Study of Aqueous Acetone Solution at Various Concentrations: Low-Frequency Raman and Molecular Dynamics Simulations

Does arginine aggregate formation in aqueous solutions follow a two-step mechanism?

The formation of aggregates was studied in arginine aqueous solutions using light scattering. The main driving force for aggregate formation is hydrogen bonding between the arginine (Arg) amino acids, which is partially verified using density functional theory calculations. The measurement of energy loss during this process, coupled with Cryo-EM morphology data, indicates that these aggregates are in the solid state. The aggregation occurs in two steps, with a liquid intermediate stage. The investigation of the effect of pH and solute concentration on aggregate formation for other amino acid aqueous solutions verifies that aggregate formation is amino-acid specific, while small-sized clusters formed by weak interactions lead to large-sized aggregation. The water structure around amino acid molecules sheds light on the prediction of their aggregate formation. Homochirality is observed in the aggregates; its existence sheds light on the origin of protein homochirality.

Roles of hydrogen bonding interactions and hydrophobic effects on enhanced water structure in aqueous solutions of amphiphilic organic molecules

Insights into the solute-induced water structural transformations are essential to understand the role of water in biological and chemical reaction processes. Herein, the structural changes in water induced by amphiphilic organic molecules were investigated using concentration-dependent derivative Raman spectroscopy (DRS) combined with two-dimensional Raman correlation spectroscopy (2D Raman-COS). We shall restrict our attention in this work to binary mixtures of water with dimethyl sulfoxide (DMSO), acetone, and isopropanol (IPA), all of which have similar chemical structures. The spectral changes in O:H and OH stretching modes illustrate that the solute molecules induce an enhancement of the water structure in dilute solutions, where the enhanced degree of water structure is closely related to the size of the dipole moment of organic molecules. In addition, the transformations of solute-induced water-specific structures were evaluated by 2D Raman-COS, which shows that the strong hydrogen bond (H-bond) structure of water is more sensitive to organic molecules and induces a transition to the weak H-bond structure of water.

Infrared Spectra and Hydrogen-Bond Configurations of Water Molecules at the Interface of Water-Insoluble Polymers under Humidified Conditions

Elucidating the state of interfacial water, especially the hydrogen-bond configurations, is considered to be key for a better understanding of the functions of polymers that are exhibited in the presence of water. Here, an analysis in this direction is conducted for two water-insoluble biocompatible polymers, poly(2-methoxyethyl acrylate) and cyclic(poly(2-methoxyethyl acrylate)), and a non-biocompatible polymer, poly(n-butyl acrylate), by measuring their IR spectra under humidified conditions and by carrying out theoretical calculations on model complex systems. It is found that the OH stretching bands of water are decomposed into four components, and while the higher-frequency components (with peaks at ∼3610 and ∼3540 cm^-1) behave in parallel with the C═O and C-O-C stretching and CH deformation bands of the polymers, the lower-frequency components (with peaks at ∼3430 and ∼3260 cm^-1) become pronounced to a greater extent with increasing humidity. From the theoretical calculations, it is shown that the OH stretching frequency that is distributed from ∼3650 to ∼3200 cm^-1 is correlated to the hydrogen-bond configurations and is mainly controlled by the electric field that is sensed by the vibrating H atom. By combining these observed and calculated results, the configurations of water at the interface of the polymers are discussed.

Investigated hydrogen-bond network kinetics of acetone-water solutions by spontaneous and stimulated Raman spectroscopy

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.

Harmonic Infrared and Raman Spectra in Molecular Environments Using the Polarizable Embedding Model

We present a fully analytic approach to calculate infrared (IR) and Raman spectra of molecules embedded in complex molecular environments modeled using the fragment-based polarizable embedding (PE) model. We provide the theory for the calculation of analytic second-order geometric derivatives of molecular energies and first-order geometric derivatives of electric dipole moments and dipole-dipole polarizabilities within the PE model. The derivatives are implemented using a general open-ended response theory framework, thus allowing for an extension to higher-order derivatives. The embedding-potential parameters used to describe the environment in the PE model are derived through first-principles calculations, thus allowing a wide variety of systems to be modeled, including solvents, proteins, and other large and complex molecular environments. Here, we present proof-of-principle calculations of IR and Raman spectra of acetone in different solvents. This work is an important step toward calculating accurate vibrational spectra of molecules embedded in realistic environments.

