511 resultados para 4D-QSAR
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Hepatitis C is a worldwide public health problem. The available therapies are limited by their partial effectiveness and with meaningful side-effects. Sesquiterpene lactones (SLs) are a group of natural products with a wide variety of chemical structures and biological activities associated. There are few studies about the influence of the molecular structure of SLs for the anti-hepatitis C virus activity. In the present work, SLs are investigated in a subgenomic RNA replicon assay system and were analyzed using multiple linear regression along with self-organizing maps with DRAGON descriptors in order to identify the structural requirements for their biological activity and to predict the inhibitory potency of SLs. Characteristics such as stereochemistry and electronic effects demonstrated to be important for their anti-HCV activity, and the SOM produced a clear separation betwenn active and inactive compounds. Therefore, it is possible to use this map as a filter for virtual screening to predict the anti-HCV activity of SLs.
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Drug discovery has moved toward more rational strategies based on our increasing understanding of the fundamental principles of protein-ligand interactions. Structure( SBDD) and ligand-based drug design (LBDD) approaches bring together the most powerful concepts in modern chemistry and biology, linking medicinal chemistry with structural biology. The definition and assessment of both chemical and biological space have revitalized the importance of exploring the intrinsic complementary nature of experimental and computational methods in drug design. Major challenges in this field include the identification of promising hits and the development of high-quality leads for further development into clinical candidates. It becomes particularly important in the case of neglected tropical diseases (NTDs) that affect disproportionately poor people living in rural and remote regions worldwide, and for which there is an insufficient number of new chemical entities being evaluated owing to the lack of innovation and R&D investment by the pharmaceutical industry. This perspective paper outlines the utility and applications of SBDD and LBDD approaches for the identification and design of new small-molecule agents for NTDs.
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Background: We describe the first occurrence in the fossil record of an aquatic avian twig-nest with five eggs in situ (Early Miocene Tudela Formation, Ebro Basin, Spain). Extensive outcrops of this formation reveal autochthonous avian osteological and oological fossils that represent a single taxon identified as a basal phoenicopterid. Although the eggshell structure is definitively phoenicopterid, the characteristics of both the nest and the eggs are similar to those of modern grebes. These observations allow us to address the origin of the disparities between the sister taxa Podicipedidae and Phoenicopteridae crown clades, and traces the evolution of the nesting and reproductive environments for phoenicopteriforms. Methodology/Principal Findings: Multi-disciplinary analyses performed on fossilized vegetation and eggshells from the eggs in the nest and its embedding sediments indicate that this new phoenicopterid thrived under a semi-arid climate in an oligohaline (seasonally mesohaline) shallow endorheic lacustine environment. High-end microcharacterizations including SEM, TEM, and EBSD techniques were pivotal to identifying these phoenicopterid eggshells. Anatomical comparisons of the fossil bones with those of Phoenicopteriformes and Podicipediformes crown clades and extinct palaelodids confirm that this avian fossil assemblage belongs to a new and basal phoenicopterid. Conclusions/Significance: Although the Podicipediformes-Phoenicopteriformes sister group relationship is now well supported, flamingos and grebes exhibit feeding, reproductive, and nesting strategies that diverge significantly. Our multi-disciplinary study is the first to reveal that the phoenicopteriform reproductive behaviour, nesting ecology and nest characteristics derived from grebe-like type strategies to reach the extremely specialized conditions observed in modern flamingo crown groups. Furthermore, our study enables us to map ecological and reproductive characters on the Phoenicopteriformes evolutionary lineage. Our results demonstrate that the nesting paleoenvironments of flamingos were closely linked to the unique ecology of this locality, which is a direct result of special climatic (high evaporitic regime) and geological (fault system) conditions.
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Aldolase has emerged as a promising molecular target for the treatment of human African trypanosomiasis. Over the last years, due to the increasing number of patients infected with Trypanosoma brucei, there is an urgent need for new drugs to treat this neglected disease. In the present study, two-dimensional fragment-based quantitative-structure activity relationship (QSAR) models were generated for a series of inhibitors of aldolase. Through the application of leave-one-out and leave-many-out cross-validation procedures, significant correlation coefficients were obtained (r(2) = 0.98 and q(2) = 0.77) as an indication of the statistical internal and external consistency of the models. The best model was employed to predict pK(i) values for a series of test set compounds, and the predicted values were in good agreement with the experimental results, showing the power of the model for untested compounds. Moreover, structure-based molecular modeling studies were performed to investigate the binding mode of the inhibitors in the active site of the parasitic target enzyme. The structural and QSAR results provided useful molecular information for the design of new aldolase inhibitors within this structural class.
