Collective Spectroscopy of Solvation Phenomena: Conflicts, Challenges, and Opportunities.

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 interpretation of this complex observable aided by computational spectroscopy.

Nuclear Overhauser spectroscopy in hyperpolarized water - chemical magnetic exchange.

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 hyperpolarization transfer mechanisms remain yet unclear, not least due to an often-encountered dilemma of dDNP experiments: The strongly enhanced signal intensities are accompanied by limited structural information as data acquisition is restricted to short time series of only one-dimensional spectra or a single correlation spectrum.

Collectivity in ionic liquids: a temperature dependent, polarizable molecular dynamics study.

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 tessellation analysis directly casts doubt on common concepts such as the alternating shells of cations and anions and the ionicity.

The Intermolecular NOE Depends on Isotope Selection: Short Range vs Long Range Behavior.

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 experimental and computational work shows that proper selection of interacting isotopes can overcome these limitations: Isotopes with strongly differing gyromagnetic ratios give rise to short-ranged intermolecular NOEs.

Synthesis and characterization of enantiopure planar-chiral phosphorus-linked diferrocenes.

In the course of an ongoing synthetic project on cyclic diferrocenylphosphines, we obtained a group of planar-chiral diferrocenyl compounds useful as precursors for subsequent cyclization. Here we report the crystal structures of two symmetric compounds [(Fc)(Ph)P], one of which contains four stereogenic centres (two C chiral and two planar chiral centres), i.e.

Dielectric spectroscopy and time dependent Stokes shift: two faces of the same coin?

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 demonstrates that the TDSS reflects local, non-collective dynamics.

Understanding the Nature of Nuclear Magnetic Resonance Relaxation by Means of Fast-Field-Cycling Relaxometry and Molecular Dynamics Simulations-The Validity of Relaxation Models.

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 dispersion contains both rotational and translational diffusion information, among others.

The nuclear Overhauser Effect (NOE) as a tool to study macromolecular confinement: Elucidation and disentangling of crowding and encapsulation effects.

We propose a methodology to capture short-lived but biophysically important contacts of biomacromolecules using the biomolecule-water nuclear Overhauser effect as an indirect microscope. Thus, instead of probing the direct correlation with the foreign biomolecule, we detect its presence by the disturbance it causes in the surrounding water. In addition, this information obtained is spatially resolved and can thus be attributed to specific sites.

The protein-water nuclear Overhauser effect (NOE) as an indirect microscope for molecular surface mapping of interaction patterns.

In this computational study, the intermolecular solute-solvent Nuclear Overhauser Effect (NOE) of the model protein ubiquitin in different chemical environments (free, bound to a partner protein and encapsulated) is investigated. Short-ranged NOE observables such as the NOE/ROE ratio reveal hydration phenomena on absolute timescales such as fast hydration sites and slow water clefts. We demonstrate the ability of solute-solvent NOE differences measured of the same protein in different chemical environments to reveal hydration changes on the relative timescale.

Changes in protein hydration dynamics by encapsulation or crowding of ubiquitin: strong correlation between time-dependent Stokes shift and intermolecular nuclear Overhauser effect.

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-dependent Stokes shift (TDSS), as well as the intermolecular Nuclear Overhauser Effect (NOE) at different sites of the protein by large-scale computer simulation of single and multiple proteins in water and confined in reverse micelles. Besides high advanced space resolved information on hydration dynamics we found a strong correlation of the change in NOE upon crowding or encapsulation and the change in the integral TDSS relaxation times in all investigated systems relative to the signals in a diluted protein solution.

Hydration dynamics of proteins in reverse micelles probed by H-NOESY/H-ROESY NMR and O-nuclear quadrupole resonance (NQR).

This study is based on extensive MD simulations of a protein in a reverse micelle to mimic the effect of confinement on biomolecules. This permits the calculation of measurable quantities appearing in NQR and Nuclear Overhauser-NMR despite the high computational effort. We address the long-standing debate about the intermolecular NOE showing that absolute quantities derived from NOESY and ROESY spectra do indeed contain considerable long-range contributions, while ratios thereof are effectively short-ranged due to almost perfect compensation effects.

Computational spectroscopy of trehalose, sucrose, maltose, and glucose: A comprehensive study of TDSS, NQR, NOE, and DRS.

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 dynamics around different saccharides.

Towards capturing cellular complexity: combining encapsulation and macromolecular crowding in a reverse micelle.

Confinement and macromolecular crowding are acknowledged to be fundamental for the understanding of biomolecular systems. This computational study combines these two phenomena by investigating a multi-protein system encapsulated in a reverse micelle. Contemporary controversies regarding force field accuracy with respect to hydration in such systems were addressed by scaling the non-bonded, non-charged interaction of water with the surfaces, i.

Revival of collective water structure and dynamics in reverse micelles brought about by protein encapsulation.

In this computational study, we investigate the behaviour of a protein in water encapsulated in a zwitterionic/neutral reverse micelle as a cellular mimetic. Addressing the discussion if current force fields are apt to correctly describe crowded/encapsulated environments, we apply an upscaling of the non-bonded, non-electrostatic interactions of protein and/or surfactants with the water component. Based on the thorough analysis of single-particle rotational motion of water and ubiquitin molecules we find retardation near the interfaces and a bulk-like core.

Macromolecular crowding and the importance of proper hydration for the structure and dynamics of protein solutions.

Recent experiments by Weingärtner et al. have given a first hint that dielectric spectroscopy is able to yield a quantitative measure of inter-protein mutual orientation. Therefore, in this computational study, we investigate crowded multi-protein solutions with a special focus on this mutual orientation and its context with dielectric spectroscopy.

Micellar confinement disrupts collective structure and accelerates collective dynamics of encapsulated water.

This computational study deals with the collective structure and dynamics as well as their interaction seen from a dielectric viewpoint in zwitterionic reverse micelles for which a force field was designed de novo. For this end, a dualistic strategy is followed: the raw data are generated by extensive microscopic molecular dynamics (MD) simulations while the subsequent analysis has a focus on mesoscopic dielectric properties. The unusually low dielectric signals as well as the remarkable acceleration of collective dynamics is elucidated in great detail.