Jens Smiatek

Jens Smiatek
Boehringer Ingelheim Pharma & University of Stuttgart · Institute for Computational Physics

PD. Dr.

About

114
Publications
18,086
Reads
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2,068
Citations
Additional affiliations
October 2017 - present
Forschungszentrum Jülich
Position
  • Group Leader
July 2012 - September 2017
Institute for Computational Physics
Position
  • University of Stuttgart
February 2009 - June 2012
University of Münster

Publications

Publications (114)
Article
Full-text available
The 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 val...
Article
Room temperature ionic liquid solutions confined between neutral and charged surfaces are investigated by means of atomistic Molecular Dynamics simulations. We study 1-ethyl-3-methylimidazolium dicyanamide ([EMIm]+[DCA]-) in water or dimethylsulfoxide (DMSO) mixtures in confinement between two interfaces. The analysis is based on the comparison of...
Article
We study the interactions between dipalmitoylphosphatidylcholine (DPPC) lipid bilayers in the gel and the fluid phase with ectoine, amino ectoine and water molecules by means of atomistic molecular dynamics (MD) simulations and conceptual density functional theory (DFT) calculations. Our results reveal a pronounced preferential exclusion of both co...
Article
Full-text available
The interaction of ionic liquids (ILs) with additives or impurities is crucial for the performance of ILs in technological applications. In order to understand the interaction between these, an insight onto the microscopic arrangement of molecules is needed. As a representative case, 1‐ethyl‐3‐methylimidazolium dicyanamide ([EMIM]+[DCA]−) mixtures...
Article
Full-text available
The calculation of temporally varying upstream process outcomes is a challenging task. Over the last years, several parametric, semi-parametric as well as non-parametric approaches were developed to provide reliable estimates for key process parameters. We present generic and product-specific recurrent neural network (RNN) models for the computatio...
Article
Advanced statistical approaches and new modeling procedures for biopharmaceutical development and manufacturing have received increasing attention. With this forum article, we would like to highlight the need for a consistent terminology and the necessity for appropriate model validation strategies.
Article
We study the solvation properties of standard lithium salts in various aprotic apolar solvents using conceptual density functional theory. The electronegativity and the chemical hardness of the species are introduced as reliable criteria for identifying suitable solvent-ion combinations. All salt solvation energies reveal positive values as a conse...
Article
We study the individual and combined influence of TMAO and urea on a basket-type DNA G-quadruplex by means of atomistic molecular dynamics (MD) simulations. In combination with the Kirkwood-Buff theory of solutions, we propose a simple mechanism to elucidate the impact of TMAO and urea on the G-quadruplex. Our results reveal the importance of the m...
Article
Donor numbers are important reference values for classifying the Lewis basicity of solvents. We present a conceptual density functional theory (DFT) formalism for the calculation of Donor numbers in order to overcome experimental challenges. Our results reveal a high degree of agreement with the experimental values for distinct protic and aprotic s...
Article
Full-text available
We 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...
Article
Compatible solutes accumulate in the cytoplasm of halophilic microorganisms, enabling their survival in a high-salinity environment. Ectoine is such a compatible solute. It is a zwitterionic molecule that strongly interacts with surrounding water molecules and changes the dynamics of the local hydration shell. Ectoine interacts with biomolecules su...
Article
Full-text available
ent 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 ar...
Article
Quantitative unit operation models for the optimization and refinement of modern late-stage biopharmaceutical drug manufacturing processes have recently attracted increasing attention. The supplementary benefits of these models include increased process robustness and control in combination with a more stringent design of the bioprocess due to a re...
Article
Full-text available
We 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 [Sanchez...
Article
Full-text available
Polyelectrolytes in solution show a broad plethora of interesting effects. In this short review article, we focus on recent theoretical and computational findings regarding specific ion and solvent effects and their impact on the polyelectrolyte behavior. In contrast to standard mean field descriptions, the properties of polyelectrolytes are signif...
