Comparison of subspace and ARX models of a waveguide's terahertz transient response after optimal wavelet filtering

A quasi-optical deembedding technique for characterizing waveguides is demonstrated using wide-band time-resolved terahertz spectroscopy. A transfer function representation is adopted for the description of the signal in the input and output port of the waveguides. The time-domain responses were discretized and the waveguide transfer function was obtained through a parametric approach in the z-domain after describing the system with an AutoRegressive with eXogenous input (ARX), as well as with a state-space model. Prior to the identification procedure, filtering was performed in the wavelet domain to minimize both signal distortion, as well as the noise propagating in the ARX and subspace models. The optimal filtering procedure used in the wavelet domain for the recorded time-domain signatures is described in detail. The effect of filtering prior to the identification procedures is elucidated with the aid of pole-zero diagrams. Models derived from measurements of terahertz transients in a precision WR-8 waveguide adjustable short are presented.

Measurement of propagation constant in waveguides with wideband coherent terahertz spectroscopy

A quasi-optical technique for characterizing micromachined waveguides is demonstrated with wideband time-resolved terahertz spectroscopy. A transfer-function representation is adopted for the description of the relation between the signals in the input and output port of the waveguides. The time-domain responses were discretized, and the waveguide transfer function was obtained through a parametric approach in the z domain after describing the system with an autoregressive with exogenous input model. The a priori assumption of the number of modes propagating in the structure was inferred from comparisons of the theoretical with the measured characteristic impedance as well as with parsimony arguments. Measurements for a precision WR-8 waveguide-adjustable short as well as for G-band reduced-height micromachined waveguides are presented. (C) 2003 Optical Society of America.

Small-angle x-ray scattering study of flow alignment of a thermotropic liquid crystal in the nematic and smectic phases

WThe capillary flow alignment of the thermotropic liquid crystal 4-n-octyl-4′-cyanobiphenyl in the nematic and smectic phases is investigated using time-resolved synchrotron small-angle x-ray scattering. Samples were cooled from the isotropic phase to erase prior orientation. Upon cooling through the nematic phase under Poiseuille flow in a circular capillary, a transition from the alignment of mesogens along the flow direction to the alignment of layers along the flow direction (mesogens perpendicular to flow) appears to occur continuously at the cooling rate applied. The transition is centered on a temperature at which the Leslie viscosity coefficient α3 changes sign. The configuration with layers aligned along the flow direction is also observed in the smectic phase. The transition in the nematic phase on cooling has previously been ascribed to an aligning-nonaligning or tumbling transition. At high flow rates there is evidence for tumbling around an average alignment of layers along the flow direction. At lower flow rates this orientation is more clearly defined. The layer alignment is ascribed to surface-induced ordering propagating into the bulk of the capillary, an observation supported by the parallel alignment of layers observed for a static sample at low temperatures in the nematic phase.

Computer simulations of structures, energetics and dynamics of myoglobin center dot center dot center dot ligand complexes

Myoglobin has been studied in considerable detail using different experimental and computational techniques over the past decades. Recent developments in time-resolved spectroscopy have provided experimental data amenable to detailed atomistic simulations. The main theme of the present review are results on the structures, energetics and dynamics of ligands ( CO, NO) interacting with myoglobin from computer simulations. Modern computational methods including free energy simulations, mixed quantum mechanics/molecular mechanics simulations, and reactive molecular dynamics simulations provide insight into the dynamics of ligand dynamics in confined spaces complementary to experiment. Application of these methods to calculate and understand experimental observations for myoglobin interacting with CO and NO are presented and discussed.

Theoretical investigation of infrared spectra and pocket dynamics of photodissociated carbonmonoxy myoglobin

