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Individual Molecules (individual + molecule)
Selected AbstractsIndividual molecules of thermostable alkaline phosphatase support different catalytic rates at room temperatureLUMINESCENCE: THE JOURNAL OF BIOLOGICAL AND CHEMICAL LUMINESCENCE, Issue 1 2002Ashley C. Dyck Abstract Thermus thermophilus cells were grown at 70°C, lysed and the lysate subjected to single molecule alkaline phosphatase assays, using a capillary electrophoresis laser-induced fluorescence detection-based method. The enzyme was found to be heterogeneous with respect to catalytic rate when assayed at room temperature. Turnover numbers ranged 12-fold, with an average of 400,±,200 reactions/min for the 80 molecules assayed. Copyright © 2002 John Wiley & Sons, Ltd. [source] Association between color doppler vascularity index, angiogenesis-related molecules, and clinical outcomes in gastric cancerJOURNAL OF SURGICAL ONCOLOGY, Issue 7 2009Chiung-Nien Chen MD Abstract Purpose This study was conducted to evaluate the correlation between color Doppler vascularity index (CDVI), clinical outcomes and five angiogenesis-related molecules including vascular endothelial growth factor (VEGF), placenta growth factor (PlGF), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), and calreticulin (CRT) in gastric cancer, and to develop an effective model selected from these five molecules to predict patient survival. Patients and Methods CDVI could be obtained preoperatively by transabdominal ultrasound from 30 patients. Enzyme immunoassay was adopted to determine protein level of VEGF and PlGF, and immunohistochemistry was used to detect COX-2, iNOS and CRT expression. Correlation between CDVI and five individual molecules was assessed. Multiple molecules model was developed using classification and regression tree (CART) analysis from five molecules, and was tested for patient survival in another 45 patients. Results CDVI was significantly correlated with patient survival (P,=,0.00907) and absolute number of metastatic lymph nodes (P,=,0.01). There was no significant association between CDVI and any individual molecule. The model, developed by CART consisting of VEGF and PlGF, could differentiate high and low CDVI and survival in testing group (P,=,0.00257). Conclusions CDVI was associated with lymph node metastasis, combined VEGF and PlGF expression status and patient survival in gastric cancer. J. Surg. Oncol. 2009;99:402,408. © 2009 Wiley-Liss, Inc. [source] Powder X-ray studies of meso -hexamethyl propylene amine oxime (meso -HMPAO) in two different phasesACTA CRYSTALLOGRAPHICA SECTION C, Issue 9 2010Mahmoud Al-Ktaifani Two different forms of meso -3,3,-[2,2-dimethylpropane-1,3-diylbis(azanediyl)]dibutan-2-one dioxime, commonly called meso -hexamethyl propylene amine oxime (HMPAO), C13H28N4O2, designated , and ,, were isolated by fractional crystallization and their crystal structures were determined by powder X-ray diffraction using the direct-space method with the parallel tempering algorithm. The , form was first crystallized from acetonitrile solution, while the , form was obtained by recrystallization of the , phase from diethyl ether. The , form crystallizes in the triclinic system (space group P), with one molecule in the asymmetric unit, while the crystal of the , form is monoclinic (space group P21/n), with one molecule in the asymmetric unit. In both phases, the molecules have similar conformations and RS/EE geometric isomerism. The crystal packing of the two phases is dominated by intermolecular hydrogen-bonding interactions between the two O,H oxime groups of an individual molecule and the amine N atoms of two different adjacent molecules, which lead to segregation of extended poly(meso -HMPAO) one-dimensional chains along the c direction. The structures of the two phases are primarily different due to the different orientations of the molecules in the chains. [source] "Tail,Tail Dimerization" of Ferrocene Amino Acid DerivativesEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2010Daniel Siebler Abstract Acid anhydrides of N-protected 1,-aminoferrocene-1-carboxylic acid (Fca) have been prepared and spectroscopically characterized (protection group Boc, Fmoc, Ac; 4a,4c). The structure of the Boc-derivative 4a has been determined by single-crystal X-ray crystallography. An intramolecular N,H···O hydrogen bond involving the carbamate units results in a ring structure containing the two ferrocene units, the anhydride moiety, and the hydrogen bond. In the