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Energy Profiles (energy + profile)
Kinds of Energy Profiles Selected AbstractsThe characteristics of Hessian singular vectors using an advanced data assimilation schemeTHE QUARTERLY JOURNAL OF THE ROYAL METEOROLOGICAL SOCIETY, Issue 642 2009A. R. Lawrence Abstract Initial condition uncertainty is a significant source of forecast error in numerical weather prediction. Singular vectors of the tangent linear propagator can identify directions in phase-space where initial errors are likely to make the largest contribution to forecast-error variance. The physical characteristics of these singular vectors depend on the choice of initial-time metric used to represent analysis-error covariances: the total-energy norm serves as a proxy to the analysis-error covariance matrix, whereas the Hessian of the cost function of a 4D-Var assimilation scheme represents a more sophisticated estimate of the analysis-error covariances, consistent with observation and background-error covariances used in the 4D-Var scheme. This study examines and compares the structure of singular vectors computed with the European Centre for Medium-Range Weather Forecasts (ECMWF) Integrated Forecasting System using these two types of initial metrics. Unlike earlier studies that use background errors derived from lagged forecast differences (the NMC method), the background-error covariance matrix in the Hessian metric is based on statistics from an ensemble of 4D-Vars using perturbed observations, which produces tighter correlations of background-error statistics than in previous formulations. In light of these new background-error statistics, this article re-examines the properties of Hessian singular vectors (and their relationship to total-energy singular vectors) using cases from different periods between 2003 and 2005. Energy profiles and wavenumber spectra reveal that the total-energy singular vectors are similar to Hessian singular vectors that use all observation types in the operational 4D-Var assimilation. This is in contrast to the structure of Hessian singular vectors without observations. Increasing the observation density tends to reduce the spatial scale of the Hessian singular vectors. Copyright © 2009 Royal Meteorological Society [source] Computational fluid dynamics modelling of boundary roughness in gravel-bed rivers: an investigation of the effects of random variability in bed elevationEARTH SURFACE PROCESSES AND LANDFORMS, Issue 4 2001A.P. Nicholas Abstract Results from a series of numerical simulations of two-dimensional open-channel flow, conducted using the computational fluid dynamics (CFD) code FLUENT, are compared with data quantifying the mean and turbulent characteristics of open-channel flow over two contrasting gravel beds. Boundary roughness effects are represented using both the conventional wall function approach and a random elevation model that simulates the effects of supra-grid-scale roughness elements (e.g. particle clusters and small bedforms). Results obtained using the random elevation model are characterized by a peak in turbulent kinetic energy located well above the bed (typically at y/h,=,0·1,0·3). This is consistent with the field data and in contrast to the results obtained using the wall function approach for which maximum turbulent kinetic energy levels occur at the bed. Use of the random elevation model to represent supra-grid-scale roughness also allows a reduction in the height of the near-bed mesh cell and therefore offers some potential to overcome problems experienced by the wall function approach in flows characterized by high relative roughness. Despite these benefits, the results of simulations conducted using the random elevation model are sensitive to the horizontal and vertical mesh resolution. Increasing the horizontal mesh resolution results in an increase in the near-bed velocity gradient and turbulent kinetic energy, effectively roughening the bed. Varying the vertical resolution of the mesh has little effect on simulated mean velocity profiles, but results in substantial changes to the shape of the turbulent kinetic energy profile. These findings have significant implications for the application of CFD within natural gravel-bed channels, particularly with regard to issues of topographic data collection, roughness parameterization and the derivation of mesh-independent solutions. Copyright © 2001 John Wiley & Sons, Ltd. [source] Interaction of FeO+ cation with benzene, aniline, and 3-methylaniline: DFT study of oxygen insertion mechanismINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 11 2008Karolina Kwapien Abstract The reaction pathways and energetics