On analytic potential functions and molecular dynamics for reactions on metal surfaces

We present a method that allows one to obtain reaction energy profiles for dissociation/recombination reactions on metal surfaces. Our method is related to the bond order conservation-Morse potential method of Shustorovich but with the differences that we employ dynamic Morse potentials and our modified bond order conservation law. Our method approximates the energy curves along the reaction coordinates and is applicable to all manner of dissociations (not just symmetric dissociations). We compare the results of our method with ab initio energy curves in the literature, experimental results and the results of the BOC-MP model of Shustorovich. Our model is able to produce reasonable representations of the reaction energy profiles for the decomposition of methane thiol and SH on gold, and, it produces energy profiles that agree with ab initio calculations and the model of Shustorovich. We also present a molecular dynamics simulation of the dissociation of H₂ on Ni(111), employing this method for obtaining reactive potential energy functions, and, demonstrate that the reciprocals of the computed reaction times obey Arrhenius kinetics.     

Analytical force constant calculation as a minimization problem

In this letter we show that the calculation of analytic second derivatives of variational potential energy surfaces with respect to nuclear coordinates is a minimization problem.     

A new fullerene complexation ligand: N-pyridylfulleropyrrolidine

The subject of this paper is a new fullerene building block design with the potential for defined geometry and good electronic communication. The synthesis and characterization of a new pyridinofullerene ligand capable of forming axially symmetric complexes with metalloporphyrins is reported. X-ray structural and molecular modeling studies, (1)H NMR, UV-vis spectroscopy, electrochemistry studies, and fluorescence quenching data support the formation of a strong complex between the new ligand and the metal center of ZnTPP. On the basis of computational studies, the highest occupied molecular orbital (HOMO) of this ligand is significantly different from a model compound with insulating carbons between the pyridine and the fullerene. The N-pyridinium fulleropyrrolidine salts of the new ligand and model compound were also prepared and their spectral and electrochemical properties are reported.     

Chiroptical properties of 2-chloropropionitrile

(S)-(-)-2-chloropropionitrile has been prepared from (S)-(+)-alanine, and the ORD curves have been obtained in several solvents and in the gas phase. A reaction field extrapolation of the solution data to the gas phase led to an estimated value of [alpha]D = -21 degrees, whereas the interpolated gas phase value is -8 degrees. The specific rotation was found to be temperature dependent in ethylcyclohexane solution over the range 0-100 degrees C. Although rotation of the methyl group leads to large calculated effects on the specific rotation, it does not lead to the temperature dependence. Rather, a low frequency mode at 224 cm(-1) was found to be responsible. This is a mixed mode involving methyl torsion and C-C[triple bond]N bending. The specific rotations calculated at the B3LYP/aug-cc-pVDZ level including electric field dependent functions are in very good agreement with the measured gas phase values.     

Monitoring multiple active sites on thiotemplate enzymes in parallel: a molecular movie of yersiniabactin bioassembly

For the uninterrupted observation of natural product bioassembly on nonribosomal peptide synthetases, Quadrupole Fourier Transform Mass Spectrometry (Q-FTMS) was utilized to directly interrogate peptides harboring covalently modified residues in yersiniabactin synthetase. After proteolysis in CNBr, the peptides corresponding to each carrier site were identified and visualized using a continuous kinetic assay. Overall, complex intermediate formation was rapid, with observation of the HPTT-beta-keto-2,2-dimethyl-S-ACP intermediate within 4 s, while each active site reached saturation within approximately 20 s. Reduction of the beta-keto group at the ACP domain was found to have the slowest rate, accumulating only after 40 s. This represents the first study to correlate five active sites in tandem with kinetic and structural resolution of the complex intermediates in addition to regiospecific information preserved in the assay.     

Error bounds for rank 1 lattice quadrature rules modulo composites

Improved estimates are established regarding the accuracy which can be achieved by a suitable choice of generator in a single-generator lattice quadrature rule (as used in the method of good lattice points) in the general case wherem, the number of quadrature points, is not necessarily prime. The result obtained for the general case is asymptotically the same as the best currently-known result for the prime case. However, it is also shown that when these rules are applied to some customary test functions the mean error (over different rules with the same number of points) can be arbitrarily large compared to the corresponding mean value for rules with a comparable but prime value ofm. These mean values are of interest in relation to computerised searches for good generators.     

Direct-writing of polymer nanostructures: poly(thiophene) nanowires on semiconducting and insulating surfaces.

A new technique for direct-writing of polymer nanostructures on insulating and semiconducting surfaces based on Electrochemical Dip-Pen Nanolithography (E-DPN) is described. The technique is based on electrochemical polymerization of monomers directly underneath the AFM tip. Sub-50 nm poly-3,4-ethylenedioxythiophene lines can be easily created. Such capability to direct-write and pattern polymeric materials with interesting electronic and electrooptical properties at the nanoscale creates a number of opportunities since a large variety of monomers are available.     

Dipole-dipole plasmon interactions in gold-on-polystyrene composites

Red-shifting of the optical absorption spectra of aggregates of gold nanoparticles by dipole-dipole interactions is of considerable interest, both for theoretical reasons and because the phenomenon can be potentially exploited in various applications. A convenient and practical way to control the effect is to assemble the aggregated ensemble of n gold nanoparticles on the outer surface of larger dielectric spheres. Here, we show by experiment and calculation how the spectra of these structures can be systematically morphed from that of isolated gold particles, through the regime of broad absorption dominated by particle-particle interactions, and finally to the limiting case of a continuous nanoshell. The experimental data were produced using the process of deposition-precipitation, which provides a facile method to decorate polystyrene microspheres with gold nanoparticles. There is no need for prior functionalization of the microsphere surface in our method of deposition-precipitation. Calculations were carried out using a code based on the discrete dipole approximation (DDA). The spectra were dominated by three effects. These were a peak absorption at about 540 nm produced by the conventional plasmon resonance of spherical gold nanoparticles, a broad absorption in the range 600-900 nm caused by diverse dipole-dipole interactions between particles, which strengthened as the number of attached gold particles increased and finally, when n was large, an absorption peak due to the onset of nanoshell-like resonances. The experimental spectra could be successfully fitted by spectra calculated using combinations of these effects.     

Relative partial molar enthalpies and apparent molar volumes of dipeptides in aqueous solution

Enthalpies of dilution at 25°C of aqueous solutions of the dipeptides glycylglycine, glycylalanine and alanylalanine have been determined and used to calculate the partial molar enthalpies of the solvent water in the solutions. The partial molar volumes of these dipeptides are also reported. The results are discussed in terms of the likely solute-solvent interactions.