Geometry determination of complexes in a molecular liquid mixture using electron-vibration-vibration two-dimensional infrared spectroscopy with a vibrational transition density cube method

On selection rules in two-dimensional terahertz-infrared-visible spectroscopy

Two-dimensional terahertz-infrared-visible (2D TIRV) spectroscopy directly measures the coupling between quantum high-frequency vibrations and classical low-frequency modes of molecular motion. In addition to coupling strength, the signal intensity in 2D TIRV spectroscopy can also depend on the selection rules of the excited transitions. Here, we explore the selection rules in 2D TIRV spectroscopy by studying the coupling between the high-frequency CH3 stretching and low-frequency vibrations of liquid dimethyl sulfoxide (DMSO). Different excitation pathways are addressed using variations in laser pulse timing and different polarizations of exciting pulses and detected signals. The DMSO signals generated via different excitation pathways can be readily distinguished in the spectrum. The intensities of different excitation pathways vary unequally with changes in polarization. We explain how this difference stems from the intensities of polarized and depolarized Raman and hyper-Raman spectra of high-frequency modes. These results apply to various systems and will help design and interpret new 2D TIRV spectroscopy experiments.

Conformation and Metal Cation Binding of Zwitterionic Alanine Tripeptide in Saline Solutions by Infrared Vibrational Spectroscopy and Molecular Dynamics Simulations

In this work, linear infrared (IR) spectroscopy and molecular dynamics (MD) simulations were used to examine the interaction of different metal cations (Na⁺, Ca²⁺, Mg²⁺, and Zn²⁺) with backbone (amide C═O) and C-terminal carboxylate (COO^-) groups in zwitterionic alanine tripeptide (Ala3) in aqueous solutions with varying saline concentrations. Circular dichroism spectra and MD results suggest that Ala3 is predominantly in polyproline-II (PP_II) conformation, whose amide-I and asymmetric carboxylate stretching IR vibration signatures are also supported by quantum-chemistry calculations. The zwitterionic form of Ala3 separates the two amide-I modes in frequency, which are weakly coupled modes, as revealed by two-dimensional IR measurement, and can be used to probe backbone-cation interactions at different scenarios (near charged or neutral chemical groups respectively). Cation concentration-dependent IR frequency red shifts in the amide-I mode are seen for both amide-I modes, whereas blue shifts are also seen in the amide-I mode far from the NH₃⁺ group. The observed spectral changes are discussed from the perspective of the salting-in and salting-out abilities of the cations. In addition, all the metal cations studied here (except Zn²⁺) can specifically coordinate to the COO^- group in bidentate and pseudo-bridging forms simultaneously. For Zn²⁺, only the pseudo-bridging form exists. Our results shed light on the macroscopic protein salting-in and salting-out phenomena from the perspective of key chemical bonds in peptides.

Photon echoes and two dimensional spectra of the amide I band of proteins measured by femtosecond IR - Raman spectroscopy

Infrared (IR) and Raman spectroscopy are fundamental techniques in chemistry, allowing the convenient determination of bond specific chemical composition and structure. Over the last decades, ultrafast multidimensional IR approaches using sequences of femtosecond IR pulses have begun to provide a new means of gaining additional information on molecular vibrational couplings, distributions of molecular structures and ultrafast molecular structural dynamics. In this contribution, new approaches to measuring multidimensional spectra involving IR and Raman processes are presented and applied to the study of the amide I band of proteins. Rephasing of the amide I band is observed using dispersed IR-Raman photon echoes and frequency domain 2D-IR-Raman spectra are measured by use of a mid-IR pulse shaper or over a broader spectral range using a tuneable picosecond laser. A simple pulse shaping approach to performing heterodyned time-domain Fourier Transform 2D-IR-Raman spectroscopy is introduced, revealing that the 2D-IR-Raman spectra distinguish homogeneous and inhomogeneous broadening in the same way as the well-established methods of 2D-IR spectroscopy. Across all datasets, the unique dependence of the amide I data on the IR and Raman strengths, vibrational anharmonicities and inhomogeneous broadening provides a fascinating spectroscopic view of the amide I band.

New ultrafast 2D-IR-Raman photon echo spectroscopy techniques are introduced and applied to the structural analysis of proteins.

