Collision energy dependence of the O(1D) + HCl --> OH + Cl(2P) reaction studied by crossed beam scattering and quasiclassical trajectory calculations on ab initio potential energy surfaces

The dynamics of the O(1D) + HCl --> OH + Cl(2P) reaction are investigated by a crossed molecular beam ion-imaging method and quasiclassical trajectory calculations on the three ab initio potential energy surfaces, the ground 1(1)A' and two excited (1(1)A' and 2(1)A') states. The scattering experiment was carried out at collision energies of 4.2, 4.5, and 6.4 kcal/mol. The observed doubly differential cross sections (DCSs) for the Cl(2P) product exhibit almost no collision energy dependence over this inspected energy range. The nearly forward-backward symmetric DCS indicates that the reaction proceeds predominantly on the ground-state potential energy surface at these energies. Variation of the forward-backward asymmetry with collision energy is interpreted using an osculating complex model. Although the potential energy surfaces obtained by CASSCF-MRCI ab initio calculations exhibit relatively low potential barriers of 1.6 and 6.5 kcal/mol for 1(1)A' and 2(1)A', respectively, the dynamics calculations indicate that contributions of these excited states are small at the collision energies lower than 15.0 kcal/mol. Theoretical DCSs calculated for the ground-state reaction pathway agree well with the observed ones. These experimental and theoretical results suggest that the titled reaction at collision energies less than 6.5 kcal/mol is predominantly via the ground electronic state.     

3s Rydberg and cationic States of pyrazine studied by photoelectron spectroscopy

We have studied 3s(n-1 and pi-1) Rydberg states and D0(n-1) and D1(pi-1) cationic states of pyrazine [1,4-diazabenzene] by picosecond (2 + 1) resonance-enhanced multiphoton ionization (REMPI), (2 + 1) REMPI photoelectron imaging, He(I) ultraviolet photoelectron spectroscopy (UPS), and vacuum ultraviolet pulsed field ionization photoelectron spectroscopy (VUV-PFI-PE). The new He(I) photoelectron spectrum of pyrazine in a supersonic jet revealed a considerably finer vibrational structure than a previous photoelectron spectrum of pyrazine vapor. We performed Franck-Condon analysis on the observed photoelectron and REMPI spectra in combination with ab initio density functional theory and molecular orbital calculations to determine the equilibrium geometries in the D0 and 3s(n-1) states. The equilibrium geometries were found to differ slightly between the D0 and 3s states, indicating the influence of a Rydberg electron on the molecular structure. The locations of the D1-D0 and 3s(pi-1)-3s(n-1) conical intersections were estimated. From the line width in the D1 <-- S0 spectrum, we estimated the lifetime of D1 to be 12 fs for pyrazine and 15 fs for fully deuterated pyrazine. A similar lifetime was estimated for the 3s(pi-1) state of pyrazine by REMPI spectroscopy. The vibrational feature of D1 observed in the VUV-PFI-PE measurement differed dramatically from that in the UPS spectrum, which suggests that the high-n Rydberg (ZEKE) states converging to the D1 vibronic state are short-lived due to electronic autoionization to the D0 continuum.     

Surface-modified carbon black for As(V) removal

This paper reports the results of the adsorption performance of As(V) removal by a commercial carbon black and its H2SO4-modified form in a single-ion situation. The influence of different process parameters and the physicochemical principles involved were studied in detail. Acid modification caused morphological changes in the virgin carbon black as evidenced by BET surface area measurements and SEM study. FTIR spectra showed the introduction of sulfonic acid group in the parent carbon due to H2SO4 treatment. TGA analysis revealed higher weight loss characteristics of the modified carbon, demonstrating the creation of functional groups. The point of zero charge (pH pzc) of the modified carbon black is highly acidic (3.5) compared to commercial carbon black (6.4). It directly infers the generation of acidic functional moieties in the carbon black. The adsorption experiments were carried out following batch equilibrium techniques. The kinetics and thermodynamics of adsorption were investigated to unveil the mechanism and nature of the adsorption process, respectively. The kinetic parameters of different models were calculated and discussed. The kinetics of adsorption can be expressed by a pseudo-second-order model and intraparticle diffusion was not the rate-determining step. Dependence of pH on adsorption showed maximum metal uptake in the range of 4-5 and inferred surface complexion as the principal mechanism of adsorption. The equilibrium adsorption data were modeled using Freundlich, Langmuir, and Dubinin-Kaganer-Radushkevich (DKR) isotherm equations and the corresponding isotherm parameters were calculated and discussed in detail.     

