Interaction non covalente | EPFL Graph Search

Une interaction non covalente diffère d'une liaison covalente en ce qu'elle n'implique pas le partage d'électrons, mais implique plutôt des variations plus dispersées des interactions électromagnétiques entre molécules ou au sein d'une molécule. L' énergie chimique libérée lors de la formation d'interactions non covalentes est généralement de l'ordre de 1 à 5 kcal / mol ( à pour 6,02 × 1023 molécules). Les interactions non covalentes peuvent être classées en différentes catégories, telles que les effets électrostatiques, les effets π, les forces de van der Waals et les effets hydrophobes. Les interactions non covalentes sont essentielles pour maintenir la structure tridimensionnelle de grosses molécules, telles que les protéines et les acides nucléiques . De plus, elles sont également impliqués dans de nombreux processus biologiques dans lesquels de grosses molécules se lient spécifiquement entre elles (voir la section propriétés de la page ADN ). Ces interaction

Mechanistic Insight into Supramolecular Polymerization in Water Tunable by Molecular Geometry

Lukas Pfeifer, Fan Xu

Supramolecular self-assembly in water based on non-covalent bonding is attracting major attention due to the potential of hydrogels and aqueous polymers in biomedical applications. Although supramolecular polymerization in organic solvents is well established, the key design features, the assembly mechanisms in water and achieving control over the aggregate structures remain challenging. Here, we present the assembly and disassembly of geometrical isomers of a stiff-stilbene bis-urea amphiphile (SA) in pure water. A remarkable feature of this system is that the (E)-isomer forms supramolecular polymers in both pure water and organic solvents. Taking advantage of this unique property, the hydrophobic effect was studied by comparing the supramolecular assembly in both systems. The assembly process in water follows an enthalpy-driven nucleation-elongation (cooperative) supramolecular polymerization mechanism with a standard Gibbs free energy (Delta G degrees = -53 kJ mol(-1)) double the value of the one found in toluene. We attributed this distinctive feature to the hydrophobic effect in water. Furthermore, we discovered an isomer-dependent assembly process, which can be used to control aggregation in aqueous media. Due to the substantial geometric difference between (E)-SA and (Z)-SA, we compared their assembly in water to study the influence of different driving forces involved in the process. The supramolecular polymerization of (E)-SA was cooperatively influenced by hydrogen bonding, pi-stacking, and hydrophobic effects, whereas the assembly of (Z)-SA was mainly driven by hydrophobic effects. As a result, the fiber length of (E)-SA in water is much longer than that of (Z)-SA, presenting opportunities for geometrical control of aggregation in aqueous media. [GRAPHICS]

CHINESE CHEMICAL SOC2022

An Atomistic Simulation Method for Oxygen Impurities in Aluminium Based on Variable Charge Molecular Dynamics

Andreas Elsener

Impurities are known to have a significant impact on materials properties. In particular, the presence of impurities can change mechanical properties and stabilize the microstructure by reducing grain growth and recrystallization processes. In the past atomistic simulations, in particular molecular dynamics, have contributed a lot to the understanding of deformation mechanisms in nanocrystalline metals. Especially, insights into details of dislocation/GB interactions have been gained. Additionally, simulations on coupled grain boundary migration in bicrystalline samples have played an important role in understanding stress assisted grain growth in nanocrystalline metals. However, all these simulations have been performed on monatomic systems. This means that the role of impurities has not yet been considered in these simulations. Some of the important difference between experiments and simulations could be removed by introducing dilute O distributions to computational Al samples. For this purpose, a simulation method is required which can deal with the oxidation of Al atoms around the O impurities and which can simulate the ionic and metallic nature of bonding simultaneously. Here, a method is suggested which fulfills the requirements by modifying the variable charge method of Streitz and Mintmire [Phys. Rev. B 50, 11996 (1994)]. A local chemical potential approach which optimizes the charge on only those atoms expected to be ionic is developed. Additionally the EAM potential for the non-electrostatic interaction given in the publication of Streitz and Mintmire is substituted by empirical potentials which treat the Al-Al interactions with a well-known Al potential. The Al-O and O-O interactions in these EAM potentials are fitted for the simulation of dilute O impurities in Al and additionally for the simulation of corundum in case of a second potential. The aforementioned developments are applied to study the effect of O impurities on the deformation of nc Al. A fully three-dimensional nc sample containing 15 grains of 12 nm grain-size is deformed with a dilute O content in the triple junction lines. The impact of O impurities on dislocation propagation is also considered in a sample which consists of a single grain extracted from a large molecular dynamics simulation. This simulation geometry contains a perfect dislocation, which is pinned at the surrounding grain boundary network. Therefore it allows the study of pinning strength and after unpinning the propagation behavior of the dislocation under various O impurity distributions. Additionally, the role of O impurities on coupled GB migration is investigated by studying two bicrystalline samples with different O distributions in both of them. In the discussion, the emphasis is on the simulation method. Especially, the significance of the samples, simulation conditions and the performance of the method in the different applications are discussed. Additionally, the different developments (local chemical potential approach and EAM potentials) are critically analyzed and improvements for future simulations of impurities are suggested.

EPFL2010

Infrared photofragment spectroscopy of charged amino acid water clusters in the gas phase

Anthi Kamariotou

We present in this work a new technique, which combines laser photofragmentation spectroscopy with tandem mass spectrometry, for structural investigations of biomolecular ions in the gas phase. A novel apparatus was designed and built for the implementation of these studies. In this instrument closed shell ions are produced in the gas phase by electrospray ionization and stored in a hexapole ion trap prior to mass selection of a parent beam in a first quadrupole and then irradiation in an octupole ion guide using laser light. Mass analysis of the photofragmentaion products in a final stage quadrupole as a function of the wavelength generates an action spectrum. We applied this new technique to follow the microsolvation of charged amino acids in the gas phase. In these studies, the nanoelectrospray ionization source generates a distribution of water clusters of charged amino acids at various hydration levels. A particular size of cluster is selected and irradiated by infrared laser pulses resulting in the dissociation of one water molecule. Detection of the photofragmentation of this weak non-covalent bond allows us to generate the vibrational action spectrum of this particular cluster. We use a two-stage difference frequency mixing setup to produce laser light in the 2900–3800 cm-1, allowing us to probe the light-atom stretching region. IR photofragmentation spectra have been obtained for the hydrates of protonated and lithiated valine and those of protonated tryptophan. By probing the region of free and hydrogen-bonded N-H and O-H stretch vibrations and with the help of density functional theory calculations at the B3LYP/6-31++G** level, we relate spectral changes to the structure of clusters. In the study of lithiated valine water clusters, we addressed the question of zwitterion formation upon the combined effect of water and an external ion. Our data indicate the presence of the non-zwitterionic form of valine upon addition of up to four water molecules. In all of the species studied here, the hydration process is driven by solvation of the charge, and upon completion of a first shell around it, water preferentially forms a second solvation shell with no strong competition from other hydration sites on the amino acid backbone. Strikingly, similar water network structures have been observed at the highest hydration level of completely different species, probably indicating the existence of stable ordered water structures. We obtained evidence for a structrual change of the valine backbone in lithiated valine upon addition of the third water molecule, while no conformational change has been identified in the clusters of the protonated species. We have thus been able to answer questions related to the conformational preferences of the amino acid and the structuring of the water network.

EPFL2006