Force field refinement for reproducing experimental infrared spectra of ionic liquids.

We employ polarizable molecular dynamics simulations with the newly developed FFGenOpt parametrization tool to reproduce IR spectra of several ionic liquid cations and anions in the gas phase. Our results show that polarizable force fields in the bulk phase provide a reasonable compromise between computational effort and accuracy for investigating IR spectra when treating the transition from gas to liquid phase carefully. Although collectivity seems to play only a minor role, the liquid phase not only changes the electrostatic environment of the molecules but also introduces friction and intermolecular interactions altering the IR spectrum significantly. In addition to the classical force field approach, we also tested if the additional computational effort of machine learning potentials justifies their application in reproducing IR spectra. However, the main purpose of this work is to improve the quality of polarizable force fields concerning vibrations and not the prediction of IR spectra which can be better done with quantum-mechanical cluster approaches.

{ScnGdn} Heterometallic Rings: Tunable Ring Topology for Spin-Wave Excitations.

Data carriers using spin waves in spintronic and magnonic logic devices offer operation at low power consumption and free of Joule heating yet requiring noncollinear spin structures of small sizes. Heterometallic rings can provide such an opportunity due to the controlled spin-wave transmission within such a confined space. Here, we present a series of {ScnGdn} (n = 4, 6, 8) heterometallic rings, which are the first Sc-Ln clusters to date, with tunable magnetic interactions for spin-wave excitations. By means of time- and temperature-dependent spin dynamics simulations, we are able to predict distinct spin-wave excitations at finite temperatures for Sc4Gd4, Sc6Gd6, and Sc8Gd8. Such a new model is previously unexploited, especially due to the interplay of antiferromagnetic exchange, dipole-dipole interaction, and ring topology at low temperatures, rendering the importance of the latter to spin-wave excitations.

Deep learning in attosecond metrology.

Time-resolved photoelectron spectroscopy provides a versatile tool for investigating electron dynamics in gaseous, liquid, and solid samples on sub-femtosecond time scales. The extraction of information from spectrograms recorded with the attosecond streak camera remains a difficult challenge. Common algorithms are highly specialized and typically computationally heavy. In this work, we apply deep neural networks to map from streaking traces to near-infrared pulses as well as electron wavepackets and extensively benchmark our results on simulated data. Additionally, we illustrate domain-shift to real-world data. We also attempt to quantify the model predictive uncertainty. Our deep neural networks display competitive retrieval quality and superior tolerance against noisy data conditions, while reducing the computational time by orders of magnitude.

Polarizable molecular dynamics simulations on the conductivity of pure 1-methylimidazolium acetate systems.

The protic ionic liquid 1-methylimidazolium acetate is in equilibrium with its neutral species 1-methylimidazole and acetic acid. Although several experimental data indicate that the equilibrium favors the neutral species, the system exhibits a significant conductivity. We developed a polarizable force field to describe the ionic liquid accurately and applied it to several mixtures of the neutral and charged species. In addition to comparing single values, such as density, diffusion coefficients, and conductivity, with experimental data, the complete frequency-dependent dielectric spectrum ranging from several MHz to THz can be used to determine the equilibrium composition of the reaction mentioned above.

Emulating proton transfer reactions in the pseudo-protic ionic liquid 1-methylimidazolium acetate.

Proton transfer reactions can enhance conductivity in protic ionic liquids. However, several proton reactions are possible in a multicomponent system of charged and neutral species, resulting in a complex reaction network. Probabilities and equilibrium concentrations of the involved species are modeled by the combination of reducible Markov chains and quantum-mechanical calculations.

Collectivity in ionic liquids: a temperature dependent, polarizable molecular dynamics study.

We use polarizable molecular dynamics simulations to study the thermal dependence of both structural and dynamic properties of two ionic liquids sharing the same cation (1-ethyl-3-methylimidazolium). The linear temperature trend in the structure is accompanied by an exponential Arrhenius-like behavior of the dynamics. Our parameter-free Voronoi tessellation analysis directly casts doubt on common concepts such as the alternating shells of cations and anions and the ionicity. The latter tries to explain the physico-chemical properties of the ionic liquids based on the association and dissociation of an ion pair. However, cations are in the majority of both ion cages, around cations and around anions. There is no preference of a cation for a single anion. Collectivity is a key factor in the dynamic properties of ionic liquids. Consequently, collective rotation relaxes faster than single-particle rotations, and the activation energies for collective translation and rotation are lower than those of the single molecules.