Molecular dynamics simulations of the photodissociated state of carbonmonoxy myoglobin (MbCO) are presented using a fluctuating charge model for CO. A new three-point charge model is fitted to high-level ab initio calculations of the dipole and quadrupole moment functions taken from the literature. The infrared spectrum of the CO molecule in the heme pocket is calculated using the dipole moment time autocorrelation function and shows good agreement with experiment. In particular, the new model reproduces the experimentally observed splitting of the CO absorption spectrum. The splitting of 3–7 cm−1 (compared to the experimental value of 10 cm−1) can be directly attributed to the two possible orientations of CO within the docking site at the edge of the distal heme pocket (the B states), as previously suggested on the basis of experimental femtosecond time-resolved infrared studies. Further information on the time evolution of the position and orientation of the CO molecule is obtained and analyzed. The calculated difference in the free energy between the two possible orientations (Fe···CO and Fe···OC) is 0.3 kcal mol−1 and agrees well with the experimentally estimated value of 0.29 kcal mol−1. A comparison of the new fluctuating charge model with an established fixed charge model reveals some differences that may be critical for the correct prediction of the infrared spectrum and energy barriers. The photodissociation of CO from the myoglobin mutant L29F using the new model shows rapid escape of CO from the distal heme pocket, in good agreement with recent experimental data. The effect of the protein environment on the multipole moments of the CO ligand is investigated and taken into account in a refined model. Molecular dynamics simulations with this refined model are in agreement with the calculations based on the gas-phase model. However, it is demonstrated that even small changes in the electrostatics of CO alter the details of the dynamics.

Kinetics and mechanism of the interconversion of inverse bicontinuous cubic mesophases

This paper describes time-resolved x-ray diffraction data monitoring the transformation of one inverse bicontinuous cubic mesophase into another, in a hydrated lipid system. The first section of the paper describes a mechanism for the transformation that conserves the topology of the bilayer, based on the work of Charvolin and Sadoc, Fogden and Hyde, and Benedicto and O'Brien in this area. We show a pictorial representation of this mechanism, in terms of both the water channels and the lipid bilayer. The second section describes the experimental results obtained. The system under investigation was 2:1 lauric acid: dilauroylphosphatidylcholine at a hydration of 50% water by weight. A pressure-jump was used to induce a phase transition from the gyroid (Q(II)(G)) to the diamond (Q(II)(D)) bicontinuous cubic mesophase, which was monitored by time-resolved x-ray diffraction. The lattice parameter of both mesophases was found to decrease slightly throughout the transformation, but at the stage where the Q(II)(D) phase first appeared, the ratio of lattice parameters of the two phases was found to be approximately constant for all pressure-jump experiments. The value is consistent with a topology-preserving mechanism. However, the polydomain nature of our sample prevents us from confirming that the specific pathway is that described in the first section of the paper. Our data also reveal signals from two different intermediate structures, one of which we have identified as the inverse hexagonal (H-II) mesophase. We suggest that it plays a role in the transfer of water during the transformation. The rate of the phase transition was found to increase with both temperature and pressure-jump amplitude, and its time scale varied from the order of seconds to minutes, depending on the conditions employed.

Ultrafast charge separation in a photoreactive rhenium-appended porphyrin assembly monitored by picosecond transient infrared spectroscopy

Rhenium(bipyridine)(tricarbonyl)(picoline) units have been linked covalently to tetraphenylmetalloporphyrins of magnesium and zinc via an amide bond between the bipyridine and one phenyl substituent of the porphyrin. The resulting complexes, abbreviated as [Re(CO)(3)(Pic)Bpy-MgTPP][OTf] and [Re(CO)(3)(Pic)Bpy-ZnTPP][OTf], exhibit no signs of electronic interaction between the Re(CO)(3)(bpy) units and the metalloporphyrin units in their ground states. However, emission spectroscopy reveals solvent-dependent quenching of porphyrin emission on irradiation into the long-wavelength absorption bands localized on the porphyrin. The characteristics of the excited states have been probed by picosecond time-resolved absorption (TRVIS) spectroscopy and time-resolved infrared (TRIR) spectroscopy in nitrile solvents. The presence of the charge-separated state involving electron transfer from MgTPP or ZnTPP to Re(bpy) is signaled in the TRIR spectra by a low-frequency shift in the nu(CO) bands of the Re(CO)(3) moiety similar to that observed by spectroelectrochemical reduction. Long-wavelength excitation of [Re(CO)(3)(Pic)Bpy-MTPP][OTf] results in characteristic TRVIS spectra of the S-1 state of the porphyrin that decay with a time constant of 17 ps (M = Mg) or 24 ps (M = Zn). The IR bands of the CS state appear on a time scale of less than 1 ps (Mg) or ca. 5 ps (Zn) and decay giving way to a vibrationally excited (i.e., hot) ground state via back electron transfer. The IR bands of the precursors recover with a time constant of 35 ps (Mg) or 55 ps (Zn). The short lifetimes of the charge-transfer states carry implications for the mechanism of reaction in the presence of triethylamine.