Fine structures in Raman spectra of tetrahedral tetrachloride molecules in femtosecond coherent spectroscopy

Herewith, we present fast Fourier transforms of time resolved signals, obtained by use of the femtosecond transient transmission (TT) spectroscopy, for three tetrachlorides, CCl₄, SiCl₄, and GeCl₄, and chloroform, CHCl₃. Due to coherent excitation of molecules, the isotopic splitting of their spectral bands in the range of symmetric stretching vibration can be observed with high resolution not available in spontaneous Raman scattering. The intensity distribution in the isotopic fine structure pattern appears to differ for various studied molecules, which is explained by the role of intermolecular interactions and the local order of molecules in the liquids. In particular, in SiCl₄, the vibrational band exhibits anomalous ratios of the peak amplitudes, which do not agree with the natural abundance of the isotopologues. Using the simple oscillatory model of the liquid and fitting theoretical curves to the experimental results, we have been able to find the intermolecular force constants for all three liquids and to formulate the conclusion that the anomalous spectral pattern in SiCl₄ results from strong interactions between the closest Cl atoms belonging to adjacent molecules. Application of the windowed Fourier transform enables us to study the dynamics of intermolecular interactions. The strength of intermolecular interactions in CCl₄, SiCl₄, and GeCl4, found by the TT technique, is compared with the results obtained by means of the femtosecond optical Kerr effect spectroscopy.

Hydrogen Bond Networks in Binary Mixtures of Water and Organic Solvents

We here present an approach for the optical in situ characterization of hydrogen bond networks (HBNs) in binary mixtures of water and organic solvents (OSs), such as methanol, ethanol, and acetonitrile. HBNs are characterized based on (i) the analysis of experimental molar Raman spectra of the mixture, (ii) partial molar Raman spectra of the mixture constituents, and (iii) computed ideal molar Raman spectra of the mixture. Especially, the consideration of the partial molar Raman spectra provides insights into the development of hydrogen bonds of molecules of one species with their neighbors. The obtained Raman spectra are evaluated with respect to the centroid of the symmetric stretching vibration Raman signal of water and to the hydroxyl stretching vibration of alcohols. We show the influence of composition and temperature on the development of the HBN of the mixtures, the HBN of water, and the HBN of the OS molecules.

The influence of interactions between isotopoloques on coherent, ultrafast vibrational dynamics of liquid C2Cl4

The dynamics of intramolecular and intermolecular vibrations in liquid tetrachloroethylene are studied for the first time by use of femtosecond time-resolved techniques, such as transient transmission spectroscopy and optical Kerr effect spectroscopy. Fourier transforms of time signals are compared with spontaneous Raman spectra for both isotropic and anisotropic components. The isotopic effect resulting from natural abundance of chlorine isotopes manifests itself as splitting of the isotropic spectra of intramolecular symmetric vibrations. Application of windowed Fourier transform enables us to study the dynamics of both spectral responses in real time and to analyze the role of intermolecular interactions on the coherence in the system. In order to describe the dynamics of molecules in a liquid and to explain the experimental results, we use a simple theoretical model taking into account intermolecular interactions, which allowed us to find vibrational and rotational life times.

Inferential monitoring of chlorinated solvents through Raman spectroscopic observation of the vibrational modes of water

Recent improvements in diode laser, fiber optic, and data acquisition technology have rejuvenated interest in field applications of Raman spectroscopy in a wide range of settings. One such application involves the observation of chlorinated solvents to facilitate the practice of "monitored natural attenuation." In this context, this manuscript focuses on means to improve the sensitivity of in-situ Raman analysis of chlorinated solvents. In particular, the work explores the performance limits of a Time-Resolved Raman Spectroscopy (TRRS) system employed to observe chlorinated solvents in aqueous samples via laboratory tests conducted on both liquid standards of trichloroethylene (TCE) and simulated biodegraded field samples. Quantitative assessment of TCE in solution is carried out through both direct observation of TCE Raman functional groups (381 cm(-1) (δ skeletal), 840 cm(-1) (νCCl) and 1242 cm(-1) (δCH)) and indirect observation of the broad OH stretching (2700-3800 cm(-1)) Raman modes of water. Results from tests on simple solutions show that the TRRS system can detect TCE at aqueous concentrations as low as 70 ppm by directly monitoring the 381 cm(-1) TCE line, whereas observation of the OH stretching line of water (3393 cm(-1)) provides an indirect indication of TCE presence with nearly a 9× improvement in detection level. This unique and counterintuitive mechanism to detect the presence of chlorinated compounds in solution takes advantage of the influence of chlorine on the vibrational modes of water. This influence, which is believed to be attributed to the formation of hydrogen bonds and their resultant interactions with the solvation shell, may serve as a more sensitive and robust indication of the presence of aggregate chlorinated solvent contamination in aqueous systems. Tests performed on simulated biodegraded field samples demonstrate that the indirect detection mechanism is apparent even in complex samples representative of typical field conditions.

