Two-dimensional infrared spectroscopy of peptides by phase-controlled femtosecond vibrational photon echoes

Simplified and economical 2D IR spectrometer design using a dual acousto-optic modulator

Over the last decade two-dimensional infrared (2D IR) spectroscopy has proven to be a very useful extension of infrared spectroscopy, yet the technique remains restricted to a small group of specialized researchers because of its experimental complexity and high equipment cost. We report on a spectrometer that is compact, mechanically robust, and is much less expensive than previous designs because it uses a single pixel MCT detector rather than an array detector. Moreover, each axis of the spectrum can be collected in either the time or frequency domain via computer programming. We discuss pulse sequences for scanning the probe axis, which were not previously possible. We present spectra on metal carbonyl compounds at 5 µm and a model peptide at 6 µm. Data collection with a single pixel MCT takes longer than using an array detector, but publishable quality data are still achieved with only a few minutes of averaging.

Determining equilibrium fluctuations using temperature-dependent 2D-IR

We demonstrate the capability of temperature-dependent 2D-IR to characterize sources of vibrational population transfer. In a model system of iron diene tricarbonyl "piano stool" complexes, this approach reveals symmetry breaking associated with equilibrium fluctuations and differentiates these from fluxional rearrangement. Tricarbonyl(1,3-butadiene)iron and tricarbonyl(1,5-cyclooctadiene)iron are shown to undergo intramolecular vibrational redistribution (IVR) coupled to the wagging motion of their carbonyl ligands. In the case of both molecules, these equilibrium fluctuations are distinguished from chemical exchange behaviors by their temperature dependence and arguments of molecular symmetry.

Modeling the thermal unfolding 2DIR spectra of a β-hairpin peptide based on the implicit solvent MD simulation

We simulated the equilibrium isotope-edited FTIR and 2DIR spectra of a β-hairpin peptide trpzip2 at a series of temperatures. The simulation was based on the configuration distributions generated using the GB(OBC) implicit solvent model and the integrated tempering sampling (ITS) technique. A soaking procedure was adapted to generate the peptide in explicit solvent configurations for the spectroscopy calculations. The nonlinear exciton propagation (NEP) method was then used to calculate the spectra. Agreeing with the experiments, the intensities and ellipticities of the isotope-shifted peaks in our simulated signals have the site-specific temperature dependences, which suggest the inhomogeneous local thermal stabilities along the peptide chain. Our simulation thus proposes a cost-effective means to understand a peptide's conformational change and related IR spectra across its thermal unfolding transition.

Molecular dynamics simulation and computational two-dimensional infrared spectroscopic study of model amyloid β-peptide oligomers

Molecular dynamics simulations were carried out to study the structure stability of model amyloid β40 (Aβ40) peptide oligomers, from monomer to hexamer, in aqueous solution at room temperature. The initial oligomer models were built by using the parallel in-register β-sheet fibril structure and then allowed to relax in the simulations. Our simulation results indicated that the stable Aβ40 monomer was a random coil, while the oligomer structures became more fibril-like with the increase of the peptide strands. Linear absorption and two-dimensional infrared spectra of the isotope-labeled oligomers were calculated and analyzed in detail, which revealed the differential secondary structural features characteristic of Aβ40 aggregation. A quantitative relation was established to make connection between the calculated spectra and experimental ensemble measurements.

Continuously tunable optical multidimensional Fourier-transform spectrometer

A multidimensional optical nonlinear spectrometer (MONSTR) is a robust, ultrastable platform consisting of nested and folded Michelson interferometers that can be actively phase stabilized. The MONSTR provides output pulses for nonlinear excitation of materials and phase-stabilized reference pulses for heterodyne detection of the induced signal. This platform generates a square of identical laser pulses that can be adjusted to have arbitrary time delays between them while maintaining phase stability. This arrangement is ideal for performing coherent optical experiments, such as multidimensional Fourier-transform spectroscopy. The present work reports on overcoming some important limitations on the original design of the MONSTR apparatus. One important advantage of the MONSTR is the fact that it is a closed platform, which provides the high stability. Once the optical alignment is performed, it is desirable to maintain the alignment over long periods of time. The previous design of the MONSTR was limited to a narrow spectral range defined by the optical coating of the beam splitters. In order to achieve tunability over a broad spectral range the internal optics needed to be changed. By using broadband coated and wedged beam splitters and compensator plates, combined with modifications of the beam paths, continuous tunability can be achieved from 520 nm to 1100 nm without changing any optics or performing alignment of the internal components of the MONSTR. Furthermore, in order to achieve continuous tunability in the spectral region between 520 nm and 720 nm, crucially important for studies on numerous biological molecules, a single longitudinal mode laser at 488.5 nm was identified and used as a metrology laser. The shorter wavelength of the metrology laser as compared to the usual HeNe laser has also increased the phase stability of the system. Finally, in order to perform experiments in the reflection geometry, a simple method to achieve active phase stabilization between the signal and the reference beams has been developed.

