Deconvolution of lignin fluorescence spectra: A contribution to the comparative structural studies of lignins

In this work, we deconvoluted the fluorescence spectra of lignin and a lignin model compound using a combination of one symmetric (Gaussian) and the most appropriate number of asymmetric (Log-normal) models. We aimed to obtain new data on the structural characteristics of lignin as a complex molecule using fluorescence spectroscopy in combination with FTIR spectra. We analyzed the emission spectra of the lignin model compound, DHP, and isolated lignins from a deciduous tree, poplar, and a coniferous tree, spruce. The number of applied asymmetric components was varied for each sample until the component positions obtained from deconvolution of a series of spectra became constant. The lignin model compound contains fewer components in the emission spectrum. The same components in the spectra of all three samples show that they contain the same fluorophores. The small shift of the peak position can be attributed to the influence of different environments. The FTIR spectra of the three polymers show a small difference between their structures. The main difference among the IR spectra of the three samples is in the intensity of some peaks. The text was submitted by the authors in English.     

Efforts toward developing direct probes of protein dynamics

We report the first IR characterization of a single C-D bond within a protein, methyl-d1 Met80 of horse heart cytochrome c. A comparison was made to methyl-d1/d3 methionine as well as methyl-d3 Met80. We found that for methyl-d1 and the asymmetric stretches of methyl-d3, line widths/line shapes are dominated by inhomogeneous broadening, whereas the symmetric stretch of methyl-d3 has a significant homogeneous component. Vibrational energy relaxation calculations found that a significantly stronger Fermi resonance exists for the symmetric stretch than for the asymmetric stretches, thereby suggesting that a difference in intramolecular vibrational relaxation (IVR) causes the observed line width/line shape difference between the symmetric and asymmetric stretches.     

Molecular dynamics simulation of liquid methanol. II. Unified assignment of infrared, Raman, and sum frequency generation vibrational spectra in methyl C-H stretching region

Vibrational spectra of methyl C-H stretching region are notoriously complicated, and thus a theoretical method of systematic assignment is strongly called for in condensed phase. Here we develop a unified analysis method of the vibrational spectra, such as infrared (IR), polarized and depolarized Raman, and ssp polarized sum frequency generation (SFG), by flexible and polarizable molecular dynamics simulation. The molecular model for methanol has been developed by charge response kernel model to allow for analyzing the methyl C-H stretching vibrations. The complicated spectral structure by the Fermi resonance has been unraveled by empirically shifting potential parameters, which provides clear information on the coupling mechanism. The analysis confirmed that for the IR, polarized Raman, and SFG spectra, two-band structure at about 2830 and 2950 cm(-1) results from the Fermi resonance splitting of the methyl C-H symmetric stretching and bending overtones. In the IR spectrum, the latter, higher-frequency band is overlapped with prominent asymmetric C-H stretching bands. In the depolarized Raman spectrum, the high frequency band at about 2980 cm(-1) is assigned to the asymmetric C-H stretching mode. In the SFG spectrum, the two bands of the splitted symmetric C-H stretching mode have negative amplitudes of imaginary nonlinear susceptibility χ(2), while the higher-frequency band is partly cancelled by positive imaginary components of asymmetric C-H stretching modes.     

Infrared spectroscopic ellipsometry of n-alkylthiol (C5-C18) self-assembled monolayers on gold

