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Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results—2nd Edition

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

Deadline for manuscript submissions: 30 November 2024 | Viewed by 9876

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Department of Civil and Environmental Engineering, Università degli Studi di Perugia, Perugia, Italy
Interests: computational chemistry; theoretical chemistry Ab initio calculations; density functional calculations; astrochemistry astrobiology; catalysis; atmospheric chemistry
Special Issues, Collections and Topics in MDPI journals

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Guest Editor
Department of Civil & Environmental Engineering, Universita degli Studi di Perugia, Perugia, Italy
Interests: dynamics of elementary chemical processes (combustion and atmospheric chemistry); production and characterization of excited and ionic species relevant in planetary ionospheres and astrochemistry; double photoionization of chiral molecules; photo-degradation mechanisms of biomolecules exposed to ionizing radiation; photocatalytic efficiency of TiO2 powders in the degradation of atmospheric pollutants species; analytical and environmental chemistry; environmental radioactivity; green fuels production by carbon dioxide hydrogenation reaction with and without solid phase catalysis; chemical characterization of officinal plants and fruits (nutritional and pharmacological properties)
Special Issues, Collections and Topics in MDPI journals

Special Issue Information

Dear Colleagues,

This Special Issue aims to collect papers investigating recent theoretical and experimental efforts exploiting new insights, methods, and techniques applied to the study of the microscopic dynamics of elementary chemical reactions. In particular, an overview of the most powerful calculation methods currently available will be published for the identification and characterization of the nature and strength of intermolecular interactions able to describe chemical reactivity. Topics include reactions between neutral species of interest in combustion, including ion–molecule reactions and those involving excited and radical species, from processes relevant for surface physics to the fundamentals of gas-phase stereodynamics, up to the physical chemistry of plasmas, planetary ionospheres, and astrochemistry, as well as complex systems of biochemical interest.

Prof. Dr. Marzio Rosi
Prof. Dr. Stefano Falcinelli
Guest Editors

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Keywords

  • potential energy surface
  • molecular reaction dynamics
  • theoretical chemistry ab initio calculations
  • combustion
  • astrochemistry
  • astrobiology
  • atmospheric chemistry
  • catalysis
  • calculation of kinetic parameters
  • modeling dust and icy grain structures and properties
  • modeling processes at the grain surfaces

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Published Papers (12 papers)

