Structure and stress of Re(11%21); chiral terraces at a racemic surface

The surface structure and morphology of the clean Re(11%21) surface has been investigated through combined low energy electron diffraction intensity analysis of data taken at multiple angles of incidence, scanning tunneling microscopy, and first-principles density functional calculations. The results show how this globally racemic surface terminates in two chirally distinct terraces, which show largescale out-of-plane atomic relaxations and in-plane lateral movement of the uppermost atoms. We further identify and discuss the initial stages of step bunching upon adsorption of oxygen that leads ultimately to the large-scale faceting of the surface. Finally, we present calculations of surface stress and the response to applied surface strain, which suggest routes to the exertion of control over the expression of chirality at the surface.

New opportunities for secure communication networks using shaped femtosecond laser pulses inducing filamentation processes in the atmosphere

The current study discusses new opportunities for secure ground to satellite communications using shaped femtosecond pulses that induce spatial hole burning in the atmosphere for efficient communications with data encoded within super-continua generated by femtosecond pulses. Refractive index variation across the different layers in the atmosphere may be modelled using assumptions that the upper strata of the atmosphere and troposphere behaving as layered composite amorphous dielectric networks composed of resistors and capacitors with different time constants across each layer. Input-output expressions of the dynamics of the networks in the frequency domain provide the transmission characteristics of the propagation medium. Femtosecond pulse shaping may be used to optimize the pulse phase-front and spectral composition across the different layers in the atmosphere. A generic procedure based on evolutionary algorithms to perform the pulse shaping is proposed. In contrast to alternative procedures that would require ab initio modelling and calculations of the propagation constant for the pulse through the atmosphere, the proposed approach is adaptive, compensating for refractive index variations along the column of air between the transmitter and receiver.

Weak intermolecular interactions in an ionically bound molecular adsorbate: cyclopentadienyl=Cu(111)

The dissociative adsorption of cyclopentadiene (C5H6) on Cu(111) yields a cyclopentadienyl (Cp) species with strongly anionic characteristics. The Cp potential energy surface and frictional coupling to the substrate are determined from measurements of dynamics of the molecule together with density functional calculations. The molecule is shown to occupy degenerate threefold adsorption sites and molecular motion is characterized by a low diffusional energy barrier of 40 +/- 3 meV with strong frictional dissipation. Repulsive dipole-dipole interactions are not detected despite charge transfer from substrate to adsorbate.

A case of four-coordinate silver(I) adopting a high energy planar geometry. Experiment and theory

The ligands PhL and MeL are obtained by condensing 2-formylpyridine with benzil dihydrazone and diacetyl dihydrazone, respectively, in 2: 1 molar proportion. With silver( I), PhL yields a double-stranded dinuclear cationic helicate 1 in which the metal is tetrahedral but MeL gives a cationic one-dimensional polymeric complex 2 where silver( I) is distorted square planar and the ligand backbone is nearly planar. In both complexes, metal: ligand ratio is 1: 1. Ab initio calculations on the ligands at the HF/6-31+G* level reveal that while PhL strongly prefers a helical conformation, MeL has a natural inclination to remain in a planar conformation. Density functional theory calculations on model silver( I) complexes show that formation of the linear polymer in the case of MeL is also an important factor in imposing the planar geometry of Ag(I) in 2.

A DFT study of free radicals formed from artemisinin and related compounds

Ab initio calculations using density functional theory have shown that the reactions that occur between artemisinin, 1, a cyclic trioxane active against malaria, and some metal ions and complexes lead to a series of radicals which are probably responsible for its therapeutic activity. In particular it has been shown that the interaction of Fe(H) with artemisinin causes the O-O bond to be broken as indeed does Fe(III) and Cu(I), while Zn(II) does not. Calculations were carried out with Fe(II) in several different forms including the bare ion, [Fe(H2O)(5)](2+) and [FeP(Im)] (P, porphyrin; Im, imadazole) and similar results were obtained. The resulting oxygen-based radicals are readily converted to more stable carbon-based radicals and/or. stable products. Similar radicals and products are also formed from two simple model trioxanes 2 and 3 that show little or no therapeutic action against malaria although some subtle differences were obtained. This suggests that the scaffold surrounding the pharmacophore may be involved in molecular recognition events allowing efficient uptake of this trioxane warhead into the parasite. (C) 2004 Elsevier B.V. All rights reserved.

