Artículos de revistas: "Structure des complexes de surface"

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Terebinska, M. I., O. I. Tkachuk, A. M. Datsyuk, O. V. Filonenko, and V. V. Lobanov. "Electronic structure of complexes of oligomers of 3,4-ethylene-dietoxythiophene with polystyrlesulphonic acid." Surface 13(28) (December 30, 2021): 84–93. http://dx.doi.org/10.15407/surface.2021.13.084.

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By the method of density functional theory (B3LYP, 6-31G **) the electronic structures of poly 3,4-ethylenedioxythiophene containing 12 links in charge states 0, +1, +2, +3 and +4 were calculated. It is shown that the oligomer of 12 units is sufficient to reflect the properties of the conductive polymer. To estimate the probability of electron density movement along the polymer chain, the width of the energy gap between NOMO and LUMO was calculated. It is shown that the molecules of oligomers EDOT and SS do not remain parallel to each other after polymerization, but rather, with increasing chain length, the latter gradually bends around the anionic unit SS; the charge distribution in the EDOT and SS oligomer complexes indicates the presence of two separated polarons at the two ends of the chain, and the asymmetry in the charge distribution also implies the presence of a curved spiral structure of the formed complex.

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Karpenko, O. S., V. V. Lobanov, and M. T. Kartel. "Stability of single-atom iron complexes on graphene double vacancy." Surface 15(30) (December 30, 2023): 3–11. http://dx.doi.org/10.15407/surface.2023.15.003.

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The equilibrium and spatial structure of the polycyclic aromatic hydrocarbon C96H24, chosen as a model of the graphene plane, as well as the systems obtained from it by removing the diatomic molecule C2 (C94H24) and then replacing four carbon atoms with four nitrogen atoms (C90N4H24) have been studied by the DFT method (B3LYP) in the 6-31G** basis using Grimme corrections to account for dispersion interactions. In the same approximation, the energetics of the formation of a complex of an iron atom in zero oxidation degree (Fe0) with C90N4H24 ([C90N4H24Fe]0) in the square planar field of the ligand has been studied. The types of molecular orbitals of the ligand, which correspond to the symmetry of the atomic d-orbitals of the Fe atom, have been determined. Interaction diagrams of the d-orbitals of the Fe atom with some molecular orbitals of the ligand C90N4H24 of the corresponding symmetry are constructed. It is concluded that the binding of the transition metal atom on the double vacancy of the graphene plane can be rationally described based on the local symmetry of the coordination center and molecular orbitals of the ligand and the formed complex.

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FUKUOKA, Atsushi, Toshiyuki FUJIMOTO, Feng-show XIAO, and Masaru ICHIKAWA. "Structure and catalysis of surface-grafted cluster complexes." Journal of The Japan Petroleum Institute 34, no. 2 (1991): 125–37. http://dx.doi.org/10.1627/jpi1958.34.125.

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Kremleva, Alena, Sven Krüger, and Notker Rösch. "Uranyl adsorption at solvated edge surfaces of 2 : 1 smectites. A density functional study." Physical Chemistry Chemical Physics 17, no. 20 (2015): 13757–68. http://dx.doi.org/10.1039/c5cp01074h.

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DUAN, YUHUA, BOOJALA V. B. REDDY, and YIANNIS N. KAZNESSIS. "RESIDUE CONSERVATION INFORMATION FOR GENERATING NEAR-NATIVE STRUCTURES IN PROTEIN–PROTEIN DOCKING." Journal of Bioinformatics and Computational Biology 04, no. 04 (2006): 793–806. http://dx.doi.org/10.1142/s0219720006002223.

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Motivation: Protein–protein docking algorithms typically generate large numbers of possible complex structures with only a few of them resembling the native structure. Recently (Duan et al., Protein Sci, 14:316–218, 2005), it was observed that the surface density of conserved residue positions is high at the interface regions of interacting protein surfaces, except for antibody–antigen complexes, where a lesser number of conserved positions than average is observed at the interface regions. Using this observation, we identified putative interacting regions on the surface of interacting partners and significantly improved docking results by assigning top ranks to near-native complex structures. In this paper, we combine the residue conservation information with a widely used shape complementarity algorithm to generate candidate complex structures with a higher percentage of near-native structures (hits). What is new in this work is that the conservation information is used early in the generation stage and not only in the ranking stage of the docking algorithm. This results in a significantly larger number of generated hits and an improved predictive ability in identifying the native structure of protein–protein complexes. Results: We report on results from 48 well-characterized protein complexes, which have enough residue conservation information from the same 59 benchmark complexes used in our previous work. We compute conservation indices of residue positions on the surfaces of interacting proteins using available homologous sequences from UNIPROT and calculate the solvent accessible surface area. We combine this information with shape-complementarity scores to generate candidate protein–protein complex structures. When compared with pure shape-complementarity algorithms, performed by FTDock, our method results in significantly more hits, with the improvement being over 100% in many instances. We demonstrate that residue conservation information is useful not only in refinement and scoring of docking solutions, but also helpful in enrichment of near-native-structures during the generation of candidate geometries of complex structures.

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Funk, Felix, Beat Flühmann, and Amy E. Barton. "Criticality of Surface Characteristics of Intravenous Iron–Carbohydrate Nanoparticle Complexes: Implications for Pharmacokinetics and Pharmacodynamics." International Journal of Molecular Sciences 23, no. 4 (2022): 2140. http://dx.doi.org/10.3390/ijms23042140.

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Un-complexed polynuclear ferric oxyhydroxide cannot be administered safely or effectively to patients. When polynuclear iron cores are formed with carbohydrates of various structures, stable complexes with surface carbohydrates driven by multiple interacting sites and forces are formed. These complexes deliver iron in a usable form to the body while avoiding the serious adverse effects of un-complexed forms of iron, such as polynuclear ferric oxyhydroxide. The rate and extent of plasma clearance and tissue biodistribution is variable among the commercially available iron–carbohydrate complexes and is driven principally by the surface characteristics of the complexes which dictate macrophage opsonization. The surface chemistry differences between the iron–carbohydrate complexes results in significant differences in in vivo pharmacokinetic and pharmacodynamic profiles as well as adverse event profiles, demonstrating that the entire iron–carbohydrate complex furnishes the pharmacologic action for these complex products. Currently available physicochemical characterization methods have limitations in biorelevant matrices resulting in challenges in defining critical quality attributes for surface characteristics for this class of complex nanomedicines.

