The relationship between dynamics and structure in the far infrared absorption spectrum of liquid water

Modeling of protein hydration dynamics is supported by THz spectroscopy of highly diluted solutions

In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in highly dilute (HD) solutions of initial proteins. THz spectroscopy measurements have been conducted as a means to analyze and characterize the collective dynamics of the HD samples. MD simulations have also been performed that have successfully reproduced the observed signatures from experimental measurement. Using this joint experimental-computational approach we determine that the HD process associated with the preparation of the highly diluted samples used in this investigation induces a dynamical transition that results in collective changes in the hydrogen-bond network of the solvent. The dynamical transition in the solvent is triggered by changes in the mobility and hydrogen-bonding interactions of the surface molecules in the HD samples and is characterized by dynamical heterogeneity. We have uncovered that the reorganization of the sample surface residue dynamics at the solvent-protein interface leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen-antibody affinity and recognition.

New insights into the microscopic interactions associated with the physical mechanism of action of highly diluted biologics

In this investigation, we report the effect on the microscopic dynamics and interactions of the cytokine interferon gamma (IFN-γ) and antibodies to IFN-γ (anti-IFN-γ) and to the interferon gamma receptor 1 (anti-IFNGR1) prepared in exceptionally dilute solutions of initial proteins. Using both THz spectroscopy and molecular dynamics simulations we have uncovered that the high dilution method of sample preparation results in the reorganization of the sample surface residue dynamics at the solvent–protein interface that leads to both structural and kinetic heterogeneous dynamics that ultimately create interactions that enhance the binding probability of the antigen binding site. Our results indicate that the modified interfacial dynamics of anti-IFN-γ and anti-IFGNR1 that we probe experimentally are directly associated with alterations in the complementarity regions of the distinct antibodies that designate both antigen–antibody affinity and recognition.

Effect of temperature on the low-frequency vibrational spectrum and relative structuring of hydration water around a single-stranded DNA

Molecular dynamics simulations of the single-stranded DNA oligomer (5'-CGCGAAT TCGCG-3') in aqueous solution have been carried out at different temperatures between 160 K and 300 K. The effects of temperature on the low-frequency vibrational spectrum and local structural arrangements of water molecules hydrating the DNA strand have been explored in detail. The low-frequency density of states distributions reveal that increasingly trapped transverse water motions play a dominant role in controlling the band corresponding to O⋯O⋯O bending or transverse oscillations of hydration water at supercooled temperatures. In addition, presence of a broad band around 260 (±20) cm(-1) under supercooled conditions indicates transformation from high density liquid-like structuring of hydration water at higher temperatures to that of a low density liquid at lower temperatures. It is found that long-range correlations between the supercooled hydration water molecules arise due to such local structural transition around the DNA oligomer.

Dielectric relaxation in liquid water: two fractions or two dynamics?

Dielectric relaxation in liquid water is studied using molecular dynamics (MD) simulations in the temperature range of 240 to 340 K at atmospheric pressure. The main dielectric and fast relaxation mode are identified in the spectra of dipole moment autocorrelation functions. The microscopic origin of the fast dielectric relaxation process, which takes place on a time scale of subpicoseconds at room temperature, is discussed. A new hypothesis for the fast dielectric mode is presented. It is based on the assumption of the intrawell rotational relaxation taking place during the waiting period between thermally activated large angle jumps occurring in the course of changing H-bond partners.

Intermolecular vibrational study in liquid water and ice by using far infrared spectroscopy with synchrotron radiation of MIRRORCLE 20

Far infrared absorption measurements for distilled water and ice Ih were performed in the frequency range from 20 cm(-1) to 1000 cm(-1) with Fourier Transform Infrared Spectrometer (FTIR) utilizing SR of a portable synchrotron. Four vibrational bands were separated from measured spectra in liquid water. We found that a peak frequency of 40±1 cm(-1) did not depend on the temperature in a range between 10.0°C and 70.0°C; however, any low energy excitation modes were not observed in the ice spectrum. It is concluded that this band is caused by collective vibrations specific to the dynamical structure in liquid water.

