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Secondary Interactions (secondary + interaction)
Selected AbstractsChemical Approach for the Study of the ,Kissing Complex' of Moloney murine leukaemia VirusHELVETICA CHIMICA ACTA, Issue 7 2008Sébastien Porcher Abstract The replication of Moloney murine leukaemia virus relies on the formation of a stable homodimeric ,kissing complex' of a GACG tetraloop interacting through only two C,G base pairs flanked of 5,-adjacent unpaired adenosines A9. Previous NMR investigations of a model stem loop 1 has not permitted to reveal the origin of this interaction. Therefore, with the aim of deeper comprehension of the phenomena, the model sequence 10 was prepared where position 9 has been substituted for a nucleoside offering a wider , -stacking. In this context, the wyosine phosphoramidite building block 2 was prepared and incorporated by adapting the conditions of the automated synthesis and developing original templated enzymatic ligation. However, no ,kissing interaction' has been observed for this model sequence 10 due to steric hindrance as confirmed by computational simulation. Consequently, several other model sequences, 18, 23,26, containing modified nucleosides were prepared. Finally, the importance of the cross-loop H-bond between G8 and G11 nucleobases was revealed by preparing a 18mer RNA hairpin 27, where the guanosine G8 has been substituted for inosine. The latter, which does not possess a C3 amino function compared to guanosine, is unable to form any ,kissing complex' demonstrating the importance of this secondary interaction in the formation of the complex. [source] An NH3+,phenyl interaction in l -phenylalanyl- l -valineACTA CRYSTALLOGRAPHICA SECTION C, Issue 12 2000Carl Henrik Görbitz One of the amino H atoms of l -phenylalanyl- l -valine, C14H20N2O3, participates in a rare secondary interaction in being accepted by the aromatic ring of the phenylalanine side chain. The phenyl group is also a donor in a weak hydrogen bond to the peptide carbonyl group. [source] Electronic and Vibrational Properties of Fluorenone in the Channels of Zeolite LCHEMISTRY - A EUROPEAN JOURNAL, Issue 10 2004André Devaux Dr. Abstract Fluorenone (C13H8O) was inserted into the channels of zeolite L by using gas-phase adsorption. The size, structure, and stability of fluorenone are well suited for studying host,guest interactions. The Fourier transform IR, Raman, luminescence, and excitation spectra, in addition to thermal analysis data, of fluorenone in solution and fluorenone/zeolite L are reported. Normal coordinate analysis of fluorenone was performed, based on which IR and Raman bands were assigned, and an experimental force field was determined. The vibrational spectra can be used for nondestructive quantitative analysis by comparing a characteristic dye band with a zeolite band that has been chosen as the internal standard. Molecular orbital calculations were performed to gain a better understanding of the electronic structure of the system and to support the interpretation of the electronic absorption and luminescence spectra. Fluorenone shows unusual luminescence behavior in that it emits from two states. The relative intensity of these two bands depends strongly on the environment and changes unexpectedly in response to temperature. In fluorenone/zeolite L, the intensity of the 300 nm band (lifetime 9 ,s) increases with decreasing temperature, while the opposite is true for the 400 nm band (lifetime 115 ,s). A model of the host,guest interaction is derived from the experimental results and calculations: the dye molecule sits close to the channel walls with the carbonyl group pointing to an Al3+ site of the zeolite framework. A secondary interaction was observed between the fluorenone's aromatic ring and the zeolite's charge-compensating cations. [source] Synthesis and Binding Properties of Dendritic Oxybathophenanthroline Ligands towards Copper(II)EUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 22 2005Holger Stephan Abstract Dendritic oxybathophenanthroline ligands (generation 0 to 3) have been synthesized by treatment of 4,7-bis(4,-hydroxyphenyl)-1,10-phenanthroline with the corresponding Fréchet-type dendrons carrying a benzylic bromide function at the focal point. The complexation of copper(II) has been studied by liquid,liquid extraction using the radioisotope 64Cu and time-resolved laser-induced fluorescence spectroscopy (TRLFS) in organic media indicating the formation of 1:3 complexes (Cu:dendritic ligand). Electronic and EPR spectroscopy were used to characterize the copper(II) chromophore, which is shown to have the expected distorted square-planar geometry with two phenanthroline donors coordinated to the copper(II) center. The third dendritic ligand therefore is proposed to be bound by secondary interactions. The stability constants of the 1:3 complexes were found to be in the order of log K , 16 in CHCl3. On the other hand, increasing generation of the dendritic Fréchet-type branches leads to enhanced shielding of the copper ion from the environment. Additional information about this behaviour was obtained by the fluorescence lifetimes, which are much less influenced upon addition of copper(II) salt to solutions of the higher generation ligands. