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Search Results (177)

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Keywords = protonation/deprotonation

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14 pages, 857 KB  
Article
Rapid and Effective Recovery of Oleanolic and Maslinic Acids from Olive Leaves Using SFE and pH-Zone Centrifugal Partition Chromatography
by Lemonia Antoniadi, Apostolis Angelis, Theodora Nikou, Dimitris Michailidis and Leandros A. Skaltsounis
Molecules 2025, 30(13), 2709; https://doi.org/10.3390/molecules30132709 - 24 Jun 2025
Viewed by 635
Abstract
Olive leaves, the main byproducts of olive cultivation, are characterized by a plethora of bioactive metabolites with significant nutritional value. Their main pentacyclic triterpenes, Oleanolic Acid (OA) and Maslinic Acid (MA), are two high added-value compounds with remarkable activities. This study aimed to [...] Read more.
Olive leaves, the main byproducts of olive cultivation, are characterized by a plethora of bioactive metabolites with significant nutritional value. Their main pentacyclic triterpenes, Oleanolic Acid (OA) and Maslinic Acid (MA), are two high added-value compounds with remarkable activities. This study aimed to develop an efficient methodology for extracting and purifying OA and MA, utilizing Supercritical Fluid Extraction (SFE) and Centrifugal Partition Chromatography (CPC)—two modern, scalable, and green techniques. A total of 21 g of olive leaves were subjected to SFE using supercritical CO2 and ethanol as co-solvent. The extraction employed a step gradient mode, starting with 100% CO2 and incrementally increasing ethanol (0–10% w/w) every 20 min. Fractions rich in OA and MA (500 mg) were further purified via CPC, utilizing pH zone refining to exploit the protonation and deprotonation properties of acidic triterpenes. The biphasic solvent system consisted of n-hexane, ethyl acetate, ethanol, and water (8:2:5:5 v/v/v/v), with trifluoroacetic acid added to the stationary phase and triethylamine added to the mobile phase. This two-step process yielded 89.5 mg of OA and 28.5 mg of MA with over 95% purity, as confirmed by HPLC-ELSD and 1H-NMR. Moreover, purified compounds and SFE fractions exhibited promising elastase and collagenase inhibition, highlighting them as dermocosmetic agents. Full article
(This article belongs to the Special Issue Supercritical Fluid Extraction of Natural Bioactive Compounds)
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35 pages, 16650 KB  
Article
Membrane Charge Effects on Solute Transport in Nanofiltration: Experiments and Molecular Dynamics Simulations
by Suwei Liu, Zihao Foo, John H. Lienhard, Sinan Keten and Richard M. Lueptow
Membranes 2025, 15(6), 184; https://doi.org/10.3390/membranes15060184 - 18 Jun 2025
Viewed by 1128
Abstract
Polyamide membranes, such as nanofiltration (NF) membranes, are widely used for water purification. However, the mechanisms of solute transport and solute rejection due to solute charge interactions with the membrane remain unclear at the molecular level. Here, we use molecular dynamics simulations to [...] Read more.
Polyamide membranes, such as nanofiltration (NF) membranes, are widely used for water purification. However, the mechanisms of solute transport and solute rejection due to solute charge interactions with the membrane remain unclear at the molecular level. Here, we use molecular dynamics simulations to examine the transport of single-solute feeds through charged nanofiltration membranes with different membrane charge concentrations of COO and NH+2 resulting from the deprotonation or protonation of polymeric end groups according to the pH level that the membrane experiences. The results show that Na+ and Cl solute ions are better rejected when the membrane has a higher concentration of negatively charged groups, corresponding to a higher pH, whereas CaCl2 is well rejected at all pH levels studied. These results are consistent with those of experiments performed at the same pH conditions as the simulation setup. Moreover, solute transport behavior depends on the membrane functional group distribution. When COO functional groups are concentrated at membrane feed surface, ion permeation into the membrane is reduced. Counter-ions tend to associate with charged functional groups while co-ions seem to pass by the charged groups more easily. In addition, steric effects play a role when ions of opposite charge cluster in pores of the membrane. This study reveals solute transport and rejection mechanisms related to membrane charge and provides insights into how membranes might be designed to achieve specific desired solute rejection. Full article
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14 pages, 4293 KB  
Article
Highly Stable Covalent Organic Framework for Palladium Removal from Nuclear Wastewater
by Wenchen Song, Junli Wang, Wentao Wang, Hui Wang and Yao Liu
Processes 2025, 13(6), 1784; https://doi.org/10.3390/pr13061784 - 5 Jun 2025
Viewed by 628
Abstract
The effective management of High-Level Liquid Waste (HLLW) is critical for environmental and human health protection. The presence of platinum group metals (PGMs) in HLLW, particularly their refractory nature due to their high melting points, complicates vitrification processes. This study presents a targeted [...] Read more.