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Selective modulation of liver X receptor beta (LXR beta) has been recognized as an important approach to prevent or reverse the atherosclerotic process. In the present work, we have developed robust conformation-independent fragment-based quantitative structure-activity and structure-selectivity relationship models for a series of quinolines and cinnolines as potent modulators of the two LXR sub-types. The generated models were then used to predict the potency of an external test set and the predicted values were in good agreement with the experimental results, indicating the potential of the models for untested compounds. The final 2D molecular recognition patterns obtained were integrated to 3D structure-based molecular modeling studies to provide useful insights into the chemical and structural determinants for increased LXR beta binding affinity and selectivity. (C) 2011 Elsevier Inc. All rights reserved.
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Abstract Background High astigmatisms are usually induced during corneal suturing subsequent to tissue transplantation or any other surgery which involves corneal suturing. One of the reasons is that the procedure is intimately dependent on the surgeon's skill for suturing identical stitches. In order to evaluate the influence of the irregularity on suturing for the residual astigmatism, a prototype for ophthalmic surgical support has been developed. The final intention of this prototype is to be an evaluation tool for guided suture and as an outcome diminish the postoperative astigmatism. Methods The system consists of hand held ring with 36 infrared LEDs, that is to be projected onto the lachrymal film of the cornea. The image is reflected back through the optics of the ocular microscope and its distortion from the original circular shape is evaluated by developed software. It provides keratometric and circularity measurements during surgery in order to guide the surgeon for uniformity in suturing. Results The system is able to provide up to 23D of astigmatism (32D - 55D range) and is ± 0.25D accurate. It has been tested in 14 volunteer patients intraoperative and has been compared to a commercial keratometer Nidek Oculus Hand-held corneal topographer. The correlation factors are 0.92 for the astigmatism and 0.97 for the associated axis. Conclusion The system is potentially efficient for guiding the surgeon on uniformity of suturing, presenting preliminary data indicating an important decrease on the residual astigmatism, from an average of 8D - for patients not submitted to the prototype guidance - to 1.4D - for patients who have actually been submitted to the prototype guidance - after the first 24 hours post-surgery and in the subsequent weeks. It also indicates that the surgeon should achieve circularity greater or equal to 98% in order to avoid postoperative astigmatisms over 1D. Trial Registration Trial registration number: CAAE - 0212.0.004.000-09.
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Human African trypanosomiasis, also known as sleeping sickness, is a major cause of death in Africa, and for which there are no safe and effective treatments available. The enzyme aldolase from Trypanosoma brucei is an attractive, validated target for drug development. A series of alkyl‑glycolamido and alkyl-monoglycolate derivatives was studied employing a combination of drug design approaches. Three-dimensional quantitative structure-activity relationships (3D QSAR) models were generated using the comparative molecular field analysis (CoMFA). Significant results were obtained for the best QSAR model (r2 = 0.95, non-cross-validated correlation coefficient, and q2 = 0.80, cross-validated correlation coefficient), indicating its predictive ability for untested compounds. The model was then used to predict values of the dependent variables (pKi) of an external test set,the predicted values were in good agreement with the experimental results. The integration of 3D QSAR, molecular docking and molecular dynamics simulations provided further insight into the structural basis for selective inhibition of the target enzyme.
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The discovery and development of a new drug are time-consuming, difficult and expensive. This complex process has evolved from classical methods into an integration of modern technologies and innovative strategies addressed to the design of new chemical entities to treat a variety of diseases. The development of new drug candidates is often limited by initial compounds lacking reasonable chemical and biological properties for further lead optimization. Huge libraries of compounds are frequently selected for biological screening using a variety of techniques and standard models to assess potency, affinity and selectivity. In this context, it is very important to study the pharmacokinetic profile of the compounds under investigation. Recent advances have been made in the collection of data and the development of models to assess and predict pharmacokinetic properties (ADME - absorption, distribution, metabolism and excretion) of bioactive compounds in the early stages of drug discovery projects. This paper provides a brief perspective on the evolution of in silico ADME tools, addressing challenges, limitations, and opportunities in medicinal chemistry.
