Excited and ground state vibrational dynamics revealed by two-dimensional electronic spectroscopy

Broadband two-dimensional electronic spectroscopy (2DES) can assist in understanding complex electronic and vibrational signatures. In this paper, we use 2DES to examine the electronic structure and dynamics of a long chain cyanine dye (1,1-diethyl-4,4-dicarbocyanine iodide, or DDCI-4), a system with a vibrational progression. Using broadband pulses that span the resonant electronic transition, we measure two-dimensional spectra that show a characteristic six peak pattern from coherently excited ground and excited state vibrational modes. We model these features using a spectral density formalism and the vibronic features are assigned to Feynman pathways. We also examine the dynamics of a particular set of peaks demonstrating anticorrelated peak motion, a signature of oscillatory wavepacket dynamics on the ground and excited states. These dynamics, in concert with the general structure of vibronic two-dimensional spectra, can be used to distinguish between pure electronic and vibrational quantum coherences.     

Calculations of intermode coupling constants and simulations of amide I,II, and III vibrational spectra of dipeptides

Amide I, II, and III vibrations of polypeptides are important marker modes whose vibrational spectra can provide critical information on structure and dynamics of proteins in solution. The extent of delocalization and vibrational properties of amide normal mode can be described by the amide local mode frequencies and intermode coupling constants between a pair of amide local modes. To determine these fundamental quantities, the previous Hessian matrix reconstruction method has been generalized here and applied to the density functional theory results for various dipeptide conformers. The calculation results are then used to simulate IR absorption, vibrational circular dichroism, and 2D IR spectra of dipeptides. The relationships between dipeptide backbone conformations and these vibrational spectra are discussed. It is believed that the present computational method and results will be of use to quantitatively simulate vibrational spectra of complicated polypeptides beyond simple dipeptides     

Study of the dynamics of surface molecules by time-resolved sum-frequency generation spectroscopy

Sum-frequency generation (SFG) is a nonlinear laser-spectroscopy technique suitable for analysis of adsorbed molecules. The sub-monolayer sensitivity of SFG spectroscopy enables vibrational spectra to be obtained with high specificity for a variety of molecules on a range of surfaces, including metals, oxides, and semiconductors. The use of ultra-short laser pulses on time-scales of picoseconds also makes time-resolved measurements possible; this can reveal ultrafast transient changes in molecular arrangements. This article reviews recent time-resolved SFG spectroscopy studies revealing site-hopping of adsorbed CO on metal surfaces and the dynamics of energy relaxation at water/metal interfaces. Time-resolved sum frequency generation spectroscopy at surfaces with non-resonant laser pulse irradiation     

On the Resolution Limit of Femtosecond Stimulated Raman Spectroscopy: Modelling Fifth‐Order Signals with Overlapping Pulses

Femtosecond stimulated Raman scattering (FSRS) spectroscopy is a powerful pump–probe technique that can track electronic and vibrational dynamics with high spectral and temporal resolution. The investigation of extremely short‐lived species, however, implies deciphering complex signals and is ultimately hampered by unwanted nonlinear effects once the time resolution limit is approached and the pulses overlap temporally. Using the loop diagrams formalism we calculate the fifth‐order response of a model system and address the limiting case where the relevant dynamics timescale is comparable to the pump–pulse duration and, consequently, the pump and the probe overlap temporally. We find that in this regime, additional diagrams that do not contribute for temporally well separated pulses need to be taken into account, giving rise to new time‐dependent features, even in the absence of photoinduced dynamics and for negative delays.     

Photoelectron spectroscopy of S1 toluene: I. Photoionization propensities of selected vibrational levels in S1 toluene

Laser photoelectron spectra have been obtained following the preparation of eight vibrational states in S(1) toluene. For four of the vibrational states (up to approximately 550 cm(-1) excess energy) excitation and ionization with nanosecond laser pulses give rise to photoelectron spectra with well-resolved vibrational peaks. For the other states (>750 cm(-1) excess energy) the photoelectron spectra show a loss of structure when nanosecond pulses are used, as a result of intramolecular dynamics [see Whiteside et al., J. Chem. Phys. 123, 204317 (2005), following paper]. A number of vibrational peaks in the photoelectron spectra are assigned, and we find that the common series of ion vibrational peaks observed following the ionization of p-fluorotoluene in various S(1) vibrational states is not reproduced in toluene.     

