Filtern
Erscheinungsjahr
Dokumenttyp
- Zeitschriftenartikel (18)
- Beitrag zu einem Tagungsband (2)
- Vortrag (1)
- Posterpräsentation (1)
Sprache
- Englisch (22)
Schlagworte
- Molecular dynamics (3)
- Crystallization (2)
- HBCD (2)
- Polymorphism (2)
- Raman spectroscopy (2)
- Affinity (1)
- Algorithm (1)
- Analysis (1)
- Anion receptors (1)
- Beta-cyclodextrin (1)
Organisationseinheit der BAM
Eingeladener Vortrag
- nein (1)
In this paper, we investigate the interconversion processes of the major flame retardant - 1,2,5,6,9,10-hexabromocyclododecane (HBCD) - by the means of statistical thermodynamics based on classical force-fields. Three ideas will be presented. First, the application of classical hybrid Monte-Carlo simulations for quantum mechanical processes will be justified. Second, the problem of insufficient convergence properties of hybrid Monte-Carlo methods for the generation of low temperature canonical ensembles will be solved by an interpolation approach. Furthermore, it will be shown how free energy differences can be used for a rate matrix computation. The results of our numerical simulations will be compared to experimental results.
The binding affinities of the six main hexabromocyclododecane (HBCD) stereoisomers and all of their possible 48 allylic pentabromocyclododecene (PBCD) metabolites to the endocrinous human transthyretin receptor (hTTR) were investigated and compared to the natural binder thyroxine, and the two brominated diphenyl ethers BDE-47 and 3-hydroxy-BDE-47. The endocrine disrupting potency was approximated by a combination of two methods: a surface matching with the natural binder thyroxine (T4) followed by approximation of free binding energies for various binding modes within hTTR. The results indicate slightly higher binding affinities for both BDE structures than for T4 itself and similarly high affinities for two trans-configurated PBCD isomers. For many other PBCD isomers, intermediate values were computed, whereas all HBCD diastereomers yielded significantly lower binding affinities.
Ergopeptides, like ergocornine and a-ergocryptine, exist in an S- and in an R-configuration. Kinetic experiments imply that certain configurations are preferred depending on the solvent. The experimental methods are explained in this article. Furthermore, computational methods are used to understand this configurational preference. Standard quantum chemical methods can predict the favored configurations by using minimum energy calculations on the potential energy landscape. However, the explicit role of the solvent is not revealed by this type of methods. In order to better understand its influence, classical mechanical molecular simulations are applied. It appears from our research that 'folding' the ergopeptide molecules into an intermediate state (between the S- and the R-configuration) is mechanically hindered for the preferred configurations.
Infraredmatrix-assisted laser dispersion and ionization(IR-MALDI) in combination with on mobility (IM) spectrometry enables the direct Analysis of biomolecules in aqueous solution. The release of ions directly from an aqueous solution is based on a phase explosion, induced by the Absorption of an IR laser pulse, which disperses the liquid as vapor, nano- and micro-droplets. The ionization process is characterized initially by a broad spatial distribution of the ions, which is a result of complex fluid dynamics and desolvation kinetics. These processes have a profound effect on the shape and width of the peaks in the IM spectra. In this work, the Transport of ions by the phase explosion-induced shockwave could be studied independently from the transport by the electric field. The shockwave-induced mean velocities of the ions at different time scales were determined through IM spectrometry and shadowgraphy. The results show a deceleration of the Ions from 118m∙s−1 at a distance of 400 μm from the liquid surface to 7.1 m∙s−1 at a distance of 10 mm, which is caused by a pileup effect. Furthermore, the desolvation kinetics were investigated
and a first-order desolvation constant of 325 ± 50 s−1
was obtained. In the second part, the IR-MALDI-IM
spectrometer is used as an HPLC detector for the twodimensional separation of a pesticide mixture.
