Letteratura scientifica selezionata sul tema "Analyse des interactions non covalentes"
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Articoli di riviste sul tema "Analyse des interactions non covalentes":
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Kumar, Prashant, Małgorzata Katarzyna Cabaj e Paulina Maria Dominiak. "Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions". Crystals 9, n. 12 (11 dicembre 2019): 668. http://dx.doi.org/10.3390/cryst9120668.
Abstract (sommario):
Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.
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Savoo, Nandini, Frederick P. Malan, Lydia Rhyman e Ponnadurai Ramasami. "Molecular insights of metal–metal interactions in transition metal complexes using computational methods". Pure and Applied Chemistry 93, n. 5 (1 maggio 2021): 579–89. http://dx.doi.org/10.1515/pac-2020-1212.
Abstract (sommario):
Abstract Computational methods were used to analyse the interactions around the metal centres in three transition metal (TM) complexes for which the X-ray data are available. We were particularly interested in understanding the metal–metal interactions. We used concepts of bond order, natural population, quantum theory of atom in molecules, electron localisation functions (ELFs) and non-covalent interactions (NCIs). Our results indicate that these tools can be used effectively to help in having insights into the bonding of TM complexes.
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Creste, Geordie, Sihem Groni, Claire Fave, Mathieu Branca e Bernd Schöllhorn. "Comparative study of non-covalent interactions between cationic N-phenylviologens and halides by electrochemistry and NMR: the halogen bonding effect". Faraday Discussions 203 (2017): 301–13. http://dx.doi.org/10.1039/c7fd00082k.
Abstract (sommario):
Five N-phenylviologen (PV2+) derivatives have been synthesized and their electrochemical behavior in the presence of halide anions has been studied. Further investigations were carried out by 1H and 19F NMR spectroscopy at different chloride concentrations. This is the first time a systematic study combines cyclic voltammetry and NMR spectroscopy in order to analyse the contribution of halogen bonding among the various non-covalent interactions between iodinated N-phenylviologens. The results show strong evidence for a significant “halogen bonding effect” in the interaction between halides and the iodo-tetrafluoro-phenylviologen PV2+-C6F4I. A significant influence of halogen bonding on reduction potentials of the novel halogen bond donor PV2+-C6F4I has been evidenced resulting in the first example of “inverse redox switching” of an XB-donor being partially deactivated upon reduction. Furthermore the particular binding properties of the perfluorinated derivative PV2+-C6F5 towards chloride are discussed considering a possible contribution of π–anion interaction in solution.
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Vonderviszt, F., J. Török, S. Lakatos, F. Kilár e P. Závodszky. "Quantitative analysis of the interaction between immune complex and Clq complement subcomponent. The role of interdomain interactions in rabbit IgG in binding of Clq to immune precipitates". Biochemical Journal 243, n. 2 (15 aprile 1987): 449–55. http://dx.doi.org/10.1042/bj2430449.
Abstract (sommario):
A novel method was developed for the analysis of the interaction of large multivalent ligands with surfaces (matrices) to analyse the binding of complement subcomponent C1q to immune precipitates. Our new evaluation method provides quantitative data characteristic of the C1q-immune-complex interaction and of the structure of the immune complex as well. To reveal the functional role of domain-domain interactions in the Fc part of IgG the binding of C1q to different anti-ovalbumin IgG-ovalbumin immune complexes was studied. Immune-complex precipitates composed of rabbit IgG in which the non-covalent or covalent bonds between the heavy chains had been eliminated were used. Non-covalent bonds were abolished by splitting off the CH3 domains, i.e. by using Facb fragments, and the covalent contact was broken by reduction and alkylation of the single inter-heavy-chain disulphide bond. The quantitative analysis of the binding curves provides a dissociation constant (K) of 200 nM for the interaction between C1q and immune precipitate formed from native IgG. Surprisingly, for immune precipitates composed of Facb fragments or IgG in which the inter-heavy-chain disulphide bond had been selectively reduced and alkylated, stronger binding (K = 30 nM) was observed. In this case, however, changes in the structure of the immune-complex matrix were also detected. These structural changes may account for the strengthening of the C1q-immune-complex interaction, which can be strongly influenced by the flexibility and the binding-site pattern of the immune-complex precipitates. These results suggest that domain-domain interactions in the Fc part of IgG affect the segmental mobility of IgG molecules and the spatial arrangement of the immune-complex matrix rather than the affinity of individual C1q-binding sites on IgG.
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Singh, Omkar, Kunal Sawariya e Polamarasetty Aparoy. "Graphlet signature-based scoring method to estimate protein–ligand binding affinity". Royal Society Open Science 1, n. 4 (dicembre 2014): 140306. http://dx.doi.org/10.1098/rsos.140306.
Abstract (sommario):
Over the years, various computational methodologies have been developed to understand and quantify receptor–ligand interactions. Protein–ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein–ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein–ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC 50 was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein–ligand complexes.
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Jungclas, Hartmut, Viacheslav V. Komarov, Anna M. Popova e Lothar Schmidt. "Molecular Interactions in Particular Van der Waals Nanoclusters". Zeitschrift für Naturforschung A 72, n. 1 (1 gennaio 2017): 17–23. http://dx.doi.org/10.1515/zna-2016-0213.
Abstract (sommario):
AbstractA method is presented to analyse the interaction energies in a nanocluster, which is consisting of three neutral molecules bound by non-covalent long range Van der Waals forces. One of the molecules (M0) in the nanocluster has a permanent dipole moment, whereas the two other molecules (M1 and M2) are non-polar. Analytical expressions are obtained for the numerical calculation of the dispersion and induction energies of the molecules in the considered nanocluster. The repulsive forces at short intermolecular distances are taken into account by introduction of damping functions. Dispersion and induction energies are calculated for a nanocluster with a definite geometry, in which the polar molecule M0 is a linear hydrocarbon molecule C5H10 and M1 and M2 are pyrene molecules. The calculations are done for fixed distances between the two pyrene molecules. The results show that the induction energies in the considered three-molecular nanocluster are comparable with the dispersion energies. Furthermore, the sum of induction energies in the substructure (M0, M1) of the considered nanocluster is much higher than the sum of induction energies in a two-molecular nanocluster with similar molecules (M0, M1) because of the absence of an electrostatic field in the latter case. This effect can be explained by the essential intermolecular induction in the three-molecular nanocluster.
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Maza, Susana, José L. de Paz e Pedro M. Nieto. "Synthesis of a Fluorous-Tagged Hexasaccharide and Interaction with Growth Factors Using Sugar-Coated Microplates". Molecules 24, n. 8 (22 aprile 2019): 1591. http://dx.doi.org/10.3390/molecules24081591.
Abstract (sommario):
Here, we report the synthesis of a sulfated, fully protected hexasaccharide as a glycosaminoglycan mimetic and the study of its interactions with different growth factors: midkine, basic fibroblast growth factor (FGF-2) and nerve growth factor (NGF). Following a fluorous-assisted approach, monosaccharide building blocks were successfully assembled and the target oligosaccharide was prepared in excellent yield. The use of more acid stable 4,6-O-silylidene protected glucosamine units was crucial for the efficiency of this strategy because harsh reaction conditions were needed in the glycosylations to avoid the formation of orthoester side products. Fluorescence polarization experiments demonstrated the strong interactions between the synthesized hexamer, and midkine and FGF-2. In addition, we have developed an alternative assay to analyse these molecular recognition events. The prepared oligosaccharide was non-covalently attached to a fluorous-functionalized microplate and the direct binding of the protein to the sugar-immobilized surface was measured, affording the corresponding KD,surf value.
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Etxabide, Alaitz, Maite Arregi, Sara Cabezudo, Pedro Guerrero e Koro de la Caba. "Whey Protein Films for Sustainable Food Packaging: Effect of Incorporated Ascorbic Acid and Environmental Assessment". Polymers 15, n. 2 (11 gennaio 2023): 387. http://dx.doi.org/10.3390/polym15020387.
Abstract (sommario):
The management of food waste and by-products has become a challenge for the agri-food sector and an example are whey by-products produced in dairy industries. Seeking other whey valorisation alternatives and applications, whey protein films for food packaging applications were developed in this study. Films containing different amounts (0, 5, 10, and 15 wt%) of ascorbic acid were manufactured via compression-moulding and their physicochemical, thermal, barrier, optical, and mechanical properties were analysed and related to the film structure. Additionally, the environmental assessment of the films was carried out to analyse the impact of film manufacture. Regarding physicochemical properties, both FTIR and water uptake analyses showed the presence of non-covalent interactions, such as hydrogen bonding, between whey protein and ascorbic acid as band shifts at the 1500–1700 cm−1 region as well as a water absorption decrease from 380% down to 240% were observed. The addition of ascorbic acid notably improved the UV-Vis light absorbance capacity of whey protein films up to 500 nm, a relevant enhancement for protecting foods susceptible to UV-Vis light-induced lipid oxidation. In relation to the environmental assessment, it was concluded that scaling up film manufacture could lead to a reduction in the environmental impacts, mainly electricity consumption.
