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Small Organic Molecules (small + organic_molecule)
Selected AbstractsA Novel Proline-Valinol Thioamide Small Organic Molecule for a Highly Enantioselective Direct Aldol ReactionADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 14-15 2009Bing Wang Abstract A new prolinethioamide compound 4, prepared from readily available natural amino acid L -proline and amino alcohol L -valinol, has been found to be an active catalyst for the direct aldol reaction of various aldehydes with acetone, cyclohexanone or cyclopentanone at 0,°C. Using only 2,mol% loading of this organocatalyst, the reaction could give high enantioselectivity with up to 96% enantiomeric excess for the reaction of 2-nitrobenzaldehyde with acetone. And as for the cyclohexanone, the excellent diastereoselectivity (anti/syn: 99/1) and enantioselectivity (99% ee) could be achieved when reacted with 3-nitrobenzaldehyde in water in the presence of this thioamide 4. This structurally simple catalyst is a highly efficient prolinethioamide derivative, and the terminal hydroxy group in this catalyst is a primary alcohol which is different from the previously reported prerequisite secondary or tertiary alcohol of prolinamides. Our results suggest a new strategy in the design of diversiform organic catalysts for direct asymmetric aldol reactions and related transformations. [source] Size-Selective Sorption of Small Organic Molecules in One-Dimensional Channels of an Ionic Crystalline Organic,Inorganic Hybrid Compound Stabilized by ,,, Interactions,ANGEWANDTE CHEMIE, Issue 33 2009Hanae Tagami Sehr selektiv: Der Durchmesser der engsten Kanalöffnung in einem organisch-anorganischen porösen Ionenkristall mit eindimensionalen Kanälen beträgt etwa 30,Å2. Die Verbindung sorbiert Moleküle wie Propan, 1-Propanol und 1,2-Dichlorethan, deren Querschnitte kleiner als die Kanalöffnung sind, während n -Butan, 1-Butanol und 1,2-Dichlorpropan ausgeschlossen bleiben (siehe Bild). [source] Signal Transducers and Activators of Transcription as Targets for Small Organic MoleculesCHEMBIOCHEM, Issue 13 2008Thorsten Berg Dr. Abstract Signal transducers and activators of transcription (STATs) are a family of transcription factors that are of central importance for cellular signaling and have therefore emerged as attractive target proteins for cell-permeable small molecules. This review outlines the basic concept of STAT signaling, the relevance of individual members of the STAT family for cellular signaling and human disease, and generally applicable approaches taken to the identification of small-molecule inhibitors of STATs. [source] Photoswitches: From Molecules to MaterialsADVANCED MATERIALS, Issue 31 2010Maria-Melanie Russew Abstract Small organic molecules, capable of undergoing efficient and reversible photochemical reactions to switch them between (at least) two (meta)stable isomers associated with markedly different properties, continue to impact the materials world. Such photoswitches are being implemented in a variety of materials for applications ranging from optical devices to "smart" polymers. All approaches exploit the photoswitching molecular entities as gates, which translate an incoming light stimulus to trigger macroscopic property changes of the materials. In this progress report, the most promising recent examples in this field are highlighted and put in perspective. Moving from supramolecular systems in solution to surfaces and finally to bulk materials, important design concepts are discussed, emphasizing both the challenges as well as the great promise of such truly advanced materials. [source] A Computational Study of the Sub-monolayer Growth of PentaceneADVANCED FUNCTIONAL MATERIALS, Issue 13 2006D. Choudhary Abstract A computational study of organic thin-film growth using a combination of ab,initio based energy calculations and kinetic Monte Carlo (KMC) simulations is provided. A lattice-based KMC model is used in which binding energies determine the relative rates of diffusion of the molecules. This KMC approach is used to present "landscapes" or "maps" that illustrate the possible structural outcomes of growing a thin film of small organic molecules, represented as a two-site dimer, on a substrate in which the strength of organic,substrate interactions is allowed to vary. KMC provides a mesoscopic-scale view of sub-monolayer deposition of organic thin films on model substrates, mapped out as a function of the flux of depositing molecules and the temperature of the substrate. The morphology of the