for oxygen insertion into CH bond in benzene, aniline, and 3-methylaniline by FeO+ in the gas phase were investigated by means of the DFT methodology with the B3LYP exchange-correlation functional and 6-311G** basis set. The main aim of this work was to elucidate the influence of substituents in phenyl ring on stationary points along the energy profile on sextet and quartet surfaces for the reaction of FeO+ with substituted benzenes. The studies show that the amino and methyl groups change the energetics of oxygen insertion by lowering the energy profile along the reaction pathway. The substituents studied in this work facilitate the insertion of oxygen into the aromatic CH bond by stabilizing the intermediate sigma complex (,-complex), the amino group being by far more effective. On the other hand, both functional groups increase the activation energy of the rate-determining step in the gas phase, so that they have unfavorable influence on the kinetics. The comparison of the energy diagrams for the sextet and quartet spin states indicates the dominance of the low-spin reactivity in oxygen insertion into aromatic CH bond. Aniline and 3-methylaniline oxidation occurs via electrophilic addition while the conversion of benzene to phenol by FeO+ is mediated by a ,-complex with mixed radical and cationic character. Present results are also discussed in the context of oxyferryl group reactivity. © 2008 Wiley Periodicals, Inc. Int J Quantum Chem, 2008 [source] Molecular dynamics simulations of the detoxification of paraoxon catalyzed by phosphotriesteraseJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 15 2009Xin Zhang Abstract Combined QM(PM3)/MM molecular dynamics simulations together with QM(DFT)/MM optimizations for key configurations have been performed to elucidate the enzymatic catalysis mechanism on the detoxification of paraoxon by phosphotriesterase (PTE). In the simulations, the PM3 parameters for the phosphorous atom were reoptimized. The equilibrated configuration of the enzyme/substrate complex showed that paraoxon can strongly bind to the more solvent-exposed metal ion Zn,, but the free energy profile along the binding path demonstrated that the binding is thermodynamically unfavorable. This explains why the crystal structures of PTE with substrate analogues often exhibit long distances between the phosphoral oxygen and Zn,. The subsequent SN2 reaction plays the key role in the whole process, but controversies exist over the identity of the nucleophilic species, which could be either a hydroxide ion terminally coordinated to Zn, or the ,-hydroxo bridge between the ,- and ,-metals. Our simulations supported the latter and showed that the rate-limiting step is the distortion of the bound paraoxon to approach the bridging hydroxide. After this preparation step, the bridging hydroxide ion attacks the phosphorous center and replaces the diethyl phosphate with a low barrier. Thus, a plausible way to engineer PTE with enhanced catalytic activity is to stabilize the deformed paraoxon. Conformational analyses indicate that Trp131 is the closest residue to the phosphoryl oxygen, and mutations to Arg or Gln or even Lys, which can shorten the hydrogen bond distance with the phosphoryl oxygen, could potentially lead to a mutant with enhanced activity for the detoxification of organophosphates. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009 [source] Isomers of C20: An energy profile IIJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 11 2003Kyle A. Beran Abstract Semi-empirical calculations, at the PM3 level provided within the Winmopac v2.0 software package, are used to geometrically optimize and determine the absolute energies (heats of formation) of a variety of C20 isomers that are predicted to exist in and around the bowl and cage isomers. Using the optimized Cartesian coordinates for the bowl and the cage isomers, a saddle-point calculation was performed. The output file generated, containing energy, distance, and geometry information, is then organized into a graphical format. The resulting graph, which plots the energy of the 20-atom system as a function of the distance from the geometric midpoint, is a two-dimensional energy profile. This profile illustrates an estimation of the contours on the potential energy surface, showing energy minima and maxima that are encountered as the bowl evolves into the cage structure, or vice-versa. To expand the surface into three dimensions, geometry optimizations were performed on the sets of Cartesian coordinates that correspond to energy minima in the bowl-cage profile. Based on these optimizations, eight additional isomers of C20 have been identified and are predicted to be