a dsDNA Oligonucleotide and Imidazolium Chloride Ionic Liquids: Effect of Alkyl Chain Length, Part I
by Fatemeh Fadaei, Michelle Seifert, Joshua R. Raymond, David Řeha, Natalia Kulik, Babak Minofar and Mark P. Heitz
Molecules 2022, 27(1), 116; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules27010116 - 25 Dec 2021
Cited by 1 | Viewed by 2643
Abstract
Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium [...] Read more.
Ionic liquids (ILs) have become nearly ubiquitous solvents and their interactions with biomolecules has been a focus of study. Here, we used the fluorescence emission of DAPI, a groove binding fluorophore, coupled with molecular dynamics (MD) simulations to report on interactions between imidazolium chloride ([Imn,1]+) ionic liquids and a synthetic DNA oligonucleotide composed entirely of T/A bases (7(TA)) to elucidate the effects ILs on a model DNA duplex. Spectral shifts on the order of 500–1000 cm−1, spectral broadening (~1000 cm−1), and excitation and emission intensity ratio changes combine to give evidence of an increased DAPI environment heterogeneity on added IL. Fluorescence lifetimes for DAPI/IL solutions yielded two time constants 0.15 ns (~80% to 60% contribution) and 2.36–2.71 ns for IL up to 250 mM. With DNA, three time constants were required that varied with added IL (0.33–0.15 ns (1–58% contribution), ~1.7–1.0 ns (~5% contribution), and 3.8–3.6 ns (94–39% contribution)). MD radial distribution functions revealed that π-π stacking interactions between the imidazolium ring were dominant at lower IL concentration and that electrostatic and hydrophobic interactions become more prominent as IL concentration increased. Alkyl chain alignment with DNA and IL-IL interactions also varied with IL. Collectively, our data showed that, at low IL concentration, IL was primarily bound to the DNA minor groove and with increased IL concentration the phosphate regions and major groove binding sites were also important contributors to the complete set of IL-DNA duplex interactions. Full article
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Review

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28 pages, 7424 KiB  
Review
Effects of Ionic Liquids on Metalloproteins
by Aashka Y. Patel, Keertana S. Jonnalagadda, Nicholas Paradis, Timothy D. Vaden, Chun Wu and Gregory A. Caputo
Molecules 2021, 26(2), 514; https://0-doi-org.brum.beds.ac.uk/10.3390/molecules26020514 - 19 Jan 2021
Cited by 15 | Viewed by 3356
Abstract
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the [...] Read more.
In the past decade, innovative protein therapies and bio-similar industries have grown rapidly. Additionally, ionic liquids (ILs) have been an area of great interest and rapid development in industrial processes over a similar timeline. Therefore, there is a pressing need to understand the structure and function of proteins in novel environments with ILs. Understanding the short-term and long-term stability of protein molecules in IL formulations will be key to using ILs for protein technologies. Similarly, ILs have been investigated as part of therapeutic delivery systems and implicated in numerous studies in which ILs impact the activity and/or stability of protein molecules. Notably, many of the proteins used in industrial applications are involved in redox chemistry, and thus often contain metal ions or metal-associated cofactors. In this review article, we focus on the current understanding of protein structure-function relationship in the presence of ILs, specifically focusing on the effect of ILs on metal containing proteins. Full article
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