Bibliographies thématiques / Bader’s topological analysis

Littérature scientifique sur le sujet « Bader’s topological analysis »

Auteur : Grafiati
Publié le 11 mars 2023

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Articles de revues sur le sujet "Bader’s topological analysis"

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Khrustalev, Victor N., Anna O. Savchenko, Anna I. Zhukova, Natalia Yu Chernikova, Michael A. Kurykin, Alexander S. Novikov et Alexander G. Tskhovrebov. « Attractive fluorine···fluorine interactions between perfluorinated alkyl chains : a case of perfluorinated Cu(II) diiminate Cu[C2F5–C(NH)–CF=C(NH)–CF3]2 ». Zeitschrift für Kristallographie - Crystalline Materials 236, no 3-4 (26 mars 2021) : 117–22. http://dx.doi.org/10.1515/zkri-2021-2009.

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Abstract A synthesis of the perfluorinated copper diiminate complex Cu[C2F5–C(NH)–CF=C(NH)–CF3]2 (3) and its self-assembly into infinite 1D chains in the crystal via Type II C(sp3)–F···F–C(sp3) contacts between perfluoroethyl substituents is reported. Rare Type II F···F interactions were studied by DFT calculations and topological analysis of the electron density distribution within the formalism of Bader’s theory (QTAIM method). This is the first report which discusses Type II contacts between perfuoroalkyl chains.
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Bulatova, Margarita, Anna A. Melekhova, Alexander S. Novikov, Daniil M. Ivanov et Nadezhda A. Bokach. « Redox reactive (RNC)CuII species stabilized in the solid state via halogen bond with I2 ». Zeitschrift für Kristallographie - Crystalline Materials 233, no 6 (27 juin 2018) : 371–77. http://dx.doi.org/10.1515/zkri-2017-2107.

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AbstractThe crystal structure of [Cu2(μ-O)(μ-I)2(CNXyl)4]·I2(2·I2) was determined from single-crystal X-ray diffraction data. The adduct2·I2represents the first example of structurally characterized isocyanide-copper(II) complexes. In the structure of2·I2,2forms independent chains connected through molecular iodine via I···I–I···I halogen bonding. The DFT calculations and topological analysis of the electron density distribution within the formalism of Bader’s theory (QTAIM method) were performed for model complex2·I2and the obtained results allowed the attribution of these contacts to moderate strength (3.8–5.3 kcal/mol) non-covalent contacts exhibiting some covalent character.
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Nenajdenko, Valentine G., Namiq G. Shikhaliyev, Abel M. Maharramov, Gulnar T. Atakishiyeva, Aytan A. Niyazova, Naila A. Mammadova, Alexander S. Novikov, Ivan V. Buslov, Victor N. Khrustalev et Alexander G. Tskhovrebov. « Structural Organization of Dibromodiazadienes in the Crystal and Identification of Br···O Halogen Bonding Involving the Nitro Group ». Molecules 27, no 16 (11 août 2022) : 5110. http://dx.doi.org/10.3390/molecules27165110.

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Nitro functionalized dibromodiazadiene dyes were prepared and fully characterized including X-ray single crystal analysis. Electron deficient dibromodiazadienes were found to be able to act as donors of halogen bonding (XB), while the nitro group acted as an acceptor of the XB. Depending on the substituents, the Br···O XB competed with other weak interactions, and for some of the dyes, they even outcompeted the XB involving the nitro group. However, the nitro functionalized dibromoalkenes 6a and 10a, which had only the nitro moiety as the most plausible acceptor of the XB, reliably formed 1D chains via Br⋯O XB. Experimental work was supported by the DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method).
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Nenajdenko, Valentine G., Namiq G. Shikhaliyev, Abel M. Maharramov, Khanim N. Bagirova, Gulnar T. Suleymanova, Alexander S. Novikov, Victor N. Khrustalev et Alexander G. Tskhovrebov. « Halogenated Diazabutadiene Dyes : Synthesis, Structures, Supramolecular Features, and Theoretical Studies ». Molecules 25, no 21 (29 octobre 2020) : 5013. http://dx.doi.org/10.3390/molecules25215013.