Ultrafast spectroscopy with sub-10 fs deep-ultraviolet pulses

Time-resolved transient absorption spectroscopy with sub-9 fs ultrashort laser pulses in the deep-ultraviolet (DUV) region is reported for the first time. Single 8.7 fs DUV pulses with a spectral range of 255-290 nm are generated by a chirped-pulse four-wave mixing technique for use as pump and probe pulses. Electronic excited state and vibrational dynamics are simultaneously observed for an aqueous solution of thymine over the full spectral range using a 128-channel lock-in detector. Vibrational modes of the electronic ground state and excited states can be observed as well as the decay dynamics of the electronic excited state. Information on the initial phase of the vibrational modes is extracted from the measured difference absorbance trace, which contains oscillatory structures arising from the vibrational modes of the molecule. Along with other techniques such as time-resolved infrared spectroscopy, spectroscopy with sub-9 fs DUV pulses is expected to contribute to a detailed understanding of the photochemical dynamics of biologically significant molecules that absorb in the DUV region such as DNA and amino acids.     

New perspectives on iron-ligand vibrations of oxyheme complexes

We report our studies of the vibrational dynamics of iron for three imidazole-ligated oxyheme derivatives that mimic the active sites of histidine-ligated heme proteins complexed with dioxygen. The experimental vibrational data are obtained from nuclear resonance vibrational spectroscopy (NRVS) measurements conducted on both powder samples and oriented single crystals, and which includes several in-plane (ip) and out-of-plane (oop) measurements. Vibrational spectral assignments have been made through a combination of the oriented sample spectra and predictions based on density functional theory (DFT) calculations. The two Fe-O(2) modes that have been previously observed by resonance Raman spectroscopy in heme proteins are clearly shown to be very strongly mixed and are not simply either a bending or stretching mode. In addition, a third Fe-O(2) mode, not previously reported, has been identified. The long-sought Fe-Im stretch, not observed in resonance Raman spectra, has been identified and compared with the frequencies observed for the analogous CO and NO species. The studies also suggest that the in-plane iron motion is anisotropic and is controlled by the orientation of the Fe-O(2) group and not sensitive to the in-plane Fe-N(p) bonds and/or imidazole orientations.     

Experimental and Theoretical Investigation of the 3sp(d) Rydberg States of Fenchone by Polarized Laser Resonance-Enhanced-Multiphoton-Ionization and Fourier Transform VUV Absorption Spectroscopy

The VUV absorption spectrum of fenchone is re-examined using synchrotron radiation Fourier transform spectrometry, revealing new vibrational structure. Picosecond laser (2+1) resonance enhanced multiphoton ionization (REMPI) spectroscopy complements this, providing an alternative view of the 3spd Rydberg excitation region. These spectra display broadly similar appearance, with minor differences that are largely explained by referring to calculated one- and two-photon electronic excitation cross-sections. Both show good agreement with Franck-Condon simulations of the relevant vibrational structures. Parent ion REMPI ionization yields with both femtosecond and picosecond excitation laser pulses are studied as a function of laser polarization and intensity, the latter providing insight into the relative two-photon excitation and one-photon ionization rates. The experimental circular-linear dichroism observed in the parent ion yields varies strongly between the 3s and 3p Rydberg states, in good overall agreement with the calculated two-photon excitation circular-linear dichroism, while corroborating other evidence that the 3p_z sub-state plays no more than a very minor role in the (2+1) REMPI spectrum. Vibrationally resolved photoelectron spectra are recorded with picosecond pulse duration (2+1) REMPI at selected intermediate vibrational excitations. The 3s intermediate state displays a very strong Δv=0 propensity on ionization, but the 3p intermediate evidences more complex vibronic dynamics, and we infer some 3p→3s internal conversion prior to ionization.     