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Research

17 pages, 5422 KiB  
Article
Ab Initio Neural Network Potential Energy Surface and Quantum Dynamics Calculations on Na(2S) + H2 → NaH + H Reaction
by Siwen Liu, Huiying Cheng, Furong Cao, Jingchang Sun and Zijiang Yang
Molecules 2024, 29(20), 4871; https://doi.org/10.3390/molecules29204871 - 14 Oct 2024
Viewed by 512
Abstract
The collisions between Na atoms and H2 molecules are of great significance in the field of chemical reaction dynamics, but the corresponding dynamics results of ground-state reactions have not been reported experimentally or theoretically. Herein, a global and high-precision potential energy surface [...] Read more.
The collisions between Na atoms and H2 molecules are of great significance in the field of chemical reaction dynamics, but the corresponding dynamics results of ground-state reactions have not been reported experimentally or theoretically. Herein, a global and high-precision potential energy surface (PES) of NaH2 (12A′) is constructed by the neural network model based on 21,873 high-level ab initio points. On the newly constructed PES, the quantum dynamics calculations on the Na(2S) + H2(v0 = 0, j0 = 0) → NaH + H reaction are carried out using the time-dependent wave packet method to study the microscopic reaction mechanism at the state-to-state level. The calculated results show that the low-vibrational products are mainly formed by the dissociation of the triatomic complex; whereas, the direct reaction process dominates the generation of the products with high-vibrational states. The reaction generally follows the direct H-abstraction process, and there is also the short-lived complex-forming mechanism that occurs when the collision energy exceeds the reaction threshold slightly. The PES could be used to further study the stereodynamics effects of isotope substitution and rovibrational excitations on the title reaction, and the presented dynamics data would provide an important reference on the corresponding experimental research at a higher level. Full article
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17 pages, 6266 KiB  
Article
Mono- and Binuclear Complexes in a Centrifuge-Less Cloud-Point Extraction System for the Spectrophotometric Determination of Zinc(II)
by Kiril B. Gavazov, Petya V. Racheva, Antoaneta D. Saravanska, Fatma Genc and Vassil B. Delchev
Molecules 2024, 29(18), 4511; https://doi.org/10.3390/molecules29184511 - 23 Sep 2024
Viewed by 431
Abstract
The hydrophobic reagent 6-hexyl-4-(2-thiazolylazo)resorcinol (HTAR) was investigated as part of a cloud-point extraction (CPE) system for the spectrophotometric determination of Zn(II). In the system, complexes with different stoichiometries, including 1:1 and 2:2 (Zn:HTAR), are formed. Their ground-state equilibrium geometries were optimized at the [...] Read more.
The hydrophobic reagent 6-hexyl-4-(2-thiazolylazo)resorcinol (HTAR) was investigated as part of a cloud-point extraction (CPE) system for the spectrophotometric determination of Zn(II). In the system, complexes with different stoichiometries, including 1:1 and 2:2 (Zn:HTAR), are formed. Their ground-state equilibrium geometries were optimized at the B3LYP/6-31G level of theory. The obtained structures were then used to calculate vertical excitation energies in order to generate theoretical UV/Vis absorption spectra. The comparison between theoretical and experimental spectra demonstrated that, under optimal conditions, a binuclear complex containing oxygen-bridging atoms is the dominant species. The absorbance was found to be linearly dependent on the concentration of Zn(II) within the range of 15.7 to 209 ng mL−1 (R2 = 0.9996). The fraction extracted (%E), logarithm of the conditional extraction constant (log Kex), and molar absorption coefficient (ε) at λmax = 553 nm were calculated to be 98.3%, 15.9, and 4.47 × 105 L mol−1 cm−1, respectively. The method developed is characterized by simplicity, convenience, profitability, sensitivity, and ecological friendliness. It has been successfully applied to the analysis of pharmaceutical and industrial samples. Full article
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13 pages, 1145 KiB  
Article
On the Simulation of Photoreactions Using Restricted Open-Shell Kohn–Sham Theory
by Ralf Büchel, Luis Álvarez, Jan Grage, Dominykas Maniscalco and Irmgard Frank
Molecules 2024, 29(18), 4509; https://doi.org/10.3390/molecules29184509 - 23 Sep 2024
Viewed by 578
Abstract
