Terahertz (THz) spectroscopic investigations of condensed-phase biological samples are reviewed ranging from the simple crystalline forms of amino acids, carbohydrates and polypeptides to the more complex aqueous forms of small proteins, DNA and RNA. Vibrationally resolved studies of crystalline samples have revealed the exquisite sensitivity of THz modes to crystalline order, temperature, conformational form, peptide sequence and local solvate environment and have given unprecedented measures of the binding force constants and anharmonic character of the force fields, properties necessary to improve predictability but not readily obtainable using any other method. These studies have provided benchmark vibrational data on extended periodic structures for direct comparisons with classical (CHARMm) and quantum chemical (density functional theory) theories. For the larger amorphous and/or aqueous phase samples, the THz modes form a continuum-like absorption that arises because of the full accessibility to conformational space and/or the rapid time scale for inter-conversion in these environments. Despite severe absorption by liquid water, detailed investigations have uncovered the photo- and hydration-induced conformational flexibility of proteins, the solvent shell depth of the water/biomolecule boundary layers and the solvent reorientation dynamics occurring in these interfacial layers that occur on sub-picosecond time scales. As such, THz spectroscopy has enhanced and extended the accessibility to intermolecular forces, length- and timescales important in biological structure and activity.

High-resolution terahertz absorption spectra (0.06-3 THz) have been obtained at 4.2 K for three crystalline forms of trialanine [H2+-(Ala)3-O-]. The crystal structures differ in their beta-sheet forms (parallel vs antiparallel) and in their water composition (hydrated vs dehydrated antiparallel beta-sheet). The spectra are nearly vibrationally resolved, with little absorption below 1 THz. In sharp contrast to observations made in the mid-IR region, the spectral patterns of all three forms are qualitatively different, illustrating the extreme sensitivity to changes in the intermolecular hydrogen-bonding networks that stabilize peptide crystals. Predictions obtained from a classical force field model (CHARMM) and density functional theory (DFT/PW91) for periodic solids are compared with the X-ray structural data and the terahertz absorption spectra. In general, the results for the parallel beta-sheet are in better agreement with experiment than those for the antiparallel beta-sheet. For all three structures, however, most hydrogen bond distances are underestimated at both levels of theory, and the predicted absorption features are significantly red-shifted for the two antiparallel beta-sheet structures. Moreover, the nuclear motions predicted at the two levels of theory are qualitatively different. These results indicate that the PW91 functional is not sufficient to treat the weak intersheet hydrogen bonding present in the different beta-sheet forms and strongly suggest the need for improved force field models that include three-atom hydrogen-bonding terms for periodic solids.

Terahertz (THz) vibrational modes are characterized by nonlocal, collective molecular motions which are relevant to conformational changes and molecular functions in biological systems. We have investigated the THz spectra of a set of small bionanotubes which can serve as very simple models of membrane pores, and have examined the character of the THz modes which can impact transport processes. In this work, THz spectra of the crystalline VA class dipeptide nanotubes were calculated at both the harmonic and vibrational self-consistent field (VSCF) level using the CHARMM22 force field with periodic boundary conditions. Comparison of the calculated THz spectra against the experimental spectra revealed that the VSCF corrections generally improved the predictions in the low-frequency region. The improvements were especially manifested in the overall blue-shifts of the VSCF frequencies relative to the harmonic values, and blue shifts were attributed to the overall positive coupling strengths in all systems. Closer examination of the motions in the most significantly coupled normal mode pairs leads us to propose that, when two similar side-chain squeezing modes are coupled, the rapidly increased van der Waals interactions can lead to a stiffening of the effective potential, which in turn leads to the observed blue-shifts. However, we also noted that when the side-chain atoms become unphysically proximate and the van der Waals repulsion becomes too large, the VSCF calculations tend to deviate in the high frequency region and for the system of l-isoleucyl-l-valine. In addition, normal-mode analysis revealed a series of channel-breathing motions in all systems except l-valyl-l-alanine. We show that the inner products of the backbone vibrations between these channel-breathing motions divided the remaining VA class dipeptide systems into two subgroups. It is suggested that these modes may facilitate a pathway for the guest molecule absorption, substitution and removal in the VA class dipeptide nanotubes. Normal mode analysis also demonstrated that the THz motions may contribute to the pore permeability either directly by changing the pore size, or indirectly by affecting the solvent-host effective potentials.