Article
Full-text available
In the quest for ever higher energy and power densities of lithium‐based batteries, numerous functional materials are being utilized, however in many cases their highly reactive nature is likely to increase the risk of danger in case of battery failures. This especially affects the aprotic non‐aqueous organic carbonate‐based electrolyte, still cons...
Article
We study the principles behind specific ion effects for alkali and halide ions in various protic and aprotic solvents with simple expressions of conceptual density functional theory (DFT). The results of our calculations are in good agreement with experimental data and underline the crucial role of frontier molecular orbital energies. Further analy...
Article
The crystalline dihydrate of the compatible solute ectoine undergoes a loss of water at ambient conditions and transforms into a highly hygroscopic anhydrate form. This unexpected transition is studied combining...
Article
Full-text available
By employing large-scale molecular dynamics simulations of atomistically resolved oligoelectrolytes in aqueous solutions, we study in detail the first four layer-by-layer deposition cycles of an oligoelectrolyte multilayer made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS). The multilayers are grown o...
Preprint
Full-text available
By employing large-scale molecular dynamics simulations of atomistically resolved oligoelectrolytes in aqueous solutions, we study in detail the first four layer-by-layer deposition cycles of an oligoelectrolyte multilayer made of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) (PDADMAC/PSS). The multilayers are grown o...
Article
Propylene carbonate (PC) together with cyclic sulfur compounds such as tetrahydrothiophene 1-oxide (THT1oxide) as co-solvent and lithium hexafluorophosphate (LiPF6) as conducting salt are introduced as new aprotic liquid electrolytes for lithium-ion batteries. Starting with the single solvent electrolyte LiPF6 in PC, by addition of THT1oxide, the i...
Article
Solvation in mixtures of 1-ethyl-3-methylimidazolium acetate ionic liquid with water in a molar concentration of 5% is studied by means of atomistic molecular dynamics (MD) simulations. We employed a spherical coarse-grained parameterization to describe a model solute and we performed MD simulations with positively charged, negatively charged and n...
Article
At certain mixing ratios, urea and lithium bis(trifluorosulfonyl)imide (LiTFSI) form deep eutectic solvents with a pronounced lowering of the melting temperature when compared to the individual components. Using atomistic molecular dynamics (MD) simulations and density functional theory (DFT) calculations, we study the structural and dynamic proper...
Article
Due to its well-balanced properties, lithium hexafluorophosphate (LiPF6) remains the most widely adopted conducting salt in state-of-the-art non-aqueous, aprotic liquid electrolytes used in lithium ion batteries (LIBs). However, the relatively high reactivity of LiPF6 can cause issues such as bulk electrolyte deterioration including formation of to...
Article
This work investigates the influence of uncharged interfaces on the distribution of water molecules in three aqueous dialkylimidazolium-based ionic liquid mixtures at various water concentrations. The results are based on atomistic molecular dynamics (MD) simulations supported by sum-frequency generation (SFG) experiments. All outcomes highlight an...
Article
We present a theoretical and numerical framework for the study of molecular attraction mechanisms between species in solution. The respective approach provides detailed insight into the enthalpic contributions of solvation and relies on molecular exchange reactions in combination with electronic perturbations. Associated values for chemical reactiv...
Article
Trimethylamine-N-oxide (TMAO) and urea are commonly produced in many extremophilic microorganisms that live in harsh environments. In view of high temperature, high pressure or high salt content, TMAO is known as a protein structure stabilizer, whereas urea destabilizes protein structures even under ambient conditions. Despite clear evidence, desta...
Article
Two selected and designed fluorinated cyclic phosphorus(III)-based compounds, namely 2-(2,2,3,3,3-pentafluoropropoxy)-1,3,2-dioxaphospholane (PFPOEPi) and 2-(2,2,3,3,3-pentafluoro-propoxy)-4-(trifluormethyl)-1,3,2-dioxaphospholane (PFPOEPi-1CF3) were synthesized and comprehensively characterized for high-voltage application in lithium ion batteries...