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Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui e Mahmoud Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase Through Target-Focused Modelling". Proceedings 22, n. 1 (14 novembre 2019): 103. http://dx.doi.org/10.3390/proceedings2019022103.
Abstract (sommario):
The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the Nedd4-1 E3 Ubiquitin ligase is an enzyme that may be targeted either covalently, or non-covalently, there are few studies that demonstrate effective inhibitors of the enzyme. In this work, we aimed to identify covalent inhibitors of Nedd4-1. This task however, proved to be challenging due to the limited available electrophilic moieties in virtual libraries. We therefore opted to divide an existing covalent Nedd4-1 inhibitor in two parts: A non-covalent binding part and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on the active site binding investigations followed by validating the covalent conjugation. Thirty compounds were selected and covalently docked into the catalytic site of the Nedd4-1. Multiple filtrations were effected before selecting 5 hits that were later analysed by molecular dynamic simulations to check their stability and explore their binding landscape in complex with the protein. All in all, two inhibitors with optimum overall stability and more stabilising interactions were kept for eventual biological evaluation. Our improved pharmacophore model approach serves as a robust method that will illuminate the screening for novel covalent inhibitor in drug discovery.
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Hammud, Hassan H., Muhammad Yar, Imene Bayach e Khurshid Ayub. "Covalent Triazine Framework C6N6 as an Electrochemical Sensor for Hydrogen-Containing Industrial Pollutants. A DFT Study". Nanomaterials 13, n. 6 (21 marzo 2023): 1121. http://dx.doi.org/10.3390/nano13061121.
Abstract (sommario):
Industrial pollutants pose a serious threat to ecosystems. Hence, there is a need to search for new efficient sensor materials for the detection of pollutants. In the current study, we explored the electrochemical sensing potential of a C6N6 sheet for H-containing industrial pollutants (HCN, H2S, NH3 and PH3) through DFT simulations. The adsorption of industrial pollutants over C6N6 occurs through physisorption, with adsorption energies ranging from −9.36 kcal/mol to −16.46 kcal/mol. The non-covalent interactions of analyte@C6N6 complexes are quantified by symmetry adapted perturbation theory (SAPT0), quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses. SAPT0 analyses show that electrostatic and dispersion forces play a dominant role in the stabilization of analytes over C6N6 sheets. Similarly, NCI and QTAIM analyses also verified the results of SAPT0 and interaction energy analyses. The electronic properties of analyte@C6N6 complexes are investigated by electron density difference (EDD), natural bond orbital analyses (NBO) and frontier molecular orbital analyses (FMO). Charge is transferred from the C6N6 sheet to HCN, H2S, NH3 and PH3. The highest exchange of charge is noted for H2S (−0.026 e−). The results of FMO analyses show that the interaction of all analytes results in changes in the EH-L gap of the C6N6 sheet. However, the highest decrease in the EH-L gap (2.58 eV) is observed for the NH3@C6N6 complex among all studied analyte@C6N6 complexes. The orbital density pattern shows that the HOMO density is completely concentrated on NH3, while the LUMO density is centred on the C6N6 surface. Such a type of electronic transition results in a significant change in the EH-L gap. Thus, it is concluded that C6N6 is highly selective towards NH3 compared to the other studied analytes.
Tesi sul tema "Analyse des interactions non covalentes":
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Ohara, Keiichiro. "Interactions non covalentes de dérivés guanidylés avec l'ADN : synthèse, évaluation biologique et analyse par spectrométrie de masse MALDI-TOF". Montpellier 2, 2008. http://www.theses.fr/2008MON20154.
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Wieduwilt, Erna K. "Quantum mechanics-based methods for the refinement of crystal structures and the analysis of non-covalent interactions". Electronic Thesis or Diss., Université de Lorraine, 2021. http://www.theses.fr/2021LORR0167.
Abstract (sommario):
Dans cette thèse, les orbitales moléculaires extrêmement localisées (ELMOs) ont été utilisées comme briques LEGO électroniques pour accomplir deux objectifs : (i) améliorer la précision des structures cristallines aux rayons X pour des petits et grands systèmes, et (ii) analyser les interactions non-covalentes dans les biomolécules. Les ELMOs sont des orbitales moléculaires strictement localisées sur des petits fragments. Pour cette raison, elles peuvent être calculées sur des petites molécules, stockées dans des bases de données, puis transférées sur des systèmes plus grands pour reconstruire leurs fonctions d’onde et leurs densités électroniques. Dans ce but, nous avons exploité les bibliothèques contenant les ELMOs de tous les fragments élémentaires (atomes, liaisons et groupes fonctionnels) des acides aminés. Dans les situations où une plus grande précision s’avère nécessaire, nous avons utilisé la technique de «~embed-ding~» QM/ELMO, dans laquelle la partie cruciale du système examiné est traitée à un niveau quantique supérieur tandis que le reste du système est décrit par des ELMOs gelées. En ce qui concerne le premier des objectifs mentionnés ci-dessus, il est important de noter que les raffinements cristallographiques standards sont basés sur le « independent atom model~» (IAM), qui estime la densité électronique à partir d’une somme de densités atomiques sphériques. Cependant, les longueurs des liaisons élément-hydrogène résultant des raffinements IAM sont systématiquement trop courtes. Une méthode qui résout ce problème est la technique « Hirshfeld atom refinement » (HAR), qui est basée sur le calcul direct de la densité électronique en utilisant des méthodes de mécanique quantique. Pour les petites molécules, il a été prouvé que la technique HAR donne des longueurs de liaison élément-hydrogène en très bon accord avec les valeurs de référence neutroniques. Toutefois, pour les grands systèmes, l’applicabilité de la méthode HAR traditionnelle est limitée, car les calculs entièrement QM sous-jacents deviennent trop coûteux. Pour pallier ce problème, dans le travail décrit dans cette thèse, les bibliothèques ELMO et les techniques QM/ELMO ont été couplées avec la méthode HAR dans le but de raffiner les structures de grands systèmes moléculaires, mais également pour obtenir des structures plus précises dans le cas de petites molécules. En outre, la nécessité ou non d’utiliser des méthodes post-HF pour HAR a été évaluée.Le deuxième objectif de cette thèse concerne l’analyse des interactions non covalentes, qui pose des problèmes similaires à ceux rencontrés en cristallographie aux rayons X. En effet, les techniques « non-covalent interaction » (NCI) et « independent gradient model~» (IGM), qui sont couramment appliquées dans l’analyse des interactions non covalentes, dépendent du calcul de la densité électronique. Ainsi, pour analyser les interactions non covalentes dans des grands systèmes, les deux techniques ont recours aux mêmes densités électroniques pro-moléculaires utilisées dans le « independent atom model ». Cependant, dans le cas des analyses NCI et IGM, ces densités fournissent également des résultats biaisés. Pour surmonter cet inconvénient, nous avons couplé les deux méthodes avec les bibliothèques ELMO, donnant naissance aux techniques NCI-ELMO et IGM-ELMO, qui ont ensuite été appliquées pour identifier, classer et quantifier approximativement les interactions non covalentes dans des polypeptides et des protéinesIn the work presented in this thesis, extremely localized molecular orbitals (ELMOs) were used as electronic LEGO building blocks to accomplish mainly two goals: (i) obtaining more accurate X-ray crystal structures for small and large systems, and (ii) analyzing non-covalent interactions in biomolecules. In fact, ELMOs are molecular orbitals that are strictly localized on small molecular fragments. Due to this strict localization, they may be computed on small molecules, stored in databases and then transferred to larger systems to reconstruct their wavefunctions and electron densities. To this end, we exploited the ELMO libraries, which contain the ELMOs for all the elementary fragments (atoms, bonds and functional groups) of the twenty natural amino acids. In situations where a higher accuracy was needed, we used the QM/ELMO embedding technique, in which the crucial part of the system under exam is treated at a higher quantum mechanical level, while the rest is described using frozen ELMOs. Concerning the first of the goals mentioned above, it is important to note that standard crystallographic refinements are based on the so-called independent atom model (IAM), which approximates the electron density as a sum of spherically averaged atomic densities. However, the element-hydrogen bond lengths resulting from IAM refinements are systematically too short. A method that solves this problem is the Hirshfeld atom refinement (HAR), a technique based on directly computing the electron density for the molecule under exam using quantum mechanical calculations. For small molecules, HAR has been proven to give element-hydrogen bond lengths that are in very good agreement with neutron reference values. However, for large systems, the applicability of the traditional HAR method is limited because the underlying fully QM calculations become computationally too expensive. Therefore, in the work presented in this thesis, the ELMO libraries and the QM/ELMO techniques have been coupled with the HAR method to refine large systems and also to obtain more accurate structures of small molecules. Furthermore, the necessity of using post-HF methods for HAR has been also evaluated. Concerning the second goal addressed in this dissertation, a similar problem as the one met in X-ray crystallography also arises in the analysis of non-covalent interactions. In fact, also the non-covalent interaction (NCI) and independent gradient model (IGM) techniques, which are commonly applied in analyses of non-covalent interactions, crucially depend on the computation of the electron density. Therefore, to analyze non-covalent interactions in large systems, both techniques had to resort to promolecular electron densities, which are the same densities used in the IAM. However, also in the cases of NCI and IGM analyses, these densities provide biased results. To overcome this drawback, we have coupled both methods with the ELMO libraries, giving rise to the NCI-ELMO and IGM-ELMO techniques, which were then applied to identify, classify and approximately quantify non-covalent interactions in polypeptides and proteins
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Imani, Zeynab. "Le rôle d’interactions N-H···S proximales dans des peptides". Thesis, université Paris-Saclay, 2021. http://www.theses.fr/2021UPASF015.
