Low-frequency vibrational modes in G-quadruplexes reveal the mechanical properties of nucleic acids.

Low-frequency vibrations play an essential role in biomolecular processes involving DNA such as gene expression, charge transfer, drug intercalation, and DNA-protein recognition. However, understanding the vibrational basis of these mechanisms relies on theoretical models due to the lack of experimental evidence. Here we present the low-frequency vibrational spectra of G-quadruplexes (structures formed by four strands of DNA) and B-DNA characterized using femtosecond optical Kerr-effect spectroscopy. Contrary to expectation, we found that G-quadruplexes show several strongly underdamped delocalized phonon-like modes that have the potential to contribute to the biology of the DNA at the atomic level. In addition, G-quadruplexes present modes at a higher frequency than B-DNA demonstrating that changes in the stiffness of the molecule alter its gigahertz to terahertz vibrational profile.

Low-Frequency (Gigahertz to Terahertz) Depolarized Raman Scattering Off n-Alkanes, Cycloalkanes, and Six-Membered Rings: A Physical Interpretation.

Molecular liquids have long been known to undergo various distinct intermolecular motions, from fast librations and cage-rattling oscillations to slow orientational and translational diffusion. However, their resultant gigahertz to terahertz spectra are far from simple, appearing as broad shapeless bands that span many orders of magnitude of frequency, making meaningful interpretation troublesome. Ad hoc spectral line shape fitting has become a notoriously fine art in the field; a unified approach to handling such spectra is long overdue. Here we apply ultrafast optical Kerr-effect (OKE) spectroscopy to study the intermolecular dynamics of room-temperature n-alkanes, cycloalkanes, and six-carbon rings, as well as liquid methane and propane. This work provides stress tests and converges upon an experimentally robust model across simple molecular series and range of temperatures, providing a blueprint for the interpretation of the dynamics of van der Waals liquids. This will enable the interpretation of low-frequency spectra of more complex liquids.

Spectrum of Slow and Super-Slow (Picosecond to Nanosecond) Water Dynamics around Organic and Biological Solutes.

Water dynamics in the solvation shell of solutes plays a very important role in the interaction of biomolecules and in chemical reaction dynamics. However, a selective spectroscopic study of the solvation shell is difficult because of the interference of the solute dynamics. Here we report on the observation of heavily slowed down water dynamics in the solvation shell of different solutes by measuring the low-frequency spectrum of solvation water, free from the contribution of the solute. A slowdown factor of ∼50 is observed even for relatively low concentrations of the solute. We go on to show that the effect can be generalized to different solutes including proteins.

Observation of coherent delocalized phonon-like modes in DNA under physiological conditions.

Underdamped terahertz-frequency delocalized phonon-like modes have long been suggested to play a role in the biological function of DNA. Such phonon modes involve the collective motion of many atoms and are prerequisite to understanding the molecular nature of macroscopic conformational changes and related biochemical phenomena. Initial predictions were based on simple theoretical models of DNA. However, such models do not take into account strong interactions with the surrounding water, which is likely to cause phonon modes to be heavily damped and localized. Here we apply state-of-the-art femtosecond optical Kerr effect spectroscopy, which is currently the only technique capable of taking low-frequency (GHz to THz) vibrational spectra in solution. We are able to demonstrate that phonon modes involving the hydrogen bond network between the strands exist in DNA at physiologically relevant conditions. In addition, the dynamics of the solvating water molecules is slowed down by about a factor of 20 compared with the bulk.

Plasmon enhanced terahertz emission from single layer graphene.

We show that surface plasmons, excited with femtosecond laser pulses on continuous or discontinuous gold substrates, strongly enhance the generation and emission of ultrashort, broadband terahertz pulses from single layer graphene. Without surface plasmon excitation, for graphene on glass, 'nonresonant laser-pulse-induced photon drag currents' appear to be responsible for the relatively weak emission of both s- and p-polarized terahertz pulses. For graphene on a discontinuous layer of gold, only the emission of the p-polarized terahertz electric field is enhanced, whereas the s-polarized component remains largely unaffected, suggesting the presence of an additional terahertz generation mechanism. We argue that in the latter case, 'surface-plasmon-enhanced optical rectification', made possible by the lack of inversion symmetry at the graphene on gold surface, is responsible for the strongly enhanced emission. The enhancement occurs because the electric field of surface plasmons is localized and enhanced where the graphene is located: at the surface of the metal. We believe that our results point the way to small, thin, and more efficient terahertz photonic devices.

