Structure and Dynamics of Microhydrated Complexes Revealed with Rotational Spectroscopy.

Chapter 21 Architecture of Hydrates and Local Structure of Acetic Acid Aqueous Solution: Ab Initio Calculations and Car–Parrinello Molecular Dynamics (CPMD) Simulations on Hydrogen-Bonding Rings, Network, and Intra-Hydrate Protonation in Multi-Hydrates of Acetic Acid Monomer

Intermolecular interactions of pyridine in liquid and in aqueous solution are studied by using soft X-ray absorption spectroscopy (XAS) at the C, N, and O K-edges. XAS of liquid pyridine shows that the N 1s→π* peak is blue shifted and the C 1s→π* peak of the meta and para sites is red shifted, respectively, as compared with XAS of pyridine gas. These shifts in liquid are smaller than those in clusters, indicating that the intermolecular interaction of liquid pyridine is weaker than that of pyridine cluster, as supported by the combination of quantum chemical calculations of the core excitation and molecular dynamics simulations of the liquid structure. On the other hand, XAS spectra of aqueous pyridine solutions (C5H5N)x(H2O)1−x measured at different molar fractions show that in the pyridine rich region, x>0.7, the C and N 1s→π* peak energies are not so different from pure liquid pyridine (x=1.0). In this region, antiparallel displaced structures of pyridine molecules are dominant as in pure pyridine liquid. In the O K-edge XAS, the pre-edge peaks sensitive to the hydrogen bond (HB) network of water molecules show the red shift of −0.15 eV from that of bulk water, indicating that small water clusters with no large-scale HB network are formed in the gap space of structured pyridine molecules. In the water rich region, 0.7>x, the N 1s→π* peaks and the O 1s pre-edge peaks are blue shifted, and the C 1s→π* peaks of the meta and para sites are red-shifted by increasing molar fraction of water. The HB network of bulk water is dominant, but quantum chemical calculations indicate that small pyridine clusters with the HB interaction between the H atom in water and the N atom in pyridine are still existent even in very dilute pyridine solutions.

Hydrogen bond (HB) networks are essential for stabilizing molecular structures in solution and govern the solubility and functionality of molecules in an aqueous environment. HBs are important in biological processes such as enzyme-substrate interactions, protein folding, and DNA replication. However, the exact role of weakly polarized C-H bonds as HB proton donors in solution, such as CH/n HBs, remains mostly unknown. Here, we employ a novel approach focusing on vibrational dephasing to investigate the coherence relaxation of induced dipoles in C-H bonds within CH/n HB networks, utilizing time-resolved coherent anti-Stokes Raman scattering (T-CARS) spectroscopy. Using a representative binary system of dimethyl sulfoxide (DMSO)-water, known for its C-H backboned HB system (i.e., C-H⋯S), we observed an increase in the dephasing time of the C-H bending mode with increasing water content until a percolation threshold at a 6 : 1 water : DMSO molar ratio, where the trend is reversed. These results provide compelling evidence for the existence of C-H⋯S structures and underscore the presence of a percolation effect, suggesting a critical threshold where long-range connectivity is disputed.

The presence of solute in water, even in small quantities, changes the properties of water. The ability of water molecules to form hydrogen-bonds is decisive for the structural and thermodynamic properties. When the solute is added to water, the network of hydrogen bonds is disrupted, changing the structure and properties of the water. In this work, we have used a simple two-dimensional rose water model together with orientation-dependent integral equation theory (ODIET) to gain insight into the effects of nonpolar solutes on the local structure of aqueous solutions. The theory shows good agreement with the radial distribution functions and enthalpies of solvation obtained with simulations, while improving the results of the orientation-averaged version of the theory. The advantage of the two-dimensional water model together with ODIET is that angle-dependent properties can be calculated relatively quickly and easily visualised. Using the potential of the mean force derivatives, the effect of added nonpolar solute on the local structure of the solution was investigated. Depending on the size of the solute, two different regimes of the effect of the solute on the structure of the solution were identified. Small solutes increase the tendency of water to form hydrogen-bonds and at the same time decrease solvation and association of the solute. On the other hand, large solutes have the opposite effect - they decrease the HB tendency of water and increase solvation and association of the solute.