crystalline thin films is shown to be a strong function of the molecule,molecule and molecule,substrate interactions. A rich variety of maps is shown to occur in which the small organic molecules either stand up or lie down in a variety of different patterns depending on the nature of the binding to the surface. In this way, it is possible to suggest how to tailor the substrate or the small organic molecule in order to create a desired growth habit. In order to demonstrate how this set of allowable maps is reduced in the case where the set of energy barriers between substrate and organic molecule are reliably known, we have used Gaussian,98 calculations to establish binding energies for the weak van der Waals interactions between a),pairs of pentacene molecules as a function of orientation and b),pentacene and two substrates, silicon surfaces passivated with cyclopentene molecules and a crystalline model of silicon dioxide. The critical nucleation size and the mode of diffusion of this idealized two-site dimer model for pentacene molecules are found to be in good agreement with experimental data. [source] Prediction of interactiveness between small molecules and enzymes by combining gene ontology and compound similarityJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 8 2010Lei Chen Abstract Determination of whether a small organic molecule interacts with an enzyme can help to understand the molecular and cellular functions of organisms, and the metabolic pathways. In this research, we present a prediction model, by combining compound similarity and enzyme similarity, to predict the interactiveness between small molecules and enzymes. A dataset consisting of 2859 positive couples of small molecule and enzyme and 286,056 negative couples was employed. Compound similarity is a measurement of how similar two small molecules are, proposed by Hattori et al., J Am Chem Soc 2003, 125, 11853 which can be availed at http://www.genome.jp/ligand-bin/search_compound, while enzyme similarity was obtained by three ways, they are blast method, using gene ontology items and functional domain composition. Then a new distance between a pair of couples was established and nearest neighbor algorithm (NNA) was employed to predict the interactiveness of enzymes and small molecules. A data distribution strategy was adopted to get a better data balance between the positive samples and the negative samples during training the prediction model, by singling out one-fourth couples as testing samples and dividing the rest data into seven training datasets,the rest positive samples were added into each training dataset while only the negative samples were divided. In this way, seven NNAs were built. Finally, simple majority voting system was applied to integrate these seven models to predict the testing dataset, which was demonstrated to have better prediction results than using any single prediction model. As a result, the highest overall prediction accuracy achieved 97.30%. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010 [source] Two-dimensional hydrogen-bonded networks in 1-(diaminomethylene)thiouron-1-ium nitrate and bis[1-(diaminomethylene)thiouron-1-ium] phosphonate monohydrateACTA CRYSTALLOGRAPHICA SECTION C, Issue 3 2009Jan Janczak Crystals of the title compounds, C2H7N4S+·NO3,, (I), and 2C2H7N4S+·HPO32,·H2O, (II), are built up from 1-(diaminomethylene)thiouron-1-ium cations and nitrate anions in (I), and from phosphonate anions and water molecules in (II). In both crystals, the cations and anions are linked together via N,H...O hydrogen bonds. The 1-(diaminomethylene)thiouron-1-ium cations exhibit a twisted conformation. Both arms of the cations are planar and are turned in opposite directions around the C,N bond involving the central N atom. Hydrogen-bonding interactions join oppositely charged units into layers in the nitrate salt and into double layers in the phosphonate monohydrate salt. In addition, the structures are stabilized by ,,, interactions between the delocalized , bonds of the cations. The significance of this study lies in the illustration of the differences between the supramolecular aggregations in the nitrate and phosphonate salts of a small organic molecule. The different geometries of the counter-ions and their different potential for hydrogen-bond formation results in markedly different hydrogen-bond arrangements. [source] A Computational Study of the Sub-monolayer Growth of PentaceneADVANCED FUNCTIONAL MATERIALS, Issue 13 2006D. Choudhary Abstract A computational study of organic thin-film growth using