@article{RewitzKeitzlTuchschereretal.2012,
  author    = {Rewitz, Christian and Keitzl, Thomas and Tuchscherer, Philip and Goetz, Sebastian and Geisler, Peter and Razinskas, Gary and Hecht, Bert and Brixner, Tobias},
  title     = {Spectral-interference microscopy for characterization of functional plasmonic elements},
  series = {Optics Express},
  journal   = {Optics Express},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-85922},
  year      = {2012},
  abstract  = {Plasmonic modes supported by noble-metal nanostructures offer strong subwavelength electric-field confinement and promise the realization of nanometer-scale integrated optical circuits with well-defined functionality. In order to measure the spectral and spatial response functions of such plasmonic elements, we combine a confocal microscope setup with spectral interferometry detection. The setup, data acquisition, and data evaluation are discussed in detail by means of exemplary experiments involving propagating plasmons transmitted through silver nanowires. By considering and experimentally calibrating any setup-inherent signal delay with an accuracy of 1 fs, we are able to extract correct timing information of propagating plasmons. The method can be applied, e.g., to determine the dispersion and group velocity of propagating plasmons in nanostructures, and can be extended towards the investigation of nonlinear phenomena.},
  language  = {en}
}
@article{ReuschHolzmeierGerlachetal.2019,
  author    = {Reusch, Engelbert and Holzmeier, Fabian and Gerlach, Marius and Fischer, Ingo and Hemberger, Patrick},
  title     = {Decomposition of Picolyl Radicals at High Temperature: A Mass Selective Threshold Photoelectron Spectroscopy Study},
  series = {Chemistry - A European Journal},
  volume    = {25},
  journal   = {Chemistry - A European Journal},
  number    = {72},
  doi       = {10.1002/chem.201903937},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-208132},
  pages     = {16652-16659},
  year      = {2019},
  abstract  = {The reaction products of the picolyl radicals at high temperature were characterized by mass-selective threshold photoelectron spectroscopy in the gas phase. Aminomethylpyridines were pyrolyzed to initially produce picolyl radicals (m /z =92). At higher temperatures further thermal reaction products are generated in the pyrolysis reactor. All compounds were identified by mass-selected threshold photoelectron spectroscopy and several hitherto unexplored reactive molecules were characterized. The mechanism for several dissociation pathways was outlined in computations. The spectrum of m /z =91, resulting from hydrogen loss of picolyl, shows four isomers, two ethynyl pyrroles with adiabatic ionization energies (IE\(_{ad}\)) of 7.99 eV (2-ethynyl-1H -pyrrole) and 8.12 eV (3-ethynyl-1H -pyrrole), and two cyclopentadiene carbonitriles with IE′s of 9.14 eV (cyclopenta-1,3-diene-1-carbonitrile) and 9.25 eV (cyclopenta-1,4-diene-1-carbonitrile). A second consecutive hydrogen loss forms the cyanocyclopentadienyl radical with IE′s of 9.07 eV (T\(_0\)) and 9.21 eV (S\(_1\)). This compound dissociates further to acetylene and the cyanopropynyl radical (IE=9.35 eV). Furthermore, the cyclopentadienyl radical, penta-1,3-diyne, cyclopentadiene and propargyl were identified in the spectra. Computations indicate that dissociation of picolyl proceeds initially via a resonance-stabilized seven-membered ring.},
  language  = {en}
}
@article{RestPhilipsDuennebackeetal.2020,
  author    = {Rest, Christina and Philips, Divya Susan and D{\"u}nnebacke, Torsten and Sutar, Papri and Sampedro, Angel and Droste, J{\"o}rn and Stepanenko, Vladimir and Hansen, Michael Ryan and Albuquerque, Rodrigo Q. and Fern{\´a}ndez, Gustavo},
  title     = {Tuning Aqueous Supramolecular Polymerization by an Acid-Responsive Conformational Switch},
  series = {Chemistry - A European Journal},
  volume    = {26},
  journal   = {Chemistry - A European Journal},
  number    = {44},
  doi       = {10.1002/chem.202001566},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-218118},
  pages     = {10005 -- 10013},
  year      = {2020},
  abstract  = {Besides their widespread use in coordination chemistry, 2,2'-bipyridines are known for their ability to undergo cis-trans conformational changes in response to metal ions and acids, which has been primarily investigated at the molecular level. However, the exploitation of such conformational switching in self-assembly has remained unexplored. In this work, the use of 2,2'-bipyridines as acid-responsive conformational switches to tune supramolecular polymerization processes has been demonstrated. To achieve this goal, we have designed a bipyridine-based linear bolaamphiphile, 1, that forms ordered supramolecular polymers in aqueous media through cooperative aromatic and hydrophobic interactions. Interestingly, addition of acid (TFA) induces the monoprotonation of the 2,2'-bipyridine moiety, leading to a switch in the molecular conformation from a linear (trans) to a V-shaped (cis) state. This increase in molecular distortion along with electrostatic repulsions of the positively charged bipyridine-H\(^{+}\) units attenuate the aggregation tendency and induce a transformation from long fibers to shorter thinner fibers. Our findings may contribute to opening up new directions in molecular switches and stimuli-responsive supramolecular materials.},
  language  = {en}
}
@article{RangFantuzziArrowsmithetal.2021,
  author    = {Rang, Maximilian and Fantuzzi, Felipe and Arrowsmith, Merle and Krummenacher, Ivo and Beck, Eva and Witte, Robert and Matler, Alexander and Rempel, Anna and Bischof, Tobias and Radacki, Krzysztof and Engels, Bernd and Braunschweig, Holger},
  title     = {Reduktion und Umlagerung eines Bor(I)-Carbonylkomplexes},
  series = {Angewandte Chemie},
  volume    = {133},
  journal   = {Angewandte Chemie},
  number    = {6},
  doi       = {10.1002/ange.202014167},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-224409},
