Solvation Dynamics of Model Peptides Probed by Terahertz Spectroscopy. Observation of the Onset of Collective Network Motions

Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation

The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2 O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2 O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2 O to D2 O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2 O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.

Decreased Water Mobility Contributes To Increased α-Synuclein Aggregation

The solvation shell is essential for the folding and function of proteins, but how it contributes to protein misfolding and aggregation has still to be elucidated. We show that the mobility of solvation shell H2O molecules influences the aggregation rate of the amyloid protein α-synuclein (αSyn), a protein associated with Parkinson's disease. When the mobility of H2O within the solvation shell is reduced by the presence of NaCl, αSyn aggregation rate increases. Conversely, in the presence CsI the mobility of the solvation shell is increased and αSyn aggregation is reduced. Changing the solvent from H2O to D2O leads to increased aggregation rates, indicating a solvent driven effect. We show the increased aggregation rate is not directly due to a change in the structural conformations of αSyn, it is also influenced by a reduction in both the H2O mobility and αSyn mobility. We propose that reduced mobility of αSyn contributes to increased aggregation by promoting intermolecular interactions.

Terahertz Kerr Effect of Liquids

In recent years, tremendous advancements have been made in various technologies such as far-infrared, low-frequency Raman, and two-dimensional (2D) Raman terahertz (THz) spectroscopies. A coherent method has emerged from numerous experimental and theoretical investigations of molecular dynamics in liquids by comparing linear and non-linear spectroscopic techniques. Intermolecular hydrogen bond vibration, molecular reorientation motion, and interaction between molecule/ionic solute and hydrogen bonds have been demonstrated to occur in the THz region, which are closely related to their physical/chemical properties and structural dynamics. However, precise probing of various modes of motion is difficult because of the complexity of the collective and cooperative motion of molecules and spectral overlap of related modes. With the development of THz science and technology, current state-of-the-art THz sources can generate pulsed electric fields with peak intensities of the order of microvolts per centimeter (MV/cm). Such strong fields enable the use of THz waves as the light source for non-linear polarization of the medium and in turn leads to the development of the emerging THz Kerr effect (TKE) technique. Many low-frequency molecular motions, such as the collective directional motion of molecules and cooperative motion under the constraint of weak intermolecular interactions, are resonantly excited by an intense THz electric field. Thus, the TKE technique provides an interesting prospect for investigating low-frequency dynamics of different media. In view of this, this paper first summarizes the research work on TKE spectroscopy by taking a solid material without low-frequency molecular motions as an example. Starting from the principle of TKE technology and its application in investigating the properties of solid matter, we have explored the low-frequency molecular dynamics of liquid water and aqueous solutions using TKE. Liquid water is a core of life and possesses many extraordinary physical and biochemical properties. The hydrogen bond network plays a crucial role in these properties and is the main reason for its various kinetic and thermodynamic properties, which differ from those of other liquids. However, the structure of the hydrogen bond network between water and solutes is not well known. Therefore, evaluating the hydrogen bond-related kinetic properties of liquid water is important.

Amide Spectral Fingerprints are Hydrogen Bonding-Mediated

The origin of the peculiar amide spectral features of proteins in aqueous solution is investigated, by exploiting a combined theoretical and experimental approach to study UV Resonance Raman (RR) spectra of peptide molecular models, namely N-acetylglycine-N-methylamide (NAGMA) and N-acetylalanine-N-methylamide (NALMA). UVRR spectra are recorded by tuning Synchrotron Radiation at several excitation wavelengths and modeled by using a recently developed multiscale protocol based on a polarizable QM/MM approach. Thanks to the unparalleled agreement between theory and experiment, we demonstrate that specific hydrogen bond interactions, which dominate hydration dynamics around these solutes, play a crucial role in the selective enhancement of amide signals. These results further argue the capability of vibrational spectroscopy methods as valuable tools for refined structural analysis of peptides and proteins in aqueous solution.