The infrared spectroscopic ellipsometry (IRSE) of n-alkylthiol (CH3(CH2)xSH, x = 4, 6, 7, 8, 10, 13, 15, and 17, self-assembled monolayers (SAMs), with 5-18 carbon atoms (C5-C18), grown on gold-coated Si(100) substrates) was investigated at room temperature. The C-H stretching vibrations could be resolved even for pentathiol, the shortest chain studied. The symmetric and asymmetric stretching vibrations of the CH2 groups are located at about 2850 and 2920 cm(-1), and those of CH3 are at about 2877 and 2962 cm(-1), respectively; they show a slight shift with the number of CH2 units. In addition, Fermi resonance of the symmetric CH3 stretching vibration at 2940 cm(-1) appears with decreasing chain length due to weak coupling with the asymmetric CH2 stretching vibration. The "odd-even effect" of the n-alkylthiol SAMs with varying CH2 units could be distinguished by the two interactive IRSE parameters. The relative ellipsometric spectra for the four longest chains could be reproduced quite well by using a Lorentz multioscillator model with a three-phase optical model (air/SAMs/gold). On the basis of the theoretical calculations, the vibrational strength of these oscillators is very weak, its magnitude being 10(-4)-10(-5). The full width at half-maximum (fwhm) of the peaks varies from 7 to 33 cm(-1). Moreover, the intensity of the C-H vibrations increases with the number of methylene units, due to strong lateral interactions and ordering effects occurring for longer chains.     

Controlling the isomerization dynamics of iodide acetonitrile dimer complex by optimally designed electromagnetic field: A wave packet based approach

Both symmetric and asymmetric forms of the iodide acetonitrile dimer complex are known to exist with a higher stability shown by the symmetric isomer. Dynamics of this isomerization has been investigated on reduced dimensional surface in absence/presence of external electromagnetic field using Gaussian wave packet as the starting wave function. When the symmetric isomer has been taken as the initial structure, isomerization does not takes place without the external field due to high energy barrier, whereas with the asymmetric isomer as the starting one, isomerization takes place spontaneously with an equal population of both isomers. Our target in this study has been to get a dominant population of asymmetric isomer which is not possible without the application of electromagnetic field. However, it has also been seen that a simple monochromatic field cannot achieve this goal. Only by application of optimally designed polychromatic field the dominating population of asymmetric isomer can be obtained.     

Effect of chain length and asymmetry on material properties of bilayer membranes

Dissipative particle dynamics is used to extract the material parameters (bending and area stretch moduli) of a bilayer membrane patch. Some experiments indicate that the area stretch modulus of lipid vesicles varies little as the chain length of the lipids composing the bilayer increases. Here we show that making the interactions between the hydrophilic head groups of the model amphiphiles proportional to the hydrophobic tail length reproduces the above result for the area stretch modulus. We also show that the area stretch modulus of bilayers composed of amphiphiles with the same number of tail beads but with asymmetric chains is less than that of bilayers with symmetric chains. The effects on the bilayer density and lateral stress profiles of changes to the amphiphile architecture are also presented.     

Are recent water models obtained by fitting diffraction data consistent with infrared/Raman and x-ray absorption spectra?

X-ray absorption (XA) spectra have been computed based on water structures obtained from a recent fit to x-ray and neutron diffraction data using models ranging from symmetrical to asymmetrical local coordination of the water molecules [A. K. Soper, J. Phys.: Condens. Matter 17, S3273 (2005)]. It is found that both the obtained symmetric and asymmetric structural models of water give similar looking XA spectra, which do not match the experiment. The fitted models both contain unphysical structures that are allowed by the diffraction data, where, e.g., hydrogen-hydrogen interactions may occur. A modification to the asymmetric model, in which the non-hydrogen-bonded OH intramolecular distance is allowed to become shorter while the bonded OH distance becomes longer, improves the situation somewhat, but the overall agreement is still unsatisfactory. The electric field (E-field) distributions and infrared (IR) spectra are also calculated using two established theoretical approaches, which, however, show significant discrepancies in their predictions for the asymmetric structural models. Both approaches predict the Raman spectrum of the symmetric model fitted to the diffraction data to be significantly blueshifted compared to experiment. At the moment no water model exists that can equally well describe IR/Raman, x-ray absorption spectroscopy, and diffraction data.     

