Tuning high aqueous phase uptake in nonionic water-in-oil microemulsions for the synthesis of Mn-Zn ferrite nanoparticles: phase behavior, characterization, and nanoparticle synthesis

In this work, the formation of water-in-oil (w/o) microemulsions with high aqueous phase uptake in a nonionic surfactant system is investigated as potential media for the synthesis of Mn-Zn ferrite nanoparticles. A comprehensive study based on the phase behavior of systems containing precursor salts, on one hand, and precipitating agent, on the other hand, was carried out to identify key regions on (a) pseudoternary phase diagrams at constant temperature (50 °C), and (b) pseudobinary phase diagrams at constant surfactant (S):oil(O) weight ratio (S:O) as a function of temperature. The internal structure and dynamics of microemulsions were studied systematically by conductivity and self-diffusion coefficient determinations (FT PGSE (1)H NMR). It was found that nonpercolated w/o microemulsions could be obtained by appropriate tuning of composition variables and temperature, with aqueous phase concentrations as high as 36 wt % for precursor salts and 25 wt % for precipitating agent systems. Three compositions with three different dynamic behaviors (nonpercolated and percolated w/o, as well as bicontinuous microemulsions) were selected for the synthesis of Mn-Zn ferrites, resulting in nanoparticles with different characteristics. Spinel structure and superparamagnetic behavior were obtained. This study sets firm basis for a systematic study of Mn-Zn ferrite nanoparticle synthesis via different scenarios of microemulsion dynamics, which will contribute to a better understanding on the relationship of the characteristics of the obtained materials with the properties of the reaction media.     

Broadband pump-probe spectroscopy with sub-10-fs resolution for probing ultrafast internal conversion and coherent phonons in carotenoids

We use pump-probe spectroscopy with broadband detection to study electronic energy relaxation and coherent vibrational dynamics in carotenoids. A fast optical multichannel analyzer combined with a non-collinear optical parametric amplifier allows simultaneous acquisition of the differential transmission dynamics on the 500–700 nm wavelength range with sub-10-fs temporal resolution. The broad spectral coverage enables on the one hand a detailed study of the ultrafast bright-to-dark state internal conversion process; on the other hand, the tracking of the motion of the vibrational wavepacket launched on the ground state multidimensional potential energy surface. We present results on all-trans β-carotene and on a long-chain polyene in solution. The developed experimental setup enables the straightforward acquisition and analysis of coherent vibrational dynamics, highlighting time–frequency domain features with extreme resolution.     

微波波谱法研究分子系统内基团大幅度运动动力学

分子中基团的运动方式、机制对分子体系性质、分子功能的表达等具有重要作用。微波波谱法在研究分子系统内部动力学、分子结构、构象变化、弱相互作用、基团大幅度运动以及探索量子溶剂等方面具有独特的能力,特别适合研究分子的精细结构、分子系统基团的内部转动运动,具有高灵敏度、高分辨率的特点。本文讨论了微波波谱法在研究分子系统基团大幅度运动动力学方面的应用,包括分子系统中甲基基团的内部转动、OH基团的运动、氨和氨基化合物的反演以及环状有机分子环运动等的动力学,同时结合作者使用微波波谱法研究的部分体系进行了分析。     

Carbon nanotubes in benzene: internal and external solvation

The structure and dynamics of benzene inside and outside of single-walled carbon nanotubes (SWNTs) in the (n,n) armchair configuration are studied via molecular dynamics computer simulations. Irrespective of the nanotube diameter, benzene molecules form cylindrical solvation shell structures on the outside of the nanotubes. Their molecular planes near the SWNTs in the first external solvation shell are oriented parallel to the nanotube surface, forming a π-stacked structure between the two. By contrast, the benzene distributions in the interior of the SWNTs are found to vary markedly with the nanotube diameter. In the case of the (7,7) and (8,8) nanotubes, internal benzene forms a single-file distribution, either in a vertex-to-vertex (n = 7) or face-to-face (n = 8) orientation between two neighboring molecules. Inside a slightly wider (9,9) nanotube channel, however, a cylindrical single-shell distribution of benzene arises. A secondary solvation structure, which begins to appear inside (10,10), develops into a full structure separate from the first internal solvation shell in (12,12). The ring orientation of internal benzene is generally parallel to the nanotube wall for n = 9-12, while it becomes either slanted with respect to (n = 7), or perpendicular to (n = 8), the nanotube axis. The confinement inside the small nanotube pores exerts a strong influence on the dynamics of benzene. Both translational and rotational dynamics inside SWNTs are slower and more anisotropic than in liquid benzene. It is also found that reorientational dynamics of internal benzene deviate dramatically from the rotational diffusion regime and change substantially with the nanotube diameter.     

