TY - JOUR A1 - Weber, M. A1 - Becker, Roland A1 - Köppen, Robert A1 - Durmaz, V. T1 - Classical hybrid Monte-Carlo simulations of the interconversion of hexabromocyclododecane N2 - 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. KW - Markov process KW - Molecular dynamics KW - Rate matrix PY - 2007 SN - 1438-0064 VL - 07-31 SP - 1 EP - 18 PB - ZIB CY - Berlin AN - OPUS4-17841 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Köppen, Robert A1 - Becker, Roland A1 - Weber, M. A1 - Durmaz, V. A1 - Nehls, Irene T1 - HBCD stereoisomers: Thermal interconversion and enantiospecific trace analysis in biota T2 - DIOXIN 2008, 28th International Symposium on Halogenated Persistent Organic Pollutants (POPs) CY - Birmingham, UK DA - 2008-08-17 KW - HBCD KW - Stereoisomerie KW - Persistent Organic Pollutant KW - HPLC-MS PY - 2008 UR - http://www.dioxin20xx.org/pdfs/2008/08-819.pdf IS - Paper #154 SP - 1 EP - 4 AN - OPUS4-17842 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Weber, M. A1 - Becker, Roland A1 - Durmaz, V. A1 - Köppen, Robert T1 - Classical hybrid Monte-Carlo simulation of the interconversion of hexabromocyclododecane stereoisomers KW - HBCD KW - Isomerisation KW - Statistical thermodynamics KW - Kinetics PY - 2008 U6 - https://doi.org/10.1080/08927020802208968 SN - 0892-7022 SN - 1029-0435 VL - 34 IS - 6-7 SP - 727 EP - 736 PB - Gordon and Breach CY - New York, NY AN - OPUS4-18261 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Durmaz, V. A1 - Schmidt, Sebastian A1 - Sabri, P. A1 - Piechotta, Christian A1 - Weber, M. T1 - Hands-off linear interaction energy approach to binding mode and affinity estimation of estrogens N2 - 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. KW - Estrogenes KW - Modeling KW - Affinity PY - 2013 U6 - https://doi.org/10.1021/ci400392p SN - 1549-9596 SN - 0095-2338 SN - 1549-960X VL - 53 IS - 10 SP - 2681 EP - 2688 CY - Washington, DC AN - OPUS4-29611 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Durmaz, V. A1 - Weber, M. A1 - Becker, Roland T1 - Multi-Mode Molecular Dynamics Simulation of the Chromatographic Elution Order of Hexabromocyclododecane Stereoisomers T2 - 25th Molecular Modelling Workshop 2011, Friedrich-Alexander-Universität Nürnberg-Erlangen CY - Nuremberg-Erlangen, Germany DA - 2011-04-04 PY - 2011 AN - OPUS4-23511 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Durmaz, V. A1 - Weber, M. A1 - Becker, Roland T1 - Multi-Mode Molecular Dynamics Simulation of the Chromatographic Elution Order of Hexabromocyclododecane Stereoisomers T2 - 25th Molecular Modelling Workshop 2011, Friedrich-Alexander-Universität Nürnberg-Erlangen CY - Nuremberg-Erlangen, Germany DA - 2011-04-04 PY - 2011 AN - OPUS4-23512 LA - deu AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - CONF A1 - Weber, M. A1 - Durmaz, V. A1 - Becker, Roland A1 - Esslinger, Susanne T1 - Predictive identification of Pentabromocyclododecene (PBCD) isomers with high binding affinity to hTTR N2 - 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. T2 - Dioxin 2009 - 29th International symposium on halogenated persistent organic pollutants / Organohalogen compounds CY - Beijing, China DA - 2009-08-23 KW - Flammschutzmittel KW - Thyroxin KW - Molecular modeling PY - 2009 UR - http://www.dioxin20xx.org/pdfs/2009/09-54.pdf VL - 71 SP - 000247 EP - 000252 CY - Beijing, China AN - OPUS4-20980 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Durmaz, V. A1 - Weber, M. A1 - Becker, Roland T1 - How to simulate affinities for host-guest systems lacking binding mode information: application to the liquid chromatographic separation of hexabromocyclododecane stereoisomers N2 - A novel approach for the simulation of host.guest systems by systematically scanning the host moleculefs 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. KW - Molecular simulation KW - Molecular dynamics KW - Binding affinity KW - Elution order KW - Beta-cyclodextrin PY - 2012 U6 - https://doi.org/10.1007/s00894-011-1239-5 SN - 1610-2940 SN - 0948-5023 VL - 18 IS - 6 SP - 2399 EP - 2408 PB - Springer CY - Berlin; Heidelberg AN - OPUS4-26112 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Köppen, Robert A1 - Riedel, Juliane A1 - Proske, Matthias A1 - Drzymala, Sarah A1 - Rasenko, Tatjana A1 - Durmaz, V. A1 - Weber, M. A1 - Koch, Matthias T1 - Photochemical trans-/cis-isomerization and quantitation of zearalenone in edible oils N2 - 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. KW - Fusarium mycotoxins KW - Food KW - Analysis KW - Occurrence PY - 2012 U6 - https://doi.org/10.1021/jf3037775 SN - 0021-8561 SN - 1520-5118 VL - 60 IS - 47 SP - 11733 EP - 11740 PB - American Chemical Society CY - Columbus, Ohio AN - OPUS4-27375 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER - TY - JOUR A1 - Andrae, K. A1 - Merkel, Stefan A1 - Durmaz, V. A1 - Fackeldey, K. A1 - Köppen, Robert A1 - Weber, M. A1 - Koch, Matthias T1 - Investigation of the ergopeptide epimerization process N2 - 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. KW - Ergopeptide KW - Epimerization KW - Hybrid monte carlo KW - Molecular dynamics KW - Conformation KW - Quantum mechanics PY - 2014 U6 - http://nbn-resolving.de/urn/resolver.pl?urn:nbn:de:kobv:b43-324632 SN - 2079-3197 VL - 2 IS - 3 SP - 102 EP - 111 PB - MDPI CY - Basel AN - OPUS4-32463 LA - eng AD - Bundesanstalt fuer Materialforschung und -pruefung (BAM), Berlin, Germany ER -