TY - JOUR A1 - Ganose, Alex M. A1 - Sahasrabuddhe, Hrushikesh A1 - Asta, Mark A1 - Beck, Kevin A1 - Biswas, Tathagata A1 - Bonkowski, Alexander A1 - Bustamante, Joana A1 - Chen, Xin A1 - Chiang, Yuan A1 - Chrzan, Daryl C. A1 - Clary, Jacob A1 - Cohen, Orion A. A1 - Ertural, Christina A1 - Gallant, Max C. A1 - George, Janine A1 - Gerits, Sophie A1 - Goodall, Rhys E. A. A1 - Guha, Rishabh D. A1 - Hautier, Geoffroy A1 - Horton, Matthew A1 - Inizan, T. J. A1 - Kaplan, Aaron D. A1 - Kingsbury, Ryan S. A1 - Kuner, Matthew C. A1 - Li, Bryant A1 - Linn, Xavier A1 - McDermott, Matthew J. A1 - Mohanakrishnan, Rohith Srinivaas A1 - Naik, Aakash A. A1 - Neaton, Jeffrey B. A1 - Parmar, Shehan M. A1 - Persson, Kristin A. A1 - Petretto, Guido A1 - Purcell, Thomas A. R. A1 - Ricci, Francesco A1 - Rich, Benjamin A1 - Riebesell, Janosh A1 - Rignanese, Gian-Marco A1 - Rosen, Andrew S. A1 - Scheffler, Matthias A1 - Schmidt, Jonathan A1 - Shen, Jimmy-Xuan A1 - Sobolev, Andrei A1 - Sundararaman, Ravishankar A1 - Tezak, Cooper A1 - Trinquet, Victor A1 - Varley, Joel B. A1 - Vigil-Fowler, Derek A1 - Wang, Duo A1 - Waroquiers, David A1 - Wen, Mingjian A1 - Yang, Han A1 - Zheng, Hui A1 - Zheng, Jiongzhi A1 - Zhu, Zhuoying A1 - Jain, Anubhav T1 - Atomate2: Modular workflows for materials science N2 - High-throughput density functional theory (DFT) calculations have become a vital element of computational materials science, enabling materials screening, property database generation, and training of “universal” machine learning models. While several software frameworks have emerged to support these computational efforts, new developments such as machine learned force fields have increased demands for more flexible and programmable workflow solutions. This manuscript introduces atomate2, a comprehensive evolution of our original atomate framework, designed to address existing limitations in computational materials research infrastructure. Key features include the support for multiple electronic structure packages and interoperability between them, along with generalizable workflows that can be written in an abstract form irrespective of the DFT package or machine learning force field used within them. Our hope is that atomate2's improved usability and extensibility can reduce technical barriers for high-throughput research workflows and facilitate the rapid adoption of emerging methods in computational material science. KW - Automation KW - Materials design KW - DFT workflows KW - Phonons KW - Thermal conductivity KW - Bonding analysis PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-635759 DO - https://doi.org/10.1039/d5dd00019j SN - 2635-098X SP - 1 EP - 30 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-63575 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - GEN A1 - Ganose, Alex M. A1 - Sahasrabuddhe, Hrushikesh A1 - Asta, Mark A1 - Beck, Kevin A1 - Biswas, Tathagata A1 - Bonkowski, Alexander A1 - Bustamante, Joana A1 - Chen, Xin A1 - Chiang, Yuan A1 - Chrzan, Daryl C. A1 - Clary, Jacob A1 - Cohen, Orion A. A1 - Ertural, Christina A1 - Gallant, Max C. A1 - George, Janine A1 - Gerits, Sophie A1 - Goodall, Rhys E. A. A1 - Guha, Rishabh D. A1 - Hautier, Geoffroy A1 - Horton, Matthew A1 - Inizan, T. J. A1 - Kaplan, Aaron D. A1 - Kingsbury, Ryan S. A1 - Kuner, Matthew C. A1 - Li, Bryant A1 - Linn, Xavier A1 - McDermott, Matthew J. A1 - Mohanakrishnan, Rohith Srinivaas A1 - Naik, Aakash A. A1 - Neaton, Jeffrey B. A1 - Parmar, Shehan M. A1 - Persson, Kristin A. A1 - Petretto, Guido A1 - Purcell, Thomas A. R. A1 - Ricci, Francesco A1 - Rich, Benjamin A1 - Riebesell, Janosh A1 - Rignanese, Gian-Marco A1 - Rosen, Andrew S. A1 - Scheffler, Matthias A1 - Schmidt, Jonathan A1 - Shen, Jimmy-Xuan A1 - Sobolev, Andrei A1 - Sundararaman, Ravishankar A1 - Tezak, Cooper A1 - Trinquet, Victor A1 - Varley, Joel B. A1 - Vigil-Fowler, Derek A1 - Wang, Duo A1 - Waroquiers, David A1 - Wen, Mingjian A1 - Yang, Han A1 - Zheng, Hui A1 - Zheng, Jiongzhi A1 - Zhu, Zhuoying A1 - Jain, Anubhav T1 - Correction: Atomate2: Modular workflows for materials science N2 - Correction for “Atomate2: modular workflows for materials science” by Alex M. Ganose et al., Digital