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Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results
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Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results

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

Deadline for manuscript submissions: closed (30 April 2023) | Viewed by 23616

Special Issue Editors

Prof. Dr. Marzio Rosi

E-Mail Website
Guest Editor
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
Prof. Dr. Stefano Falcinelli

E-Mail Website
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 at collecting 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 given to the interested reader for the identification and characterization of the nature and strength of intermolecular interactions able to describe chemical reactivity: 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, astrochemistry, as well as complex systems of biochemical interest.

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

Manuscript Submission Information

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Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Molecules is an international peer-reviewed open access semimonthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 2700 CHF (Swiss Francs). Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

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

Published Papers (16 papers)

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Research

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14 pages, 2298 KiB  
Article
Graphene as Nanocarrier for Gold(I)-Monocarbene Complexes: Strength and Nature of Physisorption
by Cahit Orek, Massimiliano Bartolomei, Cecilia Coletti and Niyazi Bulut
Molecules 2023, 28(9), 3941; https://doi.org/10.3390/molecules28093941 - 07 May 2023
Cited by 2 | Viewed by 1219
Abstract
Gold(I) metal complexes are finding increasing applications as therapeutic agents against a variety of diseases. As their potential use as effective metallodrugs is continuously confirmed, the issue of their administration, distribution and delivery to desired biological targets emerges. Graphene and its derivatives possess [...] Read more.
Gold(I) metal complexes are finding increasing applications as therapeutic agents against a variety of diseases. As their potential use as effective metallodrugs is continuously confirmed, the issue of their administration, distribution and delivery to desired biological targets emerges. Graphene and its derivatives possess attractive properties in terms of high affinity and low toxicity, suggesting that they can efficaciously be used as drug nanocarriers. In the present study, we computationally address the adsorption of a gold(I) N-heterocyclic monocarbene, namely, IMeAuCl (where IMe = 1,3-dimethylimidazol-2-ylidene), on graphene. The Au(I) N-heterocyclic carbene family has indeed shown promising anticancer activity and the N-heterocyclic ring could easily interact with planar graphene nanostructures. By means of high-level electronic structure approaches, we investigated the strength and nature of the involved interaction using small graphene prototypes, which allow us to benchmark the best-performing DFT functionals as well as assess the role of the different contributions to total interaction energies. Moreover, realistic adsorption enthalpies and free energy values are obtained by exploiting the optimal DFT method to describe the drug adsorption on larger graphene models. Such values (ΔHads = −18.4 kcal/mol and ΔGads= −7.20 kcal/mol for the largest C150H30 model) indicate a very favorable adsorption, mainly arising from the dispersion component of the interaction, with the electrostatic attraction also playing a non-negligible role. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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14 pages, 3529 KiB  
Article
Development of AMBER Parameters for Molecular Simulations of Selected Boron-Based Covalent Ligands
by Maria Assunta Chiacchio, Laura Legnani, Enrico Mario Alessandro Fassi, Gabriella Roda and Giovanni Grazioso
Molecules 2023, 28(6), 2866; https://doi.org/10.3390/molecules28062866 - 22 Mar 2023
Viewed by 1715
Abstract
Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies [...] Read more.
Boron containing compounds (BCCs) aroused increasing interest in the scientific community due to their wide application as drugs in various fields. In order to design new compounds hopefully endowed with pharmacological activity and also investigate their conformational behavior, the support of computational studies is crucial. Nevertheless, the suitable molecular mechanics parameterization and the force fields needed to perform these simulations are not completely available for this class of molecules. In this paper, Amber force field parameters for phenyl-, benzyl-, benzylamino-, and methylamino-boronates, a group of boron-containing compounds involved in different branches of the medicinal chemistry, were created. The robustness of the obtained data was confirmed through molecular dynamics simulations on ligand/β-lactamases covalent complexes. The ligand torsional angles, populated over the trajectory frames, were confirmed by values found in the ligand geometries, located through optimizations at the DFT/B3LYP/6-31g(d) level, using water as a solvent. In summary, this study successfully provided a library of parameters, opening the possibility to perform molecular dynamics simulations of this class of boron-containing compounds. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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28 pages, 1181 KiB  
