Computation of X-ray and Neutron Scattering Patterns to Benchmark Atomistic Simulations against Experiments.

Molecular Dynamics simulations study material structure and dynamics at the atomic level. X-ray and neutron scattering experiments probe exactly the same time- and length scales as the simulations. In order to benchmark simulations against measured scattering data, a program is required that computes scattering patterns from simulations with good single-core performance and support for parallelization. In this work, the existing program Sassena is used as a potent solution to this requirement for a range of scattering methods, covering pico- to nanosecond dynamics, as well as the structure from some Ångströms to hundreds of nanometers. In the case of nanometer-level structures, the finite size of the simulation box, which is referred to as the finite size effect, has to be factored into the computations for which a method is described and implemented into Sassena. Additionally, the single-core and parallelization performance of Sassena is investigated, and several improvements are introduced.

Revealing the interfacial nanostructure of a deep eutectic solvent at a solid electrode.

Deep eutectic solvents (DESs) are both green and sustainable, making them an increasingly attractive alternative to conventional solvents. One of their applications is the electrochemical deposition of metals that cannot be deposited from aqueous solution because of the limited electrochemical window of water. The electrodeposition process is influenced by the structure and dynamics of the solvent at the solid-liquid interface. Therefore,the nanoscale structure of the interface between a silicon substrate and deep eutectic solvent (choline chloride-ethylene glycol) was studied by neutron reflectometry (NR) and molecular dynamics (MD) simulations. It is not possible to model NR measurements of this system without simulating a dense DES layer at the solid-liquid interface. This study used an MD simulation trajectory to extract the density, thickness, and roughness of this DES layer. With this input, the model reproduces the reflectometry data at all measured H/D contrasts very well. The thickness of the layer does not change appreciably when applying charge or at higher temperatures. Further analysis revealed a reorganization of ions and reorientation of the choline cations in the interface layer when the electrodes are charged. These changes in ion orientation are not observed with the NR technique since they do not influence the neutron scattering length density profile due to the high number of ethylene glycol molecules at the interface. However, the agreement between measured neutron reflectometry data and model parameters obtained from MD simulations justified subnanoscale analysis of the MD trajectory and confirmed that these two complementary techniques can be successfully combined to reveal the solid/DES interface structure.

On the microscopic origin of the cryoprotective effect in lysine solutions.

The amino acid lysine has been shown to prevent water crystallization at low temperatures in saturated aqueous solutions [S. Cerveny and J. Swenson, Phys. Chem. Chem. Phys., 2014, 16, 22382-22390]. Here, we investigate two ratios of water and lysine (5.4 water molecules per lysine (saturated) and 11 water molecules per lysine) by means of the complementary use of computer simulations and neutron diffraction. By performing a detailed structural analysis we have been able to explain the anti-freeze properties of lysine by the strong hydrogen bond interactions of interstitial water molecules with lysine that prevent them from forming crystalline seeds. Additional water molecules beyond the 1 : 5.4 proportion are no longer tightly bonded to lysine and therefore are free to form crystals.

Comparison of lipidic carrier systems for integral membrane proteins - MsbA as case study.

Membrane protein research suffers from the drawback that detergents, which are commonly used to solubilize integral membrane proteins (IMPs), often lead to protein instability and reduced activity. Recently, lipid nanodiscs (NDs) and saposin-lipoprotein particles (Salipro) have emerged as alternative carrier systems that keep membrane proteins in a native-like lipidic solution environment and are suitable for biophysical and structural studies. Here, we systematically compare nanodiscs and Salipros with respect to long-term stability as well as activity and stability of the incorporated membrane protein using the ABC transporter MsbA as model system. Our results show that both systems are suitable for activity measurements as well as structural studies in solution. Based on our results we suggest screening of different lipids with respect to activity and stability of the incorporated IMP before performing structural studies.

In Situ Small-Angle Neutron Scattering Investigation of Adsorption-Induced Deformation in Silica with Hierarchical Porosity.

Adsorption-induced deformation of a series of silica samples with hierarchical porosity has been studied by in situ small-angle neutron scattering (SANS) and in situ dilatometry. Monolithic samples consisted of a disordered macroporous network of struts formed by a 2D lattice of hexagonally ordered cylindrical mesopores and disordered micropores within the mesopore walls. Strain isotherms were obtained at the mesopore level by analyzing the shift of the Bragg reflections from the ordered mesopore lattice in SANS data. Thus, SANS essentially measured the radial strain of the cylindrical mesopores including the volume changes of the mesopore walls due to micropore deformation. A H2O/D2O adsorbate with net zero coherent neutron scattering length density was employed in order to avoid apparent strain effects due to intensity changes during pore filling. In contrast to SANS, the strain isotherms obtained from in situ dilatometry result from a combination of axial and radial mesopore deformation together with micropore deformation. Strain data were quantitatively analyzed with a theoretical model for micro-/mesopore deformation by combining information from nitrogen and water adsorption isotherms to estimate the water-silica interaction. It was shown that in situ SANS provides complementary information to dilatometry and allows for a quantitative estimate of the elastic properties of the mesopore walls from water adsorption.