Hydration Dynamics of Model Peptides with Different Hydrophobic Character

The multi-scale dynamics of aqueous solutions of the hydrophilic peptide N-acetyl-glycine-methylamide (NAGMA) have been investigated through extended frequency-range depolarized light scattering (EDLS), which enables the broad-band detection of collective polarizability anisotropy fluctuations. The results have been compared to those obtained for N-acetyl-leucinemethylamide (NALMA), an amphiphilic peptide which shares with NAGMA the same polar backbone, but also contains an apolar group. Our study indicates that the two model peptides induce similar effects on the fast translational dynamics of surrounding water. Both systems slow down the mobility of solvating water molecules by a factor 6–8, with respect to the bulk. Moreover, the two peptides cause a comparable far-reaching spatial perturbation extending to more than two hydration layers in diluted conditions. The observed concentration dependence of the hydration number is explained considering the random superposition of different hydration shells, while no indication of solute aggregation phenomena has been found. The results indicate that the effect on the dynamics of water solvating the amphiphilic peptide is dominated by the hydrophilic backbone. The minor impact of the hydrophobic moiety on hydration features is consistent with structural findings derived by Fourier transform infrared (FTIR) measurements, performed in attenuated total reflectance (ATR) configuration. Additionally, we give evidence that, for both systems, the relaxation mode in the GHz frequency range probed by EDLS is related to solute rotational dynamics. The rotation of NALMA occurs at higher timescales, with respect to the rotation of NAGMA; both processes are significantly slower than the structural dynamics of hydration water, suggesting that solute and solvent motions are uncoupled. Finally, our results do not indicate the presence of super-slow water (relaxation times in the order of tens of picoseconds) around the peptides investigated.

Detection and discrimination of SARS-CoV-2 spike protein-derived peptides using THz metamaterials

The development of effective assay techniques for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) has recently received research attention due to its rapid worldwide spread and considerable risk to human health. The receptor-binding domain (RBD) of the spike (S) protein in SARS-CoV-2, a key component for viral entry that has a unique sequence compared to other structural proteins, has been considered an important diagnostic target. In this respect, low-frequency vibrational modes have the advantage of providing information about compositional and structural dependencies at the peptide level. In this study, the sensitive and selective detection of peptides derived from the RBD in SARS-CoV-2 and SARS-CoV was investigated using metamaterial-based sensing chips with a terahertz time-domain spectroscopy (THz-TDS) system. Based on their RBD sequences, two pairs of peptides with 20 residues each were prepared. The sensitivity, specificity, and reproducibility of the proposed system were examined via quantitative analysis using THz metamaterials at three resonance frequencies, and it was found that the species could be discriminated based on their sequences. The THz signals were analyzed with regard to the major amino acid components of the peptides, and the molecular distributions were also investigated based on the hydropathy and net charge of the peptides.

Water-Based Coherent Detection of Broadband Terahertz Pulses

Both solids and gases have been demonstrated as the materials for terahertz (THz) coherent detection. The gas-based coherent detection methods require a high-energy probe laser beam and the detection bandwidth is limited in the solid-based methods. Whether liquids can be used for THz detection and relax these problems has not yet been reported, which becomes a timely and interesting topic due to the recent observation of efficient THz wave generation in liquids. Here, we propose a THz coherent detection scheme based on liquid water. When a THz pulse and a fundamental laser beam are mixed on a free-flowing water film, a second harmonic (SH) beam is generated as the plasma is formed. Combining this THz-induced SH beam with a control SH beam, we successfully achieve the time-resolved waveform of the THz field with the frequency range of 0.1-18 THz. The required probe laser energy is as low as a few microjoules. The sensitivity of our scheme is 1 order of magnitude higher than that of the air-based method under comparable detection conditions. The scheme is sensitive to the THz polarization and the phase difference between the fundamental and control SH beams, which brings direct routes for optimization and polarization sensitive detection. Energy scaling and polarization properties of the THz-induced beam indicate that its generation can be attributed to a four-wave mixing process. This generation mechanism makes simple relationships among the probe laser, THz-induced SH, and THz field, favorable for robustness and flexibility of the detection device.