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Novel halogenated aromatic dichlorodiazadienes were prepared via copper-mediated oxidative coupling between the corresponding hydrazones and CCl4. These rare azo-dyes were characterized using 1H and 13C NMR techniques and X-ray diffraction analysis for five halogenated dichlorodiazadienes. Multiple non-covalent halogen···halogen interactions were detected in the solid state and studied by DFT calculations and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method). Theoretical studies demonstrated that non-covalent halogen···halogen interactions play crucial role in self-assembly of highly polarizable dichlorodiazadienes. Thus, halogen bonding can dictate a packing preference in the solid state for this class of dichloro-substituted heterodienes, which could be a convenient tool for a fine tuning of the properties of this novel class of dyes.
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Merli, Marcello, et Luciana Sciascia. « Bader’s topological analysis of the electron density in the pressure-induced phase transitions/amorphization in α-quartz from the catastrophe theory viewpoint ». Physics and Chemistry of Minerals 40, no 6 (23 mars 2013) : 455–66. http://dx.doi.org/10.1007/s00269-013-0583-7.

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Parisi, Filippo, Luciana Sciascia, Francesco Princivalle et Marcello Merli. « The pressure-induced ringwoodite to Mg-perovskite and periclase post-spinel phase transition : a Bader’s topological analysis of the ab initio electron densities ». Physics and Chemistry of Minerals 39, no 2 (1 novembre 2011) : 103–13. http://dx.doi.org/10.1007/s00269-011-0465-9.

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Kinzhalov, Mikhail A., Svetlana A. Katkova, Elizaveta P. Doronina, Alexander S. Novikov, Ivan I. Eliseev, Vasiliy A. Ilichev, Andrey A. Kukinov, Galina L. Starova et Nadezhda A. Bokach. « Red photo- and electroluminescent half-lantern cyclometalated dinuclear platinum(II) complex ». Zeitschrift für Kristallographie - Crystalline Materials 233, no 11 (25 octobre 2018) : 795–802. http://dx.doi.org/10.1515/zkri-2018-2075.

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Abstract New cyclometalated dinuclear platinum(II) complex bearing bridged 4,6-dimethylpyrimidine-2(1H)-thiolate (μ-C6H7N2S-κN,S) ligands, [{Pt(ppy)(μ-C6H7N2S-κN,S)}2] (3) (ppy=(2-phenylpyridinato-C2,N)) was prepared via the reaction of chloro-bridged dimer [{Pt(ppy)Cl}2] with 4,6-dimethylpyrimidine-2(1H)-thione (C6H8N2S) in the presence of t-BuOK. The complex holds dinuclear frameworks with short Pt(II)···Pt(II) distance (2.8877(3) Å), and exhibit red intense luminescence from the triplet metal-metal-to-ligand charge-transfer at 697 nm in CH2Cl2 solution and at 649 nm in solid state at RT. Single crystal XRD analysis reveals the metallophilic interactions Pt···Pt with significant covalent contribution in the structure of 3 which were studied by quasi-relativistic and relativistic DFT calculations (viz., M06/MWB60(Pt) and 6-311+G* (other atoms); M06/DZP-DKH levels of theory) and topological analysis of the electron density distribution within the framework of Bader’s theory (QTAIM method). Estimated strength of the Pt···Pt contact is 8.1–12.2 kcal/mol and it is mostly determined by crystal packing effects and weak attractive interactions between the adjacent metal centers due to overlapping of their dz2 and pz orbitals. An organic light-emitting diode based on this complex showed red electroluminescence with maximal luminance of 115 cd/m2 and current efficiency of 2.45 cd/A at this luminance.
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Kandhakumar, Gopal, Chinnasamy Kalaiarasi et Poomani Kumaradhas. « Structure and charge density distribution of amine azide based hypergolic propellant molecules : a theoretical study ». Canadian Journal of Chemistry 94, no 2 (février 2016) : 126–36. http://dx.doi.org/10.1139/cjc-2015-0416.

