Water OH Groups Research Articles

Sulfonylation of RNA 2'-OH groups.

The nucleophilic reactivity of RNA 2'-OH groups in water has proven broadly useful in probing, labeling, and conjugating RNA. To date, reactions selective to ribose 2'-OH have been limited to bond formation with short-lived carbonyl electrophiles. Here we report that many activated small-molecule sulfonyl species can exhibit extended lifetimes in water and retain 2'-OH reactivity. The data establish favorable aqueous solubility for selected reagents and successful RNA-selective reactions at stoichiometric and superstoichiometric yields, particularly for aryl sulfonyltriazole species. We report that the latter are considerably more stable than most prior carbon electrophiles in aqueous environments and tolerate silica chromatography. Furthermore, an azide-substituted sulfonyltriazole reagent is developed to introduce labels into RNA via click chemistry. In addition to high-yield reactions, we find that RNA sulfonylation can also be performed under conditions that give trace yields necessary for structure mapping. Like acylation, the reaction occurs with selectivity for unpaired nucleotides over those in the duplex structure, and a sulfonate adduct causes reverse transcriptase stops, suggesting potential use in RNA structure analysis. Probing of rRNA is demonstrated in human cells, indicating possible cell permeability. The sulfonyl reagent class enables a new level of control, selectivity, versatility, and ease of preparation for RNA applications.

On the Trail of Molecular Hydrophilicity and Hydrophobicity at Aqueous Interfaces

Uncovering microscopic hydrophilicity and hydrophobicity at heterogeneous aqueous interfaces is essential as it dictates physico/chemical properties such as wetting, the electrical double layer, and reactivity. Several molecular and spectroscopic descriptors were proposed, but a major limitation is the lack of connections between them. Here, we combine density functional theory-based MD simulations (DFT-MD) and SFG spectroscopy to explore how interfacial water responds in contact with self-assembled monolayers (SAM) of tunable hydrophilicity. We introduce a microscopic metric to track the transition from hydrophobic to hydrophilic interfaces. This metric combines the H/V descriptor, a structural descriptor based on the preferential orientation within the water network in the topmost binding interfacial layer (BIL) and spectroscopic fingerprints of H-bonded and dangling OH groups of water carried by BIL-resolved SFG spectra. This metric builds a bridge between molecular descriptors of hydrophilicity/hydrophobicity and spectroscopically measured quantities and provides a recipe to quantitatively or qualitatively interpret experimental SFG signals.

Space-Resolved OH Vibrational Spectra of the Hydration Shell around CO2.

The CO2 molecule is weakly bound in water. Here we analyze the influence of a dissolved CO2 molecule on the structure and OH vibrational spectra of the surrounding water. From the analysis of ab initio molecular dynamics simulations (BLYP-D3) we present static (structure, coordination, H-bonding, tetrahedrality) and dynamical (OH vibrational spectra) properties of the water molecules as a function of distance from the solute. We find a weakly oscillatory variation (“ABBA”) in the ‘solution minus bulk water’ spectrum. The origin of these features can largely be traced back to solvent–solute hard-core interactions which lead to variations in density and tetrahedrality when moving from the solute’s vicinity out to the bulk region. The high-frequency peak in the solute-affected spectra is specifically analyzed and found to originate from both water OH groups that fulfill the geometric H-bond criteria, and from those that do not (dangling ones). Effectively, neither is hydrogen-bonded.

IR Spectroscopy of the Cesium Iodide-Water Complex.

There has been much interest in I-(H2O) as a simple model for a hydrated iodide ion. Here we explore how this fundamental ion-solvent interaction is modified by the presence of a counterion, specifically Cs+. This has been achieved by forming the CsI(H2O) complex in superfluid helium nanodroplets and then probing this system using infrared spectroscopy. The complex retains the ionic hydrogen bond between the I- and a water OH group seen in I-(H2O), but the Cs+ ion substantially alters the anion-water interaction through formation of a cyclic Cs+-O-H-I- bonding motif. As with I-(H2O), the OH stretching band derived from the hydrogen-bonded OH group shows substructure, splitting into a clear doublet. However, in contrast to I-(H2O), where a tunneling splitting arising from hydrogen atom exchange plays a role, the doublet we observe is attributed solely to an anharmonic vibrational coupling effect.

