Density-functional theory-based molecular simulation study of liquid methanol

We present a density-functional theory based molecular dynamics study of the structural, dynamical, and electronic properties of liquid methanol under ambient conditions. The calculated radial distribution functions involving the oxygen and hydroxyl hydrogen show a pronounced hydrogen bonding and compare well with recent neutron diffraction data. We observe that, in line with infrared spectroscopic data, the hydroxyl-stretching mode is significantly redshifted in the liquid, whereas the hydroxyl bending mode shows a blueshift. A substantial enhancement of the molecular dipole moment is accompanied by significant fluctuations due to thermal motion. We compute a value of 32 for the relative permittivity, almost identical to the experimental value of 33. Our results provide valuable data for improvement of empirical potentials.     

SINGLET OXYGEN INVOLVEMENT IN THE INACTIVATION OF CULTURED HUMAN FIBROBLASTS BY UVA (334 nm, 365 nm) AND NEAR-VISIBLE (405 nm) RADIATIONS

The UVA (320-380 nm) radiation inactivation of mammalian cells is dependent upon the presence of oxygen. In order to examine the intermediates involved, we have irradiated cells in the presence of chemical probes which are able to modify the activity of various oxygen species. We have also examined the possibility that UVA inactivates cultured human fibroblasts via generation of intracellular hydrogen peroxide. An iron scavenger (desferrioxamine) and a hydroxyl radical scavenger (dimethylsulfoxide) protect the cells against hydrogen peroxide. Diethyldithiocarbamate (a superoxide dismutase inhibitor) and aminotriazole (a catalase inhibitor) sensitize the cells to this oxidizing agent. These data support previous reports that hydrogen peroxide inactivates as a result of the iron-catalyzed generation of hydroxyl radical. None of these agents significantly alter the fluence-dependent inactivation of cell populations by radiation at 365 nm. In contrast, the cells are sensitized to radiation at 334, 365 and 405 nm in the presence of deuterium (an enhancer of singlet oxygen lifetime) and are protected against radiation at 365 nm by sodium azide (a quencher of singlet oxygen). These results are consistent with the conclusion that the generation of singlet oxygen, but not hydrogen peroxide or hydroxyl radical, plays an important role in the inactivation of cultured human cells by UVA and near-visible radiations.     

A statistical model of hydrogen bond networks in liquid alcohols

We here present a statistical model of hydrogen bond induced network structures in liquid alcohols. The model generalises the Andersson-Schulz-Flory chain model to allow also for branched structures. Two bonding probabilities are assigned to each hydroxyl group oxygen, where the first is the probability of a lone pair accepting an H-bond and the second is the probability that given this bond also the second lone pair is bonded. The average hydroxyl group cluster size, cluster size distribution, and the number of branches and leaves in the tree-like network clusters are directly determined from these probabilities. The applicability of the model is tested by comparison to cluster size distributions and bonding probabilities obtained from Monte Carlo simulations of the monoalcohols methanol, propanol, butanol, and propylene glycol monomethyl ether, the di-alcohol propylene glycol, and the tri-alcohol glycerol. We find that the tree model can reproduce the cluster size distributions and the bonding probabilities for both mono- and poly-alcohols, showing the branched nature of the OH-clusters in these liquids. Thus, this statistical model is a useful tool to better understand the structure of network forming hydrogen bonded liquids. The model can be applied to experimental data, allowing the topology of the clusters to be determined from such studies.     

Solvation structure of hydroxyl radical by Car-Parrinello molecular dynamics

Car-Parrinello molecular dynamics simulations of a hydroxyl radical in liquid water have been performed. Structural and dynamical properties of the solvated structure have been studied in details. The partial atom-atom radial distribution functions for the hydrated hydroxyl do not show drastic differences with the radial distribution functions for liquid water. The OH is found to be a more active hydrogen bond donor and acceptor than the water molecule, but the accepted hydrogen bonds are much weaker than for the hydroxide OH- ion. The first solvation shell of the OH is less structured than the water's one and contains a considerable fraction of water molecules that are not hydrogen bonded to the hydroxyl. Part of them are found to come closer to the solvated radical than the hydrogen bonded molecules do. The lifetime of the hydrogen bonds accepted by the hydroxyl is found to be shorter than the hydrogen bond lifetime in water. A hydrogen transfer between a water molecule and the OH radical has been observed, though it is a much rarer event than a proton transfer between water and an OH- ion. The velocity autocorrelation power spectrum of the hydroxyl hydrogen shows the properties both of the OH radical in clusters and of the OH- ion in liquid.     

