The nature of the intermolecular interaction in (H2X)2 (X = O, S, Se)

2021 ◽  
Author(s):  
Alberto Fernández-Alarcón ◽  
José Manuel Guevara-Vela ◽  
José Luis Casals-Sainz ◽  
Evelio Francisco ◽  
Aurora Costales ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Intermolecular Interaction ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Hydrogen Bonds (HBs) are crucial non-covalent interactions in chemistry. Recently, the occurrence of an HB in (H2S)2 has been reported (Arunan et al., Angew. Chem. Int. Ed. 2018, 57, 15199.),...

scholarly journals New approaches to organocatalysis based on C–H and C–X bonding for electrophilic substrate activation

2016 ◽  
Vol 12 ◽  
pp. 2834-2848 ◽  
Author(s):  
Pavel Nagorny ◽  
Zhankui Sun
Keyword(s):  
Hydrogen Bond ◽  
Hydrogen Bonds ◽  
Recent Progress ◽  
Halogen Bonds ◽  
Hydrogen Bond Donor ◽  
New Approaches ◽  
Substrate Activation ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Hydrogen Bond Donors

Hydrogen bond donor catalysis represents a rapidly growing subfield of organocatalysis. While traditional hydrogen bond donors containing N–H and O–H moieties have been effectively used for electrophile activation, activation based on other types of non-covalent interactions is less common. This mini review highlights recent progress in developing and exploring new organic catalysts for electrophile activation through the formation of C–H hydrogen bonds and C–X halogen bonds.

Direct Immobilization of Ru-Based Catalysts on Silica: Hydrogen Bonds as Non-Covalent Interactions for Recycling in Metathesis Reactions

ChemCatChem ◽  
2015 ◽  
Vol 7 (16) ◽  
pp. 2493-2500 ◽  
Author(s):  
Houssein Nasrallah ◽  
Diana Dragoe ◽  
Caroline Magnier ◽  
Christophe Crévisy ◽  
Marc Mauduit ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Metathesis Reactions ◽  
Non Covalent Interactions ◽  
Direct Immobilization ◽  
Covalent Interactions

Study of non-covalent interactions on dendriplex formation: Influence of hydrophobic, electrostatic and hydrogen bonds interactions

2018 ◽  
Vol 162 ◽  
pp. 380-388 ◽  
Author(s):  
María Sánchez-Milla ◽  
Isabel Pastor ◽  
Marek Maly ◽  
M. Jesús Serramía ◽  
Rafael Gómez ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Non Covalent Interactions ◽  
Covalent Interactions

scholarly journals Columnar Aggregates of Azobenzene Stars: Exploring Intermolecular Interactions, Structure, and Stability in Atomistic Simulations

Molecules ◽  
2021 ◽  
Vol 26 (24) ◽  
pp. 7598
Author(s):  
Markus Koch ◽  
Marina Saphiannikova ◽  
Olga Guskova
Keyword(s):  
Hydrogen Bonds ◽  
Md Simulations ◽  
Binding Energies ◽  
Atomistic Simulations ◽  
Π Interactions ◽  
Different Types ◽  
Non Covalent Interactions ◽  
Experimental Works ◽  
Supramolecular Aggregates ◽  
Covalent Interactions

We present a simulation study of supramolecular aggregates formed by three-arm azobenzene (Azo) stars with a benzene-1,3,5-tricarboxamide (BTA) core in water. Previous experimental works by other research groups demonstrate that such Azo stars assemble into needle-like structures with light-responsive properties. Disregarding the response to light, we intend to characterize the equilibrium state of this system on the molecular scale. In particular, we aim to develop a thorough understanding of the binding mechanism between the molecules and analyze the structural properties of columnar stacks of Azo stars. Our study employs fully atomistic molecular dynamics (MD) simulations to model pre-assembled aggregates with various sizes and arrangements in water. In our detailed approach, we decompose the binding energies of the aggregates into the contributions due to the different types of non-covalent interactions and the contributions of the functional groups in the Azo stars. Initially, we investigate the origin and strength of the non-covalent interactions within a stacked dimer. Based on these findings, three arrangements of longer columnar stacks are prepared and equilibrated. We confirm that the binding energies of the stacks are mainly composed of π–π interactions between the conjugated parts of the molecules and hydrogen bonds formed between the stacked BTA cores. Our study quantifies the strength of these interactions and shows that the π–π interactions, especially between the Azo moieties, dominate the binding energies. We clarify that hydrogen bonds, which are predominant in BTA stacks, have only secondary energetic contributions in stacks of Azo stars but remain necessary stabilizers. Both types of interactions, π–π stacking and H-bonds, are required to maintain the columnar arrangement of the aggregates.