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[ES] La Universidad de Rutgers y la Universidad de Las Palmas de Gran Canaria, a través de su Estación de Oceanografía Espacial SEAS Canarias que dirige el Dr. Antonio González Ramos, han colaborado en cinco proyectos de recogida de datos oceánicos desarrollados en el 2008 y el 2013. Estos proyectos son considerados hitos científicos al usar minisubmarinos no tripulados que han batido récords de distancia y tiempo en el agua nunca antes conseguidos. El Dr. González Ramos (Facultad de Ciencias del Mar) recibió el premio en una gala en esta universidad norteamericana, celebrada con motivo del 20 aniversario de su Instituto de Ciencias Marinas y Costeras (RU COOL). González Ramos desarrolló la herramienta Pinzon4D, un sistema de predicción que permite mostrar predicciones de las corrientes oceánicas de 0 a 1000 metros para el mismo día, así como una predicción de tres días, a través de la aplicación Google Earth. La novedad y utilidad de esta herramienta han hecho que se convierta en el protocolo del pilotaje para las dos misiones globales actuales. La herramienta Pinzon-4D se presentará como parte de la Challenger Mission en la próxima sesión plenaria de la Comisión Oceanográfica Internacional (UNESCO). El equipo de trabajo considera que el éxito de este tipo de proyectos radica en tres pilares: la innovación tecnológica, la cooperación internacional y la visibilidad de la información
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[ES] En este proyecto se trata el proceso de análisis y desarrollo llevado a cabo con el objetivo de construir un prototipo funcional de simulador virtual de endoscopia rígida monocanal orientado a la histeroscopia. Para el desarrollo del prototipo se toma como base el entorno ESQUI, un entorno de simulación virtual médica de código libre. Este entorno provee una librería, basada a su vez en la conocida librería gráfica VTK(Visual ToolKit), cuyo propósito es poner a disposición del programador toda la algoritmia necesaria para construir una simulación médica virtual. En este proyecto, esta librería se depuró y amplió para mejorar el soporte a las técnicas de endoscopia rígida que se persiguen simular. Por otro lado se emplea el Simball 4D, un dispositivo de interfaz humana de la empresa G-coder Systems, para capturar la interacción del usuario emulando la morfología y dinámica de un endoscopio rígido. Todos estos elementos se conectan con una interfaz gráfica sencilla, intuitiva y práctica soportada por wxWidgets y utilizando Python como lenguaje de scripting. Finalmente, se analiza el prototipo resultante y se proponen una serie de líneas futuras de cara a la aplicación didáctica del mismo, tanto en relación a los objetivos conceptuales del prototipo como a los aspectos específicos del entorno ESQUI.
