1,555 results on '"General Chemistry"'
Search Results
2. Crystalline structures of l-cysteine and l-cystine
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Yangyang Su, Etienne P. Hessou, Estefania Colombo, Gustavo Belletti, Ali Moussadik, Ivan T. Lucas, Vincent Frochot, Michel Daudon, Stéphan Rouzière, Dominique Bazin, Kezhi Li, Paola Quaino, Frederik Tielens, Chemistry, Faculty of Sciences and Bioengineering Sciences, General Chemistry, General Chemistry [Brussel] (ALGC), Vrije Universiteit Brussel [Bruxelles] (VUB), State Key Laboratory of Solidification Processing, Northwestern Polytechnical University [Xi'an] (NPU), Instituto de Matemática Aplicada del Litoral (IMAL-CONICET-UNL). Santa Fe, Laboratoire Interfaces et Systèmes Electrochimiques (LISE), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Maladies rénales fréquentes et rares : des mécanismes moléculaires à la médecine personnalisée (CoRaKID), Institut National de la Santé et de la Recherche Médicale (INSERM)-Sorbonne Université (SU), Laboratoire de Physique des Solides (LPS), Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), and Martin, Véronique
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Cystinuria ,[SDV]Life Sciences [q-bio] ,Cystinosis ,Organic Chemistry ,Clinical Biochemistry ,L-cystine ,l-cysteine ,l-cystine ,[SDV.SP]Life Sciences [q-bio]/Pharmaceutical sciences ,Biochemistry ,[PHYS.PHYS.PHYS-CHEM-PH] Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,[SDV.SP] Life Sciences [q-bio]/Pharmaceutical sciences ,[SDV] Life Sciences [q-bio] ,Biominerals ,Cystine ,Humans ,characterization ,[PHYS.PHYS.PHYS-CHEM-PH]Physics [physics]/Physics [physics]/Chemical Physics [physics.chem-ph] ,Cysteine ,Disulfides ,Crystalline structure ,Computer simulations - Abstract
International audience; It is assumed that genetic diseases affecting the metabolism of cysteine and the kidney function lead to two different kinds of pathologies, namely cystinuria and cystinosis whereby generate L-cystine crystals. Recently, the presence of L-cysteine crystal has been underlined in the case of cystinosis. Interestingly, it can be strikingly seen that cystine ([-S-CH2-CH-(NH2)-COOH]2) consists of two cysteine (C3H7NO2S) molecules connected by a disulfide (S-S) bond. Therefore, the study of cystine and cysteine is important for providing a better understanding of cystinuria and cystinosis. In this paper, we elucidate the discrepancy between L-cystine and L-cysteine by investigating the theoretical and experimental infrared spectra (IR), X-ray diffraction (XRD) as well as Raman spectra aiming to obtain a better characterization of abnormal deposits related to these two genetic pathologies.
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- 2022
3. Theoretical and experimental insight into zinc loading on mesoporous silica
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Maria Ziolek, Frederik Tielens, Tomasz Siodła, Izabela Sobczak, Faculty of Chemistry [Adam Mickiewicz], Adam Mickiewicz University in Poznań (UAM), Spectroscopie, Modélisation, Interfaces pour L'Environnement et la Santé (LCMCP-SMiLES), Laboratoire de Chimie de la Matière Condensée de Paris (LCMCP), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Departement of General Chemistry (ALGC) (ALG), Université libre de Bruxelles (ULB), National Science Centre in Poland (Grant No. 2013/10/E/ST5/00642), GENCI-[CCRT/CINES/IDRIS] (Grant 2016-[x2016082022]), CCRE of Université Pierre et Marie Curie, PL-Grid Infrastructure, and General Chemistry
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Materials science ,Chemistry(all) ,Silicon ,Inorganic chemistry ,Basicity ,chemistry.chemical_element ,02 engineering and technology ,Zinc ,010402 general chemistry ,DFT ,01 natural sciences ,Metal ,Molecular level ,Materials Science(all) ,X-ray photoelectron spectroscopy ,XPS ,General Materials Science ,Fourier transform infrared spectroscopy ,[CHIM.MATE]Chemical Sciences/Material chemistry ,General Chemistry ,Mesoporous silica ,021001 nanoscience & nanotechnology ,Condensed Matter Physics ,Zn/MCF ,0104 chemical sciences ,[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,Trigonal bipyramidal molecular geometry ,FTIR ,chemistry ,Chemical engineering ,Mechanics of Materials ,visual_art ,visual_art.visual_art_medium ,0210 nano-technology - Abstract
International audience; Zinc oxide species grafted on mesostructured cellular foam (MCF) silica are investigated using a combination of experimental and theoretical techniques. MCF is modelled using a realistic amorphous silica surface model surface slab. The most energetically favorable complexes grafted on the silica surface were identified and characterized at the molecular level. The Zn metal center was found in tetrahedral coordination. Moreover, the Si-O-Zn-OH species is found to be stabilized in a 5 fold coordinated silicon with an unusual trigonal bipyramidal geometry. A mechanism for the grafting process of the metal species on the support is proposed.
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- 2018
4. Tin(<scp>ii</scp>) cations stabilized by non-symmetric N,N′,O-chelating ligands: synthesis and stability
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Miroslav Novák, Jan Turek, Yaraslava Milasheuskaya, Miriam Syková, Libor Dostál, Jesse Stalmans, Zdeňka Růžičková, Klaus Jurkschat, Roman Jambor, Chemistry, and General Chemistry
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Inorganic Chemistry - Abstract
A series of novel non-symmetric neutral N,N′,O-chelating ligands derived from the α-iminopyridine 2-(C(R1)[double bond, length as m-dash]N(C6H3-2,6-iPr2))-6-(R2R3P[double bond, length as m-dash]O)C5H3N (L1: R1 = H, R2 = R3 = Ph; L2: R1 = Me, R2 = R3 = Ph; L3: R1 = H; R2 = Ph, R3 = EtO; L4: R1 = Me, R2 = Ph, R3 = EtO; L5: R1 = H, R2 = R3 = iPrO; L6: R1 = Me, R2 = R3 = iPrO) were synthesized. Ligands L1–6 were reacted with SnCl2 and Sn(OTf)2 with the aim of studying the influence of different R2R3P[double bond, length as m-dash]O functional groups on the Lewis base mediated ionization of SnCl2 and Sn(OTf)2. While all ligands L1–6 provided the corresponding ionic tin(II) complexes [L1–6 → SnCl]+[SnCl3]− (1–6), only ligands L1, L4 and L6 were able to stabilize tin(II) dications [L1,4,6 → Sn(H2O)][OTf]2 (7–9). The auto-ionized compounds [L3–6 → SnCl]+[SnCl3]− possessing ethylphenyl phosphinate and diisopropylphosphite substituents undergo elimination of EtCl and iPrCl, respectively, yielding compounds 10–13. Thesecan either be interpreted as neutral tin(II)phosphinate chloride (10, 11) and tin(II)phosphonate chloride (12, 13), respectively, containing Sn–O and Sn–Cl bonds, and a P[double bond, length as m-dash]O → SnCl2 interaction, or as zwitterionic compounds, where the positive charge of the central tin atom is compensated by an [OSnCl2]− anion. Finally, DFT studies were performed to better understand the steric and electronic properties of the ligands L1–6 as well as the nature of the bonds in the resulting products, with a particular focus on complexes 10–13.
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- 2023
5. Photoactivation of titanium-oxo cluster [Ti6O6(OR)6(O2CtBu)6]: mechanism, photoactivated structures, and onward reactivity with O2 to a peroxide complex
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Stephen E. Brown, Ioanna Mantaloufa, Ryan T. Andrews, Thomas J. Barnes, Martin R. Lees, Frank De Proft, Ana V. Cunha, Sebastian D. Pike, Faculty of Sciences and Bioengineering Sciences, Chemistry, and General Chemistry
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General Chemistry - Abstract
The molecular titanium-oxo cluster [Ti6O6(OiPr)6(O2CtBu)6] (1) can be photoactivated by UV light, resulting in a deeply coloured mixed valent (photoreduced) Ti (III/IV) cluster, alongside alcohol and ketone (photooxidised) organic products. Mechanistic studies indicate that a two-electron (not free-radical) mechanism occurs in this process, which utilises the cluster structure to facilitate multielectron reactions. The photoreduced products [Ti6O6(OiPr)4(O2CtBu)6(sol)2], sol = iPrOH (2) or pyridine (3), can be isolated in good yield and are structurally characterized, each with two, uniquely arranged, antiferromagnetically coupled d-electrons. 2 and 3 undergo onward oxidation under air, with 3 cleanly transforming into peroxide complex, [Ti6O6(OiPr)4(O2CtBu)6(py)(O2)] (5). 5 reacts with isopropanol to regenerate the initial cluster (1) completing a closed cycle, and suggesting opportunities for the deployment of these easily made and tuneable clusters for sustainable photocatalytic processes using air and light. The redox reactivity described here is only possible in a cluster with multiple Ti sites, which can perform multi-electron processes and can adjust its shape to accommodate changes in electron density.
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- 2023
6. Scanning electron microscopy—a powerful imaging technique for the clinician
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Frederik Tielens, Raphaël Weil, Dominique Bazin, Michel Daudon, Jean-Philippe Haymann, Emmanuel Letavernier, Vincent Frochot, Elise Bouderlique, Laboratoire de Chimie-Physique (LCP), Université de Cocody, Chemistry, and General Chemistry
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0303 health sciences ,Materials science ,Chemistry(all) ,Scanning electron microscope ,kidney stones ,030232 urology & nephrology ,Building and Construction ,3. Good health ,03 medical and health sciences ,breast cancer ,0302 clinical medicine ,Chemical Engineering(all) ,[CHIM]Chemical Sciences ,Imaging technique ,Electrical and Electronic Engineering ,Pathological calcifications ,Breast calcifications ,scanning electron microscopy ,ComputingMilieux_MISCELLANEOUS ,[SDV.MHEP]Life Sciences [q-bio]/Human health and pathology ,030304 developmental biology ,Biomedical engineering - Abstract
Since its first use several decades ago, scanning electron microscopy has been used in numerous investigations dedicated to biological systems. This contribution focuses on observations on pathological calcifications in order to review several major applications of primary importance to the clinician. Among these, we highlight such observations as medical diagnostic tools in pathologies arising from primary hyperoxaluria and urinary infections.
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- 2022
7. Assessing the Reactivity of the Na3PS4 Solid-State Electrolyte with the Sodium Metal Negative Electrode Using Total Trajectory Analysis with Neural-Network Potential Molecular Dynamics
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Bekaert, Lieven, Akatsuka, Suzuno, Tanibata, Naoto, Proft, Frank De, Hubin, Annick, Mamme, Mesfin Haile, Nakayama, Masanobu, Materials and Chemistry, Electrochemical and Surface Engineering, Faculty of Engineering, General Chemistry, and Chemistry
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- 2023
8. Molecular Resolution Nanostructure and Dynamics of the Deep Eutectic Solvent—Graphite Interface as a Function of Potential
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Justin S. Freeman, Mesfin Haile Mamme, Jon Ustarroz, Gregory G. Warr, Hua Li, Rob Atkin, Materials and Chemistry, General Chemistry, and Electrochemical and Surface Engineering
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Biomaterials ,General Materials Science ,General Chemistry ,Biotechnology - Abstract
Interest in deep eutectic solvents (DESs), particularly for electrochemical applications, has boomed in the past decade because they are more versatile than conventional electrolyte solutions and are low cost, renewable, and non-toxic. The molecular scale lateral nanostructures as a function of potential at the solid–liquid interface—critical design parameters for the use of DESs as electrochemical solvents—are yet to be revealed. In this work, in situ amplitude modulated atomic force microscopy complemented by molecular dynamics simulations is used to probe the Stern and near-surface layers of the archetypal and by far most studied DES, 1:2 choline chloride:urea (reline), at the highly orientated pyrolytic graphite surface as a function of potential, to reveal highly ordered lateral nanostructures with unprecedented molecular resolution. This detail allows identification of choline, chloride, and urea in the Stern layer on graphite, and in some cases their orientations. Images obtained after the potential isswitched from negative to positive show the dynamics of the Stern layer response, revealing that several minutes are required to reach equilibrium. These results provide valuable insight into the nanostructure and dynamics of DESs at the solid–liquid interface, with implications for the rational design of DESs for interfacial applications.
