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Exclusive Papers of the Editorial Board Members (EBMs) of the Physical Chemistry Section of Molecules

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

Deadline for manuscript submissions: closed (15 December 2021) | Viewed by 62626

Special Issue Editor

Department of Pharmacy, Kobenhavns Universitet, Copenhagen, Denmark
Interests: biophysical characterization of nano-self-assemblies, cubosomes, hexosomes; nanodispersions of inverse non-lamellar liquid crystalline phases; drug and functional food soft self-assembled nanocarriers; lyotropic liquid crystalline phases; microemulsions
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Dear Colleagues,

This Special Issue of Molecules is dedicated to recent advances in physical chemistry research areas and comprises a diverse selection of exclusive papers of the Editorial Board Members (EBMs) of the Physical Chemistry Section. It focuses on highlighting recent interesting investigations conducted in the laboratories of our section’s EBMs and represents our young section as an attractive open-access publishing platform for physical chemistry research data.

Prof. Dr. Anan Yaghmur
Guest Editor

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Published Papers (20 papers)

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16 pages, 2374 KiB  
Article
Green Synthesis of Gold, Iron and Selenium Nanoparticles Using Phytoconstituents: Preliminary Evaluation of Antioxidant and Biocompatibility Potential
by Abeer Jabra Shnoudeh, Lana Qadumii, Malek Zihlif, Hamzeh J. Al-Ameer, Ruba Anwar Salou, Abdulmutalleb Yousef Jaber and Islam Hamad
Molecules 2022, 27(4), 1334; https://doi.org/10.3390/molecules27041334 - 16 Feb 2022
Cited by 11 | Viewed by 2740
Abstract
This study aimed at fabricating gold (Au), iron (Fe) and selenium (Se) nanoparticles (NPs) using various natural plant extracts from the Fertile Crescent area and evaluating their potential application as antioxidant and biocompatible agents to be used in the pharmaceutical field, especially in [...] Read more.
This study aimed at fabricating gold (Au), iron (Fe) and selenium (Se) nanoparticles (NPs) using various natural plant extracts from the Fertile Crescent area and evaluating their potential application as antioxidant and biocompatible agents to be used in the pharmaceutical field, especially in drug delivery. The Au-NPs were synthesized using Ephedra alata and Pistacia lentiscus extracts, whereas the Fe-NPs and Se-NPs were synthesized using peel, fruit and seed extracts of Punica granatum. The phytofabricated NPs were characterized by the UV-visible spectroscopy, scanning electron microscope, Fourier transform infrared spectroscopy, X-ray diffraction (XRD) and energy-dispersive X-ray (EDS) spectroscopy. Scanning electron microscope technique showed that the synthesized NPs surface was spherical, and the particle size analysis confirmed a particle size of 50 nm. The crystalline nature of the NPs was confirmed by the XRD analysis. All synthesized NPs were found to be biocompatible in the fibroblast and human erythroleukemic cell lines. Se-NPs showed a dose-dependent antitumor activity as evidenced from the experimental results with breast cancer (MCF-7) cells. A dose-dependent, free-radical scavenging effect of the Au-NPs and Se-NPs was observed in the DPPH (2,2-Diphenyl-1-picrylhydrazyl) assay, with the highest effect recorded for Au-NPs. Full article
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22 pages, 17237 KiB  
Article
Acid Dissociation Constants of the Benzimidazole Unit in the Polybenzimidazole Chain: Configuration Effects
by Liudmil Antonov, Susumu Kawauchi and Kei Shirata
Molecules 2022, 27(3), 1064; https://doi.org/10.3390/molecules27031064 - 04 Feb 2022
Cited by 1 | Viewed by 2222
Abstract
The acid dissociation constant of three benzimidazoles, namely 2,2′-bibenzo[d]imidazole, 2,5′-bibenzo[d]imidazole, and 5,5′-bibenzo[d]imidazole, have been investigated by means of density functional theory calculations in gas phase and in aqueous solution. The theoretical approach was validated by the comparing of predicted and experimentally determined p [...] Read more.