a combination of ab,initio based energy calculations and kinetic Monte Carlo (KMC) simulations is provided. A lattice-based KMC model is used in which binding energies determine the relative rates of diffusion of the molecules. This KMC approach is used to present "landscapes" or "maps" that illustrate the possible structural outcomes of growing a thin film of small organic molecules, represented as a two-site dimer, on a substrate in which the strength of organic,substrate interactions is allowed to vary. KMC provides a mesoscopic-scale view of sub-monolayer deposition of organic thin films on model substrates, mapped out as a function of the flux of depositing molecules and the temperature of the substrate. The morphology of the crystalline thin films is shown to be a strong function of the molecule,molecule and molecule,substrate interactions. A rich variety of maps is shown to occur in which the small organic molecules either stand up or lie down in a variety of different patterns depending on the nature of the binding to the surface. In this way, it is possible to suggest how to tailor the substrate or the small organic molecule in order to create a desired growth habit. In order to demonstrate how this set of allowable maps is reduced in the case where the set of energy barriers between substrate and organic molecule are reliably known, we have used Gaussian,98 calculations to establish binding energies for the weak van der Waals interactions between a),pairs of pentacene molecules as a function of orientation and b),pentacene and two substrates, silicon surfaces passivated with cyclopentene molecules and a crystalline model of silicon dioxide. The critical nucleation size and the mode of diffusion of this idealized two-site dimer model for pentacene molecules are found to be in good agreement with experimental data. [source] Continuous, Atmospheric Process to Create Organic Clusters and Nanostructured, Functional Films,ADVANCED FUNCTIONAL MATERIALS, Issue 5 2006R. Jagannathan Abstract An atmospheric process based on compressed CO2 is used to create stable clusters of small organic molecules. These clusters, 1,10,nm in size, are used as building blocks to assemble thin films on various substrates. Cluster assembly of these films is verified by using low-angle X-ray diffraction. The surface quality of these cluster-assembled films is similar to that of films usually prepared via the vacuum process. Several functional organic light-emitting diode devices have been prepared, in which only the doped emissive layer has been deposited by our process. The radiometric features and efficiencies of these devices match those of vacuum-built devices. Atomic force microscopy of these molecular clusters reveals that they are liquid-like at standard atmospheric conditions. Coatings of these clusters on cloth and stainless steel have been found to be superhydrophobic in nature. [source] Soft Contact Deposition onto Molecularly Modified GaAs.ADVANCED FUNCTIONAL MATERIALS, Issue 11-12 2002Electrical Effects, Thin Metal Film Flotation: Principles Abstract We describe and analyze a process to position a ,,1 nm thick molecular layer between two solid surfaces without damage to the molecules. The method is used to deposit a metal film in a soft, gentle manner on a semiconductor, yielding functional semiconductor/molecule/metal junctions. It is a combination of the lift-off procedure, known from, for example, lithography, and the bonding process, known from, for example, wafer bonding. The combined method may find application also outside the area described here. We point out its major difficulties as well as solutions to overcome them. For this we rely on concepts from the physics of liquid and solid surfaces and interfaces. Conditions are found, in terms of choice of solvents, under which the method will be effective. The efficacy of floatation as a soft contacting procedure is demonstrated by the preparation of Au and Al contacts on GaAs single crystal surfaces, modified by a self-assembled monolayer of small organic molecules. The resulting electrical properties of the contacts depend crucially on how the molecular interface with the contacting metal is formed. This type of wet contacting procedure to make dry devices may be advantageous especially if biomolecules are used. [source] Assessing the performances of some recently proposed density functionals for the description of bond dissociations involving organic radicalsINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 12 2010Vincent Tognetti Abstract In this article, we