Abstract (sommario):
Les interactions non covalentes jouent un rôle clé dans des phénomènes de la biologie chimique tel que la stabilisation de la structure tertiaire et quaternaire des protéines ou la reconnaissance entre des biomolécules tel que protéine-protéine et protéine-ligand. Parmi ces interactions, la liaison hydrogène classique de type amide NH···O=C a fait l’objet de nombreuses études approfondies. En revanche, l’étude d’autres types de liaisons hydrogène impliquant le NH de la fonction amide est plus rare. Nos travaux ont été focalisés sur l’impact d’une liaison NH···S sur les préférences conformationnelles d’amino acides soufrés et de leurs oligomères courts. Nous avons préparé un panel de dérivés protégés des amino acides soufrés non-canoniques suivants : Cys(Me) (acyclique), Attc (thiétane), Atlc (thiolane), Atc (thiane). Ces dérivés ont été caractérisés par des calculs théoriques, par spectroscopie double résonance IR/UV en phase gazeuse, par spectroscopie IR et RMN en solution, et à l’état solide. Nous avons mis en évidence pour ces quatre composés l’existence concomitante d’une liaison hydrogène NH···S inter-résidus formant une structure C6ˠ et d’une interaction NH···O=C formant une structure C5. Une succession de ces motifs combinés C5-C6ˠ stabilisants a été retrouvée dans les oligomères d’Attc. Un autre type de liaison hydrogène NH···S, cette fois-ci intra-résidu et formant une structure C5ˠ, a été caractérisé dans des dimères d’Atlc et d’Atc, associée parfois à une interaction NH···O=C formant un coude ˠ. La force de l’interaction NH···X dans le motif structural combiné C5-C6ˠ a été évaluée par comparaison avec des dérivés protégés amino acides cycliques à 4 chaînons : Attc (X = soufre), (Aatc(Me) (X = azoté), Aotc (X = oxygéné). Le motif C5-C6ˠ était présent dans les trois cas et la comparaison des spectres IR en phase gazeuse et en solution, aidée par des calculs théoriques, nous a permis de déduire une force croissante de la liaison hydrogène NH···X en allant de X=O vers X=S puis X=NNon-covalent interactions play a key role in chemical biology phenomena such as the stabilization of protein tertiary and quaternary structure or protein-protein and protein-substrate recognition. Among these interactions, the classical amide-type NH···O=C hydrogen bond has been thoroughly studied. The study of other types of non-covalent interactions implicating peptide backbone NH groups is much rarer. This work focused on the impact of NH···S hydrogen bonding on the conformational preferences of thioether amino acid residues and their short oligomers. A panel of capped derivatives of the following non-canonical sulfur-containing amino acids was prepared: Cys(Me) (acyclic), Attc (thietane), Atlc (thiolane), Atc (thiane). These derivatives were characterized computationally, by IR/UV double resonance laser spectroscopy in the gas phase, by IR and NMR spectroscopy in solution, and in the solid state. We demonstrated the concomitant existence of inter-residue C6ˠ NH···S hydrogen bonds and C5 NH···O=C interactions in each of these four compounds. This combined stabilizing feature was also prevalent in Attc oligomers. A different intra-residue C5ˠ NH···S hydrogen bond was characterized in short oligomers of Atlc and Atc, in some cases associated with a ˠ-turn NH···O=C interaction. The significance of NH···S bonding in the combined C5-C6ˠ structural feature of Attc was evaluated by comparison with capped derivatives of other four-membered ring amino acids: Ac4c (cyclobutane), Aatc(Me) (azetidine), Aotc (oxetane). The C5–C6ˠ feature was present in the three heterocyclic residues: comparison of their IR spectra in gas phase and in solution, aided by theoretical calculations, allowed us to identify an increasing strength of NH···X hydrogen bonding from X=O to X=S to X=N
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Yahia-Ouahmed, Meziane. "Caractérisation topologique d'interactions non-covalentes inter- et intramoléculaires". Thesis, Normandie, 2017. http://www.theses.fr/2017NORMR091/document.
Abstract (sommario):
Ces travaux de thèse ont pour but l’étude théorique et la caractérisation d’interactions non-covalentes par des méthodes QCT (Quantum Chemical Topology), qui sont des outils interprétatifs de chimie quantique. Plusieurs interactions furent étudiées du point de vue de la densité électronique (calculs DFT), notamment des interactions intramoléculaires entre atomes halogènes ainsi que des liaisons halogène inter- et intramoléculaires. L’analyse topologique QTAIM complétée par la décomposition énergétique IQA (Interacting Quantum Atoms) nous a permis de dévoiler la nature physique des interactions étudiées, i.e. la part d’interaction électrostatique et la part d’échange (covalence). Il a été montré que l’échange tient un rôle majeur dans la stabilisation de telles interactions et permet de rationnaliser les différentes topologies observées en terme de compétition entre canaux d’échange primaires et secondaires. Aussi, la formation et la rupture d’une liaison hydrogène au cours de transferts de protons a été étudiée grâce à la décomposition de grandeurs globales (de DFTConceptuelle) en contributions monoatomiques ; le schéma de décomposition proposé se base sur la partition QTAIM et la décomposition énergétique IQA. Cette approche permet de suivre l’évolution, le long d’un chemin réactionnel, de la contribution de chaque atome à la réactivité du système. Une nouvelle façon de caractériser les barrières d’énergie potentielle et les états de transition a ainsi été proposéeThis work aims to theoretically investigate and characterize non-covalent interactions by means of Quantum Chemical Topology (QCT) methods, which are quantum chemistry interpretative tools. Several interactions were studied from the point of view of the electron density (DFT calculations), including intramolecular interactions between halogen atoms as well as inter- and intramolecular halogen bonds. The QTAIM topological analysis complemented by the Interacting Quantum Atoms (IQA) energy decomposition revealed the physical nature of those interactions, i. e. the part of electrostatics and the part of exchange (covalency). It has been shown that exchange plays a significant role in stabilizing such interactions and enables rationalizing the different topologies observed in terms of competition between primary and secondary exchange channels. Also, the formation and breaking of a hydrogen bond during proton transfer reactions has been analyzed by utilizing an atomic decomposition of global quantities (from Conceptual DFT), the new decompositionscheme being based on the QTAIM partition and the IQA energy decomposition. This approach allows following the contribution of every atom to the reactivity of the whole system along a reaction path, introducing a new way of characterizing energy barriers and transition
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Riffet, Vanessa. "Interactions non-covalentes et propriétés physico-chimiques de petits systèmes biologiques : approches théoriques". Palaiseau, Ecole polytechnique, 2014. https://tel.archives-ouvertes.fr/tel-01084858/document.
