Journal articles: 'Analyse des interactions non covalentes'

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Kumar, Prashant, Małgorzata Katarzyna Cabaj, and Paulina Maria Dominiak. "Intermolecular Interactions in Ionic Crystals of Nucleobase Chlorides—Combining Topological Analysis of Electron Densities with Energies of Electrostatic Interactions." Crystals 9, no. 12 (December 11, 2019): 668. http://dx.doi.org/10.3390/cryst9120668.

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Understanding intermolecular interactions in crystals of molecular ions continues to be difficult. On the one hand, the analysis of interactions from the point of view of formal charges of molecules, similarly as it is commonly done for inorganic ionic crystals, should be performed. On the other hand, when various functional groups are present in the crystal, it becomes natural to look at the interactions from the point of view of hydrogen bonding, π…π stacking and many other kinds of non-covalent atom–atom bonding. Often, these two approaches seem to lead to conflicting conclusions. On the basis of experimental charge densities of cytosinium chloride, adeninium chloride hemihydrate, and guanine dichloride crystals, with the help of theoretical simulations, we have deeply analysed intermolecular interactions among protonated nucleobases, chloride anions and water molecules. Here, in the second paper of the series of the two (Kumar et al., 2018, IUCrJ 5, 449–469), we focus on applying the above two approaches to the large set of dimers identified in analysed crystals. To understand electrostatic interactions, we analysed electrostatic interaction energies (Ees) computed directly from molecular charge densities and contrasted them with energies computed only from net molecular charges, or from a sum of electric multipolar moments, to find the charge penetration contribution to Ees. To characterize non-covalent interactions we performed topological analyses of crystal electron densities and estimated their interaction energies (EEML) from properties of intermolecular bond critical points. We show that the overall crystal architecture of the studied compounds is governed by the tight packing principle and strong electrostatic attractions and repulsions between ions. Many ions are oriented to each other in a way to strengthen attractive electrostatic interactions or weaken strong repulsion, but not all of them. Numerous bond critical points and bond paths were found between ions, including nucleobase cations despite their overall repulsive interactions. It is clear there is no correlation between EEML and Ees. However, strong relation between EEML and the charge penetration component of Ees is observed. The relation holds regardless of interaction types or whether or not interacting molecules bear the same or opposite charges. Thus, a charge density-based approach for computing intermolecular interaction energies and the atom–atom approach to analyse non-covalent interactions do complement each other, even in ionic systems.

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Savoo, Nandini, Frederick P. Malan, Lydia Rhyman, and Ponnadurai Ramasami. "Molecular insights of metal–metal interactions in transition metal complexes using computational methods." Pure and Applied Chemistry 93, no. 5 (May 1, 2021): 579–89. http://dx.doi.org/10.1515/pac-2020-1212.

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Abstract Computational methods were used to analyse the interactions around the metal centres in three transition metal (TM) complexes for which the X-ray data are available. We were particularly interested in understanding the metal–metal interactions. We used concepts of bond order, natural population, quantum theory of atom in molecules, electron localisation functions (ELFs) and non-covalent interactions (NCIs). Our results indicate that these tools can be used effectively to help in having insights into the bonding of TM complexes.

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Creste, Geordie, Sihem Groni, Claire Fave, Mathieu Branca, and Bernd Schöllhorn. "Comparative study of non-covalent interactions between cationic N-phenylviologens and halides by electrochemistry and NMR: the halogen bonding effect." Faraday Discussions 203 (2017): 301–13. http://dx.doi.org/10.1039/c7fd00082k.

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Five N-phenylviologen (PV²⁺) derivatives have been synthesized and their electrochemical behavior in the presence of halide anions has been studied. Further investigations were carried out by ¹H and ¹⁹F NMR spectroscopy at different chloride concentrations. This is the first time a systematic study combines cyclic voltammetry and NMR spectroscopy in order to analyse the contribution of halogen bonding among the various non-covalent interactions between iodinated N-phenylviologens. The results show strong evidence for a significant “halogen bonding effect” in the interaction between halides and the iodo-tetrafluoro-phenylviologen PV2+-C6F4I. A significant influence of halogen bonding on reduction potentials of the novel halogen bond donor PV2+-C6F4I has been evidenced resulting in the first example of “inverse redox switching” of an XB-donor being partially deactivated upon reduction. Furthermore the particular binding properties of the perfluorinated derivative PV2+-C6F5 towards chloride are discussed considering a possible contribution of π–anion interaction in solution.

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Vonderviszt, F., J. Török, S. Lakatos, F. Kilár, and P. Závodszky. "Quantitative analysis of the interaction between immune complex and Clq complement subcomponent. The role of interdomain interactions in rabbit IgG in binding of Clq to immune precipitates." Biochemical Journal 243, no. 2 (April 15, 1987): 449–55. http://dx.doi.org/10.1042/bj2430449.

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A novel method was developed for the analysis of the interaction of large multivalent ligands with surfaces (matrices) to analyse the binding of complement subcomponent C1q to immune precipitates. Our new evaluation method provides quantitative data characteristic of the C1q-immune-complex interaction and of the structure of the immune complex as well. To reveal the functional role of domain-domain interactions in the Fc part of IgG the binding of C1q to different anti-ovalbumin IgG-ovalbumin immune complexes was studied. Immune-complex precipitates composed of rabbit IgG in which the non-covalent or covalent bonds between the heavy chains had been eliminated were used. Non-covalent bonds were abolished by splitting off the CH3 domains, i.e. by using Facb fragments, and the covalent contact was broken by reduction and alkylation of the single inter-heavy-chain disulphide bond. The quantitative analysis of the binding curves provides a dissociation constant (K) of 200 nM for the interaction between C1q and immune precipitate formed from native IgG. Surprisingly, for immune precipitates composed of Facb fragments or IgG in which the inter-heavy-chain disulphide bond had been selectively reduced and alkylated, stronger binding (K = 30 nM) was observed. In this case, however, changes in the structure of the immune-complex matrix were also detected. These structural changes may account for the strengthening of the C1q-immune-complex interaction, which can be strongly influenced by the flexibility and the binding-site pattern of the immune-complex precipitates. These results suggest that domain-domain interactions in the Fc part of IgG affect the segmental mobility of IgG molecules and the spatial arrangement of the immune-complex matrix rather than the affinity of individual C1q-binding sites on IgG.

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Singh, Omkar, Kunal Sawariya, and Polamarasetty Aparoy. "Graphlet signature-based scoring method to estimate protein–ligand binding affinity." Royal Society Open Science 1, no. 4 (December 2014): 140306. http://dx.doi.org/10.1098/rsos.140306.

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Over the years, various computational methodologies have been developed to understand and quantify receptor–ligand interactions. Protein–ligand interactions can also be explained in the form of a network and its properties. The ligand binding at the protein-active site is stabilized by formation of new interactions like hydrogen bond, hydrophobic and ionic. These non-covalent interactions when considered as links cause non-isomorphic sub-graphs in the residue interaction network. This study aims to investigate the relationship between these induced sub-graphs and ligand activity. Graphlet signature-based analysis of networks has been applied in various biological problems; the focus of this work is to analyse protein–ligand interactions in terms of neighbourhood connectivity and to develop a method in which the information from residue interaction networks, i.e. graphlet signatures, can be applied to quantify ligand affinity. A scoring method was developed, which depicts the variability in signatures adopted by different amino acids during inhibitor binding, and was termed as GSUS (graphlet signature uniqueness score). The score is specific for every individual inhibitor. Two well-known drug targets, COX-2 and CA-II and their inhibitors, were considered to assess the method. Residue interaction networks of COX-2 and CA-II with their respective inhibitors were used. Only hydrogen bond network was considered to calculate GSUS and quantify protein–ligand interaction in terms of graphlet signatures. The correlation of the GSUS with pIC 50 was consistent in both proteins and better in comparison to the Autodock results. The GSUS scoring method was better in activity prediction of molecules with similar structure and diverse activity and vice versa. This study can be a major platform in developing approaches that can be used alone or together with existing methods to predict ligand affinity from protein–ligand complexes.

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Jungclas, Hartmut, Viacheslav V. Komarov, Anna M. Popova, and Lothar Schmidt. "Molecular Interactions in Particular Van der Waals Nanoclusters." Zeitschrift für Naturforschung A 72, no. 1 (January 1, 2017): 17–23. http://dx.doi.org/10.1515/zna-2016-0213.