The acid dissociation constant of three benzimidazoles, namely 2,2′-bibenzo[d]imidazole, 2,5′-bibenzo[d]imidazole, and 5,5′-bibenzo[d]imidazole, have been investigated by means of density functional theory calculations in gas phase and in aqueous solution. The theoretical approach was validated by the comparing of predicted and experimentally determined pKa values in imidazole, benzimidazole, and 2-phenylbenzimidazole. From the studied compounds, 2,2′-bibenzo[d]imidazole was found to be the most acidic, which made it a valuable candidate as a material for polymer electrolyte membrane fuel cells. Full article
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11 pages, 2648 KiB  
Article
Gas-Phase Chemistry of 1,1,2,3,3,4,4-Heptafluorobut-1-ene Initiated by Chlorine Atoms
by Ramesh Sapkota and Paul Marshall
Molecules 2022, 27(3), 647; https://doi.org/10.3390/molecules27030647 - 19 Jan 2022
Cited by 1 | Viewed by 1814
Abstract
The possibility of mitigating climate change by switching to materials with low global warming potentials motivates a study of the spectroscopic and kinetic properties of a fluorinated olefin. The relative rate method was used to determine the rate constant for the reaction of [...] Read more.
The possibility of mitigating climate change by switching to materials with low global warming potentials motivates a study of the spectroscopic and kinetic properties of a fluorinated olefin. The relative rate method was used to determine the rate constant for the reaction of heptafluorobut-1-ene (CF2=CFCF2CF2H) with chlorine atoms in air. A mercury UV lamp was used to generate atomic chlorine, which initiated chemistry monitored by FTIR spectroscopy. Ethane was used as the reference compound for kinetic studies. Oxidation of heptafluorobut-1-ene initiated by a chlorine atom creates carbonyl difluoride (CF2=O) and 2,2,3,3 tetrafluoropropanoyl fluoride (O=CFCF2CF2H) as the major products. Anharmonic frequency calculations allowing for several low-energy conformations of 1,1,2,3,3,4,4 heptafluorobut-1-ene and 2,2,3,3 tetrafluoropropanoyl fluoride, based on density functional theory, are in good accord with measurements. The global warming potentials of these two molecules were calculated from the measured IR spectra and estimated atmospheric lifetimes and found to be small, less than 1. Full article
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12 pages, 3455 KiB  
Article
Gold Nanoclusters Grown on MoS2 Nanosheets by Pulsed Laser Deposition: An Enhanced Hydrogen Evolution Reaction
by Yuting Jing, Ruijing Wang, Qiang Wang and Xuefeng Wang
Molecules 2021, 26(24), 7503; https://doi.org/10.3390/molecules26247503 - 11 Dec 2021
Cited by 6 | Viewed by 2419
Abstract
Au nanoparticles were decorated on a 2H MoS2 surface to form an Au/MoS2 composite by pulse laser deposition. Improved HER activity of Au/MoS2 is evidenced by a positively shifted overpotential (−77 mV) at a current density of −10 mA cm [...] Read more.
Au nanoparticles were decorated on a 2H MoS2 surface to form an Au/MoS2 composite by pulse laser deposition. Improved HER activity of Au/MoS2 is evidenced by a positively shifted overpotential (−77 mV) at a current density of −10 mA cm−2 compared with pure MoS2 nanosheets. Experimental evidence shows that the interface between Au and MoS2 provides more sites to combine protons to form an active H atom. The density functional theory calculations found that new Au active sites on the Au and MoS2 interface with improved conductivity of the whole system are essential for enhancing HER activity of Au/MoS2. Full article
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27 pages, 737 KiB  
Article
Vibrational Energy Transfer in CO+N2 Collisions: A Database for V–V and V–T/R Quantum-Classical Rate Coefficients
by Qizhen Hong, Massimiliano Bartolomei, Cecilia Coletti, Andrea Lombardi, Quanhua Sun and Fernando Pirani
Molecules 2021, 26(23), 7152; https://doi.org/10.3390/molecules26237152 - 25 Nov 2021
Cited by 11 | Viewed by 2024
Abstract
Knowledge of energy exchange rate constants in inelastic collisions is critically required for accurate characterization and simulation of several processes in gaseous environments, including planetary atmospheres, plasma, combustion, etc. Determination of these rate constants requires accurate potential energy surfaces (PESs) that describe in [...] Read more.