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A quantum chemical calculation and charge density analysis of some amine azide based propellants (DMAZ, DMAEH, ADMCPA, AMCBA and ACPA) have been carried out to understand the geometry, bond topological, electrostatic, and energetic properties. The topological properties of electron density of the molecules were determined using Bader’s theory of atoms in molecules from the wave functions obtained from the density functional method (B3LYP) with the 6-311G** basis set. The electron density distribution of these molecules reveals the nature of chemical bonding in the molecules. The azide group attached C−N bonds of all molecules exhibit the electron density of ρbcp(r) ∼1.639 e Å−3 and the Laplacian of electron density ∇2ρbcp(r) is ∼–14.0 e Å−5, in which the corresponding values of the ADMCPA molecule are relatively high, 1.725 e Å–3 and –15.2 e Å−5 respectively, whereas for the methylamine group attached C–N bonds, these values are found to be higher (1.824 e Å–3 and –17.25 e Å−5). The Laplacian of terminal N–N bonds of the azide group is highly negative, indicating that these charges are highly concentrated, whereas the charge concentration of the dimethylamine group attached N–N bond of DMEAH is very much less, confirming that the bond is the weakest bond among the molecules. The energy density has been calculated for each bond of the molecules, which insights the energy density distribution of the molecules. Relatively, the molecules exhibit distinct electrostatic properties that are related to different charge distribution in the molecules. Large negative electrostatic potential regions are found at the vicinity of the amine and azide groups of the molecules. The charge imbalance parameter of the molecules has been determined and shows that the DMAEH molecule is the least sensitive molecule in this series.
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Yazdani-Kachoei, M., et S. Jalali-Asadabadi. « Topological analysis of electron density in half-Heusler ZrXBi (X = Co, Rh) compounds : A density functional theory study accompanied by Bader’s quantum theory of atoms in molecules ». Journal of Alloys and Compounds 828 (juillet 2020) : 154287. http://dx.doi.org/10.1016/j.jallcom.2020.154287.

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Mikherdov, Alexander, Alexander Novikov, Mikhail Kinzhalov et Andrey Zolotarev. « Intra-/Intermolecular Bifurcated Chalcogen Bonding in Crystal Structure of Thiazole/Thiadiazole Derived Binuclear (Diaminocarbene)PdII Complexes ». Crystals 8, no 3 (27 février 2018) : 112. http://dx.doi.org/10.3390/cryst8030112.

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The coupling of cis-[PdCl2(CNXyl)2] (Xyl = 2,6-Me2C6H3) with 4-phenylthiazol-2-amine in molar ratio 2:3 at RT in CH2Cl2 leads to binuclear (diaminocarbene)PdII complex 3c. The complex was characterized by HRESI+-MS, 1H NMR spectroscopy, and its structure was elucidated by single-crystal XRD. Inspection of the XRD data for 3c and for three relevant earlier obtained thiazole/thiadiazole derived binuclear diaminocarbene complexes (3a EYOVIZ; 3b: EYOWAS; 3d: EYOVOF) suggests that the structures of all these species exhibit intra-/intermolecular bifurcated chalcogen bonding (BCB). The obtained data indicate the presence of intramolecular S•••Cl chalcogen bonds in all of the structures, whereas varying of substituent in the 4th and 5th positions of the thiazaheterocyclic fragment leads to changes of the intermolecular chalcogen bonding type, viz. S•••π in 3a,b, S•••S in 3c, and S•••O in 3d. At the same time, the change of heterocyclic system (from 1,3-thiazole to 1,3,4-thiadiazole) does not affect the pattern of non-covalent interactions. Presence of such intermolecular chalcogen bonding leads to the formation of one-dimensional (1D) polymeric chains (for 3a,b), dimeric associates (for 3c), or the fixation of an acetone molecule in the hollow between two diaminocarbene complexes (for 3d) in the solid state. The Hirshfeld surface analysis for the studied X-ray structures estimated the contributions of intermolecular chalcogen bonds in crystal packing of 3a–d: S•••π (3a: 2.4%; 3b: 2.4%), S•••S (3c: less 1%), S•••O (3d: less 1%). The additionally performed DFT calculations, followed by the topological analysis of the electron density distribution within the framework of Bader’s theory (AIM method), confirm the presence of intra-/intermolecular BCB S•••Cl/S•••S in dimer of 3c taken as a model system (solid state geometry). The AIM analysis demonstrates the presence of appropriate bond critical points for these interactions and defines their strength from 0.9 to 2.8 kcal/mol indicating their attractive nature.
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Thèses sur le sujet "Bader’s topological analysis"

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Parisi, Filippo. « A Bader’s topological approach for the characterization of pressure induced phase transitions ». Doctoral thesis, Università degli studi di Trieste, 2012. http://hdl.handle.net/10077/7420.

