@article{KnorrRudolfNuernberger2013,
  author    = {Knorr, Johannes and Rudolf, Philipp and Nuernberger, Patrick},
  title     = {A comparative study on chirped-pulse upconversion and direct multichannel MCT detection},
  doi       = {10.1364/OE.21.030693},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-111334},
  year      = {2013},
  abstract  = {A comparative study is carried out on two spectroscopic techniques employed to detect ultrafast absorption changes in the mid-infrared spectral range, namely direct multichannel detection via HgCdTe (MCT) photodiode arrays and the newly established technique of chirped-pulse upconversion (CPU). Whereas both methods are meanwhile individually used in a routine manner, we directly juxtapose their applicability in femtosecond pump-probe experiments based on 1 kHz shot-to-shot data acquisition. Additionally, we examine different phase-matching conditions in the CPU scheme for a given mid-infrared spectrum, thereby simultaneously detecting signals which are separated by more than 200 cm-1.},
  language  = {en}
}
@article{BrixnerAeschlimannFischeretal.2013,
  author    = {Brixner, T. and Aeschlimann, M. and Fischer, A. and Geisler, P. and Goetz, S. and Hecht, B. and Huang, J. S. and Keitzl, T. and Kramer, C. and Melchior, P. and Pfeiffer, W. and Razinskas, G. and Rewitz, C. and Schneider, C. and Str{\"u}ber, C. and Tuchscherer, P. and Voronine, D. V.},
  title     = {Coherent spectroscopies on ultrashort time and length scales},
  series = {EPJ Web of Conferences},
  volume    = {41},
  journal   = {EPJ Web of Conferences},
  doi       = {10.1051/epjconf/20134109017},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-129073},
  pages     = {09017},
  year      = {2013},
  abstract  = {Three spectroscopic techniques are presented that provide simultaneous spatial and temporal resolution: modified confocal microscopy with heterodyne detection, space-time-resolved spectroscopy using coherent control concepts, and coherent two-dimensional nano-spectroscopy. Latest experimental results are discussed.},
  language  = {en}
}
@article{BrixnerKochKullmannetal.2013,
  author    = {Brixner, Tobias and Koch, Federico and Kullmann, Martin and Selig, Ulrike and Nuernberger, Patrick and G{\"o}tz, Daniel C. G. and Bringmann, Gerhard},
  title     = {Coherent two-dimensional electronic spectroscopy in the Soret band of a chiral porphyrin dimer},
  series = {New Journal of Physics},
  journal   = {New Journal of Physics},
  doi       = {10.1088/1367-2630/15/2/025006},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-96139},
  year      = {2013},
  abstract  = {Using coherent two-dimensional (2D) electronic spectroscopy in fully noncollinear geometry, we observe the excitonic coupling of β,β'-linked bis[tetraphenylporphyrinato-zinc(II)] on an ultrafast timescale in the excited state. The results for two states in the Soret band originating from an excitonic splitting are explained by population transfer with approximately 100 fs from the energetically higher to the lower excitonic state. This interpretation is consistent with exemplary calculations of 2D spectra for a model four-level system with coupling.},
  language  = {en}
}
@phdthesis{Lee2013,
  author    = {Lee, Wook},
  title     = {Computational study on the catalytic mechanism of mtKasA},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-83989},
  school      = {Universit{\"a}t W{\"u}rzburg},
  year      = {2013},
  abstract  = {Das Enzym KasA spielt eine entscheidende Rolle in der Biosynthese von Mykols{\"a}uren, den Bausteinen der Zellw{\"a}nde von Mycobacteriumtuberculosis. Dessen essentielle Notwendigkeit zeigt sich bei Abwesenheit von KasA in einer Zelllyse (Aufl{\"o}sung von Zellen) bei Mycobacteriumtuberculosis. Durch seine Bedeutung f{\"u}r Mycobacteriumtuberculosis, dem Erreger von Tuberkulose und damit der zweith{\"a}ufigsten Todesursache durch Infektionskrankheiten, stellt KasA ein vielversprechendes Ziel f{\"u}r die Entwicklung neuer Medikamente gegen Tuberkulose dar. Durch das Auftreten von extensiv resistenten St{\"a}mmen welche die meisten bekannten Antibiotika zur Bek{\"a}mpfung von Tuberkulose inaktivieren wird es dringend notwendig neue Medikamente gegen Tuberkulose zu entwickeln. In Kapitel 3.1 wird der Protonierungszustand der katalytischen Reste im Ruhezustand