Articles you may be interested inFabrication and characterization of metal-molecule-silicon devices Appl. Phys. Lett. 91, 033508 (2007); Trapping and detrapping of electrons photoinjected from silicon to ultrathin SiO 2 overlayers. I. In vacuum and in the presence of ambient oxygen Photoelectron emission microscopy ͑PEEM͒ has been used to investigate simple device structures buried under ultrathin oxides. In particular, we have imaged Au-SiO 2 and p-type Si-SiO 2 structures and have demonstrated that PEEM is sensitive to these buried structures. Oxide overlayers ranging up to 15.3 nm were grown by systematically varying the exposure time of the structures to a plasma-enhanced chemical-vapor deposition process. The change in image contrast as the oxide thickness increases was used to quantify the inelastic mean-free path of low-energy photoelectrons ͑ϳ1 eV͒ in amorphous silicon dioxide. For Au structures we find that the dominant mean-free path for photoelectrons in the overlying oxide is about 1.18Ϯ0.2 nm. Yet, we find a residual observable signal from the buried Au structure through roughly 13 oxide attenuation lengths. The signal attenuation from the Au can be explained by the spread of the photoelectron energies and the energy dependence of the electron-phonon interaction. Similar intensity attenuation behavior is also seen from heavily p-doped silicon (10 20 cm Ϫ3 ) regions, but the signal is only observable through roughly 3.0 nm of oxide, and the signal from the 10 18 cm Ϫ3 regions is not detectable through the thinnest oxide layer of approximately 2.5 nm. Here, the energy spread ͑ϳ2.0 eV͒ is more narrowly distributed about the phonon loss energies, leading to the observed attenuation behavior from heavily p-doped silicon.

We report on a quantitative investigation of doping-induced contrast in photoelectron emission microscopy (PEEM) images of Si devices. The calibration samples were fabricated using standard photolithography and focussed ion beam (FIB) writing, and consisted of p-type (B) stripes of different nominal dopant concentrations (10 18 -10 20 cm -3 ) and line separations, written on n-type (N d =10 14 cm -3 ) Si(001) substrates.Using a near-threshold light source, we find that the signal intensity increases monotonically with B concentration over the measured range of doping. The measured intensity ratios are in good agreement with a calculation based on photoemission from the valence band.

Vibrationally state-resolved THz spectra are obtained at cryogenic temperatures for three crystalline peptide-water systems that represent different structural motifs. The systems include two types of secondary structures and a hydrophobic peptide nanopore structure. Almost all of these systems are shown to undergo exchange with water at room temperature that alters the hydrogen bonding network in ways easily detectable in the THz region at cryogenic temperatures. Stark differences are observed in the spectra of model a-helical and b-sheet structures upon water removal at hydrophilic binding sites. However, within the confined pore of a hydrophobic nanotube, water in the form of helical wires has a subtle but significant impact on the phonon modes of the tube. The THz spectra are shown to easily distinguish between the different hydration states of the system that have been independently characterized by mass change measurements. Spectral comparisons with quantum chemical predictions of fully relaxed crystal structures confirm the hydration states and give detailed information about the free energies associated with dehydration. The vibrational free energies are shown to make significant contributions to the overall energy balance of the dehydration processes.

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Articles you may be interested inElectrical transport properties of boron-doped single-walled carbon nanotubes J. Appl. Phys. 113, 054313 (2013); 10.1063/1.4790505 Valence band structure in boron-zinc oxide films characterized by secondary electron emission J. Appl. Phys. 111, 053302 (2012); 10.1063/1.3689848Resonant field emission from two-dimensional density of state on hydrogen-terminated intrinsic diamond We present a model that describes doping-induced contrast in photoelectron emission microscopy by including the effect of surface state distributions and doping-induced band gap reduction. To quantify the contrast, the photoyield from the valence band for near-threshold photoemission is calculated as a function of p-type doping concentration in Si͑001͒. Various surface state distributions appropriate for a native-oxide covered Si device are investigated in order to determine the effect on doping-induced contrast. The lower limit on the number of surface states necessary for doping-induced contrast to occur is approximately 5ϫ10 13 cm Ϫ3 . An interesting result is that neither the position nor the energy distribution of the surface donor states affects the contrast, which corresponds to approximately a factor of 2 change in intensity for each decade change in doping density. However, the overall intensity increases with any one of: increased surface state density, narrowing of surface state distribution, or increased energy of surface states with respect to the valence band. The band bending profile generated by the model predicts that doping-induced contrast will be affected by varying the incident photon energy. Experimentally, we verify this prediction by imaging with photon energies between 4.5 and 5.2 eV.