Christian Schröder | University of Vienna (original) (raw)

Papers by Christian Schröder

The Journal of chemical physics, Jan 28, 2016

Studying the changed water dynamics in the hydration layers of biomolecules is an important step ... more Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overa...

The Journal of chemical physics, Jan 28, 2016

The influence of the partial charge distribution obtained from quantum mechanics of the solute 1-... more The influence of the partial charge distribution obtained from quantum mechanics of the solute 1-methyl-6-oxyquinolinium betaine in the ground- and first excited state on the time-dependent Stokes shift is studied via molecular dynamics computer simulation. Furthermore, the effect of the employed solvent model - here the non-polarizable SPC, TIP4P and TIP4P/2005 and the polarizable SWM4 water model - on the solvation dynamics of the system is investigated. The use of different functionals and calculation methods influences the partial charge distribution and the magnitude of the dipole moment of the solute, but not the orientation of the dipole moment. Simulations based on the calculated charge distributions show nearly the same relaxation behavior. Approximating the whole solute molecule by a dipole results in the same relaxation behavior, but lower solvation energies, indicating that the time scale of the Stokes shift does not depend on peculiarities of the solute. However, the SP...

Zeitschrift für Physikalische Chemie, 2001

Quantum yields of photodissociation were determined for iodine in compressed liquid

Physical Review Letters, 2015

In the present study we combine dielectric relaxation spectroscopy with generalized Born simulati... more In the present study we combine dielectric relaxation spectroscopy with generalized Born simulations to explore the role of orientational order for protein aggregation in solutions of bovine pancreatic insulin at various pH conditions. Under aggregation-prone conditions at low pH, insulin monomers prefer antiparallel dipole alignments, which are consistent with the orientation of the monomeric subunits in the dimer structure. This alignment is also true for two dimers, suggesting that already at moderate protein concentrations the species assemble in equilibrium clusters, in which the molecules adopt preferred orientations also found for the protomers of the corresponding oligomers.

The Journal of chemical physics, Jan 28, 2016

We report a molecular dynamics study on the effect of electronic polarization on the structure an... more We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed qui...

Physical Chemistry Chemical Physics, 2015

This work compares the two major methods to introduce polarisability in Molecular Dynamics simula... more This work compares the two major methods to introduce polarisability in Molecular Dynamics simulations: induced point-dipoles and Drude oscillators.

Physical Chemistry Chemical Physics, 2011

This work reports for the first time the computational, frequency-dependent dielectric spectrum o... more This work reports for the first time the computational, frequency-dependent dielectric spectrum of the polarizable molecular ionic liquid 1-ethyl-3-methylimidazolium triflate as well as its experimental analogue. In the frequency range from 500 MHz up to 20 GHz the agreement between the computational and the experimental spectrum is quantitative. For higher frequencies up to 10 THz the agreement is still remarkably good. The experimental asymptotic limit e N is 2.3. The difference in the computational value of 1.9 comes solely from the neglect of polarizability of the hydrogen atoms. For reasons of efficiency the simulations are based on the Lagrangian algorithm for the Drude oscillator model which cannot handle polarizable hydrogens. In the computational analysis the complete spectrum of the generalized dielectric constant P Ã 0 ðnÞ is splitted into its translational and non-translational components, called dielectric conductivity W 0 (n) and dielectric permittivity e(n). For 1-ethyl-3-methylimidazolium triflate both components contribute with equal weight and overlap in the complete frequency range. The inclusion of polarization forces, however, is quite different for the two components: the collective non-translational dynamics is accelerated and hence the dielectric permittivity is shifted to higher frequencies. The low frequency region of the dielectric conductivity is also affected while its high frequency part remains almost unchanged. Inductive effects are not only visible at high frequencies but also contribute in the sub-GHz region. The computational peak found in this region correlates with the experimental OKE-spectrum. It may be interpreted as the correlation between the induced dipole moment of the cations and the local electric field exerted by the anionic cage.

Phys. Chem. Chem. Phys., 2014

Using the reaction field continuum model the dielectric spectra of three selected ionic liquids w... more Using the reaction field continuum model the dielectric spectra of three selected ionic liquids were converted to the solvation dynamics of coumarin 153. It is shown in detail that the inclusion of the static conductivity in this model is essential.

