Home About us Contact
|
Home About us Contact | ||
|
|
||
Computational Study (computational + study)
Selected AbstractsAn Unusual Anion,, Interaction in an ;rido Organometallic Assembly: Synthesis, First Crystal Structure, and Computational StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 25 2009Jamal Moussa Abstract The organometallic assembly [Cp*Ir(,6 -C6H2O4)(BF2)2(CF3SO3)][Cp*Ir(,-Cl)3IrCp*] (3) was prepared from [Cp*Ir(solvent)3][OTf]2 (2) and 1,2,4,5 tetrahydroxybenzene (THB, 1) in acetone, in the presence of an excess amount of BF3·2H2O. Assembly 3 was fully characterized by multinuclear NMR spectroscopy. Remarkably, the X-ray molecular structure of 3 shows that an anion,, interaction occurs between the neutral component Cp*Ir(,6 -C6H2O4)(BF2)2 of the assembly and the CF3SO3 anion of the cationic species [Cp*Ir(,-Cl)3IrCp*]. Computational analysis was carried out on 3 to unravel the nature of this noncovalent interaction. Such an example could serve as a model to explain the important role of anions in organometallic chemistry and asymmetric catalysis. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] The Role of Amine,B(C6F5)3 Adducts in the Catalytic Reduction of Imines with H2: A Computational StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 15 2009Timofei Privalov Abstract This study thoroughly examines the potential energy surfaces (PESs) of two possible mechanisms for reduction of imines by B(C6F5)3 and H2. The key reaction steps of the first catalytic mechanism, which is the focus of our study, are: (i) the uptake of H2 by a thermally activated amine,B(C6F5)3 species; (ii) proton transfer from the NH2+ moiety of [RNH2CH2R,]+[HB(C6F5)3], to the imine; (iii) nucleophillic attack of the C-center of the iminium ion by the BH, group. The potential energy barriers of the latter, as determined by calculating the evolution of the H-bonded complex of an imine and [RNH2CH2R,]+[HB(C6F5)3], in toluene, are around 10 kcal,mol,1 each. In the second mechanism, only imines serve as basic partners of B(C6F5)3 in the H2 activation, which affords an [RN(H)CHR,]+[HB(C6F5)3], ion pair; direct reduction then proceeds via nucleophilic attack of the C-center by the BH, in [RN(H)CHR,]+[HB(C6F5)3],. This route becomes catalytic when the product amine is released into the solvent and B(C6F5)3 is re-used for H2 activation. Upon taking into account the association energy of an amine,B(C6F5)3 adduct [,9.5 kcal,mol,1 for tBuN(H)CH2Ph and B(C6F5)3 in toluene], the potential energy barrier for H2 uptake by an imine and B(C6F5)3 increases to 14.5 kcal,mol,1. We report a somewhat lower potential energy barrier for H2 uptake by thermally activated amine,B(C6F5)3 adducts [12.7 kcal,mol,1 for the B-N adduct of tBuN(H)CH2Ph and B(C6F5)3 in toluene], although the difference between the two H2 activationbarriers is within the expected error of the computational method. Two catalytic routes are compared based on B3LYP-computed PESs in solvent (toluene).(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2009) [source] Isostructural Potassium and Thallium Salts of Sterically Crowded Thio- and Selenophenols: A Structural and Computational StudyEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 36 2008Denis Bubrin Abstract Because of their similar cationic radii, potassium and thallium(I) compounds are usually regarded as closely related. Homologous molecular species containing either K+ or Tl+ are very rare, however. We have synthesized potassium and thallium salts MEAr* [M, E = K, S (2a); K, Se (2b); Tl, S (3a); Tl, Se (3b); Ar* = 2,6-Trip2C6H3, Trip = 2,4,6- iPr3C6H2] derived from terphenyl-substituted thio- and selenophenols. In the solid-state structures of dimeric 2a, 2b, 3a, and 3b additional metal-,n,,-arene interactions to the flanking arms of the terphenyl substituents of different hapticity n are observed. Remarkably, the homologous potassium and thallium complexes 2b and 3b crystallize in isomorphous cells. For 2a, 3a, and model complexes of the composition METph (Tph = C6H4 -2-Trip) the nature of the M,E and M···C(arene) bonding was studied by density functional theory calculations.