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Feature Papers in 'Physical Chemistry and Chemical Physics'

A topical collection in International Journal of Molecular Sciences (ISSN 1422-0067). This collection belongs to the section "Physical Chemistry and Chemical Physics".

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Editor

Topical Collection Information

Dear Colleagues,

This collection on Physical Chemistry and Chemical Physics deals with the pure science and technology of different research fields, ranging from chemistry and physics to biological materials and functions. Examples of such research areas include biophysics and studies of nanostructured materials. As the study of the forces that govern the structure and dynamics of molecular systems, chemical physics encompasses these and many emerging research directions. We aim to collect high-quality research and review articles on the many open questions of relevant interest. The collection is open to experimental and theoretical research, including molecular dynamics simulations studies. We intend to present comprehensive analyses of the studied subjects and to encourage the expression of individual points of view.

Editorial Board Members of this Section of IJMS are highly encouraged to contribute by submitting their reports on relevant advances in their field. We look forward to receiving your submissions of top-quality papers covering the main findings of the latest research in the related fields.

Original research articles and reviews on these and related topics are welcome in this Topical Collection.

Prof. Dr. Francesco Mallamace
Collection Editor

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Keywords

  • Complex materials 
  • Polymers and polyelectrolytes 
  • Self-aggregation and folding processes 
  • Water 
  • Hydrophilic and hydrophobic interactions 
  • Meso- and nano-systems 
  • Soft matter 
  • Thermodynamic 
  • Catalysis 
  • Biological macromolecules

Published Papers (36 papers)

2023

Jump to: 2022, 2021, 2020

27 pages, 9640 KiB  
Article
Synthesis, X-ray Structure, Hirshfeld, DFT Conformational, Cytotoxic, and Anti-Toxoplasma Studies of New Indole-Hydrazone Derivatives
by Eman M. Hassan, Saied M. Soliman, Esraa A. Moneer, Mohamed Hagar, Assem Barakat, Matti Haukka and Hanaa Rasheed
Int. J. Mol. Sci. 2023, 24(17), 13251; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms241713251 - 26 Aug 2023
Viewed by 774
Abstract
The hydrazones 3ac, were synthesized from the reaction of indole-3-carbaldehyde and nicotinic acid hydrazide, isonicotinic acid hydrazide, and benzoic acid hydrazide, respectively. Their structures were confirmed using FTIR, 1HNMR, and 13CNMR spectroscopic techniques. Exclusively, hydrazones 3b and 3c [...] Read more.
The hydrazones 3ac, were synthesized from the reaction of indole-3-carbaldehyde and nicotinic acid hydrazide, isonicotinic acid hydrazide, and benzoic acid hydrazide, respectively. Their structures were confirmed using FTIR, 1HNMR, and 13CNMR spectroscopic techniques. Exclusively, hydrazones 3b and 3c were confirmed using single crystal X-ray crystallography to exist in the Eanti form. With the aid of DFT calculations, the most stable configuration of the hydrazones 3ac in gas phase and in nonpolar solvents (CCl4 and cyclohexane) is the ESyn form. Interestingly, the DFT calculations indicated the extrastability of the EAnti in polar aprotic (DMSO) and polar protic (ethanol) solvents. Hirshfeld topology analysis revealed the importance of the N…H, O…H, H…C, and π…π intermolecular interactions in the molecular packing of the studied systems. Distribution of the atomic charges for the hydrazones 3ac was presented. The hydrazones 3ac showed a polar character where 3b has the highest polarity of 5.7234 Debye compared to the 3a (4.0533 Debye) and 3c (5.3099 Debye). Regarding the anti-toxoplasma activity, all the detected results verified that 3c had a powerful activity against chronic toxoplasma infection. Compound 3c showed a considerable significant reduction percent of cyst burden in brain homogenates of toxoplasma infected mice representing 49%. Full article
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13 pages, 3913 KiB  
Article
A Dynamic Recurrent Neural Network for Predicting Higher Heating Value of Biomass
by Babak Aghel, Salah I. Yahya, Abbas Rezaei and Falah Alobaid
Int. J. Mol. Sci. 2023, 24(6), 5780; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24065780 - 17 Mar 2023
Cited by 4 | Viewed by 1201
Abstract
The higher heating value (HHV) is the main property showing the energy amount of biomass samples. Several linear correlations based on either the proximate or the ultimate analysis have already been proposed for predicting biomass HHV. Since the HHV relationship with the proximate [...] Read more.
The higher heating value (HHV) is the main property showing the energy amount of biomass samples. Several linear correlations based on either the proximate or the ultimate analysis have already been proposed for predicting biomass HHV. Since the HHV relationship with the proximate and ultimate analyses is not linear, nonlinear models might be a better alternative. Accordingly, this study employed the Elman recurrent neural network (ENN) to anticipate the HHV of different biomass samples from both the ultimate and proximate compositional analyses as the model inputs. The number of hidden neurons and the training algorithm were determined in such a way that the ENN model showed the highest prediction and generalization accuracy. The single hidden layer ENN with only four nodes, trained by the Levenberg–Marquardt algorithm, was identified as the most accurate model. The proposed ENN exhibited reliable prediction and generalization performance for estimating 532 experimental HHVs with a low mean absolute error of 0.67 and a mean square error of 0.96. In addition, the proposed ENN model provides a ground to clearly understand the dependency of the HHV on the fixed carbon, volatile matter, ash, carbon, hydrogen, nitrogen, oxygen, and sulfur content of biomass feedstocks. Full article
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12 pages, 3093 KiB  
Article
A Competition between Relative Stability and Binding Energy in Caffeine Phenyl-Glucose Aggregates: Implications in Biological Mechanisms
by Camilla Calabrese, Ander Camiruaga, Maider Parra-Santamaria, Luca Evangelisti, Sonia Melandri, Assimo Maris, Imanol Usabiaga and José A. Fernandez
Int. J. Mol. Sci. 2023, 24(5), 4390; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24054390 - 23 Feb 2023
Viewed by 1357
Abstract
Hydrogen bonds and stacking interactions are pivotal in biological mechanisms, although their proper characterisation within a molecular complex remains a difficult task. We used quantum mechanical calculations to characterise the complex between caffeine and phenyl-β-D-glucopyranoside, in which several functional groups of the sugar [...] Read more.
Hydrogen bonds and stacking interactions are pivotal in biological mechanisms, although their proper characterisation within a molecular complex remains a difficult task. We used quantum mechanical calculations to characterise the complex between caffeine and phenyl-β-D-glucopyranoside, in which several functional groups of the sugar derivative compete with each other to attract caffeine. Calculations at different levels of theory (M06-2X/6-311++G(d,p) and B3LYP-ED=GD3BJ/def2TZVP) agree to predict several structures similar in stability (relative energy) but with different affinity (binding energy). These computational results were experimentally verified by laser infrared spectroscopy, through which the caffeine·phenyl-β-D-glucopyranoside complex was identified in an isolated environment, produced under supersonic expansion conditions. The experimental observations correlate with the computational results. Caffeine shows intermolecular interaction preferences that combine both hydrogen bonding and stacking interactions. This dual behaviour had already been observed with phenol, and now with phenyl-β-D-glucopyranoside, it is confirmed and maximised. In fact, the size of the complex’s counterparts affects the maximisation of the intermolecular bond strength because of the conformational adaptability given by the stacking interaction. Comparison with the binding of caffeine within the orthosteric site of the A2A adenosine receptor shows that the more strongly bound caffeine·phenyl-β-D-glucopyranoside conformer mimics the interactions occurring within the receptor. Full article
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19 pages, 5676 KiB  
Article
Effect of Synthesis Method on Reaction Mechanism for Hydrogen Evolution over CuxOy/TiO2 Photocatalysts: A Kinetic Analysis
by Laura Clarizia, Giuseppe Vitiello, Robert Bericat Vadell, Jacinto Sá, Raffaele Marotta, Ilaria Di Somma, Roberto Andreozzi and Giuseppina Luciani
Int. J. Mol. Sci. 2023, 24(3), 2004; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms24032004 - 19 Jan 2023
Cited by 1 | Viewed by 1653
Abstract
The existing literature survey reports rare and conflicting studies on the effect of the preparation method of metal-based semiconductor photocatalysts on structural/morphological features, electronic properties, and kinetics regulating the photocatalytic H2 generation reaction. In this investigation, we compare the different copper/titania-based photocatalysts [...] Read more.
The existing literature survey reports rare and conflicting studies on the effect of the preparation method of metal-based semiconductor photocatalysts on structural/morphological features, electronic properties, and kinetics regulating the photocatalytic H2 generation reaction. In this investigation, we compare the different copper/titania-based photocatalysts for H2 generation synthesized via distinct methods (i.e., photodeposition and impregnation). Our study aims to establish a stringent correlation between physicochemical/electronic properties and photocatalytic performances for H2 generation based on material characterization and kinetic modeling of the experimental outcomes. Estimating unknown kinetic parameters, such as charge recombination rate and quantum yield, suggests a mechanism regulating charge carrier lifetime depending on copper distribution on the TiO2 surface. We demonstrate that H2 generation photoefficiency recorded over impregnated CuxOy/TiO2 is related to an even distribution of Cu(0)/Cu(I) on TiO2, and the formation of an Ohmic junction concertedly extended charge carrier lifetime and separation. The outcomes of the kinetic analysis and the related modeling investigation underpin photocatalyst physicochemical and electronic properties. Overall, the present study lays the groundwork for the future design of metal-based semiconductor photocatalysts with high photoefficiencies for H2 evolution. Full article
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2022