Molecular Dynamics Simulations of Ionic Liquids and Electrolytes Using Polarizable Force Fields.

Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g., liquid electrolytes for battery applications, the presence of ions in these materials results in strong local electric fields polarizing solvent molecules and large ions. To predict properties of such systems from molecular simulations often requires either explicit or mean-field inclusion of the influence of polarization on electrostatic interactions. In this manuscript, we review the pros and cons of different treatments of polarization ranging from the mean-field approaches to the most popular explicit polarization models in molecular dynamics simulations of ionic materials. For each method, we discuss their advantages and disadvantages and emphasize key assumptions as well as their adjustable parameters. Strategies for the development of polarizable models are presented with a specific focus on extracting atomic polarizabilities. Finally, we compare simulations using polarizable and nonpolarizable models for several classes of ionic systems, discussing the underlying physics that each approach includes or ignores, implications for implementation and computational efficiency, and the accuracy of properties predicted by these methods compared to experiments.

Organic Matter from Redoximorphic Soils Accelerates and Sustains Microbial Fe(III) Reduction.

Microbial reduction of Fe(III) minerals is a prominent process in redoximorphic soils and is strongly affected by organic matter (OM). We herein determined the rate and extent of microbial reduction of ferrihydrite (Fh) with either adsorbed or coprecipitated OM by Geobacter sulfurreducens. We focused on OM-mediated effects on electron uptake and alterations in Fh crystallinity. The OM was obtained from anoxic soil columns (effluent OM, efOM) and included-unlike water-extractable OM-compounds released by microbial activity under anoxic conditions. We found that organic molecules in efOM had generally no or only very low electron-accepting capacity and were incorporated into the Fh aggregates when coprecipitated with Fh. Compared to OM-free Fh, adsorption of efOM to Fh decelerated the microbial Fe(III) reduction by passivating the Fh surface toward electron uptake. In contrast, coprecipitation of Fh with efOM accelerated the microbial reduction, likely because efOM disrupted the Fh structure, as noted by Mössbauer spectroscopy. Additionally, the adsorbed and coprecipitated efOM resulted in a more sustained Fe(III) reduction, potentially because efOM could have effectively scavenged biogenic Fe(II) and prevented the passivation of the Fh surface by the adsorbed Fe(II). Fe(III)-OM coprecipitates forming at anoxic-oxic interfaces are thus likely readily reducible by Fe(III)-reducing bacteria in redoximorphic soils.

The physical significance of the Kamlet-Taft π* parameter of ionic liquids.

The Kamlet-Taft dipolarity/polarizability parameters π* for various ionic liquids were determined using 4-tert-butyl-2-((dicyanomethylene)-5-[4-N,N-diethylamino)-benzylidene]-Δ3-thiazoline and 5-(N,N-dimethylamino)-5'-nitro-2,2'-bithiophene as solvatochromic probes. In contrast to the established π*-probe N,N-diethylnitroaniline, the chromophores presented here show excellent agreement with polarity measurement using the chemical shift of 129Xe. They do not suffer from additional bathochromic UV/vis shifts caused by hydrogen-bonding resulting in too high π*-values for some ionic liquids. In combination with large sets of various ionic liquids, these new chromophores thereby allow for detailed analysis of the physical significance of π* and the comparison to quantum-mechanical methods. We find that π* correlates strongly with the ratio of molar refractivity to molar volume, and thus with the refractive index.

The influence of the cation structure on the basicity-related polarity of ionic liquids.