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Spectroscopic and Computational Study on New Blue Emitting ReL(CO)3Cl Complexes Containing Pyridylimidazo[1,5- a]pyridine LigandsEUROPEAN JOURNAL OF INORGANIC CHEMISTRY, Issue 23 2008Claudio Garino Abstract The structural and photophysical properties of three new ReL(CO)3Cl complexes (ReL1,ReL3) and their 1-(2-pyridyl)imidazo[1,5- a]pyridine ligands, namely 3-methyl-1-(2-pyridyl)imidazo[1,5- a]pyridine (L1), 1-(2-pyridyl)-3-[4-(trifluoromethyl)phenyl]imidazo[1,5- a]pyridine (L2), and 3-(4-nitrophenyl)-1-(2-pyridyl)imidazo[1,5- a]pyridine (L3), were studied by spectroscopy, X-ray diffraction, and computational methods. ReL1,ReL3 have high-energy singlet emissions arising from a , , ,* ligand-centered state. In oxygen-free acetonitrile solutions, the complexes display dual fluorescence due to intense ligand-centered triplet emission.(© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2008) [source] Lewis Acid Activated Aza-Diels,Alder Reaction of N -(3-Pyridyl)aldimines: An Experimental and Computational StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 11 2010Francisco Palacios Abstract A combined theoretical and experimental study of a Povarov-type cycloaddition reaction suggests an asynchronous concerted process that is favored by double Lewis acid activation with BF3·Et2O; endo selectivity was observed in the reactions between N -(3-pyridyl)aldimines and styrene, cyclopentadiene, or indene, and substituted tetrahydro-1,5-naphthyridine derivatives were obtained in a regio- and stereoselective fashion. [source] Cycloadditions and Methylene Transfer in Reactions of Substituted Thiocarbonyl S -Methylides with Thiobenzophenone: A Computational StudyEUROPEAN JOURNAL OF ORGANIC CHEMISTRY, Issue 8 2005Reiner Sustmann Abstract Regiochemistry and methylene transfer reactions in cycloadditions of aliphatic thiocarbonyl S -methylides and thiobenzophenone are analyzed by ab initio [(U)HF/3-21G*] and DFT calculations [(U)B3LYP/6-31G*//(U)HF/3-21G* and (U)B3LYP/6-31G*]. The formation of regioisomeric 1,3-dithiolanes is explained by the competition of concerted (2,4-substituted 1,3-dithiolane) and stepwise cycloaddition via C,C -biradicals (4,5-substituted 1,3-dithiolane). Aliphatic thiocarbonyl S -methylides with sterically demanding substituents undergo substantial methylene transfer in the reaction with thiobenzophenone. This process involves dissociation of the C,C -biradical intermediate with liberation of thiobenzophenone S -methylide which, in turn, combines with a second molecule of thiobenzophenone. Calculated activation parameters for the different processes are in agreement with the experimental observations. (© Wiley-VCH Verlag GmbH & Co. KGaA, 69451 Weinheim, Germany, 2005) [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] The Ludwig-Soret Effect on the Thermally Induced Phase Separation Process in Polymer Solutions: A Computational StudyMACROMOLECULAR THEORY AND SIMULATIONS, Issue 2 2009Sureshkumar B. Kukadiya Abstract The Ludwig-Soret effect was investigated in the thermally induced phase separation process via SD in polymer solutions under an externally imposed spatial linear temperature gradient using mathematical modeling and computer simulation. The mathematical model incorporated non-linear Cahn-Hilliard theory for SD, Flory-Huggins theory for thermodynamics, and the Ludwig-Soret effect for thermal diffusion. 2D simulation results revealed that the Ludwig-Soret effect had negligible impact on the phase separation mechanism in binary polymer solutions under a non-uniform temperature field, as reflected by the time evolution of the dimensionless structure factor and the transition time from the early to the intermediate stages of SD. [source] A Photodissociation Reaction: Experimental and Computational Study of 2-Hydroxy-2,2-dimethylacetophenone,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2006X. Allonas ABSTRACT The photophysical parameters controlling the cleavage process of 2-hydroxy-2,2-dimethylacetophenone (HDMA) were investigated in detail. Time-resolved picosecond absorption experiments show that the formation of the triplet state occurs within 20 ps after excitation and decays within hundreds of picoseconds depending on the solvent polarity. Molecular modeling reveals that three stable conformations exist in the ground state, the most stable one exhibiting an intramolecular hydrogen bond that modifies the electronic properties of the molecule. This explains quite well the steady-state