untersucht. F{\"u}r diese Untersuchungen wurden Free Energy Perturbation (FEP) Rechnungen und MD Simulationen verwendet. Die Ergebnisse zeigten, dass der zwitterionische Zustand am wahrscheinlichsten ist. Um diese Aussage mit weiteren handfesten Daten zu untermauern wurden Potential(hyper)fl{\"a}chen (PES) f{\"u}r den Protonentransfer zwischen neutralen und zwitterionischen Zustand mit Hilfe von QM/MM Methoden berechnet. Durch die starke Abh{\"a}ngigkeit der QM/MM Optimierung von der Ausgangsstruktur war es nicht m{\"o}glich konsistente Ergebnisse f{\"u}r diese Berechnungen zu bekommen. Um dieses Problem zu umgehen wurde ein auf QM/MM basierendes Umbrella Sampling mit Semiempirischen Methoden (RM1) durchgef{\"u}hrt. Die sich daraus ergebende PMF Fl{\"a}che zeigt das der zwitterionische Zustand stabiler ist als der neutrale Zustand. In Kapitel 3.2 wurde der Protonierungszustand der entsprechenden Reste im Acyl-Enzym Zustand untersucht. Im Unterschied zu anderen katalytischen Resten ist der Protonierungszustand von His311 ist nicht eindeutig im Acyl-Enzym Zustand und es ergeben sich aus den verschiedenen Protonierungszust{\"a}nden verschiedene Decarboxylierungsmechanismen. Um den wahrscheinlichsten Protonierungszustand bez{\"u}glich der freien Energie zu bestimmen wurden FEP Rechnungen durchgef{\"u}hrt. Die Ergebnisse zeigen, dass der pKa Wert an Nδ betr{\"a}chtlich durch die Enzymumgebung verringert wird, w{\"a}hrend dies f{\"u}r Nε nicht der Fall ist. Zus{\"a}tzlich dazu wurden die PMF Profile f{\"u}r den Protonentransfer zwischen Lys340 und Glu354 mit der QM/MM basierten Umbrella Sampling Methode berechnet. Die Ergebnisse zeigen, dass das Lys340/Glu354 Paar eher neutral als ionisch ist, wenn His311 an Nε protoniert ist. Ein relativ hoher ionischer Charakter des Lys340/Glu354 Paares, wenn His311 doppelt protoniert ist, gibt einen wertvollen Einblick in die Rolle welche das Lys340/Glu354 Paar beim verschieben des Protonierungszustandes von Nδ zu Nε im His311 nach dem Acyltransferschritt spielt. Die Ergebnisse zeigen, dass His311 neutral und an Nε protoniert ist. Ebenso ist das Lys340/Glu354 Paar neutral im Acyl-Enzym Zustand. Diese berechneten Ergebnisse f{\"u}hren zu dem Schluss, dass die Decarboxylierung durch ein Oxyanion Loch erleichtert wird welches aus zwei katalytischen Histidin Resten besteht. In Kapitel 3.3 wurde der Protonierungszustand der katalytischen Reste im Ruhezustand erneut untersucht da eine aktuelle Benchmarkstudie zeigte, dass die verwendete Semiempirische Methode (RM1) in Kapitel 3.1 dazu tendiert die Stabilisation des zwitterionischen Zustandes zu {\"u}bersch{\"a}tzen. Auch wurde in Kapitel 3.1 das Lys340/Glu354 Paar als rein ionisch angesehen, w{\"a}hrend sich in Kapitel 3.2 herausstellte, dass es sich um eine Mischung aus neutralen und ionischen Charakter handelt. Die neuen Untersuchungen beinhalten eine gr{\"o}ßere QM Region inklusive des Lys340/Glu354 Paares. Der daf{\"u}r verwendete BLYP/6-31G** Ansatz ist ausreichend akkurat f{\"u}r die aktuelle Fragestellung, was durch Vergleichsrechnungen bewiesen wurde. Die neuen Ergebnisse der QM/MM MD und FEP Rechnungen deuten an, dass die katalytischen Reste im Ruhezustand h{\"o}chst wahrscheinlich neutral vorliegen. Dies wiederum f{\"u}hrt zu der Frage wie KasA aktiviert werden kann um die katalytische Reaktion zu initiieren. Auf der Basis der Ergebnisse der MD Simulationen und FEP Rechnungen f{\"u}r den His311Ala Mutanten in Kapitel 3.1 stellten wir die Hypothese auf, dass die offene Konformation von Phe404 die Aktivierung der katalytischen Reste durch die (Aus)bildung einer starken Wasserstoffbindung einleitet. Die QM/MM MD Simulation best{\"a}tigt dass diese Aktivierung der katalytischen Reste durch die offene Konformation des Phe404 bewerkstelligt werden kann. Das entsprechende auf Kraftfeld basierende PMF Profil zeigt auch, dass dieser Konformationswechsel energetisch realisierbar ist. Die Verteilung der hydrophilen und hydrophoben Reste in der Malonyl Bindungstasche in Verbindung mit unseren berechneten Ergebnissen geben einen Einblick in den detaillierten},
  subject      = {Tuberkelbakterium},
  language  = {en}
}
@article{RuetzelKullmannBubacketal.2013,
  author    = {Ruetzel, S. and Kullmann, M. and Buback, J. and Nuernberger, P. and Brixner, T.},