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AbstractA method is presented to analyse the interaction energies in a nanocluster, which is consisting of three neutral molecules bound by non-covalent long range Van der Waals forces. One of the molecules (M0) in the nanocluster has a permanent dipole moment, whereas the two other molecules (M1 and M2) are non-polar. Analytical expressions are obtained for the numerical calculation of the dispersion and induction energies of the molecules in the considered nanocluster. The repulsive forces at short intermolecular distances are taken into account by introduction of damping functions. Dispersion and induction energies are calculated for a nanocluster with a definite geometry, in which the polar molecule M0 is a linear hydrocarbon molecule C5H10 and M1 and M2 are pyrene molecules. The calculations are done for fixed distances between the two pyrene molecules. The results show that the induction energies in the considered three-molecular nanocluster are comparable with the dispersion energies. Furthermore, the sum of induction energies in the substructure (M0, M1) of the considered nanocluster is much higher than the sum of induction energies in a two-molecular nanocluster with similar molecules (M0, M1) because of the absence of an electrostatic field in the latter case. This effect can be explained by the essential intermolecular induction in the three-molecular nanocluster.

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Maza, Susana, José L. de Paz, and Pedro M. Nieto. "Synthesis of a Fluorous-Tagged Hexasaccharide and Interaction with Growth Factors Using Sugar-Coated Microplates." Molecules 24, no. 8 (April 22, 2019): 1591. http://dx.doi.org/10.3390/molecules24081591.

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Here, we report the synthesis of a sulfated, fully protected hexasaccharide as a glycosaminoglycan mimetic and the study of its interactions with different growth factors: midkine, basic fibroblast growth factor (FGF-2) and nerve growth factor (NGF). Following a fluorous-assisted approach, monosaccharide building blocks were successfully assembled and the target oligosaccharide was prepared in excellent yield. The use of more acid stable 4,6-O-silylidene protected glucosamine units was crucial for the efficiency of this strategy because harsh reaction conditions were needed in the glycosylations to avoid the formation of orthoester side products. Fluorescence polarization experiments demonstrated the strong interactions between the synthesized hexamer, and midkine and FGF-2. In addition, we have developed an alternative assay to analyse these molecular recognition events. The prepared oligosaccharide was non-covalently attached to a fluorous-functionalized microplate and the direct binding of the protein to the sugar-immobilized surface was measured, affording the corresponding KD,surf value.

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Etxabide, Alaitz, Maite Arregi, Sara Cabezudo, Pedro Guerrero, and Koro de la Caba. "Whey Protein Films for Sustainable Food Packaging: Effect of Incorporated Ascorbic Acid and Environmental Assessment." Polymers 15, no. 2 (January 11, 2023): 387. http://dx.doi.org/10.3390/polym15020387.

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The management of food waste and by-products has become a challenge for the agri-food sector and an example are whey by-products produced in dairy industries. Seeking other whey valorisation alternatives and applications, whey protein films for food packaging applications were developed in this study. Films containing different amounts (0, 5, 10, and 15 wt%) of ascorbic acid were manufactured via compression-moulding and their physicochemical, thermal, barrier, optical, and mechanical properties were analysed and related to the film structure. Additionally, the environmental assessment of the films was carried out to analyse the impact of film manufacture. Regarding physicochemical properties, both FTIR and water uptake analyses showed the presence of non-covalent interactions, such as hydrogen bonding, between whey protein and ascorbic acid as band shifts at the 1500–1700 cm−1 region as well as a water absorption decrease from 380% down to 240% were observed. The addition of ascorbic acid notably improved the UV-Vis light absorbance capacity of whey protein films up to 500 nm, a relevant enhancement for protecting foods susceptible to UV-Vis light-induced lipid oxidation. In relation to the environmental assessment, it was concluded that scaling up film manufacture could lead to a reduction in the environmental impacts, mainly electricity consumption.

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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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Hammud, Hassan H., Muhammad Yar, Imene Bayach, and Khurshid Ayub. "Covalent Triazine Framework C6N6 as an Electrochemical Sensor for Hydrogen-Containing Industrial Pollutants. A DFT Study." Nanomaterials 13, no. 6 (March 21, 2023): 1121. http://dx.doi.org/10.3390/nano13061121.

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Industrial pollutants pose a serious threat to ecosystems. Hence, there is a need to search for new efficient sensor materials for the detection of pollutants. In the current study, we explored the electrochemical sensing potential of a C6N6 sheet for H-containing industrial pollutants (HCN, H2S, NH3 and PH3) through DFT simulations. The adsorption of industrial pollutants over C6N6 occurs through physisorption, with adsorption energies ranging from −9.36 kcal/mol to −16.46 kcal/mol. The non-covalent interactions of analyte@C6N6 complexes are quantified by symmetry adapted perturbation theory (SAPT0), quantum theory of atoms in molecules (QTAIM) and non-covalent interaction (NCI) analyses. SAPT0 analyses show that electrostatic and dispersion forces play a dominant role in the stabilization of analytes over C6N6 sheets. Similarly, NCI and QTAIM analyses also verified the results of SAPT0 and interaction energy analyses. The electronic properties of analyte@C6N6 complexes are investigated by electron density difference (EDD), natural bond orbital analyses (NBO) and frontier molecular orbital analyses (FMO). Charge is transferred from the C6N6 sheet to HCN, H2S, NH3 and PH3. The highest exchange of charge is noted for H2S (−0.026 e−). The results of FMO analyses show that the interaction of all analytes results in changes in the EH-L gap of the C6N6 sheet. However, the highest decrease in the EH-L gap (2.58 eV) is observed for the NH3@C6N6 complex among all studied analyte@C6N6 complexes. The orbital density pattern shows that the HOMO density is completely concentrated on NH3, while the LUMO density is centred on the C6N6 surface. Such a type of electronic transition results in a significant change in the EH-L gap. Thus, it is concluded that C6N6 is highly selective towards NH3 compared to the other studied analytes.

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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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Boro, Mridul, Trishnajyoti Baishya, Antonio Frontera, Miquel Barceló-Oliver, and Manjit K. Bhattacharyya. "Energetic Features of H-Bonded and π-Stacked Assemblies in Pyrazole-Based Coordination Compounds of Mn(II) and Cu(II): Experimental and Theoretical Studies." Crystals 14, no. 4 (March 29, 2024): 318. http://dx.doi.org/10.3390/cryst14040318.

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Two new coordination compounds comprising Mn(II) and Cu(II) viz. [Mn(bz)2(Hdmpz)2(H2O)] (1) and [Cu(crot)2(Hdmpz)2] (2) (where, bz = benzoate; crot = crotonate; Hdmpz = 3, 5-dimethyl pyrazole) were synthesized and characterized. The characterization involved a single crystal X-ray diffraction technique, FT-IR spectroscopy, electronic spectroscopy, TGA, and elemental analyses. Compounds 1 and 2 crystallize as mononuclear entities of Hdmpz with penta-coordinated Mn(II) and hexa-coordinated Cu(II), respectively. These complexes exhibit distorted trigonal bipyramidal and distorted octahedral geometries, respectively. A crystal structure analysis of compound 1 elucidates the existence of C–H⋯π and π-stacking interactions alongside O–H⋯O, N–H⋯O, and C–H⋯O H-bonding interactions contributing to the stabilization of the compound’s layered assembly. Similarly, in compound 2, the crystal structure stability is attributed to the presence of hydrogen bonding in conjugation with π-stacking interactions. We conducted theoretical investigations to analyze π⋯π, H-bonding, and antiparallel CH···π non-covalent interactions observed in compounds 1 and 2. DFT calculations were performed to find out the strength of these interactions energetically. Moreover, QTAIM and non-covalent interaction (NCI) plot index theoretical tools were employed to characterize them and evaluate the contribution of the H-bonds.

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Lan, Qiuyu, Lin Li, Hongmin Dong, Dingtao Wu, Hong Chen, Derong Lin, Wen Qin, Wenyu Yang, Thava Vasanthan, and Qing Zhang. "Effect of Soybean Soluble Polysaccharide on the Formation of Glucono-δ-Lactone-Induced Soybean Protein Isolate Gel." Polymers 11, no. 12 (December 3, 2019): 1997. http://dx.doi.org/10.3390/polym11121997.

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The effect of soybean soluble polysaccharide (SSPS) on the formation of glucono-δ-lactone (GDL)-induced soybean protein isolate (SPI) gel was investigated. Electrophoretic analysis showed the SSPS did not change the electrophoretic behavior of SPI during the formation of SPI gel. However, infrared analysis indicated the β-sheet content increased, and the contents of random coil and α-helix decreased in both cooked SPI and SPI gel. The SSPS and SPI might conjugate via the Maillard reaction according to the results of grafting degree, color change, and infrared analyses. The main interactions during the formation of SPI gel changed from non-covalent to electrostatic interaction after adding SSPS. Sulfhydryl group content also increased in both cooked SPI and SPI gel. The water-holding capacity and gel strength of SPI gel decreased as the SSPS concentration increased. Larger aggregate holes were observed in the microstructure of SPI gel at higher SSPS concentration. Thus, SSPS could covalently conjugate with SPI and influence the formation of hydrogen bonds, disulfide bonds, and electrostatic interaction among SPI molecules to eventually form a loose gel network.