absorption properties. The conformation of the most stable triplet state is twisted by 180° with respect to the ground state. Computation of the potential energy surface along the molecular coordinate for the dissociation reaction evidences an electronic state crossing yielding a final ,,* state, in perfect agreement with the state correlation diagram. Optimization of the transition state allows the calculation of the activation energy and the use of the transition-state theory leads to an estimate of 100 ps for the cleavage process in the gas phase. Single-point energy calculations using a solvent model predict an increase of the dissociation rate constant with the increase of the solvent polarity, in good agreement with the value deduced from kinetic measurements. [source] Ultraviolet Absorption Spectra of Substituted Phenols: A Computational Study,PHOTOCHEMISTRY & PHOTOBIOLOGY, Issue 1 2006Lei Zhang ABSTRACT Vertical excitation energies for electronic transitions from the ground state to the first two excited states of phenol, mono- and disubstituted methoxyphenols and methyl-substituted phenols have been characterized with the Time-Dependent Density Functional Theory (TD-DFT), the Complete Active Space Self-Consistent Field method (CASSCF) and the Coupled Cluster with Single and Double Excitations Equation-of-Motion approach (CCSD-EOM) to simulate and interpret experimental ultraviolet absorption spectra. While CASSCF excitation energies for the first two transitions either are grossly overestimated or exhibit a weak correlation with experimental data, both TD-DFT and CCSD-EOM perform very well, reproducing the spectral shifts of both the primary band and secondary band observed upon substitution. The conformational dependence of the calculated excitation energies is generally smaller than the shifts caused by substitution. [source] Evolution of O2 in a Seven-Coordinate RuIV Dimer Complex with a [HOHOH], Bridge: A Computational Study,ANGEWANDTE CHEMIE, Issue 10 2010Jonas Nyhlén Das fehlende Glied? Nach DFT-Rechnungen ist ein Mechanismus der O2 -Entwicklung unter Beteiligung zweikerniger, siebenfach koordinierter Rutheniumspezies wahrscheinlich, bei dem Sauerstoffradikale direkt gekuppelt werden und keine unüberwindlich hohen Potentialenergiebarrieren im Wege stehen (siehe Schema). [source] A Computational Study of Feedback Effects on Signal Dynamics in a Mitogen-Activated Protein Kinase (MAPK) Pathway ModelBIOTECHNOLOGY PROGRESS, Issue 2 2001Anand R. Asthagiri Exploiting signaling pathways for the purpose of controlling cell function entails identifying and manipulating the information content of intracellular signals. As in the case of the ubiquitously expressed, eukaryotic mitogen-activated protein kinase (MAPK) signaling pathway, this information content partly resides in the signals' dynamical properties. Here, we utilize a mathematical model to examine mechanisms that govern MAPK pathway dynamics, particularly the role of putative negative feedback mechanisms in generating complete signal adaptation, a term referring to the reset of a signal to prestimulation levels. In addition to yielding adaptation of its direct target, feedback mechanisms implemented in our model also indirectly assist in the adaptation of signaling components downstream of the target under certain conditions. In fact, model predictions identify conditions yielding ultra-desensitization of signals in which complete adaptation of target and downstream signals culminates even while stimulus recognition (i.e., receptor-ligand binding) continues to increase. Moreover, the rate at which signal decays can follow first-order kinetics with respect to signal intensity, so that signal adaptation is achieved in the same amount of time regardless of signal intensity or ligand dose. All of these features are consistent with experimental findings recently obtained for the Chinese hamster ovary (CHO) cell lines (Asthagiri et al., J. Biol. Chem.1999, 274, 27119,27127). Our model further predicts that although downstream effects are independent of whether an enzyme or adaptor protein is targeted by negative feedback, adaptor-targeted feedback can "back-propagate" effects upstream of the target, specifically resulting in increased steady-state upstream signal. Consequently, where these upstream components serve