Computational spectroscopy of solvation phenomena in soft matter

Unter dem Überbegriff Spektroskopie versteht man Messungen der Interaktion zwischen Materie und elektromagnetischer Strahlung. In Abhängigkeit der Frequenz der einfallenden Strahlung treten dabei verschiedene Bestandteile der Materie auf charakteristische Weise mit ihr in Resonanz. Spektroskopische Methoden wie zum Beispiel dielektrische Spektroskopie, Terahertzspektroskopie oder der zeitabhängige Stokes-Shift messen verschiedene Aspekte der Kernbewegung von Molekülen. Insbesondere erlauben die genannten Methoden das Studium der gekoppelten Bewegung vieler Moleküle und ermöglichen so eine Beschreibung des Verhaltens von kondensierter Materie auf mesoskopischer Ebene. In dieser Arbeit liegt der Fokus auf dem Studium von sogenannter Weicher Materie. Darunter versteht man kondensierte Materie, die schon bei Raumtemperatur vielfältige dynamische Prozesse auf mikro- und mesoskopischer Ebene aufweist, welche man mittels der oben genannten spektroskopischen Methoden messen kann. Bei der Interpretation spektroskopischer Resultate stellen Computersimulationen der molekularen Dynamik solcher Systeme eine wertvolle Ergänzung zum Experiment dar. Im Experiment betrachtet man stets nur einen Ausschnitt der gesamten vorhandenen Dynamik, während man in Computersimulationen eine große Vielfalt molekularer Dynamik greifbar machen kann. Computergestützte Spektroskopie stellt die Kombination von Beidem dar, indem man spektroskopische Messgrößen aus der simulierten Moleküldynamik berechnet. Dies erlaubt den direkten Vergleich von aus der Simulationen berechneten Spektren mit experimentellen Resultaten und somit auch eine Validierung der Simulation. Die Simulation kann darüber hinaus verwendet werden, um die spektroskopisch gemessene Dynamik im größeren Kontext der gesamten molekularen Dynamik zu betrachten. Außerdem kann das gemessene Signal mit Hilfe der Simulation zerlegt werden in verschiedene Komponenten des Systems, was eine direkte und tiefgreifende Analyse des Messergebnisses erlaubt. Die vorliegende Arbeit besteht aus drei Teilen. Im ersten Teil liegt der Fokus auf den dielektrischen Eigenschaften Reverser Mizellen. Darunter versteht man von einem hydrophoben Medium und Detergens umschlossenene Wassertröpfchen in der Größe von Nanometern, welche als Modellsysteme für subzelluläre membranumschlossene Strukturen dienen. Es wird die gesamte mit klassischen Simulation beschreibbare Dynamik des kollektiven Dipolmoments beschrieben und in dielektrische Spektren sowie in Terahertzspektren umgerechnet. Dabei werden reverse Mizellen mit unterschiedlichem Wassergehalt betrachtet. Weiters wird untersucht, wie die Inklusion des Proteins Ubiquitin die dielektrischen Eigenschaften verändert. Im zweiten Teil der Arbeit wird zunächst die Verbindung zwischen dielektrischen Spektren und dem zeitabängigen Stokes-Shift in ionischen Flüssigkeiten untersucht. Darauf folgt eine detaillierte Studie zu den molekularen Ursprüngen des zeitabhängigen Stokes-Shift in ionischen Flüssigkeiten durch umfangreiche Nichtgleichgewichtssimulationen unter Zuhilfenahme eines vereinfachten coarse-grained Modells. Im dritten Teil dieser Dissertation werden zwei methodische Studien präsentiert, die den Einfluss von Polarisierbarkeit auf Struktur und Dynamik ionischer Flüssigkeiten untersuchen. Dabei werden verschiedene Methoden einander direkt gegenüber gestellt.The umbrella term spectroscopy encompasses various kinds of measurements of the interaction between matter and electromagnetic waves. Depending on the latter’s frequency, different constituents of physical matter will resonate with the incoming radiation. Spectroscopic methods such as dielectric spektroscopy, terahertz spectroscopy and the time-dependent Stokes shift measure different aspects of nuclear motion. In particular, these methods allow for a description of the coupled motion of many molecules and thus can characterize the behaviour of matter on a mesoscopic level. In this present work the focus lies on the study of so-called Soft Matter, i.e. condensed matter, that already at room temperature exhibits manifold dynamical processes on a microscopic as well as on a mesoscopic level, which are typically described using the abovementioned spectroscopic techniques. In the interpretation of experimental spectroscopic results computer simulations of molecular dynamics are a valuable additional source of information. While experiments can always show only a part of a system’s dynamical capacity, computer simulation can make tangible directly the diversity of molecular dynamics. Computational spectroscopy represents the combination of both, as one calculates spectroscopic observables directly from computer simulations of molecular dynamics. This allows for a direct comparison of computational results to experimental data, which also provides a source of validation for the models used in the simulation. Furthermore, computer simulation can be used to study the origin of the experimentally measured signal in the greater context of the whole dynamics of the system. Additionally, the total signal can often be decomposed into contributions from various components of a system, which allows for an immediate and profound analysis of experimental results. This work consists of three parts. The first part has its focus on the dielectric properties of reverse micelles. These are nano-scale water droplets surrounded by a detergent and a hydrophobic medium, which can be seen as a model system for sub-cellular membrane-enclosed structures. The whole dynamical range of the collective dipole moment is characterized within the boundaries of classical simulations and transformed into dielectric spectra and terahertz absorption spectra. Reverse micelles with different amounts of water loading are compared. Additionally, the influence of the inclusion of a strongly dipolar biomolecule is studied using the example of the protein ubiquitin. The second part of this work starts out with a study of the connection between dielectric spectra and the time-dependent Stokes shift in ionic liquids. This is followed by a detailed study concerning the molecular origins of the time-dependent Stokes shift in ionic liquids via comprehensive non-equilibrium simulations employing coarse-grained modelling. In the third and last part of this thesis two methodical studies concerning the use of charge polarizability in molecular dynamics simulations of ionic liquids are presented. Two techniques, induced point-dipoles and Drude oscillators, are directly compared in their consequences on structural and dynamical properties. Additionally, the influence of different so-called Thole functions is thoroughly investigated

