Neighboring Hydroxyl Research Articles

Control of hydroxyl group conformation by the pentafluorosulfanyl group

The unique properties of the pentafluorosulfanyl group lead to previously unrecognized interactions with neighboring hydroxyl groups that differ substantially from those of alkyl or fluoroalkyl chains. Computational methods (B3LYP/6-31++G(d,p)) were utilized to assess the geometries and barriers to rotation. Conformational control was derived primarily from restricted rotation about the SF5CCOH bond.

Phase transitions and proton ordering in hemimorphite: new insights from single-crystal EPR experiments and DFT calculations

Single-crystal electron paramagnetic resonance spectra of gamma-ray-irradiated hemimorphite (Mapimi, Durango, Mexico) after storage at room temperature for 3 months, measured from 4 to 275 K, reveal a hydroperoxy radical HO2 derived from the water molecule in the channel. The EPR spectra of the HO2 radical confirm that hemimorphite undergoes two reversible phase transitions at ~98 and ~21 K and allow determinations of its spin Hamiltonian parameters, including superhyperfine coupling constants of two more-distant protons from the neighboring hydroxyl groups, at 110, 85, 40 and 7 K. These EPR results show that the HO2 radical changes in site symmetry from monoclinic to triclinic related to the ordering and rotation of its precursor water molecule in the channel at <98 K. The monoclinic structure of hemimorphite with completely ordered O–H systems at low temperature has been evaluated by both the EPR spectra of the HO2 radical at <21 K and periodic density functional theory calculations.

Structural insights into the specific anti-HIV property of actinohivin: structure of its complex with the α(1-2)mannobiose moiety of gp120.

Actinohivin (AH) is an actinomycete lectin with a potent specific anti-HIV activity. In order to clarify the structural evidence for its specific binding to the α(1-2)mannobiose (MB) moiety of the D1 chains of high-mannose-type glycans (HMTGs) attached to HIV-1 gp120, the crystal structure of AH in complex with MB has been determined. The AH molecule is composed of three identical structural modules, each of which has a pocket in which an MB molecule is bound adopting a bracket-shaped conformation. This conformation is stabilized through two weak C-H...O hydrogen bonds facilitated by the α(1-2) linkage. The binding features in the three pockets are quite similar to each other, in accordance with the molecular pseudo-threefold symmetry generated from the three tandem repeats in the amino-acid sequence. The shape of the pocket can accept two neighbouring hydroxyl groups of the O(3) and O(4) atoms of the equatorial configuration of the second mannose residue. To recognize these atoms through hydrogen bonds, an Asp residue is located at the bottom of each pocket. Tyr and Leu residues seem to block the movement of the MB molecules. Furthermore, the O(1) atom of the axial configuration of the second mannose residue protrudes from each pocket into an open space surrounded by the conserved hydrophobic residues, suggesting an additional binding site for the third mannose residue of the branched D1 chain of HMTGs. These structural features provide strong evidence indicating that AH is only highly specific for MB and would facilitate the highly specific affinity of AH for any glycoprotein carrying many HMTGs, such as HIV-1 gp120.

Phosphatidylinositol-4,5-bisphosphate ionization and domain formation in the presence of lipids with hydrogen bond donor capabilities