as nodes within a signaling network, feedback can transfer signaling through these nodes into alternate pathways, thereby promoting the sort of signaling cross-talk that is becoming more widely appreciated. [source] Computational Study of the Lipase-Mediated Desymmetrisation of 2-Substituted-Propane-1,3-DiaminesCHEMBIOCHEM, Issue 18 2009Eduardo García-Urdiales Dr. Abstract The enantioselectivity displayed by the lipase from Pseudomonas cepacia towards a wide range of prochiral 2-substituted-propane-1,3-diamines was studied by means of molecular dynamics simulations (MDS). In all cases the enzyme allows the recovery of the corresponding amino carbamates of R configuration. However, the enantioselectivity is only synthetically useful if no ortho substituent is present and the aromatic ring is directly bonded to the 2-carbon of the 1,3-diamine core. Analysis of the MDS trajectories revealed that the homologation of 2-aryl substituents by means of a methylene group lowers enantioselectivity by alleviating the conformational tension of the slow-reacting orientations due to unfavourable intramolecular contacts between the ortho carbons of the aryl group and the nucleophilic nitrogen, as well as between the chiral carbon and the oxyanion. Additionally, the relative solvent accessible surfaces of the atoms of the aryl ring nicely correlate with the effect of the location of the substituent on enantioselectivity. [source] ChemInform Abstract: Computational Study of the Zr4+ Tetranuclear Polymer, [Zr4(OH)8(H2O)16]8+CHEMINFORM, Issue 8 2008Niny Rao Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Computational Study of the Release of H2 from Ammonia Borane Dimer (BH3NH3)2 and Its Ion Pair Isomers.CHEMINFORM, Issue 48 2007Vinh Son Nguyen Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Computational Study on the Catalytic Mechanism of Oxygen Reduction on La0.5Sr0.5MnO3 in Solid Oxide Fuel Cells.CHEMINFORM, Issue 47 2007YongMan Choi Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] A Photoelectron Spectroscopic and Computational Study of Sodium Auride Clusters, NanAun - (n = 1,3).CHEMINFORM, Issue 42 2007Li-Feng Cui Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 200 leading journals. To access a ChemInform Abstract, please click on HTML or PDF. [source] Computational Study of Enthalpies of Formation of OXO (X: Cl, Br, and I) and Their AnionsCHEMINFORM, Issue 6 2005Sang Yeon Lee Abstract For Abstract see ChemInform Abstract in Full Text. [source] Formation of Silicon Analogues of Thio-isocyanic Acid, HNSiS, and Its Isomers by Neutral,Neutral Reactions of the Fragments: A Computational Study.CHEMINFORM, Issue 51 2004P. Raghunath No abstract is available for this article. [source] Isolated Pentagon Rule in Buckybowls: A Computational Study on Thermodynamic Stabilities and Bowl-to-Bowl Inversion Barriers.CHEMINFORM, Issue 51 2003T. C. Dinadayalane No abstract is available for this article. [source] Computational Study of the Protonation of AlXH2 and AlX2H (X: F, Cl, and Br).CHEMINFORM, Issue 48 2003AlX2H+, AlX2H+4., Structures of AlXH+, Their Dihydrogen Complexes AlXH+ No abstract is available for this article. [source] Silaaromaticity in Polycyclic Systems: A Computational Study.CHEMINFORM, Issue 20 2003D. Manjula Dhevi No abstract is available for this article. [source] ChemInform Abstract: The Structure and Possible Catalytic Sites of Mo3S9 as a Model of Amorphous Molybdenum Trisulfide: A Computational Study.CHEMINFORM, Issue 45 2001Haijun Jiao Abstract ChemInform is a weekly Abstracting Service, delivering concise information at a glance that was extracted from about 100 leading journals. To access a ChemInform Abstract of an article which was published elsewhere, please select a "Full Text" option. The original article is trackable via the "References" option. [source] Stabilization of High-Valent FeIVS6 -Cores by Dithiocarbamate(1,) and 1,2-Dithiolate(2,) Ligands in Octahedral [FeIV(Et2dtc)3,n(mnt)n](n,1), Complexes (n=0, 1, 2, 3): A Spectroscopic and Density Functional Theory Computational Study,CHEMISTRY - A EUROPEAN JOURNAL, Issue 12 2010Carsten Milsmann Dr. Abstract A detailed spectroscopic and quantum chemical analysis is presented to elucidate the electronic structures of the octahedral complexes [Fe(Et2dtc)3,n(mnt)n]n, (1,4, n=3, 2, 1, 0) and their one-electron