Solvent-induced backbone fluctuations and the collective librational dynamics of lysozyme studied by terahertz spectroscopy

THz spectroscopy is used to investigate the dynamics of the globular protein hen egg white lysozyme under varying hydration and temperature conditions. An analysis of the experimental spectra has revealed that the amount of solvent in the hydration shell has a strong influence on the low-frequency protein conformational dynamics and also the arrangement of hydrogen bonds in the protein secondary structure. Furthermore at a hydration level >0.2 we identify collective backbone fluctuations in the protein secondary structure that are not present at low hydration. It is possible that these solvent induced modes are important for the biological function of the protein.

Ultrafast dynamics of hydrogen bond exchange in aqueous ionic solutions

The structural and dynamical properties of aqueous ionic solutions influence a wide range of natural and biological processes. In these solutions, water has the opportunity to form hydrogen bonds with other water molecules and anions. Knowing the time scale with which these configurations interconvert represents a key factor to understanding the influence of molecular scale heterogeneity on chemical events in aqueous ionic solutions. We have used ultrafast IR spectroscopy and Car-Parrinello molecular dynamics (CPMD) simulations to investigate the hydrogen bond (H-bond) structural dynamics in aqueous 6 M sodium perchlorate (NaClO4) solution. We have measured the H-bond exchange dynamics between spectrally distinct water-water and water-anion H-bond configurations with 2DIR spectroscopy and the orientational relaxation dynamics of water molecules in different H-bond configurations with polarization-selective IR pump-probe experiments. The experimental H-bond exchange time correlates strongly with the experimental orientational relaxation time of water molecules. This agrees with prior observations in water and aqueous halide solutions, and has been interpreted within the context of an orientational jump model for the H-bond exchange. The CPMD simulations performed on aqueous 6 M NaClO4 solution clearly demonstrate that water molecules organize into two radially and angularly distinct structural subshells within the first solvation shell of the perchlorate anion, with one subshell possessing the majority of the water molecules that donate H-bonds to perchlorate anions and the other subshell possessing predominantly water molecules that donate two H-bonds to other water molecules. Due to the high ionic concentration used in the simulations, essentially all water molecules reside in the first ionic solvation shells. The CPMD simulations also demonstrate that the molecular exchange between these two structurally distinct subshells proceeds more slowly than the H-bond exchange between the two spectrally distinct H-bond configurations. We interpret this to indicate that orientational motions predominantly dictate the rate of H-bond exchange, while translational diffusion must occur to complete the molecular exchange between the two structurally distinct subshells around the perchlorate anions. The 2DIR measurements observe the H-bond exchange between the two spectrally distinct H-bond configurations, but the lifetime of the hydroxyl stretch precludes the observation of the slower molecular exchange. Our 2DIR experiments and CPMD simulations demonstrate that orientational motions predominantly equilibrate water molecules within their local solvation subshells, but the full molecular equilibration within the first solvation shell around the perchlorate anion necessitates translational motion.

The influence of chain dynamics on the far-infrared spectrum of liquid methanol-water mixtures

Far-infrared-absorption spectroscopy has been used to study the low-frequency (<or=100 cm-1) intermolecular modes of methanol in mixtures with water. With the aid of a first-principles molecular-dynamics simulation on an equivalent system, a detailed understanding about the origin of the low-frequency IR modes has been established. The total dipole spectrum from the simulation suggests that the bands appearing in the experimental spectra at approximately 55 and 70 cm-1 in methanol and methanol-rich mixtures arise from both fluctuations and torsional motions occurring within the methanol hydrogen-bonded chains. The influence of these modes on both the solvation dynamics and the relaxation mechanisms in the liquid is discussed within the context of recent experimental and theoretical results that have emerged from studies focusing on the short-time dynamics in the methanol hydrogen bond network.

The influence of chain dynamics on the far-infrared spectrum of liquid methanol

Far-infrared-absorption spectroscopy is used to investigate the low-frequency (<or=100 cm-1) intermolecular interactions in liquid methanol. Using an intense source of far-infrared radiation, modes are elucidated at approximately 30 and 70 cm-1 in the absorption spectrum. These modes are believed to arise from intermolecular bending and librational motions, respectively, and are successfully reproduced in an ab initio molecular-dynamics simulation of methanol.