have assessed the performances of some recently proposed density functionals for the prediction of reaction energies involving radicals, notably bond dissociations of small organic molecules or of TEMPO-based ones, and ,-scissions, focusing on our TCA family and on range-separated hybrids. It is found that no functional belonging to these two families is able to compete with the M0x one. We have tried to improve the performances of the range-separated hybrids by the optimization of the attenuation parameter, but the improvements for one dataset lead to an unavoidable deterioration for the others. Furthermore, the differences between two different approaches to the long-range/short-range separation are discussed in terms of average enhancement factors, emphasizing the crucial choice of the approximate scheme used for the short-range part. Finally, the influence of the geometries has been considered and found to be negligible for this kind of molecular sets, validating the usual single point energies strategies developed in such benchmarking assessments. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] Establishment of Azotobacter on plant roots: chemotactic response, development and analysis of root exudates of cotton (Gossypium hirsutum L.) and wheat (Triticum aestivum L.)JOURNAL OF BASIC MICROBIOLOGY, Issue 5 2007Rakesh Kumar Abstract Biofertilizers contribute in N2 fixation, P solubilization, phytohormone production and thus enhance plant growth. Beneficial plant-microbe interactions and the stability and effectiveness of biofertilizer depend upon the establishment of bacterial strains in the rhizosphere of the plant. This interaction depends upon many factors, one of them being plant exudates. Root exudates are composed of small organic molecules like carbonic acids, amino acids or sugars etc., which are released into the soil and bacteria can be attracted towards these exudates due to chemotaxis. The chemotactic behaviour of Azotobacter strains was studied using cotton (Desi HD 123 and American H 1098) and wheat (WH 711) seedlings and the root exudates of these two plants were chemically characterized. Analysis of the root exudates revealed the presence of sugars and simple polysaccharides (glucose), amino acids (glutamate, lysine) and organic acids (citric acid, succinic acid, maleic acid, malonic acid). Differences between cotton cultivars in root exudates were observed which influenced chemotactic response in Azotobacter. These results indicate colonization with rhizobacteria which implies that optimal symbionts, on the sides of both plant cultivar and bioinoculant bacteria can lead to better plant growth under cultivation conditions. (© 2007 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim) [source] The antioxidant capacity of salivaJOURNAL OF CLINICAL PERIODONTOLOGY, Issue 3 2002M. Battino Abstract Background/aims: Saliva, a heterogeneous fluid comprising proteins, glycoproteins, electrolytes, small organic molecules and compounds transported from the blood, constantly bathes the teeth and oral mucosa. It acts as a cleansing solution, an ion reservoir, a lubricant and a buffer. In addition to its other host-protective properties, saliva could constitute a first line of defence against free radical-mediated oxidative stress, since the process of mastication and digestion of ingested foods promotes a variety of reactions, including lipid peroxidation. Moreover, during gingival inflammation, gingival crevicular fluid flow increases the change of saliva composition with products from the inflammatory response; this, in turn, could have some rôle in controlling and/or modulating oxidative damages in the oral cavity. This is the reason why the antioxidant capacity of saliva has led to increasing interest, and the development of techniques suitable for saliva antioxidant evaluation. Materials and Methods: Here, we review the current peer-reviewed literature concerning the nature and characteristics of free radicals, reactive oxygen species, oxidants, pro-oxidants and antioxidants in saliva, especially pro-oxidant and antioxidant features, as well as current methods for assessing the antioxidant capacity of saliva. Results and Conclusions: In the last decade, several methods have been developed for assaying the antioxidant activity of saliva, indicating an increasing interest of researchers and clinicians. Unfortunately, systematic studies of saliva are still lacking, even in healthy populations. Zusammenfassung Hintergrund/Zielsetzung: Der Speichel, eine heterogene Flüssigkeit bestehend aus