Structure and Dynamics in the Nucleosome Revealed by Solid‐State NMR

Eukaryotic chromatin structure and dynamics play key roles in genomic regulation. In the current study, the secondary structure and intramolecular dynamics of human histone H4 (hH4) in the nucleosome core particle (NCP) and in a nucleosome array are determined by solid‐state NMR (SSNMR). Secondary structure elements are successfully localized in the hH4 in the NCP precipitated with Mg²⁺. In particular, dynamics on nanosecond to microsecond and microsecond to millisecond timescales are elucidated, revealing diverse internal motions in the hH4 protein. Relatively higher flexibility is observed for residues participating in the regulation of chromatin mobility and DNA accessibility. Furthermore, our study reveals that hH4 in the nucleosome array adopts the same structure and show similar internal dynamics as that in the NCP assembly while exhibiting relatively restricted motions in several regions consisting of residues in the N‐terminus, Loop 1, and the α3 helix region.     

Properties and structure of aromatic ester solvents

This paper reports on an experimental and theoretical study of the aromatic ester solvents family. Several compounds were selected to analyze the different factors that influence their liquid-state properties and structures. The pressure-volume-temperature behavior of these fluids was measured accurately over wide temperature and pressure ranges and correlated successfully with the empirical TRIDEN equation. From the measured data the relevant derived coefficients of isothermal compressibility, isobaric expansibility, and internal pressure were calculated. The statistical associating fluid theory (SAFT) and perturbed chain statistical associating fluid theory (PC-SAFT) molecularly based equations of state were used to predict the PVT behavior with model parameters obtained from the correlation of available saturation literature data; the results provided by PC-SAFT equations of state were clearly superior for all of the studied solvents. The fluid's molecular level structure was studied by quantum computations at the B3LYP/6-311++g** level and classical molecular dynamics simulations in the NPT ensemble with the OPLS-AA forcefield. Molecular parameters, such as torsional barriers or cluster energetics, were analyzed as a function of ester structures. The molecular dynamics study provides, on one hand, theoretical values of thermophysical properties, which are compared with the experimental ones, and, on the other hand, valuable molecular level structural information. On the basis of both macroscopic and microscopic studies complex fluid structures were inferred with important effects arising from the geometries of the studied molecules and from the existence of remarkable intermolecular forces of dominating dipolar nature.     

Probing dynamic protein ensembles with atomic proximity measures

The emerging role of internal dynamics in protein fold and function requires new avenues of structure analysis. We analyzed the dynamically restrained conformational ensemble of ubiquitin generated from residual dipolar coupling data, in terms of protruding and buried atoms as well as interatomic distances, using four proximity-based algorithms, CX, DPX, PRIDE and PRIDE-NMR (http://hydra.icgeb.trieste.it/protein/). We found that Ubiquitin, this relatively rigid molecule has a highly diverse dynamic ensemble. The environment of protruding atoms is highly variable across conformers, on the other hand, only a part of buried atoms tends to fluctuate. The variability of the ensemble cautions against the use of single conformers when explaining functional phenomena. We also give a detailed evaluation of PRIDE-NMR on a wide dataset and discuss its usage in the light of the features of available NMR distance restraint sets in public databases.     

