Atmospheric fate of diketones and OH radical–kinetics,reaction force,ETS-NOCV analysis

In this work, we have focused on the atmospheric reaction chemistry of two α-diketones 2,3-Pentanedione (2,3-PTD) and 2,3-hexanedione (2,3-HEX) with OH radical. The full reaction pathway was studied theoretically under H-atom abstraction reaction using density functional theory and wave-function-based MP2 calculations. Single-point energy calculations were performed at CCSD(T) level of theory with 6–31+G(d,p) basis set. The H-atom abstraction from –CH₂ group is the most dominant channel in both 2,3-PTD and 2,3-HEX with OH radical. The fate of secondary reactions of peroxy and alkoxy radical is studied in detail. The reaction force analysis shows that abstraction process is dominated by structural rearrangement than electronic reordering. The ETS-NOCV-based reaction scheme is studied in order to find out the pair wise interaction energy of the chemical bonding. The ETS-NOCV method for all the transition states shows π-bonding nature for the bond breaking (C–H) and bond formation (O–H) due to the presence of hydrogen bond. The theoretical rate constant value matches well with the experimental rate constant value for both α-diketones. Normal linear Arrhenius behaviour for all the pathways is found in the range of 278–350 K. The short atmospheric lifetime indicates the removal process of diketones with OH radical.     

Cross section for the H+H2O abstraction reaction: experiment and theory

The absolute value of the cross section for the abstraction reaction between fast H atoms and H2O has been determined experimentally at a mean collision energy of 2.46 eV. The OH population distribution at the same mean energy has also been determined. The new measurements are compared with state-of-the-art quantum mechanical and quasiclassical scattering calculations on the most recently developed potential energy surface.     

Hydrogen bonding in mixed OH+H2O overlayers on Pt(111)

The stability of OH on Pt(111) has been investigated to determine the role of hydrogen bonding in stabilizing the overlayer. We find that the optimal structure is a mixed (OH+H2O) phase, confirming recent density-functional theory predictions. The reaction O+3H(2)O forms a hexagonal (sqrt[3]xsqrt[3])R30 degrees -(OH+H2O) lattice with a weak (3x3) superstructure, caused by ordering of the hydrogen bonds. The mixed overlayer can accommodate a range of H(2)O/OH compositions but becomes less stable as the H2O content is reduced, causing defects in the hydrogen-bonding network that lift the (3 x 3) superstructure and destabilize the overlayer.     

Comparison of hydrogen and halogen bonds between dimethyl sulfoxide and hypohalous acid: competition and cooperativity

A theoretical study of the complexes formed between dimethyl sulfoxide (DMSO) and hypohalous acid (HOX, X = Cl, Br, and I) has been carried out at the MP2/aug-cc-pVTZ level. For each HOX, four minima binary complexes were found, two mainly with an OH???O hydrogen bond and the other two with an OX???O halogen bond. The hydrogen-bonded complexes are more stable than the halogen-bonded analogues for HOCl and HOBr, while both types of complexes have similar stability in the iodine case. A red shift was found for the associated H–O and X–O bond stretch vibrations and a small blue shift for the distant bonds. As the oxygen of DMSO simultaneously binds with two HOCl molecules, the corresponding interactions are weakened with diminutive effect. This diminutive effect is the largest in the complexes with two OH???O hydrogen bonds but the smallest in those with two OCl???O halogen bonds.     

Theoretical study on the mechanism of the reaction of FOX-7 with OH and NO2 radicals: bimolecular reactions with low barrier during the decomposition of FOX-7

The decomposition of 1,1-diamino-2,2-dinitroethene (FOX-7) attracts great interests, while the studies on bimolecular reactions during the decomposition of FOX-7 are scarce. This study for the first time investigated the bimolecular reactions of OH and NO₂ radicals, which are pyrolysis products of ammonium perchlorate (an efficient oxidant usually used in solid propellant), with FOX-7 by computational chemistry methods. The molecular geometries and energies were calculated using the (U)B3LYP/6-31++G(d,p) method. The rate constants of the reactions were calculated by canonical variational transition state theory. We found three mechanisms (H-abstraction, OH addition to C and N atom) for the reaction of OH + FOX-7 and two mechanisms (O abstraction and H abstraction) for the reaction of NO₂ + FOX-7. OH radical can abstract H atom or add to C atom of FOX-7 with barriers near to zero, which means OH radical can effectively degrade FOX-7. The O abstraction channel of the reaction of NO₂ + FOX-7 results in the formation of NO₃ radical, which has never been detected experimentally during the decomposition of FOX-7.     