How strongly does trehalose interact with lysozyme in the solid state? Insights from molecular dynamics simulation and inelastic neutron scattering

Therapeutic proteins are usually conserved in glassy matrixes composed of stabilizing excipients and a small amount of water, which both control their long-term stability, and thus their potential use in medical treatments. To shed some light on the protein-matrix interactions in such systems, we performed molecular dynamics (MD) simulations on matrixes of (i) the model globular protein lysozyme (L), (ii) the well-known bioprotectant trehalose (T), and (iii) the 1:1 (in weight) lysozyme/trehalose mixture (LT), at hydration levels h of 0.0, 0.075, and 0.15 (in g of water/g of protein or sugar). We also supplemented these simulations with complementary inelastic neutron scattering (INS) experiments on the L, T, and LT lyophilized (freeze-dried) samples. The densities and free volume distributions indicate that trehalose improves the molecular packing of the LT glass with respect to the L one. Accordingly, the low-frequency vibrational densities of states (VDOS) and the mean square displacements (MSDs) of lysozyme reveal that it is less flexible-and thus less likely to unfold-in the presence of trehalose. Furthermore, at low contents (h = 0.075), water systematically stiffens the vibrational motions of lysozyme and trehalose, whereas it increases their MSDs on the nanosecond (ns) time scale. This stems from the hydrogen bonds (HBs) that lysozyme and trehalose form with water, which, interestingly, are stronger than the ones they form with each other but which, nonetheless, relax faster on the ns time scale, given the larger mobility of water. Moreover, lysozyme interacts preferentially with water in the hydrated LT mixtures, and trehalose appears to slow down significantly the relaxation of lysozyme-water HBs. Overall, our results suggest that the stabilizing efficiency of trehalose arises from its ability to (i) increase the number of HBs formed by proteins in the dry state and (ii) make the HBs formed by water with proteins stable on long (>ns) time scales.

Modeling of mixing acetone and water: how can their full miscibility be reproduced in computer simulations?

The free energy of mixing of acetone and water is calculated at 298 K by means of thermodynamic integration considering combinations of three acetone and six water potentials. The Anisotropic United Atom 4 (AUA4) and Transferable Potential for phase Equilibria (TraPPE) models of acetone are found not to be miscible with any of the six water models considered, although the free energy cost of the mixing of any of these model pairs is very small, being below the mean kinetic energy of the molecules along one degree of freedom of 0.5RT. On the other hand, the combination of the Pereyra, Asar, and Carignano (PAC) acetone and TIP5P-E water models turns out to be indeed fully miscible, and it is able to reproduce the change of the energy, entropy, and Helmholtz free energy of mixing of the two neat components very accurately (i.e., within 0.8 kJ/mol, 2.5 J/(mol K), and 0.3 kJ/mol, respectively) in the entire composition range. The obtained results also suggest that the PAC model of acetone is likely to be fully miscible with other water models, at least with SPC and TIP4P, as well.

Thermostabilization mechanism of bovine serum albumin by trehalose

Thermal denaturation of bovine serum albumin (BSA) is analyzed from differential scanning calorimetry (DSC) and Raman spectroscopy investigations. DSC curves exhibit a marked dependence on protein concentration. BSA thermal denaturation becomes broader and bimodal, and the temperature of denaturation increases with increasing protein concentration. Raman scattering investigations simultaneously carried out in the low-frequency range (10-350 cm(-1)) and in the amide I band region (1500-1800 cm(-1)) indicate that the denaturation process is described as a biphasic process independent of protein concentration. The dependence of the protein stability upon the protein concentration can be interpreted from the coupling of protein and solvent dynamics. The confrontation of previous results obtained from Raman investigations on lysozyme (LYS) and the present study of BSA brings out significant information on protein dynamics and the coupling of protein and hydration-water dynamics in relation with the solvent accessible surface area. Contrary to LYS, the modification of the dynamics of hydration water by the protein is clearly observed on BSA. The influence of trehalose on the protein dynamics was analyzed. We found that trehalose reduces the dynamic fluctuations of polar side chains at the protein-solvent interface. The mechanism of thermostabilization by trehalose is related to the reduction of the exposure of hydrophobic groups of BSA to the water molecules, and to a strengthening of intermolecular O-H interactions in the hydrogen-bond network of water, leading to the stabilization of the tertiary structure.

Diffusion coefficient and the secondary structure of poly-L-glutamic acid in aqueous solution

The diffusion coefficients (D) of poly-L-glutamic acid (PLG) at various pHs are investigated by the laser-induced transient-grating method with a new photoreactive probe molecule. The pH dependence of D is compared with that of the helical content of PLG measured by circular dichroism. It is found that the pH dependences of both quantities are very similar. Since the frictions of the translational diffusion of charged and protonated carboxyl groups are found to be similar each other, it is concluded that the conformation of the main polymer chain is the main factor in determining the diffusion process; in other words, the alpha-helix conformation makes the molecular diffusion faster. This result indicates that the conformational change of a protein can be detected by monitoring the diffusion coefficient.