Infrared absorption spectra, radiative efficiencies, and global warming potentials of perfluorocarbons: Comparison between experiment and theory

Experimentally and theoretically determined infrared spectra are reported for a series of straight-chain perfluorocarbons: C2F6, C3F8, C4F10, C5F12, C6F14, and C8F18. Theoretical spectra were determined using both density functional (DFT) and ab initio methods. Radiative efficiencies (REs) were determined using the method of Pinnock et al. (1995) and combined with atmospheric lifetimes from the literature to determine global warming potentials (GWPs). Theoretically determined absorption cross sections were within 10% of experimentally determined values. Despite being much less computationally expensive, DFT calculations were generally found to perform better than ab initio methods. There is a strong wavenumber dependence of radiative forcing in the region of the fundamental C-F vibration, and small differences in wavelength between band positions determined by theory and experiment have a significant impact on the REs. We apply an empirical correction to the theoretical spectra and then test this correction on a number of branched chain and cyclic perfluoroalkanes. We then compute absorption cross sections, REs, and GWPs for an additional set of perfluoroalkenes.

Harmonic force fields from scaled SCF calculations: Program ASYM40

We report an extended version of our normal coordinate program ASYM40, which may be used to transform Cartesian force constants from ab initio calculations to a force field in nonredundant internal (symmetry) coordinates. When experimental data are available, scale factors for the theoretical force field may then be optimized by least-squares refinement. The alternative of refining an empirical force field to fit a wide variety of data, as with the previous version ASYM20, has been retained. We compare the results of least-squares refinement of the full harmonic force field with least-squares refinement of only the scale factors for an SCF calculated force field and conclude that the latter approach may be useful for large molecules where more sophisticated calculations are impractical. The refinement of scale factors for a theoretical force field is also useful when there are only limited spectroscopic data. The program will accept ab initio calculated force fields from any program that presents Cartesian force constants as output. The program is available through Quantum Chemistry Program Exchange.

Molecular structure of 2,5-dihydropyrrole (C4NH7), obtained by gas-phase electron diffraction and theoretical calculations

The structure of 2,5-dihydropyrrole (C4NH7) has been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing third-order Moller-Plesset (MP3) level of theory and the 6-311+G(d,p) basis set. Several theoretical calculations were performed. From theoretical calculations using MP3/6-311+G(d,p) evidence was obtained for the presence of an axial (63%) (N-H bond axial to the CNC plane) and an equatorial conformer (37%) (N-H bond equatorial to the CNC plane). The five-membered ring was found to be puckered with the CNC plane inclined at 21.8 (38)° to the plane of the four carbon atoms.

Molecular structures of trimethylchlorogermane, (CH3)(3)GeCl, and trimethylbromogermane, (CH3)(3)GeBr, obtained by gas-phase electron diffraction and theoretical calculations

The structures of trimethylchlorogermane ((CH3)(3)GeCl) and trimethylbromogermane ((CH3)(3)GeBr) have been determined by gas-phase electron diffraction (GED), augmented by the results from ab initio calculations employing second-order Moller-Plesset (MP2) level of theory and the 6-311+G(d) basis set. All the electrons were included in the correlation calculation. The results from the ab initio calculations indicated that these molecules have C-3v symmetry, and models with this symmetry were used in the electron diffraction analysis. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylchlorogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.950(4) Angstrom, r(Ge-Cl) = 2.173(4) Angstrom, r(C-H) = 1.090(9) Angstrom, angleCGeC = 112.7(7)degrees, angleCGeCl = 106.0(8)degrees, angleGeCH = 107.8(12)degrees. The results for the principal distances (r(g)) and angles (angle(alpha)) from the combined GED/ab initio study of trimethylbromogermane (with estimated 2sigma uncertainties) are: r(Ge-C) = 1.952(7) Angstrom, r(Ge-Br) = 2.325(4) Angstrom, r(C-H) = 1. 140(28) Angstrom, angleCGeC = 114.2(11)degrees, angleCGeBr = 104.2(13)degrees, angleGeCH 106.9(43)degrees. Local C-3v symmetry and staggered conformation were assumed for the methyl groups.