The effective management of High-Level Liquid Waste (HLLW) is critical for environmental and human health protection. The presence of platinum group metals (PGMs) in HLLW, particularly their refractory nature due to their high melting points, complicates vitrification processes. This study presents a targeted adsorption strategy using COF-42 for Pd2+ sequestration in HLLW systems. The comprehensive characterization of COF-42 and its Pd-loaded counterpart (Pd@COF-42) via PXRD, FT-IR, TGA, XPS, and SEM confirms structural robustness and successful Pd2+ incorporation. Kinetic and thermodynamic analyses reveal pseudo-second-order adsorption behavior with a maximum capacity of 170.6 mg/g, highlighting the exceptional Pd2+ affinity. Systematic optimization identifies HNO3 concentration (≤3 M) and adsorbent dosage (≤30 mg) as critical parameters governing adsorption efficiency through protonation–deprotonation equilibria. Furthermore, COF-42 exhibits superior selectivity for Pd2+ over 13 competing metal ions and maintains ~80% adsorption efficiency after four regeneration cycles. These performance metrics originate from the synergistic interplay of (1) framework flexibility enabling adaptive Pd2+ coordination, (2) hierarchical porosity facilitating ion diffusion, and (3) dense –NH/–NH2 groups acting as electron-rich chelation sites. Full article
(This article belongs to the Section Environmental and Green Processes)
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28 pages, 3280 KB  
Article
Structural, Computational, and Biomolecular Interaction Study of Europium(III) and Iron(III) Complexes with Pyridoxal-Semicarbazone Ligand
by Violeta Jevtovic, Stefan Perendija, Aljazi Abdullah Alrashidi, Maha Awjan Alreshidi, Elham A. Alzahrani, Odeh A. O. Alshammari, Mostafa Aly Hussien, Jasmina Dimitrić Marković and Dušan Dimić
Int. J. Mol. Sci. 2025, 26(11), 5289; https://doi.org/10.3390/ijms26115289 - 30 May 2025
Viewed by 793
Abstract
The coordination chemistry, structural characterization, and biomolecular interactions of europium(III) and iron(III) complexes with the pyridoxal-semicarbazone (PLSC) ligand were thoroughly examined using experimental and computational approaches. Single-crystal X-ray diffraction revealed that the europium complex exhibits a nine-coordinate geometry with one protonated and one [...] Read more.