Discovery, 2025, 4, 1944–1973, https://doi.org/10.1039/D5DD00019J. PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-640297 DO - https://doi.org/10.1039/d5dd90036k SN - 2635-098X SP - 1 EP - 2 PB - Royal Society of Chemistry (RSC) CY - Cambridge AN - OPUS4-64029 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Jahnke, Annika A1 - Beck, Aaron J. A1 - Becker, Richard L. A1 - Bedulina, Daria A1 - Braun, Ulrike A1 - Gerdts, Gunnar A1 - Hildebrandt, Lars A1 - Joerss, Hanna A1 - Klein, Ole A1 - Korduan, Janine A1 - Laforsch, Christian A1 - Lannig, Gisela A1 - Leslie, Heather A. A1 - Lips, Stefan A1 - Menger, Frank A1 - Nabi, Deedar A1 - Oberbeckmann, Sonja A1 - Primpke, Sebastian A1 - Pröfrock, Daniel A1 - Ramsperger, Anja F.R.M. A1 - Römerscheid, Mara A1 - Schmitt-Jansen, Mechthild A1 - Scholz-Böttcher, Barbara M. A1 - Tröppner, Oliver A1 - Wendt-Potthoff, Katrin A1 - Kühnel, Dana T1 - Perspective article: Multisectoral considerations to enable a circular economy for plastics N2 - Plastics are widely used but improper disposal and release lead to increasing global pollution, threatening environmental and human health. To address this issue, we suggest intersectoral collaboration to achieve zero plastic pollution. The outcomes of the project P-LEACH demonstrated the enormous complexity and range of potential toxic effects of plastic-associated chemicals and micro-/nanoplastics released into water from UV-weathered plastics. We initiated an intersectoral dialogue amongst scientists, manufacturers, regulators and representatives of civil society about how to alleviate the negative impacts of plastic pollution. Circular economy offers a framework for selecting non-toxic chemicals, extending product (re)use, and waste reduction, which act to alleviate pollution when applied to plastics. We suggest three measures to advance a circular economy of plastics: 1.) Increase simplicity of chemicals in virgin plastics combined with transparent information on the contents; 2.) Consider recyclability already in plastic material and product design; 3.) Foster communication through intersectoral dialogue. Major cornerstones are the provision of standardized, easy-to-use tools to characterize plastics and plastic leachates chemically and (eco)toxicologically, the enhancement of citizen awareness enabling them to make informed choices, the creation of economic incentives for manufacturers, and sector-specific regulations to provide products that safeguard environmental and human health. KW - Plastics KW - Circular economy KW - Cross-sectoral dialogue KW - Recyclability KW - Plastic-associated chemicals PY - 2025 UR - https://nbn-resolving.org/urn:nbn:de:kobv:b43-638280 DO - https://doi.org/10.1016/j.jhazmat.2025.139326 SN - 0304-3894 VL - 496 SP - 1 EP - 9 PB - Elsevier B.V. AN - OPUS4-63828 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ruhe, L. A1 - Ickert, Stefanie A1 - Hochkirch, U. A1 - Hofmann, J. A1 - Beck, S. A1 - Thomale, J. A1 - Linscheid, M. W. T1 - Comprehensive molecular characterization of a cisplatin-specific monoclonal antibody N2 - Despite their immense and rapidly increasing importance as analytical tools or therapeutic drugs, the detailed structural features of particular monoclonal antibodies are widely unknown. Here, an antibody already in use for diagnostic purposes and for molecular dosimetry studies in cancer therapy with very high affinity and specificity for cisplatin-induced DNA modifications was studied extensively. The molecular structure and modifications as well as the antigen specificity were investigated mainly by mass spectrometry. Using nano electrospray ionization mass spectrometry, it was possible to characterize the antibody in its native state. Tandem-MS experiments not only revealed specific fragments but also gave information on the molecular structure. The detailed primary structure was further elucidated by proteolytic treatment with a selection of enzymes and high resolution tandem-MS. The data were validated by comparison with known antibody sequences. Then, the complex glycan structures bound to the antibody were characterized in all detail. The Fc-bound oligosaccharides were released