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Digurova, Anna I., та Natalia A. Lvova. "“Boron + vacancy” complexes on the hydrogenated diamond surface С(100)-(2×1)". Image Journal of Advanced Materials and Technologies 6, № 4 (2021): 256–66. http://dx.doi.org/10.17277/jamt.2021.04.pp.256-266.

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The paper presents the results of quantum-chemical modeling of structural and electronic states of “boron + vacancy” complex defects on the hydrogenated and clean diamond surface, with a variation in the position of BV complexes in the upper six surface layers. Neutral, positive and negatively charged states of the complexes are considered. Two different positions of impurity and intrinsic defects in the composition of the BV complex have been considered for the third and fourth layers: under the dimer row and between the rows. The influence of the surface passivation on the position of BV complexes on the energy scale is analyzed. It has been found that hydrogenation of the surface leads to a change in the configuration of the most stable BV complex. The formation of a local graphite-like structure with π-conjugation is the main stabilizing factor for the defect structures, regardless of the considered charge state. It was shown that the distribution of the spin density of the studied negative BV complexes located directly in the near-surface layers of the clean and hydrogenated surface is similar to the spin properties of complexes in the bulk of diamond.

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Караулова, Дарья Александровна, Владимир Георгиевич Алексеев, and Мариана Александровна Феофанова. "DFT CALCULATION OF THE STRUCTURE OF COPPER COMPLEXES." Вестник Тверского государственного университета. Серия: Химия, no. 2(48) (July 7, 2022): 79–85. http://dx.doi.org/10.26456/vtchem2022.2.9.

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DFT расчёт структуры комплексов меди (II) c лигандами различной химической природы (ацетат-анион, хлорид-анион, N,N- диэтилэтилендиамин) проведён с использованием базисов LACV3P**++, LACVP**++, def2-SVPD и гибридных функционалов B3LYP-D3, M05-2XD3, M06-D3, M06-2X-D3, M08-HX, PW6B95-D3. Лучшее соответствие результатов расчёта экспериментальным данным обеспечивает использование функционала PW6B95-D3. DFT calculation of the structure of copper (II) complexes with ligands of various chemical nature (acetate anion, chloride anion, N,Ndiethylethylenediamine) was carried out using the LACV3P**++, LACVP**++, def2-SVPD basis and hybrid-GGA functionals B3LYP-D3, M05-2X-D3, M06-D3, M06-2X-D3, M08-HX, PW6B95-D3. The best correspondence between the calculation results and experimental data is ensured by the use of the PW6B95-D3 functional.

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9

Newton, Aric G., Jin-Yong Lee, and Kideok D. Kwon. "Na-Montmorillonite Edge Structure and Surface Complexes: An Atomistic Perspective." Minerals 7, no. 5 (2017): 78. http://dx.doi.org/10.3390/min7050078.

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10

Spadini, Lorenzo, Alain Manceau, Paul W. Schindler, and Laurent Charlet. "Structure and Stability of Cd2+ Surface Complexes on Ferric Oxides." Journal of Colloid and Interface Science 168, no. 1 (1994): 73–86. http://dx.doi.org/10.1006/jcis.1994.1395.

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11

Behnke, Craig A., Isolde Le Trong, Jeff W. Godden, et al. "Atomic resolution studies of carbonic anhydrase II." Acta Crystallographica Section D Biological Crystallography 66, no. 5 (2010): 616–27. http://dx.doi.org/10.1107/s0907444910006554.

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Carbonic anhydrase has been well studied structurally and functionally owing to its importance in respiration. A large number of X-ray crystallographic structures of carbonic anhydrase and its inhibitor complexes have been determined, some at atomic resolution. Structure determination of a sulfonamide-containing inhibitor complex has been carried out and the structure was refined at 0.9 Å resolution with anisotropic atomic displacement parameters to anRvalue of 0.141. The structure is similar to those of other carbonic anhydrase complexes, with the inhibitor providing a fourth nonprotein ligand to the active-site zinc. Comparison of this structure with 13 other atomic resolution (higher than 1.25 Å) isomorphous carbonic anhydrase structures provides a view of the structural similarity and variability in a series of crystal structures. At the center of the protein the structures superpose very well. The metal complexes superpose (with only two exceptions) with standard deviations of 0.01 Å in some zinc–protein and zinc–ligand bond lengths. In contrast, regions of structural variability are found on the protein surface, possibly owing to flexibility and disorder in the individual structures, differences in the chemical and crystalline environments or the different approaches used by different investigators to model weak or complicated electron-density maps. These findings suggest that care must be taken in interpreting structural details on protein surfaces on the basis of individual X-ray structures, even if atomic resolution data are available.

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Johansson-Åkhe, Isak, Claudio Mirabello, and Björn Wallner. "InterPep2: global peptide–protein docking using interaction surface templates." Bioinformatics 36, no. 8 (2020): 2458–65. http://dx.doi.org/10.1093/bioinformatics/btaa005.

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Abstract Motivation Interactions between proteins and peptides or peptide-like intrinsically disordered regions are involved in many important biological processes, such as gene expression and cell life-cycle regulation. Experimentally determining the structure of such interactions is time-consuming and difficult because of the inherent flexibility of the peptide ligand. Although several prediction-methods exist, most are limited in performance or availability. Results InterPep2 is a freely available method for predicting the structure of peptide–protein interactions. Improved performance is obtained by using templates from both peptide–protein and regular protein–protein interactions, and by a random forest trained to predict the DockQ-score for a given template using sequence and structural features. When tested on 252 bound peptide–protein complexes from structures deposited after the complexes used in the construction of the training and templates sets of InterPep2, InterPep2-Refined correctly positioned 67 peptides within 4.0 Å LRMSD among top10, similar to another state-of-the-art template-based method which positioned 54 peptides correctly. However, InterPep2 displays a superior ability to evaluate the quality of its own predictions. On a previously established set of 27 non-redundant unbound-to-bound peptide–protein complexes, InterPep2 performs on-par with leading methods. The extended InterPep2-Refined protocol managed to correctly model 15 of these complexes within 4.0 Å LRMSD among top10, without using templates from homologs. In addition, combining the template-based predictions from InterPep2 with ab initio predictions from PIPER-FlexPepDock resulted in 22% more near-native predictions compared to the best single method (22 versus 18). Availability and implementation The program is available from: http://wallnerlab.org/InterPep2. Supplementary information Supplementary data are available at Bioinformatics online.