Heme Pocket Architecture in Human Serum Albumin: Regulation of O2 Binding Affinity of a Prosthetic Heme Group by Site-Directed Mutagenesis

Summary : We present the O₂ binding properties of recombinant human serum albumin (rHSA) mutants complexed with an iron(II) protoporphyrin IX as a prosthetic heme group. Iron(III) protoporphyrin IX (hemin) is bound within subdomain IB of HSA with weak axial coordination by Tyr-161. In order to confer O₂ binding capability to this naturally occurring hemoprotein: (i) a proximal histidine was introduced into position Ile-142; and (ii) the coordinated Tyr-161 was replaced with hydrophobic Leu using site-directed mutagenesis. It provided a recombinant HSA double-mutant [rHSA(I142H/Y161L) = rHSA(HL)]. The rHSA(HL)–heme formed a ferrous five-coordinate high-spin complex with axial ligation of His-142 under an Ar atmosphere. This artificial hemoprotein binds O₂ at room temperature. Laser flash photolysis experiments demonstrated that O₂ rebinidng to rHSA(HL)–heme displays monophasic kinetics, whereas the CO recombination process obeyed a double-exponential pattern. This might be attributable to the two different geometries of the axial imidazole coordination arising from the two orientations of the porphyrin plane in the heme pocket. The O₂ binding affinity of rHSA(HL)–heme was considerably lower than those of R-state hemoglobin (Hb) and myoglobin (Mb), principally because of the high O₂ dissociation rate constant. The third mutations have been introduced into the distal side of the heme (at position Leu-185 or Arg-186) to increase the O₂ binidng affinity. The rHSA(HL/L185N)–heme showed high O₂ binding affinity ( : 1 Torr), which is 18-fold greater than that of the original double mutant rHSA(HL)–heme and which is rather close to those of Hb (R-state) and Mb. Furthermore, replacement of polar Arg-186 with Leu or Phe adjusted the O₂ binding affinity ( ) to 10 Torr, which is almost equivalent to value for human red blood cells.     

Intensive optimization and evaluation of global DNA methylation quantification using LC-MS/MS

Analytical and Bioanalytical Chemistry - DNA methylation is a typical epigenetic phenomenon. Numerous methods for detecting global DNA methylation levels have been developed, among which LC-MS/MS...     

A coarse-grained model of the effective interaction for charged amino acid residues and its application to formation of GCN4-pLI tetramer

ABSTRACT

We present a simple coarse-grained model of the effective interaction for charged amino acid residues, such as Glu and Lys, in a water solvent. The free-energy profile as a function of the distance between two charged amino acid side-chain analogues in an explicit water solvent is calculated with all-atom molecular dynamics simulation and thermodynamic integration method. The calculated free-energy profile is applied to the coarse-grained potential of the effective interaction between two amino acid residues. The Langevin dynamics simulations with our coarse-grained potential are performed for association of a small protein complex, GCN4-pLI tetramer. The tetramer conformation reproduced by our coarse-grained model is similar to the X-ray crystallographic structure. We show that the effective interaction between charged amino acid residues stabilises association and orientation of protein complex. We also investigate the association pathways of GCN4-pLI tetramer.     

3‐Chloro­propion­amide

The crystal structure of 3‐chloro­propion­amide, C₃H₆ClNO, (I), was determined in order to obtain coordinates for molecular‐orbital calculations. Intermolecular N—H?O and C—H?O hydrogen bonds link the mol­ecules into continuous two‐dimensional sheets parallel to the (100) plane. The bond distances are C—Cl 1.793 (3), C=O 1.233 (3) and C—N 1.320 (3) Å.     

FT-EPR study of the pH dependence of the photochemistry of sesamol in aqueous solution

A Fourier transform electron paramagnetic resonance (FT-EPR) study was made of the photochemistry of 3,4-methylenedioxyphenol (sesamol, SEOH)) in aqueous solution. FT-EPR measurements show that in alkaline (pH 11) solution, pulsed-laser excitation of SECT leads to photoionization giving the hydrated electron and SEO^⋅ free radical. Resonance signals from these paramagnetic species develop with instrument-controlled rise time. They exhibit a low-field emission/ high-field absorption (E/A) CIDEP pattern with the transition from emission to absorption occurring at the resonance of the hydrated electron. It is shown that the spin polarization stems from contributions from the ST₀ radical pair mechanism (E/A) and triplet mechanism (A). From this it is concluded that photoionization of sesamol occurs via the triplet excited state. In neutral and acidic (pH 4–7) aqueous solution, photoexcitation generates SEO^⋅ and cyclohexadienyl-type radicals. In this case, radicals grow in over a period of 1–2 μs and FT-EPR spectra display an E/A pattern with the inversion point in the center. The lowering of the pH of the solution apparently is accompanied by a strong reduction in the relative importance of photoionization. From the FT-EPR data it can be deduced that in neutral and acidic solutions the dominant reaction channel is H-atom transfer. In this respect, the photochemistry of sesamol differs from that of phenol andp-cresol. For these phenols the change in pH does not affect the appearance of the FT-EPR spectra. Apparently, the change in electronic structure caused by the methylenedioxy substituent strongly affects the excited state reactivity of sesamol.