Knowledge of energy exchange rate constants in inelastic collisions is critically required for accurate characterization and simulation of several processes in gaseous environments, including planetary atmospheres, plasma, combustion, etc. Determination of these rate constants requires accurate potential energy surfaces (PESs) that describe in detail the full interaction region space and the use of collision dynamics methods capable of including the most relevant quantum effects. In this work, we produce an extensive collection of vibration-to-vibration (V–V) and vibration-to-translation/rotation (V–T/R) energy transfer rate coefficients for collisions between CO and N2 molecules using a mixed quantum-classical method and a recently introduced (A. Lombardi, F. Pirani, M. Bartolomei, C. Coletti, and A. Laganà, Frontiers in chemistry, 7, 309 (2019)) analytical PES, critically revised to improve its performance against ab initio and experimental data of different sources. The present database gives a good agreement with available experimental values of V–V rate coefficients and covers an unprecedented number of transitions and a wide range of temperatures. Furthermore, this is the first database of V–T/R rate coefficients for the title collisions. These processes are shown to often be the most probable ones at high temperatures and/or for highly excited molecules, such conditions being relevant in the modeling of hypersonic flows, plasma, and aerospace applications. Full article
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13 pages, 1995 KiB  
Article
Enthalpies of Adduct Formation between Boron Trifluoride and Selected Organic Bases in Solution: Toward an Accurate Theoretical Entry to Lewis Basicity
by Jean-François Gal, Pierre-Charles Maria, Manuel Yáñez and Otilia Mó
Molecules 2021, 26(21), 6659; https://doi.org/10.3390/molecules26216659 - 04 Nov 2021
Cited by 7 | Viewed by 2345
Abstract
The Lewis basicity of selected organic bases, modeled by the enthalpies of adduct formation between gaseous BF3 and bases in dichloromethane (DCM) solution, is critically examined. Although experimental enthalpies for a large number of molecules have been reported in the literature, it [...] Read more.
The Lewis basicity of selected organic bases, modeled by the enthalpies of adduct formation between gaseous BF3 and bases in dichloromethane (DCM) solution, is critically examined. Although experimental enthalpies for a large number of molecules have been reported in the literature, it may be desirable to estimate missing or uncertain data for important Lewis bases. We decided to use high-level ab initio procedures, combined with a polarized continuum solvation model, in which the solvated species were the clusters formed by specific hydrogen bonding of DCM with the Lewis base and the Lewis base/BF3 adduct. This mode of interaction with DCM corresponds to a specific solvation model (SSM). The results essentially showed that the enthalpy of BF3 adduct formation in DCM solution was clearly influenced by specific interactions, with DCM acting as hydrogen-bonding donor (HBD) molecule in two ways: base/DCM and adduct/DCM, confirming that specific solvation is an important contribution to experimentally determined Lewis basicity scales. This analysis allowed us to conclude that there are reasons to suspect some gas-phase values to be in error by more than the stated experimental uncertainty. Some experimental values in DCM solution that were uncertain for identified reasons could be complemented by the computed values. Full article
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42 pages, 1128 KiB  
Article
Revision and Extension of a Generally Applicable Group-Additivity Method for the Calculation of the Standard Heat of Combustion and Formation of Organic Molecules
by Rudolf Naef and William E. Acree, Jr.
Molecules 2021, 26(20), 6101; https://doi.org/10.3390/molecules26206101 - 10 Oct 2021
Cited by 11 | Viewed by 2875
Abstract
The calculation of the heats of combustion ΔH°c and formation ΔH°f of organic molecules at standard conditions is presented using a commonly applicable computer algorithm based on the group-additivity method. This work is a continuation and extension of an earlier publication. [...] Read more.
The calculation of the heats of combustion ΔH°c and formation ΔH°f of organic molecules at standard conditions is presented using a commonly applicable computer algorithm based on the group-additivity method. This work is a continuation and extension of an earlier publication. The method rests on the complete breakdown of the molecules into their constituting atoms, these being further characterized by their immediate neighbor atoms. The group contributions are calculated by means of a fast Gauss–Seidel fitting calculus using the experimental data of 5030 molecules from literature. The applicability of this method has been tested by a subsequent ten-fold cross-validation procedure, which confirmed the extraordinary accuracy of the prediction of ΔH°c with a correlation coefficient R2 and a cross-validated correlation coefficient Q2 of 1, a standard deviation σ of 18.12 kJ/mol, a cross-validated standard deviation S of 19.16 kJ/mol, and a mean absolute deviation of 0.4%. The heat of formation ΔH°f has been calculated from ΔH°c using the standard enthalpies of combustion for the elements, yielding a correlation coefficient R2 for ΔH°f of 0.9979 and a corresponding standard deviation σ of 18.14 kJ/mol. Full article
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18 pages, 3144 KiB  
Article
Establishing a New Link between Fuzzy Logic, Neuroscience, and Quantum Mechanics through Bayesian Probability: Perspectives in Artificial Intelligence and Unconventional Computing
by Pier Luigi Gentili
Molecules 2021, 26(19), 5987; https://doi.org/10.3390/molecules26195987 - 02 Oct 2021
Cited by 30 | Viewed by 5968
Abstract
Human interaction with the world is dominated by uncertainty. Probability theory is a valuable tool to face such uncertainty. According to the Bayesian definition, probabilities are personal beliefs. Experimental evidence supports the notion that human behavior is highly consistent with Bayesian probabilistic inference [...] Read more.
