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Institute
- Biochemie und Chemie (1978) (remove)
PELDOR (pulse electron-electron double resonance) is an established method to study intramolecular distances and can give evidence for conformational changes and flexibilities. However, it can also be used to study intermolecular interactions as for example oligerimization. Here, we used PELDOR to study the ‘end-to-end’ stacking of small double stranded (ds)RNAs. For this study, the dsRNA molecules were only singly labelled with the spin label TPA to avoid multi-spin effects and to measure only the intermolecular stacking interactions. It can be shown that small dsRNAs tend to assemble to rod-like structures due to π-π-interactions between the base pairs at the end of the strands. On the one hand, these interactions can influence or complicate measurements aimed at the determining of the structure and dynamics of the dsRNA molecule itself. On the other hand, it can be interesting to study such intermolecular stacking interactions in more detail, as for example their dependence on ion concentration. We quantitatively determined the stacking probability as a function of the monovalent NaCl salt and the dsRNA concentration. From this data the dissociation constant Kd was deduced and found to depend on the ratio between the NaCl salt and dsRNA concentrations. Additionally, the distances and distance distributions obtained predict a model for the stacking geometry of dsRNAs. Introducing a nucleotide overhangs at one end of the dsRNA molecule restricts the stacking to the other end, leading only to dimer formations. Introducing such an overhang at both ends of the dsRNA molecule fully suppresses stacking, as we could demonstrate by PELDOR experiments quantitatively.
Kraftfelder sind ein vielseitiges Werkzeug zur schnellen Berechnung vielfältiger Moleküleigenschaften. Die Qualität der damit erhaltenen Vorhersagen ist auch ein Maß, wie gut die wichtigen Einflussgrößen verstanden und vor allem in das Kraftfeld-Modell integriert sind. Bei der Parametrisierung müssen viele Effekte gegeneinander ausbalanciert werden, da die Kraftfeldterme nicht unabhängig voneinander betrachtet werden können. Umfangreiche Testrechnungen sind erforderlich, um die notwendige Qualität der Parameter sicher zu stellen. Eine Automatisierung dieses Prozesses bringt nicht nur eine enorme Zeitersparnis, sie zwingt auch zur sorgfältigen Definition von Vorgaben und Qualitätskriterien. Die Formulierung einer Strategie in einem Programm anstelle von „intelligentem Raten“ fördert zudem ein tieferes Verständnis. Bei einer Änderung der Strategie muss nur das entsprechende Programm geändert werden, dem Entwickler bleibt der manuelle Test erspart. Automatische Methoden zur Plausibilitätsprüfung vermeiden Probleme durch Fehler bei der Dateneingabe von Hand. Die programmgesteuerte Erstellung aussagekräftiger Protokolle und Grafiken macht die Fülle der bei der Parametrisierung und Evaluierung eines Kraftfeldes anfallenden Informationen für den Benutzer überschaubar. Probleme und deren Zusammenhang können so leichter erfasst werden. Für das MOMO-Kraftfeld konnten auf diese Weise verbesserte und neue Parameter für Wasserstoffbrücken abgeleitet werden, zwei empirische Punktladungsmodelle und deren Verträglichkeit mit zwei quantenchemischen Modellen verbessert und prinzipielle Probleme bei deren Vereinbarkeit erkannt werden sowie die automatische Parametrisierung von Bindungslängen, Bindungswinkeln und Torsionswinkeln ermöglicht werden. Bei Letzterem konnte jedoch keine Verbesserung gegenüber den Originalparametern erreicht werden, was nicht weiter verwunderlich ist, da diese seit Jahrzehnten entwickelt worden sind, wohingegen Wasserstoffbrücken und Partialladungen erst später hinzugekommen sind und nicht so umfangreich wie die bindenden Kraftfeldterme getestet wurden. Voraussetzung für die hier gewählte Vorgehensweise, alle Arbeiten weitgehend zu automatisieren und Strategien immer in Programme umzusetzen, waren sehr umfangreiche Programmierarbeiten. Ziel war es, auf einfache Weise die Steuerung des Kraftfeldes aus kleineren Programmen, die spezielle Probleme bearbeiten, zuzulassen. Durch die Nutzung zahlreicher Open-Source-Projekte, die gemeinsam die gewünschte Funktionalität zur Verfügung stellen, konnte der Aufwand auf die dazu passende Implementierung des MOMO-Kraftfeldes und das Verbinden mit der von diesen Projekten bereitgestellten Software beschränkt werden. Der Kern des MOMO-Kraftfeldes wurde aus Geschwindigkeitsgründen in der Compilersprache C geschrieben, Datenein- und -ausgabe und die Programme zur Parametrisierung und Auswertung wurden in Python geschrieben.
Seit einigen Jahrzehnten wollen Biochemiker, Mediziner, Biologen und Pharmazeuten weltweit nicht mehr auf eine bioanalytische Methode verzichten, an deren Entwicklung der Frankfurter Wissenschaftler Prof. Dr. Michael Karas vom Institut für Pharmazeutische Chemie der Goethe-Universität maßgeblich beteiligt war. Die Rede ist von der Matrix-unterstützten Laser-Desorptions- / Ionisations-Massenspektrometrie – kurz MALDI-MS.
"Ästhetisch ist, was hilft"
(2017)
The title compound, [Na(CF3O3S)(C12H24O6)], features a sodium cation that is coordinated by eight O atoms in an irregular hexagonal bipyramidal environment. The equatorial positions are occupied by the six O atoms of an 18-crown-6 ether ring. In the axial positions, there is one O atom of a trifluoromethanesulfonate anion and an ether O atom of a symmetry-equivalent crown ether ring. In this way, centrosymmetric dimers are formed.
The asymmetric unit of the title compound, [K(C3H3N2)(C12H24O6)], is composed of a potassium cation bonded to the six O atoms of a crown ether molecule and the two N atoms of a pyrazolate anion. The K...O distances range from 2.8416 (8) to 3.0025 (8) Å, and the two K...N distances are 2.7441 (11) and 2.7654 (11) Å. The K cation is displaced by 0.8437 (4) Å from the best plane through the six O atoms. The latter plane is almost perpendicular to the plane of the pyrazolate ring [dihedral angle 83.93 (3)°]. Key indicators: single-crystal X-ray study; T = 173 K; mean σ(C–C) = 0.002 A°; R factor = 0.026; wR factor = 0.066; data-to-parameter ratio = 16.5.
The title compound, C(19)H(14)ClNO(3)·0.2H(2)O, crystallizes with five mol-ecules and a disordered water mol-ecule in the asymmetric unit. Four of the five mol-ecules form hydrogen-bonded dimers via N-H⋯O hydrogen bonds towards another symmetry-independent mol-ecule, whereas the fifth mol-ecule forms a hydrogen-bonded dimer with its symmetry equivalent, also via N-H⋯O hydrogen bonds. The dihedral angle between the planes of the fused benzene ring and the five-membered ring to which it is attached is 79.45 (13), 49.00 (15), 72.49 (16), 81.91 (18) and 76.38 (16)° for the five mol-ecules in the asymmetric unit.