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Sugawa, Kosuke, Kaichi Ono, Ritsurai Tomii, et al. "Development of Au Nanoparticle Two-Dimensional Assemblies Dispersed with Au Nanoparticle-Nanostar Complexes and Surface-Enhanced Raman Scattering Activity." Nanomaterials 14, no. 9 (2024): 764. http://dx.doi.org/10.3390/nano14090764.

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We recently found that polyvinylpyrrolidone (PVP)-protected metal nanoparticles dispersed in water/butanol mixture spontaneously float to the air/water interface and form two-dimensional assemblies due to classical surface excess theory and Rayleigh–Bénard–Marangoni convection induced by butanol evaporation. In this study, we found that by leveraging this principle, a unique structure is formed where hetero gold nanospheres (AuNPs)/gold nanostars (AuNSs) complexes are dispersed within AuNP two-dimensional assemblies, obtained from a mixture of polyvinylpyrrolidone-protected AuNPs and AuNSs that interact electrostatically with the AuNPs. These structures were believed to form as a result of AuNPs/AuNSs complexes formed in the water/butanol mixture floating to the air/water interface and being incorporated into the growth of AuNP two-dimensional assemblies. These structures were obtained by optimizing the amount of mixed AuNSs, with excessive addition resulting in the formation of random three-dimensional network structures. The AuNP assemblies dispersed with AuNPs/AuNSs complexes exhibited significantly higher Raman (surface-enhanced resonance Raman scattering: SERRS) activity compared to simple AuNP assemblies, while the three-dimensional network structure did not show significant SERRS activity enhancement. These results demonstrate the excellent SERRS activity of AuNP two-dimensional assemblies dispersed with hetero AuNPs/AuNSs complexes.

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14

Ramachandra, Srinidhi, Federico Polo, Fabio Edafe, et al. "Luminescent acetylthiol derivative tripodal osmium(II) and iridium(III) complexes: Spectroscopy in solution and on surfaces." Pure and Applied Chemistry 83, no. 4 (2011): 779–99. http://dx.doi.org/10.1351/pac-con-10-11-07.

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Luminescent Os(II) and Ir(III) complexes containing a tripodal-type structure terminalized with three thiol derivatives are described. The tripod is introduced through derivatization, with a rigid spacer, of a phenanthroline ligand coordinated to the metal ion, and the entire structure possesses axial geometry. The geometry of the complexes combined with the three anchoring sites, the thiol groups, allows the complexes to adopt an almost perpendicular arrangement to the surfaces and the formation of a well-packed monolayer on Au substrates. The photophysical and electrochemical behavior of the complexes is studied in solution and on surfaces. Furthermore, a self-assembled monolayer (SAM) of Os(II) complexes on an ultraflat Au surface is used to fabricate a metal–molecule–metal junction with Au and In Ga eutectic as electrodes. The Os(II) SAM in the tunneling junction exhibits rectification behavior which is opposite in direction to that which we have previously shown for Ru(II) SAMs.

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Varadachari, Chandrika, Tarit Chattopadhyay, and Kunal Ghosh. "The crystallo-chemistry of oxide-humus complexes." Soil Research 38, no. 4 (2000): 789. http://dx.doi.org/10.1071/sr99053.

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Complexation of humic substances with goethite, hematite, gibbsite, and boehmite has been explained from a viewpoint of crystal structure of the minerals. Theoretical analysis of crystal surface structures revealed the following. (i) Residual charge carried by O or OH on surfaces of gibbsite is –1/2; on boehmite it is –3/2 or –1/2; on goethite it is –4/3, –2/3, or –1/3; and on hematite it is –3/2, –1, or –1/2. Cations adsorbed to neutralise these charges can form bridging links with humic acid; higher charges form stronger links. (ii) Surfaces of goethite, hematite, and gibbsite also contain octahedral sites in which one O/OH position is vacant. These may provide centres for the formation of strong coordination bonds. (iii) Such vacant octahedral positions are absent in boehmite. It follows that in gibbsite, cation bridging links would be weak and vacant octahedral sites would be the dominant bonding sites; in goethite and hematite, both cation bridging and surface coordination sites would be present; in boehmite, cation bridging would be the only strong bonding mode. Derivations from crystallochemical analysis are supported by experimental observations. Infrared studies also show strong OH involvement in boehmite complexation in contrast to the weakness of OH involvement in gibbsite complexes.

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Harvey, Sophie R., Justin T. Seffernick, Royston S. Quintyn, et al. "Relative interfacial cleavage energetics of protein complexes revealed by surface collisions." Proceedings of the National Academy of Sciences 116, no. 17 (2019): 8143–48. http://dx.doi.org/10.1073/pnas.1817632116.

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To fulfill their biological functions, proteins must interact with their specific binding partners and often function as large assemblies composed of multiple proteins or proteins plus other biomolecules. Structural characterization of these complexes, including identification of all binding partners, their relative binding affinities, and complex topology, is integral for understanding function. Understanding how proteins assemble and how subunits in a complex interact is a cornerstone of structural biology. Here we report a native mass spectrometry (MS)-based method to characterize subunit interactions in globular protein complexes. We demonstrate that dissociation of protein complexes by surface collisions, at the lower end of the typical surface-induced dissociation (SID) collision energy range, consistently cleaves the weakest protein:protein interfaces, producing products that are reflective of the known structure. We present here combined results for multiple complexes as a training set, two validation cases, and four computational models. We show that SID appearance energies can be predicted from structures via a computationally derived expression containing three terms (number of residues in a given interface, unsatisfied hydrogen bonds, and a rigidity factor).

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Polly, R., B. Schimmelpfennig, M. Flörsheimer, et al. "Quantum chemical study of inner-sphere complexes of trivalent lanthanide and actinide ions on the corundum (110) surface." ract 101, no. 9 (2013): 561–70. http://dx.doi.org/10.1524/ract.2013.2054.