Molecular dynamics simulation of liquid water confined inside graphite channels: dielectric and dynamical properties

Electric and dielectric properties and microscopic dynamics of liquid water confined between graphite slabs are analyzed by means of molecular dynamics simulations for several graphite-graphite separations at ambient conditions. The electric potential across the interface shows oscillations due to water layering, and the overall potential drop is about -0.28 V. The total dielectric constant is larger than the corresponding value for the bulklike internal region of the system. This is mainly due to the preferential orientations of water nearest the graphite walls. Estimation of the capacitance of the system is reported, indicating large variations for the different adsorption layers. The main trend observed concerning water diffusion is 2-fold: on one hand, the overall diffusion of water is markedly smaller for the closest graphite-graphite separations, and on the other hand, water molecules diffuse in interfaces slightly slower than those in the bulklike internal areas. Molecular reorientational times are generally larger than those corresponding to those of unconstrained bulk water. The analysis of spectral densities revealed significant spectral shifts, compared to the bands in unconstrained water, in different frequency regions, and associated to confinement effects. These findings are important because of the scarce information available from experimental, theoretical, and computer simulation research into the dielectric and dynamical properties of confined water.     

Low-temperature dynamics in amorphous polymers and low-molecular-weight glasses--what is the difference?

Numerous experiments have shown that the low-temperature dynamics of a wide variety of disordered solids is qualitatively universal. However, most of these results were obtained with ensemble-averaging techniques which hide the local parameters of the dynamic processes. We used single-molecule (SM) spectroscopy for direct observation of the dynamic processes in disordered solids with different internal structure and chemical composition. The surprising result is that the dynamics of low-molecular-weight glasses and short-chain polymers does not follow, on a microscopic level, the current concept of low-temperature glass dynamics. An extra contribution to the dynamics was detected causing irreproducible jumps and drifts of the SM spectra on timescales between milliseconds and minutes. In most matrices consisting of small molecules and oligomers, the spectral dynamics was so fast that SM spectra could hardly or not at all be recorded and only irregular fluorescence flares were observed. These results provide new mechanistic insight into the behavior of glasses in general: At low temperatures, the local dynamics of disordered solids is not universal but depends on the structure and chemical composition of the material.     

Thermal analysis via molecular dynamics simulation

Thermal analysis by classical molecular dynamics simulations is discussed on hand of heat capacity of crystals of 9600 atoms. The differences between quantum mechanical and classical mechanical calculations are shown. Anharmonicity is proven to be an important factor. Finally, it is found that defects contribute to an increase in heat capacity before melting. The energy of conformational gauche defects within the crystal is only about 10% due to internal rotation. The other energy must be generated by cooperative strain. The conclusion is that the next generation of faster computers may permit wider use of molecular dynamics simulations in support of the interpretation of thermal analysis.Dedicated to Professor Bernhard Wunderlich on the occasion of his 65th birthday     

Combining Neutron Scattering,Deuteration Technique,and Molecular Dynamics Simulations to Study Dynamics of Protein and Its Surface Water Molecules

Protein internal dynamics is essential for its function.Exploring the internal dynamics of protein molecules as well as its connection to protein structure and function is a central topic in biophysics.However,the atomic motions in protein molecules exhibit a great degree of complexities.These complexities arise from the complex chemical composition and superposition of different types of atomic motions on the similar time scales,and render it challenging to explicitly understand the microscopic mechanism governing protein motions,functions,and their connections.Here,we demonstrate that,by using neutron scattering,molecular dynamics simulation,and deuteration technique,one can address this challenge to a large extent.     

Coupling of the overall molecular motion with the conformational transitions. II. The full rotational problem

The method proposed in the companion paper for analysing the coupling between overall and internal dynamics is applied to the study of the full rotational motion of a molecule with one internal degree of freedom. For systems characterized by a finite set of stable conformers determined by the minima of the intramolecular potential, a simplified time evolution operator of mixed type is derived, with the continuous diffusion equation and the generalized random walk operator representing the overall rotation and the internal dynamics, respectively. The dependence on the conformational state of the rotational diffusion tensor is one source of coupling between these two types of motion. Another source is represented by the recoil rotations acting on each subunit during a conformational transition. Both conformational-dependent rotational diffusion tensors and recoil rotations can be calculated from a model for the friction exerted by the solvent. Some applications of the theory are presented in relation to the butane molecule and the molecules having the structure of biphenyl, with particular emphasis on the calculation of the experimental observables in NMR and dielectric relaxation measurements.     