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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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Lai, Hien T. T., and Toan T. Nguyen. "Investigating structural features of dimeric SARS-CoV-2 Mpro catalytic site with bound covalent ligands at physiological temperature." Journal of Physics: Conference Series 2485, no. 1 (April 1, 2023): 012006. http://dx.doi.org/10.1088/1742-6596/2485/1/012006.

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Abstract The SARS-CoV-2 main protease (Mpro) plays an important role in the viral transcription and replication of the SARS-CoV-2 virus that is causing the Covid-19 pandemic worldwide. Therefore, it represents a very attractive target for drug development for treatment of this disease. It is a cysteine protease because it has in the active site the catalytic dyad composed of cysteine (C145) and histidine (H41). The catalytic site represents the binding site for inhibitors, many of them bind to Mpro with a covalent bond. In this research, structural and physiochemical characteristics of the Mpro binding site are investigated when the ligand 11a is covalently and non-covalently bound. All-atom molecular dynamics (MD) simulations were run for 500 ns at physiological temperature (310 K). It is found that conformations of both the Mpro protein and the ligand are stable during the simulation with covalently bound complex showing stronger stability. When the ligand is covalently bound (its final state), residues that stably interact with the ligand are H41, C145, H163, H164 and E166. The optimal conformation of these residues is stabilized also via the Hbond interactions with the catalytic water present in the Mpro binding site. In the case of the non-covalently bound ligand (state before the covalent bond is formed), the binding site residues retain their conformations similar to the covalent binding site, and they still form Hbonds with the catalytic water, except H41. This residue, instead, adopts a different conformation and looses the Hbond with the catalytic water, leaving more freedom to move to the ligand. We hypothesize that H41 could play a role in guiding the ligand to the optimal position for final covalent bonding. Further analyses are in process to check this hypothesis. These results represent an important basis for studying drug candidates against SARS-CoV-2 by means of computer aided drug design.

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Srivastava, Devyani, Om Prakash, Gabriele Kociok-Köhn, Abhinav Kumar, Abdullah Alarifi, Naaser A. Y. Abduh, Mohd Afzal, and Mohd Muddassir. "Centrosymmetric Nickel(II) Complexes Derived from Bis-(Dithiocarbamato)piperazine with 1,1′-Bis(diphenylphosphino)ferrocene and 1,2-Bis(diphenylphosphino)ethane) as Ancillary Ligands: Syntheses, Crystal Structure and Computational Studies." Crystals 13, no. 2 (February 17, 2023): 343. http://dx.doi.org/10.3390/cryst13020343.

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Two Ni(II) complexes with the formula [{Ni(dppf)}2{(L1)2}](PF6)2 (Ni-I) and [{Ni(dppe)}2{(L1)2}](PF6)2 (Ni-II) were prepared by reacting [Ni(dppf)Cl2] and [Ni(dppe)Cl2] (dppf = 1,1′-Bis(diphenylphosphino)ferrocene; dppe = 1,2-Bis(diphenylphosphino)ethane) with secondary amine piperazine derived ligand disodium bis-(dithiocarbamate)piperazine ((piper(dtc)2 = L1) and counter anion PF6−. These complexes were characterized by elemental analyses, FT-IR, 1H, 13C and 31P NMR, UV-Vis. spectroscopy and single crystal X-ray diffraction. The X-ray analyses reveal centrosymmetric structures where each Ni(II) centre adopts distorted square planar geometry defined by two sulfur centres of dithiocarbamate ligand and two phosphorus centres of dppf and dppe ligands in Ni-I and Ni-II, respectively. The supramolecular framework of both Ni-I and Ni-II are sustained by C-H⋯π and C-H⋯F interactions, and they also display interesting intramolecular C-H⋯Ni anagostic interactions. Further, the nature of these interactions are studied using Hirshfeld surface analyses, DFT and quantum theory of atoms in molecules (QTAIM) calculations. Additionally, non-covalent interaction (NCI) plot analyses were conducted to gain additional insight into these non-covalent interactions. This work is vital in a new approach towards the rational designing of the centrosymmetric molecules with interesting architectures.

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Contreras-Riquelme, Sebastián, Jose-Antonio Garate, Tomas Perez-Acle, and Alberto J. M. Martin. "RIP-MD: a tool to study residue interaction networks in protein molecular dynamics." PeerJ 6 (December 7, 2018): e5998. http://dx.doi.org/10.7717/peerj.5998.

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Protein structure is not static; residues undergo conformational rearrangements and, in doing so, create, stabilize or break non-covalent interactions. Molecular dynamics (MD) is a technique used to simulate these movements with atomic resolution. However, given the data-intensive nature of the technique, gathering relevant information from MD simulations is a complex and time consuming process requiring several computational tools to perform these analyses. Among different approaches, the study of residue interaction networks (RINs) has proven to facilitate the study of protein structures. In a RIN, nodes represent amino-acid residues and the connections between them depict non-covalent interactions. Here, we describe residue interaction networks in protein molecular dynamics (RIP-MD), a visual molecular dynamics (VMD) plugin to facilitate the study of RINs using trajectories obtained from MD simulations of proteins. Our software generates RINs from MD trajectory files. The non-covalent interactions defined by RIP-MD include H-bonds, salt bridges, VdWs, cation-π, π–π, Arginine–Arginine, and Coulomb interactions. In addition, RIP-MD also computes interactions based on distances between Cαs and disulfide bridges. The results of the analysis are shown in an user friendly interface. Moreover, the user can take advantage of the VMD visualization capacities, whereby through some effortless steps, it is possible to select and visualize interactions described for a single, several or all residues in a MD trajectory. Network and descriptive table files are also generated, allowing their further study in other specialized platforms. Our method was written in python in a parallelized fashion. This characteristic allows the analysis of large systems impossible to handle otherwise. RIP-MD is available at http://www.dlab.cl/ripmd.

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Farias, Sergio A. de S., Kelvyn M. L. Rocha, Érica C. M. Nascimento, Rafael do C. C. de Jesus, Paulo R. Neres, and João B. L. Martins. "Docking and Electronic Structure of Rutin, Myricetin, and Baicalein Targeting 3CLpro." International Journal of Molecular Sciences 24, no. 20 (October 12, 2023): 15113. http://dx.doi.org/10.3390/ijms242015113.

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Understanding the role of 3CLpro protease for SARS-CoV-2 replication and knowing the potential of flavonoid molecules like rutin, myricetin, and baicalein against 3CLpro justify an investigation into their inhibition. This study investigates possible bonds and reactivity descriptors of rutin, myricetin, and baicalein through conformational and electronic properties. Density functional theory was used to determine possible interactions. Analyses were carried out through the molecular electrostatic potential, electron localization function, Fukui function descriptors based on frontier orbitals, and non-covalent interactions. A docking study was performed using a resolution of 1.55 Å for 3CLpro to analyze the interactions of rutin, myricetin, and baicalein. Scores of structures showed that rutin is the best ligand, followed by myricetin and baicalein. Docking studies showed that baicalein and rutin can establish effective interactions with residues of the catalytic dyad (Cys145 and His41), but just rutin forms a hydrogen bond. Myricetin, in turn, could not establish an effective interaction with Cys145. Baicalein interaction arose with active residues such as Arg188, Val186, Gln189, and Gln192. Interactions of rutin and myricetin with Arg188 and Gln189 were also found. A critical interaction was observed only for rutin with the hydroxyls of ring A with His41, and also for Cys145 with rings B and C, which is probably related to the highest score of rutin.

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Russo, Simona, Maria Rosaria Acocella, Annaluisa Mariconda, Valentina Volpe, Roberto Pantani, and Pasquale Longo. "Mechano Chemical Compatibilization of Polyethylene with Graphite by Means of a Suitable Ester." Polymers 15, no. 13 (June 21, 2023): 2770. http://dx.doi.org/10.3390/polym15132770.

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An effective non-covalent compatibilization method for graphite and low-density polyethylene is reported. To obtain this result, pyren-1-yl-stearate (P1S) was synthesized, characterized and mixed with graphite to provide a better dispersion in polyethylene matrix. The P1S improves the dispersion of carbon filler in polyethylene through non-covalent compatibilization: the pyrenyl group gives π−π stacking interactions with graphite and the stearyl chain provides van der Waals interaction with the polymer chain (specifically London dispersion forces). In this study, different P1S/graphite fillers were prepared with a ratio by weight of 90/10 and 50/50, respectively, by using manual and ball-milling mixing. Their stability, interaction and morphology were evaluated through TGA, RX, and SEM. Thermogravimetric analyses showed that ball-milling mixing is more effective than manual mixing in promoting π−π stacking interactions of molecules such as P1S ester containing an alkyl chain and aromatic rings. The role of ball milling is confirmed by X-ray diffraction measurements since it was possible to observe both exfoliation and intercalation phenomena when this technique was used to mix the P1S ester with graphite. SEM analyses of polyethylene containing 1% of the carbon fillers again highlighted the importance of ball milling to promote the interaction of the ester with graphite and, simultaneously, the importance of the alkyl chain in order to achieve polyethylene-graphite compatibilization.