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2010/2011
In questo lavoro è stata messa a punto una metodologia basata sull’analisi topologica della densità elettronica secondo la teoria di Bader che ha permesso di indagare la stabilità di fasi mineralogiche in condizioni di alta pressione. In una prima fase è stata caratterizzata la decomposizione della ringwoodite (olivina-γ) in Mg-perovskite e periclasio ( post spinel phase transition) che si ritiene essere responsabile della discontinuità sismica che si osserva a 660 Km di profondità, tra la zona di transizione del mantello ed il mantello inferiore. Lo scopo del lavoro è stato quello di ottenere informazioni sulla disposizione degli elettroni nella struttura cristallina e sulla evoluzione al variare delle condizioni di pressione. L’analisi effettuata ha mostrato l’instaurarsi di una forte instabiltà strutturale (caratterizzata da una “conflict catastrophe”) nella ringwoodite a circa 30 GPa. Tale risultato conferma il coinvolgimento della transizione di fase “post-spinel”nella discontinuità sismica a 660 Km. In una seconda fase la procedura è stata applicata alla fase Mg-perovskite allo scopo di testarne la validità. Lo studio dell’evoluzione della topologia della densità elettronica nel range di pressione da 0 a 200 GPa ha permesso di individuare una regione di stabilità della fase perovskitica (da circa 22 a circa 124 GPa) delimitata tra due “fold catastrophes”. Le due “fold catastrophes” si hanno entrambe in prossimità di discontinuità sismiche: la prima, attribuita alla transizione di fase da ringwoodite a Mg-perovskite + periclasio corrisponde alla discontinuità sismica a 660 Km e la seconda, attribuita alla transizione da Mg-perovskite a post-perovskite a circa 130 GPa, osservata a circa 2600 Km di profondità, tra il mantello profondo e il D′′-layer, poco prima della discontinuità di Gutemberg a 2900 Km.
XXIV Ciclo
1975
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Orlando, A. M. « NEW INSIGHT IN ELECTRON DENSITY AND ELECTRON SPIN DENSITY THROUGH TOPOLOGICAL DESCRIPTORS BASED ON BADER'S THEORY OF ATOM IN MOLECULES ». Doctoral thesis, Università degli Studi di Milano, 2016. http://hdl.handle.net/2434/374929.

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This Ph.D. thesis is focused on the application of quantum theory of atoms in molecules (QTAIM) based chemical descriptors to challenging chemical test-cases, as well as on the development of novel topological descriptors, like the Source Function for the spin density. The thesis is organized as follows: In chapter 1 the electron density (ED) of a very unusual structural feature in a synthetic beta–sultamic analogue (DTC), has been explored by both low-T single–crystal X–ray diffraction and quantum mechanical simulations to gain insights into the subtle interplay between structure, electron delocalization and crystal field polarization effects. The core chemical moiety in DTC is an uncommon 4–membered thiazete–1,1–dioxide heterocycle, where the formally single N–C bond is, on average, 0.018 Å shorter than the formally double N=C bond. Both local and non–local topological descriptors provided by QTAIM have been employed in the analysis of DTC in comparison with chemically related derivatives and possible implications from the viewpoint of the accurate in silico modelling of crystal structures are discussed. Particular attention is dedicated on such kind of issues in chemical and pharmaceutical industries, because the control of the crystal structure is really problematic in some cases; in fact different polymorphs of the same substance have different intensive physical properties, such as solubility, refraction index and conductivity and problems may arise in industrial processes related to the synthesis of chemicals and drugs on large scale. In chapter 2, we focused on the source function (SF) QTAIM based topological descriptor. The electron density (ED) at any point r within a system may be regarded as consisting of a sum of SF contributions S(r; X) representing a measure of how the various atomic basins (X) or groups of atomic basins defined through QTAIM contribute to determine the ρ(r) at r. Recently it was shown that the SF is able to reveal electron delocalization effects in planar electron conjugated systems, in terms of an increased capability of determining the ED along a given bond by the distant, though through-bonds connected, atomic basins and, at the same time, into a decreased ability to do so by the two atoms directly involved in the bond. Such an adjustment of sources then translates into a pictorial pattern of enhanced and reduced atomic SF contributions from, respectively, distant and nearby atoms, compared to the case of a partially or fully saturated network of bonds. Then we have extended such an analysis to the non planar conjugated systems, where the usual electron separation does no longer apply. Being based on the total ED, the SF analysis may be safely applied also in these less conventional electron delocalized systems. In the present Ph. D. thesis we have extended the SF reconstruction approach also to the electron density spin counterparts in vacuo. Such reconstruction was investigated both on simple (but chemically meaningful) spin-polarized molecular systems and on more complex single-molecule magnets. This investigation has showed that the difference between the two spin counterparts of electron density distribution can be reconstructed with a sufficient accuracy, analogously to the case of the total ED. Moreover, it was found that the SF for the electron spin density brings in precious chemical information, neatly distinguishing the quite different roles played by the unpaired electrons ED and the spin polarized ED due to the remaining electrons. Furthermore, quantitative answers to questions related to the transferability of the spin density in alkyl radicals or to the transmission of spin information in metal(s)-ligand systems were provided. Understanding, from a real space perspective, by which mechanisms spin information transmits, might be of relevance to interpret the fundamental magnetic interactions present in complex materials, such as for example coordination polymers or Heussler and half-Heussler alloys. As these interactions have a key role in spintronics, characterization of the chemical bond and interpretation of the electron spin density distributions in these systems through the SF analysis, could hopefully disclose structure-property relationships extremely useful for the design of materials with particular physical properties.
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Chapitres de livres sur le sujet "Bader’s topological analysis"

