Journal articles: 'Covalent Interactions'

1

Alkorta, Ibon, and Sławomir J. Grabowski. "Non-covalent interactions." Computational and Theoretical Chemistry 998 (October 2012): 1. http://dx.doi.org/10.1016/j.comptc.2012.07.025.

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FINKELSTEIN, ALEXEI V., MICHAEL Y. LOBANOV, NIKITA V. DOVIDCHENKO, and NATALIA S. BOGATYREVA. "MANY-ATOM VAN DER WAALS INTERACTIONS LEAD TO DIRECTION-SENSITIVE INTERACTIONS OF COVALENT BONDS." Journal of Bioinformatics and Computational Biology 06, no. 04 (August 2008): 693–707. http://dx.doi.org/10.1142/s0219720008003606.

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Strict physical theory and numerical calculations show that a specific coupling of many-atom van der Waals interactions with covalent bonding can significantly (half as much) increase the strength of attractive dispersion interactions when the direction of interaction coincides with the direction of the covalent bond, and decrease this strength when the direction of interaction is perpendicular to the direction of the covalent bond. The energy effect is comparable to that caused by the replacement of atoms (e.g. N by C or O ) in conventional pairwise van der Waals interactions. Analysis of protein structures shows that they bear an imprint of this effect. This means that many-atom van der Waals interactions cannot be ignored in refinement of protein structures, in simulations of their folding, and in prediction of their binding affinities.

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Bagus, Paul S., and Connie J. Nelin. "Covalent interactions in oxides." Journal of Electron Spectroscopy and Related Phenomena 194 (June 2014): 37–44. http://dx.doi.org/10.1016/j.elspec.2013.11.004.

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Schneider, Hans-J�rg. "EDITORIAL: NON-COVALENT INTERACTIONS." Journal of Physical Organic Chemistry 10, no. 5 (May 1997): 253. http://dx.doi.org/10.1002/(sici)1099-1395(199705)10:5<253::aid-poc1875>3.0.co;2-r.

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5

Olson, R. E. "Ionic-covalent collision interactions." International Journal of Quantum Chemistry 24, S17 (July 9, 2009): 49–64. http://dx.doi.org/10.1002/qua.560240807.

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Majumdar, Dhrubajyoti, A. Frontera, Rosa M. Gomila, Sourav Das, and Kalipada Bankura. "Synthesis, spectroscopic findings and crystal engineering of Pb(ii)–Salen coordination polymers, and supramolecular architectures engineered by σ-hole/spodium/tetrel bonds: a combined experimental and theoretical investigation." RSC Advances 12, no. 10 (2022): 6352–63. http://dx.doi.org/10.1039/d1ra09346k.

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We report σ-hole interaction/spodium/tetrel bonding and other non-covalent interactions in a heteronuclear Pb(ii)–Salen coordination polymer using DFT, HSA, QTAIM/NCI, and QTAIM/ELF plots. The non-covalent interactions predominantly drive the formation of extended architectures.

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Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud E. S. Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase through Target-Focused Modelling." Molecules 24, no. 17 (August 28, 2019): 3125. http://dx.doi.org/10.3390/molecules24173125.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the enzyme may be targeted both covalently and non-covalently, minimal studies provide effective inhibitors against it. Recently, research has focused on covalent inhibitors based on their characteristic, highly-selective warheads and ability to prevent drug resistance. This prompted us to screen for new covalent inhibitors of Nedd4-1 using a combination of computational approaches. However, this task proved challenging due to the limited number of electrophilic moieties available in virtual libraries. Therefore, we opted to divide an existing covalent Nedd4-1 inhibitor into two parts: a non-covalent binding group and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on molecular interactions at the binding site. The pharmacophore was then subjected to virtual screening to identify structurally similar hit compounds. Multiple filtrations were implemented prior to selecting four hits, which were validated with a covalent conjugation and later assessed by molecular dynamic simulations. The results showed that, of the four hit molecules, Zinc00937975 exhibited advantageous molecular groups, allowing for favourable interactions with one of the characteristic cysteine residues. Predictive pharmacokinetic analysis further justified the compound as a potential lead molecule, prompting its recommendation for confirmatory biological evaluation. Our inhouse, refined, pharmacophore model approach serves as a robust method that will encourage screening for novel covalent inhibitors in drug discovery.

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Novikov, Alexander S. "Non-Covalent Interactions in Polymers." Polymers 15, no. 5 (February 24, 2023): 1139. http://dx.doi.org/10.3390/polym15051139.

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Non-covalent interactions are one of the key topics in modern chemical science. These inter- and intramolecular weak interactions (e.g., hydrogen, halogen, and chalcogen bonds, stacking interactions and metallophilic contacts) have a significant effect on the properties of polymers. In this Special Issue, “Non-covalent interactions in polymers”, we tried to collect fundamental and applied research manuscripts (original research articles and comprehensive review papers) focused on non-covalent interactions in polymer chemistry and related fields. The scope of the Special Issue is very broad: we welcome all the contributions that deal with the synthesis, structure, functionality and properties of polymer systems involving non-covalent interactions.

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Wang, Zhifang, Geng An, Ye Zhu, Xuemin Liu, Yunhua Chen, Hongkai Wu, Yingjun Wang, Xuetao Shi, and Chuanbin Mao. "3D-printable self-healing and mechanically reinforced hydrogels with host–guest non-covalent interactions integrated into covalently linked networks." Materials Horizons 6, no. 4 (2019): 733–42. http://dx.doi.org/10.1039/c8mh01208c.

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Černý, Jiří, and Pavel Hobza. "Non-covalent interactions in biomacromolecules." Physical Chemistry Chemical Physics 9, no. 39 (2007): 5291. http://dx.doi.org/10.1039/b704781a.