  pages     = {3000 -- 3005},
  year      = {2021},
  abstract  = {Bei der Einelektronenreduktion eines durch eine cyclisches (Alkyl)(amino)carben (CAAC) stabilisierten Arylborylen-Carbonylkomplexes erfolgt die Bildung eines dimeren Borylketyl-Radikalanions, bedingt durch eine intramolekulare Arylmigration zum CO Kohlenstoffatom. Computergest{\"u}tzte Analyse liefert Hinweise auf eine radikalanionische [(CAAC)B(CO)Ar]\(^{.-}\) Zwischenstufe. Weiterf{\"u}hrende Reduktion des entstandenen Komplexes liefert ein hoch nukleophiles (Boranyliden)methanolat.},
  language  = {de}
}
@phdthesis{Quast2012,
  author    = {Quast, Tatjana},
  title     = {Spectroscopic investigation of charge-transfer processes and polarisation pulse shaping in the visible spectral range},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-74265},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2012},
  abstract  = {The first part deals with the spectroscopic investigation of ultrafast light-induced charge-transfer processes in different molecular compounds. In the second part, the question of the generation and characterisation of broadband visible polarisation-shaped laser pulses is treated.},
  subject      = {Polarisiertes Licht},
  language  = {en}
}
@article{PreitschopfSturmStroganovaetal.2023,
  author    = {Preitschopf, Tobias and Sturm, Floriane and Stroganova, Iuliia and Lemmens, Alexander K. and Rijs, Anouk M. and Fischer, Ingo},
  title     = {IR/UV Double Resonance Study of the 2-Phenylallyl Radical and its Pyrolysis Products},
  series = {Chemistry - A European Journal},
  volume    = {29},
  journal   = {Chemistry - A European Journal},
  number    = {13},
  doi       = {10.1002/chem.202202943},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-312338},
  year      = {2023},
  abstract  = {Isolated 2-phenylallyl radicals (2-PA), generated by pyrolysis from a nitrite precursor, have been investigated by IR/UV ion dip spectroscopy using free electron laser radiation. 2-PA is a resonance-stabilized radical that is considered to be involved in the formation of polycyclic aromatic hydrocarbons (PAH) in combustion, but also in interstellar space. The radical is identified based on its gas-phase IR spectrum. Furthermore, a number of bimolecular reaction products are identified, showing that the self-reaction as well as reactions with unimolecular decomposition products of 2-PA form several PAH efficiently. Possible mechanisms are discussed and the chemistry of 2-PA is compared with the one of the related 2-methylallyl and phenylpropargyl radicals.},
  language  = {en}
}
@phdthesis{Pfister2011,
  author    = {Pfister, Johannes},
  title     = {On the correlation between the electronic structure and transport properties of [2.2]paracyclophanes and other aromatic systems},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-65362},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2011},
  abstract  = {Die vorliegende Arbeit pr{\"a}sentiert theoretische Untersuchungen zu Energie- und Ladungs-Transporteigenschaften in organischen Kristallen. Kapitel 4 behandelt Exzitonentransport in Anthracen bei dem der Fall einer schwachen Kopplung zwischen den π-Systemen vorliegt. Die elektronische Kopplung wird mit dem „monomer transition density" (MTD) Ansatz berechnet. Aus den Kopplungen und Reorganisationsenergien werden mit der Marcus-Theorie H{\"u}pfraten berechnet. Mit Kenntnis der Kristallstrukturen werden daraus in die experimentell zug{\"a}nglichen Exzitonendiffusionsl{\"a}ngen berechnet, deren isotroper Anteil im Rahmen der Streuung der experimentell zug{\"a}nglichen Daten reproduziert werden. Auch die Anisotropie der Exzitonendiffusionsl{\"a}ngen wird qualitativ und quantitativ im Rahmen der zu erwartenden Messgenauigkeit richtig wiedergegeben. Weiterhin enth{\"a}lt Kapitel 4 Untersuchungen zum Elektronen- und Lochtransport in den zwei verschiedenen Modifikationen (α und β) von Perylen. Reorganisationsenergien sowie Diffusionskonstanten wurden f{\"u}r beide beide Kristallstrukturen und Typen des Ladungstransports berechnet. Den besten Transport stellt dabei Lochtransport in β-Perylen dar, jedoch ist dieser stark isotrop. Die bevorzugte Transportrichtung is entlang der b-Achse der Einheitszelle mit elektronischen Kopplungen von gr{\"o}ßer als 100 meV. Allerdings gibt es hier keinerlei Lochtransport in Richtung der c-Achse. Die Diffusionskonstante in Richtung der b-Achse ist um zwei Gr{\"o}ßenordnungen gr{\"o}ßer als die in c-Richtung (62.7•10-6 m2/s vs. 0.4•10-6 m2/s). Der Ladungstransport wird sowohl f{\"u}r L{\"o}cher, als auch f{\"u}r Elektronen in beiden Perylenmodifikationen immer stark anisotrop berechnet. Um diese Resultate zu verifizieren wurden experimentelle Elektronenmobilit{\"a}ten in α-Perylen mit den Simulationen verglichen. Es stellte sich eine sehr gute {\"U}bereinstimmung heraus mit Fehlern von nur maximal 27\%. Wie oben gezeigt, ist es m{\"o}glich Transporteigenschaften in zwischen schwach wechselwirkenden Systemen zu berechnen und zu messen. Allerdings ist es hier schwierig, die G{\"u}te der zu Grunde liegenden Kopplungsparameter genau anzugeben. Aus diesem Gunde wurde eine Zusammenarbeit {\"u}ber stark wechselwirkede Systeme zwischen uns sowie den Arbeitskreis von Prof. Ingo Fischer begonnen. Dort wurden [2.2]Paracyclophane und dessen Derivate untersucht um zu zeigen, wie Substitution mit Hydroxylgruppen deren Absorptionseigenschaften beeinflusst. Eine Kombination der SCS-MP2 und SCS-CC2-Methoden liefert hierbei insgesamt die besten Ergebnisse um die geometrischen und elektronischen Strukturen f{\"u}r Grund- und angeregte Zust{\"a}nde dieser Modellsysteme sowie deren Stammmolek{\"u}len Benzol und Phenol zu beschreiben. Strukturell weist nur [2.2]Paracyclophan im Grundzustand ein Doppelminimumspotenzial bzgl. Verschiebung und Verdrillung der Benzol/Phenol-einheiten untereinander auf. Alle anderen Systeme sind aufgrund ihrer Substitution