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Several activities were conducted during my PhD activity. For the NEMO experiment a collaboration between the INFN/University groups of Catania and Bologna led to the development and production of a mixed signal acquisition board for the Nemo Km3 telescope. The research concerned the feasibility study for a different acquisition technique quite far from that adopted in the NEMO Phase 1 telescope. The DAQ board that we realized exploits the LIRA06 front-end chip for the analog acquisition of anodic an dynodic sources of a PMT (Photo-Multiplier Tube). The low-power analog acquisition allows to sample contemporaneously multiple channels of the PMT at different gain factors in order to increase the signal response linearity over a wider dynamic range. Also the auto triggering and self-event-classification features help to improve the acquisition performance and the knowledge on the neutrino event. A fully functional interface towards the first level data concentrator, the Floor Control Module, has been integrated as well on the board, and a specific firmware has been realized to comply with the present communication protocols. This stage of the project foresees the use of an FPGA, a high speed configurable device, to provide the board with a flexible digital logic control core. After the validation of the whole front-end architecture this feature would be probably integrated in a common mixed-signal ASIC (Application Specific Integrated Circuit). The volatile nature of the configuration memory of the FPGA implied the integration of a flash ISP (In System Programming) memory and a smart architecture for a safe remote reconfiguration of it. All the integrated features of the board have been tested. At the Catania laboratory the behavior of the LIRA chip has been investigated in the digital environment of the DAQ board and we succeeded in driving the acquisition with the FPGA. The PMT pulses generated with an arbitrary waveform generator were correctly triggered and acquired by the analog chip, and successively they were digitized by the on board ADC under the supervision of the FPGA. For the communication towards the data concentrator a test bench has been realized in Bologna where, thanks to a lending of the Roma University and INFN, a full readout chain equivalent to that present in the NEMO phase-1 was installed. These tests showed a good behavior of the digital electronic that was able to receive and to execute command imparted by the PC console and to answer back with a reply. The remotely configurable logic behaved well too and demonstrated, at least in principle, the validity of this technique. A new prototype board is now under development at the Catania laboratory as an evolution of the one described above. This board is going to be deployed within the NEMO Phase-2 tower in one of its floors dedicated to new front-end proposals. This board will integrate a new analog acquisition chip called SAS (Smart Auto-triggering Sampler) introducing thus a new analog front-end but inheriting most of the digital logic present in the current DAQ board discussed in this thesis. For what concern the activity on high-resolution vertex detectors, I worked within the SLIM5 collaboration for the characterization of a MAPS (Monolithic Active Pixel Sensor) device called APSEL-4D. The mentioned chip is a matrix of 4096 active pixel sensors with deep N-well implantations meant for charge collection and to shield the analog electronics from digital noise. The chip integrates the full-custom sensors matrix and the sparsifification/readout logic realized with standard-cells in STM CMOS technology 130 nm. For the chip characterization a test-beam has been set up on the 12 GeV PS (Proton Synchrotron) line facility at CERN of Geneva (CH). The collaboration prepared a silicon strip telescope and a DAQ system (hardware and software) for data acquisition and control of the telescope that allowed to store about 90 million events in 7 equivalent days of live-time of the beam. My activities concerned basically the realization of a firmware interface towards and from the MAPS chip in order to integrate it on the general DAQ system. Thereafter I worked on the DAQ software to implement on it a proper Slow Control interface of the APSEL4D. Several APSEL4D chips with different thinning have been tested during the test beam. Those with 100 and 300 um presented an overall efficiency of about 90% imparting a threshold of 450 electrons. The test-beam allowed to estimate also the resolution of the pixel sensor providing good results consistent with the pitch/sqrt(12) formula. The MAPS intrinsic resolution has been extracted from the width of the residual plot taking into account the multiple scattering effect.
