X–H rotational-echo double-resonance NMR for torsion angle determination of peptides

C–H and N–H rotational-echo double-resonance (REDOR) NMR is developed for determining torsion angles in peptides. The distance between an X spin such as ¹³C or ¹⁵N and a proton is measured by evolving the proton magnetization under REDOR-recoupled X–H dipolar interaction. The proton of interest is selected through its directly bonded heteronuclear spin Y. The sidechain torsion angle χ₁ is extracted from a ¹³Cβ-detected Hβ–N distance, while the backbone torsion angle φ is extracted from an ¹⁵N-detected H^N–C^′ distance. The approach is demonstrated on three model peptides with known crystal structures to illustrate its utility.     

Dipolar double-quantum filtered rotational-echo double resonance

The homonuclear dipolar coupling of a directly bonded (13)C-(13)C pair has been used to create a dipolar double-quantum filter (D-DQF) to remove the natural-abundance (13)C background in (13)C[(2)H] rotational-echo double-resonance (REDOR) experiments. The most efficient version of this experiment has the D-DQF excitation and reconversion preceding the REDOR evolution period. Calculated and observed (13)C[(2)H]D-DQF-REDOR dephasings were in agreement for a test sample of mixed recrystallized labeled alanines.     

Conductivity of water-in-oil microemulsions: Comparison of the Boltzmann statistics and the charge fluctuation model

The electrical conductivity of water-in-oil microemulsions is interpreted on the basis of the distribution of ionic charges among the droplets. The charging energy is approximated by the Born energy. In the interpretation, the hydrodynamic radius is distinguished from the water core radius. The Boltzmann statistics are compared with the fluctuation theory. The former approach is more realistic due to its consideration of the discrete nature of charge, while the latter better fits the data obtained with the AOT-water-isooctane system.     

Laser double-resonance studies of Rydberg states of HgAr

The first Rydberg states of the HgAr van der Waals molecule have been characterized by a laser double-resonance technique. Two states have been observed, which correlate to Hg(7s³S₁)+Ar(¹S₀), a strongly bound state, C, in accord with theoretical expectations and a very weakly bound state, D, which is unexplained.     

Infrared double-resonance lineshapes in strongly pumped spherical-top molecules

Strong double-resonance signals are observed in silane pumped with a TEA-CO₂ laser and probed with a tunable diode laser. The lineshapes of these signals have been modeled with an extension of three level density-matrix theory to the case of a large bandwidth pump laser. Up to 50% of the ground state population can be transferred to specific rotational levels of the dyad by CO₂ laser pumping. Collision-mediated two-photon excitation to triad levels has also been observed.     

Random grafting statistics in graft distribution analysis

Graft distribution functions have been derived from random grafting statistics. Among the functions, the weight fraction of ungrafted backbone chains, the molecular weight distribution of the ungrafted backbone chains and the GPC apparent molecular weight distribution of the graft copolymer have been found to agree with experimental values determined for a graft copolymer system in which grafting was expected to be random. The other functions, which are not directly measurable, are therefore probably also correct. In analytical work the entire set of graft distribution functions may be computed for a graft copolymer system from the following experimental data: (1) molecular weight distribution of the starting backbone chains; (2) the chemical composition of the mixture of the graft copolymer and ungrafted backbone; (3) the graft side-chain molecular weight distribution, which may be assumed to be identical to that of the ungrafted homopolymer separable from the reaction mixture.     

Infrared double-resonance spectroscopy of bromoform with picosecond pulses

Using independently tunable pump and probe pulses in the infrared, time- and frequency-resolved spectroscopy of vibrationally excited, polyatomic molecules in liquids is demonstrated for the first time. Experimental data are presented for CHBr₃, measuring the population lifetime via excited-state absorption of the CH-stretching mode; for larger probe delay, the non-equilibrium population of intermediate vibrational levels in the relaxation ladder of bromoform is observed.     