weniger flexibel. Fast alle untersuchten [2.2]Paracyclophane zeigen nur geringe Struktur{\"a}nderungen bei der Anregung in den S1 Zustand: Der Abstand zwischen den Ringen wird k{\"u}rzer, aber qualitativ behalten sie ihre Verdrillung und Verschiebung bei, wenn auch das Ausmaß dieser Verzerrungen reduziert wird. Die Ausnahme hierbei ist p-DHPC, welches von einer verschoben Struktur im Grundzustand in eine verdrillte Struktur im angeregten Zustand {\"u}bergeht. Dies hat zur Konsequenz, dass die Intensit{\"a}t des 0-0-{\"U}bergangs aufgrund der Franck-Condon Faktoren f{\"u}r p-DHPC experimentell nicht mehr beobachtet werden kann und von Verunreinigungen durch o-DHPC {\"u}berdeckt wird. Die Strukturen der Paracyclophane und deren {\"A}nderung durch elektronische {\"U}berg{\"a}nge werden in dieser Arbeit durch elektrostatische Potenziale sowie den antibindenen (bindenden) HOMO (LUMO) Orbitalen erkl{\"a}rt. Adiabatische Anregungsenergien wurden mit Nullpunktsschwingungsenergien korrigiert und liefern Genauigkeiten deren Fehler weniger als 0,1 eV betr{\"a}gt. Hierbei ist zu beachten, dass eine Korrektur auf B3LYP Niveau die Ergebnisse verschlechtert und man die Berechnung der Schwingungsfrequenzen auf SCS-CC2 durchf{\"u}hren muss um diese Genauigkeit zu erhalten. Aufgrund dieser Rechnungen wurde eine Interpretation der experimentellen [1+1]REMPI Spektren m{\"o}glich. Bandenprogressionen f{\"u}r die Schwingungen der Verschiebung, der Verdrillung und einer Atmung im [2.2]Paracyclophanskelett wurden identifiziert und zeigen gute {\"U}bereinstimmung zum Experiment. Diese Arbeiten zeigen, dass das Substitutionsschema von [2.2]Paracyclophanen eine erhebliche Auswirkung auf die spektroskopischen Eigenschaften haben kann. Da diese Eigenschaften direkt mit den Transporteigenschaften dieser Materialien verbunden ist, kann das hier gewonnene Verst{\"a}ndnis der spektroskopischen Eigenschaften genutzt werden, um Materialien mit maßgeschneiderten Transporteigenschaften zu designen. Es konnte gezeigt werden, dass die SCS-CC2-Methode sehr gut geeignet ist, die zu Grunde liegende Wechselwirkung zwischen den π-Systemen vorherzusagen.},
  subject      = {Ladungstransport},
  language  = {en}
}
@phdthesis{Petry2002,
  author    = {Petry, Renate},
  title     = {Spektroskopische Strukturanalytik synthetischer Polypeptide},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-664},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2002},
  abstract  = {In der vorliegenden Arbeit wurden zwei spektroskopische Methoden (Raman- und Circulardichroismus-Spektroskopie) und die Kernspinresonanz zur Untersuchung der Sekund{\"a}rstruktur von synthetischen Polypeptiden eingesetzt. Dabei wurden die Struktur-Funktions-Beziehungen der dritten extrazellul{\"a}ren Schleife des Gonadotropin-freisetzenden Rezeptors (GnRH-R) untersucht. Die spektroskopischen Ergebnisse belegten, dass die zuvor getroffene Aussage {\"u}ber eine vorhandene helikale Struktur revidiert werden musste. Die Strukturanalysen mit Hilfe der CD-, Raman- und 2D NMR-Experimente an zwei Serien von Polypeptiden lieferten Aussagen {\"u}ber die Sekund{\"a}rstruktur. Insbesondere die Raman-Untersuchungen in Verbindung mit einer statistischen Datenanalyse lieferten detaillierte Information {\"u}ber subtile Konformations{\"a}nderungen, die einerseits durch die Addition und andererseits durch die Substitution einzelner Aminos{\"a}uren in den synthetischen Polypeptiden ausgel{\"o}st wurden. Anhand der ausgew{\"a}hlten Raman-Linien konnte nachgewiesen werden, dass sowohl die {\"A}nderungen der Polypeptidkettenl{\"a}nge als auch die {\"A}nderung der Polypeptidsequenzen mit den beobachteten Intensit{\"a}ten der Raman-Linien korreliert sind.},
  subject      = {Synthetische Polypeptide},
  language  = {de}
}
@phdthesis{Peica2006,
  author    = {Peica, Niculina},
  title     = {Vibrational spectroscopy and density functional theory calculations on biological molecules},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-20913},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2006},
  abstract  = {Infrared (IR) and Raman spectroscopy are among the most widely used techniques in the physical and natural sciences today. Vibrational spectroscopy, including IR and Raman spectroscopy, has both a long and interesting history and an illustrious record of contributions to science. Spectroscopy in the pharmaceutical industry is dominated by techniques such as nuclear magnetic resonance (NMR) and mass spectrometry (MS) for the elucidation of chemical structures. Despite this, the versatility of infrared spectroscopy ensures it still remains a key technique in quality control laboratories, and in applications where solid form characterization or minimal sample preparation is a necessity. Raman spectroscopy has many uses in the pharmaceutical and chemical industry, but its strengths is in solid form analysis. It is regularly used to identify compounds, and results are used in the release of pharmaceutical and chemical products. This work consists of 8 chapters, which cover the vibrational spectroscopy beginning with the theory and instrumentation, continuing with the experimental setup and probes description, and completing with results and discussions of the experiments. The first chapter of this work introduces Raman spectroscopy as a dominant technique used in pharmaceutical and chemical industry. The theoretical background regarding vibrational spectroscopy (IR and Raman) is accounted for in the second chapter of this work, while the samples presentation, the experimental procedures, and the description of the apparatus together with the computational details are briefly specified in the third chapter. The fourth chapter investigates the concentration dependent wavenumber shifts and linewidth changes of tetrahydrofuran in a binary system. Many of the applications in food science rely heavily on Raman spectroscopy, often preceding the biomedical applications. The characterization and identification of food additives using Raman, surface-enhanced Raman spectroscopy, and theoretical calculations is in detail depicted in the fifth chapter, whereas in the sixth and seventh chapters the monitoring of several medicines and various lanthanide complexes with anticancer properties, respectively, employing IR and Raman techniques are treated. These last two chapters address applications of vibrational spectroscopy to pharmaceutical products, and include the use of vibrational spectroscopy in combinatorial chemistry and density functional theory, a modality increasingly used by the pharmaceutical industry for the discovery if new pharmacologically active substances.},