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- 2023
9. Unravelling the Mechanism and Governing Factors in Lewis Acid and Non-Covalent Diels–Alder Catalysis: Different Perspectives
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Lise Vermeersch, Frank De Proft, Vicky Faulkner, Freija De Vleeschouwer, Faculty of Sciences and Bioengineering Sciences, Chemistry, and General Chemistry
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Inorganic Chemistry ,activation strain model ,Organic Chemistry ,Lewis acids ,non-covalent interaction donors ,General Medicine ,Physical and Theoretical Chemistry ,Molecular Biology ,energy decomposition analysis ,Spectroscopy ,Catalysis ,Diels–Alder catalysis ,Computer Science Applications - Abstract
In the current literature, many non-covalent interaction (NCI) donors have been proposed that can potentially catalyze Diels-Alder (DA) reactions. In this study, a detailed analysis of the governing factors in Lewis acid and non-covalent catalysis of three types of DA reactions was carried out, for which we selected a set of hydrogen-, halogen-, chalcogen-, and pnictogen-bond donors. We found that the more stable the NCI donor–dienophile complex, the larger the reduction in DA activation energy. We also showed that for active catalysts, a significant part of the stabilization was caused by orbital interactions, though electrostatic interactions dominated. Traditionally, DA catalysis was attributed to improved orbital interactions between the diene and dienophile. Recently, Vermeeren and co-workers applied the activation strain model (ASM) of reactivity, combined with the Ziegler-Rauk-type energy decomposition analysis (EDA), to catalyzed DA reactions in which energy contributions for the uncatalyzed and catalyzed reaction were compared at a consistent geometry. They concluded that reduced Pauli repulsion energy, and not enhanced orbital interaction energy, was responsible for the catalysis. However, when the degree of asynchronicity of the reaction is altered to a large extent, as is the case for our studied hetero-DA reactions, the ASM should be employed with caution. We therefore proposed an alternative and complementary approach, in which EDA values for the catalyzed transition-state geometry, with the catalyst present or deleted, can be compared one to one, directly measuring the effect of the catalyst on the physical factors governing the DA catalysis. We discovered that enhanced orbital interactions are often the main driver for catalysis and that Pauli repulsion plays a varying role.
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- 2023
- Full Text
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10. Mechanochemical Felkin-Anh Model: Achieving Forbidden Reaction Outcomes with Mechanical Force
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Tom Bettens, Mercedes Alonso, Paul Geerlings, Frank De Proft, Chemistry, Vriendenkring VUB, and General Chemistry
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Organic Chemistry - Abstract
Anti-Felkin-Anh diastereoselectivity can be achieved for nucleophilic additions to α-chiral ketones upon stretching the ketone with a mechanical pulling force. Herein, a mechanochemical Felkin-Anh model is proposed for predicting the outcome of a nucleophilic addition to an α-chiral ketone. Essentially, the fully stretched chiral ketone has one substituent shielding each side of the carbonyl, in contrast to the Felkin-Anh model, in which free rotation around a bond is required to achieve the two rotamers of the ketone. Depending on the pulling scenario, either Felkin-Anh or anti-Felkin-Anh diastereoselectivity is obtained. The model is entirely based on the distance between the pulling points, which is maximized in the anti-periplanar arrangement. The major diastereomer is associated with the approach with the least steric interactions. The intuitive model is validated by means of mechanochemical density functional theory calculations. Importantly, the ketone is fully stretched in the sub 1 nN force regime, thus minimizing the risk of undesired homolytic bond rupture. Moreover, the mechanical force is not used for lowering the reaction barriers associated with the nucleophilic addition; instead, it is solely applied for locking the conformation of a molecule and provoking otherwise inaccessible reaction pathways on the force-modified potential energy surface.
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- 2023
11. The Halogen Bond in Weakly Bonded Complexes and the Consequences for Aromaticity and Spin-Orbit Coupling
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Ana V. Cunha, Remco W. A. Havenith, Jari van Gog, Freija De Vleeschouwer, Frank De Proft, Wouter Herrebout, Molecular Energy Materials, Chemistry, and General Chemistry
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Organic Chemistry ,halogen bonds ,Pharmaceutical Science ,density functional theory ,energy decomposition analysis ,ring current analysis ,spin-orbit coupling ,Analytical Chemistry ,Chemistry ,Chemistry (miscellaneous) ,Drug Discovery ,Molecular Medicine ,Physical and Theoretical Chemistry ,Biology - Abstract
The halogen bond complexes CF (Formula presented.) X⋯Y and C (Formula presented.) F (Formula presented.) X⋯Y, with Y = furan, thiophene, selenophene and X = Cl, Br, I, have been studied by using DFT and CCSD(T) in order to understand which factors govern the interaction between the halogen atom X and the aromatic ring. We found that PBE0-dDsC/QZ4P gives an adequate description of the interaction energies in these complexes, compared to CCSD(T) and experimental results. The interaction between the halogen atom X and the (Formula presented.) -bonds in perpendicular orientation is stronger than the interaction with the in-plane lone pairs of the heteroatom of the aromatic cycle. The strength of the interaction follows the trend Cl < Br < I; the chalcogenide in the aromatic ring nor the hybridization of the C–X bond play a decisive role. The energy decomposition analysis shows that the interaction energy is dominated by all three contributions, viz., the electrostatic, orbital, and dispersion interactions: not one factor dominates the interaction energy. The aromaticity of the ring is undisturbed upon halogen bond formation: the (Formula presented.) -ring current remains equally strong and diatropic in the complex as it is for the free aromatic ring. However, the spin-orbit coupling between the singlet and triplet (Formula presented.) states is increased upon halogen bond formation and a faster intersystem crossing between these states is therefore expected.
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- 2023
12. SuFEx-enabled, chemoselective synthesis of triflates, triflamides and triflimidates
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Steven Verhelst, Fien Hoppenbrouwers, Mercedes Alonso, Wim De Borggraeve, Lauren Voets, Joachim Demaerel, Ruben Van Lommel, Bing-Yu Li, Faculty of Sciences and Bioengineering Sciences, Chemistry, and General Chemistry
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Chemistry ,Science & Technology ,Chemistry, Multidisciplinary ,Physical Sciences ,General Chemistry - Abstract
Sulfur(VI) Fluoride Exchange (SuFEx) chemistry has emerged as a next-generation click reaction, designed to assemble functional molecules quickly and modularly. Here, we report the ex situ generation of trifluoromethanesulfonyl fluoride (CF3SO2F) gas in a two chamber system, and its use as a new SuFEx handle to efficiently synthesize triflates and triflamides. This broadly tolerated protocol lends itself to peptide modification or to telescoping into coupling reactions. Moreover, redesigning the SVI–F connector with a S=O → S=NR replacement, furnished the analogous triflimidoyl fluorides as SuFEx electrophiles, which were engaged in the synthesis of rarely reported triflimidate esters. Notably, experiments showed H2O to be the key towards achieving chemoselective trifluoromethanesulfonation of phenols vs. amine groups, a phenomenon best explained—using ab initio metadynamics simulations—by a hydrogen bonded termolecular transition state for the CF3SO2F triflylation of amines. Sulfur(VI) Fluoride Exchange (SuFEx) chemistry has emerged as a next-generation click reaction, designed to assemble functional molecules quickly and modularly. Here, we report the ex situ generation of trifluoromethanesulfonyl fluoride (CF3SO2F) gas in a two chamber system, and its use as a new SuFEx handle to efficiently synthesize triflates and triflamides. This broadly tolerated protocol lends itself to peptide modification or to telescoping into coupling reactions. Moreover, redesigning the SVI–F connector with a S=O → S=NR replacement, furnished the analogous triflimidoyl fluorides as SuFEx electrophiles, which were engaged in the synthesis of rarely reported triflimidate esters. Notably, experiments showed H2O to be the key towards achieving chemoselective trifluoromethanesulfonation of phenols vs. amine groups, a phenomenon best explained—using ab initio metadynamics simulations—by a hydrogen bonded termolecular transition state for the CF3SO2F triflylation of amines. ispartof: Chemical Science vol:13 issue:8 pages:1-10 ispartof: location:England status: published
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- 2022
13. Can the Philicity of Radicals Be Influenced by Oriented External Electric Fields?
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Thijs Stuyver, Rik H. Verschueren, Freija De Vleeschouwer, Ruben Van Lommel, Wim M. De Borggraeve, Chemistry, General Chemistry, and Faculty of Sciences and Bioengineering Sciences
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Dipole ,Chemical physics ,Chemistry ,Polarizability ,Electric field ,Radical ,Organic Chemistry ,Moment (physics) ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Biochemistry - Abstract
Herein, the effects of an electric field on radicals are investigated for a set of model radicals with varying complexity. An electric field impacts the intrinsic philicity of a radical, as quantified by the global electrophilicity index, ω. The extent of change in philicity depends on the directionality and strength of the applied electric field and the dipole moment and polarizability of the radical.