Revival of the Intermolecular Nuclear Overhauser Effect for Mapping Local Protein Hydration Dynamics

The highly heterogeneous hydration dynamics of protein–water interfaces is considered important for protein stability and dynamics, protein folding, enzymatic activity, and even drug design. The nuclear Overhauser effect (NOE) between protein and water protons is the only experimental observable which, in principle, can provide a map of locally resolved hydration dynamics. However, its utility was questioned in various theoretical studies that emphasized the contributions of long-range NOE interactions. We show by a detailed analysis based on molecular dynamics simulations that, contrary to recent claims, the protein–water NOE is an excellent observable to map local hydration dynamics at the protein surface

Changes in the real structure and magnetoresistance of Co90Fe10/Cu and Co90Fe10/Cu85Ag10Au5 multilayers after annealing

Annealing of the (1.1 nm Co90Fe10/2.2 nm Cu)×20 and (1.1 nm Co90Fe10/2.2 nm Cu85Ag10Au5)×20 multilayers at 235 °C improved their magnetoresistance as compared to the virgin samples. Annealing at higher temperatures resulted in degradation of the magnetoresistance effect. This observation raised the motivation of a detailed structural study using small-angle X-ray scattering, wide-angle X-ray diffraction, electron diffraction and transmission electron microscopy with the aim to link the structural changes in the system to the changes in the magnetoresistance. The structure studies have shown that the maximum of the magnetoresistance observed after annealing at 235 °C is related to the separation of Co90Fe10 and Cu, which are partly intermixed at interfaces after the deposition process. The decay of the GMR effect at higher annealing temperatures is caused by an increase of the interface roughness, which led in the Co90Fe10/Cu multilayers to occurrence of non-continuous interfaces and to short-circuiting of magnetic layers. In the Cu85Ag10Au5 multilayers, the combination of small-angle X-ray scattering and wide-angle X-ray diffraction has shown that Cu85Ag10Au5 did not form an alloy with the nominal composition: Only a part of Au and Ag was dissolved in the copper structure; the remainder of Ag and Au formed precipitates

ForConX: A forcefield conversion tool based on XML

International audienceThe force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the force field conversion on the basis of an XML document. The force field is converted to and from this XML structure facilitating the implementation of new MD programs for the conversion. Furthermore, the XML structure is human readable and can be manipulated before continuing the conversion. We report, as testcases, the conversions of topologies for acetonitrile, dimethylformamide, and 1-ethyl-3-methylimidazolium trifluoromethanesulfonate comprising also Urey–Bradley and Ryckaert–Bellemans potentials