Home About us Contact
|
Home About us Contact | ||
|
|
||
Ionic Bonds (ionic + bond)
Selected AbstractsExploring the binding site of the human muscarinic M3 receptor: Homology modeling and docking studyINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 8 2007Liliana Ostopovici Abstract The human muscarinic M3 receptor (hM3) and its interactions with selective agonists and antagonists were investigated by means of combined homology and docking approach. Also, two pharmacophoric models for the hM3 agonist and antagonist binding sites were proposed. The three-dimensional (3D) structure of hM3 receptor was modeled based on the high-resolution X-ray structure of bovine rhodopsin from the Protein Data Bank (PDB). To validate the reliability of the model obtained, the main chain torsion angles phi (,) and psi (,) were examined in a Ramachandran plot, and all omega angles were measured for peptidic bond planarity. The characteristics of the active site, the position, and the orientation of ligands in situ, as well as the binding modes of the representative agonists and antagonists, were analyzed by applying a molecular docking technique using the AutoDock 3.0.5 program. Specific interactions responsible for recognition of the hM3 receptor, like ionic bond formed between protonated amine of the ligands and the Asp3.6 side chain were identified. Structure,reactivity relationships have been explained by analyzing the 3D structure of the hM3 model and the ligand conformations resulted from molecular docking simulation. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Surface-enhanced Raman and steady fluorescence study of interaction between antitumoral drug 9-aminoacridine and trypsin-like protease related to metastasis processes, guanidinobenzoataseBIOPOLYMERS, Issue 2 2001Adrian Murza Abstract Fluorescence spectroscopy and surface-enhanced Raman spectroscopy (SERS) were applied to study the interaction of the antitumoral drug 9-aminoacridine (9AA) with a trypsin-like protease guanidinobenzoatase (GB) extracted from a mouse Erlich tumor. As a consequence of this interaction, a strong 9AA exciplex emission was detected in the emission fluorescence spectra at certain drug and enzyme concentrations. A SERS study was accomplished on silver colloids at several excitation wavelengths in order to obtain more information about the interaction mechanism. The results derived from Raman spectroscopy indicated that 9AA in the amino monomeric form may interact with the enzyme by means of two different bonds: an ionic bond with a negatively charged amino acid and a ring stacking interaction with an aromatic residue placed in the catalytic site of GB. This interaction mechanism was responsible for a strong exciplex emission detected at a longer wavelength than the expected value of the normal fluorescence emission. Moreover, the GB concentration dependence of the interaction suggested that the drug was sensitive to the quaternary structure of the enzyme. © 2001 John Wiley & Sons, Inc. Biopolymers (Biospectroscopy) 62: 85,94, 2001 [source] Polyamines interact with DNA as molecular aggregatesFEBS JOURNAL, Issue 17 2002Luciano D'Agostino New compounds, named nuclear aggregates of polyamines, having a molecular mass of 8000, 4800 and <,1000 Da, were found in the nuclear extracts of several replicating cells. Their molecular structure is based on the formation of ionic bonds between polyamine ammonium and phosphate groups. The production of the 4800 Da compound, resulting from the aggregation of five or more <,1000 Da units, was increased in Caco-2 cells treated with the mitogen gastrin. Dissolving single polyamines in phosphate buffer resulted in the in vitro aggregation of polyamines with the formation of compounds with molecular masses identical to those of natural aggregates. After the interaction of the 4800 Da molecular aggregate with the genomic DNA at 37 °C, both the absorbance of DNA in phosphate buffer and the DNA mobility in agarose gel increased greatly. Furthermore, these compounds were able to protect the genomic DNA from digestion by DNase I, a phosphodiesterasic endonuclease. Our data indicate that the nuclear aggregate of polyamines interacts with DNA phosphate groups and influence, more efficaciously than single polyamines, both the conformation and the protection of the DNA. [source] Optimizing the formula of rare earth-bearing materials: A computational chemistry investigationINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 3 2007Marjorie Bertolus Abstract We present a computational investigation into the nature of bonds formed by rare earth elements (REE) in materials. This study focuses on