Optimized Magnesium Force Field Parameters for Biomolecular Simulations with Accurate Solvation, Ion-Binding, and Water-Exchange Properties

Magnesium ions play an essential role in many vital processes. To correctly describe their interactions in molecular dynamics simulations, an accurate parametrization is crucial. Despite the importance and considerable scientific effort, current force fields based on the commonly used 12-6 Lennard-Jones interaction potential fail to reproduce a variety of experimental solution properties. In particular, no parametrization exists so far that simultaneously reproduces the solvation free energy and the distance to the water oxygens in the first hydration shell. Moreover, current Mg2+ force fields significantly underestimate the rate of water exchange leading to unrealistically slow exchange kinetics. In order to make progress in the development of improved models, we systematically optimize the Mg2+ parameters in combination with the TIP3P water model in a much larger parameter space than previously done. The results show that a long-ranged interaction potential and modified Lorentz-Berthelot combination rules allow us to accurately reproduce multiple experimental properties including the solvation free energy, the distances to the oxygens of the first hydration shell, the hydration number, the activity coefficient derivative in MgCl2 solutions, the self-diffusion coefficient, and the binding affinity to the phosphate oxygen of RNA. Matching this broad range of thermodynamic properties, we present two sets of optimal parameters: MicroMg yields water exchange on the microsecond timescale in agreement with experiments. NanoMg yields water exchange on the nanosecond timescale facilitating the direct observation of ion-binding events. As shown for the example of the add A-riboswitch, the optimized parameters correctly reproduce the structure of specifically bound ions and permit the de novo prediction of Mg2+-binding sites in biomolecular simulations.

Kinetic pathways of water exchange in the first hydration shell of magnesium

Water exchange between the coordination shells of metal cations in aqueous solutions is fundamental in understanding their role in biochemical processes. Despite the importance, the microscopic mechanism of water exchange in the first hydration shell of Mg²⁺ has not been resolved since the exchange dynamics is out of reach for conventional all-atom simulations. To overcome this challenge, transition path sampling is applied to resolve the kinetic pathways, to characterize the reaction mechanism and to provide an accurate estimate of the exchange rate. The results reveal that water exchange involves the concerted motion of two exchanging water molecules and the collective rearrangement of all water molecules in the first hydration shell. Using a recently developed atomistic model for Mg²⁺, water molecules remain in the first hydration shell for about 40 ms, a time considerably longer compared to the 0.1 ms predicted by transition state theory based on the coordinates of a single water molecule. The discrepancy between these timescales arises from the neglected degrees of freedom of the second exchanging water molecule that plays a decisive role in the reaction mechanism. The approach presented here contributes molecular insights into the dynamics of water around metal cations and provides the basis for developing accurate atomistic models or for understanding complex biological processes involving metal cations.

A Comprehensive Review on Food Applications of Terahertz Spectroscopy and Imaging

Food product safety is a public health concern. Most of the food safety analytical and detection methods are expensive, labor intensive, and time consuming. A safe, rapid, reliable, and nondestructive detection method is needed to assure consumers that food products are safe to consume. Terahertz (THz) radiation, which has properties of both microwave and infrared, can penetrate and interact with many commonly used materials. Owing to the technological developments in sources and detectors, THz spectroscopic imaging has transitioned from a laboratory-scale technique into a versatile imaging tool with many practical applications. In recent years, THz imaging has been shown to have great potential as an emerging nondestructive tool for food inspection. THz spectroscopy provides qualitative and quantitative information about food samples. The main applications of THz in food industries include detection of moisture, foreign bodies, inspection, and quality control. Other applications of THz technology in the food industry include detection of harmful compounds, antibiotics, and microorganisms. THz spectroscopy is a great tool for characterization of carbohydrates, amino acids, fatty acids, and vitamins. Despite its potential applications, THz technology has some limitations, such as limited penetration, scattering effect, limited sensitivity, and low limit of detection. THz technology is still expensive, and there is no available THz database library for food compounds. The scanning speed needs to be improved in the future generations of THz systems. Although many technological aspects need to be improved, THz technology has already been established in the food industry as a powerful tool with great detection and quantification ability. This paper reviews various applications of THz spectroscopy and imaging in the food industry.