Phosphatidylinositol-4,5-bisphosphate (PI(4,5)P2) is an important lipidic signaling molecule that is involved in a broad range of cellular processes. Its interaction with proteins and its lateral distribution are governed by the ionization state of the phosphomonoester groups and its ability to form intra- and intermolecular hydrogen bonds. In this study we have investigated the ionization state of PI(4,5)P2 in ternary lipid vesicle systems that contain in addition to PI(4,5)P2 and phosphatidylcholine (PC) either phosphatidylethanolamine (PE), phosphatidylserine (PS) or phosphatidylinositol (PI). In the presence of PE we find an increased ionization of PI(4,5)P2, which can be attributed to increased deprotonation due to hydrogen bond formation between PE and the PI(4,5)P2 phosphomonoester groups. However, the effect of PE on PI(4,5)P2 ionization is significantly smaller than it had been found previously for phosphatidic acid in the presence of PE (Kooijman et al., 2005). The reduced impact of PE on PI(4,5)P2 ionization can be attributed to competing intramolecular hydrogen bond formation between the phosphomonoester groups and neighboring hydroxyl groups. It is noteworthy that the presence of PE affects more strongly the ionization of the 5-phosphate group than that of the 4-phosphate, suggesting that the interaction of PE with the 5-phosphate is stronger. In PI(4,5)P2/PS/PC lipid vesicles, the presence of PS was expected to yield an increased protonation of the PI(4,5)P2 phosphomonoester groups due to a decreased interfacial pH as a result of the increased negative interfacial charge. However, the effect of PS on PI(4,5)P2 ionization is only minor, potentially suggesting that PS and PI(4,5)P2 are demixed. The PI(4,5)P2/PI/PC vesicle system was characterized by a surprising mixing behavior that has potentially far reaching consequences: fluorescence microscopy measurements of giant unilammellar vesicles composed of PI(4,5)P2/PI/PC at physiological concentrations show that PI and PI(4,5)P2 form macroscopic, fluid phase domains in contact with a fluid PC rich phase (fluid/fluid demixing). Despite the fact that PI and PI(4,5)P2 co-localize, the effect of PI on PI(4,5)P2 ionization behavior is only noticeable above pH 7. Apparently two opposing effects lead to the observed behavior: Due to the presence of the anionic PI, the interfacial pH drops, which is expected to lead to an enhanced protonation of the PI(4,5)P2 phosphomonoester groups. In turn, hydrogen bond formation between PI and PI(4,5)P2 would lead to the opposite, i.e. increased deprotonation of the phosphomonoester group. Apparently these two effects compensate each other for pH values smaller than about 7, while for higher pH values the increased interfacial pH in the presence of PI has a stronger impact than PI/PI(4,5)P2 hydrogen bond formation. The cooperative formation of PI/PI(4,5)P2 mixed domains has potentially important ramifications for the spatial organization of phosphoinositide mediated signaling events.

The first example of amine-induced reversal of diastereoselectivity in acylation of some trans-2-substituted cyclohexanols

The reaction between racemic acyl chlorides and racemic trans -2-substituted-cyclohexanols proceeds diastereoselectively. We found for the first time that addition of a tertiary amine not only accelerates the acylation, but for some substituents leads to complete inversion of diastereoselectivity. These observations have been rationalized in terms of a possible stereoselective intramolecular assistance by the substituent group during the acylation of the neighboring hydroxyl group.

Novel Cytotoxic Polyoxygenated Steroids from an Okinawan SpongeDysideasp.

A library of extracts established from hundreds of marine organisms was screened by a cytotoxicity test. The active organic extract of an Okinawan marine sponge of the genus Dysidea was subjected to bioassay-guided fractionation to give three new polyoxygenated steroids dysideasterols F-H (1-3), together with two known related compounds (4 and 5). Their structures were confirmed by NMR and mass spectroscopic analyses. A characteristic structural feature of 2, 4 and 5 is an allylic epoxide, whereas this epoxide undergoes ring-opening by a neighbouring hydroxyl group to give a tetrahydrofuran ring in 1 and 3. All compounds 1-5 exhibited a similar cytotoxic effect with IC50 values of 0.15-0.3 µM against human epidermoid carcinoma A431 cells, demonstrating that the allylic epoxide moiety was not responsible for this cytotoxic effect.

Model of cooperative character of hydrogen bonds in water

A quantitative description of hydrogen bonds in liquid water is developed using a simple model. The proposed approach is based on the notion of a hydrogen bond as mediated by proton exchange between neighboring hydroxyl groups under adiabatic conditions with respect to the electron subsystem. Application of the model is illustrated by means of the example of analysis of the IR absorption spectrum of a thin water layer. It is shown that the structure of water in layers with thicknesses on the order of 1 μm differs from the structure of bulk water.