  subject      = {Schwingungsspektroskopie},
  language  = {en}
}
@phdthesis{Pavel2003,
  author    = {Pavel, Ioana-Emilia},
  title     = {Vibrational spectroscopy and density functional theory calculations, a powerful approach for the characterization of pharmaceuticals and new organometallic complexes},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-7186},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2003},
  abstract  = {In the current work, several well-known pharmaceuticals (1,4-dihydrazinophthalazine sulfate, caffeine, and papaverine hydrochloride) and new organometallic compounds (nickel(II) cupferronato complexes NiL2An, L = PhN2O2-, n = 1, A = o-phenanthroline (1), o,o'-bipyridine (2) and n = 2, A = H2O (3), o-NH2Py (4), o-C6H4(NH2)2 (5); silylene-bridged dinuclear iron complexes [Cp(OC)2Fe]2SiX2 (X = H (6), F (7), Cl (8), Br (9), I (10)); 3-silaoxetane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-oxa-3-silacyclobutane (11) and 3-silathietane 3,3-dimethyl-2,2,4,4-tetraphenyl-1-sila-3-thiacyclobutane (12) compounds), which have successfully been characterized by using vibrational spectroscopy in conjunction with accurate density functional theory (DFT) calculations, are presented. The DFT computed molecular geometries of the species of interest reproduced the crystal structure data very well and in conjunction with IR and Raman measurements helped us to clarify the structures of the compounds, for which no experimental data were available; and this, especially for the new organometallic compounds, where the X-Ray analysis was limited by the non-availability of single crystals (3, 5, 10). Furthermore, a natural population analysis (NPA) and natural bond orbital (NBO) calculations together with a detailed analysis of the IR and Raman experimental as well as calculated spectra of the new organometallic compounds, allowed us to study some special bonding situations (1-12) or to monitor the structural changes observed with the change in temperature during the Raman experiments (11, 12). By combining these two methods (DFT and vibrational spectroscopy), the auspicious results obtained on the organometallic compounds 6-12 and overall in literature, made us confident of the power of theoretical calculations in aiding the interpretation of rich SERS spectra by solving some interesting issues. Consequently, the Raman and SERS spectra of well-known pharmaceuticals (1,4-dihydrazinophthalazine sulfate, caffeine, and papaverine hydrochloride) or new potentially biological active organometallic complexes (1-5), that were synthetized by our coworkers, were discussed with the assistance of the accurate results obtained from DFT calculations (structural parameters, harmonic vibrational wavenumbers, Raman scattering activities), and many previous incomplete assignments have been analyzed and improved. This allowed us to establish the vibrational behavior of these biological compounds near a biological artificial model at different pH values or concentrations (Ag substrate), taking into account that information about the species present under particular conditions could be of great importance for the interpretation of biochemical processes. The total electron density of molecules and the partial charges situated on selected atoms, which were determined theoretically by NPA, allowed us to establish the probability of different atoms acting as an adsorptive site for the metal surface. Moreover, a closer examination of the calculated orbitals of molecules brought further arguments on the presence or absence of the photoproducts at the Ag surface during the irradiation (1,4-dihydrazinophthalazine sulfate). Overall, the results provide a benchmark illustration of the virtues of DFT in aiding the interpretation of rich vibrational spectra attainable for larger polyatomic adsorbates by using SERS, as well as in furnishing detailed insight into the relation between the vibrational properties and the nature of the Ag substrate-adsorbate bonding. Therefore, we strongly believe that theoretical calculations will become a matter of rapidly growing scientific and practical interest in SERS.},
  subject      = {Arzneimittel},
  language  = {en}
}
@phdthesis{Paasche2013,
  author    = {Paasche, Alexander},
  title     = {Mechanistic Insights into SARS Coronavirus Main Protease by Computational Chemistry Methods},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-79029},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {The SARS virus is the etiological agent of the severe acute respiratory syndrome, a deadly disease that caused more than 700 causalities in 2003. One of its viral proteins, the SARS coronavirus main protease, is considered as a potential drug target and represents an important model system for other coronaviruses. Despite extensive knowledge about this enzyme, it still lacks an effective anti-viral drug. Furthermore, it possesses some unusual features related to its active-site region. This work gives atomistic insights into the SARS coronavirus main protease and tries to reveal mechanistic aspects that control catalysis and inhibition. Thereby, it applies state-of-the-art computational methods to develop models for this enzyme that are capable to reproduce and