The Journal of chemical physics, Jan 14, 2014

Combining simulation and model theories, this paper analyses the impact of pair dynamics on the i... more Combining simulation and model theories, this paper analyses the impact of pair dynamics on the intermolecular nuclear Overhauser effect (NOE) in liquids. For the first time, we give a distance resolved NOE. When applied to the ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate the NOE turns out to be of long-range nature. This behaviour translates to the experimentally measured cross- and longitudinal relaxation rates. We were able to calculate the heteronuclear NOE from simulation data, despite the high computational effort. Model theories are computationally less demanding and cover the complete frequency range of the respective spectral density function, they are usually based on a very simple pair distribution function and the solution of the diffusion equation. In order to model the simulated data sufficiently, these simplifications in structure and dynamics have to be generalised considerably.

Physical Chemistry Chemical Physics, 2012

Molecular ionic liquids are typically characterized by strong electrostatic interactions resultin... more Molecular ionic liquids are typically characterized by strong electrostatic interactions resulting in a charge ordering and retardation of their translational and rotational behaviour. Unfortunately, this effect is often overestimated in classical molecular dynamics simulations. This can be circumvented in a twofold way: the easiest way is to reduce the partial charges of the ions to sub-integer values of ±0.7-0.9 e. The more realistic model is to include polarizable forces, e.g. Drude-oscillators, but it comes along with an increasing computational effort. On the other hand, charge-scaled models are claimed to take an average polarizability into account. But do both models have the same impact on structure and dynamics of molecular ionic liquids? In the present study several molecular dynamics simulations of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate are performed with different levels of polarization as well as with varying charge scaling factors of 0.74 to 0.90. The analysis of the structural and dynamical results are performed in different levels: from the atomic point of view over the molecular level to collective properties determined by the complete sample.

Physical Chemistry Chemical Physics, 2011

The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was stu... more The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was studied at varying water content. 1-Ethyl-3-methylimidazolium and trifluoromethanesulfonate were the cation and anion, respectively. The protein stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations. The lengths of the respective trajectories extended up to 200 nanoseconds in order to cover the complete solvent dynamics. Considering the above mentioned properties as a function of the water content they all exhibit a maximum or minimum at the very same mole fraction. While the exact value x(H(2)O) = 0.927 depends on the underlying force field, its origin may be traced back to the competition between the van der Waals and the electrostatic energy of the protein as well as to the transition from aqueous dielectric screening to ionic charge screening with decreasing water content. The parameter-free Voronoi decomposition of space served as a basis for the analysis of most results. In particular, solvation shells were naturally inferred from this concept. In addition to the molecular analysis a mesoscopic view is given in terms of dielectric properties. Thereby, the net dielectric constant is decomposed into contributions from the protein, the first and second solvation shells as well as the bulk. Cross-terms between these components are given, too.

Journal of Chemical Theory and Computation, 2012

The Journal of Chemical Physics, 2011

In this computational study, the collective translational motions of 1-ethyl-3-methylimidazolium ... more In this computational study, the collective translational motions of 1-ethyl-3-methylimidazolium triflate, characterized by its current correlation function and its collective dipolar displacement, are interpreted in terms of an ion cage around a central ion. Thereby, a coincidence of the relevant time constants is observed. Furthermore, the ion cage is long living and its composition is rather heterogeneous. Besides high numbers of counter ions, several ions of like charge populate the first shell around a central ion. In contrast to the strong influence of the local environment on the collective translational motion, rotations are strictly collective. In other words, a local picture falls short of describing the overall antiparallel alignment of ionic dipoles. A further issue of this work is the interpretation of the initial region of the collective dipolar displacement. It can be related to all collective translational processes showing up in the computational dielectric spectrum. In particular, slow translational processes which are invisible in the current correlation function can be detected. The inclusion of these slow processes allow for an excellent computational reconstruction of the experimental spectrum of the generalized dielectric constant.

