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Sequence-selective bis-intercalating dyes exhibit large increases in fluorescence in the presence of specific DNA sequences. This property makes this class of fluorophore of particular importance to biosensing and super-resolution imaging. Here we report ultrafast transient anisotropy measurements of resonance energy transfer (RET) between thiazole orange (TO) molecules in a complex formed between the homodimer TOTO and double-stranded (ds) DNA. Biexponential homo-RET dynamics suggest two subpopulations within the ensemble: 80% intercalated and 20% non-intercalated. Based on the application of the transition density cube method to describe the electronic coupling and Monte Carlo simulations of the TOTO/dsDNA geometry, the dihedral angle between intercalated TO molecules is estimated to be 81° ± 5°, corresponding to a coupling strength of 45 ± 22 cm[superscript −1]. Dye intercalation with this geometry is found to occur independently of the underlying DNA sequence, despite the known preference of TOTO for the nucleobase sequence CTAG. The non-intercalated subpopulation is inferred to have a mean inter-dye separation distance of 19 Å, corresponding to coupling strengths between 0 and 25 cm[superscript −1]. This information is important to enable the rational design of energy transfer systems that utilize TOTO as a relay dye. The approach used here is generally applicable to determining the electronic coupling strength and intercalation configuration of other dimeric bis-intercalators., United States. Army Research Office. Multidisciplinary University Research Initiative (W911NF1210420), United States. Office of Naval Research (DURIP Award N00014-15-1-2830), United States. Office of Naval Research (DURIP Award N00014-13-1-0664), Naval Research Laboratory (U.S.) Nanoscience Institute and the Laboratory University Collaborative Initiative

The influence of the metal substrate on the measurement of high resolution THz vibrational modes of molecular solids with the waveguide THz-TDS technique is investigated. The sample film of salicylic acid is studied using waveguide THz-TDS on three different metal substrates and two-surface passivated substrates. The independence of the observed THz vibrational modes to the metal substrate is demonstrated. Independently, surface passivation is presented as a viable experimental addition to the waveguide THz-TDS technique to aid the characterization of samples with known reactivity to metal surfaces., Published in the Journal of Applied Physics, v111 article 023105 p1-7, 2012. Sponsored in part by the Defense Threat Reduction Agency and the Office of Naval Research.

Using a low power beam of ultrashort THz pulses that propagate in the ambient laboratory environment we have measured the rotational signatures of small molecule vapors at frequencies within the atmospheric transmission windows. We investigate two types of apparatus. In the first type the THz beam propagates along a 6.7 meter round trip path that is external to the spectrometer, and which contains a long sample tube (5.4 meter round trip path) that holds the analyte vapor. The environment of the tube is controlled to simulate dry or humid conditions. In the second apparatus the THz beam propagates over a much longer 170 meter round trip path with analyte vapor contained in a relatively short 1.2 meter round trip path sample chamber. We describe the rotational signatures for each apparatus in the presence of the strong interference from water vapor absorption. For the shorter path long-tube apparatus we find that the peak detection sensitivity is sufficient to resolve a 1% absorption feature. For the more challenging 170 meter path apparatus we find that the peak detection sensitivity is sufficient to resolve a 3-5% absorption feature. The experiments presented here represent a first step towards using ultrashort THz pulses for coherent broad band detection of small molecule gases and vapors under ambient conditions., Pub. in Optics Express, v20, n6, 12 March 2012. The original document contains color images.

Waveguide terahertz time-domain spectroscopy (THz-TDS) is used to characterize the temperature dependent vibrational properties of three threat-related materials: 4-amino-dinitrotoluene (4A-DNT), pentaerythritol tetranitrate (PETN), and octahydro-1,3,5,7-tetranitro-1,3,5,7-tetrazocine (HMX). These materials are characterized as thin polycrystalline layers deposited in the 50 micron gap of a metal parallel plate waveguide. For each material waveguide THz-TDS at least partially resolves the underlying vibrational spectrum and reveals new features that have not been observed in previous free space measurements of these materials. Strong experimental evidence for a phase transformation is observed for 4A-DNT as the polycrystalline layer on the waveguide surface is cooled to near 200 K. For PETN a highly resolved spectrum containing eleven vibrational lines is observed at 11 K with full-width at half maximum linewidths ranging from 7 GHz to 40 GHz. Based on comparison to measurements in the literature, our PETN measurement suggests that it is possible to produce narrow linewidths from a polycrystalline layer that approach those from a single crystal. Finally, for HMX, a highly resolved vibrational spectrum is measured that is assigned to the metastable gamma polymorph., Supported in part by Defense Threat Reduction Agency (10-2960M). The original document contains color images. Published in Optics Express, v18 n26 p27239-27250, 20 Dec 2010.