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Casals-Sainz, José Luis, Aurora Costales Castro, Evelio Francisco, and Ángel Martín Pendás. "Tetrel Interactions from an Interacting Quantum Atoms Perspective." Molecules 24, no. 12 (June 12, 2019): 2204. http://dx.doi.org/10.3390/molecules24122204.

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Tetrel bonds, the purportedly non-covalent interaction between a molecule that contains an atom of group 14 and an anion or (more generally) an atom or molecule with lone electron pairs, are under intense scrutiny. In this work, we perform an interacting quantum atoms (IQA) analysis of several simple complexes formed between an electrophilic fragment (A) (CH3F, CH4, CO2, CS2, SiO2, SiH3F, SiH4, GeH3F, GeO2, and GeH4) and an electron-pair-rich system (B) (NCH, NCO-, OCN-, F-, Br-, CN-, CO, CS, Kr, NC-, NH3, OC, OH2, SH-, and N3-) at the aug-cc-pvtz coupled cluster singles and doubles (CCSD) level of calculation. The binding energy ( E bind AB ) is separated into intrafragment and inter-fragment components, and the latter in turn split into classical and covalent contributions. It is shown that the three terms are important in determining E bind AB , with absolute values that increase in passing from electrophilic fragments containing C, Ge, and Si. The degree of covalency between A and B is measured through the real space bond order known as the delocalization index ( δ AB ). Finally, a good linear correlation is found between δ AB and E xc AB , the exchange correlation (xc) or covalent contribution to E bind AB .

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12

Miyanaga, Akimasa, Risako Ouchi, Fumitaka Kudo, and Tadashi Eguchi. "Complex structure of the acyltransferase VinK and the carrier protein VinL with a pantetheine cross-linking probe." Acta Crystallographica Section F Structural Biology Communications 77, no. 9 (August 26, 2021): 294–302. http://dx.doi.org/10.1107/s2053230x21008761.

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Acyltransferases are responsible for the selection and loading of acyl units onto carrier proteins in polyketide and fatty-acid biosynthesis. Despite the importance of protein–protein interactions between the acyltransferase and the carrier protein, structural information on acyltransferase–carrier protein interactions is limited because of the transient interactions between them. In the biosynthesis of the polyketide vicenistatin, the acyltransferase VinK recognizes the carrier protein VinL for the transfer of a dipeptidyl unit. The crystal structure of a VinK–VinL covalent complex formed with a 1,2-bismaleimidoethane cross-linking reagent has been determined previously. Here, the crystal structure of a VinK–VinL covalent complex formed with a pantetheine cross-linking probe is reported at 1.95 Å resolution. In the structure of the VinK–VinL–probe complex, the pantetheine probe that is attached to VinL is covalently connected to the side chain of the mutated Cys106 of VinK. The interaction interface between VinK and VinL is essentially the same in the two VinK–VinL complex structures, although the position of the pantetheine linker slightly differs. This structural observation suggests that interface interactions are not affected by the cross-linking strategy used.

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13

Bjij, Imane, Pritika Ramharack, Shama Khan, Driss Cherqaoui, and Mahmoud Soliman. "Tracing Potential Covalent Inhibitors of an E3 Ubiquitin Ligase Through Target-Focused Modelling." Proceedings 22, no. 1 (November 14, 2019): 103. http://dx.doi.org/10.3390/proceedings2019022103.

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The Nedd4-1 E3 Ubiquitin ligase has been implicated in multiple disease conditions due its overexpression. Although the Nedd4-1 E3 Ubiquitin ligase is an enzyme that may be targeted either covalently, or non-covalently, there are few studies that demonstrate effective inhibitors of the enzyme. In this work, we aimed to identify covalent inhibitors of Nedd4-1. This task however, proved to be challenging due to the limited available electrophilic moieties in virtual libraries. We therefore opted to divide an existing covalent Nedd4-1 inhibitor in two parts: A non-covalent binding part and a pre-selected α, β-unsaturated ester that forms the covalent linkage with the protein. A non-covalent pharmacophore model was built based on the active site binding investigations followed by validating the covalent conjugation. Thirty compounds were selected and covalently docked into the catalytic site of the Nedd4-1. Multiple filtrations were effected before selecting 5 hits that were later analysed by molecular dynamic simulations to check their stability and explore their binding landscape in complex with the protein. All in all, two inhibitors with optimum overall stability and more stabilising interactions were kept for eventual biological evaluation. Our improved pharmacophore model approach serves as a robust method that will illuminate the screening for novel covalent inhibitor in drug discovery.

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14

Nicolle, Laura, Céline M. A. Journot, and Sandrine Gerber-Lemaire. "Chitosan Functionalization: Covalent and Non-Covalent Interactions and Their Characterization." Polymers 13, no. 23 (November 26, 2021): 4118. http://dx.doi.org/10.3390/polym13234118.

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Chitosan (CS) is a natural biopolymer that has gained great interest in many research fields due to its promising biocompatibility, biodegradability, and favorable mechanical properties. The versatility of this low-cost polymer allows for a variety of chemical modifications via covalent conjugation and non-covalent interactions, which are designed to further improve the properties of interest. This review aims at presenting the broad range of functionalization strategies reported over the last five years to reflect the state-of-the art of CS derivatization. We start by describing covalent modifications performed on the CS backbone, followed by non-covalent CS modifications involving small molecules, proteins, and metal adjuvants. An overview of CS-based systems involving both covalent and electrostatic modification patterns is then presented. Finally, a special focus will be given on the characterization techniques commonly used to qualify the composition and physical properties of CS derivatives.

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15

Yu, Xinlei, Tong Jin, Kun Wang, Dan Li, and Longjiu Cheng. "Benchmark studies on the large errors of calculated binding energies in metallophilic interactions." Journal of Chemical Physics 156, no. 10 (March 14, 2022): 104103. http://dx.doi.org/10.1063/5.0085213.

