Disentangling multidimensional femtosecond spectra of excitons by pulse shaping with coherent control

C-Terminal Truncated α-Synuclein Fibrils Contain Strongly Twisted β-Sheets

C-terminal truncations of monomeric wild-type alpha-synuclein (henceforth WT-αS) have been shown to enhance the formation of amyloid aggregates both in vivo and in vitro and have been associated with accelerated progression of Parkinson’s disease (PD). The correlation with PD may not solely be a result of faster aggregation, but also of which fibril polymorphs are preferentially formed when the C-terminal residues are deleted. Considering that different polymorphs are known to result in distinct pathologies, it is important to understand how these truncations affect the organization of αS into fibrils. Here we present high-resolution microscopy and advanced vibrational spectroscopy studies that indicate that the C-terminal truncation variant of αS, lacking residues 109–140 (henceforth referred to as 1–108-αS), forms amyloid fibrils with a distinct structure and morphology. The 1–108-αS fibrils have a unique negative circular dichroism band at ∼230 nm, a feature that differs from the canonical ∼218 nm band usually observed for amyloid fibrils. We show evidence that 1–108-αS fibrils consist of strongly twisted β-sheets with an increased inter-β-sheet distance and a higher solvent exposure than WT-αS fibrils, which is also indicated by the pronounced differences in the 1D-IR (FTIR), 2D-IR, and vibrational circular dichroism spectra. As a result of their distinct β-sheet structure, 1–108-αS fibrils resist incorporation of WT-αS monomers.

Coherent control protocol for separating energy-transfer pathways in photosynthetic complexes by chiral multidimensional signals

Adaptive optimizations performed using a genetic algorithm are employed to construct optimal laser pulse configurations that separate spectroscopic features associated with the two main energy-transfer pathways in the third-order nonlinear optical response simulated for the Fenna-Matthews-Olson (FMO) photosynthetic complex from the green sulfur bacterium Chlorobium tepidum. Superpositions of chirality-induced tensor components in both collinear and noncollinear pulse configurations are analyzed. The optimal signals obtained by manipulating the ratios of various 2D spectral peaks reveal detailed information about the excitation dynamics.

Coherently-controlled two-dimensional photon echo electronic spectroscopy

Optical two-dimensional photon-echo spectroscopy is realized with shaped excitation pulses, allowing coherent control of twodimensional spectra. This development enables probing of state-selective quantum decoherence and phase/time sensitive couplings between states. The coherently-controlled two-dimensional photon-echo spectrometer with two pulse shapers is based on a passively stabilized four-beam interferometer with diffractive optic, and allows heterodyne detection of signals with a long-term phase stability of approximately Lambda/100. The two-dimensional spectra of Rhodamine 101 in a methanol solution, measured with unshaped and shaped pulses, exhibit significant differences. We observe in particular, the appearance of fine structure in the spectra obtained using shaped excitation pulses.

How to turn your pump-probe instrument into a multidimensional spectrometer: 2D IR and Vis spectroscopies via pulse shaping

We have recently developed a new and simple way of collecting 2D infrared and visible spectra that utilizes a pulse shaper and a partly collinear beam geometry. 2D IR and Vis spectroscopies are powerful tools for studying molecular structures and their dynamics. They can be used to correlate vibrational or electronic eigenstates, measure energy transfer rates, and quantify the dynamics of lineshapes, for instance, all with femtosecond time-resolution. As a result, they are finding use in systems that exhibit fast dynamics, such as sub-millisecond chemical and biological dynamics, and in hard-to-study environments, such as in membranes. While powerful, these techniques have been difficult to implement because they require a series of femtosecond pulses to be spatially and temporally overlapped with precise time-resolution and interferometric phase stability. However, many of the difficulties associated with implementing 2D spectroscopies are eliminated by using a pulse shaper and a simple beam geometry, which substantially lowers the technical barriers required for researchers to enter this exciting field while simultaneously providing many new capabilities. The aim of this paper is to provide an overview of the methods for collecting 2D spectra so that an outsider considering using 2D spectroscopy in their own research can judge which approach would be most suitable for their research aims. This paper focuses primarily on 2D IR spectroscopy, but also includes our recent work on adapting this technology to collecting 2D Vis spectra. We review work that has already been published as well as cover several topics that we have not reported previously, including phase cycling methods to remove background signals, eliminate unwanted scatter, and shift data collection into the rotating frame.

Coherent control of pump-probe signals of helical structures by adaptive pulse polarizations

The simplification of the pump-probe spectrum of excitons by pure-phase-polarization pulse shaping is investigated by a simulation study. The state of light is manipulated by varying the phases of two perpendicular polarization components of the pump, holding its total spectral and temporal intensity profiles fixed. Genetic and iterative Fourier transform algorithms are used to search for pulse phase functions that optimize the ratio of the signal at two frequencies. New features are extracted from the congested pump-probe spectrum of a helical pentamer by selecting a combination of Liouville space pathways. Tensor components which dominate the optimized spectra are identified.