Proteinen, Glykoproteinen, Elektrolyten, kleinen organischen Molekülen und Bestandteilen aus dem Blut, umspült andauernd Zähne und Mundschleimhäute. Er wirkt als Reinigungslösung, Reservoir für Ionen, als Schmiermittel und als Puffer. Zusätzlich zu seinen anderen Abwehreigenschaften könnte der Speichel eine erste Verteidigungslinie gegen durch freie Radikal verursachten oxidativen Stress sein, da der Prozess der Nahrungszerkleinerung und -verdauung eine Vielzahl von Reaktionen auslöst einschließlich der Lipidperoxidation. Darüber hinaus erhöht sich während gingivaler Entzündung der Sulkusflüssigkeitsfluss und verändert die Zusammensetzung des Speichels durch Produkte der Entzündungsreaktion. Dies könnte eine Rolle bei der Kontrolle und/oder Beeinflussung oxidativer Schäden in der Mundhöhle spielen. Dies sind die Gründe dafür, warum die antioxidative Kapazität des Speichels zu einem wachsenden Interesse und zur Entwicklung von Techniken geführt hat, die die Bestimmung der antioxidativen Kapazität des Speichels erlauben. Material und Methoden: In diesem Übersichtsartikel wird die akutelle Literatur hinsichtlich der Natur und Charakteristika freier Radikale, reaktiver Sauerstoffarten, Oxidantien, Prooxidantien und Antioxidantien im Speichel, insbesondere Eigenschaften der Pro- und Antioxidantien sowie aktuelle Methoden zur Bestimmung der antioxidative Kapazität des Speichels, dargestellt. Ergebnisse/Schlussfolgerungen: Während des vergangenen Jahrzehnts wurden mehrere Methoden für die Bestimmung der antioxidativen Kapazität des Speichels entwickelt, was für ein wachsendes wissenschaftliches und klinisches Interesse spricht. Unglücklicherweise fehlen noch systematische Studien zum Speichel selbst für gesunde Kollektive. Résumé Origine/but: La salive, fluide hétérogène constitué de protéines, de glycoprotéines, d'électrolytes, de petites molécules organiques et de composés transportés du sang, baigne constamment les dents et les muqueuses buccales. Elle agit comme une solution nettoyante, comme réservoir d'ions, comme lubrifiant et comme tampon. En plus de ces propriétés protectrices pour l'hôte, la salive pourrait constituer une première ligne de défense contre le stress oxydatif dû aux radicaux libres puisque le processus de mastication et de digestion des nourritures ingérées induit une variété de réactions, telle la peroxidation des lipides. De plus, pendant l'inflammation gingivale, le flux gingival sulculaire augmente et altère la compositon de la salive par les produits de la réponse inflammatoire. Cela, à son tour, pourrait avoir un rôle dans le contrôle ou la modulation des dommages oxydatifs dans la cavité buccale. C'est la raison pour laquelle la capacité antioxydant de la salive a connu un intérêt croissant et le développement de techniques fiables pour l'évaluation des antioxydants salivaires. Matériaux et méthodes: Ici, nous passons en revue de façon concise la littérature actuelle concernant la nature et les caractéristiques des radicaux libres, des espèces réactives à l'oxygène, des oxydants, des pro-oxydants et des antioxydants dans la salive, particulièrement les caractéristiques pro-oxydante et antioxydante et les méthodes actuelles de mise en évidence des capacités antioxydantes de la salive. Résultats et conclusions: Lors de la dernière décade, plusieurs méthodes ont été développées pour tester l'activité antioxydante de la salive, ce qui prouve un intérêt grandissant des chercheurs et des cliniciens. Malheureusement, des études systématiques sur la salive manquent même pour les populations saines. [source] CHARMM fluctuating charge force field for proteins: I parameterization and application to bulk organic liquid simulationsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 1 2004Sandeep Patel Abstract A first-generation fluctuating charge (FQ) force field to be ultimately applied for protein simulations is presented. The electrostatic model parameters, the atomic hardnesses, and electronegativities, are parameterized by fitting to DFT-based charge responses of small molecules perturbed by a dipolar probe mimicking a water dipole. The nonbonded parameters for atoms based on the CHARMM atom-typing scheme are determined via simultaneously optimizing vacuum water-solute geometries and energies (for a set of small organic molecules) and condensed phase properties (densities and vaporization enthalpies) for pure bulk liquids. Vacuum solute-water geometries, specifically hydrogen bond distances, are fit to 0.19 Å r.m.s. error, while dimerization energies are fit to 0.98 kcal/mol r.m.s. error. Properties