energetically stable. These additional isomers were subsequently subjected to saddle-point calculations in order to identify those isomers that lie adjacent to one another on the three-dimensional surface. Two isomers that are adjacent to each other will exhibit an energy profile that progresses smoothly from the potential well of each isomer up to the saddle point separating them. Consequently, these adjacent pairs of isomers establish a step-wise transformation between the bowl and the cage. This process, which extends out over the three-dimensional surface, is predicted to require less energy than that of the direct, two-dimensional transformation predicted in the bowl-cage profile. © 2003 Wiley Periodicals, Inc. J Comput Chem 24: 1287,1290, 2003 [source] Effect of Oxygen Partial Pressure During Firing on the High AC Field Response of BaTiO3 DielectricsJOURNAL OF THE AMERICAN CERAMIC SOCIETY, Issue 4 2010Ichiro Fujii The effect of oxygen partial pressure during firing on the high field dielectric response of formulated and undoped BaTiO3 ceramics was investigated. For formulated ceramics, the dielectric constant of both oxygen- and air-fired samples increased almost linearly with the amplitude of the ac-driving field. Formulated BaTiO3 samples sintered in a reducing atmosphere produced a sublinear increase in the permittivity with the ac field amplitude. For undoped BaTiO3 ceramics, the dielectric constant increased sublinearly over a wide range of oxygen partial pressures during firing. It is proposed for the formulated ceramics that the dopant-oxygen vacancy defect dipoles in the shell region accounted for the curvature in the field dependence of the permittivity. These defects appear to add a concentration of weak pinning centers to the potential energy profile through which domain walls move. [source] Transport Processes at ,-Quartz,Water Interfaces: Insights from First-Principles Molecular Dynamics SimulationsCHEMPHYSCHEM, Issue 7 2008Waheed A. Adeagbo Dr. Abstract Car,Parrinello molecular dynamics (CP,MD) simulations are performed at high temperature and pressure to investigate chemical interactions and transport processes at the ,-quartz,water interface. The model system initially consists of a periodically repeated quartz slab with O-terminated and Si-terminated (1000) surfaces sandwiching a film of liquid water. At a temperature of 1000 K and a pressure of 0.3 GPa, dissociation of H2O molecules into H+ and OH, is observed at the Si-terminated surface. The OH, fragments immediately bind chemically to the Si-terminated surface while Grotthus-type proton diffusion through the water film leads to protonation of the O-terminated surface. Eventually, both surfaces are fully hydroxylated and no further chemical reactions are observed. Due to the confinement between the two hydroxylated quartz surfaces, water diffusion is reduced by about one third in comparison to bulk water. Diffusion properties of dissolved SiO2 present as Si(OH)4 in the water film are also studied. We do not observe strong interactions between the hydroxylated quartz surfaces and the Si(OH)4 molecule as would have been indicated by a substantial lowering of the Si(OH)4 diffusion coefficient along the surface. No spontaneous dissolution of quartz is observed. To study the mechanism of dissolution, constrained CP,MD simulations are done. The associated free energy profile is calculated by thermodynamic integration along the reaction coordinate. Dissolution is a stepwise process in which two SiO bonds are successively broken. Each bond breaking between a silicon atom at the surface and an oxygen atom belonging to the quartz lattice is accompanied by the formation of a new SiO bond between the silicon atom and a water molecule. The latter loses a proton in the process which eventually leads to protonation of the oxygen atom in the cleaved quartz SiO bond. The final solute species is Si(OH)4. [source] Ab initio Study of Mechanism of Forming a Germanic Hetero-Polycyclic Compound between Germylidene (H2C=Ge:) and AcetoneCHINESE JOURNAL OF CHEMISTRY, Issue 8 2010Xiuhui Lu Abstract The mechanism of the cycloaddition reaction of forming a germanic hetero-polycyclic compound between singlet germylidene (R1) and acetone (R2) has been investigated with CCSD(T)//MP2/6-31G* method. From the surface energy profile, it can be predicted that the dominant reaction pathway for this reaction consists of three steps: (1) the two reactants (R1, R2) firstly form a twisted four-membered ring intermediate (INT2); (2) the intermediate (INT2) reacts further with acetone (R2) to give another intermediate (INT4); (3) intermediate (INT4) isomerizes to a hetero-polycyclic germanic compound (P4) via a transition state TS4. The presented rule of this reaction: the [2+2] cycloaddition effect between the , orbital of germylidene and the , orbital of ,-bonded compounds leads to the formation of four-membered ring intermediate (INT2). The 4p unoccupied orbital and the lone-pair sp electrons of Ge in the four-membered ring intermediate (INT2) react with the , orbital and the antibonding ,* orbital of ,-bonded compounds, respectively, forming the ,,p and sp, ,* cyclic donor-acceptor bonds, resulting in the generation of a stable germanic hetero-polycyclic compound (P4). [source] Theoretical Study on the Mechanism of the Petasis-type Boronic Mannich Reaction of Organoboronic Acids, Amines, and , -Hydroxy AldehydesCHINESE JOURNAL OF CHEMISTRY, Issue 1 2010Jingcong Tao Abstract The mechanism of a typical Petasis-type boronic mannich reaction (the styrylboronic acid, dibenzylamine, and , -hydroxylpropionaldehyde) has been investigated using density functional theory calculations. According to our calculations, the reaction is most likely to proceed through the following steps: 1) the nucleophilic addition of the amine to the aldehyde to form the carbinolamine; 2) the dehydration of the carbinolamine; 3) the formation of the tetra-coordinated borate intermediate; 4) the CC bond formation by the intramolecular transfer of the styryl group; 5) the hydrolysis of the resulting intermediate to give the final products. The highest point on the energy profile is the transition state for the CC bond formation (118.8 kJ·mol,1 above the reactants in ethanol). Our results can give reasonable explanations on some experimental facts observed for many Petasis-type boronic Mannich reactions. [source] A DFT study on the hydrolysis mechanism of NH-tautomeric antitumors of [HL][trans -RuCl4L(dmso- S)]INTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 6 2010Jin Can Chen Abstract The hydrolysis process of Ru (III) complex [Htrz][trans -RuCl4(1- H -1,2,4-triazole)(dmso- S)] 1, a potential antitumor complex similar to the well-known anticancer agent [ImH][trans -RuCl4(Im)(dmso- S)] (NAMI-A), has been investigated by using density functional theory (DFT) method, and the solvent effect was also considered and calculated by conductor-like polarizable calculation model (CPCM). Meanwhile, the hydrolysis process of the NH-tautomeric isomer, [Htrz][trans -RuCl4(4- H -1,2,4-triazole)(dmso- S)] 2, was also modeled and predicted by the same methods. The structural characteristics and the detailed energy profiles for the hydrolysis processes of two isomers have been obtained. The analysis of thermodynamic and kinetic characteristics of hydrolysis reaction suggests the following: for the first hydrolysis step, the Complex 1 has lower hydrolysis rate than the reported anticancer drug NAMI-A, and the result is in accordance with experimental one. However, Complex 1 has obviously higher hydrolysis rate than its isomer Complex 2, and the result was reasonably explained in theory. For the second hydrolysis step, the formation of cis -diaqua species is thermodynamic preferred to that of trans isomers. In addition, the trend in nucleophilic attack abilities (A) of hydrolysis products by pertinent biomolecules was revealed and predicted. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010 [source] BSSE-free hardness profiles of hydrogen bond exchange in the hydrogen fluoride dimerINTERNATIONAL JOURNAL OF QUANTUM CHEMISTRY, Issue 14 2006David Asturiol Abstract Hardness profiles are calculated for the hydrogen bond interchange in the hydrogen fluoride dimer; the study is carried out at the Hartree,Fock and second-order Møller,Plesset (MP2) levels of theory with three different basis sets. The basis set superposition error (BSSE) is corrected by means of the chemical Hamiltonian approach (CHA). Uncorrected and BSSE-corrected energy and hardness profiles are compared. Their analysis shows that hardness profiles do not lead to spurious minima as energy profiles do in various cases. The CHA methodology is shown to be valuable in the analysis of intermolecular interactions, with BSSE observed to carry smaller modifications on hardness profiles than on energy curves. © 2006 Wiley Periodicals, Inc. Int J Quantum Chem, 2006 [source] Rheological and electrical properties of bentonite in anionic polystyrene sulfonate and nonionic poly(vinyl alcohol)JOURNAL OF APPLIED POLYMER SCIENCE, Issue 6 2007Bassem A. Mostafa Abstract The flow properties of bentonite were studied with a combination of anionic polystyrene sulfonate (molecular weight = 70,000 g/mol) and nonionic poly(vinyl alcohol) (molecular weight = 50,000 g/mol). This combination had a significant effect on clay suspensions