Article
Scattering of e± by C2H6 Molecule over a Wide Range of Energy: A Theoretical Investigation
by N. M. B. Sathee, M. Mousumi Khatun, Anita Rani, M. Masum Billah, M. Nure Alam Abdullah, Mahmudul H. Khandker, Hiroshi Watabe, A. K. Fazlul Haque and M. Alfaz Uddin
Molecules 2023, 28(3), 1255; https://doi.org/10.3390/molecules28031255 - 27 Jan 2023
Cited by 2 | Viewed by 1205
Abstract
The present work reports the theoretical investigation of the scattering of electrons and positrons by the ethane (C2H6) molecule over the energy range 1 eV–1 MeV. The investigation was carried out by taking into account the screening correction arising [...] Read more.
The present work reports the theoretical investigation of the scattering of electrons and positrons by the ethane (C2H6) molecule over the energy range 1 eV–1 MeV. The investigation was carried out by taking into account the screening correction arising from a semiclassical analysis of the atomic geometrical overlapping of the scattering observables calculated in the independent atom approximation. The study is presented through the calculations of a broad spectrum of observable quantities, namely differential, integrated elastic, momentum transfer, viscosity, inelastic, grand total, and total ionization cross-sections and the Sherman functions. A comparative study was carried out between scattering observables for electron impact with those for positron impact to exhibit the similarity and dissimilarity arising out of the difference of the collisions of impinging projectiles with the target. Partial-wave decomposition of the scattering states within the Dirac relativistic framework employing a free-atom complex optical model potential was used to calculate the corresponding observable quantities of the constituent atoms. The results, calculated using our recipe, were compared with the experimental and theoretical works available in the literature. The Sherman function for a e±–C2H6 scattering system is presented for the first time in the literature. The addition of the screening correction to the independent atom approximation method was found to substantially reduce the scattering cross-sections, particularly at forward angles for lower incident energies. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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14 pages, 2503 KiB  
Article
The Peroxymonocarbonate Anion HCO4− as an Effective Oxidant in the Gas Phase: A Mass Spectrometric and Theoretical Study on the Reaction with SO2
by Chiara Salvitti, Federico Pepi, Anna Troiani, Marzio Rosi and Giulia de Petris
Molecules 2023, 28(1), 132; https://doi.org/10.3390/molecules28010132 - 23 Dec 2022
Cited by 1 | Viewed by 1423
Abstract
The peroxymonocarbonate anion, HCO4−, the covalent adduct between the carbon dioxide and hydrogen peroxide anion, effectively reacts with SO2 in the gas phase following three oxidative routes. Mass spectrometric and electronic structure calculations show that sulphur dioxide is oxidised [...] Read more.
The peroxymonocarbonate anion, HCO4−, the covalent adduct between the carbon dioxide and hydrogen peroxide anion, effectively reacts with SO2 in the gas phase following three oxidative routes. Mass spectrometric and electronic structure calculations show that sulphur dioxide is oxidised through a common intermediate to the hydrogen sulphate anion, sulphur trioxide, and sulphur trioxide anion as primary products through formal HO2−, oxygen atom, and oxygen ion transfers. The hydrogen sulphite anion is also formed as a secondary product from the oxygen atom transfer path. The uncommon nucleophilic behaviour of HCO4− is disclosed by the Lewis acidic properties of SO2, an amphiphilic molecule that forms intermediates with characteristic and diagnostic geometries with peroxymonocarbonate. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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15 pages, 4187 KiB  
Article
Coupling Effect of Non-Ignition Impact and Heat on the Decay of FOX-7
by Chongchong She, Kun Chen, Minglei Chen, Zhiyan Lu, Nana Wu, Lijie Li, Junfeng Wang and Shaohua Jin
Molecules 2022, 27(23), 8255; https://doi.org/10.3390/molecules27238255 - 26 Nov 2022
Viewed by 928
Abstract
Non-ignition impact and heat stimuli are the most common external stimuli loaded on energetic materials. Nevertheless, there is thereby an urgent need, but it is still a significant challenge to comprehend their coupling effects on the decay and safety mechanisms of energetic materials. [...] Read more.
