Ellen H. G. Backus

Energy transport in peptide helices

We investigate energy transport through an α-aminoisobutyric acid-based 310-helix dissolved in chloroform in a combined experimental-theoretical approach. Vibrational energy is locally deposited at the N terminus of the helix by ultrafast internal conversion of a covalently attached, electronically excited, azobenzene moiety. Heat flow through the helix is detected with subpicosecond time resolution by employing vibrational probes as local thermo meters at various distances from the heat source. The experiment is supplemented by detailed nonequilibrium molecular dynamics (MD) simulations of the process, revealing good qualitative agreement with experiment: Both theory and experiment exhibit an almost instantaneous temperature jump of the reporter units next to the heater which is attributed to the direct impact of the isomerizing azobenzene moiety. After this impact event, helix and azobenzene moiety appear to be thermally decoupled. The energy deposited in the helix thermalizes on a subpicosecond timescale and propagates along the helix in a diffusive-like process, accompanied by a significant loss into the solvent. However, in terms of quantitative numbers, theory and experiment differ. In particular, the MD simulation seems to overestimate the heat diffusion constant (2 Å2 ps−1 from the experiment) by a factor of five.

Real-time observation of molecular motion on a surface

The laser-induced movement of CO molecules over a platinum surface was followed in real time by means of ultrafast vibrational spectroscopy. Because the CO molecules bound on different surface sites exhibit different C–O stretch vibrational frequencies, the site-to-site hopping, triggered by excitation with a laser pulse, can be determined from subpicosecond changes in the vibrational spectra. The unexpectedly fast motion—characterized by a 500-femtosecond time constant—reveals that a rotational motion of the CO molecules, rather than pure translation, is required for this diffusion process. This conclusion is corroborated by density functional theory calculations.

α-Helix folding in the presence of structural constraints

We have investigated the site-specific folding kinetics of a photoswitchable cross-linked α-helical peptide by using single 13C = 18O isotope labeling together with time-resolved IR spectroscopy. We observe that the folding times differ from site to site by a factor of eight at low temperatures (6°C), whereas at high temperatures (45°C), the spread is considerably smaller. The trivial sum of the site signals coincides with the overall folding signal of the unlabeled peptide, and different sites fold in a noncooperative manner. Moreover, one of the sites exhibits a decrease of hydrogen bonding upon folding, implying that the unfolded state at low temperature is not unstructured. Molecular dynamics simulations at low temperature reveal a stretched-exponential behavior which originates from parallel folding routes that start from a kinetically partitioned unfolded ensemble. Different metastable structures (i.e., traps) in the unfolded ensemble have a different ratio of loop and helical content. Control simulations of the peptide at high temperature, as well as without the cross-linker at low temperature, show faster and simpler (i.e., single-exponential) folding kinetics. The experimental and simulation results together provide strong evidence that the rate-limiting step in formation of a structurally constrained α-helix is the escape from heterogeneous traps rather than the nucleation rate. This conclusion has important implications for an α-helical segment within a protein, rather than an isolated α-helix, because the cross-linker is a structural constraint similar to those present during the folding of a globular protein.

Liquid flow along a solid surface reversibly alters interfacial chemistry

Monitoring water interfaces in motion Water behaves differently at interfaces—where it meets the air, or a solid surface—than it does in the middle of the liquid. Past laboratory studies of this phenomenon have mainly focused on still samples, despite the fact that in natural settings such as rivers and rain, the water moves along the surfaces. Lis et al. used a microfluidics apparatus and a spectroscopy technique called sum frequency generation to study the effects of flow on aqueous chemistry at silica and fluorite surfaces (see the Perspective by Waychunas). The flow of fresh water along the surfaces disrupts the equilibrium of dissolved ions, substantially changing the surface charge and the molecular orientation of the water at the interface. Science, this issue p. 1138; see also p. 1094 A combination of microfluidics and surface-specific spectroscopy enables the study of flow effects at aqueous interfaces. [Also see Perspective by Waychunas] In nature, aqueous solutions often move collectively along solid surfaces (for example, raindrops falling on the ground and rivers flowing through riverbeds). However, the influence of such motion on water-surface interfacial chemistry is unclear. In this work, we combine surface-specific sum frequency generation spectroscopy and microfluidics to show that at immersed calcium fluoride and fused silica surfaces, flow leads to a reversible modification of the surface charge and subsequent realignment of the interfacial water molecules. Obtaining equivalent effects under static conditions requires a substantial change in bulk solution pH (up to 2 pH units), demonstrating the coupling between flow and chemistry. These marked flow-induced variations in interfacial chemistry should substantially affect our understanding and modeling of chemical processes at immersed surfaces.