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [source] Structural disorder in amyloid fibrils: its implication in dynamic interactions of proteinsFEBS JOURNAL, Issue 19 2009P. Tompa Proteins are occasionally converted from their normal soluble state to highly ordered fibrillar aggregates (amyloids), which give rise to pathological conditions that range from neurodegenerative disorders to systemic amyloidoses. Recent methodological advances in solid-state NMR and EPR spectroscopy have enabled determination of the 3D structure of several amyloids at residue-level resolution. The general picture that emerges is that amyloids constitute parallel , sheets, in which individual polypeptide chains run roughly perpendicular to the major axis of the fibril and are stacked in-register. Thus, the unifying theme of amyloid formation is the structural transition from an initial globular or intrinsically disordered state to a highly ordered regular form. In this minireview, we show that this description is somewhat oversimplified, because part of the polypeptide chain in the amyloid remains intrinsically disordered and does not become part of the ordered core. As demonstrated through examples such as the amyloids of ,-synuclein and A, peptide and the yeast prions HET-s and Ure2p, these disordered segments are depleted in amino acids NQFYV and are enriched in DEKP. They are also significantly more charged and have a higher predicted disordered value than segments in the cross-, core. We suggest that structural disorder in amyloid is a special case of ,fuzziness', i.e. disorder in the bound state that may serve different functions, such as the accommodation of destabilizing residues and the mediation of secondary interactions between protofibrils. [source] Investigations on regio- and stereoselectivities in cycloadditions involving ,- (3-pyridyl)- N -phenylnitrone: Development of an efficient route to novel nicotine analogsJOURNAL OF HETEROCYCLIC CHEMISTRY, Issue 6 2005Gurpinder Singh Thermal reactions of hitherto ,-(3-pyridyl)- N -phenylnitrone (1) with mono-substituted electron-rich and electron-neutral dipolarophiles are regio-, and stereo-selective (exo -selective), controlled by LUMO - dipole - HOMO- dipolarophile interaction, and furnish syn -5-substituted-3-(3-pyridyl)-isoxazolidines (5) in high yields. With electron deficient dipolarophiles such as acrylonitrile there is observed a loss of regioselectivity as well as stereoselectivity and the regioselectivity is reversed in reactions with methyl vinyl ketone and methyl acrylate, due to intervention of HOMO-dipole - LUMO-dipolarophile interaction, affording 4-substi-tuted-3-(3-pyridyl)-isoxazolidines (7) as major products. Reactions of nitrone (1) with disubstituted dipolarophiles such as methyl methacrylate and ethyl coronate furnish methyl syn -5-methy-3-pyridyl-1-phenyl-isoxazolidine-5-carboxylate (8) and ethyl anti -5-methy-3-pyridyl-1-phenyl-isoxazolidine-4-carboxylate (10), respectively, in high yields. Reaction with N -Phenylmaleimide affords novel isoxazolidino-pyrro-lidinediones bearing a 3-pyridyl moiety (11, 12). A mechanistic rationalization of the obtained results in terms of electronic, steric and secondary interactions is proffered. [source] Supramolecular polymers: from scientific curiosity to technological realityMACROMOLECULAR SYMPOSIA, Issue 1 2003A.W. Bosnian Abstract Supramolecular polymers[1] are introduced as a new approach to come to materials in which the repeating units are not connected by covalent bonds but by specific secondary interactions. Self-complementary quadruple hydrogen bonded structures with high association constants are presented as easy to synthesize fragments in supramolecular polymers. Some of the many possibilities of equilibrium polymers are discussed, while it is shown that these supramolecular polymers can obtain materials properties normally only obtained with macromolecules. [source] Weak interactions in chain polymers [M(,- X)2L2], (M = Zn, Cd; X = Cl, Br; L = substituted pyridine) , an