crystal, the individual molecules are connected by intermolecular N,H···O hydrogen bonds of the carbamate unit. Experimental and theoretical studies suggest that the ring motif is also a dominant species in solution. Electronic communication across the anhydride moiety is found to be very weak as judged from electrochemical, spectroscopic, and theoretical experiments. [source] Electronic Structure of Self-Assembled Monolayers on Au(111) Surfaces: The Impact of Backbone PolarizabilityADVANCED FUNCTIONAL MATERIALS, Issue 23 2009LinJun Wang Abstract Modifying metal electrodes with self-assembled monolayers (SAMs) has promising applications in organic and molecular electronics. The two key electronic parameters are the modification of the electrode work function because of SAM adsorption and the alignment of the SAM conducting states relative to the metal Fermi level. Through a comprehensive density-functional-theory study on a series of organic thiols self-assembled on Au(111), relationships between the electronic structure of the individual molecules (especially the backbone polarizability and its response to donor/acceptor substitutions) and the properties of the corresponding SAMs are described. The molecular backbone is found to significantly impacts the level alignment; for molecules with small ionization potentials, even Fermi-level pinning is observed. Nevertheless, independent of the backbone, polar head-group substitutions have no effect on the level alignment. For the work-function modification, the larger molecular dipole moments achieved when attaching donor/acceptor substituents to more polarizable backbones are largely compensated by increased depolarization in the SAMs. The main impact of the backbone on the work-function modification thus arises from its influence on the molecular orientation on the surface. This study provides a solid theoretical basis for the fundamental understanding of SAMs and significantly advances the understanding of structure,property relationships needed for the future development of functional organic interfaces. [source] Alkali Metal Doped Organic Molecules on Insulators: Charge Impact on the Optical PropertiesADVANCED MATERIALS, Issue 36 2010Thomas Dienel Doping-induced absorption changes of organic molecules on an insulating solid are reported. The charge transfer between alkali metal atoms and individual molecules on a surface leads to new electronic transitions identified with optical absorption spectroscopy. Progressive doping allows the discrimination of neutral, monoanionic and dianionic molecules in the solid state through examination of the spectra and rate equation modeling. [source] Reversible Conductance Switching of Single Diarylethenes on a Gold Surface,ADVANCED MATERIALS, Issue 11 2006N. Katsonis Light-controlled conductance switching of diarylethenes attached to Au(111) is reported (see figure). First, scanning tunneling microscopy is used to demonstrate reversible photoswitching for individual molecules. Second, reversible switching in self-assembled monolayers is established by means of optical spectroscopy. [source] Reconstruction of atomistic details from coarse-grained structuresJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2010Andrzej J. Rzepiela Abstract We present an algorithm to reconstruct atomistic structures from their corresponding coarse-grained (CG) representations and its implementation into the freely available molecular dynamics (MD) program package GROMACS. The central part of the algorithm is a simulated annealing MD simulation in which the CG and atomistic structures are coupled via restraints. A number of examples demonstrate the application of the reconstruction procedure to obtain low-energy atomistic structural ensembles from their CG counterparts. We reconstructed individual molecules in vacuo (NCQ tripeptide, dipalmitoylphosphatidylcholine, and cholesterol), bulk water, and a WALP transmembrane peptide embedded in a solvated lipid bilayer. The first examples serve to optimize the parameters for the reconstruction procedure, whereas the latter examples illustrate the applicability to condensed-phase biomolecular systems. © 2010 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Association between color doppler vascularity index, angiogenesis-related molecules, and clinical outcomes in gastric cancerJOURNAL OF SURGICAL ONCOLOGY, Issue 7 2009Chiung-Nien Chen MD Abstract Purpose This study was conducted to evaluate the correlation between color Doppler vascularity index (CDVI), clinical outcomes