Numerical study of the accuracy and efficiency of various approaches for Monte Carlo surface hopping calculations

A one-dimensional, two-state model problem with two well-separated avoided crossing points is employed to test the efficiency and accuracy of a semiclassical surface hopping technique. The use of a one-dimensional model allows for the accurate numerical evaluation of both fully quantum-mechanical and semiclassical transition probabilities. The calculations demonstrate that the surface hopping procedure employed accounts for the interference between different hopping trajectories very well and provides highly accurate transition probabilities. It is, in general, not computationally feasible to completely sum over all hopping trajectories in the semiclassical calculations for multidimensional problems. In this case, a Monte Carlo procedure for selecting important trajectories can be employed. However, the cancellation due to the different phases associated with different trajectories limits the accuracy and efficiency of the Monte Carlo procedure. Various approaches for improving the accuracy and efficiency of Monte Carlo surface hopping procedures are investigated. These methods are found to significantly reduce the statistical sampling errors in the calculations, thereby increasing the accuracy of the transition probabilities obtained with a fixed number of trajectories sampled.     

Ion-chromatographic analysis of mixtures of ferrous and ferric iron

Determinations of the aqueous iron species Fe(II) and Fe(III) are essential for a fully-informed understanding of redox processes involving iron. Most previous methods for speciation of iron have been based on the calorimetric determination of Fe(II) followed by reduction of Fe(III) and analysis for total iron. The indirect determination of Fe(III) and the consumption of relatively large sample volumes have limited the accuracy and utility of such methods. A method based on ion-chromatography has been developed for simultaneous direct determination of Fe(II) and Fe(III). Sample pretreatment involves only conventional filtration and acidification. No interferences with the iron(II) determination were found; in determination of iron(III) the only interference observed was an artifact peak (of unknown origin) that occurred only when iron(II) was present, and had an area that was a function of the iron(II) concentration and could hence be corrected for. Solutions of iron(II) free from iron(III) can be prepared by treatment with a mixture of hydrogen and nitrogen in the presence of palladium black as catalyst, to reduce the iron(III). Photoreduction of iron(III) in acidified samples increases the Fe(II)/Fe(III) ratio; no means of circumventing this effect is known, other than storing the samples in the dark and analysing them as soon as possible.     

GROMACS: fast, flexible, and free

This article describes the software suite GROMACS (Groningen MAchine for Chemical Simulation) that was developed at the University of Groningen, The Netherlands, in the early 1990s. The software, written in ANSI C, originates from a parallel hardware project, and is well suited for parallelization on processor clusters. By careful optimization of neighbor searching and of inner loop performance, GROMACS is a very fast program for molecular dynamics simulation. It does not have a force field of its own, but is compatible with GROMOS, OPLS, AMBER, and ENCAD force fields. In addition, it can handle polarizable shell models and flexible constraints. The program is versatile, as force routines can be added by the user, tabulated functions can be specified, and analyses can be easily customized. Nonequilibrium dynamics and free energy determinations are incorporated. Interfaces with popular quantum-chemical packages (MOPAC, GAMES-UK, GAUSSIAN) are provided to perform mixed MM/QM simulations. The package includes about 100 utility and analysis programs. GROMACS is in the public domain and distributed (with source code and documentation) under the GNU General Public License. It is maintained by a group of developers from the Universities of Groningen, Uppsala, and Stockholm, and the Max Planck Institute for Polymer Research in Mainz. Its Web site is http://www.gromacs.org.     

Highly oriented self-assembled monolayers as templates for epitaxial calcite growth

The lateral alignment of [012] habit-modified calcite crystals with respect to a carboxylic acid terminated self-assembled monolayer (SAM) of thiols has been determined. The crystals were grown from a Kitano solution (pH 5.6-6.0), and the samples were investigated with scanning electron microscopy, X-ray diffraction, and polarization microscopy. For the first time, a lattice match in one direction, which is the nearest neighbor direction of the SAM and the calcite <100> direction, has been experimentally shown. The experimental results are in good agreement with the theoretical models proposed in previous work, and it is expected that this method can be applied to similar systems where inorganic crystals nucleate with a preferred orientation to a SAM.     