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Aurophilicity is a d10–d10 closed-shell interaction, which is repulsively calculated by the Hartree–Fork (HF) method, whereas binding energies ( Eb) are largely overestimated under the second-order Møller–Plesset (MP2) method, compared to the coupled cluster singles and doubles with perturbative triples [CCSD(T)] method. The unusual energy errors between different wave functional methods were also verified in other closed-shell metallophilic systems and even were taken as a label of metallophilic interaction. Here, we performed a benchmark study on a collection of structures with weak interactions, sp–sp bonds, sp–d bonds, and d–d bonds, to investigate the influence factor of the errors of HF and MP2 methods. It was found that the large energy errors of HF and MP2 methods were not specified for closed-shell interactions, and the errors could also be very large for many covalent bonds, which was strongly related to the azimuthal quantum number of interaction orbitals. Compared to the CCSD(T) method, the MP2 method weakens the s–s covalent interactions slightly, strengthens the p–p covalent interactions slightly, and overestimates the d–d covalent interactions largely (can be −170 kcal/mol for the Re–Re quadruple bond). This benchmark study suggests that the special energy errors in metallophilicity may result from the participation of d orbitals. Benchmark studies on various density functional methods were also given for calculating binding energies of d–d bonds.

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Tanti, Jonathan, Meghan Lincoln, and Andy Kerridge. "Decomposition of d- and f-Shell Contributions to Uranium Bonding from the Quantum Theory of Atoms in Molecules: Application to Uranium and Uranyl Halides." Inorganics 6, no. 3 (August 30, 2018): 88. http://dx.doi.org/10.3390/inorganics6030088.

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The electronic structures of a series of uranium hexahalide and uranyl tetrahalide complexes were simulated at the density functional theoretical (DFT) level. The resulting electronic structures were analyzed using a novel application of the Quantum Theory of Atoms in Molecules (QTAIM) by exploiting the high symmetry of the complexes to determine 5f- and 6d-shell contributions to bonding via symmetry arguments. This analysis revealed fluoride ligation to result in strong bonds with a significant covalent character while ligation by chloride and bromide species resulted in more ionic interactions with little differentiation between the ligands. Fluoride ligands were also found to be most capable of perturbing an existing electronic structure. 5f contributions to overlap-driven covalency were found to be larger than 6d contributions for all interactions in all complexes studied while degeneracy-driven covalent contributions showed significantly greater variation. σ-contributions to degeneracy-driven covalency were found to be consistently larger than those of individual π-components while the total π-contribution was, in some cases, larger. Strong correlations were found between overlap-driven covalent bond contributions, U–O vibrational frequencies, and energetic stability, which indicates that overlap-driven covalency leads to bond stabilization in these complexes and that uranyl vibrational frequencies can be used to quantitatively probe equatorial bond covalency. For uranium hexahalides, degeneracy-driven covalency was found to anti-correlate with bond stability.

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17

Novikov, Alexander S. "Theoretical Investigation on Non-Covalent Interactions." Crystals 12, no. 2 (January 24, 2022): 167. http://dx.doi.org/10.3390/cryst12020167.

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This editorial is dedicated to announcing the Special Issue “Theoretical investigation on non-covalent interactions” of Crystals. The Special Issue covers the most recent progress in the rapidly growing fields of data science, artificial intelligence, and quantum and computational chemistry in topics relevant to the problem of theoretical investigation on non-covalent interactions (including, but not limited to, hydrogen, halogen, chalcogen, pnictogen, tetrel, and semi-coordination bonds; agosic and anagosic interactions; stacking, anion-/cation–π interactions; metallophilic interactions, etc.). The main successes of my colleagues and I in the field of fundamental theoretical studies of non-covalent interactions in various chemical compounds over the past year are briefly highlighted.

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Kizior, Beata, Mariusz Michalczyk, Jarosław J. Panek, Wiktor Zierkiewicz, and Aneta Jezierska. "Unraveling the Nature of Hydrogen Bonds of “Proton Sponges” Based on Car-Parrinello and Metadynamics Approaches." International Journal of Molecular Sciences 24, no. 2 (January 12, 2023): 1542. http://dx.doi.org/10.3390/ijms24021542.

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The nature of intra- and intermolecular non-covalent interactions was studied in four naphthalene derivatives commonly referred to as “proton sponges”. Special attention was paid to an intramolecular hydrogen bond present in the protonated form of the compounds. The unsubstituted “proton sponge” served as a reference structure to study the substituent influence on the hydrogen bond (HB) properties. We selected three compounds substituted by methoxy, amino, and nitro groups. The presence of the substituents either retained the parent symmetry or rendered the compounds asymmetric. In order to reveal the non-covalent interaction properties, the Hirshfeld surface (HS) was computed for the crystal structures of the studied compounds. Next, quantum-chemical simulations were performed in vacuo and in the crystalline phase. Car–Parrinello molecular dynamics (CPMD), Path Integral Molecular Dynamics (PIMD), and metadynamics were employed to investigate the time-evolution changes of metric parameters and free energy profile in both phases. Additionally, for selected snapshots obtained from the CPMD trajectories, non-covalent interactions and electronic structure were studied. Quantum theory of atoms in molecules (QTAIM) and the Density Overlap Regions Indicator (DORI) were applied for this purpose. It was found based on Hirshfeld surfaces that, besides intramolecular hydrogen bonds, other non-covalent interactions are present and have a strong impact on the crystal structure organization. The CPMD results obtained in both phases showed frequent proton transfer phenomena. The proton was strongly delocalized in the applied time-scale and temperature, especially in the PIMD framework. The use of metadynamics allowed for tracing the free energy profiles and confirming that the hydrogen bonds present in “proton sponges” are Low-Barrier Hydrogen Bonds (LBHBs). The electronic and topological analysis quantitatively described the temperature dependence and time-evolution changes of the electronic structure. The covalency of the hydrogen bonds was estimated based on QTAIM analysis. It was found that strong hydrogen bonds show greater covalency, which is additionally determined by the proton position in the hydrogen bridge.