Understanding proton affinity of tyrosine sidechain in hydrophobic confinement#

Tyrosine is an important amino acid residue that plays a key role in several biochemical transformations such as, abstraction/donation of proton from/by its sidechain. We present here a density functional study on the proton affinity of tyrosine sidechain suspended inside the core of a single walled carbon nanotube that mimics the environment of protein structural pores and molecular channels. Tyrosine is found to exhibit a lower reactivity on confinement and unlike several other polar amino acid sidechains, its reactivity does not respond to hydrogen bonding with neighbouring hydroxyl groups. A density functional study is presented on the effect of hydrophobic confinement on the proton affinity of a tyrosine sidechain suspended within a single-walled carbon nanotube. The bulky sidechain encounters unfavorable steric interactions with the surrounding wall that primarily determines the observed lower reactivity of the sidechain.

Formation mechanisms of precursors of radiation-induced color centers during fabrication of silica optical fiber preform

Samples in the form of transverse slices of rods and optical fiber preforms made from the high-hydroxyl KU-1 and low-hydroxyl KS-4V silica by the plasma outside deposition (POD) method are γ-irradiated to a dose of ∼1 MGy (SiO2). Next, the radial dependences of the radiation-induced nonbridging oxygen hole center (NBOHC) and E′-center (three-coordinated silicon) in the samples are constructed by measuring the amplitudes of their 4.8 and 5.8 eV absorption bands, respectively. Based on the analysis of these radial dependences and considering the temperature and duration of the preirradiation heat treatment of the rods and preforms at the POD-installation, we determine the ratio of the oscillator strengths of the above bands and the microscopic thermoinduced processes occurring during preform fabrication and producing precursors of the radiation-induced NBOHC and E′-center. These processes are found to be associated with the escape of either H2 or H2O from neighboring hydroxyl groups, and, therefore, can occur in high-hydroxyl silica only. It is concluded that enhancement of the radiation resistance of high-hydroxyl silica optical fibers requires decreasing the temperature and duration of the preform fabrication process, in particular, changing from the POD-technology to the low-temperature plasmachemical vapor deposition (PCVD) or surface PCVD (SPCVD)-technology.

LABORATORY STUDIES ON THE FORMATION OF FORMIC ACID (HCOOH) IN INTERSTELLAR AND COMETARY ICES

Mixtures of water (H2O) and carbon monoxide (CO) ices were irradiated at 10 K with energetic electrons to simulate the energy transfer processes that occur in the track of galactic cosmic-ray particles penetrating interstellar ices. We identified formic acid (HCOOH) through new absorption bands in the infrared spectra at 1690 and 1224 cm–1 (5.92 and 8.17 μm, respectively). During the subsequent warm-up of the irradiated samples, formic acid is evident from the mass spectrometer signal at the mass-to-charge ratio, m/z = 46 (HCOOH+) as the ice sublimates. The detection of formic acid was confirmed using isotopically labeled water-d2 with carbon monoxide, leading to formic acid-d2 (DCOOD). The temporal fits of the reactants, reaction intermediates, and products elucidate two reaction pathways to formic acid in carbon monoxide-water ices. The reaction is induced by unimolecular decomposition of water forming atomic hydrogen (H) and the hydroxyl radical (OH). The dominating pathway to formic acid (HCOOH) was found to involve addition of suprathermal hydrogen atoms to carbon monoxide forming the formyl radical (HCO); the latter recombined with neighboring hydroxyl radicals to yield formic acid (HCOOH). To a lesser extent, hydroxyl radicals react with carbon monoxide to yield the hydroxyformyl radical (HOCO), which recombined with atomic hydrogen to produce formic acid. Similar processes are expected to produce formic acid within interstellar ices, cometary ices, and icy satellites, thus providing alternative processes for the generation of formic acid whose abundance in hot cores such as Sgr-B2 cannot be accounted for solely by gas-phase chemistry.

