Home About us Contact
|
Home About us Contact | ||
|
|
||
Molecule Interactions (molecule + interaction)
Selected AbstractsUnderstanding the Nature of the States Responsible for the Green Emission in Oxidized Poly(9,9-dialkylfluorene)s: Photophysics and Structural Studies of Linear Dialkylfluorene/Fluorenone Model CompoundsADVANCED FUNCTIONAL MATERIALS, Issue 13 2009Khai Leok Chan Abstract Here, the optical properties of a series of structurally well-defined model compounds for oxidatively degraded poly(dialkylfluorenes) (PFs) are reported. Specifically, linear compounds comprising one, two, or four dihexylfluorene (F) moieties together with one fluorenone (O) moiety placed either at the end or in the center of each chain (i.e., FO, FFO, FOF, FFOFF) are studied. The results support the recent observation that the photophysics of the fluorenone-centered "pentamer" (FFOFF) is most similar to that of oxidized PFs. They further demonstrate that molecule,molecule interaction is essential to activate the green emission band. Investigations by X-ray diffraction (XRD) identify the solid-state structure of a representative member of this class of compounds and reveal inter-molecular interaction through dipole,dipole coupling between neighboring fluorenone moieties. [source] Energy density analysis of cluster size dependence of surface,molecule interactions (II): Formate adsorption onto a Cu(111) surfaceJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2006Hiromi Nakai Abstract Adsorption of formate (HCOO) onto a Cu(111) surface has been treated theoretically using 18 kinds of Cun (6 , n , 56) clusters. The energy density analysis (EDA) proposed by Nakai has been adopted to examine surface,molecule interactions for different cluster sizes. EDA results for the largest model cluster Cu56 have shown that the adsorption-induced energy density variation in Cu atoms decays with distance from the adsorption site. Analysis of this decay, which can be carried out using the EDA technique, is important because it enables verification of the reliability of the model cluster used. In the case of formate adsorption onto the Cu(111) surface, it is found that at least a four-layer model cluster is necessary to treat the surface,molecule interaction with chemical accuracy. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 917,925, 2006 [source] Analysis of fluid-structure interaction in low pressure MEMS by Integral EquationsPROCEEDINGS IN APPLIED MATHEMATICS & MECHANICS, Issue 1 2008Attilio FrangiArticle first published online: 25 FEB 200 The evaluation of gas dissipation occurring in inertial polysilicon MEMS is addressed focusing the attention on the free,molecule flow. In this regime, which is very often of interest for industrial applications, collisions between molecules can be neglected and the momentum transfer to the moving shuttle can be easily computed. Since the surfaces of silicon MEMS are generally very rough, a complete diffusion model is adopted to describe the wall,molecule interaction. A Boundary Integral Equation approach is proposed and it is shown that the introduction of the key assumption of small perturbations is crucial in the development of a robust and fast numerical tool. (© 2008 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] Energy density analysis of cluster size dependence of surface,molecule interactions (II): Formate adsorption onto a Cu(111) surfaceJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2006Hiromi Nakai Abstract Adsorption of formate (HCOO) onto a Cu(111) surface has been treated theoretically using 18 kinds of Cun (6 , n , 56) clusters. The energy density analysis (EDA) proposed by Nakai has been adopted to examine surface,molecule interactions for different cluster sizes. EDA results for the largest model cluster Cu56 have shown that the adsorption-induced energy density variation in Cu atoms decays with distance from the adsorption site. Analysis of this decay, which can be carried out using the EDA technique, is important because it enables verification of the reliability of the model cluster used. In the case of formate adsorption onto the Cu(111) surface, it is found that at least a four-layer model cluster is necessary to treat the surface,molecule interaction with chemical accuracy. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 917,925, 2006 [source] THE STRUCTURE AND NANOMECHANICAL PROPERTIES OF THE ADHESIVE MUCILAGE THAT MEDIATES DIATOM-SUBSTRATUM ADHESION AND MOTILITY,JOURNAL OF PHYCOLOGY, Issue 6 2003Michael J. Higgins We investigated the adhesive mucilage and mechanism of cell-substratum adhesion of two benthic raphid diatoms, the marine species Craspedostauros australis E. J. Cox and the freshwater species Pinnularia viridis (Nitzsch) Ehrenberg. SEM images of P. viridis and C. australis cells revealed the presence of multistranded tethers that appear to arise along the raphe openings and extend for a considerable distance from the cell before forming a "holdfast-like" attachment with the substratum. We propose that the tethers result from the elongation/stretching of composite adhesive mucilage strands secreted from raphes during the onset of cell adhesion and reorientation. Atomic force microscopy (AFM) force measurements reveal that the adhesive strands originating from the nondriving raphe of live C. australis and P. viridis are highly extensible and accumulate to form tethers. During force measurements tethers can be chemically stained and are seen to extend between the cantilever tip and a cell during elongation and relaxation. In most cases, AFM force measurements recorded an interaction with