A reinvestigation of the Raman spectrum of water

Molecular dynamics study of collective water vibrations in a DNA hydration shell

The structure of DNA double helix is stabilized by water molecules and metal counterions that form the ion-hydration shell around the macromolecule. Understanding the role of the ion-hydration shell in the physical mechanisms of the biological functioning of DNA requires detailed studies of its structure and dynamics at the atomistic level. In the present work, the study of collective vibrations of water molecules around the DNA double helix was performed within the framework of classical all-atom molecular dynamics methods. Calculating the vibrational density of states, the vibrations of water molecules in the low-frequency spectra ranged from [Formula: see text]30 to [Formula: see text]300 [Formula: see text] were analyzed for the case of different regions of the DNA double helix (minor groove, major groove, and phosphate groups). The analysis revealed significant differences in the collective vibrations behavior of water molecules in the DNA hydration shell, compared to the vibrations of bulk water. All low-frequency modes of the DNA ion-hydration shell are shifted by about 15-20 [Formula: see text] towards higher frequencies, which is more significant for water molecules in the minor groove region of the double helix. The interactions of water molecules with the atoms of the macromolecule induce intensity decrease of the mode of hydrogen-bond symmetrical stretching near 150 [Formula: see text], leading to the disappearance of this mode in the DNA spectra. The obtained results can provide an interpretation of the experimental data for DNA low-frequency spectra and may be important for the understanding of the processes of indirect protein-nucleic recognition.

Nitrate Capture Investigation in Plasma-Activated Water and Its Antifungal Effect on Cryptococcus pseudolongus Cells

This research investigated the capture of nitrate by magnesium ions in plasma-activated water (PAW) and its antifungal effect on the cell viability of the newly emerged mushroom pathogen Cryptococcus pseudolongus. Optical emission spectra of the plasma jet exhibited several emission bands attributable to plasma-generated reactive oxygen and nitrogen species. The plasma was injected directly into deionized water (DW) with and without an immersed magnesium block. Plasma treatment of DW produced acidic PAW. However, plasma-activated magnesium water (PA-Mg-W) tended to be neutralized due to the reduction in plasma-generated hydrogen ions by electrons released from the zero-valent magnesium. Optical absorption and Raman spectra confirmed that nitrate ions were the dominant reactive species in the PAW and PA-Mg-W. Nitrate had a concentration-dependent antifungal effect on the tested fungal cells. We observed that the free nitrate content could be controlled to be lower in the PA-Mg-W than in the PAW due to the formation of nitrate salts by the magnesium ions. Although both the PAW and PA-Mg-W had antifungal effects on C. pseudolongus, their effectiveness differed, with cell viability higher in the PA-Mg-W than in the PAW. This study demonstrates that the antifungal effect of PAW could be manipulated using nitrate capture. The wide use of plasma therapy for problematic fungus control is challenging because fungi have rigid cell wall structures in different fungal groups.

A Remote Raman System and Its Applications for Planetary Material Studies

A remote Raman prototype with a function of excitation energy adjusting for the purpose of obtaining a Raman signal with good signal-to-noise ratio (SNR), saving power consumption, and possibly avoiding destroying a target by high energy pulses, which may have applications for Chinese planetary explorations, has been setup and demonstrated for detecting different minerals. The system consists of a spectrograph equipped with a thermoelectrically cooled charge-coupled device (CCD) detector, a telescope with 150 mm diameter and 1500 mm focus length, and a compact 1064 nm Nd:YAG Q-switched laser with an electrical adjusted pulse energy from 0 to 200 mJ/pulse. A KTP crystal was used for second harmonic generation in a 1064 nm laser to generate a 532 nm laser, which is the source of Raman scatting. Different laser pulse energies and integration time were used to obtain distinguishable remote Raman spectra of various samples. Results show that observed remote Raman spectra at a distance of 4 m enable us to identify silicates, carbonates, sulfates, perchlorates, water/water ice, and organics that have been found or may exist on extraterrestrial planets. Detailed Raman spectral assignments of the measured planetary materials and the feasible applications of remote Raman system for planetary explorations are discussed.