Reaction of OH radical and ozone with methyl salicylate – a DFT study

A theoretical study on the reaction mechanism of methyl salicylate (MeSA), a green leaf volatile organic compound with OH radical and ozone, has been carried out using density functional theory methods using B3LYP, M06‐2X and MPW1K functionals with 6‐311++G(d,p) basis set. The atmospheric degradation pathways of MeSA with OH radical are studied under two different pathways, viz. H‐atom abstraction and electrophilic addition of OH radical. The hydrogen abstraction from –OH group is found to be the dominant reaction channel with small barrier height. Likewise, the electrophilic addition of OH radicals at the para position of MeSA is found to be favourable rather than the ortho and meta positions because of the small barrier height. However, the reaction of MeSA with respect to the addition of O₃ is initiated only through the cycloaddition to the C?C bond, resulting in primary ozonide. The Arrhenius plot for most of the addition reaction shows positive temperature dependence, while for the abstraction reaction, it exhibits negative temperature dependence over the temperature range of 278–350 K. The calculated theoretical rate constants are in good agreement with available experimental data. Overall, the addition of both OH radical and ozone possesses ability to degrade MeSA, but slower when compared with the Cl radical. Copyright © 2015 John Wiley & Sons, Ltd.     

(R)-1,3丁二醇的手性不对称性：微分键极化率的研究

本文从(R)-(-)-1,3-丁二醇 ((R)-(-)-1,3-Butanediol) 的拉曼峰强和拉曼旋光峰强, 求得其键极化率和微分键极化率, 得出在拉曼过程中, 电荷主要沿H16 (或H15) O6C3C2C1O5所形成的 (六边) 环向外围的OH键和CH 键流动. 而此环内外化学键的微分键极化率的符号正好相反, 此意味着这个分子具有相当好的手性不对称性质. 关键词： 旋光拉曼 键极化率 微分键极化率 1,3-丁二醇     

A theoretical study on the ESPT mechanism for a novel Bis‐HPBT fluorophore

In this work, based on the density functional theory and time‐dependent density functional theory methods, the properties of the 2 intramolecular hydrogen bonds (O1‐H2···N3 and O4‐H5···N6) of a new photochemical sensor 4‐(3‐(benzo[d]thiazol‐2‐yl)‐5‐tert‐butyl‐4‐hydroxybenzyl)‐2‐(benzo[d]thiazol‐2‐yl)‐6‐tert‐butyl phenol (Bis‐HPBT) have been investigated in detail. The calculated dominating bond lengths and bond angles about these 2 hydrogen bonds (O1‐H2···N3 and O4‐H5···N6) demonstrate that the intramolecular hydrogen bonds should be strengthened in the S₁ state. In addition, the variations of hydrogen bonds of Bis‐HPBT have been also testified based on infrared vibrational spectra. Our theoretical results reproduced absorption and emission spectra of the experiment, which verifies that the theoretical level we used is reasonable and effective in this work. Further, hydrogen bonding strengthening manifests the tendency of excited state intramolecular proton transfer (ESIPT) process. Frontier molecular orbitals depict the nature of electronically excited state and support the ESIPT reaction. According to the calculated results of potential energy curves along stepwise and synergetic O1‐H2 and O4‐H5 coordinates, the potential energy barrier of approximately 1.399 kcal/mol is discovered in the S₁ state, which supports the single ESIPT process along with 1 hydrogen bond of Bis‐HPBT. In other words, the proton transfer reaction can be facilitated based on the electronic excitation effectively. In turn, through the process of radiative transition, the proton‐transfer Bis‐HPBT‐SPT form regresses to the ground state with the fluorescence of 539 nm.     

H2O分子OH键振动能谱的代数计算

用U(2)代数模型,对H2O分子OH键的高激发振动能谱进行了理论计算,并与其它模型的计算相比较,结果表明,代数模型能以较小的标准偏差描述这一分子OH键的振动能谱。     

Evidence of the weakness of the OH⋯F hydrogen bond from a conformational study of 3-fluoro-1-propanol by microwave spectroscopy

The rotational spectra of the OH and OD isotopic species have been observed for three rotamers of 3-fluoro-1-propanol. One of them (HBC form) displays an internal hydrogen bond with a distorted chair conformation of the six-membered ring. The other two rotamers have the oxygen atom gauche with respect to the C₂C₃ bond, the hydroxyl hydrogen trans with respect to the C₁C₂ bond and the fluorine atom gauche (GGT form) and trans (TGT form), respectively, with respect to the C₂C₁ bond. The energies of the vibrational ground states of the HBC and TGT forms are ～0.4 and 1.0 kcal/mole higher than that of the GGT form, respectively (from relative intensity measurements). The hydrogen bond is therefore rather weak in this compound. With compounds capable of forming OH?O or OH?N bonds, the conformation appropriate for hydrogen bonding is normally the most stable form. Several excited states have been analyzed for the TGT and GGT rotamers in order to have additional data with respect to the potential function for the internal rotation about the C₃C₂ bond.     