Analysis of the Effect of Translation−Rotation Coupling on Diffusion along the Molecular Axes

The analysis of the microscopic diffusion processes of CO(2) and H(2)O in the coordinate system defined by the molecular orientation allows a new criterion to be introduced which provides information on the short and long time behavior of the rotation-translation coupling as well as to quantify the strength of this coupling. We discuss the general conditions under which this affects the translation diffusion "seen" by the molecule along its molecular axes. The results show that the translation-rotation coupling is correlated to the local environment in shaping the longitudinal and transversal translation dynamics of a molecule at a microscopic level.

Liquid Structure and Preferential Solvation of Metal Ions in Solvent Mixtures of N,N-Dimethylformamide and N-Methylformamide

Raman spectra of aprotic N,N-dimethylformamide (DMF) and protic N-methylformamide (NMF) mixtures containing manganese(II), nickel(II), and zinc(II) perchlorate were obtained, and the individual solvation numbers around the metal ions were determined over the whole range of solvent compositions. Variation profiles of the individual solvation numbers with solvent composition showed no significant difference among the metal systems examined. In all of these metal systems, no preferential solvation occurs in mixtures with DMF mole fraction of x(DMF) < 0.5, whereas DMF preferentially solvates the metal ions at x(DMF) > 0.5. The liquid structure of the mixtures was also studied by means of small-angle neutron scattering (SANS) and low-frequency Raman spectroscopy. SANS experiments demonstrate that DMF molecules do not appreciably self-aggregate in the mixtures over the whole range of solvent composition. Low-frequency Raman spectroscopy suggests that DMF molecules are extensively hydrogen-bonded with NMF in NMF-rich mixtures, whereas NMF molecules extensively self-aggregate in DMF-rich mixtures, although the liquid structure in neat NMF is partly ruptured. The bulk solvent structure in the mixtures thus varies with solvent composition, which plays a decisive role in developing the varying profiles of the individual solvation numbers of metal ions in the solvent mixtures.

Low-frequency Raman spectra of sub- and supercritical CO2: qualitative analysis of the diffusion coefficient behavior

We report the results of the low-frequency Raman experiments on CO(2) which were carried out in a wide density range, along the liquid-gas coexistence curve in a temperature range of 293-303 K, and on the critical isochore of 94.4 cm(3) mol(-1) in a temperature range of 304-315 K. In our approach, the qualitative behavior of the diffusion coefficient D is predicted, assuming the following: first, that the low-frequency Raman spectra can be interpreted in terms of the translation rotation motions; second, that the random force could be replaced by the total force to calculate the friction coefficient; and finally, that the Einstein frequency is associated with the position of the maximum of the low-frequency Raman spectrum. The results show that the diffusion coefficient increases along the coexistence curve, and its values are almost constant on the critical isochore. The predicted values reproduce qualitatively those obtained by other techniques. The values of D were also calculated by molecular-dynamics simulation and they qualitatively reproduce the behavior of D.

Structural Fluctuation and Dynamics of Ribose Puckering in Aqueous Solution from First Principles

Using the method of ab initio molecular dynamics, we examine the structural fluctuation and the low-frequency dynamics of beta-ribofuranose puckering in aqueous solution. Our analysis suggests that the distance between the anomeric and hydroxymethyl oxygens is a simple relevant geometrical parameter that dynamically correlates with the phase angle in the north region. The time-frequency analysis using the Hilbert-Huang transform also confirms the correlation, and most of the instantaneous frequencies for the phase angle and the above distance are found to be concentrated on the region below about 100 cm(-1). Our analysis of ab initio molecular dynamics trajectories suggests that the molecular origin of the hydration effects on the low-frequency dynamics of beta-ribofuranose puckering is closely related to this correlation and thus primarily attributed to the relatively local interactions among the anomeric and hydroxymethyl oxygens and the surrounding water molecules near them. Additionally, we discuss the difference in the low-frequency dynamics of beta-ribofuranose puckering between two hydroxymethyl rotamers.

Molecular structure and dynamics of liquids: aqueous urea solutions

In this review a multi-technical approach to the analysis of the structure and dynamics of the urea/water system is described. The reorientational movement of the solute molecule is investigated by the analysis of spectral band-shapes, as well as with the use of the optical Kerr effect (OKE) and molecular dynamics simulation (MDS). The effect of solute concentration on the structure and dynamics of the aqueous solutions (aggregation, orientational distribution, solvation...) is studied by molecular dynamics simulation and neutron scattering. The results obtained by other techniques are included to provide a critical analysis. Finally, the low-frequency Raman spectra of the system are interpreted on the basis of the semi-quantitative information obtained by molecular dynamics simulation.