Toward theoretical terahertz spectroscopy of glassy aqueous solutions: partially frozen solute-solvent couplings of glycine in water

The molecular-level understanding of THz spectra of aqueous solutions under ambient conditions has been greatly advanced in recent years. Here, we go beyond previous analyses by performing ab initio molecular dynamics simulations of glycine in water with artificially frozen solute or solvent molecules, respectively, while computing the total THz response as well as its decomposition into mode-specific resonances based on the "supermolecular solvation complex" technique. Clamping the water molecules and keeping glycine moving breaks the coupling of glycine to the structural dynamics of the solvent, however, the polarization and dielectric solvation effects in the static solvation cage are still at work since the full electronic structure of the quenched solvent is taken into account. The complementary approach of fixing glycine reveals both the dynamical and electronic response of the solvation cage at the level of its THz response. Moreover, to quantitatively account for the electronic contribution solely due to solvent embedding, the solute species is "vertically desolvated", thus preserving the fully coupled solute-solvent motion in terms of the solute's structural dynamics in solution, while its electronic structure is no longer subject to solute-solvent polarization and charge transfer effects. When referenced to the free simulation of Gly(aq), this three-fold approach allows us to decompose the THz spectral contributions due to the correlated solute-solvent dynamics into entirely structural and purely electronic effects. Beyond providing hitherto unknown insights, the observed systematic changes of THz spectra in terms of peak shifts and lineshape modulations due to conformational freezing and frozen solvation cages might be useful to investigate the solvation of molecules in highly viscous H-bonding solvents such as ionic liquids and even in cryogenic ices as relevant to polar stratospheric and dark interstellar clouds.

Calculated Terahertz Spectra of Glycine Oligopeptide Solutions Confined in Carbon Nanotubes

To reduce the intense terahertz (THz) wave absorption of water and increase the signal-to-noise ratio, the THz spectroscopy detection of biomolecules usually operates using the nanofluidic channel technologies in practice. The effects of confinement due to the existence of nanofluidic channels on the conformation and dynamics of biomolecules are well known. However, studies of confinement effects on the THz spectra of biomolecules are still not clear. In this work, extensive all-atom molecular dynamics simulations are performed to investigate the THz spectra of the glycine oligopeptide solutions in free and confined environments. THz spectra of the oligopeptide solutions confined in carbon nanotubes (CNTs) with different radii are calculated and compared. Results indicate that with the increase of the degree of confinement (the reverse of the radius of CNT), the THz absorption coefficient decreases monotonically. By analyzing the diffusion coefficient and dielectric relaxation dynamics, the hydrogen bond life, and the vibration density of the state of the water molecules in free solution and in CNTs, we conclude that the confinement effects on the THz spectra of biomolecule solutions are mainly to slow down the dynamics of water molecules and hence to reduce the THz absorption of the whole solution in confined environments.

Label-free protein detection using terahertz time-domain spectroscopy

Protein analysis is the foundation to understanding the mechanisms of complex biological processes. As one of the most widely used techniques to determine protein species and contents, protein dot blot aids biology research but needs corresponding antibodies for marking. A label-free detection method based on terahertz time-domain spectroscopy (THz-TDS) is proposed and demonstrated to improve this traditional technology. A membrane loaded with protein samples is directly scanned using a transmission THz-TDS system for spectral imaging. Different kinds of proteins can be distinguished by the refractive index extracted from the THz transmission spectrum. The intensity or shade imaged with the THz transmission spectrum can help detect the protein quantitatively. The feasibility of this new protein assay is demonstrated by the results of systematic testing with actual samples prepared with the dot-blot protocol.

