PGx01 series

We use vibrational sum-frequency generation (VSFG) spectroscopy to study the structure of hen egg-white lysozyme (HEWL) aggregates adsorbed to DOPG/D₂O and air/D₂O interfaces. We find that aggregates with a parallel and antiparallel β-sheet structure together with smaller unordered aggregates and a denaturated protein are adsorbed to both interfaces. We demonstrate that to retrieve this information, fitting of the VSFG spectra is essential. The number of bands contributing to the VSFG spectrum might be misinterpreted, due to interference between peaks with opposite orientation and a nonresonant background. Our study identified hydrophobicity as the main driving force for adsorption to the air/D₂O interface. Adsorption to the DOPG/D₂O interface is also influenced by hydrophobic interaction; however, electrostatic interaction between the charged protein’s groups and the lipid’s headgroups has the most significant effect on the adsorption. We find that the intensity of the VSFG spectrum at the DOPG/D₂O interface is strongly enhanced by varying the pH of the solution. We show that this change is not due to a change of lysozyme’s and its aggregates’ charge but due to dipole reorientation at the DOPG/D₂O interface. This finding suggests that extra care must be taken when interpreting the VSFG spectrum of proteins adsorbed at the lipid/water interface.

Ion hydration and interfacial water play crucial roles in numerous phenomena ranging from biological to industrial systems. Although biologically relevant (and mostly smaller) ions have been studied extensively in this context, very little experimental data exist about molecular-scale behavior of heavy ions and their complexes at interfaces, especially under technologically significant conditions. It has recently been shown that PtCl₆^2– complexes adsorb at positively charged interfaces in a two-step process that cannot fit into well-known empirical trends, such as Hofmeister series. Here, a combined vibrational sum frequency generation and molecular dynamics study reveals that a unique interfacial water structure is connected to this peculiar adsorption behavior. A novel subensemble analysis of molecular dynamics simulation results shows that after adsorption PtCl₆^2– complexes partially retain their first and second hydration spheres and that it is possible to identify three different types of water molecules around them on the basis of their orientational structures and hydrogen-bonding strengths. These results have important implications for relating interfacial water structure and hydration enthalpy to the general understanding of specific ion effects. This in turn influences interpretation of heavy metal ion distribution across, and reactivity within, liquid interfaces.

The response of DNA and RNA bases to ultraviolet (UV) radiation has been receiving increasing attention for a number of important reasons: (i) the selection of the building blocks of life on an early earth may have been mediated by UV photochemistry, (ii) radiative damage of DNA depends critically on its photochemical properties, and (iii) the processes involved are quite general and play a role in more biomolecules as well as in other compounds. A growing number of groups worldwide have been studying the photochemistry of nucleobases and their derivatives. Here we focus on gas phase studies, which (i) reveal intrinsic properties distinct from effects from the molecular environment, (ii) allow for the most detailed comparison with the highest levels of computational theory, and (iii) provide isomeric selectivity. From the work so far a picture is emerging of rapid decay pathways following UV excitation. The main understanding, which is now well established, is that canonical nucleobases, when absorbing UV radiation, tend to eliminate the resulting electronic excitation by internal conversion (IC) to the electronic ground state in picoseconds or less. The availability of this rapid “safe” de-excitation pathway turns out to depend exquisitely on molecular structure. The canonical DNA and RNA bases are generally short-lived in the excited state, and thus UV protected. Many closely related compounds are longer lived, and thus more prone to other, potentially harmful, photochemical processes. It is this structure dependence that suggests a mechanism for the chemical selection of the building blocks of life on an early earth. However, the picture is far from complete and many new questions now arise.

Long-lived excitons formed upon visible light absorption play an essential role in photovoltaics, photocatalysis, and even in high-density information storage. Here, we describe a self-assembled two-dimensional metal-organic crystal, composed of graphene-supported macrocycles, each hosting a single FeN₄ center, where a single carbon monoxide molecule can adsorb. In this heme-like biomimetic model system, excitons are generated by visible laser light upon a spin transition associated with the layer 2D crystallinity, and are simultaneously detected via the carbon monoxide ligand stretching mode at room temperature and near-ambient pressure. The proposed mechanism is supported by the results of infrared and time-resolved pump-probe spectroscopies, and by ab initio theoretical methods, opening a path towards the handling of exciton dynamics on 2D biomimetic crystals.

Molecular scale information about the structure of surfactants at interfaces underlies their application in consumer products. In this study the non-linear optical technique of Sum Frequency Generation (SFG) vibrational spectroscopy has been used to investigate the structure and temporal behaviour of two cationic surfactants used frequently in hair conditioners. SFG spectra of films of behenyltrimethylammonium methosulfate (BTMS) and behenyltrimethylammonium chloride (BTAC) were recorded at the air/water interface and on glass slides following Langmuir Blodgett (LB) deposition. The assignment of the BTMS and BTAC spectral features (resonances) to the C—H stretching modes of the surfactants was consolidated by comparison with the SFG spectrum of deuterated cetyltrimethylammonium bromide (d-CTAB) and by recording spectra on D₂O as well as on water. The C—H resonances arise from the methylene and methyl groups of the tail and head-groups of the surfactants. A slow collapse mechanism was observed following film compression of both BTAC and BTMS. The change in molecular structure of the films undergoing this slow collapse was followed by recording sequential SFG spectra in the C—H region, and by monitoring the SFG intensity at specific wavenumbers over time. Additionally, LB deposition onto glass was used to capture the state of the film during the slow collapse, and these SFG spectra showed close similarity to the corresponding spectra on water. Complementary Atomic Force Microscopy (AFM) was used to elucidate the layering of the compressed and relaxed films deposited onto mica by LB deposition.

