2013, Nedelcu, S., Sommer, J.-U.

By molecular dynamics simulations, we investigated the transport of charged polymers in applied electric fields in confining environments, which were straight cylinders of uniform or non-uniform diameter. In the simulations, the solvent was modeled explicitly and, also, the counterions and coions of added salt. The electrophoretic velocities of charged chains in relation to electrolyte friction, hydrodynamic effects due to the solvent, and surface friction were calculated. We found that the velocities were higher if counterions were moved away from the polymeric domain, which led to a decrease in hydrodynamic friction. The topology of the surface played a key role in retarding the motion of the polyelectrolyte and, even more so, in the presence of transverse electric fields. The present study showed that a possible way of improving separation resolution is by controlling the motion of counterions or electrolyte friction effects.

2019, Holm, Alexander, Mayr, Stefan G.

Ferromagnetic shape memory alloys, including the Fe7Pd3 system, constitute an upcoming class of functional materials, whose atomic-scale physical foundations are still insufficiently understood. The present work employs molecular dynamics simulations, based on ab initio derived embedded atom method potentials, to study martensitic transformations and twin variant reorientation. We address thermal and stress induced austenite-martensite transitions, twinning, as well as twin boundary mobility. While the predicted thermal properties are in accordance with experimental observations, we explore the detailed crystallography underlying transformation as well as twin boundary motion. © 2019 The Author(s).

2021, Elsaesser, Thomas, Schauss, Jakob, Kundu, Achintya, Fingerhut, Benjamin P.

Electric interactions have a strong impact on the structure and dynamics of biomolecules in their native water environment. Given the variety of water arrangements in hydration shells and the femto- to subnanosecond time range of structural fluctuations, there is a strong quest for sensitive noninvasive probes of local electric fields. The stretching vibrations of phosphate groups, in particular the asymmetric (PO2)− stretching vibration νAS(PO2)−, allow for a quantitative mapping of dynamic electric fields in aqueous environments via a field-induced redshift of their transition frequencies and concomitant changes of vibrational line shapes. We present a systematic study of νAS(PO2)− excitations in molecular systems of increasing complexity, including dimethyl phosphate (DMP), short DNA and RNA duplex structures, and transfer RNA (tRNA) in water. A combination of linear infrared absorption, two-dimensional infrared (2D-IR) spectroscopy, and molecular dynamics (MD) simulations gives quantitative insight in electric-field tuning rates of vibrational frequencies, electric field and fluctuation amplitudes, and molecular interaction geometries. Beyond neat water environments, the formation of contact ion pairs of phosphate groups with Mg2+ ions is demonstrated via frequency upshifts of the νAS(PO2)− vibration, resulting in a distinct vibrational band. The frequency positions of contact geometries are determined by an interplay of attractive electric and repulsive exchange interactions.

2015, Buchner, Franziska, Nakayama, Akira, Yamazaki, Shohei, Ritze, Hans-Hermann, Lübcke, Andrea

Time-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.

2018, Tkachov, Roman, Stepien, Lukas, Grafe, Robert, Guskova, Olga, Kiriy, Anton, Simon, Frank, Reith, Heiko, Nielsch, Kornelius, Schierning, Gabi, Kasinathan, Deepa, Leyens, Christoph

1,1,2,2-Ethenetetrathiolate (ett4-) coordination polymers, such as poly[Kx(Ni-ett)], have been known for decades for their excellent thermoelectric properties. However in reality, ett4- is neither a "true" comonomer which participates in the polymerization, nor represents a "true" repeat unit of the target polymer. Indeed, poly[K2(Ni-ett)], which is formally the product of Ni-induced polymerization of ett4-, has a poor conductivity and needs to be oxidized to show attractive thermoelectric characteristics. The polymerization and oxidation processes are poorly controllable which causes irreproducibility of the polymer properties. To improve the synthesis reproducibility, we studied polymerization of potassium tetrathiooxalate (K2tto), the convenient synthesis of which was developed in our recent work. Because K2tto is the "true monomer", and not its precursor, a high quality product is reproducibly formed simply by mixing K2tto with NiCl2 at room temperature. The procedure does not require additional components (bases), or special conditions (prolonged heating), which are usually needed for the preparation of this polymer from the monomer precursor 1,3,4,6-tetrathiapentalene-2,5-dione (TPD). Furthermore, as tto2- is formally the product of two-electron oxidation of ett4-, the poorly controllable oxidation process is avoided and poly[Ni-tto] almost free from K is directly formed upon the complexation of Ni2+ and tto2-. Thus-obtained poly[Ni-tto] possesses conductivity in the range of 27-47 S cm-1 and a Seebeck coefficient in the range of -38 to -55 μV K-1, which are superior thermoelectric properties compared to poly[Kx(Ni-ett)] samples obtained by the previously reported methods. Redox and structural properties of poly[Ni-tto] were compared with those of poly[Kx(Ni-ett)] obtained by the reported methods. Furthermore, DFT calculations were performed to shed more light on generally promising properties of this class of materials. Particularly, possible packing models have been predicted for polymers, and the molecular dynamics simulations have been used to simulate the molecular arrangements under ambient conditions.

2021, El Harrar, Till, Frieg, Benedikt, Davari, Mehdi D., Jaeger, Karl-Erich, Schwaneberg, Ulrich, Gohlke, Holger

Ionic liquids (IL) and aqueous ionic liquids (aIL) are attractive (co-)solvents for biocatalysis due to their unique properties. On the other hand, the incubation of enzymes in IL or aIL often reduces enzyme activity. Recent studies proposed various aIL-induced effects to explain the reduction, classified as direct effects, e.g., local dehydration or competitive inhibition, and indirect effects, e.g., structural perturbations or disturbed catalytic site integrity. However, the molecular origin of indirect effects has largely remained elusive. Here we show by multi-μs long molecular dynamics simulations, free energy computations, and rigidity analyses that aIL favorably interact with specific residues of Bacillus subtilis Lipase A (BsLipA) and modify the local structural stability of this model enzyme by inducing long-range perturbations of noncovalent interactions. The perturbations percolate over neighboring residues and eventually affect the catalytic site and the buried protein core. Validation against a complete experimental site saturation mutagenesis library of BsLipA (3620 variants) reveals that the residues of the perturbation pathways are distinguished sequence positions where substitutions highly likely yield significantly improved residual activity. Our results demonstrate that identifying these perturbation pathways and specific IL ion-residue interactions there effectively predicts focused variant libraries with improved aIL tolerance.

2014, Nedelcu, S., Sommer, J.-U.

By molecular dynamics simulations we investigate the transport of charged polymers in confinement, under externally applied electric fields, in straight cylinders of uniform diameter and in the presence of monovalent or multivalent counterions. The applied electric field has two components; a longitudinal component along the axis of the cylinder and a transversal component perpendicular to the cylinder axis. The direction of electrophoretic velocity depends on the polyelectrolyte length, valency of the counterions present in solution and transversal electric field value. A statistical model is put forward in order to explain these observations.