of the liquids studied include bulk liquid structure and polarization. The FQ model does indeed show a condensed phase effect in the shifting of molecular dipole moments to higher values relative to the gas phase. The FQ liquids also appear to be more strongly associated, in the case of hydrogen bonding liquids, due to the enhanced dipolar interactions as evidenced by shifts toward lower energies in pair energy distributions. We present results from a short simulation of NMA in bulk TIP4P-FQ water as a step towards simulating solvated peptide/protein systems. As expected, there is a nontrivial dipole moment enhancement of the NMA (although the quantitative accuracy is difficult to assess). Furthermore, the distribution of dipole moments of water molecules in the vicinity of the solutes is shifted towards larger values by 0.1,0.2 Debye in keeping with previously reported work. © 2003 Wiley Periodicals, Inc. J Comput Chem 25: 1,15, 2004 [source] Modeling the crystallization of proteins and small organic molecules in nanoliter dropsAICHE JOURNAL, Issue 1 2010Richard D. Dombrowski Abstract Drop-based crystallization techniques are used to achieve a high degree of control over crystallization conditions in order to grow high-quality protein crystals for X-ray diffraction or to produce organic crystals with well-controlled size distributions. Simultaneous crystal growth and stochastic nucleation makes it difficult to predict the number and size of crystals that will be produced in a drop-based crystallization process. A mathematical model of crystallization in drops is developed using a Monte Carlo method. The model incorporates key phenomena in drop-based crystallization, including stochastic primary nucleation and growth rate dispersion (GRD) and can predict distributions of the number of crystals per drop and full crystal size distributions (CSD). Key dimensionless parameters are identified to quickly screen for crystallization conditions that are expected to yield a high fraction of drops containing one crystal and a narrow CSD. Using literature correlations for the solubilities, growth, and nucleation rates of lactose and lysozyme, the model is able to predict the experimentally observed crystallization behavior over a wide range of conditions. Model-based strategies for use in the design and optimization of a drop-based crystallization process for producing crystals of well-controlled CSD are identified. © 2009 American Institute of Chemical Engineers AIChE J, 2010 [source] Heavy atom motions and tunneling in hydrogen transfer reactions: the importance of the pre-tunneling stateJOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 7 2010Hans-Heinrich Limbach Abstract Arrhenius curves of selected hydrogen transfer reactions in organic molecules and enzymes are reviewed with the focus on systems exhibiting temperature-independent kinetic isotope effects. The latter can be rationalized in terms of a ,pre-tunneling state' which is formed from the reactants by heavy atom motions and which represents a suitable molecular configuration for tunneling to occur. Within the Bell,Limbach tunneling model, formation of the pre-tunneling state dominates the Arrhenius curves of the H and the D transfer even at higher temperatures if a large energy Em is required to reach the pre-tunneling state. Tunneling from higher vibrational levels and the over-barrier reaction via the transition state which lead to temperature-dependent kinetic isotope effects dominate the Arrhenius curves only if Em is small compared to the energy of the transition state. Using published data on several hydrogen transfer systems, the type of motions leading to the pre-tunneling state is explored. Among the phenomena which lead to large energies of the pre-tunneling state are (i) cleavage of hydrogen bonds or coordination bonds of the donor or acceptor atoms to molecules or molecular groups in order to allow the formation of the pre-tunneling state, (ii) the occurrence of an energetic intermediate on the reaction pathway within which tunneling takes place, and (iii) major reorganization of a molecular skeleton, requiring the excitation of specific vibrations in order to reach the pre-tunneling state. This model suggests a solution to the puzzle of Kwart's findings of temperature-independent kinetic isotope effects for hydrogen transfer in small organic molecules. Copyright © 2010 John Wiley & Sons, Ltd. [source] Confined space regulated polymerizationJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 5 2008Ye-Zi You Abstract The confined space