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Modelowanie właściwosci wiązań wodorowych na przykładzie kompleksów układ amidowy - woda

Rzepiela Kacper, Buczek Aneta, Kupka Teobald, Kar Tapas, Broda Małgorzta A.

Wiadomości Chemiczne

2023

[Z] 77, 7-8

629--645

The energy and structure of intermolecular hydrogen bonds between water molecule and N-methylamide (NMA) or uracil (U) are discussed on the basis of DFT calculations. Theoretical methods are applied to calculate properties of cis- and trans- NMA complexes with one water molecule. Subsequently, H-bonds in six uracil – water complexes are analyzed. The influence of dispersion interactions and the polar environment on the hydrogen bond energy was analyzed. Results obtained by B3LYP functional with and without Grimme D3 dispersion correction indicate that dispersion interaction plays a significant role in an association process. In addition, the polar solvent reduces the hydrogen bond energy and this reduction is directly proportional to the hydrogen bond energy.

Efekt kooperatywności oddziaływań niekowalencyjnych w wybranych układach molekularnych stabilizowanych wiązaniami wodorowymi i halogenowymi

Domagała Małgorzata, Dominikowska Justyna, Palusiak Marcin

Wiadomości Chemiczne

2019

[Z] 73, 1-2

33--52

Among various so-called weak interactions, a halogen bond [8 and references therein] is currently probably one of more explored by researchers. This is due to the fact that it has several properties in common with the hydrogen bonding, and thus, similarly as already well characterised H-bond, it may have a crucial role in different physical, chemical, and biological processes. This bond is formed due to stabilising interactions between a region of positive charge located on a surface of the halogen atom and the other atomic center possessing the electron charge surplus (e.g. a lone pair) [8]. The region of positive charge appears on the halogen atom surface due to deformation of its electron cloud resulting in its ellipsoidal shape with the short axis opposite the covalent bond and the long axis in the perpendicular direction [11]. This results in a particular distribution of local charges on the atomic surface, as shown in Figure 1. As a consequence the halogen atom may exhibit a dual character, acting as either electron charge donor or acceptor, depending on the type of interaction and the direction of the appearing interactomic contact. A good example of such situation is shown in Figure 2. Thus, one may consider the situation when two interactions are formed simultaneously and the halogen atom acts as an electron charge donor and acceptor at the same time. For such situation the synergism of both interactions may strengthen complexation. In order to analyze that case, various representative complexes were investigated [13, 17, 18, 20, 21] by means of many-body interaction approach [5, 6]. In general, it appears that as distinct to hydrogen bond [2–4], the synergism is rather weak, with some exceptions for iodine atom due to stronger halogen bonds formed by that atomic centre [13, 17, 18]. In the case of halo-amine tetramers [21] the additional stabilising effect derived from back bonding of π type was found – for the first time for a halogen bond.