and five angiogenesis-related molecules including vascular endothelial growth factor (VEGF), placenta growth factor (PlGF), cyclooxygenase-2 (COX-2), inducible nitric oxide synthase (iNOS), and calreticulin (CRT) in gastric cancer, and to develop an effective model selected from these five molecules to predict patient survival. Patients and Methods CDVI could be obtained preoperatively by transabdominal ultrasound from 30 patients. Enzyme immunoassay was adopted to determine protein level of VEGF and PlGF, and immunohistochemistry was used to detect COX-2, iNOS and CRT expression. Correlation between CDVI and five individual molecules was assessed. Multiple molecules model was developed using classification and regression tree (CART) analysis from five molecules, and was tested for patient survival in another 45 patients. Results CDVI was significantly correlated with patient survival (P,=,0.00907) and absolute number of metastatic lymph nodes (P,=,0.01). There was no significant association between CDVI and any individual molecule. The model, developed by CART consisting of VEGF and PlGF, could differentiate high and low CDVI and survival in testing group (P,=,0.00257). Conclusions CDVI was associated with lymph node metastasis, combined VEGF and PlGF expression status and patient survival in gastric cancer. J. Surg. Oncol. 2009;99:402,408. © 2009 Wiley-Liss, Inc. [source] Multi-wavelength fluorescence lifetime spectroscopy: a new approach to the study of endogenous fluorescence in living cells and tissuesLASER PHYSICS LETTERS, Issue 3 2009D. Chorvat Jr. Abstract The study of biological systems in their real environmental conditions is crucial to decipher the true image of structures and processes underlying their functionality. In this regard, development of non-invasive optical techniques that do not require labelling, such as the investigation of tissue endogenous fluorescence, is particularly important and, as reflected in the increasing number of contributions published recently on this subject, was recognized by many leading groups. Multi-spectral and lifetime detection of fluorescence provides an effective experimental tool to discriminate between multiple naturally-occurring fluorophores in living tissues. At the same time, however, data analysis allowing us to understand the spectral, temporal and spatial information gathered, describing individual molecules involved in the autofluorescence of intact biological systems, represents a tough scientific challenge that has not yet been fully resolved. In this review, we discuss the latest advances in technologies that record and assess spectrally-resolved fluorescence lifetime data as well as their biological and clinical applications. We show how these methods provide efficient sensing of molecules correlated with changes in the mitochondrial metabolic redox state in pathological conditions and/or of cell ultrastructures in diseased tissue, based on the presence of oxidation/reductionsensitive fluorophores and/or cell-specific chromophores. Future directions are also outlined. (© 2009 by Astro Ltd., Published exclusively by WILEY-VCH Verlag GmbH & Co. KGaA) [source] Reconstruction from a single diffraction pattern of azimuthally projected electron density of molecules aligned parallel to a single axisACTA CRYSTALLOGRAPHICA SECTION A, Issue 1 2010D. K. Saldin Diffraction from the individual molecules of a molecular beam, aligned parallel to a single axis by a strong electric field or other means, has been proposed as a means of structure determination of individual molecules. As in fiber diffraction, all the information extractable is contained in a diffraction pattern from incidence of the diffracting beam normal to the molecular alignment axis. The limited size of the object results in continuous diffraction patterns characterized by neither Bragg spots nor layer lines. Equations relating the scattered amplitudes to the molecular electron density may be conveniently formulated in terms of cylindrical harmonics. For simulated diffraction patterns from short C nanotubes aligned along their axes, iterative solution of the equation for the zeroth-order cylindrical harmonic and its inverse with appropriate constraints in real and reciprocal space enables the phasing of the measured amplitudes, and hence a reconstruction of the azimuthal projection of the molecule. [source] Patenting Nanotechnology in Europe: Making a Good Start?THE JOURNAL OF WORLD INTELLECTUAL PROPERTY, Issue 1 2010An Analysis of Issues in Law, Regulation Nanotechnology