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Gómez, Santiago, Sara Gómez, Jorge David, Doris Guerra, Chiara Cappelli, and Albeiro Restrepo. "Dissecting Bonding Interactions in Cysteine Dimers." Molecules 27, no. 24 (December 7, 2022): 8665. http://dx.doi.org/10.3390/molecules27248665.

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Neutral (n) and zwitterionic (z) forms of cysteine monomers are combined in this work to extensively explore the potential energy surfaces for the formation of cysteine dimers in aqueous environments represented by a continuum. A simulated annealing search followed by optimization and characterization of the candidate structures afforded a total of 746 structurally different dimers held together via 80 different types of intermolecular contacts in 2894 individual non-covalent interactions as concluded from Natural Bond Orbitals (NBO), Quantum Theory of Atoms in Molecules (QTAIM) and Non-Covalent Interactions (NCI) analyses. This large pool of interaction possibilities includes the traditional primary hydrogen bonds and salt bridges which actually dictate the structures of the dimers, as well as the less common secondary hydrogen bonds, exotic X⋯Y (X = C, N, O, S) contacts, and H⋯H dihydrogen bonds. These interactions are not homogeneous but have rather complex distributions of strengths, interfragment distances and overall stabilities. Judging by their Gibbs bonding energies, most of the structures located here are suitable for experimental detection at room conditions.

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Lei, Fengying, Qingyu Liu, Yeshuang Zhong, Xinai Cui, Jie Yu, Zuquan Hu, Gang Feng, Zhu Zeng, and Tao Lu. "Computational Insight into the Nature and Strength of the π-Hole Type Chalcogen∙∙∙Chalcogen Interactions in the XO2∙∙∙CH3YCH3 Complexes (X = S, Se, Te; Y = O, S, Se, Te)." International Journal of Molecular Sciences 24, no. 22 (November 10, 2023): 16193. http://dx.doi.org/10.3390/ijms242216193.

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In recent years, the non-covalent interactions between chalcogen centers have aroused substantial research interest because of their potential applications in organocatalysis, materials science, drug design, biological systems, crystal engineering, and molecular recognition. However, studies on π-hole-type chalcogen∙∙∙chalcogen interactions are scarcely reported in the literature. Herein, the π-hole-type intermolecular chalcogen∙∙∙chalcogen interactions in the model complexes formed between XO2 (X = S, Se, Te) and CH3YCH3 (Y = O, S, Se, Te) were systematically studied by using quantum chemical computations. The model complexes are stabilized via one primary X∙∙∙Y chalcogen bond (ChB) and the secondary C−H∙∙∙O hydrogen bonds. The binding energies of the studied complexes are in the range of −21.6~−60.4 kJ/mol. The X∙∙∙Y distances are significantly smaller than the sum of the van der Waals radii of the corresponding two atoms. The X∙∙∙Y ChBs in all the studied complexes except for the SO2∙∙∙CH3OCH3 complex are strong in strength and display a partial covalent character revealed by conducting the quantum theory of atoms in molecules (QTAIM), a non-covalent interaction plot (NCIplot), and natural bond orbital (NBO) analyses. The symmetry-adapted perturbation theory (SAPT) analysis discloses that the X∙∙∙Y ChBs are primarily dominated by the electrostatic component.

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Di Martino, Jessica, Manuel Arcieri, Francesco Madeddu, Michele Pieroni, Giovanni Carotenuto, Paolo Bottoni, Lorenzo Botta, Tiziana Castrignanò, Sofia Gabellone, and Raffaele Saladino. "Molecular Dynamics Investigations of Human DNA-Topoisomerase I Interacting with Novel Dewar Valence Photo-Adducts: Insights into Inhibitory Activity." International Journal of Molecular Sciences 25, no. 1 (December 23, 2023): 234. http://dx.doi.org/10.3390/ijms25010234.

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Chronic exposure to ultraviolet (UV) radiation is known to induce the formation of DNA photo-adducts, including cyclobutane pyrimidine dimers (CPDs) and Dewar valence derivatives (DVs). While CPDs usually occur at higher frequency than DVs, recent studies have shown that the latter display superior selectivity and significant stability in interaction with the human DNA/topoisomerase 1 complex (TOP1). With the aim to deeply investigate the mechanism of interaction of DVs with TOP1, we report here four all-atom molecular dynamic simulations spanning one microsecond. These simulations are focused on the stability and conformational changes of two DNA/TOP1-DV complexes in solution, the data being compared with the biomimetic thymine dimer counterparts. Results from root-mean-square deviation (RMSD) and root-mean-square fluctuation (RMSF) analyses unequivocally confirmed increased stability of the DNA/TOP1-DV complexes throughout the simulation duration. Detailed interaction analyses, uncovering the presence of salt bridges, hydrogen bonds, water-mediated interactions, and hydrophobic interactions, as well as pinpointing the non-covalent interactions within the complexes, enabled the identification of specific TOP1 residues involved in the interactions over time and suggested a potential TOP1 inhibition mechanism in action.

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Quiñonero, David, and Antonio Frontera. "Benzene, an Unexpected Binding Unit in Anion–π Recognition: The Critical Role of CH/π Interactions." Sci 4, no. 3 (August 22, 2022): 32. http://dx.doi.org/10.3390/sci4030032.

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We report high-level ab initio calculations (CCSD(T)(full)/CBS//SCS-RI-MP2(full)/aug-cc-pwCVTZ) that demonstrate the importance of cooperativity effects when Anion–π and CH/π interactions are simultaneously established with benzene as the π-system. In fact, most of the complexes exhibit high cooperativity energies that range from 17% to 25.3% of the total interaction energy, which is indicative of the strong influence of the CH/π on the Anion–π interaction and vice versa. Moreover, the symmetry-adapted perturbation theory (SAPT) partition scheme was used to study the different energy contributions to the interaction energies and to investigate the physical nature of the interplay between both interactions. Furthermore, the Atoms in Molecules (AIM) theory and the Non-Covalent Interaction (NCI) approach were used to analyze the two interactions further. Finally, a few examples from the Protein Data Bank (PDB) are shown. All results stress that the concurrent formation of both interactions may play an important role in biological systems due to the ubiquity of CH bonds, phenyl rings, and anions in biomolecules.

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Park, Hyunhang, and Sung Hoon Lee. "Review on Interfacial Bonding Mechanism of Functional Polymer Coating on Glass in Atomistic Modeling Perspective." Polymers 13, no. 14 (July 8, 2021): 2244. http://dx.doi.org/10.3390/polym13142244.

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Atomistic modeling methods are successfully applied to understand interfacial interaction in nanoscale size and analyze adhesion mechanism in the organic–inorganic interface. In this paper, we review recent representative atomistic simulation works, focusing on the interfacial bonding, adhesion strength, and failure behavior between polymer film and silicate glass. The simulation works are described under two categories, namely non-bonded and bonded interaction. In the works for non-bonded interaction, three main interactions, namely van der Waals interaction, polar interaction, and hydrogen bonds, are investigated, and the contributions to interfacial adhesion energy are analyzed. It is revealed that the most dominant interaction for adhesion is hydrogen bonding, but flexibility of the polymer film and modes of adhesion measurement test do affect adhesion and failure behavior. In the case of bonded interactions, the mechanism of covalent silane bond formation through condensation and hydrolysis process is reviewed, and surface reactivity, molecular density, and adhesion properties are calculated with an example of silane functionalized polymer. Besides interfacial interactions, effects of external conditions, such as surface morphology of the glass substrate and relative humidity on the adhesion and failure behavior, are presented, and modeling techniques developed for building interfacial system and calculating adhesion strengths are briefly introduced.

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Gholivand, Khodayar, Kaveh Farshadfar, S. Mark Roe, Mahdieh Hosseini, and Akram Gholami. "Investigation of structure-directing interactions within copper(i)thiocyanate complexes through X-ray analyses and non-covalent interaction (NCI) theoretical approach." CrystEngComm 18, no. 37 (2016): 7104–15. http://dx.doi.org/10.1039/c6ce01339b.

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Falcioni, Fabio, Sophie Bennett, Pallas Stroer-Jarvis, and Paul L. A. Popelier. "Probing Non-Covalent Interactions through Molecular Balances: A REG-IQA Study." Molecules 29, no. 5 (February 28, 2024): 1043. http://dx.doi.org/10.3390/molecules29051043.