oxidized analogues [Fe(Et2dtc)3,n(mnt)n](n,1), (1ox,4ox); (mnt)2, represents maleonitriledithiolate(2,) and (Et2dtc)1, is the diethyldithiocarbamato(1,) ligand. By using X-ray crystallography, Mössbauer spectroscopy, and Fe and S K-edge X-ray absorption spectroscopy (XAS) it is convincingly shown that, in contrast to our previous studies on [Fe(cyclam)(mnt)]1+ (cyclam=1,4,8,11-tetraazacyclotetradecane), the oxidation of 1,4 is metal-centered yielding the genuine FeIV complexes 1ox,4ox. For the latter complexes, a spin ground state of S=1 has been established by magnetic susceptibility measurements, which indicates a low-spin d4 configuration. DFT calculations at the B3LYP level support this electronic structure and exclude the presence of a ligand , radical coordinated to an intermediate-spin ferric ion. Mössbauer parameters and XAS spectra have been calculated to calibrate our computational results against the experiment. Finally, a simple ligand-field approach is presented to correlate the structural features obtained from X-ray crystallography (100,K) with the spectroscopic data. [source] Pincer-Type Heck Catalysts and Mechanisms Based on PdIV Intermediates: A Computational StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 5 2010Olivier Blacque Dr. Abstract Pincer-type palladium complexes are among the most active Heck catalysts. Due to their exceptionally high thermal stability and the fact that they contain PdII centers, controversial PdII/PdIV cycles have been often proposed as potential catalytic mechanisms. However, pincer-type PdIV intermediates have never been experimentally observed, and computational studies to support the proposed PdII/PdIV mechanisms with pincer-type catalysts have never been carried out. In this computational study the feasibility of potential catalytic cycles involving PdIV intermediates was explored. Density functional calculations were performed on experimentally applied aminophosphine-, phosphine-, and phosphite-based pincer-type Heck catalysts with styrene and phenyl bromide as substrates and (E)-stilbene as coupling product. The potential-energy surfaces were calculated in dimethylformamide (DMF) as solvent and demonstrate that PdII/PdIV mechanisms are thermally accessible and thus a true alternative to formation of palladium nanoparticles. Initial reaction steps of the lowest energy path of the catalytic cycle of the Heck reaction include dissociation of the chloride ligands from the neutral pincer complexes [{2,6-C6H3(XPR2)2}Pd(Cl)] [X=NH, R=piperidinyl (1,a); X=O, R=piperidinyl (1,b); X=O, R=iPr (1,c); X=CH2, R=iPr (1,d)] to yield cationic, three-coordinate, T-shaped 14e, palladium intermediates of type [{2,6-C6H3(XPR2)2}Pd]+ (2). An alternative reaction path to generate complexes of type 2 (relevant for electron-poor pincer complexes) includes initial coordination of styrene to 1 to yield styrene adducts [{2,6-C6H3(XPR2)2}Pd(Cl)(CH2CHPh)] (4) and consecutive dissociation of the chloride ligand to yield cationic square-planar styrene complexes [{2,6-C6H3(XPR2)2}Pd(CH2CHPh)]+ (6) and styrene. Cationic styrene adducts of type 6 were additionally found to be the resting states of the catalytic reaction. However, oxidative addition of phenyl bromide to 2 result in pentacoordinate PdIV complexes of type [{2,6-C6H3(XPR2)2}Pd(Br)(C6H5)]+ (11), which subsequently coordinate styrene (in trans position relative to the phenyl unit of the pincer cores) to yield hexacoordinate phenyl styrene complexes [{2,6-C6H3(XPR2)2}Pd(Br)(C6H5)(CH2CHPh)]+ (12). Migration of the phenyl ligand to the olefinic bond gives cationic, pentacoordinate phenylethenyl complexes [{2,6-C6H3(XPR2)2}Pd(Br)(CHPhCH2Ph)]+ (13). Subsequent ,-hydride elimination induces direct HBr liberation to yield cationic, square-planar (E)-stilbene complexes with general formula [{2,6-C6H3(XPR2)2}Pd(CHPhCHPh)]+ (14). Subsequent liberation of (E)-stilbene closes the catalytic cycle. [source] Aromatic,Carbohydrate Interactions: An NMR and Computational Study of Model SystemsCHEMISTRY - A EUROPEAN JOURNAL, Issue 25 2008Sophie Vandenbussche Ir. Abstract The interactions of simple carbohydrates with aromatic moieties have been investigated experimentally by NMR spectroscopy. The analysis of the changes in the chemical shifts of the sugar proton signals induced upon addition of aromatic entities