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19

Novikov, Alexander S. "Plethora of Non-Covalent Interactions in Coordination and Organometallic Chemistry Are Modern Smart Tool for Materials Science, Catalysis, and Drugs Design." International Journal of Molecular Sciences 23, no. 23 (November 25, 2022): 14767. http://dx.doi.org/10.3390/ijms232314767.

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Non-covalent interactions are one of the key topics in coordination and organometallic chemistry. Examples of such weak interactions are hydrogen, halogen, and chalcogen bonds, stacking interactions, metallophilic contacts, etc. Non-covalent interactions play an important role in materials science, catalysis, and medicinal chemistry. The aim of this Special Issue of International Journal of Molecular Sciences, entitled “Non-Covalent Interactions in Coordination and Organometallic Chemistry”, is to cover the most recent progress in the rapidly growing field of non-covalent interactions in coordination and organometallic chemistry. Both experimental and theoretical studies, fundamental and applied research and any types of manuscripts are welcome for consideration.

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20

Miret-Casals, Laia, Willem Vannecke, Kurt Hoogewijs, Gianluca Arauz-Garofalo, Marina Gay, Mireia Díaz-Lobo, Marta Vilaseca, Christophe Ampe, Marleen Van Troys, and Annemieke Madder. "Furan warheads for covalent trapping of weak protein–protein interactions: cross-linking of thymosin β4 to actin." Chemical Communications 57, no. 49 (2021): 6054–57. http://dx.doi.org/10.1039/d1cc01731d.

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Furan is used as a caged warhead to covalently target weak protein–protein interactions. Furan-thymosin β4 cross-links selectively and irreversibly with actin targeting lysine. Furan technology could be further exploited for covalent drug design.

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Rehman, Sayeed Ur, Tarique Sarwar, Mohammed Amir Husain, Hassan Mubarak Ishqi, and Mohammad Tabish. "Studying non-covalent drug–DNA interactions." Archives of Biochemistry and Biophysics 576 (June 2015): 49–60. http://dx.doi.org/10.1016/j.abb.2015.03.024.

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22

Rinaudo, Marguerite. "Non-Covalent Interactions in Polysaccharide Systems." Macromolecular Bioscience 6, no. 8 (August 7, 2006): 590–610. http://dx.doi.org/10.1002/mabi.200600053.

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23

Hanssen, Eric, Betty Reinboth, and Mark A. Gibson. "Covalent and Non-covalent Interactions of βig-h3 with Collagen VI." Journal of Biological Chemistry 278, no. 27 (April 27, 2003): 24334–41. http://dx.doi.org/10.1074/jbc.m303455200.

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24

Varadwaj, Arpita, Pradeep Varadwaj, Helder Marques, and Koichi Yamashita. "The Stibium Bond or the Antimony-Centered Pnictogen Bond: The Covalently Bound Antimony Atom in Molecular Entities in Crystal Lattices as a Pnictogen Bond Donor." International Journal of Molecular Sciences 23, no. 9 (April 23, 2022): 4674. http://dx.doi.org/10.3390/ijms23094674.

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A stibium bond, i.e., a non-covalent interaction formed by covalently or coordinately bound antimony, occurs in chemical systems when there is evidence of a net attractive interaction between the electrophilic region associated with an antimony atom and a nucleophile in another, or the same molecular entity. This is a pnictogen bond and are likely formed by the elements of the pnictogen family, Group 15, of the periodic table, and is an inter- or intra-molecular non-covalent interaction. This overview describes a set of illustrative crystal systems that were stabilized (at least partially) by means of stibium bonds, together with other non-covalent interactions (such as hydrogen bonds and halogen bonds), retrieved from either the Cambridge Structure Database (CSD) or the Inorganic Crystal Structure Database (ICSD). We demonstrate that these databases contain hundreds of crystal structures of various dimensions in which covalently or coordinately bound antimony atoms in molecular entities feature positive sites that productively interact with various Lewis bases containing O, N, F, Cl, Br, and I atoms in the same or different molecular entities, leading to the formation of stibium bonds, and hence, being partially responsible for the stability of the crystals. The geometric features, pro-molecular charge density isosurface topologies, and extrema of the molecular electrostatic potential model were collectively examined in some instances to illustrate the presence of Sb-centered pnictogen bonding in the representative crystal systems considered.

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Hobza, Pavel, Rudolf Zahradník, and Klaus Müller-Dethlefs. "The World of Non-Covalent Interactions: 2006." Collection of Czechoslovak Chemical Communications 71, no. 4 (2006): 443–531. http://dx.doi.org/10.1135/cccc20060443.

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The review focusses on the fundamental importance of non-covalent interactions in nature by illustrating specific examples from chemistry, physics and the biosciences. Laser spectroscopic methods and both ab initio and molecular modelling procedures used for the study of non-covalent interactions in molecular clusters are briefly outlined. The role of structure and geometry, stabilization energy, potential and free energy surfaces for molecular clusters is extensively discussed in the light of the most advanced ab initio computational results for the CCSD(T) method, extrapolated to the CBS limit. The most important types of non-covalent complexes are classified and several small and medium size non-covalent systems, including H-bonded and improper H-bonded complexes, nucleic acid base pairs, and peptides and proteins are discussed with some detail. Finally, we evaluate the interpretation of experimental results in comparison with state of the art theoretical models: this is illustrated for phenol...Ar, the benzene dimer and nucleic acid base pairs. A review with 270 references.

