Christian Schröder

University of Vienna | UniWien · Institut für Computergestützte Biologische Chemie

Protex is an open-source program that enables proton exchanges of solvent molecules during molecular dynamics simulations. While conventional molecular dynamics simulations do not allow for bond breaking or formation, protex offers an easy-to-use interface to augment these simulations and define multiple proton sites for (de-)protonation using a si...

Different spectroscopy types reveal different aspects of molecular processes in soft matter. In particular, collective observables can provide insights into intermolecular correlations invisible to the more popular single-particle methods. In this perspective we feature the dielectric relaxation spectroscopy (DRS) with an emphasis on the proper int...

This study investigates the possibilities and limitations of reproducing experimental infrared spectra of ionic liquids via polarizable molecular dynamics force fields. The force field refinement is based on FFGenOpt, an...

Dissolution dynamic nuclear polarization (dDNP) is a versatile hyperpolarization technique to boost signal intensities in nuclear magnetic resonance (NMR) spectroscopy. The possibility to dissolve biomolecules in a hyperpolarized aqueous buffer under mild conditions has recently widened the scope of NMR by dDNP. The water-to-target hyperpolarizatio...

We use polarizable molecular dynamics simulations to study the thermal dependence of both structural and dynamic properties of two ionic liquids sharing the same cation (1-ethyl-3-methylimidazolium). The linear temperature trend in the structure is accompanied by an exponential Arrhenius-like behavior of the dynamics. Our parameter-free Voronoi tes...

The protic ionic liquid 1-methylimidazolium acetate is in equilibrium with its neutral species 1-methylimidazole and acetic acid. Although several experimental data indicate that the equilibrium favors the neutral species, the system exhibits a significant conductivity. We developed a polarizable force field to describe the ionic liquid accurately...

Proton transfer reactions can enhance conductivity in protic ionic liquids. However, several proton reactions are possible in a multicomponent system of charged and neutral species, resulting in a complex reaction...

The combination of water and surface-active ionic liquids provides a unique reaction medium, facilitating aggregation and micellization of the ionic liquid to allow for chemical reactions in bulk water. With a growing focus on sustainable technologies, ionic liquids have emerged as tunable solvents for multiple applications but are often too viscou...

UV/Vis absorption data of (E)-4-(2-[5-{4,4,5,5-tetramethyl-1,3,2-dioxaborolane-2-yl}thiene-2-yl]vinyl)-2-(dicyano-methylene)-3-cyano-5,5-dimethyl-2,5-dihydrofuran (ThTCF) as a solvatochromic probe is applied to examine the anion coordination strength (e.g. of N(CN)2, BF4, PF6, N(Tf)2, CF3COO) as a function of the cation structure of ionic liquids....

In this work the role that charge delocalization plays in the non-linear optical response of ionic liquids is evaluated. The first hyperpolarizability for the non-linear process of second harmonic generation (SHG) and second hyperpolarizability for the non-linear process of electro-optical Kerr-Effect (EOKE) of a large number of ionic liquid formin...

The nuclear Overhauser effect (NOE) is a powerful tool in molecular structure elucidation, combining the subtle chemical shift of NMR and three-dimensional information independent of chemical connectivity. Its usage for intermolecular studies, however, is fundamentally limited by an unspecific long-ranged interaction behavior. This joint experiment...

Redox-active molecules are of interest in many fields, such as medicine, catalysis, or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is oft...

Electronic charge delocalization on the molecular backbones of ionic liquid-forming ions substantially impacts their molecular polarizabilities. Density functional theory calculations of polarizabilities and volumes of many cations and anions are reported and applied to yield refractive indices of 1216 ionic liquids. A novel expression for the prec...

Redox active molecules are of interest in many fields such as medicine, catalysis or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often...

Redox active molecules are of interest in many fields such as medicine, catalysis or energy storage. In particular, in supercapacitor applications, they can be grafted to ionic liquids to form so-called biredox ionic liquids. To completely understand the structural and transport properties of such systems, an insight at the molecular scale is often...

The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption measurements published in the companion paper revealed an influence of hydrophobic sidechain alterations on th...

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...

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 this study we compare the results of three different polarizable molecular dynamics force fields with an ab initio trajectory of the aqueous mixture of 1-butyl-3-methylimidazolium tetrafluoroborate and chloride, especially regarding their ability to describe static and dynamic phenomena. The discrepancies are discussed in terms of intra- and int...

An extended Designed regression analysis of experimental data on density and refractive indices of several classes of ionic liquids yielded statistically averaged atomic volumes and polarizabilities of the constituting atoms. These values can be used to predict the molecular volume and polarizability of an unknown ionic liquid as well as its mass d...