The coordination chemistry, structural characterization, and biomolecular interactions of europium(III) and iron(III) complexes with the pyridoxal-semicarbazone (PLSC) ligand were thoroughly examined using experimental and computational approaches. Single-crystal X-ray diffraction revealed that the europium complex exhibits a nine-coordinate geometry with one protonated and one deprotonated PLSC ligand and nitrato and aqua ligands. In contrast, the iron complex adopts a six-coordinate structure featuring a monoprotonated PLSC, two chlorido, and an aqua ligand. Hirshfeld surface analysis confirmed the significance of intermolecular contacts in stabilizing the crystal lattice. Theoretical geometry optimizations using DFT methods demonstrated excellent agreement with experimental bond lengths and angles, thereby validating the reliability of the chosen computational levels for subsequent quantum chemical analyses. Quantum Theory of Atoms in Molecules (QTAIM) analysis was employed to investigate the nature of metal–ligand interactions, with variations based on the identity of the donor atom and the ligand’s protonation state. The biological potential of the complexes was evaluated through spectrofluorimetric titration and molecular docking. Eu-PLSC displayed stronger binding to human serum albumin (HSA), while Fe-PLSC showed higher affinity for calf thymus DNA (CT-DNA), driven by intercalation. Thermodynamic data confirmed spontaneous and enthalpy-driven interactions. These findings support using PLSC-based metal complexes as promising candidates for future biomedical applications, particularly in drug delivery and DNA targeting. Full article
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14 pages, 3746 KB  
Article
Theoretical Insights into the Impact of Pyrrole and Imidazole Substituents on the BODIPY Chromophore
by Patrycja Piękoś, Paweł Lipkowski, Wim Dehaen, Robert Wieczorek and Aleksander Filarowski
Molecules 2025, 30(10), 2209; https://doi.org/10.3390/molecules30102209 - 18 May 2025
Viewed by 1442
Abstract
This paper concerns the in silico studies of the influence of heterocyclic substituents as well as their protonated and deprotonated forms on the spectral characteristics of BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes. Computational studies were carried out in order to reveal the most effective [...] Read more.
This paper concerns the in silico studies of the influence of heterocyclic substituents as well as their protonated and deprotonated forms on the spectral characteristics of BODIPY (4,4-difluoro-4-bora-3a,4a-diaza-s-indacene) dyes. Computational studies were carried out in order to reveal the most effective method of modeling of the spectral features of fluorescent BODIPY dyes. To perform these studies, the pyrrole and imidazole derivatives of BODIPY dyes were selected, and their spectral features were investigated with DFT and TD-DFT calculations. The calculations showed that the deprotonation of the substituents leads to a bathochromic shift of the calculated absorption wavelength, while the protonation (imidazole derivative) brings about a hypsochromic shift with respect to the neutral form of the dye. The calculated spectral characteristics, considering the influence of the solvent polarity (PCM model), were correlated with the ETN solvatochromic parameter. These correlations show that the increase in the solvent polarity causes a hypsochromic shift of the calculated absorption and emission wavelengths, whereas the bathochromic shift of the wavelengths is observed for the protonated form. Full article
(This article belongs to the Special Issue Quantum Chemical Calculations of Molecular Reaction Processes)
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23 pages, 12241 KB  
Article
Biodiesel Isomerization Using Sulfated Tin(IV) Oxide as a Superacid Catalyst to Improve Cold Flow Properties
by Yano Surya Pradana, I Gusti Bagus Ngurah Makertihartha, Tirto Prakoso, Tatang Hernas Soerawidjaja and Antonius Indarto
Technologies 2025, 13(5), 203; https://doi.org/10.3390/technologies13050203 - 16 May 2025
Cited by 1 | Viewed by 692
Abstract
The development of alternative energies has become a concern for all countries to ensure domestic energy supply and provide environmental friendliness. One of the providential alternative energies is biodiesel. Biodiesel, commonly stated as fatty acid alkyl ester (FAAE), is a liquid fuel intended [...] Read more.