Abstract (sommario):
La structure tridimensionnelle et les propriétés physico-chimiques des biomolécules telles que les peptides sont gouvernées non seulement par leur composition primaire mais aussi par diverses interactions non-covalentes, inter- et intra-moléculaires. La description, la mesure et les effets de ces interactions sont actuellement au cœur de nombreux travaux de recherches à l’interface entre la biologie et la physico-chimie. Dans ce cadre, nos travaux de thèse visent à une meilleure compréhension de ces interactions au sein de biomolécules et d’agrégats en utilisant les outils de la chimie quantique et de la modélisation moléculaire. Pour cela, du fait de la complexité et de la taille des systèmes biologiques réels, des modèles chimiques simplifiés ont été élaborés. Ceux-ci nous ont permis d’étudier et de comprendre la nature et les effets de ces interactions prises « individuellement » sur la structure géométrique et électronique de systèmes moléculaires tels que de petits peptides et des agrégats de la glycine bétaïne. Le rôle des interactions non-covalentes sur la réactivité dans des conditions physico-chimiques variées (réduction électronique, phase gazeuse, microsolvatation) constitue également une des approches de notre travail. Parmi les systèmes étudiés, nombres d’entre eux comportent un ou plusieurs groupes chargés ammonium, guanidinium ou imidazolium, présents dans les chaines latérales des acides aminés lysine, arginine et histidine. Nous avons montré que l’environnement chimique et électronique de ces groupes chargés influence largement la structure et la réactivité des molécules qui les contiennent. Enfin, au cours de nos travaux, nous avons réalisé une calibration des méthodes de modélisation pour l’étude des propriétés électroniques de peptides radicalaires et mis au point des protocoles d’exploration de surface d’énergie potentielle à partir du champ de force polarisable AMOEBA, ceci afin d’optimiser l’exhaustivité des recherches conformationnelles pour des systèmes biologiques flexiblesThe three-dimensional structure and physico-chemical properties of biomolecules such as peptides are not only governed by their elementary composition but also various non-covalent intra-and inter-molecular interactions. The characterization, measurement and effects of these interactions are currently at the center of many researches at the interface between biology and physical chemistry. In this context, the aim of our thesis is a better understanding of these interactions in biomolecules and aggregates using the tools of quantum chemistry and molecular modeling. In this regard, due to the complexity and size of the real biological systems, chemical models have been developed. These have allowed us to study and understand the nature and effects of these interactions taken "individually" on the geometric and electronic structure of molecular systems such as small peptides and aggregates of glycine betaine. The role of non-covalent interactions on the reactivity of various physico-chemical conditions (electronic reduction, gas phase, microsolvation) is also one of the several approaches of our work. Among the systems examined, many of them included at least one ammonium, guanidinium or imidazolium charged groups, which are founded in the side chains of the amino acids lysine, arginine and histidine. We have shown that the chemical environment of these electronic charges greatly influences the structure and reactivity of the molecules that contain these groups. Eventually, we both performed a calibration of modeling methods for the study of the electronic properties of radical peptides and developed new protocols for the potential energy surface exploration starting from the AMOEBA polarizable force field, in order to optimize the conformational searches exhaustivity for flexible biological systems
6
Hardouin, Julie. "Etude de glutathiones S-transférases par spectrométrie de masse : séquences et interactions non covalentes". Rouen, 2003. http://www.theses.fr/2003ROUES031.
Abstract (sommario):
L'apparition des ionisations MALDI et ESI a permis à la spectrométrie de masse de devenir la technique de choix dans l'analyse protéomique et pour l'étude des complexes non-covalents. L'objectif de cette étude était de caractériser, par spectrométrie de masse, les structures primaire et quaternaire des glutathiones S-transférases (GST) ainsi que son interaction avec des toxines afin d'expliciter un processus de détoxication. Dans un premier temps, nous avons déterminé les séquences de GST porcines ainsi que certaines modifications post-traductionnelles par MALDI-TOF-MS et LC-ESI-IT/MS. Dans un deuxième temps, nous avons étudié les complexes non-covalents des GST porcine et humaine, sous ionisation ESI sur un appareil à secteurs. Les interactions de faible énergie entre l'enzyme dimérique, le glutathion (GSH) et un cyclodepsipeptide, la DTXE (toxine fongique) ont été mises en évidence. L'observation de ces complexes non-covalents exige l'optimisation de la préparation de l'échantillon et le réglage des paramètres source ESI. Cette étude met en relief la capacité de la spectrométrie de masse à effectuer des " screening " de ligands, de substrats et d'inhibiteurs d'une protéine. Cette approche ouvre une voie ultérieure sur le devenir des substrats c'est-à-dire de métabolisation, établissant ainsi un lien entre le protéome et le métabolomeMass spectrometry coupled with the ionizations MALDI or ESI is the analytical technique in proteomic and for the study of non-covalent complexes. The goal of this work is to characterize the primary and quaternary structures of glutathiones S-transferases (GST) with mass spectrometry. Their interactions with toxins is studied to explain the detoxication processes. First, the sequences of porcine GST and post-translational modifications were determined by MALDI-TOF-MS and LC-ESI-IT/MS. Secondly, the non-covalent complexes of porcine and human GST were studied by ESI on a magnetic analyzer. The non-covalent interactions between the dimeric enzyme, the glutathion (GSH) and a cyclodepsipeptide (DTXE) were analyzed. The observation of these species needed the optimization of the sample preparation and the source parameters. This study showed the high efficiency of mass spectrometry to perform screenings of ligands, substrates and inhibitors of proteins. This approach opens up for the future studies of drugs and their metabolites linked with enzymes. The proteome has a direct link with the metabolome
7
Chamoun, Jean. "Contribution du couplage CE-ICP/MS dans l'étude des interactions métals-protéine non-covalentes". Université Louis Pasteur (Strasbourg) (1971-2008), 2005. http://www.theses.fr/2005STR13090.
Abstract (sommario):
Le criblage des interactions protéine/métal grâce à l’utilisation du couplage CE-ICP/MS a été étudié. La mise au point de ce nouvel outil analytique nécessite, outre un interfaçage de ces deux techniques, ine séparation efficace des protéines et une détection sensible des métaux. L’optimisation de la séparation électrophorétique d’un mélange de protéines-test a conduit à l’utilisation d’un tampon borate à pH 9,2, qui minimise l’adsorption et permet la séparation de toutes les protéines du mélange avec une bonne reproductibilité des temps de migration. L’interfaçage entre l’électrophorèse capillaire et l’ICP/MS a été réalisé à l’aide d’une interface avec une solution conductrice. L’optimisation des paramètres tels que débits des gaz, débit et composition de la solution conductrice et position du capillaire dans le micronébuliseur a été réalisée afin d’obtenir les meilleures sensibilité de détection et efficacité de séparation. Toutefois, ce type d’interface entraîne des dilutions importantes des échantillons, qui nous ont conduits à développer un système de préconcentration en ligne afin d’améliorer les limites de détection. Le calcul des limites de détection réalisé sur le cuivre et le zinc contenus dans l’anhydrase carbonique, protéine la moins efficacement concentrée, montre une amélioration des limites de détection en CE-ICP/MS de 6 fois pour le cuivre et 5 fois pour le zinc. Ce couplage a ensuite été utilisé dans l’étude des interactions de trois métaux de transition (Cd, Co et Ni) avec un mélange de protéines constitué de métalloprotéines et protéines majeures du sérum sanguin. Ces études montrent un comportement similaire du cobalt et du nickel, différant totalement de celui du cadmium. Dans le cas des métalloprotéines, le couplage CE-ICP/MS permet également de conclure quant à la nature probable des sites d’interaction. De plus, cette méthode a permis d’étudier l’affinité relative des différents métaux vis-à-vis du mélange de protéines. L’aspect dissociatif du couplage a également été exploité pour obtenir des données cinétiques, permettant l’accès aux constantes de dissociation des complexes et dans certains cas, à la mise en évidence de sites d’interaction multiples. Enfin, la technique a été appliquée à des cations dits « durs » : lanthanides et uranyle (UO22+). Les premiers résultats démontrent une adsorption massive de ces cations à la surface des capillaires. Néanmoins, les études réalisées sur un mélange de six protéines, préalablement identifiées comme cibles de l’uranium, montrent que quatre d’entre elles interagissent avec l’uranium, parmi lesquelles l’albumine et la transferrineThe screening of metal/protein interactions using CE coupled to ICP/MS was investigated. The development of this new analytical tool requires, besides the hyphenation of the two techniques, both an efficient separation of the proteins and a sensitive detection of metals. The optimization of the electrophoretic separation of a protein-test mixture led to the use of a borate buffer, pH 9. 2, which both minimizes adsorption and allows the separation of all proteins’ mixture with a good migration times reproducibility. The hyphenation between capillary electrophoresis and ICP/MS was performed using a sheath flow interface. The optimization of parameters, such as coolant, auxiliary and nebulizer gases, composition and flowrate of the sheath flow solution and position of the capillary in the nebulizer was carried out in order to obtain the best detection sensitivity and separation efficiency. However, this type of interface involves important samples dilutions, which led us to develop an on-line preconcentration technique in order to improve the detection limits. The detection limits calculated for the copper and zinc contained in the carbonic anhydrase, the less efficiently concentrated protein, showed an improvement of the detection limits in CE-ICP/MS of 6 times for copper and 5 times for zinc. CE-ICP/MS was then used in the study of the interactions of three transition metals (Cd, Co and Ni) with a mixture of proteins made of metalloproteins and major blood serum proteins. These studies revealed a similar behavior of cobalt and nickel, completely different from that of cadmium. In the case of the metalloproteins, hyphenated CE-ICP/MS allowed to identify the probable nature of the interaction sites. Moreover, this method allowed studies on the relative affinity of various metals with a mixture of proteins. The dissociative aspect of the separation was also exploited in order to obtain kinetic data which allowed the access to the dissociation constants of the complexes and in certain cases, highlighted the presence of multiple interaction sites. Finally, the technique was applied to so-called “hard cations”: lanthanides and uranyl ion (UO22+). The first results showed a massive adsorption of these cations on the capillaries surface. Nevertheless, the studies, carried out on a mixture of six proteins, previously identified as uranium-targets, showed that four of them interact with the uranium, among which albumin and transferrin
8
Bayach, Imene. "Non-covalent interactions in natural products". Thesis, Limoges, 2014. http://www.theses.fr/2014LIMO0050/document.
