Probing Backbone Coupling within Hydrated Proteins with Two-Color 2D Infrared Spectroscopy.

The vibrational coupling between protein backbone modes and the role of water interactions are important topics in biomolecular spectroscopy. Our work reports the first study of the coupling between amide I and amide A modes within peptides and proteins with secondary structure and water contacts. We use two-color two-dimensional infrared (2D IR) spectroscopy and observe cross peaks between amide I and amide A modes. In experiments with peptides with different secondary structures and side chains, we observe that the spectra are sensitive to secondary structure. Water interactions affect the cross peaks, which may be useful as probes for the accessibility of protein sites to hydration water. Moving to two-color 2D IR spectra of proteins, the data demonstrate that the cross peaks integrate the sensitivities of both amide I and amide A spectra and that a two-color detection scheme may be a promising tool for probing secondary structures in proteins.

Aqueous pyruvate partly dissociates under deep ultraviolet irradiation but is resilient to near ultraviolet excitation.

The deep ultraviolet photochemistry of aqueous pyruvate is believed to have been essential to the origin of life, and near ultraviolet excitation of pyruvate in aqueous aerosols is assumed to contribute significantly to the photochemistry of the Earth's atmosphere. However, the primary photochemistry of aqueous pyruvate is unknown. Here we study the susceptibility of aqueous pyruvate to photodissociation by deep ultraviolet and near ultraviolet irradiation with femtosecond spectroscopy supported by density functional theory calculations. The primary photo-dynamics of the aqueous pyruvate show that upon deep-UV excitation at 200 nm, about one in five excited pyruvate anions have dissociated by decarboxylation 100 ps after the excitation, while the rest of the pyruvate anions return to the ground state. Upon near-UV photoexcitation at a wavelength of 340 nm, the dissociation yield of aqueous pyruvate 200 ps after the excitation is insignificant and no products are observed. The experimental results are explained by our calculations, which show that aqueous pyruvate anions excited at 200 nm have sufficient excess energy for decarboxylation, whereas excitation at 340 nm provides the aqueous pyruvate anions with insufficient energy to overcome the decarboxylation barrier.

Theoretical Sum Frequency Generation Spectra of Protein Amide with Surface-Specific Velocity-Velocity Correlation Functions.

Vibrational sum frequency generation (vSFG) spectroscopy is widely used to probe the protein structure at interfaces. Because protein vSFG spectra are complex, they can only provide detailed structural information if combined with computer simulations of protein molecular dynamics and spectra calculations. We show how vSFG spectra can be accurately modeled using a surface-specific velocity-velocity scheme based on ab initio normal modes. Our calculated vSFG spectra show excellent agreement with the experimental sum frequency spectrum of LTα14 peptide and provide insight into the origin of the characteristic α-helical amide I peak. Analysis indicates that the peak shape can be explained largely by two effects: (1) the uncoupled response of amide groups located on opposite sides of the α-helix will have different orientations with respect to the interface and therefore different local environments affecting the local mode vibrations and (2) vibrational splitting from nearest neighbor coupling evaluated as inter-residue vibrational correlation. The conclusion is consistent with frequency mapping techniques with an empirically based ensemble of peptide structures, thus showing how time correlation approaches and frequency mapping techniques can give independent yet complementary molecular descriptions of protein vSFG. These models reveal the sensitive relationship between protein structure and their amide I response, allowing exploitation of the complicated molecular vibrations and their interference to derive the structures of proteins under native conditions at interfaces.

Structure and Orientation of the SARS-Coronavirus-2 Spike Protein at Air-Water Interfaces.

The SARS coronavirus 2 (SARS-CoV-2) spike protein is located at the outermost perimeter of the viral envelope and is the first component of the virus to make contact with surrounding interfaces. The stability of the spike protein when in contact with surfaces plays a deciding role for infection pathways and for the viability of the virus after surface contact. While cryo-EM structures of the spike protein have been solved with high resolution and structural studies in solution have provided information about the secondary and tertiary structures, only little is known about the folding when adsorbed to surfaces. We here report on the secondary structure and orientation of the S1 segment of the spike protein, which is often used as a model protein for in vitro studies of SARS-CoV-2, at the air-water interface using surface-sensitive vibrational sum-frequency generation (SFG) spectroscopy. The air-water interface plays an important role for SARS-CoV-2 when suspended in aerosol droplets, and it serves as a model system for hydrophobic surfaces in general. The SFG experiments show that the S1 segment of the spike protein remains folded at the air-water interface and predominantly binds in its monomeric state, while the combination of small-angle X-ray scattering and two-dimensional infrared spectroscopy measurements indicate that it forms hexamers with the same secondary structure in aqueous solution.

Electrostatics Trigger Interfacial Self-Assembly of Bacterial Ice Nucleators.