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- 2021
14. DFT exchange: sharing perspectives on the workhorse of quantum chemistry and materials science
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Andrew M. Teale, Trygve Helgaker, Andreas Savin, Carlo Adamo, Bálint Aradi, Alexei V. Arbuznikov, Paul W. Ayers, Evert Jan Baerends, Vincenzo Barone, Patrizia Calaminici, Eric Cancès, Emily A. Carter, Pratim Kumar Chattaraj, Henry Chermette, Ilaria Ciofini, T. Daniel Crawford, Frank De Proft, John F. Dobson, Claudia Draxl, Thomas Frauenheim, Emmanuel Fromager, Patricio Fuentealba, Laura Gagliardi, Giulia Galli, Jiali Gao, Paul Geerlings, Nikitas Gidopoulos, Peter M. W. Gill, Paola Gori-Giorgi, Andreas Görling, Tim Gould, Stefan Grimme, Oleg Gritsenko, Hans Jørgen Aagaard Jensen, Erin R. Johnson, Robert O. Jones, Martin Kaupp, Andreas M. Köster, Leeor Kronik, Anna I. Krylov, Simen Kvaal, Andre Laestadius, Mel Levy, Mathieu Lewin, Shubin Liu, Pierre-François Loos, Neepa T. Maitra, Frank Neese, John P. Perdew, Katarzyna Pernal, Pascal Pernot, Piotr Piecuch, Elisa Rebolini, Lucia Reining, Pina Romaniello, Adrienn Ruzsinszky, Dennis R. Salahub, Matthias Scheffler, Peter Schwerdtfeger, Viktor N. Staroverov, Jianwei Sun, Erik Tellgren, David J. Tozer, Samuel B. Trickey, Carsten A. Ullrich, Alberto Vela, Giovanni Vignale, Tomasz A. Wesolowski, Xin Xu, Weitao Yang, Chemistry, General Chemistry, Vriendenkring VUB, Laboratoire de chimie théorique (LCT), Institut de Chimie du CNRS (INC)-Sorbonne Université (SU)-Centre National de la Recherche Scientifique (CNRS), Université Paris Dauphine-PSL, Université Paris sciences et lettres (PSL), CEntre de REcherches en MAthématiques de la DEcision (CEREMADE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Groupe Méthodes et outils de la chimie quantique (LCPQ) (GMO), Laboratoire de Chimie et Physique Quantiques Laboratoire (LCPQ), Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut de Chimie du CNRS (INC)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Institut National des Sciences Appliquées - Toulouse (INSA Toulouse), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS)-Université Toulouse III - Paul Sabatier (UT3), Institut National des Sciences Appliquées (INSA)-Université de Toulouse (UT)-Institut National des Sciences Appliquées (INSA)-Centre National de la Recherche Scientifique (CNRS), Institut de Chimie Physique (ICP), Institut de Chimie du CNRS (INC)-Université Paris-Saclay-Centre National de la Recherche Scientifique (CNRS), Systèmes de Fermions Finis - Agrégats (LPT), Laboratoire de Physique Théorique (LPT), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS)-Fédération de recherche « Matière et interactions » (FeRMI), ANR-10-LABX-0026,CSC,Center of Chemistry of Complex System(2010), ANR-19-CE07-0024,Co-LAB,Acide/base de Lewis confinées(2019), and European Project: 863481,PTEROSOR
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[CHIM.THEO]Chemical Sciences/Theoretical and/or physical chemistry ,[PHYS.MPHY]Physics [physics]/Mathematical Physics [math-ph] ,Materials Science ,ddc:540 ,General Physics and Astronomy ,Humans ,Physical and Theoretical Chemistry - Abstract
In this paper, the history, present status, and future of density-functional theory (DFT) is informally reviewed and discussed by 70 workers in the field, including molecular scientists, materials scientists, method developers and practitioners. The format of the paper is that of a roundtable discussion, in which the participants express and exchange views on DFT in the form of 300 individual contributions, formulated as responses to a preset list of 26 questions. Supported by a bibliography of 776 entries, the paper represents a broad snapshot of DFT, anno 2022.
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- 2022
15. Does Supramolecular Gelation Require an External Trigger?
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Ruben Van Lommel, Julie Van Hooste, Johannes Vandaele, Gert Steurs, Tom Van der Donck, Frank De Proft, Susana Rocha, Dimitrios Sakellariou, Mercedes Alonso, Wim M. De Borggraeve, Chemistry, and General Chemistry
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Biomaterials ,Single Particle Tracking ,Polymers and Plastics ,Organic Chemistry ,single particle tracking ,Bioengineering ,self-assembly ,gels ,Gels ,external stimuli ,LMWG - Abstract
The supramolecular gelation of small molecules is typically preceded by an external stimulus to trigger the self-assembly. The need for this trigger stems from the metastable nature of most supramolecular gels and can limit their applicability. Herein, we present a small urea-based molecule that spontaneously forms a stable hydrogel by simple mixing without the addition of an external trigger. Single particle tracking experiments and observations made from scanning electron microscopy indicated that triggerless gelation occurred in a similar fashion as the archetypical heat-triggered gelation. These results could stimulate the search for other supramolecular hydrogels that can be obtained by simple mixing. Furthermore, the mechanism of the heat-triggered supramolecular gelation was elucidated by a combination of molecular dynamics simulations and quantitative NMR experiments. Surprisingly, hydrogelation seemingly occurs via a stepwise self-assembly in which spherical nanoparticles mature into an entangled fibrillary network. ispartof: GELS vol:8 issue:12 ispartof: location:Switzerland status: published
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- 2022
16. Modulation of Metal Carbonyl Stretching Frequencies in the Second Coordination Sphere through the Internal Stark Effect
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Gemma L. Parker, Ruben Van Lommel, Nil Roig, Mercedes Alonso, Adrian B. Chaplin, Chemistry, and General Chemistry
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DYNAMICS ,Science & Technology ,bond theory ,Chemistry, Multidisciplinary ,Organic Chemistry ,NICKEL ,Molecular Conformation ,General Chemistry ,RHODIUM ,Ligands ,electrostatic interactions ,Ruthenium ,Catalysis ,REACTIVITY ,IRIDIUM COMPLEXES ,MACROCYCLIC PNP ,ELECTRONIC-PROPERTIES ,Chemistry ,rotaxanes ,carbonyl ligands ,Physical Sciences ,Rhodium ,LIGANDS ,macrocyclic ligands ,BASIS-SETS - Abstract
Spectroscopic and computational examination of a homologous series of rhodium(I) pybox carbonyl complexes has revealed a correlation between the conformation of the flanking aryl-substituted oxazoline donors and the carbonyl stretching frequency. This relationship is also observed experimentally for octahedral rhodium(III) and ruthenium(II) variants and cannot be explained through the classical, Dewar-Chatt-Duncanson, interpretation of metal-carbonyl bonding. Instead, these findings are reconciled by local changes in the magnitude of the electric field that is projected along the metal-carbonyl vector: the internal Stark effect. ispartof: CHEMISTRY-A EUROPEAN JOURNAL vol:28 issue:69 ispartof: location:Germany status: published
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- 2022
17. Theoretical study of Li2Ti6O13, Li2Sn6O13 and Li2Zr6O13 as possible cathode in Li-ion batteries
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J.R. Fernández-Gamboa, Frederik Tielens, Yohandys A. Zulueta, Faculty of Sciences and Bioengineering Sciences, Chemistry, and General Chemistry
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Mechanics of Materials ,Mechanical Engineering ,General Materials Science ,Condensed Matter Physics - Abstract
Efficient energy storage devices, such as batteries and capacitors play an important role in the development of renewable energy sources. C2/m space group Li2B6O13 (B = Ti4+, Sn4+, or Zr4+) compounds are expected to be materials with high potential for use as negative electrodes in high-performance batteries. The structural and electronic properties of these materials were studied in this article using density functional theory. The increase of the ionic radius of the B ions in the studied materials expands the unit cell parameters and the Li–Li distance in the channel of the Li2B6O13 (B = Ti4+, Sn4+, or Zr4+) compounds. Electronic structure calculations confirm that all structures present semiconductor characteristics. Li2Sn6O13 presents the best semiconductor properties with a band gap of 1.24 eV. The open cell voltages are found to be 2.20, 2.70 and 1.95 V per Li+/Li intercalation in Li2B6O13 structures, respectively. These predicted properties bring in new evidence to consider of these Li2B6O13 for use asan alternative battery materials.
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- 2022
18. Quest for the Most Aromatic Pathway in Charged Expanded Porphyrins
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Irene Casademont‐Reig, Tatiana Woller, Victor García, Julia Contreras‐García, William Tiznado, Miquel Torrent‐Sucarrat, Eduard Matito, Mercedes Alonso, European Commission, Chemistry, and General Chemistry
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charged macrocycles ,annulene model ,Organic Chemistry ,porphyrinoids ,aromaticity ,General Chemistry ,ring currents ,Catalysis - Abstract
Despite the central role of aromaticity in the chemistry of expanded porphyrins, the evaluation of aromaticity remains difficult for these extended macrocycles. The presence of multiple conjugation pathways and different planar and nonplanar π-conjugation topologies makes the quantification of global and local aromaticity even more challenging. In neutral expanded porphyrins, the predominance of the aromatic conjugation pathway passing through the imine-type nitrogens and circumventing the amino NH groups is established. However, for charged macrocycles, the question about the main conjugation circuit remains open. Accordingly, different conjugation pathways in a set of neutral, anionic, and cationic expanded porphyrins were investigated by means of several aromaticity indices rooted in the structural, magnetic, and electronic criteria. Overall, our results reveal the predominance of the conjugation pathway that passes through all nitrogen atoms to describe the aromaticity of deprotonated expanded porphyrins, while the outer pathway through the perimeter carbon atoms becomes the most aromatic in protonated macrocycles. In nonplanar and charged macrocycles, a discrepancy between electronic and magnetic descriptors is observed. Nevertheless, our work demonstrates AVmin remains the best tool to determine the main conjugation pathway of expanded porphyrins. M.A. and I.C.R. wish to acknowledge the VUB for a Strategic Research Program awarded to ALGC. The resources and services used in this work were provided by the Flemish Supercomputer Center (VSC), funded by the Research Foundation - Flanders (FWO), and the Flemish Government. I.C.R. acknowledges co-funding from the European Union′s Horizon 2020 research and innovation Maria Skłodowska-Curie Actions, under grant agreement number 945380. It has been also supported by grants from the Spanish government MICINN (PGC2018-098212-B-C21, PID2019-104772GB, PID2019-105488GB-I00, and PCI2019-103657), Diputación Foral de Gipuzkoa (2019-CIEN-000092-01), Gobierno Vasco (IT1346-19, IT1254-19, and PIBA19-0004), and the DIPC (DIPC_INV_003132). Open Access funding provided by University of Basque Country.
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- 2022
19. Reactivity of a N‐Coordinated Germylene‐Borane Complex: From Ge→B to Ge→Ga Coordination
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Dominik Vítek, Aleš Růžička, Lise Vermeersch, Libor Dostál, Jan Turek, Roman Jambor, Chemistry, Faculty of Sciences and Bioengineering Sciences, and General Chemistry
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germylene ,NMR spectroscopy ,Organic Chemistry ,proton affinity ,group 13 metals ,General Chemistry ,coordination bond ,Catalysis - Abstract
Reactivity studies of the GeII→B complex L(Cl)Ge⋅BH3 (1; L=2-Et2NCH2-4,6-tBu2-C6H2) were performed to determine the effect on the GeII→B donation. N-coordinated compounds L(OtBu)Ge⋅BH3 (2) and [LGe⋅BH3]2 (3) were prepared. The possible tuning of the GeII→B interaction was proved experimentally, yielding compounds 1-PPh2-8-(LGe)-C10H6 (4) and L(Cl)Ge⋅GaCl3 (5) without a GeII→B interaction. In 5, an unprecedented GeII→Ga coordination was revealed. The experimental results were complemented by a theoretical study focusing on the bonding in 1−5. The different strength of the GeII→E (E=B, Ga) donation was evaluated by using energy decomposition analysis. The basicity of different L(X)Ge groups through proton affinity is also assessed.
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- 2022
20. Properties of the density functional response kernels and its implications on chemistry
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Stijn Fias, Paul W. Ayers, Frank De Proft, Paul Geerlings, Chemistry, General Chemistry, and Vriendenkring VUB
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General Physics and Astronomy ,Physical and Theoretical Chemistry - Abstract
An overview of mathematical properties of the non-local second order derivatives of the canonical, grand canonical, isomorphic, and grand isomorphic ensembles is given. The significance of their positive or negative semidefiniteness and the implications of these properties for atoms and molecules are discussed. Based on this property, many other interesting properties can be derived, such as the expansion in eigenfunctions, bounds on the diagonal and off-diagonal elements, and the eigenvalues of these kernels. We also prove Kato’s theorem for the softness kernel and linear response and the dissociation limit of the linear responses as the sum of the linear responses of the individual fragments when dissociating a system into two non-interacting molecular fragments. Finally, strategies for the practical calculation of these kernels, their eigenfunctions, and their eigenvalues are discussed.