Hippocampal sclerosis (HS) is observed in many intractable, mesial temporal lobe epilepsy (MTLE) patients. We aimed to delineate the internal structural changes (ISC) shown as loss of internal architecture in the hippocampus on 3-Tesla magnetic resonance imaging (3T-MRI) due to its higher spatial resolution. We studied 12 MTLE patients who exhibited unilateral HS on conventional 1.5 Tesla-MRI. Using 3T-MRI, high resolution T2-weighted coronal images of the hippocampus were investigated by visual inspection without the use of detailed clinical information. In addition, tissue samples obtained from four patients who underwent epilepsy surgery were analyzed histopathologically. In addition to hippocampal atrophy (HA) in the abnormal side, blurring of the low-intensity streak, i.e., ISC, in the hippocampus was seen in 12 patients and atrophy or high signal intensity was observed in Ammon's horn or the dentate gyrus in nine patients. After four patients underwent epilepsy surgery, tissue samples showed astrogliosis and a loss of pyramidal neurons in the hippocampal body, concordant with ISC or HA on MRI examination. High-resolution MRI suggests that minute internal structural changes in the hippocampus reflect neuronal cell loss or gliosis, possibly in the early stage, and also show laterality of changes more sensitively. Different internal structural changes could further subclassify HS and may predict the surgical outcomes of seizure control based on the clinicopathological correlation.

Recognition of poly(C) DNA and RNA sequences in mammalian cells is achieved by a subfamily of the KH (hnRNP K homology) domain-containing proteins known as poly(C)-binding proteins (PCBPs). To reveal the molecular basis of poly(C) sequence recognition, we have determined the crystal structure, at 1.7-A resolution, of PCBP2 KH1 in complex with a 7-nucleotide DNA sequence (5'-AACCCTA-3') corresponding to one repeat of the human C-rich strand telomeric DNA. The protein-DNA interaction is mediated by the combination of several stabilizing forces including hydrogen bonding, electrostatic interactions, van der Waals contacts, and shape complementarities. Specific recognition of the three cytosine residues is realized by a dense network of hydrogen bonds involving the side chains of two conserved lysines and one glutamic acid. The co-crystal structure also reveals a protein-protein dimerization interface of PCBP2 KH1 located on the opposite side of the protein from the DNA binding groove. Numerous stabilizing protein-protein interactions, including hydrophobic contacts, stacking of aromatic side chains, and a large number of hydrogen bonds, indicate that the protein-protein interaction interface is most likely genuine. Interaction of PCBP2 KH1 with the C-rich strand of human telomeric DNA suggests that PCBPs may participate in mechanisms involved in the regulation of telomere/telomerase functions.

Isolation of RuIII-bda (17-electron specie) complex with an aqua ligand (2-electron donor) is challenging due to violation of the 18-electron rule. Although considerable efforts have been dedicated to mechanistic studies of water oxidation by the Ru-bda family, the structure and initial formation of the RuIII-bda aqua complex are still controversial. Herein, we challenge this often overlooked step by designing a pocket-shape Ru-based complex 1. The computational studies showed that 1 possesses the crucial hydrophobicity at the RuV(O) state as well as similar probability of access of terminal O to solvent water molecules when compared with classic Ru-bda catalysts. Through characterization of single-crystal structures at the RuII and RuIII states, a pseudo seven-coordinate “ready-to-go” aqua ligand with RuIII...O distance of 3.62 Å was observed. This aqua ligand was also found to be part of a formed hydrogen-bonding network, providing a good indication of how the RuIII-OH2 complex is formed.

A binary complex of the ammonia channel Amt1 from Methanococcus jannaschii and its cognate P(II) signalling protein GlnK1 has been produced and characterized. Complex formation is prevented specifically by the effector molecules Mg-ATP and 2-ketoglutarate. Single-particle electron microscopy of the complex shows that GlnK1 binds on the cytoplasmic side of Amt1. Three high-resolution X-ray structures of GlnK1 indicate that the functionally important T-loop has an extended, flexible conformation in the absence of Mg-ATP, but assumes a compact, tightly folded conformation upon Mg-ATP binding, which in turn creates a 2-ketoglutarate-binding site. We propose a regulatory mechanism by which nitrogen uptake is controlled by the binding of both effector molecules to GlnK1. At normal effector levels, a 2-ketoglutarate molecule binding at the apex of the compact T-loop would prevent complex formation, ensuring uninhibited ammonia uptake. At low levels of Mg-ATP, the extended loops would seal the ammonia channels in the complex. Binding of both effector molecules to P(II) signalling proteins may thus represent an effective feedback mechanism for regulating ammonium uptake through the membrane.