Article
Recent experimental results indicate that the stability of non‐Watson‐Crick DNA i‐motif structures can be influenced by the presence of various metal cations. Whereas Au+, Cu+, and Ag+ are stabilizing agents, alkali metal ions like Na+ or Li+ are known to destabilize the i‐motif. In terms of reduced ion‐cytosine complexes, we rationalize the experi...
Article
Full-text available
Polyelectrolytes constitute an important group of materials, used for such different purposes as the stabilization of emulsions and suspensions or oil recovery. They are also studied and utilized in the field of microfluidics. With respect to the latter, a part of the interest in polyelectrolytes inside microchannels stems from genetic analysis, co...
Article
Many organic co-solutes are known to stabilize or to destabilize native structures of proteins or DNA. Most of these effects can be explained by co-solute binding or exclusion mechanisms. A beneficial approach to study the underlying principles relies on the computation of Kirkwood–Buff integrals, which can be also used to derive detailed expressio...
Article
Full-text available
Electrolyte formulations in standard lithium ion and lithium metal batteries are complex mixtures of various components. In this article, we review molecular key principles of ion complexes in multicomponent electrolyte solutions in regards of their influence on charge transport mechanisms. We outline basic concepts for the description of ion–solve...
Article
We present a new polarizable coarse-grained martini force field for monovalent ions, called refIon, which is developed mainly for the accurate reproduction of electrostatic properties in aqueous electrolyte solutions. The ion model relies on full long-range Coulomb interactions and introduces satellite charges around the central interaction site in...
Article
In nature, the cellular environment of DNA includes not only water and ions, but also other components and co-solutes, which can exert both stabilizing and destabilizing effects on particular oligonucleotide conformations. Among them, ectoine, known as an important osmoprotectant organic co-solute in a broad range of pharmaceutical products, turns...
Article
We studied dynamic and structural properties of two lithium conducting salts in the aprotic organic solvent adiponitrile by a combination of atomistic molecular dynamics (MD) simulations, quantum chemical calculations, and experimental findings. The outcomes of our simulations reveal significant differences between both lithium salts, namely lithiu...
Article
We study the relaxation of surface-tethered polymers in microchannels under moderate confinement (i.e. h ∼ Rg, where h is the channel height and Rg is the radius of gyration of the polymer) by experiments with fluorescence-marked DNA molecules and coupled lattice-Boltzmann/molecular dynamics simulations. The determined scaling exponent suggests tha...
Article
We present the results of atomistic molecular dynamics simulations regarding specific ion effects in water, methanol and N,N-dimethylacetamide (DMAc). As reference system, we introduce rigid and rod-like models of polyanions and polycations in combination with alkali metal cations and halide anions as counterions. Pronounced specific ion effects ca...
Article
We study generic properties of poly(ionic liquid)s (PILs) via coarse-grained molecular dynamics simulations in bulk solution and under confinement. The influence of different side chain lengths on the spatial properties of the PIL systems and on the ionic transport mechanism is investigated in detail. Our results reveal the formation of apolar and...
Article
We present an application of the Kirkwood–Buff theory, which is introduced to describe the influence of cosolutes on the chemical equilibrium between dissociated and associated ion pairs in ternary electrolyte solutions. Our approach makes use of Kirkwood–Buff integrals and the introduction of a local/bulk partition model. The cosolute species can...
Article
Ionic liquids (ILs) are versatile solvents for a broad range of biotechnological applications. Recent experimental and simulation results highlight the potential benefits of dilute ILs in aqueous solution (aqueous ILs) in order to modify protein and DNA structures systematically. In contrast to a limited number of standard co-solutes like urea, ect...
Article
In nature, a wide range of biological processes such as transcription termination and intermolecular binding depend on the formation of specific DNA secondary and tertiary structures. These structures can be both stabilized or destabilized by different cosolutes coexisting with nucleic acids in the cellular environment. In our molecular dynamics si...
Article
We present an ab initio parameterization scheme for explicitly dipole-polarizable force fields for simulation of molecular liquids. The scheme allows for, in principle, arbitrarily coarse-grained representations. All parameters in the force field are derived from first principles, based on simple physical arguments. Only one fit parameter enters th...