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Summary Sorption plays a major role in the safety assessment of nuclear waste disposal. In the present theoretical study we focused on understanding the interaction of trivalent lanthanides and actinides (La3+, Eu3+ and Cm3+) with the corundum (110) surface. Optimization of the structures were carried out using density functional theory with different basis sets. Additionally, Møller-Plesset perturbation theory of second order was used for single point energy calculations. We studied the structure of different inner-sphere complexes depending on the surface deprotonation and the number of water molecules in the first coordination shell. The most likely structure of the inner-sphere complex (tri- or tetradentate) was predicted. For the calculations we used a cluster model for the surface. By deprotonating the cluster a chemical environment at elevated pH values was mimicked. Our calculations predict the highest stability for a tetradentate inner-sphere surface complexes with five water molecules remaining in the first coordination sphere of the metal ions. The formation of the inner-sphere complexes is favored when a coordination takes place with at most one deprotonated surface aluminol group located beneath the inner-sphere complex. The mutual interaction between sorbing metal ions at the surface is studied as well. The minimal possible distance between two inner-sphere sorbed metal ions at the surface was determined to be 530 pm.

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YAKOVKIN, I. N. "FAVORABLE SILICA MONOLAYER STRUCTURES ON THE Mo(112) SURFACE." Surface Review and Letters 12, no. 03 (2005): 449–56. http://dx.doi.org/10.1142/s0218625x05007281.

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Favored structures of SiO n monolayers on Mo (112) surface have been studied using the total energy minimization technique based on DFT semirelativistic approach. In the [ SiO 4] complexes, which form the c (2 × 2) silica structure on the Mo (112), the bonding of the Si atoms with the surface is accomplished through the oxygen atoms. The structure with a symmetric position of oxygen atoms has been found to be the most favorable. In this structure, two oxygen atoms occupy bridge-on-row sites on the Mo (112) surface, with Si atoms between them, while oxygen atoms in the troughs appear not in expected threefold sites, but adjust their positions along the middle lines of the troughs. Estimated main phonon frequency and density of states for the symmetric [ SiO 4] structure agree well with experimental results.

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Aiassa, Virginia, Claudia Garnero, Ariana Zoppi, and Marcela R. Longhi. "Cyclodextrins and Their Derivatives as Drug Stability Modifiers." Pharmaceuticals 16, no. 8 (2023): 1074. http://dx.doi.org/10.3390/ph16081074.

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Cyclodextrins (CDs) are cyclic oligosaccharides that contain a relatively hydrophobic central cavity and a hydrophilic outer surface. They are widely used to form non-covalent inclusion complexes with many substances. Although such inclusion complexes typically exhibit higher aqueous solubility and chemical stability than pure drugs, it has been shown that CDs can promote the degradation of some drugs. This property of stabilizing certain drugs while destabilizing others can be explained by the type of CD used and the structure of the inclusion complex formed. In addition, the ability to form complexes of CDs can be improved through the addition of suitable auxiliary substances, forming multicomponent complexes. Therefore, it is important to evaluate the effect that binary and multicomponent complexes have on the chemical and physical stability of complexed drugs. The objective of this review is to summarize the studies on the stabilizing and destabilizing effects of complexes with CDs on drugs that exhibit stability problems.

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Liu, Lina, Ruifei Qin, Xiaofeng Fan, et al. "Electrospinning Preparation, Structure, and Properties of Fe3O4/Tb(acac)3phen/Polystyrene Bifunctional Microfibers." Materials 16, no. 12 (2023): 4409. http://dx.doi.org/10.3390/ma16124409.

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Compared to single functional materials, multifunctional materials with magnetism and luminescence are more attractive and promising; Thus, it has become an important subject. In our work, bifunctional Fe3O4/Tb(acac)3phen/polystyrene) microfibers with magnetic and luminescent properties (acac: acetylacetone, phen: 1,10-phenanthroline) were synthesized by simple electrospinning process. The doping of Fe3O4 and Tb(acac)3phen made the fiber diameter larger. The surface of pure polystyrene microfibers and microfibers doped only with Fe3O4 nanoparticles were chapped similar to bark, whereas the surface of the microfibers was smoother after doping with Tb(acac)3phen complexes. The luminescent properties of the composite microfibers were systematically studied in contrast to pure Tb(acac)3phen complexes, including excitation and emission spectra, fluorescence dynamics, and the temperature dependence of intensity. Compared with the pure complexes, the thermal activation energy and thermal stability of composite microfiber was significantly improved, and the luminescence of the unit mass of Tb(acac)3phen complexes in composite microfibers was stronger than that in pure Tb(acac)3phen complexes. The magnetic properties of the composite microfibers were also investigated using hysteresis loops, and an interesting experimental phenomenon was found that the saturation magnetization of the composite microfibers gradually increased with the increase in the doping proportion of terbium complexes.

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Jing, JIN, GONG Yuan-Yuan, WU Han-Qing, LI Lei, and NIU Shu-Yun. "Crystal Structure and Surface Photoelectric Property of Mn(II) Coordination Complexes." Acta Physico-Chimica Sinica 27, no. 07 (2011): 1587–94. http://dx.doi.org/10.3866/pku.whxb20110705.

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22

Ashford, Dennis L., M. Kyle Brennaman, Robert J. Brown, et al. "Varying the Electronic Structure of Surface-Bound Ruthenium(II) Polypyridyl Complexes." Inorganic Chemistry 54, no. 2 (2014): 460–69. http://dx.doi.org/10.1021/ic501682k.

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23

Jin, Jing, Yu Ding, Yuan-Yuan Gong, et al. "Synthesis, structure and surface photo-electric property of Ni(II) complexes." Inorganica Chimica Acta 399 (April 2013): 227–35. http://dx.doi.org/10.1016/j.ica.2013.01.034.

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Marco-Brown, Jose L., María Alcira Trinelli, Eric M. Gaigneaux, Rosa M. Torres Sánchez, and María dos Santos Afonso. "New insights on the structure of the picloram–montmorillonite surface complexes." Journal of Colloid and Interface Science 444 (April 2015): 115–22. http://dx.doi.org/10.1016/j.jcis.2014.12.045.

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25

Olson, Norman H., Thomas J. Smith, Prasanna R. Kolatkar, et al. "Cryoelectron microscopy of complexes of human rhinovirus with a monoclonal FAB and the viral cellular receptor." Proceedings, annual meeting, Electron Microscopy Society of America 50, no. 1 (1992): 524–25. http://dx.doi.org/10.1017/s0424820100123027.