Three-dimensional structures by two-dimensional vibrational spectroscopy

The development of experiments that can generate molecular movies of changing chemical structures is a major challenge for physical chemistry. But to realize this dream, we not only need to significantly improve existing approaches but also must invent new technologies. Most of the known protein structures have been determined by X-ray diffraction and to lesser extent by NMR. Though powerful, X-ray diffraction presents limitations for acquiring time-dependent structures. In the case of NMR, ultrafast equilibrium dynamics might be inferred from line shapes, but the structures of conformations interconverting on such time scales are not realizable. This Account highlights two-dimensional infrared spectroscopy (2D IR), in particular the 2D vibrational echo, as an approach to time-resolved structure determination. We outline the use of the 2D IR method to completely determine the structure of a protein of the integrin family in a time window of few picoseconds. As a transmembrane protein, this class of structures has proved particularly challenging for the established structural methodologies of X-ray crystallography and NMR. We describe the challenges facing multidimensional spectroscopy and compare it with some other methods of structural biology. Then we succinctly discuss the basic principles of 2D IR methods as they relate to time domain and frequency domain experimental and theoretical properties required for protein structure determination. By means of the example of the transmembrane protein, we describe the essential aspects of combined carbon-13-oxygen-18 isotope labels to create vibrational resonance pairs that allow the determination of protein and peptide structures in motion. Finally, we propose a three-dimensional structure of the αIIb transmembrane homodimer that includes optimum locations of all side chains and backbone atoms of the protein.

Two-Dimensional Electronic Spectroscopy in the Ultraviolet Wavelength Range

Coherent two-dimensional (2D) spectroscopies conducted at visible and infrared wavelengths are having a transformative impact on the understanding of numerous processes in condensed phases. The extension of 2D spectroscopy to the ultraviolet spectral range (2DUV) must contend with several challenges, including the attainment of adequate laser bandwidth, interferometric phase stability, and the suppression of undesired nonlinearities in the sample medium. Solutions to these problems are motivated by the study of a wide range of biological systems whose lowest-frequency electronic resonances are found in the UV. The development of 2DUV spectroscopy also makes possible the attainment of new insights into elementary chemical reaction dynamics (e.g., electrocyclic ring opening in cycloalkenes). Substantial progress has been made in both the implementation and application of 2DUV spectroscopy in the past several years. In this Perspective, we discuss 2DUV methodology, review recent applications, and speculate on what the future will hold.

Interplay between vibrational energy transfer and excited state deactivation in DNA components

Femtosecond laser spectroscopies are used to examine a thymine family of systems chosen to expose the interplay between excited state deactivation and two distinct vibrational energy transfer (VET) pathways: (i) VET from the base to the deoxyribose ring; (ii) VET between neighboring units in a dinucleotide. We find that relaxation in the ground electronic state accelerates markedly as the molecular sizes increase from the nucleobase to the dinucleotide. This behavior directly reflects growth in the density of vibrational quantum states on the substituent of the base. Excited state lifetimes are studied at temperatures ranging from 100 to 300 K to characterize the thermal fluctuations that connect the Franck-Condon geometries and the conical intersections leading back to the ground state. An Arrhenius analysis yields an approximate excited state energy barrier of 13 meV in the thymine dinucleotide. In addition, we find that the transfer of vibrational energy from the base to the substituent suppresses thermal fluctuations across this energy barrier. The possibility that the solvent viscosity imposes friction on the reaction coordinate is examined by comparing thymine and adenine systems. Experiments suggest that the solvent viscosity has little effect on barrier crossing dynamics in thymine because the conical intersection is accessed through relatively small out-of-plane atomic displacements. Overall, we conclude that the transfer of vibrational quanta from thymine to the deoxyribose ring couples significantly to the internal conversion rate, whereas the neighboring unit in the dinucleotide serves as a secondary heat bath. In natural DNA, it follows that (local) thermal fluctuations in the geometries of subunits involving the base and deoxyribose ring are most important to this subpicosecond relaxation process.