Article
We present a coarse-grained polarizable molecular dynamics force field for the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate ([BMIm][PF₆]). For the treatment of electronic polarizability, we employ the Drude model. Our results show that the new explicitly polarizable force field reproduces important static and dynamic properties such...
Article
Five molecular models for trimethylamine N-oxide (TMAO) to be used in conjunction with compatible models for liquid water are evaluated by comparison of molecular dynamics (MD) simulation results to experimental data as functions of TMAO molality. The experimental data comprise thermodynamic properties (density, apparent molar volume and partial mo...
Article
Full-text available
Using quantum mechanical calculations within the density functional theory, we provide a comprehensive analysis of the infrared-active excitations of water molecules confined within nanocages formed by the beryl crystal lattice. We calculate the infrared-active modes including the translational, librational, and mixed-type resonances of regular and...
Article
We study the stretching of a surface-tethered polyelectrolyte confined between parallel surfaces under the application of a dc electric field. We explore the influence of the electric-field strength, the length of the polyelectrolyte, and the degree of confinement on the conformation of the polyelectrolyte by single-molecule experiments and coarse-...
Article
We study the effect of pressure-driven flow on a single surface-tethered DNA molecule confined between parallel surfaces. The influence of flow and channel parameters as well as the length of the molecules on their extension and orientation is explored. In the experiments the chain conformations are imaged by laser scanning confocal microscopy. We...
Article
We use mesoscopic lattice-Boltzmann/molecular dynamics simulations to study the stretching behavior of a single tethered polymer in micro- and nanochannels. In particular, we are interested in the connection between fluid flow properties and the force on the polymer chain. An analytical expression for the stretching force is proposed, which linearl...
Article
We study the properties of residual water molecules at different mole fractions in dialkylimidazolium based ionic liquids (ILs), namely 1-ethyl-3-methylimidazolium tetrafluoroborate (EMIM/BF4) and 1-butyl-3-methylimidazolium tetrafluoroborate (BMIM/BF4) by means of atomistic molecular dynamics (MD) simulations. The corresponding Kirkwood-Buff (KB)...
Article
Low concentrated aqueous ionic liquids (ILs) and their influence on protein structures attracted a lot of interest over the last years. This can be mostly attributed to the fact that aqueous ILs, depending on the involved ion species, can be used as protein protectants or protein denaturants. Atomistic molecular dynamics (MD) simulations are perfor...
Article
Ionic liquids (ILs) are used in a variety of technological and biological applications. Recent experimental and simulation results reveal the influence of aqueous ionic liquids on the stability of protein and enzyme structures. Depending on different parameters like the concentration and the ion composition, one can observe distinct stabilization o...
Article
The reaction ensemble and the constant pH method are well-known chemical equilibrium approaches to simulate protonation and deprotonation reactions in classical molecular dynamics and Monte Carlo simulations. In this article, we show similarity between both methods {under certain conditions}. We perform molecular dynamics simulations of a weak poly...
Article
Core-level spectra of liquids can be difficult to interpret due to the presence of a range of local environments. We present computational methods for investigating core-level spectra based on the idea that both local structural parameters and the X-ray spectra behave as functions of the local atomic configuration around the absorbing site. We iden...
Article
We present a refined version of the polarizable Martini water model - coined refPOL - designed specifically for the use with long-range electrostatics. The refPOL model improves the agreement with the experimentally measured dielectric constant and the mass density of water at room temperature compared to the original polarizable Martini water forc...
Chapter
We present an overview of free energy methods and rare event sampling techniques which are commonly used in the context of biomolecular simulations at different length scales. Our intention is to focus on the description of the main principles behind these methods. A large number of methods introduce an artificial biasing energy for the calculation...
Article
We present a novel method for the study of weak polyelectrolytes and general acid-base reactions in molecular dynamics and Monte Carlo simulations. The approach combines the advantages of the reaction ensemble and the Wang-Landau sampling method. Deprotonation and protonation reactions are simulated explicitly with the help of the reaction ensemble...