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Novikov, Alexander S. "Non-Covalent Interactions in Coordination and Organometallic Chemistry." Crystals 10, no. 6 (June 23, 2020): 537. http://dx.doi.org/10.3390/cryst10060537.

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The problem of non-covalent interactions in coordination and organometallic compounds is a hot topic in modern chemistry, material science, crystal engineering and related fields of knowledge. Researchers in various fields of chemistry and other disciplines (physics, crystallography, computer science, etc.) are welcome to submit their works on this topic for our Special Issue “Non-Covalent Interactions in Coordination and Organometallic Chemistry”. The aim of this Special Issue is to highlight and overview modern trends and draw the attention of the scientific community to various types of non-covalent interactions in coordination and organometallic compounds. In this editorial, I would like to briefly highlight the main successes of our research group in the field of the fundamental study of non-covalent interactions in coordination and organometallic compounds over the past 5 years.

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Giese, M., M. Albrecht, and K. Rissanen. "Experimental investigation of anion–π interactions – applications and biochemical relevance." Chemical Communications 52, no. 9 (2016): 1778–95. http://dx.doi.org/10.1039/c5cc09072e.

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Weinhold, Frank. "“Noncovalent Interaction”: A Chemical Misnomer That Inhibits Proper Understanding of Hydrogen Bonding, Rotation Barriers, and Other Topics." Molecules 28, no. 9 (April 27, 2023): 3776. http://dx.doi.org/10.3390/molecules28093776.

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We discuss the problematic terminology of “noncovalent interactions” as commonly applied to hydrogen bonds, rotation barriers, steric repulsions, and other stereoelectronic phenomena. Although categorization as “noncovalent” seems to justify classical-type pedagogical rationalizations, we show that these phenomena are irreducible corollaries of the same orbital-level conceptions of electronic covalency and resonance that govern all chemical bonding phenomena. Retention of such nomenclature is pedagogically misleading in supporting superficial dipole–dipole and related “simple, neat, and wrong” conceptions as well as perpetuating inappropriate bifurcation of the introductory chemistry curriculum into distinct “covalent” vs. “noncovalent” modules. If retained at all, the line of dichotomization between “covalent” and “noncovalent” interaction should be re-drawn beyond the range of quantal exchange effects (roughly, at the contact boundary of empirical van der Waals radii) to better unify the pedagogy of molecular and supramolecular bonding phenomena.

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Percherancier, Yann, Delphine Germain-Desprez, Frédéric Galisson, Xavier H. Mascle, Laurent Dianoux, Patricia Estephan, Mounira K. Chelbi-Alix, and Muriel Aubry. "Role of SUMO in RNF4-mediated Promyelocytic Leukemia Protein (PML) Degradation." Journal of Biological Chemistry 284, no. 24 (April 20, 2009): 16595–608. http://dx.doi.org/10.1074/jbc.m109.006387.

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Promyelocytic leukemia protein (PML) is a tumor suppressor acting as the organizer of subnuclear structures called PML nuclear bodies (NBs). Both covalent modification of PML by the small ubiquitin-like modifier (SUMO) and non-covalent binding of SUMO to the PML SUMO binding domain (SBD) are necessary for PML NB formation and maturation. PML sumoylation and proteasome-dependent degradation induced by the E3 ubiquitin ligase, RNF4, are enhanced by the acute promyelocytic leukemia therapeutic agent, arsenic trioxide (As2O3). Here, we established a novel bioluminescence resonance energy transfer (BRET) assay to dissect and monitor PML/SUMO interactions dynamically in living cells upon addition of therapeutic agents. Using this sensitive and quantitative SUMO BRET assay that distinguishes PML sumoylation from SBD-mediated PML/SUMO non-covalent interactions, we probed the respective roles of covalent and non-covalent PML/SUMO interactions in PML degradation and interaction with RNF4. We found that, although dispensable for As2O3-enhanced PML sumoylation and RNF4 interaction, PML SBD core sequence was required for As2O3- and RNF4-induced PML degradation. As confirmed with a phosphomimetic mutant, phosphorylation of a stretch of serine residues, contained within PML SBD was needed for PML interaction with SUMO-modified protein partners and thus for NB maturation. However, mutation of these serine residues did not impair As2O3- and RNF4-induced PML degradation, contrasting with the known role of these phosphoserine residues for casein kinase 2-promoted PML degradation. Altogether, these data suggest a model whereby sumoylation- and SBD-dependent PML oligomerization within NBs is sufficient for RNF4-mediated PML degradation and does not require the phosphorylation-dependent association of PML with other sumoylated partners.

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Mustoe, Chantal L., Mathusan Gunabalasingam, Darren Yu, Brian O. Patrick, and Pierre Kennepohl. "Probing covalency in halogen bonds through donor K-edge X-ray absorption spectroscopy: polyhalides as coordination complexes." Faraday Discussions 203 (2017): 79–91. http://dx.doi.org/10.1039/c7fd00076f.

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The properties of halogen bonds (XBs) in solid-state I₂X⁻and I₄X⁻materials (where X = Cl, Br) are explored using donor K-edge X-ray absorption spectroscopy (XAS) to experimentally determine the degree of charge transfer in such XB interactions. The degree of covalency in these bonds is substantial, even in cases where significantly weaker secondary interactions are observed. These data, in concert with previous work in this area, suggests that certain halogen bonds have covalent contributions to bonding that are similar to, and even exceed, those observed in transition metal coordinate bonds. For this reason, we suggest that XB interactions of this type be denoted in a similar way to coordination bonds (X → Y) as opposed to using a representation that is the same as for significantly less covalent hydrogen bonds (X⋯Y).