The Journal of Chemical Physics, 2009

The Journal of Chemical Physics, 2008

In this study we present the results of the molecular dynamics simulation of the ionic liquids: 1... more In this study we present the results of the molecular dynamics simulation of the ionic liquids: 1-butyl-3-methyl-imidazolium tetrafluoroborate and trifluoromethylacetate as well as 1-ethyl-3-methyl-imidazolium dicyanamide. Ionic liquids are characterized by both a molecular dipole moment and a net charge. Thus, in contrast to a solution of simple ions in a (non-) polar solvent, rotational and translational effects influence the very same molecule. This study works out the theoretical framework necessary to compute the conductivity spectrum and its low frequency limit of ionic liquids. Merging these computed conductivity spectra with previous simulation results on the dielectric spectra of ionic liquids yields the spectrum of the generalized dielectric constant, which may be compared to experiments. This spectrum was calculated for the three ionic liquids over six orders of magnitude in frequency ranging from 10 MHz to 50 THz. The role of rotation and translation and their coupling term on the generalized dielectric constant is discussed in detail with a special emphasis on the zero-frequency limit. Thereby, the frequency dependence of the cross correlation between the collective rotational dipole moment and the current is discussed.

Chemical Communications, 2012

The Journal of chemical physics, Jan 28, 2016

Studying the changed water dynamics in the hydration layers of biomolecules is an important step ... more Studying the changed water dynamics in the hydration layers of biomolecules is an important step towards fuller understanding of their function and mechanisms, but has shown to be quite difficult. The measurement of the time-dependent Stokes shift of a chromophore attached to the biomolecule is a promising method to achieve this goal, as published in Sajadi et al. [J. Phys. Chem. Lett., 5, 1845 (2014).] where trehalose was used as biomolecule, 1-methyl-6-oxyquinolinium betaine as chromophore, and water as solvent. An overall retardation of solvent molecules is then obtained by comparison of the linked system to the same system without trehalose, but contributions from different subgroups of solvent molecules, for example, molecules close to or far from trehalose, are unknown. The difficulty arising from these unknown contributions of retarded and possibly unretarded solvent molecules is overcome in this work by conducting computer simulations on this system and decomposing the overa...

The Journal of chemical physics, Jan 28, 2016

The influence of the partial charge distribution obtained from quantum mechanics of the solute 1-... more The influence of the partial charge distribution obtained from quantum mechanics of the solute 1-methyl-6-oxyquinolinium betaine in the ground- and first excited state on the time-dependent Stokes shift is studied via molecular dynamics computer simulation. Furthermore, the effect of the employed solvent model - here the non-polarizable SPC, TIP4P and TIP4P/2005 and the polarizable SWM4 water model - on the solvation dynamics of the system is investigated. The use of different functionals and calculation methods influences the partial charge distribution and the magnitude of the dipole moment of the solute, but not the orientation of the dipole moment. Simulations based on the calculated charge distributions show nearly the same relaxation behavior. Approximating the whole solute molecule by a dipole results in the same relaxation behavior, but lower solvation energies, indicating that the time scale of the Stokes shift does not depend on peculiarities of the solute. However, the SP...

Zeitschrift für Physikalische Chemie, 2001

Quantum yields of photodissociation were determined for iodine in compressed liquid

Physical Review Letters, 2015

In the present study we combine dielectric relaxation spectroscopy with generalized Born simulati... more In the present study we combine dielectric relaxation spectroscopy with generalized Born simulations to explore the role of orientational order for protein aggregation in solutions of bovine pancreatic insulin at various pH conditions. Under aggregation-prone conditions at low pH, insulin monomers prefer antiparallel dipole alignments, which are consistent with the orientation of the monomeric subunits in the dimer structure. This alignment is also true for two dimers, suggesting that already at moderate protein concentrations the species assemble in equilibrium clusters, in which the molecules adopt preferred orientations also found for the protomers of the corresponding oligomers.