UV/Vis absorption data of (E)-4-(2-[5-{4,4,5,5-tetramethyl-1,3,2-dioxaborolane-2-yl}thiene-2-yl]vinyl)-2-(dicyano-methylene)-3-cyano-5,5-dimethyl-2,5-dihydrofuran (ThTCF) as a solvatochromic probe is applied to examine the anion coordination strength (e.g. of N(CN)2, BF4, PF6, N(Tf)2, CF3COO) as a function of the cation structure of ionic liquids. Several 1-n-alky-3-methylimidazolium- and tetraalkylammonium CH3-NR3+-based ILs with different n-alkyl chain lengths (R = -C4H9, -C6H11, -C8H17, -C10H21) are considered. UV/Vis absorption data of ThTCF show subtle correlations with hydrogen bond accepting (HBA) ability-related measurands such as Kamlet-Taft ß, Freire's EHB, and Laurence ß1 parameter as a function of anion and cation structure. The different influence of the n-alkyl chain length of imidazolium- and tetraalkylammonium-based ILs on the dipolarity and HBA strength is confirmed by comparison with the 14N isotropic hyperfine coupling constants (Aiso) of a positively (CATI) and negatively charged spin probe (TSKCr) of TEMPO-type [(2,2,6,6-tetramethylpiperidin-1-yl)oxyl] and quantum chemically derived dipoles of the cations. The Aiso values correlate with the absorption energy of ThTCF and EHB, but in different ways depending on the anion or charge of the spin probe. In a final discussion of the ß, EHB, and ß1 scales in relation to ThTCF, the importance of the molar concentration N of ionic liquids for the physical significance of the respective parameters is discussed.

Solvation of anthraquinone and TEMPO redox-active species in acetonitrile using a polarizable force field.

Redox-active molecules are of interest in many fields, such as medicine, catalysis, or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often required, but few force fields are developed ad hoc for these molecules. Moreover, they do not include polarization effects, which can lead to inaccurate solvation and dynamical properties. In this work, we developed polarizable force fields for redox-active species anthraquinone (AQ) and 2,2,6,6-tetra-methylpiperidinyl-1-oxyl (TEMPO) in their oxidized and reduced states as well as for acetonitrile. We validate the structural properties of AQ, AQ•-, AQ2-, TEMPO•, and TEMPO+ in acetonitrile against density functional theory-based molecular dynamics simulations and we study the solvation of these redox molecules in acetonitrile. This work is a first step toward the characterization of the role played by AQ and TEMPO in electrochemical and catalytic devices.

LEDGF/p75 Is Required for an Efficient DNA Damage Response.

Lens epithelium-derived growth factor splice variant of 75 kDa (LEDGF/p75) plays an important role in cancer, but its DNA-damage repair (DDR)-related implications are still not completely understood. Different LEDGF model cell lines were generated: a complete knock-out of LEDGF (KO) and re-expression of LEDGF/p75 or LEDGF/p52 using CRISPR/Cas9 technology. Their proliferation and migration capacity as well as their chemosensitivity were determined, which was followed by investigation of the DDR signaling pathways by Western blot and immunofluorescence. LEDGF-deficient cells exhibited a decreased proliferation and migration as well as an increased sensitivity toward etoposide. Moreover, LEDGF-depleted cells showed a significant reduction in the recruitment of downstream DDR-related proteins such as replication protein A 32 kDa subunit (RPA32) after exposure to etoposide. The re-expression of LEDGF/p75 rescued all knock-out effects. Surprisingly, untreated LEDGF KO cells showed an increased amount of DNA fragmentation combined with an increased formation of γH2AX and BRCA1. In contrast, the protein levels of ubiquitin-conjugating enzyme UBC13 and nuclear proteasome activator PA28γ were substantially reduced upon LEDGF KO. This study provides for the first time an insight that LEDGF is not only involved in the recruitment of CtIP but has also an effect on the ubiquitin-dependent regulation of DDR signaling molecules and highlights the role of LEDGF/p75 in homology-directed DNA repair.

Streptavidin Homologues for Applications on Solid Surfaces at High Temperatures.