The development of alternative energies has become a concern for all countries to ensure domestic energy supply and provide environmental friendliness. One of the providential alternative energies is biodiesel. Biodiesel, commonly stated as fatty acid alkyl ester (FAAE), is a liquid fuel intended to substitute petroleum diesel. Nevertheless, implementation of pure biodiesel is not recommended for conventional diesel engines. It holds poor values of cold flow properties, as the effect of high saturated FAAE content contributes to this constraint. Several processes have been proposed to enhance cold flow properties of biodiesel, but this work focuses on the skeletal isomerization process. This process rearranges the skeletal carbon chain of straight-chain FAAE into branched isomeric products to lower the melting point, related to the good cold flow behavior. This method specifically requires an acid catalyst to elevate the isomerization reaction rate. And then, sulfated tin(IV) oxide emerged as a solid superacid catalyst due to its superiority in acidity. The results of biodiesel isomerization over this catalyst and its modification with iron had not satisfied the expectation of high isomerization yield and significant CFP improvement. However, they emphasized that the skeletal isomers demonstrated minimum impact on biodiesel oxidation stability. They also affirmed the role of an acid catalyst in the reaction mechanism in terms of protonation, isomerization, and deprotonation. Furthermore, the metal promotion was theoretically necessary to boost the catalytic activity of this material. It initiated the dehydrogenation of linear hydrocarbon before protonation and terminated the isomerization by hydrogenating the branched carbon chain after deprotonation. Finally, the overall findings indicated promising prospects for further enhancement of catalyst performance and reusability. Full article
(This article belongs to the Topic Advances in Green Energy and Energy Derivatives)
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34 pages, 10030 KB  
Article
Seven New Irbesartan Salts: Significantly Improved Dissolution, Excellent Hygrothermal Stability, and Characteristic Supramolecular Synthons
by Junxiao Wang, Chuanhua Wu, Menglong Zhang, Lingli Hou, Wei Chen, Dingding Jing and Ying Bao
Crystals 2025, 15(4), 342; https://doi.org/10.3390/cryst15040342 - 4 Apr 2025
Viewed by 630
Abstract
Irbesartan (IRB) is a commonly used BCS Class II antihypertensive drug requiring dissolving capacity enhancement to address oral bioavailability limitations. In this work, seven new IRB salts were successfully synthesized, including one carboxylate (IRB-MAL) and six sulfonate salts (IRB-TOSA, IRB-BSA, IRB-4-CBSA, IRB-2, 5-CBSA, [...] Read more.
Irbesartan (IRB) is a commonly used BCS Class II antihypertensive drug requiring dissolving capacity enhancement to address oral bioavailability limitations. In this work, seven new IRB salts were successfully synthesized, including one carboxylate (IRB-MAL) and six sulfonate salts (IRB-TOSA, IRB-BSA, IRB-4-CBSA, IRB-2, 5-CBSA, IRB-MSA, and IRB-CPSA). Their vitro dissolution, intrinsic dissolution rates (IDRs), thermal/hygroscopic stability (via thermal analysis, dynamic vapor sorption, and accelerated stability tests), and phase transition process (monitored by in situ Raman spectroscopy) were evaluated. The results revealed that IRB-TOSA, IRB-MAL, IRB-BSA, IRB-4-CBSA, and IRB-MSA salts exhibited IDRs of 0.3194–0.7383 mg/(cm2·min), all significantly higher than IRB, with dissolution concentrations increased by 14.9–113.6%. IRB-TOSA and IRB-4-CBSA salts demonstrated excellent hydrothermal stability. Single crystal structure analysis confirmed proton transfer from coformers’ sulfonic/carboxylic acids (deprotonation site, H-out) to IRB’s diazaheterocycles (protonation site, H-in) in IRB salts. Six sulfonate salts exhibited NH-in–H···OH-out and Nnon-H-in–H···OH-out hydrogen bonds, with the former absent in IRB-MAL. Furthermore, supramolecular synthon studies revealed distinct hydrogen-bonding patterns (e.g., bifurcated bonds in 2,5-CBSA and CPSA salts) that correlate with moisture resistance. Quantitative analysis of IRB salts suggested hydrogen bond strengths may influence their melting points (decomposition temperatures). This study demonstrates that IRB salts hold promise for advanced pharmaceutical applications. Full article
(This article belongs to the Section Crystal Engineering)
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14 pages, 5324 KB  
Article
Electrocatalytic CO2 Reduction Coupled with Water Oxidation by bi- and Tetranuclear Copper Complexes Based on di-2-pyridyl Ketone Ligand
by Siyuan Yang, Tian Liu, Wenbo Huang, Chengwen Zhang and Mei Wang
Molecules 2025, 30(7), 1544; https://doi.org/10.3390/molecules30071544 - 31 Mar 2025
Viewed by 789
Abstract
In the field of sustainable energy conversion and storage technologies, copper-based complexes have become a research hotspot due to their efficient and stable catalytic performance. The development of bifunctional catalysts that can simplify catalytic steps, enhance efficiency, and reduce catalyst usage has become [...] Read more.