has been interpreted in terms of interaction geometries. Phenol and aromatic amino acids (phenylalanine, tyrosine, tryptophan) have been used. The observed sugar,aromatic interactions depend on the chemical nature of the sugar, and thus on the stereochemistries of the different carbon atoms, and also on the solvent. A preliminary study of the solvation state of a model monosaccharide (methyl ,-galactopyranoside) in aqueous solution, both alone and in the presence of benzene and phenol, has also been carried out by monitoring of intermolecular homonuclear solvent,sugar and aromatic,sugar NOEs. These experimental results have been compared with those obtained by density functional theory methods and molecular mechanics calculations. [source] Computational Study of the Phosphoryl Transfer Catalyzed by a Cyclin-Dependent KinaseCHEMISTRY - A EUROPEAN JOURNAL, Issue 30 2007Marco De, Vivo Dr. Abstract A cyclin-dependent kinase, Cdk2, catalyzes the transfer of the ,-phosphate from ATP to a threonine or serine residue of its polypeptide substrates. Here, we investigate aspects of the reaction mechanism of Cdk2 by gas-phase density functional calculations, classical molecular dynamics, and Car,Parrinello QM/MM simulations. We focus on the role of the conserved Asp127 and on the nature of the phosphoryl transfer reaction mechanism catalyzed by Cdk2. Our findings suggest that Asp127 is active in its deprotonated form by assisting the formation of the near-attack orientation of the substrate serine or threonine. Therefore, the residue does not act as a general base during the catalysis. The mechanism for the phosphoryl transfer is a single SN2-like concerted step, which shows a phosphorane-like transition state geometry. Although the resulting reaction mechanism is in agreement with a previous density functional study of the same catalytic reaction mechanism (Cavalli et,al., Chem. Comm.2003, 1308,1309), the reaction barrier is considerably lower when QM/MM calculations are performed, as in this study (,42,kcal,mol,1 QM vs. ,24,kcal,mol,1 QM/MM); this indicates that important roles for the catalysis are played by the protein environment and solvent waters. Because of the high amino acid sequence conservation among the whole family of cyclin-dependent kinases (CDKs), these results could be general for the CDK family. [source] [(NHC)AuI]-Catalyzed Formation of Conjugated Enones and Enals: An Experimental and Computational StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 22 2007Nicolas Marion Abstract The [(NHC)AuI]-catalyzed (NHC = N-heterocyclic carbene) formation of ,,,-unsaturated carbonyl compounds (enones and enals) from propargylic acetates is described. The reactions occur at 60,°C in 8,h in the presence of an equimolar mixture of [(NHC)AuCl] and AgSbF6 and produce conjugated enones and enals in high yields. Optimization studies revealed that the reaction is sensitive to the solvent, the NHC, and, to a lesser extent, to the silver salt employed, leading to the use of [(ItBu)AuCl]/AgSbF6 in THF as an efficient catalytic system. This transformation proved to have a broad scope, enabling the stereoselective formation of (E)-enones and -enals with great structural diversity. The effect of substitution at the propargylic and acetylenic positions has been investigated, as well as the effect of aryl substitution on the formation of cinnamyl ketones. The presence or absence of water in the reaction mixture was found to be crucial. From the same phenylpropargyl acetates, anhydrous conditions led to the formation of indene compounds via a tandem [3,3] sigmatropic rearrangement/intramolecular hydroarylation process, whereas simply adding water to the reaction mixture produced enone derivatives cleanly. Several mechanistic hypotheses, including the hydrolysis of an allenol ester intermediate and SN2, addition of water, were examined to gain an insight into this transformation. Mechanistic investigations and computational studies support [(NHC)AuOH], produced in situ from [(NHC)AuSbF6] and H2O, instead of cationic [(NHC)AuSbF6] as the catalytically active species. Based on DFT calculations performed at the B3LYP level of theory, a full catalytic cycle featuring an unprecedented transfer of the OH moiety bound to the gold center to the CC bond leading to the formation of a gold,allenolate is