Influence of Polyols on the Formation of Iron Oxide Nanoparticles in Solvothermal System

We reported a simple solvothermal route in phase-controllable synthesis of iron oxide nanoparticles by using polyols as solvent. Magnetite and hematite are selectively synthesized while Fe(NO3)3.9H2O is used as single iron source and without any additives. While ethylene glycol, 1,2propanediol, 1,3-butanediol, or glycerol is used as solvents, magnetite nanoparticles are obtained, and the average particle sizes vary from 10 to 40 nm. While 1,4-butanediol or 1,5-pentanediol is used as solvents, hematite nanoparticles are obtained. Our results suggest that the polyols with neighboring hydroxyl groups is favorable for the formation of magnetite nanoparticles.

ChemInform Abstract: Acid-Catalyzed Hydrolysis of Triacylglycerols Obeys Monoexponential Kinetics

The acid-catalyzed hydrolyses of triacetyl-glycerol and of tributyryl-glycerol take place following a simple monoexponential kinetic scheme. The result can be interpreted as all three ester groups reacting with approximately the same specific rate. This observation reported in 1920 is unusual, because the intrinsic reactivities of primary and secondary esters are different, and because as far as the reaction proceeds, the remaining ester groups have neighboring hydroxyl groups, which undoubtly alter the reactivity of the reaction centers, relative to the situation in the initial reactant structure

Hydrogen-Promoted Chlorination of RuO2(110)

High-resolution core-level photoemission spectroscopy and temperature-programmed reaction experiments together with density functional theory calculations were used to elucidate on the atomic scale the chlorination mechanism of ruthenium dioxide RuO2(110) by hydrogen chloride exposure. The surface-selective chlorination accounts for the extraordinary stability of the RuO2 catalyst in the Sumitomo process-the heterogeneously catalyzed oxidation of hydrogen chloride by oxygen. The selective replacement of bridging oxygen atoms by chlorine atoms depends on the formation of water molecules serving as leaving groups. Water is produced by the chlorine-assisted recombination of two neighboring surface hydroxyl groups at around 450 K, a temperature where water instantaneously leaves the surface. Finally, the bridging vacancy is rapidly filled in by chlorine atoms, thereby forming bridging chlorine atoms. Preadsorbed hydrogen has shown to facilitate the chlorination process for stoichiometry reasons. The general strategy of transforming bridging O atoms into a good leaving group has been corroborated by the chlorination of RuO2(110) via CO pretreatment with CO2 as the leaving group and subsequent Cl-2 exposure. (Less)

Structural investigation of some important Chinese diatomites

The structure of some important diatomites has been investigated systematically. It has been revealed that the Zhejiang white soil contains bound, isolated, and neighboring hydroxyl groups and that other diatomites involve hydroxyl groups of two types, i.e., isolated and neighboring hydroxyl groups. The IR spectra exhibit bands associated with the Si-O and Al-O bonds. The acid treatment and calcination lead to a change in the size, size distribution, and structure of pores. The calcination results in a change in the diatomite structure, the removal of free water, and a decrease in the content of bound water. Upon calcination at a temperature of 1150°C, amorphous silica constituting the diatomite crystallizes into α-cristobalite. The Jilin diatomite has primary pores, the Yunnan diatomite has tertiary pores, and the other diatomites have secondary pores.

A Clean, Mild, and Selective Oxidation of Sulfides to Sulfoxides Using NaClO/H2SO4 in Aqueous Media

A range of sulfides can be selectively oxidized to the corresponding sulfoxides in good yields using NaClO/H2SO4 in both water and 50:50 water:EtOH as solvent. Two new compounds are reported that show a diastereoselective oxidation in 2-phenylthioalcohols with possible neighboring hydroxyl group participation with a logic proposed mechanism.

