Vibrational Dynamics and Couplings of the Hydrated RNA Backbone: A Two-Dimensional Infrared Study.

The equilibrium structure of the RNA sugar-phosphate backbone and its hydration shell is distinctly different from hydrated DNA. Applying femtosecond two-dimensional infrared (2D-IR) spectroscopy in a range from 950 to 1300 cm-1, we elucidate the character, dynamics, and couplings of backbone modes of a double-stranded RNA A-helix geometry in its aqueous environment. The 2D-IR spectra display a greater number of backbone modes than for DNA, with distinctly different lineshapes of diagonal peaks. Phosphate-ribose interactions and local hydration structures are reflected in the complex coupling pattern of RNA modes. Interactions with the fluctuating water shell give rise to spectral diffusion on a 300 fs time scale, leading to a quasi-homogeneous line shape of the symmetric (PO2)- stretching mode of the strongly hydrated phosphate groups. The RNA results are benchmarked by 2D-IR spectra of DNA oligomers in water and analyzed by molecular dynamics and quantum mechanical molecular mechanics simulations.

Water Librations in the Hydration Shell of Phospholipids.

The hydrophilic phosphate moiety in the headgroup of phospholipids forms strong hydrogen bonds with water molecules in the first hydration layer. Time-domain terahertz spectroscopy in a range from 100 to 1000 cm-1 reveals the influence of such interactions on rotations of water molecules. We determine librational absorption spectra of water nanopools in phospholipid reverse micelles for a range from w0 = 2 to 16 waters per phospholipid molecule. A pronounced absorption feature with maximum at 830 cm-1 is superimposed on a broad absorption band between 300 and 1000 cm-1. Molecular dynamics simulations of water in the reverse micelles suggest that the feature at 830 cm-1 arises from water molecules forming one or two strong hydrogen bonds with phosphate groups, while the broad component comes from bulk-like environments. This behavior is markedly different from water interacting with less polar surfaces.

Molecular couplings and energy exchange between DNA and water mapped by femtosecond infrared spectroscopy of backbone vibrations.

Molecular couplings between DNA and water together with the accompanying processes of energy exchange are mapped via the ultrafast response of DNA backbone vibrations after OH stretch excitation of the water shell. Native salmon testes DNA is studied in femtosecond pump-probe experiments under conditions of full hydration and at a reduced hydration level with two water layers around the double helix. Independent of their local hydration patterns, all backbone vibrations in the frequency range from 940 to 1120 cm-1 display a quasi-instantaneous reshaping of the spectral envelopes of their fundamental absorption bands upon excitation of the water shell. The subsequent reshaping kinetics encompass a one-picosecond component, reflecting the formation of a hot ground state of the water shell, and a slower contribution on a time scale of tens of picoseconds. Such results are benchmarked by measurements with resonant excitation of the backbone modes, resulting in distinctly different absorption changes. We assign the fast changes of DNA absorption after OH stretch excitation to structural changes in the water shell which couple to DNA through the local electric fields. The second slower process is attributed to a flow of excess energy from the water shell into DNA, establishing a common heated ground state in the molecular ensemble. This interpretation is supported by theoretical calculations of the electric fields exerted by the water shell at different temperatures.

Range, Magnitude, and Ultrafast Dynamics of Electric Fields at the Hydrated DNA Surface.

Range and magnitude of electric fields at biomolecular interfaces and their fluctuations in a time window down to the subpicosecond regime have remained controversial, calling for electric-field mapping in space and time. Here, we trace fluctuating electric fields at the surface of native salmon DNA via their interactions with backbone vibrations in a wide range of hydration levels by building the water shell layer by layer. Femtosecond two-dimensional infrared spectroscopy and ab initio based theory establish water molecules in the first two layers as the predominant source of interfacial electric fields, which fluctuate on a 300 fs time scale with an amplitude of 25 MV/cm due to thermally excited water motions. The observed subnanometer range of these electric interactions is decisive for biochemical structure and function.

Ultrafast vibrational dynamics of the DNA backbone at different hydration levels mapped by two-dimensional infrared spectroscopy.

DNA oligomers are studied at 0% and 92% relative humidity, corresponding to N < 2 and N > 20 water molecules per base pair. Two-dimensional (2D) infrared spectroscopy of DNA backbone modes between 920 and 1120 cm(-1) maps fluctuating interactions at the DNA surface. At both hydration levels, a frequency fluctuation correlation function with a 300 fs decay and a slow decay beyond 10 ps is derived from the 2D lineshapes. The fast component reflects motions of DNA helix, counterions, and water shell. Its higher amplitude at high hydration level reveals a significant contribution of water to the fluctuating forces. The slow component reflects disorder-induced inhomogeneous broadening.