Influence of molecular stiffness on the dynamic structure factor

Characteristic features of the influence of molecular stiffness on the dynamic structure factor of macromolecules are briefly outlined. The relaxation times characterizing the internal dynamics of the macro‐molecules exhibit a crossover from Rouse‐Zimm to bending modes with increasing mode number. As a consequence the dynamic structure factor is strongly influenced by the molecular stiffness. In particular, a stretched exponential relaxation of the dynamic structure factor at scattering vectors larger than the inverse persistence length is predicted and confirmed by a comparison with experimental data. Moreover, the influence of polydispersity is discussed.     

Molecular dynamics study of triosephosphate isomerase from Trypanosoma cruzi in water/decane mixtures

A comprehensive study of the triosephosphate isomerase from the parasite Trypanosoma cruzi (TcTIM) in water, in decane, and in three water/decane mixtures was performed using molecular dynamics (MD) simulations in a time scale of 40 ns. The structure and dynamics of the enzyme, as well as the solvent molecules' distribution and mobility, were analyzed in detail. In the presence of decane, the amplitudes of the most important internal motions of the enzyme backbone were observed to depend on the solvent concentration: the higher the water concentration, the greater the amplitudes. Contrary to this trend, the amplitudes of the TcTIM motions in pure water were similar to those of the simulation with the lowest water concentration. The enzyme was observed to be almost motionless in pure decane due to a sharp increase of the number of intramolecular hydrogen bonds. This caused a contraction of the enzyme structure accompanied by a loss of secondary structure and of a decrease of the hydrophilic solvent accessible surface. A similar behavior, although to a lesser extent, was observed in the simulation at the lowest water concentration. Our results suggest that the presence of decane molecules located at specific sites of the enzyme might accelerate its internal movements, although a minimum number of water molecules is needed for the protein to keep its structure and dynamics. Altogether, this work provides new insight into protein and water behavior in organic solvents as well as into the dynamics of TcTIM itself.     

Hydrogen-bond structure and dynamics at the interface between water and carboxylic acid-functionalized self-assembled monolayers

Molecular dynamics computer simulations are used to study hydrogen-bond structure and dynamics at the interface between water and carboxylic acid-functionalized self-assembled monolayers (CAFSAMs). Water-water, water-CAFSAM, and internal CAFSAM hydrogen bonds are examined. Roughly half of all adjacent carboxylic acid-terminated hydrocarbon chains are hydrogen-bonded to one another. This is consistent with experimental results reflecting two pKa values for CAFSAMs. Hydrogen-bond dynamics are expressed in terms of hydrogen-bond population autocorrelation functions and are found to be nonexponential. The water-water hydrogen-bond dynamics are slower at the interface than in the bulk, which is similar to what was found at the interface between water and weakly polar liquids such as nitrobenzene. The water-CAFSAM hydrogen bonds are found to be long-lived, on the order of tens of picoseconds. Internal CAFSAM chain-chain hydrogen bonds show almost no relaxation on the simulation time scale.     

Oxoanion binding by guanidiniocarbonylpyrrole cations in water: a combined DFT and MD investigation

Structures and properties of nonbonding interactions involving guanidinium-functionalized hosts and carboxylate substrates were investigated by a combination of ab initio and molecular dynamics approaches. The systems under study are on one hand intended to be a model of the arginine-anion bond, so often observed in proteins and nucleic acids, and on the other to provide an opportunity to investigate the influence of molecular structure on the formation of supramolecular complexes in detail. Use of DFT calculations, including extended basis sets and implicit water treatment, allowed us to determine minimum-energy structures and binding enthalpies that compared well with experimental data. Intermolecular forces were found to be mostly due to electrostatic interactions through three hydrogen bonds, one of which is bifurcate, and are sufficiently strong to induce a conformational change in the ligand consisting of a rotation of about 180 degrees around the guanidiniocarbonylpyrrole axis. Free binding energies of the complexes were evaluated through MD simulations performed in the presence of explicit water molecules by use of the molecular mechanics Poisson-Boltzmann solvent accessible surface area (MM-PBSA) and linear interaction energy (LIE) approaches. LIE energies were in quantitative agreement with experimental data. A detailed analysis of the MD simulations revealed that the complexes cannot be described in terms of a single binding structure, but that they are characterized by a significant internal mobility responsible for several low-energy metastable structures.     