Vibrational dynamics of 9-fluorenemethanol using infrared-ultraviolet double-resonance spectroscopy

Vibrational spectroscopy of jet-cooled 9-fluorenemethanol and its clusters 9-fluorenemethanol-H2O, 9-fluorenemethanol-CH3OH, 9-fluorenemethanol-C2H5OH, and 9-fluorenemethanol-C3H7OH has been carried out using an IR-UV double-resonance method. The spectrum of the OH stretching vibration, v(OH), has been measured for the 9-fluorenemethanol monomer and for each of the clusters. Two conformers of 9-fluorenemethanol, symmetric (sym) and unsymmetric (unsym), have been identified using a combination of spectroscopy and quantum chemical calculations with B3LYP and HF methods using the 6-31G(d) basis set. Vibrational dynamics resulting from IR excitation has also been studied using the S0-S1 transition probed by a nanosecond-time-delayed UV laser. The data suggest that isomerization occurs as a result of the IR excitation, but the breadth of the probe spectra makes an unequivocal conclusion difficult. The effect of hydrogen bonding on the v(OH) of 9-fluorenemethanol has also been studied in clusters with water, methanol, ethanol, and propanol by measuring the IR spectra. Cluster dissociation dynamics have also been studied following IR excitation. It is observed that upon excitation of the cluster of a particular conformation the monomer product is generally produced in both conformer forms. Energetic considerations indicate that isomerization occurs before dissociation.     

Laser induced double-resonance ionic fluorescence in an inductively coupled plasma

Two pulsed dye lasers pumped by an excimer laser are simultaneously directed into the analytical zone of an inductively coupled argon plasma. When the two beams are tuned to the appropriate ionic transitions, highly excited ionic levels can be efficiently populated in saturated conditions, the resulting fluorescence being then spectrally isolated with a monochromator and measured. A theoretical outline of this technique, variously called double-resonance fluorescence or two-step fluorescence, is given. The experimental results obtained with the alkaline-earth metals Ca, Sr, Ba and Mg show that the technique does provide excellent sensitivity, freedom from scattering problems and unprecedented spectral selectivity. The laser characteristics, the time overlap between the pulses and the spectral characteristics of the transitions used are discussed. Finally, ionic fluorescence in the plasma is the most suitable analytical application of such double-resonance technique since its use in flame atomic fluorescence suffers from the strong depletion of the excited levels due to collisionally assisted ionization.     

Lineshapes and optical selectivity in high-resolution double-resonance ionization mass spectrometry

Lineshapes expected in high-resolution double-resonance ionization spectroscopy are calculated using the density matrix formalism, integrated over experimentally realistic conditions including atomic velocity and angular distributions as well as laser intensity profiles. The results of these calculations are compared with experimental measurements on the system 4s^{2 1}S₀ → 4s4p ¹P₁ → 4s4d ¹D₁ → ion for calcium. The measurements of lineshape, with a dynamic range of >10⁶, reveal and confirm subtle effects predicted by theory. These include the shape, position and intensity of the laser-induced structure in the spectra and the simultaneous presence of coherent and incoherent excitation processes. The calculations are able to accurately predict isotopic selectivities achieved in experimental resonance ionization measurements and are used to evaluate these values for the detection of minor calcium isotopes, including the radionuclide ⁴¹Ca.     

Estimating sufficient statistics in co-evolutionary analysis by mutual information

Mutual information (MI) is a standard measure in information theory to observe and quantify correlated signals and events in both, empirical data sets and theoretical models. In the field of computational biology the MI turned out to be particularly useful in studies on co-evolutionary signals of sites within biomolecules. A key issue in the applicability of the MI is, however, a correct reference system or null model to understand finite-size effects in the underlying, finite data set. Although some bioinformatics studies exist with rigorous results for theoretical, well-designed random distributions, data from real-world proteins was never used to quantify the effect of finite-size samples. The impact of real-world statistics is, however, most relevant for researchers in all fields concerned with detecting evolutionary signals within biological sequences. We present results on such effects in finite-sized biological data sets and point to future research directions. We are most of all concerned with bacterial, ribosomal proteins as a prototypical example in molecular evolution. We compare to previous published suggestions, give an empirical formula, and propose a protocol to guide future research projects.     

