scholarly journals Noncovalent Bonds through Sigma and Pi-Hole Located on the Same Molecule. Guiding Principles and Comparisons

Molecules ◽  
2021 ◽  
Vol 26 (6) ◽  
pp. 1740
Author(s):  
Wiktor Zierkiewicz ◽  
Mariusz Michalczyk ◽  
Steve Scheiner

Over the last years, scientific interest in noncovalent interactions based on the presence of electron-depleted regions called σ-holes or π-holes has markedly accelerated. Their high directionality and strength, comparable to hydrogen bonds, has been documented in many fields of modern chemistry. The current review gathers and digests recent results concerning these bonds, with a focus on those systems where both σ and π-holes are present on the same molecule. The underlying principles guiding the bonding in both sorts of interactions are discussed, and the trends that emerge from recent work offer a guide as to how one might design systems that allow multiple noncovalent bonds to occur simultaneously, or that prefer one bond type over another.

2021 ◽  
Author(s):  
Garima Shrivastava ◽  
Alaa AA Aljabali ◽  
Seyed Hossein Shahcheraghi ◽  
Marzieh Lotfi ◽  
Madhur D Shastri ◽  
...  

The mortality and morbidity rates for prostate cancer have recently increased to alarming levels, rising higher than lung cancer. Due to a lack of drug targets and molecular probes, existing theranostic techniques are limited. Human LIN28A and its paralog LIN28B overexpression are associated with a number of tumors resulting in a remarkable increase in cancer aggression and poor prognoses. The current review aims to highlight recent work identifying the key roles of LIN28A and LIN28B in prostate cancer, and to instigate further preclinical and clinical research in this important area.


Crystals ◽  
2019 ◽  
Vol 9 (10) ◽  
pp. 506 ◽  
Author(s):  
Irina Yushina ◽  
Natalya Tarasova ◽  
Dmitry Kim ◽  
Vladimir Sharutin ◽  
Ekaterina Bartashevich

The interrelation between noncovalent bonds and physicochemical properties is in the spotlight due to the practical aspects in the field of crystalline material design. Such study requires a number of similar substances in order to reveal the effect of structural features on observed properties. For this reason, we analyzed a series of three substituted thiazolo[2,3-b][1,3]thiazinium triiodides synthesized by an iodocyclization reaction. They have been characterized with the use of X-ray diffraction, Raman spectroscopy, and thermal analysis. Various types of noncovalent interactions have been considered, and an S…I chalcogen bond type has been confirmed using the electronic criterion based on the calculated electron density and electrostatic potential. The involvement of triiodide anions in the I…I halogen and S…I chalcogen bonding is reflected in the Raman spectroscopic properties of the I–I bonds: identical bond lengths demonstrate different wave numbers of symmetric triiodide vibration and different values of electron density at bond critical points. Chalcogen and halogen bonds formed by the terminal iodine atom of triiodide anion and numerous cation…cation pairwise interactions can serve as one of the reasons for increased thermal stability and retention of iodine in the melt under heating.


Crystals ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 455 ◽  
Author(s):  
Saikat Seth

In this study, a new equimolar (1:1:1) mixed ligand Cu(II) polymer, [Cu(IDA)(ImP)]n (1) with iminodiacetato (IDA) and imidazo[1,2-a]-pyridine (ImP) was synthesized and characterized by single crystal X-ray diffraction analysis. X-ray crystallography reveals that compound (1) consists of polymeric zigzag chain along [010] the carboxylate carbonyl oxygen atom by two-fold symmetry screw axis. The solid-state structure is stabilized through C–H···O hydrogen bonds and C–H···π interactions that lead the molecules to generate two-dimensional supramolecular assemblies. The intricate combinations of hydrogen bonds and C–H···π interactions are fully described along with computational studies. A thorough analysis of Hirshfeld surface and fingerprint plots elegantly quantify the interactions involved within the structure. The binding energies associated with the noncovalent interactions observed in the crystal structure and the interplay between them were calculated using theoretical DFT calculations. Weak noncovalent interactions were analyzed and characterized using Bader’s theory of ‘‘atoms-in-molecules’’ (AIM). Finally, the solid-state supramolecular assembly was characterized by the “Noncovalent Interaction” (NCI) plot index.