Abstract (sommario):
Les polyphénols naturels forment des complexes non-covalents dans lesquels le π-stacking et les liaisons hydrogène jouent un rôle clé dans la stabilisation. Les calculs DFT incluant la dispersion (DFT-D), la description des processus d'agrégation non-covalente de produits naturels devient fiable. Dans ce travail, les méthodes DFT-D sont appliquées à i) la compréhension de la biosynthèse stéréo- et régio-sélective des oligostilbenoïdes, ii) la prédiction de l'agrégation des antioxydants naturels au sein de la membrane bicouche lipidique, qui pourrait rationaliser la synergie de la vitamine E, la vitamine C et polyphénols dans leur action antioxydante, et iii) la modulation des propriétés optiques de dérivés de chalconesNatural polyphenols form non-covalent complexes in which π-stacking and H-bonding play a key stabilizing role. The dispersion-corrected DFT calculations have paved the way towards reliable description of aggregation processes of natural products. In this work, these methods are applied at i) understanding of stereo- and regio-selective oligostilbenoids biosynthesis; ii) predicting natural antioxidant aggregation within lipid bilayer membrane, which may allow rationalizing the synergism of vitamin E, vitamin C and polyphenols in their antioxidant action; and iii) modulating optical properties of chalcone derivatives
9
Watrelot, Aude. "Interactions non-covalentes entre les polyphénols et les pectines : Etude sur un substrat modèle : la pomme". Thesis, Avignon, 2013. http://www.theses.fr/2013AVIG0656/document.
Abstract (sommario):
Les paramètres thermodynamiques et les cinétiques d’interactions entre des polyphénols (des procyanidines et des anthocyanes) et des fractions pectiques ont été déterminés par des méthodes physico-chimiques en solution et sur support solide. Les expériences ont été réalisées avec les anthocyanes majoritaires de cassis ou des procyanidines de type B (extraites de pomme) avec différents degrés de polymérisation et des fractions pectiques issues de pectines de pomme présentant divers degrés de méthylation et différentes chaines latérales d’oses neutres.Les interactions entre les anthocyanes et les pectines sont influencées par les substituants osidiques et le nombre de groupements hydoxyles du noyau B des anthocyanes ainsi que par la composition des fractions pectiques. Les constantes d’affinité entre les pectines et les procyanidines en solution sont les plus élevées quand le degré de polymérisation des procyanidines et le degré de méthylation des pectines sont les plus élevés. De plus, le niveau de ramification des pectines limite leur association avec les procyanidines. Ces interactions impliquent à la fois des liaisons hydrogènes et des interactions hydrophobes. Après les modifications chimiques et l’immobilisation des procyanidines sur une surface, les unités de résonance obtenues par résonance plasmonique de surface entre la (-)-épicatéchine ou le dimère DP2 et les pectines de pomme sont similaires à celles obtenues avec la protéine riche en proline IB5, mais plus faible qu’avec la sérum albumine bovineThermodynamical parameters and kinetics of interactions between polyphenols (procyanidins and anthocyanins) and pectic fractions were defined by physico-chemical methods in solution and with a solid support. Experiments confronted major anthocyanins presents in blackcurrant or B-type procyanidins from apple with various degrees of polymerization to pectic fractions from apple pectins presenting different degree of methylation and different neutral sugar side chains.Interactions between anthocyanins and pectins are influenced by the glycosyl substituent and the number of hydroxyl groups in the B-ring of anthocyanins, and by the composition of pectins. The affinity constant of procyanidins – pectins interaction in solution are the highest when both the procyanidins degree of polymerization and the pectins degree of methylation are the highest. Moreover, the ramification state of pectins limits their association with procyanidins. Those interactions are due to hydrogen bonds and hydrophobic interactions.After chemical modifications of procyanidins and immobilization on a solid support, the resonance units obtained by surface plasmon resonance between (-)-epicatechin or dimer B2 and apple pectins are similar to those obtained with the prolin-rich protein IB5 and lower than with bovine serum albumin
10
Didier, Dorian. "Recyclage de complexes bis(oxazolines)- cuivre chiraux pour la catalyse asymétrique : hétérogénéisation par interactions non-covalentes". Phd thesis, Université Paris Sud - Paris XI, 2011. http://tel.archives-ouvertes.fr/tel-00856579.
Abstract (sommario):
Les ligands de type bis(oxazolines) associés à des sels métalliques ont montré leur efficacité dans de nombreuses réactions de formation de liaisons C-C. L'utilisation de tels complexes chiraux en tant que catalyseurs asymétriques permet l'accès à une large variété de synthons fonctionnalisés énantioenrichis pour la synthèse de composés d'intérêt biologique. Cependant, un taux catalytique important (souvent 10 mol%) est nécessaire à l'obtention de bonnes activités et énantiosélectivités. Il est donc intéressant de pouvoir recycler ces complexes de manière à réduire le coût de leur emploi mais également d'augmenter le turn-over de ces réactions énantiosélectives.La structure des bis(oxazolines) a donc été choisie de manière à permettre le recyclage de catalyseurs par hétérogénéisation. Un nouveau concept a ainsi été mis en place, impliquant la formation de complexes à transfert de charge (CTC) entre un groupement anthracényle et la trinitrofluorénone. La formation de telles interactions non-covalentes permet la précipitation du catalyseur sous forme de CTC en milieu apolaire par ajout de pentane. Ce procédé ayant donné de très bons résultats pour la cycloaddition de Diels-Alder avec des complexes de cuivre, nous l'avons l'appliqué à d'autres transformations stéréosélectives dans le but d'étendre le champ d'application de notre méthode. Nous avons ainsi étudié cette méthode de recyclage pour les réactions de nitroaldolisation, ène-carbonyle et de cyclopropanation, à la fois dans des procédures mono- et multi-substrats mais également dans une procédure multi-réactions. Les rendements et les excès énantiomériques obtenus grâce à ces nouveaux complexes de cuivre chiraux sont analogues aux valeurs observées dans des conditions de catalyse homogène décrites dans la bibliographie. Dans une grande majorité des cas, une excellente stabilité du catalyseur en termes de sélectivité et d'activité est relevée à travers ses différentes réutilisations.La synthèse et l'utilisation de nouveaux supports permettant la formation de CTC ou d'interactions π ont également été réalisées de manière à éviter l'ajout de pentane jusqu'alors nécessaire à la précipitation de notre espèce catalytique. Ce type de catalyseur a pu être mis à l'épreuve dans les mêmes réactions que celles citées ci-dessus, avec des supports modifiés tels que le polystyrène ou la silice, mais également en présence de charbon actif. Cela nous a permis d'obtenir de bons résultats quant à l'efficacité des catalyseurs dans différentes procédures de catalyse hétérogène, avec une bonne conservation des valeurs de rendements et d'énantiosélectivités.