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- 2022
21. A sustainable way of recycling polyamides: dissolution and ammonolysis of polyamides to diamines and diamides using ammonia and biosourced glycerol
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Wouter Stuyck, Kwinten Janssens, Mats Denayer, Free De Schouwer, Robin Coeck, Katrien V. Bernaerts, Jelle Vekeman, Frank De Proft, Dirk E. De Vos, Chemistry, General Chemistry, Faculty of Sciences and Bioengineering Sciences, Faculty of Arts and Philosophy, AMIBM, and RS: FSE AMIBM
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DECOMPOSITION ,Chemistry ,DEPOLYMERIZATION ,Environmental Chemistry ,HYDROGENATION ,DEGRADATION ,POLYMERS ,NYLON-6 ,Pollution ,TOXICITY ,AMIDES - Abstract
Graphical representation of Lewis acid catalyzed ammonolysis of polyamide 66. In order to make recycling a viable strategy for post-consumer plastics, economically feasible revalorization processes must be developed. The ammonolysis of polyamides can be such a cutting-edge recycling technology; however, due to the rigid structure of these polyamide plastics, operating conditions of current ammonolysis processes are harsh, including high temperatures (>300 degrees C) and high NH3 pressures. Here, we report a very green and elegant ammonolysis process of the widely abundant polyamide 66 by using a hard Lewis acid catalyst and 1 bar of NH3 in a simple glycol solvent at 200 degrees C. Computational studies revealed that especially the vicinal diol moiety of these glycol solvents plays a key role in activation of the ammonia nucleophile, with glycerol being the most effective solvent, reaching the depolymerization equilibrium after 20 h even without a catalyst. To our delight, a biosourced glycerol (obtained from the saponification of triglycerides) could also directly serve as a suitable solvent, even outperforming the ammonolysis process in highly purified glycerol.
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- 2022
22. From Density Functional Theory to Conceptual Density Functional Theory and Biosystems
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Geerlings, Paul, Chemistry, Vriendenkring VUB, and General Chemistry
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response functions ,enzymatic catalysis ,computational peptidology ,reactivity descriptors ,toxicity ,Pharmaceutical Science ,biological activity ,DFT ,conceptual DFT ,CDFT principles ,applications ,conceptual dft ,Applications ,Drug Discovery ,Molecular Medicine - Abstract
The position of conceptual density functional theory (CDFT) in the history of density functional theory (DFT) is sketched followed by a chronological report on the introduction of the various DFT descriptors such as the electronegativity, hardness, softness, Fukui function, local version of softness and hardness, dual descriptor, linear response function, and softness kernel. Through a perturbational approach they can all be characterized as response functions, reflecting the intrinsic reactivity of an atom or molecule upon perturbation by a different system, including recent extensions by external fields. Derived descriptors such as the electrophilicity or generalized philicity, derived from the nature of the energy vs. N behavior, complete this picture. These descriptors can be used as such or in the context of principles such as Sanderson’s electronegativity equalization principle, Pearson’s hard and soft acids and bases principle, the maximum hardness, and more recently, the minimum electrophilicity principle. CDFT has known an ever-growing use in various subdisciplines of chemistry: from organic to inorganic chemistry, from polymer to materials chemistry, and from catalysis to nanotechnology. The increasing size of the systems under study has been coped with thanks to methodological evolutions but also through the impressive evolution in software and hardware. In this flow, biosystems entered the application portfolio in the past twenty years with studies varying (among others) from enzymatic catalysis to biological activity and/or the toxicity of organic molecules and to computational peptidology. On the basis of this evolution, one can expect that “the best is yet to come”.
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- 2022
- Full Text
- View/download PDF
23. Sn,P-Peri-Substituted Naphthalene as a Ligand for Transition Metals
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Michal Aman, Libor Dostál, Zdeňka Růžičková, Jan Turek, Roman Jambor, Chemistry, and General Chemistry
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Inorganic Chemistry ,Organic Chemistry ,Physical and Theoretical Chemistry - Abstract
Peri-substituted naphthalene 1-PPh2-8-SnL-C10H6 (1) [L = 2,6-(Me2NCH2)2C6H3] was used as a ligand for the complexation of transition metals (TMs). The presence of two donor atoms provided rigid κ2P,Sn-coordinated complexes of TM. Correspondingly, reactions of 1 with binuclear Mn2(CO)10 and Co2(CO)8 yielded ionic complexes [(κ2-1)Mn(CO)4]+ [Mn(CO)5]− (2) and [(κ2-1)Co(CO)3]+ [Co(CO)4]− (3), first examples of Sn-coordinated Mn(CO)4+ and Co(CO)3+ cations. The reactivity of 1 toward TM–Cl complexes is quite different. During these reactions, transmetallation with subsequent elimination of L(Cl)Sn was observed. However, L(Cl)Sn remained in the coordination sphere of the TM, yielding P-coordinated heterobimetallic TM complexes 1-PPh2-8-[Rh(COD){Sn(Cl)L}]C10H6 (7), 1-PPh2-8-[Ir(COD){Sn(Cl)L}]C10H6 (8), and 1-PPh2-8-[Pd(Cl){Sn(Cl)L}]-C10H6 (9) with additional Sn→TM intermolecular coordination. These transmetallations may be kinetically driven, as suggested by density functional theory calculations and isolation of the κ2P,Sn-coordinated complex of PtCl2, [(κ2-1)PtCl2] (10). Thus, the reactivity of 1 clearly deviates from the P,Sn-based ligands studied so far.
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- 2022
24. Non-fluorinated non-solvating cosolvent enabling superior performance of lithium metal negative electrode battery
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Junyeob Moon, Dong Ok Kim, Lieven Bekaert, Munsoo Song, Jinkyu Chung, Danwon Lee, Annick Hubin, Jongwoo Lim, Materials and Chemistry, Faculty of Engineering, General Chemistry, Earth System Sciences, and Electrochemical and Surface Engineering
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Multidisciplinary ,General Physics and Astronomy ,General Chemistry ,General Biochemistry, Genetics and Molecular Biology - Abstract
The growth of dendrites on lithium metal electrodes is problematic because it causes irreversible capacity loss and safety hazards. Localised high-concentration electrolytes (LHCEs) can form a mechanically stable solid-electrolyte interphase and prevent uneven growth of lithium metal. However, the optimal physicochemical properties of LHCEs have not been clearly determined which limits the choice to fluorinated non-solvating cosolvents (FNSCs). Also, FNSCs in LHCEs raise environmental concerns, are costly, and may cause low cathodic stability owing to their low lowest unoccupied molecular orbital level, leading to unsatisfactory cycle life. Here, we spectroscopically measured the Li+ solvation ability and miscibility of candidate non-fluorinated non-solvating cosolvents (NFNSCs) and identified the suitable physicochemical properties for non-solvating cosolvents. Using our design principle, we proposed NFNSCs that deliver a coulombic efficiency up to 99.0% over 1400 cycles. NMR spectra revealed that the designed NFNSCs were highly stable in electrolytes during extended cycles. In addition, solvation structure analysis by Raman spectroscopy and theoretical calculation of Li+ binding energy suggested that the low ability of these NFNSCs to solvate Li+ originates from the aromatic ring that allows delocalisation of electron pairs on the oxygen atom.
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- 2022
25. Conceptual density functional theory under pressure
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J. Eeckhoudt, T. Bettens, P. Geerlings, R. Cammi, B. Chen, M. Alonso, F. De Proft, Chemistry, Faculty of Sciences and Bioengineering Sciences, General Chemistry, and Vriendenkring VUB
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General Chemistry - Abstract
High pressure chemistry offers the chemical community a range of possibilities to control chemical reactivity, develop new materials and fine-tune chemical properties. Despite the large changes that extreme pressure brings to the table, the field has mainly been restricted to the effects of volume changes and thermodynamics with less attention devoted to electronic effects at the molecular scale. This paper combines the conceptual DFT framework for analyzing chemical reactivity with the XP-PCM method for simulating pressures in the GPa range. Starting from the new derivatives of the energy with respect to external pressure, an electronic atomic volume and an atomic compressibility are found, comparable to their enthalpy analogues, respectively. The corresponding radii correlate well with major known sets of this quantity. The ionization potential and electron affinity are both found to decrease with pressure using two different methods. For the electronegativity and chemical hardness, a decreasing and increasing trend is obtained, respectively, and an electronic volume-based argument is proposed to rationalize the observed periodic trends. The cube of the softness is found to correlate well with the polarizability, both decreasing under pressure, while the interpretation of the electrophilicity becomes ambiguous at extreme pressures. Regarding the electron density, the radial distribution function shows a clear concentration of the electron density towards the inner region of the atom and periodic trends can be found in the density using the Carbó quantum similarity index and the Kullback-Leibler information deficiency. Overall, the extension of the CDFT framework with pressure yields clear periodic patterns.
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- 2022
26. Elucidation of the IR of Cu and Mn substituted intraframework SiBEA zeolites
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Etienne P. Hessou, Michael Badawi, Laetitia Valentin, Guy Atohoun, Stanislaw Dzwigaj, Monica Calatayud, Frederik Tielens, Chemistry, and General Chemistry
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CuSiBEA ,Chemistry(all) ,IR ,MnSiBEA ,zeolites ,General Chemistry ,DFT ,Catalysis - Abstract
Copper and manganese modified zeolites play key roles in selective oxidation catalytic reactions. Combining Density Functional Perturbation Theory (DFPT) implemented in VASP, and infrared spectroscopy experiments, we have studied and elucidated the incorporation of Cu2+ and Mn2+ in the framework of SiBEA zeolite. Six isomers are investigated for both models CuSiBEA and MnSiBEA. The energy stability study identified the most stable isomer in each case, which correspond to M-O2 bent moieties in the vicinity of hydroxyl groups. The isomers are then characterized by experimental and theoretical IR spectra. Both experimental and calculated IR spectra are in good agreement highlighting the presence of active sites (Cu-OH and Mn-OH) in the obtained models. The accurate molecular description of the nature of the active sites presented in this work will be important for understanding the catalysis going on and for developing novel catalytic processes.
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- 2022
27. Reaction Mechanisms for Graphene and Carbon Nanotube Fluorination
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Miquel Torrent-Sucarrat, Gregory Van Lier, Miquel Solà, Paul Geerlings, Sílvia Osuna, Christopher P. Ewels, Institut de biologie et chimie des protéines [Lyon] (IBCP), Université Claude Bernard Lyon 1 (UCBL), Université de Lyon-Université de Lyon-Centre National de la Recherche Scientifique (CNRS), Departement of General Chemistry (ALGC) (ALG), Université libre de Bruxelles (ULB), Institut des Matériaux Jean Rouxel (IMN), Université de Nantes - UFR des Sciences et des Techniques (UN UFR ST), Université de Nantes (UN)-Université de Nantes (UN)-Centre National de la Recherche Scientifique (CNRS)-Institut de Chimie du CNRS (INC)-Ecole Polytechnique de l'Université de Nantes (EPUN), Université de Nantes (UN)-Université de Nantes (UN), General and Organic Chemistry, General Chemistry, and Chemistry
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Reaction mechanism ,Nanotube ,Materials science ,Selective chemistry of single-walled nanotubes ,chemistry.chemical_element ,Nanotechnology ,02 engineering and technology ,Carbon nanotube ,010402 general chemistry ,01 natural sciences ,law.invention ,Condensed Matter::Materials Science ,law ,Physics::Atomic and Molecular Clusters ,Physics::Chemical Physics ,Physical and Theoretical Chemistry ,Nuclear Experiment ,Astrophysics::Galaxy Astrophysics ,reaction Mechanisms ,Graphene ,021001 nanoscience & nanotechnology ,0104 chemical sciences ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,Carbon nanotube quantum dot ,General Energy ,chemistry ,Chemical engineering ,Fluorine ,[PHYS.COND.CM-MS]Physics [physics]/Condensed Matter [cond-mat]/Materials Science [cond-mat.mtrl-sci] ,Density functional theory ,0210 nano-technology - Abstract
International audience; Via density functional theory calculations, we explore the process of graphene and carbon nanotube fluorination. Contrary to graphene, HF-catalyzed carbon nanotube fluorination adds fluorine pairs at (1,4) spacing, naturally leading to a self-organized C4F coverage, which call subsequently rearrange into dense axial C2F lines by fluorine diffusion upon solubilization or heat treatment. Controlling the fluorination process and subsequent nanotube processing results in fluorinated material types with unexplored electronic and chemical properties.