高岭石-水体系中水分子结构的分子动力学模拟

以Hendricks模型为初始结构, 利用CLAYFF力场对高岭石-水体系进行无晶体学限制的分子动力学模拟. 结果表明, 层间水有三种类型: I型类似于Costanzo提出的“洞水”分子, 其HH矢量(水分子中从一个氢原子位置指向另一个氢原子位置的方向矢量)平行于(001)平面, 而C2轴稍微倾斜于(001)面法线; II型类似于“连接水”, 一个氢氧键指向临近的层间四面体氧形成氢键, 另一个氢氧键与(001)面近似平行; III型水分子在层间近似保持为竖直状, 一个氢与层间四面体氧形成氢键, 而另一个氢与对面层的羟基氧形成氢键. 高岭石羟基氢沿(001)晶面法线的浓度曲线显示一部分羟基指向变为近似平行于(001)面, 羟基氧因此能够暴露出来与层间水分子氢形成氢键. 此外, 模拟中还观察到部分II型水分子氧偏离于层间的平均位置而更靠近四面体层, 这和Costanzo的实验结果一致, 可能是X射线谱图中(002)弱衍射峰出现的原因.     

Mechanistic insights on how hydroquinone disarms OH and OOH radicals

Phenol derivatives are distinguished as successful free radical scavengers. We present a detailed analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radical with emphasis on changes that take place in the vicinity of the transition state. Quantum theory of atoms in molecules is employed to elucidate the sequence of positive and negative charge transfer by studying selected properties of the three key atoms (the transferring hydrogen, the donor atom, and the acceptor atom) along intrinsic reaction path. The presented results imply that in both reactions, which are examples of proton coupled electron transfer, proton, and electron get simultaneously transferred to the radical oxygen atom. The fact that the hydrogen's charge and volume do not monotonously change in the vicinity of the transition state in the product valley results from the adjacency of the proton and the electron to the donor and the acceptor oxygen atoms. Obtaining a detailed understanding of mechanisms by which free radicals are disarmed is of paramount importance given the effects of those highly reactive species on biological systems. A comprehensive analysis of hydroxyl hydrogen abstraction from hydroquinone by hydroxyl and hydroperoxyl radicals, based on changes of selected electronic properties of the three most relevant atoms (hydrogen donor, hydrogen acceptor, and the hydrogen itself), along the reaction coordinate, can be obtained by first‐principles calculations.     

Structural and kinetic effects on a simple catalytic reaction: oxygen reduction on Ni(110)

Oxygen hydrogenation at 100 K by gas phase atomic hydrogen on Ni(110) has been studied under ultrahigh vacuum conditions by temperature programmed desorption (TPD) and x-ray photoelectron spectroscopy (XPS). Formation of adsorbed water and hydroxyl species was observed and characterized. The coverage of the reaction products was monitored as a function of both temperature and initial oxygen precoverage. On the contrary, when high coverage oxygen overlayers were exposed to gas phase molecular hydrogen, no hydrogenation reaction took place. The results are compared to the inverse process, exposing the hydrogen covered surface to molecular oxygen. In this case, at 100 K, simple Langmuir-Hinshelwood modeling yields an initial sticking coefficient for oxygen adsorption equal to 0.26, considerably lower than for the clean surface. Moreover, formation of hydroxyl groups is found to be twice as fast as the final hydrogenation of OH groups to water. Assuming a preexponential factor of 10(13) s(-1), an activation barrier of 6.7 kcal/mol is obtained for OH formation, thus confirming the high hydrogenating activity of nickel with respect to other transition metals, for which higher activation energies are reported. However, oxygen is hardly removed by hydrogen on nickel: this is explained on the basis of the strong Ni-O chemical bond. The hydrogen residual coverage is well described including a contribution from the adsorption-induced H desorption process which takes place during the oxygen uptake and which is clearly visible from the TPD data.     

Combined Monte Carlo and molecular dynamics simulation of hydrated 18:0 sphingomyelin-cholesterol lipid bilayers

We have carried out atomic level molecular dynamics and Monte Carlo simulations of hydrated 18:0 sphingomyelin (SM)-cholesterol (CHOL) bilayers at temperatures of 20 and 50 degrees C. The simulated systems each contained 266 SM, 122 CHOL, and 11861 water molecules. Each simulation was run for 10 ns under semi-isotropic pressure boundary conditions. The particle-mesh Ewald method was used for long-range electrostatic interactions. Properties of the systems were calculated over the final 3 ns. We compare the properties of 20 and 50 degrees C bilayer systems with each other, with experimental data, and with experimental and simulated properties of pure SM bilayers and dipalmitoyl phospatidyl choline (DPPC)-CHOL bilayers. The simulations reveal an overall similarity of both systems, despite the 30 degrees C temperature difference which brackets the pure SM main phase transition. The area per molecule, lipid chain order parameter profiles, atom distributions, and electron density profiles are all very similar for the two simulated systems. Consistent with simulations from our lab and others, we find strong intramolecular hydrogen bonding in SM molecules between the phosphate ester oxygen and the hydroxyl hydrogen atoms. We also find that cholesterol hydroxyl groups tend to form hydrogen bonds primarily with SM carbonyl, methyl, and amide moieties and to a lesser extent methyl and hydroxyl oxygens.     