interpreting the experimental observations. The theoretical investigations are elaborated over four main fields that assess the accuracy of the used methods, and employ them to understand the function of the active-site region, the inhibition mechanism, and the ligand binding. The testing of different quantum chemical methods reveals that their performance depends partly on the employed model. This can be a gas phase description, a continuum solvent model, or a hybrid QM/MM approach. The latter represents the preferred method for the atomistic modeling of biochemical reactions. A benchmarking uncovers some serious problems for semi-empirical methods when applied in proton transfer reactions. To understand substrate cleavage and inhibition of SARS coronavirus main protease, proton transfer reactions between the Cys/His catalytic dyad are calculated. Results show that the switching between neutral and zwitterionic state plays a central role for both mechanisms. It is demonstrated that this electrostatic trigger is remarkably influenced by substrate binding. Whereas the occupation of the active-site by the substrate leads to a fostered zwitterion formation, the inhibitor binding does not mimic this effect for the employed example. The underlying reason is related to the coverage of the active-site by the ligand, which gives new implications for rational improvements of inhibitors. More detailed insights into reversible and irreversible inhibition are derived from in silico screenings for the class of Michael acceptors that follow a conjugated addition reaction. From the comparison of several substitution patterns it becomes obvious that different inhibitor warheads follow different mechanisms. Nevertheless, the initial formation of a zwitterionic catalytic dyad is found as a common precondition for all inhibition reactions. Finally, non-covalent inhibitor binding is investigated for the case of SARS coranavirus main protease in complex with the inhibitor TS174. A novel workflow is developed that includes an interplay between theory and experiment in terms of molecular dynamic simulation, tabu search, and X-ray structure refinement. The results show that inhibitor binding is possible for multiple poses and stereoisomers of TS174.},
  subject      = {SARS},
  language  = {en}
}
@article{OjhaForsterKumaretal.2013,
  author    = {Ojha, Animesh K. and Forster, Stefan and Kumar, Sumeet and Vats, Siddharth and Negi, Sangeeta and Fischer, Ingo},
  title     = {Synthesis of well-dispersed silver nanorods of different aspect ratios and their antimicrobial properties against gram positive and negative bacterial strains},
  series = {Journal of Nanobiotechnology},
  volume    = {11},
  journal   = {Journal of Nanobiotechnology},
  number    = {42},
  doi       = {10.1186/1477-3155-11-42},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-132222},
  year      = {2013},
  abstract  = {In the present contribution, we describe the synthesis of highly dispersed silver nanorods (NRs) of different aspect ratios using a chemical route. The shape and size of the synthesized NRs were characterized by Transmission Electron Microscopy (TEM) and UV-visible spectroscopy. Longitudinal and transverse absorptions bands confirm the rod type structure. The experimentally recorded UV-visible spectra of NRs solutions were fitted by using an expression of the extinction coefficient for rod like nano structures under the dipole approximation. Simulated and experimentally observed UV-visible spectra were compared to determine the aspect ratios (R) of NRs. The average values of R for NR1, NR2 and NR3 solutions are estimated to be 3.0 ± 0.1, 1.8 ± 0.1 and 1.2 ± 0.1, respectively. These values are in good agreement with those obtained by TEM micrographs. The silver NRs of known aspect ratios are used to study antimicrobial activities against B. subtilis (gram positive) and E. coli (gram negative) microbes. We observed that the NRs of intermediate aspect ratio (R = 1.8) have greater antimicrobial effect against both, B. subtilis (gram positive) and E. coli (gram negative). The NRs of aspect ratio, R = 3.0 has better antimicrobial activities against gram positive than on the gram negative.},
  language  = {en}
}
@article{MuellerMetaMeidneretal.2023,
  author    = {M{\"u}ller, Patrick and Meta, Mergim and Meidner, Jan Laurenz and Schwickert, Marvin and Meyr, Jessica and Schwickert, Kevin and Kersten, Christian and Zimmer, Collin and Hammerschmidt, Stefan Josef and Frey, Ariane and Lahu, Albin and de la Hoz-Rodr{\´i}guez, Sergio and Agost-Beltr{\´a}n, Laura and Rodr{\´i}guez, Santiago and Diemer, Kira and Neumann, Wilhelm and Gonz{\`a}lez, Florenci V. and Engels, Bernd and Schirmeister, Tanja},
  title     = {Investigation of the compatibility between warheads and peptidomimetic sequences of protease inhibitors — a comprehensive reactivity and selectivity study},
  series = {International Journal of Molecular Sciences},
  volume    = {24},
  journal   = {International Journal of Molecular Sciences},
  number    = {8},
  issn      = {1422-0067},
  doi       = {10.3390/ijms24087226},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-313596},
  year      = {2023},
  abstract  = {Covalent peptidomimetic protease inhibitors have gained a lot of attention in drug development in recent years. They are designed to covalently bind the catalytically active amino acids through electrophilic groups called warheads. Covalent inhibition has an advantage in terms of pharmacodynamic properties but can also bear toxicity risks due to non-selective off-target protein binding. Therefore, the right combination of a reactive warhead with a well-suited peptidomimetic sequence is of great importance. Herein, the selectivities of well-known warheads combined with peptidomimetic sequences suited for five different proteases were investigated, highlighting the impact of both structure parts (warhead and peptidomimetic sequence) for affinity and selectivity. Molecular docking gave insights into the predicted binding modes of the inhibitors inside the binding pockets of the different enzymes. Moreover, the warheads were investigated by NMR and LC-MS reactivity assays against serine/threonine and cysteine nucleophile models, as well as by quantum mechanics simulations.},