Non-ignition impact and heat stimuli are the most common external stimuli loaded on energetic materials. Nevertheless, there is thereby an urgent need, but it is still a significant challenge to comprehend their coupling effects on the decay and safety mechanisms of energetic materials. Then, reactive molecular dynamics simulation was employed to mimic practical situations and reveal the impact heat coupling effect on the decay mechanism of FOX-7. The temperature and the degree of compression of the crystal caused by the impact are considered variables in the simulation. Both increasing the degree of compression and elevating the temperature promotes the decay of FOX-7. However, their underlying response mechanism is not the same. The acceleration of decomposition is due to the elevated potential energy of the FOX-7 molecules because of elevating the temperature. In addition to the elevated potential energy of the molecule, the main contribution to the decomposition from the compression is to change the decomposition path. The results of the analysis show that compression reduces the stability of the C=C bond, so that chemical reactions related to the double bond occur. In addition, interestingly, the compression along the c direction has an almost equal effect on the final product as the compression along the b direction. Finally, the decay reaction networks are proposed to provide insights into the decomposition mechanism on atomic level. All these findings are expected to pave a way to understand the underlying response mechanism for the FOX-7 against external stimuli. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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19 pages, 3210 KiB  
Article
Near-Threshold and Resonance Effects in Rotationally Inelastic Scattering of D2O with Normal-H2
by Astrid Bergeat, Alexandre Faure, Laurent Wiesenfeld, Chloé Miossec, Sébastien B. Morales and Christian Naulin
Molecules 2022, 27(21), 7535; https://doi.org/10.3390/molecules27217535 - 03 Nov 2022
Cited by 2 | Viewed by 1117
Abstract
We present a combined experimental and theoretical study on the rotationally inelastic scattering of heavy water, D2O, with normal-H2. Crossed-molecular beam measurements are performed in the collision energy range between 10 and 100 cm−1, corresponding to [...] Read more.
We present a combined experimental and theoretical study on the rotationally inelastic scattering of heavy water, D2O, with normal-H2. Crossed-molecular beam measurements are performed in the collision energy range between 10 and 100 cm−1, corresponding to the near-threshold regime in which scattering resonances are most pronounced. State-to-state excitation cross-sections are obtained by probing three low-lying rotational levels of D2O using the REMPI technique. These measurements are complemented by quantum close-coupling scattering calculations based on a high-accuracy D2O–H2 interaction potential. The agreement between experiment and theory is within the experimental error bars at 95% confidence intervals, leading to a relative difference of less than 7%: the near-threshold rise and the overall shape of the cross-sections, including small undulations due to resonances, are nicely reproduced by the calculations. Isotopic effects (D2O versus H2O) are also discussed by comparing the shape and magnitude of the respective cross-sections. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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19 pages, 2745 KiB  
Article
Scattering of N2 Molecules from Silica Surfaces: Effect of Polymorph and Surface Temperature
by Maria Rutigliano and Fernando Pirani
Molecules 2022, 27(21), 7445; https://doi.org/10.3390/molecules27217445 - 02 Nov 2022
Cited by 4 | Viewed by 882
Abstract
The inelastic scattering of N2 molecules from silica surfaces, taken at 100 K, has been investigated by adopting a semiclassical collision model in conjunction with the appropriate treatment of the long-range interaction forces. Such forces promote the formation of the precursor state [...] Read more.
The inelastic scattering of N2 molecules from silica surfaces, taken at 100 K, has been investigated by adopting a semiclassical collision model in conjunction with the appropriate treatment of the long-range interaction forces. Such forces promote the formation of the precursor state that controls all basic elementary processes occurring at the gas–surface interphase. The probabilities for the different elementary surface processes triggered by quartz are determined and compared with those recently obtained for another silica polymorph (cristobalite). In addition, the final roto-vibrational distributions of N2 molecules undergoing inelastic scattering have been characterized. N2 molecules, impinging on both considered surfaces in low-medium vibrational states, preserve the initial vibrational state, while those inelastically scattered are rotationally excited and translationally colder. The surface temperature effect, investigated by raising the temperature itself from 100 K up to 1000 K, emerges more sharply for the cristobalite polymorph, mainly for the molecules impinging in the ground roto-vibrational state and with low collision energies. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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15 pages, 3319 KiB  