This article describes a simple and quick in silico method for the prediction of cytochrome P450 (CYP)-mediated hydroxylation of drug-like compounds. Testosterone and progesterone, two known substrates of CYP3A4, are used to test the method. Further, we apply the procedure to predict sites of hydroxylation of isomers of the flame retardant hexabromocyclododecane by CYP3A4. Within the method, the compound is rotated in the binding pocket of the cytochrome, so that each hydrogen under consideration is placed near the active centre. Afterwards, short molecular dynamics simulations are provided for each step of the rotation. All steps of the simulation are compared concerning the distances between the hydrogens and the active centre and the corresponding energies. The computational results correlate well with experimental results.
The emphasis of the present work was to investigate the photochemical conversion of trans- to cis-zearalenone in edible oils under real-life conditions. For quantitation purposes a cis-zearalenone standard was synthesized and characterized for its identity and purity (≥95%) by 1H NMR, X-ray crystallography, HPLC fluorescence and mass spectrometric detection. In a sample survey of 12 edible oils (9 corn oils, 3 hempseed oils) from local supermarkets all corn oils contained trans-zearalenone (median 194 µg/kg), but no cis-zearalenone was detected. For alteration studies trans-zearalenone contaminated corn oils were exposed to sunlight over 4 and 30 weeks, revealing an obvious shift toward cis-zearalenone up to a cis/trans ratio of 9:1 by storage in colorless glass bottles. Irradiation experiments of trans-zearalenone in different organic solvents confirmed the preferred formation of cis-zearalenone possibly caused by entropic effects rather than by enthalpic entities as investigated by quantum chemical and classical force field simulations.
Hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens
(2013)
With this work we target the development of a predictictive model for the identification of small molecules which bind to the estrogen receptor alpha and, thus, may act as endocrine disruptors. We propose a combined thermodynamic approach for the estimation of preferential binding modes along with corresponding free energy differences using a linear interaction energy (LIE) ansatz. The LIE model is extended by a Monte Carlo approach for the computation of conformational entropies as recently developed by our group. Incorporating the entropy contribution substantially increased the correlation with experimental affinity values. Both squared coefficients for the fitted data as well as the more meaningful leave-one-out cross-validation of predicted energies were elevated up to rFit2 = 0.87 and qLOO2 = 0.82, respectively. All calculations have been performed on a set of 31 highly diverse ligands regarding their structural properties and affinities to the estrogen receptor alpha. Comparison of predicted ligand orientations with crystallographic data retrieved from the Protein database pdb.org revealed remarkable binding mode predictions.
Guideline ICH Q3D on elemental impurities (EI) was adopted by the International Council for Harmonisation of Technical Requirements for Pharmaceuticals for Human Use (ICH) and published in December 2014.
The European Medicines Agency (EMA) Committee for Medicinal Products for Human use (CHMP) adopted guideline Q3D in December 2014 and defined the dates for coming into effect .
ICH Q3D is the first globally harmonised guidance to control 24 elemental impurities in drug products administered by oral, parenteral and inhalation routes. The policy entails a paradigm shift, moving away from substance-based testing towards risk-based assessment and control strategy.
In the context of implementing Q3D in Europe, several texts and monographs of the European Pharmacopoeia (Ph. Eur.) were revised, rendering the guideline legally binding in 38 European countries. Ph. Eur. general chapter 5.20. has been modified to reflect ICH Q3D guideline and the old fashioned heavy metals test, Ph. Eur. 2.4.8., has been deleted from individual Ph. Eur. monographs for substances for human use. Furthermore, general chapter Ph. Eur. 2.4.20. Determination of metal catalyst and metal reagent residues has been completely revised and renamed Determination of elemental impurities.
Whatever the chosen analytical method, reference materials with a known content of the target element are required for the quantification of elemental impurities. This led EDQM to consider the establishment of suitable reference materials. However, due to lack of specific experience and technical equipment, external partners were sought. Three key European institutes (JRC, BAM and PTB) were identified and involved in the project.
To mitigate the overall risk at first the project focussed on the elements classified by ICH Q3D as Class 1: lead, cadmium, mercury and arsenic.