Human interaction with the world is dominated by uncertainty. Probability theory is a valuable tool to face such uncertainty. According to the Bayesian definition, probabilities are personal beliefs. Experimental evidence supports the notion that human behavior is highly consistent with Bayesian probabilistic inference in both the sensory and motor and cognitive domain. All the higher-level psychophysical functions of our brain are believed to take the activities of interconnected and distributed networks of neurons in the neocortex as their physiological substrate. Neurons in the neocortex are organized in cortical columns that behave as fuzzy sets. Fuzzy sets theory has embraced uncertainty modeling when membership functions have been reinterpreted as possibility distributions. The terms of Bayes’ formula are conceivable as fuzzy sets and Bayes’ inference becomes a fuzzy inference. According to the QBism, quantum probabilities are also Bayesian. They are logical constructs rather than physical realities. It derives that the Born rule is nothing but a kind of Quantum Law of Total Probability. Wavefunctions and measurement operators are viewed epistemically. Both of them are similar to fuzzy sets. The new link that is established between fuzzy logic, neuroscience, and quantum mechanics through Bayesian probability could spark new ideas for the development of artificial intelligence and unconventional computing. Full article
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10 pages, 4313 KiB  
Communication
From Critical Point to Critical Point: The Two-States Model Describes Liquid Water Self-Diffusion from 623 to 126 K
by Carmelo Corsaro and Enza Fazio
Molecules 2021, 26(19), 5899; https://doi.org/10.3390/molecules26195899 - 29 Sep 2021
Cited by 2 | Viewed by 1793
Abstract
Liquid’s behaviour, when close to critical points, is of extreme importance both for fundamental research and industrial applications. A detailed knowledge of the structural–dynamical correlations in their proximity is still today a target to reach. Liquid water anomalies are ascribed to the presence [...] Read more.
Liquid’s behaviour, when close to critical points, is of extreme importance both for fundamental research and industrial applications. A detailed knowledge of the structural–dynamical correlations in their proximity is still today a target to reach. Liquid water anomalies are ascribed to the presence of a second liquid–liquid critical point, which seems to be located in the very deep supercooled regime, even below 200 K and at pressure around 2 kbar. In this work, the thermal behaviour of the self-diffusion coefficient for liquid water is analyzed, in terms of a two-states model, for the first time in a very wide thermal region (126 K < T < 623 K), including those of the two critical points. Further, the corresponding configurational entropy and isobaric-specific heat have been evaluated within the same interval. The two liquid states correspond to high and low-density water local structures that play a primary role on water dynamical behavior over 500 K. Full article
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11 pages, 1717 KiB  
Article
Seven Conformations of the Macrocycle Cyclododecanone Unveiled by Microwave Spectroscopy
by Ecaterina Burevschi and M. Eugenia Sanz
Molecules 2021, 26(17), 5162; https://doi.org/10.3390/molecules26175162 - 26 Aug 2021
Cited by 6 | Viewed by 2713
Abstract
The physicochemical properties and reactivity of macrocycles are critically shaped by their conformations. In this work, we have identified seven conformations of the macrocyclic ketone cyclododecanone using chirped-pulse Fourier transform microwave spectroscopy in combination with ab initio and density functional theory calculations. Cyclododecanone [...] Read more.