is the technology that concerns itself with the smallest units of matter and promises manipulation of matter on the level of individual molecules. It is expected that vastly improved quality of many kinds of products will be the result. The patenting of nanotech inventions is well under way in Europe, but going down to the most elemental level raises new and important questions. For example, how does patenting at the nano level relate to similar technology on the super-nano level? Also fundamental questions can be asked, such as: should matter at all be patentable at the most elemental level? This article seeks to give a first overview of questions of law and regulation concerning the patentability of inventions in the field of nanotechnology under the European Patent Convention. [source] The Molecular Phenotype of Kidney TransplantsAMERICAN JOURNAL OF TRANSPLANTATION, Issue 10 2010P. F. Halloran Microarray studies of kidney transplant biopsies provide an opportunity to define the molecular phenotype. To facilitate this process, we used experimental systems to annotate transcripts as members of pathogenesis-based transcript sets (PBTs) representing biological processes in injured or diseased tissue. Applying this annotation to microarray results revealed that changes in single molecules and PBTs reflected a large-scale coordinate disturbance, stereotyped across various diseases and injuries, without absolute specificity of individual molecules or PBTs for rejection. Nevertheless, expression of molecules and PBTs was quantitatively specific: IFNG effects for rejection; T cell and macrophage transcripts for T cell-mediated rejection; endothelial and NK transcripts for antibody-mediated rejection. Various diseases and injuries induced the same injury,repair response, undetectable by histopathology, involving epithelium, stroma and endothelium, with increased expression of developmental, cell cycle and apoptosis genes and decreased expression of differentiated epithelial features. Transcripts reflecting this injury,repair response were the best correlates of functional disturbance and risk of future graft loss. Late biopsies with atrophy-fibrosis, reflecting their cumulative burden of injury, displayed more transcripts for B cells, plasma cells and mast cells. Thus the molecular phenotype is best described in terms of three elements: specific diseases, including rejection; the injury,repair response and the cumulative burden of injury. [source] An aza-cyclophane stacked in racemic columnar assemblies: whole-molecule disorder in a two-dimensional solid solutionACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Matthias Zeller The oxime derivative of [1.1.1]cyclophane cyclotriveratrylene (CTV) was ring expanded utilizing a Beckmann rearrangement to provide a ten-membered N -acetyl macrocyclic amide that crystallizes as a chloroform monosolvate in columnar assemblies manifesting an unusual disorder within the crystal. Columns made up of this structure consist of infinite columnar assemblies of alternating d and l enantiomers and therefore necessarily are made up of a racemate, yet the chiralities of individual molecules in adjacent columns are independent of one another, leading to the overall formation of a two-dimensional solid solution. The random arrangement of the columns within the structure leads to the emergence of a crystallographic mirror plane not reflected by the molecular symmetry, to a change of symmetry from Pna21 to Pnma and to whole-molecule disorder of the bowl-shaped molecules within the columns. [source] Ultralow-resolution ab initio phasing of filamentous proteins: crystals from a six-Ig fragment of titin as a case studyACTA CRYSTALLOGRAPHICA SECTION D, Issue 5 2008Alexandre Urzhumtsev Low-resolution diffraction data (resolution below 12,Å) from crystals of a filamentous six-Ig fragment of titin, I65,I70, were used in ab initio phasing with the aim of calculating its lattice packing and molecular envelope. Filamentous molecules, characterized by marked anisometry and idiosyncratic crystal lattices, have not been addressed before using this methodology. In this study, low-resolution phasing (19,122,Å) successfully identified the region of the unit cell occupied by the molecule. Phase extension to a higher resolution (12,Å) yielded regions of high density that corresponded either to the positions of individual Ig domains or to zones of dense intermolecular contacts, hindering the identification of individual domains and the interpretation of electron-density