A key necessity was the traceability of the element content to the SI (International System of Units Measurement) to allow metrologically reliable and reproducible determination. This required new and specific approaches to be developed by the partners in charge (BAM and PTB).
Since January 2018 lead solution CRS, cadmium solution CRS, mercury solution CRS and arsenic solution CRS are available to the users of the Ph. Eur. .
Small-molecule oxoanions are often imprinted noncovalently as carboxylates into molecularly imprinted polymers (MIPs), requiring the use of an organic counterion. Popular species are either pentamethylpiperidine (PMP) as a protonatable cation or tetraalkylammonium (TXA) ions as permanent cations. The present work explores the influence of the TXA as a function of their alkyl chain length, from methyl to octyl, using UV/vis absorption, fluorescence titrations, and HPLC as well as MD simulations. Protected phenylalanines (Z-L/D-Phe) served as templates/analytes. While the influence of the counterion on the complex stability constants and anion-induced spectral changes shows a monotonous trend with increasing alkyl chain length at the prepolymerization stage, the cross-imprinting/rebinding studies showed a unique pattern that suggested the presence of adaptive cavities in the MIP matrix, related to the concept of induced fit of enzyme−substrate interaction. Larger cavities formed in the presence of larger counterions can take up pairs of Z-X-Phe and smaller TXA, eventually escaping spectroscopic detection. Correlation of the experimental data with the MD simulations revealed that counterion mobility, the relative distances between the three partners, and the hydrogen bond lifetimes are more decisive for the response features observed than actual distances between interacting atoms in a complex or the orientation of binding moieties. TBA has been found to yield the highest imprinting factor, also showing a unique dual behavior regarding the interaction with template and fluorescent monomer. Finally, interesting differences between both enantiomers have been observed in both theory and experiment, suggesting true control of enantioselectivity. The contribution concludes with suggestions for translating the findings into actual MIP development.
Elemental impurities (EI) in medicinal products for human use are limited according to ICH guideline Q3D, which is in force since December 2017 in Europe and US.
As a consequenceconsequence, the relevant texts of the European Pharmacopoeia (Ph. Eur.) and the United States Pharmacopeia (USP) have been modified to reflect and complement ICH Q3D, providing details on the analytical methods to be used. In those chapters (Ph. Eur. 2.4.20., USP <233>), it is stated that for the quantification of elemental impurities, certified reference materials (CRM) from a national metrology institute (NMI) or reference materials that are traceable to the CRM of an NMI should be used.
The Ph. Eur. has so far implemented elemental impurity standards of this type for the four most important elemental impurities i.e. those corresponding to ICH Q3D Class 1: lead, cadmium, mercury and arsenic.
The poster provides details on the development of those four reference standards, which was undertaken in partnership with a major institute accredited CRM producer (JRC, European Commission), and a national metrology institute (BAM and PTB, Germany), and a Designated Institute and accredited CRM producer (BAM, Germany). The reference standards were established and characterised according to rigorous metrological principles and are supplied with extended supporting information as required for the intended use.
After successful completion of the project, the four reference standards have been added to the Ph.Eur. catalogue and are in distribution. It is expected that another three elemental impurity standards will be implemented and made available to users within the next three years.
A novel approach for the simulation of host.guest systems by systematically scanning the host moleculefs orientations within the guest cavity is presented along with a thermodynamic strategy for determining preferential binding modes and corresponding optimal interaction energies between host and guest molecules. By way of example, the elution order of hexabromocyclododecane stereoisomers from high performance liquid chromatography separation on a permethylated β-cyclcodextrin stationary phase has been computed using classical molecular dynamics simulations with the explicit solvents water and acetonitrile. Comparison of estimated with experimental separation data reveals remarkable squared coefficients of correlation with R2=0.87 and a very high correlation RLOO2 . 0:72 using the leaveone-out cross-validation method and water as solvent. In particular, the approach presented shapes up as very robust in terms of the evaluated time range under consideration, reflecting well thermodynamic equilibria. These and further observations correlating with experimental results suggest the suitability of the underlying force fields and our multi-mode approach for the estimation of relative binding affinities for host–guest systems with unknown binding modes.
