Amber T. Krummel

Droplet Microfluidics for Fabrication of Non-Spherical Particles

We describe new developments for controlled fabrication of monodisperse non-spherical particles using droplet microfluidics. The high degree of control afforded by microfluidic technologies enables generation of single and multiple emulsion droplets. We show that these droplets can be transformed to non-spherical particles through further simple, spontaneous processing steps, including arrested coalescence, asymmetric polymer solidification, polymerization in microfluidic flow, and evaporation-driven clustering. These versatile and scalable microfluidic approaches can be used for producing large quantities of non-spherical particles that are monodisperse in both size and shape; these have great potential for commercial applications.

Site-specific vibrational dynamics of the CD3ζ membrane peptide using heterodyned two-dimensional infrared photon echo spectroscopy

Heterodyned two-dimensional infrared (2D IR) spectroscopy has been used to study the amide I vibrational dynamics of a 27-residue peptide in lipid vesicles that encompasses the transmembrane domain of the T-cell receptor CD3zeta. Using 1-(13)C[Double Bond](18)O isotope labeling, the amide I mode of the 49-Leucine residue was spectroscopically isolated and the homogeneous and inhomogeneous linewidths of this mode were measured by fitting the 2D IR spectrum collected with a photon echo pulse sequence. The pure dephasing and inhomogeneous linewidths are 2 and 32 cm(-1), respectively. The population relaxation time of the amide I band was measured with a transient grating, and it contributes 9 cm(-1) to the linewidth. Comparison of the 49-Leucine amide I mode and the amide I band of the entire CD3zeta peptide reveals that the vibrational dynamics are not uniform along the length of the peptide. Possible origins for the large amount of inhomogeneity present at the 49-Leucine site are discussed.

A pulse sequence for directly measuring the anharmonicities of coupled vibrations: Two-quantum two-dimensional infrared spectroscopy

We have experimentally demonstrated a pulse sequence for the acquisition of heterodyned two-dimensional infrared (2D IR) spectra that correlates the overtone and combination bands to the fundamental frequencies. The spectra are generated by Fourier transforming the time domain signal that is allowed to evolve during one- and two-quantum coherence times. In this manner, the overtone and combination bands appear along the two-quantum axis, resulting in a direct determination of the diagonal and off-diagonal anharmonicities. To demonstrate this pulse sequence, we have collected two-quantum 2D IR spectra of a ruthenium dicarbonyl complex, extracted the diagonal and off-diagonal anharmonicities, and simulated the spectra using an exciton model. Several polarization conditions are presented that suppress the diagonal or cross peaks and we have used them to improve the accuracy of the measurement.

Molecular Orientation of Asphaltenes and PAH Model Compounds in Langmuir−Blodgett Films Using Sum Frequency Generation Spectroscopy

Asphaltenes are an important class of compounds in crude oil whose surface activity is important for establishing reservoir rock wettability which impacts reservoir drainage. While many phenomenological interfacial studies with crude oils and asphaltenes have been reported, there is very little known about the molecular level interactions between asphaltenes and mineral surfaces. In this study, we analyze Langmuir-Blodgett films of asphaltenes and related model compounds with sum frequency generation (SFG) vibrational spectroscopy. In SFG, the polarization of the input (vis, IR) and output (SFG) beams can be varied, which allows the orientation of different functional groups at the interface to be determined. SFG clearly indicates that asphaltene polycyclic aromatic hydrocarbons (PAHs) are highly oriented in the plane of the interface and that the peripheral alkanes are transverse to the interface. In contrast, model compounds with oxygen functionality have PAHs oriented transverse to the interface. Computational quantum chemistry is used to support corresponding band assignments, enabling robust determination of functional group orientations.

