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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.
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.
Coherent two-dimensional electronic spectroscopy in the Soret band of a chiral porphyrin dimer
(2013)
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.
KasA is a key enzyme which plays an essential part in the biosynthetic pathway of mycolic acids, the building block of cell wall in Mycobacterium tuberculosis. Its importance was demonstrated by the finding that the depletion of KasA leads to the cell lysis of Mycobacterium tuberculosis. Since Mycobacterium tuberculosis is a pathogen of tuberculosis, the second leading cause of death from an infectious disease worldwide, KasA has drawn attention as one of the attractive drug targets against tuberculosis. Due to the emergence of extensively drug-resistant strains which make most of the known antibiotics for treating tuberculosis ineffective, it became an urgent issue to develop new drugs against tuberculosis. In chapter 3.1, the protonation state of the catalytic residues in the resting state was mainly addressed. The FEP computation and MD simulations were employed for this investigation, and the results showed that the zwitterionic state is most probable. To underpin this conclusion with more solid data, The PESs for the proton transfer between the neutral and zwitterionic state were computed in the context of QM/MM. However, due to the strong dependency of the QM/MM optimization on the initial structure, it was not possible to obtain consistent results from these computations. To circumvent this problem, QM/MM based umbrella sampling was carried out with a semi-empirical method (RM1), and the resulting PMF surface indicated that the zwitterionic state is more stable than the neutral state. In chapter 3.2, the protonation state of significant residues in the acyl-enzyme state was investigated. Unlike other catalytic residues, the protonation state of His311 is ambiguous in the acyl-enzyme state, and different decarboxylation mechanisms can be derived depending on the protonation state of His311 in the acyl-enzyme state. Therefore, FEP computations were carried out to find most probable protonation state of His311 in terms of free energy, and the results showed that the pKa value at Nδ is considerably lowered by the enzyme environment while that of Nε is not. Additionally, the PMF profiles for the proton transfer between Lys340 and Glu354 were computed using QM/MM based umbrellas sampling method, and the results showed that the property of the Lys340/Glu354 pair is neutral rather than ionic when His311 is protonated at Nε. Moreover, a relatively larger ionic character of the Lys340/Glu354 pair when His311 is doubly protonated provides a valuable insight into how the Lys340/Glu354 pair plays a role in shifting the protonated state from Nδ to Nε in His311 after the acyl-transfer step. Overall, the results demonstrated that His311 is neutral and protonated at Nε, and the Lys340/Glu354 pair is also neutral in the acyl-enzyme state. Those computational results lead to the conclusion that the decarboxylation reaction is facilitated by an oxyanion hole which is comprised of two catalytic histidines. In chapter 3.3, the protonation state of catalytic residues in the resting state was revisited because a recent benchmark study showed that the employed semi-empirical method (RM1) in chapter 3.1 tends to overestimate the stabilization of the zwitterionic state. Furthermore, the Lys340/Glu354 pair was considered as purely ionic in chapter 3.1, while it actually has a mixed neutral and ionic character as demonstrated in chapter 3.2. The new investigations employed a larger QM region including the Lys340/Glu354 pair with the BLYP/6-31G** approach, which was proven to be accurate enough for the present purpose by benchmark computations. The new results from the QM/MM MD and FEP computations indicated the catalytic residues to be neutral most probably in the resting state, and this in turn brought up the question how KasA can be activated to initiate the catalytic reaction. On the basis of the results from the MD simulations and FEP computations for the His311Ala mutant in chapter 3.1, we hypothesized that the open conformation of Phe404 would trigger the activation of the catalytic residues by the formation of a strong hydrogen bond. The QM/MM MD simulation proved that the activation of the catalytic residues can indeed be accomplished by the open conformation of Phe404 we suggested, and the corresponding force field based PMF profile also indicated that this conformational change is energetically feasible. The distribution of hydrophilic and hydrophobic residues in the malonyl binding pocket in conjunction with our computational results further provided a valuable insight into the detailed process how the catalytic residues is activated upon the substrate entering.
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.
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.
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.
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 \(C_2H_2\).
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.
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.
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.