Ballistic energy transport along PEG chains: distance dependence of the transport efficiency

Dual-frequency relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy was used to investigate energy transport in polyethylene glycol (PEG) oligomers of different length, having 0, 4, 8, and 12 repeating units and end-labeled with azido and succinimide ester moieties (azPEGn). The energy transport initiated by excitation of the N≡N stretching mode of the azido group in azPEGn in CCl(4) at ca. 2100 cm(-1) was recorded by probing the C=O stretching modes (reporters) of the succinimide ester moiety. Sensitive to the excess energy delivered to the reporter modes, RA 2DIR permits observation of both the through-bond and through-solvent energy transport contributions. The cross-peak data involving the reporter modes with different thermal sensitivity and the data for mixtures of compounds permitted concluding that through-bond energy transport is the dominant mechanism for most cross peaks in all four azPEGn compounds. The through-bond energy transport time, evaluated as the waiting time at which the cross peak maximum is reached, was found to be linearly dependent on the chain length of up to 60 Å, suggesting a ballistic energy transport regime. The through-bond energy transport speed determined from the chain-length dependence of T(max) in CCl(4) is found to be ca. 450 m s(-1). The cross-peak amplitude at the maximum decays exponentially with the chain length; a characteristic decay distance is found to be 15.7 ± 1 Å. The cross-peak amplitude at zero waiting time, determined by the end-to-end distance distribution, is found to decay with the chain length (L) as ∼L(-1.4), which is close to predictions of the free flight chain model. The match indicates that the end-group interaction does not strongly perturb the end-to-end distribution, which is close to the ideal random coil distribution with the Gaussian probability density.

Constant-speed vibrational signaling along polyethyleneglycol chain up to 60-Å distance

A series of azido-PEG-succinimide ester oligomers with a number of repeating PEG units of 0, 4, 8, and 12 (azPEG0, 4, 8, and 12) was investigated using a relaxation-assisted two-dimensional infrared (RA 2DIR) spectroscopy method. The RA 2DIR method relies on the energy transport in molecules and is capable of correlating the frequencies of vibrational modes separated by large through-bond distances. Excitation of the azido group in the compounds at ca. 2,100 cm(-1) generates an excess energy which propagates in the molecule as well as dissipates into the solvent. We discovered that a part of the excess energy propagates ballistically via the covalent backbone of the molecules with a constant speed of ca. 550 m/s. The transport is described as a propagation of a vibrational wavepacket having a mean-free-path length of 10-15 Å. The discovery has the potential for developing new efficient signal transduction strategies for molecular electronics and biochemistry. It also permits extending the distances accessible in RA 2DIR structural measurements up to ca. 60 Å.

Vibrational spectroscopic determination of local solvent electric field, solute-solvent electrostatic interaction energy, and their fluctuation amplitudes

IR probes have been extensively used to monitor local electrostatic and solvation dynamics. Particularly, their vibrational frequencies are highly sensitive to local solvent electric field around an IR probe. Here, we show that the experimentally measured vibrational frequency shifts can be inversely used to determine local electric potential distribution and solute-solvent electrostatic interaction energy. In addition, the upper limits of their fluctuation amplitudes are estimated by using the vibrational bandwidths. Applying this method to fully deuterated N-methylacetamide (NMA) in D(2)O and examining the solvatochromic effects on the amide I' and II' mode frequencies, we found that the solvent electric potential difference between O(═C) and D(-N) atoms of the peptide bond is about 5.4 V, and thus, the approximate solvent electric field produced by surrounding water molecules on the NMA is 172 MV/cm on average if the molecular geometry is taken into account. The solute-solvent electrostatic interaction energy is estimated to be -137 kJ/mol, by considering electric dipole-electric field interaction. Furthermore, their root-mean-square fluctuation amplitudes are as large as 1.6 V, 52 MV/cm, and 41 kJ/mol, respectively. We found that the water electric potential on a peptide bond is spatially nonhomogeneous and that the fluctuation in the electrostatic peptide-water interaction energy is about 10 times larger than the thermal energy at room temperature. This indicates that the peptide-solvent interactions are indeed important for the activation of chemical reactions in aqueous solution.

Decelerated water dynamics and vibrational couplings of hydrated DNA mapped by two-dimensional infrared spectroscopy

Double-stranded DNA oligomers containing 23 alternating adenine-thymine base pairs are studied at different hydration levels by femtosecond two-dimensional (2D) infrared spectrosopy. Coupled NH stretching modes of the A-T pairs and OH stretching excitations of the water shell are discerned in the 2D spectra. Limited changes of NH stretching frequencies and line shapes with increasing hydration suggest spectral dynamics governed by DNA rather than water fluctuations. In contrast, OH stretching excitations of the water shell around fully hydrated DNA undergo spectral diffusion on a ~500 fs time scale. The center line slopes of the 2D spectra of hydrated DNA demonstrate a slower decay of the frequency-time correlation function (TCF) than that in neat water, as is evident from a comparison with 2D spectra of neat H(2)O and theoretical TCFs. We attribute this behavior to reduced structural fluctuations of the water shell and a reduced rate of resonant OH stretching energy transfer.