depending on the sequence of the polymer addition. The addition of 50 mg/L anionic polystyrene sulfonate followed by 200 mg/L nonionic poly(vinyl alcohol) improved the rheological properties with a 7% bentonite suspension, especially at 20°C and after 24 h of aging. However, by the reversal of this addition sequence, the rheological properties of bentonite suspensions were reduced. The , potential of bentonite suspensions of the individual polymers at the same concentration was ,42 mV for polystyrene sulfonate and ,63 mV for poly(vinyl alcohol). The combined effect of anionic polystyrene sulfonate followed by nonionic poly(vinyl alcohol) noticeably changed the , potential (,95 mV). With the reversal of the addition sequence, this parameter did not change. Potential energy profiles were constructed to investigate the suspension stability. Potential energy profiles of polystyrene sulfonate added to bentonite suspensions and followed by poly(vinyl alcohol) produced high repulsion potential energy between clay surfaces, reflecting high suspension stability. By the reversal of this sequence, a significant reduction of the energy barrier was observed. On the basis of the rheological and electrical properties of this system, the addition of polystyrene sulfonate followed by poly(vinyl alcohol) provides a promising tendency for a 7% clay concentration to meet desirable drilling mud properties. © 2007 Wiley Periodicals, Inc. J Appl Polym Sci 104: 3886,3894, 2007 [source] DFT conformational studies of ,-maltotriose,JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2008Udo Schnupf Abstract Recent DFT optimization studies on ,-maltose improved our understanding of the preferred conformations of ,-maltose. The present study extends these studies to ,-maltotriose with three ,- D -glucopyranose residues linked by two ,-[1,4] bridges, denoted herein as DP-3's. Combinations of gg, gt, and tg hydroxymethyl groups are included for both "c" and "r" hydroxyl rotamers. When the hydroxymethyl groups are for example, gg-gg-gg, and the hydroxyl groups are rotated from all clockwise, "c", to all counterclockwise, "r", the minimum energy positions of the bridging dihedral angles (,H and ,H) move from the region of conformational space of (,, ,), relative to (0°, 0°), to a new position defined by (+, +). Further, it was found previously that the relative energies of ,-maltose gg-gg-c and "r" conformations were very close to one another; however, the DP-3's relative energies between hydroxyl "c" or "r" rotamers differ by more than one kcal/mol, in favor of the "c" form, even though the lowest energy DP-3 conformations have glycosidic dihedral angles similar to those found in the ,-maltose study. Preliminary solvation studies using COSMO, a dielectric solvation method, point to important solvent contributions that reverse the energy profiles, showing an energy preference for the "r" forms. Only structures in which the rings are in the chair conformation are presented here. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2008 [source] Combined DFT, QCISD(T), and G2 mechanism investigation for the reactions of carbon monophosphide CP with unsaturated hydrocarbons allene CH2CCH2 and methylacetylene CH3CCHJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 7 2007YAn-Li Zhao Abstract The possible reaction product distribution and mechanism of carbon monophosphide CP with unsaturated hydrocarbons allene CH2CCH2 and methylacetylene CH3CCH are investigated at the B3LYP/6-311+G(d,p), QCISD(T)/6-311++G(2df,2p), and G2 levels of theory. Corresponding reactants, products, intermediates, and interconversion and dissociation transition states are located on the reaction potential energy profiles. Computation results show that in the reaction of CP with CH2CCH2 the dominant reaction product should be species CH2CCHCP. Also, we can suggest species HCCCH2CP as a secondary reaction product despite of only minor contribution to reaction products. In the reaction of CP with CH3CCH, the primary and secondary products are suggested to be two important molecules HCCCP and CH3CCCP, respectively. The predicted mechanisms for the two reactions are not in parallel with the reactions of CN with allene CH2CCH2 and methylacetylene CH3CCH given in previous studies. The present calculations provide some useful information for future possible experimental isolation and observation for some interesting unsaturated carbon,phosphorus-bearing species. © 2007 Wiley Periodicals, Inc. J Comput Chem, 2007 [source] Ab initio calculations of intramolecular parameters for a class of arylamide polymersJOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 6 2006Satyavani Vemparala Abstract Using