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- 2010
28. Reactivity of Single Transition Metal Atoms on a Hydroxylated Amorphous Silica Surface: A Periodic Conceptual DFT Investigation
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Frederik Tielens, Stefaan Cottenier, Mercedes Alonso, Bert M. Weckhuysen, Paul W. Ayers, Frank De Proft, Xavier Deraet, Jan Turek, General Chemistry, Chemistry, and Faculty of Sciences and Bioengineering Sciences
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010405 organic chemistry ,Chemistry ,Organic Chemistry ,Fermi level ,General Chemistry ,010402 general chemistry ,01 natural sciences ,London dispersion force ,Catalysis ,0104 chemical sciences ,symbols.namesake ,Chemical physics ,Atom ,symbols ,Density of states ,Oxophilicity ,Reactivity (chemistry) ,Density functional theory ,van der Waals force - Abstract
The drive to develop maximal atom-efficient catalysts coupled to the continuous striving for more sustainable reactions has led to an ever-increasing interest in single-atom catalysis. Based on a periodic conceptual density functional theory (cDFT) approach, fundamental insights into the reactivity and adsorption of single late transition metal atoms supported on a fully hydroxylated amorphous silica surface have been acquired. In particular, this investigation revealed that the influence of van der Waals dispersion forces is especially significant for a silver (98 %) or gold (78 %) atom, whereas the oxophilicity of the Group 8–10 transition metals plays a major role in the interaction strength of these atoms on the irreducible SiO2 support. The adsorption energies for the less-electronegative row 4 elements (Fe, Co, Ni) ranged from −1.40 to −1.92 eV, whereas for the heavier row 5 and 6 metals, with the exception of Pd, these values are between −2.20 and −2.92 eV. The deviating behavior of Pd can be attributed to a fully filled d-shell and, hence, the absence of the hybridization effects. Through a systematic analysis of cDFT descriptors determined by using three different theoretical schemes, the Fermi weighted density of states approach was identified as the most suitable for describing the reactivity of the studied systems. The main advantage of this scheme is the fact that it is not influenced by fictitious Coulomb interactions between successive, charged reciprocal cells. Moreover, the contribution of the energy levels to the reactivity is simultaneously scaled based on their position relative to the Fermi level. Finally, the obtained Fermi weighted density of states reactivity trends show a good agreement with the chemical characteristics of the investigated metal atoms as well as the experimental data.
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- 2021
29. Investigation of electronic and photocatalytic properties of AgTi2(PO4)3 NASICON-type phosphate: Combining experimental data and DFT calculations
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Ali Moussadik, Nour-eddine Lazar, Driss Mazkad, Flavio Siro Brigiano, Kitty Baert, Tom Hauffman, Abdellah Benzaouak, Younes Abrouki, Mohamed Kacimi, Frederik Tielens, Mohammed Halim, Adnane El Hamidi, Faculty of Sciences and Bioengineering Sciences, Chemistry, General Chemistry, Electrochemical and Surface Engineering, Materials and Chemistry, and Materials Characterisation
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General Chemical Engineering ,General Physics and Astronomy ,General Chemistry - Abstract
Ag-based semiconductors have attracted significant attention as promising visible-light photocatalysts for environmental purification. In this study, electronic and photocatalytic properties of AgTi2(PO4)3 NASICON-type phosphate, have been addressed in detail, combining experimental results and theoretical calculations. The as-prepared sample was characterized for its morphological, structural and optical properties by various techniques. The generalized gradient approximation by Perdew-Burke-Ernzerhof (GGA-PPE) within density functional theory (DFT) was used to investigate the electronic structure. We have applied corrective Hubbard U terms to Ti 3d orbitals in order to better reproduce the experimental band gap of 2.6 eV. The photocatalytic activity has then been performed for rhodamine B dye degradation under visible light illumination. Efficient dye degradation up to 97.2% was achieved in 120 min. In addition, the catalyst exhibited good stability over four consecutive cycles. Finally, combining experimental and theoretical findings, the origin of the photocatalytic activity was identified and a photodegradation mechanism was proposed.
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- 2023
30. <Review>Porphyrin Analogs as Photosensitizers in a Photodynamic Cancer Therapy
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MIKIO, SUZUKI, MIKA, HIROSE, SHIGEO, KAI, MATSUHIRO, HORI, TAKAHIRO, HAYASHI, 岐阜薬科大学一般化学研究室/岐阜薬科大学一般化学研究室/岐阜薬科大学一般化学研究室/岐阜薬科大学一般化学研究室/岐阜薬科大学一般化学研究室, and Department of General Chemistry, Gifu Pharmaceutical University/Department of General Chemistry, Gifu Pharmaceutical University/Department of General Chemistry, Gifu Pharmaceutical University/Department of General Chemistry, Gifu Pharmaceutical University/Department of General Chemistry, Gifu Pharmaceutical University
- Abstract
近年, 癌の光力学療法(PDT)が注目され, 精力的な研究が広範に進められている。現在, PDTの臨床試験に用いられている光増感剤としては, ヘマトポルフィリン誘導体(Hpd)が挙げられる。しかしながら, このHpdは, 高い組織透過性を有する600nm以上の可視光に対して弱い吸収を示すにとどまり, さらにHpd中の活性成分が腫瘍組織に取り込まれる割合は, 正常組織に比べてけた外れに大きいわけではない。したがって, より効果的なPDTを実施するにあたり, 適用される光増感剤としては, 組織透過性の高い赤色光領域に強い吸収を持ち, 腫瘍組織に対して高い選択性および親和性を具備するものが望まれる。このような理由で, 最近, 多種多様な新しい光増感剤が登場してきた。なかでも, メソ置換ポルフィリン, クロリン誘導体, バクテリオクロリンおよびフタロシアニンが, PDTにおける第二世代光増感剤として注目を集めている。, There is currently worldwide activity in the development of a photodynamic therapy (PDT) for cancer. The sensitizer currently used in clinical trials of PDT for cancer consists of a mixture of hematoporphyrin derivatives (Hpd). Hpd, however, absorbs only weakly above 600nm where light exhibits the deepest penetration into tissues. Furthermore, the uptake by the tumour of the active component in Hpd is only marginally higher than that by most normal tissues. Thus it has been evident for some time that the effectiveness of PDT could be enhanced by the use of photosensitizers that absorb more strongly towards the red end of the light spectrum and are more selectively retained by neoplastic tissues. For these reasons, several new classes of photosensitizers for PDT have been suggested over the past few years. Among them, substituted porphyrins, chlorin analogs, bacteriochlorins, and phtalocyanines have received increasing attention as a second- gereration photosensitizer in PDT.
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- 1990
31. Hydrogen-Bond-Assisted Diels–Alder Kinetics or Self-Healing in Reversible Polymer Networks? A Combined Experimental and Theoretical Study
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Jessica Mangialetto, Kiano Gorissen, Lise Vermeersch, Bruno Van Mele, Niko Van den Brande, Freija De Vleeschouwer, Materials and Chemistry, Faculty of Engineering, Faculty of Sciences and Bioengineering Sciences, Chemistry, Vriendenkring VUB, Physical Chemistry and Polymer Science, and General Chemistry
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Kinetics ,Chemistry (miscellaneous) ,Polymers ,Organic Chemistry ,Drug Discovery ,Molecular Medicine ,Pharmaceutical Science ,Hydrogen Bonding ,Physical and Theoretical Chemistry ,Models, Theoretical ,hydrogen bonding ,Diels–Alder catalysis ,microcalorimetry ,density functional theory ,Analytical Chemistry ,Hydrogen - Abstract
Diels–Alder (DA) cycloadditions in reversible polymer networks are important for designing sustainable materials with self-healing properties. In this study, the DA kinetics of hydroxyl-substituted bis- and tetrafunctional furans with bis- and tris-functional maleimides, both containing ether-functionalized spacers, is investigated by modelling two equilibria representing the endo and exo cycloadduct formation. Concretely, the potential catalysis of the DA reaction through hydrogen bonding between hydroxyl of the furans and carbonyl of the maleimides or ether of the spacers is experimentally and theoretically scrutinized. Initial reaction rates and forward DA rate constants are determined by microcalorimetry at 20 °C for a model series of reversible networks, extended with (i) a hydroxyl-free network and hydroxyl-free linear or branched systems, and (ii) polypropylene glycol additives, increasing the hydroxyl concentration. A computational density-functional theory study is carried out on the endo and exo cycloadditions of furan and maleimide derivatives, representative for the experimental ones, in the absence and presence of ethylene glycol as additive. Additionally, an ester-substituted furan was investigated as a hydroxyl-free system for comparison. Experiment and theory indicate that the catalytic effect of H-bonding is absent or very limited. While increased concentration of H-bonding could in theory catalyze the DA reaction, the experimental results rule out this supposition.
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- 2022
- Full Text
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32. Nanostructured materials and heterogeneous catalysis : a succinct review regarding DeNox catalysis
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Dominique Bazin, Jelle Vekeman, Qing Wang, Xavier Deraet, Frank De Proft, Hazar Guesmi, Frederik Tielens, Chemistry, Faculty of Sciences and Bioengineering Sciences, and General Chemistry
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NO adsorption ,NANOMETER-SCALE ,General Chemical Engineering ,SURFACES ,IN-SITU ,DeNox catalysis ,DFT approach ,NOBLE-METAL ,Building and Construction ,General Chemistry ,CLOSE-PACKED TRANSITION ,Metallic cluster ,DENSITY-FUNCTIONAL THEORY ,SYNCHROTRON-RADIATION ,Chemistry ,Nanoscience ,BIMETALLIC CATALYSTS ,RH(111) SURFACE ,X-RAY ,Electrical and Electronic Engineering - Abstract
In this contribution, we would like to underline the peculiar chemical properties of nanome-ter scale metallic particles. To attain this goal, we select the case of DeNox catalysis (NOx reduction to nitrogen molecule) for which such nanomaterials play a crucial role. Experimental data as well as re-cent theoretical calculation through density functional theory are used to assess the relationship be-tween the adsorption mode of NO and the behaviour of nanometre scale metallic particles. Resume. Les oxydes d'azote NOx issus des gaz d'echappement des moteurs Diesel participent a la de-terioration de l'environnement, la moitie des emissions de NO leur etant imputable. Le monoxyde d'azote provient essentiellement des reactions chimiques entre l'azote de l'air et l'oxygene qui s'eta-blissent a tres haute temperature. Le defi consiste a reduire cette emission qui doit etre selective en azote (eviter la formation de N2O ou de NO2). En ce qui concerne les catalyseurs mis en & OELIG;uvre, on en distingue trois groupes : les oxydes de metaux, les metaux nobles et les zeolites. A partir de donnees ex-perimentales obtenues sur l'adsorption du NO sur des agregats monometalliques, une relation entre les modes d'adsorption de cette molzcule (adsorption molzculaire/chimisorption) et la rzponse de l'agrzgat mztallique face a cette adsorption (croissance/dissociation) a ztz proposze. Les ztudes thzo-riques baszes sur la thzorie de la fonctionnelle de la densitz confortent cette relation. Cette contri-bution przsente l'ensemble de ces rzsultats expzrimentaux et thzoriques et tache de montrer l'aspect przdictif d'une telle relation.