maps in terms of a molecular model. This problem resulted from the acutely uneven packing of the molecules in the crystal and it was further accentuated by the presence of partially disordered regions in the molecule. Addition of low-resolution reflections with phases computed ab initio to those obtained experimentally using MIRAS improved the initial electron-density maps of the atomic model, demonstrating the generic utility of low-resolution phases for the structure-elucidation process, even when individual molecules cannot be resolved in the lattice. [source] Unexpected Deformations Induced by Surface Interaction and Chiral Self-Assembly of CoII -Tetraphenylporphyrin (Co-TPP) Adsorbed on Cu(110): A Combined STM and Periodic DFT StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 38 2010Philip Donovan Abstract In a combined scanning tunnelling microscopy (STM) and periodic density functional theory (DFT) study, we present the first comprehensive picture of the energy costs and gains that drive the adsorption and chiral self-assembly of highly distorted CoII -tetraphenylporphyrin (Co-TPP) conformers on the Cu(110) surface. Periodic, semi-local DFT calculations reveal a strong energetic preference for Co-TPP molecules to adsorb at the short-bridge site when organised within a domain. At this adsorption site, a substantial chemical interaction between the molecular core and the surface causes the porphyrin macrocycle to accommodate close to the surface and in a flat geometry, which induces considerable tilting distortions in the phenyl groups. Experimental STM images can be explained in terms of these conformational changes and adsorption-induced electronic effects. For the ordered structure we unambiguously show that the substantial energy gain from the molecule,surface interaction recuperates the high cost of the induced molecular and surface deformations as compared with gas phase molecules. Conversely, singly adsorbed molecules prefer a long-bridge adsorption site and adopt a non-planar, saddle-shape conformation. By using a van der Waals density functional correction scheme, we found that the intermolecular ,,, interactions make the distorted conformer more stable than the saddle conformer within the organic assembly. These interactions drive supramolecular assembly and also generate chiral expression in the system, pinning individual molecules in a propeller-like conformation and directing their assembly along non-symmetric directions that lead to the coexistence of mirror-image chiral domains. Our observations reveal that a strong macrocycle,surface interaction can trigger and stabilise highly unexpected deformations of the molecular structure and thus substantially extend the range of chemistries possible within these systems. [source] Mode-Selective Electrical Excitation of a Molecular RotorCHEMISTRY - A EUROPEAN JOURNAL, Issue 38 2009Heather Batteries not included: The rotation of individual molecular rotors can be driven electrically using electrons from a scanning tunneling microscope tip (see picture). Above the threshold energy of the CH stretch excitation, tunneling electrons are effective at selectively driving rotation, but not translation of the thioether rotors. The ability to rotate individual molecules on command will permit the interrogation of many important effects like rotational energy transfer along 1D molecular chains and rotational orientation switching in ordered arrays. [source] Non-Covalent Polyvalent Ligands by Self-Assembly of Small Glycodendrimers: A Novel Concept for the Inhibition of Polyvalent Carbohydrate,Protein Interactions In Vitro and In VivoCHEMISTRY - A EUROPEAN JOURNAL, Issue 1 2006Gebhard Thoma Dr. Abstract Polyvalent carbohydrate,protein interactions occur frequently in biology, particularly in recognition events on cellular membranes. Collectively, they can be much stronger than corresponding monovalent interactions, rendering it difficult to control them with individual small molecules. Artificial macromolecules have been used as polyvalent ligands to inhibit polyvalent processes; however, both reproducible synthesis and appropriate characterization of such complex entities is demanding. Herein, we present an alternative concept avoiding conventional macromolecules. Small glycodendrimers which fulfill single molecule entity criteria self-assemble to form non-covalent nanoparticles. These particles,not the individual molecules,function as polyvalent ligands, efficiently inhibiting polyvalent processes both in vitro and in vivo. The