It is a well-established standard to describe ground-state chemical reactions at an ab initio level of multi-electron theory. Fast reactions can be directly simulated. The most widely used approach is density functional theory for the electronic structure in combination with molecular dynamics for [...] Read more.
It is a well-established standard to describe ground-state chemical reactions at an ab initio level of multi-electron theory. Fast reactions can be directly simulated. The most widely used approach is density functional theory for the electronic structure in combination with molecular dynamics for the nuclear motion. This approach is known as ab initio molecular dynamics. In contrast, the simulation of excited-state reactions at this level of theory is significantly more difficult. It turns out that the self-consistent solution of the Kohn–Sham equations is not easily reached in excited-state simulations. The first program that solved this problem was the Car–Parrinello molecular dynamics code, using restricted open-shell Kohn–Sham theory. Meanwhile, there are alternatives, most prominently the Q-Chem code, which widens the range of applications. The present study investigates the suitability of both codes for the molecular dynamics simulation of excited-state motion and presents applications to photoreactions. Full article
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18 pages, 6880 KiB  
Article
Why Does the Optimal Tuning Method of the Range Separation Parameter of a Long-Range Corrected Density Functional Fail in Intramolecular Charge Transfer Excitation Calculations?
by Han-Seok Bae, Dae-Hwan Ahn and Jong-Won Song
Molecules 2024, 29(18), 4423; https://doi.org/10.3390/molecules29184423 - 18 Sep 2024
Viewed by 412
Abstract
We performed intra- and intermolecular charge transfer (CT) excitation energy calculations of (a) conjugated carbon chain [H2N–(CH=CH)n–X] and (b) its equidistant H2NH∙∙∙HX (n = 2~8) with various electron acceptors (X = NH2, [...] Read more.
We performed intra- and intermolecular charge transfer (CT) excitation energy calculations of (a) conjugated carbon chain [H2N–(CH=CH)n–X] and (b) its equidistant H2NH∙∙∙HX (n = 2~8) with various electron acceptors (X = NH2, OH, Cl, CHO, CN, and NO2) using EOM-CCSD, time-dependent (TD) Hartree–Fock (HF) and various density functional theory (DFT) functionals, such as BLYP, B3LYP, long-range corrected (LC) DFT, and LC-DFT with an optimally tuned (OT) range separation parameter (µ) using Koopman’s theorem to investigate the effect of the electron-withdrawing (or -donating) strength of end-capped functional group (X) and CT distance (R) on intra- and intermolecular CT excitation energies. As the electron-withdrawing strength of X increases, both intra- and intermolecular CT excitation energies tend to decrease, since energy gaps between orbitals corresponding to CT excitations (e.g., HOMO and LUMO) decrease. However, the effect of the electron-withdrawing group on intramolecular CT excitation energy is negligible (at most 0.5 eV). OT-LC-DFT shows accurate intermolecular CT excitation energy, but worse results in intramolecular CT excitation energy than LC-DFT with the default µ value (0.47). Therefore, we conclude that the optimal tuning method is not effective in predicting intramolecular CT excitation energy. While intermolecular CT excitation energy has excitonic binding energy with asymptotic behavior to CT distance that is not affected by the choice of range separation parameter, intramolecular CT excitation energy is affected by orbital relaxation energy, which strongly depends on the choice of range separation parameter, which makes the OT method of range separation parameter ineffective in predicting intramolecular CT excitation energy as well as local excitation with high accuracy. Full article
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17 pages, 3647 KiB  
Article
Profoxydim in Focus: A Structural Examination of Herbicide Behavior in Gas and Aqueous Phases
by María Cobos-Escudero, Paula Pla, Álvaro Cervantes-Diaz, José Luis Alonso-Prados, Pilar Sandín-España, Manuel Alcamí and Al Mokhtar Lamsabhi
Molecules 2024, 29(18), 4371; https://doi.org/10.3390/molecules29184371 - 14 Sep 2024
Viewed by 591
Abstract
This study investigates the chemical structure of profoxydim, focusing on its E–isomer, the main commercial form. The research aimed to determine the predominant tautomeric forms under various environmental conditions. Using proton and carbon–13 NMR spectroscopy alongside theoretical modeling, we examined tautomers and their [...] Read more.