the incorporation of neodymium in minerals called apatites, which are derived from fluorapatite: Ca10(PO4)6F2. These minerals, which allow many substitutions on all three Ca, P, and F sites, are considered as potential host phases for radioactive elements separated from nuclear waste. Nd and trivalent actinides have very similar physical and chemical properties, and Nd is not radioactive and much more easily handled. It is therefore very often used as a surrogate for actinides with oxidation degree three in experimental studies. Several formulas can be considered to substitute Nd3+ to Ca2+ and maintain charge balance of the apatite. Existing experimental and theoretical studies, however, mostly concern the Ca9Nd(PO4)5SiO4F2 formula, where the Nd incorporation is compensated by the replacement of one PO by a SiO group. Moreover, only the cation position has been studied, whereas the silicate position and its influence on stability are unknown. We present a more general investigation of possible charge compensations on the one hand, and of the various resulting configurations on the other. All possible configurations of the two formulas Ca9Nd(PO4)5 SiO4F2 and Ca8NdNa(PO4)6F2 have been considered. Calculations have been performed within the framework of density functional theory (DFT). A computation scheme that permits good accuracy in these systems within reasonable computation times is determined. The results obtained for cohesion energies, geometries, and electronic densities are discussed. As for the formulation, it is shown that the Ca8NdNa(PO4)6F2 formula is less stable than the fluorapatite, while Ca9Nd(PO4)5 SiO4F2 is more stable. For the structures, it is found that Nd substitutes preferably in the second cationic site. Moreover, the most stable structures exhibit the shortest Na,Nd or Nd,Si distances. Local charge balance therefore seems favorable. Then, it is shown that Nd forms covalent bonds both in apatite and in britholite, while Na forms ionic bonds. Finally, a first correlation between the material stability and the covalent character of the bonds formed is established. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2007 [source] Self-assembly and recrystallization of bacterial S-layer proteins at silicon supports imaged in real time by atomic force microscopyJOURNAL OF MICROSCOPY, Issue 3 2003E. S. Györvary Summary The self-assembly of bacterial surface-layer (S-layer) proteins (SbpA of Bacillus sphaericus CCM 2177) at silicon supports (hydrophobic, non-plasma-treated and hydrophilic, O2 plasma-treated silicon supports) was imaged in real time by atomic force microscopy (AFM). A closed mosaic layer consisting of small crystals (less than 200 nm in diameter) was formed at a hydrophobic silicon support, whereas a coherent crystalline lattice consisting of large domains (2,10 µm in size) was generated at O2 plasma-treated, hydrophilic silicon wafers. The structure of the formed layers was a monolayer (9 nm in height) at the hydrophobic silicon and a bilayer (15 nm in height) at the hydrophilic silicon. In situ AFM measurements confirmed the importance of ionic bonds in the formation of crystalline SbpA layers at silicon supports. Rupture of the protein subunits with a metal chelator from the crystalline lattice of SbpA was visualized in situ by AFM. The stability of solid-supported SbpA layers could be enhanced by cross-linking the S-layers with amino,amino or amino,carboxyl group directed cross-linkers. [source] A strategy for synthesis of ion-bonded amphiphilic miktoarm star copolymers via supramolecular macro-RAFT agentJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 17 2008Dairen Lu Abstract Amphiphilic supramolecular miktoarm star copolymers linked by ionic bonds with controlled molecular weight and low polydispersity have been successfully synthesized via reversible addition-fragmentation chain transfer (RAFT) polymerization using an ion-bonded macromolecular RAFT agent (macro-RAFT agent). Firstly, a new tetrafunctional initiator, dimethyl 4,6-bis(bromomethyl)-isophthalate, was synthesized and used as an initiator for atom transfer radical polymerization (ATRP) of styrene to form polystyrene (PSt) containing two ester groups at the middle of polymer chain. Then, the ester groups were converted into tertiary amino groups and the ion-bonded supramolecular macro-RAFT agent was obtained through the interaction between the tertiary amino group and 2-dodecylsulfanylthiocarbonylsulfanyl-2-methyl propionic acid (DMP). Finally, ion-bonded amphiphilic miktoarm star copolymer, (PSt)2 -poly(N -isopropyl-acrylamide)2, was prepared by RAFT polymerization of N -isopropylacrylamide (NIPAM) in the presence of the supramolecular macro-RAFT agent. The polymerization kinetics was investigated and the molecular weight and the architecture of the resulting star polymers were characterized by means of 1H-NMR, FTIR, and GPC techniques. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 5805,5815, 2008 [source] Nonclassical forces: Seemingly insignificant but a powerful tool to control macromolecular structuresJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 14 2008Michiya Fujiki Abstract Strong chemical forces such as covalent and ionic bonds are responsible for building discrete molecules, nature dwells on noncovalent forces weaker by three orders in magnitude, like the hydrophobic effect, hydrogen bonding, and van der Waals forces. Despite being weak, they possess the potential to drive spontaneous folding or unfolding of proteins and nucleic acids and the recognition between complimentary molecular surfaces. The power of these forces lies in the cooperativity with which they act, thereby generating a cumulative effect of many bonding interactions occurring together. Many ongoing research aims to translate the potential of these forces to the synthetic world to create desired structures with specific chemical functions. Achieving this offers unlimited opportunities for designing and synthesizing the most complex structures with specific applications. This highlight aims to reflect the critical role these noncovalent forces play in controlling macromolecular structures, which hold immense untapped potential for applications defying conventions, and briefly touches on the concept of homochirality in nature based on chiral and weak noncovalent interactions in synthetic nonpolar Si-catenated polymers. It sheds some light on the discovery and characterization of Si/F-C interactions in fluoroalkylated polysilanes in chemosensing of fluoride ions and nitroaromatics with a great sensitivity and selectivity. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 4637,4650, 2008 [source] Preparation of Stable Colloidal Crystals and Macroporous Materials Using Diazoresin as a Thermosetting AgentMACROMOLECULAR RAPID COMMUNICATIONS, Issue 4 2004Hailin Cong Abstract Summary: Two kinds of stable colloidal crystals have been prepared from polymeric or SiO2 colloids in the presence of diazoresin (DR) as a thermosetting agent combining thermal treatment. Following the decomposition of N groups of DR under heating, the ionic bonds between the DR molecules and colloids change to covalent bonds and the colloidal crystals become very stable toward ultrasonic washing. The colloids were then removed by tetrahydrofuran (THF) in the case of organics or by hydrofluoric acid (HF) for the inorganics to leave the macroporous DR materials. Reactions between the DR molecules and the colloids during thermal treatment. [source] Charge-Shift Bonding,A Class of Electron-Pair Bonds That Emerges from Valence Bond Theory and Is Supported by the Electron Localization Function ApproachCHEMISTRY - A EUROPEAN JOURNAL, Issue 21 2005Sason Shaik Prof. Abstract This paper deals with a central paradigm of chemistry, the electron-pair bond. Valence bond (VB) theory and electron-localization function (ELF) calculations of 21 single bonds demonstrate that along the two classical bond families of covalent and ionic bonds, there exists a class of charge-shift bonds (CS bonds) in which the fluctuation of the electron pair density plays a dominant role. In VB theory, CS bonding manifests by way of a large covalent-ionic resonance energy, RECS, and in ELF by a depleted basin population with large variances (fluctuations). CS bonding is shown to be a fundamental mechanism that is necessary to satisfy the equilibrium condition, namely the virial ratio of the kinetic and potential energy contributions to the bond energy. The paper defines the atomic propensity and territory for CS bonding: Atoms (fragments) that are prone to CS bonding are compact electronegative and/or lone-pair-rich species. As such, the territory of CS bonding transcends considerations of static charge distribution, and involves: a) homopolar bonds of heteroatoms with zero static ionicity, b) heteropolar , and , bonds of the electronegative and/or electron-pair-rich elements among themselves and to other atoms (e.g., the higher metalloids, Si, Ge, Sn, etc), c) all hypercoordinate molecules. Several experimental manifestations of charge-shift bonding are discussed, such as depleted bonding density, the rarity of ionic chemistry of silicon in condensed phases, and the high barriers of halogen-transfer reactions as compared to hydrogen-transfers. [source] | |||||||||||||