Anharmonic Backbone Vibrations in Ultrafast Processes at the DNA-Water Interface.

The vibrational modes of the deoxyribose-phosphodiester backbone moiety of DNA and their interactions with the interfacial aqueous environment are addressed with two-dimensional (2D) infrared spectroscopy on a femto- to picosecond time scale. Beyond the current understanding in the harmonic approximation, the anharmonic character and delocalization of the backbone modes in the frequency range from 900 to 1300 cm(-1) are determined with both diagonal anharmonicities and intermode couplings on the order of 10 cm(-1). Mediated by the intermode couplings, energy transfer between the backbone modes takes place on a picosecond time scale, parallel to vibrational relaxation and energy dissipation into the environment. Probing structural dynamics noninvasively via the time evolution of the 2D lineshapes, limited structural fluctuations are observed on a 300 fs time scale of low-frequency motions of the helix, counterions, and water shell. Structural disorder of the DNA-water interface and DNA-water hydrogen bonds are, however, preserved for times beyond 10 ps. The different interactions of limited strength ensure ultrafast vibrational relaxation and dissipation of excess energy in the backbone structure, processes that are important for the structural integrity of hydrated DNA.

Supercontinuum pulse shaping in the few-cycle regime.

The synthesis of nearly arbitrary supercontinuum pulse forms is demonstrated with sub-pulse structures that maintain a temporal resolution in the few-cycle regime. Spectral broadening of the 35 fs input pulses to supercontinuum bandwidths is attained in a controlled two-stage sequential filamentation in air at atmospheric pressure, facilitating a homogeneous power density over the full spectral envelope in the visible to near infrared spectral range. Only standard optics and a liquid crystal spatial light modulator (LC-SLM) are employed for achieving pulse compression to the sub 5 fs regime with pulse energies of up to 60 µJ and a peak power of 12 GW. This constitutes the starting point for further pulse form synthesis via phase modulation within the sampling limit of the pulse shaper. Transient grating frequency-resolved optical gating (TG-FROG) allows for the characterization of pulse forms that extend over several hundred femtoseconds with few-cycle substructures.

On the role of thermal activation in selective photochemistry: mechanistic insight into the oxidation of propene on the V4O11- cluster.

An experimental methodology for a mechanistic analysis of gas phase chemical reactions is presented in the context of structure-reactivity relationships of metal oxide clusters relevant to photocatalysis. The spectroscopic approach is demonstrated with the investigation of the photoinduced oxygenation of propene on the V(4)O(11)(-) cluster, where the thermal activation and subsequent photoreaction are deduced with the information from (i) the temperature dependency of the aggregation kinetics in the propene-seeded helium atmosphere of an ion-trap reactor; (ii) the fluence dependency in the yield of different product channels of the photoreaction and (iii) the intensity dependency in the fragmentation of neutral reaction products that are probed via in situ multi-photon ionization. For the thermal reaction, selective hydrogen abstraction from the allylic position of propene accompanied by the linkage to the cluster at the dioxo moiety is postulated as the mechanism in the aggregation of propene on the V(4)O(11)(-) cluster. In accordance with an insightful neutralization-reionization study (Schröder et al., J. Mass. Spectrom., 2010, 301, 84), the subsequent photoinduced reaction is defined by an allylic oxidation in the formation of acrolein from the initial allyloxy radical photoproduct. The relevance of the observed selectivity is discussed in view of the electronic structure and bond motifs offered by high valence oxide systems such as the V(4)O(11)(-) cluster.

Standoff spectroscopy via remote generation of a backward-propagating laser beam.

In an earlier publication we demonstrated that by using pairs of pulses of different colors (e.g., red and blue) it is possible to excite a dilute ensemble of molecules such that lasing and/or gain-swept superradiance is realized in a direction toward the observer. This approach is a conceptual step toward spectroscopic probing at a distance, also known as standoff spectroscopy. In the present paper, we propose a related but simpler approach on the basis of the backward-directed lasing in optically excited dominant constituents of plain air, N(2) and O(2). This technique relies on the remote generation of a weakly ionized plasma channel through filamentation of an ultraintense femtosecond laser pulse. Subsequent application of an energetic nanosecond pulse or series of pulses boosts the plasma density in the seed channel via avalanche ionization. Depending on the spectral and temporal content of the driving pulses, a transient population inversion is established in either nitrogen- or oxygen-ionized molecules, thus enabling a transient gain for an optical field propagating toward the observer. This technique results in the generation of a strong, coherent, counterpropagating optical probe pulse. Such a probe, combined with a wavelength-tunable laser signal(s) propagating in the forward direction, provides a tool for various remote-sensing applications. The proposed technique can be enhanced by combining it with the gain-swept excitation approach as well as with beam shaping and adaptive optics techniques.