Frequency-frequency correlation functions and apodization in two-dimensional infrared vibrational echo spectroscopy: a new approach

Ultrafast two-dimensional infrared (2D-IR) vibrational echo spectroscopy can probe structural dynamics under thermal equilibrium conditions on time scales ranging from femtoseconds to approximately 100 ps and longer. One of the important uses of 2D-IR spectroscopy is to monitor the dynamical evolution of a molecular system by reporting the time dependent frequency fluctuations of an ensemble of vibrational probes. The vibrational frequency-frequency correlation function (FFCF) is the connection between the experimental observables and the microscopic molecular dynamics and is thus the central object of interest in studying dynamics with 2D-IR vibrational echo spectroscopy. A new observable is presented that greatly simplifies the extraction of the FFCF from experimental data. The observable is the inverse of the center line slope (CLS) of the 2D spectrum. The CLS is the inverse of the slope of the line that connects the maxima of the peaks of a series of cuts through the 2D spectrum that are parallel to the frequency axis associated with the first electric field-matter interaction. The CLS varies from a maximum of 1 to 0 as spectral diffusion proceeds. It is shown analytically to second order in time that the CLS is the T(w) (time between pulses 2 and 3) dependent part of the FFCF. The procedure to extract the FFCF from the CLS is described, and it is shown that the T(w) independent homogeneous contribution to the FFCF can also be recovered to yield the full FFCF. The method is demonstrated by extracting FFCFs from families of calculated 2D-IR spectra and the linear absorption spectra produced from known FFCFs. Sources and magnitudes of errors in the procedure are quantified, and it is shown that in most circumstances, they are negligible. It is also demonstrated that the CLS is essentially unaffected by Fourier filtering methods (apodization), which can significantly increase the efficiency of data acquisition and spectral resolution, when the apodization is applied along the axis used for obtaining the CLS and is symmetrical about tau=0. The CLS is also unchanged by finite pulse durations that broaden 2D spectra.     

Detection of electronic and vibrational coherences in molecular systems by 2D electronic photon echo spectroscopy

Two-dimensional optical photon echo spectra are simulated for model systems which exhibit vibrational, electronic and a combination of electronic and vibrational coherent dynamics. The coherent motion manifests itself as periodic beatings of the spectrum cross-peak intensity with the population time. The intensity modulations are compared to evolution of the excited-state population and coordinate expectation value. The advantageous capabilities of the technique as well as possible difficulties in spectra interpretations are outlined. Possibilities for distinguishing electronic and vibrational coherences are discussed.     

Spectrally resolved femtosecond two-color three-pulse photon echoes: study of ground and excited state dynamics in molecules

We report the use of spectrally resolved femtosecond two-color three-pulse photon echoes as a potentially powerful multidimensional technique for studying vibrational and electronic dynamics in complex molecules. The wavelengths of the pump and probe laser pulses are found to have a dramatic effect on the spectrum of the photon echo signal and can be chosen to select different sets of energy levels in the vibrational manifold, allowing a study of the dynamics and vibrational splitting in either the ground or the excited state. The technique is applied to studies of the dynamics of vibrational electronic states in the dye molecule Rhodamine 101 in methanol.     

Molecular vibrational dynamics of rhodamine B dye in solution studied by femtosecond CARS

Spectrally dispersed femtosecond time-resolved coherent anti-Stokes Raman spectroscopy is utilized to study the ultrafast vibrational dynamics in rhodamine B dye in solution at room temperature. The anti-Stokes intensities are monitored as a function of time and wavenumber. By simply changing the timing of laser pulses, the vibrational dynamics of excited Raman transitions in rhodamine B molecules can be tracked and detected.     