AFM Research in Catalysis and Medicine

2020 ◽  
Vol 7 (3) ◽  
pp. 248-255
Author(s):  
Ludmila Matienko ◽  
Mil Elena Mickhailovna ◽  
Binyukov Vladimir Ivanovich ◽  
Goloshchapov Alexandr Nikolaevich
Keyword(s):  
Hydrogen Bonds ◽  
Active Sites ◽  
Morphological Changes ◽  
Iron Complexes ◽  
Supramolecular Structures ◽  
Intermolecular Hydrogen Bonds ◽  
Force Microscopy ◽  
Atomic Force ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Background: In this study, we show that the AFM method not only allows monitoring the morphological changes in biological structures fixed on the surface due to H-bonds, but also makes it possible to study the self-organization of metal complexes by simulating the active center of enzymes due to intermolecular H-bonds into stable nanostructures; the sizes of which are much smaller than the studied biological objects. The possible role of intermolecular hydrogen bonds in the formation of stable supramolecular metal complexes, which are effective catalysts for the oxidation of alkyl arenes to hydroperoxides by molecular oxygen and mimic the selective active sites of enzymes, was first studied by AFM. Methods and Results: The formation of supramolecular structures due to intermolecular hydrogen bonds and, possibly, other non-covalent interactions, based on homogenous catalysts and models of active centers enzymes, heteroligand nickel and iron complexes, was proven by AFM-technique. AFM studies of supramolecular structures were carried out using NSG30 cantilever with a radius of curvature of 2 nm, in the tapping mode. To form nanostructures on the surface of a hydrophobic, chemically modified silicon surface as a substrate, the sample was prepared using a spin-coating process from solutions of the nickel and iron complexes. The composition and the structure of the complex Ni2(acac)(OAc)3·NMP·2H2O were determined in earlier works using various methods: mass spectrometry, UV- and IR-spectroscopy, elemental analysis, and polarography. Self-assembly of supramolecular structures is due to intermolecular interactions with a certain coordination of these interactions, which may be a consequence of the properties of the components themselves, the participation of hydrogen bonds and other non-covalent interactions, as well as the balance of the interaction of these components with the surface. Using AFM, approaches have been developed for fixing on the surface and quantifying parameters of cells. Conclusion: This study summarizes the authors' achievements in using the atomic force microscopy (AFM) method to study the role of intermolecular hydrogen bonds (and other non-covalent interactions) and supramolecular structures in the mechanisms of catalysis. The data obtained from AFM based on nickel and iron complexes, which are effective catalysts and models of active sites of enzymes, indicate a high probability of the formation of supramolecular structures in real conditions of catalytic oxidation, and can bring us closer to understanding enzymes activity. With a sensitive AFM method, it is possible to observe the self-organization of model systems into stable nanostructures due to H-bonds and possibly other non-covalent interactions, which can be considered as a step towards modeling the active sites of enzymes. Methodical approaches of atomic force microscopy for the study of morphological changes of cells have been developed.

Computational evidence that hyperconjugative orbital interactions are responsible for the stability of intramolecular Te⋯O/Te⋯S non-covalent interactions and comparable to hydrogen bonds in quasi-cyclic systems

2016 ◽  
Vol 40 (11) ◽  
pp. 9132-9138 ◽  
Author(s):  
Mrinal Kanti Si ◽  
Bishwajit Ganguly
Keyword(s):  
Hydrogen Bonds ◽  
Bond Strength ◽  
Orbital Interactions ◽  
Non Covalent Interactions ◽  
Cyclic Systems ◽  
The Stability ◽  
Covalent Interactions ◽  
Secondary Bonding

The intramolecular secondary bonding interactions involving quasi-cyclic tellurium are comparable to H-bond strength and partially governed by orbital interactions.

scholarly journals The subtle balance of weak supramolecular interactions: The hierarchy of halogen and hydrogen bonds in haloanilinium and halopyridinium salts

2010 ◽  
Vol 6 ◽  
Author(s):  
Kari Raatikainen ◽  
Massimo Cametti ◽  
Kari Rissanen
Keyword(s):  
Hydrogen Bonds ◽  
Single Crystal ◽  
Halogen Bonding ◽  
Relative Strength ◽  
Supramolecular Interactions ◽  
X Ray Diffraction ◽  
X Ray ◽  
Structural Database ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The series of haloanilinium and halopyridinium salts: 4-IPhNH3Cl (1), 4-IPhNH3Br (5), 4-IPhNH3H2PO4 (6), 4-ClPhNH3H2PO4 (8), 3-IPyBnCl (9), 3-IPyHCl (10) and 3-IPyH-5NIPA (3-iodopyridinium 5-nitroisophthalate, 13), where hydrogen or/and halogen bonding represents the most relevant non-covalent interactions, has been prepared and characterized by single crystal X-ray diffraction. This series was further complemented by extracting some relevant crystal structures: 4-BrPhNH3Cl (2, CCDC ref. code TAWRAL), 4-ClPhNH3Cl (3, CURGOL), 4-FPhNH3Cl (4, ANLCLA), 4-BrPhNH3H2PO4, (7, UGISEI), 3-BrPyHCl, (11, CIHBAX) and 3-ClPyHCl, (12, VOQMUJ) from Cambridge Structural Database for sake of comparison. Based on the X-ray data it was possible to highlight the balance between non-covalent forces acting in these systems, where the relative strength of the halogen bonding C–X···A− (X = I, Br or Cl) and the ratio between the halogen and hydrogen bonds [C–X···A− : D–H···A−] varied across the series.

