2D IR Photon Echo Research Articles

Simulations of the infrared, Raman, and 2D-IR photon echo spectra of water in nanoscale silica pores

Vibrational spectroscopy is frequently used to characterize nanoconfined liquids and probe the effect of the confining framework on the liquid structure and dynamics relative to the corresponding bulk fluid. However, it is still unclear what molecular-level information can be obtained from such measurements. In this paper, we address this question by using molecular dynamics (MD) simulations to reproduce the linear infrared (IR), Raman, and two-dimensional IR (2D-IR) photon echo spectra for water confined within hydrophilic (hydroxyl-terminated) silica mesopores. To simplify the spectra the OH stretching region of isotopically dilute HOD in D2O is considered. An empirical mapping approach is used to obtain the OH vibrational frequencies, transition dipoles, and transition polarizabilities from the MD simulations. The simulated linear IR and Raman spectra are in good general agreement with measured spectra of water in mesoporous silica reported in the literature. The key effect of confinement on the water spectrum is a vibrational blueshift for OH groups that are closest to the pore interface. The blueshift can be attributed to the weaker hydrogen bonds (H-bonds) formed between the OH groups and silica oxygen acceptors. Non-Condon effects greatly diminish the contribution of these OH moieties to the linear IR spectrum, but these weaker H-bonds are readily apparent in the Raman spectrum. The 2D-IR spectra have not yet been measured and thus the present results represent a prediction. The simulated spectra indicates that it should be possible to probe the slower spectral diffusion of confined water compared to the bulk liquid by analysis of the 2D-IR spectra.

Two-Dimensional Infrared Spectroscopy and Electron Microscopy of Seeded and Non-Seeded Amyloid β Peptide Fibrils

Seeded and non-seeded fibrils from amyloid β 40-residue (Aβ40) peptides have been studied with two-dimensional infrared (2D-IR) spectroscopy and electron microscopy (EM). For the former, 13C=18O isotope labels were placed in various residues to probe residue-specific amide-I' vibrations of Aβ40 peptides. 2D-IR spectroscopy (2D-IR photon echo) of both kinds of fibrils shows distinct linear chain excitons of amide units due to the interamide vibrational coupling. Structural differences between the seeded and the non-seeded fibrils vary across the sequence. However, seeded fibrils tend to have a better aligned tertiary structure than non-seeded fibrils. Negatively stained EM images indicate that non-seeded fibrils had no discernible narrowing or nodes. In comparison, seeded fibrils tend to appear twisted like a ribbon, with periodic narrowing or nodes. The distances between nodes (the “internodal” distances) were relatively homogeneous distributions (∼75 nm) and the same in all isotopically labeled peptides. The apparent width of the fibrils in these images indicate that seeded fibrils are two kinds and that the width of the narrower fibrils is the same as the width of non-seeded fibrils. The mass-per-length evaluated from dark-field EM images indicates that the most prevalent number of filaments in seeded fibrils is 6, which is twice as many as the number in non-seeded fibrils (3 filaments per fibril). Overall, these results demonstrate that seeded and non-seeded fibrils have distinctly different tertiary structures.

2D IRphoton echo of azido-probes for biomolecular dynamics

The vibrations in the azido-, N(3), asymmetric stretching region of 2'-azido-2'-deoxyuridine (N(3)dU) are examined by two-dimensional infrared spectroscopy. In water and tetrahydrofuran (THF), the spectra display a single sharp diagonal peak that shows solvent sensitivity. The frequency-frequency correlation time in water is 1.5 ps, consistent with H-bond making and breaking dynamics. The 2D IR spectrum is reproduced for N(3)dU in water based on a model correlation function and known linear response functions. Its large extinction coefficient, vibrational frequency outside the protein and nucleic acid IR absorption, and sensitivity to water dynamics render -N(3) a very useful probe for 2D IR and other nonlinear IR studies: its signal is ca. 100 times that of nitriles.