One of the most commonly used bonds between two biomolecules is the bond between biotin and streptavidin (SA) or streptavidin homologues (SAHs). A high dissociation constant and the consequent high-temperature stability even allows for its use in nucleic acid detection under polymerase chain reaction (PCR) conditions. There are a number of SAHs available, and for assay design, it is of great interest to determine as to which SAH will perform the best under assay conditions. Although there are numerous single studies on the characterization of SAHs in solution or selected solid phases, there is no systematic study comparing different SAHs for biomolecule-binding, hybridization, and PCR assays on solid phases. We compared streptavidin, core streptavidin, traptavidin, core traptavidin, neutravidin, and monomeric streptavidin on the surface of microbeads (10-15 µm in diameter) and designed multiplex microbead-based experiments and analyzed simultaneously the binding of biotinylated oligonucleotides and the hybridization of oligonucleotides to complementary capture probes. We also bound comparably large DNA origamis to capture probes on the microbead surface. We used a real-time fluorescence microscopy imaging platform, with which it is possible to subject samples to a programmable time and temperature profile and to record binding processes on the microbead surface depending on the time and temperature. With the exception of core traptavidin and monomeric streptavidin, all other SA/SAHs were suitable for our investigations. We found hybridization efficiencies close to 100% for streptavidin, core streptavidin, traptavidin, and neutravidin. These could all be considered equally suitable for hybridization, PCR applications, and melting point analysis. The SA/SAH-biotin bond was temperature-sensitive when the oligonucleotide was mono-biotinylated, with traptavidin being the most stable followed by streptavidin and neutravidin. Mono-biotinylated oligonucleotides can be used in experiments with temperatures up to 70 °C. When oligonucleotides were bis-biotinylated, all SA/SAH-biotin bonds had similar temperature stability under PCR conditions, even if they comprised a streptavidin variant with slower biotin dissociation and increased mechanostability.

Polarizable MD simulations of ionic liquids: How does additional charge transfer change the dynamics?

Both experimental and computational evidence exist that Coulomb interactions between the molecular ions in ionic liquids are significantly damped by almost a factor of two. This circumstance is often used to justify charge scaling. However, as polarizable MD simulations are also capable of explaining the reduced Coulomb interaction between the ionic liquid ions [C. Schröder, Phys. Chem. Chem. Phys., 2012, 14, 3089], the question arises, if the reduced Coulomb interactions are due to a charge transfer between the molecules or due to an overall effect of induced dipolar interactions. We aim to contribute to this discussion using polarizable MD simulations of 1-ethyl-3-methylimidazolium tetrafluoroborate including a new model for treating charge transfer between the cations and anions. The diffusion time scales are not changed significantly with the inclusion of charge transfer, but individual ions show a strong dependence on charge transfer amounts. Ions which have transferred more charge, and have a charge with a smaller magnitude, diffuse slower. The charge transfer model shows a slightly larger conductivity, despite having smaller charges, and shows a much stronger contribution of the anions to the conductivity. With charge transfer, the anions become the dominant species for charge transport, while the polarizable models show a roughly equal contribution from the anions and the cations.

Dielectric spectroscopy and time dependent Stokes shift: two faces of the same coin?

Different types of spectroscopy capture different aspects of dynamics and different ranges of intermolecular contributions. In this article, we investigate the dielectric relaxation spectroscopy (DRS) of collective nature and the time-dependent Stokes shift (TDSS) of disputed nature. Our computational study of unconfined and confined water clearly demonstrates that the TDSS reflects local, non-collective dynamics. Surprisingly, we found that the reaction field continuum model (RFCM) used to estimate TDSS curves solely from collective DRS spectra correctly transforms collective dynamics to local ones even in cases when the relaxation time trends are quite different. This correct transformation is possible due to structural information available in the DRS amplitude in a Kivelsen-Madden like context.

Polarizable molecular dynamics simulations of ionic liquids: Influence of temperature control.

Ionic liquids are an interesting class of soft matter with viscosities of one or two orders of magnitude higher than that of water. Unfortunately, classical, non-polarizable molecular dynamics (MD) simulations of ionic liquids result in too slow dynamics and demonstrate the need for explicit inclusion of polarizability. The inclusion of polarizability, here via the Drude oscillator model, requires amendments to the employed thermostat, where we consider a dual Nosé-Hoover thermostat, as well as a dual Langevin thermostat. We investigate the effects of the choice of a thermostat and the underlying parameters such as the masses and force constants of the Drude particles on static and dynamic properties of ionic liquids. Here, we show that Langevin thermostats are not suitable for investigating the dynamics of ionic liquids. Since polarizable MD simulations are associated with high computational costs, we employed a self-developed graphics processing unit enhanced code within the MD program CHARMM to keep the overall computational effort reasonable.

Varus or valgus positioning of the tibial component of a unicompartmental fixed-bearing knee arthroplasty does not increase wear.