Article
Multilayer Graphtriyne Membranes for Separation and Storage of CO2: Molecular Dynamics Simulations of Post-Combustion Model Mixtures
by Yusuf Bramastya Apriliyanto, Noelia Faginas-Lago, Stefano Evangelisti, Massimiliano Bartolomei, Thierry Leininger, Fernando Pirani, Leonardo Pacifici and Andrea Lombardi
Molecules 2022, 27(18), 5958; https://doi.org/10.3390/molecules27185958 - 13 Sep 2022
Cited by 3 | Viewed by 1555
Abstract
The ability to remove carbon dioxide from gaseous mixtures is a necessary step toward the reduction of greenhouse gas emissions. As a contribution to this field of research, we performed a molecular dynamics study assessing the separation and adsorption properties of multi-layered graphtriyne [...] Read more.
The ability to remove carbon dioxide from gaseous mixtures is a necessary step toward the reduction of greenhouse gas emissions. As a contribution to this field of research, we performed a molecular dynamics study assessing the separation and adsorption properties of multi-layered graphtriyne membranes on gaseous mixtures of CO2, N2, and H2O. These mixtures closely resemble post-combustion gaseous products and are, therefore, suitable prototypes with which to model possible technological applications in the field of CO2 removal methodologies. The molecular dynamics simulations rely on a fairly accurate description of involved force fields, providing reliable predictions of selectivity and adsorption coefficients. The characterization of the interplay between molecules and membrane structure also permitted us to elucidate the adsorption and crossing processes at an atomistic level of detail. The work is intended as a continuation and a strong enhancement of the modeling research and characterization of such materials as molecular sieves for CO2 storage and removal. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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14 pages, 4323 KiB  
Article
Chemoselective Oxidation of Isoxazolidines with Ruthenium Tetroxide: A Successful Intertwining of Combined Theoretical and Experimental Data
by Laura Legnani, Salvatore V. Giofré, Daniela Iannazzo, Consuelo Celesti, Lucia Veltri and Maria Assunta Chiacchio
Molecules 2022, 27(17), 5390; https://doi.org/10.3390/molecules27175390 - 24 Aug 2022
Cited by 2 | Viewed by 1048
Abstract
The direct oxidation reaction of isoxazolidines plays an important role in organic chemistry, leading to the synthesis of biologically active compounds. In this paper, we report a computational mechanistic study of RuO4-catalyzed oxidation of differently N-substituted isoxazolidines 1a–c [...] Read more.
The direct oxidation reaction of isoxazolidines plays an important role in organic chemistry, leading to the synthesis of biologically active compounds. In this paper, we report a computational mechanistic study of RuO4-catalyzed oxidation of differently N-substituted isoxazolidines 1a–c. Attention was focused on the endo/exo oxidation selectivity. For all the investigated compounds, the exo attack is preferred to the endo one, showing exo percentages growing in parallel with the stability order of transient carbocations found along the reaction pathway. The study has been supported by experimental data that nicely confirm the modeling results. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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13 pages, 7127 KiB  
Article
Sensing the ortho Positions in C6Cl6 and C6H4Cl2 from Cl2− Formation upon Molecular Reduction
by Sarvesh Kumar, José Romero, Michael Probst, Thana Maihom, Gustavo García and Paulo Limão-Vieira
Molecules 2022, 27(15), 4820; https://doi.org/10.3390/molecules27154820 - 27 Jul 2022
Viewed by 1654
Abstract
The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl2−. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of [...] Read more.
The geometrical effect of chlorine atom positions in polyatomic molecules after capturing a low-energy electron is shown to be a prevalent mechanism yielding Cl2−. In this work, we investigated hexachlorobenzene reduction in electron transfer experiments to determine the role of chlorine atom positions around the aromatic ring, and compared our results with those using ortho-, meta- and para-dichlorobenzene molecules. This was achieved by combining gas-phase experiments to determine the reaction threshold by means of mass spectrometry together with quantum chemical calculations. We also observed that Cl2− formation can only occur in 1,2-C6H4Cl2, where the two closest C–Cl bonds are cleaved while the chlorine atoms are brought together within the ring framework due to excess energy dissipation. These results show that a strong coupling between electronic and C–Cl bending motion is responsible for a positional isomeric effect, where molecular recognition is a determining factor in chlorine anion formation. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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16 pages, 3157 KiB  