Article
We study the effect of the organic co-solute trimethylamine N-oxide (TMAO) on the volume phase transition of microgel particles made from poly(N-isopropylacrylamide) (PNIPAM) using dynamic light scattering (DLS) and all-atom molecular dynamics (MD) simulations. The DLS measurements reveal a continuous TMAO-induced shrinking process from a coil to a...
Article
Full-text available
We study the solvation and the association properties of ion pairs in aqueous dimethyl sulfoxide (DMSO) solution by atomistic molecular dynamics (MD) simulations. The ion pair is composed of two lithium and a single sulfonated diphenyl sulfone ion whose properties are studied under the influence of different DMSO concentrations. For increasing mole...
Article
Full-text available
The influence of urea on the conducting salt lithium bis-(trifluoromethanesulfonyl)-imide (LiTFSI) in terms of lithium ion coordination numbers and lithium ion transport properties is studied via atomistic molecular dynamics simulations. Our results indicate that the presence of urea favors the formation of a deep eutectic electrolyte with pronounc...
Article
Full-text available
Ectoine is an important osmolyte, which allows microorganisms to survive in extreme environmental salinity. The hygroscopic effects of ectoine in pure water can be explained by a strong water binding behavior whereas a study on the effects of ectoine in salty solution is yet missing. We provide Raman spectroscopic evidence that the influence of ect...
Article
Full-text available
The following materials were used as received without further purification: Ectoine (pu-rity > 99%) from Biotop (Germany), high purified water for chromatography (Lichrosolv) and deuterium oxide (Magnisolv 99.96% for NMR) from Merck (Germany), and NaCl from Sigma-Aldrich (Germany). The solutes were weighted within the cuvette on a Sartorius balance...
Chapter
In the reporting period July 2014 to June 2015, we performed molecular dynamics (MD) simulations with the software packages ESPResSo and Gromacs as well as custom MD-code to investigate different models of room temperature ionic liquids (RTILs) in confined environment and bulk solution. The application in mind is an IL-based electric double-layer c...
Article
Full-text available
The binding effects of osmolytes on the conformational behavior of grafted polymers are studied in this work. In particular, we focus on the interactions between urea and poly(N-isopropylacrylamide) (PNIPAM) brushes by monitoring the ellipsometric brush thickness for varying urea concentrations over a broad temperature range. The interpretation of...
Chapter
We simulate at the atomistic scale the layer-by-layer growth of a four layers thin film of poly(diallyl dimethyl ammonium chloride)/poly(styrene sulfonate sodium salt) oligomers adsorbed on a silica substrate. The simulation is intended to provide atomistic details on the structure of a swollen multilayer in solutions with different concentrations...
Article
Full-text available
There is a large body of literature investigating the static and dynamic properties of polyelectrolytes due both to their widespread application in industrial processes and their ubiquitous presence in biology. Because of their highly charged nature, polyelectrolytes tend to alter the local dielectric permittivity of the solution within a few nanom...
Article
We present simulations of aqueous polyelectrolyte complexes with new MARTINI models for the charged polymers poly(styrene sulfonate) and poly(diallyldimethylammonium). Our coarse-grained polyelectrolyte models allow us to study large length and long time scales with regard to chemical details and thermodynamic properties. The results are compared t...
Article
We study the solvation and the dynamic properties of apolar model solutes in alkyl-imidazolium based ionic liquids (IL) via all-atom molecular dynamics simulations. In regards of specific IL effects, we focused on the often used 1-Ethyl-3-Methylimidazolium cation in combination with the anions tetrafluoroborate, acetate, and bis-(trifluoromethanesu...
Article
Full-text available
Microorganisms accumulate molar concentrations of compatible solutes like ectoine to prevent proteins from denaturation. Direct structural or spectroscopic information on the mechanism and about the hydration shell around ectoine are scarce. We combined surface plasmon resonance (SPR), confocal Raman spectroscopy, molecular dynamics simulations and...