Toward the understanding of the environmental effects on core ionizations

Experimental X‐ray absorption spectra are extensively used to determine electronic structure of small molecules but remain difficult to exploit for proteins due to the large number of peaks within their spectra. For such complex systems, theoretical tools like quantum mechanics/molecular mechanics methodology can greatly ease the assignment of the spectra. This study presents a systematic methodology to evaluate core‐ionization energies (E_ion) in proteins with the help of the asymptotic projection approach (Glushkov and Tsaune, Z. Vichislit. Matem. Mat. Fiz. 1985, 25, 298; Glushkov, Chem. Phys. Lett. 1997, 273, 122; Glushkov, Chem. Phys. Lett. 1998, 287, 189; Glushkov, J. Math. Chem. 2002, 31, 91; Glushkov, Opt. Spectrosc. 2002, 93, 15). An in‐depth inspection of E_ion of systems of increasing complexity is considered, going from amino acids to polyglycine and to glycine in human serum albumin (HSA). Computational analysis can help to better understand experimental data and to discriminate environmental effects by tracing them back to individual and collective electrostatic contributions. In the present work, it was found that E_ion of alpha carbon of glycine residues in HSA ranges from 285 to 295 eV depending on their surroundings. © 2014 Wiley Periodicals, Inc.     

Dynamic measurement of room impulse responses using a moving microphone

A technique for the recording of large sets of room impulse responses or head-related transfer functions is presented. The technique uses a microphone moving with constant speed. Given a setup (e.g., length of the room impulse response), a careful choice of the recording parameters (excitation signal, speed of movement) leads to the reconstruction of all impulse responses along the trajectory. In the case of a moving microphone along a circle, the maximal angular speed is given as a function of the length of the impulse response, its maximal temporal frequency, the speed of sound propagation, and the radius of the circle. As a result of the presented algorithm, head-related transfer functions sampled at 44.1 kHz can be measured at all angular positions along the horizontal plane in less than 1 s. The presented theory is compared with a real system implementation using a precision moving microphone holder. The practical setup is discussed together with its limitations.     

Multireversible redox processes in pentanuclear bis(triple-helical) manganese complexes featuring an oxo-centered triangular {Mn(II)2Mn(III)(μ3-O)}5+ or {Mn(II)Mn(III)2(μ3-O)}6+ core wrapped by two {Mn(II)2(bpp)3}-

A new pentanuclear bis(triple-helical) manganese complex has been isolated and characterized by X-ray diffraction in two oxidation states: [{Mn(II)(μ-bpp)(3)}(2)Mn(II)(2)Mn(III)(μ-O)](3+) (1(3+)) and [{Mn(II)(μ-bpp)(3)}(2)Mn(II)Mn(III)(2)(μ-O)](4+) (1(4+)). The structure consists of a central {Mn(3)(μ(3)-O)} core of Mn(II)(2)Mn(III) (1(3+)) or Mn(II)Mn(III)(2) ions (1(4+)) which is connected to two apical Mn(II) ions through six bpp(-) ligands. Both cations have a triple-stranded helicate configuration, and a pair of enantiomers is present in each crystal. The redox properties of 1(3+) have been investigated in CH(3)CN. A series of five distinct and reversible one-electron waves is observed in the -1.0 and +1.50 V potential range, assigned to the Mn(II)(4)Mn(III)/Mn(II)(5), Mn(II)(3)Mn(III)(2)/Mn(II)(4)Mn(III), Mn(II)(2)Mn(III)(3)/Mn(II)(3)Mn(III)(2), Mn(II)Mn(III)(4)/Mn(II)(2)Mn(III)(3), and Mn(III)(5)/Mn(II)Mn(III)(4) redox couples. The two first oxidation processes leading to Mn(II)(3)Mn(III)(2) (1(4+)) and Mn(II)(2)Mn(III)(3) (1(5+)) are related to the oxidation of the Mn(II) ions of the central core and the two higher oxidation waves, close in potential, are thus assigned to the oxidation of the two apical Mn(II) ions. The 1(4+) and 1(5+) oxidized species and the reduced Mn(4)(II) (1(2+)) species are quantitatively generated by bulk electrolyses demonstrating the high stability of the pentanuclear structure in four oxidation states (1(2+) to 1(5+)). The spectroscopic characteristics (X-band electron paramagnetic resonance, EPR, and UV-visible) of these species are also described as well as the magnetic properties of 1(3+) and 1(4+) in solid state. The powder X- and Q-band EPR signature of 1(3+) corresponds to an S = 5/2 spin state characterized by a small zero-field splitting parameter (|D| = 0.071 cm(-1)) attributed to the two apical Mn(II) ions. At 40 K, the magnetic behavior is consistent for 1(3+) with two apical S = 5/2 {Mn(II)(bpp)(3)}(-) and one S = 2 noninteracting spins (11.75 cm(3) K mol(-1)), and for 1(4+) with three S = 5/2 noninteracting spins (13.125 cm(3) K mol(-1)) suggesting that the {Mn(II)(2)Mn(III)(μ(3)-O)}(5+) and {Mn(II)Mn(III)(2)(μ(3)-O)}(6+) cores behave at low temperature like S = 2 and S = 5/2 spin centers, respectively. The thermal behavior below 40 K highlights the presence of intracomplex magnetic interactions between the two apical spins and the central core, which is antiferromagnetic for 1(3+) leading to an S(T) = 3 and ferromagnetic for 1(4+) giving thus an S(T) = 15/2 ground state.     