DFT methods, we have determined intramolecular parameters for an important class of arylamide polymers displaying antimicrobial and anticoagulant inhibitory properties. A strong link has been established between these functions and the conformation that the polymers adopt in solution and at lipid bilayer interfaces. Thus, it is imperative for molecular dynamics simulations designed to probe the conformational behavior of these systems to accurately describe the torsional degrees of freedom. Standard force fields were shown to be deficient in this respect. Therefore, we have computed the relevant torsional energy profiles using a series of constrained geometry optimizations. We have also determined electrostatic parameters using our results in combination with standard RESP charge optimization. Force constants for bond and angle potentials were calculated by iteratively matching quantum and classical normal modes via a Monte Carlo scheme. The resulting new set of parameters accurately described the conformation and dynamical behavior of the arylamide polymers. © 2006 Wiley Periodicals, Inc. J Comput Chem 27: 693,700, 2006 [source] Comparison of linear-scaling semiempirical methods and combined quantum mechanical/molecular mechanical methods for enzymic reactions.JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 14 2002Abstract QM/MM methods have been developed as a computationally feasible solution to QM simulation of chemical processes, such as enzyme-catalyzed reactions, within a more approximate MM representation of the condensed-phase environment. However, there has been no independent method for checking the quality of this representation, especially for highly nonisotropic protein environments such as those surrounding enzyme active sites. Hence, the validity of QM/MM methods is largely untested. Here we use the possibility of performing all-QM calculations at the semiempirical PM3 level with a linear-scaling method (MOZYME) to assess the performance of a QM/MM method (PM3/AMBER94 force field). Using two model pathways for the hydride-ion transfer reaction of the enzyme dihydrofolate reductase studied previously (Titmuss et al., Chem Phys Lett 2000, 320, 169,176), we have analyzed the reaction energy contributions (QM, QM/MM, and MM) from the QM/MM results and compared them with analogous-region components calculated via an energy partitioning scheme implemented into MOZYME. This analysis further divided the MOZYME components into Coulomb, resonance and exchange energy terms. For the model in which the MM coordinates are kept fixed during the reaction, we find that the MOZYME and QM/MM total energy profiles agree very well, but that there are significant differences in the energy components. Most significantly there is a large change (,16 kcal/mol) in the MOZYME MM component due to polarization of the MM region surrounding the active site, and which arises mostly from MM atoms close to (<10 Å) the active-site QM region, which is not modelled explicitly by our QM/MM method. However, for the model where the MM coordinates are allowed to vary during the reaction, we find large differences in the MOZYME and QM/MM total energy profiles, with a discrepancy of 52 kcal/mol between the relative reaction (product,reactant) energies. This is largely due to a difference in the MM energies of 58 kcal/mol, of which we can attribute ,40 kcal/mol to geometry effects in the MM region and the remainder, as before, to MM region polarization. Contrary to the fixed-geometry model, there is no correlation of the MM energy changes with distance from the QM region, nor are they contributed by only a few residues. Overall, the results suggest that merely extending the size of the QM region in the QM/MM calculation is not a universal solution to the MOZYME- and QM/MM-method differences. They also suggest that attaching physical significance to MOZYME Coulomb, resonance and exchange components is problematic. Although we conclude that it would be possible to reparameterize the QM/MM force field to reproduce MOZYME energies, a better way to account for both the effects of the protein environment and known deficiencies in semiempirical methods would be to parameterize the force field based on data from DFT or ab initio QM linear-scaling calculations. Such a force field could be used efficiently in MD simulations to calculate free energies. © 2002 Wiley Periodicals, Inc. J Comput Chem 23: 1314,1322, 2002 [source] [2,+,3] Cycloaddition of C,C,N -triphenylnitrone to trans -substituted nitroethylenes in the light of an AM1 and AM1/COSMO computational study,JOURNAL OF PHYSICAL ORGANIC CHEMISTRY, Issue 5 2003Andrzej Baranski Abstract AM1 calculations suggest