Jump to: 2023, 2021, 2020

13 pages, 2797 KiB  
Article
The Interplay between ESIPT and TADF for the 2,2′-Bipyridine-3,3′-diol: A Theoretical Reconsideration
by Xin Zhao, Lixia Zhu, Qi Li, Hang Yin and Ying Shi
Int. J. Mol. Sci. 2022, 23(22), 13969; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232213969 - 12 Nov 2022
Cited by 9 | Viewed by 1477
Abstract
Organic molecules with excited-state intramolecular proton transfer (ESIPT) and thermally activated delayed fluorescence (TADF) properties have great potential for realizing efficient organic light-emitting diodes (OLEDs). Furthermore, 2,2′-bipyridine-3,3′-diol (BP(OH)2) is a typical molecule with ESIPT and TADF properties. Previously, the double ESIPT [...] Read more.
Organic molecules with excited-state intramolecular proton transfer (ESIPT) and thermally activated delayed fluorescence (TADF) properties have great potential for realizing efficient organic light-emitting diodes (OLEDs). Furthermore, 2,2′-bipyridine-3,3′-diol (BP(OH)2) is a typical molecule with ESIPT and TADF properties. Previously, the double ESIPT state was proved to be a luminescent state, and the T2 state plays a dominant role in TADF for the molecule. Nevertheless, whether BP(OH)2 undergoes a double or single ESIPT process is controversial. Since different ESIPT channels will bring different TADF mechanisms, the previously proposed TADF mechanism based on the double ESIPT structure for BP(OH)2 needs to be reconsidered. Herein, reduced density gradient, potential energy surface, IR spectra and exited-state hydrogen-bond dynamics computations confirm that BP(OH)2 undergoes the barrierless single ESIPT process rather than the double ESIPT process with a barrier. Moreover, based on the single ESIPT structure, we calculated spin-orbit coupling matrix elements, nonradiative rates and electron-hole distributions. These results disclose that the T3 state plays a predominant role in TADF. Our investigation provides a better understanding on the TADF mechanism in hydrogen-bonded molecular systems and the interaction between ESIPT and TADF, which further provides a reference for developing efficient OLEDs. Full article
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27 pages, 785 KiB  
Article
The Lattice Model of Particles with Orientation-Dependent Interactions at Solid Surfaces: Wetting Scenarios
by Andrzej Patrykiejew
Int. J. Mol. Sci. 2022, 23(21), 12802; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms232112802 - 24 Oct 2022
Cited by 1 | Viewed by 877
Abstract
Wetting phenomena in a lattice model of particles having two chemically different halves (A and B) and being in contact with solid substrates have been studied with Monte Carlo methods. The energy of the interaction between a pair of neighboring particles has been [...] Read more.
Wetting phenomena in a lattice model of particles having two chemically different halves (A and B) and being in contact with solid substrates have been studied with Monte Carlo methods. The energy of the interaction between a pair of neighboring particles has been assumed to depend on the degree to which the AA, AB and BB regions face each other. In this work, we have assumed that uAA=1.0 and considered three series of systems with uAB=uBB, uAB=0 and uBB=0. The phase behavior of bulk systems has been determined. In particular, it has been shown that at sufficiently low temperatures the bulk systems order into the superantiferromagnetic (SAF) phase, or into the antiferromagnetic (AF) phase, depending on the magnitudes of AA, AB and BB interaction energies, uAA, uAB and uBB. The SAF structure occurs whenever ϵ=uAA+uBB2uAB is lower than zero and the AF structure is stable when ϵ is greater than zero. The wetting behavior has been demonstrated to depend strongly on the structure of the bulk condensed phase, the interactions between fluid particles and the strength of the surface potential. In all series, we have found the dewetting transition, resulting from the limited stability of different ordered structures of surface phases. However, in the systems that exhibit the gas–liquid transition in the bulk, the reentrant wetting transition has been observed at sufficiently high temperatures. The mechanism of dewetting and reentrant wetting transitions has been determined. Moreover, we have also demonstrated, how the dewetting transition in the series with uAB=0 is affected by the wall selectivity, i.e., when the interaction between the parts A and B of fluid particles and the solid is different. Full article
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12 pages, 2086 KiB  
Article
Towards Sustainable Carbon Return from Waste to Industry via C2-Type Molecular Unit
by Konstantin S. Rodygin, Kristina A. Lotsman, Dmitriy E. Samoylenko, Viktor M. Kuznetsov and Valentine P. Ananikov
Int. J. Mol. Sci. 2022, 23(19), 11828; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911828 - 05 Oct 2022
Cited by 6 | Viewed by 1475
Abstract
A general possibility of a sustainable cycle for carbon return to high-value-added products is discussed by turning wastes into acetylene. Pyrolyzed solid municipal wastes, pyrolyzed used cationic exchangers, and other waste carbon sources were studied in view of the design of a sustainable [...] Read more.
A general possibility of a sustainable cycle for carbon return to high-value-added products is discussed by turning wastes into acetylene. Pyrolyzed solid municipal wastes, pyrolyzed used cationic exchangers, and other waste carbon sources were studied in view of the design of a sustainable cycle for producing calcium carbide and acetylene. The yields of calcium carbide from carbon wastes were as high as those from industrial fossil raw materials (coke, charcoal, etc.). Conversion of carbon-containing wastes to calcium carbide provides an excellent opportunity to make acetylene, which is directly compatible with modern industry. Overall, the process returns carbon-containing wastes back to sustainable cycles to produce high-value-added products involving only C2-type molecules (calcium carbide and acetylene). Calcium carbide may be stored and transported, and on-demand acetylene generation is easy to realize. Upon incorporation into the waste processing route, calcium carbide may be an efficient carbon reservoir for quick industrial uptake. Full article
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18 pages, 696 KiB  
Article
Theoretical Study of the Exciton Binding Energy and Exciton Absorption in Different Hyperbolic-Type Quantum Wells under Applied Electric, Magnetic, and Intense Laser Fields
by Melike Behiye Yücel, Huseyin Sari, Carlos M. Duque, Carlos A. Duque and Esin Kasapoglu
Int. J. Mol. Sci. 2022, 23(19), 11429; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms231911429 - 28 Sep 2022
Cited by 3 | Viewed by 1439
Abstract
In this study, we investigated the exciton binding energy and interband transition between the electron and heavy-hole for the single and double quantum wells which have different hyperbolic-type potential functions subject to electric, magnetic, and non-resonant intense laser fields. The results obtained show [...] Read more.
In this study, we investigated the exciton binding energy and interband transition between the electron and heavy-hole for the single and double quantum wells which have different hyperbolic-type potential functions subject to electric, magnetic, and non-resonant intense laser fields. The results obtained show that the geometric shapes of the structure and the applied external fields are very effective on the electronic and optical properties. In the absence of the external fields, the exciton binding energy is a decreasing function of increasing well sizes except for the strong confinement regime. Therefore, for all applied external fields, the increase in the well widths produces a red-shift at the absorption peak positions. The magnetic field causes an increase in the exciton binding energy and provides a blue-shift of the absorption peak positions corresponding to interband transitions. The effect of the electric field is quite pronounced in the weak confinement regime, it causes localization in opposite directions of the quantum wells of the electron and hole, thereby weakening the Coulomb interaction between them, causing a decrease in exciton binding energy, and a red-shift of the peak positions corresponding to the interband transitions. Generally, an intense laser field causes a decrease in the exciton binding energy and produces a red-shift of the peak positions corresponding to interband transitions. Full article
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61 pages, 14169 KiB  
Review
The Pnictogen Bond, Together with Other Non-Covalent Interactions, in the Rational Design of One-, Two- and Three-Dimensional Organic-Inorganic Hybrid Metal Halide Perovskite Semiconducting Materials, and Beyond
by Arpita Varadwaj, Pradeep R. Varadwaj, Helder M. Marques and Koichi Yamashita
Int. J. Mol. Sci. 2022, 23(15), 8816; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23158816 - 08 Aug 2022
Cited by 11 | Viewed by 2553
Abstract
The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel [...] Read more.
The pnictogen bond, a somewhat overlooked supramolecular chemical synthon known since the middle of the last century, is one of the promising types of non-covalent interactions yet to be fully understood by recognizing and exploiting its properties for the rational design of novel functional materials. Its bonding modes, energy profiles, vibrational structures and charge density topologies, among others, have yet to be comprehensively delineated, both theoretically and experimentally. In this overview, attention is largely centered on the nature of nitrogen-centered pnictogen bonds found in organic-inorganic hybrid metal halide perovskites and closely related structures deposited in the Cambridge Structural Database (CSD) and the Inorganic Chemistry Structural Database (ICSD). Focusing on well-characterized structures, it is shown that it is not merely charge-assisted hydrogen bonds that stabilize the inorganic frameworks, as widely assumed and well-documented, but simultaneously nitrogen-centered pnictogen bonding, and, depending on the atomic constituents of the organic cation, other non-covalent interactions such as halogen bonding and/or tetrel bonding, are also contributors to the stabilizing of a variety of materials in the solid state. We have shown that competition between pnictogen bonding and other interactions plays an important role in determining the tilting of the MX6 (X = a halogen) octahedra of metal halide perovskites in one, two and three-dimensions. The pnictogen interactions are identified to be directional even in zero-dimensional crystals, a structural feature in many engineered ordered materials; hence an interplay between them and other non-covalent interactions drives the structure and the functional properties of perovskite materials and enabling their application in, for example, photovoltaics and optoelectronics. We have demonstrated that nitrogen in ammonium and its derivatives in many chemical systems acts as a pnictogen bond donor and contributes to conferring stability, and hence functionality, to crystalline perovskite systems. The significance of these non-covalent interactions should not be overlooked, especially when the focus is centered on the rationale design and discovery of such highly-valued materials. Full article