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- 2022
33. Peculiar opportunities given by XPS spectroscopy for the clinician
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Flavio Siro Brigiano, Dominique Bazin, Frederik Tielens, Chemistry, and General Chemistry
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Biomaterials ,medicine ,Chemistry(all) ,XPS ,Chemical Engineering(all) ,Pathological calcification ,Building and Construction ,Electrical and Electronic Engineering ,Prothesis - Abstract
X-ray Photoelectron Spectroscopy (XPS) constitutes an elegant way to describe the chemical characteristics of the surface of biological materials. It is thus a unique approach to decipher the interaction between biological materials and tissues. In the case of medical implants, it is thus possible to understand its biocompatibility as well as its integration in the body which can be wanted in the case of prothesis or avoided in the case of JJ-stents. More precisely, XPS can bring valuable information of the interaction between physiological calcification (here bone) and the prosthesis as well as the interaction between pathological calcifications (lithiasis) and the JJ-stent. This mini overview is dedicated to two communities, the physical chemists and the clinicians. In the first part of this overview, after an introduction on the basic principles of XPS, we focus on the theoretical techniques adopted for the computation of XPS spectra of materials. The second part, dedicated to clinicians, describes the useof XPS for the characterization of biological materials. We report which kind of chemical information can be gained by this surface-sensitive technique and how this information has a relevant impact on medical applications. Through different examples, we show that XPS is a strong and very useful tool, and thus receiving a crucial place in medical research.
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- 2022
34. Extending conceptual DFT to include external variables: the influence of magnetic fields
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Robin Francotte, Tom J. P. Irons, Andrew M. Teale, Frank de Proft, Paul Geerlings, Vriendenkring VUB, Chemistry, General Chemistry, and Faculty of Sciences and Bioengineering Sciences
- Subjects
General Chemistry - Abstract
An extension of conceptual DFT to include the influence of an external magnetic field is proposed in the context of a program set up to cope with the ever increasing variability of reaction conditions and concomitant reactivity. The two simplest global reactivity descriptors, the electronic chemical potential (μ) and the hardness (η), are considered for the main group atoms H-Kr using current density-functional theory. The magnetic field strength, |B|, is varied between 0.0 and 1.0 B0 = ħe−1a0−2 ≈ 2.3505 × 105 T, encompassing the Coulomb and intermediate regimes. The carbon atom is studied as an exemplar system to gain insight into the behaviour of the neutral, cationic and anionic species under these conditions. Their electronic configurations change with increasing |B|, leading to a piecewise behaviour of the ionization energy (I) and electron affinity (A) values as a function of |B|. This results in complex behaviour of properties such as the electronegativity χ = −1/2(I + A) = −μ and hardness η = 1/2(I − A). This raises an interesting question: to what extent are atomic properties periodic in the presence of a magnetic field? In the Coulomb regime, close to |B| = 0, we find the familiar periodicity of the atomic properties, and make the connections to response functions central to conceptual DFT. However, as the field increases in the intermediate regime configurational changes of the atomic species lead to discontinuous changes in their properties; fundamentally changing their behaviour, which is illustrated by constructing a periodic table of χ and η values at |B| = 0.5 B0. These values tend to increase for groups 1-2 and decrease for groups 16-18, leading to a narrower range overall and suggesting substantial changes in the chemistry of the main group elements. Changes within each group are also examined as a function of |B|. These are more complex to interpret due to the larger number of configurations accessible to heavier elements at high field. This is illustrated for group 17 where Cl and Br have qualitatively different configurations to their lighter cogener at |B| = 0.5 B0. The insight into periodic trends in strong magnetic fields may provide a crucial starting point for predicting chemical reactivity under these exotic conditions.
- Published
- 2022
35. Conceptual density functional theory for temporary anions stabilized by scaled nuclear charges
- Author
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Titeca, Charlotte, De Proft, Frank, Jagau, Thomas-C., Faculty of Sciences and Bioengineering Sciences, General Chemistry, and Chemistry
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General Physics and Astronomy ,Physical and Theoretical Chemistry - Abstract
The charge stabilization method has often been used before for obtaining energies of temporary anions. Herein, we combine this method for the first time with conceptual density functional theory and quantum theory of atoms in molecules, by extending it to the study of nuclear Fukui functions, atom-condensed electronic Fukui functions and bond critical points. This is applied to temporary anions of ethene and chlorinated ethene compounds, which are known to undergo dissociative electron attachment (DEA). It appears that the method is able to detect multiple valence resonance states in the same molecule, namely a Π and a Σ state. The accuracy of the method is assessed by comparing the obtained electron affinities with experimental affinities reported in literature. The obtained nuclear and atom-condensed electronic Fukui functions are interpreted as nuclear forces and electron distributions respectively, and show clear differences between the Π and Σ states. This allows a more profound characterization and understanding of how the DEA process proceeds. The conclusions are in line with findings from earlier publications, proving that the combination of conceptual DFT with the charge stabilization method yields reasonable results at rather low computational cost.
- Published
- 2022
- Full Text
- View/download PDF
36. Mechanistic characterization of zeolite-catalyzed aromatic electrophilic substitution at realistic operating conditions
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Massimo Bocus, Louis Vanduyfhuys, Frank De Proft, Bert M. Weckhuysen, Veronique Van Speybroeck, Chemistry, and General Chemistry
- Subjects
STABILITY ,BENZENE ,water ,ALKYLATION ,FRAMEWORK ,DFT ,molecular dynamics ,REACTIVITY ,SIMULATIONS ,Chemistry ,RATE CONSTANTS ,Physics and Astronomy ,enhanced sampling mechanism ,MONTE-CARLO ,ETHYLATION ,benzene ethylation ,zeolite ,ETHENE - Abstract
Zeolite-catalyzed benzene ethylation is an important industrial reaction, as it is the first step in the production of styrene for polymer manufacturing. Furthermore, it is a prototypical example of aromatic electrophilic substitution, a key reaction in the synthesis of many bulk and fine chemicals. Despite extensive research, the reaction mechanism and the nature of elusive intermediates at realistic operating conditions is not properly understood. More in detail, the existence of the elusive arenium ion (better known as Wheland complex) formed upon electrophilic attack on the aromatic ring is still a matter of debate. Temperature effects and the presence of protic guest molecules such as water are expected to impact the reaction mechanism and lifetime of the reaction intermediates. Herein, we used enhanced sampling ab initio molecular dynamics simulations to investigate the complete mechanism of benzene ethylation with ethene and ethanol in the H-ZSM-5 zeolite. We show that both the stepwise and concerted mechanisms are active at reaction conditions and that the Wheland intermediate spontaneously appears as a shallow minimum in the free energy surface after the electrophilic attack on the benzene ring. Addition of water enhances the protonation kinetics by about 1 order of magnitude at coverages of one water molecule per Brønsted acidic site. In the fully solvated regime, an overstabilization of the BAS as hydronium ion occurs and the rate enhancement disappears. The obtained results give critical atomistic insights in the role of water to selectively tune the kinetics of protonation reactions in zeolites.
- Published
- 2022
37. Strengthening Engineered Nanocrystal Three-Dimensional Superlattices via Ligand Conformation and Reactivity
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Plunkett, Alexander, Kampferbeck, Michael, Bor, Buesra, Sazama, Uta, Krekeler, Tobias, Bekaert, Lieven, Noei, Heshmat, Giuntini, Diletta, Fröba, Michael, Stierle, Andreas, Weller, Horst, Vossmeyer, Tobias, Schneider, Gerold A., Domènech, Berta, Materials and Chemistry, Faculty of Engineering, General Chemistry, Publica, and Mechanics of Materials
- Subjects
nanocrystals ,nanoindentation ,supercrystals ,ddc:540 ,Ingenieurwissenschaften [620] ,robustness ,self-assembly ,ddc:620 ,organic ligands ,Cross-linking ,cross-linking - Abstract
ACS nano 16(8), 11692 - 11707 (2022). doi:10.1021/acsnano.2c01332, Nanocrystal assembly into ordered structures provides mesostructural functional materials with a precise control that starts at the atomic scale. However, the lack of understanding on the self-assembly itself plus the poor structural integrity of the resulting supercrystalline materials still limits their application into engineered materials and devices. Surface functionalization of the nanobuilding blocks with organic ligands can be used not only as a means to control the interparticle interactions during self-assembly but also as a reactive platform to further strengthen the final material via ligand cross-linking. Here, we explore the influence of the ligands on superlattice formation and during cross-linking via thermal annealing. We elucidate the effect of the surface functionalization on the nanostructure during self-assembly and show how the ligand-promoted superlattice changes subsequently alter the cross-linking behavior. By gaining further insights on the chemical species derived from the thermally activated cross-linking and its effect in the overall mechanical response, we identify an oxidative radical polymerization as the main mechanism responsible for the ligand cross-linking. In the cascade of reactions occurring during the surface-ligands polymerization, the nanocrystal core material plays a catalytic role, being strongly affected by the anchoring group of the surface ligands. Ultimately, we demonstrate how the found mechanistic insights can be used to adjust the mechanical and nanostructural properties of the obtained nanocomposites. These results enable engineering supercrystalline nanocomposites with improved cohesion while preserving their characteristic nanostructure, which is required to achieve the collective properties for broad functional applications., Published by Soc., Washington, DC
- Published
- 2022
38. Urinary tract infection inducing stones
- Author
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Michel Daudon, Margaux Petay, Sophie Vimont, Ariane Deniset, Frederik Tielens, Jean-Philippe Haymann, Emmanuel Letavernier, Vincent Frochot, Dominique Bazin, Chemistry, and General Chemistry
- Subjects
Carbonation rate ,Chemistry(all) ,Struvite ,Amorphous carbonated calcium phosphate ,Whitlockite ,Chemical Engineering(all) ,Carbapatite ,Infection-induced calculi ,Building and Construction ,Electrical and Electronic Engineering ,Urease-splitting bacteria - Abstract
Most papers on kidney stones arising from infection concentrate on the mineral struvite. In this contribution, we would like to call attention to other mineral phases such as highly carbonated calcium phosphate apatite, ammonium urate, and whitlockite, by presenting clinical and chemical data. We start with epidemiological data which emphasize the increase in the prevalence of kidney stones related to infection. Then we present a statistical analysis of more than 85,000 stones which have been analysed at the Laboratoire des Lithiases of Assistance Publique-Hôpitaux de Paris which gives insights regarding the link between urinary tract infection and struvite, carbonated calcium phosphate apatite (carbapatite), and also surprisingly whitlockite. Some information regarding the pathogenesis of kidney stones linked to infection, the nature of the bacteria which have been identified, and the approach to precisely analyse infrared spectra to identify struvite, carbapatite, and whitlockite, conclude this first part. To complete this clinical description, we describe the crystallographic structure and the chemistry of three relevant compounds namely carbonated calcium phosphate, struvite, and whitlockite. To conclude this second part, the dependence of crystallite morphology of struvite on pH and on the presence, or absence, of bacteria, is described. Based on clinical and chemical data, it is becoming clear that struvite is not the only mineral intimately related to renal infectious processes, but that whitlockite and carbapatite with a high carbonation rate are strongly associated with urinary tract infection as well.