Time-dependent fifth-order bands in nominally third-order 2D IR vibrational echo spectra

Progress in the field of 2D IR vibrational spectroscopy has been bolstered by the production of intense mid-IR laser pulses. As higher-energy pulses are employed, a concomitant increase occurs in the likelihood of fifth-order contributions to the 2D IR spectra. We report the appearance of fifth-order signals in 2D IR spectra of CO bound to the active site of the enzyme cytochrome P450(cam) with the substrate norcamphor. Two bands with novel time dependences, one on the diagonal and one off-diagonal, are not accounted for by normal third-order interactions. These bands are associated with a ν = 1-2 vibrational transition frequency. Both bands decay to 0 and then grow back in with opposite sign. The diagonal band is positive at short time, decays to 0, reappears with negative sign, before eventually decaying to 0. The off-diagonal band is negative at short time, decays to 0, reappears positive, and then decays to 0. The appearance and time dependence of these bands are characterized. Understanding these fifth-order bands is useful because they may be misidentified with time-dependent bands that arise from other processes, such as chemical exchange, vibrational coupling, or energy transfer. The presence and unusual time dependences of the fifth-order bands are reproduced with model calculations that account for the fact that vibrational relaxation from the ν = 2 to 1 level is approximately a factor of 2 faster than that from the ν = 1 to 0 level.

Strong correlation of electronic and lattice excitations in GaAs/AlGaAs semiconductor quantum wells revealed by two-dimensional terahertz spectroscopy

Coulomb-mediated interactions between intersubband excitations of electrons in GaAs/AlGaAs double quantum wells and longitudinal optical phonons are studied by two-dimensional spectroscopy in the terahertz frequency range. The multitude of diagonal and off-diagonal peaks in the 2D spectrum gives evidence of strong polaronic signatures in the nonlinear response. A quantitative theoretical analysis reveals a dipole coupling of electrons to the polar lattice that is much stronger than in bulk GaAs, due to a dynamic localization of the electron wave function by scattering processes.

Probing ultrafast dynamics in adenine with mid-UV four-wave mixing spectroscopies

Heterodyne-detected transient grating (TG) and two-dimensional photon echo (2DPE) spectroscopies are extended to the mid-UV spectral range in this investigation of photoinduced relaxation processes of adenine in aqueous solution. These experiments are the first to combine a new method for generating 25 fs laser pulses (at 263 nm) with the passive phase stability afforded by diffractive optics-based interferometry. We establish a set of conditions (e.g., laser power density, solute concentration) appropriate for the study of dynamics involving the neutral solute. Undesired solute photoionization is shown to take hold at higher peak powers of the laser pulses. Signatures of internal conversion and vibrational cooling dynamics are examined using TG measurements with signal-to-noise ratios as high as 350 at short delay times. In addition, 2DPE line shapes reveal correlations between excitation and emission frequencies in adenine, which reflect electronic and nuclear relaxation processes associated with particular tautomers. Overall, this study demonstrates the feasibility of techniques that will hold many advantages for the study of biomolecules whose lowest-energy electronic resonances are found in the mid-UV (e.g., DNA bases, amino acids).

Measurement of Raman χ(3) and theoretical estimation of DOVE four wave mixing of hydrogen peroxide

Hydrogen peroxide has strong infrared (IR) transitions ν(6) and its combination band ν(2)+ν(6), which may provide a unique opportunity to implement doubly vibrationally enhanced (DOVE) four wave mixing (FWM) for directly measuring hydrogen peroxide in spectrally overcrowded mixtures. In this work, the magnitude of the DOVE third-order susceptibility χ(3) was theoretically estimated. By using a FWM interferometric method, one of the strongest Raman bands, O-O stretch ν(3) Raman χ(3) of 30 wt % H(2)O(2), was first measured to be 1.2 × 10(-14) esu. The Raman χ(3) of ν(2) was then determined to be 5.3 × 10(-15) esu based on their relative Raman intensities. The resulting Raman χ(3) of ν(2) was used to calculate the DOVE χ(3) of (ν(6), ν(2)+ν(6)), together with the dipolar moments of the two IR transitions determined from IR absorption measurement. The calculated value of DOVE-IR χ(3) was 1.1 × 10(-13) esu for pure H(2)O(2), about 1.5 times larger than that of the strong ring breathing Raman band of benzene. The large DOVE χ(3) suggests the feasibility of direct measurement of hydrogen peroxide in an aqueous environment using DOVE four wave mixing.

