TY - JOUR A1 - Kramer, Markus A1 - Kleinpeter, Erich T1 - A conformational study of N-acetyl glucosamine derivatives utilizing residual dipolar couplings JF - Journal of magnetic resonance N2 - The conformational analyses of six non-rigid N-acetyl glucosamine (NAG) derivatives employing residual dipolar couplings (RDCs) and NOEs together with molecular dynamics (MD) simulations are presented. Due to internal dynamics we had to consider different conformer ratios existing in solution. The good quality of the correlation between theoretically and experimentally obtained RDCs show the correctness of the calculated conformers even if the ratios derived from the MD simulations do not exactly meet the experimental data. If possible, the results were compared to former published data and commented. KW - NMR KW - Residual dipolar couplings KW - Molecular dynamics KW - N-acetyl glucosamine derivatives KW - Carbohydrates Y1 - 2011 U6 - https://doi.org/10.1016/j.jmr.2011.06.029 SN - 1090-7807 VL - 212 IS - 1 SP - 174 EP - 185 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Beye, Martin A1 - Wernet, Ph. A1 - Schüßler-Langeheine, Christian A1 - Föhlisch, Alexander T1 - Time resolved resonant inelastic X-ray scattering: a supreme tool to understand dynamics in solids and molecules JF - Journal of electron spectroscopy and related phenomena : the international journal on theoretical and experimental aspects of electron spectroscopy N2 - Dynamics in materials typically involve different degrees of freedom, like charge, lattice, orbital and spin in a complex interplay. Time-resolved resonant inelastic X-ray scattering (RIXS) as a highly selective tool can provide unique insight and follow the details of dynamical processes while resolving symmetries, chemical and charge states, momenta, spin configurations, etc. In this paper, we review examples where the intrinsic scattering duration time is used to study femtosecond phenomena. Free-electron lasers access timescales starting in the sub-ps range through pump-probe methods and synchrotrons study the time scales longer than tens of ps. In these examples, time-resolved resonant inelastic X-ray scattering is applied to solids as well as molecular systems. KW - Resonant inelastic X-ray scattering KW - Ultrafast spectroscopy KW - Phase transitions KW - Molecular dynamics Y1 - 2013 U6 - https://doi.org/10.1016/j.elspec.2013.04.013 SN - 0368-2048 VL - 188 IS - 3 SP - 172 EP - 182 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Escribano, Bruno A1 - Akhmatskaya, Elena A1 - Reich, Sebastian A1 - Azpiroz, Jon M. T1 - Multiple-time-stepping generalized hybrid Monte Carlo methods JF - Journal of computational physics N2 - Performance of the generalized shadow hybrid Monte Carlo (GSHMC) method [1], which proved to be superior in sampling efficiency over its predecessors [2-4], molecular dynamics and hybrid Monte Carlo, can be further improved by combining it with multi-time-stepping (MTS) and mollification of slow forces. We demonstrate that the comparatively simple modifications of the method not only lead to better performance of GSHMC itself but also allow for beating the best performed methods, which use the similar force splitting schemes. In addition we show that the same ideas can be successfully applied to the conventional generalized hybrid Monte Carlo method (GHMC). The resulting methods, MTS-GHMC and MTS-GSHMC, provide accurate reproduction of thermodynamic and dynamical properties, exact temperature control during simulation and computational robustness and efficiency. MTS-GHMC uses a generalized momentum update to achieve weak stochastic stabilization to the molecular dynamics (MD) integrator. MTS-GSHMC adds the use of a shadow (modified) Hamiltonian to filter the MD trajectories in the HMC scheme. We introduce a new shadow Hamiltonian formulation adapted to force-splitting methods. The use of such Hamiltonians improves the acceptance rate of trajectories and has a strong impact on the sampling efficiency of the method. Both methods were implemented in the open-source MD package ProtoMol and were tested on a water and a protein systems. Results were compared to those obtained using a Langevin Molly (LM) method [5] on the same systems. The test results demonstrate the superiority of the new methods over LM in terms of stability, accuracy and sampling efficiency. This suggests that putting the MTS approach in the framework of hybrid Monte Carlo and using the natural stochasticity offered by the generalized hybrid Monte Carlo lead to improving stability of MTS and allow for achieving larger step sizes in the simulation of complex systems. KW - Force splitting KW - Mollification KW - Generalized hybrid