This study investigates the chemical structure of profoxydim, focusing on its E–isomer, the main commercial form. The research aimed to determine the predominant tautomeric forms under various environmental conditions. Using proton and carbon–13 NMR spectroscopy alongside theoretical modeling, we examined tautomers and their conformers in different solvents (MeOD, DMSO, CDCl3, benzene) to mimic gas and aqueous phases. The findings reveal that the enolic form dominates in the gas phase, while the ketonic form prevails in aqueous environments, providing key insights into the herbicide’s environmental behavior. We also observed an isomeric transition from E to Z under acidic conditions, which could affect profoxydim’s reactivity in natural environments. The theoretical calculations indicated that in acidic conditions, the E and Z forms are nearly degenerate, with the E form remaining dominant in neutral environments. Additionally, QSAR models assessed the toxicity of various tautomers, revealing significant differences that could impact bioactivity and environmental fate. This research offers crucial insights into the structural dynamics of profoxydim, contributing to cyclohexanedione chemistry and the development of more effective herbicides. Full article
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18 pages, 2206 KiB  
Article
Effects of Surface Charge Distribution and Electrolyte Ions on the Nonlinear Spectra of Model Solid–Water Interfaces
by Konstantin S. Smirnov
Molecules 2024, 29(16), 3758; https://doi.org/10.3390/molecules29163758 - 8 Aug 2024
Viewed by 848
Abstract
Molecular dynamics simulations of model charged solid/water interfaces were carried out to provide insight about the relationship between the second-order nonlinear susceptibility χ(2) and the structure of the interfacial water layer. The results of the calculations reveal that the density [...] Read more.
Molecular dynamics simulations of model charged solid/water interfaces were carried out to provide insight about the relationship between the second-order nonlinear susceptibility χ(2) and the structure of the interfacial water layer. The results of the calculations reveal that the density fluctuations of water extend to about 12 Å from the surface regardless of the system, while the orientational ordering of molecules is long-ranged and is sensitive to the presence of electrolytes. The charge localization on the surface was found to affect only the high-frequency part of the Im[χ(2)] spectrum, and the addition of salt has very little effect on the spectrum of the first water layer. For solid/neat water interfaces, the spectroscopically active part of the liquid phase has a thickness largely exceeding the region of density fluctuations, and this long-ranged nonlinear activity is mediated by the electric field of the molecules. The electrolyte ions and their hydration shells act in a destructive way on the molecular field. This effect, combined with the screening of the surface charge by ions, drastically reduces the thickness of the spectroscopic diffuse layer. There is an electrolyte concentration at which the nonlinear response of the diffuse layer is suppressed and the χ(2) spectrum of the interface essentially coincides with that of the first water layer. Full article
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11 pages, 2616 KiB  
Article
Do Molecules Tunnel through Nanoporous Graphene?
by Liudmyla Barabanova and Alper Buldum
Molecules 2024, 29(14), 3306; https://doi.org/10.3390/molecules29143306 - 13 Jul 2024
Viewed by 712
Abstract
The molecular transport and quantum tunneling of H2 and H2O molecules through nanoporous graphene is studied using computational modeling and first-principles density functional theory. It is demonstrated that molecules with sufficiently high kinetic energies can tunnel through nanopores. It is [...] Read more.
The molecular transport and quantum tunneling of H2 and H2O molecules through nanoporous graphene is studied using computational modeling and first-principles density functional theory. It is demonstrated that molecules with sufficiently high kinetic energies can tunnel through nanopores. It is also demonstrated that molecules can be trapped in front of a nanopore or behind it. These investigations help us learn the behavior of molecules in and around the nanopores of graphene. They also help us learn the fundamentals of molecular tunneling. We believe nanoporous graphene can play important roles for gas separation and nanofiltration. Full article
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18 pages, 4418 KiB  
Article
Unpredictable Dynamic Behaviour of Ruthenium Chelate Pyrrole Derivatives
by Giacomo Drius, Riccardo Tarroni, Matteo Birchmeier, Carola Parolin, Carla Boga, Magda Monari and Silvia Bordoni
