Kevin J. Kubarych

Site-Specific Coupling of Hydration Water and Protein Flexibility Studied in Solution with Ultrafast 2D-IR Spectroscopy

There is considerable evidence for the slaving of biomolecular dynamics to the motions of the surrounding solvent environment, but to date there have been few direct experimental measurements capable of site-selectively probing both the dynamics of the water and the protein with ultrafast time resolution. Here, two-dimensional infrared spectroscopy (2D-IR) is used to study the ultrafast hydration and protein dynamics sensed by a metal carbonyl vibrational probe covalently attached to the surface of hen egg white lysozyme dissolved in D(2)O/glycerol solutions. Surface labeling provides direct access to the dynamics at the protein-water interface, where both the hydration and the protein dynamics can be observed simultaneously through the vibrational probes frequency-frequency correlation function. In pure D(2)O, the correlation function shows a fast initial 3 ps decay corresponding to fluctuations of the hydration water, followed by a significant static offset attributed to fluctuations of the protein that are not sampled within the <20 ps experimental window. Adding glycerol increases the bulk solvent viscosity while leaving the protein structurally intact and hydrated. The hydration dynamics exhibit a greater than 3-fold slowdown between 0 and 80% glycerol (v/v), and the contribution from the proteins dynamics is found to slow in a nearly identical fashion. In addition, the magnitude of the dynamic slowdown associated with hydrophobic hydration is directly measured and shows quantitative agreement with predictions from molecular dynamics simulations.

Diffractive optics-based six-wave mixing: Heterodyne detection of the full χ(5) tensor of liquid CS2

This work exploits the passive phase stabilization of diffractive optics to implement heterodyne detection of the complete χ(5) tensor of liquid CS2 as an example of a simple liquid. This approach permits the use of two different colors for the excitation, probe, and detection beam protocols and enables full optimization of the signal with respect to discrimination against lower order cascaded third-order responses. This work extends the previous study of polarization selectivity, in combination with heterodyne detection, to all independent polarization components to provide further insight into the origins of the fifth-order response and its connection to the multitime correlation of the liquid dynamics. The characteristic feature that clearly distinguishes the direct fifth-order response from lower order cascades is the pronounced ridge along the τ4 axis (probe pulse delay) with very rapid decay along the τ2 axis (excitation pulse delay). This observation is in contrast to recent related work using one-...

Crowding induced collective hydration of biological macromolecules over extended distances.

Ultrafast two-dimensional infrared (2D-IR) spectroscopy reveals picosecond protein and hydration dynamics of crowded hen egg white lysozyme (HEWL) labeled with a metal-carbonyl vibrational probe covalently attached to a solvent accessible His residue. HEWL is systematically crowded alternatively with polyethylene glycol (PEG) or excess lysozyme in order to distinguish the chemically inert polymer from the complex electrostatic profile of the protein crowder. The results are threefold: (1) A sharp dynamical jamming-like transition is observed in the picosecond protein and hydration dynamics that is attributed to an independent-to-collective hydration transition induced by macromolecular crowding that slows the hydration dynamics up to an order of magnitude relative to bulk water. (2) The interprotein distance at which the transition occurs suggests collective hydration of proteins over distances of 30-40 Å. (3) Comparing the crowding effects of PEG400 to our previously reported experiments using glycerol exposes fundamental differences between small and macromolecular crowding agents.

Chapter 5 Multidimensional Electronic and Vibrational Spectroscopy: An Ultrafast Probe of Molecular Relaxation and Reaction Dynamics

Abstract Multidimensional optical spectroscopy in the visible and infrared is a rapidly developing technique enabling direct observation of complex dynamics of molecules in complex environments such as liquids and proteins. Measuring the correlation between excited and detected frequencies with sub‐picosecond resolution has enabled the resolution of long‐standing problems such as energy transfer in photosynthesis and the life‐sustaining structural rearrangements of liquid water. This chapter aims to provide a bridge between the concepts familiar in the AMO physics community and how those ideas and experimental methods are applied to condensed phase molecular spectroscopy. We outline the technical challenges of these powerful methods while considering a few examples of experiments that showcase the unique perspective offered by 2D electronic and vibrational spectroscopy.