Deciphering complex dynamics of water counteraction around secondary structural elements of allosteric protein complex: Case study of SAP-SLAM system in signal transduction cascade

The first hydration shell of a protein exhibits heterogeneous behavior owing to several attributes, majorly local polarity and structural flexibility as revealed by solvation dynamics of secondary structural elements. We attempt to recognize the change in complex water counteraction generated due to substantial alteration in flexibility during protein complex formation. The investigation is carried out with the signaling lymphocytic activation molecule (SLAM) family of receptors, expressed by an array of immune cells, and interacting with SLAM-associated protein (SAP), composed of one SH2 domain. All atom molecular dynamics simulations are employed to the aqueous solutions of free SAP and SLAM-peptide bound SAP. We observed that water dynamics around different secondary structural elements became highly affected as well as nicely correlated with the SLAM-peptide induced change in structural rigidity obtained by thermodynamic quantification. A few instances of contradictory dynamic features of water to the change in structural flexibility are explained by means of occluded polar residues by the peptide. For βD, EFloop, and BGloop, both structural flexibility and solvent accessibility of the residues confirm the obvious contribution. Most importantly, we have quantified enhanced restriction in water dynamics around the second Fyn-binding site of the SAP due to SAP-SLAM complexation, even prior to the presence of Fyn. This observation leads to a novel argument that SLAM induced more restricted water molecules could offer more water entropic contribution during the subsequent Fyn binding and provide enhanced stability to the SAP-Fyn complex in the signaling cascade. Finally, SLAM induced water counteraction around the second binding site of the SAP sheds light on the allosteric property of the SAP, which becomes an integral part of the underlying signal transduction mechanism.

The dynamics of peptide-water interactions in dialanine: An ultrafast amide I 2D IR and computational spectroscopy study

We present a joint experimental and computational study of the dynamic interactions of dialanine (Ala-Ala) with water, comparing the results of ultrafast 2D IR and infrared transient absorption spectroscopy of its amide I vibration with spectra modeled from molecular dynamics (MD) simulations. The experimental data are analyzed to describe vibrational frequency fluctuations, vibrational energy relaxation, and chemical exchange processes. The origin of these processes in the same underlying fluctuating forces allows a common description in terms of the fluctuations and conformational dynamics of the peptide and associated solvent. By comparing computational spectroscopy from MD simulations with multiple force fields and water models, we describe how the dynamics of water hydrogen bond fluctuations and switching processes act as a source of friction that governs the dephasing and vibrational relaxation, and provide a description of coupled water and peptide motions that give rise to spectroscopic exchange processes.

Quantum Mechanics Approach to Hydration Energies and Structures of Alanine and Dialanine

A systematic approach to the phenomena related to hydration of biomolecules is reported at the state of the art of electronic-structure methods. Large-scale CCSD(T), MP4-SDQ, MP2, and DFT(M06-2X) calculations for some hydrated complexes of alanine and dialanine (Ala⋅13 H₂ O, Ala₂ H⁺ ⋅18 H₂ O, and Ala₂ ⋅18 H₂ O) are compared with experimental data and other elaborate modeling to assess the reliability of a simple bottom-up approach. The inclusion of a minimal number of water molecules for microhydration of the polar groups together with the polarizable continuum model is sufficient to reproduce the relative bulk thermodynamic functions of the considered biomolecules. These quantities depend on the adopted electronic-structure method, which should be chosen with great care. Nevertheless, the computationally feasible MP2 and M06-2X functionals with the aug-cc-pVTZ basis set satisfactorily reproduce values derived by high-level CCSD(T) and MP4-SDQ methods, and thus they are suitable for future developments of more elaborate and hence more biochemically significant peptides.

Improved thickness estimation of liquid water using Kramers-Kronig relations for determination of precise optical parameters in terahertz transmission spectroscopy

In terahertz transmission spectroscopy, there is a typical problem of thickness uncertainty, which hampers to determine precise optical parameters of samples. In order to resolve this experimental problem, a method optimizing sample thickness using singly subtractive Kramers-Kronig relations is proposed. For tens of micrometers thick water samples, we improved the accuracy of sample thickness by an order of magnitude (up to sub-micrometer) using the algorithm leading to obtain precise optical parameters of water. The broad applicability of the method is demonstrated for measuring various materials in addition to highly absorbing liquid water in the spectral range from 0.3 to 1.6 THz.