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18 pages, 4036 KiB  
Article
Synthesis of 1-Amino-3-oxo-2,7-naphthyridines via Smiles Rearrangement: A New Approach in the Field of Chemistry of Heterocyclic Compounds
by Samvel N. Sirakanyan, Domenico Spinelli, Athina Geronikaki, Luca Zuppiroli, Riccardo Zuppiroli, Victor G. Kartsev, Elmira K. Hakobyan, Hasmik A. Yegoryan and Anush A. Hovakimyan
Int. J. Mol. Sci. 2022, 23(11), 5904; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23115904 - 25 May 2022
Cited by 3 | Viewed by 1527
Abstract
In this paper we describe an efficient method for the synthesis of new heterocyclic systems: furo[2,3-c]-2,7-naphthyridines 6, as well as a new method for the preparation of 1,3-diamino-2,7-naphthyridines 11. For the first time, a Smiles rearrangement was carried out [...] Read more.
In this paper we describe an efficient method for the synthesis of new heterocyclic systems: furo[2,3-c]-2,7-naphthyridines 6, as well as a new method for the preparation of 1,3-diamino-2,7-naphthyridines 11. For the first time, a Smiles rearrangement was carried out in the 2,7-naphthyridine series, thus gaining the opportunity to synthesize 1-amino-3-oxo-2,7-naphthyridines 4, which are the starting compounds for obtaining furo[2,3-c]-2,7-naphthyridines. The cyclization of alkoxyacetamides 9 proceeds via two different processes: the expected formation of furo[2,3-c]-2,7-naphthyridines 10 and the ‘unexpected’ formation of 1,3-diamino-2,7-naphthyridines 11 (via a Smiles type rearrangement). Full article
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18 pages, 3129 KiB  
Article
Aurivillius Oxides Nanosheets-Based Photocatalysts for Efficient Oxidation of Malachite Green Dye
by David A. Collu, Cristina Carucci, Marco Piludu, Drew F. Parsons and Andrea Salis
Int. J. Mol. Sci. 2022, 23(10), 5422; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23105422 - 12 May 2022
Cited by 8 | Viewed by 1699
Abstract
Aurivillius oxides ferroelectric layered materials are formed by bismuth oxide and pseu-do-perovskite layers. They have a good ionic conductivity, which is beneficial for various photo-catalyzed reactions. Here, we synthesized ultra-thin nanosheets of two different Aurivillius oxides, Bi2WO6 (BWO) and Bi [...] Read more.
Aurivillius oxides ferroelectric layered materials are formed by bismuth oxide and pseu-do-perovskite layers. They have a good ionic conductivity, which is beneficial for various photo-catalyzed reactions. Here, we synthesized ultra-thin nanosheets of two different Aurivillius oxides, Bi2WO6 (BWO) and Bi2MoO6 (BMO), by using a hard-template process. All materials were characterized through XRD, TEM, FTIR, TGA/DSC, DLS/ELS, DRS, UV-Vis. Band gap material (Eg) and potential of the valence band (EVB) were calculated for BWO and BMO. In contrast to previous reports on the use of multi composite materials, a new procedure for photocatalytic efficient BMO nanosheets was developed. The procedure, with an additional step only, avoids the use of composite materials, improves crystal structure, and strongly reduces impurities. BWO and BMO were used as photocatalysts for the degradation of the water pollutant dye malachite green (MG). MG removal kinetics was fitted with Langmuir—Hinshelwood model obtaining a kinetic constant k = 7.81 × 10−2 min−1 for BWO and k = 9.27 × 10−2 min−1 for BMO. Photocatalytic dye degradation was highly effective, reaching 89% and 91% MG removal for BWO and BMO, respectively. A control experiment, carried out in the absence of light, allowed to quantify the contribution of adsorption to MG removal process. Adsorption contributed to MG removal by a 51% for BWO and only by a 19% for BMO, suggesting a different degradation mechanism for the two photocatalysts. The advanced MG degradation process due to BMO is likely caused by the high crystallinity of the material synthetized with the new procedure. Reuse tests demonstrated that both photocatalysts are highly active and stable reaching a MG removal up to 95% at the 10th reaction cycle. These results demonstrate that BMO nanosheets, synthesized with an easy additional step, achieved the best degradation performance, and can be successfully used for environmental remediation applications. Full article
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52 pages, 3400 KiB  
Review
Radiopharmaceuticals for PET and SPECT Imaging: A Literature Review over the Last Decade
by George Crișan, Nastasia Sanda Moldovean-Cioroianu, Diana-Gabriela Timaru, Gabriel Andrieș, Călin Căinap and Vasile Chiș
Int. J. Mol. Sci. 2022, 23(9), 5023; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23095023 - 30 Apr 2022
Cited by 62 | Viewed by 9232
Abstract
Positron emission tomography (PET) uses radioactive tracers and enables the functional imaging of several metabolic processes, blood flow measurements, regional chemical composition, and/or chemical absorption. Depending on the targeted processes within the living organism, different tracers are used for various medical conditions, such [...] Read more.
Positron emission tomography (PET) uses radioactive tracers and enables the functional imaging of several metabolic processes, blood flow measurements, regional chemical composition, and/or chemical absorption. Depending on the targeted processes within the living organism, different tracers are used for various medical conditions, such as cancer, particular brain pathologies, cardiac events, and bone lesions, where the most commonly used tracers are radiolabeled with 18F (e.g., [18F]-FDG and NA [18F]). Oxygen-15 isotope is mostly involved in blood flow measurements, whereas a wide array of 11C-based compounds have also been developed for neuronal disorders according to the affected neuroreceptors, prostate cancer, and lung carcinomas. In contrast, the single-photon emission computed tomography (SPECT) technique uses gamma-emitting radioisotopes and can be used to diagnose strokes, seizures, bone illnesses, and infections by gauging the blood flow and radio distribution within tissues and organs. The radioisotopes typically used in SPECT imaging are iodine-123, technetium-99m, xenon-133, thallium-201, and indium-111. This systematic review article aims to clarify and disseminate the available scientific literature focused on PET/SPECT radiotracers and to provide an overview of the conducted research within the past decade, with an additional focus on the novel radiopharmaceuticals developed for medical imaging. Full article
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15 pages, 516 KiB  
Review
Aluminium Nanoparticles as Efficient Adjuvants Compared to Their Microparticle Counterparts: Current Progress and Perspectives
by Ali Nazarizadeh, Alexander H. Staudacher, Nicole L. Wittwer, Tyron Turnbull, Michael P. Brown and Ivan Kempson
Int. J. Mol. Sci. 2022, 23(9), 4707; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094707 - 24 Apr 2022
Cited by 13 | Viewed by 2811
Abstract
Aluminium (Al) compounds are used as adjuvants in human and veterinary prophylactic vaccines due to their improved tolerability compared to other adjuvants. These Al-based adjuvants form microparticles (MPs) of heterogeneous sizes ranging from ~0.5 to 10 µm and generally induce type 2 (Th2)-biased [...] Read more.
Aluminium (Al) compounds are used as adjuvants in human and veterinary prophylactic vaccines due to their improved tolerability compared to other adjuvants. These Al-based adjuvants form microparticles (MPs) of heterogeneous sizes ranging from ~0.5 to 10 µm and generally induce type 2 (Th2)-biased immune responses. However, recent literature indicates that moving from micron dimension particles toward the nanoscale can modify the adjuvanticity of Al towards type 1 (Th1) responses, which can potentially be exploited for the development of vaccines for which Th1 immunity is crucial. Specifically, in the context of cancer treatments, Al nanoparticles (Al-NPs) can induce a more balanced (Th1/Th2), robust, and durable immune response associated with an increased number of cytotoxic T cells compared to Al-MPs, which are more favourable for stimulating an oncolytic response. In this review, we compare the adjuvant properties of Al-NPs to those of Al-MPs in the context of infectious disease vaccines and cancer immunotherapy and provide perspectives for future research. Full article
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52 pages, 19052 KiB  
Review
The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor
by Arpita Varadwaj, Pradeep R. Varadwaj, Helder M. Marques and Koichi Yamashita
Int. J. Mol. Sci. 2022, 23(9), 4674; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094674 - 23 Apr 2022
Cited by 10 | Viewed by 2244
Abstract
A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the [...] Read more.
A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered. Full article
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20 pages, 732 KiB  
Review
Uranium: The Nuclear Fuel Cycle and Beyond
by Bárbara Maria Teixeira Costa Peluzo and Elfi Kraka
Int. J. Mol. Sci. 2022, 23(9), 4655; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23094655 - 22 Apr 2022
Cited by 20 | Viewed by 9024
Abstract
This review summarizes the recent developments regarding the use of uranium as nuclear fuel, including recycling and health aspects, elucidated from a chemical point of view, i.e., emphasizing the rich uranium coordination chemistry, which has also raised interest in using uranium compounds in [...] Read more.