Libri sul tema "Analyse des interactions non covalentes":
1
Karshikoff, Andrey. Non-Covalent Interactions in Proteins. World Scientific Publishing Co Pte Ltd, 2021.
2
Karshikoff, Andrey. Non-covalent Interactions in Proteins. Imperial College Press, 2006.
3
Samah, Posse-Ousmane. Les conditions d'admission et de séjour des travailleurs hautement qualifiés dans l'UE. Carl Grossmann Verlag, 2017. http://dx.doi.org/10.24921/2017.94115913.
Abstract (sommario):
Cet ouvrage analyse le dispositif mis en place par la Directive Carte bleue, non pas en tant que système à part entière, mais comme partie intégrante de la politique européenne en matière dimmigration. Une telle démarche savère nécessaire compte tenu de lapproche sectorielle adoptée par lUE dans ce domaine et la fragmentation juridique quelle occasionne. Dans ce contexte, ce travail présente une analyse des éléments essentiels et des problèmes juridiques de la Directive Carte bleue ainsi que les interactions et les liens du système avec dautres instruments adoptés dans le cadre de la migration légale. En particulier, des parallèles sont établis entre linterprétation de certaines dispositions de la directive et la jurisprudence de la CJUE rendue sur la base de dispositions similaires prévues dans dautres instruments. Cette analyse intègre la proposition de refonte de la directive, présentée en juin 2016.
4
Ruiz-Villalba, Adrián, Nikolaos Frangogiannis e José Maria Pérez-Pomares. Origin and diversity of cardiac fibroblasts: developmental substrates of adult cardiac fibrosis. A cura di José Maria Pérez-Pomares, Robert G. Kelly, Maurice van den Hoff, José Luis de la Pompa, David Sedmera, Cristina Basso e Deborah Henderson. Oxford University Press, 2018. http://dx.doi.org/10.1093/med/9780198757269.003.0012.
Abstract (sommario):
Cardiac connective tissues are primarily formed by cardiac fibroblasts (CF) of diverse embryonic origins. Whereas CF specific roles in cardiac morphogenesis remain under-researched, their involvement in adult cardiac fibrosis is clinically relevant. Cardiac fibrosis is a common element of several chronic cardiac conditions characterized by the loss of ventricular wall mechanical function, ultimately driving to heart failure. In the ischaemic heart early reparative fibrosis evidences the very restricted regenerative potential of the myocardium. In non-ischaemic diseases fibrosis is activated by unknown signals. We summarize current knowledge on the origin of CFs and their developmental roles, and discuss the differential disease-dependent response of different CF subpopulations to various pathological stimuli. We also describe the characteristic cell-cell and cell-matrix interactions that determine the fibrotic remodelling of the myocardium. We analyse experimental models for the study of cardiac fibrosis, and suggest future directions in the search for new markers and therapeutic targets.
Capitoli di libri sul tema "Analyse des interactions non covalentes":
1
Brandenburg, D., W. Thevis, D. Glasmacher, J. Pirrwitz, M. Fabry, E. Schaefer e L. Ellis. "Analysis of the interaction between insulin and its receptor by means of covalent and non-covalent techniques". In Peptides, 574–76. Dordrecht: Springer Netherlands, 1994. http://dx.doi.org/10.1007/978-94-011-0683-2_189.
2
Seth, Saikat Kumar, Antonio Bauzá e Antonio Frontera. "CHAPTER 9. Quantitative Analysis of Weak Non-covalent σ-Hole and π-Hole Interactions". In Monographs in Supramolecular Chemistry, 285–333. Cambridge: Royal Society of Chemistry, 2018. http://dx.doi.org/10.1039/9781788013086-00285.
3
Schoenmaker, Dirk, e Willem Schramade. "Calculating Social and Environmental Value". In Springer Texts in Business and Economics, 115–44. Cham: Springer International Publishing, 2023. http://dx.doi.org/10.1007/978-3-031-35009-2_5.
Abstract (sommario):
AbstractThe previous chapters described the importance of balancing the various types of value, but how to calculate those types of value? The core model in corporate finance is the discounted cash flow (DCF) model, used to determine the financial value (FV) of a project or a company. This chapter explains how social (S) and environmental (E) issues can be expressed in value terms to arrive at social value (SV) and environmental value (EV). Recent advances in impact measurement enable companies to measure social and environmental quantities (such as life years saved by medical treatment or carbon emissions from using fossil fuels) and then to multiply these quantities by their respective shadow price, derived from welfare theory.The reason for monetary valuation of (non-market priced) social and environmental impact is to make them visible, and part of the decision-making process, by integrating SV and EV in the accounting system and business language. A common unit ($, € or any other currency) for financial, social, and environmental aspects of business impacts enables managers (and stakeholders) to compare different value components and to analyse the interactions between these value components. The mental challenge for many managers is to start thinking, analysing, and acting in this way, in spite of data gaps and other hurdles.
4
Gomendio, Montserrat, e José Ignacio Wert. "7. Education Reforms". In Dire Straits-Education Reforms, 269–98. Cambridge, UK: Open Book Publishers, 2023. http://dx.doi.org/10.11647/obp.0332.07.
Abstract (sommario):
In Chapter 7, we analyse the interactions between ideology, governance, conflicts of interest and the evidence provided by ILSAs. We argue that the evidence can be split into three main categories. The first category includes strong evidence which has no impact on policy. The most robust evidence suggests that is reduced impact for greater levels of investment, i.e. decreases in class size and increases in teacher salaries, does not work in education. The reason why this approach has had no influence is because it generates a head-on conflict between the vested interests of unions and those of most stakeholders who strongly oppose them, because they are recommending a decrease in the amount of resources received from public funds. The second category includes variables that are strongly context-dependent (such as enhanced school autonomy), which may be difficult for policymakers to interpret. Furthermore, policy recommendations often ignore this fact and recommend such policies universally with dire consequences. Finally, the third category includes variables that attempt to measure equity, which tend to be inconclusive and partial, meaning that the policy recommendations have been heavily influenced by ideology. This has led to a universal recommendation to apply comprehensive policies and avoid those that are regarded as ‘discriminatory’ (such as ability grouping and early tracking). Such policies lead to the worst outcomes in terms of equity among non-egalitarian societies.
5
Laplaza, Rubén, Francesca Peccati, David Arias-Olivares e Julia Contreras-García. "14 Visualizing non-covalent interactions with NCIPLOT". In Complementary Bonding Analysis, 353–78. De Gruyter, 2021. http://dx.doi.org/10.1515/9783110660074-014.
6
Francisco, E., e A. Martín Pendás. "Energy Partition Analyses: Symmetry-Adapted Perturbation Theory and Other Techniques". In Non-Covalent Interactions in Quantum Chemistry and Physics, 27–64. Elsevier, 2017. http://dx.doi.org/10.1016/b978-0-12-809835-6.00003-7.
7
Herberg, Friedrich W., e Bastian Zimmermann. "Analysis of protein kinase interactions using biomolecular interaction analysis". In Protein Phosphorylation, 315–34. Oxford University PressOxford, 1999. http://dx.doi.org/10.1093/oso/9780199637294.003.0015.
Abstract (sommario):
Abstract Novel technologies employing surface plasmon resonance (Biacore AB) or resonance mirrors (lAsys, Lab Systems) can be used for the characterization of protein-protein, protein-DNA and ligand-receptor interactions (for review see refs 1-3). These techniques directly measure the binding of a molecule in the soluble phase (the ‘analyte’, also called the ‘ligate’) to a ‘ligand’ molecule immobilized on a sensor surface. Thereby the association (k a) and dissociation rate constants (k d) are determined separately. With a known concentration of the analyte, apparent equilibrium binding constants (K D or K A) can be calculated. The chemistries for coupling molecules to the surface via amine, sulfhydryl, carboxyl, and other groups are well defined and reproducible. Non-covalent, site-directed immobilization can be achieved by avidin-biotin interaction, by the use of antibodies, or by binding fusion proteins to specific surfaces. Surfaces containing lipid monolayers are also available. This technology can be used for monitoring interactions, in real time without the use of labels, between two or more molecules, e.g. between proteins, peptides, nucleic acids, or pharmaceuticals.
8
Boto, Roberto A., e Julia Contreras-García. "Beyond QTAIM: NCI Indexes as a Tool to Reveal Intermolecular Bonds in Molecular Aggregates". In Intermolecular Interactions in Crystals: Fundamentals of Crystal Engineering, 222–57. The Royal Society of Chemistry, 2017. http://dx.doi.org/10.1039/bk9781782621737-00222.