We herein report an ab initio molecular dynamics study on a natural DES composed of urea and betaine in a 3 : 2 ratio, as a test case for evaluating the water effect. The article deals with a theoretical study using both ab initio molecular dynamics and quantum chemistry computations in order to unravel the role of water in the nanostructure of a urea-betaine mixture. Preliminary molecular dynamics outcomes (both radial and spatial distribution functions) suggest that water promotes the association between urea and betaine by increasing the hydrogen bond network and precluding the aggregation of urea molecules. In other words, the presence of water allows a less restrictive hydrogen bond network, presenting a regimen where the strong hydrogen bond interactions are replaced by a wide variety of weaker hydrogen bond interactions. On the other hand, in a water free DES there is a regimen where strong urea-betaine interactions are dominant. It is shown that second order perturbation theory energy analysis provides cogent insights into charge spreading and hydrogen bond patterns. A vibrational analysis (both IR and power spectrum) over the ab initio molecular dynamics trajectories in the water free DES as well as in the urea-betaine-water systems reveals that our results are consistent with the second order perturbation theory analysis and with the hydrogen bond network pattern.

High spatial resolution and deep detection depths of seismic reflection surveying are conducive to studying the fine structure of the internal solitary wave. However, seismic images are instantaneous, which are not conducive to observing kinematic processes of the internal solitary waves. We improved the scheme of seismic data processing and used common-offset gathers to continuously image the same location. In this way, we can observe internal fine structure changes during the movement of the internal solitary waves, especially the part in contact with the seafloor. We observed a first-mode depression internal solitary wave on the continental slope near the Dongsha Atoll of the South China Sea and short-term shoaling processes of the internal solitary wave by using our improved method. We found that the change in shape of waveform varies at different depths. We separately analyzed the evolution of the six waveforms at different depths. The results showed that the waveform in deep water deforms before that in shallow water and the waveform in shallow water deforms to a greater degree. We measured four parameters of the six waveforms during the shoaling including phase velocity, amplitude, wavelength, and slopes of leading and trailing edge. The phase velocity and amplitudes of waveforms in shallow water increase, the wavelengths decrease, and the slopes of trailing edge gradually become larger than that of the leading edge, while the amplitudes of the deep water waveforms do not change significantly and the phase velocities decrease. Our results are consistent with previous studies made by numerical simulations, which suggest the effectiveness of the new processing scheme. This improved scheme cannot only study the internal solitary waves shoaling, but also has great potential in the study of other ocean dynamics.

The hydrogen bond (HB) network structure and kinetics of the acetone-water mixed solutions were investigated by the spontaneous Raman and stimulated Raman scattering (SRS) spectra. The HB network of water molecules was enhanced when the volume fraction of acetone ranged from 0 to 0.25. Two new SRS peaks of water at 3272 and 3380 cm-1 were obtained, resulting from the cooperation of the polar carbonyl (C = O)-enhanced HB and the ice-like structure formed around the methyl groups. However, when the volume fraction went beyond 0.25, the spontaneous Raman main peak at 3445 cm-1 showed a significant blue-shift, and the corresponding SRS signal disappeared, indicating that the HB of water was weakened, which originated from the self-association of acetone. In the meantime, the fully tetrahedral HB structure among water molecules was destroyed at the higher volume fraction (≥ 0.8). Hopefully, our study here would advance the study of HB network structures and kinetics in other aqueous solutions.

Rotational spectra, nuclear quadrupole coupling tensors, and structures for CF3CF2X, X = Cl, Br

Memory effects and internal changes of a material†

The maturity of tomato fruit is normally characterized by external color, and it is often difficult to know when fruit have achieved commercial maturity or become over-mature. The internal structure of tomato fruit changes during development and this study investigates the utility of nondestructive measurement of tomato fruit structure as a function of maturity using magnetic resonance imaging (MRI). The objective of this work is to use analysis of internal tomato fruit structural measurements to characterize maturity. Intact cherry tomato fruit were harvested at six different maturity stages. At each stage of maturity, the internal structure of the fruit was measured using a series of two-dimensional (2D) magnetic resonance (MR) images. Qualitative and quantitative image analyses were performed to correlate internal fruit structure with maturity. Internal structural changes observed in the pericarp region of the tomato fruit are highly correlated with fruit maturity. MR image information combined with classical analysis techniques provides a more complete understanding of structure and physicochemical changes in tomato fruit during maturation. This study demonstrates that MRI is a useful analytical tool to characterize internal changes in agricultural produce as the produce matures. This technique can be applied to almost any agricultural produce to monitor internal physical changes due to external impact, maturity stage, variation in climate, storage time, and condition, or other factors impacting quality.

Site selective analysis of water in hydrogen bond network of aqueous dimethyl sulfoxide solutions by oxygen K-edge X-ray absorption spectroscopy