This review summarizes the recent developments regarding the use of uranium as nuclear fuel, including recycling and health aspects, elucidated from a chemical point of view, i.e., emphasizing the rich uranium coordination chemistry, which has also raised interest in using uranium compounds in synthesis and catalysis. A number of novel uranium coordination features are addressed, such the emerging number of U(II) complexes and uranium nitride complexes as a promising class of materials for more efficient and safer nuclear fuels. The current discussion about uranium triple bonds is addressed by quantum chemical investigations using local vibrational mode force constants as quantitative bond strength descriptors based on vibrational spectroscopy. The local mode analysis of selected uranium nitrides, N≡U≡N, U≡N, N≡U=NH and N≡U=O, could confirm and quantify, for the first time, that these molecules exhibit a UN triple bond as hypothesized in the literature. We hope that this review will inspire the community interested in uranium chemistry and will serve as an incubator for fruitful collaborations between theory and experimentation in exploring the wealth of uranium chemistry. Full article
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36 pages, 3396 KiB  
Review
Tracing the Primordial Chemical Life of Glycine: A Review from Quantum Chemical Simulations
by Albert Rimola, Nadia Balucani, Cecilia Ceccarelli and Piero Ugliengo
Int. J. Mol. Sci. 2022, 23(8), 4252; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084252 - 12 Apr 2022
Cited by 12 | Viewed by 3281
Abstract
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial [...] Read more.
Glycine (Gly), NH2CH2COOH, is the simplest amino acid. Although it has not been directly detected in the interstellar gas-phase medium, it has been identified in comets and meteorites, and its synthesis in these environments has been simulated in terrestrial laboratory experiments. Likewise, condensation of Gly to form peptides in scenarios resembling those present in a primordial Earth has been demonstrated experimentally. Thus, Gly is a paradigmatic system for biomolecular building blocks to investigate how they can be synthesized in astrophysical environments, transported and delivered by fragments of asteroids (meteorites, once they land on Earth) and comets (interplanetary dust particles that land on Earth) to the primitive Earth, and there react to form biopolymers as a step towards the emergence of life. Quantum chemical investigations addressing these Gly-related events have been performed, providing fundamental atomic-scale information and quantitative energetic data. However, they are spread in the literature and difficult to harmonize in a consistent way due to different computational chemistry methodologies and model systems. This review aims to collect the work done so far to characterize, at a quantum mechanical level, the chemical life of Gly, i.e., from its synthesis in the interstellar medium up to its polymerization on Earth. Full article
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18 pages, 6660 KiB  
Review
Metal Coordination Enhances Chalcogen Bonds: CSD Survey and Theoretical Calculations
by Antonio Frontera and Antonio Bauza
Int. J. Mol. Sci. 2022, 23(8), 4188; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23084188 - 10 Apr 2022
Cited by 14 | Viewed by 1893
Abstract
In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where [...] Read more.
In this study the ability of metal coordinated Chalcogen (Ch) atoms to undergo Chalcogen bonding (ChB) interactions has been evaluated at the PBE0-D3/def2-TZVP level of theory. An initial CSD (Cambridge Structural Database) inspection revealed the presence of square planar Pd/Pt coordination complexes where divalent Ch atoms (Se/Te) were used as ligands. Interestingly, the coordination to the metal center enhanced the σ-hole donor ability of the Ch atom, which participates in ChBs with neighboring units present in the X-ray crystal structure, therefore dictating the solid state architecture. The X-ray analyses were complemented with a computational study (PBE0-D3/def2-TZVP level of theory), which shed light into the strength and directionality of the ChBs studied herein. Owing to the new possibilities that metal coordination offers to enhance or modulate the σ-hole donor ability of Chs, we believe that the findings presented herein are of remarkable importance for supramolecular chemists as well as for those scientists working in the field of solid state chemistry. Full article
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23 pages, 12577 KiB  
Article
Theoretical Characterization of the Step-by-Step Mechanism of Conversion of Leukotriene A4 to Leukotriene B4 Catalysed by the Enzyme Leukotriene A4 Hydrolase
by Miquel Canyelles-Niño, Àngels González-Lafont and José M. Lluch
Int. J. Mol. Sci. 2022, 23(6), 3140; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063140 - 15 Mar 2022
Cited by 3 | Viewed by 1718
Abstract
LTA4H is a bifunctional zinc metalloenzyme that converts leukotriene A4 (LTA4) into leukotriene B4 (LTB4), one of the most potent chemotactic agents involved in acute and chronic inflammatory diseases. In this reaction, LTA4H [...] Read more.
LTA4H is a bifunctional zinc metalloenzyme that converts leukotriene A4 (LTA4) into leukotriene B4 (LTB4), one of the most potent chemotactic agents involved in acute and chronic inflammatory diseases. In this reaction, LTA4H acts as an epoxide hydrolase with a unique and fascinating mechanism, which includes the stereoselective attachment of one water molecule to the carbon backbone of LTA4 several methylene units away from the epoxide moiety. By combining Molecular Dynamics simulations and Quantum Mechanics/Molecular Mechanics calculations, we obtained a very detailed molecular picture of the different consecutive steps of that mechanism. By means of a rather unusual 1,7-nucleophilic substitution through a clear SN1 mechanism, the epoxide opens and the triene moiety of the substrate twists in such a way that the bond C6-C7 adopts its cis (Z) configuration, thus exposing the R face of C12 to the addition of a water molecule hydrogen-bonded to ASP375. Thus, the two stereochemical features that are required for the bioactivity of LTB4 appear to be closely related. The noncovalent π-π stacking interactions between the triene moiety and two tyrosines (TYR267 and, especially, TYR378) that wrap the triene system along the whole reaction explain the preference for the cis configuration inside LTA4H. Full article
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18 pages, 5262 KiB  
Review
Chiral Linked Systems as a Model for Understanding D-Amino Acids Influence on the Structure and Properties of Amyloid Peptides
by Aleksandra A. Ageeva, Alexander B. Doktorov, Nikolay E. Polyakov and Tatyana V. Leshina
Int. J. Mol. Sci. 2022, 23(6), 3060; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23063060 - 11 Mar 2022
Cited by 5 | Viewed by 1998
Abstract
In this review, we provide an illustration of the idea discussed in the literature of using model compounds to study the effect of substitution of L- for D-amino acid residues in amyloid peptides. The need for modeling is due to the inability to [...] Read more.
In this review, we provide an illustration of the idea discussed in the literature of using model compounds to study the effect of substitution of L- for D-amino acid residues in amyloid peptides. The need for modeling is due to the inability to study highly disordered peptides by traditional methods (high-field NMR, X-ray). At the same time, the appearance of such peptides, where L-amino acids are partially replaced by D-analogs is one of the main causes of Alzheimer’s disease. The review presents examples of the use diastereomers with L-/D-tryptophan in model process—photoinduced electron transfer (ET) for studying differences in reactivity and structure of systems with L- and D-optical isomers. The combined application of spin effects, including those calculated using the original theory, fluorescence techniques and molecular modeling has demonstrated a real difference in the structure and efficiency of ET in diastereomers with L-/D-tryptophan residues. In addition, the review compared the factors governing chiral inversion in model metallopeptides and Aβ42 amyloid. Full article
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15 pages, 18114 KiB  
Article
Seedless Cu Electroplating on Ru-W Thin Films for Metallisation of Advanced Interconnects
by Rúben F. Santos, Bruno M. C. Oliveira, Liliane C. G. Savaris, Paulo J. Ferreira and Manuel F. Vieira
Int. J. Mol. Sci. 2022, 23(3), 1891; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23031891 - 08 Feb 2022
Cited by 2 | Viewed by 2037
Abstract
For decades, Ta/TaN has been the industry standard for a diffusion barrier against Cu in interconnect metallisation. The continuous miniaturisation of transistors and interconnects into the nanoscale are pushing conventional materials to their physical limits and creating the need to replace them. Binary [...] Read more.
For decades, Ta/TaN has been the industry standard for a diffusion barrier against Cu in interconnect metallisation. The continuous miniaturisation of transistors and interconnects into the nanoscale are pushing conventional materials to their physical limits and creating the need to replace them. Binary metallic systems, such as Ru-W, have attracted considerable attention as possible replacements due to a combination of electrical and diffusion barrier properties and the capability of direct Cu electroplating. The process of Cu electrodeposition on Ru-W is of fundamental importance in order to create thin, continuous, and adherent films for advanced interconnect metallisation. This work investigates the effects of the current density and application method on the electro-crystallisation behaviour of Cu. The film structure, morphology, and chemical composition were assessed by digital microscopy, atomic force microscopy, scanning and transmission electron microscopies, energy-dispersive X-ray spectroscopy, and X-ray diffraction. The results show that it was possible to form a thin Cu film on Ru-W with interfacial continuity for current densities higher than 5 mA·cm−2; however, the substrate regions around large Cu particles remained uncovered. Pulse-reverse current application appears to be more beneficial than direct current as it decreased the average Cu particle size. Full article
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2021