The physicochemical properties and reactivity of macrocycles are critically shaped by their conformations. In this work, we have identified seven conformations of the macrocyclic ketone cyclododecanone using chirped-pulse Fourier transform microwave spectroscopy in combination with ab initio and density functional theory calculations. Cyclododecanone is strongly biased towards adopting a square configuration of the heavy atom framework featuring three C–C bonds per side. The substitution and effective structures of this conformation have been determined through the observation of its 13C isotopologues. The minimisation of transannular interactions and, to a lesser extent, HCCH eclipsed configurations drive conformational preferences. Our results contribute to a better understanding of the intrinsic forces mediating structural choices in macrocycles. Full article
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7 pages, 2410 KiB  
Article
A QM/MM Study on the Initiation Reaction of Firefly Bioluminescence—Enzymatic Oxidation of Luciferin
by Mohan Yu and Yajun Liu
Molecules 2021, 26(14), 4222; https://doi.org/10.3390/molecules26144222 - 12 Jul 2021
Cited by 5 | Viewed by 2174
Abstract
Among all bioluminescent organisms, the firefly is the most famous, with a high luminescent efficiency of 41%, which is widely used in the fields of biotechnology, biomedicine and so on. The entire bioluminescence (BL) process involves a series of complicated in-vivo chemical reactions. [...] Read more.
Among all bioluminescent organisms, the firefly is the most famous, with a high luminescent efficiency of 41%, which is widely used in the fields of biotechnology, biomedicine and so on. The entire bioluminescence (BL) process involves a series of complicated in-vivo chemical reactions. The BL is initiated by the enzymatic oxidation of luciferin (LH2). However, the mechanism of the efficient spin-forbidden oxygenation is far from being totally understood. Via MD simulation and QM/MM calculations, this article describes the complete process of oxygenation in real protein. The oxygenation of luciferin is initiated by a single electron transfer from the trivalent anionic LH2 (L3−) to O2 to form 1[L•2−…O2•−]; the entire reaction is carried out along the ground-state potential energy surface to produce the dioxetanone (FDO) via three transition states and two intermediates. The low energy barriers of the oxygenation reaction and biradical annihilation involved in the reaction explain this spin-forbidden reaction with high efficiency. This study is helpful for understanding the BL initiation of fireflies and the other oxygen-dependent bioluminescent organisms. Full article
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20 pages, 4646 KiB  
Article
The Physico-Chemical Properties of Glipizide: New Findings
by Giovanna Bruni, Ines Ghione, Vittorio Berbenni, Andrea Cardini, Doretta Capsoni, Alessandro Girella, Chiara Milanese and Amedeo Marini
Molecules 2021, 26(11), 3142; https://doi.org/10.3390/molecules26113142 - 24 May 2021
Cited by 4 | Viewed by 5987
Abstract
The present work is a concrete example of how physico-chemical studies, if performed in depth, are crucial to understand the behavior of pharmaceutical solids and constitute a solid basis for the control of the reproducibility of the industrial batches. In particular, a deep [...] Read more.
The present work is a concrete example of how physico-chemical studies, if performed in depth, are crucial to understand the behavior of pharmaceutical solids and constitute a solid basis for the control of the reproducibility of the industrial batches. In particular, a deep study of the thermal behavior of glipizide, a hypoglycemic drug, was carried out with the aim of clarifying whether the recognition of its polymorphic forms can really be done on the basis of the endothermic peak that the literature studies attribute to the melting of the compound. A number of analytical techniques were used: thermal techniques (DSC, TGA), X-ray powder diffraction (XRPD), FT-IR spectroscopy and scanning electron microscopy (SEM). Great attention was paid to the experimental design and to the interpretation of the combined results obtained by all these techniques. We proved that the attribution of the endothermic peak shown by glipizide to its melting was actually wrong. The DSC peak is no doubt triggered by a decomposition process that involves gas evolution (cyclohexanamine and carbon dioxide) and formation of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which remains as decomposition residue. Thermal treatments properly designed and the combined use of DSC with FT-IR and XRPD led to identifying a new polymorphic form of 5-methyl-N-[2-(4-sulphamoylphenyl) ethyl] pyrazine-2-carboxamide, which is obtained by crystallization from the melt. Hence, our results put into evidence that the check of the polymorphic form of glipizide cannot be based on the temperature values of the DSC peak, since such a peak is due to a decomposition process whose Tonset value is strongly affected by the particle size. Kinetic studies of the decomposition process show the high stability of solid glipizide at room temperature. Full article
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12 pages, 12901 KiB  
Article
Tris(Butadiene) Compounds versus Butadiene Oligomerization in Second-Row Transition Metal Chemistry: Effects of Increased Ligand Fields
by Yi Zhao, Qun Chen, Mingyang He, Zhihui Zhang, Xuejun Feng, Yaoming Xie, Robert Bruce King and Henry F. Schaefer
Molecules 2021, 26(8), 2220; https://doi.org/10.3390/molecules26082220 - 12 Apr 2021
Viewed by 1708
Abstract
The geometries, energetics, and preferred spin states of the second-row transition metal tris(butadiene) complexes (C4H6)3M (M = Zr–Pd) and their isomers, including the experimentally known very stable molybdenum derivative (C4H6)3Mo, have [...] Read more.