Aromatic C-H bond activation revealed by infrared multiphoton dissociation spectroscopy

Metal-oxide cations are models of catalyst mediating the C-H bond activation of organic substrates. One of the most powerful reagents suggested in the gas phase is based on CuO(+) . Here, we describe the activation of the aromatic C-H bonds of phenanthroline in its complex with CuO(+) . The reaction sequence starts with a hydrogen atom abstraction by the oxygen atom from the 2-position of the phenanthroline ring, followed by OH migration to the ring. Using infrared multiphoton spectroscopy, it is shown that the reaction can be energetically facilitated by additional coordination of a water ligand to the copper ion. As the reaction is intramolecular, a spectroscopic characterization of the product is mandatory in order to unambiguously address the reaction mechanism.     

Inducing H/D exchange in ultrathin ice films by proton deficiency

We show that H/D exchange between H(2)O and D(2)O in ultrathin ice films adsorbed on Cu(100) does not occur through autoionization at temperatures below 140 K. The exchange is, however, facile if a proton deficiency is induced in the ice films by having small amounts of OH preadsorbed on the copper surface. The system was studied using surface infrared vibrational spectroscopy with the aid of density functional theory calculations.     

Solid state water motions revealed by deuterium relaxation in 2H2O-synthesized kanemite and 2H2O-hydrated Na+-zeolite A

Deuterium NMR relaxation experiments, low temperature deuterium NMR lineshape analysis, and FTIR spectra are consistent with a new model for solid state jump dynamics of water in (2)H(2)O-synthesized kanemite and (2)H(2)O-hydrated Na(+)-Zeolite A. Exchange occurs between two populations of water: one in which water molecules are directly coordinated to sodium ions and experience C(2) symmetry jumps of their OH bonds, and a population of interstitial water molecules outside the sodium ion coordination sphere that experience tetrahedral jumps of their OH bonds. For both samples the C(2) jump rate is much faster than the tetrahedral jump rate. (2)H NMR relaxation experiments match well with the fast exchange regime of the model over a wide range of temperatures, including room temperature and above. For hydrated Zeolite A, the kinetic activation parameters for the tetrahedral and C(2) symmetry jumps are Delta H tet++=+17 kJ/mol, Delta S tet++=-109 J/(mol K), Delta H C2++=+19 kJ/mol, and Delta S C2++=-20 J/(mol K). For kanemite, Delta H tet++ =+23 kJ/mol, Delta S tet++=-69 J/(mol K), Delta H C2++ =+23 kJ/mol, and Delta S C2++ =-11 J/(mol K).     

第一性原理研究H_2O分子在CaCO_3(104)表面吸附

基于密度泛函理论的第一性原理方法模拟研究H_2O在CaCO_3(104)表面的吸附特征.首先,研究H_2O分子在CaCO_3(104)表面的顶位、桥位(短桥位、长桥位)和穴位上垂直和平行表面两种类型下的8种高对称吸附结构模型,结合吸附能和稳定吸附构象确定最优吸附位.而后,基于H_2O/CaCO_3(104)最优吸附结构模型,研究吸附前后H_2O和CaCO_3(104)表面的物理结构、电子结构(Mulliken电荷布居数、态密度、电子局域函数)的特征,分析H_2O/CaCO_3(104)表面之间的相互作用以及成键机理.研究结果:吸附能和体系稳定构象显示H_2O分子/CaCO_3(104)表面的最稳定吸附结构为穴位-平行.在穴位-平行位吸附后,H_2O分子的O-H键长和H-O-H键角均发生改变; CaCO_3晶体平行和垂直(104)表面方向上原子位置均发生改变,表面层变化最大;即吸附作用对H_2O分子和CaCO_3晶体的物理结构均产生较大影响; H_2O/CaCO3(104)最优吸附体系的Mulliken电荷布居数、电子态密度、电子局域函数的研究均说明H_2O分子与CaCO3(104)之间存在电子的转移形成化学键.其中,Ca-O(H_2O)形成离子键,H(H_2O)-O(CaCO_3)之间存在氢键作用.本文研究揭示了方解石表面水湿性的原因,同时为方解石润湿性的深入研究奠定基础.     