The vibrational spectrum and ultimate modulus of polyethylene

We have performed the first completely ab initio lattice dynamics calculation of the full orthorhombic cell of polyethylene using periodic density functional theory in the local density approximation (LDA) and the generalized gradient approximation (GGA). Contrary to current perceptions, we show that LDA accurately describes the structure whereas GGA fails. We emphasize that there is no parametrization of the results. We then rigorously tested our calculation by computing the phonon dispersion curves across the entire Brillouin zone and comparing them to the vibrational spectra, in particular the inelastic neutron scattering (INS) spectra, of polyethylene (both polycrystalline and aligned) and perdeuteriopolyethylene. The F-point frequencies (where the infrared and Raman active modes occur) are in good agreement with the latest low temperature data. The near-perfect reproduction of the INS spectra, gives confidence in the results and allows Lis to deduce a number of physical properties including the elastic moduli, parallel and perpendicular to the chain. We find that the Young's modulus for an infinitely long, perfectly crystalline polyethylene is 360.2 GPa at 0 K. The highest experimental value is 324 GPa, indicating that current high modulus fibers are similar to 90% of their maximum possible strength.

An investigation of the germylene addition reaction, GeH2+C2H2: Time-resolved gas-phase kinetic studies and quantum chemical calculations of the reaction energy surface

Time resolved studies of germylene, GeH2, generated by laser flash photolysis of 3,4-dimethylgermacyclopentene-3, have been carried out to obtain rate constants for its bimolecular reaction with acetylene, C2H2. The reaction was studied in the gas-phase over the pressure range 1-100 Tort, with SF6 as bath gas, at 5 temperatures in the range 297-553 K. The reaction showed a very slight pressure dependence at higher temperatures. The high pressure rate constants (obtained by extrapolation at the three higher temperatures) gave the Arrhenius equation: log(k(infinity)/cm(3) molecule(-1) s(-1)) (-10.94 +/- 0.05) + (6.10 +/- 0.36 kJ mol(-1))/RTln10. These Arrhenius parameters are consistent with a fast reaction occurring at approximately 30% of the collision rate at 298 K. Quantum chemical calculations (both DFT and ab initio G2//B3LYP and G2//QCISD) of the GeC2H4 potential energy surface (PES), show that GeH2 + C2H2 react initially to form germirene which can isomerise to vinylgermylene with a relatively low barrier. RRKM modelling, based on a loose association transition state, but assuming vinylgermylene is the end product (used in combination with a weak collisional deactivation model) predicts a strong pressure dependence using the calculated energies, in conflict with the experimental evidence. The detailed GeC2H4 PES shows considerable complexity with ten other accessible stable minima (B3LYP level), the three most stable of which are all germylenes. Routes through this complex surface were examined in detail. The only product combination which appears capable of satisfying the (P-3) + C2H4.C2H4 was confirmed as a product by GC observed lack of a strong pressure dependence is Ge(P-3) + C2H4. C2H4 was confirmed as a product by GC analysis. Although the formation of these products are shown to be possible by singlet-triplet curve crossing during dissociation of 1-germiranylidene (1-germacyclopropylidene), it seems more likely (on thermochernical grounds) that the triplet biradical, (GeCH2CH2.)-Ge-., is the immediate product precursor. Comparisons are made with the reaction of SiH2 with C2H2.