In this contribution we simulate the refractive index of several ion combinations yielding ionic liquids. The results show that their structural tunability can be exploited to successfully design liquids with task-specific refractive indices over a wide range of values, even higher than 2.0. Some designing clues are provided, being charge delocaliz...

The Kamlet-Taft dipolarity/polarizability parameters π* for various ionic liquids were determined by 4-tert-butyl-2-(dicyanomethylene)-5-[4-N,N-diethylamino)-benzylidene]-Δ3-thiazoline and 5-(N,N-dimethylamino)-5`-nitro-2,2`-bithiophene as solvatochromic probes. In contrast to the established π*-probe N,N-diethylnitroaniline, the chromophores prese...

In this study, we investigate the influence of chiral and achiral cations on the enantiomerization of biphenylic anions in n-butylmethylether and water. In addition to the impact of the cations and solvent molecules on the free energy profile of rotation, we also explore if chirality transfer between a chiral cation and the biphenylic anion is poss...

Different types of spectroscopy capture different aspects of dynamics and different ranges of intermolecular contributions. In this article, we investigate the dielectric relaxation spectroscopy (DRS) of collective nature and the time-dependent Stokes shift (TDSS) of disputed nature. Our computational study of unconfined and confined water clearly...

The time-dependent Stokes shift is frequently used to study solvation dynamics experimentally and on the computer. Its ability to provide locally resolved information on solvent properties opens up a number of interesting applications. We present the methodology behind the calculation of solvation dynamics from molecular dynamics simulations with f...

We present a novel strategy for organocatalytic transfer hydrogenations relying on an ion‐paired catalyst of natural l ‐amino acids as main source of chirality in combination with racemic, atropisomeric phosphoric acids as counteranion. The combination of a chiral cation with a structurally flexible anion resulted in a novel chiral framework for as...

Ionic liquids are an interesting class of soft matter with viscosities of one or two orders of magnitude higher than that of water. Unfortunately, classical, non-polarizable molecular dynamics (MD) simulations of ionic liquids result in too slow dynamics and demonstrate the need for explicit inclusion of polarizability. The inclusion of polarizabil...

Fast-Field cycling relaxometry is a nuclear magnetic resonance method growing in popularity, yet theoretical interpretation is limited to analytical models of uncertain accuracy. We present the first study calculating fast field cycling dipolar coupling directly from a molecular dynamics simulation trajectory. In principle, the frequency-resolved d...

Both, experimental and computational evidences exist that Coulomb interactions between the molecular ions in ionic liquids are significantly damped by almost a factor of two. On the one hand, this fact explains why non-polarizable simulations with integer molecular charges tend to underestimate the dynamics, sometimes by an order of magnitude. On t...

The local changes in protein hydration dynamics upon encapsulation of the protein or macromolecular crowding are essential to understand protein function in cellular environments. We were able to obtain a spatially-resolved picture of the influence of confinement and crowding on the hydration dynamics of the protein ubiquitin by analyzing the time-...

The inclusion of explicit polarization in molecular dynamics simulation has gained increasing interest during the last several years. An understudied area is the role of polarizability in computer simulations of solvation dynamics around chromophores, particularly for the large solutes used in experimental studies. In this work, we present fully po...

Many applications in chemistry, biology, and energy storage/conversion research rely on molecular simulations to provide fundamental insight into structural and transport properties of materials with high ionic concentrations. Whether the system is comprised entirely of ions, like ionic liquids, or is a mixture of a polar solvent with a salt, e.g.,...

The bioprotective nature of monosaccharides and disaccharides is often attributed to their ability to slow down the dynamics of adjacent water molecules. Indeed, solvation dynamics close to sugars is indisputably retarded compared to bulk water. However, further research is needed on the qualitative and quantitative differences between the water dy...

Ionic liquid mixtures not only possess the well-known advantages of pure ionic liquids, but allow for a continuous and very exact fine-tuning of physico-chemical properties. Molecular dynamics simulations are a valuable tool for understanding the molecular processes that govern the behavior of IL mixtures. Considering electrochemical applications,...

The derivation of atomic polarizabilities for polarizable force eld development has been a long standing problem. Atomic polarizabilities were often rened manually starting from tabulated values, rendering an automated assignment of parameters difcult and hampering reproducibility and transferability of the obtained values. To overcome this, we tra...

We report the design and synthesis of novel ion-tagged chiral ligands for asymmetric transfer hydrogenation (ATH) in aqueous medium. Based on (R,R)-1,2-diphenylethylene diamine (DPEN) as structural motif, a straightforward three-step protocol was developed that gave access to novel chiral ligands with carbamate-substructure and pyridinium head grou...