  language  = {en}
}
@article{MuessigLisinetskayaDewhurstetal.2020,
  author    = {Muessig, Jonas H. and Lisinetskaya, Polina and Dewhurst, Rian D. and Bertermann, R{\"u}diger and Thaler, Melanie and Mitric, Roland and Braunschweig, Holger},
  title     = {Tetraiododiborane(4) (B\(_2\)I\(_4\)) is a Polymer based on sp\(^3\) Boron in the Solid State},
  series = {Angewandte Chemie International Edition},
  volume    = {59},
  journal   = {Angewandte Chemie International Edition},
  doi       = {10.1002/anie.201913590},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-209428},
  pages     = {5531-5535},
  year      = {2020},
  abstract  = {Herein we present the first solid-state structures of tetraiododiborane(4) (B\(_2\)I\(_4\)), which was long believed to exist in all phases as discrete molecules with planar, tricoordinate boron atoms, like the lighter tetrahalodiboranes(4) B\(_2\)F\(_4\), B\(_2\)Cl\(_4\), and B\(_2\)Br\(_4\). Single-crystal X-ray diffraction, solid-state NMR, and IR measurements indicate that B\(_2\)I\(_4\) in fact exists as two different polymeric forms in the solid state, both of which feature boron atoms in tetrahedral environments. DFT calculations are used to simulate the IR spectra of the solution and solid-state structures, and these are compared with the experimental spectra.},
  language  = {en}
}
@phdthesis{Moigno2001,
  author    = {Moigno, Damien},
  title     = {Study of the ligand effects on the metal-ligand bond in some new organometallic complexes using FT-Raman and -IR spectroscopy, isotopic substitution and density functional theory techniques},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-3101},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2001},
  abstract  = {The present studies which have been performed in the work-group C-2 (Prof. W. Kiefer) within the program of the Sonderforschungsbereichs 347, deal with the FT-Raman and -IR spectroscopy on new organometallic complexes, synthesized in the work-groups B-2 (Prof. W. Malisch), B-3 (Prof. W. A. Schenk), D-1 (Prof. H. Werner) and D-4 (Prof. D. Stalke). The FT-Raman spectra recorded at 1064 nm led to very useful and interesting information. Furthermore, the DFT calculations which are known to offer promise of obtaining accurate vibrational wavenumbers, were successfully used for the assignment of the vibrational spectra. For the first time it has been possible to ascribe exactly the n(RhC) stretching mode in the vinylidene rhodium(I) complex trans-[RhF(=C=CH2)(PiPr3)2] by using isotopic substitution, in conjunction with theoretical calculations. This is also true for the complexes trans-[RhF(CO)(PiPr3)2], trans-[RhF(C2H4)(PiPr3)2], trans-[RhX(=C=CHPh)(PiPr3)2] (X = F, Cl, Br, I, Me, PhCºC) and trans-[RhX(CN-2,6-xylyl)(PiPr3)2] (X = F, Cl, Br, I, CºCPh). In addition, the comparison between the n(RhC) wavenumbers of the complexes trans-[RhF(=13C=13CH2)(PiPr3)2] and trans-[RhF(CO)(PiPr3)2], containing the isoelectronic ligands 13C=13CH2 and CO, which have the same reduced mass, indicated that the Rh-C bond is stronger in the carbonyl than in the vinylidene complex. Besides, the n(RhF) stretching mode, which has been observed at higher wavenumbers in the FT-Raman and -IR spectra of trans-[RhF(CO)(PiPr3)2], showed that the carbonyl ligand is a better p-acceptor and a less effective s-donor than the vinylidene one. Moreover, the comparison of the n(CºC) and n(Rh-C) modes from the FT-Raman spectrum of the complexes trans-[Rh(CºCPh)(L)(PiPr3)2] (L = C=CHPh, CO, CN-2,6-xylyl) point out that the p-acceptor ability of the ligand trans to CºCPh should rise in the order C=CH2 < CO < CN-2,6-xylyl \pounds C=CHPh. The investigated sensitivity of the n(RhC), n(CC), n(CO) and n(CN) vibrational modes to the electronic modifications occuring in the vinylidene, carbonyl, ethylene and isonitrile complexes, should allow in the future the examination of the p-acceptor or p-donor properties of further ligands. Likewise, we were able to characterize the influence of various X ligands on the RhC bond by using the n(RhC) stretching mode as a probe for the weakening of this. The calculated wavenumbers of the n(RhC) for the vinylidene complexes trans-[RhX(=C=CHR)(PiPr3)2], where R = H or Ph, suggested that the strength of the Rh=C bond increases along the sequence X = CºCPh < CH3 < I < Br < Cl < F. For the series of carbonyl compounds trans-[RhX(CO)(PiPr3)2], where X = F, Cl, Br and I, analogous results have been obtained and confirmed from the model compounds trans-[RhX(CO)(PMe3)2]. Since, the calculated vibrational modes for the ethylene complex trans-[RhF(C2H4)(PiPr3)2] were in good agreement with the experimental results and supported the description of this complex as a metallacyclopropane, we were interested in getting more information upon this class of compounds. In this context, we have recorded the FT-Raman and -IR spectra of the thioaldehyde complexes mer-[W(CO)3(dmpe)(h2-S=CH2)] and mer-[W(CO)3(dmpe)(h2-S=CD2)] which have been synthezised by B-3. The positions of the different WL vibrational modes anticipated by the DFT calculations, were consistent with the experimental results. Indeed, the analysis of the band shifts in the FT-Raman and -IR spectra of the isotopomer mer-[W(CO)3(dmpe)(h2-S=CD2)] confirmed our assignment. The different stereoisomers of complex mer-[W(CO)3(dmpe)(h2-S=CH2)] were investigated too, since RMN and IR-data have shown that complex mer-[W(CO)3(dmpe)(h2-S=CH2)] lead in solution to an equilibrium. Since the information on the vibrational spectra of the molybdenum and tungsten complexes Cp(CO)2M-PR2-X (M = Mo, W; R = Me, tBu, Ph; X = S, Se) is very