enzymatically and studied by matrix-assisted laser desorption/ionization mass spectrometry. Overall 16 different major glycan structures were identified. The binding specificity of the antibody was investigated by applying synthetic single and double stranded DNA oligomers harboring distinct Pt adducts. The antibody− antigen complexes were analyzed by mass spectrometry under native conditions. The stability of the complex with double stranded DNA was also investigated. KW - Antibody KW - Native MS KW - Cisplatin KW - PTM PY - 2017 DO - https://doi.org/10.1021/acs.molpharmaceut.7b00575 SN - 1543-8384 SN - 1543-8392 VL - 14 IS - 12 SP - 4454 EP - 4461 AN - OPUS4-43997 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ruhe, L. A1 - Ickert, Stefanie A1 - Beck, S. A1 - Linscheid, M. W. T1 - A new strategy for metal labeling of glycan structures in antibodies N2 - Quantitative analysis of complex proteins is a challenging task in modern bioanalytical chemistry. Commonly available isotope labels are still suffering from limitations and drawbacks, whereas new metal labels open numerous possibilities in mass spectrometric analyses. In this work, we have developed a newmetal labeling strategy to tag glycan structures of proteins, more particularly antibodies. The oligosaccharide glycans were selectively trimmed to the last N-acetylglucosamine to which an artificial azide containing galactose residue was bound. This azide can be used for subsequent cycloaddition of an alkyne. Therefore, we developed a lanthanide-containing macrocyclic reagent to selectively connect to this azido galactose. In summary, the glycan structures of an antibody can be labeled with a metal functionality using this approach. Furthermore, the functionality of the antibodies can be fully maintained by labeling the Fc glycans instead of using labeling reagents that target amino or thiol groups. This approach enables the possibility of using elemental, besides molecular mass spectrometry, for quantitative analyses or imaging experiments of antibodies in complex biological samples. KW - Antibody KW - Metal labeling KW - Glycans KW - DOTA KW - Lanthanide PY - 2018 DO - https://doi.org/10.1007/s00216-017-0683-1 SN - 1618-2650 SN - 1618-2642 VL - 410 IS - 1 SP - 21 EP - 25 PB - Springer AN - OPUS4-44000 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Stockmann, Jörg M. A1 - Hertwig, Andreas A1 - Beck, Uwe T1 - Visualization of low-contrast surface modifications: Thin films, printed pattern, laser-induced changes, imperfections, impurities, and degradation N2 - Visualization of surface modifications may be very challenging for coating/substrate systems of either almost identical optical constants, e.g. transparent films on substrates of the same material, or minor film thickness, substance quantity and affected area, e.g. ultra-thin or island films. Methods for visualization are optical microscopy (OM), imaging ellipsometry (IE), and referenced spectroscopic ellipsometry (RSE). Imaging ellipsometry operates at oblique incidence near Brewster angle of the bare, clean or unmodified substrate. In this configuration, reflected intensities are rather weak. However, the contrast to add-on and sub-off features may be superior. Referenced spectroscopic ellipsometry operates in a two-sample configuration but with much higher intensities. In many cases, both ellipsometric techniques reveal and visualize thin films, printed-pattern, laser-induced changes, and impurities better than optical microscopy. In particular for stratified homogeneous modifications, ellipsometric techniques give access to modelling and hence thickness determination. Modifications under investigation are polymer foil residue on silicon, laser-induced changes of ta-C:H coatings on 100Cr6 steel, imperfections of ta-C:H on thermal silicon oxide, degradation of glass, thin film tin oxide pattern on silicon, printed and dried pattern of liquids such as deionized water, cleaning agents, and dissolved silicone. © 2016 Elsevier B.V. All rights reserved. T2 - International Conference on Spectroscopic Ellipsometry (ICSE-7) CY - Berlin, Germany DA - 06.06.2016 KW - Optical microscopy (OM) KW - Imaging