Ultrafast vibrational dynamics of interfacial water

We report investigations of the vibrational dynamics of water molecules at the water–air and at the water–lipid interface. Following vibrational excitation with an intense femtosecond infrared pulse resonant with the O–H stretch vibration of water, we follow the subsequent relaxation processes using the surface-specific spectroscopic technique of sum frequency generation. This allows us to selectively follow the vibrational relaxation of the approximately one monolayer of water molecules at the interface. Although the surface vibrational spectra of water at the interface with air and lipids are very similar, we find dramatic variations in both the rates and mechanisms of vibrational relaxation. For water at the water–air interface, very rapid exchange of vibrational energy occurs with water molecules in the bulk, and this intermolecular energy transfer process dominates the response. For membrane-bound water at the lipid interface, intermolecular energy transfer is suppressed, and intramolecular relaxation dominates. The difference in relaxation mechanism can be understood from differences in the local environments experienced by the interfacial water molecules in the two different systems.     

Transient phenomena in time- and frequency-gated spontaneous emission

The effect of overlapping pump and gate pulses on time- and frequency-gated spontaneous emission spectra is explored for a model of material dynamics that accounts for strong nonadiabatic and electron-vibrational coupling effects, vibrational relaxation, and optical dephasing, thus representing characteristic features of photoinduced excited-state dynamics in large molecules in the gas phase or in condensed phases. The behaviors of the sequential, coherent, and doorway-window contributions to the spontaneous emission spectrum are studied separately. The interrelation between the sequential and coherent contributions is demonstrated to be sensitive to the carrier frequencies of the pump and gate pulses and also to the optical dephasing rate, opening the possibility of an experimental determination of the latter. The coherent contribution is shown to dominate the spectrum at specific emission frequencies.     

C-H stretching vibrations of methyl, methylene and methine groups at the vapor/alcohol (N = 1-8) interfaces

In IR and Raman spectral studies, the congestion of the vibrational modes in the C-H stretching region between 2800 and 3000 cm(-1) has complicated spectral assignment, conformational analysis, and structural and dynamics studies, even with quite a few of the simplest molecules. To resolve these issues, polarized spectra measurement on a well aligned sample is generally required. Because the liquid interface is generally ordered and molecularly thin, and sum frequency generation vibrational spectroscopy (SFG-VS) is an intrinsically coherent polarization spectroscopy, SFG-VS can be used for discerning details in vibrational spectra of the interfacial molecules. Here we show that, from systematic molecular symmetry and SFG-VS polarization analysis, a set of polarization selection rules could be developed for explicit assignment of the SFG vibrational spectra of the C-H stretching modes. These polarization selection rules helped assignment of the SFG-VS spectra of vapor/alcohol (n = 1-8) interfaces with unprecedented details. Previous approach on assignment of these spectra relied on IR and Raman spectral assignment, and they were not able to give such detailed assignment of the SFG vibrational spectra. Sometimes inappropriate assignment was made, and consequently misleading conclusions on interfacial structure, conformation and even dynamics were reached. With these polarization rules in addition to knowledge from IR and Raman studies, new structural information and understanding of the molecular interactions at these interfaces were obtained, and some new spectral features for the C-H stretching modes were also identified. Generally speaking, these new features can be applied to IR and Raman spectroscopic studies in the condensed phase. Therefore, the advancement on vibrational spectra assignment may find broad applications in the related fields using IR and Raman as vibrational spectroscopic tools.     

Vibrational Spectra of Zeolite Y as a Function of Ion Exchange

Zeolite Y is one of the earliest known and most widely used synthetic zeolites. Many experimental investigations verify the valuable ion exchange capability of this zeolite. In this study, we assessed the effects of ion exchange on its vibrational spectra. We applied classical lattice dynamics methods for IR and Raman intensity calculations. Computed spectra of optimized zeolite Y structures with different cations were compared with experimental data. The spectra obtained in this study are in agreement with previous experimental and computational studies on zeolites from the faujasite group.     