A complete reactant-product analysis of the oxygen transfer reaction in [V4O11 x C3H6]-: a cluster complex for modeling surface activation and reactivity.

The anionic V4O11 cluster is presented as a gas-phase system of low dimensionality for modeling surface activation of molecular oxygen and the reactivity toward unsaturated hydrocarbons. Together with the charged cluster aggregates and fragments taking part in the reaction, neutral reactant and product species are monitored via multiphoton ionization for the first time within the instrumentation of tandem mass spectrometry and ion trap reactors. This novel approach allows for a comprehensive analysis of the photoinduced oxygen transfer reaction to propene within the defined aggregate complex [V4O11 x C3H6]- that simulates coadsorption and activation under fully controlled conditions.

Identification of conical structures in small aluminum oxide clusters: infrared spectroscopy of (Al2O3)1-4(AlO)+.

The vibrational spectroscopy of the electronically closed-shell (Al 2O 3) n (AlO) (+) cations with n = 1-4 is studied in the 530-1200 cm (-1) range by infrared predissociation spectroscopy of the corresponding ion-He atom complexes in combination with quantum chemical calculations. In all cases we find, assisted by a genetic algorithm, global minimum structures that differ considerably from those derived from known modifications of bulk alumina. The n = 1 and n = 4 clusters exhibit an exceptionally stable conical structure of C 3 v symmetry, whereas for n = 2 and n = 3, multiple isomers of lower symmetry and similar energy may contribute to the recorded spectra. A blue shift of the highest energy absorption band is observed with increasing cluster size and attributed to a shortening of Al-O bonds in the larger clusters. This intense band is assigned to vibrational modes localized on the rim of the conical structures for n = 1 and n = 4 and may aid in identifying similar, highly symmetric structures in larger ions.

Poor man's source for sub 7 fs: a simple route to ultrashort laser pulses and their full characterization.

A practicable and economic method for the generation and full characterization of laser pulses ranging down to sub 7 fs duration with energies spanning the full microJ domain is presented. The method utilizes a self-induced and self-guiding filamentation of titanium-sapphire based, amplified pulses in air for spectral broadening, a standard chirp mirror compression scheme and transient grating frequency resolved optical gating for determining the spectral phase over the full visible to near infrared range. In this manner, few-cycle laser pulses with a high quality in the spatial beam profile have been generated in an robust arrangement with a minimal amount of standard optical components for their full characterization. The optical scheme demonstrates an uncomplicated, versatile access to this regime of pulsed laser radiation accompanied by a comprehensive analysis.

Optically reconfigurable azobenzene polymer-based fiber Bragg filter.

Optically writable, thermally erasable surface relief gratings in thin Disperse Red 1 polymethyl methacrylate azopolymer films were used to demonstrate an arbitrarily reconfigurable fiber Bragg filter. Gratings were optically written on azopolymer-coated side-polished fiber blocks, and a write-erase-write cycle was demonstrated. Finite difference time domain simulations reveal that this optically reconfigurable device concept can be optimized in a silicon-on-insulator waveguide platform.

Visible and UV coherent Raman spectroscopy of dipicolinic acid.

We use time-resolved coherent Raman spectroscopy to obtain molecule-specific signals from dipicolinic acid (DPA), which is a marker molecule for bacterial spores. We use femtosecond laser pulses in both visible and UV spectral regions and compare experimental results with theoretical predictions. By exciting vibrational coherence on more than one mode simultaneously, we observe a quantum beat signal that can be used to extract the parameters of molecular motion in DPA. The signal is enhanced when an UV probe pulse is used, because its frequency is near-resonant to the first excited electronic state of the molecule. The capability for unambiguous identification of DPA molecules will lead to a technique for real-time detection of spores.

Population dynamics in vibrational modes during non-Born-Oppenheimer processes: CARS spectroscopy used as a mode-selective filter.

The coupling of specific nuclear and electronic degrees of freedom of a molecular system during non-radiative electronic transitions plays a central role in photochemistry and photobiology. This breakdown of the Born-Oppenheimer approximation during processes such as internal conversion determines the mechanism and product distribution of photochemical reactions and is responsible for the high efficiency of photobiological processes. In order to explore this phenomena in beta-carotene, a molecule that plays a primary role as an auxiliary light-harvesting pigment in photosynthesis, a spectroscopic method was employed that allows for the individual vibrational modes to be monitored selectively within the dynamics of an internal conversion process. This spectroscopic technique employs an initial pump laser to excite the molecule into an excited electronic state and resolves the subsequent relaxation process by interrogating the system with a time-delayed, coherent anti-Stokes Raman process (CARS), which acts as a mode-selective filter for observing the population flow within specific vibrational modes with a time resolution in the femtosecond regime.