Quantum mechanical effects in zwitterionic amino acids: The case of proline, hydroxyproline, and alanine in water.

In this work, we use ab initio molecular dynamics simulations to elucidate the electronic properties of three hydrated zwitterionic amino acids, namely proline, hydroxyproline, and alanine, the former two forming an important constituent of collagen. In all three systems, we find a substantial amount of charge transfer between the amino acids and surrounding solvent, which, rather surprisingly, also involves the reorganization of electron density near the hydrophobic non-polar groups. Water around proline appears to be slightly more polarized, as reflected by the enhanced water dipole moment in its hydration shell. This observation is also complemented by an examination of the IR spectra of the three systems where there is a subtle red and blue shift in the O-H stretch and bend regions, respectively, for proline. We show that polarizability of these amino acids as revealed by a dipole moment analysis involves a significant enhancement from the solvent and that this also involves non-polar groups. Our results suggest that quantum mechanical effects are likely to be important in understanding the coupling between biomolecules and water in general and in hydrophobic interactions.

Structure-activity relationships in carbohydrates revealed by their hydration.

One of the more intriguing aspects of carbohydrate chemistry is that despite having very similar molecular structures, sugars have very different properties. For instance, there is a sensible difference in sweet taste between glucose and trehalose, even though trehalose is a disaccharide that comprised two glucose units, suggesting a different ability of these two carbohydrates to bind to sweet receptors. Here we have looked at the hydration of specific sites and at the three-dimensional configuration of water molecules around three carbohydrates (glucose, cellobiose, and trehalose), combining neutron diffraction data with computer modelling. Results indicate that identical chemical groups can have radically different hydration patterns depending on their location on a given molecule. These differences can be linked with the specific activity of glucose, cellobiose, and trehalose as a sweet substance, as building block of cellulose fiber, and as a bioprotective agent, respectively. This article is part of a Special Issue entitled "Recent Advances in Bionanomaterials" Guest Editors: Dr. Marie-Louise Saboungi and Dr. Samuel D. Bader.

The structure of liquid water beyond the first hydration shell.

To date there is a general consensus on the structure of the first coordination shells of liquid water, namely tetrahedral short range order of molecules. In contrast, little is known about the structure at longer distances and the influence of the tetrahedral molecular arrangement of the first shells on the order at these length scales. An expansion of the distance dependent excess entropy is used in this contribution to find out which molecular arrangements are important at each distance range. This was done by splitting the excess entropy into two parts: one connected to the relative position of two molecules and the other one related to their relative orientation. A transition between two previously unknown regimes in liquid water is identified at a distance of about ∼6 Å: from a predominantly orientational order at shorter distances to a regime at larger distances of up to ∼9 Å where the order is predominantly positional and molecules are distributed with the same tetrahedral symmetry as the very first molecules.

On the atomic structure of cocaine in solution.

Cocaine is an amphiphilic drug which has the ability to cross the blood-brain barrier (BBB). Here, a combination of neutron diffraction and computation has been used to investigate the atomic scale structure of cocaine in aqueous solutions. Both the observed conformation and hydration of cocaine appear to contribute to its ability to cross hydrophobic layers afforded by the BBB, as the average conformation yields a structure which might allow cocaine to shield its hydrophilic regions from a lipophilic environment. Specifically, the carbonyl oxygens and amine group on cocaine, on average, form ∼5 bonds with the water molecules in the surrounding solvent, and the top 30% of water molecules within 4 Šof cocaine are localized in the cavity formed by an internal hydrogen bond within the cocaine molecule. This water mediated internal hydrogen bonding suggests a mechanism of interaction between cocaine and the BBB that negates the need for deprotonation prior to interaction with the lipophilic portions of this barrier. This finding also has important implications for understanding how neurologically active molecules are able to interact with both the blood stream and BBB and emphasizes the use of structural measurements in solution in order to understand important biological function.

A robust comparison of dynamical scenarios in a glass-forming liquid.

We use Bayesian inference methods to provide fresh insights into the sub-nanosecond dynamics of glycerol, a prototypical glass-forming liquid. To this end, quasielastic neutron scattering data as a function of temperature have been analyzed using a minimal set of underlying physical assumptions. On the basis of this analysis, we establish the unambiguous presence of three distinct dynamical processes in glycerol, namely, translational diffusion of the molecular centre of mass and two additional localized and temperature-independent modes. The neutron data also provide access to the characteristic length scales associated with these motions in a model-independent manner, from which we conclude that the faster (slower) localized motions probe longer (shorter) length scales. Careful Bayesian analysis of the entire scattering law favors a heterogeneous scenario for the microscopic dynamics of glycerol, where molecules undergo either the faster and longer or the slower and shorter localized motions.

