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

Deadline for manuscript submissions: closed (30 June 2021) | Viewed by 23976

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Dr. Caroline Dessent

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Guest Editor

Department of Chemistry, University of York, Heslington, York YO10 5DD, UK
Interests: biological molecules in the gas-phase; gaseous ions; laser spectroscopy; molecular clusters; photoionization spectroscopy; computational chemistry; electron-molecule scattering; molecular anions; nucleobase photophysics; collision-induced dissociation; photodegradation
Special Issues, Collections and Topics in MDPI journals

Dr. Angelina Angelova

E-Mail Website
Guest Editor

CNRS UMR 8612 "Institut Galien Paris-Saclay", Paris-Saclay University, F-92296 Châtenay Malabry, France
Interests: lipid/protein nanoassemblies; liquid crystalline phases; cubosomes; self-assembled nanostructures and nanoparticles with neuroprotective properties; protein- and peptide-based nanomedicines; nanocarriers for macromolecular drug delivery; membrane receptor nanoscale organization; lipids; peptides; BDNF; cyclodextrin; soft nanomaterials; nanocrystallization
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear colleagues,

Research communities in many areas of chemistry are actively seeking to promote the career progression of women towards the goal of achieving gender balance amongst senior scientists. As physical chemists, we are part of a community of scientists that now includes many outstanding female scientists, engaged in internationally leading research across all of the sub-fields of physical chemistry. The growing profile of eminent female physical chemists has led to a research field in which younger scientists embrace gender equality, and fosters an environment where wider diversity is valued. To celebrate the achievements of women in physical chemistry, our journal Molecules will launch a Special Issue on “Women in Physical Chemistry”, to be published in 2020. This Special Issue will include high-quality papers and comprehensive review articles in all areas of physical chemistry. Contributions are encouraged from research groups led by women or men.

We look forward to receiving your contributions!

Dr. Caroline Dessent
Dr. Angelina Angelova
Guest Editors

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Published Papers (7 papers)

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10 pages, 6783 KiB

Open AccessArticle

Cross-Correlated Motions in Azidolysozyme

by Seyedeh Maryam Salehi and Markus Meuwly

Molecules 2022, 27(3), 839; https://doi.org/10.3390/molecules27030839 - 27 Jan 2022

Cited by 3 | Viewed by 2822

Abstract

The changes in the local and global dynamics of azide-labelled lysozyme compared with that of the wild type protein are quantitatively assessed for all alanine residues along the polypeptide chain. Although attaching -N

_{3}

to alanine residues has been considered to be a [...] Read more.

_{3}

to alanine residues has been considered to be a minimally invasive change in the protein it is found that depending on the location of the alanine residue, the local and global changes in the dynamics differ. For Ala92, the change in the cross-correlated motions are minimal, whereas attaching -N

_{3}

to Ala90 leads to pronounced differences in the local and global correlations as quantified by the cross-correlation coefficients of the C

_{α}

atoms. We also demonstrate that the spectral region of the asymmetric azide stretch distinguishes between alanine attachment sites, whereas changes in the low frequency, far-infrared region are less characteristic. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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16 pages, 3396 KiB

Open AccessArticle

Photodegradation of Riboflavin under Alkaline Conditions: What Can Gas-Phase Photolysis Tell Us about What Happens in Solution?

by Natalie G. K. Wong, Chris Rhodes and Caroline E. H. Dessent

Molecules 2021, 26(19), 6009; https://doi.org/10.3390/molecules26196009 - 3 Oct 2021