Comparative study of direct and phase-specific vibrational sum-frequency generation spectroscopy: advantages and limitations.

As a surface-specific technique, vibrational sum-frequency generation (SFG) is used in a wide range of applications where soft matter or solid interfaces are to be probed on a molecular level through their vibrational modes. In recent years, phase-specific sum-frequency generation (PS-SFG, also known as heterodyne-detected SFG) spectroscopy has been increasingly replacing its predecessor (direct SFG, also known as homodyne SFG) as the experimental technique of choice for characterizing interfacial structure. The technique enables phase sensitive measurements, allowing for the determination of the real and imaginary parts of the interfacial vibrational response function and thereby the unambiguous identification of molecular orientation. This phase-sensitivity requires, however, a complete understanding of the complex optical properties of the sample and of their effect on the signal. These optical properties significantly influence the raw spectral data from which the real and imaginary parts of the second-order susceptibility are retrieved. We show that it is essential to correct the data appropriately to infer the true molecular response. The current study presents a detailed description of the physical contributions to the phase-resolved spectrum, allowing a direct comparison between the phase-resolved spectrum and that obtained using the well-understood direct detection method in a step-by-step data analysis process. In addition to phase sensitivity, PS-SFG has been shown to increase the sensitivity compared to traditional (direct) SFG spectroscopy. We present a quantitative comparison between theoretical limits of the signal-to-noise ratio of both techniques, which shows that for many systems the signal-to-noise ratio is very similar for direct- and phase-specific SFG signals.

Energy transport in peptide helices: a comparison between high- and low-energy excitations.

Energy transport in a short helical peptide in chloroform solution is studied by time-resolved femtosecond spectroscopy and accompanying nonequilibrium molecular dynamics (MD) simulations. In particular, the heat transport after excitation of an azobenzene chromophore attached to one terminus of the helix with 3 eV (UV) photons is compared to the excitation of a peptide C=O oscillator with 0.2 eV (IR) photons. The heat in the helix is detected at various distances from the heat source as a function of time by employing vibrational pump-probe spectroscopy. As a result, the carbonyl oscillators at different positions along the helix act as local thermometers. The experiments show that heat transport through the peptide after excitation with low-energy photons is at least 4 times faster than after UV excitation. On the other hand, the heat transport obtained by nonequilibrium MD simulations is largely insensitive to the kind of excitation. The calculations agree well with the experimental results for the low-frequency case; however, they give a factor of 5 too fast energy transport for the high-energy case. Employing instantaneous normal mode calculations of the MD trajectories, a simple harmonic model of heat transport is adopted, which shows that the heat diffusivity decreases significantly at temperatures initially reached by high-energy excitation. This finding suggests that the photoinduced energy gets trapped, if it is deposited in high amounts. The various competing mechanisms, such as vibrational T(1) relaxation, resonant transfer between excitonic states, cascading down relaxation, and low-frequency mode transfer, are discussed in detail.

Aqueous Heterogeneity at the Air/Water Interface Revealed by 2D‐HD‐SFG Spectroscopy

Water molecules interact strongly with each other through hydrogen bonds. This efficient intermolecular coupling causes strong delocalization of molecular vibrations in bulk water. We study intermolecular coupling at the air/water interface and find intermolecular coupling 1) to be significantly reduced and 2) to vary strongly for different water molecules at the interface--whereas in bulk water the coupling is homogeneous. For strongly hydrogen-bonded OH groups, coupling is roughly half of that of bulk water, due to the lower density in the near-surface region. For weakly hydrogen-bonded OH groups that absorb around 3500 cm(-1), which are assigned to the outermost, yet hydrogen-bonded OH groups pointing towards the liquid, coupling is further reduced by an additional factor of 2. Remarkably, despite the reduced structural constraints imposed by the interfacial hydrogen-bond environment, the structural relaxation is slow and the intermolecular coupling of these water molecules is weak.