PURPOSE: Higher revision rates were shown in varus- or valgus-positioned tibias in unicompartmental knee arthroplasty (UKA), but more than 15% of UKA prostheses are implanted with more than 5° of varus or valgus. This study aimed to analyze the wear rate in UKA when implanting the tibial component in either varus or valgus position versus a neutral placement at 90° to the tibial anatomical axis. The study hypothesized that a 5° varus or valgus positioning of the tibial plateau will generate less wear compared to a neutral alignment. METHODS: Wear was experimentally analyzed on a medial anatomical fixed-bearing unicompartmental knee prosthesis (Univation, Aesculap, Germany) in vitro with a customized, four-station, servohydraulic knee wear simulator, reproducing the walking cycle. The forces, loading and range of motion were applied as specified in the ISO 14243-1:2002, 5 million cycles were analyzed. The tibial components of the medial prostheses were inserted in a neutral position, with 5° varus, and 5° valgus (n = 3, each group). RESULTS: The wear rate decreased significantly with a 5° varus positioning (6.30 ± 1.38 mg/million cycles) and a 5° valgus positioning (4.96 ± 2.47 mg/million cycles) compared to the neutral position (12.16 ± 1.26 mg/million cycles) (p < 0.01 for the varus and the valgus position). The wear area on the inlay was slightly reduced in the varus and valgus group. CONCLUSION: A varus or valgus "malpositioning" up to 5° will not lead to an increased wear. Wear was even less because of the reduced articulating contact area between the inlay and the femur. A slight varus positioning of the tibial component (parallel to the anatomical joint line) positioning can be advocated from a point of wear. LEVEL OF EVIDENCE: Experimental study.

Reviewing Magnetic Particle Preparation: Exploring the Viability in Biosensing.

In this review article, we conceptually investigated the requirements of magnetic nanoparticles for their application in biosensing and related them to example systems of our thin-film portfolio. Analyzing intrinsic magnetic properties of different magnetic phases, the size range of the magnetic particles was determined, which is of potential interest for biosensor technology. Different e-beam lithography strategies are utilized to identify possible ways to realize small magnetic particles targeting this size range. Three different particle systems from 500 µm to 50 nm are produced for this purpose, aiming at tunable, vertically magnetized synthetic antiferromagnets, martensitic transformation in a single elliptical, disc-shaped Heusler Ni50Mn32.5Ga17.5 particle and nanocylinders of Co2MnSi-Heusler compound. Perspectively, new applications for these particle systems in combination with microfluidics are addressed. Using the concept of a magnetic on-off ratchet, the most suitable particle system of these three materials is validated with respect to magnetically-driven transport in a microfluidic channel. In addition, options are also discussed for improving the magnetic ratchet for larger particles.

Enantiomerization of Axially Chiral Biphenyls: Polarizable MD Simulations in Water and Butylmethylether.

In this study, we investigate the influence of chiral and achiral cations on the enantiomerization of biphenylic anions in n-butylmethylether and water. In addition to the impact of the cations and solvent molecules on the free energy profile of rotation, we also explore if chirality transfer between a chiral cation and the biphenylic anion is possible, i.e., if pairing with a chiral cation can energetically favour one conformer of the anion via diastereomeric complex formation. The quantum-mechanical calculations are accompanied by polarizable MD simulations using umbrella sampling to study the impact of solvents of different polarity in more detail. We also discuss how accurate polarizable force fields for biphenylic anions can be constructed from quantum-mechanical reference data.

Attosecond Dynamics of sp-Band Photoexcitation.

We report measurements of the temporal dynamics of the valence band photoemission from the magnesium (0001) surface across the resonance of the Γ[over ¯] surface state at 134 eV and link them to observations of high-resolution synchrotron photoemission and numerical calculations of the time-dependent Schrödinger equation using an effective single-electron model potential. We observe a decrease in the time delay between photoemission from delocalized valence states and the localized core orbitals on resonance. Our approach to rigorously link excitation energy-resolved conventional steady-state photoemission with attosecond streaking spectroscopy reveals the connection between energy-space properties of bound electronic states and the temporal dynamics of the fundamental electronic excitations underlying the photoelectric effect.