Direct dynamics study of ultrafast vibrational energy relaxation in ice Ih

Car-Parrinello molecular dynamics (CPMD) and a previously developed wave packet model are used to study ultrafast relaxation in water clusters. Water clusters of 15 water molecules are used to represent ice Ih. The relaxation is studied by exciting a symmetric or an asymmetric stretch mode of the central water molecule. The CPMD results suggest that relaxation occurs within 100 fs. This is in agreement with experimental work by Woutersen and Bakker and the earlier wave packet calculations. The CPMD results further indicate that the excitation energy is transferred both intramolecularly and intermolecularly on roughly the same time scale. The intramolecular energy transfer occurs predominantly between the symmetric and asymmetric modes while the bend mode is largely left unexcited on the short time scale studied here.     

Model shape transitions of micelles: spheres to cylinders and disks

We present a microscopic analysis of shape transitions of micelles of model linear nonionic surfactants. In particular, symmetric H(4)T(4) and asymmetric H(3)T(6) surfactants have been chosen for the study. In a previous work, it has been observed that symmetric surfactants have a strong tendency to prefer spherical micelles over a wide range of chemical potentials, while asymmetric surfactants undergo shape transitions between a spherical micelle at low concentration to other forms, mainly finite cylindrical micelles. This study combines the application of a two-dimensional single-chain mean-field theory (SCMFT) with Monte Carlo (MC) simulations of exactly the same systems. On the one hand, the characteristics of the SCMFT make this method suitable for free energy calculations, especially for small surfactants, due to the incorporation of relevant microscopic details in the model. On the other hand, MC simulations permit us to obtain a complete picture of the statistical mechanical problem, for the purpose of validation of the mean-field calculations. Our results reveal that the spherical shape for the symmetric surfactant is stable over a large range of surfactant concentrations. However, the asymmetric surfactant undergoes a complex shape transition that we have followed by calculating the standard chemical potential as a function of the aggregation number. The results indicate that the system forms prolate spheroids prior to developing short capped cylinders that gradually grow in length, with some oscillations in the energy of formation. The most important result of our work is the evidence of a bifurcation where, together with the elongated objects, the system can develop oblate aggregates and finally a torus shape similar to a red blood cell.     

Distorted wave Born and three-body distorted wave Born approximation calculations of the fully differential cross section for electron-impact ionization of nitrogen molecules

Currently there are no reliable theoretical approaches for calculating fully differential cross sections (FDCSs) for low-energy electron-impact ionization of large molecules. We have recently proposed the orientation-averaged molecular orbital (OAMO) for calculating cross sections averaged over molecular orientations. In this paper, we use the OAMO to calculate distorted wave Born approximation (DWBA) and molecular three-body distorted wave (M3DW) Born approximation FDCS for electron-impact ionization of the nitrogen molecule. Both coplanar symmetric and asymmetric FDCSs are investigated in the energy range of 35.6-400 eV. By comparing with the experimental data, we found that the M3DW is reasonably accurate in this energy range. We also found that the postcollision interaction plays a sufficiently important role and that the DWBA is not reliable.     

A combined experimental and theoretical study of carboxylate coordination modes: a structural probe

The variations of the frequency differences of symmetric and asymmetric stretching vibrations in a series of carboxylato Fe(II) complexes have been theoretically studied. It is shown that structural information can be obtained from a direct comparison between the difference (Delta = nu(as) - nu(s)) in the asymmetric (nu(as)) and symmetric (nu(s)) carboxylate vibrations of the free anion and that of the coordinated species. The coordination mode approaches C(2v) symmetry as Delta decreases with respect to its value for the noncoordinated carboxylate. The use of IR spectroscopy in the resolution of speculated crystallographic structures is suggested.     

Small-angle neutron scattering studies of dynamics and hierarchical pattern formation in binary mixtures of polymers and small molecules

We present the dynamics of the composition fluctuations and pattern formation of two-component systems in both single-phase and two-phase states as studied by time-resolved small-angle neutron scattering and light scattering. Two-component systems to be covered here include not only dynamically symmetric systems, in which each component has nearly identical self-diffusion coefficients, but also dynamically asymmetric systems, in which each component has different self-diffusion coefficients. We compare the dynamic behaviors of the two systems and illuminate their important differences. The scattering studies presented for dynamically asymmetric systems highlight that stress–diffusion coupling and viscoelastic effects strongly affect the dynamics and pattern formation. For dynamically symmetric systems, we examine the universality existing in both polymer systems and small-molecule systems as well as new features concerning the time evolution of hierarchical structures during phase separation via spinodal decomposition over a wide range of wave numbers (up to four orders of magnitude). For both systems, we emphasize that polymers provide good model systems for studying the dynamics and pattern formation. © 2004 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 42: 3027–3062, 2004     