Jump to: 2023, 2022, 2020

25 pages, 5507 KiB  
Article
A Holistic Approach to Determining Stereochemistry of Potential Pharmaceuticals by Circular Dichroism with β-Lactams as Test Cases
by Marcin Górecki and Jadwiga Frelek
Int. J. Mol. Sci. 2022, 23(1), 273; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010273 - 27 Dec 2021
Viewed by 2485
Abstract
This paper’s main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods [...] Read more.
This paper’s main objective is to show that many different factors must be considered when solving stereochemical problems to avoid misleading conclusions and obtain conclusive results from the analysis of spectroscopic properties. Particularly in determining the absolute configuration, the use of chiroptical methods is crucial, especially when other techniques, including X-ray crystallography, fail, are not applicable, or give inconclusive results. Based on various β-lactam derivatives as models, we show how to reliably determine their absolute configuration (AC) and preferred conformation from circular dichroism (CD) spectra. Comprehensive CD analysis, employing both approaches, i.e., traditional with their sector and helicity rules, and state-of-the-art supported by quantum chemistry (QC) calculations along with solvation models for both electronic (ECD) and vibrational (VCD) circular dichroism ranges, allows confident defining stereochemistry of the β-lactams studied. Based on an in-depth analysis of the results, we have shown that choosing a proper chiroptical method/s strictly depends on the specific case and certain structural features. Full article
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32 pages, 8578 KiB  
Review
An Overview on the Performance of 1,2,3-Triazole Derivatives as Corrosion Inhibitors for Metal Surfaces
by Meryem Hrimla, Lahoucine Bahsis, My Rachid Laamari, Miguel Julve and Salah-Eddine Stiriba
Int. J. Mol. Sci. 2022, 23(1), 16; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms23010016 - 21 Dec 2021
Cited by 22 | Viewed by 3062
Abstract
This review accounts for the most recent and significant research results from the literature on the design and synthesis of 1,2,3-triazole compounds and their usefulness as molecular well-defined corrosion inhibitors for steels, copper, iron, aluminum, and their alloys in several aggressive media. Of [...] Read more.
This review accounts for the most recent and significant research results from the literature on the design and synthesis of 1,2,3-triazole compounds and their usefulness as molecular well-defined corrosion inhibitors for steels, copper, iron, aluminum, and their alloys in several aggressive media. Of particular interest are the 1,4-disubstituted 1,2,3-triazole derivatives prepared in a regioselective manner under copper-catalyzed azide-alkyne cycloaddition (CuAAC) click reactions. They are easily and straightforwardly prepared compounds, non-toxic, environmentally friendly, and stable products to the hydrolysis under acidic conditions. Moreover, they have shown a good efficiency as corrosion inhibitors for metals and their alloys in different acidic media. The inhibition efficiencies (IEs) are evaluated from electrochemical impedance spectroscopy (EIS) parameters with different concentrations and environmental conditions. Mechanistic aspects of the 1,2,3-triazoles mediated corrosion inhibition in metals and metal alloy materials are also overviewed. Full article
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13 pages, 4068 KiB  
Article
Fluorescence Recognition of Anions Using a Heteroditopic Receptor: Homogenous and Two-Phase Sensing
by Marta Zaleskaya-Hernik, Łukasz Dobrzycki, Marcin Karbarz and Jan Romański
Int. J. Mol. Sci. 2021, 22(24), 13396; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms222413396 - 13 Dec 2021
Cited by 8 | Viewed by 2098
Abstract
In contrast to monotopic receptor 3, the anthracene functionalized squaramide dual-host receptor 1 is capable of selectively extracting sulfate salts, as was evidenced unambiguously by DOSY, mass spectrometry, fluorescent and ion chromatography measurements. The receptors were investigated in terms of anion and [...] Read more.
In contrast to monotopic receptor 3, the anthracene functionalized squaramide dual-host receptor 1 is capable of selectively extracting sulfate salts, as was evidenced unambiguously by DOSY, mass spectrometry, fluorescent and ion chromatography measurements. The receptors were investigated in terms of anion and ion pair binding using the UV–vis and 1H NMR titrations method in acetonitrile. The reference anion receptor 3, lacking a crown ether unit, was found to lose the enhancement in anion binding induced by the presence of cations. Besides the ability to bind anions in an enhanced manner exhibited by ion pair receptors 2 and 4, changing the 1-aminoanthracene substituent resulted in their exhibiting a lower anion affinity than receptor 1. By using receptor 1 and adjusting the water content in organic phase it was possible to selectively detect sulfates both by “turn-off” and “turn-on” fluorescence, and to do so homogenously and under interfacial conditions. Such properties of receptor 1 have allowed the development of a new type of sensor capable of recognizing and extracting potassium sulfate from the aqueous medium across a phase boundary, resulting in an appropriate fluorescent response in the organic solution. Full article
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17 pages, 3336 KiB  
Article
Synthesis of Oxidized 3β,3′β-Disteryl Ethers and Search after High-Temperature Treatment of Sterol-Rich Samples
by Adam Zmysłowski, Jerzy Sitkowski, Katarzyna Bus, Katarzyna Michalska and Arkadiusz Szterk
Int. J. Mol. Sci. 2021, 22(19), 10421; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms221910421 - 27 Sep 2021
Cited by 1 | Viewed by 1535
Abstract
It was proven that sterols subjected to high-temperature treatment can be concatenated, which results in polymeric structures, e.g., 3β,3′β-disteryl ethers. However, it was also proven that due to increased temperature in oxygen-containing conditions, sterols can undergo various oxidation reactions. This study aimed to [...] Read more.
It was proven that sterols subjected to high-temperature treatment can be concatenated, which results in polymeric structures, e.g., 3β,3′β-disteryl ethers. However, it was also proven that due to increased temperature in oxygen-containing conditions, sterols can undergo various oxidation reactions. This study aimed to prove the existence and perform quantitative analysis of oxidized 3β,3′β-disteryl ethers, which could form during high-temperature treatment of sterol-rich samples. Samples were heated at 180, 200 and 220 °C for 0.5 to 4 h. Quantitative analyses of the oxidized 3β,3′β-disteryl ethers were performed with liquid extraction, solid-phase extraction and liquid chromatography coupled with mass spectrometry. Additionally, to perform this analysis, the appropriate standards of all oxidized 3β,3′β-disteryl ethers were prepared. Eighteen various oxidized 3β,3′β-disteryl ethers (derivatives of 3β,3′β-dicholesteryl ether, 3β,3′β-disitosteryl ether and 3β,3′β-distigmasteryl ether) were prepared. Additionally, the influence of metal compounds on the mechanism of ether formation at high temperatures was investigated. Full article
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18 pages, 445 KiB  
Article
“Water Association” Band in Saccharide Amorphous Matrices: Role of Residual Water on Bioprotection
by Sergio Giuffrida, Antonio Cupane and Grazia Cottone
Int. J. Mol. Sci. 2021, 22(5), 2496; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052496 - 02 Mar 2021
Cited by 6 | Viewed by 1893
Abstract
Saccharides protect biostructures against adverse environmental conditions mainly by preventing large scale motions leading to unfolding. The efficiency of this molecular mechanism, which is higher in trehalose with respect to other sugars, strongly depends on hydration and sugar/protein ratio. Here we report an [...] Read more.
Saccharides protect biostructures against adverse environmental conditions mainly by preventing large scale motions leading to unfolding. The efficiency of this molecular mechanism, which is higher in trehalose with respect to other sugars, strongly depends on hydration and sugar/protein ratio. Here we report an Infrared Spectroscopy study on dry amorphous matrices of the disaccharides trehalose, maltose, sucrose and lactose, and the trisaccharide raffinose. Samples with and without embedded protein (Myoglobin) are investigated at different sugar/protein ratios, and compared. To inspect matrix properties we analyse the Water Association Band (WAB), and carefully decompose it into sub-bands, since their relative population has been shown to effectively probe water structure and dynamics in different matrices. In this work the analysis is extended to investigate the structure of protein-sugar-water samples, for the first time. Results show that several classes of water molecules can be identified in the protein and sugar environment and that their relative population is dependent on the type of sugar and, most important, on the sugar/protein ratio. This gives relevant information on how the molecular interplay between residual waters, sugar and protein molecules affect the biopreserving properties of saccharides matrices. Full article