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Wojtkowiak, Kamil, Mariusz Michalczyk, Wiktor Zierkiewicz, Aneta Jezierska, and Jarosław J. Panek. "Chalcogen Bond as a Factor Stabilizing Ligand Conformation in the Binding Pocket of Carbonic Anhydrase IX Receptor Mimic." International Journal of Molecular Sciences 23, no. 22 (November 8, 2022): 13701. http://dx.doi.org/10.3390/ijms232213701.

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It is postulated that the overexpression of Carbonic Anhydrase isozyme IX in some cancers contributes to the acidification of the extracellular matrix. It was proved that this promotes the growth and metastasis of the tumor. These observations have made Carbonic Anhydrase IX an attractive drug target. In the light of the findings and importance of the glycoprotein in the cancer treatment, we have employed quantum–chemical approaches to study non-covalent interactions in the binding pocket. As a ligand, the acetazolamide (AZM) molecule was chosen, being known as a potential inhibitor exhibiting anticancer properties. First-Principles Molecular Dynamics was performed to study the chalcogen and other non-covalent interactions in the AZM ligand and its complexes with amino acids forming the binding site. Based on Density Functional Theory (DFT) and post-Hartree–Fock methods, the metric and electronic structure parameters were described. The Non-Covalent Interaction (NCI) index and Atoms in Molecules (AIM) methods were applied for qualitative/quantitative analyses of the non-covalent interactions. Finally, the AZM–binding pocket interaction energy decomposition was carried out. Chalcogen bonding in the AZM molecule is an important factor stabilizing the preferred conformation. Free energy mapping via metadynamics and Path Integral molecular dynamics confirmed the significance of the chalcogen bond in structuring the conformational flexibility of the systems. The developed models are useful in the design of new inhibitors with desired pharmacological properties.

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CAMARERO, JULIO A. "NEW DEVELOPMENTS FOR THE SITE-SPECIFIC ATTACHMENT OF PROTEIN TO SURFACES." Biophysical Reviews and Letters 01, no. 01 (January 2006): 1–28. http://dx.doi.org/10.1142/s1793048006000045.

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Protein immobilization on surfaces is of great importance in numerous applications in biology and biophysics. The key for the success of all these applications relies on the immobilization technique employed to attach the protein to the corresponding surface. Protein immobilization can be based on covalent or noncovalent interaction of the molecule with the surface. Noncovalent interactions include hydrophobic interactions, hydrogen bonding, van der Waals forces, electrostatic forces, or physical adsorption. However, since these interactions are weak, the molecules can get denatured or dislodged, thus causing loss of signal. They also result in random attachment of the protein to the surface. Site–specific covalent attachment of proteins onto surfaces, on the other hand, leads to molecules being arranged in a definite, orderly fashion and uses spacers and linkers to help minimize steric hindrances between the protein and the surface. This work reviews in detail some of the methods most commonly used as well as the latest developments for the site-specific covalent attachment of protein to solid surfaces.

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Driver, Mark D., Mark J. Williamson, Joanne L. Cook, and Christopher A. Hunter. "Functional group interaction profiles: a general treatment of solvent effects on non-covalent interactions." Chemical Science 11, no. 17 (2020): 4456–66. http://dx.doi.org/10.1039/d0sc01288b.

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Borocci, Stefano, Felice Grandinetti, Francesca Nunzi, and Nico Sanna. "Classifying the chemical bonds involving the noble-gas atoms." New Journal of Chemistry 44, no. 34 (2020): 14536–50. http://dx.doi.org/10.1039/d0nj01927e.

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Qie, Xuejiao, Yao Chen, Wei Quan, Zhaojun Wang, Maomao Zeng, Fang Qin, Jie Chen, and Zhiyong He. "Analysis of β-lactoglobulin–epigallocatechin gallate interactions: the antioxidant capacity and effects of polyphenols under different heating conditions in polyphenolic–protein interactions." Food & Function 11, no. 5 (2020): 3867–78. http://dx.doi.org/10.1039/d0fo00627k.

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A β-Lg-EGCG covalent conjugate is formed by linking the amino group of a lysine residue and EGCG; the antioxidant capacity of EGCG induced by β-Lg–EGCG covalent conjugates causes a significant decrease.

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36

Piestrzeniewicz, Mariola K., Dorota Wilmańska, Janusz Szemraj, Kazimierz Studzian, and Marek Gniazdowski. "Interactions of Novel Morpholine and Hexamethylene Derivatives of Anthracycline Antibiotics with DNA." Zeitschrift für Naturforschung C 59, no. 9-10 (October 1, 2004): 739–48. http://dx.doi.org/10.1515/znc-2004-9-1020.

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Abstract Doxorubicin (DOX), daunorubicin (DRB), epidoxorubicin (EDOX) and their analogues with a 3′-NH2 group in daunosamine form a covalent bond with a 2-NH2 group of guanine via a methylene group from formaldehyde (CH2O). It is assumed that a Schiff base type intermediate is formed between CH2O and the 3′-NH2 group in the reaction. This reaction is supposed to occur in the cell. New analogues of anthracyclines with formamidine functionality bound to C-3′ of daunosamine and containing the bulky morpholine (DRBM, DOXM and EDOXM) or hexamethyleneimine rings attached are studied in our laboratory. These substituents decrease the association of the drugs to DNA and potentially hinder the formation of Schiff base-intermediates. Our experiments indicate that the formation of the covalent complexes by DRB, DOX and EDOX under these conditions is confirmed by a high enhancement (17-40x) of the inhibition of overall RNA synthesis by E. coli RNA polymerase on T7 DNA. DRBM and DOXM exhibit a lower enhancement of the inhibition by CH2O (7-13x). The other analogues show a 1.6-3x increase of inhibition. Hence, their covalent binding is lower than that of the parent compounds. These conclusions are confirmed by spectrophotometric estimations following removal of non-covalently associated drugs. Electrophoretic analysis of drug-DNA complexes formed in the presence of CH2O indicates that DRBM and DOXM as their parent compounds induce labile cross-links in DNA. Comparison of the results obtained at the subcellular level with cytotoxicity estimations indicates that there is a correlation between cytotoxicity of the anthracyclines on L1210 cells and transcriptional template activity of drug-DNA complexes formed in the presence of CH2O (r = 0.64; n = 9). These data confirm a notion that covalent attachment of anthracyclines to DNA is an essential event leading to cytotoxicity.