In the field of sustainable energy conversion and storage technologies, copper-based complexes have become a research hotspot due to their efficient and stable catalytic performance. The development of bifunctional catalysts that can simplify catalytic steps, enhance efficiency, and reduce catalyst usage has become an important research area. In this study, we successfully synthesized two copper complexes with different geometries utilizing di(2-pyridyl) ketone as the ligand, [CuII2L2Cl2]·0.5H2O (1) and [Cu4IIL4(OCH3)2](NO3)2 (2) (L = deprotonated methoxy-di-pyridin-2-yl-methanol), which can serve as homogeneous electrocatalysts for water oxidation and CO2 reduction simultaneously. The turnover frequency (TOF) of complexes 1 and 2 for electrocatalytic water oxidation are 7.23 s−1 and 0.31 s−1 under almost neutral condition (pH = 8.22), respectively. Meanwhile, the TOF of complexes 1 and 2 for the catalytic reduction of CO2 to CO are 4.27 s−1 and 8.9 s−1, respectively. In addition, both complexes remain essentially unchanged during the electrocatalytic water oxidation and electrocatalytic CO2 reduction processes, demonstrating good stability. Structural analysis reveals that the distinct catalytic efficiencies originate from their geometric configurations: the binuclear structure of complex 1 facilitates proton-coupled electron transfer during water oxidation, whereas the tetranuclear architecture of complex 2 enhances CO2 activation. Complexes 1 and 2 represent the first two copper molecular electrocatalysts capable of catalyzing both water oxidation and CO2 reduction. The findings in this work can open up new avenues for the advancement of artificial photosynthesis simulation and the development of bifunctional catalysts for water oxidation and CO2 reduction. Full article
(This article belongs to the Special Issue Design, Synthesis, and Catalytic Applications of Metal Complexes)
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15 pages, 2472 KB  
Article
Meta-Xylene-Based Diamines with Protected Benzyl Sites: Potential NCN Pincer Ligands with Tunable Steric Profiles
by Tamina Z. Kirsch, Toren Hynes, Jason D. Masuda and Saurabh S. Chitnis
Molecules 2025, 30(6), 1331; https://doi.org/10.3390/molecules30061331 - 16 Mar 2025
Viewed by 836
Abstract
Bulky NCN aryl-diamides featuring methyl groups in the benzyl positions were synthesized with the aim of creating a new class of meta-xylene-based trianionic pincer ligands where the common decomposition pathway of metal pincer complexes via C-H activation is prevented. Sterically demanding substituents [...] Read more.
Bulky NCN aryl-diamides featuring methyl groups in the benzyl positions were synthesized with the aim of creating a new class of meta-xylene-based trianionic pincer ligands where the common decomposition pathway of metal pincer complexes via C-H activation is prevented. Sterically demanding substituents on the ligands furthermore provide steric protection of the metal centre and can help prevent the dimerization of the complexes. While a double deprotonation of the ligands and the formation of a dilithium salt was straightforward, difficulties were encountered when attempting to deprotonate the ipso-CH proton on the central aryl ring to yield trianionic ligands. This stands in contrast to related pincer ligands without methyl groups in the benzylic positions. Experimental and theoretical investigations led to the conclusion that the challenges encountered when attempting the third deprotonation are likely caused by an interplay of increased electron density at the nitrogen atoms and steric hindrance. Both effects originate in the introduction of methyl groups in the benzylic positions, which make the targeted proton less accessible. These results provide further insight into the impact of methyl groups in the benzyl positions on both steric and electronic properties of NCN pincer ligands, which may find utility in coordination chemistry applications where metalation can be achieved by direct C-H activation rather than requiring triple deprotonation. Full article
(This article belongs to the Special Issue Advances in Main Group Chemistry)
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15 pages, 6972 KB  
Article
Preparation of Mechanically Strong Aramid Nanofiber Gel Film with Surprising Entanglements and Orientation Structure Through Aprotic Donor Solvent Exchange
by Zeyu Chen, Chuying Yu and Wenbin Zhong
Materials 2025, 18(5), 1142; https://doi.org/10.3390/ma18051142 - 4 Mar 2025
Viewed by 1102
Abstract
Aramid nanofiber (ANF), a nanoscale building block with a prominently complex structure, can be prepared by splitting poly(p-phenylene terephthalamide) (PPTA) fibers into negatively charged ANFs in a deprotonating manner in a DMSO/KOH solvent system, followed by a subsequent re-protonation process using a proton-donor [...] Read more.