that the [2,+,3] cycloaddition of triphenylnitrone 1 to nitroalkenes 2a,c in the gas phase takes place in a concerted manner. However, the azolidine ring bonds C3,C4 and O1,C5 are not formed fully synchronously. Kinetic factors favor the formation of cycloadducts with nitro group in position C-4 of the azolidine ring (path A). Introduction of toluene, acetone or acetonitrile as a reaction medium increases the activation barriers for both regioisomeric paths. Simultaneously, the energy profiles for path A undergo qualitative change. In this case, two transition states and an intermediate with zwitterionic character were localized by means of the AM1/COSMO method. Copyright © 2003 John Wiley & Sons, Ltd. [source] Deactivation reactions in the modeled 2,2,6,6-tetramethyl-1-piperidinyloxy-mediated free-radical polymerization of styrene: A comparative study with the 2,2,6,6-tetramethyl-1-piperidinyloxy/acrylonitrile systemJOURNAL OF POLYMER SCIENCE (IN TWO SECTIONS), Issue 2 2007Andrzej Kaim Abstract The competitiveness of the combination and disproportionation reactions between a 1-phenylpropyl radical, standing for a growing polystyryl macroradical, and a 2,2,6,6-tetramethyl-1-piperidinyloxy (TEMPO) radical in the nitroxide-mediated free-radical polymerization of styrene was quantitatively evaluated by the study of the transition geometry and the potential energy profiles for the competing reactions with the use of quantum-mechanical calculations at the density functional theory (DFT) UB3-LYP/6-311+G(3df, 2p)//(unrestricted) Austin Model 1 level of theory. The search for transition geometries resulted in six and two transition structures for the radical combination and disproportionation reactions, respectively. The former transition structures, mainly differing in the out-of-plane angle of the NO bond in the transition structure TEMPO molecule, were correlated with the activation energy, which was determined to be in the range of 8.4,19.4 kcal mol,1 from a single-point calculation at the DFT UB3-LYP/6-311+G(3df, 2p)//unrestricted Austin Model 1 level. The calculated activation energy for the disproportionation reaction was less favorable by a value of more than 30 kcal mol,1 in comparison with that for the combination reaction. The approximate barrier difference for the TEMPO addition and disproportionation reaction was slightly smaller for the styrene polymerization system than for the acrylonitrile polymerization system, thus indicating that a ,-proton abstraction through a TEMPO radical from the polymer backbone could diminish control over the radical polymerization of styrene with the nitroxide even more than in the latter system. © 2006 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem 45: 232,241, 2007 [source] Ligand diffusion in the catalase from Proteus mirabilis: A molecular dynamics studyPROTEIN SCIENCE, Issue 10 2001Patricia Amara Abstract The role of the channels and cavities present in the catalase from Proteus mirabilis (PMC) was investigated using molecular dynamics (MD) simulations. The reactant and products of the reaction, H2O2 ,1/2 O2 + H2O, catalyzed by the enzyme were allowed to diffuse to and from the active site. Dynamic fluctuations in the structure are found necessary for the opening of the major channel, ideied in the X-ray model, which allows access to the active site. This channel is the only pathway to the active site observed during the dynamics, and both the products and reactant use it. H2O and O2 are also detected in a cavity defined by the heme and Ser196, which could play an important role during the reaction. Free energy profiles of the ligands diffusing through the major channel indicate that the barriers to ligand diffusion are less than 20 kJ mol,1 for each of the species. It is not clear from our study that minor channels play a role for access to the protein active site or to the protein surface. [source] Understanding African easterly waves: a moist singular vector approachATMOSPHERIC SCIENCE LETTERS, Issue 3 2009Rosalind J. Cornforth Abstract Moist singular vectors (MSV) have been applied successfully to predicting mid-latitude storms growing in association with latent heat of condensation. Tropical cyclone sensitivity has also been assessed. Extending this approach to more general tropical weather systems here, MSVs are evaluated for understanding and predicting African easterly waves, given the importance of moist processes in their development. First results, without initial moisture perturbations, suggest MSVs may be used advantageously. Perturbations bear similar structural and energy profiles to previous idealised non-linear studies and observations. Strong sensitivities prevail in the