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The interaction energies of two series of molecular balances (1-X with X = H, Me, OMe, NMe2 and 2-Y with Y = H, CN, NO2, OMe, NMe2) designed to probe carbonyl…carbonyl interactions were analysed at the B3LYP/6-311++G(d,p)-D3 level of theory using the energy partitioning method of Interacting Quantum Atoms/Fragments (IQA/IQF). The partitioned energies are analysed by the Relative Energy Gradient (REG) method, which calculates the correlation between these energies and the total energy of a system, thereby explaining the role atoms have in the energetic behaviour of the total system. The traditional “back-of-the-envelope” open and closed conformations of molecular balances do not correspond to those of the lowest energy. Hence, more care needs to be taken when considering which geometries to use for comparison with the experiment. The REG-IQA method shows that the 1-H and 1-OMe balances behave differently to the 1-Me and 1-NMe2 balances because the latter show more prominent electrostatics between carbonyl groups and undergoes a larger dihedral rotation due to the bulkiness of the functional groups. For the 2-Y balance, REG-IQA shows the same behaviour across the series as the 1-H and 1-OMe balances. From an atomistic point of view, the formation of the closed conformer is favoured by polarisation and charge-transfer effects on the amide bond across all balances and is counterbalanced by a de-pyramidalisation of the amide nitrogen. Moreover, focusing on the oxygen of the amide carbonyl and the α-carbon of the remaining carbonyl group, electrostatics have a major role in the formation of the closed conformer, which goes against the well-known n-π* interaction orbital overlap concept. However, REG-IQF shows that exchange–correlation energies overtake electrostatics for all the 2-Y balances when working with fragments around the carbonyl groups, while they act on par with electrostatics for the 1-OMe and 1-NMe2. REG-IQF also shows that exchange–correlation energies in the 2-Y balance are correlated to the inductive electron-donating and -withdrawing trends on aromatic groups. We demonstrate that methods such as REG-IQA/IQF can help with the fine-tuning of molecular balances prior to the experiment and that the energies that govern the probed interactions are highly dependent on the atoms and functional groups involved.

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Dong, Wen-Shuai, Lu Zhang, Wen-Li Cao, Zu-Jia Lu, Qamar-un-Nisa Tariq, Chao Zhang, Xiao-Wei Wu, Zong-You Li, and Jian-Guo Zhang. "Synthesis, Crystal Structure, and Characterization of Energetic Salts Based on 3,5-Diamino-4H-Pyrazol-4-One Oxime." Molecules 28, no. 1 (January 3, 2023): 457. http://dx.doi.org/10.3390/molecules28010457.

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In order to broaden the study of energetic cations, a cation 3,5-diamino-4H-pyrazol-4-one oxime (DAPO) with good thermal stability was proposed, and its three salts were synthesized by a simple and efficient method. The structures of the three salts were verified by infrared spectroscopy, mass spectrometry, elemental analysis, and single crystal X-ray diffraction. The thermal stabilities of the three salts were verified by differential scanning calorimetry and thermos-gravimetric analysis. DAPO-based energetic salts are analysed using a variety of theoretical techniques, such as 2D fingerprint, Hirshfeld surface, and non-covalent interaction. Among them, the energy properties of perchlorate (DAPOP) and picrate (DAPOT) were determined by EXPLO5 program combined with the measured density and enthalpy of formation. These compounds have high density, acceptable detonation performance, good thermal stability, and satisfactory sensitivity. The intermolecular interactions of the four compounds were studied by Hirshfeld surface and non-covalent interactions, indicating that hydrogen bonds and π–π stacking interactions are the reasons for the extracellular properties of perchlorate (DAPOP) and picrate (DAPOT), indicating that DAPO is an optional nitrogen-rich cation for the design and synthesis of novel energetic materials with excellent properties.

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Mohammad Fuad, Nur Adlin Sofiya, Lee Sin Ang, Nur Najwa Alyani Mohd Nabil, and Norlin Shuhaime. "Theoretical Investigations on the Interactions of Urea with Hydroxyl and Non-Hydroxyl Hydroxyapatite Surface." Trends in Sciences 20, no. 6 (March 16, 2023): 6558. http://dx.doi.org/10.48048/tis.2023.6558.

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We performed an investigation on urea interacting with hydroxyapatite (HA). The oxygen atoms on HA are either left alone or added with hydrogen to create hydroxyl to resemble the HA surface. Using B3LYP and 3 different basis sets, it was found that urea was able to interact positively with either hydroxyl or non-hydroxyl surface of HA. The Gaussian 09 and Multiwfn software were employed to conduct the calculations. The most favorable interaction has interaction energy of –1.36 eV, which was obtained with the 2 largest basis sets considered, on the pure hydroxyl surface. From the topology analysis on electron density and the non-covalent interaction analysis, it was found that the main attractions between urea and HA were due to the carbonyl oxygen and hydrogen of urea, and hydrogen, oxygen, and calcium on the HA surface. The bond length of newly bonded atoms ranges from 1.62 to 5.18 Å, whereas the energy gap has range between 0.46 to 1.14 eV. All the analysis performed in this study agreed with the results obtained in the formation of favorable interactions and complement previous experimental results that HA can bond with urea molecule. HIGHLIGHTS First known attempt to compare hydrogen-terminated and non-terminated surface of HA in urea adsorption The atoms involved in the adsorption were identified, and electronic structure of the possible combination was analysed and studied using topology and non-covalent interaction analysis Urea attached to both surfaces are stable, with negative interaction energy, confirming experiments’ results that urea can be adsorbed to HA GRAPHICAL ABSTRACT

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Aarabi, Mohammad, Samira Gholami, and Sławomir J. Grabowski. "Hydrogen and Lithium Bonds—Lewis Acid Units Possessing Multi-Center Covalent Bonds." Molecules 26, no. 22 (November 17, 2021): 6939. http://dx.doi.org/10.3390/molecules26226939.

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MP2/aug-cc-pVTZ calculations were carried out on complexes wherein the proton or the lithium cation is located between π-electron systems, or between π-electron and σ-electron units. The acetylene or its fluorine and lithium derivatives act as the Lewis base π-electron species similarly to molecular hydrogen, which acts as the electron donor via its σ-electrons. These complexes may be classified as linked by π-H∙∙∙π/σ hydrogen bonds and π-Li∙∙∙π/σ lithium bonds. The properties of these interactions are discussed, and particularly the Lewis acid units are analyzed, because multi-center π-H or π-Li covalent bonds may occur in these systems. Various theoretical approaches were applied here to analyze the above-mentioned interactions—the Quantum Theory of Atoms in Molecules (QTAIM), the Symmetry-Adapted Perturbation Theory (SAPT) and the Non-Covalent Interaction (NCI) method.

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Nagurniak, Glaucio R., Maurício J. Piotrowski, Àlvaro Muñoz-Castro, João B. S. Cascaldi, Renato L. T. Parreira, and Giovanni F. Caramori. "What is the driving force behind molecular triangles and their guests? A quantum chemical perspective about host–guest interactions." Physical Chemistry Chemical Physics 22, no. 34 (2020): 19213–22. http://dx.doi.org/10.1039/d0cp01821j.

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The physical nature of host–guest interactions occurring between molecular triangles and linear anions was explored using DFT calculations combined with energy decomposition analyses, nuclear independent chemical shift, and non-covalent interactions.

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Xie, Lei, Nan Xiao, Lu Li, Xinan Xie, and Yan Li. "Theoretical Insight into the Interaction between Chloramphenicol and Functional Monomer (Methacrylic Acid) in Molecularly Imprinted Polymers." International Journal of Molecular Sciences 21, no. 11 (June 10, 2020): 4139. http://dx.doi.org/10.3390/ijms21114139.

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Molecular imprinting technology is a promising method for detecting chloramphenicol (CAP), a broad-spectrum antibiotic with potential toxicity to humans, in animal-derived foods. This work aimed to investigate the interactions between the CAP as a template and functional monomers required for synthesizing efficient molecularly imprinted polymers for recognition and isolation of CAP based on density functional theory. The most suitable monomer, methacrylic acid (MAA), was determined based on interaction energies and Gibbs free energy changes. Further, the reaction sites of CAP and MAA was predicted through the frontier molecular orbitals and molecular electrostatic potentials. Atoms in molecules topology analysis and non-covalent interactions reduced density gradient were applied to investigate different types of non-covalent and inter-atomic interactions. The simulation results showed that CAP was the main electron donor, while MAA was the main electron acceptor. Moreover, the CAP–MAA complex simultaneously involved N-H···O and C=O···H double hydrogen bonds, where the strength of the latter was greater than that of the former. The existence of hydrogen bonds was also confirmed by theoretical and experimental hydrogen nuclear magnetic resonance and Fourier transform infrared spectroscopic analyses. This research can act as an important reference for intermolecular interactions and provide strong theoretical guidance regarding CAP in the synthesis of molecularly imprinted polymers.