  title     = {Exploring higher-lying electronic states of a molecular switch by coherent triggered-exchange 2D electronic spectroscopy},
  series = {EPJ Web of Conferences},
  volume    = {41},
  journal   = {EPJ Web of Conferences},
  number    = {05001},
  doi       = {10.1051/epjconf/20134105001},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-129117},
  year      = {2013},
  abstract  = {We use pump-repump-probe transient absorption spectroscopy to investigate the role of higher-lying electronic states in the photochemistry of a molecular switch. Moreover, replacing the pump pulse by a pulse-shaper-generated phase-stable double pulse, triggered-exchange two-dimensional (TE2D) electronic spectroscopy is established in the visible regime.},
  language  = {en}
}
@article{RudolfKanalGehrigetal.2013,
  author    = {Rudolf, P. and Kanal, F. and Gehrig, D. and Niesel, J. and Brixner, T. and Schatzschneider, U. and Nuernberger, P.},
  title     = {Femtosecond mid-infrared study of the aqueous solution photochemistry of a CO-releasing molecule (CORM)},
  series = {EPJ Web of Conferences},
  volume    = {41},
  journal   = {EPJ Web of Conferences},
  doi       = {10.1051/epjconf/20134105004},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-129104},
  pages     = {05004},
  year      = {2013},
  abstract  = {Ultraviolet irradiation of CO-releasing molecules (CORMs) in water eventually leads to the loss of several carbon monoxide ligands.We show for an exemplary manganese tricarbonyl CORM that only one ligand is photolyzed off on an ultrafast timescale and that some molecules may undergo geminate recombination.},
  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{FischerHembergerBodietal.2013,
  author    = {Fischer, Kathrin H. and Hemberger, Patrick and Bodi, Andras and Fischer, Ingo},
  title     = {Photoionisation of the tropyl radical},
  series = {Beilstein Journal of Organic Chemistry},
  volume    = {9},
  journal   = {Beilstein Journal of Organic Chemistry},
  doi       = {10.3762/bjoc.9.77},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-128652},
  pages     = {681-688},
  year      = {2013},
  abstract  = {We present a study on the photoionisation of the cycloheptatrienyl (tropyl) radical, \(C_7H_7\), using tunable vacuum ultraviolet synchrotron radiation. Tropyl is generated by flash pyrolysis from bitropyl. Ions and electrons are detected in coincidence, permitting us to record mass-selected photoelectron spectra. The threshold photoelectron spectrum of tropyl, corresponding to the \(X^{+1}A1' ← X^2E_2"\) transition, reveals an ionisation energy of 6.23 ± 0.02 eV, in good agreement with Rydberg extrapolations, but slightly lower than the value derived from earlier photoelectron spectra. Several vibrations can be resolved and are reassigned to the C-C stretch mode \(ν_{16}^+\) and to a combination of \(ν_{16}^+\) with the ring breathing mode \(ν_2^+\). Above 10.55 eV dissociative photoionisation of tropyl is observed, leading to the formation of \(C_5H_5^+\) and \(C_2H_2\).},
  language  = {en}
}
@article{SteinbacherBubackNuernbergeretal.2013,
  author    = {Steinbacher, A. and Buback, J. and Nuernberger, P. and Brixner, T.},
  title     = {Precise and rapid detection of optical activity for accumulative femtosecond spectroscopy},
  series = {EPJ Web of Conferences},
  volume    = {41},
  journal   = {EPJ Web of Conferences},
  doi       = {10.1051/epjconf/20134112011},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-129124},
  pages     = {12011},
  year      = {2013},
  abstract  = {We present a fast and sensitive polarimeter combining common-path optical heterodyne interferometry and accumulative spectroscopy to detect rotatory power. The sensitivity of rotatory detection is determined to be 0.10 milli-degrees for a measurement time of only one second and an interaction length of 250 µm. Its suitability for femtosecond studies is demonstrated in a non-resonant two-photon photodissociation experiment.},
  language  = {en}
}
@article{OjhaForsterKumaretal.2013,
  author    = {Ojha, Animesh K. and Forster, Stefan and Kumar, Sumeet and Vats, Siddharth and Negi, Segeeta 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},
  issn      = {1477-3155},
  doi       = {10.1186/1477-3155-11-42},
  url       = {http://nbn-resolving.de/urn:nbn:de:bvb:20-opus-122837},
  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}
}