Molecules 2024, 29(13), 3068; https://doi.org/10.3390/molecules29133068 - 27 Jun 2024
Viewed by 935
Abstract
Reaction of [Ru(H)2(CO)(PPh3)3] 1 with an equimolar amount of pyrrole-2-carboxylic acid (H2L1) leads to the homoleptic chelate derivative k2(O,O)-[RuH(CO)(HL1)(PPh3)2] 2. Prolonged acetonitrile refluxing [...] Read more.
Reaction of [Ru(H)2(CO)(PPh3)3] 1 with an equimolar amount of pyrrole-2-carboxylic acid (H2L1) leads to the homoleptic chelate derivative k2(O,O)-[RuH(CO)(HL1)(PPh3)2] 2. Prolonged acetonitrile refluxing promotes an unusual k2(O,O)- → k2(N,O)- dynamic chelate conversion, forming a neutral, stable, air- and moisture- insensitive, solvento-species k2(N,O)-[Ru(MeCN)(CO)(L1)(PPh3)2] 3. Analogously, reaction of 1 with the pyrrole-2-carboxyaldehyde (HL2) affords k2(N,O)-[RuH(CO)(HL2)(PPh3)2] 4, 5, as a couple of functional isomers. Optimized reaction conditions such as temperature and solvent polarity allow the isolation of dominant configurations. Structure 5 is a pyrrolide Ru-carbaldehyde, obtained from cyclization of the pendant CHO function, whereas species 4 can be viewed as an ethanoyl-conjugated Ru-pyrrole. Derivatives 35 were characterized by single crystal X-ray diffraction, ESI-Ms, IR, and NMR spectroscopy, indicating distinct features for the Ru-bonded pyrrolyl groups. DFT computational results, coplanarity, bond equalization, and electron delocalization along the fused five-membered rings support aromatic features. In accordance with the antisymbiotic trans-influence, both the isolated isomers 4 and 5 disclose CO ligands opposite to N- or O-anionic groups. The quantitative Mayer bond order evidences a stabilizing backbonding effect. Antibacterial and antifungal trials on Gram-positive (Staphylococcus aureus), Gram-negative (Escherichia coli), and Candida albicans were further carried out. Full article
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21 pages, 2867 KiB  
Article
Computational Insights into Cyclodextrin Inclusion Complexes with the Organophosphorus Flame Retardant DOPO
by Le Ma, Yongguang Zhang, Puyu Zhang and Haiyang Zhang
Molecules 2024, 29(10), 2244; https://doi.org/10.3390/molecules29102244 - 10 May 2024
Viewed by 872
Abstract
Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, [...] Read more.
Cyclodextrins (CDs) were used as green char promoters in the formulation of organophosphorus flame retardants (OPFRs) for polymeric materials, and they could reduce the amount of usage of OPFRs and their release into the environment by forming [host:guest] inclusion complexes with them. Here, we report a systematic study on the inclusion complexes of natural CDs (α-, β-, and γ-CD) with a representative OPFR of DOPO using computational methods of molecular docking, molecular dynamics (MD) simulations, and quantum mechanical (QM) calculations. The binding modes and energetics of [host:guest] inclusion complexes were analyzed in details. α-CD was not able to form a complete inclusion complex with DOPO, and the center of mass distance [host:guest] distance amounted to 4–5 Å. β-CD and γ-CD allowed for a deep insertion of DOPO into their hydrophobic cavities, and DOPO was able to frequently change its orientation within the γ-CD cavity. The energy decomposition analysis based on the dispersion-corrected density functional theory (sobEDAw) indicated that electrostatic, orbital, and dispersion contributions favored [host:guest] complexation, while the exchange–repulsion term showed the opposite. This work provides an in-depth understanding of using CD inclusion complexes in OPFRs formulations. Full article
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11 pages, 931 KiB  
Article
Ionic Route to Atmospheric Relevant HO2 and Protonated Formaldehyde from Methanol Cation and O2
by Mauro Satta, Daniele Catone, Mattea Carmen Castrovilli, Francesca Nicolanti and Antonella Cartoni
Molecules 2024, 29(7), 1484; https://doi.org/10.3390/molecules29071484 - 27 Mar 2024
Viewed by 1029
Abstract
Gas-phase ion chemistry influences atmospheric processes, particularly in the formation of cloud condensation nuclei by producing ionic and neutral species in the upper troposphere–stratosphere region impacted by cosmic rays. This work investigates an exothermic ionic route to the formation of hydroperoxyl radical (HO [...] Read more.