Aramid nanofiber (ANF), a nanoscale building block with a prominently complex structure, can be prepared by splitting poly(p-phenylene terephthalamide) (PPTA) fibers into negatively charged ANFs in a deprotonating manner in a DMSO/KOH solvent system, followed by a subsequent re-protonation process using a proton-donor reagent. There are rare reports regarding the utilization of an aprotic donor reagent to convert deprotonated ANF dispersion into film or gel with a controllable structure and high mechanical properties. In this work, dichloromethane, as an anhydrous aprotic donor solvent, has been introduced into the deprotonated ANF dispersion to replace DMSO, containing PPTA molecules and hydroxyl ions, leading to the gelation of deprotonated ANF dispersions, forming a film (ANFDCM) possessing a surprisingly highly entangled and oriented structure, as proven by SEM results. Due to the attenuation of electrostatic repulsion in the dispersion, partially deprotonated ANFs intertwined and cross-linked through π–π conjugation among a large number of benzene rings in PPTA molecules. After treating ANFDCM with water for re-protonation, the as-prepared film (ANFDCM-W) exhibited high tensile strength (307.7 MPa) and toughness (74.7 MJ m−3). Full article
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13 pages, 1479 KB  
Article
Computation of the pKa Values of Gallic Acid and Its Anionic Forms in Aqueous Solution: A Self-Similar Transformation Approach for Accurate Proton Hydration Free Energy Estimation
by Marcin Molski
Molecules 2025, 30(3), 742; https://doi.org/10.3390/molecules30030742 - 6 Feb 2025
Cited by 1 | Viewed by 1503
Abstract
The Gibbs free energies of gallic acid (GA) and its anionic forms in aqueous solution were computed utilizing density functional theory (DFT) at the LSDA, M062X, B3LYP/QZVP levels, in conjunction with the SMD solvation model. The pKa values corresponding to the [...] Read more.
The Gibbs free energies of gallic acid (GA) and its anionic forms in aqueous solution were computed utilizing density functional theory (DFT) at the LSDA, M062X, B3LYP/QZVP levels, in conjunction with the SMD solvation model. The pKa values corresponding to the four-step deprotonation of GA were determined through a non-linear self-similar transformation expressed as, pKa = a⋅pKa(the)c which establishes a link between theoretical and experimental pKa values. This approach replaces the previously employed linear relationship, pKa = a⋅pKa(the) + b. The proposed model demonstrates high accuracy in reproducing the experimental pKa1 = 4.16 ± 0.02, pKa2 = 8.55 ± 0.01, pKa3 =11.40 ± 0.10, pKa4 =12.8 ± 0.40 values of GA, with a standard error (SE) of 0.045 and a mean absolute error (MAE) of 0.019 in pKa unit. Furthermore, it facilitates the precise determination of the Gibbs free energy of the proton hydration, yielding ∆G(H+)aq = 259.4272(75) [kcal mol−1]. This result conforms acceptably with the experimental value of ∆G(H+)aq = −259.5 [kcal mol−1]. Full article
(This article belongs to the Special Issue Computational Chemistry Insights into Molecular Interactions)
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21 pages, 2871 KB  
Article
Protolytic Reactions at Electrified TiO2 P25 Interface: Quantitative and Thermodynamic Characterization
by Etelka Tombácz, Dániel Nesztor, Márta Szekeres, Hans Lewandowski, Erwin Klumpp and Renáta Gerencsér-Berta
Molecules 2025, 30(3), 696; https://doi.org/10.3390/molecules30030696 - 5 Feb 2025
Cited by 1 | Viewed by 1470
Abstract
Protolytic reactions on the surface of a titania photocatalyst (TiO2 P25 containing chlorine impurities) were studied using potentiometric and calorimetric acid-base titration. The impurity was removed by either washing or heat treatment. The efficiency of purification was tested by chlorine (TOX) analysis [...] Read more.