Fractional Brownian dynamics in proteins

Correlation functions describing relaxation processes in proteins and other complex molecular systems are known to exhibit a nonexponential decay. The simulation study presented here shows that fractional Brownian dynamics is a good model for the internal dynamics of a lysozyme molecule in solution. We show that both the dynamic structure factor and the associated memory function fit well the corresponding analytical functions calculated from the model. The numerical analysis is based on autoregressive modeling of time series.     

Synthesis of μ2-Oxo-Bridged Iron(III) Tetraphenylporphyrin–Spacer–Nitroxide Dimers and their Structural and Dynamics Characterization by using EPR and MD Simulations

Iron(III) porphyrins have the propensity to form μ₂-oxo-dimers, the structures of which resemble two wheels on an axle. Whereas their crystal structure is known, their solution structure and internal dynamics is not. In the present work, the structure and dynamics of such dimers were studied by means of electron paramagnetic resonance (EPR) spectroscopy and quantum chemistry based molecular dynamics (MD) simulations by using the semiempirical tight-binding method (GFN-xTB). To enable EPR investigation of the dimers, a nitroxide was attached to each of the tetraphenylporphyrin cores through a linear and a bent linker. The inter-nitroxide distance distributions within the dimers were determined by continuous-wave (cw)-EPR and pulsed electron–electron double resonance (PELDOR or DEER) experiments and, with the help of MD, interpreted in terms of the rotation of the porphyrin planes with respect to each other around the Fe–O–Fe axis. It was found that such rotation is restricted to the four registers defined by the phenyl substituents. Within the registers, the rotation angle swings between 30° and 60° in the proximal and between 125° and 145° in the distal register. With EPR, all four angles were found to be equally populated, whereas the 30° and 145° angles are strongly favored to the expense of the 60° and 125° angles in the MD simulation. In either case, the internal dynamics of these dimers thus resemble the motion of a step motor.     

Microscopic analysis of protein oxidative damage: effect of carbonylation on structure, dynamics, and aggregability of villin headpiece

One of the most important irreversible oxidative modifications of proteins is carbonylation, the process of introducing a carbonyl group in reaction with reactive oxygen species. Notably, carbonylation increases with the age of cells and is associated with the formation of intracellular protein aggregates and the pathogenesis of age-related disorders such as neurodegenerative diseases and cancer. However, it is still largely unclear how carbonylation affects protein structure, dynamics, and aggregability at the atomic level. Here, we use classical molecular dynamics simulations to study structure and dynamics of the carbonylated headpiece domain of villin, a key actin-organizing protein. We perform an exhaustive set of molecular dynamics simulations of a native villin headpiece together with every possible combination of carbonylated versions of its seven lysine, arginine, and proline residues, quantitatively the most important carbonylable amino acids. Surprisingly, our results suggest that high levels of carbonylation, far above those associated with cell death in vivo, may be required to destabilize and unfold protein structure through the disruption of specific stabilizing elements, such as salt bridges or proline kinks, or tampering with the hydrophobic effect. On the other hand, by using thermodynamic integration and molecular hydrophobicity potential approaches, we quantitatively show that carbonylation of hydrophilic lysine and arginine residues is equivalent to introducing hydrophobic, charge-neutral mutations in their place, and, by comparison with experimental results, we demonstrate that this by itself significantly increases the intrinsic aggregation propensity of both structured, native proteins and their unfolded states. Finally, our results provide a foundation for a novel experimental strategy to study the effects of carbonylation on protein structure, dynamics, and aggregability using site-directed mutagenesis.