The interaction of self-assembled dendritic amphiphiles with drugs and dyes in aqueous solutions is of great significance for designing and optimizing shape-persistent delivery systems. Here we present deeper insight for two examples of low molecular weight (LMW) nonionic dendritic amphiphiles as host molecules and a series of selected aromatic guest model molecules (benzene, naphthalene, biphenyl, terphenyl, anthracene, and pyrene). Aromatic guest molecules were incorporated into the self-assemblies of dendritic nanocarriers, and the resultant complexes were studied by a combination of UV, NMR, computational simulation, and small-angle X-ray-scattering (SAXS) techniques in order to determine the loading capacity, localization, and specific interactions in dendritic amphiphiles with guest molecules. Our findings revealed that the localization of guest molecules in the hydrophobic region and the loading capacity of guest molecules are dependent on their size and the arrangement of aromatic rings instead of the loading amount. Furthermore, the shape of self-assembled host molecules was found to be ellipsoidal and highly persistent even after loading the guest molecules. To the best of our knowledge, this is the first systematic host–guest study, particularly with low molecular weight nonionic dendritic amphiphilies and aromatic guest molecules. Thus, this study opens new possibilities and ways to explore the transport behavior of aromatic drugs with such nanocarriers.
A novel, cost-efficient method for the analytical extraction of the Fusarium mycotoxin zearalenone (ZON) from edible oils by dynamic covalent hydrazine chemistry (DCHC) was developed and validated for its application with high performance liquid chromatography-fluorescence detection (HPLC-FLD). ZON is extracted from the edible oil by hydrazone formation on a polymer resin functionalised with hydrazine groups and subsequently released by hydrolysis. Specifity and precision of this approach are superior to liquid partitioning or gel permeation chromatography (GPC). DCHC also extracts zearalanone (ZAN) but not α-/β-zearalenol or -zearalanol. The hydrodynamic properties of ZON, which were estimated using molecular simulation data, indicate that the compound is unaffected by nanofiltration through the resin pores and thus selectively extracted. The method's levels of detection and quantification are 10 and 30 µg/kg, using 0.2 g of sample. Linearity is given in the range of 10-20,000 µg/kg, the average recovery being 89%. Bias and relative standard deviations do not exceed 7%. In a sample survey of 44 commercial edible oils based on various agricultural commodities (maize, olives, nuts, seeds, etc.) ZON was detected in four maize oil samples, the average content in the positive samples being 99 µg/kg. The HPLC-FLD results were confirmed by HPLC-tandem mass spectrometry and compared to those obtained by a liquid partitioning based sample preparation procedure.