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13 pages, 2214 KiB  
Article
Electron-Induced Decomposition of Uracil-5-yl O-(N,N-dimethylsulfamate): Role of Methylation in Molecular Stability
by Eugene Arthur-Baidoo, Karina Falkiewicz, Lidia Chomicz-Mańka, Anna Czaja, Sebastian Demkowicz, Karol Biernacki, Witold Kozak, Janusz Rak and Stephan Denifl
Int. J. Mol. Sci. 2021, 22(5), 2344; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22052344 - 26 Feb 2021
Cited by 9 | Viewed by 2045
Abstract
The incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron [...] Read more.
The incorporation of modified uracil derivatives into DNA leads to the formation of radical species that induce DNA damage. Molecules of this class have been suggested as radiosensitizers and are still under investigation. In this study, we present the results of dissociative electron attachment to uracil-5-yl O-(N,N-dimethylsulfamate) in the gas phase. We observed the formation of 10 fragment anions in the studied range of electron energies from 0–12 eV. Most of the anions were predominantly formed at the electron energy of about 0 eV. The fragmentation paths were analogous to those observed in uracil-5-yl O-sulfamate, i.e., the methylation did not affect certain bond cleavages (O-C, S-O and S-N), although relative intensities differed. The experimental results are supported by quantum chemical calculations performed at the M06-2X/aug-cc-pVTZ level of theory. Furthermore, a resonance stabilization method was used to theoretically predict the resonance positions of the fragment anions O and CH3. Full article
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14 pages, 7889 KiB  
Article
Effects of the Mixing Protocol on the Self-Assembling Process of Water Soluble Porphyrins
by Maria Angela Castriciano, Sergio Cardillo, Roberto Zagami, Mariachiara Trapani, Andrea Romeo and Luigi Monsù Scolaro
Int. J. Mol. Sci. 2021, 22(2), 797; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020797 - 14 Jan 2021
Cited by 10 | Viewed by 2031
Abstract
The hierarchical self-assembling kinetics of the porphyrin 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (H2TPPS44−) into J-aggregates at high ionic strength under acidic conditions and eventually in the presence of an added chiral templating agent (tartrate) were investigated through UV/Vis spectroscopy, resonance [...] Read more.
The hierarchical self-assembling kinetics of the porphyrin 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (H2TPPS44−) into J-aggregates at high ionic strength under acidic conditions and eventually in the presence of an added chiral templating agent (tartrate) were investigated through UV/Vis spectroscopy, resonance light scattering, and circular dichroism (CD). The effect of changing the mixing order of the various components in the solution on the kinetic parameters and the expression of chirality on the final J-aggregates was evaluated. In this latter case, only when the chiral tartrate anion is premixed with the porphyrin, the resulting nano-architectures exhibit CD spectra that reflect the handedness of the chiral inducer. We discuss a general mechanistic scheme, with the involvement of ion pairs or dimers that offer an alternative pathway to the aggregation process. Full article
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14 pages, 2941 KiB  
Article
Adsorption of Malachite Green and Alizarin Red S Dyes Using Fe-BTC Metal Organic Framework as Adsorbent
by Giulia Rossella Delpiano, Davide Tocco, Luca Medda, Edmond Magner and Andrea Salis
Int. J. Mol. Sci. 2021, 22(2), 788; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020788 - 14 Jan 2021
Cited by 64 | Viewed by 5105
Abstract
Synthetic organic dyes are widely used in various industrial sectors but are also among the most harmful water pollutants. In the last decade, significant efforts have been made to develop improved materials for the removal of dyes from water, in particular, on nanostructured [...] Read more.
Synthetic organic dyes are widely used in various industrial sectors but are also among the most harmful water pollutants. In the last decade, significant efforts have been made to develop improved materials for the removal of dyes from water, in particular, on nanostructured adsorbent materials. Metal organic frameworks (MOFs) are an attractive class of hybrid nanostructured materials with an extremely wide range of applications including adsorption. In the present work, an iron-based Fe-BTC MOF, prepared according to a rapid, aqueous-based procedure, was used as an adsorbent for the removal of alizarin red S (ARS) and malachite green (MG) dyes from water. The synthesized material was characterized in detail, while the adsorption of the dyes was monitored by UV-Vis spectroscopy. An optimal adsorption pH of 4, likely due to the establishment of favorable interactions between dyes and Fe-BTC, was found. At this pH and at a temperature of 298 K, adsorption equilibrium was reached in less than 30 min following a pseudo-second order kinetics, with k″ of 4.29 × 10−3 and 3.98 × 10−2 g∙mg−1 min−1 for ARS and MG, respectively. The adsorption isotherm followed the Langmuir model with maximal adsorption capacities of 80 mg∙g−1 (ARS) and 177 mg∙g−1 (MG), and KL of 9.30·103 L∙mg−1 (ARS) and 51.56·103 L∙mg−1 (MG). Full article
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22 pages, 5345 KiB  
Article
Spectral Probe for Electron Transfer and Addition Reactions of Azide Radicals with Substituted Quinoxalin-2-Ones in Aqueous Solutions
by Konrad Skotnicki, Slawomir Ostrowski, Jan Cz. Dobrowolski, Julio R. De la Fuente, Alvaro Cañete and Krzysztof Bobrowski
Int. J. Mol. Sci. 2021, 22(2), 633; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22020633 - 10 Jan 2021
Cited by 3 | Viewed by 1917
Abstract
The azide radical (N3) is one of the most important one-electron oxidants used extensively in radiation chemistry studies involving molecules of biological significance. Generally, it was assumed that N3 reacts in aqueous solutions only by electron transfer. However, [...] Read more.
The azide radical (N3) is one of the most important one-electron oxidants used extensively in radiation chemistry studies involving molecules of biological significance. Generally, it was assumed that N3 reacts in aqueous solutions only by electron transfer. However, there were several reports indicating the possibility of N3 addition in aqueous solutions to organic compounds containing double bonds. The main purpose of this study was to find an experimental approach that allows a clear assignment of the nature of obtained products either to its one-electron oxidation or its addition products. Radiolysis of water provides a convenient source of one-electron oxidizing radicals characterized by a very broad range of reduction potentials. Two inorganic radicals (SO4●−, CO3●−) and Tl2+ ions with the reduction potentials higher, and one radical (SCN)2●− with the reduction potential slightly lower than the reduction potential of N3 were selected as dominant electron-acceptors. Transient absorption spectra formed in their reactions with a series of quinoxalin-2-one derivatives were confronted with absorption spectra formed from reactions of N3 with the same series of compounds. Cases, in which the absorption spectra formed in reactions involving N3 differ from the absorption spectra formed in the reactions involving other one-electron oxidants, strongly indicate that N3 is involved in the other reaction channel such as addition to double bonds. Moreover, it was shown that high-rate constants of reactions of N3 with quinoxalin-2-ones do not ultimately prove that they are electron transfer reactions. The optimized structures of the radical cations (7-R-3-MeQ)●+, radicals (7-R-3-MeQ) and N3 adducts at the C2 carbon atom in pyrazine moiety and their absorption spectra are reasonably well reproduced by density functional theory quantum mechanics calculations employing the ωB97XD functional combined with the Dunning’s aug-cc-pVTZ correlation-consistent polarized basis sets augmented with diffuse functions. Full article
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2020