- Published
- 2022
39. Autobiography of Paul Geerlings
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Paul Geerlings, Vriendenkring VUB, Quantum Chemistry - Molecular Modelling, Chemistry, and General Chemistry
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Literature ,business.industry ,Chemistry ,Biography ,Physical and Theoretical Chemistry ,business - Published
- 2020
40. How Do Local Reactivity Descriptors Shape the Potential Energy Surface Associated with Chemical Reactions? The Valence Bond Delocalization Perspective
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Sason Shaik, Frank De Proft, Paul Geerlings, Thijs Stuyver, Chemistry, Vriendenkring VUB, Quantum Chemistry - Molecular Modelling, and General Chemistry
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Chemistry ,Perspective (graphical) ,General Chemistry ,010402 general chemistry ,01 natural sciences ,Biochemistry ,Chemical reaction ,Catalysis ,Article ,Addition/Correction ,0104 chemical sciences ,Delocalized electron ,Colloid and Surface Chemistry ,Chemical physics ,Potential energy surface ,Valence bond theory ,Density functional theory ,Reactivity (chemistry) ,Fukui function - Abstract
How do local reactivity descriptors, such as the Fukui function and the local spin density distribution, shape the potential energy surface (PES) associated with chemical reactions and thus govern reactivity trends and regioselective preferences? This is the question that is addressed here through a qualitative valence bond (VB) analysis. We demonstrate that common density functional theory (DFT)-based local reactivity descriptors can essentially be regarded-in one way or another-as indirect measures of delocalization, i.e., resonance stabilization, of the reactants within VB theory. The inherent connection between (spatial) delocalization and (energetic) resonance stabilization embedded in VB theory provides a natural and elegant framework for analyzing and comprehending the impact of individual local reactivity descriptors on the global PES. Our analysis provides new insights into the role played by local reactivity descriptors and illustrates under which conditions they can sometimes fail to predict reactivity trends and regioselective preferences, e.g., in the case of ambident reactivity. This treatment constitutes a first step toward a unification of VB theory and conceptual DFT.
- Published
- 2020
41. Switching between Hückel and Möbius aromaticity: a density functional theory and information-theoretic approach study
- Author
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Paul Geerlings, Mercedes Alonso, Frank De Proft, Tian Lu, Shubin Liu, Chunying Rong, Donghai Yu, Chemistry, Vriendenkring VUB, Quantum Chemistry - Molecular Modelling, and General Chemistry
- Subjects
Physics ,Möbius ,information-theoretic approach ,010405 organic chemistry ,General Physics and Astronomy ,Aromaticity ,aromaticity ,010402 general chemistry ,Ring (chemistry) ,benziporphyrins ,DFT ,Hückel ,01 natural sciences ,0104 chemical sciences ,Möbius aromaticity ,Chemical physics ,Close relationship ,Phenylene ,Density functional theory ,Physical and Theoretical Chemistry ,Topology (chemistry) ,Antiaromaticity - Abstract
Benziporphyrins are versatile macrocycles exhibiting aromaticity switching behaviors. The existence of both Hückel and Möbius (anti)aromaticity has been reported in these systems, whose validity is respectively governed by the [4n + 2] and [4n] π-electron rule on the macrocyclic pathway. Despite the experimental evidence on the floppiness of benziporphyrins, the switching mechanism between Hückel and Möbius structures is still not clear, as well as the factors influencing the stability of the different π-conjugation topologies. For these reasons, we performed a systematic study on A,D-di-p-benzihexaphyrins(1.1.1.1.1.1) with two redox states corresponding to [28] and [30] π-electron conjugation pathways. Whereas benzi[28]hexaphyrin obeys Möbius aromaticity, benzi[30]hexaphyrin follows Hückel aromaticity. The dynamic interconversion between Möbius and Hückel aromaticity is investigated through the rotation of a phenylene ring, which acts as the topology selector. Further analyses of the energy profiles using energy decomposition and information-theoretic approaches provide new insights into conformational stability, aromaticity and antiaromaticity for these species. Strong and opposite cross correlations between aromaticity indexes and information-theoretic quantities were found for the two macrocyclic systems with opposite global aromaticity and antiaromaticity behaviors. These results indicate that Hückel and Möbius aromaticity and antiaromaticity, though qualitatively different, are closely related and can be interchanged, and information-theoretic quantities provide a novel understanding about their relevance. Our present results should provide in-depth insights to appreciate the nature and origin about Möbius (anti)aromaticity and its close relationship with Hückel (anti)aromaticity.
- Published
- 2020
42. The hunt for reactive alkynes in bio-orthogonal click reactions: insights from mechanochemical and conceptual DFT calculations†
- Author
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Frank De Proft, Paul Geerlings, Mercedes Alonso, Tom Bettens, Chemistry, Faculty of Sciences and Bioengineering Sciences, Vriendenkring VUB, Quantum Chemistry - Molecular Modelling, and General Chemistry
- Subjects
Chemistry ,Materials science ,Nucleophile ,Chemical physics ,Bent molecular geometry ,Molecule ,Density functional theory ,Linear molecular geometry ,Reactivity (chemistry) ,Context (language use) ,General Chemistry ,Physics::Chemical Physics ,Triple bond - Abstract
In our effort to implement the mechanical force used to activate single molecules in mechanochemistry in the context of conceptual density functional theory, we present a theoretical investigation of strained alkynes for rationalizing structural trends as well as the reactivity of cyclic alkynes that are of great importance in in vivo click reactions. The strain on the triple bond in cyclic alkynes is modeled by angular constraints in a 2-butyne fragment and the corresponding bending force is calculated by means of an extended COGEF (constrained geometries simulate external forces) model. In general, the force required to bend the triple bond is smaller with electron-withdrawing groups on the propargylic C-atom, which elegantly results in smaller angles around the triple bond in cyclic alkynes with such substitution pattern. By means of conceptual DFT descriptors, the electrophilic and nucleophilic character of bent triple bonds was investigated revealing moderate activation for small distortions from the linear geometry (0° to 15°) and a drastically more reactive π-space if the triple bond is bent further. This analysis of the intrinsic reactivity of the triple bond is in line with experimental observations, explaining the reactive nature of cyclooctynes and cycloheptynes, whereas larger cyclic systems do not drastically activate the triple bond., The force required to bend alkynes increases linearly with the angle and depends on the substituent pattern. The reactivity of the triple bond does not readily increase and is less influenced by the substituent pattern for larger bends.
- Published
- 2019
43. Sn,P-coordinated Ru cation: a robust catalyst for aerobic oxidations of benzylamine and benzyl alcohol
- Author
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Jens Beckmann, Jan Turek, Jiří Tydlitát, Aleš Růžička, Roman Jambor, Libor Dostál, Michal Aman, Chemistry, and General Chemistry
- Subjects
Ligand ,Reducing agent ,Metals and Alloys ,Ionic bonding ,General Chemistry ,Medicinal chemistry ,Catalysis ,Surfaces, Coatings and Films ,Electronic, Optical and Magnetic Materials ,chemistry.chemical_compound ,Benzylamine ,chemistry ,Benzyl alcohol ,Materials Chemistry ,Ceramics and Composites ,Naphthalene - Abstract
A stable ionic κ2Sn,P-coordinated Ru complex shows excellent catalytic activity in aerobic oxidations of benzylamine and benzyl alcohol. This complex is stabilized by a stannylene-phosphine peri-substituted naphthalene ligand, which can act as either a reducing agent for a Ru(III) complex or as a κ2Sn,P-chelating ligand for Ru(II) compounds.
- Published
- 2021
44. N-Donor stabilized tin(ii) cations as efficient ROP catalysts for the synthesis of linear and star-shaped PLAs via the activated monomer mechanism
- Author
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Miroslav Novák, Yaraslava Milasheuskaya, Zdeňka Růžičková, Jan Turek, Roman Jambor, Štěpán Podzimek, Chemistry, and General Chemistry
- Subjects
Steric effects ,Ligand ,ring-opening polymerization ,iminopyridine ,Imine ,Substituent ,Ionic bonding ,tin(II) cation ,DFT calculation ,iminopyridin ,ring-opening polymerace ,Medicinal chemistry ,Adduct ,Inorganic Chemistry ,chemistry.chemical_compound ,Monomer ,chemistry ,L-lactide ,cínatý kation ,L-laktid ,Lewis acids and bases ,DFT kalkulace - Abstract
Alpha-Iminopyridine ligands L-1(2-(CH=N(C6H2-2,4,6-Ph-3))C5H4N), L-2 (2-(CH=N(C6H2-2,4,6-tBu(3)))C5H4N) and L-3 (1,2-(C5H4N-2-CH=N)(2)CH2CH2) differing by the steric demand of the substituent on the imine CH=N group and by the number of donating nitrogen atoms were utilized to initiate a Lewis base mediated ionization of SnCl2 in an effort to prepare ionic tin(II) species [L1-3 -> SnCl][SnCl3]. The reaction of L-1 and L-2 with SnCl2 led to the formation of neutral adducts [L-1 -> SnCl2] (2) and [L-2 -> SnCl2] (3). The preparation of the desired ionic compounds was achieved by subsequent reactions of 2 and 3 with an equivalent of SnCl2 or GaCl3. In contrast, ligand L-3 containing four donor nitrogen atoms showed the ability to ionize SnCl2 and also Sn(OTf)(2), yielding [L-3 -> SnCl][SnCl3] (7) and [L-3 -> Sn(H2O)][OTf](2) (8). The study thus revealed that the reaction is dependent on the type of the ligand. The prepared complexes 4-8 together with the previously reported [{2-((CH3)C=N(C6H3-2,6-iPr(2)))-6-CH3O-C5H3N}SnCl][SnCl3] (1) were tested as catalysts for the ROP of L-lactide, which could operate via an activated monomer mechanism. Finally, a DFT computational study was performed to evaluate the steric and electronic properties of the ionic tin(II) species 1 and 4-8 together with their ability to interact with the L-lactide monomer. Alfa-iminopyridinové ligandy L-1(2-(CH=N(C6H2-2,4,6-Ph-3))C5H4N), L-2 (2-(CH=N(C6H2-2,4,6- tBu(3)))C5H4N) a L-3 (1,2-(C5H4N-2-CH=N)(2)CH2CH2) lišící se stericitou substituentu na iminové skupině CH=N a počtem donorových atomů dusíku byly použity k autoionizaci SnCl2 zprostředkované Lewisovou bází ve snaze připravit cínaté iontové komplexy [L1-3 -> SnCl][SnCl3]. Reakce L-1 a L-2 se SnCl2 vedla ke vzniku neutrálních aduktů [L-1 -> SnCl2] (2) a [L-2 -> SnCl2] (3). Příprava požadovaných iontových sloučenin byla dosažena následnými reakcemi s ekvivalentem SnCl2 nebo GaCl3. Naproti tomu ligand L-3 obsahující čtyři donorové atomy dusíku vykazoval schopnost ionizovat SnCl2 a také Sn(OTf)(2), čímž vznikl [L-3 -> SnCl][SnCl3] (7) a [L-3 -> Sn(H20)][OTf](2) (8). Studie tak odhalila, že reakce je závislá na typu ligandu. Připravené komplexy 4-8 spolu s dříve uvedeným [{2-((CH3)C=N(C6H3-2,6-iPr(2)))-6-CH3O-C5H3N}SnCl][SnCl3] (1) byly testovány jako katalyzátory pro ROP L-laktidu prostřednictvím mechanismu aktivovaného monomeru. Nakonec byla provedena výpočetní DFT studie, aby se vyhodnotily sterické a elektronické vlastnosti cínatých iontových komplexů 1 a 4-8 spolu s jejich schopností interagovat s monomerem L-laktidu.