Article
Bound Electron Enhanced Radiosensitisation of Nimorazole upon Charge Transfer
by Sarvesh Kumar, Islem Ben Chouikha, Boutheïna Kerkeni, Gustavo García and Paulo Limão-Vieira
Molecules 2022, 27(13), 4134; https://doi.org/10.3390/molecules27134134 - 28 Jun 2022
Cited by 1 | Viewed by 1406
Abstract
This novel work reports nimorazole (NIMO) radiosensitizer reduction upon electron transfer in collisions with neutral potassium (K) atoms in the lab frame energy range of 10–400 eV. The negative ions formed in this energy range were time-of-flight mass analyzed and branching ratios were [...] Read more.
This novel work reports nimorazole (NIMO) radiosensitizer reduction upon electron transfer in collisions with neutral potassium (K) atoms in the lab frame energy range of 10–400 eV. The negative ions formed in this energy range were time-of-flight mass analyzed and branching ratios were obtained. Assignment of different anions showed that more than 80% was due to the formation of the non-dissociated parent anion NIMO•− at 226 u and nitrogen dioxide anion NO2− at 46 u. The rich fragmentation pattern revealed that significant collision induced the decomposition of the 4-nitroimidazole ring, as well as other complex internal reactions within the temporary negative ion formed after electron transfer to neutral NIMO. Other fragment anions were only responsible for less than 20% of the total ion yield. Additional information on the electronic state spectroscopy of nimorazole was obtained by recording a K+ energy loss spectrum in the forward scattering direction (θ ≈ 0°), allowing us to determine the most accessible electronic states within the temporary negative ion. Quantum chemical calculations on the electronic structure of NIMO in the presence of a potassium atom were performed to help assign the most significant lowest unoccupied molecular orbitals participating in the collision process. Electron transfer was shown to be a relevant process for nimorazole radiosensitisation through efficient and prevalent non-dissociated parent anion formation. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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18 pages, 7222 KiB  
Article
Poly(o-methoxyaniline) Chain Degradation Based on a Heat Treatment (HT) Process: Combined Experimental and Theoretical Evaluation
by Jéssica Montenegro Santana da Silva, Adriano de Souza Carolino, Lilian Rodrigues de Oliveira, Douglas de Souza Gonçalves, Matheus Moraes Biondo, Pedro Henrique Campelo, Jaqueline de Araújo Bezerra, Ştefan Ţălu, Henrique Duarte da Fonseca Filho, Hidembergue Ordozgoith da Frota and Edgar Aparecido Sanches
Molecules 2022, 27(12), 3693; https://doi.org/10.3390/molecules27123693 - 08 Jun 2022
Cited by 1 | Viewed by 1592
Abstract
Poly(o-methoxyaniline) emeraldine-salt form (ES-POMA) was chemically synthesized using hydrochloric acid and subjected to a heat treatment (HT) process for 1 h at 100 °C (TT100) and 200 °C (TT200). The HT process promoted a progressive decrease in [...] Read more.
Poly(o-methoxyaniline) emeraldine-salt form (ES-POMA) was chemically synthesized using hydrochloric acid and subjected to a heat treatment (HT) process for 1 h at 100 °C (TT100) and 200 °C (TT200). The HT process promoted a progressive decrease in crystallinity. The Le Bail method revealed a decomposition from tetrameric to trimeric-folded chains after the HT process. The unheated POMA-ES presented a globular vesicular morphology with varied micrometric sizes. The heat treatment promoted a reduction in these globular structures, increasing the non-crystalline phase. The boundary length (S) and connectivity/Euler feature (χ) parameters were calculated from the SEM images, revealing that ES-POMA presented a wide distribution of heights. The TT100 and TT200 presented a narrow boundary distribution, suggesting smoother surfaces with smaller height variations. The UV-VIS analysis revealed that the transition at 343 nm (nonlocal π → π*) was more intense in the TT200 due to the electronic delocalization, which resulted from the reduced polymer chain caused by the HT process. In addition to the loss of conjugation, counter ion withdrawal reduced the ion-chain interaction, decreasing the local electron density. This result shows the influence of the chlorine counter ions on the peaks position related to the HOMO → LUMO transition, since the π → polaron transition occurs due to the creation of the energy states due to the presence of counter ions. Finally, the electrical conductivity decreased after the HT process from 1.4 × 10−4 S.cm−1 to 2.4 × 10−6 S.cm−1 as result of the polymer deprotonation/degradation. Thus, this paper proposed a systematic evaluation of the POMA molecular structure and crystallite size and shape after heat treatment. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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17 pages, 12223 KiB  
Article
Reactivity of 4,5-Dichlorophthalic Anhydride towards Thiosemicarbazide and Amines: Synthesis, Spectroscopic Analysis, and DFT Study