Gas-phase ion chemistry influences atmospheric processes, particularly in the formation of cloud condensation nuclei by producing ionic and neutral species in the upper troposphere–stratosphere region impacted by cosmic rays. This work investigates an exothermic ionic route to the formation of hydroperoxyl radical (HO2) and protonated formaldehyde from methanol radical cation and molecular oxygen. Methanol, a key atmospheric component, contributes to global emissions and participates in various chemical reactions affecting atmospheric composition. The two reactant species are of fundamental interest due to their role in atmospheric photochemical reactions, and HO2 is also notable for its production during lightning events. Our experimental investigations using synchrotron radiation reveal a fast hydrogen transfer from the methyl group of methanol to oxygen, leading to the formation of CH2OH+ and HO2. Computational analysis corroborates the experimental findings, elucidating the reaction dynamics and hydrogen transfer pathway. The rate coefficients are obtained from experimental data and shows that this reaction is fast and governed by capture theory. Our study contributes to a deeper understanding of atmospheric processes and highlights the role of ion-driven reactions in atmospheric chemistry. Full article
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12 pages, 2532 KiB  
Article
AlF–AlF Reaction Dynamics between 200 K and 1000 K: Reaction Mechanisms and Intermediate Complex Characterization
by Weiqi Wang, Xiangyue Liu and Jesús Pérez-Ríos
Molecules 2024, 29(1), 222; https://doi.org/10.3390/molecules29010222 - 31 Dec 2023
Cited by 1 | Viewed by 1216
Abstract
AlF is a relevant molecule in astrochemistry as a tracer of F-bearing molecules. Additionally, AlF presents diagonal Franck-Condon factors and can be created very efficiently in the lab, which makes it a prototypical molecular for laser cooling. However, very little is known about [...] Read more.
AlF is a relevant molecule in astrochemistry as a tracer of F-bearing molecules. Additionally, AlF presents diagonal Franck-Condon factors and can be created very efficiently in the lab, which makes it a prototypical molecular for laser cooling. However, very little is known about the reaction dynamics of AlF. In this work, we report on the reaction dynamics of AlF–AlF between 200 and 1000 K using ab initio molecular dynamics and a highly efficient active learning approach for the potential energy surface, including all degrees of freedom. As a result, we identify the main reaction mechanisms and the lifetime of the intermediate complex AlF–AlF relevant to astrochemistry environments and regions in buffer gas cells. Full article
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13 pages, 1723 KiB  
Article
The Sticking of N2 on W(100) Surface: An Improvement in the Description of the Adsorption Dynamics Further Reconciling Theory and Experiment
by Maria Rutigliano and Fernando Pirani
Molecules 2023, 28(22), 7546; https://doi.org/10.3390/molecules28227546 - 11 Nov 2023
Cited by 1 | Viewed by 889
Abstract
The adsorption of nitrogen molecules on a (100) tungsten surface has been studied using a new potential energy surface in which long-range interactions are suitably characterized and represented by the Improved Lennard–Jones function. The new potential energy surface is used to carry out [...] Read more.
The adsorption of nitrogen molecules on a (100) tungsten surface has been studied using a new potential energy surface in which long-range interactions are suitably characterized and represented by the Improved Lennard–Jones function. The new potential energy surface is used to carry out molecular dynamics simulations by adopting a semiclassical collisional method that explicitly includes the interaction with the surface phonons. The results of the sticking probability, evaluated as a function of the collision energy, are in good agreement with those obtained in the experiments and improve the already good comparison recently obtained with calculations performed using interactions from the Density Functional Theory method and corrected for long-range van der Waals contributions. The dependence of trapping probability on the surface temperature for a well-defined collision energy has also been investigated. Full article
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Planned Papers

The below list represents only planned manuscripts. Some of these manuscripts have not been received by the Editorial Office yet. Papers submitted to MDPI journals are subject to peer-review.

Title: Ab initio study of electron capture in collisions of protons with CO2 molecules.
Authors: Ismanuel Rabadán; Luis Méndez
Affiliation: Departamento de Química, Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain

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