The absolute stereochemistry of several cis-dihydrodiols microbially produced from substituted benzenes

The absolute stereochemistry of a series of 3-substituted cis-dihydrodiols obtained by microbial oxidation of toluene, ethylbenzene, chlorobenzene, and biphenyl has been assigned from chemical and spectrophotometric studies. ?-Halogenated toluenes also have been investigated as substrates in these oxidations, and the corresponding cis-dihydrodiols isolated. Implications from the observation that some of the cis-dihydrodiols are racemic are discussed. Oxidation of an olefin, (±)-3-methylcyclohexene, by these microorganisms leads only to cis-diols whose absolute stereochemistry about the hydroxyl-bearing carbons is the same as that found for the cis-dihydrodiols formed from the aromatic substrates.     

Ab initio calculation of the effective valence shell hamiltonian of carbon: Simultaneous treatment of neutral and ion states

The n = 2 effective valence shell hamiltonian, $\text{H}$^v, of carbon is evaluated through second order using ³P Hartree—Fock orbitals (5s4p) with added d functions to provide results within a few percent of the spd convergence limits. The calculated $\text{H}$^v is employed to evaluate the n = 2 valence states of C, C^?, C⁺, C²⁺ and C³⁺ with an average deviation of the 21 excitation energies, ionization potentials and electron affinity from experimental values of 0.32 eV. Three-electron parts of $\text{H}$^v contribute substantially to a number of these excitation energies.     

Synthesis and elaboration of functionalised carbohydrate-derived spiroketals

The scope of a stereoselective three-step approach for the synthesis of sugar derived spiroketals is presented. The methodology consists of Grignard addition of vinyl- or allylmagnesium bromide to a carbohydrate lactone, followed by K-10 clay mediated glycosidation with a terminal alkenol and subsequent ring-closing metathesis of the resulting diene. The generality of this procedure is demonstrated by the synthesis of various pyranose- and furanose-derived spiroketals, as well as more advanced tricyclic spiroketal derivatives. It is shown that functionalisation of the double bond in the resulting spiroketals leads to fused polycyclic ethers.     

Highly selective tritium-from-deuterium isotope separation by pulsed NH3 laser multiple-photon dissociation of chloroform

Infrared multiple-photon dissociation of CTCl₃ was investigated using a pulsed CO₂ laser-pumped NH₃ laser at 12.08 μm. No evidence of any CDCl₃ depletion or decomposition product was observed in photolyzed CTCl₃/CDCl₃ mixtures. A lower limit of the single-step T/D enrichment factor, β, was found to be ≈ 165, based on the sensitivity in measuring CDCl₃ depletion. The low-fluene CTCl₃/CDCl₃ optical selectivity in absorptions is > 9000 at the 835 cm^?1 CTCl₃ ν₄ peak.     

The vibrational analysis of methylarsonic acid,trideuteromethylarsonic acid and their anions

Raman and IR spectra of methylarsonic acid, CH₃AsO₃H₂, trideuteromethylarsonic acid, CD₃AsO₃H₂ and their anions in aqueous solution and the solid state are discussed. Some results of a general valence force field and a Urey-Bradley force field are reported.     

Vibrational analysis of chlorinated methylphosphonic acids: Part 2. Vibrational analysis of CHCl2PO3H2 and its anions

The vibrational spectra (IR and Raman) of CHCl₂PO₃H₂ and its anions in H₂O and D₂O solutions are reported. The IR spectra of the solid dibasic sodium and potassium salts, the solid normal and O-deuterated monobasic sodium and potassium salt and the solid normal and O-deuterated acid are discussed. The principal results of the normal coordinate analysis of the compounds are tabulated.