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Coppens, Philip. « Space Partitioning and Topological Analysis of the Total Charge Density ». Dans X-Ray Charge Densities and Chemical Bonding. Oxford University Press, 1997. http://dx.doi.org/10.1093/oso/9780195098235.003.0008.

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In partitioning space in the analysis of a continuous charge distribution, the requirement of locality, formulated by Kurki-Suonio (Kurki-Suonio 1968, 1971; Kurki-Suonio and Salmo 1971), should be preserved. It states that density at a point should be assigned to a center in the proximity of that point. In discrete boundary partitioning schemes, the density at each point is assigned to a specific basin, while in fuzzy boundary partitioning, the density at the point may be assigned to overlapping functions centered at different locations. The least-squares formalisms described in chapter 3 implicitly define a space partitioning scheme, based on the density functions used in the refinement that are each centered on a specific nucleus. Since the density functions are continuous, they overlap, so the fragments interpenetrate rather than meet at a discrete boundary. Such fuzzy boundaries correspond to smoothly varying functions, both in real and reciprocal space, and therefore to well-behaved fragment scattering factors, and reasonable fragment electrostatic moments. The interpenetratingfragment partitioning schemes are related to the Mulliken and Løwdin population analyses of theoretical chemistry. The topological analysis of the total density, developed by Bader and coworkers, leads to a scheme of natural partitioning into atomic basins which each obey the virial theorem. The sum of the energies of the individual atoms defined in this way equals the total energy of the system. While the Bader partitioning was initially developed for the analysis of theoretical densities, it is equally applicable to model densities based on the experimental data. The density obtained from the Fourier transform of the structure factors is generally not suitable for this purpose, because of experimental noise, truncation effects, and thermal smearing. The topological analysis of the density leads to a powerful classification of bonding based on the electron density. It is discussed in the final sections of this chapter. The stockholder partitioning concept is one of the important contributions to charge density analysis made by Hirshfeld (1977b). It defines a continuous sampling function wi(r), which assigns the density among the constituent atoms. The sampling function is based on the spherical-atom promolecule density—the sum of the spherically averaged ground-state atom densities.
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Khanmohammadi, Azadeh. « Investigation of Non-Covalent Interactions of Copper (II) Complexes with Small Biomolecules ». Dans Copper - From the Mineral to the Final Application [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.106216.

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In this chapter, the influence of non-covalent interactions on the complexes formed by the various biomolecules (mesalazine, para-aminosalicylic acid, acetaminophen, psoralen, and methyl salicylate) with the Cu2+ cation is investigated using the density functional theory (DFT) method. Since the interactions involving aromatic rings are crucial binding forces in chemical systems, this is exciting research trying to understand and control the effect of non-covalent interactions responsible for complicated functions in nature. Herein, the calculations are performed in the gas phase and water solvent. The results show that the absolute amounts of energy are reduced by going from the gas phase to the solution. The topological properties of the electron density and the values of charge transfer are evaluated by the Bader theory of atoms in molecules (AIM) and the natural bond orbital (NBO) analysis, respectively. These results are useful for understanding the role of the drug-receptor interactions in the complexes. The electronic descriptors are also important factors in forming a charge-transfer complex between cation and biological target. The results of this study that are ubiquitous in biological systems may be useful for the design and synthesis of a variety of supramolecular complexes with the desired properties.
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