Quantification of singlet oxygen production in the reaction of superoxide with hydrogen peroxide using a selective chemiluminescent probe

A sensitive chemiluminescent probe that selectively reacts with singlet oxygen in the presence of superoxide and hydrogen peroxide has been used to quantify the production of singlet oxygen in the reaction of superoxide with hydrogen peroxide. The yield of singlet oxygen from this reaction was found to be low (0.2% relative to the initial superoxide concentration). No evidence for the formation of hydroxyl radical was observed in this reaction, ruling out the Haber-Weiss mechanism as a major singlet oxygen formation pathway. No singlet oxygen production was observed in the reaction of superoxide with 2-nitrobenzoic acid, which has a pKa similar to that of hydrogen peroxide, rendering the protonation of superoxide, followed by its disproportionation, an unlikely explanation for the formation of singlet oxygen in this system. The low yields of singlet oxygen and hydroxyl radical suggest that their formation in this reaction should be relatively unimportant in biological systems.     

Computational studies for reduced graphene oxide in hydrogen-rich environment

We employ molecular dynamic simulations to study the reduction process of graphene oxide (GO) in a chemically active environment enriched with hydrogen. We examine the concentration and pressure of hydrogen gas as a function of temperature in which abstraction of oxygen is possible with minimum damage to C-sp(2) bonds, hence preserving the integrity of the graphene sheet. Through these studies we find chemical pathways that demonstrate beneficiary mechanisms for the quality of graphene including formation of water as well as suppression of carbonyl pair holes in favor of hydroxyl and epoxide formation facilitated by hydrogen gas in the environment.     

2,2,6,6-四甲基哌啶-1-氧自由基促进的钒基催化剂催化苯直接氧化制苯酚

以钒基化合物为催化剂,在TEMPO(2,2,6,6-四甲基哌啶-1-氧自由基)存在下,能形成快速催化分子氧氧化苯制苯酚的催化体系.在反应过程中,由类似芬顿试剂反应过程生成的羟基自由基亲核进攻苯环,形成羟基环己二烯自由基;该羟基氢可在TEMPO存在的催化体系中消除,同时苯环氢可立即转移至氧原子而生成苯酚.在以[(CH3)...     

The microenvironment effect on the generation of reactive oxygen species by Pd-bacteriopheophorbide

Generation of reactive oxygen species (ROS) is the hallmark of important biological processes and photodynamic therapy (PDT), where ROS production results from in situ illumination of certain dyes. Here we test the hypothesis that the yield, fate, and efficacy of the species evolved highly depend on the dye's environment. We show that Pd-bacteriopheophorbide (Pd-Bpheid), a useful reagent for vascular targeted PDT (VTP) of solid tumors, which has recently entered into phase II clinical trials under the code name WST09 (trade name TOOKAD), forms appreciable amounts of hydroxyl radicals, superoxide radicals, and probably hydrogen peroxide in aqueous medium but not in organic solvents where singlet oxygen almost exclusively forms. Evidence is provided by pico- and nanosecond time-resolved spectroscopies, ESR spectroscopy with spin-traps, time-resolved singlet oxygen phosphorescence, and chemical product analysis. The quantum yield for singlet oxygen formation falls from approximately 1 in organic solvents to approximately 0.5 in membrane-like systems (micelles or liposomes), where superoxide and hydroxyl radicals form at a minimal quantum yield of 0.1%. Analysis of photochemical products suggests that the formation of oxygen radicals involves both electron and proton transfer from (3)Pd-Bpheid at the membrane/water interface to a colliding oxygen molecule, consequently forming superoxide, then hydrogen peroxide, and finally hydroxyl radicals, with no need for metal catalysis. The ability of bacteriochlorophyll (Bchl) derivatives to form such radicals upon excitation at the near infrared (NIR) domain opens new avenues in PDT and research of redox regulation in animals and plants.     