Optical characterization of gold-cuprous oxide interfaces for terahertz emission applications.

We show that the interface between gold and thermally formed cuprous oxide, which emits terahertz radiation when illuminated with ultrafast femtosecond lasers, is in fact an AuCu/Cu2O interface due to the formation of the thermal diffusion alloy AuCu. The alloy enables the formation of a Schottky-barrier-like electric field near the interface which is essential to explain the THz emission from these samples. We confirm the formation of this AuCu layer by x-ray diffraction measurements, ellipsometry, and visual inspection. We determined the frequency-dependent complex refractive indices of the Cu2O and AuCu layer and verified them using reflection spectroscopy measurements. These refractive indices can be used for optimizing the thickness of Cu2O for maximum THz emission from these interfaces.

Enhanced terahertz emission by coherent optical absorption in ultrathin semiconductor films on metals.

We report on the surprisingly strong, broadband emission of coherent terahertz pulses from ultrathin layers of semiconductors such as amorphous silicon, germanium and polycrystalline cuprous oxide deposited on gold, upon illumination with femtosecond laser pulses. The strength of the emission is surprising because the materials are considered to be bad (amorphous silicon and polycrystalline cuprous oxide) or fair (amorphous germanium) terahertz emitters at best. We show that the strength of the emission is partly explained by cavity-enhanced optical absorption. This forces most of the light to be absorbed in the depletion region of the semiconductor/metal interface where terahertz generation occurs. For an excitation wavelength of 800 nm, the strongest terahertz emission is found for a 25 nm thick layer of amorphous germanium, a 40 nm thick layer of amorphous silicon and a 420 nm thick layer of cuprous oxide, all on gold. The emission from cuprous oxide is similar in strength to that obtained with optical rectification from a 300 µm thick gallium phosphide crystal. As an application of our findings we demonstrate how such thin films can be used to turn standard optical components, such as paraboloidal mirrors, into self-focusing terahertz emitters.

Terahertz emission from surface-immobilized gold nanospheres.

Electromagnetic wave emission based on optical rectification at terahertz (THz) wavelengths was observed from surface-immobilized gold nanospheres (SIGNs) above a gold surface. Although the excitation wavelength is off-resonant with the localized surface plasmons, the THz emission field was observed to be approximately 4.8 times greater than that from a percolated gold thin film of 10 nm thickness. A theoretical calculation predicts that the light electric field is enhanced in the SIGN system, even at off-resonance wavelengths. The observed THz field amplitude was quadratic with the illumination light field, suggesting that the THz generation is due to a second-order nonlinear optical process.

Surface plasmon-enhanced terahertz emission from a hemicyanine self-assembled monolayer.

Emission of terahertz radiation is observed when surface plasmons are excited on a thin film of gold, in the Kretschmann geometry. When a hemicyanine-terminated alkanethiol self-assembled monolayer of thickness 1.2 nm is deposited on the gold film, stronger terahertz emission is observed. Our experimental results confirm that enhanced terahertz emission is possible from planar gold surfaces when surface plasmons are excited.

Percolation-enhanced generation of terahertz pulses by optical rectification on ultrathin gold films.

Emission of pulses of electromagnetic radiation in the terahertz range is observed when ultrathin gold films on glass are illuminated with femtosecond near-IR laser pulses. A distinct maximum is observed in the emitted terahertz amplitude from films of average thickness just above the percolation threshold. Our measurements suggest that the emission is through a second-order nonlinear optical rectification process, enhanced by the excitation of localized surface plasmon hot spots on the percolated metal film.

Terahertz generation from graphite.

Generation of subpicosecond terahertz pulses is observed when graphite surfaces are illuminated with femtosecond near-infrared laser pulses. The nonlinear optical generation of THz pulses from graphite is unexpected since, in principle, the material possesses a centre of inversion symmetry. Experiments with highly oriented pyrolytic graphite crystals suggest that the THz radiation is generated by a transient photocurrent in a direction normal to the graphene planes, along the c-axis of the crystal. This is supported by magnetic-field induced changes in the THz electric-field polarization, and consequently, the direction of the photocurrent. We show that other forms of graphite, such as a pencil drawing on paper, are also capable of emitting THz pulses.