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Cryo-electron microscopy and image analysis techniques make it possible to study structural and functional relationships of macromolecular complexes that currently are not easily examined with crystallographic techniques. We have recorded images of frozen-hydrated human rhinovirus serotype-14 (HRV-14) complexed with a neutralizing, monoclonal, antibody fragment (Fab-17Ia; Fig. 1 A); and HRV-16 complexed with the amino-terminal, two-domain fragment (D1D2) of its cellular receptor (intercellular adhesion molecule-1, ICAM-1; Fig. 1B). Three-dimensional reconstructions (Figs. 2A,B) were calculated to ∽3nm resolution from 35 and 44 images of each complex, respectively. The HRV-14/Fab structure clearly identified the footprint of the Fab on the surface of the virion. The HRV-16/D1D2 reconstruction presents, for the first time, the three-dimensional structure of a complete virus complexed with its cellular receptor.

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Xiao, Zuobing, Juan Deng, Yunwei Niu та ін. "Preparation of sustained-release fragrance based on the cavity structure of β-cyclodextrin and its application in cotton fabric". Textile Research Journal 89, № 17 (2018): 3466–74. http://dx.doi.org/10.1177/0040517518813647.

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The present study reported the formation of fragrance/β-cyclodextrin (β-CD) inclusion complexes aimed to promote thermal stability and controlled release. Then, the fragrance/β-CD inclusion complexes were applied in cotton fabrics through impregnation to obtain aromatic cotton fabrics. The surface morphology and structures of the fragrance/β-CD inclusion complexes were examined via scanning electron microscopy (SEM) and Fourier transform infrared spectroscopy; these analysis results confirmed the formation of inclusion complexes. The stability tests were performed by thermogravimetric analysis and the results confirmed these inclusion complexes had good thermal stability. The surface morphology of the cotton fabrics impregnated by fragrance/β-CD inclusion complexes were tested by SEM. Slow-release experiments of the aromatic cotton fabrics performed by gas chromatography-mass spectrometry and an electronic nose proved that the cotton fabrics impregnated by fragrance/β-CD inclusion complexes had excellent slow-release properties. Moreover, the continuous aroma release time of the cotton fabrics impregnated by fragrance/β-CD inclusion complexes reached up to 80 days.

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Petsalakis, Ioannis D., Giannoula Theodorakopoulos, and Jerry Whitten. "Electronic structure and spectra of (Cu2O)n–H2O complexes." Physical Chemistry Chemical Physics 17, no. 1 (2015): 428–33. http://dx.doi.org/10.1039/c4cp04303k.

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(Cu2O)n clusters form nanobarrels with a square mesh surface structure. Low-lying charge-transfer electronic excited states of (Cu2O)n–H2O are determined.

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28

Dan, Nily, and Dganit Danino. "Structure and kinetics of lipid–nucleic acid complexes." Advances in Colloid and Interface Science 205 (March 2014): 230–39. http://dx.doi.org/10.1016/j.cis.2014.01.013.

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Seoane, Beatriz, and Alessandra Carbone. "Soft disorder modulates the assembly path of protein complexes." PLOS Computational Biology 18, no. 11 (2022): e1010713. http://dx.doi.org/10.1371/journal.pcbi.1010713.

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The relationship between interactions, flexibility and disorder in proteins has been explored from many angles over the years: folding upon binding, flexibility of the core relative to the periphery, entropy changes, etc. In this work, we provide statistical evidence for the involvement of highly mobile and disordered regions in complex assembly. We ordered the entire set of X-ray crystallographic structures in the Protein Data Bank into hierarchies of progressive interactions involving identical or very similar protein chains, yielding 40205 hierarchies of protein complexes with increasing numbers of partners. We then examine them as proxies for the assembly pathways. Using this database, we show that upon oligomerisation, the new interfaces tend to be observed at residues that were characterised as softly disordered (flexible, amorphous or missing residues) in the complexes preceding them in the hierarchy. We also rule out the possibility that this correlation is just a surface effect by restricting the analysis to residues on the surface of the complexes. Interestingly, we find that the location of soft disordered residues in the sequence changes as the number of partners increases. Our results show that there is a general mechanism for protein assembly that involves soft disorder and modulates the way protein complexes are assembled. This work highlights the difficulty of predicting the structure of large protein complexes from sequence and emphasises the importance of linking predictors of soft disorder to the next generation of predictors of complex structure. Finally, we investigate the relationship between the Alphafold2’s confidence metric pLDDT for structure prediction in unbound versus bound structures, and soft disorder. We show a strong correlation between Alphafold2 low confidence residues and the union of all regions of soft disorder observed in the hierarchy. This paves the way for using the pLDDT metric as a proxy for predicting interfaces and assembly paths.

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30

Cao, Weiwei, Junliang Chen, Shuhua Ma, et al. "Structure Characterization and Functional Properties of Flaxseed Protein–Chlorogenic Acid Complex." Foods 12, no. 24 (2023): 4449. http://dx.doi.org/10.3390/foods12244449.

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This study aimed to investigate the effects of the covalent binding of flaxseed protein (FP) and chlorogenic acid (CA) on the structure and functional properties of FP–CA complexes fabricated using the alkali method. The results suggested that the encapsulation efficiency of CA encapsulated by FP ranged from 66.11% to 72.20% and the loading capacity of CA increased with an increasing addition ratio of CA with a dose-dependent relationship, which increased from 2.34% to 10.19%. The particle size, turbidity, zeta potential and PDI of FP and the FP–CA complexes had no significant discrepancy. UV–Vis and fluorescence spectra showed the existence of the interaction between FP and CA. SEM images showed that the surface of the FP–0.35%CA complex had more wrinkles compared to FP. Differential scanning calorimetry analysis indicated the decomposition temperature of FP at 198 °C was higher than that (197 °C) of the FP–0.35%CA complex, implying that the stability of the FP–CA complexes was lower than FP. The functional properties suggested that the FP–CA complex with 1.40% CA had a higher water holding capacity (500.81%), lower oil holding capacity (273.495%) and lower surface hydrophobicity. Moreover, the FP–CA complexes had better antioxidant activities than that of FP. Therefore, this study provides more insights for the potential application of FP–CA covalent complexes in functional food processing.

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31

Geneve, Robert L., Carol C. Baskin, Jerry M. Baskin, K. M. G. Gehan Jayasuriya, and Nalin S. Gama-Arachchige. "Functional morpho-anatomy of water-gap complexes in physically dormant seed." Seed Science Research 28, no. 3 (2018): 186–91. http://dx.doi.org/10.1017/s0960258518000089.