Ice active bacteria can catalyze water freezing at high subzero temperatures using ice nucleating proteins (INPs) located at their outer cell walls. INPs are the most effective ice nucleators known and are of significant interest for agriculture, climate research, and freeze/antifreeze technologies. The aggregation of INPs into large ice nucleation sites is a key step for effective ice nucleation. It has been proposed that ice active bacteria can drive the aggregation of INPs and thereby trigger ice nucleation. However, the mechanism of INP aggregate assembly and the molecular processes behind the activation are still unclear. Both biochemical pathways and activation through electrostatics have been proposed based on experiments with lysed ice active bacteria. For a more direct view on the assembly of INPs, we follow the structure and water interactions of a synthetic model INP of the well-studied ice bacterium Pseudomonas syringae at the air-water interface as a function of the subphase pH. By combining sum frequency generation spectroscopy with two-dimensional infrared spectra, we conclude that self-assembly and electrostatic interactions drive the formation of ordered INP structures capable of aligning interfacial water.

Excitation Conditions for Surface-Enhanced Hyper Raman Scattering With Biocompatible Gold Nanosubstrates.

Surface enhanced hyper Raman scattering (SEHRS) can provide many advantages to probing of biological samples due to unique surface sensitivity and vibrational information complementary to surface-enhanced Raman scattering (SERS). To explore the conditions for an optimum electromagnetic enhancement of SEHRS by dimers of biocompatible gold nanospheres and gold nanorods, finite-difference time-domain (FDTD) simulations were carried out for a broad range of excitation wavelengths from the visible through the short-wave infrared (SWIR). The results confirm an important contribution by the enhancement of the intensity of the laser field, due to the two-photon, non-linear excitation of the effect. For excitation laser wavelengths above 1,000 nm, the hyper Raman scattering (HRS) field determines the enhancement in SEHRS significantly, despite its linear contribution, due to resonances of the HRS light with plasmon modes of the gold nanodimers. The high robustness of the SEHRS enhancement across the SWIR wavelength range can compensate for variations in the optical properties of gold nanostructures in real biological environments.

Surface-Enhanced Hyper Raman Spectra of Aromatic Thiols on Gold and Silver Nanoparticles.

We report the two-photon excited nonresonant surface-enhanced hyper Raman scattering (SEHRS) spectra of six aromatic thiol molecules during their interaction with gold and silver nanostructures. SEHRS spectra were obtained from thiophenol, benzyl mercaptan, and phenylethyl mercaptan and from the three isomers 2-aminothiophenol (2-ATP), 3-aminothiophenol (3-ATP), and 4-aminothiophenol (4-ATP). All SEHRS spectra were excited off-resonance at a wavelength of 1064 nm and compared to surface-enhanced Raman scattering (SERS) spectra excited at 785 nm or at 633 nm. The SEHRS spectra show a different interaction of thiophenol, benzyl mercaptan, and phenylethyl mercaptan with silver and gold nanostructures. Density functional theory calculations were used to support band assignments, in particular, for the unknown SERS spectrum of 3-ATP, and identify a band of phenylethyl mercaptan as a vibrational mode unique to the SEHRS spectrum and very weak in the Raman and infrared spectra. 2-ATP, 3-ATP, and 4-ATP show a different interaction with gold nanostructures that was found to depend on pH. Bands in the SEHRS spectrum of 2-ATP could be assigned to 2,2'-dimercaptoazobenzene, suggested to be obtained in a plasmon-assisted reaction that occurred during the SEHRS experiment. The results provide the basis for a better characterization of organic thiols at surfaces in a variety of fields, including surface functionalization and plasmonic catalysis.

In Situ Complementary Doping, Thermoelectric Improvements, and Strain-Induced Structure within Alternating PEDOT:PSS/PANI Layers.

Although the deposition of alternating layers from poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and polyaniline (PANI) salts has recently provided a breakthrough in the field of conductive polymers, the cause for the conductivity improvement has remained unclear. In this work, we report a cooperative doping effect between alternating PANI base and PEDOT:PSS layers, resulting in electrical conductivities of 50-100 S cm-1 and power factors of up to 3.0 ± 0.5 µW m-1 K-2, which surpass some of the recent values obtained for protonated PANI/PEDOT:PSS multilayers by a factor of 20. In this case, the simultaneous improvement in the electrical conductivity of both types of layers is caused by the in situ protonation of PANI, which corresponds to the removal of the excess acidic PSS chains from the PEDOT:PSS grains. The interplay between the functional groups' reactivity and the supramolecular chain reorganization leads to an array of preparation-dependent phenomena, including a stepwise increase in the film thickness, an alternation in the electrical conductivity, and the formation of a diverse surface landscape. The latter effect can be traced to a buildup of strain within the layers, which results in either the formation of folds or the shrinkage of the film. These results open new paths for designing nanostructured thin-film thermoelectrics.