Counting the monomers in nanometer-sized oligomers by pulsed electron-electron double resonance

In a lot of cases active biomolecules are complexes of higher order, thus methods capable of counting the number of building blocks and elucidating their geometric arrangement are needed. Therefore, we experimentally validate here spin-counting via 4-pulse electron-electron double resonance (PELDOR) on well-defined test samples. Two biradicals, a symmetric and an asymmetric triradical, and a tetraradical were synthesized in a convergent reaction scheme via palladium-catalyzed cross-coupling reactions. PELDOR was then used to obtain geometric information and the number of spin centers per molecule in a single experiment. The measurement yielded the expected distances (2.2-3.8 nm) and showed that different spin-spin distances in one molecule can be resolved even if the difference amounts to only 5 A. The number of spins n has been determined to be 2.1 in both biradicals, to 3.1 and 3.0 in the symmetric and asymmetric triradicals, respectively, and to 3.9 in the tetraradical. The overall error of PELDOR spin-counting was found to be 5% for up to four spins. Thus, this method is a valuable tool to determine the number of constituting spin-bearing monomers in biologically relevant homo- and heterooligomers and how their oligomerization state and geometric arrangement changes during function.     

Pervaporation of water-ethanol mixtures through symmetric and asymmetric TPX membranes

In this work, the pervaporation performance and mechanism of water-ethanol mixtures through symmetric and asymmetric TPX [poly(4-methyl-1-pentene)] membranes were investigated. The results show that TPX is a highly water permselective material although it is strongly hydrophobic. It was found that, for a symmetric dense TPX membrane, the feed solution vaporizes first and then permeates through the membrane. The water selectivity stems from the huge difference in diffusivity between water and ethanol vapors. To improve the permeation flux, asymmetric TPX membranes were prepared by a wet inversion method. However, due to the swelling effect of ethanol on TPX, small pores occur when the dense skin contacts the feed solution, resulting in a loss of water selectivity. Stain experiments were carried out to verify this mechanism. In addition, it was found that a parallel model can describe the mechanism quite accurately. Good agreement between the theoretical calculation and experimental measurement has been obtained. Furthermore, we also found that the loss of selectivity can be avoided by turning the asymmetric membrane over; that is, let the dense skin face the permeate.     

Vibrational coherence transfer characterized with Fourier-transform 2D IR spectroscopy

Two-dimensional infrared (2D IR) spectroscopy of the symmetric and asymmetric C[Triple Bond]O stretching vibrations of Rh(CO)(2)acac in hexane has been used to investigate vibrational coherence transfer, dephasing, and population relaxation in a multilevel vibrational system. The transfer of coherence between close-lying vibrational frequencies results in extra relaxation-induced peaks in the 2D IR spectrum, whose amplitude depends on the coherence transfer rate. Coherence transfer arises from the mutual interaction of the bright CO stretches with dark states, which in this case reflects the mutual d-pi(*) back bonding of the Rh center to both the terminal carbonyls and the acetylacenonate ligand. For 2D IR relaxation experiments with variable waiting times, coherent dynamics lead to the modulation of peak amplitudes, while incoherent population relaxation and exchange results in the growth of the relaxation-induced peaks. We have modeled the data by propagating the density matrix with the Redfield equation, incorporating all vibrational relaxation processes during all three experimental time periods and including excitation reorientation effects arising from relaxation. Coherence and population transfer time scales from the symmetric to the asymmetric stretch were found to be 350 fs and 3 ps, respectively. We also discuss a diagrammatic approach to incorporating all vibrational relaxation processes into the nonlinear response function, and show how coherence transfer influences the analysis of structural variables from 2D IR spectroscopy.     