Jump to: 2023, 2022, 2021

18 pages, 2588 KiB  
Review
Comparing Molecular Mechanisms in Solar NH3 Production and Relations with CO2 Reduction
by Domenico Mallamace, Georgia Papanikolaou, Siglinda Perathoner, Gabriele Centi and Paola Lanzafame
Int. J. Mol. Sci. 2021, 22(1), 139; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010139 - 25 Dec 2020
Cited by 12 | Viewed by 2841
Abstract
Molecular mechanisms for N2 fixation (solar NH3) and CO2 conversion to C2+ products in enzymatic conversion (nitrogenase), electrocatalysis, metal complexes and plasma catalysis are analyzed and compared. It is evidenced that differently from what is present in [...] Read more.
Molecular mechanisms for N2 fixation (solar NH3) and CO2 conversion to C2+ products in enzymatic conversion (nitrogenase), electrocatalysis, metal complexes and plasma catalysis are analyzed and compared. It is evidenced that differently from what is present in thermal and plasma catalysis, the electrocatalytic path requires not only the direct coordination and hydrogenation of undissociated N2 molecules, but it is necessary to realize features present in the nitrogenase mechanism. There is the need for (i) a multi-electron and -proton simultaneous transfer, not as sequential steps, (ii) forming bridging metal hydride species, (iii) generating intermediates stabilized by bridging multiple metal atoms and (iv) the capability of the same sites to be effective both in N2 fixation and in COx reduction to C2+ products. Only iron oxide/hydroxide stabilized at defective sites of nanocarbons was found to have these features. This comparison of the molecular mechanisms in solar NH3 production and CO2 reduction is proposed to be a source of inspiration to develop the next generation electrocatalysts to address the challenging transition to future sustainable energy and chemistry beyond fossil fuels. Full article
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14 pages, 10843 KiB  
Article
Role of Cobalt(III) Cationic Complexes in the Self-Assembling Process of a Water Soluble Porphyrin
by Nadia Manganaro, Roberto Zagami, Mariachiara Trapani, Maria Angela Castriciano, Andrea Romeo and Luigi Monsù Scolaro
Int. J. Mol. Sci. 2021, 22(1), 39; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms22010039 - 22 Dec 2020
Cited by 2 | Viewed by 2500
Abstract
Under moderate acidic conditions, the cationic (+3) complexes ions tris(1,10-phenanthroline)cobalt(III), [Co(phen)3]3+, and hexamminecobalt(III), [Co(NH3)6]3+, efficiently promote the self-assembling process of the diacid 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (H2TPPS4) into [...] Read more.
Under moderate acidic conditions, the cationic (+3) complexes ions tris(1,10-phenanthroline)cobalt(III), [Co(phen)3]3+, and hexamminecobalt(III), [Co(NH3)6]3+, efficiently promote the self-assembling process of the diacid 5,10,15,20-tetrakis(4-sulfonatophenyl)porphyrin (H2TPPS4) into J-aggregates. The growth kinetics have been analyzed according to a well-established autocatalytic model, in which the rate determining step is the initial formation of a nucleus containing m porphyrin units (in the range 2–3), followed by a stage whose rate constant kc evolves as a power of time. The observed catalytic rate constants and the extent of J-aggregation increase on increasing the metal complex concentration, with the phen complex being the less active. The UV/Vis extinction spectra display quite broad envelops at the J-band, especially for the amino-complex, suggesting that electronic dipolar coupling between chromophores is operative in these species. The occurrence of spontaneous symmetry breaking has been revealed by circular dichroism and the measured dissymmetry g-factor decreases on increasing the aggregation rates. The role of these metal complexes on the growth and stabilization of porphyrin nano-assemblies is discussed in terms of the different degree of hydrophilicity and hydrogen bonding ability of the ligands present in the coordination sphere around the metal center. Full article
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16 pages, 2947 KiB  
Article
Gold Nanoparticle Formation via X-ray Radiolysis Investigated with Time-Resolved X-ray Liquidography
by Hosung Ki, Sungjun Park, Seunghwan Eom, Jain Gu, Siin Kim, Changwon Kim, Chi Woo Ahn, Minseo Choi, Sena Ahn, Doo-Sik Ahn, Jungkweon Choi, Mu-Hyun Baik and Hyotcherl Ihee
Int. J. Mol. Sci. 2020, 21(19), 7125; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21197125 - 27 Sep 2020
Cited by 4 | Viewed by 2798
Abstract
We report the generation of gold nanoparticles (AuNPs) from the aqueous solution of chloro(2,2′,2″-terpyridine)gold(III) ion ([Au(tpy)Cl]2+) through X-ray radiolysis and optical excitation at a synchrotron. The original purpose of the experiment was to investigate the photoinduced structural changes of [Au(tpy)Cl]2+ [...] Read more.
We report the generation of gold nanoparticles (AuNPs) from the aqueous solution of chloro(2,2′,2″-terpyridine)gold(III) ion ([Au(tpy)Cl]2+) through X-ray radiolysis and optical excitation at a synchrotron. The original purpose of the experiment was to investigate the photoinduced structural changes of [Au(tpy)Cl]2+ upon 400 nm excitation using time-resolved X-ray liquidography (TRXL). Initially, the TRXL data did not show any signal that would suggest structural changes of the solute molecule, but after an induction time, the TRXL data started to show sharp peaks and valleys. In the early phase, AuNPs with two types of morphology, dendrites, and spheres, were formed by the reducing action of hydrated electrons generated by the X-ray radiolysis of water, thereby allowing the detection of TRXL data due to the laser-induced lattice expansion and relaxation of AuNPs. Along with the lattice expansion, the dendritic and spherical AuNPs were transformed into smaller, raspberry-shaped AuNPs of a relatively uniform size via ablation by the optical femtosecond laser pulse used for the TRXL experiment. Density functional theory calculations confirm that the reduction potential of the metal complex relative to the hydration potential of X-ray-generated electrons determines the facile AuNP formation observed for [Au(tpy)Cl]2+. Full article
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17 pages, 5901 KiB  
Article
The Product of Matrix Metalloproteinase Cleavage of Doxorubicin Conjugate for Anticancer Drug Delivery: Calorimetric, Spectroscopic, and Molecular Dynamics Studies on Peptide–Doxorubicin Binding to DNA
by Kamila Butowska, Krzysztof Żamojć, Mateusz Kogut, Witold Kozak, Dariusz Wyrzykowski, Wiesław Wiczk, Jacek Czub, Jacek Piosik and Janusz Rak
Int. J. Mol. Sci. 2020, 21(18), 6923; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21186923 - 21 Sep 2020
Cited by 7 | Viewed by 3735
Abstract
Matrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide–DOX, the product of the MMPs’ cleavage of carrier-linked [...] Read more.