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Xie, Yixuan, Siyu Chen, Qiongyu Li, Ying Sheng, Michael Russelle Alvarez, Joeriggo Reyes, Gege Xu, Kemal Solakyildirim, and Carlito B. Lebrilla. "Glycan–protein cross-linking mass spectrometry reveals sialic acid-mediated protein networks on cell surfaces." Chemical Science 12, no. 25 (2021): 8767–77. http://dx.doi.org/10.1039/d1sc00814e.

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The cell surface glycocalyx is highly interactive defined by extensive covalent and non-covalent interactions. A method for cross-linking and characterizing glycan–peptide interactions in situ is developed.

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Buaksuntear, Kwanchai, Phakamat Limarun, Supitta Suethao, and Wirasak Smitthipong. "Non-Covalent Interaction on the Self-Healing of Mechanical Properties in Supramolecular Polymers." International Journal of Molecular Sciences 23, no. 13 (June 21, 2022): 6902. http://dx.doi.org/10.3390/ijms23136902.

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Supramolecular polymers are widely utilized and applied in self–assembly or self–healing materials, which can be repaired when damaged. Normally, the healing process is classified into two types, including extrinsic and intrinsic self–healable materials. Therefore, the aim of this work is to review the intrinsic self–healing strategy based on supramolecular interaction or non-covalent interaction and molecular recognition to obtain the improvement of mechanical properties. In this review, we introduce the main background of non-covalent interaction, which consists of the metal–ligand coordination, hydrogen bonding, π–π interaction, electrostatic interaction, dipole–dipole interaction, and host–guest interactions, respectively. From the perspective of mechanical properties, these interactions act as transient crosslinking points to both prevent and repair the broken polymer chains. For material utilization in terms of self–healing products, this knowledge can be applied and developed to increase the lifetime of the products, causing rapid healing and reducing accidents and maintenance costs. Therefore, the self–healing materials using supramolecular polymers or non-covalent interaction provides a novel strategy to enhance the mechanical properties of materials causing the extended cycling lifetime of products before replacement with a new one.

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Novikov, Alexander S. "Non-Covalent Catalysts." Catalysts 13, no. 2 (February 3, 2023): 339. http://dx.doi.org/10.3390/catal13020339.

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The elementary stages of chemical reactions (including catalytic ones) are caused by such weak inter- and intramolecular contacts as hydrogen, halogen, chalcogen, and tetrel bonds as well as stacking (and other π-system-involved) interactions [...]

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Valley, Christopher C., Anthony R. Braun, and Jonathan N. Sachs. "Pre-Ligand Assembly of TNF Receptors Through Covalent and Non-Covalent Interactions." Biophysical Journal 100, no. 3 (February 2011): 419a—420a. http://dx.doi.org/10.1016/j.bpj.2010.12.2485.

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Carnerero, Jose M., Aila Jimenez-Ruiz, Paula M. Castillo, and Rafael Prado-Gotor. "Covalent and Non-Covalent DNA-Gold-Nanoparticle Interactions: New Avenues of Research." ChemPhysChem 18, no. 1 (October 27, 2016): 17–33. http://dx.doi.org/10.1002/cphc.201601077.

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Oliveira, Boaz Galdino de. "Why much of Chemistry may be indisputably non-bonded?" Semina: Ciências Exatas e Tecnológicas 43, no. 2 (January 18, 2023): 211–29. http://dx.doi.org/10.5433/1679-0375.2022v43n2p211.

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In this compendium, the wide scope of all intermolecular interactions ever known has been revisited, in particular giving emphasis the capability of much of the elements of the periodic table to form non-covalent contacts. Either hydrogen bonds, dihydrogen bonds, halogen bonds, pnictogen bonds, chalcogen bonds, triel bonds, tetrel bonds, regium bonds, spodium bonds or even the aerogen bond interactions may be cited. Obviously that experimental techniques have been used in some works, but it was through the theoretical methods that these interactions were validate, wherein the QTAIM integrations and SAPT energy partitions have been useful in this regard. Therefore, the great goal concerns to elucidate the interaction strength and if the intermolecular system shall be total, partial or non-covalently bonded, wherein this last one encompasses the most majority of the intermolecular interactions what leading to affirm that chemistry is debatably non-bonded.

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BELOSLUDOV, V. R., M. YU LAVRENTIEV, and S. A. SYSKIN. "MODEL OF INTERATOMIC INTERACTIONS AND VIBRATIONAL SPECTRUM OF Tl2CaBa2Cu2O8." International Journal of Modern Physics B 05, no. 19 (November 20, 1991): 3109–14. http://dx.doi.org/10.1142/s021797929100122x.

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A model of interatomic interactions of Tl2CaBa2Cu2O8 , which takes into account coulombic interaction and covalent bonds, is presented. Vibrational spectrum is calculated using that model, and a comparison with experiments on Raman scattering is given.

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Yau, Tak-Yu, William Sander, Christian Eidson, and Albert J. Courey. "SUMO Interacting Motifs: Structure and Function." Cells 10, no. 11 (October 21, 2021): 2825. http://dx.doi.org/10.3390/cells10112825.