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AbstractPhysical dormancy (PY) occurs in at least 18 angiosperm plant families and is caused by water-impermeable palisade cells in seed (or fruit) coats. Breaking of PY involves disruption or dislodgement of water-gap structures causing the seeds/fruits to become water permeable (non-dormant). The water-gap region is a morphologically distinct area of the seed or fruit coat that forms a water-gap complex. The location, anatomy, morphology and origin of water-gaps can differ between and even within families and genera. Water-gap structures sense environmental conditions that allow seeds with PY to become permeable just prior to the commencement of conditions favourable for germination and plant establishment. There are three basic water-gap morpho-anatomies characterized by the way the water-gap opens: Type-I, Type-II and Type-III. In Type-I water-gaps, specific kinds of cells pull apart to form a surface opening, while in Type-II a portion of the surface structure is pulled away from adjacent cells, opening the water-gap. Type-III is the least common type and has a circular, plug-like structure that is dislodged, whereby water entry occurs. In addition, water-gap complexes are either simple or compound, depending on whether only a single primary water-gap structure is involved in dormancy release or an additional secondary water-gap structure opens, permitting water entry.

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32

Nastasiienko, Nataliia, Borys Palianytsia, Mykola Kartel, Mats Larsson, and Tetiana Kulik. "Thermal Transformation of Caffeic Acid on the Nanoceria Surface Studied by Temperature Programmed Desorption Mass-Spectrometry, Thermogravimetric Analysis and FT–IR Spectroscopy." Colloids and Interfaces 3, no. 1 (2019): 34. http://dx.doi.org/10.3390/colloids3010034.

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The studies of pyrolysis of caffeic acid (CA) and its surface complexes is important for the development of technologies of heterogeneous catalytic pyrolysis of plant- and wood- based renewable biomass components. In this work, the structure and thermal transformations of the surface complexes of CA on the surface of nanoceria were investigated using Fourier transform–infrared (FT–IR) spectroscopy, thermogravimetric analysis (TGA) and temperature-programmed desorption mass spectrometry (TPD MS). It was found that CA on the surface of cerium dioxide forms several types of complexes: bidentate carboxylates, monodentate carboxylates and complexes formed as a result of interaction with phenolic hydroxyl groups. This is due to the ability of nanosized cerium dioxide to generate basic hydroxyl groups that can deprotonate phenolic groups to form phenolates on the surface. The main pyrolysis products were identified. The possible ways of forming 3,4-dihydroxyphenylethylene, acetylene carboxylic acid, pyrocatechol and phenol from surface complexes of CA were suggested. It was established that on the nanoceria surface effectively occur the decarboxylation, decarbonylation, and dehydration reactions of the CA, which are the desirable processes in biomass conversion technologies.

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33

Ogenko, V. M. "Surface Chemistry in Modern Nanotechnologies." Adsorption Science & Technology 14, no. 5 (1996): 295–300. http://dx.doi.org/10.1177/026361749601400504.

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A review of the properties of fine oxide surfaces at the nano level is given based on the author's work. It includes a scheme related to the structure of pyrogenic silica and the changes induced by dehydroxylation as studied by quantum chemical and spectroscopic methods. The application of non-linear optical methods has appeared to be useful for the investigation of disperse solid structures. Quantitative measurements of intermolecular interaction have been obtained by light scattering. Alteration of the surface activity due to gas-phase electron–donor molecule action on chemisorbed complexes or functional groups on the surface is considered. It is also shown how the physicochemical properties of a solid surface can be changed as a result of chemical modification. The investigations discussed could lead in practice to the creation of new lightweight ceramic materials, adsorbents, catalyst supports, hollow-body microspherical fillers and medicinal preparations. Some of these are useful for nano electronics and instrument design as well as for the solution of some meteorological problems.

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34

Waleh, Ahmad, Nan Ho, Lek Chantranupong, and Gilda H. Loew. "Electronic structure of nitrosyl ferrous heme complexes." Journal of the American Chemical Society 111, no. 8 (1989): 2767–72. http://dx.doi.org/10.1021/ja00190a004.

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35

Manceau, Alain, Kathryn L. Nagy, Lorenzo Spadini, and K. Vala Ragnarsdottir. "Influence of Anionic Layer Structure of Fe-Oxyhydroxides on the Structure of Cd Surface Complexes." Journal of Colloid and Interface Science 228, no. 2 (2000): 306–16. http://dx.doi.org/10.1006/jcis.2000.6922.

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36

F. Alshdoukhi, Ibtehaj, Alyaa S.M.O. Al-barwari, Nazk Mohammed Aziz, et al. "Pd(II), Pt(II), Zn(II), Cd(II) and Hg(II) complexes of the newly prepared 1,2-benzo- isothiazol-3(2H)-dithiocarbamate (BIT-DTC) ligand." Bulletin of the Chemical Society of Ethiopia 38, no. 4 (2024): 889–99. http://dx.doi.org/10.4314/bcse.v38i4.6.

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In the current work, we report the synthesis and characterization of new dithiocarbamate complexes derived from 1,2-benzoisothiazol-3(2H)-one (BitH). The ligand was synthesized by treating the BitH with carbon disulfide in a basic solution. The NMR technique confirmed the preparation of the ligand. The treatment of the Bit-dtcNa with the metal salt’s solution afforded the complexes of the type [M(Bit-dtc)2]; M = Zn, Cd, Hg, Pd, and Pt. The complexes were characterized via FT-IR and 1H-NMR techniques. The Zn, Pd, and Pt complexes were investigated theoretically, and some of their quantum properties were determined. These parameters include HOMO-LUMO energies, electron affinity, ionization potential, chemical hardness, dipole moment and the total energies of the optimized structures. Moreover, the surface structure of Zn and Hg complexes were investigated by SEM and XRD techniques. The SEM pattern showed a cubic structures for the Zn complex while the Hg complex appeared as a nano rods structure. The calculated average particle sizes for Zn and Hg complexes were 23 and 26 nm, respectively. KEY WORDS: Dithiocarbamate, 1,2-Benzoisothiazol-3(2H)-one, DFT, SEM, XRD Bull. Chem. Soc. Ethiop. 2024, 38(3), 889-899. DOI: https://dx.doi.org/10.4314/bcse.v38i4.6

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37

Shores, E. W., T. Nakayama, D. L. Wiest, Y. Takahama, S. Sharrow, and A. Singer. "Structurally distinct T cell receptor complexes on developmentally distinct T cell populations in severe combined immunodeficiency mice expressing a TCR beta transgene." Journal of Immunology 150, no. 4 (1993): 1263–75. http://dx.doi.org/10.4049/jimmunol.150.4.1263.