Hydrodynamic effects on the energy transfer from dipoles to metal slab

A systematic study of nonlocal and size effects on the energy transfer of a dipole (e.g., a molecule or a quantum dot) induced by the proximity of a metal slab is presented. Nonlocal effects are accounted for using the hydrodynamic model (HDM). We derive a general relation that connects the energy transfer rate to the linear charge density-density response function of the slab. This function is explicitly evaluated for the HDM and the local Drude model. We show that a thin metal slab can support a series of higher-frequency surface plasma wave (SPW) modes in addition to the normal SPW modes, thanks to the nonlocal effects. These modes markedly alter the response and the energy transfer process, as revealed in the structure of the energy transfer rate in the parameter space. Our findings are important for applications such as the recently developed metal-induced energy transfer imaging, which relies on accurate modeling of the energy transfer rate.

Targeting acute myeloid leukemia cells by CD33 receptor-specific MoS2-based nanoconjugates

Acute myeloid leukemia (AML) is a highly aggressive type of cancer caused by the uncontrolled proliferation of undifferentiated myeloblasts, affecting the bone marrow and blood. Systemic chemotherapy is considered the primary treatment strategy; unfortunately, healthy cells are also affected to a large extent, leading to severe side effects of this treatment. Targeted drug therapies are becoming increasingly popular in modern medicine, as they bypass normal tissues and cells. Two-dimensional MoS₂-based nanomaterials have attracted attention in the biomedical field as promising agents for cancer diagnosis and therapy. Cancer cells typically (over)express distinctive cytoplasmic membrane-anchored or -spanning protein-based structures (e.g., receptors, enzymes) that distinguish them from healthy, non-cancerous cells. Targeting cancer cells via tumor-specific markers using MoS₂-based nanocarriers loaded with labels or drugs can significantly improve specificity and reduce side effects of such treatment. SKM-1 is an established AML cell line that has been employed in various bio-research applications. However, to date, it has not been used as the subject of studies on selective cancer targeting by inorganic nanomaterials. Here, we demonstrate an efficient targeting of AML cells using MoS₂nanoflakes prepared by a facile exfoliation route and functionalized with anti-CD33 antibody that binds to CD33 receptors expressed by SKM-1 cells. Microscopic analyses by confocal laser scanning microscopy supplemented by label-free confocal Raman microscopy proved that (anti-CD33)-MoS₂conjugates were present on the cell surface and within SKM-1 cells, presumably having been internalized via CD33-mediated endocytosis. Furthermore, the cellular uptake of SKM-1 specific (anti-CD33)-MoS₂conjugates assessed by flow cytometry analysis was significantly higher compared with the cellular uptake of SKM-1 nonspecific (anti-GPC3)-MoS₂conjugates. Our results indicate the importance of appropriate functionalization of MoS₂nanomaterials by tumor-recognizing elements that significantly increase their specificity and hence suggest the utilization of MoS₂-based nanomaterials in the diagnosis and therapy of AML.

Effects of interfaces on structure and dynamics of water droplets on a graphene surface: A molecular dynamics study

The structure and dynamics of water droplets on a bilayer graphene surface are investigated using molecular dynamics simulations. The effects of solid/water and air/water interfaces on the local structure of water droplets are analyzed in terms of the hydrogen bond distribution and tetrahedral order parameter. It is found that the local structure in the core region of a water droplet is similar to that in liquid water. On the other hand, the local structure of water molecules at the solid/water and air/water interfaces, referred to as the interface and surface regions, respectively, consists mainly of three-coordinated molecules that are greatly distorted from a tetrahedral structure. This study reveals that the dynamics in different regions of the water droplets affects the intermolecular vibrational density of states: It is found that in the surface and interface regions, the intensity of vibrational density of states at ∼50 cm^-1 is enhanced, whereas those at ∼200 and ∼500 cm^-1 are weakened and redshifted. These changes are attributed to the increase in the number of molecules having fewer hydrogen bonds in the interface and surface regions. Both single-molecule and collective orientation relaxations are also examined. Single-molecule orientation relaxation is found to be marginally slower than that in liquid water. On the other hand, the collective orientation relaxation of water droplets is found to be significantly faster than that of liquid water because of the destructive correlation of dipole moments in the droplets. The negative correlation between distinct dipole moments also yields a blueshifted libration peak in the absorption spectrum. It is also found that the water-graphene interaction affects the structure and dynamics of the water droplets, such as the local water structure, collective orientation relaxation, and the correlation between dipole moments. This study reveals that the water/solid and water/air interfaces strongly affect the structure and intermolecular dynamics of water droplets and suggests that the intermolecular dynamics, such as energy relaxation dynamics, in other systems with interfaces are different from those in liquid water.