Water-Induced Relaxation of a Degenerate Vibration of Guanidinium Using 2D IR Echo Spectroscopy

The nearly degenerate asymmetric stretch vibrations near 1600 cm(-1) of the guanidinium cation in D-glycerol/D(2)O mixtures having different viscosity were studied by 2D IR photon echo spectroscopy. The polarization-dependent photon echo signal shows two separate frequency distributions in the 2D spectrum in D(2)O, even though only one band is evident from inspection of the linear FTIR spectrum. The split components are more clearly seen at higher viscosity where the distortion of the molecule from 3-fold symmetry is even more evident. The interactions with solvent induce energy transfer between the degenerate component modes on the time scale of 0.5 ps. The energy transfer between modes is directly observed in 2D IR and distinguished by the waiting time dependence of the cross peaks from the transfers between configurations of the distorted ion and solvent. The 2D IR analysis carried out for various polarization conditions gave frequency-frequency auto- and cross-correlation functions for the degenerate components which derive from the solvent induced wagging of the -ND(2) groups of the guanidinium ion.

2D IR photon echo study of the anharmonic coupling in the OCN region of phenyl cyanate

The vibrations in the OCN stretching region of phenyl cyanate are examined by two-dimensional infrared spectroscopy. In water and THF, these spectra display three diagonal peaks having cross peaks characteristic of anharmonically coupled transitions. The pattern of the spectra is reproduced by coupling of two overtones with the OCN fundamental.

Two-Dimensional Circularly Polarized IR Photon Echo Spectroscopy of Polypeptides: Four-Wave-Mixing Optical Activity Measurement

A coherent two-dimensional (2D) optical spectroscopy utilizing circularly polarized (CP) beams, which was shown to be useful in studying molecular chirality in condensed phases, was theoretically proposed recently [Cho et al. J. Chem. Phys. 2003, 119, 7003]. A photon echo (PE) version of 2D optical activity spectroscopy is discussed in this paper. Considering various dipeptide and polypeptide systems, where the amide I local modes constitute the set of basis modes used to describe exciton and biexciton states as linear combinations of those basis modes, we present numerically simulated 2D circularly polarized IR PE spectra. It is shown that this novel spectroscopic method can provide additional information on the angles between the transition magnetic dipole and the transition electric dipole of two different vibrationally excited states, which are highly sensitive to the 3D structure and chirality of a given polypeptide. Also, a hierarchical relation of IR absorption, vibrational circular dichroism, 2D IR PE, and 2D CP-IR PE is discussed to show advantages of 2D optical activity spectroscopy in general.

Coupling between C–D and C [dbnd]O motions using dual-frequency 2D IR photon echo spectroscopy

Coupling between C–D and C O vibrational modes of formamide has been characterized by dual-frequency 2D IR spectroscopy. The signals are consistent with those computed assuming an optically dense system at the C O frequency. A negative off-diagonal anharmonicity of ∼0.85 ± 0.20 cm −1 was obtained and the coupled modes have anticorrelated frequency distributions. Other features including relaxation times, diagonal anharmonicities for the individual C O and C–D modes and the dephasing dynamics of the cross peak have been determined to characterize the coupling between modes.

Vibrational spectroscopic characteristics of secondary structure polypeptides in liquid water: Constrained MD simulation studies

Using the constrained MD simulation method in combination with quantum chemistry calculation, Hessian matrix reconstruction, and fragmentation approximation methods, we established a computational scheme for numerical simulations of amide I IR absorption, vibrational circular dichroism (VCD), and 2D IR photon echo spectra of peptides in solution. Six different secondary structure peptides, i.e., alpha-helix, 3(10)-helix, pi-helix, antiparallel and parallel beta-sheets, and polyproline II (P(II)), are considered, and the vibrational characteristic features in their linear and nonlinear spectra in the amide I band region are discussed. Isotope-labeling effects on IR and VCD spectra are notable only for alpha- and pi-helical peptides due to the strong vibrational couplings between two nearest neighboring amide I local oscillators. The amplitudes of difference 2D IR spectra are shown to be strongly dependent on both the extent of mode delocalization and the relative orientation of local mode transition dipoles determined by secondary structure.

Dual-frequency 2D IR photon echo of a hydrogen bond

Dual-frequency 2D IR heterodyned photon echo experiments with independently tunable mid-IR pulses are presented. Two-dimensional IR spectra acquired using three pulses in a sequence of 3, 3 and 6 μm allow observation of NH and CO stretching mode interactions. Intermolecular hydrogen bonding between NH and CO groups is characterized via observation of interaction of the NH and CO vibrational modes. Structural and dynamical parameters determined include the cross anharmonicity, angular constraints, and a correlation factor for the frequency distributions.