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Lim, Jaebum, Vincent M. Lynch, Ramakrishna Edupuganti, Andrew Ellington, and Eric V. Anslyn. "Synthesis and structural analyses of phenylethynyl-substituted tris(2-pyridylmethyl)amines and their copper(ii) complexes." Dalton Transactions 45, no. 26 (2016): 10585–98. http://dx.doi.org/10.1039/c6dt00473c.

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Three new tris(2-pyridylmethyl)amine-based ligands possessing phenylethynyl units have been prepared using Sonogashira couplings and substitution reactions. Various non-covalent interactions of copper (ii) complexes of these ligands have been presented in detail.

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Moreno-Alcántar, Guillermo, José Manuel Guevara-Vela, Rafael Delgadillo-Ruíz, Tomás Rocha-Rinza, Ángel Martín Pendás, Marcos Flores-Álamo, and Hugo Torrens. "Structural effects of trifluoromethylation and fluorination in gold(i) BIPHEP fluorothiolates." New Journal of Chemistry 41, no. 19 (2017): 10537–41. http://dx.doi.org/10.1039/c7nj02202f.

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Stondus, Jigmat, and Rajni Kant. "CAMBRIDGE STRUCTURE DATABASE ANALYSIS OF MOLECULAR INTERACTION ENERGIES IN BROMINESUBSTITUTED COUMARIN STRUCTURES." RASAYAN Journal of Chemistry 15, no. 02 (2022): 991–1008. http://dx.doi.org/10.31788/rjc.2022.1526853.

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Although the non-covalent interactions such as hydrogen bonds and Van der Waals bonds are considered as weak but have a significant impact on the characteristics of the molecule in solution and the crystalline phase. The nature and strength of such intermolecular interactions result in various physicochemical and biological properties in crystal structures. In the present study, a quantitative analysis of intermolecular interaction in the crystal packing of some bromine substituted coumarin derivatives has been undertaken for lattice energy and intermolecular interaction energies analyses using a computational approach. The analysis shows that the energy contribution of halogen bonds such as C-Br…O and C-Br…π is quite significant in the crystal structures of bromine substituted coumarins. Besides, the C-H…O, C-H…Br and π…π interactions are also found to have a profound effect on the molecular packing of these structures. Molecular interactions with reference to the packing mechanism in each molecule are studied in detail. It is expected that empirical analysis of molecular energy interactions will help in understanding the role of various structural motifs in crystal packing

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Brinda, K. V., Avadhesha Surolia, and Sarawathi Vishveshwara. "Insights into the quaternary association of proteins through structure graphs: a case study of lectins." Biochemical Journal 391, no. 1 (September 26, 2005): 1–15. http://dx.doi.org/10.1042/bj20050434.

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The unique three-dimensional structure of both monomeric and oligomeric proteins is encoded in their sequence. The biological functions of proteins are dependent on their tertiary and quaternary structures, and hence it is important to understand the determinants of quaternary association in proteins. Although a large number of investigations have been carried out in this direction, the underlying principles of protein oligomerization are yet to be completely understood. Recently, new insights into this problem have been gained from the analysis of structure graphs of proteins belonging to the legume lectin family. The legume lectins are an interesting family of proteins with very similar tertiary structures but varied quaternary structures. Hence they have become a very good model with which to analyse the role of primary structures in determining the modes of quaternary association. The present review summarizes the results of a legume lectin study as well as those obtained from a similar analysis carried out here on the animal lectins, namely galectins, pentraxins, calnexin, calreticulin and rhesus rotavirus Vp4 sialic-acid-binding domain. The lectin structure graphs have been used to obtain clusters of non-covalently interacting amino acid residues at the intersubunit interfaces. The present study, performed along with traditional sequence alignment methods, has provided the signature sequence motifs for different kinds of quaternary association seen in lectins. Furthermore, the network representation of the lectin oligomers has enabled us to detect the residues which make extensive interactions (‘hubs’) across the oligomeric interfaces that can be targetted for interface-destabilizing mutations. The present review also provides an overview of the methodology involved in representing oligomeric protein structures as connected networks of amino acid residues. Further, it illustrates the potential of such a representation in elucidating the structural determinants of protein–protein association in general and will be of significance to protein chemists and structural biologists.

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Swierczynski, Dariusz, Roman Luboradzki, Grigori Dolgonos, Janusz Lipkowski, and Hans-Jörg Schneider. "Non-Covalent Interactions of Organic Halogen Compounds with Aromatic Systems – Analyses of Crystal Structure Data." European Journal of Organic Chemistry 2005, no. 6 (March 2005): 1172–77. http://dx.doi.org/10.1002/ejoc.200400446.

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Sharma, Pranay, Rosa M. Gomila, Miquel Barceló-Oliver, Akalesh K. Verma, Diksha Dutta, Antonio Frontera, and Manjit K. Bhattacharyya. "Unconventional Dual Donor-Acceptor Topologies of Aromatic Rings in Amine-Based Polymeric Tetrahedral Zn(II) Compounds Involving Unusual Non-Covalent Contacts: Antiproliferative Evaluation and Theoretical Studies." Crystals 13, no. 3 (February 23, 2023): 382. http://dx.doi.org/10.3390/cryst13030382.

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Two Zn(II) coordination polymers, viz., [Zn2Cl2(H2O)2(µ-4-AmBz)2]n (1) and [ZnCl2(µ-3-AmPy)2]n (2) (4-AmBz = 4-aminobenzoate, 3-AmPy = 3-aminopyridine) have been prepared at room temperature and characterized using elemental analysis, FT-IR, electronic spectroscopy, TGA (thermogravimetric analysis) and single crystal XRD. Crystal structure analyses of the polymers unfold the presence of non-covalent anion–π, π-stacking and unusual NH2(amino)⋯π interactions which provide rigidity to the crystal structures. Unconventional Type I Cl⋯Cl interactions also play a pivotal role in the stability of compound 1. Molecular electrostatic potential (MEP) surface analysis reveals that the MEP values over the center of the aromatic rings of coordinated 4-AmBz and 3-AmPy moieties are positive on one side and negative on the other side which confirms the dual non-covalent donor-acceptor topologies of the aromatic rings and explains the concurrent formation of unusual non-covalent NH2···π and anion–π interactions. DFT (density functional theory) calculations, QTAIM (quantum theory of atoms in molecules) and NCI plot (non-covalent index) index analyses reveal that among various non-covalent contacts involved in the crystal packing of the compounds, H-bonds in compound 1 and π-interactions (NH2···π, π-π, anion–π) in compound 2 are energetically significant. We have explored in vitro cytotoxic potential of the compounds in Dalton’s lymphoma (DL) cancer cells using trypan blue and apoptosis assays. The studies show that compounds 1 and 2 can significantly exhibit cytotoxicity in DL cells with minimum cytotoxicity in healthy PBMC cells. Molecular docking studies reveal that the compounds effectively bind with the antiapoptotic target proteins; thereby establishing a structure activity relationship of the compounds.

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Kia, Reza, and Azadeh Kalaghchi. "Structural, Non-Covalent Interaction, and Natural Bond Orbital Studies on Bromido-Tricarbonyl Rhenium(I) Complexes Bearing Alkyl-Substituted 1,4-Diazabutadiene (DAB) Ligands." Crystals 10, no. 4 (April 1, 2020): 267. http://dx.doi.org/10.3390/cryst10040267.

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The synthesis, characterization, structural and computational studies of Re(I) tricarbonyl bromo complexes bearing alkyl-substituted 1,4-diazabutadiene ligands, [Re(CO)3(1,4-DAB)Br], where 1,4-DAB = N,N-bis(2,4-dimethylbenzene)-1,4-diazabutadiene, 2,4-Me2DAB (1); N,N-bis(2,4-dimethylbenzene)-2,3-dimethyl-1,4-diazabutadiene, 2,4-Me2DABMe (2); N,N-bis(2,4,6-trimethylbenzene)-1,4-diazabutadiene, 2,4,6-Me3DAB (3); and N,N-bis(2,6-diisopropylbenzene)-1,4-diazabutadiene, 2,6-ipr2DAB (4) are reported. The complexes were characterized by different spectroscopic methods such as FT-IR, 1H-NMR, 13C-NMR, and elemental analyses and their solid-state structures were confirmed by X-ray diffraction. In each complex, the Re(I) centre shows a distorted octahedral shape with a facial geometry of carbonyl groups. The gas phase geometry of the complexes was identified by density functional theory. Interesting intermolecular n…π* interactions of complexes 1 and 3 were investigated by non-covalent interaction index (NCI), and natural bond orbital (NBO) analyses. The intramolecular n…σ*, σ…π*, π…σ* interactions were also studied in complexes 3 and 4.