The geometries, energetics, and preferred spin states of the second-row transition metal tris(butadiene) complexes (C4H6)3M (M = Zr–Pd) and their isomers, including the experimentally known very stable molybdenum derivative (C4H6)3Mo, have been examined by density functional theory. Such low-energy structures are found to have low-spin singlet and doublet spin states in contrast to the corresponding derivatives of the first-row transition metals. The three butadiene ligands in the lowest-energy (C4H6)3M structures of the late second-row transition metals couple to form a C12H18 ligand that binds to the central metal atom as a hexahapto ligand for M = Pd but as an octahapto ligand for M = Rh and Ru. However, the lowest-energy (C4H6)3M structures of the early transition metals have three separate tetrahapto butadiene ligands for M = Zr, Nb, and Mo or two tetrahapto butadiene ligands and one dihapto butadiene ligand for M = Tc. The low energy of the experimentally known singlet (C4H6)3Mo structure contrasts with the very high energy of its experimentally unknown singlet chromium (C4H6)3Cr analog relative to quintet (C12H18)Cr isomers with an open-chain C12H18 ligand. Full article
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13 pages, 2576 KiB  
Article
Photoproducts of the Photodynamic Therapy Agent Verteporfin Identified via Laser Interfaced Mass Spectrometry
by Chris Furlan, Jacob A. Berenbeim and Caroline E. H. Dessent
Molecules 2020, 25(22), 5280; https://doi.org/10.3390/molecules25225280 - 12 Nov 2020
Cited by 4 | Viewed by 2518
Abstract
Verteporfin, a free base benzoporphyrin derivative monoacid ring A, is a photosensitizing drug for photodynamic therapy (PDT) used in the treatment of the wet form of macular degeneration and activated by red light of 689 nm. Here, we present the first direct study [...] Read more.
Verteporfin, a free base benzoporphyrin derivative monoacid ring A, is a photosensitizing drug for photodynamic therapy (PDT) used in the treatment of the wet form of macular degeneration and activated by red light of 689 nm. Here, we present the first direct study of its photofragmentation channels in the gas phase, conducted using a laser interfaced mass spectrometer across a broad photoexcitation range from 250 to 790 nm. The photofragmentation channels are compared with the collision-induced dissociation (CID) products revealing similar dissociation pathways characterized by the loss of the carboxyl and ester groups. Complementary solution-phase photolysis experiments indicate that photobleaching occurs in verteporfin in acetonitrile; a notable conclusion, as photoinduced activity in Verteporfin was not thought to occur in homogenous solvent conditions. These results provide unique new information on the thermal break-down products and photoproducts of this light-triggered drug. Full article
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19 pages, 2359 KiB  
Article
Versatility of the Cyano Group in Intermolecular Interactions
by Steve Scheiner
Molecules 2020, 25(19), 4495; https://doi.org/10.3390/molecules25194495 - 30 Sep 2020
Cited by 8 | Viewed by 2862
Abstract
Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, [...] Read more.
Several cyano groups are added to an alkane, alkene, and alkyne group so as to construct a Lewis acid molecule with a positive region of electrostatic potential in the area adjoining these substituents. Although each individual cyano group produces only a weak π-hole, when two or more such groups are properly situated, they can pool their π-holes into one much more intense positive region that is located midway between them. A NH3 base is attracted to this site, where it forms a strong noncovalent bond to the Lewis acid, amounting to as much as 13.6 kcal/mol. The precise nature of the bonding varies a bit from one complex to the next but typically contains a tetrel bond to the C atoms of the cyano groups or the C atoms of the linkage connecting the C≡N substituents. The placement of the cyano groups on a cyclic system like cyclopropane or cyclobutane has a mild weakening effect upon the binding. Although F is comparable to C≡N in terms of electron-withdrawing power, the replacement of cyano by F substituents substantially weakens the binding with NH3. Full article
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13 pages, 3940 KiB  
Article
The Role of Structural Representation in the Performance of a Deep Neural Network for X-ray Spectroscopy
by Marwah M.M. Madkhali, Conor D. Rankine and Thomas J. Penfold
Molecules 2020, 25(11), 2715; https://doi.org/10.3390/molecules25112715 - 11 Jun 2020
Cited by 12 | Viewed by 3761
Abstract
An important consideration when developing a deep neural network (DNN) for the prediction of molecular properties is the representation of the chemical space. Herein we explore the effect of the representation on the performance of our DNN engineered to predict Fe K-edge X-ray [...] Read more.