a number of adhesive strands that are secreted from the raphe. The force curves of C. australis and P. viridis revealed a sawtooth pattern, suggesting the successive unbinding of modular domains when the adhesive strands were placed under stress. In addition, we applied the "fly-fishing" technique that allowed the cantilever, suspended a distance above the cell, to interact with single adhesive strands protruding from the raphe. These force curves revealed sawtooth patterns, although the binding forces recorded were in the range for single molecule interactions. [source] The lines-of-force landscape of interactions between molecules in crystals; cohesive versus tolerant and `collateral damage' contactACTA CRYSTALLOGRAPHICA SECTION B, Issue 3 2010Angelo Gavezzotti A quantitative analysis of relative stabilities in organic crystal structures is possible by means of reliable calculations of interaction energies between pairs of molecules. Such calculations have been performed by the PIXEL method for 1108 non-ionic and 98 ionic organic crystals, yielding total energies and separate Coulombic polarization and dispersive contributions. A classification of molecule,molecule interactions emerges based on pair energy and its first derivative, the interaction force, which is estimated here explicitly along an approximate stretching path. When molecular separation is not at the minimum-energy value, as frequently happens, forces may be attractive or repulsive. This information provides a fine structural fingerprint and may be relevant to the mechanical properties of materials. The calculations show that the first coordination shell includes destabilizing contacts in ,,9% of crystal structures for compounds with highly polar chemical groups (e.g. CN, NO2, SO2). Calculations also show many pair contacts with weakly stabilizing (neutral) energies; such fine modulation is presumably what makes crystal structure prediction so difficult. Ionic organic salts or zwitterions, including small peptides, show a Madelung-mode pairing of opposite ions where the total lattice energy is stabilized from sums of strongly repulsive and strongly attractive interactions. No obvious relationships between atom,atom distances and interaction energies emerge, so analyses of crystal packing in terms of geometrical parameters alone should be conducted with due care. [source] In this issue: Biotechnology Journal 11/2009BIOTECHNOLOGY JOURNAL, Issue 11 2009Article first published online: 13 NOV 200 Forensic identification on chips Choi and Seo et al., Biotechnol. J. 2009, 4, 1530,1541 Short tandem repeat (STR) analysis can be used for genetic fingerprinting of individuals as it is done for forensic human identification. However, the current state-of-the-art STR genotyping processes and instruments are labor intensive, expensive, time consuming, and lack portability. Micro-total-analysis systems or lab-on-a-chip platforms based on microfabrication technologies have the capability to miniaturize and integrate bioanalysis steps in a single format and have already been successfully applied for forensic STR typing. Researchers from Daejeon, Korea, highlight up-to-date work on advanced microdevices for high-throughput STR genotyping, and a portable integrated microsystem for on-site forensic DNA analysis. Surface plasmon resonance on chips Maynard et al., Biotechnol. J. 2009, 4, 1542,1558 Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are promising targets for drug and biomarker development. This team of authors from Austin, Minneapolis and Rochester (all USA) describe current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G-protein coupled receptor ligands and applications in cellular biology. Nucleotide immobilization on chips Sethi et al., Biotechnol. J. 2009, 4, 1513,1529 The development of oligonucleotide-based microarrays (biochips) is of major interest in science and biotechnology industry and has applications in a wide range of research areas including genomics, proteomics, computational biology and pharmaceuticals. Especially microarrays have proven to be a unique method for time and cost efficient analysis of thousands of genes at one. Authors from Delhi and Lucknow, India discuss currently used chemical strategies for immobilization of oligonucleotides and put a special emphasis on post-synthetic immobilization on glass surfaces. Recent advances on these synthesis pathways are presented in detail. [source] Surface plasmon resonance for high-throughput ligand screening of membrane-bound proteinsBIOTECHNOLOGY JOURNAL, Issue 11 2009Jennifer A. Maynard Dr. Abstract Technologies based on surface plasmon resonance (SPR) have allowed rapid, label-free characterization of protein-protein and protein-small molecule interactions. SPR has become the gold standard in industrial and academic settings, in which the interaction between a pair of soluble binding partners is characterized in detail or a library of molecules is screened for binding against a single soluble protein. In spite of these successes, SPR is only beginning to be adapted to the needs of membrane-bound proteins which are difficult to study in situ but represent promising targets for drug and biomarker development. Existing technologies, such as BIAcoreTM, have been adapted for membrane protein analysis by building supported lipid layers or capturing lipid vesicles on existing chips. Newer technologies, still in development, will allow membrane proteins to be presented in native or near-native formats. These include SPR nanopore arrays, in which lipid bilayers containing membrane proteins stably span small pores that are