ellipsometry (IE) KW - Referenced spectroscopic ellipsometry (RSE) KW - Thin films KW - Impurities KW - Degradation PY - 2016 DO - https://doi.org/10.1016/j.apsusc.2016.10.145 SN - 0196-4332 VL - 2017 IS - 421 SP - 807 EP - 812 PB - Elsevier B.V. AN - OPUS4-42136 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Hofmann, J. A1 - Riedel, Jens A1 - Beck, S. A1 - Pagel, K. A1 - Linscheid, M. W. T1 - Charge-induced geometrical reorganization of DNA oligonucleotides studied by tandem mass spectrometry and ion mobility N2 - Mass spectrometry is applied as a tool for the elucidation of molecular structures. This premises that gas-phase structures reflect the original geometry of the analytes, while it requires a thorough understanding and investigation of the forces controlling and affecting the gas-phase structures. However, only little is known about conformational changes of oligonucleotides in the gas phase. In this study, a series of multiply charged DNA oligonucleotides (n¼15–40) has been subjected to a comprehensive tandem mass spectrometric study to unravel transitions between different ionic gas-phase structures. The nucleobase sequence and the chain length were varied to gain insights into their influence on the geometrical oligonucleotide organization. Altogether, 23 oligonucleotides were analyzed using collision-induced fragmentation. All sequences showed comparable correlation regarding the characteristic collision energy. This value that is also a measure for stability, strongly correlates with the net charge density of the precursor ions. With decreasing charge of the oligonucleotides, an increase in the fragmentation energy was observed. At a distinct charge density, a deviation from linearity was observed for all studied species, indicating a structural reorganization. To corroborate the proposed geometrical change, collisional cross-sections of the oligonucleotides at different charge states were determined using ion mobility-mass spectrometry. The results clearly indicate that an increase in charge density and thus Coulomb repulsion results in the transition from a folded, compact form to elongated structures of the precursor ions. Our data show this structural transition to depend mainly on the charge density, whereas sequence and size do not have an influence. KW - Ion mobility KW - Collision-induced dissociation KW - Mass spectrometry KW - Oligonucleotide KW - Fragmentation KW - Tandem-MS PY - 2018 DO - https://doi.org/10.1177/1469066717746896 SN - 1469-0667 SN - 1751-6838 VL - 24 IS - 2 SP - 225 EP - 230 PB - Sage AN - OPUS4-44429 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Ickert, Stefanie A1 - Riedel, Jens A1 - Beck, S. A1 - Linscheid, M. W. T1 - Negative nucleotide ions as sensitive probes for energy specificity in collision‐induced fragmentation in mass spectrometry N2 - Rationale: The most commonly used fragmentation methods in tandem mass spectrometry (MS/MS) are collision‐induced dissociation (CID) and higher energy collisional dissociation (HCD). While in CID the preselected ions in the trap are resonantly (and m/z exclusively) excited, in HCD the entire m/z range experiences the dissociative acceleration. The different excitation is reflected in different fragment distributions. Methods: As a test‐bed for particularly pronounced fragmentation specificity, here MS/MS experiments on several 4‐mer oligonucleotides were conducted employing both collision methods and the results were thoroughly compared. Oligonucleotides are shown to be sensitive probes to subtle changes, especially in the negative ion mode. A detailed analysis of these differences reveals insight into the dissociation mechanics. Results: Thedifferencesarerepresentedinheat‐maps,whichallowforadirectvisualinspection oflargeamountsofdata.Inthesefalsecolourrepresentationsthe,sometimessubtle,changesinthe individual dissociation product distributions become distinct. Another advantage of these graphic plots can be found in the formation of systematic patterns. These patterns reflect trends in dissociation specificity which allow for the formulation of general rules in fragmentation behavior. Conclusions: Instruments equipped with