Spectroscopic and Theoretical Studies of Some Bivalent Metal Complexes of a Quinoline Schiff Base Derivative

Interaction of M(II) ions, M=Co, Ni, Cu, Zn, and Pd, with a Schiff base ligand (HL), derived from the condensation of 2-hydroxy-5-nitrobenzaldehyde and 8-aminoquinoline, gave the complexes [Co(L)2(H2O)2], [Ni(L)2(H2O)2], [Cu(L)(H2O)]CH3COO, [Zn(L)(H2O)]CH3COO, and [Pd(HL)Cl2]. The ligand and its complexes were characterized by means of elemental and thermal analyses, molar conductance, and magnetic moment measurements along with the different spectroscopic techniques. Theoretical calculations based on DFT were carried out to verify the optimized structures of ligand and complexes. The relative reactivity of the compounds was estimated from chemical descriptors analysis using the HOMO and LUMO frontier orbitals. Molecular docking of ligand and its zinc complex revealed that the interaction of Zn(L) with DNA is comparable to that of HL due to the presence of water OH groups instead of the hydroxyl group of ligand.

Gold(I)-catalyzed intermolecular dioxolane addition to alkynes: the role of water

Density functional theory (DFT) calculations have been performed on a homogeneous gold-catalyzed reaction between acetylene/propyne and the cyclic ketal 2,2-dimethyl-1,3-dioxolane, DMDO, in the presence of water, with the aim of understanding the actual role played by water. After the addition of DMDO to the alkyne, hydrolysis may happen through two possible reaction routes. In the so-called H-route (previously proposed for similar intramolecular reactions), a water proton is initially added to the alkyne C atom still linked to gold and, afterwards, an OH group adds to a DMDO C atom to allow the release of acetone, whereas in the newly proposed OH-route, a water OH group firstly adds to the most substituted DMDO C atom with simultaneous addition of H to the alkyne C atom linked to gold. A 1,3-H transposition from the just added OH group allows the release of acetone. An intramolecular nucleophilic OH addition to the gold-activated alkene intermediate formed from both hydrolysis paths drives the system to the corresponding 1,3-dioxolane product. The H-route is unable to explain the formation of the dioxolane addition products (observed in similar intramolecular reactions) instead of those coming from the direct addition of water to the alkyne, since it is energetically more demanding than the direct hydration. However, OH-route goes through structures that are more stable than those in the water addition, so, it is the one actually happening for the reaction under study. The regioselective addition of DMDO to the internal C atom of propyne is predicted on the basis of the large polarity of the structures formed in this approach, which makes them capable of strong interactions with water.

Molecular hydrophobicity at a macroscopically hydrophilic surface

Interfaces between water and silicates are ubiquitous and relevant for, among others, geochemistry, atmospheric chemistry, and chromatography. The molecular-level details of water organization at silica surfaces are important for a fundamental understanding of this interface. While silica is hydrophilic, weakly hydrogen-bonded OH groups have been identified at the surface of silica, characterized by a high O-H stretch vibrational frequency. Here, through a combination of experimental and theoretical surface-selective vibrational spectroscopy, we demonstrate that these OH groups originate from very weakly hydrogen-bonded water molecules at the nominally hydrophilic silica interface. The properties of these OH groups are very similar to those typically observed at hydrophobic surfaces. Molecular dynamics simulations illustrate that these weakly hydrogen-bonded water OH groups are pointing with their hydrogen atom toward local hydrophobic sites consisting of oxygen bridges of the silica. An increased density of these molecular hydrophobic sites, evident from an increase in weakly hydrogen-bonded water OH groups, correlates with an increased macroscopic contact angle.

Water-Soluble Leaving Group Enables Hydrophobic Functionalization of RNA.

