scholarly journals Chiral Cocrystal Solid Solutions, Molecular Complexes, and Salts of N-Triphenylacetyl-l-Tyrosine and Diamines

2019 ◽  
Vol 20 (20) ◽  
pp. 5004 ◽  
Author(s):  
Agnieszka Czapik ◽  
Maciej Jelecki ◽  
Marcin Kwit
Keyword(s):  
Solid Solution ◽  
Hydrogen Bonds ◽  
Molecular Complexes ◽  
Structural Motif ◽  
Supramolecular Systems ◽  
Racemic Mixtures ◽  
Non Covalent Interactions ◽  
Covalent Interactions ◽  
Racemic Crystals ◽  
Triphenylacetic Acid

The molecular recognition process and the ability to form multicomponent supramolecular systems have been investigated for the amide of triphenylacetic acid and l-tyrosine (N-triphenylacetyl-l-tyrosine, TrCOTyr). The presence of several supramolecular synthons within the same amide molecule allows the formation of various multicomponent crystals, where TrCOTyr serves as a chiral host. Isostructural crystals of solvates with methanol and ethanol and a series of binary crystalline molecular complexes with selected organic diamines (1,5-naphthyridine, quinoxaline, 4,4′-bipyridyl, and DABCO) were obtained. The structures of the crystals were planned based on non-covalent interactions (O–H···N or N–H+···O− hydrogen bonds) present in a basic structural motif, which is a heterotrimeric building block consisting of two molecules of the host and one molecule of the guest. The complex of TrCOTyr with DABCO is an exception. The anionic dimers built off the TrCOTyr molecules form a supramolecular gutter, with trityl groups located on the edge and filled by DABCO cationic dimers. Whereas most of the racemic mixtures crystallize as racemic crystals or as conglomerates, the additional tests carried out for racemic N-triphenylacetyl-tyrosine (rac-TrCOTyr) showed that the compound crystallizes as a solid solution of enantiomers.

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.

Non-Covalent Interactions Atlas Benchmark Data Sets 3: Repulsive Contacts

2020 ◽  
Author(s):  
Kristian Kříž ◽  
Martin Nováček ◽  
Jan Řezáč
Keyword(s):  
Organic Molecules ◽  
Energy Surface ◽  
Molecular Complexes ◽  
Data Sets ◽  
Interaction Energies ◽  
Data Set ◽  
Benchmark Data ◽  
Mechanical Methods ◽  
Non Covalent Interactions ◽  
Covalent Interactions

The new R739×5 data set from the Non-Covalent Interactions Atlas series (www.nciatlas.org) focuses on repulsive contacts in molecular complexes, covering organic molecules, sulfur, phosphorus, halogens and noble gases. Information on the repulsive parts of the potential energy surface is crucial for the development of robust empirically parametrized computational methods. We use the new data set of highly accurate CCSD(T)/CBS interaction energies to test existing DFT and semiempirical quantum-mechanical methods. On the example of the PM6 method, we analyze the source of the error and its relation to the difficulties in the description of conformational energies, and we also devise an immediately applicable correction that fixes the most serious uncorrected issues previously encountered in practical calculations.

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.

Supramolecular organization of phthalocyanines: from solution to surface

2009 ◽  
Vol 13 (04n05) ◽  
pp. 471-480 ◽  
Author(s):  
M. Victoria Martínez-Díaz ◽  
Giovanni Bottari
Keyword(s):  
Photophysical Properties ◽  
Building Blocks ◽  
Supramolecular Interactions ◽  
Supramolecular Organization ◽  
Supramolecular Systems ◽  
Ligand Interactions ◽  
Donor Acceptor ◽  
Interesting Class ◽  
Non Covalent Interactions ◽  
Covalent Interactions

Phthalocyanines are an interesting class of aromatic macrocycles which possess exciting electrical, redox and photophysical properties that make them ideal building blocks for applications in different technological fields. However, the incorporation of phthalocyanines into devices is often tied to the possibility of organizing these macrocycles into arrays using supramolecular interactions. To date, several supramolecular motifs such as hydrogen-bonding, donor-acceptor or metal-ligand interactions have been used to promote the phthalocyanines' organization in solution. Furthermore, such weak, non-covalent interactions have also been widely employed to foster the organization of these macrocycles in condensed phases such as liquid-crystals or thin films. This micro-review provides a brief overview of the contribution made by some research groups in Spain towards the preparation of organized phthalocyanine-based supramolecular systems.

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 Photoinduced electron transfer in supramolecular ruthenium–porphyrin assemblies

2017 ◽  
Vol 46 (7) ◽  
pp. 2255-2262 ◽  
Author(s):  
Diego Rota Martir ◽  
Mattia Averardi ◽  
Daniel Escudero ◽  
Denis Jacquemin ◽  
Eli Zysman-Colman
Keyword(s):  
Electron Transfer ◽  
Photoinduced Electron Transfer ◽  
Supramolecular Systems ◽  
Non Covalent Interactions ◽  
Ruthenium Porphyrin ◽  
Covalent Interactions

We present dynamic supramolecular systems composed of a Ru(ii) complex of the form of [Ru(dtBubpy)2(qpy)][PF6]2 (where dtBubpy is 4,4′-di-tert-butyl-2,2′-dipyridyl and qpy is 4,4′:2′,2′′:4′′,4′′′-quaterpyridine) and zinc tetraphenylporphyrins (ZnTPP), through non-covalent interactions between the distal pyridines of the qpy and the zinc of ZnTPP.

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