The Building Blocks of Cellulose: The Intrinsic Conformational Structures of Cellobiose, Its Epimer, Lactose, and Their Singly Hydrated Complexes

A combination of vibrational spectroscopy conducted under molecular beam conditions and quantum chemical calculation has established the intrinsic three-dimensional structures of the cellulose disaccharide and, focusing on the critical beta1,4-linkage at the nonreducing end of the growing cellulose polymer, its C-4' epimer. Left to their own devices they both adopt a cis (anti-phi/syn-psi) glycosidic configuration, supported in the epimer by strong, cooperative inter-ring hydrogen bonding. In the cellulose disaccharide, however, where the OH-4'(Glc) group is equatorial, the cooperativity is reduced and the corresponding inter-ring hydrogen bonding is relatively weak. The cis conformational preference is still retained in their singly hydrated complexes. In the cellulose disaccharide insertion of the water molecule at the favored binding site between OH-4' and the neighboring hydroxyl group OH-6' promotes a structural reorganization to create a configuration that parallels that of its unhydrated epimer and greatly strengthens the inter-ring hydrogen bonding. In the C-4' epimer, the axial orientation of OH-4' blocks this binding site and the bound water molecule simply adds on at the end of the (OH-O)(n) chain, which has a negligible effect on the (already strong) inter-ring bonding. The implications of these results are discussed with respect to the structure and insolubility of native cellulose polymers.

Adsorption and Protonation of CO2 on Partially Hydroxylated γ-Al2O3 Surfaces: A Density Functional Theory Study

Adsorption and protonation of CO2 on the (110) and (100) surfaces of gamma-Al2O3 have been studied using density functional theory slab calculations. On the dry (110) and (100) surfaces, the O-Al bridge sites were found to be energetically favorable for CO2 adsorption. The adsorbed CO2 was bound in a bidentate configuration across the O-Al bridge sites, forming a carbonate species. The strongest binding with an adsorption energy of 0.80 eV occurs at the O3c-Al5c bridge site of the (100) surface. Dissociation of water across the O-Al bridge sites resulted in partially hydroxylated surfaces, and the dissociation is energetically favorable on both surfaces. Water dissociation on the (110) surface has a barrier of 0.42 eV, but the same process on the (100) surface has no barrier with respect to the isolated water molecule. On the partially hydroxylated gamma-Al2O3 surfaces, a bicarbonate species was formed by protonating the carbonate species with the protons from neighboring hydroxyl groups. The energy difference between the bicarbonate species and the coadsorbed bidentate carbonate species and hydroxyls is only 0.04 eV on the (110) surface, but the difference reaches 0.97 eV on the (100) surface. The activation barrier for forming the bicarbonate species on the (100) surface, 0.42 eV, is also lower than that on the (110) surface (0.53 eV).

Treatment of electrostatic interactions in simulations of the interface between transition metal surfaces and organic matter: the discrete classical model and the reaction-field dielectric method

A more efficient molecular dynamics model is devised to study the interface between platinum(111) and liquid isopropanol. The faster reaction-field dielectric method (RFD) is investigated as the alternative to the very accurate discrete classical model (DCM) (M. W. Finnis, Surf. Sci., 1991, 241, 61) to account for the electrostatic interactions at the interface. Differences in static and dynamic properties of the interface are examined. The mass-density and number-density distributions showed only a little sensitivity towards the choice of the method. The orientational structure revealed notable but still small quantitative changes for highly-polarized parts of the isopropanol molecules if the RFD is used instead of the DCM. The general qualitative picture is still preserved. The simulations of the platinum(111)/isopropanol interface with the DCM or the Ewald summation were carried out for longer times than in our previous contribution (K. B. Tarmyshov and F. Müller-Plathe, J. Chem. Phys., 2007, 126, 74702). The analysis disclosed that the influence of chemical or electrostatic interactions at the interface on the relative orientation of the neighbouring hydroxyl groups, which are adsorbed on the surface, is notably smaller than reported before. Overall, the reaction-field dielectric method can be used to study the properties of the interface between transition metals and organic matter, if there appears a chemical bond of 10 kT or higher between the surface and adsorbate molecules or their parts.