A sensitive fluorescent probe for the polar solvation dynamics at protein–surfactant interfaces

Relaxation dynamics at the surface of biologically important macromolecules is important taking into account their functionality in molecular recognition.

Terahertz spectroscopy for the isothermal detection of bacterial DNA by magnetic bead-based rolling circle amplification

A terahertz biosensor based on rolling circle amplification was developed for the isothermal detection of bacterial DNA.

Rapid and label-free detection and assessment of bacteria by terahertz time-domain spectroscopy

Here we demonstrated the potential and applicability of terahertz (THz) spectroscopy to detect four commonly found bacteria in the infectious diseases. Besides the different spectral characteristics between bacterial species, THz absorption differences for living bacteria, dead bacteria and bacterial powder of the same species were also investigated. Our results revealed that small differences in water contents between bacterial cells account for distinct discrepancies of the absorption coefficients, which can be used for bacterial species identification. Furthermore, living and dead bacteria showed different absorption coefficients as a result of their different hydration levels, suggesting that THz spectroscopy can be used to rapidly assess the living state of bacteria under test. Our results clearly demonstrated the ability of THz spectroscopy for time-saving and label-free detection of bacteria with minimal sample preparation, potentially to be utilized for point-of-care tests in the near future. Schematic representation of bacterial detection by THz spectroscopy. Different bacteria have distinctive absorption coefficients as a result of their different water contents.

Molecular properties of aqueous solutions: a focus on the collective dynamics of hydration water

When a solute is dissolved in water, their mutual interactions determine the molecular properties of the solute on one hand, and the structure and dynamics of the surrounding water particles (the so-called hydration water) on the other. The very existence of soft matter and its peculiar properties are largely due to the wide variety of possible water-solute interactions. In this context, water is not an inert medium but rather an active component, and hydration water plays a crucial role in determining the structure, stability, dynamics, and function of matter. This review focuses on the collective dynamics of hydration water in terms of retardation with respect to the bulk, and of the number of molecules whose dynamics is perturbed. Since water environments are in a dynamic equilibrium, with molecules continuously exchanging from around the solute towards the bulk and vice versa, we examine the ability of different techniques to measure the water dynamics on the basis of the explored time scales and exchange rates. Special emphasis is given to the collective dynamics probed by extended depolarized light scattering and we discuss whether and to what extent the results obtained in aqueous solutions of small molecules can be extrapolated to the case of large biomacromolecules. In fact, recent experiments performed on solutions of increasing complexity clearly indicate that a reductionist approach is not adequate to describe their collective dynamics. We conclude this review by presenting current ideas that are being developed to describe the dynamics of water interacting with macromolecules.

Microfluidic Devices for Terahertz Spectroscopy of Live Cells Toward Lab-on-a-Chip Applications

THz spectroscopy is an emerging technique for studying the dynamics and interactions of cells and biomolecules, but many practical challenges still remain in experimental studies. We present a prototype of simple and inexpensive cell-trapping microfluidic chip for THz spectroscopic study of live cells. Cells are transported, trapped and concentrated into the THz exposure region by applying an AC bias signal while the chip maintains a steady temperature at 37 °C by resistive heating. We conduct some preliminary experiments on E. coli and T-cell solution and compare the transmission spectra of empty channels, channels filled with aqueous media only, and channels filled with aqueous media with un-concentrated and concentrated cells.

A study of the relationship between water and anions of the Hofmeister series using pressure perturbation calorimetry

Pressure perturbation calorimetry (PPC) was used to study the relationship between water and sodium salts with a range of different anions. At temperatures around 25 °C the heat on pressurisation (ΔQ) from 1 to 5 bar was negative for all solutions relative to pure water. The raw data showed that as the temperature rose, the gradient was positive relative to pure water and the transition temperature where ΔQ was zero was related to anion surface charge density and was more pronounced for the low-charge density anions. A three component model was developed comprising bulk water, the hydration layer and the solute to calculate the molar expansivity of the hydration layer around the ions in solution. The calculated molar expansivities of water in the hydration layer around the ions were consistently less than pure water. ΔQ at different disodium hydrogen phosphate concentrations showed that the change in molar enthalpy relative to pure water was not linear even as it approached infinite dilution suggesting that while hydration layers can be allocated to the water around ions this does not rule out interactions between water and ions extending beyond the immediate hydration layer.