Protolytic reactions on the surface of a titania photocatalyst (TiO2 P25 containing chlorine impurities) were studied using potentiometric and calorimetric acid-base titration. The impurity was removed by either washing or heat treatment. The efficiency of purification was tested by chlorine (TOX) analysis and acid-base titration. Common intersection points of −0.023 and −0.021 mmol/g were obtained for the original and 400 °C heat-treated samples, which are in good agreement with the measured TOX value of 28 mmol/kg. The point of zero charge of the purified sample was determined to be 6.50. Titration data were fitted to simulate protolytic reactions during isothermal calorimetric titrations of purified titania. The evolved heat was measured, and data points were corrected with the heat of mixing and neutralization. The quantity of charged surface species formed in each step of titration was calculated using the parameters from the constant capacitance model fit. The partial molar enthalpy values of the exothermic and endothermic processes of surface protonation (ΔHpr, −17.47 to −16.10 kJ/mol) and deprotonation (ΔHdepr, 32.53 to 27.08 kJ/mol) depend slightly on the ionic strength of suspensions. The average standard enthalpy of one proton transfer reaction is −23.54 ± 1.75 kJ/mol, which is consistent with the literature. Full article
(This article belongs to the Section Physical Chemistry)
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24 pages, 1331 KB  
Article
Acid-Base Equilibria for Tautomeric Heterocycles in the Gas-Phase: A Case of Uracil
by Ewa Daniela Raczyńska
Symmetry 2025, 17(2), 177; https://doi.org/10.3390/sym17020177 - 24 Jan 2025
Cited by 1 | Viewed by 1238
Abstract
Prototropic conversion (prototropy) for heterocyclic nucleobases was already signaled by Watson and Crick about seventy years ago as one of the reasons for nucleic acids mutations. This isomeric phenomenon has been investigated for neutral derivatives by means of both experimental and theoretical procedures, [...] Read more.
Prototropic conversion (prototropy) for heterocyclic nucleobases was already signaled by Watson and Crick about seventy years ago as one of the reasons for nucleic acids mutations. This isomeric phenomenon has been investigated for neutral derivatives by means of both experimental and theoretical procedures, and their favored tautomers discussed in numerous articles published in the last fifty years. Protonation/deprotonation reactions in the gas phase have also been studied using both quantum-chemical calculations and experimental techniques. Some thermochemical parameters of these processes have been documented. However, prototropy has not always been taken into account in protonation/deprotonation reactions. Most frequently, tautomeric heterocycles have been treated as simple polyfunctional compounds without possible intramolecular protontransfers. Taking into account the lack of data for the complete tautomeric mixtures, quantum-chemical investigations have been undertaken by us about twenty-five years ago for prototropic heterosystems. In this work, the pyrimidine base uracil (U) was chosen. It possesses two identical exo groups (=O/OH) at the 2- and 4-positions, two labile (tautomeric) protons, and five conjugated sites (N1, N3, C5, O7, and O8). Different types of isomerism, prototropy and OH-rotation, were considered for the neutral, protonated, and deprotonated forms. Using quantum-chemical methods, thermochemical stabilities of all possible tautomers-rotamers were examined in vacuo and the potential isomers selected. The selected isomeric mixtures for the neutral and ionic forms were applied for the determination of the thermochemical parameters in the four-step acid/base equilibria: B2− BH BH2 BH3+ BH42+, where BH2 indicates U. For each step, the microscopic (kinetic) and macroscopic (thermodynamic) acid/base parameters were estimated, and sites of the proton gain and proton loss examined. The similarities and differences between the acid/base equilibria for uracil and other pyrimidine nucleobases were discussed. Full article
(This article belongs to the Section Chemistry: Symmetry/Asymmetry)
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13 pages, 2060 KB  
Article
Enhancing HDAC Inhibitor Screening: Addressing Zinc Parameterization and Ligand Protonation in Docking Studies
by Rocco Buccheri, Alessandro Coco, Lorella Pasquinucci, Emanuele Amata, Agostino Marrazzo and Antonio Rescifina
Int. J. Mol. Sci. 2025, 26(2), 850; https://doi.org/10.3390/ijms26020850 - 20 Jan 2025
Cited by 2 | Viewed by 1915
Abstract
Precise binding free-energy predictions for ligands targeting metalloproteins, especially zinc-containing histone deacetylase (HDAC) enzymes, require specialized computational approaches due to the unique interactions at metal-binding sites. This study evaluates a docking algorithm optimized for zinc coordination to determine whether it could accurately differentiate [...] Read more.