Water Bending Mode at the Water–Vapor Interface Probed by Sum-Frequency Generation Spectroscopy: A Combined Molecular Dynamics Simulation and Experimental Study

We present a combined molecular dynamics simulation and experimental study on the water bending mode at the water-vapor interface using sum-frequency generation (SFG) spectroscopy. The SFG spectrum simulated using an ab initio-based water model shows good agreement with the experimental data. The imaginary part of the SFG response shows a negative peak at ∼1650 cm(-1) and a positive peak at ∼1730 cm(-1). Our results reveal that these widely (∼80 cm(-1)) separated peaks result from the interference of two closely spaced (∼29 cm(-1)) peaks of opposite sign. The positive peak at ∼1689 cm(-1) originates from water with two donor hydrogen atoms with the HOH angular bisector pointing down toward the bulk, and the negative peak at ∼1660 cm(-1) from water with free O-H groups, pointing up. The small frequency difference of 29 cm(-1) indicates that the HOH bending mode frequency of interfacial water is relatively insensitive to the number of hydrogen bonds.

Extreme surface propensity of halide ions in water.

Water possesses an extremely high polarity, making it a unique solvent for salts. Indeed, aqueous electrolyte solutions are ubiquitous in the atmosphere, biology, energy applications and industrial processes. For many processes, chemical reactions at the water surface are rate determining, and the nature and concentration of the surface-bound electrolytes are of paramount importance, as they determine the water structure and thereby surface reactivity. Here we investigate the dynamics of water molecules at the surface of sodium chloride and sodium iodide solutions, using surface-specific femtosecond vibrational spectroscopy. We quantify the interfacial ion density through the reduced energy transfer rates between water molecules resulting from the lowered effective interfacial density of water molecules, as water is displaced by surface active ions. Our results reveal remarkably high surface propensities for halogenic anions, higher for iodide than for chloride ions, corresponding to surface ion concentrations several times that of the bulk.

Determining In Situ Protein Conformation and Orientation from the Amide-I Sum-Frequency Generation Spectrum: Theory and Experiment

Vibrational sum-frequency generation (VSFG) spectra of the amide-I band of proteins can give detailed insight into biomolecular processes near membranes. However, interpreting these spectra in terms of the conformation and orientation of a protein can be difficult, especially in the case of complex proteins. Here we present a formalism to calculate the amide-I infrared (IR), Raman, and VSFG spectra based on the protein conformation and orientation distribution. Based on the protein conformation, we set up the amide-I exciton Hamiltonian for the backbone amide modes that generate the linear and nonlinear spectroscopic responses. In this Hamiltonian, we distinguish between nearest-neighbor and non-nearest-neighbor vibrational couplings. To determine nearest-neighbor couplings we use an ab initio 6-31G+(d) B3LYP-calculated map of the coupling as a function of the dihedral angles. The other couplings are estimated using the transition-dipole coupling model. The local-mode frequencies of hydrogen-bonded peptide bonds and of peptide bonds to proline residues are red-shifted. To obtain realistic hydrogen-bond shifts we perform a molecular dynamics simulation in which the protein is solvated by water. As a first application, we measure and calculate the amide-I IR, Raman, and VSFG spectra of cholera toxin B subunit docked to a model cell membrane. To deduce the orientation of the protein with respect to the membrane from the VSFG spectra, we compare the experimental and calculated spectral shapes of single-polarization results, rather than comparing the relative amplitudes of VSFG spectra recorded for different polarization conditions for infrared, visible, and sum-frequency light. We find that the intrinsic uncertainty in the interfacial refractive index--essential to determine the overall amplitude of the VSFG spectra--prohibits a meaningful comparison of the intensities of the different polarization combinations. In contrast, the spectral shape of most of the VSFG spectra is independent of the details of the interfacial refractive index and provides a reliable way of determining molecular interfacial orientation. Specifically, we find that the symmetry axis of the cholera toxin B subunit is oriented at an angle of 6° ± 17° relative to the surface normal of the lipid monolayer, in agreement with 5-fold binding between the toxins five subunits and the receptor lipids in the membrane.