Cited by 8 | Viewed by 4040

Abstract

The application of electrospray ionisation mass spectrometry (ESI-MS) as a direct method for detecting reactive intermediates is a technique of developing importance in the routine monitoring of solution-phase reaction pathways. Here, we utilise a novel on-line photolysis ESI-MS approach to detect the photoproducts of riboflavin in aqueous solution under mildly alkaline conditions. Riboflavin is a constituent of many food products, so its breakdown processes are of wide interest. Our on-line photolysis setup allows for solution-phase photolysis to occur within a syringe using UVA LEDs, immediately prior to being introduced into the mass spectrometer via ESI. Gas-phase photofragmentation studies via laser-interfaced mass spectrometry of deprotonated riboflavin, [RF − H]⁻, the dominant solution-phase species under the conditions of our study, are presented alongside the solution-phase photolysis. The results obtained illustrate the extent to which gas-phase photolysis methods can inform our understanding of the corresponding solution-phase photochemistry. We determine that the solution-phase photofragmentation observed for [RF − H]⁻ closely mirrors the gas-phase photochemistry, with the dominant m/z 241 condensed-phase photoproduct also being observed in gas-phase photodissociation. Further gas-phase photoproducts are observed at m/z 255, 212, and 145. The value of exploring both the gas- and solution-phase photochemistry to characterise photochemical reactions is discussed. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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10 pages, 1466 KiB

Open AccessArticle

Intramolecular Photo-Oxidation as a Potential Source to Probe Biological Electron Damage: A Carboxylated Adenosine Analogue as Case Study

by Maria Elena Castellani and Jan R. R. Verlet

Molecules 2021, 26(10), 2877; https://doi.org/10.3390/molecules26102877 - 13 May 2021

Cited by 1 | Viewed by 2413

Abstract

A carboxylated adenosine analog (C-Ado⁻) has been synthesized and probed via time-resolved photoelectron spectroscopy in order to induce intra-molecular charge transfer from the carboxylic acid moiety to the nucleobase. Intra-molecular charge transfer can be exploited as starting point to probe low-energy electron (LEE) damage in DNA and its derivatives. Time-dependent density functional theory (TD-DFT) calculations at the B3LYP-6311G level of theory have been performed to verify that the highest occupied molecular orbital (HOMO) was located on carboxylic acid and that the lowest occupied molecular orbital (LUMO) was on the nucleobase. Hence, the carboxylic acid could work as electron source, whilst the nucleobase could serve the purpose of electron acceptor. The dynamics following excitation at 4.66 eV (266 nm) were probed using time-resolved photoelectron spectroscopy using probes at 1.55 eV (800 nm) and 3.10 eV (400 nm). The data show rapid decay of the excited state population and, based on the similarity of the overall dynamics to deoxy-adenosine monophosphate (dAMP^–), it appears that the dominant decay mechanism is internal conversion following ¹ππ* excitation of the nucleobase, rather than charge-transfer from the carboxylic acid to the nucleobase. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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12 pages, 2090 KiB

Open AccessArticle

Cross-Talk between Overlap Interactions in Biomolecules: A Case Study of the β-Turn Motif

by Jayashree Nagesh

Molecules 2021, 26(6), 1533; https://doi.org/10.3390/molecules26061533 - 11 Mar 2021

Cited by 1 | Viewed by 2071

Abstract

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions,

n \to π^{*}

is the best understood with studies ranging from small molecules to

β

-turns of model proteins such as [...] Read more.

Noncovalent interactions play a pivotal role in regulating protein conformation, stability and dynamics. Among the quantum mechanical (QM) overlap-based noncovalent interactions,

n \to π^{*}

is the best understood with studies ranging from small molecules to

β

-turns of model proteins such as GB1. However, these investigations do not explore the interplay between multiple overlap interactions in contributing to local structure and stability. In this work, we identify and characterize all noncovalent overlap interactions in the

β

-turn, an important secondary structural element that facilitates the folding of a polypeptide chain. Invoking a QM framework of natural bond orbitals, we demonstrate the role of several additional interactions such as

n \to σ^{*}

and

π \to π^{*}

that are energetically comparable to or larger than

n \to π^{*}

. We find that these interactions are sensitive to changes in the side chain of the residues in the

β

-turn of GB1, suggesting that the

n \to π^{*}

may not be the only component in dictating

β

-turn conformation and stability. Furthermore, a database search of

n \to σ^{*}

and

π \to π^{*}

in the PDB reveals that they are prevalent in most proteins and have significant interaction energies (∼1 kcal/mol). This indicates that all overlap interactions must be taken into account to obtain a comprehensive picture of their contributions to protein structure and energetics. Lastly, based on the extent of QM overlaps and interaction energies, we propose geometric criteria using which these additional interactions can be efficiently tracked in broad database searches. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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16 pages, 2393 KiB