produced during the polymerization has access for all small organic molecules or oligomers with small size to enter this confined space; however, it can prevent the macromolecules with big size from entering. Therefore, the reaction between two branched macromolecules is excluded in A2+B3 polymerization system, resulting uncrosslinked branched polymers, and there was no gel point observed throughout the polymerization. © 2008 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 46: 1730,1737, 2008 [source] Compensating for variation in 1JCH coupling constants in HSQC spectra acquired on small organic moleculesMAGNETIC RESONANCE IN CHEMISTRY, Issue 11 2010Peter W. A. Howe Abstract The HSQC sequence provides a sensitive way of determining the 13C chemical shift of protonated carbons. It uses INEPT elements for magnetization transfer, which can only be optimized for one value of 1JCH, but small organic molecules contain a wide range of 1JCH values. One popular method of compensating for 1JCH variation is to incorporate adiabatic pulses into the INEPT elements. This article shows that this method fails for a significant subset of functional groups. It also shows that the effects of this failure can be reduced by avoiding refocusing delays and by using a J -compensated excitation element. Copyright © 2010 John Wiley & Sons, Ltd. [source] Studies on inclusion complexes of calix[4]arenes capped by diamide bridges with small organic molecules,MAGNETIC RESONANCE IN CHEMISTRY, Issue 8 2008Barbara Balázs Abstract The inclusion of small neutral organic guests (acetonitrile, toluene, pyrazine, butylamine, nitromethane) by cyclic calix[4]arene diamide receptors was studied by 1H NMR spectroscopy. The binding constants determined by 1H NMR titration, and the results obtained by T1 relaxation measurements and DOSY confirm the importance of the acidity of the CH bond of the guests and highlight the role of steric interactions including conformational properties of the receptors in the recognition process. Copyright © 2008 John Wiley & Sons, Ltd. [source] Toward an "omic" physiopathology of reactive chemicals: Thirty years of mass spectrometric study of the protein adducts with endogenous and xenobiotic compoundsMASS SPECTROMETRY REVIEWS, Issue 5 2009Federico Maria Rubino Abstract Cancer and degenerative diseases are major causes of morbidity and death, derived from the permanent modification of key biopolymers such as DNA and regulatory proteins by usually smaller, reactive molecules, present in the environment or generated from endogenous and xenobiotic components by the body's own biochemical mechanisms (molecular adducts). In particular, protein adducts with organic electrophiles have been studied for more than 30 [see, e.g., Calleman et al., 1978] years essentially for three purposes: (a) as passive monitors of the mean level of individual exposure to specific chemicals, either endogenously present in the human body or to which the subject is exposed through food or environmental contamination; (b) as quantitative indicators of the mean extent of the individual metabolic processing which converts a non-reactive chemical substance into its toxic products able to damage DNA (en route to cancer induction through genotoxic mechanisms) or key proteins (as in the case of several drugs, pesticides or otherwise biologically active substances); (c) to relate the extent of protein modification to that of biological function impairment (such as enzyme inhibition) finally causing the specific health damage. This review describes the role that contemporary mass spectrometry-based approaches employed in the qualitative and quantitative study of protein,electrophile adducts play in the discovery of the (bio)chemical mechanisms of toxic substances and highlights the future directions of research in this field. A particular emphasis is given to the measurement of often high levels of the protein adducts of several industrial and environmental pollutants in unexposed human populations, a phenomenon which highlights the possibility that a number of small organic molecules are generated in the human organism through minor metabolic processes, the imbalance of which may be the cause of "spontaneous" cases of cancer and of other degenerative diseases of still uncharacterized etiology. With all this in mind, it is foreseen that a holistic description of cellular functions will take advantage of new analytical methods based on time-integrated metabolomic measurements of a new biological compartment, the "adductome," aimed at better understanding