Nanomaterials ◽  
2020 ◽  
Vol 10 (4) ◽  
pp. 651 ◽  
Author(s):  
Huacheng Zhang ◽  
Zhaona Liu ◽  
Hui Fu

Pillararenes trimer with particularly designed structural geometry and excellent capacity of recognizing guest molecules is a very efficient and attractive building block for the fabrication of advanced self-assembled materials. Pillararenes trimers could be prepared via both covalent and noncovalent bonds. The classic organic synthesis reactions such as click reaction, palladium-catalyzed coupling reaction, amidation, esterification, and aminolysis are employed to build covalent bonds and integrate three pieces of pillararenes subunits together into the “star-shaped” trimers and linear foldamers. Alternatively, pillararenes trimers could also be assembled in the form of host-guest inclusions and mechanically interlocked molecules via noncovalent interactions, and during those procedures, pillararenes units contribute the cavity for recognizing guest molecules and act as a “wheel” subunit, respectively. By fully utilizing the driving forces such as host-guest interactions, charge transfer, hydrophobic, hydrogen bonding, and C–H…π and π–π stacking interactions, pillararenes trimers-based supramolecular self-assemblies provide a possibility in the construction of multi-dimensional materials such as vesicular and tubular aggregates, layered networks, as well as frameworks. Interestingly, those assembled materials exhibit interesting external stimuli responsiveness to e.g., variable concentrations, changed pH values, different temperature, as well as the addition/removal of competition guests and ions. Thus, they could further be used for diverse applications such as detection, sorption, and separation of significant multi-analytes including metal cations, anions, and amino acids.


2020 ◽  
Author(s):  
Sergey A. Shteingolts ◽  
Adam I. Stash ◽  
Vladimir G. Tsirelson ◽  
Robert Fayzullin

A detailed analysis of a complete set of the local potentials that appear in the Euler equation for electron density is carried out for noncovalent interactions in the uracil derivative using experimental X-ray charge density. The interplay between the quantum theory of atoms in molecules and crystals and the local potentials and corresponding inner-crystal electronic forces of electrostatic and kinetic origin is explored. Novel physically grounded bonding descriptors derived within the orbital-free quantum crystallography provided the detailed examination of pi-stacking and intricate C=O...pi interactions and nonclassical hydrogen bonds. The donor-acceptor character of these interactions is revealed by analysis of Pauli and von Weizsäcker potentials together with more well-known functions. Partitioning of crystal space into atomic-like potential basins led us to the definite description of the charge transfer. In this way, our analysis throws light on aspects of these closed-shell interactions hitherto hidden from the description.


Author(s):  
Huacheng Zhang

Pillararenes trimer with particularly designed structural geometry and excellent capacity of recognizing guest molecules is a very efficient and attractive building block for the fabrication of advanced self-assembled materials. Pillararenes trimers could be prepared via both covalent and noncovalent bonds. The classic organic synthesis reactions such as click reaction, Palladium-catalyzed coupling reaction, amidation, esterification and aminolysis are employed to build covalent bonds and integrate three pieces of pillararenes subunits together into the “star-shaped” trimers and linear foldamers. Alternatively, pillararenes trimers could also be assembled in the form of host-guest inclusions and mechanically interlocked molecules via noncovalent interactions, and during those procedures, pillararenes units contribute the cavity for recognizing guest molecules and act as a “wheel” subunit, respectively. By fully utilizing the driving forces such as host-guest interactions, charge transfer, hydrophobic, hydrogen bonding, C—H…π and π—π stacking interactions, pillararenes trimers-based supramolecular self-assemblies provide a possibility in the construction of multi-dimensional materials such as vesicular and tubular aggregates, layered networks, as well as frameworks. Interestingly, those assembled materials exhibit interesting external stimuli responsiveness to e.g., variable concentrations, changed pH values, different temperature, as well as the addition/removal of competition guests and ions. Thus, they could further be used for diverse applications such as detection, sorption and separation of significant multi-analytes including metal cations, anions and amino acids.


Crystals ◽  
2021 ◽  
Vol 11 (9) ◽  
pp. 1032
Author(s):  
Sonia Khemaissa ◽  
Sandrine Sagan ◽  
Astrid Walrant

Tryptophan is an aromatic amino acid with unique physico-chemical properties. It is often encountered in membrane proteins, especially at the level of the water/bilayer interface. It plays a role in membrane protein stabilization, anchoring and orientation in lipid bilayers. It has a hydrophobic character but can also engage in many types of interactions, such as π–cation or hydrogen bonds. In this review, we give an overview of the role of tryptophan in membrane proteins and a more detailed description of the underlying noncovalent interactions it can engage in with membrane partners.