Two-Dimensional Correlation Spectroscopy (2D-COS) Studies of Solution Mixtures in the Low Frequency Raman Region

Raman spectra of a series of binary solution mixtures, including chloroform (CHCl₃), ethanol (EtOH), and 1,1,1,3,3,3-hexafluoro-2-propanol (HFIP), were analyzed using the two-dimensional correlation spectroscopic (2D-COS) technique in the low frequency region. Numerous asynchronous cross-peaks ubiquitously appeared in the concentration-dependent Raman spectra of these organic solvent mixtures. The result clearly demonstrated a deviation from ideal solution behavior, reflecting the presence of specific molecular interactions causing a subtle nonlinear spectral intensity response of Raman bands to the concentration changes. Furthermore, the combination of 2D-COS and low frequency Raman spectroscopy was extended to poly[(R)-3-hydroxybutyrate-co-(R)-3-hydroxyhexanoate] (PHBHx) copolymer solutions in CHCl₃-HFIP co-solvents. The results suggest the existence of hydrogen bonding interaction between the PHBHx and HFIP, which is consistent with the previous infrared spectroscopic study of PHBHx solutions.

Femtosecond infrared pump-stimulated Raman probe spectroscopy: the first application of the method to studies of vibrational relaxation pathways in the liquid HDO/D2O system

We have proposed and constructed a setup for a novel method of ultrafast vibrational spectroscopy: femtosecond infrared pump-stimulated Raman probe spectroscopy. This is the first time-resolved spectroscopy providing simultaneously a sub-100 fs time resolution, a spectral resolution better than 10 cm^-1 and a spectral window covering an extremely broad range of molecular vibrations (at least: 200-4000 cm^-1) with a "single laser shot". The new method was applied to study vibrational relaxation pathways in the liquid HDO/D₂O system. We determined the lifetimes of OH stretching vibrations to be in the range 310-500 fs depending on the isotopic dilution, which is in good agreement with the results from pump-probe femtosecond infrared spectroscopy. Moreover, we observed a strong coupling of OH stretch to OD stretch vibrations and possibly also to the librational modes of water.

Delocalization and stretch-bend mixing of the HOH bend in liquid water

Liquid water's rich sub-picosecond vibrational dynamics arise from the interplay of different high- and low-frequency modes evolving in a strong yet fluctuating hydrogen bond network. Recent studies of the OH stretching excitations of H₂O indicate that they are delocalized over several molecules, raising questions about whether the bending vibrations are similarly delocalized. In this paper, we take advantage of an improved 50 fs time-resolution and broadband infrared (IR) spectroscopy to interrogate the 2D IR lineshape and spectral dynamics of the HOH bending vibration of liquid H₂O. Indications of strong bend-stretch coupling are observed in early time 2D IR spectra through a broad excited state absorption that extends from 1500 cm^-1 to beyond 1900 cm^-1, which corresponds to transitions from the bend to the bend overtone and OH stretching band between 3150 and 3550 cm^-1. Pump-probe measurements reveal a fast 180 fs vibrational relaxation time, which results in a hot-ground state spectrum that is the same as observed for water IR excitation at any other frequency. The fastest dynamical time scale is 80 fs for the polarization anisotropy decay, providing evidence for the delocalized or excitonic character of the bend. Normal mode analysis conducted on water clusters extracted from molecular dynamics simulations corroborate significant stretch-bend mixing and indicate delocalization of δ_HOH on 2-7 water molecules.

Interaction of NaOH solutions with silica surfaces

HYPOTHESIS

Sodium adsorption on silica surfaces depends on the solution counter-ion. Here, we use NaOH solutions to investigate basic environments.

SIMULATIONS

Sodium adsorption on hydroxylated silica surfaces from NaOH solutions were investigated through molecular dynamics with a dissociative force field, allowing for the development of secondary molecular species.