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Bei inäqual furchenden Spiraliern, wie Platynereis dumerilii, entstehen durch die ersten beiden Furchungen vier unterschiedlich große und auch bereits unterschiedlich determinierte Blastomeren. Im allgemeinen ist die größte der vier Blastomeren die Gründerzelle des D-Quadranten (Dorresteijn und Fischer 1988). Dieser Quadrant etabliert die dorsoventrale Körperachse im Keim, indem er das Schicksal benachbarter Blastomeren über Zell-Zell-Interaktionen positionsgerecht bestimmt (Damen und Dictus 1996). Der D-Quadrant erhält bei Platynereis einen überproportional großen Anteil (60%) des gesamten dotterfreien Zytoplasmas im Keim (Dorresteijn 1990). Sein Schicksal wird durch morphogenetische Faktoren innerhalb des dotterfreien Zytoplasmas bestimmt. Der Gehalt an dotterfreiem Zytoplasma bestimmt nicht nur das Schicksal der Blastomeren, sondern korreliert auch direkt mit den jeweils unterschiedlichen Zellzyklusgeschwindigkeiten der Blastomeren. Die plasmareichen Zellen des D-Quadranten, aber auch bereits die Vorläuferzelle CD, teilen sich im Vergleich mit den jeweils anderen Blastomeren im Keim besonders rasch (Dorresteijn 1990). In dieser Arbeit wurde unter verschiedenen Aspekten untersucht (a) inwieweit die Etablierung der dorsoventralen Körperachse von der raschen Proliferation der D-Zellinie abhängt, (b) inwieweit Zellzyklusregulatoren Bestandteil der oben genannten morphogenetischen Faktoren sein könnten und (c) wie die unterschiedlichen Zellzyklusgeschwindigkeiten auf molekularer Ebene reguliert werden.Zum einen wurden die frühen Furchungsstadien von Aplysia californica volumetrisch vermessen. Anders als bei den meisten inäqual furchenden Spiraliern wird bei Aplysia nicht der größte, sondern einer der kleineren embryonalen Quadranten als D-Quadrant determiniert. Ich konnte zeigen, daß die CD-Blastomere (27% des Eivolumens) dennoch, ähnlich wie bei Platynereis, bei der ersten Furchungsteilung überproportional viel dotterfreies Zytoplasma (40%) erhält und so als Vorläuferzelle des D-Quadranten determiniert wird. Bei der zweiten Furchung teilt sich die CD-Blastomere jedoch, anders als bei Platynereis, symmetrisch. Welche der beiden Tochterzellen von CD als definitiver D-Quadrant determiniert wird, erfordert also zusätzliche (induktive?) Mechanismen. Auch bei Aplysia sind die Zellzyklusgeschwindigkeiten der Blastomeren mit ihren jeweiligen Anteilen am dotterfreiem Zytoplasma korreliert. Das Postulat, daß die rasche Proliferation des D-Quadranten und seiner Vorläuferzelle CD für die Etablierung der dorsoventralen Körperachse und für die Determination der Blastomeren in Keimen inäqual furchender Spiralier erforderlich sind, konnte ich zusätzlich bestätigen, indem ich die Teilungsabfolge im Keim von Platynereis mit Hilfe des Cdc2-spezifischen Inhibitors Olomoucin experimentell abänderte. Durch pulse chase-Behandlung mit Olomoucin wurde erreicht, daß die Blastomeren die vierte Mitose, anders als im normalen Keim, synchron einleiteten. Die so behandelten Keime entwickelten sich zu Trochophorae, die keine oder nur eine stark reduzierte dorsoventrale Polarität erkennen ließen. Das dorsoventrale Muster entsteht in Keimen von Spiraliern durch die Organisatorwirkung der Blastomeren 3D und 4d und bei Platynereis eventuell auch 2d (Damen und Dictus 1996, Dorresteijn und Eich 1991). Der Teilungsvorsprung, den diese Blastomeren normalerweise gegenüber anderen Zellinien haben, war in den mit Olomoucin-behandelten Keimen stark vermindert. Dadurch haben diese Blastomeren ihre induktiven Kapazitäten möglicherweise nicht, oder nicht rechtzeitig erwerben können, um die benachbarten Zellen gemäß ihrer Position entlang der dorsoventralen Körperachse zu determinieren. Insofern ist die differentielle Zellzyklusregulation fest in das Determinationsgeschehen integriert. Das bedeutet auch, daß zellzyklusregulierende Faktoren Bestandteil der anfangs genannten
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Die Zellgenealogie des Polychaeten Platynereis dumerilii wurde durch Farbstoffinjektion in die Blastomeren des 2-, 4- und 8-Zellstadiums, sowie die Zellen 2d, 2d112, 4d und 4d1 untersucht. Injektionen gelangen durch Aufweichung der Vitellinhülle mittels Dithioerythritol und Trypsin. Die injizierten Keime wurden zur Trochophora bzw zum dreisegmentigen Jungwurm aufgezogen, fixiert und mit dem konfokalen Rasterlichtmikroskop dreidimensional aufgenommen. Die animal-vegetale Achse des Frühkeims entspricht der antero-posterioren Achse des Jungwurms. Die Mikromeren des ersten Quartetts sind radiär um die antero-posteriore Achse angeordnet und bilden den Kopf. Die Mikromere 2d proliferiert bilateralsymmetrisch von der dorsalen Mittellinie aus und liefert das gesamte Rumpfektoderm. Indirekt ließ sich ableiten, daß die Mikromeren 2a1 bis 2c1 schmale ektodermale Streifen zwischen Kopf und Rumpf bilden und aus 2a2 und 2c2 das ektodermale Stomodaeum hervorgeht. Die Mikromeren des dritten Quartetts sowie möglicherweise 2b2 bilden 'Ektomesoderm'. 4d proliferiert ebenfalls bilateralsymmetrisch von der dorsalen Mittellinie aus zum Rumpfmesoderm und liefert vielleicht noch kleine Beiträge zum Aufbau des Darmes. Der Mitteldarm stammt von den dotterreichen Makromeren 4A bis 4D.