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Krupka, Katarzyna M., Sylwia Banach, Michał Pocheć, Jarosław J. Panek, and Aneta Jezierska. "Making and Breaking—Insight into the Symmetry of Salen Analogues." Symmetry 15, no. 2 (February 5, 2023): 424. http://dx.doi.org/10.3390/sym15020424.

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This study focuses on selected members of the general salen-analogues family possessing two O-H⋯N hydrogen bonds, namely three isomers of N,N’-bis(salicylidene)-X-phenylenediamine, denoted as ortho, meta and para. Two of the isomers are not planar in the published crystal structures. The current study tackles the problem of symmetry and interactions within the molecules, as well as in the crystal lattice. The aromaticity of the phenyl rings is evaluated using the Harmonic Oscillator Model of Aromaticity (HOMA) index. Intra- and inter-molecular non-covalent interactions are studied via Hirshfeld surface analysis, Independent Gradient Model (IGM), Quantum Theory of Atoms in Molecules (QTAIM), Non-Covalent Interaction (NCI) index, Electron Localisation Function (ELF), Core-Valence Bifurcation (CVB) index and Symmetry-Adapted Perturbation Theory (SAPT). Density Functional Theory (DFT) simulations were carried out in vacuo and with solvent reaction field based on Polarisable Continuum Model (IEF-PCM formulation) at the ωB97XD/6-311+G(2d,2p) level. Crystal structure analyses were performed for the data reported previously in the literature. The obtained results demonstrate that the three isomers differ greatly in their structural properties (molecular symmetry is broken for the ortho and meta isomers in the solid state) and ability to form intermolecular interactions, while retaining overall similar physico-chemical characteristics, e.g., aromaticity of the phenyl rings. It was found that the presence of the polar solvent does not significantly affect the structure of the studied compounds. An application of the Hirshfeld surface analysis revealed the nature of the non-covalent interactions present in the investigated crystals. The SAPT results showed that the stability of the dimers extracted from the crystals of the Schiff base derivatives arises from electrostatics and dispersion.

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Sáenz-Tavera, Isabel del Carmen, and Victor M. Rosas-García. "Ab initio calculations and reduced density gradient analyses of the structure and energetics of hydrated calcium fluoride and calcium carbonate." Physical Chemistry Chemical Physics 21, no. 10 (2019): 5744–58. http://dx.doi.org/10.1039/c8cp06353b.

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We studied microhydrated calcium fluoride, calcium carbonate and their ions at the MP2/6-311++G** level of theory and found that water–water non-covalent interactions destabilize the solvation shell, and are compensated by cooperative hydrogen bonds.

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Freitas-Marques, Maria Betânia de, Wagner da Nova Mussel1, Maria Irene Yoshida, Christian Fernandes, Tércio Assunção Pedros, and Pedro Henrique Reis da Silva. "Interações químicas entre monômero e molécula molde em polímeros com impressão molecular, o EGDMA: 2-VP (4: 1) - estudo de caso MIP lumefantrina." Journal of Experimental Techniques and Instrumentation 4, no. 04 (December 19, 2021): 56–76. http://dx.doi.org/10.30609/jeti.v4i04.14486.

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Molecularly Imprinted Polymers (MIP) are synthetic materials used as a tool to enhance the selectivity in different analytical approaches, such as solid-phase extraction, chromatography, and sensing devices. Knowing the mechanism involved in the interaction between the template and monomer is essential for a further successful application. However, studies on this topic are scarce. This work evaluates the involved mechanisms in the template-monomer interaction for a lumefantrine MIP system, an antimalarial drug. Field-emission gun scanning electron microscopy, thermal analysis, X-ray diffraction, and density functional theory were applied to determine the mechanism involved in two MIPs obtained in different conditions. A new parameter, named Molecularly Imprinting Factor (MIF), was proposed to evaluate the contribution of specific interactions in the sorption of the analyte by the MIP structure. MIF allows direct insights into specific binding, non-specific contributions, interaction nature, behavior predictability, system acid-base behavior, pre-screening pairs capability, and binding site affinities evaluation. Two interaction types were observed, covalent and non-covalent, when methacrylic acid and 2-vinyl pyridine were used as monomers, respectively. Therefore, the use of methacrylic acid formed a sorbent inappropriate for solid-phase extraction since the binding is not reversible. On the other hand, 2-vinyl pyridine-lumefantrine binding was reversible, and MIF = 0.59 (59.02% of specific site sorption) indicates that the predominant mechanism in the sorption is specific.

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Hosseinzadeh, Maryamossadat, Shiva Masoudi, Nasrin Masnabadi, and Fatemeh Azarakhshi. "Theoretical study of encapsulation of diethylstilbestrol drug into the inner surface of BNNT toward designing a new nanocarrier for drug delivery systems." Materials Research Express 9, no. 4 (April 1, 2022): 045002. http://dx.doi.org/10.1088/2053-1591/ac60e1.

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Abstract In this research, the encapsulation and intermolecular non-bonded interactions of an anticancer drug, Diethylstilbestrol (DES), into the inner surfaces of BNNT (8,8–12) were investigated. All Density Functional Theory (DFT) calculations were performed in a gas phase. So, this research focuses on intermolecular hydrogen bonding, van der Waals and steric interactions between active sites of the BNNT and DES by quantum theory of atom in molecule (QTAIM) theory. QTAIM and non-covalent interaction index (NCI) analyses showed the interactions between the DES drug and the BNNT nanotube. The HOMO-LUMO orbitals, Density of States (DOS) plots, and reduced density gradient (RDG) analyses were carried out to determine the effect of DES adsorption into the nanotube. Furthermore, the effect of the abovementioned interactions between the DES and BNNT (8,8–12) on the electronic characteristics, and natural charges have also been estimated. Based on the results, the thermodynamic parameters of BNNT (8,8-12)/DES are in very close agreement with the NCI analysis and showed that the BNNT (8,8–12) adsorb DES via a physisorption process rather than chemical one and the sorption procedure was exothermic in benign and thermodynamically favorable. Therefore, the use of BNNT (8,8–12) as a carrier for DES drug has been confirmed theoretically.

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Shen, Jian-Xin, Wen-Wen Du, Yuan-Ling Xia, Zhi-Bi Zhang, Ze-Fen Yu, Yun-Xin Fu, and Shu-Qun Liu. "Identification of and Mechanistic Insights into SARS-CoV-2 Main Protease Non-Covalent Inhibitors: An In-Silico Study." International Journal of Molecular Sciences 24, no. 4 (February 20, 2023): 4237. http://dx.doi.org/10.3390/ijms24044237.

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The indispensable role of the SARS-CoV-2 main protease (Mpro) in the viral replication cycle and its dissimilarity to human proteases make Mpro a promising drug target. In order to identify the non-covalent Mpro inhibitors, we performed a comprehensive study using a combined computational strategy. We first screened the ZINC purchasable compound database using the pharmacophore model generated from the reference crystal structure of Mpro complexed with the inhibitor ML188. The hit compounds were then filtered by molecular docking and predicted parameters of drug-likeness and pharmacokinetics. The final molecular dynamics (MD) simulations identified three effective candidate inhibitors (ECIs) capable of maintaining binding within the substrate-binding cavity of Mpro. We further performed comparative analyses of the reference and effective complexes in terms of dynamics, thermodynamics, binding free energy (BFE), and interaction energies and modes. The results reveal that, when compared to the inter-molecular electrostatic forces/interactions, the inter-molecular van der Waals (vdW) forces/interactions are far more important in maintaining the association and determining the high affinity. Given the un-favorable effects of the inter-molecular electrostatic interactions—association destabilization by the competitive hydrogen bond (HB) interactions and the reduced binding affinity arising from the un-compensable increase in the electrostatic desolvation penalty—we suggest that enhancing the inter-molecular vdW interactions while avoiding introducing the deeply buried HBs may be a promising strategy in future inhibitor optimization.

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Mahmoudi, Ghodrat, Marjan Abedi, Simon E. Lawrence, Ennio Zangrando, Maria G. Babashkina, Axel Klein, Antonio Frontera, and Damir A. Safin. "Tetrel Bonding and Other Non-Covalent Interactions Assisted Supramolecular Aggregation in a New Pb(II) Complex of an Isonicotinohydrazide." Molecules 25, no. 18 (September 4, 2020): 4056. http://dx.doi.org/10.3390/molecules25184056.