electron density studyACTA CRYSTALLOGRAPHICA SECTION B, Issue 5 2009Ruimin Wang The experimental electron-density distributions in crystals of five chain polymers [M(,- X)2(py)2] (M = Zn, Cd; X = Cl, Br; py = 3,5-substituted pyridine) have been obtained from high-resolution X-ray diffraction data sets (sin,,/, > 1.1,Å,1) at 100,K. Topological analyses following Bader's `Atoms in Molecules' approach not only confirmed the existence of (3, ,1) critical points for the chemically reasonable and presumably strong covalent and coordinative bonds, but also for four different secondary interactions which are expected to play a role in stabilizing the polymeric structures which are unusual for Zn as the metal center. These weaker contacts comprise intra- and inter-strand C,H...X,M hydrogen bonds on the one hand and C,X...X,C interhalogen contacts on the other hand. According to the experimental electron-density studies, the non-classical hydrogen bonds are associated with higher electron density in the (3, ,1) critical points than the halogen bonds and hence are the dominant interactions both with respect to intra- and inter-chain contacts. [source] A 1,2,4-diazaphospholane complex of rhodiumACTA CRYSTALLOGRAPHICA SECTION C, Issue 4 2003Robert W. Clark The crystal structure of a prospective olefin catalyst, namely {2-[1-acetyl-5-(2-hydroxyphenyl)-4-phenyl-1,2,4-diazaphospholan-3-yl]phenyl acetate-,P}chloro(,4 -cycloocta-1,5-diene)rhodium(I) dichloromethane solvate, [RhCl(C8H12)(C24H23N2O4P)]·CH2Cl2, has been determined at 173,K. The five-membered heterocycle of the phosphine ligand is in a slightly distorted twist conformation. An intramolecular N1,H1,Cl1 hydrogen bond contributes to the adopted conformation and may additionally participate in secondary interactions with substrates during catalysis. [source] Characterization and design of chemically selective cationic displacers using a robotic high-throughput screenBIOTECHNOLOGY PROGRESS, Issue 3 2009Christopher J. Morrison Abstract A robotic high-throughput displacer screen was developed and employed to identify chemically selective displacers for several protein pairs in cation exchange chromatography. This automated screen enabled the evaluation of a wide range of experimental conditions in a relatively short period of time. Displacers were evaluated at multiple concentrations for these protein pairs, and DC-50 plots were constructed. Selectivity pathway plots were also constructed and different regimes were established for selective and exclusive separations. Importantly, selective displacement was found to be conserved for multiple protein pairs, demonstrating the technique to be applicable for a range of protein systems. Although chemically selective displacers were able to separate protein pairs that had similar retention in ion exchange but different surface hydrophobicities, they were not able to distinguish protein pairs with similar surface hydrophobicities. This corroborates that displacer-protein hydrophobic interactions play an important role for this class of selective displacers. Important functional group moieties were established and efficient displacers were identified. These results demonstrate that the design of chemically selective displacers requires a delicate balance between the abilities to displace proteins from the resin and to bind to a selected protein. The use of robotic screening of displacers will enable the extension of chemically selective displacement chromatography beyond hydrophobic displacer-protein interactions to other secondary interactions and more selective displacement systems. © 2009 American Institute of Chemical Engineers Biotechnol. Prog., 2009 [source] Ligand Association/Dissociation Paths and Ill-Defined Coordination NumbersCHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2010Antonio Ruiz-Martínez Abstract The continuous shape measures approach provides a means for handling the common situation in which a metal atom presents an ill-defined coordination number. Those cases are characterized by the presence of secondary interactions to Lewis bases at distances significantly longer than those expected for a chemical bond. Systematic ways of analyzing ligand association/dissociation pathways that describe such structures and their application to a variety of specific cases are presented. The concepts and methodology presented here apply to molecules and extended solids as well and provide, when needed, a more flexible and precise stereochemical description of the metal coordination sphere than that of an integer coordination number and the associated polyhedral shape. El mètode de les mesures contínues de forma ens permet tractar la situació trobada freqüentment, en què un àtom metàl,lic presenta un nombre de coordinació no ben definit, caracteritzat per la presència d,interaccions secundàries amb bases de Lewis a distàncies significativament més llargues que les que correspondrien a un enllaç químic. Aquí es presenten formes sistemàtiques d,analitzar els camins d,associació/dissociació de lligands que descriuen aquestes estructures, així com llur aplicació a diverses famílies de compostos. Els conceptes i la metodologia presentats en aquest article s'apliquen tant a molècules com a sòlids infinits i ens proporcionen una descripció estereoquímica més flexible i alhora precisa de les esferes de coordinació que no pas un nombre de coordinació enter i la forma polièdrica associada. [source] A QM/MM Study of Cisplatin,DNA Oligonucleotides: From Simple Models to Realistic SystemsCHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2006Arturo Robertazzi Abstract QM/MM calculations were employed to investigate the role of hydrogen bonding and , stacking in several single- and double-stranded cisplatin,DNA structures. Computed geometrical parameters reproduce experimental structures of cisplatin and its complex with guanine,phosphate,guanine. Following QM/MM optimisation, single-point DFT calculations allowed estimation of intermolecular forces through atoms in molecules (AIM) analysis. Binding energies of platinated single-strand DNA qualitatively agree with myriad experimental and theoretical studies showing that complexes of guanine are stronger than those of adenine. The topology of all studied complexes confirms that platination strongly affects the stability of both single- and double-stranded DNAs: PtNH,,,X (X = N or O) interactions are ubiquitous in these complexes and account for over 70,% of all H-bonding interactions. The , stacking is greatly reduced by both mono- and bifunctional complexation: the former causes a loss of about 3,4 kcal,mol,1, whereas the latter leads to more drastic disruption. The effect of platination on Watson,Crick GC is similar to that found in previous studies: major redistribution of energy occurs, but the overall stability is barely affected. The BH&H/AMBER/AIM approach was also used to study platination of a double-stranded DNA octamer d(CCTG*G*TCC),d(GGACCAGG), for which an experimental structure is available. Comparison between theory and experiment is satisfactory, and also reproduces previous DFT-based studies of analogous structures. The effect of platination is similar to that seen in model systems, although the effect on GC pairing was more pronounced. These calculations also reveal weaker, secondary interactions of the form Pt,,,O and Pt,,,N, detected in several single- and double-stranded DNA. [source] Chiral recognition mechanisms with macrocyclic glycopeptide selectors,CHIRALITY, Issue 1 2009Alain Berthod Abstract Macrocyclic glycopeptide selectors are naturally occurring antibiotics produced by microorganisms. They were found to be excellent chiral selectors for a wide range of enantiomers, including amino acids. Four selectors are commercialized as chiral stationary phases (CSP) for chromatography. They are ristocetin, teicoplanin, vancomycin, and the teicoplanin aglycone (TAG). The key docking interaction for amino acid recognition was established to be a charge,charge interaction between the anionic carboxylate group of the amino acid and a cationic amine group of the macrocyclic peptidic selector basket. The carbohydrate units are responsible for secondary interactions. However, they hinder somewhat the charge,charge docking interaction. The TAG selector is more effective for amino acid enantioseparations than the other CSPs. The "sugar" units are however useful allowing for chiral recognitions of other analytes, e.g., ,-blockers, not possible with the aglycone. Thermodynamic studies established that normal phase and reversed phase enantioseparations were enthalpy-driven. With polar waterless mobile phases used in the polar ionic mode, some separations were enthalpy-driven and others were entropy-driven. The linear solvation energy method was tentatively used to gain knowledge about the chiral recognition mechanism. It appeared to be a viable approach with neutral molecules but it failed with ionizable solutes. With molecular solutes and the teicoplanin CSP, the study showed a significant role of the surface charge-induced dipole interaction and steric effects. The remarkable complementary enantioselectivity effect observed with the four CSPs is discussed. Chirality, 2009. © 2008 Wiley-Liss, Inc. [source] | |||||||||||||||||||||||||