Second-harmonic phonon spectroscopy of α\alpha-quartz

We demonstrate midinfrared second-harmonic generation as a highly sensitive phonon spectroscopy technique that we exemplify using $\alpha$-quartz (SiO$_2$) as a model system. A midinfrared free-electron laser provides direct access to optical phonon resonances ranging from $350\ \mathrm{cm}^{-1}$ to $1400\ \mathrm{cm}^{-1}$. While the extremely wide tunability and high peak fields of an free-electron laser promote nonlinear spectroscopic studies---complemented by simultaneous linear reflectivity measurements---azimuthal scans reveal crystallographic symmetry information of the sample. Additionally, temperature-dependent measurements show how damping rates increase, phonon modes shift spectrally and in certain cases disappear completely when approaching$T_c=846\ \mathrm{K}$where quartz undergoes a structural phase transition from trigonal$\alpha$-quartz to hexagonal$\beta$-quartz, demonstrating the technique's potential for studies of phase transitions

Second Harmonic Generation from Critically Coupled Surface Phonon Polaritons

Mid-infrared nanophotonics can be realized using sub-diffractional light localization and field enhancement with surface phonon polaritons in polar dielectric materials. We experimentally demonstrate second harmonic generation due to the optical field enhancement from critically coupled surface phonon polaritons at the 6H-SiC-air interface, employing an infrared free-electron laser for intense, tunable, and narrowband mid-infrared excitation. Critical coupling to the surface polaritons is achieved using a prism in the Otto geometry with adjustable width of the air gap, providing full control over the excitation conditions along the polariton dispersion. The calculated reflectivity and second harmonic spectra reproduce the full experimental data set with high accuracy, allowing for a quantification of the optical field enhancement. We also reveal the mechanism for low out-coupling efficiency of the second harmonic light in the Otto geometry. Perspectives on surface phonon polariton-based nonlinear sensing and nonlinear waveguide coupling are discussed

Resonant enhancement of second harmonic generation in the mid-infrared using localized surface phonon polaritons in sub-diffractional nanostructures

We report on strong enhancement of mid-infrared second harmonic generation (SHG) from SiC nanopillars due to the resonant excitation of localized surface phonon-polaritons within the Reststrahlen band. The magnitude of the SHG peak at the monopole mode experiences a strong dependence on the resonant frequency beyond that described by the field localization degree and the dispersion of linear and nonlinear-optical SiC properties. Comparing the results for the identical nanostructures made of 4H and 6H SiC polytypes, we demonstrate the interplay of localized surface phonon polaritons with zone-folded weak phonon modes of the anisotropic crystal. Tuning the monopole mode in and out of the region where the zone-folded phonon is excited in 6H-SiC, we observe a prominent increase of the already monopole-enhanced SHG output when the two modes are coupled. Envisioning this interplay as one of the showcase features of mid-infrared nonlinear nanophononics, we discuss its prospects for the effective engineering of nonlinear-optical materials with desired properties in the infrared spectral range.Comment: 16 pages, 3 figure

Gas phase structures and charge localization in small aluminum oxide anions: Infrared photodissociation spectroscopy and electronic structure calculations

We use cryogenic ion trap vibrational spectroscopy in combination with quantum chemical calculations to study the structure of mono- and dialuminum oxide anions. The infrared photodissociation spectra of D2-tagged AlO1-4 − and Al2O3-6 − are measured in the region from 400 to 1200 cm−1. Structures are assigned based on a comparison to simulated harmonic and anharmonic IR spectra derived from electronic structure calculations. The monoaluminum anions contain an even number of electrons and exhibit an electronic closed-shell ground state. The Al2O3-6 − anions are oxygen-centered radicals. As a result of a delicate balance between localization and delocalization of the unpaired electron, only the BHLYP functional is able to qualitatively describe the observed IR spectra of all species with the exception of AlO3 −. Terminal Al–O stretching modes are found between 1140 and 960 cm−1. Superoxo and peroxo stretching modes are found at higher (1120-1010 cm−1) and lower energies (850-570 cm−1), respectively. Four modes in-between 910 and 530 cm−1 represent the IR fingerprint of the common structural motif of dialuminum oxide anions, an asymmetric four-member Al–(O)2–Al ring