An important consideration when developing a deep neural network (DNN) for the prediction of molecular properties is the representation of the chemical space. Herein we explore the effect of the representation on the performance of our DNN engineered to predict Fe K-edge X-ray absorption near-edge structure (XANES) spectra, and address the question: How important is the choice of representation for the local environment around an arbitrary Fe absorption site? Using two popular representations of chemical space—the Coulomb matrix (CM) and pair-distribution/radial distribution curve (RDC)—we investigate the effect that the choice of representation has on the performance of our DNN. While CM and RDC featurisation are demonstrably robust descriptors, it is possible to obtain a smaller mean squared error (MSE) between the target and estimated XANES spectra when using RDC featurisation, and converge to this state a) faster and b) using fewer data samples. This is advantageous for future extension of our DNN to other X-ray absorption edges, and for reoptimisation of our DNN to reproduce results from higher levels of theory. In the latter case, dataset sizes will be limited more strongly by the resource-intensive nature of the underlying theoretical calculations. Full article
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14 pages, 7341 KiB  
Article
Plasmon-Enhanced Controlled Drug Release from Ag-PMA Capsules
by Giulia Neri, Carmelo Corsaro and Enza Fazio
Molecules 2020, 25(9), 2267; https://doi.org/10.3390/molecules25092267 - 11 May 2020
Cited by 15 | Viewed by 3494
Abstract
Silver (Ag)-grafted PMA (poly-methacrylic acid, sodium salt) nanocomposite loaded with sorafenib tosylate (SFT), an anticancer drug, showed good capability as a drug carrier allowing on-demand control of the dose, timing and duration of the drug release by laser irradiation stimuli. In this study, [...] Read more.
Silver (Ag)-grafted PMA (poly-methacrylic acid, sodium salt) nanocomposite loaded with sorafenib tosylate (SFT), an anticancer drug, showed good capability as a drug carrier allowing on-demand control of the dose, timing and duration of the drug release by laser irradiation stimuli. In this study, the preparation of Ag-PMA capsules loaded with SFT by using sacrificial silica microparticles as templates was reported. A high drug loading (DL%) of ∼13% and encapsulation efficiency (EE%) of about 76% were obtained. The photo-release profiles were regulated via the adjustment of light wavelength and power intensity. A significant improvement of SFT release (14% vs. 21%) by comparing SFT-Ag-PMA capsules with Ag-PMA colloids under the same experimental conditions was observed. Moreover, an increase of drug release by up to 35% was reached by tuning the laser irradiation wavelength near to Ag nanoparticles’ surface plasmon resonance (SPR). These experimental results together with more economical use of the active component suggest the potentiality of SFT-Ag-PMA capsules as a smart drug delivery system. Full article
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18 pages, 2763 KiB  
Article
An Oxalate-Bridged Copper(II) Complex Combining Monodentate Benzoate, 2,2′-bipyridine and Aqua Ligands: Synthesis, Crystal Structure and Investigation of Magnetic Properties
by Francielli Sousa Santana, Matteo Briganti, Rafael A. Allão Cassaro, Federico Totti, Ronny Rocha Ribeiro, David L. Hughes, Giovana Gioppo Nunes and Dayane Mey Reis
Molecules 2020, 25(8), 1898; https://doi.org/10.3390/molecules25081898 - 20 Apr 2020
Cited by 7 | Viewed by 5023
Abstract
A dinuclear copper(II) complex of formula [{Cu(bipy)(bzt)(OH2)}2(μ-ox)] (1) (where bipy = 2,2′-bipyridine, bzt = benzoate and ox = oxalate) was synthesised and characterised by diffractometric (powder and single-crystal XRD) and thermogravimetric [...] Read more.