Monte Carlo KW - Molecular dynamics KW - Modified Hamiltonians Y1 - 2015 U6 - https://doi.org/10.1016/j.jcp.2014.08.052 SN - 0021-9991 SN - 1090-2716 VL - 280 SP - 1 EP - 20 PB - Elsevier CY - San Diego ER - TY - JOUR A1 - Poghosyan, Armen H. A1 - Shahinyan, A. A. A1 - Koetz, Joachim T1 - Self-assembled monolayer formation of distorted cylindrical AOT micelles on gold surfaces JF - Colloids and surfaces : an international journal devoted to the principles and applications of colloid and interface science ; A, Physicochemical and engineering aspects N2 - Self-assembling features of sodium dioctyl sulfosuccinate (AOT) molecules and micelle adsorption on gold Au (111) surfaces have been examined using molecular dynamics simulation. We argue that AOT micelles display a strong adsorption on gold surfaces resulting in distorted cylindrical micelles attached to the (111) facets. The well protected Au(111) facets decorated by a dense packed elongated ellipsoidal AOT layer hinder the diffusion of the reactant to the (111) facets and could result in the preferential growth of ultra-thin gold nanoplatelets. KW - Surfactant micelles KW - Adsorption KW - Gold surface KW - Molecular dynamics Y1 - 2018 U6 - https://doi.org/10.1016/j.colsurfa.2018.02.067 SN - 0927-7757 SN - 1873-4359 VL - 546 SP - 20 EP - 27 PB - Elsevier CY - Amsterdam ER - TY - JOUR A1 - Poghosyan, Armen H. A1 - Shahinyan, A. A. A1 - Koetz, Joachim T1 - Catanionic AOT/BDAC micelles on gold {111} surfaces JF - Colloid and polymer science : official journal of the Kolloid-Gesellschaft N2 - A sodium dioctyl sulfosuccinate (AOT)/benzyl hexadecyl dimethyl ammonium chloride (BDAC) mixed micelle self-organization and adsorption on gold Au(111) surfaces have been investigated using a molecular dynamics approach. The spherical AOT/BDAC mixed micelle is strongly adsorbed on the gold surface and is disoriented to a cylinder-like shape. KW - AOT/BDAC micelles KW - Gold surfaces KW - Molecular dynamics Y1 - 2018 U6 - https://doi.org/10.1007/s00396-018-4348-1 SN - 0303-402X SN - 1435-1536 VL - 296 IS - 8 SP - 1301 EP - 1306 PB - Springer CY - New York ER - TY - JOUR A1 - Villatoro, José Andrés A1 - Weber, M. A1 - Zühlke, Martin A1 - Lehmann, A. A1 - Zenichowski, Karl A1 - Riebe, Daniel A1 - Beitz, Toralf A1 - Löhmannsröben, Hans-Gerd A1 - Kreuzer, O. T1 - Structural characterization of synthetic peptides using electrospray ion mobility spectrometry and molecular dynamics simulations JF - International Journal of Mass Spectrometry N2 - Electrospray ionization-ion mobility spectrometry was employed for the determination of collision cross sections (CCS) of 25 synthetically produced peptides in the mass range between 540-3310 Da. The experimental measurement of the CCS is complemented by their calculation applying two different methods. One prediction method is the intrinsic size parameter (ISP) method developed by the Clemmer group. The second new method is based on the evaluation of molecular dynamics (MD) simulation trajectories as a whole, resulting in a single, averaged collision cross-section value for a given peptide in the gas phase. A high temperature MD simulation is run in order to scan through the whole conformational space. The lower temperature conformational distribution is obtained through thermodynamic reweighting. In the first part, various correlations, e.g. CCS vs. mass and inverse mobility vs. m/z correlations, are presented. Differences in CCS between peptides are also discussed in terms of their respective mass and m/z differences, as well as their respective structures. In the second part, measured and calculated CCS are compared. The agreement between the prediction results and the experimental values is in the same range for both calculation methods. While the calculation effort of the ISP method is much lower, the MD method comprises several tools providing deeper insights into the conformations of peptides. Advantages and limitations of both methods are discussed. Based on the separation of two pairs of linear and cyclic peptides of virtually the same mass, the influence of the structure on the cross sections is discussed. The shift in cross section differences and peak shape after transition from the linear to the cyclic peptide can be well understood by applying different MD tools, e.g. the root-mean-square deviation (RMSD) and the root mean square fluctuation (RMSF). (C) 2018 Elsevier B.V. All rights reserved. KW - Ion mobility spectrometry KW - Electrospray ionization KW - Peptides KW - Collision cross-section KW - Molecular dynamics Y1 - 2019 U6 - https://doi.org/10.1016/j.ijms.2018.10.036 SN - 1387-3806 SN - 1873-2798 VL - 436 SP - 108 EP - 117 PB - Elsevier CY - Amsterdam ER -