FINDINGS

Across the NaOH concentrations (0.01 M - 1.0 M), ∼50% of the Na⁺ ions were concentrated in the surface region, developing silica surface charges between - 0.01 C/m² (0.01 M NaOH) and - 0.76 C/m² (1.0 M NaOH) due to surface site deprotonation. Five inner-sphere adsorption complexes were identified, including monodentate, bidentate, and tridentate configurations and two additional structures, with Na⁺ ions coordinated by bridging oxygen and hydroxyl groups or water molecules. Coordination of Na⁺ ions by bridging oxygen atoms indicates partial or complete incorporation of Na⁺ ions into the silica surface. Residence time analysis identified that Na⁺ ions coordinated by bridging oxygen atoms stayed adsorbed onto the surface four times longer than the mono/bi/tridentate species, indicating formation of relatively stable and persistent Na⁺ ion adsorption structures. Such inner-sphere complexes form only at NaOH concentrations of > 0.5 M. Na⁺ adsorption and lifetimes have implications for the stability of silica surfaces.

DFT Study of Hydrogen-Bonding Interaction, Solvation Effect, and Electric-Field Effect on Raman Spectra of Hydrated Proton

Strong hydrogen-bonding interaction and Raman spectra of hydrated proton have been investigated using hybrid density functional theory method B3LYP. The solvation model of density (SMD) approach is employed in the present calculation to simulate hydrated protons in aqueous solution. Focusing on the different hydrogen-bonded Eigen-water and Zundel-water interactions, we present a better assignment of Raman signals of hydrated proton on the basis of vibrational analysis in different environments. Our results showed that B3LYP calculations could give a good prediction for characteristic vibrational frequencies of Eigen and Zundel isomers in liquid phase. The O-H stretching vibrational frequencies from Eigen and Zundel units are very sensitive to hydrogen-bonding interaction with solvent water molecules. Moreover, the solvation effect and the external electric-field effect lead to the proton deviating from the central position of Zundel structure and finally resulting in a transition to Eigen one in aqueous solution. Furthermore, by combining theoretical prediction and Raman scattering theory, we calculate absolute Raman intensities of characteristic signals based on the polarizability tensor derivatives of hydrated proton clusters. This is very helpful to infer the microstructure of hydrated protons in aqueous solution by using Raman measurements.

Diffusion and spectroscopy of water and lipids in fully hydrated dimyristoylphosphatidylcholine bilayer membranes

Microscopic structure and dynamics of water and lipids in a fully hydrated dimyristoylphosphatidylcholine phospholipid lipid bilayer membrane in the liquid-crystalline phase have been analyzed with all-atom molecular dynamics simulations based on the recently parameterized CHARMM36 force field. The diffusive dynamics of the membrane lipids and of its hydration water, their reorientational motions as well as their corresponding spectral densities, related to the absorption of radiation, have been considered for the first time using the present force field. In addition, structural properties such as density and pressure profiles, a deuterium-order parameter, surface tension, and the extent of water penetration in the membrane have been analyzed. Molecular self-diffusion, reorientational motions, and spectral densities of atomic species reveal a variety of time scales playing a role in membrane dynamics. The mechanisms of lipid motion strongly depend on the time scale considered, from fast ballistic translation at the scale of picoseconds (effective diffusion coefficients of the order of 10(-5) cm(2)/s) to diffusive flow of a few lipids forming nanodomains at the scale of hundreds of nanoseconds (diffusion coefficients of the order of 10(-8) cm(2)/s). In the intermediate regime of sub-diffusion, collisions with nearest neighbors prevent the lipids to achieve full diffusion. Lipid reorientations along selected directions agree well with reported nuclear magnetic resonance data and indicate two different time scales, one about 1 ns and a second one in the range of 2-8 ns. We associated the two time scales of reorientational motions with angular distributions of selected vectors. Calculated spectral densities corresponding to lipid and water reveal an overall good qualitative agreement with Fourier transform infrared spectroscopy experiments. Our simulations indicate a blue-shift of the low frequency spectral bands of hydration water as a result of its interaction with lipids. We have thoroughly analyzed the physical meaning of all spectral features from lipid atomic sites and correlated them with experimental data. Our findings include a "wagging of the tails" frequency around 30 cm(-1), which essentially corresponds to motions of the tail-group along the instantaneous plane formed by the two lipid tails, i.e., in-plane oscillations are clearly of bigger importance than those along the normal-to-the plane direction.