The validity of linear response theory (LRT) in computer simulations of solvation dynamics, i.e. the time-dependent Stokes shift, has been debated widely during the last decades. Since the use of LRT is computationally less expensive than the calculation of the true nonequilibrium response, it is often invoked for large systems exhibiting a particu...

In this computational study, we investigate the morphology and dynamics of nanostructures formed by the ionic liquid 1‑dodecyl‑3‑methylimidazolium chloride [C12mim]Cl dissolved in water. Recent works emphasize the positive impact of this additive on various catalytic transformations. The assembling process revealed by molecular dynamics simulation...

A biphasic process for the hydrogenation of aldehydes was developed using a well‐defined iron (II) PNP pincer complex as model system to investigate the performance of various ionic liquids. A number of suitable hydrophobic ionic liquids based on the N(Tf)2⁻ anion were identified, allowing to immobilize the iron (II) catalyst in the ionic liquid la...

The design of room-temperature ionic liquids featuring high refractive indices is desirable for a number of applications. Introducing strongly polarizable (poly)halides as anions is a promising route to increase the polarizability of an ionic liquid and thus the refractive index. Based on the experimental refractive indices and mass densities of im...

Ionic liquids increase the solubility of various coffee ingredients in aqueous solution but little is known about the underlying mechanism. Kirkwood-Buff integrals as well as the potential of mean force indicate that the imidazolium cations are accumulated at the surface of the solutes, removing water molecules from the solute surface. Although hyd...

We present large scale polarizable simulations of mixtures of the ionic liquids 1-ethyl-3-methylimidazolium trifluoromethylsulfonate and 1-ethyl-3-methylimidazolium dicyanamide with water, where the dielectric spectra, the ion hydration and the conductivity were evaluated. The dielectric decrement, the depression of the dielectric constant of water...

Based on their tunable properties, ionic liquids attracted significant interest to replace conventional, organic solvents in biomolecular applications. Following a Gartner cycle, the expectations on this new class of solvents dropped after the initial hype due to the high viscosity, hydrolysis, and toxicity problems as well as their high cost. Sinc...

The distribution of a molecule's polarizability to individual atomic sites is inevitable to develop accurate polarizable force fields. We present the direct quantum mechanical calculation of atomic polarizabilities of 27...

Ground and excited state dipoles and polarizabilities of the chromophores N-methyl-6-oxyquinolinium betaine (MQ) and coumarin 153 (C153) in solution have been evaluated using time-dependent density functional theory (TD-DFT). A method for determining the atomic polarizabilities has been developed; the molecular dipole has been decomposed into atomi...

This study presents the large scale computer simulations of two common fluorophores, N-methyl-6-oxyquinolinium betaine and coumarin 153, in five polar or ionic solvents. The validity of linear response approximations to calculate the time-dependent Stokes shift is evaluated in each system. In most studied systems linear response theory fails. In io...

The current computational study investigates the changes in solvation dynamics of water when introducing hydrophobic side chains to the molecular probe N-methyl-6-oxyquinolinium betaine. High precision transient fluorescence and absorption measurements published in the companion paper revealed an influence of hydrophobic sidechain alterations on th...

The time-dependent fluorescence of a chromophore can be calculated from either nonequilibrium simulations, or, as long as linear response theory holds true, from equilibrium solvent fluctuations in the ground or excited state if the perturbation inflicted by the chromophore is small. The assumption of Gaussian statistics, in contrast, links the non...

The disaccharide trehalose is known to protect cells of some plants and microorganisms from freezing and desiccation injury via the protection of proteins, membranes and liposomes and is probably the most famous cryoprotectant among the carbohydrates. Proposed mechanisms range from water replacement or suppressed crystallization to changed water dy...

We studied the extraction behavior of two thioglycolate-based ionic liquids (ILs), for heavy metals from aqueous solutions; substances of interest were methyltrioctylammonium S-hexyl thioglycolate [N1888][C6SAc] and methyltrioctylphosphonium S-hexyl thioglycolate [P1888][C6SAc]. Theses ILs previously have shown very good extraction abilities toward...

The time-dependent fluorescence of a chromophore can be calculated from either nonequilibrium simulations, or, as long as linear response theory holds true, from equilibrium solvent fluctuations in the ground or excited state if the perturbation inflicted by the chromophore is small. The assumption of Gaussian statistics, in contrast, links the non...

The force field conversion from one MD program to another one is exhausting and error-prone. Although single conversion tools from one MD program to another exist not every combination and both directions of conversion are available for the favorite MD programs Amber, Charmm, Dl-Poly, Gromacs, and Lammps. We present here a general tool for the forc...