Attachment of hydrophobic groups to RNA is challenging because of their poor aqueous solubility. One-step acylation of RNA 2'-OH groups in water using a water-soluble imidazole leaving group is described. The effect of the hydrophobic groups on hybridization is reported. Furthermore, propargyl-functionalized RNA is shown to be readily labeled with a fluorophore. Lastly, heptyl-functionalized RNA is found to exhibit the unusual property of solubility in organic solvents.

Reorientation of OH-group connecting bifurcated H-bond acceptors in liquid water

The OH-group connecting bifurcated H-bond (HB) acceptors is one case of the three-centered HBs found in physical and biological systems. An example is the transition state of molecular reorientation jump mechanism in liquid water, ionic solutions, and hydration shells of biomolecules. In this Letter, the orientational time correlation functions of these special OH-groups in water were studied by performing molecular dynamics simulations and using the normal-mode approach developed recently. The reorientation angle of the OH-group before entering the diffusive regime can be estimated through the plateau in the mean-square rotational displacement calculated by several methods.

Environment of the Al3+ ion in Water–Acetone Solutions of Aluminum Chloride

Water–acetone solutions in the AlCl3–(CH3)2CO–H2O and AlCl3–(CH3)2CO–H2O–HCl systems were obtained and studied. In both cases, the solution separated into layers to form liquid fractions of lower and higher density. The IR spectra of the fractions were studied. In the light fraction, no AlCl3 was present, but hydrogen-bonded acetone–water complexes were detected. The spectra of the heavy fraction exhibited a broad band at ~3020–3040 cm–1 corresponding to the OH groups of water from aluminum hexahydrate. As the solvent is evaporated, the band narrows down, with its position being retained. The IR spectrum of the obtained solid becomes identical to the IR spectrum of the crystal hydrate AlCl3.(H2O)6. The structures and spectral and energetic parameters of Al(H2O) 6 3+ , Al(H2O) 6+12 3+ , Al((CH3)2CO) 6 3+ , Al((CH3)2CO) 4 3+ , and (CH3)2CO.H2O were calculated by the density functional theory method (B3LYP/6-31++G(d,p)). Relying on the results, an explanation was proposed for the experimentlly observed absence of acetone molecules in the Al3+ first coordination shell.

Luminescent amorphous silicon carbide ultrafine nanoparticles fabricated by pulsed-laser ablation

Bulk quantities of amorphous silicon carbide(SiC) ultrafine nanoparticles have been prepared via pulsed-laser ablation on a polished 3C–SiC polycrystalline target immersed in de-ionized water. The diameter of the nanoparticles is ~10 ± 2.0 nm. The surface of the nanoparticles binds to the –H and –OH groups in water, suggesting that the ultrafine nanoparticles are hydrophilic. A direct band gap energy of 5.3 eV and an indirect band gap energy of 2.4 eV were determined via the ultraviolet–visible absorption characterization, which implies that the nanoparticles are of SiC. As excited at 320 nm, the suspension exhibited strong and stable violet emissions centered at 430 nm.

Photodegradation of organic pollutants RhB dye using UV simulated sunlight on ceria based TiO2 nanomaterials for antibacterial applications.

To photo-catalytically degrade RhB dye using solar irradiation, CeO2 doped TiO2 nanocomposites were synthesized hydrothermally at 700 °C for 9 hrs. All emission spectra showed a prominent band centered at 442 nm that was attributed to oxygen related defects in the CeO2-TiO2 nanocrystals. Two sharp absorption bands at 1418 cm−1 and 3323 cm−1 were attributed to the deformation and stretching vibration, and bending vibration of the OH group of water physisorbed to TiO2, respectively. The photocatalytic activities of Ce-TiO2 nanocrystals were investigated through the degradation of RhB under UV and UV+ visible light over a period of 8 hrs. After 8 hrs, the most intense absorption peak at 579 nm disappeared under the highest photocatalytic activity and 99.89% of RhB degraded under solar irradiation. Visible light-activated TiO2 could be prepared from metal-ion incorporation, reduction of TiO2, non-metal doping or sensitizing of TiO2 using dyes. Studying the antibacterial activity of Ce-TiO2 nanocrystals against E. coli revealed significant activity when 10 μg was used, suggesting that it can be used as an antibacterial agent. Its effectiveness is likely related to its strong oxidation activity and superhydrophilicity. This study also discusses the mechanism of heterogeneous photocatalysis in the presence of TiO2.