Studying the Key Intermediate of RNA Autohydrolysis by Cryogenic Gas-Phase Infrared Spectroscopy

Over the course of the COVID-19 pandemic, mRNA-based vaccines have gained tremendous importance. The development and analysis of modified RNA molecules benefit from advanced mass spectrometry and require sufficient understanding of fragmentation processes. Analogous to the degradation of RNA in solution by autohydrolysis, backbone cleavage of RNA strands was equally observed in the gas phase; however, the fragmentation mechanism remained elusive. In this work, autohydrolysis-like intermediates were generated from isolated RNA dinucleotides in the gas phase and investigated using cryogenic infrared spectroscopy in helium nanodroplets. Data from both experiment and density functional theory provide evidence for the formation of a five-membered cyclic phosphate intermediate and rule out linear or six-membered structures. Furthermore, the experiments show that another prominent condensed-phase reaction of RNA nucleotides can be induced in the gas phase: the tautomerization of cytosine. Both observed reactions are therefore highly universal and intrinsic properties of the investigated molecules

Unravelling the structural complexity of glycolipids with cryogenic infrared spectroscopy

Glycolipids are complex glycoconjugates composed of a glycan headgroup and a lipid moiety. Their modular biosynthesis creates a vast amount of diverse and often isomeric structures, which fulfill highly specific biological functions. To date, no gold-standard analytical technique can provide a comprehensive structural elucidation of complex glycolipids, and insufficient tools for isomer distinction can lead to wrong assignments. Herein we use cryogenic gas-phase infrared spectroscopy to systematically investigate different kinds of isomerism in immunologically relevant glycolipids. We show that all structural features, including isomeric glycan headgroups, anomeric configurations and different lipid moieties, can be unambiguously resolved by diagnostic spectroscopic fingerprints in a narrow spectral range. The results allow for the characterization of isomeric glycolipid mixtures and biological applications

Resolving sphingolipid isomers using cryogenic infrared spectroscopy

1‐Deoxysphingolipids are a recently described class of sphingolipids that have been shown to be associated with several disease states including diabetic and hereditary neuropathy. The identification and characterization of 1‐deoxysphingolipids and their metabolites is therefore highly important. However, exact structure determination requires a combination of sophisticated analytical techniques due to the presence of various isomers, such as ketone/alkenol isomers, carbon–carbon double‐bond (C=C) isomers and hydroxylation regioisomers. Here we demonstrate that cryogenic gas‐phase infrared (IR) spectroscopy of ionized 1‐deoxysphingolipids enables the identification and differentiation of isomers by their unique spectroscopic fingerprints. In particular, C=C bond positions and stereochemical configurations can be distinguished by specific interactions between the charged amine and the double bond. The results demonstrate the power of gas‐phase IR spectroscopy to overcome the challenge of isomer resolution in conventional mass spectrometry and pave the way for deeper analysis of the lipidome