2020 ◽  
Vol 76 (8) ◽  
pp. 795-809
Author(s):  
Konstantin L'vovich Obydennov ◽  
Tatiana Andreevna Kalinina ◽  
Olga Alexandrovna Vysokova ◽  
Pavel Alexandrovich Slepukhin ◽  
Varvara Alexandrovna Pozdina ◽  
...  

The crystal structures of four new chiral [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines are described, namely, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C20H24N4O4S, ethyl 6,6-dimethyl-5-(4-methylbenzoyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C17H20N4O3S, and ethyl 5-benzoyl-6-(4-methoxyphenyl)-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C21H20N4O4S. The crystallographic data and cell activities of these four compounds and of the structures of three previously reported similar compounds, namely, ethyl 5′-(4-methylbenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O3S, ethyl 5′-(4-methoxybenzoyl)-5′H,7′H-spiro[cyclopentane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate, C19H22N4O4S, and ethyl 6-methyl-5-(4-methylbenzoyl)-6-phenyl-6,7-dihydro-5H-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine-3-carboxylate, C22H22N4O3S, are contrasted and compared. For both crystallization and an MTT assay, racemic mixtures of the corresponding [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines were used. The main manner of molecular packing in these compounds is the organization of either enantiomeric pairs or dimers. In both cases, the formation of two three-centre hydrogen bonds can be detected resulting from intramolecular N—H...O and intermolecular N—H...O or N—H...N interactions. Molecules of different enantiomeric forms can also form chains through N—H...O hydrogen bonds or form layers between which only weak hydrophobic contacts exist. Unlike other [1,2,3]triazolo[5,1-b][1,3,4]thiadiazines, ethyl 5′-benzoyl-5′H,7′H-spiro[cyclohexane-1,6′-[1,2,3]triazolo[5,1-b][1,3,4]thiadiazine]-3′-carboxylate contains molecules of only the (R)-enantiomer; moreover, the N—H group does not participate in any significant intermolecular interactions. Molecular mechanics methods (force field OPLS3e) and the DFT B3LYP/6-31G+(d,p) method show that the compound forming enantiomeric pairs via weak N—H...N hydrogen bonds is subject to greater distortion of the geometry under the influence of the intermolecular interactions in the crystal. For intramolecular N—H...O and S...O interactions, an analysis of the noncovalent interactions (NCIs) was carried out. The cellular activities of the compounds were tested by evaluating their antiproliferative effect against two normal human cell lines and two cancer cell lines in terms of half-maximum inhibitory concentration (IC50). Some derivatives have been found to be very effective in inhibiting the growth of Hela cells at nanomolar and submicromolar concentrations with minimal cytotoxicity in relation to normal cells.


1970 ◽  
Vol 64 (2) ◽  
pp. 41-45
Author(s):  
Theodor D. Sterling

□ In summary, we can say that as a result of recent work in implanting visual prostheses in correlated work in visual physiology, data processing, and materials technology and in the development of sophisticated simulation techniques, we have approached several steps closer to a vantage point from which we can state the conditions under which a reliable visual prosthesis in the armamentarium of sensory aids has been clarified as a result of the conference and the interest of the scientific community in the development of such a system has been stimulated. It is significant that Dr. MacNichol (the new director of NINDS) has made our computer program for simulating the output of a prosthesis available to scientists at the National Institutes of Health as well as members of the newly-formed National Eye Institute. It is also obvious that we can sustain scientific interest in the problems involved in the development of experiments toward a visual prosthesis, because of the simultaneously human and personal involvement of researchers in alleviating the problems of blindness.


2019 ◽  
Author(s):  
Teresa Naranjo ◽  
Rubén Álvarez-Asencio ◽  
Patricia Pedraz ◽  
Belén Nieto-Ortega ◽  
Enrique Burzurí ◽  
...  

Hydrogen bonds are arguably the most important of noncovalent interactions. The physical properties of water and the information storage in DNA depend on H-bonding, for instance. To this day, the balance between the Coulombic and covalent contributions to H-bonds is still under debate. Here, we show that H-bonded host-guest systems associate in ionic liquids, pure salts with melting point below room temperature, in which dipole-dipole electrostatic interactions should be negligible in comparison with dipole-charge interactions. Binding constants (<i>K</i><sub>a</sub>) obtained from titrations of four H-bonded host-guest systems in two organic solvents and two ionic liquids yield smaller yet comparable <i>K</i><sub>a</sub>values in ionic liquids than in organic solvents. We also detect the association event using force spectroscopy. Our results indicate that strong H-bonds are only moderately affected by surroundings composed entirely of charges, suggesting that the balance of Coulombic to covalent forces is not tipped towards the former.


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