by Hatem A. Abuelizz, Ahmed H. Bakheit, Mohamed Marzouk, Mohamed M. Abdellatif and Rashad Al-Salahi
Molecules 2022, 27(11), 3550; https://doi.org/10.3390/molecules27113550 - 31 May 2022
Cited by 5 | Viewed by 1543
Abstract
The cyclic anhydrides are broadly employed in several fields, such as the chemical, plastic, agrochemical, and pharmaceutical industries. This study describes the chemical reactivity of 4,5-dichlorophthalic anhydride towards several nucleophiles, including thiosemicarbazide and different amines, to produce the carboxylic acid derivatives resulting from [...] Read more.
The cyclic anhydrides are broadly employed in several fields, such as the chemical, plastic, agrochemical, and pharmaceutical industries. This study describes the chemical reactivity of 4,5-dichlorophthalic anhydride towards several nucleophiles, including thiosemicarbazide and different amines, to produce the carboxylic acid derivatives resulting from anhydride’s opening, namely, phthalimide and dicarboxylic acid (1–12) products. Their chemical structures are confirmed by NMR, IR and MS spectra analyses. Density–functional theory (DFT) studies are performed using (DFT/B3LYP) with the 6-311G(d, p) basis sets to recognize different chemical and physical features of the target compounds. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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13 pages, 3778 KiB  
Article
Modelling the Interaction between Carboxylic Acids and Zinc Oxide: Insight into Degradation of ZnO Pigments
by Jihan Lubani, Filippo De Angelis, Daniele Meggiolaro, Laura Cartechini and Simona Fantacci
Molecules 2022, 27(11), 3362; https://doi.org/10.3390/molecules27113362 - 24 May 2022
Cited by 1 | Viewed by 1810
Abstract
Computational modelling applied to cultural heritage can assist the characterization of painting materials and help to understand their intrinsic and external degradation processes. The degradation of the widely employed zinc oxide (ZnO)—a white pigment mostly used in oil paints—leads to the formation of [...] Read more.
Computational modelling applied to cultural heritage can assist the characterization of painting materials and help to understand their intrinsic and external degradation processes. The degradation of the widely employed zinc oxide (ZnO)—a white pigment mostly used in oil paints—leads to the formation of metal soaps, complexes of Zn ions and long-chain fatty acids coming from the degradation of the oil binder. Being a serious problem affecting the appearance and the structural integrity of many oil paintings, it is relevant to characterize the structure of these complexes and to understand the reaction pathways associated with this degradation process. Density functional theory (DFT) calculations were performed to investigate the adsorption of the acetate and acetic acid on relatively large ZnO clusters and the formation of Zn–acetate complexes. Carboxylic acids with longer alkyl chains were then investigated as more realistic models of the fatty acids present in the oil medium. In addition, DFT calculations using a periodic ZnO slab were performed in order to compare the obtained results at different levels of theory. Optimization calculations as well as the formation energies of the ZnO@carboxylate coupled systems and the thermodynamics leading to possible degradation products were computed. Our results highlight the potential for DFT calculations to provide a better understanding of oil paint degradation, with the aim of contributing to the development of strengthening and conservation strategies of paintings. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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14 pages, 1509 KiB  
Article
Semiempirical Potential in Kinetics Calculations on the HC3N + CN Reaction
by Emília Valença Ferreira de Aragão, Luca Mancini, Noelia Faginas-Lago, Marzio Rosi, Dimitrios Skouteris and Fernando Pirani
Molecules 2022, 27(7), 2297; https://doi.org/10.3390/molecules27072297 - 01 Apr 2022
Cited by 3 | Viewed by 1433
Abstract
The reaction between the cyano radical CN and cyanoacetylene molecule HC3N is of great interest in different astronomical fields, from star-forming regions to planetary atmospheres. In this work, we present a new synergistic theoretical approach for the derivation of the rate [...] Read more.
The reaction between the cyano radical CN and cyanoacetylene molecule HC3N is of great interest in different astronomical fields, from star-forming regions to planetary atmospheres. In this work, we present a new synergistic theoretical approach for the derivation of the rate coefficient for gas phase neutral-neutral reactions. Statistic RRKM calculations on the Potential Energy Surface are coupled with a semiempirical analysis of the initial bimolecular interaction. The value of the rate coefficient for the HC3N + CN → H + NCCCCN reaction obtained with this method is compared with previous theoretical and experimental investigations, showing strengths and weaknesses of the new presented approach. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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Review