two different excitation schemes for MS/MS are today widely available. Nonetheless, direct comparisons between the individual results are scarcely made. Such comparative studies bear a powerful analytical potential to elucidate fragmentation reaction mechanism. KW - DNA KW - Tandem MS KW - HCD KW - CID PY - 2018 DO - https://doi.org/10.1002/rcm.8062 SN - 0951-4198 SN - 1097-0231 VL - 32 IS - 7 SP - 597 EP - 603 PB - Wiley & Sons, Ltd. AN - OPUS4-44430 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Fischer, Daniel A1 - Hertwig, Andreas A1 - Beck, Uwe A1 - Negendank, Detlef A1 - Lohse, Volkmar A1 - Kormunda, M. A1 - Esser, N. T1 - Dependence of the optical constants and the performance in the SPREE gas measurement on the thickness of doped tin oxide over coatings N2 - In this study, thickness related changes of the optical properties of doped tin oxide were studied. Two different sets of samples were prepared. The first set was doped with iron or nickel on silicon substrate with thicknesses of 29–56 nm, the second was iron doped on gold/glass substrate with 1.6–6.3 nm. The optical constants were determined by using spectral ellipsometry (SE) followed by modelling of the dielectric function with an oscillator model using Gaussian peaks. The analysis of the optical constants shows a dependence of the refraction and the absorption on the thickness of the doped tin oxide coating. In addition to the tin oxide absorption in the UV, one additional absorption peak was found in the near-IR/red which is related to plasmonic effects due to the doping. This peak shifts from the near-IR to the red part of the visible spectrum and becomes stronger by reducing the thickness, probably due to the formation of metal nanoparticles in this layer. These results were found for two different sets of samples by using the same optical model. Afterwards the second sample set was tested in the Surface Plasmon Resonance Enhanced Ellipsometric (SPREE) gas measurement with CO gas. It was found that the thickness has significant influence on the sensitivity and thus the adsorption of the CO gas. By increasing the thickness from 1.6 nm to 5.1 nm, the sensing ability is enhanced due to a higher coverage of the surface with the over coating. This is explained by the high affinity of CO molecules to the incorporated Fe-nanoparticles in the tin oxide coating. By increasing the thickness further to 6.3 nm, the sensing ability drops because the layer disturbs the SPR sensing effect too much. T2 - 7th International Conference on Spectroscopic Ellipsometry (ICSE-7) DA - 06.06.2016 KW - Surface plasmon resonance KW - Spectroscopic ellipsometry KW - Doped tin oxide KW - Gas sensing KW - Plasmonic absorption PY - 2017 DO - https://doi.org/10.1016/j.apsusc.2016.11.188 SN - 0169-4332 VL - 421, Teil B SP - 480 EP - 486 PB - Elsevier B.V. AN - OPUS4-42692 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Rosu, Dana Maria A1 - Petrik, P. A1 - Rattmann, G. A1 - Schellenberger, M. A1 - Beck, Uwe A1 - Hertwig, Andreas T1 - Optical characterization of patterned thin films N2 - The present study investigates the use of imaging and mapping ellipsometry to determine the properties of non-ideal and patterned thin film samples. Samples which are candidates for future references and standards were prepared for this purpose. The samples investigated were lithographically patterned SiO2 and photoresist layers. The thickness and the optical constants of the two materials were determined using spectroscopic ellipsometry in the visible spectral range. On a larger lateral scale of several mm lateral resolution, the homogeneity was investigated using a goniospectral rotating compensator ellipsometer. A nulling imaging ellipsometer was used to determine the properties of the sample on a smaller scale of 25–150 µm. KW - Spectroscopic imaging and mapping ellipsometry KW - Inhomogeneous and patterned thin films KW - SiO2 KW - Photoresist KW - Ellipsometrie KW - Patterned films PY - 2014 DO - https://doi.org/10.1016/j.tsf.2013.11.052 SN - 0040-6090 VL - 571 IS - 3 SP - 601 EP - 604 PB - Elsevier CY - Amsterdam AN - OPUS4-32695 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -