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Ligand Atoms (ligand + atom)
Selected AbstractsLigand Influence on Metathesis Activity of Ruthenium Carbene Catalysts: A DFT StudyADVANCED SYNTHESIS & CATALYSIS (PREVIOUSLY: JOURNAL FUER PRAKTISCHE CHEMIE), Issue 1-2 2007Bernd Abstract A survey of the concept of active and inactive ligand conformations in ruthenium alkene carbene complexes of the Grubbs catalyst type is presented. This concept is extended to a variety of anionic ligand atoms. Density functional theory calculations at the B3LYP/LACV3P**+//B3LYP/LACVP* level of theory were performed on the precatalyst, 14 valence-electron intermediate, alkene carbene conformers and ruthena(IV)cyclobutane model intermediates for several ligands, such as methoxide, methanethiolate, fluoride, mesylate, water, and ammonia. The rule of the superiority of metathesis catalysts with small and electron-withdrawing halogens does not apply to fluoride ligands. Alkoxides and thiolates also destabilize active carbene conformations, while mesylate ligands lead to a balanced energetic relation of active and inactive carbene orientations. Cationic ruthenium carbene species with aqua or ammine ligands are limited by unfavored ligand dissociation to 14 valence-electron intermediates. A guideline for the design of novel ligand systems for ruthenium carbene complexes as metathesis catalysts is proposed. [source] Low- and high-spin iron (II) complexes studied by effective crystal field method combined with molecular mechanicsJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2003M. B. Darkhovskii Abstract A computational method targeted to Werner-type complexes is developed on the basis of quantum mechanical effective Hamiltonian crystal field (EHCF) methodology (previously proposed for describing electronic structure of transition metal complexes) combined with the Gillespie,Kepert version of molecular mechanics (MM). It is a special version of the hybrid quantum/MM approach. The MM part is responsible for representing the whole molecule, including ligand atoms and metal ion coordination sphere, but leaving out the effects of the d -shell. The quantum mechanical EHCF part is limited to the metal ion d -shell. The method reproduces with reasonable accuracy geometry and spin states of the Fe(II) complexes with monodentate and polydentate aromatic ligands with nitrogen donor atoms. In this setting a single set of MM parameters set is shown to be sufficient for handling all spin states of the complexes under consideration. © 2003 Wiley Periodicals, Inc. J Comput Chem 14: 1703,1719, 2003 [source] X-ray absorption spectroscopy to watch catalysis by metalloenzymes: status and perspectives discussed for the water-splitting manganese complex of photosynthesisJOURNAL OF SYNCHROTRON RADIATION, Issue 1 2003Holger Dau Understanding structure,function relations is one of the main interests in the molecular biosciences. X-ray absorption spectroscopy of biological samples (BioXAS) has gained the status of a useful tool for characterization of the structure of protein-bound metal centers with respect to the electronic structure (oxidation states, orbital occupancies) and atomic structure (arrangement of ligand atoms). Owing to progress in the performance characteristics of synchrotron radiation sources and of experimental stations dedicated to the study of (ultra-dilute) biological samples, it is now possible to carry out new types of BioXAS experiments, which have been impracticable in the past. Of particular interest are approaches to follow biological catalysis at metal sites by characterization of functionally relevant structural changes. In this article, the first steps towards the use of BioXAS to `watch' biological catalysis are reviewed for the water-splitting reactions occurring at the manganese complex of photosynthesis. The following aspects are considered: the role of BioXAS in life sciences; methodological aspects of BioXAS; catalysis at the Mn complex of photosynthesis; combination of EXAFS and crystallographic information; the freeze-quench technique to capture semi-stable states; time-resolved BioXAS using a freeze-quench approach; room-temperature experiments and `real-time' BioXAS; tasks and perspectives. [source] Neutral Pentacoordinate Silicon(IV) Complexes with Silicon,Chalcogen (S, Se, Te) BondsCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2009Bastian Theis Dipl.-Chem. Abstract The neutral pentacoordinate silicon(IV) complexes 1 (SiS2ONC skeleton), 2 (SiSeSONC), 3 (SiTeSONC), 6/9 (SiSe2O2C), 7 (SiSe2S2C), and 8/10 (SiSe4C) were synthesized and structurally characterized by using single-crystal X-ray diffraction and multinuclear solid-state and solution-state (except for 6,9) NMR spectroscopy. With the synthesis of compounds 1,3 and 6,10, it has been demonstrated that pentacoordinate silicon compounds with soft chalcogen ligand atoms (S, Se, Te) can be stable in the solid state and in solution. [source] Reduced vdW Radius Improves Site of Metabolism Predictions Using X-Ray Structure of CYP2D6MOLECULAR INFORMATICS, Issue 8 2009Peteris Prusis Abstract The major oxidative metabolic degradation of drugs occurs through cytochrome P450 enzymes, which has very wide substrate specificity. Therefore it is crucial to be able to determine the exact position for enzymatic oxidation. Several methods have been developed for site of metabolism (SOM) prediction in silico, including docking based methods. One of the benefits of docking based methods is that it visualizes the drug-enzyme complex and facilitate antidesign towards specific interactions. Recently, the crystal structure of one of the cytochrome P450 enzyme isoforms, CYP2D6, has been published. Here we investigate the feasibility to utilize this structure for SOM predictions using docking. It was found that the intact structure was not well suited for SOM predictions. Reduction of vdW radius of enzyme atoms in the docking grid significantly improved predictions, indicating that the atoms of some of the sidechains of the solved CYP2D6 crystal structure conformation interfere with docked ligands atoms, thus, preventing accurate dockings and SOM predictions. [source] | ||||||||||