proposed. Es descriu la reacció de formació de compostos de carbonil ,,, -insaturats (enones i enals) a partir d,acetats propargílics catalitzada per [(NHC)AuI] (NHC=carbè N-heterocíclic). Les reaccions tenen lloc a 60,°C en 8,h en presència d,una mescla equimolar de [(NHC)AuCl] i AgSbF6 i produeix rendiments alts d,enones i enals conjugats. Estudis d,optimització van mostrar que la reacció era sensible al solvent, el NHC, i, en menor grau, a la natura de la sal de plata emprada; això va portar a escollir [(ItBu)AuCl]/AgSbF6 en THF com a sistema catalític eficient. La transformació va mostrar posseir un ampli espectre, i es va aconseguir la formació estereoselectiva d,(E)-enones i -enals amb gran diversitat estructural. La influència de la substitució en les posicions propargílica i acetilènica va ser investigada, així com la substitució d,aril per donar lloc a la formació de cinamilcetones. La presència o absència d,aigua en el medi de reacció es va mostrar com a crucial. A partir dels mateixos fenilpropargilacetats, condicions anhidres van portar a la formació de compostos indènics mitjançant una reacció tàndem de reorganització sigmatròpica [3,3] i hidroarilació intramolecular, mentre que l,addició d,aigua a la reacció portava de manera neta a derivats del tipus enona. Diverses hipòtesis mecanístiques, entre elles la hidròlisi d,un intermedi del tipus al.lenol ester i l,addició SN2, d,aigua, han estat examinades per millorar la comprensió del procés. Les dades mecanístiques i els estudis computacionals suggereixen que l,espècie catalítica activa és [(NHC)AuOH], produït in situ a partir de [(NHC)AuSbF6] i H2O, i no el complex catiònic [(NHC)AuSbF6]. A partir d,estudis DFT realitzats al nivell B3LYP, es proposa un cicle catalític complet, que inclou un nou tipus d,etapa consistent en la transferència d,un grup OH des de l,or cap a l,enllaç CC per produir un complex or-al.lenolat. [source] An Experimental and Computational Study on Intramolecular Charge Transfer: A Tetrathiafulvalene-Fused Dipyridophenazine MoleculeCHEMISTRY - A EUROPEAN JOURNAL, Issue 13 2007Chunyang Jia Prof. Abstract To study the electronic interactions in donor,acceptor (D,A) ensembles, D and A fragments are coupled in a single molecule. Specifically, a tetrathiafulvalene (TTF)-fused dipyrido[3,2- a:2,,3,- c]phenazine (dppz) compound having inherent redox centers has been synthesized and structurally characterized. Its electronic absorption, fluorescence emission, photoinduced intramolecular charge transfer, and electrochemical behavior have been investigated. The observed electronic properties are explained on the basis of density functional theory. [source] Mechanism and exo -Regioselectivity of Organolanthanide-Mediated Intramolecular Hydroamination/Cyclization of 1,3-Disubstituted Aminoallenes: A Computational StudyCHEMISTRY - A EUROPEAN JOURNAL, Issue 9 2006Sven Tobisch Priv.-Doz. Abstract The complete catalytic reaction course for the organolanthanide-assisted intramolecular hydroamination/cyclization (IHC) of 4,5-heptadien-1-ylamine by a prototypical [(,5 -Me5C5)2LuCH(SiMe3)2] precatalyst has been critically scrutinized by employing a reliable DFT method. A computationally verified mechanistic scenario for the IHC of 1,3-disubstituted aminoallene substrates has been proposed that is consistent with the empirical rate law determined by experiment and accounts for crucial experimental observations. It involves kinetically rapid substrate association and dissociation equilibria, facile and reversible intramolecular allenic CC insertion into the LnN bond, and turnover-limiting protonation of the azacycle's tether functionality, with the amine-amidoalleneLn adduct complex representing the catalyst's resting state. This mechanistic scenario bears resemblance to the mechanism that has been recently proposed in a computational exploration of aminodiene IHC. The unique features of the IHC of the two substrate classes are discussed. Furthermore, the thermodynamic and kinetic factors that control the regio- and stereoselectivity of aminoallene IHC have been elucidated. These achievements have provided a deeper insight into the catalytic structure,reactivity relationships in organolanthanide-assisted cyclohydroamination of unsaturated CC functionalities. [source] | |||||||||||||||||||||||||||||||||||||||||||||||||