Open AccessArticle

Towards the Application of Supramolecular Self-Associating Amphiphiles as Next-Generation Delivery Vehicles

by Lisa J. White, Jessica E. Boles, Kira L. F. Hilton, Rebecca J. Ellaby and Jennifer R. Hiscock

Molecules 2020, 25(18), 4126; https://doi.org/10.3390/molecules25184126 - 9 Sep 2020

Cited by 12 | Viewed by 3787

Abstract

Herein, we present a series of supramolecular self-associating amphiphilic (SSA) salts and establish the potential for these molecular constructs to act as next-generation solution-state molecular delivery vehicles. We characterise the self-association of these SSAs, both alone and when co-formulated with a variety of drug(like) competitive guest species. Single crystal X-ray diffraction studies enable the observation of hydrogen-bonded self-association events in the solid state, whilst high resolution mass spectrometry confirms the presence of anionic SSA dimers in the gas-phase. These same anionic SSA dimeric species are also identified within a competitive organic solvent environment (DMSO-d₆/0.5% H₂O). However, extended self-associated aggregates are observed to form under aqueous conditions (H₂O/5.0% EtOH) in both the absence and presence of these competitive guest species. Finally, through the completion of these studies, we present a framework to support others in the characterisation of such systems. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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17 pages, 3524 KiB

Open AccessArticle

Observation of Enhanced Dissociative Photochemistry in the Non-Native Nucleobase 2-Thiouracil

by Kelechi O. Uleanya, Rosaria Cercola, Maria Nikolova, Edward Matthews, Natalie G. K. Wong and Caroline E. H. Dessent

Molecules 2020, 25(14), 3157; https://doi.org/10.3390/molecules25143157 - 10 Jul 2020

Cited by 13 | Viewed by 3185

Abstract

We present the first study to measure the dissociative photochemistry of 2-thiouracil (2-TU), an important nucleobase analogue with applications in molecular biology and pharmacology. Laser photodissociation spectroscopy is applied to the deprotonated and protonated forms of 2-TU, which are produced in the gas-phase using electrospray ionization mass spectrometry. Our results show that the deprotonated form of 2-thiouracil ([2-TU-H]⁻) decays predominantly by electron ejection and hence concomitant production of the [2-TU-H]· free-radical species, following photoexcitation across the UVA-UVC region. Thiocyanate (SCN⁻) and a m/z 93 fragment ion are also observed as photodecay products of [2-TU-H]⁻ but at very low intensities. Photoexcitation of protonated 2-thiouracil ([2-TU·H]⁺) across the same UVA-UVC spectral region produces the m/z 96 cationic fragment as the major photofragment. This ion corresponds to ejection of an HS· radical from the precursor ion and is determined to be a product of direct excited state decay. Fragment ions associated with decay of the hot ground state (i.e., the ions we would expect to observe if 2-thiouracil was behaving like UV-dissipating uracil) are observed as much more minor products. This behaviour is consistent with enhanced intersystem crossing to triplet excited states compared to internal conversion back to the ground state. These are the first experiments to probe the effect of protonation/deprotonation on thionucleobase photochemistry, and hence explore the effect of pH at a molecular level on their photophysical properties. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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15 pages, 2203 KiB

Open AccessReview

Women in the Singlet Fission World: Pearls in a Semi-Open Shell

by Joanna Stoycheva, Julia Romanova and Alia Tadjer

Molecules 2021, 26(10), 2922; https://doi.org/10.3390/molecules26102922 - 14 May 2021

Cited by 1 | Viewed by 3928

Abstract

Singlet fission, a multiple exciton generation process, can revolutionize existing solar cell technologies. Offering the possibility to double photocurrent, the process has become a focal point for physicists, chemists, software developers, and engineers. The following review is dedicated to the female investigators, predominantly theorists, who have contributed to the field of singlet fission. We highlight their most significant advances in the subject, from deciphering the mechanism of the process to designing coveted singlet fission materials. Full article

(This article belongs to the Special Issue Women in Physical Chemistry)

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