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Small ubiquitin-related modifier (SUMO) is a member of the ubiquitin-related protein family. SUMO modulates protein function through covalent conjugation to lysine residues in a large number of proteins. Once covalently conjugated to a protein, SUMO often regulates that protein’s function by recruiting other cellular proteins. Recruitment frequently involves a non-covalent interaction between SUMO and a SUMO-interacting motif (SIM) in the interacting protein. SIMs generally consist of a four-residue-long hydrophobic stretch of amino acids with aliphatic non-polar side chains flanked on one side by negatively charged amino acid residues. The SIM assumes an extended β-strand-like conformation and binds to a conserved hydrophobic groove in SUMO. In addition to hydrophobic interactions between the SIM non-polar core and hydrophobic residues in the groove, the negatively charged residues in the SIM make favorable electrostatic contacts with positively charged residues in and around the groove. The SIM/SUMO interaction can be regulated by the phosphorylation of residues adjacent to the SIM hydrophobic core, which provide additional negative charges for favorable electrostatic interaction with SUMO. The SUMO interactome consists of hundreds or perhaps thousands of SIM-containing proteins, but we do not fully understand how each SUMOylated protein selects the set of SIM-containing proteins appropriate to its function. SIM/SUMO interactions have critical functions in a large number of essential cellular processes including the formation of membraneless organelles by liquid–liquid phase separation, epigenetic regulation of transcription through histone modification, DNA repair, and a variety of host–pathogen interactions.

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DOLOCAN, ANDREI, VOICU OCTAVIAN DOLOCAN, and VOICU DOLOCAN. "APPLICATION OF A NEW HAMILTONIAN OF INTERACTION TO THREE-DIMENSIONAL STRUCTURES." International Journal of Modern Physics B 18, no. 09 (April 10, 2004): 1351–68. http://dx.doi.org/10.1142/s0217979204024707.

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Using a new Hamiltonian of interaction we have calculated the cohesive energy in three-dimensional structures. We have found the news dependences of this energy on the distance between the atoms. The obtained results are in a good agreement with experimental data in ionic, covalent and noble gases crystals. The coupling constant γ between the interacting field and the atoms is somewhat smaller than unity in ionic crystals and is some larger than unity in covalent and noble gases crystals. The formulae found by us are general and may be applied, also, to the other types of interactions, for example, gravitational interactions.

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Kee, Choon Wee, and Ming Wah Wong. "Pentanidium-Catalyzed Asymmetric Phase-Transfer Conjugate Addition: Prediction of Stereoselectivity via DFT Calculations and Docking Sampling of Transition States, and Origin of Stereoselectivity." Australian Journal of Chemistry 69, no. 9 (2016): 983. http://dx.doi.org/10.1071/ch16225.

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Density functional theory (DFT) study, at the M06–2X/6–311+G(d,p)//M06–2X/6–31G(d,p) level, was carried out to examine the catalytic mechanism and origin of stereoselectivity of pentanidium-catalyzed asymmetric phase-transfer conjugate addition. We employed a hybrid approach by combining automated conformation generation through molecular docking followed by subsequent DFT calculation to locate various possible transition states for the enantioselective conjugate addition. The calculated enantioselectivity (enantiomeric excess), based on the key diastereomeric C–C bond-forming transition states, is in good accord with experimental result. Non-covalent interaction analysis of the key transition states reveals extensive non-covalent interactions, including aromatic interactions, hydrogen bonds, and non-classical C–H⋯O interactions between the pentanidium catalyst and substrates. The origin of stereoselectivity was analysed using a strain-interaction model.

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Jing, Zhanxin, Xueying Xian, Qiuhong Huang, Qiurong Chen, Pengzhi Hong, Yong Li, and Aihua Shi. "Biocompatible double network poly(acrylamide-co-acrylic acid)–Al3+/poly(vinyl alcohol)/graphene oxide nanocomposite hydrogels with excellent mechanical properties, self-recovery and self-healing ability." New Journal of Chemistry 44, no. 25 (2020): 10390–403. http://dx.doi.org/10.1039/d0nj01725f.

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Biocompatible double network PAmAA–Al³⁺/PVA/GO nanocomposite hydrogels based on non-covalent interactions were synthesized, and the non-covalent interactions endow the materials with good self-recovery and self-healing performances.

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Jiao, Tianyu, Kang Cai, Zhichang Liu, Guangcheng Wu, Libo Shen, Chuyang Cheng, Yuanning Feng, Charlotte L. Stern, J. Fraser Stoddart, and Hao Li. "Guest recognition enhanced by lateral interactions." Chemical Science 10, no. 19 (2019): 5114–23. http://dx.doi.org/10.1039/c9sc00591a.

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Armentrout, P. B., and M. T. Rodgers. "Thermochemistry of Non-Covalent Ion–Molecule Interactions." Mass Spectrometry 2, Special_Issue (2013): S0005. http://dx.doi.org/10.5702/massspectrometry.s0005.

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Buntkowsky, Gerd, and Michael Vogel. "Small Molecules, Non-Covalent Interactions, and Confinement." Molecules 25, no. 14 (July 21, 2020): 3311. http://dx.doi.org/10.3390/molecules25143311.

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This review gives an overview of current trends in the investigation of small guest molecules, confined in neat and functionalized mesoporous silica materials by a combination of solid-state NMR and relaxometry with other physico-chemical techniques. The reported guest molecules are water, small alcohols, and carbonic acids, small aromatic and heteroaromatic molecules, ionic liquids, and surfactants. They are taken as characteristic role-models, which are representatives for the typical classes of organic molecules. It is shown that this combination delivers unique insights into the structure, arrangement, dynamics, guest-host interactions, and the binding sites in these confined systems, and is probably the most powerful analytical technique to probe these systems.

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Journal articles on the topic 'Covalent Interactions'

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