Accurate measurements of the Raman scattering coefficient and the depolarization ratio in liquid water

Despite a long history, the Raman scattering coefficient of water has so far only been measured with 10% uncertainty using a 95% confidence interval. In this paper, we present an experiment where we have achieved 1.5% uncertainty by using a low concentration of Rhodamine 6G in ethanol as a reference along with accurate consideration of polarization-related effects and the geometry of the experimental setup. We have found that the photon-to-photon Raman scattering coefficient of the OH stretching band of liquid water is (1.84±0.03)×10(-4) m(-1) when integrated over the spectral frequency range from 620 to 700 nm while the exciting laser operates at 532 nm. We have also accurately measured the depolarization ratio across this band.

MOLECULAR DYNAMICS SIMULATION ON THE STRUCTURE AND DYNAMICS OF WATER IN THE 1-BUTYL-3-METHYLIMIDAZOLIUM TETRAFLUOROBORATE/WATER MIXTURE

The micro-structure, and IR spectrum of water molecules in 1-butyl-3-methylimi- dazolium tetrafluoroborate( [Bmim]BF4 )/water mixture with different concentrations (x1 = 25.0%, 50.0%, 75.0%, and 90.0%) were studied with molecular dynamics simulation at room temperature. It was shown that water molecules tend to be isolated from each other in mixtures with more ions than water molecules in pure water. With the increase of the molar fraction of water in the mixture, the rotation bands and the bending bands of water display red shift from 566.2 to 651.4 cm-1 and from 1638.4 to 1683.2 cm-1 respectively, whereas the O–H stretch bands show blue shift from 3519.8 to 3452 cm-1, which agree well with the experimental results. This suggests that the molecules are hindered and their motions are difficult and slow, due to the hydrogen-bond interactions and the inharmonic interactions between the inter- or intra-molecular modes of water molecules.

Theoretical study of binding interactions and vibrational Raman spectra of water in hydrogen-bonded anionic complexes: (H2O)n- (n = 2 and 3), H2O...X- (X = F, Cl, Br, and I), and H2O...M- (M = Cu, Ag, and Au)

Binding interactions and Raman spectra of water in hydrogen-bonded anionic complexes have been studied by using the hybrid density functional theory method (B3LYP) and ab initio (MP2) method. In order to explore the influence of hydrogen bond interactions and the anionic effect on the Raman intensities of water, model complexes, such as the negatively charged water clusters ((H2O)n-, n = 2 and 3), the water...halide anions (H2O...X-, X = F, Cl, Br, and I), and the water-metal atom anionic complexes (H2O...M-, M = Cu, Ag, and Au), have been employed in the present calculations. These model complexes contained different types of hydrogen bonds, such as O-H...X-, O-H...M-, O-H...O, and O-H...e-. In particular, the last one is a dipole-bound electron involved in the anionic water clusters. Our results showed that there exists a large enhancement in the off-resonance Raman intensities of both the H-O-H bending mode and the hydrogen-bonded O-H stretching mode, and the enhancement factor is more significant for the former than for the latter. The reasons for these spectral properties can be attributed to the strong polarization effect of the proton acceptors (X-, M-, O, and e-) in these hydrogen-bonded complexes. We proposed that the strong Raman signal of the H-O-H bending mode may be used as a fingerprint to address the local microstructures of water molecules in the chemical and biological systems.

Theory of Time-Resolved Sum-Frequency Generation and Its Applications to Vibrational Dynamics of Water

A molecular theory of time-resolved sum-frequency generation (SFG) has been developed. The theoretical framework is constructed using the coupled-oscillator model in the adiabatic approximation. This theory can treat not only the vibrational spectroscopy but also vibrational dynamics. An application of this theory is also provided for estimation of the time constants of the intermolecular vibrational energy transfer between water molecules. This approach can be used for molecular analysis of the experimental results of Shen at al. on the SFG studies of vibrational dynamics of water.

Detection of bacteria by surface-enhanced Raman spectroscopy

The detection and identification of dilute bacterial samples by surface-enhanced Raman spectroscopy has been explored by mixing aqueous suspensions of bacteria with a suspension of nanocolloidal silver particles. An estimate of the detection limit of E. coli was obtained by varying the concentration of bacteria. By correcting the Raman spectra for the broad librational OH band of water, reproducible spectra were obtained for E. coli concentrations as low as approximately 10(3) cfu/mL. To aid in the assignment of Raman bands, spectra for E. coli in D(2)O are also reported.

