Potential for the detection of molecular complexes and determination of interaction geometry by 2DIR: Application to protein sciences

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.

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.

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

We demonstrate the use of a new vibrational transition density cube (VTDC) method for determining the geometry of complexes in a molecular liquid mixture from electron-vibration-vibration two-dimensional infrared (EVV 2DIR) spectra. The VTDC method was used to calculate the electrically-mediated intermolecular vibrational coupling and thereby the EVV 2DIR spectra. Using the 1:1 benzonitrile-phenylacetylene (BN-PA) liquid mixture as a test case, the new method leads to a distance of 3.60 Å between the interacting BN-PA pair, a much more accurate value than the distance previously obtained using a dipolar approximation for the electrical coupling. We also show that molecular dynamics simulations of the liquid mixture predict a modal geometry of complexation which agrees well with the geometry determined from the 2DIR data via VTDC analysis. We therefore conclude the combination of VTDC and EVV 2DIR data is a useful approach for the determination of the geometry of molecular complexes in the condensed phase.

Frontiers in spectroscopy

We review the frontiers of spectroscopy from a historical perspective, starting with the development of atomic spectroscopy about 150 years ago, followed by some comments on selected previous Faraday Discussions. As the spectrum of frontiers at the Faraday Discussion 150 is very broad, we give only a brief survey providing a map of the various frontiers approached today. This is followed by an exemplary discussion of one particular frontier towards the spectroscopic detection of symmetry violations in fundamental physics. In particular the understanding of parity violation in chiral molecules has recently made great progress. We briefly describe the advances made in recent decades as well as the current status of theory and experiments in this exciting field of research. We conclude with an outlook on open questions and frontiers of the future in spectroscopy.