Surface-enhanced hyper Raman hyperspectral imaging and probing in animal cells.

Hyper Raman scattering, that is, spontaneous, two-photon excited Raman scattering, of organic molecules becomes strong when it occurs as surface-enhanced hyper Raman scattering (SEHRS), in the proximity of plasmonic nanostructures. Its advantages over one-photon excited surface-enhanced Raman scattering (SERS) include complementary vibrational information resulting from different selection rules, probing of very small focal volumes, and beneficial excitation with long wavelengths. Here, imaging of macrophage cells by SEHRS is demonstrated, using SEHRS labels consisting of silver nanoparticles and two different molecules, 2-naphthalenethiol and para-mercaptobenzoic acid, that are excited off-resonance. The vibrational signatures of the molecules are discriminated using hyperspectral analysis and provide information about the subcellular localization of the SEHRS probes. The SEHRS based hyperspectral imaging approach presented here uses principal component analysis (PCA) to localize the reporter molecules inside the cells and is augmented by hierarchical cluster analysis (HCA). The high sensitivity of SEHRS spectra with respect to small environmental changes can be utilized for mapping of physiological parameters in the endosomal system of the cells. This is illustrated by discussing the spatial distribution of endosomes of varying pH inside the cytosol.

Surface enhanced hyper Raman scattering (SEHRS) and its applications.

Surface enhanced hyper Raman scattering (SEHRS) is the spontaneous, two-photon excited Raman scattering that occurs for molecules residing in high local optical fields of plasmonic nanostructures. Being regarded as a non-linear analogue of surface enhanced Raman scattering (SERS), SEHRS shares most of its properties, but also has additional characteristics. They include complementary spectroscopic information resulting from different selection rules and a stronger enhancement due to the non-linearity in excitation. In practical spectroscopy, this can translate to advantages, which include a high selectivity when probing molecule-surface interactions, the possibility of probing molecules at low concentrations due to the strong enhancement, and the advantages that come with excitation in the near-infrared. In this review, we give examples of the wealth of vibrational spectroscopic information that can be obtained by SEHRS and discuss work that has contributed to understanding the effect and that therefore provides directions for SEHRS spectroscopy. Future applications could range from biophotonics to materials research.

Post-Hartree-Fock studies of the He/Mg(0001) interaction: Anti-corrugation, screening, and pairwise additivity.

The adsorption of noble gases on metallic surfaces represents a paradigmatic case of van-der-Waals (vdW) interaction due to the role of screening effects on the corrugation of the interaction potential [J. L. F. Da Silva et al., Phys. Rev. Lett. 90, 066104 (2003)]. The extremely small adsorption energy of He atoms on the Mg(0001) surface (below 3 meV) and the delocalized nature and mobility of the surface electrons make the He/Mg(0001) system particularly challenging, even for state-of-the-art vdW-corrected density functional-based (vdW-DFT) approaches [M. P. de Lara-Castells et al., J. Chem. Phys. 143, 194701 (2015)]. In this work, we meet this challenge by applying two different procedures. First, the dispersion-corrected second-order Möller-Plesset perturbation theory (MP2C) approach is adopted, using bare metal clusters of increasing size. Second, the method of increments [H. Stoll, J. Chem. Phys. 97, 8449 (1992)] is applied at coupled cluster singles and doubles and perturbative triples level, using embedded cluster models of the metal surface. Both approaches provide clear evidences of the anti-corrugation of the interaction potential: the He atom prefers on-top sites, instead of the expected hollow sites. This is interpreted as a signature of the screening of the He atom by the metal for the on-top configuration. The strong screening in the metal is clearly reflected in the relative contribution of successively deeper surface layers to the main dispersion contribution. Aimed to assist future dynamical simulations, a pairwise potential model for the He/surface interaction as a sum of effective He-Mg pair potentials is also presented, as an improvement of the approximation using isolated He-Mg pairs.

Surface-Enhanced Hyper-Raman Spectra of Adenine, Guanine, Cytosine, Thymine, and Uracil.

Using picosecond excitation at 1064 nm, surface-enhanced hyper-Raman scattering (SEHRS) spectra of the nucleobases adenine, guanine, cytosine, thymine, and uracil with two different types of silver nanoparticles were obtained. Comparing the SEHRS spectra with SERS data from the identical samples excited at 532 nm and with known infrared spectra, the major bands in the spectra are assigned. Due to the different selection rules for the one- and two-photon excited Raman scattering, we observe strong variation in relative signal strengths of many molecular vibrations obtained in SEHRS and SERS spectra. The two-photon excited spectra of the nucleobases are found to be very sensitive with respect to molecule-nanoparticle interactions. Using both the SEHRS and SERS data, a comprehensive vibrational characterization of the interaction of nucleobases with silver nanostructures can be achieved.