Die Berechnung der induzierten Ladung

One of the main aspects of statistical mechanics is that the properties of a thermodynamics state point do not depend on the choice of the statistical ensemble. It breaks down for small systems e.g. single molecules. Hence, the choice of the statistical ensemble is crucial for the interpretation of single molecule experiments, where the outcome of measurements depends on which variables or control parameters, are held fixed and which ones are allowed to fluctuate. Following this principle, this thesis investigates the thermodynamics of a single polymer pulling experiments within two different statistical ensembles. The scaling of the conjugate chain ensembles, the fixed end-to-end vector (Helmholtz) and the fixed applied force (Gibbs), are studied in depth. This thesis further investigates the ensemble equivalence for different force regimes and polymer-chain contour lengths. Using coarse-grained molecular dynamic simulations, i.e. Langevin dynamics, the simulations were found to complement the theoretical predictions for the scaling of ensemble difference of Gaussian chains in different force-regimes, giving special attention to the zero force regime. After constructing Helmholtz and Gibbs conjugate ensembles for a Gaussian chain, two different data sets of thermodynamic states on the force-extension plane, i.e. force-extension curves, were generated. The ensemble difference is computed for different polymer-chain lengths by using force-extension curves. The scaling of the ensemble difference versus relative polymer-chain length under different force regimes has been derived from the simulation data and compared to theoretical predictions. The results demonstrate that the Gaussian chain in the zero force limit generates nonequivalent ensembles, regardless of its equilibrium bond length and polymer-chain contour length. Moreover, if polymers are charged in confinement, coarse-graining is problematic, owing to dielectric interfaces. Hence, the effect of dielectric interfaces must be taken into account when describing physical systems such as ionic channels or biopolymers inside nanopores. It is shown that the effect of dielectrics is crucial for the dynamics of a biopolymer or an ion inside a nanopore. In the simulations, the feasibility of an efficient and accurate computation of electrostatic interactions in the presence of an arbitrarily shaped dielectric domain is challenging. Several solutions for this problem have been previously proposed in the literature such as a density functional approach, or transforming problem at hand into an algebraic problem ( Induced Charge Computation (ICC) ) and boundary element methods. Even though the essential concept is the same, which is to replace the dielectric interface with a polarization charge density, these approaches have been analyzed and the ICC algorithm has been implemented. A new superior boundary element method has been devised utilizing the force computation via the Particle-Particle Particle-Mesh (P3M) method for periodic geometries (ICCP3M). This method has been compared to the ICC algorithm, the algebraic solutions, and to density functional approaches. Extensive numerical tests against analytically tractable geometries have confirmed the correctness and applicability of developed and implemented algorithms, demonstrating that the ICCP3M is the fastest and the most versatile algorithm. Further optimization issues are also discussed in obtaining accurate induced charge densities. The potential of mean force (PMF) of DNA modelled on a coarsed-grain level inside a nanopore is investigated with and without the inclusion of dielectric effects. Despite the simplicity of the model, the dramatic effect of dielectric inclusions is clearly seen in the observed force profile.Eines der wichtigsten Ergebnisse der statistischen Mechanik ist, dass unterschiedliche statistische Ensembles dieselben thermodynamischen Zustände erzeugen. Dieses Prinzip gilt nicht notwendigerweise für kleine Systeme, wie zum Beispiel einzelne Moleküle oder ein einzelnes Polymer. Deshalb ist die Wahl des statistischen Ensembles von entscheidender Bedeutung für die Interpretation von Einzelmolekülexperimenten ( im Englischen "Single Molecule Experiment" (SME) ), denn das Ergebnis der Messung hängt davon ab, welche Variablen oder Kontrollparameter festgehalten werden und welche fluktuieren können. Ausgehend von diesem Problem haben wir Zugexperimente an einem einzigen Polymer in zwei verschiedenen Ensembles durchgeführt und den thermodynamischen Limes (Anzahl der