scarce, we extended our research work to this class of compounds. We have tried to elucidate the bonding properties in these chalcogenoheterocycle complexes by taking advantage of the mass effect on the different metal atoms (W vs. Mo). Thus, the observed band shifts allowed to assign most of the ML fundamental modes of these complexes. This project and the following one were a cooperation within the work-group B-2. The Raman and IR spectra of the matrix isolated photoproducts expected by the UV irradiation of the iron silyl complex Cp(CO)2FeSiH2CH3 have been already reported by Claudia Fickert and Volker Nagel in their PhD-thesis. Since no exact assignment was feasible for these spectra, we were interested in the study of the reaction products created by irradiation of the carbonyl iron silyl complex Cp(CO)2FeCH2SiH3. Although the calculated characteristic vibrational modes of the metal ligand unit for the various photoproducts are significantly different in constitution, they are very similar in wavenumbers, which did not simplify their identification. However, the theoretical results have been found to be consistent with the earlier experimental results. Finally, the last part of this thesis has been devoted to the (2-Py)2E- anions which exhibit a high selectivity toward metal-coordination. All di(2-pyridyl) amides and -phosphides which were synthesized by D-4, coordinate the R2Al+ fragment via both ring nitrogen atoms. This already suggests that the charge density in the anions is coupled into the rings and accumulated at the ring nitrogen atoms, but the Lewis basicity of the central nitrogen atom in Et2Al(2-Py)2N is still high enough to coordinate a second equivalent AlEt3 to form the Lewis acid base adduct Et2Al(2-Py)2NAlEt3. Due to the higher electronegativity of the central nitrogen atom in Me2Al(2-Py)2N, Et2Al(2-Py)2N and Et2Al(2-Py)2NAlEt3, compared to the bridging two coordinated phosphorus atom in Me2Al(2-Py)2P and Et2Al(2-Py)2P, the di(2-pyridyl)amide is the hardest Lewis base. In the phosphides merely all charge density couples into the rings leaving the central phosphorus atom only attractive for soft metals. These results were confirmed by using DFT and MP2 calculations. Moreover, a similar behaviour has been observed and described for the benzothiazolyl complex [Me2Al{Py(Bth)P}], where complementary investigations are to be continued. The DFT calculations carried out on the model compounds analysed in these studies supply very accurate wavenumbers and molecular geometries, these being in excellent agreement with the experimental results obtained from the corresponding isolated complexes.},
  subject      = {{\"U}bergangsmetallkomplexe},
  language  = {en}
}
@phdthesis{Meuer2002,
  author    = {Meuer, Petra},
  title     = {Spektroskopische Untersuchungen an Kammerwasser},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-4974},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2002},
  abstract  = {Ziel dieser Arbeit war es, die M{\"o}glichkeiten zur Verwendung des Auges bzw. der Augenvorderkammer als spektroskopische Zelle f{\"u}r nicht-invasive In-vivo-Messungen zu untersuchen. Dabei stand vor allem die Ger{\"a}te-technische Umsetzung und die Entwicklung geeigneter Auswertestrategien im Vordergrund. In dieser Arbeit konnte gezeigt werden, dass die spektroskopische Untersuchung von Kammerwasser-Substanzen m{\"o}glich ist. Durch den Einsatz der UV/VIS-Spektroskopie konnte Fluorescein in vivo bestimmt werden. Die Anwendung der NIR-Spektroskopie eignet sich vor allem zur Bestimmung von Glucose im Kammerwasser. Die G{\"u}te der Glucose-Bestimmung ist von verschiedenen Faktoren abh{\"a}ngig, wie z. B. dem verwendeten Ger{\"a}t, den Parameter der Auswertung und der Temperatur. F{\"u}r weitergehende Studien sollten daher die in dieser Arbeit aufgedeckten Probleme und Strategien beachtet werden.},
  subject      = {Blutzucker},
  language  = {de}
}
@phdthesis{Matthaei2023,
  author    = {Matthaei, Christian Tobias},
  title     = {Studying the Photodissociation of Chlorine-Containing Molecules with Velocity Map Imaging},
  doi       = {10.25972/OPUS-32740},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-327405},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2023},
  abstract  = {The first is via direct dissociation and the second likely involves a barrier slowing down dissociation. Chlorine-containing hydrocarbons pose a great risk for the environment and especially for the atmosphere. In this thesis I present the photodissociation dynamics of multiple chlorine-containing molecules. The method of velocity map imaging was utilized for gaining information on the kinetic energy distribution of the fragments generated in the photodissociation reactions. First, the photodissociation of benzoyl chloride after excitation to the S1, S2 and the S3 state between 279 nm and 237 nm was studied. This stable molecule was an ideal candidate for demonstrating a new ionization scheme for chlorine atoms. It was shown that benzoyl chloride dissociates statistically from the ground state. Afterwards, the results from experiments on the radicals trichloromethyl and dichlorocarbene are presented in the range of 230 to 250 nm. These radicals remain after the dissociation of carbon tetrachloride and have not been studied in detail because of their instability. Trichlormethyl dissociates via two paths: The loss of a chlorine atom to dichlorocarbene and by decaying to CCl and a chlorine molecule. The dissociation to dichlorocarbene involves a barrier. If the photon exciting the molecule has enough energy to surpass the barrier, which is the case starting at around 235 nm, trichlormethyl dissociates rapidly resulting in an anisotropic VMI. However, if the the excitation energy is lower, the dissociation takes longer than a rotational period and the anisotropy is lost.The path to CCl is a statistical dissociation. Dichlorocarbene dissociates to CCl and Cl via to separate channels. The first is via direct dissociation and the second likely involves a barrier slowing down dissociation.},