Precise binding free-energy predictions for ligands targeting metalloproteins, especially zinc-containing histone deacetylase (HDAC) enzymes, require specialized computational approaches due to the unique interactions at metal-binding sites. This study evaluates a docking algorithm optimized for zinc coordination to determine whether it could accurately differentiate between protonated and deprotonated states of hydroxamic acid ligands, a key functional group in HDAC inhibitors (HDACi). By systematically analyzing both protonation states, we sought to identify which state produces docking poses and binding energy estimates most closely aligned with experimental values. The docking algorithm was applied across HDAC 2, 4, and 8, comparing protonated and deprotonated ligand correlations to experimental data. The results demonstrate that the deprotonated state consistently yielded stronger correlations with experimental data, with R2 values for deprotonated ligands outperforming protonated counterparts in all HDAC targets (average R2 = 0.80 compared to the protonated form where R2 = 0.67). These findings emphasize the significance of proper ligand protonation in molecular docking studies of zinc-binding enzymes, particularly HDACs, and suggest that deprotonation enhances predictive accuracy. The study’s methodology provides a robust foundation for improved virtual screening protocols to evaluate large ligand libraries efficiently. This approach supports the streamlined discovery of high-affinity, zinc-binding HDACi, advancing therapeutic exploration of metalloprotein targets. A comprehensive, step-by-step tutorial is provided to facilitate a thorough understanding of the methodology and enable reproducibility of the results. Full article
(This article belongs to the Collection Feature Papers in Molecular Informatics)
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14 pages, 3063 KB  
Article
Evaluation of Nanomagnetite–Biochar Composite for BTA Removal
by Carolina Guida, Nathaniel Findling, Valérie Magnin, Fabienne Favre Boivin and Laurent Charlet
Nanomaterials 2025, 15(2), 115; https://doi.org/10.3390/nano15020115 - 14 Jan 2025
Viewed by 1009
Abstract
In this study, the removal of benzotriazole (BTA), a pervasive aquatic contaminant widely used for its anti-corrosion, UV-stabilizing, and antioxidant properties, by nanomagnetite, biochar, and nanomagnetite–biochar composite is investigated. Nanomagnetite and nanomagnetite–biochar composite were synthesized under anoxic conditions and tested for BTA removal [...] Read more.
In this study, the removal of benzotriazole (BTA), a pervasive aquatic contaminant widely used for its anti-corrosion, UV-stabilizing, and antioxidant properties, by nanomagnetite, biochar, and nanomagnetite–biochar composite is investigated. Nanomagnetite and nanomagnetite–biochar composite were synthesized under anoxic conditions and tested for BTA removal efficiency at neutral pH under both oxic and anoxic conditions at different time scales. Within the short time scale (up to 8 h), the removal of BTA by nanomagnetite–biochar composite was shown to be due to BTA deprotonation by the nanomagnetite surface. Through proton liberation, Fe²⁺ is released in accordance with the reaction Fe₃O₄ + 2H⁺ → Fe₂O₃ + Fe²⁺ + H₂O, which likely influences BTA complexation and its possible redox degradation. On the longer time scale, biochar achieved higher removal efficiency: 50% BTA removed within 48 h, due to formation of a ternary complex with surface Ca2+ ions, or 75% BTA removed after HCl biochar acid wash followed by Ca2+ surface saturation. As BTA presents significant environmental risks due to its extensive industrial applications, the present study offers critical insights into the mechanisms of BTA removal by nanomagnetite–biochar composite, and highlights the potential of such materials for water treatment applications. Full article
(This article belongs to the Section Environmental Nanoscience and Nanotechnology)
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