Heterosite effects in novel heteronuclear clusters [OS2Ru(CO)(11)(PPh3)] and Os2Ru(CO)(10)(2-acetylpyridine-N-isopropylimine)]

A new synthetic route towards the mixed-metal cluster [OS2Ru(CO)(12)] is described together with the syntheses of its PPh3 and iPr-AcPy (iPr-AcPy = 2-acetylpyridine-N-isopropylimine) derivatives. The molecular structures of the novel clusters [Os2Ru(CO)(11)(PPh3)] and [Os2Ru(CO)(10)(iPr-AcPy)] were determined on the basis of crystalline solid solutions of the Os2Ru and corresponding Os-3 species. The structures reveal that coordination of the Lewis bases occurs exclusively at the ruthenium site of [Os2Ru(CO)(12)], which is in agreement with density functional theory (DFT) calculations on several structural isomers of these compounds. According to the time-dependent DFT results, the lowest optically accessible excited state of [Os2Ru(CO)(10)(iPr-AcPy)] has a prevailing sigma(Ru-Os-2)pi*(iPr-AcPy) character, with a partial sigma sigma*(Ru-Os-2) contribution. In weakly coordinating 2-chlorobutane, the excited state has a lifetime tau = 10.4 +/- 1.2 ps and produces biradicals considerably faster than observed for [Os-3(CO)10(iPr-AcPy) (tau = 25.3 +/- 0.7ps)]. In coordinating acetonitrile, the excited state of [Os2Ru(CO)(10)(iPr-AcPy)] decays mono-exponentially with a lifetime tau = 2.1 +/- 0.2 ps. In contrast to [Os-3(CO)(10)(iPr-AcPy)] that forms biradicals as the main primary photoproduct even in strongly coordinating solvents, zwitterion formation from the solvated lowest excited state is observed for the heterometallic cluster. This is concluded from time-resolved absorption studies in the microsecond time domain. Due to the lower tendency of the coordinatively unsaturated Ru+(CO)(2)(iPr-AcPy-/0) moiety to bind a Lewis base, the heteronuclear biradical and zwitterionic photoproducts live significantly shorter than their triosmium counterparts. The influence of the weaker Os-2-Ru(iPr-AcPy) bond on the redox reactivity is clearly reflected in very reactive radical anions formed upon electrochemical reduction of [Os2Ru(CO)(10)(iPr-AcPy)]. The dimer [-OS(CO)(4)-Os(CO)(4)-Ru(CO)(2)(iPr-AcPy)](2)(2-) is the only IR-detectable intermediate reduction product. The dinuclear complex [Os-2(CO)(8)](2-) and insoluble [Ru(CO)(2)(iPr-AcPy)](n), are the ultimate reduction products, proving fragmentation of the OS2Ru core.

Redox control of light-induced charge separation in a transition metal cluster: photochemistry of a methyl viologen-substituted [Os-3(CO)10(a-diimine)] cluster

Sub)picosecond transient absorption (TA) and time-resolved infrared (TRIR) spectra of the cluster [OS3(CO)(10-) (AcPy-MV)](2+) (the clication AcPy-MV = Acpy-MV2+ = [2-pyridylacetimine-N-(2-(1'-methyl-4,4'-bipyridine-1,1'-diium-1-yl) ethyl)] (PF6)(2)) (1(2+)) reveal that photoinduced electron transfer to the electron-accepting 4,4'-bipyridine-1,1'diium (MV2+) moiety competes with the fast relaxation of the initially populated sigmapi* excited state of the cluster to the ground state and/or cleavage of an Os-Os bond. The TA spectra of cluster 12 in acetone, obtained by irradiation into its lowest-energy absorption band, show the characteristic absorptions of the one-electron-reduced MV*(+) unit at 400 and 615 nm, in accordance with population of a charge-separated (CS) state in which a cluster-core electron has been transferred to the lowest pi* orbital of the remote MV2+ unit. This assignment is confirmed by picosecond TRIR spectra that show a large shift of the pilot highest-frequency nu(CO) band of 1(2+) by ca. +40 cm(-1), reflecting the photooxidation of the cluster core. The CS state is populated via fast (4.2 x 10(11) s(-1)) and efficient (88%) oxidative quenching of the optically populated sigmapi* excited state and decays biexponentially with lifetimes of 38 and 166 ps (1:2:1 ratio) with a complete regeneration of the parent cluster. About 12% of the cluster molecules in the sigmapi* excited state form long-lived open-core biradicals. In strongly coordinating acetonitrile, however, the cluster core-to-MV2+ electron transfer in cluster 12+ results in the irreversible formation of secondary photoproducts with a photooxidized cluster core. The photochemical behavior of the [Os-3(CO)(10)(alpha-diimine-MV)](2+) (donor-acceptor) dyad can be controlled by an externally applied electronic bias. Electrochemical one-electron reduction of the MV2+ moiety prior to the irradiation reduces its electron-accepting character to such an extent that the photoinduced electron transfer to MV*+ is no longer feasible. Instead, the irradiation of reduced cluster 1(.)+ results in the reversible formation of an open-core zwitterion, the ultimate photoproduct also observed upon irradiation of related nonsubstituted clusters [Os-3(CO)(10)(alpha-diimine)] in strongly coordinating solvents such as acetonitrile.