Automated 2D IR spectroscopy using a mid-IR pulse shaper and application of this technology to the human islet amyloid polypeptide

The capability of 2D IR spectroscopy to elucidate time-evolving structures is enhanced by a programmable mid-IR pulse shaper that greatly improves the ease, speed, and accuracy of data collection. Traditional ways of collecting 2D IR spectra are difficult to implement, cause distorted peak shapes, and result in poor time resolution and/or phase problems. We report on several methods for collecting 2D IR spectra by using a computer-controlled germanium acoustooptic modulator that overcomes the above problems. The accuracy and resolution of each method is evaluated by using model metal carbonyl compounds that have well defined lineshapes. Furthermore, phase cycling can now be employed to largely alleviate background scatter from heterogeneous samples. With these methods in hand, we apply 2D IR spectroscopy to study the structural diversity in amyloid fibers of aggregated human islet amyloid polypeptide (hIAPP), which is involved with type 2 diabetes. The 2D IR spectra reveal that the beta-sheet fibers have a large structural distribution, as evidenced by an inhomogeneously broadened beta-sheet peak and strong coupling to random coil conformations. Structural diversity is an important characteristic of hIAPP because it may be that partly folded peptides cause the disease. This experiment on hIAPP is an example of how computer generation of 2D IR pulse sequences is a key step toward automating 2D IR spectroscopy, so that new pulse sequences can be implemented quickly and a diverse range of systems can be studied more easily.

Manipulating multidimensional electronic spectra of excitons by polarization pulse shaping

A simulation study demonstrates how coherent control, combined with adaptive polarization pulse shaping and a genetic algorithm, may be used to simplify femtosecond coherent nonlinear optical signals of excitons. Cross peaks are amplified and resolved, and diagonal peaks are suppressed in the heterodyne-detected two-pulse echo signal from the Soret band of a porphyrin dimer coupled to a Brownian oscillator bath. Various optimization strategies involving the spectral, temporal, and polarization profiles of the second pulse are compared.

Coherent control of cross-peaks in chirality-induced two-dimensional optical signals of excitons

Polarization tuning of the interference of chirality-induced tensor components is used to simulate the suppression of diagonal peaks and amplification of cross peaks in femtosecond two-dimensional photon echo signals of excitons in a chiral porphyrin dimer. Superpositions of various tensor components which generate the optimized signals are constructed using a genetic learning algorithm. Exciton couplings and bath correlations may be extracted from these highly resolved signals.

Femtosecond pulse shaping directly in the mid-IR using acousto-optic modulation

Pulse shaping directly in the mid-IR is accomplished by using a germanium acousto-optic modulator (Ge AOM) capable of programmable phase and amplitude modulation for IR light between 2 and 18 microm. Shaped waveforms centered at 4.9 microm are demonstrated in both the frequency and the time domains. With a 50% throughput efficiency, the Ge AOM can generate much more intense pulses with higher resolution than can indirect shaping methods. Furthermore, the phase stability of the shaped pulse proved sufficient for cross correlation with unshaped mid-IR pulses. Thus, phase- and amplitude-tailored pulses can now be readily incorporated into phase-sensitive experiments, such as heterodyned 2D IR spectroscopy.

Dissecting coherent vibrational spectra of small proteins into secondary structural elements by sensitivity analysis

The response of proteins to sequences of femtosecond infrared pulses provides a multidimensional view into their equilibrium distribution of structures and snapshot pictures of fast-triggered dynamical events. Analyzing these experiments requires advanced computational tools for assigning regions in the resulting multi-dimensional correlation plots to specific secondary-structure elements and their couplings. A differential sensitivity analysis technique based on a perturbation of the local (real space) Hamiltonian is developed to achieve that goal. Application to the amide I region of a small globular protein reveals regions associated with the alpha-helix, beta-sheet, and their coupling. Comparison of signals generated in different directions shows that the double-quantum-coherence signal has a higher sensitivity to the couplings compared with the single-quantum-coherence (photon echo) technique.

The effects of connectivity, coherence, and trapping on energy transfer in simple light-harvesting systems studied using the Haken-Strobl model with diagonal disorder

The problem of electronic energy transfer in a network of two-level systems coupled to a single trapping site is investigated using a simple Haken-Strobl model with diagonal disorder. The goal is to illustrate how the trapping time T(trap), coherence time T(d), and molecular topology all affect the overall efficiency of a light-harvesting network. Several issues are identified that need to be considered in the design of an optimal energy transfer network, including the dephasing-induced decoupling the trap from the rest of the network, the nonlinear dependence of trapping rate on the coherence time, and the role of network size and connectivity in determining the effect of the coherence time on efficiency. There are two main conclusions from this work. First, there exists an optimum combination of trapping time and coherence time, which will give the most rapid population transfer to the trap. These values are not in general the shortest trapping time and the longest coherence time, as would be expected based on rate equation models and/or simple considerations from previous analytical results derived for the Haken-Strobl model in an infinite system. Second, in the coherent regime, where T(d) is longer than the other relevant timescales, population trapping in a finite system can be suppressed by quantum interference effects, whose magnitude is sensitive to the molecular geometry. Suggestions for possible methods of observing such effects are discussed. These results provide a qualitative framework for quantum coherence and molecular topology into account for the design of covalent light-harvesting networks with high energy transfer efficiencies.