integrated organism response to environmental and endogenous stressors. © 2009 Wiley Periodicals, Inc., Mass Spec Rev 28:725,784, 2009 [source] Crystallization behavior and mechanical properties of polypropylene/modified carbon black compositesPOLYMER COMPOSITES, Issue 4 2009Ping Zhu Carbon black (CB) modified with small organic molecules was filled in polypropylene (PP) matrix. The crystallization behavior and mechanical properties of PP/modified CB (MCB) composites were investigated. Compared with the original CB, MCB could be dispersed uniformly in smaller particle sizes in PP matrix, and MCB could act as a more effective nucleating, toughening, and reinforcing agent when it was filled in PP at low concentrations. Further increasing of MCB particles in PP matrix resulted in the decrease of impact and tensile strength of PP/MCB composites. It was inferred from DSC results that the existence of CB vand MCB in PP matrix could result in the decrease of crystallite size and degree of perfection of PP. POLYM. COMPOS., 2009. © 2008 Society of Plastics Engineers [source] Side-chain flexibility in protein,ligand binding: The minimal rotation hypothesisPROTEIN SCIENCE, Issue 4 2005Maria I. Zavodszky Abstract The goal of this work is to learn from nature about the magnitudes of side-chain motions that occur when proteins bind small organic molecules, and model these motions to improve the prediction of protein,ligand complexes. Following analysis of protein side-chain motions upon ligand binding in 63 complexes, we tested the ability of the docking tool SLIDE to model these motions without being restricted to rotameric transitions or deciding which side chains should be considered as flexible. The model tested is that side-chain conformational changes involving more atoms or larger rotations are likely to be more costly and less prevalent than small motions due to energy barriers between rotamers and the potential of large motions to cause new steric clashes. Accordingly, SLIDE adjusts the protein and ligand side groups as little as necessary to achieve steric complementarity. We tested the hypothesis that small motions are sufficient to achieve good dockings using 63 ligands and the apo structures of 20 different proteins and compared SLIDE side-chain rotations to those experimentally observed. None of these proteins undergoes major main-chain conformational change upon ligand binding, ensuring that side-chain flexibility modeling is not required to compensate for main-chain motions. Although more frugal in the number of side-chain rotations performed, this model substantially mimics the experimentally observed motions. Most side chains do not shift to a new rotamer, and small motions are both necessary and sufficient to predict the correct binding orientation and most protein,ligand interactions for the 20 proteins analyzed. [source] Significant progress in predicting the crystal structures of small organic molecules , a report on the fourth blind testACTA CRYSTALLOGRAPHICA SECTION B, Issue 2 2009Graeme M. Day We report on the organization and outcome of the fourth blind test of crystal structure prediction, an international collaborative project organized to evaluate the present state in computational methods of predicting the crystal structures of small organic molecules. There were 14 research groups which took part, using a variety of methods to generate and rank the most likely crystal structures for four target systems: three single-component crystal structures and a 1:1 cocrystal. Participants were challenged to predict the crystal structures of the four systems, given only their molecular diagrams, while the recently determined but as-yet unpublished crystal structures were withheld by an independent referee. Three predictions were allowed for each system. The results demonstrate a dramatic improvement in rates of success over previous blind tests; in total, there were 13 successful predictions and, for each of the four targets, at least two groups correctly predicted the observed crystal structure. The successes include one participating group who correctly predicted all four crystal structures as their first ranked choice, albeit at a considerable computational expense. The results reflect important improvements in modelling methods and suggest that, at least for the small and fairly rigid types of molecules included in this blind test, such calculations can be constructively applied to help understand crystallization and polymorphism of organic molecules. 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