Marked influence of the bridging carbonyl ligands on the photo- and electrochemistry of the clusters [Ru-3(CO)(8)(mu-CO)(2)-(alpha-diimine)] (alpha-diimine = 2,2 '-bipyridine, 4,4 '-dimethyl-2,2 '-bipyridine and 2,2 '-bipyrimidine)

Bonding, photochemical and electrochemical properties of the clusters [Ru-3(CO)(8)(mu-CO)(2)(alpha-diimine)] (alpha-diimine=2,2'-bipyridine (1), 4,4'-dimethyl-2,2'-bipyridine (2) and 2,2'-bipyrimidine (3)) are strongly influenced by the presence of bridging carbonyl ligands. Irradiation at 471 nm initially results in the population of a sigma(Ru-3)pi*(alpha-diimine) excited state. From this state, fast decay takes place to the optically hardly directly accessible pi(Ru/mu-CO) pi*(alpha-diimine) lowest excited state. These assignments agree with theoretical (TD-DFT) results, resonance Raman and picosecond time-resolved infrared spectra. The involvement of the bridging carbonyl ligands in the electron transfer increases the energetic barrier for the formation of open-structure photoproducts such as biradicals and zwitterions. Zwitterions were therefore only obtained in strongly coordinating media such as pyridine at 250 K. The bridging carbonyl ligands also stabilize the radical anions produced upon one-electron reduction of the clusters [Ru-3(CO)(8)(mu-CO)(2)(alpha-diimine)] and observed with cyclic voltammetry, EPR and IR spectroelectrochemistry (for alpha-diimine=2,2'-bipyrimidine). In contrast, open-triangle intermediates formed along the reduction path to [Ru(CO)(2)(alpha-diimine)](n) and [Ru-2(CO)(8)](2-) are more reactive than their triosmium analogues.

Kinetic studies of reactions of organosilylenes: what have they taught us?

Rate constants for bimolecular reactions, obtained through time-resolved kinetic studies both in the gas and liquid phases are reviewed. Data for reactions of MeSiH, PhSiH, ClSiH, SiCl2, SiMe2, MeSiPh, SiPh2 and SiMes(2) are covered. Where possible, substituent effects relative to SiH2 have been obtained. These demonstrate widely varying effects between different types of reaction, which aids mechanistic understanding. Reactivities are high for all silylenes, but substituents can reduce them by both electronic and steric effects. The gas and liquid phase data (mainly for SiMe2) are compared and appear to be reasonably consistent. This review, although detailed, is not comprehensive.

Gas-phase kinetics of chlorosilylene reactions II. ClSiH + C2H4: absolute rate measurements and quantum chemical and RRKM calculations for the prototype pi addition reaction

Time-resolved studies of chlorosilylene, ClSiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, are carried out to obtain rate constants for its bimolecular reaction with ethene, C2H4, in the gas-phase. The reaction is studied over the pressure range 0.13-13.3 kPa (with added SF6) at five temperatures in the range 296-562 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))=(-10.55 +/- 0.10) + (3.86 +/- 0.70) kJ mol(-1)/RT ln10. The Arrhenius parameters correspond to a loose transition state and the rate constant at room temperature is 43% of that for SiH2 + C2H4, showing that the deactivating effect of Cl-for-H substitution in the silylene is not large. Quantum chemical calculations of the potential energy surface for this reaction at the G3MP2//B3LYP level show that, as well as 1-chlorosilirane, ethylchlorosilylene is a viable product. The calculations reveal how the added effect of the Cl atom on the divalent state stabilisation of ClSiH influences the course of this reaction. RRKM calculations of the reaction pressure dependence suggest that ethylchlorosilylene should be the main product. The results are compared and contrasted with those of SiH2 and SiCl2 with C2H4.