Light-induced excitation of matter proceeds within femtoseconds, resulting in excited states. Originating from these states chemical reaction mechanisms, like isomerization or bond formation, set in. Photophysical mechanisms like energy distribution and excitonic delocalization also occur. Thus, the reaction scheme has to be disentangled by assessing the importance of each process. Spectroscopic methods based on fs laser pulses have emerged as a versatile tool to study these reactions. Within this thesis time-resolved experiments with fs laser pulses on various molecular systems were performed. Novel photosystems, with possible applications ranging from ultrathin molecular wires to molecular switches, were extensively characterized. To resolve the complex kinetics of the investigated systems, time-resolved techniques had to be newly developed. By combining a visible excitation pulse pair with an additional pulse and a continuum probe electronic triggered-exchange two-dimensional spectroscopy (TE2D) was demonstrated for the first time. This goal was accomplished by combining a three-color transient-absorption setup with a pulse shaper. Hence, 2D spectroscopy with a continuum probe was also implemented. Using these methods two different molecular systems in solution were characterized in a comprehensive manner. (ZnTPP)2, a directly beta,beta’-linked Zn-metallated bisporphyrin, and a spiropyran-merocyanine photosystem, 6,8-dinitro BIPS, were characterized. (ZnTPP)2 is a homodimer, featuring strong excitonic effects. These manifest themselves in a twofold splitting of the Soret band (S2). 6,8-Dinitro BIPS exists in one of two possible conformations. The ring closed spiropyran absorbs only in the UV, while the ring open merocyanine also absorbs in the visible. For both molecular systems photodynamics upon illumination were monitored using transient-absorption. However, the obtained results were ambiguous, necessitating more complex methods. In the case of (ZnTPP)2 first the monomeric building block was characterized. There, population transfer from the S2 state into S1 within 2 ps was identified. Afterwards, intersystem crossing proceeds within 2 ns. For (ZnTPP)2 similar pathways were found, albeit the relaxation is faster. The intersystem crossing with 1.5 ns was not only indirectly deduced but directly measured by probing in the NIR spectral range. The excitonic influence of was investigated by coherent 2D spectroscopy in the Soret band. Population transfer within S2 was directly visualized on a time-scale of 100 fs. Calculation of the 2D spectra of a simple homodimer confirmed the results. After this analysis of the distinct excitonic character, this molecule may serve as a building block for larger porphyrin arrays with applications ranging from asymmetric catalysis over biomimicry of electron-transfer to organic optical devices. The second photosystem was the molecular switch 6,8-dinitro BIPS, existing in two conformations. Merocyanine is the more stable form in thermal equilibrium. Transient-absorption measurements uncovered that the sample consisted of a mixture of two merocyanine isomers, referred to as TTC and TTT. However, both isomers are capable of ring-closure forming spiropyran. The remaining excited molecules return to the ground state radiatively. Conducting 2D measurements utilizing a continuum probe the differing photochemistry of both isomers was examined in a single measurement. No isomerization between these conformations was detected. Therefore, 6,8-dinitro BIPS performs a concerted switching without long-living intermediates. This was confirmed by a pump-repump-probe scan. 6,8-DinitroBIPS can be closed by visible and opened by UV pulses using subsequent pulses and vice versa. These mechanisms via singlet pathways satisfy an important criterion for a unimolecular switching device. A second pump-repump-probe experiment showed that the sample is ionized, resulting in a merocyanine radical cation, when the first excited state is resonantly excited. Furthermore, by implementing TE2Dspectroscopy, it was elucidated that only TTC was ionized. Taking all this into account new techniques were developed and complex molecular systems were characterized within this thesis. Deeper insight into the photodynamics of (ZnTPP)2and 6,8-dinitro BIPS was gained by adapting transient absorption for the NIR spectral range, constructing a 2D setup in pump-probe geometry, and combining it with multipulse excitation to coherent TE2D. All techniques solved the questions for which they were constructed, but they are not limited to these cases. Especially TE2D opens new roads in photochemistry. By connecting reactant, product and the corresponding intermediates, a chemical reaction can be tracked through all stages, making unambiguous identification of the reactive states feasible. Thus, fundamental insight into the photochemistry of molecular compounds is gained.
We calculate two-dimensional (2D) spectra reflecting the time-dependent electronic predissociation of a diatomic molecule. The laser-excited electronic state is coupled non-adiabatically to a fragment channel, leading to the decay of the prepared quasi-bound states. This decay can be monitored by the three-pulse configuration employed in optical 2D spectroscopy. It is shown that in this way it is possible to state-selectively characterize the time-dependent population of resonance states with different lifetimes. A model of the NaI molecule serves as a numerical example.