  subject      = {Photodissoziation},
  language  = {en}
}
@phdthesis{Marquetand2007,
  author    = {Marquetand, Philipp},
  title     = {Vectorial properties and laser control of molecular dynamics},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-24697},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2007},
  abstract  = {In this work, the laser control of molecules was investigated theoretically. In doing so, emphasis was layed on entering vectorial properties and in particular the orientation in the laboratory frame. Therefore, the rotational degree of freedom had to be included in the quantum mechanical description. The coupled vibrational and rotational dynamics was examined, which is usually not done in coherent control theory. Local control theory was applied, where the field is determined from the dynamics of a system, which reacts with an instantaneous response to the perturbation and, in turn, determines the field again. Thus, the field is entangled with the quantum mechanical motion and the presented examples document, that this leads to an intuitive interpretation of the fields in terms of the underlying molecular dynamics. The limiting case of a classical treatment was shown to give similar results and hence, eases to understand the complicated structure of the control fields. In a different approach, the phase- and amplitude shaping of laser fields was systematically studied in the context of controlling population transfer in molecules.},
  subject      = {Laserchemie},
  language  = {en}
}
@phdthesis{Margraf2010,
  author    = {Margraf, Markus Johann},
  title     = {Spektroskopie an π-konjugierten Molek{\"u}len},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-54032},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2010},
  abstract  = {Femtosekunden-zeitaufgel{\"o}ste transiente Absorptionsspektroskopie einer neutralen organischen gemischtvalenten Verbindung In einem Femtosekunden-zeitaufgel{\"o}sten Anrege-Abfrage-Experiment wurde die Dynamik des Elektronentransfers einer neutralen organischen gemischtvalenten Verbindung untersucht. Neben der Abh{\"a}ngigkeit des R{\"u}ckelektronentransfers von der Solvenspolarit{\"a}t wurde auch die Rotationsdiffusion in n-Hexan, Toluol, Dibutylether, tert-Butylmethylether und Benzonitril studiert. Die transiente Dynamik l{\"a}sst sich mit einer Lebensdauer beschreiben, verursacht durch einen R{\"u}ckelektronentransfer. W{\"a}hrend dieser in unpolaren L{\"o}semitteln relativ langsam verl{\"a}uft, beobachtet man deutlich schnellere ET-Raten mit steigender Polarit{\"a}t des L{\"o}semittels. Die Lebensdauer variiert von 1.2 ps f{\"u}r Benzonitril bis 260 ps f{\"u}r n-Hexan. Rotationsdiffusion konnte nicht beobachtet werden. Die gemessenen Raten wurden mit theoretischen Raten verglichen. F{\"u}r unpolare L{\"o}semittel konnte eine gute {\"U}bereinstimmung gefunden werden. In polaren L{\"o}semitteln bewirkt eine Korrektur, die die Solvensrelaxationszeit ber{\"u}cksichtigt, eine sehr gute {\"U}bereinstimmung von berechneten und gemessenen R{\"u}ckelektronentransferraten. Zeit- und frequenzaufgel{\"o}ste Photoionisation des C 2A2-Zustandes des Benzylradikals Die Lebensdauer des C 2A2-Zustandes des Benzylradikals wurde in Abh{\"a}ngigkeit der {\"U}berschussenergie bestimmt. Die zeitabh{\"a}ngigen Ionensignale konnten dabei mit einer biexponentiellen Dynamik beschrieben werden. Bei einer Anregung am Ursprung (305nm) betragen die Lebensdauern τ1= 400 fs und τ2 = 4.5 ps. Die k{\"u}rzere Lebensdauer τ1 beschreibt die interne Konversion vom C-Zustand zu den stark koppelnden A/B-Zust{\"a}nden, die l{\"a}ngere Lebensdauer τ2 die interne Konversion von den A/B-Zust{\"a}nden in den elektronischen Grundzustand. Mit steigender Anregungsenergie beobachtet man eine stete Abnahme beider Lebensdauern. Bei einer Anregung mit einem Puls der Wellenl{\"a}nge von 301 nm beobachtet man deutlich k{\"u}rzere Lebensdauern mit τ1 = 350 fs und τ2 = 2.8 ps. Erfolgt die Anregung mit einem Puls der Wellenl{\"a}nge von 298 nm, betragen die Zeitkonstanten τ1 = 180 fs und τ2 = 2.1 ps. Desweiteren konnte ein zeitabh{\"a}ngiges Ionensignal f{\"u}r eine Spezies mit der Zusammensetzung C7H5 beobachtet werden. Der Tr{\"a}ger des Signals ist das Fulvenallenylradikal.},
  subject      = {Valenzgemischte Verbindungen},
  language  = {de}
}
@article{MalyBrixner2021,
  author    = {Mal{\´y}, Pavel and Brixner, Tobias},
  title     = {Fluorescence-Detected Pump-Probe Spectroscopy},
  series = {Angewandte Chemie International Edition},
  volume    = {60},
  journal   = {Angewandte Chemie International Edition},
  number    = {34},
  doi       = {10.1002/anie.202102901},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-244811},
  pages     = {18867 -- 18875},
  year      = {2021},
  abstract  = {We introduce a new approach to transient spectroscopy, fluorescence-detected pump-probe (F-PP) spectroscopy, that overcomes several limitations of traditional PP. F-PP suppresses excited-state absorption, provides background-free detection, removes artifacts resulting from pump-pulse scattering, from non-resonant solvent response, or from coherent pulse overlap, and allows unique extraction of excited-state dynamics under certain conditions. Despite incoherent detection, time resolution of F-PP is given by the duration of the laser pulses, independent of the fluorescence lifetime. We describe the working principle of F-PP and provide its theoretical description. Then we illustrate specific features of F-PP by direct comparison with PP, theoretically and experimentally. For this purpose, we investigate, with both techniques, a molecular squaraine heterodimer, core-shell CdSe/ZnS quantum dots, and fluorescent protein mCherry. F-PP is broadly applicable to chemical systems in various environments and in different spectral regimes.},
  language  = {en}
}