The addition reaction between silylene and ethyne: further isotope studies, pressure dependence studies, and quantum chemical calculations

Time-resolved kinetic studies of the reaction of dideutero-silylene, SiD2, generated by laser flash photolysis of phenylsilane-d(3), have been carried out to obtain rate constants for its bimolecular reaction with C2H2. The reaction was studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas, at five temperatures in the range 297-600 K. The second-order rate constants obtained by extrapolation to the high-pressure limits at each temperature fitted the Arrhenius equation log(k(infinity)/cm(3) molecule(-1) s(-1)) = (-10.05 +/- 0.05) + (3.43 +/- 0.36 kJ mol(-1))/RT ln 10. The rate constants were used to obtain a comprehensive set of isotope effects by comparison with earlier obtained rate constants for the reactions of SiH2 with C2H2 and C2D2. Additionally, pressure-dependent rate constants for the reaction of SiH2 with C2H2 in the presence of He (1-100 Tort) were obtained at 300, 399, and 613 K. Quantum chemical (ab initio) calculations of the SiC2H4 reaction system at the G3 level support the initial formation of silirene, which rapidly isomerizes to ethynylsilane as the major pathway. Reversible formation of vinylsilylene is also an important process. The calculations also indicate the involvement of several other intermediates, not previously suggested in the mechanism. RRKM calculations are in semiquantitative agreement with the pressure dependences and isotope effects suggested by the ab initio calculations, but residual discrepancies suggest the possible involvement of the minor reaction channel, SiH2 + C2H2 - SWPO + C2H4. The results are compared and contrasted with previous studies of this reaction system.

Investigation of the prototype silylene reaction, SiH2+H2O(and D2O): time-resolved gas-phase kinetic studies, isotope effects, RRKM calculations, and quantum chemical calculations of the reaction energy surface

Time-resolved kinetic studies of the reaction of silylene, SiH2, with H2O and with D2O have been carried out in the gas phase at 296 and at 339 K, using laser flash photolysis to generate and monitor SiH2. The reaction was studied over the pressure range 10-200 Torr with SF6 as bath gas. The second-order rate constants obtained were pressure dependent, indicating that the reaction is a third-body assisted association process. Rate constants at 339 K were about half those at 296 K. Isotope effects, k(H)/k(D), were small averaging 1.076 0.080, suggesting no involvement of H- (or D-) atom transfer in the rate determining step. RRKM modeling was undertaken based on a transition state appropriate to formation of the expected zwitterionic donoracceptor complex, H2Si...OH2. Because the reaction is close to the low pressure (third order) region, it is difficult to be definitive about the activated complex structure. Various structures were tried, both with and without the incorporation of rotational modes, leading to values for the high-pressure limiting (i.e., true secondorder) rate constant in the range 9.5 x 10(-11) to 5 x 10(-10) cm(3) molecule' s(-1). The RRKM modeling and mechanistic interpretation is supported by ab initio quantum calculations carried out at the G2 and G3 levels. The results are compared and contrasted with the previous studies.

Calculations of rovibrational energies and dipole transition intensities for polyatomic molecules using MULTIMODE

We report rigorous calculations of rovibrational energies and dipole transition intensities for three molecules using a new version of the code MULTIMODE. The key features of this code which permit, for the first time, such calculations for moderately sized but otherwise general polyatomic molecules are briefly described. Calculations for the triatomic molecule BF(2) are done to validate the code. New calculations for H(2)CO and H(2)CS are reported; these make use of semiempirical potentials but ab initio dipole moment surfaces. The new dipole surface for H(2)CO is a full-dimensional fit to the dipole moment obtained with the coupled-cluster with single and double excitations and a perturbative treatment of triple excitations method with the augmented correlation consistent triple zeta basis set. Detailed comparisons are made with experimental results from a fit to relative data for H(2)CS and absolute intensities from the HITRAN database for H(2)CO.

Large vibrational variational calculations using 'multimode' and an iterative diagonalization technique

We have favoured the variational (secular equation) method for the determination of the (ro-) vibrational energy levels of polyatomic molecules. We use predominantly the Watson Hamiltonian in normal coordinates and an associated given potential in the variational code 'Multimode'. The dominant cost is the construction and diagonalization of matrices of ever-increasing size. Here we address this problem, using pertubation theory to select dominant expansion terms within the Davidson-Liu iterative diagonalization method. Our chosen example is the twelve-mode molecule methanol, for which we have an ab initio representation of the potential which includes the internal rotational motion of the OH group relative to CH3. Our new algorithm allows us to obtain converged energy levels for matrices of dimensions in excess of 100 000.