Evidence for Coupling between Nitrile Groups Using DNA Templates : A Promising New Method for Monitoring Structures with Infrared Spectroscopy

Infrared spectroscopy is a common method for monitoring biomolecular structures but suffers from spectral congestion. Non-natural vibrational probes provide a way to regain structural specificity because they provide a unique vibrational signature and can be incorporated into proteins or other biomolecules at specific locations. A popular probe is the nitrile group because its frequency is sensitive to the electrostatics of its environment. In this work, we show that pairs of nitrile groups can be used to directly probe distances and angles in dual labeled molecules. By labeling model DNA oligomers with pairs of nitrile tags, we demonstrate that the vibrational coupling between two nitrile groups is strong enough that Fourier transform infrared (FTIR) spectra can be used to probe relative nitrile distances >4.5 A. Our approach is similar in spirit to monitoring structures with fluorescence resonance energy transfer (FRET) using a pair of fluorescent labels or a pair of spin labels in electron spin resonance spectroscopy. The small sizes of nitrile groups make especially valuable probes of sterically confined regions like the inner cores of large biomolecules where other spectroscopic probes do not fit.

Detection of high levels of recombination generated during PCR amplification of RNA templates

Recombination during the PCR amplification of DNA templates can be a serious problem for those seeking to genotype heterogeneous populations, yet a boon to those seeking to enhance variation during in vitro evolution. Here, the extent to which PCR generates chimeric full-length products was estimated using a powerful restriction fragment-length polymorphism (RFLP) assay involving the use of fluorescently labeled PCR primers. Three different RNA-encoding DNA templates were assayed: (i) one for a group I ribozyme, (ii) one for a 16S ribosomal RNA (rRNA), and (iii) one for a messenger RNA (mRNA). In all cases, the observed frequency of chimeric PCR products exceeded 20%, and longer templates appear to produce more chimeric products. Although two of these templates have the potential to form secondary structures during the PCR, this tendency does not seem to heighten recombination frequency. These results corroborate previous studies that show that the production of chimeras can be best attenuated to a certain extent by varying the extension times in PCR.

2D IR spectroscopy at 100 kHz utilizing a Mid-IR OPCPA laser source.

We present a 100 kHz 2D IR spectrometer. The system utilizes a ytterbium all normal dispersion fiber oscillator as a common source for the pump and seed beams of a MgO:PPLN OPCPA. The 1030 nm OPCPA pump is generated by amplification of the oscillator in cryocooled Yb:YAG amplifiers, while the 1.68 μm seed is generated in a OPO pumped by the oscillator. The OPCPA outputs are used in a ZGP DFG stage to generate 4.65 μm pulses. A mid-IR pulse shaper delivers pulse pairs to a 2D IR spectrometer allowing for data collection at 100 kHz.

Polymeric infrared compatible microfluidic devices for spectrochemical analysis.

An innovative fabrication method is presented that affords the combination of polydimethyl-siloxane (PDMS) microfluidic technology with vibrational spectroscopy. PDMS devices are produced with uniform thicknesses ranging from 25 to 400 μm. The optical characteristics of the microfluidic devices in the mid-infrared are reported. The broad utility of this approach is demonstrated through IR imaging of flows in functional gradient generators and flow-focusing devices.

Active Bragg angle compensation for shaping ultrafast mid-infrared pulses

Active Bragg angle compensation is demonstrated for shaping ultrafast, mid-infrared pulses. The effects of angular dispersion introduced by the acousto-optic modulator on the temporal characteristics of the pulse are measured by autocorrelating the output from the pulse shaper. The time duration of the output pulses were measured to be thirty times shorter than pulses produced with a constant frequency amplitude waveform. This approach acts to mitigate angular dispersion in Bragg-regime acousto-optic devices, thus affording the ability to shape ultrafast pulses of light with broad bandwidths that are centered at mid-IR wavelengths and longer.

Probing structural features of self-assembled violanthrone-79 using two dimensional infrared spectroscopy

Two-dimensional infrared (2D IR) spectroscopy was used to characterize the structure of a self-assembled polycyclic aromatic hydrocarbon (PAH), violanthrone-79. A local mode basis was constructed using spectroscopic and computational results of anthrone and monomer violanthrone-79. The vibrational modes in the spectral region 1550-1700 cm(-1), carbonyl stretching and in-plane ring breathing, are used as vibrational probes. The local mode basis and an electrostatic coupling model were applied to three nanoaggregate structures: parallel, antiparallel, and a chiral configuration produced by a 28° rotation from parallel. Angular disorder within each nanoaggregate configuration was also explored. This investigation is a first approach to probe self-assembled PAHs with 2D IR spectroscopy. The experimental and calculated 2D IR spectra align best when the violanthrone-79 molecules are in an anti-parallel configuration within the nanoaggregate.