Glucose solvation by the ionic liquid 1,3-dimethylimidazolium chloride: a simulation study

Simulations of beta-glucose in the ionic liquid 1,3-dimethylimidazolium chloride have been performed in order to examine the solvation environment of the carbohydrate. Both single molecule and 1:5 glucose:ionic liquid (16.7 wt %) solutions are studied, and the hydrogen bonding between sugar and solvent is examined. The primary solvation shell around the perimeter of the glucose ring consists predominantly of chloride anions which hydrogen bond to the hydroxyl groups. A small presence of the cation is also found, with the association occurring through the weakly acidic hydrogen at the 2-position of the imidazolium ring interacting with the oxygen atoms of the sugar secondary hydroxyls. An average chloride coordination number of 4 is found around the glucose for both the single molecule and high concentration simulations, despite the reduced chloride:glucose ratio in the latter case. In relation to the cation, the glucose molecules occupy positions above and below the plane of the imidazolium ring. Importantly, even at high glucose concentrations, no significant change in the anion-cation interactions and overall liquid structure of the ionic liquid is found, indicating that the glucose is readily accommodated by the solvent at this concentration. Dominant contributions to the sugar-ionic liquid interaction energy come from favorable hydrogen bonding (electrostatic) interactions between hydroxyls and chlorides, although a small favorable van der Waals energy contribution is also seen between the sugar and cations suggesting that the cation could be tailored in order to further improve the dissolution of glucose/cellulose in ionic liquid systems.     

Emission of reactive oxygen species during degradation of iron gall ink

Iron gall inks are characterised by high contents of acids and transition metals, promoting degradation of cellulose due to hydrolysis and oxidation, respectively. Their chemical interaction with the environment is not well understood, especially in view of emissions of degradation products which could lead to spread of degradation processes.In order to study the emissions, we employed gas chromatography/mass spectrometry following headspace micro-extraction, and liquid chromatography following hydroxyl radical scavenging with appropriate probes. We also studied chemiluminescence of cellulose affected by ink degradation.We show that while the emissions of organic volatile degradation compounds by inks are less intense than those of surrounding paper, ink does promote the degradation of cellulose across big distances (from object to object). We were able to link this to emission of reactive oxygen species, probably hydrogen peroxide. Its emission from ink is considerably more intensive than from paper.     

The "somersault" mechanism for the p-450 hydroxylation of hydrocarbons. The intervention of transient inverted metastable hydroperoxides

A series of model theoretical calculations are described that suggest a new mechanism for the oxidation step in enzymatic cytochrome P450 hydroxylation of saturated hydrocarbons. A new class of metastable metal hydroperoxides is described that involves the rearrangement of the ground-state metal hydroperoxide to its inverted isomeric form with a hydroxyl radical hydrogen bonded to the metal oxide (MO-OH --> MO....HO). The activation energy for this somersault motion of the FeO-OH group is 20.3 kcal/mol for the P450 model porphyrin iron(III) hydroperoxide [Por(SH)Fe(III)-OOH(-)] to produce the isomeric ferryl oxygen hydrogen bonded to an *OH radical [Por(SH)Fe(III)-O....HO(-)]. This isomeric metastable hydroperoxide, the proposed primary oxidant in the P450 hydroxylation reaction, is calculated to be 17.8 kcal/mol higher in energy than the ground-state iron(III) hydroperoxide Cpd 0. The first step of the proposed mechanism for isobutane oxidation is abstraction of a hydrogen atom from the C-H bond of isobutane by the hydrogen-bonded hydroxyl radical to produce a water molecule strongly hydrogen bonded to anionic Cpd II. The hydroxylation step involves a concerted but nonsynchronous transfer of a hydrogen atom from this newly formed, bound, water molecule to the ferryl oxygen with a concomitant rebound of the incipient *OH radical to the carbon radical of isobutane to produce the C-O bond of the final product, tert-butyl alcohol. The TS for the oxygen rebound step is 2 kcal/mol lower in energy than the hydrogen abstraction TS (DeltaE() = 19.5 kcal/mol). The overall proposed new mechanism is consistent with a lot of the ancillary experimental data for this enzymatic hydroxylation reaction.     