An extensive study on Raman spectra of water from 253 to 753 K at 30 MPa: A new insight into structure of water

Raman spectra of water were systematically investigated from 253 to 753K at 30MPa. The measurement reveals that increase of temperature causes significant deformation of Raman contours as well as blue shifts of central frequency by over 200cm−1, indicating breakup of hydrogen bonding network. The widespread hydrogen bonding tetrahedrons are considered to disappear beyond 673K where water enters supercritical state with small polymers like trimers and dimers remained. The referential Gaussian deconvolution of Raman contours into five components below 533K and four components beyond 533K respectively should represent that OH groups in water are engaged in stretching vibration with different energetic states which show strong temperature dependence.

Effect of alkali halide salt additives on the structure of poly(vinyl alcohol) films cast from aqueous solutions

The molecular structures of poly(vinyl alcohol) films cast from polymer aqueous solutions (1 mol/L) containing 0.1 mol/L of LiCl, NaF, NaCl, KCl, CsCl, KBr, and KI salts are studied via FTIR spectroscopy. The addition of any of these salts except LiCl leads to an increase in the degree of crystallinity of poly(vinyl alcohol) in a film by a factor of 1.3–1.6. In contrast, LiCl significantly decreases the crystallinity of the polymer. It is found that, in the IR spectra of the films containing salt additives, the position of the maximum in the band of the stretching vibrations of OH groups of the polymer is shifted relative to its position in the IR spectra of the films free of salt additives. The magnitude and direction of this band shift depend on the types (anion or cation) and radii of ions comprising salts. The observed effects are interpreted in terms of existing ideas on the interactions of salt ions with the OH groups of water and other hydroxyl-containing molecules.

Interactions of Polyelectrolytes with Water and Ions at Air/Water Interfaces Studied by Phase-Sensitive Sum Frequency Generation Vibrational Spectroscopy

Interactions of the polyelectrolyte partially hydrolyzed polyacrylamide (HPAM) with water and cations at air/liquid interfaces were studied using phase-sensitive sum frequency generation (SFG) vibrational spectroscopy. In contrast to the conventional SFG vibrational spectroscopy which measures only the amplitude of the second-order susceptibility |χ(2)|, the heterodyne-detected SFG measures the complex χ(2) which contains information about the absolute orientation of surface molecules. While the OH groups of water near a neat air/water interface mostly pointed down to the bulk (downward), the presence of the polyelectrolyte caused flipping of water molecules with the hydrogen being oriented upward. With 10–7 M HPAM, water showed a highly ordered structure with a single peak near 3100 cm–1, but higher concentrations resulted in a less ordered water structure with multiple peaks. The addition of the monovalent cation Na+ to the polyelectrolyte solution did not affect the conformation of the polyelectrolyte, though the water molecules flipped back to a structure similar to that of a neat air/water interface with the hydrogen pointing down. On the other hand, the addition of divalent cation Ca2+ not only changed the conformation of the polyelectrolyte but also completely destroyed the ordered structure of interfacial water molecules. The observed phenomena support the polymer–ion complex model in which a divalent cation can interact with two intrachain or interchain charges and form a jointing point. The amorphous nature of the polymer–ion complex explained the disappearance of the ordered water structure in the presence of divalent cations.

From hydrogen bond donor to acceptor: the effect of ethanol fluorination on the first solvating water molecule

Supersonic jet FTIR spectra of the OH stretching vibrations in complexes of mono-, di- and trifluoroethanol with water are presented. In contrast to the non-fluorinated ethanol case, the fluorinated alcohols are all shown to act as O-H···O hydrogen bond donors towards water. This is found to be mostly a consequence of the intramolecular electron-withdrawing effect of the fluorine atoms and, with decreasing importance for increasing fluorination, due to the attractive intermolecular contact between one of the dangling water OH groups and the fluorine atoms. The findings provide a stepwise rationalization for the hydrophobic properties of the pharmaceutically important trifluoromethyl group.