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21 pages, 3433 KiB  
Review
Current Status of the X + C2H6 [X ≡ H, F(2P), Cl(2P), O(3P), OH] Hydrogen Abstraction Reactions: A Theoretical Review
by Joaquin Espinosa-Garcia, Cipriano Rangel and Jose C. Corchado
Molecules 2022, 27(12), 3773; https://doi.org/10.3390/molecules27123773 - 11 Jun 2022
Cited by 2 | Viewed by 1503
Abstract
This paper is a detailed review of the chemistry of medium-size reactive systems using the following hydrogen abstraction reactions with ethane, X + C2H6 → HX + C2H5; X ≡ H, F(2P), Cl(2 [...] Read more.
This paper is a detailed review of the chemistry of medium-size reactive systems using the following hydrogen abstraction reactions with ethane, X + C2H6 → HX + C2H5; X ≡ H, F(2P), Cl(2P), O(3P) and OH, and focusing attention mainly on the theoretical developments. These bimolecular reactions range from exothermic to endothermic systems and from barrierless to high classical barriers of activation. Thus, the topography of the reactive systems changes from reaction to reaction with the presence or not of stabilized intermediate complexes in the entrance and exit channels. The review begins with some reflections on the inherent problems in the theory/experiment comparison. When one compares kinetics or dynamics theoretical results with experimental measures, one is testing both the potential energy surface describing the nuclei motion and the kinetics or dynamics method used. Discrepancies in the comparison may be due to inaccuracies of the surface, limitations of the kinetics or dynamics methods, and experimental uncertainties that also cannot be ruled out. The paper continues with a detailed review of some bimolecular reactions with ethane, beginning with the reactions with hydrogen atoms. The reactions with halogens present a challenge owing to the presence of stabilized intermediate complexes in the entrance and exit channels and the influence of the spin-orbit states on reactivity. Reactions with O(3P) atoms lead to three surfaces, which is an additional difficulty in the theoretical study. Finally, the reactions with the hydroxyl radical correspond to a reactive system with ten atoms and twenty-four degrees of freedom. Throughout this review, different strategies in the development of analytical potential energy surfaces describing these bimolecular reactions have been critically analyzed, showing their advantages and limitations. These surfaces are fitted to a large number of ab initio calculations, and we found that a huge number of calculations leads to accurate surfaces, but this information does not guarantee that the kinetics and dynamics results match the experimental measurements. Full article
(This article belongs to the Special Issue Molecular Reactivity: Theoretical Study and Interpretation of Experimental Results)
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