scholarly journals From Supramolecular Hydrogels to Multifunctional Carriers for Biologically Active Substances

2021 ◽  
Vol 22 (14) ◽  
pp. 7402
Author(s):  
Joanna Skopinska-Wisniewska ◽  
Silvia De la Flor ◽  
Justyna Kozlowska
Keyword(s):  
Antimicrobial Activity ◽  
Hydrogen Bonds ◽  
Biologically Active ◽  
Supramolecular Hydrogel ◽  
Chemical Substances ◽  
Ligand Coordination ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Active Substances ◽  
Metal Ligand

Supramolecular hydrogels are 3D, elastic, water-swelled materials that are held together by reversible, non-covalent interactions, such as hydrogen bonds, hydrophobic, ionic, host–guest interactions, and metal–ligand coordination. These interactions determine the hydrogels’ unique properties: mechanical strength; stretchability; injectability; ability to self-heal; shear-thinning; and sensitivity to stimuli, e.g., pH, temperature, the presence of ions, and other chemical substances. For this reason, supramolecular hydrogels have attracted considerable attention as carriers for active substance delivery systems. In this paper, we focused on the various types of non-covalent interactions. The hydrogen bonds, hydrophobic, ionic, coordination, and host–guest interactions between hydrogel components have been described. We also provided an overview of the recent studies on supramolecular hydrogel applications, such as cancer therapy, anti-inflammatory gels, antimicrobial activity, controlled gene drug delivery, and tissue engineering.

scholarly journals Bromination of bis(pyridin-2-yl) diselenide in methylene chloride: the reaction mechanism and crystal structures of 1H-pyridine-2-selenenyl dibromide and its cycloadduct with cyclopentene (3aSR,9aRS)-2,3,3a,9a-tetrahydro-1H-cyclopenta[4,5][1,3]selenazolo[3,2-a]pyridinium bromide

2019 ◽  
Vol 75 (5) ◽  
pp. 675-679 ◽  
Author(s):  
Zhanna V. Matsulevich ◽  
Julia M. Lukiyanova ◽  
Vladimir I. Naumov ◽  
Galina N. Borisova ◽  
Vladimir K. Osmanov ◽  
...  
Keyword(s):  
Hydrogen Bonds ◽  
Methylene Chloride ◽  
Three Dimensional ◽  
Cycloaddition Reaction ◽  
Double Layers ◽  
Pyridinium Bromide ◽  
Square Planar ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Centrosymmetric Dimers

1H-Pyridine-2-selenenyl dibromide, C5H5NSeBr2, 1, is a product of the bromination of bis(pyridin-2-yl) diselenide in methylene chloride recrystallization from methanol. Compound 1 is essentially zwitterionic: the negative charge resides on the SeBr2 moiety and the positive charge is delocalized over the pyridinium fragment. The C—Se distance of 1.927 (3) Å is typical of a single bond. The virtually linear Br—Se—Br moiety of 178.428 (15)° has symmetrical geometry, with Se—Br bonds of 2.5761 (4) and 2.5920 (4) Å, and is twisted by 63.79 (8)° relative to the pyridinium plane. The Se atom forms an intermolecular Se...Br contact of 3.4326 (4) Å, adopting a distorted square-planar coordination. In the crystal, molecules of 1 are linked by intermolecular N—H...Br and C—H...Br hydrogen bonds, as well as by non-covalent Se...Br interactions, into a three-dimensional framework. (3aSR,(9aRS)-2,3,3a,9a-Tetrahydro-1H-cyclopenta[4,5][1,3]selenazolo[3,2-a]pyridinium-9 bromide, C10H12NSe+·Br−, 2, is a product of the cycloaddition reaction of 1 with cyclopentene. Compound 2 is a salt containing a selenazolopyridinium cation and a bromide anion. Both five-membered rings of the cation adopt envelope conformations. The dihedral angle between the basal planes of these rings is 62.45 (11)°. The Se atom of the cation forms two additional non-covalent interactions with the bromide anions at distances of 3.2715 (4) and 3.5683 (3) Å, attaining a distorted square-planar coordination. In the crystal, the cations and anions of 2 form centrosymmetric dimers by non-covalent Se...Br interactions. The dimers are linked by weak C—H...Br hydrogen bonds into double layers parallel to (001).

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