In the last two decades, while searching for interesting applications of ionic liquids as potent solvents, their solvation properties and their general impact on biomolecules, and in particular on proteins, gained interest. It turned out that ionic liquids are excellent solvents for protein refolding and crystallization. Biomolecules showed increas...

In this paper, we investigate the solvation of coffee ingredients including caffeine, gallic acid as representative for phenolic compounds and quercetin as representative for flavonoids in aqueous mixtures of the ionic liquid 1-ethyl-3-methylimidazolium acetate [C2mim][OAc] at various concentrations. Due to the anisotropy of the solutes we show tha...

In the last two decades, while searching for interesting applications of ionic liquids as potent solvents, their solvation properties and their general impact on biomolecules, and in particular on proteins, gained interest. It turned out that ionic liquids are excellent solvents for protein refolding and crystallization. Biomolecules showed increas...

In classical physics, one distinguishes three states of matter: gas, liquid and solid. In gas phase, molecules are characterised by no or hardly any interaction between them. Consequently, they display statistical disorder, i.e. arbitrary positions, and their motion is mainly of translational and/or rotational character. Their free energy A = U − T...

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 e...

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...

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...

As an example of charged, dipolar soft matter, the ionic liquid 1-ethyl-3-methyl-imidazolium dicyanamide is studied by coarse-grained molecular dynamics simulations. We focus on the link between microscopic and mesoscopic properties for both structure and dynamics. Thereby, the generalized Kirkwood g K-factor plays a central role in establishing th...

A series of surface-active ionic liquids based on the 1-dodecyl-3-methylimidazolium cation and different anions such as halides and alkylsulfates was synthesized. The aggregation behavior of these ionic liquids in water was characterized by surface tension, conductivity measurements and UV-Vis spectroscopy in order to determine the critical micelle...

An extended designed regression analysis of experimental data on density and refractive indices of several classes of ionic liquids yielded statistically averaged atomic volumes and polarizabilities of the constituting atoms. These values can be used to predict the molecular volume and polarizability of an unknown ionic liquid as well as its mass d...

We investigate by means of Molecular Dynamics simulations how the intrinsic surface structure of liquid/liquid interfaces involving ionic liquids depends on the opposite phase of varying polarity. We study 1-n-butyl-3-methylimidazolium hexafluorophosphate (BMIM PF6) and 1-n-butyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imid (BMIM NTf2). The...

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 co...

Classical Molecular Dynamics simulations describing electrostatic interactions only by point charges can be augmented by the inclusion of atomic polarisabilities modelling charge flexibility. Two widely used models, Drude oscillators and induced point-dipoles, are compared in a systematic study using their respective implementations in CHARMM and A...

Using extensive classical molecular dynamics simulations, we compute the dielectric and far infrared spectra of nine popular water models, including polarizable and non-polarizable ones. We analyze the dielectric spectra using a two-relaxation model that allows to extract the characteristic time of both the main dielectric relaxation and, of the fa...

Dielectric spectroscopy is a measure of the collective Coulomb interaction in liquid systems. Adding ionic liquids to an aqueous solution results in a decrease of the static value of the generalized dielectric constant which cannot be attributed to kinetic depolarization models characterized by the static conductivity and rotational relaxation cons...

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 t...

For the three molecular ionic liquids 1-ethyl-3-methylimidazolium tetrafluoroborate, 1-ethyl-3-methylimidazolium trifluoromethanesulfonate and 1-butyl-3-methylimidazolium tetrafluoroborate, dielectric spectra were calculated from molecular dynamics simulations based on polarizable force fields. Using the reaction field continuum model the dielectri...

Based on shikimic acid – the starting material for the important anti-influenza drug Tamiflu (oseltamivir phosphate) – we present that the dissolution properties of ionic liquids can lead to better access to the valuable ingredient embedded in the biopolymer. Different imidazolium-based ionic liquids were investigated, and the extraction yield of s...

Point-induced dipoles are used to mimic electronic degrees of freedom in molecular dynamics simulations. Ultrashort distance interactions of these induced dipoles are damped by the so-called Thole functions to avoid the "polarization catastrophe." This study aims at the overall impact of Thole functions on structure as well as single-particle and c...

The solvation dynamics of coumarin C153 dissolved in three selected molecular ionic liquids - EMIM(+)BF4 (-), EMIM(+)TfO(-), and BMIM(+)BF4 (-) - was studied by molecular dynamics simulations including polarization forces. The solvation response function was decomposed with respect to permanent and induced charge distributions, cationic and anionic...

a b s t r a c t We present design, synthesis and application of basic chiral ionic liquids based on commercially avail-able (S)-proline. This new set of chiral ionic liquids was specifically designed to replace trifluoroacetic acid in enamine-based organocatalysis for asymmetric C C bond formation. Based on their permanent charge, these chiral ioni...