08 Fakultät Mathematik und Physik
Permanent URI for this collectionhttps://elib.uni-stuttgart.de/handle/11682/9
Browse
9 results
Search Results
Item Open Access PDADMAC/PSS oligoelectrolyte multilayers : internal structure and hydration properties at early growth stages from atomistic simulations(2020) Sánchez, Pedro A.; Vögele, Martin; Smiatek, Jens; Qiao, Baofu; Sega, Marcello; Holm, ChristianWe analyze the internal structure and hydration properties of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligoelectrolyte multilayers at early stages of their layer-by-layer growth process. Our study is based on large-scale molecular dynamics simulations with atomistic resolution that we presented recently [Sánchez et al., Soft Matter 2019, 15, 9437], in which we produced the first four deposition cycles of a multilayer obtained by alternate exposure of a flat silica substrate to aqueous electrolyte solutions of such polymers at 0.1M of NaCl. In contrast to any previous work, here we perform a local structural analysis that allows us to determine the dependence of the multilayer properties on the distance to the substrate. We prove that the large accumulation of water and ions next to the substrate observed in previous overall measurements actually decreases the degree of intrinsic charge compensation, but this remains as the main mechanism within the interface region. We show that the range of influence of the substrate reaches approximately 3 nm, whereas the structure of the outer region is rather independent from the position. This detailed characterization is essential for the development of accurate mesoscale models able to reach length and time scales of technological interest.Item Open Access Insights into Hildebrand solubility parameters : contributions from cohesive energies or electrophilicity densities?(2023) Miranda‐Quintana, Ramón Alain; Chen, Lexin; Smiatek, JensWe introduce certain concepts and expressions from conceptual density functional theory (DFT) to study the properties of the Hildebrand solubility parameter. The original form of the Hildebrand solubility parameter is used to qualitatively estimate solubilities for various apolar and aprotic substances and solvents and is based on the square root of the cohesive energy density. Our results show that a revised expression allows the replacement of cohesive energy densities by electrophilicity densities, which are numerically accessible by simple DFT calculations. As an extension, the reformulated expression provides a deeper interpretation of the main contributions and, in particular, emphasizes the importance of charge transfer mechanisms. All calculated values of the Hildebrand parameters for a large number of common solvents are compared with experimental values and show good agreement for non‐ or moderately polar aprotic solvents in agreement with the original formulation of the Hildebrand solubility parameters. The observed deviations for more polar and protic solvents define robust limits from the original formulation which remain valid. Likewise, we show that the use of machine learning methods leads to only slightly better predictability.Item Open Access Theoretical insights into specific ion effects and strong‐weak acid‐base rules for ions in solution : deriving the law of matching solvent affinities from first principles(2020) Miranda‐Quintana, Ramón Alain; Smiatek, JensWe present a detailed study of specific ion effects, volcano plots and the law of matching solvent affinities by means of a conceptual density functional theory (DFT) approach. Our results highlight that specific ion effects and the corresponding implications on the solvation energy are mainly due to differences in the electric chemical potentials and chemical hardnesses of the ions and the solvent. Our approach can be further used to identify reliable criteria for the validity of the law of matching solvent affinities. Basic expressions are derived, which allow us to study the limiting conditions for this empirical observation with regard to matching chemical reactivity indices. Moreover, we show that chaotropic and kosmotropic concepts and their implications for the stability of ion pairs are directly related to a generalized strong and weak acids and bases (SWAB) principle for ions in solution, which is also applicable to rationalize the shape of volcano plots for different solvents. In contrast to previous assumptions, all empirical findings can be explained by the properties of local solvent‐ion complexes which dominate the specific global behavior of ion pairs in solution.Item Open Access Unraveling the impact of acetylation patterns in chitosan oligomers on Cu2+ ion binding : insights from DFT calculations(2023) Singh, Ratna; Smiatek, Jens; Moerschbacher, Bruno M.Chitosans are partially acetylated polymers of glucosamine, structurally characterized by their degree of polymerization as well as their fraction and pattern of acetylation. These parameters strongly influence the physico-chemical properties and biological activities of chitosans, but structure-function relationships are only poorly understood. As an example, we here investigated the influence of acetylation on chitosan-copper complexation using density functional theory. We investigated the electronic structures of completely deacetylated and partially acetylated chitosan oligomers and their copper-bound complexes. Frontier molecular orbital theory revealed bonding orbitals for electrophiles and antibonding orbitals for nucleophiles in fully deacetylated glucosamine oligomers, while partially acetylated oligomers displayed bonding orbitals for both electrophiles and nucleophiles. Our calculations showed that the presence of an acetylated subunit in a chitosan oligomer affects the structural and the electronic properties of the oligomer by generating new intramolecular interactions with the free amino group of neighboring deacetylated subunits, thereby influencing its polarity. Furthermore, the band gap energy calculated from the fully and partially deacetylated oligomers indicates that the mobility of electrons in partially acetylated chitosan oligomers is higher than in fully deacetylated oligomers. In addition, fully deacetylated oligomers form more stable complexes with higher bond dissociation energies with copper than partially acetylated ones. Interestingly, in partially acetylated oligomers, the strength of copper binding