Concentration dependence of hydration water in a model peptide

The molecular dynamics of aqueous solutions of a model amphiphilic peptide is studied as a function of concentration by broad-band light scattering experiments. Similarly to protein aqueous solutions, a considerable retardation, of about a factor 6-8, of hydration water dynamics with respect to bulk water is found, showing a slight dependence on solute concentration. Conversely, the average number of water molecules perturbed by the presence of peptide, i.e. the hydration number, appears to be strongly modified by adding solute. Its behaviour, decreasing upon increasing concentration, can be interpreted considering the random close-to-contact condition experienced by solute particles. Overall, the present findings support the view of a "long range" effect of peptides on the surrounding water, extending beyond the first two hydration shells.

Label-free detection and characterization of the binding of hemagglutinin protein and broadly neutralizing monoclonal antibodies using terahertz spectroscopy

Hemagglutinin (HA) is the main surface glycoprotein of the influenza A virus. The H9N2 subtype influenza A virus is recognized as the most possible pandemic strain as it has crossed the species barrier, infecting swine and humans. We use terahertz spectroscopy to study the hydration shell formation around H9 subtype influenza A virus's HA protein (H9 HA) as well as the detection of antigen binding of H9 HA with the broadly neutralizing monoclonal antibody. We observe a remarkable concentration dependent nonlinear response of the H9 HA, which reveals the formation process of the hydration shell around H9 HA molecules. Furthermore, we show that terahertz dielectric properties of the H9 HA are strongly affected by the presence of the monoclonal antibody F10 and that the terahertz dielectric loss tangent can be used to detect the antibody binding at lower concentrations than the standard ELISA test.

Terahertz time-domain and low-frequency Raman spectroscopy of organic materials

With the ongoing proliferation of terahertz time-domain instrumentation from semiconductor physics into applied spectroscopy over the past decade, measurements at terahertz frequencies (1 THz ≡ 10(12) Hz ≡ 33 cm(-1)) have attracted a sustained growing interest, in particular the investigation of hydrogen-bonding interactions in organic materials. More recently, the availability of Raman spectrometers that are readily able to measure in the equivalent spectral region very close to the elastic scattering background has also grown significantly. This development has led to renewed efforts in performing spectroscopy at the interface between dielectric relaxation phenomena and vibrational spectroscopy. In this review, we briefly outline the underlying technology, the physical phenomena governing the light-matter interaction at terahertz frequencies, recent examples of spectroscopic studies, and the current state of the art in assigning spectral features to vibrational modes based on computational techniques.

Interfacial water at the trialanine hydrophilic surface: a DFT electronic structure and bottom-up investigation

A model describing a network of hydrogen bonded water-trialanine has been developed to estimate hydration effects on various conformers of the peptide.

Structure and dynamics of aqueous 2-propanol: a THz-TDS, NMR and neutron diffraction study

90 mol_H2O% is identified as a critical composition at which alcohol–water interactions are maximised; with 4–5 H₂O molecules present in the hydration shell per 2-propanol.

Ion-specific solvation water dynamics: single water versus collective water effects

Recent femtosecond-resolved spectroscopy experiments demonstrate the single-water orientational dynamics in the first solvation shell around monatomic ions to be slowed down. In contrast, dielectric spectroscopy experiments exhibit a blue shift of the water dielectric relaxation time with rising salt concentration, indicative of faster water dynamics. Using molecular dynamics simulations employing nonpolarizable and thermodynamically optimized ion force fields, we reproduce both experimental trends and resolve these conflicting experimental findings by the simultaneous analysis of single-water and collective-water dynamics in the ion solvation shells. While the single-molecule reorientational dynamics of first solvation shell water around ions indeed slows down, the collective dynamics, which furnishes the dominant contribution to the dielectric response, accelerates. This collective acceleration is rationalized by a dramatically decreasing water cooperativity around ions when compared to bulk water, quantified by the Kirkwood dielectric enhancement factor. The static dielectric decrement of salt solutions is thus reinterpreted as a dielectric structure breaking rather than a water alignment effect. Both the dielectric blue shift and the dielectric decrement become stronger with increasing anion size, meaning larger halide ions such as iodide are more efficient dielectric structure breakers than small halide ions such as fluoride.