The Journal of chemical physics, Jan 28, 2016

We report a molecular dynamics study on the effect of electronic polarization on the structure an... more We report a molecular dynamics study on the effect of electronic polarization on the structure and single-particle dynamics of mixtures of the aprotic ionic liquid 1-ethyl-3-methylimidazolium bis-(trifluoromethylsulfonyl)-imide ([EMIM][TFSI]) doped with a lithium salt with the same anion at 298 K and 1 bar. In particular, we analyze the effect of electron density fluctuations on radial distribution functions, velocity autocorrelation functions, cage correlation functions, mean-squared displacements, and vibrational densities of states, comparing the predictions of the quantum-chemistry-based Atomistic Polarizable Potential for Liquids, Electrolytes, & Polymers (APPLE&P) with those of its nonpolarizable version and those of the standard non-polarizable Optimized Potentials for Liquid Simulations-All Atom (OPLS-AA). We found that the structure of the mixture is scarcely modified by the fluctuations in electron charge of their constituents, but their transport properties are indeed qui...

Physical Chemistry Chemical Physics, 2015

This work compares the two major methods to introduce polarisability in Molecular Dynamics simula... more This work compares the two major methods to introduce polarisability in Molecular Dynamics simulations: induced point-dipoles and Drude oscillators.

Physical Chemistry Chemical Physics, 2011

This work reports for the first time the computational, frequency-dependent dielectric spectrum o... more This work reports for the first time the computational, frequency-dependent dielectric spectrum of the polarizable molecular ionic liquid 1-ethyl-3-methylimidazolium triflate as well as its experimental analogue. In the frequency range from 500 MHz up to 20 GHz the agreement between the computational and the experimental spectrum is quantitative. For higher frequencies up to 10 THz the agreement is still remarkably good. The experimental asymptotic limit e N is 2.3. The difference in the computational value of 1.9 comes solely from the neglect of polarizability of the hydrogen atoms. For reasons of efficiency the simulations are based on the Lagrangian algorithm for the Drude oscillator model which cannot handle polarizable hydrogens. In the computational analysis the complete spectrum of the generalized dielectric constant P Ã 0 ðnÞ is splitted into its translational and non-translational components, called dielectric conductivity W 0 (n) and dielectric permittivity e(n). For 1-ethyl-3-methylimidazolium triflate both components contribute with equal weight and overlap in the complete frequency range. The inclusion of polarization forces, however, is quite different for the two components: the collective non-translational dynamics is accelerated and hence the dielectric permittivity is shifted to higher frequencies. The low frequency region of the dielectric conductivity is also affected while its high frequency part remains almost unchanged. Inductive effects are not only visible at high frequencies but also contribute in the sub-GHz region. The computational peak found in this region correlates with the experimental OKE-spectrum. It may be interpreted as the correlation between the induced dipole moment of the cations and the local electric field exerted by the anionic cage.

Phys. Chem. Chem. Phys., 2014

Using the reaction field continuum model the dielectric spectra of three selected ionic liquids w... more Using the reaction field continuum model the dielectric spectra of three selected ionic liquids were converted to the solvation dynamics of coumarin 153. It is shown in detail that the inclusion of the static conductivity in this model is essential.

The Journal of chemical physics, Jan 14, 2014

Combining simulation and model theories, this paper analyses the impact of pair dynamics on the i... more Combining simulation and model theories, this paper analyses the impact of pair dynamics on the intermolecular nuclear Overhauser effect (NOE) in liquids. For the first time, we give a distance resolved NOE. When applied to the ionic liquid 1-ethyl-3-methyl-imidazolium tetrafluoroborate the NOE turns out to be of long-range nature. This behaviour translates to the experimentally measured cross- and longitudinal relaxation rates. We were able to calculate the heteronuclear NOE from simulation data, despite the high computational effort. Model theories are computationally less demanding and cover the complete frequency range of the respective spectral density function, they are usually based on a very simple pair distribution function and the solution of the diffusion equation. In order to model the simulated data sufficiently, these simplifications in structure and dynamics have to be generalised considerably.