Determination of membrane Peptide orientation by 1H-detected 2H NMR spectroscopy

We demonstrate the application of the proton inverse detected deuteron (PRIDE) NMR technique to the measurement of the orientation of membrane-bound peptides with enhanced sensitivity. Gramicidin D, a transmembrane peptide, and ovispirin, a surface-bound peptide, were used as model systems. The peptides were 2H-labeled by 1H/2H exchange and oriented uniaxially on glass plates. The directly detected 2H spectra of both peptides showed only a strong D(2)O signal and no large quadrupolar splittings. In contrast, the PRIDE spectrum of gramicidin exhibited quadrupolar splittings as large as 281 kHz, consistent with its transmembrane orientation. Moreover, the large D(2)O signal in the directly detected 2H spectra was cleanly suppressed in the PRIDE spectrum. For ovispirin, the 1H indirectly detected 2H spectrum revealed a 104 kHz splitting and a zero-frequency peak. The former reflects the in-plane orientation of most of the helix axis, while the latter results from residues with a magic-angle orientation of the N-D bonds. These are consistent with previous 15N NMR results on ovispirin. The combination of PRIDE and exchange labeling provides an economical and sensitive method of studying membrane peptide orientations in lipid bilayers without the influence of D(2)O and with the ability to detect N-D bonds at the magic angle from the bilayer normal.     

A comparative study of the immunogold labeling on H(2)O(2)-treated and heated epoxy sections.

The purpose of this study was to compare the intensity of the immunogold labeling of H(2)O(2)-treated and heated epoxy sections. Renal swine tissue with glomerular immune complex deposits with reactivity against IgG was embedded in epoxy resin. Immunogold labeling with anti-IgG was performed on sections from these blocks. Some of these sections were treated by H(2)O(2), others were heated in a citrate solution, while some were not treated at all. Some epoxy sections, which had been exposed to both H(2)O(2) and heat, were also exposed to the same immunolabeling. The heated epoxy sections obtained an yield of specific immunogold labeling, which was twice as large as the labeling of the H(2)O(2)-treated sections. The yield of immunolabeling of the sections that had been exposed to both H(2)O(2) and heat was not significantly different from the sections that were only exposed to heat. The non-treated sections were very weakly labeled with anti-IgG. We believe that both H(2)O(2) and heat have the ability to break some chemical bonds between the epoxy resin and the antigens, but heating in citrate buffer has a larger potential in this respect than H(2)O(2). We interpret the results from the combined treatment with H(2)O(2) and heat in the following way; the bonds that are broken by H(2)O(2) will also be broken by heating in citrate solution. The practical significance of these results is that heating in citrate buffer is a more convenient method for enhancing the immunolabeling of epoxy sections than treatment with H(2)O(2).     

Pulse radiolysis studies of 2‐ and 3‐hydroxybenzyl alcohols: inhibition of dehydration of ·OH‐(hydroxybenzyl alcohols) adducts by H2PO4− ions

Reactions of ·OH/O ^.? radicals and H‐atoms as well as specific oxidants such as Cl₂^.? and N₃· radicals have been studied with 2‐ and 3‐hydroxybenzyl alcohols (2‐ and 3‐HBA) at various pH using pulse radiolysis technique. At pH 6.8, ·OH radicals were found to react quite fast with both the HBAs (k = 7.8 × 10⁹ dm³ mol^?1 s^?1 with 2‐HBA and 2 × 10⁹ dm³ mol^?1 s^?1 with 3‐HBA) mainly by adduct formation and to a minor extent by H‐abstraction from ? CH₂OH groups. ·OH‐(HBA) adduct were found to undergo decay to give phenoxyl type radicals in a pH dependent way and it was also very much dependent on buffer‐ion concentrations. It was seen that ·OH‐(2‐HBA) and ·OH‐(3‐HBA) adducts react with HPO₄^2? ions (k = 2.1 × 10⁷ and 2.8 × 10⁷ dm³ mol^?1 s^?1 at pH 6.8, respectively) giving the phenoxyl type radicals of HBAs. At the same time, this reaction is very much hindered in the presence of H₂PO ions indicating the role of phosphate ion concentration in determining the reaction pathway of ·OH adduct decay to final stable product. In the acidic region adducts were found to react with H⁺ ions. At pH 1, reaction of ·OH radicals with HBAs gave exclusively phenoxyl type radicals. Proportion of the reducing radicals formed by H‐abstraction pathway in ·OH/O ^.? reactions with HBAs was determined following electron transfer to methyl viologen. H‐atom abstraction is the major pathway in O ^.? reaction with HBAs compared to ·OH radical reaction. H‐atom reaction with 2‐ and 3‐HBA gave transient species which were found to transfer electron to methyl viologen quantitatively. Copyright © 2010 John Wiley & Sons, Ltd.     