Nuclear magnetic resonance chemical shifts and quadrupole couplings for different hydrogen-bonding cases occurring in liquid water: a computational study

Nuclear magnetic resonance (NMR) parameters are determined theoretically for the oxygen and hydrogen/deuterium nuclei of differently hydrogen-bonded water molecules in liquid water at 300 K. The parameters are the chemical shift, the shielding anisotropy, the asymmetry parameter of shielding, the nuclear quadrupole coupling constant, and the asymmetry parameter of the nuclear quadrupole coupling. We sample instantaneous configurations from a Car-Parrinello molecular dynamics simulation and feed nuclear coordinates into a quantum chemical program for the calculation of NMR parameters using density-functional theory with the three-parameter hybrid exchange-correlation (B3LYP) functional. In the subsequent analysis, molecules are divided into groups according to the number of hydrogen bonds they possess, and the full average NMR tensors are calculated separately for each group. The classification of the hydrogen-bonding cases is performed using a simple distance-based criterion. The analysis reveals in detail how the NMR tensors evolve as the environment changes gradually from gas to liquid upon increasing the number of hydrogen bonds to the molecule of interest. Liquid-state distributions of the instantaneous values of the NMR properties show a wide range of values for each hydrogen-bonding species with significant overlap between the different cases. Our study shows how local changes in the environment, along with classical thermal averaging, affect the NMR parameters in liquid water. For example, a broken or alternatively extra hydrogen bond induces major changes in the NMR tensors, and the effect is more pronounced for hydrogen or deuterium than for oxygen. The data sheds light on the usefulness of NMR experiments in investigating the local coordination of liquid water.     

Competitive binding of methanol and propane for water via matrix-isolation spectroscopy: implications for inhibition of clathrate nucleation

Methanol is a well-known thermodynamic inhibitor of clathrate hydrate formation. The interactions responsible for the inhibition, however, are not well-identified. Propane is a relatively simple hydrocarbon that forms a clathrate hydrate under mild conditions. This paper reports data about the interaction of methanol with water-propane complex. Methanol, water, and propane are isolated in carbon tetrachloride, and the interaction is probed with infrared spectroscopy. Water is known to interact with propane via the oxygen lone pairs and the propane methylene hydrogens. Experimental evidence indicates that methanol hydrogen bonds to water via donation of the hydroxyl hydrogen (K = 4.4 × 10(2)). Methanol does not have a direct interaction with propane. These results are consistent with an inhibitory mechanism in which methanol competes with propane for the oxygen atom of water.     

Fe(II)-EDTA chelate-induced aromatic hydroxylation of terephthalate as a new method for the evaluation of hydroxyl radical-scavenging ability.

The investigation of Fe(II)-EDTA chelate-induced aromatic hydroxylation of terephthalate in pH 7.4 phosphate buffer solution and a new method for the evaluation of hydroxyl radical-scavenging ability are reported. The method is based on attack of the hydroxyl radical on the terephthalate to produce highly fluorescent 2-hydroxyterephthalate, which is detected fluorimetrically. The formation of hydroxyl radical is believed to be the result of the reduction of molecular oxygen by Fe(II)-EDTA to form superoxide radical, which in turn dismutates to hydrogen peroxide, and then Fe(II)-EDTA catalyzes the decomposition of hydrogen peroxide to produce hydroxyl radical. The mechanism of the generation of hydroxyl radical in the proposed system was confirmed. This study established a simple and inexpensive method for the evaluation of the scavenging ability of some compounds on hydroxyl radicals.     

Excess properties and spectroscopic studies of binary system of 1-methoxy-2-propanol + dimethyl sulfoxide at T = (298.15–318.15) K

Thermophysical property data for the binary system of 1-methoxy-2-propanol (PGME) + dimethyl sulfoxide (DMSO), a potential candidate for use as the scrubbing liquid for the absorption of SO₂, are lacking in the literature. This paper presents experimental data at 0.1 MPa on the density and viscosity for this binary system measured over the whole composition range at T = (298.15, 303.15, 308.15, 313.15 and 318.15) K. The extended combined uncertainty U_c with a 0.95 level of confidence for the pycnometer method and Ubbelohde viscometer used in this study is 0.002 g·cm^?3 and 0.028 cm²·s^?1, respectively. The PGME + DMSO system shows negative values of the excess molar volume at all temperatures and compositions. Based on UV-Vis and FTIR, the intermolecular interaction of PGME with DMSO was confirmed as hydrogen bonding between the hydroxyl hydrogen atom in PGME and the oxygen atom in DMSO.     

Synthesis of alkyl (3-pyridyl)hydroxymethylphosphonates and their IR spectra

The reaction of dialkyl H-phosphonates with pyridine-3-carbaldehyde gives alkyl (3-pyridyl)hydroxymethylphosphonates. In liquid systems, the hydrogen atom is localized at the oxygen atom of the hydroxyl group; in crystals, the existence of a zwitter-ionic form could not be excluded. In CHCl₃ solutions, isolated molecules and cyclic dimeric H-complexes exist in an equilibrium.Translated fromIzvestiya Akademii Nauk. Seriya Khimicheskaya, No. 9, pp. 1674–1676, September, 1994.