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This work comprises three different types of unconventional correlated systems.rnChapters 3-5 of this work are about the open shell compounds Rb4O6 and Cs4O6. These mixed valent compounds contain oxygen in two different modifications: the closed-shell peroxide anion is nonmagnetic, whereas the hyperoxide anion contains an unpaired electrons in an antibonding pi*-orbital. Due to this electron magnetic ordering is rendered possible. In contrast to theoretical predictions, which suggested half-metallic ferromagnetism for Rb4O6,rndominating antiferromagnetic interactions were found in the experiment. Besidesrna symmetry reduction due to the mixed valency, strong electronic correlations of this highly molecular system determine its properties; it is a magnetically frustrated insulator. The corresponding Cs4O6 was found to show similar properties.rnChapters 6-9 of this work are about intermetallic Heusler superconductors. rnAll of these superconductors were rationally designed using the van Hove scenario as a working recipe. A saddle point in the energy dispersion curve of a solid leads to a van Hove singularity in the density of states. In the Ni-based and Pd-based Heusler superconductors presented in this work this sort of a valence instability occurs at the high-symmetry L point and coincides or nearly coincides with the Fermi level. The compounds escape the high density of states at the Fermi energy through a transition into the correlated superconducting state.rnChapter 10 of this work is about the tetragonally distorted ferrimagnetic DO22 phase of Mn3Ga. This hard-magnetic modification is technologically useful for spin torque transfer applications. The phase exhibits two different crystallographic sites that are occupied by Mn atoms and can thus be written as Mn2MnGa. The competition between the mainly itinerant moments of the Mn atoms at the Wyckoff position 4d and the localized moments of the Mn atoms at the Wyckoff position 2b leads to magnetic correlations. The antiferromagnetic orientation of these moments determines the compound to exhibit a resulting magnetic moment of approximately 1 µB per formula unit in a partially compensated ferrimagnetic configuration.
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A series of imidazolium salts of the type [BocNHCH2CH2ImR]X (Boc = t-Bu carbamates; Im = imidazole) (R = Me, X = I, 1a; R = Bn, X = Br, 1b; R = Trityl, X = Cl, 1c) and [BnImR’]X (R’ = Me, X = Br, 1d; R’ = Bn, X = Br, 1e; R’ = Trityl, X = Cl, 1g; R’ = tBu, X = Br, 1h) bearing increasingly bulky substituents were synthetized and characterized. Subsequently, these precursors were employed in the synthesis of silver(I)-N-heterocyclic (NHC) complexes as transmetallating reagents for the preparation of rhodium(I) complexes [RhX(NBD)(NHC)] (NHC = 1-(2-NHBoc-ethyl)-3-R-imidazolin-2-ylidene; X = Cl; R = Me, 4a; R = Bn, 4b; R = Trityl, 4c; X = I, R = Me, 5a; NHC = 1-Bn-3-R’-imidazolin-2-ylidene; X = Cl; R’ = Me, 4d, R’ = Bn, 4e, R’ = Trityl, 4g; R’ = tBu, 4h). VT NMR studies of these complexes revealed a restricted rotation barriers about the metal-carbene bond. While the rotation barriers calculated for the complexes in which R = Me, Bn (4a,b,d,e and 5a) matched the experimental values, this was not true for the complexes 4c,g, bearing a trityl group for which the values are much smaller than the calculated ones. Energy barriers for 4c,g, derived from a line shape simulation, showed a strong dependence on the temperature while for 4h the rotational energy barrier is stopped at room temperature. The catalytic activity of the new rhodium compounds was investigated in the hydrosilylation of terminal alkynes and in the addition of phenylboronic acid to benzaldehyde. The imidazolium salts 1d,e were also employed in the synthesis of new iron(II)-NHC complexes. Finally, during a six-months stay at the University of York a new ligand derived from Norharman was prepared and employed in palladium-mediated cross-coupling.