A Mechanistic and Kinetic Study of the β-Lactone Hydrolysis of Salinosporamide A (NPI-0052), A Novel Proteasome Inhibitor

The aim of the present study was to investigate the mechanism of aqueous degradation of Salinosporamide A (NPI-0052; 1), a potent proteasome inhibitor that is currently in Phase I clinical trials for the treatment of cancer and is characterized by a unique beta-lactone-gamma-lactam bicyclic ring structure. The degradation of 1 was monitored by HPLC and by both low- and high-resolution mass spectral analyses. Apparent first-order rate constants for the degradation at 25 degrees C were determined in aqueous buffer solutions (ionic strength 0.15 M adjusted with NaCl) at various pH values in the range of 1 to 9. Degradation kinetics in water and in deuterium oxide were compared as a mechanistic probe. The studies were performed at pH (pD) 4.5 at 25 degrees C. To further confirm the reaction mechanism, the degradation was also performed in (18)O-enriched water and the degradation products subjected to HPLC separation prior to mass spectral analysis. Solubility and stability in (SBE)(7m)-beta-cyclodextrin (Captisol) solutions were also determined. The hydrolytic degradation of 1, followed by both HPLC and LC/MS, showed that the drug in aqueous solutions gives a species with a molecular ion consistent with the beta-lactone hydrolysis product (NPI-2054; 2). This initial degradant further rearranges to a cyclic ether (NPI-2055; 3) via an intramolecular nucleophilic displacement reaction. The kinetic results showed that the degradation of 1 was moderately buffer catalyzed (general base) and the rate constants were pH independent in the range of 1-5 and base dependent above pH 6.5. No acid catalysis was observed. The kinetic deuterium solvent isotope effect (KSIE) was 3.1 (kH/kD) and a linear proton inventory plot showed that the rate-determining step involved only a single proton transfer. This suggested that a neighboring hydroxyl group (as opposed to a second water molecule) facilitated water attack at pD 4.5. Mass spectral analysis from the (18)O-labeling studies proved that the mechanism involves acyl-oxygen bond cleavage and not a carbonium ion mechanism. 1 is unstable in water (t(90%) <or= 33 min at pH <5) and degrades via beta-lactone hydrolysis involving a normal ester hydrolysis mechanism (addition-elimination) resulting in acyl-oxygen bond cleavage. Captisol solubilized and stabilized 1 in aqueous solutions.

Study of a Family of 40 Hydroxylated β-Cristobalite Surfaces Using Empirical Potential Energy Functions

We present a study of a family of 40 unique hydroxylated β-cristobalite surfaces generated by cleaving the β-cristobalite unit cell along crystallographic planes to include a combination of several low Miller index surfaces. The surface silicon atoms are quantified as percentages of Q 2 and Q 3 centers based on their polymeric state. We find that Q 3 centers are, on average, three times more abundant than Q 2 centers. To study the surface properties, we use two different empirical potential energy functions: the multibody potential proposed by Fueston and Garofalini (J. Phys. Chem. 1990, 94, 5351) and the newly developed CHARMM potential by Lopes et al. (J. Phys. Chem. B 2006, 110, 2782). Our results for the surface water interactions are in good agreement with previous ab initio theoretical studies by Yang et al. (Phys. Rev. B 2006, 73, 146102) for the (100) surface. We find that the most commonly studied family of {100} surfaces is unique and is the only surface with 100% abundance of Q 2 centers, whereas there are nine examples of surfaces with 100% Q 3 centers. The predominantly pure Q 3 surfaces show no hydrogen bonding with the neighboring surface hydroxyl groups and weakly adsorb water overlayers. This is markedly different from the {100} pure Q 2 surface that shows strong hydrogen bonding within the surface groups and with water. As compared to all the surfaces studied in this work, we find that the {100} surfaces are not true representations of the overall β-cristobalite surfaces and their properties. We find that the two main factors that characterize the physical properties of silica surfaces are the polymeric state of the silicon atom and surface topography. Two types of pure Q 3 crystallographic planes have been identified and are labeled as Q 3A and Q 3B based on the differences in their topological features. Using the {111} and {011} surfaces as examples, we show that the Q 3A surface adsorbs H 2 O that forms a stable monolayer, but the Q 3B surface fails to form a stable H 2 O overlayer. Other crystallographic planes with different ratios of Q 2 to Q 3 centers are contrasted by the differences in the hydrogen-bonding network and their ability to form ordered H 2 O overlayers.