Department of Chemistry

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The biosynthesis of abietadiene is the first biosynthetically relevant process shown to involve a potential energy surface with a bifurcating reaction pathway. Herein, we use gas-phase, enzyme-free direct dynamics simulations to study the behavior of the key reaction (bifurcating) step, which is conversion of the C 20 pimaradienyl cation to the abietadienyl cation. In a previous study (J. Am. Chem. Soc.2011, 133, 8335), a truncated C 10 model was used to investigate this reaction. The current work finds that the complete C 20 pimaradienyl cation gives reaction dynamics similar to that reported for the truncated C 10 model. We find that in the absence of the enzyme, the C 20 abietadienyl cation is generated in almost equal quantity (1.3:1) as an unobserved (in nature) seven-membered ring product. These simulations allude to a need for abietadiene synthase to steer the reaction to avoid generation of the seven-membered ring product. The methodology of post-transition state chemical dynamics simulations is also considered. The trajectories are initiated at the rate-controlling transition state (TS) separating the pimaradienyl and abietadienyl cations. Accurate results are expected for the short-time direct motion from this TS toward the abietadienyl cation. However, the dynamics may be less accurate for describing the unimolecular reactions that occur in moving toward the pimaradienyl cation, due to the unphysical flow of zero-point energy. © 2012 American Chemical Society.

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Journal of Chemical Theory and Computation

Gas-phase chemical dynamics simulations on the bifurcating pathway of the pimaradienyl cation rearrangement: Role of enzymatic steering in abietic acid biosynthesis

Pd grating patterns have been fabricated using the process of micromolding in capillary employing a Pd alkanethiolate precursor, which could be converted to metal in situ by thermolysis. Thus generated Pd grating were uniform in width (∼950 nm) and spacing (∼450 nm) over millimeter square areas on glass substrates. Importantly, the pattern when used as an optical grating produced a diffraction pattern with a high resolution (&gt;2000); the intensities of widely separated (diffraction angle, ∼26·8°) diffracted spots could be measured using a simple photodiode. By varying the concentration of Pd precursor (2mMto 25 mM), thickness of the resulting gratings could be adjusted in the range of ∼15-115 nm. By adjusting the grating parameters optimally, a maximum diffraction efficiency of 36% has been achieved. Thus fabricated Pd grating was used as seed catalyst to deposit Cu by electroless plating. The Cu deposition process has also been monitored by employing AFM, SEM and EDS analysis. The diffraction efficiency values corroborate well with the changes in the grating thickness due to Cu deposition. The grating structures presented can be reproducibly fabricated for rapidly emerging optical diffraction based sensing applications. This has been demonstrated in the case of aqueous Cu 2+ by depositing the latter electrolessly on Pd. © Indian Academy of Sciences.

Fulltext

Bulletin of Materials Science

Pd grating obtained by direct micromolding for use in high resolution optical diffraction based sensing

Organic fluorescent materials that enable a control of the emission color based on external influence are highly sought after in optoelectronic applications. A simple molecule, a di-methoxy substituted oligo(phenyleneethynylene), whose emission can be precisely tuned by controlling the cooling rate from the melt (1-13 °C min-1 and higher) or by changing the crystallization process on substrate surfaces, is presented. Interestingly, the emission intensity at 397 nm of the melt cooled films was found to be linearly dependent on the diffraction intensity of the (200) preferred orientation of the crystallites. The surrounding medium too seems to influence the emission behavior depending on the thermal diffusivity. Furthermore, the emission is also found to be sensitive to the substrate topography and roughness as a rough surface becomes unconducive to aggregation. © The Royal Society of Chemistry.

Journal of Materials Chemistry

Tunable solid state fluorescence behavior of a methoxy substituted oligo(phenyleneethynylene): Influence of cooling rate and surface crystallization

Extensive classical chemical dynamics simulations of gas-phase X - + CH 3Y→ XCH 3 + Y - S N2 nucleophilic substitution reactions are reviewed and discussed and compared with experimental measurements and predictions of theoretical models. The primary emphasis is on reactions for which X and Y are halogen atoms. Both reactions with the traditional potential energy surface (PES), which include pre- and postreaction potential energy minima and a central barrier, and reactions with nontraditional PESs are considered. These S N2 reactions exhibit important nonstatistical atomic-level dynamics. The X - + CH 3Y→ X --CH 3Y association rate constant is less than the capture model as a result of inefficient energy transfer from X -+ CH 3Y relative translation to CH 3Y rotation and vibration. There is weak coupling between the low-frequency intermolecular modes of the X --CH 3Y complex and higher frequency CH 3Y intramolecular modes, resulting in non-RRKM kinetics for X --CH 3Y unimolecular decomposition. Recrossings of the [X - CH 3 - Y] - central barrier is important. As a result of the above dynamics, the relative translational energy and temperature dependencies of the S N2 rate constants are not accurately given by statistical theory. The nonstatistical dynamics results in nonstatistical partitioning of the available energy to XCH 3 +Y - reaction products. Besides the indirect, complex forming atomic-level mechanism for the S N2 reaction, direct mechanisms promoted by X - + CH 3Y relative translational or CH 3Y vibrational excitation are possible, e.g., the roundabout mechanism. © 2012 American Chemical Society.