One role of hydration water in proteins: key to the "softening" of short time intraprotein collective vibrations of a specific length scale

High resolution inelastic X-ray scattering (IXS) experiments show that the "phonon energy softening" and "phonon population enhancement" observed in a hydrated native protein when increasing the temperature from 200 K to physiological temperature are not directly related to the protein structure. Such phenomena were also observed in a denatured sample without a defined tertiary structure and with a limited residual secondary structure. However, in a dry sample, such "softening" is strongly suppressed. These facts suggest that the above-mentioned protein "softening" phenomenon is water-induced. In addition, increasing the hydration level can also induce "phonon energy softening" at room temperature, but not at 200 K. This change may be due to a qualitative difference in the dynamics of hydration water at 200 K and at room temperature.

Liquid-sheet jets for terahertz spectroscopy

We investigated liquid-sheet jets with controllable thickness for application to terahertz (THz) spectroscopy. Slit-type and colliding-jet nozzles were used to generate optically flat liquid jets. The thickness of the liquid sheet was determined precisely by spectral interference and THz time-domain-spectroscopy methods. By adjusting the collision angle of the colliding-jet nozzle, we could control the thickness of the liquid sheet from 50 to 120 μm.

Nanometer-resolved radio-frequency absorption and heating in biomembrane hydration layers

Radio-frequency (RF) electromagnetic fields are readily absorbed in biological matter and lead to dielectric heating. To understand how RF radiation interacts with macromolecular structures and possibly influences biological function, a quantitative description of dielectric absorption and heating at nanometer resolution beyond the usual effective medium approach is crucial. We report an exemplary multiscale theoretical study for biomembranes that combines (i) atomistic simulations for the spatially resolved absorption spectrum at a single planar DPPC lipid bilayer immersed in water, (ii) calculation of the electric field distribution in planar and spherical cell models, and (iii) prediction of the nanometer resolved temperature profiles under steady RF radiation. Our atomistic simulations show that the only 2 nm thick lipid hydration layer strongly absorbs in a wide RF range between 10 MHz and 100 GHz. The absorption strength, however, strongly depends on the direction of the incident wave. This requires modeling of the electric field distribution using tensorial dielectric spectral functions. For a spherical cell model, we find a strongly enhanced RF absorption on an equatorial ring, which gives rise to temperature gradients inside a single cell under radiation. Although absolute temperature elevation is small under conditions of typical telecommunication usage, our study points to hitherto neglected temperature gradient effects and allows thermal RF effects to be predicted on an atomistically resolved level. In addition to a refined physiological risk assessment of RF fields, technological applications for controlling temperature profiles in nanodevices are possible.

Density functional theory investigation of cocaine water complexes

Twenty cocaine-water complexes were studied using density functional theory (DFT) B3LYP/6-311++G** level to understand their geometries, energies, vibrational frequencies, charge transfer and topological parameters. Among the 20 complexes, 12 are neutral and eight are protonated in the cocaine-water complexes. Based on the interaction energy, the protonated complexes are more stable than the neutral complexes. In both complexes, the most stable structure involves the hydrogen bond with water at nitrogen atom in the tropane ring and C=O groups in methyl ester. Carbonyl groups in benzoyl and methyl ester is the most reactive site in both forms and it is responsible for the stability order. The calculated topological results show that the interactions involved in the hydrogen bond are electrostatic dominant. Natural bond orbital (NBO) analysis confirms the presence of hydrogen bond and it supports the stability order. Atoms in molecules (AIM) and NBO analysis confirms the C-H···O hydrogen bonds formed between the cocaine-water complexes are blue shifted in nature.