Matrix metalloproteinases (MMPs) are extracellular matrix degradation factors, promoting cancer progression. Hence, they could provide an enzyme-assisted delivery of doxorubicin (DOX) in cancer treatment. In the current study, the intercalation process of DOX and tetrapeptide–DOX, the product of the MMPs’ cleavage of carrier-linked DOX, into dsDNA was investigated using stationary and time-resolved fluorescence spectroscopy, UV-Vis spectrophotometry and isothermal titration calorimetry (ITC). The molecular dynamics (MD) simulations on the same tetrapeptide–DOXDNA and DOXDNA systems were also performed. The undertaken studies indicate that DOX and tetrapeptide–DOX can effectively bond with dsDNA through the intercalation mode; however, tetrapeptide–DOX forms less stable complexes than free DOX. Moreover, the obtained results demonstrate that the differences in DNA affinity of both forms of DOX can be attributed to different intercalation modes. Tetrapeptide–DOX shows a preference to intercalate into DNA through the major groove, whereas DOX does it through the minor one. In summary, we can conclude that the tetrapeptide–DOX intercalation to DNA is significant and that even the lack of non-specific proteases releasing DOX from the tetrapeptide conjugate, the presence of which is suggested by the literature for the efficient release of DOX, should not prevent the cytostatic action of the anthracycline. Full article
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17 pages, 2858 KiB  
Article
5-(N-Trifluoromethylcarboxy)aminouracil as a Potential DNA Radiosensitizer and Its Radiochemical Conversion into N-Uracil-5-yloxamic Acid
by Paulina Spisz, Witold Kozak, Lidia Chomicz-Mańka, Samanta Makurat, Karina Falkiewicz, Artur Sikorski, Anna Czaja, Janusz Rak and Magdalena Zdrowowicz
Int. J. Mol. Sci. 2020, 21(17), 6352; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21176352 - 01 Sep 2020
Cited by 5 | Viewed by 2241
Abstract
Hypoxia—a hallmark of solid tumors—dramatically impairs radiotherapy, one of the most common anticancer modalities. The adverse effect of the low-oxygen state can be eliminated by the concomitant use of a hypoxic cell radiosensitizer. In the present paper, we show that 5-(N-trifluoromethylcarboxy) [...] Read more.
Hypoxia—a hallmark of solid tumors—dramatically impairs radiotherapy, one of the most common anticancer modalities. The adverse effect of the low-oxygen state can be eliminated by the concomitant use of a hypoxic cell radiosensitizer. In the present paper, we show that 5-(N-trifluoromethylcarboxy) aminouracil (CF3CONHU) can be considered as an effective radiosensitizer of DNA damage, working under hypoxia. The title compound was synthesized in the reaction of 5-aminouracil and trifluoroacetic anhydride in trifluoroacetic acid. Then, an aqueous and deoxygenated solution of the HPLC purified compound containing tert-butanol as a hydroxyl radical scavenger was irradiated with X-rays. Radiodegradation in a 26.67 ± 0.31% yield resulted in only one major product—N-uracil-5-yloxamic acid. The mechanism that is possibly responsible for the formation of the observed radioproduct has been elucidated with the use of DFT calculations. The cytotoxic test against the PC3 prostate cancer cell line and HDFa human dermal fibroblasts confirmed the low cytotoxicity of CF3CONHU. Finally, a clonogenic assay and flow cytometric analysis of histone H2A.X phosphorylation proved the radiosensitization in vitro. Full article
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23 pages, 4466 KiB  
Review
Point-of-Use Rapid Detection of SARS-CoV-2: Nanotechnology-Enabled Solutions for the COVID-19 Pandemic
by Navid Rabiee, Mojtaba Bagherzadeh, Amir Ghasemi, Hossein Zare, Sepideh Ahmadi, Yousef Fatahi, Rassoul Dinarvand, Mohammad Rabiee, Seeram Ramakrishna, Mohammadreza Shokouhimehr and Rajender S. Varma
Int. J. Mol. Sci. 2020, 21(14), 5126; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21145126 - 20 Jul 2020
Cited by 103 | Viewed by 10678
Abstract
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is [...] Read more.
Severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) caused the COVID-19 pandemic that has been spreading around the world since December 2019. More than 10 million affected cases and more than half a million deaths have been reported so far, while no vaccine is yet available as a treatment. Considering the global healthcare urgency, several techniques, including whole genome sequencing and computed tomography imaging have been employed for diagnosing infected people. Considerable efforts are also directed at detecting and preventing different modes of community transmission. Among them is the rapid detection of virus presence on different surfaces with which people may come in contact. Detection based on non-contact optical techniques is very helpful in managing the spread of the virus, and to aid in the disinfection of surfaces. Nanomaterial-based methods are proven suitable for rapid detection. Given the immense need for science led innovative solutions, this manuscript critically reviews recent literature to specifically illustrate nano-engineered effective and rapid solutions. In addition, all the different techniques are critically analyzed, compared, and contrasted to identify the most promising methods. Moreover, promising research ideas for high accuracy of detection in trace concentrations, via color change and light-sensitive nanostructures, to assist fingerprint techniques (to identify the virus at the contact surface of the gas and solid phase) are also presented. Full article
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19 pages, 3857 KiB  
Article
Femto- to Millisecond Time-Resolved Photodynamics of a Double-Functionalized Push–Pull Organic Linker: Potential Candidate for Optoelectronically Active MOFs
by Mario Gutiérrez, Lucie Duplouy-Armani, Lorenzo Angiolini, Mercedes Pintado-Sierra, Félix Sánchez and Abderrazzak Douhal
Int. J. Mol. Sci. 2020, 21(12), 4366; https://0-doi-org.brum.beds.ac.uk/10.3390/ijms21124366 - 19 Jun 2020
Cited by 4 | Viewed by 2663
Abstract
The design of improved organic linkers for the further engineering of smarter metal–organic framework (MOF) materials has become a paramount task for a wide number of material scientists. In this report, a luminescent double-functionalized push–pull (electron donor–acceptor) archetype organic molecule, dimethyl 4-amino-8-cyanonaphthalene-2,6-dicarboxylate (Me [...] Read more.
The design of improved organic linkers for the further engineering of smarter metal–organic framework (MOF) materials has become a paramount task for a wide number of material scientists. In this report, a luminescent double-functionalized push–pull (electron donor–acceptor) archetype organic molecule, dimethyl 4-amino-8-cyanonaphthalene-2,6-dicarboxylate (Me2CANADC), has been synthesized and characterized. The optical steady-state properties of Me2CANADC are strongly influenced by the surrounding environment as a direct consequence of its strong charge transfer (CT) character. The relaxation from its first electronically excited singlet state follows a double pathway: (1) on one side deactivating from its local excited (LE) state in the sub-picosecond or picosecond time domain, and (2) on the other side undergoing an ultrafast intramolecular charge transfer (ICT) reaction that is slowing down in viscous solvents. The deactivation to the ground state of these species with CT character is the origin of the Me2CANADC luminescence, and they present solvent-dependent lifetime values ranging from 8 to 18 ns. The slow photodynamics of Me2CANADC unveils the coexistence of a non-emissive triplet excited state and the formation of a long-lived charge separated state (2 µs). These observations highlight the promising optical properties of Me2CANADC linker, opening a window for the design of new functional MOFs with huge potential to be applied in the fields of luminescent sensing and optoelectronics. Full article
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