Decomposition of water Raman stretching band with a combination of optimization methods

In this study, an investigation of the behaviour of stretching bands of CH and OH groups of water–ethanol solutions at alcohol concentrations ranging from 0 to 96% by volume has been performed. A new approach to decomposition of the wide structureless water Raman band into spectral components based on modern mathematical methods of solution of inverse multi-parameter problems–combination of Genetic Algorithm and the method of Generalized Reduced Gradient–has been demonstrated. Application of this approach to decomposition of Raman stretching bands of water–ethanol solutions allowed obtaining new interesting results practically without a priori information. The behaviour of resolved spectral components of Raman stretching OH band in binary mixture with rising ethanol concentration is in a good agreement with the concept of clathrate-like structure of water–ethanol solutions. The results presented in this paper confirm existence of essential structural rearrangement in water–ethanol solutions at ethanol concentrations 20–30% by volume.

Two-dimensional near-infrared correlation spectroscopy study the methanol in acidic pH region

The effect of pH on the structure of methanol was investigated by FT-NIR (Fourier transform near-infrared) spectroscopy and generalized two-dimensional (2D) correlation spectroscopy. pH perturbed 2D correlation spectra are calculated for the spectra in the 5500–4000, 7500–5500 cm −1 regions at different pH values. We observed that the stretching of CH 3 was shifted because of the direct interaction of the CH 3 group of methanol with the OH group of water, the change of free OH is more sensitive to pH than the cyclic dimmer and CH·O.

A study of co-precipitated bimetallic gold catalysts for water–gas shift reaction

Synthesis, testing and characterisation of bimetallic gold, Au-M on ceria as catalysts were carried out for low temperature water-gas shift reaction (WGS). Amongst the entire screened catalysts 3 wt% (AU-Pt)/CeO2 displayed the best WGS activity than the monometallic promotors, giving the light-off curve at the lowest temperature in the range 100-300 degrees C. (Au-Pd)/CeO2 also achieved the same activity but at a higher temperature. It was also found that WGS activity was strongly correlated with the surface reducibility which in turn depended on the modified local electronic band structure of promoted ceria. These results clearly suggest that the key role of bimetallic promoter may involve in facilitating the creation of defective reduced surface by exerting its local electronic effect on ceria to form the surface germinal -OH groups in water which act as active sites for enhanced WGS activity. (C) 2008 Elsevier B.V. All rights reserved.

Femtosecond spectroscopic study of the solvation of amphiphilic molecules by water

We use polarization-resolved mid-infrared pump-probe spectroscopy to study the aqueous solvation of proline and N-methylacetamide. These molecules serve as models to study the solvation of proteins. We monitor the orientational dynamics of partly deuterated water molecules (HDO) that are present at a low concentration in the water. We find that the OD vibration of HDO relaxes via an intermediate level, that is characterized by a hydrogen-bond that is stronger than in the ground state. With increasing concentration the lifetime of the excited state increases from 1.8 ps to 2.4 ps and the lifetime of the intermediate level from 0.6 ps to 1.0 ps. Regarding the orientational dynamics we observe biexponential behavior, which finds its origin in the presence of two classes of water molecules. There is a fraction of water molecules that has bulk-like orientational dynamics ( τ rot = 2.5 ps) and a fraction of immobilized water molecules ( τ rot > 10 ps). The relative abundance of the two fractions is determined by the nature and concentration of the solute. We find that the hydrophobic solute groups are responsible for the immobilization of water molecules. Every methyl group causes the immobilization of approximately 4 water OH groups. The hydrophilic solute groups, on the other hand, do not hinder the reorientation and the water molecules solvating them reorient with the same rate as in the bulk liquid.