Here we present the excited state dynamics of jet-cooled 6-thioguanine (6-TG), using resonance-enhanced multiphoton ionization (REMPI), IR–UV double resonance spectroscopy, and pump–probe spectroscopy in the nanosecond and picosecond time domains. We report data on two thiol tautomers, which appear to have different excited state dynamics. These decay to a dark state, possibly a triplet state, with rates depending on tautomer form and on excitation wavelength, with the fastest rate on the order of 10¹⁰ s^–1. We also compare 6-TG with 9-enolguanine, for which we observed decay to a dark state with a 2 orders of magnitude smaller rate. At increased excitation energy (∼+500 cm^–1) an additional pathway appears for the predominant thiol tautomer. Moreover, the excited state dynamics for 6-TG thiols is different from that recently predicted for thiones.

We present resonant two-photon ionization (R2PI) spectra of isocytosine (isoC) and pump–probe results on two of its tautomers. IsoC is one of a handful of alternative bases that have been proposed in scenarios of prebiotic chemistry. It is structurally similar to both cytosine (C) and guanine (G). We compare the excited-state dynamics with the Watson–Crick (WC) C and G tautomeric forms. These results suggest that the excited-state dynamics of WC form of G may primarily depend on the heterocyclic substructure of the pyrimidine moiety, which is chemically identical to isoC. For WC isoC we find a single excited-state decay with a rate of ∼10¹⁰ s^–1, while the enol form has multiple decay rates, the fastest of which is 7 times slower than for WC isoC. The excited-state dynamics of isoC exhibits striking similarities with that of G, more so than with the photodynamics of C.

Quantitative concentrations measurements using time-resolved laser-induced fluorescence have been demonstrated for nitric oxide (NO) in flame. Fluorescence lifetimes measured using a picosecond Nd:YAG laser and optical parametric amplifier system have been used to directly compensate the measured signal for collisional quenching and evaluate NO concentration. The full evaluation also includes the spectral overlap between the ∼15 cm⁻¹ broad laser pulse and multiple NO absorption lines as well as the populations of the probed energy levels. Effective fluorescence lifetimes of 1.2 and 1.5 ns were measured in prepared NO/N₂/O₂ mixtures at ambient pressure and temperature and in a premixed NH₃-seeded CH₄/N₂/O₂ flame, respectively. Concentrations evaluated from measurements in NO/N₂/O₂ mixtures with NO concentrations of 100–600 ppm were in agreement with set values within 3% at higher concentrations. An accuracy of 13% was estimated by analysis of experimental uncertainties. An NO profile measured in the flame showed concentrations of ∼1000 ppm in the post-flame region and is in good agreement with NO concentrations predicted by a chemical mechanism for NH₃ combustion. An accuracy of 16% was estimated for the flame measurements. The direct concentration evaluation from time-resolved fluorescence allows for quantitative measurements in flames where the composition of major species and their collisional quenching on the probed species is unknown. In particular, this is valid for non-stationary turbulent combustion and implementation of the presented approach for measurements under such conditions is discussed.

The lipopeptide surfactin produced by certain strains of Bacillus subtilis is a powerful biosurfactant possessing potentially useful antimicrobial properties. In order to better understand its surface behavior, we have used surface sensitive sum frequency generation (SFG) vibrational spectroscopy in the C—H and C═O stretching regions to determine its structure at the air/water interface. Using surfactin with the leucine groups of the peptide ring perdeuterated, we have shown that a majority of the SFG signals arise from the 4 leucine residues. We find that surfactin forms a robust film, and that its structure is not affected by the number density at the interface or by pH variation of the subphase. The spectra show that the ring of the molecule lies in the plane of the surface rather than perpendicular to it, with the tail lying above this, also in the plane of the interface.

In recent years, efforts have been made in catalysis related surface science studies to explore the possibilities to perform experiments at conditions closer to those of a technical catalyst, in particular at increased pressures. Techniques such as high pressure scanning tunneling/atomic force microscopy (HPSTM/AFM), near ambient pressure x-ray photoemission spectroscopy (NAPXPS), surface x-ray diffraction (SXRD) and polarization-modulation infrared reflection absorption spectroscopy (PM-IRAS) at semi-realistic conditions have been used to study the surface structure of model catalysts under reaction conditions, combined with simultaneous mass spectrometry (MS). These studies have provided an increased understanding of the surface dynamics and the structure of the active phase of surfaces and nano particles as a reaction occurs, providing novel information on the structure/activity relationship. However, the surface structure detected during the reaction is sensitive to the composition of the gas phase close to the catalyst surface. Therefore, the catalytic activity of the sample itself will act as a gas-source or gas-sink, and will affect the surface structure, which in turn may complicate the assignment of the active phase. For this reason, we have applied planar laser induced fluorescence (PLIF) to the gas phase in the vicinity of an active model catalysts. Our measurements demonstrate that the gas composition differs significantly close to the catalyst and at the position of the MS, which indeed should have a profound effect on the surface structure. However, PLIF applied to catalytic reactions presents several beneficial properties in addition to investigate the effect of the catalyst on the effective gas composition close to the model catalyst. The high spatial and temporal resolution of PLIF provides a unique tool to visualize the on-set of catalytic reactions and to compare different model catalysts in the same reactive environment. The technique can be applied to a large number of molecules thanks to the technical development of lasers and detectors over the last decades, and is a complementary and visual alternative to traditional MS to be used in environments difficult to asses with MS. In this article we will review general considerations when performing PLIF experiments, our experimental set-up for PLIF and discuss relevant examples of PLIF applied to catalysis.