Surface-enhanced Raman spectroscopy of bacteria and pollen

A technique for distinguishing biological material based on surface-enhanced Raman scattering (SERS) is reported in this work. Of particular interest is biological material that can be airborne. Silver colloidal particles with diameters in the range 10 to 20 nm and with a characteristic ultraviolet-visible (UV-VIS) absorption band at 400 nm were used to obtain SERS spectra of Escherichia coli, Pseudomonas aeruginosa, and Salmonella typhimurium bacteria and a number of tree and grass pollens (Cupressus arizonica (cypress), Sequoia sempervirens (redwood), Populus deltoides (cottonwood), Poa pratensis (Kentucky bluegrass), and Anthoxanthum odoratum (sweet vernal grass)). While differences in the SERS spectra among the bacteria were small, we found that the pollen spectra we analyzed could readily be distinguished from the bacteria spectra, and there were significant differences between pollen from different families. In order to obtain reproducible results, we studied the parameters controlling the interaction between the analyte and the nanoscale metallic surface. Our results show that the volume ratio of analyte to colloidal particles must be within a narrow range of values to optimize the signal-to-noise ratio of the SERS spectra and minimize the fluorescence from the analyte. Also, we found that the time-dependent behavior of colloidal/bacterial suspensions (or adsorption rate of the silver colloid particles on the bacteria) is strongly dependent on pH, density of bacteria in solution, and even, to some extent, the type of bacteria.

Ultraviolet laser-induced fluorescence of colonic tissue: basic biology and diagnostic potential

Laser-induced fluorescence (LIF) of colonic tissue was examined both in vitro and in vivo to assess the ability of the technique to distinguish neoplastic from hyperplastic and normal tissue and to relate the LIF spectra to specific constituents of the colon. Spectra from 86 normal colonic sites, 35 hyperplastic polyps, 49 adenomatous polyps, and 7 adenocarcinomas were recorded both in vivo and in vitro. With 337-nm excitation, the fluorescence spectra all had peaks at 390 and 460 nm, believed to arise from collagen and NADH, and a minimum at 425 nm, consistent with absorption attributable to hemoglobin. The spectra of colonic tissue recorded both in vivo and in vitro are different, primarily in the NADH fluorescence component, which decays exponentially with time after resection. When normal colonic tissue is compared to hyperplastic or adenomatous polyps, the predominant changes in the fluorescence spectra are a decrease in collagen fluorescence and a slight increase in hemoglobin reabsorption. A multivariate linear regression (MVLR) analysis was used to distinguish neoplastic tissue from non-neoplastic tissue with a sensitivity, specificity, predictive value positive, and predictive value negative toward neoplastic tissue of 80%, 92%, 82%, and 91%, respectively. When the MVLR technique was used to distinguish neoplastic polyps from non-neoplastic polyps, values of 86%, 77%, 86%, and 77% respectively, were obtained. The data suggest that the LIF measurements sense changes in polyp morphology, rather than changes in fluorophores specific to polyps, and it is this change in morphology that leads indirectly to discrimination of polyps.

High-sensitivity fluorescence detector fluorescein isothiocyanate derivatives of amino acids separated by capillary zone electrophoresis

A fluorescence detector has been developed for capillary zone electrophoresis that produces a ten-fold improvement in precision compared with the previous state-of-the-art in fluorescence detection. This instrument, which is based on a sheath-flow cuvette flow chamber and a 0.05-W argon ion laser beam, combines a high numerical aperture collection optic, N.A = 0.65, with a high quantum yield photomultiplier tube, phi approximately = 0.15 at the wavelength of maximum emission. Detection limits (3 sigma) range from the injection of 1.7 . 10(-21) mol (1.3 . 10(-12) M) of fluorescein isothiocyanate (FITC)-labeled arginine, the best case, to 6 . 10(-21) mol (5.6 . 10(-12) M) of FITC-cysteine, the worse case. Signal linearity extends for at least five orders of magnitude from the detection limit to greater than 10(-16) mol (10(-7) M) injected.