- Published
- 2021
45. Towards a predictive model for polymer solubility using the noncovalent interaction index: polyethylene as a case study
- Author
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Frederik Tielens, Jelle Vekeman, Frank De Proft, Mats Denayer, Chemistry, Faculty of Sciences and Bioengineering Sciences, and General Chemistry
- Subjects
Solvent ,Folding (chemistry) ,Hildebrand solubility parameter ,Molecular dynamics ,Chemistry ,Intermolecular force ,Solvation ,General Physics and Astronomy ,Thermodynamics ,Physical and Theoretical Chemistry ,Solubility ,Accessible surface area - Abstract
In this work we present the development of a novel, quantitative solubility descriptor based on the non-covalent interaction index. It is presented as a more insightful alternative to Hansen's solubility parameters and the COSMO model to assess and predict polymer solubility in different solvents. To this end, we studied the solvation behaviour as a function of the chain length of a single chain of arguably the most simple polymer, polyethylene, in anisole (solvent) and methanol (poor solvent) via molecular dynamics simulations. It was found that in anisole the solute maximized its interface with the solvent, whereas in methanol the macromolecule formed rod-like structures by folding on itself once the chain length surpassed a certain barrier. We assessed this behaviour – which can be related to solubility – quantitatively and qualitatively via well-known descriptors, namely the solvation free energy, and the solvent accessible surface area. In addition, we propose the non-covalent interaction (NCI) index as a versatile descriptor, providing information on the strength, as well as the nature, of the solute–solvent interactions, the solute's intramolecular interactions and on the solute's conformation, both qualitatively and quantitatively. Finally, as a quantitative measure for solubility, defined in this context as the solute's tendency to maximize its interactions with the solvent, we propose two new NCI-based descriptors: the relative integrated NCI density and the integrated NCI difference. The former represents the quantitative difference in solute–solvent interactions between a fully extended coil and the actual conformation during simulation and the latter the quantitative difference between the intermolecular (solute–solvent) and the intramolecular (in the solute) non-covalent interactions. The easy interpretation and calculation of these novel quantities open up the possibility of fast, reliable and insightful high-throughput screening of different (anti)solvent and solute combinations.
- Published
- 2021
46. Effects of Structural Substituents on the Electrochemical Decomposition of Carbonyl Derivatives and Formation of the Solid-Electrolyte Interphase in Lithium-Ion Batteries
- Author
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Joeri Van Mierlo, Xinhua Zhu, Mesfin Haile Mamme, Annick Hubin, S. Hamidreza Beheshti, Mehran Javanbakht, Hamidreza Behi, Hamid Omidvar, Maitane Berecibar, Electrical Engineering and Power Electronics, Electromobility research centre, Faculty of Engineering, Materials and Chemistry, General Chemistry, Earth System Sciences, and Electrochemical and Surface Engineering
- Subjects
Technology ,Control and Optimization ,Materials science ,Passivation ,Energy Engineering and Power Technology ,chemistry.chemical_element ,Electrolyte ,Electrochemistry ,Lithium-ion battery ,Graphite ,solid–electrolyte interphase ,electrolyte additive ,molecular tunning ,SEI stability ,irreversible capacity loss ,lithium-ion battery ,Electrical and Electronic Engineering ,Engineering (miscellaneous) ,Renewable Energy, Sustainability and the Environment ,solid-electrolyte interphase ,Anode ,chemistry ,Chemical engineering ,Lithium-Ion Battery ,Interphase ,Lithium ,Energy (miscellaneous) - Abstract
The solid–electrolyte interphase (SEI), the passivation layer formed on anode particles during the initial cycles, affects the performance of lithium-ion batteries (LIBs) in terms of capacity, power output, and cycle life. SEI features are dependent on the electrolyte content, as this complex layer originates from electrolyte decomposition products. Despite a variety of studies devoted to understanding SEI formation, the complexity of this process has caused uncertainty in its chemistry. In order to clarify the role of the substituted functional groups of the SEI-forming compounds in their efficiency and the features of the resulting interphase, the performance of six different carbonyl-based molecules has been investigated by computational modeling and electrochemical experiments with a comparative approach. The performance of the electrolytes and stability of the generated SEI are evaluated in both half-cell and full-cell configurations. Added to the room-temperature studies, the cyclability of the NMC/graphite cells is assessed at elevated temperatures as an intensified aging condition. The results show that structural adjustments within the SEI-forming molecule can ameliorate the cyclability of the electrolyte, leading to a higher capacity retention of the LIB cell, where cinnamoyl chloride is introduced as a novel and more sustainable SEI forming agent with the potential of improving the LIB capacity retention.
- Published
- 2021
47. A Combined Experimental/Quantum-Chemical Study of Tetrel, Pnictogen, and Chalcogen Bonds of Linear Triatomic Molecules
- Author
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Frank De Proft, Freija De Vleeschouwer, Wouter A. Herrebout, Paul Geerlings, Özge Ergün, Chemistry, General Chemistry, and Vriendenkring VUB
- Subjects
Halogen bond ,Materials science ,Valence (chemistry) ,Triatomic molecule ,quadrupole-dipole model ,Organic Chemistry ,Pharmaceutical Science ,Article ,Analytical Chemistry ,Chalcogen ,Chemistry ,QD241-441 ,Atomic orbital ,Chemistry (miscellaneous) ,Chemical physics ,Drug Discovery ,Atom ,Molecular Medicine ,Lewis acids and bases ,Physical and Theoretical Chemistry ,infrared spectroscopy ,Pnictogen ,Biology ,tetrel/pnictogen/chalcogen bonds - Abstract
Linear triatomic molecules (CO2, N2O, and OCS) are scrutinized for their propensity to form perpendicular tetrel (CO2 and OCS) or pnictogen (N2O) bonds with Lewis bases (dimethyl ether and trimethyl amine) as compared with their tendency to form end-on chalcogen bonds. Comparison of the IR spectra of the complexes with the corresponding monomers in cryogenic solutions in liquid argon enables to determine the stoichiometry and the nature of the complexes. In the present cases, perpendicular tetrel and pnictogen 1:1 complexes are identified mainly on the basis of the lifting of the degenerate ν 2 bending mode with the appearance of both a blue and a red shift. Van ′t Hoff plots of equilibrium constants as a function of temperature lead to complexation enthalpies that, when converted to complexation energies, form the first series of experimental complexation energies on sp1 tetrel bonds in the literature, directly comparable to quantum-chemically obtained values. Their order of magnitude corresponds with what can be expected on the basis of experimental work on halogen and chalcogen bonds and previous computational work on tetrel bonds. Both the order of magnitude and sequence are in fair agreement with both CCSD(T) and DFA calculations, certainly when taking into account the small differences in complexation energies of the different complexes (often not more than a few kJ mol−1) and the experimental error. It should, however, be noted that the OCS chalcogen complexes are not identified experimentally, most probably owing to entropic effects. For a given Lewis base, the stability sequence of the complexes is first successfully interpreted via a classical electrostatic quadrupole–dipole moment model, highlighting the importance of the magnitude and sign of the quadrupole moment of the Lewis acid. This approach is validated by a subsequent analysis of the molecular electrostatic potential, scrutinizing the σ and π holes, as well as the evolution in preference for chalcogen versus tetrel bonds when passing to “higher” chalcogens in agreement with the evolution of the quadrupole moment. The energy decomposition analysis gives further support to the importance/dominance of electrostatic effects, as it turns out to be the largest attractive term in all cases considered, followed by the orbital interaction and the dispersion term. The natural orbitals for chemical valence highlight the sequence of charge transfer in the orbital interaction term, which is dominated by an electron-donating effect of the N or O lone-pair(s) of the base to the central atom of the triatomics, with its value being lower than in the case of comparable halogen bonding situations. The effect is appreciably larger for TMA, in line with its much higher basicity than DME, explaining the comparable complexation energies for DME and TMA despite the much larger dipole moment for DME.
- Published
- 2021
48. Elucidating Relaxation Phenomena in Lithium Metal Batteries with Odd-Random Phase Electrochemical Impedance Spectroscopy
- Author
-
Benny Wouters, Xinhua Zhu, Lieven Bekaert, Annick Hubin, Materials and Chemistry, Faculty of Engineering, General Chemistry, Earth System Sciences, and Electrochemical and Surface Engineering
- Subjects
Relaxation phenomena ,Materials science ,Chemical physics ,Phase (matter) ,Lithium metal ,Dielectric spectroscopy - Published
- 2021
49. Single Metal Atoms Embedded in the Surface of Pt Nanocatalysts: The Effect of Temperature and Hydrogen Pressure
- Author
-
Qing Wang, Beien Zhu, Frederik Tielens, Hazar Guesmi, Chemistry, and General Chemistry
- Subjects
single atom Pt nanocatalysts ,multi-scaled reconstruction (MSR) ,stability ,DFT ,shape & surface composition prediction ,reactive condition ,Environmental Science(all) ,Physical and Theoretical Chemistry ,Stability ,Catalysis ,General Environmental Science - Abstract
Embedding energetically stable single metal atoms in the surface of Pt nanocatalysts exposed to varied temperature (T) and hydrogen pressure (P) could open up new possibilities in selective and dynamical engineering of alloyed Pt catalysts, particularly interesting for hydrogenation reactions. In this work, an environmental segregation energy model is developed to predict the stability and the surface composition evolution of 24 Metal M-promoted Pt surfaces (with M: Cu, Ag, Au, Ni, Pd, Co, Rh and Ir) under varied T and P. Counterintuitive to expectations, the results show that the more reactive alloy component (i.e., the one forming the strongest chemical bond with the hydrogen) is not the one that segregates to the surface. Moreover, using DFT-based Multi-Scaled Reconstruction (MSR) method and by extrapolation of M-promoted Pt nanoparticles (NPs), the shape dynamics of M-Pt are investigated under the same ranges of T and P. The results show that under low hydrogen pressure and high temperature ranges, Ag and Au—single atoms (and Cu to a less extent) are energetically stable on the surface of truncated octahedral and/or cuboctahedral shaped NPs. This indicated that coinage single-atoms might be used to tune the catalytic properties of Pt surface under hydrogen media. In contrast, bulk stability within wide range of temperature and pressure is predicted for all other M-single atoms, which might act as bulk promoters. This work provides insightful guides and understandings of M-promoted Pt NPs by predicting both the evolution of the shape and the surface compositions under reaction gas condition.
- Published
- 2022
50. The spin polarized linear response from density functional theory: Theory and application to atoms
- Author
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Geerlings, Paul [General Chemistry (ALGC), Vrije Universiteit Brussel (Free University Brussels – VUB), Pleinlaan 2, 1050 Brussels (Belgium)]
- Published
- 2014
- Full Text
- View/download PDF
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