Journal of Physical Chemistry A

Chemical dynamics simulations of X - + CH 3Y → XCH 3 + Y - gas-phase S N2 nucleophilic substitution reactions. Nonstatistical dynamics and nontraditional reaction mechanisms

Previous studies have shown that classical trajectory simulations often give accurate results for short-time intramolecular and unimolecular dynamics, particularly for initial non-random energy distributions. To obtain such agreement between experiment and simulation, the appropriate distributions must be sampled to choose initial coordinates and momenta for the ensemble of trajectories. If a molecules classical phase space is sampled randomly, its initial decomposition will give the classical anharmonic microcanonical (RRKM) unimolecular rate constant for its decomposition. For the work presented here, classical trajectory simulations of the unimolecular decomposition of quantum and classical microcanonical ensembles, at the same fixed total energy, are compared. In contrast to the classical microcanonical ensemble, the quantum microcanonical ensemble does not sample the phase space randomly. The simulations were performed for CH 4, C 2H 5, and Cl - - -CH 3Br using both analytic potential energy surfaces and direct dynamics methods. Previous studies identified intrinsic RRKM dynamics for CH 4 and C 2H 5, but intrinsic non-RRKM dynamics for Cl - - -CH 3Br. Rate constants calculated from trajectories obtained by the time propagation of the classical and quantum microcanonical ensembles are compared with the corresponding harmonic RRKM estimates to obtain anharmonic corrections to the RRKM rate constants. The relevance and accuracy of the classical trajectory simulation of the quantum microcanonical ensemble, for obtaining the quantum anharmonic RRKM rate constant, is discussed. © 2012 American Institute of Physics.

Journal of Chemical Physics

Comparisons of classical chemical dynamics simulations of the unimolecular decomposition of classical and quantum microcanonical ensembles

The scattering of high kinetic energy (1-6.5 eV) xenon and krypton atoms from ice was experimentally measured and theoretically modeled. The ice efficiently accommodates translational energy, but the extent to which the energy is quenched suggests the mechanism for the highest energies and near-normal incidence angles involves more than interaction with just the molecules at the ice surface. Simulations show that for these conditions the xenon penetrates into the selvedge. This penetration into the solid manifests experimentally in that the postcollision translational energy is essentially independent of the incident translational energy. This observation is in stark contrast with what is usually the situation for scattering from a surface. Finally, postexposure desorption measurements showed that some of the incident gas atoms were trapped in the bulk of the ice at temperatures well above where the absorption is thermodynamically stable. The above evidence leads to the conclusion that under conditions of near-normal angles of incidence and high collision energy, much, if not most, of the rare gas penetrates below the ice surface and into the selvedge. A fraction is stably embedded in the near surface region of the ice, whereas the remaining rare gas escapes with two distinct velocity distributions; the first is a result of a thermal process and the second, faster distribution, is the result of ejection from the solid. © 2012 American Chemical Society.

Journal of Physical Chemistry C

Scattering of high-incident-energy Kr and Xe from ice: Evidence that a major channel involves penetration into the bulk

Structure and dynamics of acrylodan labeled A-crystallin tetramer formed in the presence of a bile salt (sodium deoxycholate, NaDC) has been studied using fluorescence correlation spectroscopy (FCS) and femtosecond up-conversion techniques. Using FCS it is shown that, the diffusion constant (D t) of the A-crystallin oligomer (mass ∼800 kDa) increases from ∼35 m 2 s -1 to ∼68 m 2 s -1. This corresponds to a decrease in hydrodynamic radius (r h) from ∼6.9 nm to ∼3.3 nm. This corresponds to about 10-fold decrease in molecular mass to ∼80 kDa and suggests formation of a tetramer (since mass of A-crystallin monomer is ∼20 kDa). The steady state emission maximum and average solvation time ( s) of acrylodan labeled at cysteine 131 position of A-crystallin is markedly affected on addition of NaDC, while the tryptophan (trp-9) becomes more exposed. This suggests that NaDC binds near the cys-131 and makes the terminal region of A-crystallin exposed. This may explain the enhanced auto-phosphorylation activity of A-crystallin near the terminus of the 173 amino acid protein (e.g., at the threonine 13, serine 45, or serine 169 and 172) and suggests that phosphorylation at ser-122 (close to cys-131) is relatively less important. © 2012 American Institute of Physics.

Deoxycholate induced tetramer of αa-crystallin and sites of phosphorylation: Fluorescence correlation spectroscopy and femtosecond solvation dynamics

Organocatalytic conjugate addition of thioacids to α,β- unsaturated ketones has been studied in the presence of cinchona alkaloid derived urea catalyst. Both the enantiomers of products are accessible with the same level of enantioselectivity using pseudoenantiomeric quinine/quinidine derived catalysts. The catalytic process provides optically active thioesters with high chemical yields (up to 99%) and useful enantioselectivity (up to 83% ee). The reaction was performed with 1 mol % of catalyst in toluene at room temperature. A transition state model has been proposed to explain the stereochemical outcome of the reaction. © 2012 Elsevier Ltd. All rights reserved.

Tetrahedron Letters

Enantioselective sulfa-Michael addition of thioacids to α,β-unsaturated ketones with bifunctional organocatalyst

An efficient enantioselective conjugate addition of malononitrile to a range of β-substituted 2-enoylpyridines catalyzed by cinchona alkaloid-based bifunctional urea catalysts has been developed. Both enantiomers of the products could be achieved with the same level of enantioselectivity by using pseudoenantiomeric catalysts in up to 97% ee and in excellent yields. One of the enantioenriched products has been transformed to a highly functionalized piperidone derivative. © 2012 American Chemical Society.