Abstract (sommario):
This chapter dwells on a novel descriptor for the visualization of non-covalent interactions, NCI (for Non-Covalent Interactions), based on the Reduced electron Density Gradient (RDG) and enabling an easy-to-catch visualization of non-covalent interactions. In this chapter we will see how this index is based on the bosonic kinetic energy density, revealing a complete spectrum of chemical structures. It recovers the shell structure and Lewis picture of ELF (covalent bonds, lone pairs), but also interactions not recovered by ELF because they are not related to localization, such as ionic and non-covalent interactions, as recovered by QTAIM bond critical points (BCPs). These QTAIM interactions are visualized as isosurfaces, which also provide a very intuitive description of delocalized interactions, overcoming the pair interactions as defined by BCPs. Finally, we will also show that weak intramolecular interactions, both attractive and repulsive, can be visualized by NCI too, even in the absence of QTAIM features. Since NCI provides a complete picture of chemical structure, it becomes an ideal tool to analyze molecular aggregates. We will finish the chapter with several examples applied to molecular solids, showing the ability of NCI to quickly characterize delocalized interactions in benzene from X-ray densities. We will also show an approximation of NCI from promolecular densities applicable to protein structures (e.g. xyz or pdb files). Finally, we will show an example where NCI has helped in revealing a new type of bonding that enables explanation of new experimental results under pressure and unexpected macroscopic properties.
9
Chowdhry, Babur Z., e Stephen E. Harding. "Protein-ligand interactions and their analysis". In Protein-Ligand Interactions: hydrodynamics and calorimetry, 1–18. Oxford University PressOxford, 2000. http://dx.doi.org/10.1093/oso/9780199637492.003.0001.
Abstract (sommario):
Abstract In each cell of an organism, a myriad of reactions, covalent and non-covalent, occur at any given point in time. These reactions are co-ordinated and regulated, both spatially and temporally. Each reaction has a specific purpose, occurs as a result of finely-tuned inter- and intramolecular recognition mechanisms, and forms part of an intricate network of interdependent multi-component linear/ non-linear reactions in interconnected compartments (organelles etc.) of the cell. Moreover the frontiers of viability of such reactions-and the living organ isms that depend on them-are marked by extreme conditions: 1-12 for pH, -5-110 °C for temperature, 0.1-120 MPa for hydrostatic pressure, and 0.6-1.0 for water activity. Amongst the many molecules that participate in such reactions in the complex-and, as yet hardly understood, milieu of the cell-are proteins.
10
Khanmohammadi, Azadeh. "Investigation of Non-Covalent Interactions of Copper (II) Complexes with Small Biomolecules". In Copper - From the Mineral to the Final Application [Working Title]. IntechOpen, 2022. http://dx.doi.org/10.5772/intechopen.106216.
Abstract (sommario):
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.
Atti di convegni sul tema "Analyse des interactions non covalentes":
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Direm, Amani, Brahim El Bali, Mohammed Lachkar, Esra Çetiner, Koray Sayin e Michal Dusek. "Towards quantitative analysis of the non-covalent interactions in a newly synthesized phenanthroline-based nickel(II) complex: A combined experimental and computational study". In 6th International Electronic Conference on Medicinal Chemistry. Basel, Switzerland: MDPI, 2020. http://dx.doi.org/10.3390/ecmc2020-07512.
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Hosszu, Alexandra, e Mihai alexandru Botezatu. "LEARNING ABOUT INTERACTIONS AND EMOTIONAL SUPPORT THROUGH CHATBOTS". In eLSE 2020. University Publishing House, 2020. http://dx.doi.org/10.12753/2066-026x-20-106.
Abstract (sommario):
In the contemporary period, social life is strongly mediated by digital technology, which influences both the knowledge of one's own person and the knowledge of others. Digital can facilitate inter-human communication, increase professional efficiency, improve the quality of life or even change the perspective on society. Digital instruments started to be used also as "emotionally intelligent bots" which might help individuals building emotional resilience, promising "no judging", "privacy", "reflective space" and being "your 4 am friend". Human - non-human relationship became a reality through friendly interactions and learning processes in both direction: from non-human to human and from human to non-human. How is the human - non-human interaction constructed through chatbots? How is the human portrayed in chatbots? How is the non-human portrayed in chatbots? How are learning processes build through emotional support chatbots? These are some of the questions which will be addressed through this paper. This paper aims to analyse the learning role of the emotional support chatbots focusing on the learning processes and the knowledge produced through the human - non-human interaction. In the first part of the paper, I will summarize a literature review of the main articles relevant for this theme. The second part of the paper will include a review of the existing apps promising emotional support and a study case on 2 of the apps following three objectives: (1) understanding the interaction built between human and chatbot, (2) examining the learning processes enhanced by the chatbots, and (3) analyzing types of knowledge produced through the interaction and the learning processes.
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Milenković, Dejan A., Marko N. Živanović, Milan S. Dekić, Marijana Stanojević Pirković e Jelena R. Đorović Jovanović. "CYTOTOXIC ACTIVITY AND MOLECULAR DOCKING STUDY OF 4- SUBSTITUTED FLAVYLIUM SALT". In 1st INTERNATIONAL Conference on Chemo and BioInformatics. Institute for Information Technologies, University of Kragujevac,, 2021. http://dx.doi.org/10.46793/iccbi21.466m.
Abstract (sommario):
In the present manuscript, the cytotoxic activity of flavylium cation substituted at 4- position with phenyl (FC-4Ph) was tested to two cells lines (human colorectal carcinoma, HCT-116, and human fibroblast lung, MRC-5). In vitro cytotoxicity experiments were performed to elucidate the possible anticancer activity of tested substance. Investigated compound did not show cytotoxic effect on HCT-116 after 24 h, while after 72 h exerted significant effect. A significant selectivity towards colorectal carcinoma cells was observed. On the other hand, this compound did not show any effect on MRC-5 cell line. The molecular interactions between receptor tyrosine kinase (RTK) and title compound was examined. The crystal structure of investigated receptor RTK was downloaded from Protein Data Bank. The native bound ligand ((E)-[4-(3,5-difluorophenyl)-3H-pyrrolo[2,3-b]pyridin-3-ylidene](3- methoxyphenyl)methanol was extracted from receptor and binding pocket analysis was performed. Re-docking was carried out with the FC-4Ph in order to generate the same docking pose as found in co-crystallized form of receptor. The obtained results of revealed that investigated compound binds at the same binding pockets to RTK, as well as native bound ligand, by weak non-covalent interactions. The most prominent interactions are hydrogen bonds, π-alkyl, and π-π interactions. The preliminary results suggest that investigated compound showed good binding affinity against RTK, as evident from the free binding energy (ΔGbind in kJ/mol).
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Ganapathy, Harish, V. Emlin, Anant Narendra Parikh e V. Sajith. "Experimental Investigation on Surface Particle Interactions During Pool Boiling of Nanofluids". In ASME 2011 9th International Conference on Nanochannels, Microchannels, and Minichannels. ASMEDC, 2011. http://dx.doi.org/10.1115/icnmm2011-58180.
Abstract (sommario):
The pool boiling characteristics of nanofluids is affected by the interaction between the nanoparticles and the heater surface which forms a sorption layer and this layer increases the surface wettability and thereby enhances the CHF. While deteriorated nucleate boiling has been attributed to the decreased activation of cavities due to the increased wettability, it fails to explain the enhanced performance observed by several researchers, which can be explained only by an increase in surface roughness and hence a direct increase in the number of cavities, thereby compensating for the increase in wettability. Attempts to characterize the roughness of heater surfaces have been restricted to magnified visualizations and intrusive probing. No non-intrusive tests have been reported on flat heaters, which are ideal to conduct surface analyses. The present work is aimed at conducting a non-intrusive experimental study to analyse the surface roughness modification due to the sorption layer on flat plate heaters. Experiments have been carried out using electro-stabilized aluminium oxide water based nanofluids of different concentrations with heaters having varying values of surface roughness. The burn-out heat flux was measured and the effect of sedimentation time was studied. The surface-particle interaction parameter (Ra/dp) was varied to capture the phenomena of plugging as well as splitting of nucleation sites. An experiment having a high value of the interaction parameter shows enhanced boiling performance and that with a value close to 1 shows deteriorated performance. Further it was seen that this behaviour is dependent on the particle concentration. Detailed surface characterization has been done using an optical measurements setup and atomic force microscopy. Boiling on nano-coated heaters has been investigated and presented as an effective solution to counter the disadvantageous transient boiling behavior of nanofluids.