Analysis of the structure of nanocomposites of triglyceride platelets and DNA.

DNA-complexes with platelet-like, cationically modified lipid nanoparticles (cLNPs) are studied with regard to the formation of nanocomposite structures with a sandwich-like arrangement of the DNA and platelets. For this purpose suspensions of platelet-like triglyceride nanocrystals, stabilized by a mixture of two nonionic (lecithin plus polysorbate 80 or poloxamer 188) and one cationic stabilizer dimethyldioctadecylammonium (DODAB), are used. The structure of the platelets in the native suspensions and their DNA-complexes, ranging from the sub-nano to the micron scale, is investigated with small- and wide-angle scattering (SAXS, SANS, WAXS), calorimetry, photon correlation spectroscopy, transmission electron microscopy and computer simulations. The appearance of strong, lamellarly ordered peaks in the SAXS patterns of the DNA-complexes suggests a stacked arrangement of the nanocrystals, with the DNA being partially condensed between the platelets. This finding is supported with computer simulated small-angle scattering patterns of nanocrystal stacks, which can reproduce the measured small-angle scattering patterns on an absolute scale. The influence of the choice of the nonionic stabilizers and the amount of the cationic stabilizer DODAB on the structure of the native suspensions and the inner structure of their DNA-complexes is studied, too. Using high amounts of DODAB, lecithins with saturated acyl chains and polysorbate 80 instead of poloxamer 188 produces thinner nanocrystals, and thus decreases their repeat distances in the nanocomposites. Such nanocomposites could be of interest as DNA carriers, where the triglyceride platelets protect the sandwiched DNA from degradation.

Collective intermolecular motions dominate the picosecond dynamics of short polymer chains.

Neutron scattering and extensive molecular dynamics simulations of an all atom C(100)H(202) system were performed to address the short-time dynamics leading to center-of-mass self-diffusion. The simulated dynamics are in excellent agreement with resolution resolved time-of-flight quasielastic neutron scattering. The anomalous subdiffusive center-of-mass motion could be modeled by explicitly accounting for viscoelastic hydrodynamic interactions. A model-free analysis of the local reorientations of the molecular backbone revealed three relaxation processes: While two relaxations characterize local bond rotation and global molecular reorientation, the third component on intermediate times could be attributed to transient flowlike motions of atoms on different molecules. The existence of these collective motions, which are clearly visualized in this Letter, strongly contribute to the chain relaxations in molecular liquids.

On the structure of water and chloride ion interactions with a peptide backbone in solution.

The arrangement of water and chloride ions around a model peptide (glycyl-L-prolyl-glycine-NH2) was investigated using Molecular Dynamics (MD) simulations and complementary Empirical Potential Structure Refinement (EPSR) simulations which adapt the modelled structure to reproduce experimentally measured neutron diffraction data. The results are in good qualitative agreement and show a common picture for all hydrogen-containing amine and amide groups: namely that there are two common chloride interactions observed - a direct contact between Cl(-) and peptide backbone and a water-mediated interaction. The geometry of this mediation depends on the distance between chloride and nitrogen and hints towards two distinct modes of interaction between water and the ion, either along one of the O-H bonds or along the water dipole.

Water mediation is essential to nucleation of ß-turn formation in peptide folding motifs.

Water-mediated bond formation: The structure of the peptide GPG-NH2 has been investigated in aqueous solution to understand the role of water in the formation of a ß-turn. Using a combination of neutron diffraction enhanced by isotopic substitution, NMR spectroscopy, and computer simulations, it was found that water is an essential component to initiate folding in solution.

Climate variability on Fit for 55 European power systems.

The use of variable renewable energy sources to generate electricity introduces a dependency on meteorological factors into power systems. With the renewables share growing globally, often driven by political pressures, the reliability and efficiency of power systems are increasingly affected by this dependency. In this paper, we investigate the impact of the natural variability of meteorological parameters on the European power system in 2030. We specifically focus on (1) analysing the main European weather patterns affecting renewable energy production and (2) understanding the co-variability of this production among European countries. The identification of a set of patterns in the behaviour of key power system operation indicators allows us to analyse the relationship between large-scale weather regimes and daily power system operations in a 2030 European energy context. Regarding renewable generation, analysis of the co-variability shows that European power systems tend to form two clusters, in each of which all the regions tend to show a positive correlation among themselves and a negative correlation with the other cluster. Our analysis of the most important large-scale weather regimes shows that during cyclonic patterns, the carbon intensity of all the European power systems is lower than normal, while the opposite happens during blocking regimes.