metrics and trajectories chosen, and benefits of initial moisture perturbations should be appraised. Copyright © 2009 Royal Meteorological Society [source] Determination of the Catalytic Pathway of a Manganese Arginase Enzyme Through Density Functional InvestigationCHEMISTRY - A EUROPEAN JOURNAL, Issue 32 2009Monica Leopoldini Dr. Abstract The catalytic mechanism of dimanganese-containing arginase enzyme has been investigated by DFT calculations. Two exchange-correlation functionals, B3,LYP and MPWB1,K, have been used to construct the potential energy profiles for the hydrolysis of an arginine substrate performed by an arginase active site model system. Two reaction mechanisms have been investigated, one involving a water molecule (mechanism,1) and the other involving a hydroxide ion (mechanism,2) as nucleophilic agent. Results obtained in the gas phase and in the protein environment have indicated that mechanism,1 involving a water molecule entails structural features as well as an activation energy for the rate-determining step that are inconsistent with experimental data available for the arginase enzyme. On the other hand, when a hydroxide ion is present at the Mn2 site, a lower activation energy and a structural arrangement closer to the experimental indication are obtained. [source] Ab Initio Molecular Dynamics Studies of Ionic Dissolution and Precipitation of Sodium Chloride and Silver Chloride in Water Clusters, NaCl(H2O)n and AgCl(H2O)n, n = 6, 10, and 14CHEMISTRY - A EUROPEAN JOURNAL, Issue 24 2006Chi-Kit Siu Dr. Abstract An ab initio molecular dynamics method was used to compare the ionic dissolution of soluble sodium chloride (NaCl) in water clusters with the highly insoluble silver chloride (AgCl). The investigations focused on the solvation structures, dynamics, and energetics of the contact ion pair (CIP) and of the solvent-separated ion pair (SSIP) in NaCl(H2O)n and AgCl(H2O)n with cluster sizes of n = 6, 10 and 14. We found that the minimum cluster size required to stabilize the SSIP configuration in NaCl(H2O)n is temperature-dependent. For n = 6, both configurations are present as two distinct local minima on the free-energy profile at 100 K, whereas SSIP is unstable at 300 K. Both configurations, separated by a low barrier (<10 kJ,mol,1), are identifiable on the free energy profiles of NaCl(H2O)n for n = 10 and 14 at 300 K, with the Na+/Cl, pairs being internally solvated in the water cluster and the SSIP configuration being slightly higher in energy (<5 kJ,mol,1). In agreement with the low bulk solubility of AgCl, no SSIP minimum is observed on the free-energy profiles of finite AgCl(H2O)n clusters. The AgCl interaction is more covalent in nature, and is less affected by the water solvent. Unlike NaCl, AgCl is mainly solvated on the surface in finite water clusters, and ionic dissolution requires a significant reorganization of the solvent structure. [source] A Theoretical Study of Surface Reduction Mechanisms of CeO2(111) and (110) by H2CHEMPHYSCHEM, Issue 6 2007Hsin-Tsung Chen Dr. Abstract Reaction mechanisms for the interactions between CeO2(111) and (110) surfaces are investigated using periodic density functional theory (DFT) calculations. Both standard DFT and DFT+U calculations to examine the effect of the localization of Ce 4f states on the redox chemistry of H2,CeO2 interactions are described. For mechanistic studies, molecular and dissociative local minima are initially located by placing an H2 molecule at various active sites of the CeO2 surfaces. The binding energies of physisorbed species optimized using the DFT and DFT+U methods are very weak. The dissociative adsorption reactions producing hydroxylated surfaces are all exothermic; exothermicities at the DFT level range from 4.1 kcal,mol,1 for the (111) to 26.5 kcal,mol,1 for the (110) surface, while those at the DFT+U level are between 65.0 kcal,mol,1 for the (111) and 81.8 kcal,mol,1 for the (110) surface. Predicted vibrational frequencies of adsorbed OH and H2O species on the surfaces are in line with available experimental and theoretical results. Potential energy profiles are constructed by connecting molecularly adsorbed and dissociatively adsorbed intermediates on each CeO2 surface with tight transition states using the nudged elastic band (NEB) method. It is found that the U correction method plays a significant role in energetics, especially for the intermediates of the exit channels and products that are partially reduced. The surface reduction reaction on CeO2(110) is energetically much more favorable. Accordingly, oxygen vacancies are more easily formed on the (110) surface than on the (111) surface. [source] | ||||||||||||||||||||||||||||