A dinuclear copper(II) complex of formula [{Cu(bipy)(bzt)(OH2)}2(μ-ox)] (1) (where bipy = 2,2′-bipyridine, bzt = benzoate and ox = oxalate) was synthesised and characterised by diffractometric (powder and single-crystal XRD) and thermogravimetric (TG/DTG) analyses, spectroscopic techniques (IR, Raman, electron paramagnetic resonance spectroscopy (EPR) and electronic spectroscopy), magnetic measurements and density functional theory (DFT) calculations. The analysis of the crystal structure revealed that the oxalate ligand is in bis(bidentate) coordination mode between two copper(II) centres. The other four positions of the coordination environment of the copper(II) ion are occupied by one water molecule, a bidentate bipy and a monodentate bzt ligand. An inversion centre located on the ox ligand generates the other half of the dinuclear complex. Intermolecular hydrogen bonds and π-π interactions are responsible for the organisation of the molecules in the solid state. Molar magnetic susceptibility and field dependence magnetisation studies evidenced a weak intramolecular–ferromagnetic interaction (J = +2.9 cm−1) between the metal ions. The sign and magnitude of the calculated J value by density functional theory (DFT) are in agreement with the experimental data. Full article
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14 pages, 1972 KiB  
Article
Non-Lamellar Liquid Crystalline Nanocarriers for Thymoquinone Encapsulation
by Anan Yaghmur, Boi Vi Tran and Seyed Moein Moghimi
Molecules 2020, 25(1), 16; https://doi.org/10.3390/molecules25010016 - 19 Dec 2019
Cited by 31 | Viewed by 3863
Abstract
Owing to their unique structural features, non-lamellar liquid crystalline nanoparticles comprising cubosomes and hexosomes are attracting increasing attention as versatile investigative drug carriers. Background: Depending on their physiochemical characteristics, drug molecules on entrapment can modulate and reorganize structural features of cubosomes and hexosomes. [...] Read more.
Owing to their unique structural features, non-lamellar liquid crystalline nanoparticles comprising cubosomes and hexosomes are attracting increasing attention as versatile investigative drug carriers. Background: Depending on their physiochemical characteristics, drug molecules on entrapment can modulate and reorganize structural features of cubosomes and hexosomes. Therefore, it is important to assess the effect of guest molecules on broader biophysical characteristics of non-lamellar liquid crystalline nanoparticles, since drug-induced architectural, morphological, and size modifications can affect the biological performance of cubosomes and hexosomes. Methods: We report on alterations in morphological, structural, and size characteristics of nanodispersions composed from binary mixtures of glycerol monooleate and vitamin E on thymoquinone (a molecule with wide therapeutic potentials) loading. Results: Thymoquinone loading was associated with a slight increase in the mean hydrodynamic nanoparticle size and led to structural transitions from an internal biphasic feature of coexisting inverse cubic Fd3m and hexagonal (H2) phases to an internal inverse cubic Fd3m phase (micellar cubosomes) or an internal inverse micellar (L2) phase (emulsified microemulsions, EMEs). We further report on the presence of “flower-like” vesicular populations in both native and drug-loaded nanodispersions. Conclusions: These nanodispersions have the potential to accommodate thymoquinone and may be considered as promising platforms for the development of thymoquinone nanomedicines. Full article
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Review

Jump to: Research

24 pages, 6220 KiB  
Review
Bonding Analysis of Compounds with Unusual Coordination of Carbon: Proposed Symmetric Systems with Six-Coordinate Carbon
by Carl Trindle, Zikri Altun and Erdi Ata Bleda
Molecules 2020, 25(17), 3937; https://doi.org/10.3390/molecules25173937 - 28 Aug 2020
Cited by 2 | Viewed by 2834
Abstract
The possibility of carbon tetravalence in geometries other than tetrahedral and of carbon hypervalence has been taken seriously since the 1970s. Computational modeling and subsequent experimental validation have established the existence of molecules with carbon atoms with planar tetravalence and as many as [...] Read more.
The possibility of carbon tetravalence in geometries other than tetrahedral and of carbon hypervalence has been taken seriously since the 1970s. Computational modeling and subsequent experimental validation have established the existence of molecules with carbon atoms with planar tetravalence and as many as six objects in carbon’s coordination sphere. In this work, we develop insight into the nature of bonding to carbon in these unusual environs as provided by Bader’s Atoms in Molecules (AIM) analysis of the electron density, along with the electron localization function (ELF) and the non-covalent index (NCI). We review several well-established systems (spiropentadiene dication, hexamethyl benzene dication, dimethanospiro[2.2]octaplane dication, and 1,8-dimethoxy-9-dimethoxyanthracene cation) and propose new D2d–symmetric variants of a hexacoordinated species. Full article
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