The influence of additives on the nanoscopic dynamics of the phospholipid dimyristoylphosphatidylcholine.

The influence of additives on the molecular dynamics of the phospholipid dimyristoylphosphatidylcholine (DMPC) in its fully hydrated liquid crystalline phase was studied. Quasielastic neutron scattering (QENS) was used to detect motions with dimensions of some Ångstroms on two different time scales, namely 60ps and 900ps. The effects of myristic acid, farnesol, cholesterol, and sodium glycocholate could consistently be explained on the basis of collective, flow-like motions of the phospholipid molecules. The influence of the additives on these motions was explained by packing effects, corresponding to the reduction of free volume. Cholesterol was found to decrease the mobility of DMPC seen on the 900ps time scale with increasing cholesterol content. In contrast, all other studied additives have no significant effect on the mobility.

Affixin (ß-parvin) promotes cardioprotective signaling via STAT3 activation.

The focal adhesion protein affixin (ß-parvin) is highly expressed in the heart and is associated with the sarcomeric z-disc as well as the cell membrane. While affixin is known to be involved in cell adhesion and migration, its functional role in cardiomyocytes remains unclear. To gain insight into the function of affixin, we performed a yeast-two-hybrid-screen employing affixin as a bait. The signal transducer and activator of transcription 3 (STAT3) was detected as a binding partner of affixin. Overexpression of affixin in neonatal rat cardiomyocytes resulted in markedly enhanced STAT3 DNA binding activity and upregulation of STAT3-dependent genes. Moreover, upregulation of affixin led to cardiomyocyte hypertrophy with an increase in cell size and enhanced protein synthesis. Consistent with STAT3 activation, overexpression of affixin also protected cardiomyocytes from doxorubicin-induced apoptosis. Finally, HUVECs that were cultivated in medium from affixin-overexpressing cardiomyocytes responded with an increase in tubuli formation, in line with a proangiogenic effect of affixin. In conclusion, we demonstrate that affixin activates STAT3 in cardiomyocytes and promotes characteristic STAT3-related effects such as hypertrophy, protection against apoptosis, and angiogenesis. This novel pathway might therefore represent a target for cardioprotective strategies.

Using polarization analysis to separate the coherent and incoherent scattering from protein samples.

Polarization analysis was used to separate experimentally the coherent and spin-incoherent nuclear static scattering functions, from a representative set of samples of interest for protein studies. This method had so far limited application in the study of amorphous materials, despite the relevance of the information that it provides. It allows, for instance, the experimental determination of the structure factor of materials containing a significant amount of hydrogen atoms, avoiding the contamination of measurements by a non-negligible incoherent background. Knowledge of the relative importance of the coherent and incoherent terms at different Q-values is also a pre-requisite for the interpretation of quasielastic neutron scattering experiments, performed at instruments in which the total dynamic scattering function is measured, such as conventional time-of-flight and backscattering spectrometers. Combining data from different instruments, it was possible to cover a wide Q-range, from the small-angle region (0.006

The influence of 2 kbar pressure on the global and internal dynamics of human hemoglobin observed by quasielastic neutron scattering.

Pressure is a ubiquitous physical parameter in life and is commonly used in the life sciences to study new protein folding pathways or association-dissociation phenomena. In this paper, an investigation of the influence of pressure on hemoglobin, a multimeric protein, at the picosecond time scale is presented using time-of-flight neutron scattering. The aim is to observe the influence of pressure on the translational diffusion and internal motions of hemoglobin in a concentrated solution and a possible dissociation of the subunits as suggested by Pin et al. (Biochemistry 29:9194, 1990) using fluorescence spectroscopy. A new flat 2 kbar pressure cell made of an aluminum alloy has been used, which allowed the effect of pressure to be studied with minimum background contribution. Within this range of pressure, the effect of this physical parameter on global diffusion can be explained in terms of the change in the water buffer viscosity and an oligomerization of hemoglobin subunits, whereas the internal motions were less affected.

Mutually Beneficial Combination of Molecular Dynamics Computer Simulations and Scattering Experiments.

We showcase the combination of experimental neutron scattering data and molecular dynamics (MD) simulations for exemplary phospholipid membrane systems. Neutron and X-ray reflectometry and small-angle scattering measurements are determined by the scattering length density profile in real space, but it is not usually possible to retrieve this profile unambiguously from the data alone. MD simulations predict these density profiles, but they require experimental control. Both issues can be addressed simultaneously by cross-validating scattering data and MD results. The strengths and weaknesses of each technique are discussed in detail with the aim of optimizing the opportunities provided by this combination.