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- ItemExcited-state relaxation of hydrated thymine and thymidine measured by liquid-jet photoelectron spectroscopy: experiment and simulation(Washington, DC : ACS Publications, 2015) Buchner, Franziska; Nakayama, Akira; Yamazaki, Shohei; Ritze, Hans-Hermann; Lübcke, AndreaTime-resolved photoelectron spectroscopy is performed on thymine and thymidine in aqueous solution to study the excited-state relaxation dynamics of these molecules. We find two contributions with sub-ps lifetimes in line with recent excited-state QM/MM molecular dynamics simulations (J. Chem. Phys.2013, 139, 214304). The temporal evolution of ionization energies for the excited ππ* state along the QM/MM molecular dynamics trajectories were calculated and are compatible with experimental results, where the two contributions correspond to the relaxation paths in the ππ* state involving different conical intersections with the ground state. Theoretical calculations also show that ionization from the nπ* state is possible at the given photon energies, but we have not found any experimental indication for signal from the nπ* state. In contrast to currently accepted relaxation mechanisms, we suggest that the nπ* state is not involved in the relaxation process of thymine in aqueous solution.
- ItemFemtosecond stimulated Raman spectroscopy of the cyclobutane thymine dimer repair mechanism: A computational study(Washington, DC : American Chemical Society, 2014) Ando, H.; Fingerhut, B.P.; Dorfman, K.E.; Biggs, J.D.; Mukamel, S.Cyclobutane thymine dimer, one of the major lesions in DNA formed by exposure to UV sunlight, is repaired in a photoreactivation process, which is essential to maintain life. The molecular mechanism of the central step, i.e., intradimer C-C bond splitting, still remains an open question. In a simulation study, we demonstrate how the time evolution of characteristic marker bands (C=O and C=C/C-C stretch vibrations) of cyclobutane thymine dimer and thymine dinucleotide radical anion, thymidylyl(3′→5′)-thymidine, can be directly probed with femtosecond stimulated Raman spectroscopy (FSRS). We construct a DFT(M05-2X) potential energy surface with two minor barriers for the intradimer C5-C′5 splitting and a main barrier for the C6-C′6 splitting, and identify the appearance of two C5=C6 stretch vibrations due to the C6-C′6 splitting as a spectroscopic signature of the underlying bond splitting mechanism. The sequential mechanism shows only absorptive features in the simulated FSRS signals, whereas the fast concerted mechanism shows characteristic dispersive line shapes. (Figure Presented).
- ItemThe Contrasting Character of Early and Late Transition Metal Fluorides as Hydrogen Bond Acceptors(Washington, DC : ACS Publications, 2015) Smith, Dan A.; Beweries, Torsten; Blasius, Clemens; Jasim, Naseralla; Nazir, Ruqia; Nazir, Sadia; Robertson, Craig C.; Whitwood, Adrian C.; Hunter, Christopher A.; Brammer, Lee; Perutz, Robin N.The association constants and enthalpies for the binding of hydrogen bond donors to group 10 transition metal complexes featuring a single fluoride ligand (trans-[Ni(F)(2-C5NF4)(PR3)2], R = Et 1a, Cy 1b, trans-[Pd(F)(4-C5NF4)(PCy3)2] 2, trans-[Pt(F){2-C5NF2H(CF3)}(PCy3)2] 3 and of group 4 difluorides (Cp2MF2, M = Ti 4a, Zr 5a, Hf 6a; Cp*2MF2, M = Ti 4b, Zr 5b, Hf 6b) are reported. These measurements allow placement of these fluoride ligands on the scales of organic H-bond acceptor strength. The H-bond acceptor capability β (Hunter scale) for the group 10 metal fluorides is far greater (1a 12.1, 1b 9.7, 2 11.6, 3 11.0) than that for group 4 metal fluorides (4a 5.8, 5a 4.7, 6a 4.7, 4b 6.9, 5b 5.6, 6b 5.4), demonstrating that the group 10 fluorides are comparable to the strongest organic H-bond acceptors, such as Me3NO, whereas group 4 fluorides fall in the same range as N-bases aniline through pyridine. Additionally, the measurement of the binding enthalpy of 4-fluorophenol to 1a in carbon tetrachloride (−23.5 ± 0.3 kJ mol–1) interlocks our study with Laurence’s scale of H-bond basicity of organic molecules. The much greater polarity of group 10 metal fluorides than that of the group 4 metal fluorides is consistent with the importance of pπ–dπ bonding in the latter. The polarity of the group 10 metal fluorides indicates their potential as building blocks for hydrogen-bonded assemblies. The synthesis of trans-[Ni(F){2-C5NF3(NH2)}(PEt3)2], which exhibits an extended chain structure assembled by hydrogen bonds between the amine and metal-fluoride groups, confirms this hypothesis.