Multi-element Saha–Boltzmann and Boltzmann plots in laser-induced plasmas

A multi-element Saha–Boltzmann plot method is proposed for the determination of the temperature and the relative number density in laser-induced plasmas, assuming local thermodynamic equilibrium and stoichiometry conservation. The method has been applied to the characterization of a plasma generated with a Cu–Fe–Ni–Mn alloy, using a Nd:YAG laser in air at atmospheric pressure. Spectra of the local emissivity have been obtained by spatial deconvolution of the intensity spectra, obtained with spatial resolution. Saha–Boltzmann plots obtained from the emissivities of 58 spectral lines of Fe I, Fe II, Ni I, Ni II, Mn I and Mn II have been fitted to linear behavior with high correlation, which shows the validity of the equation proposed. Radial distributions of the temperature and number densities of neutral atoms and ions have been determined. The results obtained reinforce the initial considerations of local thermodynamic equilibrium and conservation of stoichiometry. The proposed equation can also be applied to only one ionization species (multi-element Boltzmann plot). Spatially-integrated measurements of the plasma emission have also been performed to show that, in this case, the application of the method to the line intensities provides the two different apparent temperatures for neutral atoms and ions.     

Rotational-echo double-resonance NMR distance measurements for the tubulin-bound Paclitaxel conformation

The important anticancer drug Taxol (paclitaxel, PTX) owes its unique activity to its ability to bind to tubulin in a stoichiometric ratio and promote its assembly into microtubules. The conformation of the microtubule-bound drug has been the focus of numerous research efforts, since the inability of polymerized tubulin to form crystals precludes structure proof by X-ray crystallography. Likewise, although the alpha,beta-tubulin dimer structure has been solved by electron crystallography, the 3.7 A resolution is too low to permit direct determination of either ligand conformation or binding pose. In this article, we present experimental results from 2H{19F} REDOR NMR that provide direct confirmation that paclitaxel adopts a T-shaped conformation when it is bound to tubulin.     

Conformation of L-tyrosine studied by fluorescence-detected UV-UV and IR-UV double-resonance spectroscopy

The laser-induced fluorescence spectrum of jet-cooled L-tyrosine exhibits more than 20 vibronic bands in the 35450-35750 cm(-1) region. We attribute these bands to eight conformers by using results of UV-UV hole-burning spectroscopy. These isomers are classified into four groups; each group consists of two rotational isomers that have a similar side-chain conformation but different orientations of the phenolic OH. The splitting of band origins of rotational isomers is 31, 21, 5, and 0 cm(-1) for these groups. IR-UV spectra suggest that conformers belonging to two of the four groups have an intramolecular OH...N hydrogen bond between the COOH and NH2 groups. By comparing experimental and theoretical results of L-tyrosine with those of L-phenylalanine, we propose probable conformers of L-tyrosine.     

Sampling statistics and considerations for single-shot analysis using laser-induced breakdown spectroscopy

A statistical analysis of single-shot spectral data is reported for laser-induced breakdown spectroscopy (LIBS). Fluctuations in both atomic emission and plasma continuum emission are investigated in concert for a homogenous gaseous flow, and fluctuations in plasma temperature are reported based on iron atomic emission in an aerosol-seeded flow. Threshold irradiance for plasma initiation and plasma absorption were investigated for pure gaseous and aerosol streams, with detailed statistical measurements performed as a function of pulse energy in the breakdown regime. The ratio of the analyte atomic emission intensity to the continuum emission intensity (peak/base) provided a robust signal for single-shot LIBS analysis. Moreover, at optimal temporal delay, the precision of the LIBS signal was maximized for pulse energies within the saturation regime with respect to plasma absorption of incident energy. Finally, single-shot temperature measurements were analyzed, leading to the conclusion that spatial variations in the plasma volume formation and subsequent plasma emission collection, play important roles in the overall shot-to-shot precision of the LIBS technique for gaseous and aerosol analysis.     