Self-assembly of vertically aligned gold nanorod arrays on patterned substrates

Nanorods standing at attention! A self-assembly technique based on convective and capillary forces was used for the direct fabrication of standing arrays of gold nanorods on lithographically predefined areas. The hexagonal close-packed structure of gold nanorods creates an ideal substrate for surface-enhanced Raman spectroscopy.     

Spectral properties of polypyridyl ruthenium complexes intercalated in DNA: theoretical insights into the surrounding effects of [Ru(dppz)(bpy)(2)](2+)

The UV/Visible absorption properties of a polypyridyl ruthenium complex upon intercalation on DNA are studied at the mixed quantum mechanics molecular mechanics level of theory. Vertical excitation transitions are computed by time dependent density functional theory. Particular emphasis is put on the different levels at which the macromolecular environment is treated, and in particular on the analysis of the effect of mechanical, electrostatic and polarizable embedding. We show that with the highest level of theory the experimental absorption wavelengths are reproduced with a difference of only 2 or 3 nm for the low energy bands. The systematic analysis of the individual vertical transitions allows us to get much more insights into the role played by the environment, in particular, in metal to ligand and intra ligand charge transfer transitions that can lead to the production of DNA oxidative lesions exploitable in phototherapy.     

A first low‐resolution difference Fourier map of phosphorus in a membrane protein from near‐edge anomalous diffraction

Crystal diffraction of three membrane proteins (cytochrome bc₁ complex, sarcoplasmic reticulum Ca²⁺ ATPase, ADP‐ATP carrier) and of one nucleoprotein complex (leucyl tRNA synthetase bound to tRNAleu, leuRS:tRNAleu) was tested at wavelengths near the X‐ray K‐absorption edge of phosphorus using a new set‐up for soft X‐ray diffraction at the beamline ID01 of the ESRF. The best result was obtained from crystals of Ca²⁺ ATPase [adenosin‐5′‐(β,γ‐methylene) triphosphate complex] which diffracted out to 7 Å resolution. Data were recorded at a wavelength at which the real resonant scattering factor of phosphorus reaches the extreme value of ?20 electron units. The positions of the four triphosphates of the monoclinic unit cell of the ATPase have been obtained from a difference Fourier synthesis based on a limited set of anomalous diffraction data.     

Quantum processing of images by continuous wave optical parametric amplification

We have experimentally shown that a degenerate optical parametric oscillator pumped by a cw laser, inserted in a cavity having degenerate transverse modes such as a hemiconfocal or confocal cavity, and operating below the oscillation threshold in the regime of phase sensitive amplification, is able to process input images of various shapes in the quantum regime. More precisely, when deamplified, the image is amplitude squeezed; when amplified, its two polarization components are intensity correlated at the quantum level. In addition, the amplification process of the images is shown to take place in the noiseless regime.     

Investigation of gain ripple in two-pump fiber optical parametric amplifiers

By using the four-sideband theory, we analyze the gain spectrum in wideband two-pump fiber optical parametric amplifiers and predict gain ripples over the flat gain region. We derive an approximation of their pseudo-periods and discuss methods for reducing their amplitudes.     

Spatio-temporal dynamics of multicolor spatial Kerr solitons

We present numerical and experimental results showing the rich and complex spatio-temporal dynamics of multicolor spatial vector soliton generated by stimulated Raman scattering in a Kerr planar waveguide. By taking into account their temporal dimension, we found the precise domain of existence of multicolor soliton whose components are mutually guided and spatio-temporally superimposed. In addition, we observe the Raman Stokes component in the trailing edge of the pump pulse and show that it is associated with the slow-light process induced by the sharp resonance of the Raman gain medium.