Gas-phase kinetics of chlorosilylene reactions. I. ClSiH + Me3SiH: absolute rate measurements and theoretical calculations for prototype Si−H insertion reactions

Time-resolved studies of chlorosilylene, CISiH, generated by the 193 nm laser flash photolysis of 1-chloro-1-silacyclopent-3-ene, have been carried out to obtain rate constants for its bimolecular reaction with trimethylsilane, Me3SiH, in the gas phase. The reaction was studied at total pressures up to 100 torr (with and without added SF6) over the temperature range 297-407 K. The rate constants were found to be pressure independent and gave the following Arrhenius equation: log(k/cm(3) molecule(-1) s(-1)) = (-13.97 +/- 0.25) + (12.57 +/- 1.64) kJ mol(-1)/RT In 10. The Arrhenius parameters are consistent with a mechanism involving an intermediate complex, whose rearrangement is the rate-determining step. Quantum chemical calculations of the potential energy surface for this reaction and also the reactions of CISiH with SiH4 and the other methylsilanes support this conclusion. Comparisons of both experiment and theory with the analogous Si-H insertion processes of SiH2 and SiMe2 show that the main factor causing the lower reactivity of ClSiH is the secondary energy barrier. The calculations also show the existence of a novel intramolecular H-atom exchange process in the complex of ClSiH with MeSiH3.

The gas-phase reaction between silylene and 2-butyne: kinetics, isotope studies, pressure dependence studies and quantum chemical calculations

Time-resolved kinetic studies of the reactions of silylene, SiH2, and dideutero-silylene, SiD2, generated by laser. ash photolysis of phenylsilane and phenylsilane-d(3), respectively, have been carried out to obtain rate coefficients for their bimolecular reactions with 2-butyne, CH3C CCH3. The reactions were studied in the gas phase over the pressure range 1-100 Torr in SF6 bath gas at five temperatures in the range 294-612 K. The second-order rate coefficients, obtained by extrapolation to the high pressure limits at each temperature, fitted the Arrhenius equations where the error limits are single standard deviations: log(k(H)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.67 +/- 0.04) + (1.71 +/- 0.33) kJ mol(-1)/RTln10 log(k(D)(infinity)/cm(3) molecule(-1) s(-1)) = (-9.65 +/- 0.01) + (1.92 +/- 0.13) kJ mol(-1)/RTln10 Additionally, pressure-dependent rate coefficients for the reaction of SiH2 with 2-butyne in the presence of He (1-100 Torr) were obtained at 301, 429 and 613 K. Quantum chemical (ab initio) calculations of the SiC4H8 reaction system at the G3 level support the formation of 2,3-dimethylsilirene [cyclo-SiH2C(CH3)=C(CH3)-] as the sole end product. However, reversible formation of 2,3-dimethylvinylsilylene [CH3CH=C(CH3)SiH] is also an important process. The calculations also indicate the probable involvement of several other intermediates, and possible products. RRKM calculations are in reasonable agreement with the pressure dependences at an enthalpy value for 2,3-dimethylsilirene fairly close to that suggested by the ab initio calculations. The experimental isotope effects deviate significantly from those predicted by RRKM theory. The differences can be explained by an isotopic scrambling mechanism, involving H - D exchange between the hydrogens of the methyl groups and the D-atoms in the ring in 2,3-dimethylsilirene-1,1-d(2). A detailed mechanism involving several intermediate species, which is consistent with the G3 energy surface, is proposed to account for this.

A novel X-ray rheometer for in situ studies of polymer melts and solutions during shear flow

A novel X-ray rheometer based on a parallel plate geometry is described. This system allows time-resolved X-ray scattering intensity data to be obtained from polymeric samples subjected to shear flow. The range of quantitative structural parameters, such as molecular orientation and inter chain correlations, which can be obtained from the data is highlighted. Examples of the utility of X-ray scattering in examining optically opaque samples and the extraction of 〈P2〉 and 〈P4〉 orientation parameters are given using anisotropic hydroxypropylcellulose solutions as the sample.