Two-Dimensional Infrared Spectroscopy of Metal Carbonyls

Metal carbonyl complexes offer both rich chemistry and complex vibrational spectroscopy due to strong coupling among the carbonyl stretches. Using two-dimensional infrared (2DIR) spectroscopy, it is possible to resolve the underlying transitions between vibrational energy levels, determine the orientations and relative magnitude of the corresponding transition dipole moments, measure the coupling between modes due to the anharmonicity of the potential, and probe energy redistribution among the modes as well as energy relaxation to other degrees of freedom. Measurements on metal carbonyl complexes have played, and continue to play, a crucial role in facilitating the development of 2DIR spectroscopy. These compounds have provided powerful demonstrations of the unique ability of 2DIR spectroscopy to resolve vibrational structure and dynamics in multimode systems. In addition, invaluable new information has been obtained on metal-to-ligand charge transfer processes, solvent-solute interactions and fluxionality. Since transition metal complexes play important roles in catalysis and as dye sensitizers for semiconductor nanoparticle photocatalysis, detailed probes of equilibrium and phototriggered dynamics should aid our understanding of these key catalytic systems. The richness and level of detail provided by the 2DIR spectra of metal carbonyl complexes turn them into extremely useful model systems for testing the accuracy of ab initio quantum chemical calculations. Accurate modeling of the 2DIR spectra of solvated metal carbonyl complexes requires the development of new theoretical and computational tools beyond those employed in the standard analysis of one-dimensional IR spectra, and represents an ongoing challenge to currently available computational methodologies. These challenges are further compounded by the increasing interest in triggered 2DIR experiments that involve nonequilibrium vibrational dynamics on multiple electronic potential surfaces. In this Account, we review the various metal carbonyl complexes studied via 2DIR spectroscopy and outline the theoretical approaches used in order to model the spectra. The capabilities of 2DIR spectroscopy and its interplay with modern ab initio calculations are demonstrated in the context of the metal carbonyl complex Mn(2)(CO)(10) recently studied in our lab. Continued progress in experimental implementation and theoretical analysis will enable transient 2D spectroscopy to provide structurally sensitive details of complex, highly interacting nonequilibrium processes that are central to diverse chemical transformations.

Two-dimensional infrared spectroscopy detected by chirped pulse upconversion

A two-dimensional (2D) infrared spectrum of Mn2(CO)10 is measured by using chirped-pulse upconversion (CPU) of the nonlinear signal field plus a reference local oscillator. By converting the spectrum to the visible, a silicon CCD camera can be used. The method offers an attractive alternative to direct IR detection due to the technological maturity of silicon and its greater intrinsic detectivity over HgCdTe. Using CPU, we acquired a rephasing 2D IR spectrum in a few seconds.

Site-Specific Hydration Dynamics of Globular Proteins and the Role of Constrained Water in Solvent Exchange with Amphiphilic Cosolvents

The thermodynamic driving forces for protein folding, association, and function are often determined by protein-water interactions. With a novel covalently bound labeling approach, we have used sensitive vibrational probes, site-selectively conjugated to two lysozyme variants-in conjunction with ultrafast two-dimensional infrared (2D-IR) spectroscopy-to investigate directly the protein-water interface. By probing alternatively a topologically flat, rigid domain and a flexible domain, we find direct experimental evidence for spatially heterogeneous hydration dynamics. The hydration environment around globular proteins can vary from exhibiting bulk-like hydration dynamics to dynamically constrained water, which results from stifled hydrogen bond switching dynamics near extended hydrophobic surfaces. Furthermore, we leverage preferential solvation exchange to demonstrate that the liberation of dynamically constrained water is a sufficient driving force for protein-surface association reactions. These results provide an intuitive picture of the dynamic aspects of hydrophobic hydration of proteins, illustrating an essential function of water in biological processes.

Fourier transform measurement of two-photon excitation spectra: applications to microscopy and optimal control.

We report a novel Fourier transform method for measuring two-photon excitation spectra. We demonstrate this method using simple dye molecules and discuss its applications in two-photon fluorescence microscopy and optimal control. This method facilitates an intuitive interpretation of recent control experiments in terms of tuning the nonlinear spectrum of the exciting laser source.

Multilevel vibrational coherence transfer and wavepacket dynamics probed with multidimensional IR spectroscopy.

Multidimensional infrared (MDIR) spectroscopy of a strongly coupled multilevel vibrational system Mn(2)(CO)(10) (dimanganese decacarbonyl) in cyclohexane solution reveals fully resolved excited vibrational state coherences that exhibit slow 0.25-0.50 ps(-1) decay constants. Detailed analysis of the waiting-time dependence of certain cross-peak amplitudes shows modulation at multiple frequencies, providing a direct signature of excited vibrational coherences resulting from coherence transfer. A new signature of coherence transfer is observed as temporally modulated cross-peak amplitudes with more than one modulation frequency. The relative importance of different coherence transfer paths is considered in the context of the orientational response of a system which includes two vibrational modes with parallel dipole moments. Since MDIR spectroscopy enables spectral isolation of individual excited vibrational coherences (i.e., coherences between fundamental excitations), these experiments report directly on the frequency-frequency correlation functions of the excited states relative to each other as well as relative to the ground state. These results highlight the rich information contained in fully exploring three-dimensional third-order spectroscopy, particularly regarding chemically relevant slower dynamics and the importance of intramolecular interactions leading to dephasing by optically dark or low-frequency modes of the molecule.

Diffractive optics implementation of six-wave mixing

Diffractive optics are applied to six-wave mixing processes to provide a single optic approach to attaining the required, relatively complex, phase-matching geometry to discriminate against lower-order nonlinear responses. The diffractive optics were designed specifically for broad-bandwidth operation and passive phase locking of the appropriate pulse pairs for use in femtosecond two-dimensional Raman studies of the dynamic structure of liquids. The fifth-order signal was studied in liquid CS>(2); two different colors were used for the excitation and the probe to reduce background scatter, as were two different phase-matching geometries with different degrees of suppression of cascaded third-order processes.