The reactivity of the 5‐formylcytosine with hydroxyl radical: A theoretical perspective

Hydroxyl radical (?OH) damages DNA/RNA by attacking pyrimidine nucleobases through the addition reaction and H‐atom abstraction. It may attack on the new cytosine derivative (5‐formylCytosine [5‐fCyt]) causing DNA oxidative damage, whereas the study of the related mechanism is still in its infancy. In the present work, 2 distinct mechanisms of ?OH‐mediated 5‐fCyt at the complete basis set methods (CBS‐QB3) and CBS‐QB3/polarized continuum model approaches have firstly been explored, the addition reaction (paths R1 ~ R3) and the abstraction reaction (paths R4 ~ R6), respectively, and it shows that the addition of ?OH to the C5═C6 double bond of 5‐fCyt is more favourable than other reactions, indicating that the ?OH addition to the C5 and C6 atoms have relatively high probability to happen. The proportion of the C5 and C6 adducts is large and may be detectable experimentally, which is in agreement with the conclusions of ?OH‐mediated cytosine reaction reported experimentally and theoretically. These hint that the new DNA base (5‐fCyt) is easily damaged when exposed the surrounding of ?OH environment. Therefore, the reducing free radical production or the addition of some antioxidants should be taken in embryonic stem cells to resistance DNA damage. Our results provide some evidences between 5‐fCyt and tumor development for the experimental scientists.     

Atmospheric chemistry of HFE-7000 (i-C3F7OCH3) and isofluoro-propyl formate (i-C3F7OC(O)H): reactions with OH radicals,atmospheric lifetime and fate of alkoxy radical (i-C3F7OCH2O•) – a DFT study

ABSTRACT

The mechanism of hydrogen abstraction reaction between HFE-7000 (i-C₃F₇OCH₃) and OH radicals using M06-2X functional in conjunction with 6-31+G(d,p) basis set is investigated. The pre-reactive and post-reactive complexes from intrinsic reaction coordinate calculations are validated at entrance and exit channels, respectively. The standard enthalpies of formation for the species and bond dissociation energy for C–H bond are also estimated. The rate constants of the titled reactions over the temperature range of 250–450 K are reported. The OH-driven atmospheric life time of i-HFE-7000 is computed to be 3.19 years. The atmospheric fate of the alkoxy radical (i-C₃F₇OCH₂O^?) is also explored here for the first time. Three prominent plausible decomposition channels including oxidation are considered in detail. The thermochemical data reveal that reaction with O₂ is the dominant path for the decomposition of i-C₃F₇OCH₂O^? radical. Moreover, rate constant for the OH-initiated hydrogen abstraction of isofluoro-propyl formate (i-C₃F₇OC(O)H) is also reported.     

Theoretical studies on the adsorption and decomposition of H2O on Pd(1 1 1) surface

To provide information about the chemistry of water on Pd surfaces, we performed density functional slab model studies on water adsorption and decomposition at Pd(1 1 1) surface. We located transition states of a series of elementary steps and calculated activation energies and rate constants with and without quantum tunneling effect included. Water was found to weakly bind to the Pd surface. Co-adsorbed species OH and O that are derivable from H₂O stabilize the adsorbed water molecules via formation of hydrogen bonds. On the clean surface, the favorable sites are top and bridge for H₂O and OH, respectively. Calculated kinetic parameters indicate that dehydrogenation of water is unlikely on the clean regular Pd(1 1 1) surface. The barrier for the hydrogen abstraction of H₂O at the OH covered surface is approximately 0.2-0.3 eV higher than the value at the clean surface. Similar trend is computed for the hydroxyl group dissociation at H₂O or O covered surfaces. In contrast, the O-H bond breaking of water on oxygen covered Pd surfaces, H₂O_ad + O_ad → 2OH_ad, is predicted to be likely with a barrier of ∼0.3 eV. The reverse reaction, 2OH_ad → H₂O_ad + O_ad, is also found to be very feasible with a barrier of ∼0.1 eV. These results show that on oxygen-covered surfaces production of hydroxyl species is highly likely, supporting previous experimental findings.