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Abstract T cell differentiation and TCR expression were assessed in severe combined immunodeficiency (SCID) mice possessing an already rearranged TCRV beta 8 transgene. Unlike nontransgenic SCID mice, TCRV beta 8-transgenic SCID mice contained a broad spectrum of T cell populations, including both immature thymocytes and mature T cells. In TCRV beta 8-transgenic SCID mice, immature CD4-CD8- and CD4+CD8+ thymocytes expressed surface TCR complexes structurally distinct from those expressed by mature single-positive T cells. Immature CD4+CD8+ thymocytes expressed surface TCR beta chains without a clonotypic TCR partner chain and largely without associated CD3 components. In contrast, mature single-positive T cells expressed fully assembled surface TCR complexes containing disulfide-linked heterodimers consisting of transgenic TCR beta chains and endogenous TCR alpha chains. The surface TCR complexes on mature T cells were associated with CD3 components and were competent to transduce TCR-mediated proliferative signals. Thus, T cells at different stages of development in TCRV beta 8-transgenic SCID mice express structurally distinct surface TCR complexes, demonstrating that the developmental stage achieved by T cells in these mice is related to the structure of the surface TCR complexes they express. Indeed, the present results indicate that successful differentiation into single-positive T cells requires surface expression of fully assembled TCR complexes.

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38

Yong, R. N., A. M. O. Mohamed, and B. W. Wang. "Influence of amorphous silica and iron hydroxide on interparticle action and soil surface properties." Canadian Geotechnical Journal 29, no. 5 (1992): 803–18. http://dx.doi.org/10.1139/t92-088.

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The study of the physicochemical properties of pure amorphous materials (complexes) consisting of Fe2O3 and SiO2 in various proportions indicates that the amorphous complexes will exhibit different properties and characteristics depending on the proportions of Fe2O3 and SiO2. Addition of the amorphous complexes with illitic clay studied shows that the properties of the clay admixture will also vary according to the properties of the amorphous complex, albeit to a lesser degree. The properties and behaviour observed for the amorphous complexes and the clay admixtures can be linked directly to the large specific surface area and high surface charge of the amorphous complexes. The contribution of amorphous complexes to the clay – amorphous complex mixtures (clay admixtures) is twofold: firstly, by the amount of amorphous complex in the clay admixture, and secondly by the composition of the amorphous complex used. The contribution from the amorphous complex is in two forms: water-holding capacity and bonding action. The presence of pH-dependent surface charges associated with the amorphous complexes makes the physicochemical properties and behaviour of the clay admixtures (e.g., liquid limits and zeta potential) sensitive to the pH environment. Coating of amorphous colloids onto clay particle surfaces, shown by scanning electron microscopy, appears to, be enhanced by a decrease in pH of the system, indicating that the enhancement is likely due to the increased electrostatic attraction resulting from the increased amounts of positive charges on the amorphous colloids. Key words : amorphous materials, mass ratio, zeta potential, Bingham yield stress, clay admixtures, hydrogen bonding, specific surface area, cation exchange capacity, anion exchange capacity, fabric and soil structure.

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39

Lee, G. M., B. Johnstone, K. Jacobson, and B. Caterson. "The dynamic structure of the pericellular matrix on living cells." Journal of Cell Biology 123, no. 6 (1993): 1899–907. http://dx.doi.org/10.1083/jcb.123.6.1899.

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Although up to several microns thick, the pericellular matrix is an elusive structure due to its invisibility with phase contrast or DIC microscopy. This matrix, which is readily visualized by the exclusion of large particles such as fixed red blood cells is important in embryonic development and in maintenance of cartilage. While it is known that the pericellular matrix which surrounds chondrocytes and a variety of other cells consists primarily of proteoglycans and hyaluronan with the latter binding to cell surface receptors, the macromolecular organization is still speculative. The macromolecular organization previously could not be determined because of the collapse of the cell coat with conventional fixation and dehydration techniques. Until now, there has been no way to study the dynamic arrangement of hyaluronan with its aggregated proteoglycans on living cells. In this study, the arrangement and mobility of hyaluronan-aggrecan complexes were directly observed in the pericellular matrix of living cells isolated from bovine articular cartilage. The complexes were labeled with 30- to 40-nm colloidal gold conjugated to 5-D-4, an antibody to keratan sulfate, and visualized with video-enhanced light microscopy. From our observations of the motion of pericellular matrix macromolecules, we report that the chondrocyte pericellular matrix is a dynamic structure consisting of individual tethered molecular complexes which project outward from the cell surface. These complexes undergo restricted rotation or wobbling. When the cells were cultured with ascorbic acid, which promotes production of matrix components, the size of the cell coat and the position of the gold probes relative to the plasma membrane were not changed. However, the rapidity and extent of the tethered motion were reduced. Treatment with Streptomyces hyaluronidase removed the molecules that displayed the tethered motion. Addition of hyaluronan and aggrecan to hyaluronidase-treated cells yielded the same labeling pattern and tethered motion observed with native cell coats. To determine if aggrecan was responsible for the extended configuration of the complexes, only hyaluronan was added to the hyaluronidase-treated cells. The position and mobility of the hyaluronan was detected using biotinylated hyaluronan binding region (b-HABR) and gold streptavidin. The gold-labeled b-HABR was found only near the cell surface. Based on these observations, the hyaluronan-aggrecan complexes composing the cell coat are proposed to be extended in a brush-like configuration in an analogous manner to that previously described for high density, grafted polymers in good solvents.

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40

Rudd, T., J. T. Gallagher, D. Ron, R. J. Nichols, and D. G. Fernig. "A gravimetric analysis of protein–oligosaccharide interactions." Biochemical Society Transactions 31, no. 2 (2003): 349–51. http://dx.doi.org/10.1042/bst0310349.