The choice of solvents influences crystalline solid formed during the crystallization of active pharmaceutical ingredients (API). The underlying effects are not always well understood because of the complexity of the systems. Theoretical models are often insufficient to describe this phenomenon. In this study, the crystallization behavior of the model drug paracetamol in different solvents was studied based on experimental and molecular dynamics data. The crystallization process was followed in situ using time-resolved Raman spectroscopy. Molecular dynamics with simulated annealing algorithm was used for an atomistic understanding of the underlying processes. The experimental and theoretical data indicate that paracetamol molecules adopt a particular geometry in a given solvent predefining the crystallization of certain polymorphs
Stable isotope ratios and trace element concentrations of fossil bones and teeth are important geochemical proxies for the reconstruction of diet and past environment in archaeology and palaeontology. However, since diagenesis can significantly alter primary diet-related isotope signatures and elemental compositions, it is important to understand and quantify alteration processes. Here, we present the results of in-vitro Alteration experiments of dental tissues from a modern African elephant molar reacted in aqueous solutions at 30 °C and 90 °C for 4 to 63 days. Dental cubes with ≈ 3 mm edge length, comprising both enamel and dentin, were placed into 2 mL of acidic aqueous solution enriched in different isotopes (25Mg, 44Ca, 67Zn, 86Sr, initial pH 1). Element and isotope distribution profiles across the reacted cubes were measured with LA-(MC-)ICP-MS and EMPA, while potential effects on the bioapatite crystal structure were characterised by Raman spectroscopy. In all experiments isotope ratios measured by LA-(MC-)ICP-MS revealed an alteration of the enamel in the outer ≈ 200–300 μm. In contrast, dentin was fully altered (≈ 1.4 mm) after one week at 90 °C while the alteration did not exceed a depth of 150–200 μm during the 30 °C experiments. Then, the tracer solution started also to penetrate through the enamel-dentin junction into the innermost enamel, however, leaving the central part of the enamel unaltered, even after three months. The Raman spectra suggest an initial demineralisation in the acidic environment while organic matter (i.e. collagen) is still preserved. In the 90 °C experiment, Raman spectra of the v1 PO4) band of the dentin shift over time towards synthetic hydroxylapatite patterns and the Ca (and Sr) concentrations in the respective solutions decrease. This indicates precipitation of newly formed apatite. Isotope and element concentration profiles across the dental tissues reveal different exchange mechanisms for different isotope systems. Magnesium is leached from enamel and dentin, while Zn is incorporated into the apatite crystal structure. However, the distribution of both elements is not affected in the innermost enamel where their concentrations do not change over the whole duration of the experiments. We found no correlation of reaction depth in the cubes and experimental duration, which might be caused by natural variability of the dental material already at the beginning of the experiment. Our alteration experiments in a closed system at high temperatures ≤90 °C and low initial pH demonstrate that at least the central part of mm-thick mammalian enamel apatite seems to be resistant against alteration preserving its pristine bioapatite mineral structure as well as its in-vivo elemental and isotopic composition. The experiments assess diagenetic alteration in a novel multi-proxy approach using in-situ analyses in high spatial resolution. It is demonstrated that the isotopes of Ca, Sr, Zn and
Mg in the dentin are prone for diagenetic alteration, while enamel is more resistant against alteration and could be used for dietary and physiological reconstructions in fossil teeth.
This work addresses the problem of determining the number of components from sequential spectroscopic data analyzed by non-negative matrix factorization without separability assumption (SepFree NMF). These data are stored in a matrix M of dimension “measured times” versus “measured wavenumbers” and can be decomposed to obtain the spectral fingerprints of the states and their evolution over time. SepFree NMF assumes a memoryless (Markovian) process to underline the dynamics and decomposes M so that M = WH, with W representing the components’ fingerprints and H their kinetics. However, the rank of this decomposition (i.e., the number of physical states in the process) has to be guessed from pre-existing knowledge on the observed process. We propose a measure for determining the number of components with the computation of the minimal memory effect resulting from the decomposition; by quantifying how much the obtained factorization is deviating from the Markovian property, we are able to score factorizations of a different number of components. In this way, we estimate the number of different entities which contribute to the observed system, and we can extract kinetic information without knowing the characteristic spectra of the single components. This manuscript provides the mathematical background as well as an analysis of computer generated and experimental sequentially measured Raman spectra.
Raman spectroscopy is a well established tool for the analysis of vibration spectra, which then allow for the determination of individual substances in a chemical sample, or for their phase transitions. In the time-resolved-Raman-sprectroscopy the vibration spectra of a chemical sample are recorded sequentially over a time interval, such that conclusions for intermediate products (transients) can be drawn within a chemical process. The observed data-matrix M from a Raman spectroscopy can be regarded as a matrix product of two unknown matrices W and H, where the first is representing the contribution of the spectra and the latter represents the chemical spectra. One approach for obtaining W and H is the non-negative matrix factorization. We propose a novel approach, which does not need the commonly used separability assumption. The performance of this approach is shown on a real world chemical example.