synthesis and characterization of these glycodendrimers is described in detail. Furthermore, we report on the characterization of the non-covalent nanoparticles formed and on their biological evaluation. [source] pH-Controllable Supramolecular SystemsCHEMISTRY - AN ASIAN JOURNAL, Issue 3 2009Ken Cham-Fai Leung Prof. Abstract Proton, all that matters! This Focus Review surveys representative examples of pH-controllable supramolecular systems with interesting features and state-of-the-art applications, which can lead to the construction of meaningful molecular machines for electronic and biological applications that can be controlled by simple perturbation with acid and base. This Focus Review surveys representative examples of pH-controllable supramolecular systems with interesting features and state-of-the-art applications such as 1),conformational changes within individual molecules; 2),folding/unfolding of polymers; 3),simultaneous binding of cations and anions; 4),logic function; 5),ON,OFF switchable colorimetric sensing; 6),translocation of macrocycle-in-rotaxane molecules; 7),large-scale movement within molecules; and 8),regulation of the substrate flow in nanocontainers. In particular, systems will be discussed that involve: pH-induced conformational changes of a resorcinarene cavitand and a bis(iron porphyrin) complex; pH control in assembly and disassembly of supramolecular systems stabilized with different major noncovalent interactions; pH-driven movements of interlocked molecules involving rotaxanes, molecular elevators, and molecular muscles; and, finally, multicomponent supramolecular systems immobilized on solid supports as pH-responsive nanovalves for the controlled release of specific substrates. Recent advances in the understanding of pH-controllable supramolecular systems have led to the construction of meaningful molecular machines for electronic and biological applications that are amenable to control by simple perturbation with acids and bases. [source] Vibronic Transitions in Single MetalloporphyrinsCHEMPHYSCHEM, Issue 5 2005H. J. Lee Dr. Abstract Structural and electronic properties of single zinc etioporphyrin molecules adsorbed on Al2O3/NiAl(110) were probed by a low-temperature scanning tunneling microscope (STM). Scanning tunneling spectroscopy (STS) revealed progressions of spectral features corresponding to the vibronic states of individual molecules that depend strongly on the molecular conformations. Vibronic features observed by STS were compared with the results from fluorescence induced by tunneling electrons (tunneling-induced fluorescence, TIF). [source] Photophysical Aspects of Single-Molecule Detection by Two-Photon Excitation with Consideration of Sequential Pulsed IlluminationCHEMPHYSCHEM, Issue 5 2004R. Niesner Abstract An important goal in single molecule fluorescence correlation spectroscopy is the theoretical simulation of the fluorescence signal stemming from individual molecules and its autocorrelation function. The simulation approaches developed up to now are based exclusively on continuous-wave (cw) illumination and consequently on cw-excitation. However, this approximation is no longer valid in the case of two-photon excitation, for which pulsed illumination is usually employed. We present a novel theoretical model for the simulation of the fluorescence signal of single molecules and its autocorrelation function with consideration of the time dependence of the excitation flux and thus of all illumination-dependent photoprocesses: two-photon excitation, induced emission and photobleaching. Further important characteristics of our approach are the consideration of the dependence of the photobleaching rate on illumination and the low intersystem-crossing rates of the studied coumarins. Moreover, using our approach, we can predict quantitatively the effect of the laser pulse width on the fluorescence signal of a molecule, that is, the contributions of the photobleaching and saturation effects, and thus we can calculate the optimal laser pulse width. The theoretical autocorrelation functions were fitted to the experimental data, and we could ascertain a good agreement between the resulting and the expected parameters. The most important parameter is the photobleaching constant ,, the cross section of the transition Sn,S1, which characterises the photostability of the molecules independent of the experimental conditions. Its value is 1.7×10,23 cm2 for coumarin 153 and 5×10,23 cm2 for coumarin 314. [source] | ||||||||||||||||||||||||||||