New insights into response functions of liquids by electric field-resolved polarization emission time measurements

We resolve information about the dynamics of simple liquids that has been obscured in prior frequency and time-domain measurements by way of full field-resolved polarization emission time (FR-PET) measurements of carbon disulfide. The amplitude and phase of the field-resolved transient-grating signal is used to calculate a spectrogram of the signal field at each delay between the transient-grating (TG) pump and probe pulses. The temporal maximum of the spectrogram, defined to be the signal emission time, varies with pump-probe delay; it follows the convolution of the TG pulses while the pulses overlap and exhibits recurrences at times when the nuclear dynamics are the main component of the liquid material response. Since this is a third-order nonlinear spectroscopic method, the isotropic and anisotropic signals are constructed from the polarization tensor components. The frequency-integrated anisotropic component of the signal is equivalent to the signal measured in optical Kerr Effect (OKE) experiments. The FR-PET determination of the signal emission times is a direct measurement of the third-order nonlinear (polarizability) polarization and, hence provides new strong constraints on appropriate models of the liquid dynamics. Models for the material response function are used to calculate the signal emission times. In particular, we show that the proper treatment of the time-correlation function for orientational motion gives the best fit to the FR-PET data for rotational diffusional motion. We also establish that librational motion is not a short-time (coherent) motion that leads to rotational diffusion. Finally, we find that the Bucaro-Litovitz form for interaction-induced dynamics is not entirely correct for the CS(2) liquid we study. We suggest that the failing may result from the implicit assumption of two-body interactions, which is only appropriate for gases.

Simulating the T-jump-triggered unfolding dynamics of trpzip2 peptide and its time-resolved IR and two-dimensional IR signals using the Markov state model approach

We proposed a computational protocol of simulating the T-jump peptide unfolding experiments and the related transient IR and two-dimensional IR (2DIR) spectra based on the Markov state model (MSM) and nonlinear exciton propagation (NEP) methods. MSMs partition the conformation space into a set of nonoverlapping metastable states, and we can calculate spectra signal for each of these states using the NEP method. Thus the overall spectroscopic observable for a given system is simply the sum of spectra of different metastable states weighted by their populations. We show that results from MSMs constructed from a large number of simulations have a much better agreement with the equilibrium experimental 2DIR spectra compared to that generated from straightforward MD simulations starting from the folded state. This indicates that a sufficient sampling of important relevant conformational states is critical for calculating the accurate spectroscopic observables. MSMs are also capable of simulating the unfolding relaxation dynamics upon the temperature jump. The agreement of the simulation using MSMs and NEP with the experiment not only provides a justification for our protocol, but also provides the physical insight of the underlying spectroscopic observables. The protocol we developed has the potential to be extended to simulate a wide range of fast triggering plus optical detection experiments for biomolecules.

Sulfoxide stretching mode as a structural reporter via dual-frequency two-dimensional infrared spectroscopy

The S=O stretching mode in sulfoxides, having a frequency in the 950-1150 cm(-1) range, is tested as a structural label via dual-frequency two-dimensional infrared (2DIR) spectroscopy. The properties of this structural reporter are studied in several compounds, including (4,4(')-dimethyl-2,2(')-bipyridyl)(o-methylsulfinylbenzoate) ruthenium II, [Ru(dmb)(2)(BzSO)](+), (RuBzSO), octylsulfinylpropionic acid (OSPA), and o- and p-methylsulfinyl-benzoic acid (oMSBA and pMSBA). The mode assignment in the fingerprint region for these compounds is made using a combination of density functional theory calculations and 2DIR and relaxation-assisted 2DIR (RA 2DIR) spectroscopies. The SO stretching mode frequency and IR intensity demonstrate substantial sensitivity to the molecular structure. Multiple cross peaks of the C=O and S=O stretching modes with modes in the fingerprint region (930-1450 cm(-1)) were recorded. The 2DIR and RA 2DIR spectra focusing at interactions of a high-frequency mode of a ligand with the modes in the fingerprint region provide a spectral fingerprint of a compound and help mode assignment in the often congested fingerprint region. The cross-peak amplitudes in oMSBA, pMSBA, and OSPA were compared with the theoretical predictions based on the computed values for the off-diagonal anharmonicities and a reasonable match is found. The SO stretching mode provides means for assigning other modes in the fingerprint region and constitutes a promising structural reporter for the 2DIR and RA 2DIR spectroscopy measurements.