- ItemDefect-free Naphthalene Diimide Bithiophene Copolymers with Controlled Molar Mass and High Performance via Direct Arylation Polycondensation(Washington, DC : ACS Publications, 2015) Matsidik, Rukiya; Komber, Hartmut; Luzio, Alessandro; Caironi, Mario; Sommer, MichaelA highly efficient, simple, and environmentally friendly protocol for the synthesis of an alternating naphthalene diimide bithiophene copolymer (PNDIT2) via direct arylation polycondensation (DAP) is presented. High molecular weight (MW) PNDIT2 can be obtained in quantitative yield using aromatic solvents. Most critical is the suppression of two major termination reactions of NDIBr end groups: nucleophilic substitution and solvent end-capping by aromatic solvents via C–H activation. In situ solvent end-capping can be used to control MW by varying monomer concentration, whereby end-capping is efficient and MW is low for low concentration and vice versa. Reducing C–H reactivity of the solvent at optimized conditions further increases MW. Chain perfection of PNDIT2 is demonstrated in detail by NMR spectroscopy, which reveals PNDIT2 chains to be fully linear and alternating. This is further confirmed by investigating the optical and thermal properties as a function of MW, which saturate at Mn ≈ 20 kDa, in agreement with controls made by Stille coupling. Field-effect transistor (FET) electron mobilities μsat up to 3 cm2/(V·s) are measured using off-center spin-coating, with FET devices made from DAP PNDIT2 exhibiting better reproducibility compared to Stille controls.
- ItemMagnetofluidic platform for multidimensional magnetic and optical barcoding of droplets(Cambridge : RSC, 2014) Lin, Gungun; Makarov, Denys; Medina-Sánchez, Mariana; Guix, Maria; Baraban, Larysa; Cuniberti, Gianaurelio; Schmidt, Oliver G.We present a concept of multidimensional magnetic and optical barcoding of droplets based on a magnetofluidic platform. The platform comprises multiple functional areas, such as an encoding area, an encoded droplet pool and a magnetic decoding area with integrated giant magnetoresistive (GMR) sensors. To prove this concept, penicillin functionalized with fluorescent dyes is coencapsulated with magnetic nanoparticles into droplets. While fluorescent dyes are used as conventional optical barcodes which are decoded with an optical decoding setup, an additional dimensionality of barcodes is created by using magnetic nanoparticles as magnetic barcodes for individual droplets and integrated micro-patterned GMR sensors as the corresponding magnetic decoding devices. The strategy of incorporating a magnetic encoding scheme provides a dynamic range of ~40 dB in addition to that of the optical method. When combined with magnetic barcodes, the encoding capacity can be increased by more than 1 order of magnitude compared with using only optical barcodes, that is, the magnetic platform provides more than 10 unique magnetic codes in addition to each optical barcode. Besides being a unique magnetic functional element for droplet microfluidics, the platform is capable of on-demand facile magnetic encoding and real-time decoding of droplets which paves the way for the development of novel non-optical encoding schemes for highly multiplexed droplet-based biological assays.
- ItemX-ray imaging of chemically active valence electrons during a pericyclic reaction(London : Nature Publishing Group, 2014) Bredtmann, T.; Ivanov, M.; Dixit, G.Time-resolved imaging of chemically active valence electron densities is a long-sought goal, as these electrons dictate the course of chemical reactions. However, X-ray scattering is always dominated by the core and inert valence electrons, making time-resolved X-ray imaging of chemically active valence electron densities extremely challenging. Here we demonstrate an effective and robust method, which emphasizes the information encoded in weakly scattered photons, to image chemically active valence electron densities. The degenerate Cope rearrangement of semibullvalene, a pericyclic reaction, is used as an example to visually illustrate our approach. Our work also provides experimental access to the long-standing problem of synchronous versus asynchronous bond formation and breaking during pericyclic reactions.