Picosecond IR-UV pump-probe spectroscopic study on the intramolecular vibrational energy redistribution of NH2 and CH stretching vibrations of jet-cooled aniline

Intramolecular vibrational energy redistribution (IVR) of the NH2 symmetric and asymmetric stretching vibrations of jet-cooled aniline has been investigated by picosecond time-resolved IR-UV pump-probe spectroscopy. A picosecond IR laser pulse excited the NH2 symmetric or asymmetric stretching vibration of aniline in the electronic ground state and the subsequent time evolutions of the excited level as well as redistributed levels were observed by a picosecond UV pulse. The IVR lifetimes for symmetric and asymmetric stretches were obtained to be 18 and 34 ps, respectively. In addition, we obtained the direct evidence that IVR proceeds via two-step bath states; that is, the NH2 stretch energy first flows into the doorway state and the energy is further dissipated into dense bath states. The rate constants of the second step were estimated to be comparable to or slower than those of the first step IVR. The relaxation behavior was compared with that of IVR of the OH stretching vibration of phenol [Y. Yamada, T. Ebata, M. Kayano, and M. Mikami J. Chem. Phys. 120, 7400 (2004)]. We found that the second step IVR process of aniline is much slower than that of phenol, suggesting a large difference of the "doorway state increasing the dense bath states" anharmonic coupling strength between the two molecules. We also observed IVR of the CH stretching vibrations, which showed much faster IVR behavior than that of the NH2 stretches. The fast relaxation is described by the interference effect, which is caused by the coherent excitation of the quasistationary states.     

Peak Profile Analysis in High Field Asymmetric Wave Ion Mobility Spectrometry

High field asymmetric wave ion mobility spectrometry (FAIMS) is a powerful tool to detect and characterize gas-phase ions, while the unsolvable partial differential equation of ions moving in ion drift tube poses a big challenge to FAIMS spectral peak analysis. In this work, a universal and effective model of FAIMS spectral peak profile has been proposed by introducing ion trajectory and loss height. With this model, the influence of the structure of ion drift tube, dispersion voltages, compensation voltages, and carrier gas flow rate on the FAIMS spectral peak characteristics like peak shape, full width at half maximum and peak height is analyzed and discussed. The results show that the influence of different factors on the FAIMS spectral peak profile can be qualitatively described by the model which agrees with the experimental data.     

Absolute triple differential cross-section measurements in energy sharing kinematics and a coplanar asymmetric geometry at 100 and 200 eV on He

Results of measurements for electron impact ionization of atomic helium are reported for energy-sharing kinematics in a coplanar asymmetric geometry. Incident energies of 100 eV and 200 eV are considered and comparison with previous experiments in fully symmetric kinematics allows the results to be put on an absolute scale. The cross-sections are compared with those obtained from two variants of the distorted wave Born approximation (DWBA) model. Good general agreement is obtained for the form of the angular distributions. The absolute magnitude of the cross sections is however not compatible with the choice of half-on-shell Coulomb T-Matrix currently used in the distorted wave impulse and related approximations.     

Simulations of a lattice model of two-headed linear amphiphiles: influence of amphiphile asymmetry

Using a 2D lattice model, we conduct Monte Carlo simulations of micellar aggregation of linear-chain amphiphiles having two solvophilic head groups. In the context of this simple model, we quantify how the amphiphile architecture influences the critical micelle concentration (CMC), with a particular focus on the role of the asymmetry of the amphiphile structure. Accordingly, we study all possible arrangements of the head groups along amphiphile chains of fixed length N = 12 and 16 molecular units. This set of idealized amphiphile architectures approximates many cases of symmetric and asymmetric gemini surfactants, double-headed surfactants, and boloform surfactants. Consistent with earlier results, we find that the number of spacer units s separating the heads has a significant influence on the CMC, with the CMC increasing with s for s < N/2. In comparison, the influence of the asymmetry of the chain architecture on the CMC is much weaker, as is also found experimentally.