IR/UV and UV/UV double-resonance study of guaiacol and eugenol dimers

Guaiacol (2-methoxyphenol) and eugenol (4-allyl-2-methoxyphenol) molecules are biologically active phenol derivatives with an intramolecular -OH...OCH3 hydrogen bond (H bond). Pulsed supersonic expansions of mixtures of either of the two molecules with He yield weakly bound homodimers as well as other higher-order complexes. A number of complementary and powerful laser spectroscopic techniques, including UV-UV and IR-UV double resonances, have been employed to interrogate the species formed in the expansion in order to get information on their structures and spectroscopic properties. The interpretation of the spectra of eugenol dimer is complex and required a previous investigation on a similar but simpler molecule both to gain insight into the possible structures and support the conclusions. Guaiacol (2-methoxyphenol) has been used for that purpose. The combination of the broad laser study combined with ab initio calculations at the Becke 3 Lee-Yang-Parr/6-31+Gd level has provided the isomer structures, the potential-energy wells, and shed light on the inter- and intramolecular interactions involved. Guaiacol homodimer has been shown to have a single isomer whereas eugenol dimer has at least two. The comparison between the computed geometries of the dimers, their respective energies, and the vibrational normal modes permits the identification of the spectra.     

Monte Carlo global sensitivity analysis of Boltzmann equation for electron kinetics in H2 discharges

Global sensitivity analysis with the Monte Carlo method is applied to the Boltzmann equation for the electron energy distribution function (eedf). The results show the sensitivity of eedf and related quantities on the global variation of cross sections set. A new indicator of global sensitivity is used, which appears to be of easy applicability.     

Structural role of fluoride in aluminophosphate sol-gel glasses: high-resolution double-resonance NMR studies

The local structure of Na-Al-P-O-F glasses, prepared by a novel sol-gel route, was extensively investigated by advanced solid-state NMR techniques. 27Al{19F} rotational echo double resonance (REDOR) results indicate that the F incorporated into aluminophosphate glass is preferentially bonded to octahedral Al units and results in a significant increase in the concentration of six-coordinated aluminum. The extent of Al-F and Al-O-P connectivities are quantified consistently by analyzing 27Al{31P} and 27Al{19F} REDOR NMR data. Two distinct types of fluorine species were identified and characterized by various 19F{27Al}, 19F{23Na}, and 19F{31P} double resonance experiments, which were able to support peak assignments to bridging (Al-F-Al, -140 ppm) and terminal (Al-F, -170 ppm) units. On the basis of the detailed quantitative dipole-dipole coupling information obtained, a comprehensive structural model for these glasses is presented, detailing the structural speciation as a function of composition.     

Study of the temperature‐dependent conformational averaging of 1H NMR resonances in vinylcyclopropane through the use of ab initio methodology and Boltzmann statistics

The temperature dependence of the ¹ H NMR resonance of the C‐4 olefinic proton in vinylcyclopropane was investigated through a combination of ab initio calculations and Boltzmann statistics. A torsional energy profile as a function of the 〈?〉 dihedral angle was obtained using HF methodology with a 6–311G** basis set, while the corresponding ¹ H chemical shift profiles for the C‐4 proton were computed using the GIAO approach and either HF, DFT (B3LYP) or MP2 methods at the 6–311G** level of theory. Chemical shifts at different temperatures calculated as canonical ensemble averages in which the different ab initio ¹ H chemical shift profiles and a Boltzmann factor defined by the HF/ 6–311G** energy function are employed reproduce remarkably well the temperature dependence observed experimentally. Attempts to perform a similar study using only the GIAO‐MP2 ¹ H chemical shift profile and 〈?〉 dihedral angle trajectories obtained from molecular dynamics simulations at different temperatures failed to reproduce the experimental trends. This shortcoming was attributed to the inability of the force fields employed, Tripos 6.0 and MMFF94, to reproduce properly the three‐well torsional potential of vinylcyclopropane. The application of both methodologies to the calculation of population‐dependent chemical shifts in other systems is discussed. Copyright © 2002 John Wiley & Sons, Ltd.