Polymersegmente wächst gegen unendlich) untersucht. Wir haben zwei konjugierte Ensembles, nämlich das, in dem der End-zu-End Abstand (Helmholtz) festgehalten wurde, mit dem, wo wir die Kraft (Gibbs) festgehalten haben, gründlich und auf verschiedene Arten verglichen. Wir haben den Ensemble-Unterschied als Funktion der Anzahl der Polymersegmente in unterschiedlichen Zugkraftbereichen mittels Molekulardynamik Simulationen untersucht, wobei wir eine Langevin Dynamik benutzt haben. Die untersuchten Messgrössen waren die Bestimmung von sogenannten Kraft-Dehnungskurven, wie sie auch in AFM Experimenten gemessen werden. Diese Kurven wurden für zwei verschieden Gauss Ketten verschiedenster Polymerlänge durchgeführt, einmal mit verschwindender Bondlänge und einmal mit Bondlänge eins. Aufgrund unserer Simulationen konnten wir zeigen, das sowohl Gauss-Ketten mit endlicher, wie auch verschwindender Bondlänge für den Bereich verschwindender Zugkraft einen endlichen Ensembleunterschied besitzen, der nicht von der Kettenlänge abhängt. Dieses Phänomen wurde bereits vor 20 Jahren von R. Neumann beschrieben. Trotz der relativ einfachen Argumente von Neumann gibt es bis heute noch Arbeiten, die diesen Sachverhalt entweder anzweifeln oder verkehrt darstellen. Wir hoffen, durch diesen Teil der Arbeit den Sachverhalt zufriedenstellend aufgeklärt zu haben. Im zweiten Teil der Arbeit behandeln wir geladen Polymere unter einem räumlichen Einschluss. Dies können zum Beispiel Ionen in schmalen Kanälen sein (Ionenkanäle), oder DNA in Nanoporen. In vergröberten Simulationen werden geladene Polymere immer in einem dielektrischen Kontinuum dargestellt. Wasser hat eine relative dielektrische Konstante von 80 bei Raumtemperatur, die dann in dieses Model als Parameter gesteckt wird. Wenn feste Grenzflächen vorhanden sind, haben diese meist niedrige dielektrische Konstanten ($\approx 2$). Diese Grenzflächen haben grosse Auswirkungen auf die elektrostatischen Wechselwirkungen. In den Simulationen ist es wichtig, diese Effekte korrekt *und schnell* zu berechnen. Deshalb haben wir einen effizienten und präzisen Algorithmus entwickelt, der genau dies bewerkstelligt. In der Literatur wurden mehrere Möglichkeiten vorgeschlagen, wie dieses Problem für Simulationen lösbar sein sollte, wie zum Beispiel Dichtefunktionalmethoden, Umwandlung des Problems in ein algebraisches Problem (Induced Charge Computation, ICC) oder die Randelement Methode. Das wesentliche Konzept besteht darin, die Polarisationsladung auf dem dielektrischen Rand so zu bestimmen, dass die dielektrischen Randbedingungen erfüllt werden. Wir haben den ICCP3M Algorithmus entwickelt, dessen Kernstück darin besteht, den P3M Algorithmus zur Bestimmung der induzierten Ladung auf den Randelementen zu benutzen. Durch diesen Trick lässt sich die Ladungsberechnung in CPU Zeit $\mathscr{O}(Nlog N)$, wobei $\mathscr{O}(N)$ die Anzahl der Ladungen im System ist, durchführen. Wir haben den Algorithmus innerhalb des Espresso Programmpakets implementiert und optimiert. Im letzten Teil der Arbeit wurde das Potential der mittleren Kraft einer vergröberten DNA innerhalb einer Nanopore untersucht, wobei wir die Unterschiede zwischen korrekter Behandung der dielektrischen Ränder und der Ignorierung derselben quantifiziert haben. Trotz seiner Einfachheit zeigt unser Modell den dramatischen Einfluss, den die dielektrischen Ränder auf die gemessene efffektive Kraft und das Potential der mittleren Kraft ausüben

Gas phase vibrational spectroscopy of cold (TiO2)−n (n = 3–8) clusters

We report infrared photodissociation (IRPD) spectra for the D2-tagged titanium oxide cluster anions (TiO2)−n with n = 3–8 in the spectral region from 450 to 1200 cm−1. The IRPD spectra are interpreted with the aid of harmonic spectra from BP86/6-311+G* density functional theory calculations of energetically low-lying isomers. We conclusively assign the IRPD spectra of the n = 3 and n = 6 clusters to global minimum energy structures with Cs and C2 symmetry, respectively. The vibrational spectra of the n = 4 and n = 7 clusters can be attributed to contributions of at most two low-lying structures. While our calculations indicate that the n = 5 and n = 8 clusters have many more low-lying isomers than the other clusters, the dominant contributions to their spectra can be assigned to the lowest energy structures. Through comparison between the calculated and experimental spectra, we can draw conclusions about the size-dependent evolution of the properties of (TiO2)−n clusters, and on their potential utility as model systems for catalysis on a bulk TiO2 surface