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Direm, Amani, zina Boutobba, Koray Sayın, Brahim El Bali, Mohammed Lachkar e Nourredine Benali-Cherif. "A combined experimental and theoretical study of an oxalato-bridged copper(II) complex: Crystal structure and <em>Hirshfeld</em> surface analysis of the non-covalent interactions". In 6th International Electronic Conference on Medicinal Chemistry. Basel, Switzerland: MDPI, 2020. http://dx.doi.org/10.3390/ecmc2020-07402.
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Balogh, Lajos P., e Mohamed K. Khan. "Biodistribution of Dendrimer Nanocomposites for Nano-Radiation Therapy of Cancer". In ASME 2006 Multifunctional Nanocomposites International Conference. ASMEDC, 2006. http://dx.doi.org/10.1115/mn2006-17025.
Abstract (sommario):
Multifunctional nanocomposites have an enormous scientific and practical future in medicine, especially in biomedical imaging and targeted delivery. Multifunctional composite nanodevices (CND) possess chemical and physical properties of all components, while interactions with the environment of the nanoparticle are dominated by the contact surface of the host molecule. Thus, if the surface is dominated by the organic component of a nano-sized organic-inorganic composite particle, an inorganic particle property can be manipulated in a biologic environment as if it belonged to an organic macromolecule. Composition, charge, and size of are critical in determining nanoparticle trafficking and uptake by organs, and therefore this knowledge is crucial for the development of cancer imaging and therapies. Specific biokinetics and biodistribution then can be influenced by correctly selecting size, and modifying surface characteristics, such as covalently attaching various targeting moieties to the surface forming biohybrids, regulating the surface charge, etc. Dendrimer nanocomposites are recently developed nearly monodisperse hybrid nanoparticles composed of macromolecular hosts and very small, uniformly dispersed inorganic guest domains combining desirable properties of the components. The surface groups control the interaction of these nanodevices with the biological environment. As a result of various synthetic options, the interior and/or the exterior of the host can be cationic, anionic, or non-ionic, depending on their termini and interior functionalities and the pH, and may involve multiple targeting moieties. We have synthesized gold/dendrimer nanocomposites to carry payload radiation and/or diagnostic moiety to specific targets. We examined the biodistribution of the templates and the corresponding gold/dendrimer nanocomposites. We employed the same dendrimer template and systematically varied the size, the surface charge and the composition. Biodistribution of {Au} gold/dendrimer nanodevices of various size (5, 12 and 22 nm) and surface charge (positive, negative) was investigated in mice models (B16 melanoma and DU145 human prostate cancer). Isotope neutron activation analysis (INAA) was used to measure the presence of Au(0) in the tissue sample. All {Au} gold/dendrimer-nanocomposites were assayed for their quantitative short-term (1hr), intermediate (1 day) and long-term (4 days) biodistribution throughout organs for clinical toxicity. Delivery of radiation dose was achieved by radioactive {198Au} composites in a mice model. We have shown that modulating surface charge and composition will greatly change the biodistribution characteristics of the nanodevices. Rigorous testing of the principles that govern nanoparticle interactions with the complex environment of biological systems will be critical for an understanding of how these nanodevices will behave in vivo.
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Josserand, E., e F. Billon. "Application of Mixed Equivalent Solid and Explicit Hole Models to Analysis of Thick Perforated Plates". In ASME 2008 Pressure Vessels and Piping Conference. ASMEDC, 2008. http://dx.doi.org/10.1115/pvp2008-61885.
Abstract (sommario):
Confronted with the problem of how to conduct a complete fatigue analysis of the Tube Plate (TP) of Tubular and Shell Heat Exchangers and particularly of the Steam Generators equipping nuclear power plants of the Pressurized Water Reactor type (PWR), analysts have developed a method to analyse stress in perforated flat and thick Tube Plates with square penetration (crate) patterns, and in particular to analyse several specific zones such as the Interface Zones and various Effects, such as the Secondary (or Shell) Thermal Gradient Effect (STG Effect), the Thermal Gradient in the No-Tube Lane Effect (TGL Effect) and their interactions. The benefit of the approach is that it enables to analyze mechanical and thermal stress calculated using a full 3D Finite Element model incorporating an equivalent solid and the different Interface Zones, and allowing simulating the specific Thermo-Mechanical Effects. The Interface Zones (IZs) are those between the perforated and non-perforated area, the STG Effect is due to the strong gradient near the Secondary (or Shell) Side surface, the TGL Effect is produced by a temperature gradient across the No-Tube Lane. The method used for the fatigue analysis is based on a “Partitioning Stress Method” by means of which the stress induced by the various load types — mechanical loads, global thermal loads, local thermal effects (STG and TGL Effects), and local geometrical effects (IZs) — are first treated separately and then recombined with their appropriate Stress Multiplier Functions.
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Prieto Sanz, Helena. "Do text discussions improve the academic skills of students of HE? Andorra University case." In Sixth International Conference on Higher Education Advances. Valencia: Universitat Politècnica de València, 2020. http://dx.doi.org/10.4995/head20.2020.11211.
Abstract (sommario):
Reading is a core competency in learning processes of higher education as a tool for accessing discipline-specific knowledge. The aim of this case study is to analyse the impact of text group discussions on the academic skills of students at the Universitat d’Andorra (UdA). Qualitative techniques -non-participant observation, interviews and discussion groups- were applied to UdA students and faculty. Five student groups belonging to the Bachelor of Teaching and Learning (BTL), Bachelor of Computer Science (BCS) and Bachelor of Business Administration (BBA) were studied. After processing the data with Atlas.ti, the first results were obtained. Evidences of a positive impact on the academic skills are identified. Firstly, both students and faculty indicated an improvement of the text comprehension mainly because of the peer interactions. Improvement of the critical and analitycal attitude, the own speech as well as the metacognitive learning are also highlighted as areas on which dialogic reading has positive impact.
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Tsarau, Andrei, Marnix van den Berg, Wenjun Lu, Raed Lubbad e Sveinung Løset. "Modelling Results With a New Simulator for Arctic Marine Structures - SAMS". In ASME 2018 37th International Conference on Ocean, Offshore and Arctic Engineering. American Society of Mechanical Engineers, 2018. http://dx.doi.org/10.1115/omae2018-78593.
Abstract (sommario):
The Simulator for Arctic Marine Structures (SAMS) has emerged on the foundation of a number of scientific models developed at SAMCoT – Centre for Research-based Innovation - Sustainable Arctic Marine and Coastal Technology hosted by NTNU – as a versatile numerical tool for the analysis of sea ice actions and action effects on Arctic offshore structures. The current capabilities of SAMS allow engineers to analyse icefloe impacts and ice loads on arbitrary marine structures in various environmental conditions; simulations may involve both fixed and floating structures, non-rigid multi floe interactions, ice breaking and ice rubbling, wind, current and propeller-flow effects on both structures and ice. All these capabilities can be combined to model also complex marine operations in the Arctic and subarctic regions. As SAMS can be applied in both full- and model scales, a number of available experimental case studies from the field and ice tanks can be reanalysed with the new simulator to ensure the high fidelity of the simulations and to establish a validation basis. This paper presents several of such case studies and discusses further validation possibilities.
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Perre, Patrick, e Ian Turner. "A physical interpretation of the use of fractional operators for modelling the drying process". In 21st International Drying Symposium. Valencia: Universitat Politècnica València, 2018. http://dx.doi.org/10.4995/ids2018.2018.7885.
Abstract (sommario):
Fractional order derivatives provide useful alternatives to their integer order counterparts due to their ability to model memory and other properties of the porous medium, such as nonlocal behaviour. These phenomena are driven by the constrained interactions within the complex and non-homogeneous microstructures evident at the pore scale. In this work, we investigate the suitability of time and space fractional operators for modelling drying processes and provide a physical interpretation of these operators. At first, the concept and the general formulation in the case of a 1-D finite domain is summarised. Then a selection of simulations allowed us to analyse the physical effects of these operators on the solution. In particular, we elucidate:(I )the ability of these operators to break the fundamental relationship between mean square displacement and time in the simple example of diffusion in an open space, (ii) the caution to be taken with the formulation of boundary conditions and source terms to obtain consistent balance equations, (iii) the effect of fractional in space diffusion as a way to alter the MC profiles compared to standard diffusion, therefore potentially avoiding the dependence of the diffusivity on the variable Keywords: Fractional Calculus; Transport in Porous Media; Finite Volume Method; Matrix Transfer Technique; Matrix Functions.