Detection of Drug Binding to a Target Protein Using EVV 2DIR Spectroscopy

We demonstrate that electron-vibration-vibration two-dimensional infrared spectroscopy (EVV 2DIR) can be used to detect the binding of a drug to a target protein-active site. The EVV 2DIR spectrum of the FGFR1 kinase target protein is found to have ∼200 detectable cross-peaks in the spectral region 1250-1750 cm^-1/2600-3400 cm^-1, with additional 63 peaks caused by the addition of a drug, SU5402. Of these 63 new peaks, it is shown that only six are due to protein-drug interactions, with the other 57 being due to vibrational coupling within the drug itself. Quantum mechanical calculations employing density functional theory are used to support assignment of the six binding-dependent peaks, with one being assigned to a known interaction between the drug and a backbone carbonyl group which forms part of the binding site. None of the 57 intramolecular coupling peaks associated with the drug molecule change substantially in either intensity or frequency when the drug binds to the target protein. This strongly suggests that the structure of the drug in the target binding site is essentially identical to that when it is not bound.

Differentiation between Enamines and Tautomerizable Imines Oxidation Reaction Mechanism using Electron-Vibration-Vibration Two Dimensional Infrared Spectroscopy

Intermediates lie at the center of chemical reaction mechanisms. However, detecting intermediates in an organic reaction and understanding its role in reaction mechanisms remains a big challenge. In this paper, we used the theoretical calculations to explore the potential of the electron-vibration-vibration two-dimensional infrared (EVV-2DIR) spectroscopy in detecting the intermediates in the oxidation reactions of enamines and tautomerizable imines with 2,2,6,6-tetramethylpiperidine-1-oxyl (TEMPO). We show that while it is difficult to identify the intermediates from their infrared and Raman signals, the simulated EVV-2DIR spectra of these intermediates have well resolved spectral features, which are absent in the signals of reactants and products. These characteristic spectral signatures can, therefore, be used to reveal the reaction mechanism as well as monitor the reaction progress. Our work suggests the potential strength of EVV-2DIR technique in studying the molecular mechanism of organic reactions in general.

Applications of the New Family of Coherent Multidimensional Spectroscopies for Analytical Chemistry

A new family of vibrational and electronic spectroscopies has emerged, comprising the coherent analogs of traditional analytical methods. These methods are also analogs of coherent multidimensional nuclear magnetic resonance (NMR) spectroscopy. This new family is based on creating the same quantum mechanical superposition states called multiple quantum coherences (MQCs). NMR MQCs are mixtures of nuclear spin states that retain their quantum mechanical phase information for milliseconds. The MQCs in this new family are mixtures of vibrational and electronic states that retain their phases for picoseconds or shorter times. Ultrafast, high-intensity coherent beams rapidly excite multiple states. The excited MQCs then emit bright beams while they retain their phases. Time-domain methods measure the frequencies of the MQCs by resolving their phase oscillations, whereas frequency-domain methods measure the resonance enhancements of the output beam while scanning the excitation frequencies. The resulting spectra provide multidimensional spectral signatures that increase the spectroscopic selectivity required for analyzing complex samples.

From Ultrafast Structure Determination to Steering Reactions: Mixed IR/Non-IR Multidimensional Vibrational Spectroscopies

Ultrafast multidimensional infrared spectroscopy is a powerful method for resolving features of molecular structure and dynamics that are difficult or impossible to address with linear spectroscopy. Augmenting the IR pulse sequences by resonant or nonresonant UV, Vis, or NIR pulses considerably extends the range of application and creates techniques with possibilities far beyond a pure multidimensional IR experiment. These include surface-specific 2D-IR spectroscopy with sub-monolayer sensitivity, ultrafast structure determination in non-equilibrium systems, triggered exchange spectroscopy to correlate reactant and product bands, exploring the interplay of electronic and nuclear degrees of freedom, investigation of interactions between Raman- and IR-active modes, imaging with chemical contrast, sub-ensemble-selective photochemistry, and even steering a reaction by selective IR excitation. We give an overview of useful mixed IR/non-IR pulse sequences, discuss their differences, and illustrate their application potential.