Selective nonlinear response preparation using femtosecond spectrally resolved four-wave-mixing

A novel method is presented to assist the assignment of vibrational coherence in the homodyne degenerate four-wave-mixing technique. The dependence of vibrational coherence dynamics on the interaction sequence of chirped pump and Stokes excitation pulses is exploited to distinguish quantum beating from polarization interference. Moreover, by combining chirped excitation and variable delays between pump and Stokes pulses, it is possible to achieve a controlled excitation of response pathways from a single electronic state and separation of population dynamics and vibrational coherence dynamics within a single response pathway. Numerical simulations are performed in the response function framework, which clearly show that such an approach applies for oscillatory contributions originated in the electronically excited state as well as in the ground state. The approach is experimentally demonstrated in three different polyatomic molecules in solution.     

Electromagnetically induced transparency with quantum interferometry

We have shown that electromagnetically induced transparency can be achieved by control-probe interferometry using two delayed phase-locked ultrashort pulses. Two vibrational wavepackets on the excited state, excited by two delayed phase-locked ultrashort pulses, interfere constructively or destructively leading to enhancement or suppression of absorption to a selective set of vibrational levels. Depending on the phase difference and the delay between the pulses with same carrier frequency, one can design different transparency windows between absorption peaks at consecutive even(odd) vibrational levels by eliminating absorption at odd(even) vibrational levels. We have shown that by switching the phase difference of two delayed femtosecond pulses, one can switch to complete elimination of absorption from enhanced absorption to a particular set of vibrational levels in the excited state. Thus, switching of transparency through window between odd vibrational levels to that between even vibrational levels is possible. By properly choosing the temporal width and the carrier frequency of the pulses, lossless transmission of complete or bands of frequencies of the pulses can be achieved through these transparency windows. Hence, designing of single- or multi-mode transparency windows in NaH molecule is feasible by control-probe quantum interferometry.     

Strong enhancement of vibrational relaxation by Watson-Crick base pairing

We have studied the ultrafast dynamics of NH-stretch vibrational excitations in Watson-Crick base pairs consisting of adenine and uracil derivatives. To estimate the influence of the A:U hydrogen bonding on the vibrational dynamics, we have also studied the uracil derivative in monomeric form. The vibrational relaxation of the NH-stretching mode is found to occur much faster in the Watson-Crick base pair than in monomeric uracil. From the delay dependence of the transient vibrational spectra, it can be concluded that both in base-paired and monomeric uracil, the energy relaxation takes place in two steps, the first step being a rapid transfer of energy from the NH-stretching mode to an accepting mode, the second step the relaxation of this accepting mode. The transient spectra show evidence that in the base pair the hydrogen bond between the nucleobases acts as the accepting mode, and that the hydrogen bonding between the bases is responsible for the extremely fast vibrational relaxation in this system.     

Towards a detailed understanding of bacterial metabolism--spectroscopic characterization of Staphylococcus epidermidis.

Bacteria are a major cause of infection. To fight disease and growing resistance, research interest is focused on understanding bacterial metabolism. For a detailed evaluation of the involved mechanisms, a precise knowledge of the molecular composition of the bacteria is required. In this article, various vibrational spectroscopic techniques are applied to comprehensively characterize, on a molecular level, bacteria of the strain Staphylococcus epidermidis, an opportunistic pathogen which has evolved to become a major cause of nosocomial infections. IR absorption spectroscopy reflects the overall chemical composition of the cells, with major focus on the protein vibrations. Smaller sample volumes-down to a single cell-are sufficient to probe the overall chemical composition by means of micro-Raman spectroscopy. The nucleic-acid and aromatic amino-acid moieties are almost exclusively explored by UV resonance Raman spectroscopy. In combination with statistical evaluation methods [hierarchical cluster analysis (HCA), principal component analysis (PCA), linear discriminant analysis (LDA)], the protein and nucleic-acid components that change during the different bacterial growth phases can be identified from the in vivo vibrational spectra. Furthermore, tip-enhanced Raman spectroscopy (TERS) provides insight into the surface structures and follows the dynamics of the polysaccharide and peptide components on the bacterial cells with a spatial resolution below the diffraction limit. This might open new ways for the elucidation of host-bacteria and drug-bacteria interactions.