was found to be dependent on the pattern of acetylation. Our study provides first insight into the influence of patterns of acetylation on the electronic and ion binding properties of chitosans. Depending on the intended application, the obtained results can serve as a guide for the selection of the optimal chitosan for a specific purpose.Item Open Access Solubilization of inclusion bodies : insights from explainable machine learning approaches(2023) Walther, Cornelia; Martinetz, Michael C.; Friedrich, Anja; Tscheließnig, Anne-Luise; Voigtmann, Martin; Jung, Alexander; Brocard, Cécile; Bluhmki, Erich; Smiatek, JensWe present explainable machine learning approaches for gaining deeper insights into the solubilization processes of inclusion bodies. The machine learning model with the highest prediction accuracy for the protein yield is further evaluated with regard to Shapley additive explanation (SHAP) values in terms of feature importance studies. Our results highlight an inverse fractional relationship between the protein yield and total protein concentration. Further correlations can also be observed for the dominant influences of the urea concentration and the underlying pH values. All findings are used to develop an analytical expression that is in reasonable agreement with experimental data. The resulting master curve highlights the benefits of explainable machine learning approaches for the detailed understanding of certain biopharmaceutical manufacturing steps.Item Open Access Raman spectroscopic signature of ectoine conformations in bulk solution and crystalline state(2020) Solomun, Tihomir; Hahn, Marc Benjamin; Smiatek, JensRecent crystallographic results revealed conformational changes of zwitterionic ectoine upon hydration. By means of confocal Raman spectroscopy and density functional theory calculations, we present a detailed study of this transformation process as part of a Fermi resonance analysis. The corresponding findings highlight that all resonant couplings are lifted upon exposure to water vapor as a consequence of molecular binding processes. The importance of the involved molecular groups for water binding and conformational changes upon hydration is discussed. Our approach further shows that the underlying rapid process can be reversed by carbon dioxide saturated atmospheres. For the first time, we also confirm that the conformational state of ectoine in aqueous bulk solution coincides with crystalline ectoine in its dihydrate state, thereby highlighting the important role of a few bound water molecules.Item Open Access The solvation and ion condensation properties for sulfonated polyelectrolytes in different solvents : a computational study(2014) Smiatek, Jens; Wohlfarth, Andreas; Holm, ChristianIn contrast to the broad knowledge about aqueous polyelectrolyte solutions, less is known about the properties in aprotic and apolar solvents. We therefore investigate the behavior of sulfonated polyelectrolytes in sodium form in the presence of different solvents via all-atom molecular dynamics simulations. The results clearly reveal strong variations in ion condensation constants and polyelectrolyte conformations for different solvents like water, dimethyl sulfoxide (DMSO) and chloroform. The binding free energies of the solvent contacts with the polyelectrolyte groups validate the influence of different solvent qualities. With regard to the ion condensation behavior, the numerical findings show that the explicit values for the condensation constants depend on the preferential binding coefficient as derived by the evaluation of Kirkwood--Buff integrals. Surprisingly, the smallest ion condensation constant is observed for DMSO compared to water, whereas in the presence of chloroform, virtually no free ions are present, which is in good agreement to the donor number concept. In contrast to the results for the low condensation constants, the sodium conductivity in DMSO is smaller compared to water. We are able to relate this result to the observed smaller diffusion coefficient for the sodium ions in DMSO.Item Open Access Holistic process models : a Bayesian predictive ensemble method for single and coupled unit operation models(2022) Montano Herrera, Liliana; Eilert, Tobias; Ho, I-Ting; Matysik, Milena; Laussegger, Michael; Guderlei, Ralph; Schrantz, Bernhard; Jung, Alexander; Bluhmki, Erich; Smiatek, JensThe coupling of individual models in terms of end-to-end calculations for unit operations in manufacturing processes is a challenging task. We present a probability distribution-based approach for the combined outcomes of parametric and non-parametric models. With this so-called Bayesian predictive ensemble, the statistical moments such as mean value and standard deviation can be accurately computed without any further approximation. It is shown that the ensemble of different model predictions leads to an uninformed prior distribution, which can be transformed into a predictive posterior distribution using Bayesian inference and numerical Markov Chain Monte Carlo calculations. We demonstrate the advantages of our method using several numerical examples. Our approach is not restricted to certain unit operations, and can also be used for the more robust interpretation and assessment of model predictions in general.Item Open Access Principles of molecular evolution : concepts from non-equilibrium thermodynamics for the multilevel theory of learning(2024) Smiatek, JensWe present a non-equilibrium thermodynamics approach to the multilevel theory of learning for the study of molecular evolution. This approach allows us to study the explicit time dependence of molecular evolutionary processes and their impact on entropy production. Interpreting the mathematical expressions, we can show that two main contributions affect entropy production of molecular evolution processes which can be identified as mutation and gene transfer effects. Accordingly, our results show that the optimal adaptation of organisms to external conditions in the context of evolutionary processes is driven by principles of minimum entropy production. Such results can also be interpreted as the basis of some previous postulates of the theory of learning. Although our macroscopic approach requires certain simplifications, it allows us to interpret molecular evolutionary processes using thermodynamic descriptions with reference to well-known biological processes.