addressable from both sides of the bilayer. Here, we discuss current SPR instrumentation and the potential for SPR nanopore arrays to enable quantitative, high-throughput screening of G protein coupled receptor ligands and applications in basic cellular biology. [source] Influence of Intermolecular Interactions on the Formation of Tetra(carbomethoxy)-tetrathiafulvalene AssembliesCHEMPHYSCHEM, Issue 10 2007Núria Crivillers Abstract We study the assemblies that tetra(carbomethoxy)tetrathiafulvalene (TCM,TTF) forms in solution and when deposited on a surface depending on intermolecular interactions and on the interactions with the substrate and the solvent. Its organization on graphite and mica substrates was studied by atomic force microscopy, and different molecular assemblies were observed depending on the prevailing interactions. The promotion of molecule,molecule interactions gave rise to the formation of molecular fibers. The investigation of the influence of the solvent,molecule interactions on TCM,TTF molecular organizations was carried out by UV/Vis spectroscopy, and a new TCM,TTF polymorph was obtained by changing the nature of the solvent. Finally, an explanation for all these phenomena, supported by computational modeling, is put forward. [source] Ab initio computational study of positron emission tomography ligands interacting with lipid molecule for the prediction of nonspecific bindingJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2008Lula Rosso Abstract Nonspecific binding is a poorly understood biological phenomenon of relevance in the study of small molecules interactions in vivo and in drug development. Nonspecific binding is thought to be correlated in part to a molecule's lipophilicity, typically estimated by measuring (or calculating) octanol,water partition coefficient. This is, however, a gross simplification of a complex phenomenon. In this article, we present a computational method whose aim is to help identify positron emission tomography (PET) ligands with low nonspecific binding characteristics by investigating the molecular basis of ligand,membrane interaction. We considered a set consisting of 10 well-studied central nervous system PET radiotracers acting on a variety of molecular targets. Quantum mechanical calculations were used to estimate the strength of the interaction between each drug molecule and one phospholipid molecule commonly present in mammalian membranes. The results indicate a correlation between the computed drug,lipid interaction energy and the in vivo nonspecific distribution volume relative to the free tracer plasma concentration, calculated using standard compartmental modeling for the analysis of PET data. Significantly, the drugs whose interaction with the lipid molecule more favorably possessed, in general, a higher nonspecific binding value, whereas for the drugs taken in consideration in this study, the water-octanol partition coefficient, log P, did not show good predictive power of the nonspecific binding. This study also illustrates how ab initio chemical methods may offer meaningful and unbiased insights for the understanding of the underlying chemical mechanisms in biological systems. © 2008 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Scoring ligand similarity in structure-based virtual screeningJOURNAL OF MOLECULAR RECOGNITION, Issue 4 2009Maria I. Zavodszky Abstract Scoring to identify high-affinity compounds remains a challenge in virtual screening. On one hand, protein,ligand scoring focuses on weighting favorable and unfavorable interactions between the two molecules. Ligand-based scoring, on the other hand, focuses on how well the shape and chemistry of each ligand candidate overlay on a three-dimensional reference ligand. Our hypothesis is that a hybrid approach, using ligand-based scoring to rank dockings selected by protein,ligand scoring, can ensure that high-ranking molecules mimic the shape and chemistry of a known ligand while also complementing the binding site. Results from applying this approach to screen nearly 70,000 National Cancer Institute (NCI) compounds for thrombin inhibitors tend to support the hypothesis. EON ligand-based ranking of docked molecules yielded the majority (4/5) of newly discovered, low to mid-micromolar inhibitors from a panel of 27 assayed compounds, whereas ranking docked compounds by protein,ligand scoring alone resulted in one new inhibitor. Since the results depend on the choice of scoring function, an analysis of properties was performed on the top-scoring docked compounds according to five different protein,ligand scoring functions, plus EON scoring using three different reference compounds. The results indicate that the choice of scoring function, even among scoring functions measuring the same types of interactions, can have an unexpectedly large effect on which compounds are chosen from screening. Furthermore, there was almost no overlap between the top-scoring compounds from protein,ligand versus ligand-based scoring, indicating the two approaches provide complementary information. Matchprint analysis, a new addition to the SLIDE (Screening Ligands by Induced-fit Docking, Efficiently) screening toolset, facilitated comparison of docked molecules' interactions with those of known inhibitors. The majority of interactions conserved among top-scoring compounds for a given scoring function, and from the different scoring functions, proved to be conserved interactions in known inhibitors. This was particularly true in the S1 pocket, which was occupied by all the docked compounds. Copyright © 2009 John Wiley & Sons, Ltd. [source] | |||||||||||||