Physical Chemistry Chemical Physics, 2012

Molecular ionic liquids are typically characterized by strong electrostatic interactions resultin... more Molecular ionic liquids are typically characterized by strong electrostatic interactions resulting in a charge ordering and retardation of their translational and rotational behaviour. Unfortunately, this effect is often overestimated in classical molecular dynamics simulations. This can be circumvented in a twofold way: the easiest way is to reduce the partial charges of the ions to sub-integer values of ±0.7-0.9 e. The more realistic model is to include polarizable forces, e.g. Drude-oscillators, but it comes along with an increasing computational effort. On the other hand, charge-scaled models are claimed to take an average polarizability into account. But do both models have the same impact on structure and dynamics of molecular ionic liquids? In the present study several molecular dynamics simulations of 1-ethyl-3-methylimidazolium trifluoromethanesulfonate are performed with different levels of polarization as well as with varying charge scaling factors of 0.74 to 0.90. The analysis of the structural and dynamical results are performed in different levels: from the atomic point of view over the molecular level to collective properties determined by the complete sample.

Physical Chemistry Chemical Physics, 2011

The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was stu... more The solvation of the zinc finger protein with the PDB-ID “5ZNF” in hydrated ionic liquids was studied at varying water content. 1-Ethyl-3-methylimidazolium and trifluoromethanesulfonate were the cation and anion, respectively. The protein stability as well as the solvation structure, the shell dynamics and the shell resolved dielectric properties were investigated by means of molecular dynamics simulations. The lengths of the respective trajectories extended up to 200 nanoseconds in order to cover the complete solvent dynamics. Considering the above mentioned properties as a function of the water content they all exhibit a maximum or minimum at the very same mole fraction. While the exact value x(H(2)O) = 0.927 depends on the underlying force field, its origin may be traced back to the competition between the van der Waals and the electrostatic energy of the protein as well as to the transition from aqueous dielectric screening to ionic charge screening with decreasing water content. The parameter-free Voronoi decomposition of space served as a basis for the analysis of most results. In particular, solvation shells were naturally inferred from this concept. In addition to the molecular analysis a mesoscopic view is given in terms of dielectric properties. Thereby, the net dielectric constant is decomposed into contributions from the protein, the first and second solvation shells as well as the bulk. Cross-terms between these components are given, too.

Journal of Chemical Theory and Computation, 2012

The Journal of Chemical Physics, 2011

In this computational study, the collective translational motions of 1-ethyl-3-methylimidazolium ... more In this computational study, the collective translational motions of 1-ethyl-3-methylimidazolium triflate, characterized by its current correlation function and its collective dipolar displacement, are interpreted in terms of an ion cage around a central ion. Thereby, a coincidence of the relevant time constants is observed. Furthermore, the ion cage is long living and its composition is rather heterogeneous. Besides high numbers of counter ions, several ions of like charge populate the first shell around a central ion. In contrast to the strong influence of the local environment on the collective translational motion, rotations are strictly collective. In other words, a local picture falls short of describing the overall antiparallel alignment of ionic dipoles. A further issue of this work is the interpretation of the initial region of the collective dipolar displacement. It can be related to all collective translational processes showing up in the computational dielectric spectrum. In particular, slow translational processes which are invisible in the current correlation function can be detected. The inclusion of these slow processes allow for an excellent computational reconstruction of the experimental spectrum of the generalized dielectric constant.

The Journal of Chemical Physics, 2009

The Journal of Chemical Physics, 2008

In this study we present the results of the molecular dynamics simulation of the ionic liquids: 1... more In this study we present the results of the molecular dynamics simulation of the ionic liquids: 1-butyl-3-methyl-imidazolium tetrafluoroborate and trifluoromethylacetate as well as 1-ethyl-3-methyl-imidazolium dicyanamide. Ionic liquids are characterized by both a molecular dipole moment and a net charge. Thus, in contrast to a solution of simple ions in a (non-) polar solvent, rotational and translational effects influence the very same molecule. This study works out the theoretical framework necessary to compute the conductivity spectrum and its low frequency limit of ionic liquids. Merging these computed conductivity spectra with previous simulation results on the dielectric spectra of ionic liquids yields the spectrum of the generalized dielectric constant, which may be compared to experiments. This spectrum was calculated for the three ionic liquids over six orders of magnitude in frequency ranging from 10 MHz to 50 THz. The role of rotation and translation and their coupling term on the generalized dielectric constant is discussed in detail with a special emphasis on the zero-frequency limit. Thereby, the frequency dependence of the cross correlation between the collective rotational dipole moment and the current is discussed.

Chemical Communications, 2012