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Interactions between an immobilized, heparin-derived octasaccharide and growth factors have been observed using a quartz crystal microbalance-dissipation (QCM-D). This device can measure the amount of growth factors binding to the octasaccharide surface and also the change of dissipation of the surface. Dissipation is a measure of how the adhered material ‘damps’ the surface vibrations. The octasaccharides were anchored through their reducing ends by the intermediary of the alkanethiol molecule, which covalently binds to the crystal surface through the thiol group. As expected, heparin sulphate binding growth factors bound to the octasaccharide, but the change in mass of growth factor bound per unit change in dissipation is different for the different growth factors. Suggesting that the structures of the various growth factor–octasaccharide complexes are different, therefore, indicates that the change in dissipation can give insights into the structure, orientation and packing of the oligosaccharide-growth factor complexes.

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41

Planat, Michel, Raymond Aschheim, Marcelo M. Amaral, Fang Fang, and Klee Irwin. "Quantum Information in the Protein Codes, 3-Manifolds and the Kummer Surface." Symmetry 13, no. 7 (2021): 1146. http://dx.doi.org/10.3390/sym13071146.

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Every protein consists of a linear sequence over an alphabet of 20 letters/amino acids. The sequence unfolds in the 3-dimensional space through secondary (local foldings), tertiary (bonds) and quaternary (disjoint multiple) structures. The mere existence of the genetic code for the 20 letters of the linear chain could be predicted with the (informationally complete) irreducible characters of the finite group Gn:=Zn⋊2O (with n=5 or 7 and 2O the binary octahedral group) in our previous two papers. It turns out that some quaternary structures of protein complexes display n-fold symmetries. We propose an approach of secondary structures based on free group theory. Our results are compared to other approaches of predicting secondary structures of proteins in terms of α helices, β sheets and coils, or more refined techniques. It is shown that the secondary structure of proteins shows similarities to the structure of some hyperbolic 3-manifolds. The hyperbolic 3-manifold of smallest volume—Gieseking manifold—some other 3 manifolds and the oriented hypercartographic group are singled out as tentative models of such secondary structures. For the quaternary structure, there are links to the Kummer surface.

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42

Gao, Xue, Jian Song, Li Xian Sun, Yong Heng Xing, Feng Ying Bai, and Zhan Shi. "A family of uranium–carboxylic acid hybrid materials: synthesis, structure and mixed-dye selective adsorption." New Journal of Chemistry 40, no. 7 (2016): 6077–85. http://dx.doi.org/10.1039/c6nj00109b.

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43

Melvin, Marissa K., Brian W. Skelton, Paul K. Eggers, and Colin L. Raston. "Synthesis, crystallization and Hirshfeld surface analysis of transition metal carboxylate pentapyridines." CrystEngComm 24, no. 1 (2022): 57–69. http://dx.doi.org/10.1039/d1ce01248g.

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Single X-ray diffraction studies and Hirshfeld surface analysis of three transition metal coordination complexes of Py5Me2COOH reveals the ligand's diverse coordination utility and the structure directing effect of the carboxylate moiety.

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44

Pourayoubi, Mehrdad, Anahid Saneei, Michal Dušek, Soobiyeh Alemi Rostami, Aurelien Crochet, and Monika Kučeraková. "Two new organotin(IV)-phosphoryl complexes: crystal structure and Hirshfeld surface analysis." Journal of the Iranian Chemical Society 12, no. 12 (2015): 2093–103. http://dx.doi.org/10.1007/s13738-015-0686-9.

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45

Shi, Zhong-Feng, Jia-Ming Li, Lei Li, and Shu-Yun Niu. "Synthesis, Structure, and Surface Photoelectric Properties of Two Novel Cobalt(II) Complexes." Zeitschrift für anorganische und allgemeine Chemie 637, no. 14-15 (2011): 2282–87. http://dx.doi.org/10.1002/zaac.201100229.

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46

Schläpfer, C. W., N. N. Vlasova, S. K. Poznyak, and A. I. Kokorin. "The Structure and Properties of TiO2–Cu(II)–EDTA Ternary Surface Complexes." Journal of Colloid and Interface Science 239, no. 1 (2001): 200–208. http://dx.doi.org/10.1006/jcis.2001.7574.

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47

Gärdlund, Linda, Lars Wågberg, and Magnus Norgren. "New insights into the structure of polyelectrolyte complexes." Journal of Colloid and Interface Science 312, no. 2 (2007): 237–46. http://dx.doi.org/10.1016/j.jcis.2007.03.075.

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48

Kielb, Patrycja, Marius Horch, Pierre Wrzolek, et al. "Hydrogen evolution by cobalt hangman porphyrins under operating conditions studied by vibrational spectro-electrochemistry." Catalysis Science & Technology 8, no. 7 (2018): 1849–57. http://dx.doi.org/10.1039/c7cy02253k.

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49

Montazerozohori, M., A. Masoudiasl, Th Doert, and H. Seykens. "Structural and computational study of some new nano-structured Hg(ii) compounds: a combined X-ray, Hirshfeld surface and NBO analyses." RSC Advances 6, no. 26 (2016): 21396–412. http://dx.doi.org/10.1039/c5ra22899a.

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50

Watheq, Baraa, Emad Yousif, Mohammed H. Al-Mashhadani, et al. "A Surface Morphological Study, Poly(Vinyl Chloride) Photo-Stabilizers Utilizing Ibuprofen Tin Complexes against Ultraviolet Radiation." Surfaces 3, no. 4 (2020): 579–93. http://dx.doi.org/10.3390/surfaces3040039.

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In this work, three Ibuprofen tin complexes were synthesized and characterized by Fourier Transform Infrared spectroscopy (FTIR), 1H and 119Sn-Nuclear Magnetic Resonance (NMR), and Energy Dispersive X-ray (EDX) spectroscopies to identify the structures. The complexes were mixed separately with poly(vinyl chloride) (PVC) to improve its photo-stability properties. Their activity was demonstrated by several approaches of the FTIR to exhibit the formation of new groups within the polymer structure due to the exposure to UV light. Moreover, the polymer’s weight loss during irradiation and the average molecular weight estimation using its viscosity before and after irradiation were investigated. Furthermore, different techniques were used to study the surface morphology of the PVC before and after irradiation. Field-emission scanning electron microscopy (FESEM) and optical microscope demonstrated that applying Ibuprofen tin complexes keeps the surface of PVC smoother, with fewer cracks and spots after irradiation comparing to the blank PVC. Finally, It seems possible that such synthesized Ibuprofen tin complexes can work as excellent photo-stabilizers of PVC. In particular, complex 1 showed the best results among other stabilizers due to the large conjugation system of the stabilizer.

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