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A new supramolecular Pb(II) complex [PbL(NO2)]n was synthesized from Pb(NO3)2, N’-(1-(pyridin-2-yl)ethylidene)isonicotinohydrazide (HL) and NaNO2. [PbL(NO2)]n is constructed from discrete [PbL(NO2)] units with an almost ideal N2O3 square pyramidal coordination environment around Pb(II). The ligand L− is coordinated through the 2-pyridyl N-atom, one aza N-atom, and the carbonyl O-atom. The nitrite ligand binds in a κ2-O,O coordination mode through both O-atoms. The Pb(II) center exhibits a hemidirected coordination geometry with a pronounced coordination gap, which allows a close approach of two additional N-atoms arising from the N=C(O) N-atom of an adjacent molecule and from the 4-pyridyl N-atom from the another adjacent molecule, yielding a N4O3 coordination, constructed from two Pb–N and three Pb–O covalent bonds, and two Pb⋯N tetrel bonds. Dimeric units in the structure of [PbL(NO2)]n are formed by the Pb⋯N=C(O) tetrel bonds and intermolecular electrostatically enforced π+⋯π− stacking interactions between the 2- and 4-pyridyl rings and further stabilized by C–H⋯π intermolecular interactions, formed by one of the methyl H-atoms and the 4-pyridyl ring. These dimers are embedded in a 2D network representing a simplified uninodal 3-connected fes (Shubnikov plane net) topology defined by the point symbol (4∙82). The Hirshfeld surface analysis of [PbL(NO2)] revealed that the intermolecular H⋯X (X = H, C, N, O) contacts occupy an overwhelming majority of the molecular surface of the [PbL(NO2)] coordination unit. Furthermore, the structure is characterized by intermolecular C⋯C and C⋯N interactions, corresponding to the intermolecular π⋯π stacking interactions. Notably, intermolecular Pb⋯N and, most interestingly, Pb⋯H interactions are remarkable contributors to the molecular surface of [PbL(NO2)]. While the former contacts are due to the Pb⋯N tetrel bonds, the latter contacts are mainly due to the interaction with the methyl H-atoms in the π⋯π stacked [PbL(NO2)] molecules. Molecular electrostatic potential (MEP) surface calculations showed marked electrostatic contributions to both the Pb⋯N tetrel bonds and the dimer forming π+⋯π− stacking interactions. Quantum theory of atoms in molecules (QTAIM) analyses underlined the tetrel bonding character of the Pb⋯N interactions. The manifold non-covalent interactions found in this supramolecular assembly are the result of the proper combination of the polyfunctional multidentate pyridine-hydrazide ligand and the small nitrito auxiliary ligand.

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Domingo, Luis R., Mar Ríos-Gutiérrez, and Patricia Pérez. "An MEDT study of the carbenoid-type [3 + 2] cycloaddition reactions of nitrile ylides with electron-deficient chiral oxazolidinones." Organic & Biomolecular Chemistry 14, no. 44 (2016): 10427–36. http://dx.doi.org/10.1039/c6ob01989g.

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A combination of the bonding evolution theory and non-covalent interactions analyses of TSs makes it possible to characterise both the carbenoid-type 32CA reaction between a NY and a chiral oxazolidinone, and the diastereoselectivity experimentally observed.

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Varadwaj, Pradeep R. "Halogen Bond via an Electrophilic π-Hole on Halogen in Molecules: Does It Exist?" International Journal of Molecular Sciences 25, no. 9 (April 23, 2024): 4587. http://dx.doi.org/10.3390/ijms25094587.

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This study reveals a new non-covalent interaction called a π-hole halogen bond, which is directional and potentially non-linear compared to its sister analog (σ-hole halogen bond). A π-hole is shown here to be observed on the surface of halogen in halogenated molecules, which can be tempered to display the aptness to form a π-hole halogen bond with a series of electron density-rich sites (Lewis bases) hosted individually by 32 other partner molecules. The [MP2/aug-cc-pVTZ] level characteristics of the π-hole halogen bonds in 33 binary complexes obtained from the charge density approaches (quantum theory of intramolecular atoms, molecular electrostatic surface potential, independent gradient model (IGM-δginter)), intermolecular geometries and energies, and second-order hyperconjugative charge transfer analyses are discussed, which are similar to other non-covalent interactions. That a π-hole can be observed on halogen in halogenated molecules is substantiated by experimentally reported crystals documented in the Cambridge Crystal Structure Database. The importance of the π-hole halogen bond in the design and growth of chemical systems in synthetic chemistry, crystallography, and crystal engineering is yet to be fully explicated.

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Shen, Yu, Mengling Lv, Zhenyue Tang, Wei Liu, Yusong Zhang, Fei Teng, Xu Wang, Meili Shao, and Yujun Jiang. "Soy Protein Isolate Interacted with Acrylamide to Reduce the Release of Acrylamide in the In Vitro Digestion Model." Foods 12, no. 6 (March 8, 2023): 1136. http://dx.doi.org/10.3390/foods12061136.

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Acrylamide (AA), a common carcinogen, has been found in many dietary products.. This study aimed to explore the interaction of soybean protein isolate (SPI) with AA and further research the different effects of SPI on the AA release due to interactions in the in vitro digestion model. Analysis of variance was used to analyze the data. The results suggested that AA could bind with SPI in vitro, leading to the variation in SPI structure. The intrinsic fluorescence of SPI was quenched by AA via static quenching. The non-covalent (van der Waals forces and hydrogen bonding) and covalent bonds were the main interaction forces between SPI and AA. Furthermore, the release of AA significantly decreased due to its interaction with SPI under simulated gastrointestinal conditions. SPI had different effects on the AA release rate after different treatments. The thermal (80, 85, 90, and 95 °C for either 10 or 20 min) and ultrasound (200, 300, and 400 W for either 15, 30, or 60 min) treatments of SPI were useful in reducing the release of AA. However, the high pressure-homogenized (30, 60, 90, and 120 MPa once, twice, or thrice) treatments of SPI were unfavorable for reducing the release of AA.

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Moreno-Alcántar, Guillermo, Kristopher Hess, José Manuel Guevara-Vela, Tomás Rocha-Rinza, Ángel Martín Pendás, Marcos Flores-Álamo, and Hugo Torrens. "π-Backbonding and non-covalent interactions in the JohnPhos and polyfluorothiolate complexes of gold(i)." Dalton Transactions 46, no. 37 (2017): 12456–65. http://dx.doi.org/10.1039/c7dt00961e.

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Kim, Ju Yaen, Misaki Kinoshita, Satoshi Kume, Hanke GT, Toshihiko Sugiki, John E. Ladbury, Chojiro Kojima, et al. "Non-covalent forces tune the electron transfer complex between ferredoxin and sulfite reductase to optimize enzymatic activity." Biochemical Journal 473, no. 21 (October 27, 2016): 3837–54. http://dx.doi.org/10.1042/bcj20160658.

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Although electrostatic interactions between negatively charged ferredoxin (Fd) and positively charged sulfite reductase (SiR) have been predominantly highlighted to characterize complex formation, the detailed nature of intermolecular forces remains to be fully elucidated. We investigated interprotein forces for the formation of an electron transfer complex between Fd and SiR and their relationship to SiR activity using various approaches over NaCl concentrations between 0 and 400 mM. Fd-dependent SiR activity assays revealed a bell-shaped activity curve with a maximum ∼40–70 mM NaCl and a reverse bell-shaped dependence of interprotein affinity. Meanwhile, intrinsic SiR activity, as measured in a methyl viologen-dependent assay, exhibited saturation above 100 mM NaCl. Thus, two assays suggested that interprotein interaction is crucial in controlling Fd-dependent SiR activity. Calorimetric analyses showed the monotonic decrease in interprotein affinity on increasing NaCl concentrations, distinguished from a reverse bell-shaped interprotein affinity observed from Fd-dependent SiR activity assay. Furthermore, Fd:SiR complex formation and interprotein affinity were thermodynamically adjusted by both enthalpy and entropy through electrostatic and non-electrostatic interactions. A residue-based NMR investigation on the addition of SiR to 15N-labeled Fd at the various NaCl concentrations also demonstrated that a combination of electrostatic and non-electrostatic forces stabilized the complex with similar interfaces and modulated the binding affinity and mode. Our findings elucidate that non-electrostatic forces are also essential for the formation and modulation of the Fd:SiR complex. We suggest that a complex configuration optimized for maximum enzymatic activity near physiological salt conditions is achieved by structural rearrangement through controlled non-covalent interprotein interactions.

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Gumus, Ilkay, Ummuhan Solmaz, Gun Binzet, Ebru Keskin, Birdal Arslan, and Hakan Arslan. "Hirshfeld surface analyses and crystal structures of supramolecular self-assembly thiourea derivatives directed by non-covalent interactions." Journal of Molecular Structure 1157 (April 2018): 78–88. http://dx.doi.org/10.1016/j.molstruc.2017.12.017.

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Journal articles on the topic 'Analyse des interactions non covalentes'

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