O2 Atoms Research Articles

Mechanism of 17α,20-Lyase and New Hydroxylation Reactions of Human Cytochrome P450 17A1: 18O LABELING AND OXYGEN SURROGATE EVIDENCE FOR A ROLE OF A PERFERRYL OXYGEN

Cytochrome P450 (P450) reactions can involve C-C bond cleavage, and several of these are critical in steroid and sterol biosynthesis. The mechanisms of P450s 11A1, 17A1, 19A1, and 51A1 have been controversial, in the context of the role of ferric peroxide (FeO2 (-)) versus perferryl (FeO(3+), compound I) chemistry. We reinvestigated the 17α-hydroxyprogesterone and 17α-hydroxypregnenolone 17α,20-lyase reactions of human P450 17A1 and found incorporation of one (18)O atom (from (18)O2) into acetic acid, consonant with proposals for a ferric peroxide mechanism (Akhtar, M., Lee-Robichaud, P., Akhtar, M. E., and Wright, J. N. (1997) J. Steroid Biochem. Mol. Biol. 61, 127-132; Akhtar, M., Wright, J. N., and Lee-Robichaud, P. (2011) J. Steroid Biochem. Mol. Biol. 125, 2-12). However, the reactions were supported by iodosylbenzene (a precursor of the FeO(3+) species) but not by H2O2 We propose three mechanisms that can involve the FeO(3+) entity and that explain the (18)O label in the acetic acid, two involving the intermediacy of an acetyl radical and one a steroid 17,20-dioxetane. P450 17A1 was found to perform 16-hydroxylation reactions on its 17α-hydroxylated products to yield 16,17α-dihydroxypregnenolone and progesterone, suggesting the presence of an active perferryloxo active species of P450 17A1 when its lyase substrate is bound. The 6β-hydroxylation of 16α,17α-dihydroxyprogesterone and the oxidation of both 16α,17α-dihydroxyprogesterone and 16α,17α-dihydroxypregnenolone to 16-hydroxy lyase products were also observed. We provide evidence for the contribution of a compound I mechanism, although contribution of a ferric peroxide pathway in the 17α,20-lyase reaction cannot be excluded.

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The O atom exchange reaction, 16O(3P) + 18O18O(3Σg–) → 16O18O(3Σg–) + 18O(3P), was investigated at a hyperthermal center-of-mass (c.m.) collision energy (Ecoll) of 86 kcal mol–1, using a crossed-molecular-beams apparatus and quasiclassical trajectory (QCT) calculations. The inelastically scattered 16O and reactively scattered 16O18O products were detected with a rotatable mass spectrometer employing electron-impact ionization. The 16O atoms are scattered in inelastic collisions in the forward direction relative to their initial direction of flight, with most of the available energy partitioned into translation. The 16O18O products of reactive collisions are mainly formed through impulsive dynamics and are scattered in the forward as well as sideways directions relative to the direction of the reagent 16O atoms, with a slight majority of the available energy partitioned into translation (⟨ET⟩ = 58%) and a significant contribution to internal degrees of freedom. Excellent agreement was found between the exp...

Radiation enhanced diffusion processes in UO2 and (U,Pu)O2

The diffusion mechanisms and migration characteristics of point defects in the fluorite structures of UO2 and (U, Pu) O2 were analyzed. The possibility of complex migration mechanisms of anionic and cationic vacancy and interstitial Frenkel defects depending on the stoichiometry of materials was shown.The statistical analysis of published data on the radiation-enhanced diffusion (RED) characteristics of metal atoms in UO2 and (U, Pu)O2 for temperatures 1303-1673 K was carried out. An approximate temperature dependence of RED coefficient was obtained. Within the framework of understanding of the mechanisms of diffusion processes in fluorite structure, the approximate temperature dependence of the RED coefficient of oxygen for UO2 and (U, Pu)O2 was proposed.

Photophysics of the LOV-Based Fluorescent Protein Variant iLOV-Q489K Determined by Simulation and Experiment.

Light, oxygen, voltage (LOV) based fluorescent proteins (FPs) represent a promising alternative to fluorescent reporters of the green fluorescent protein family. For certain applications like multicolor imaging or the design of FRET-based biosensors, the generation of spectrally shifted LOV-based FPs would be required. In a recent theoretical study ( Khrenova J. Phys. Chem. B 2015 , 119 ( 16 ), pp 5176 - 5183 ), the photophysical properties of a variant of the LOV-based fluorescent protein iLOV were predicted using quantum mechanics/molecular mechanics (QM/MM) approaches. The variant contained a lysine residue at the position of a highly conserved glutamine residue (Q489K), which directly interacts with the O4 and N5 atom of the flavin mononucleotide (FMN) chromophore. On the basis of QM/MM calculations, iLOV-Q489K was suggested to possess substantially red-shifted absorption and fluorescence-emission maxima with respect to parental iLOV. Here, we describe the experimental characterization of this variant, which, surprisingly contrary to the theoretical prediction, shows blue-shifted absorption and fluorescence-emission maxima. Using molecular dynamics (MD) simulations and QM/MM calculations, the molecular basis for the contradictory theoretical and experimental results is presented. Essentially, our computational analysis suggests that, in the Q489K variant, two possible side-chain conformers exist: (i) a least populated conformer K489in forming a hydrogen bond with the O4 atom of FMN chromophore and (ii) a most populated conformer K489out with the side-chain amino group flipped away from the FMN chromophore forming a new hydrogen bond with the backbone oxygen of G487. QM/MM calculated spectra of the K489out conformer are blue-shifted compared to the calculated spectra of parental iLOV, which is in accordance with experimental data. This suggests that the change in the conformation of K489 from K498in to K489out accounts for the change in the direction of the spectral shift from red to blue, thus reconciling theory and experiment.

Synthesis, Structures and Luminescence Properties of Metal-Organic Frameworks Based on Lithium-Lanthanide and Terephthalate.

Metal-organic frameworks assembled from Ln(III), Li(I) and rigid dicarboxylate ligand, formulated as [LiLn(BDC)2(H2O)·2(H2O)] (MS1-6,7a) and [LiTb(BDC)2] (MS7b) (Ln = Tb, Dy, Ho, Er, Yb, Y0.96Eu0.04, Y0.93Tb0.07, and H2BDC = terephthalic acid), were obtained under hydrothermal conditions. The isostructural MS1-6 crystallize in monoclinic P21/c space group. While, in the case of Tb3+ a mixture of at least two phases was obtained, the former one (MS7a) and a new monoclinic C2/c phase (MS7b). All compounds have been studied by single-crystal and powder X-ray diffraction, thermal analyses (TGA), vibrational spectroscopy (FTIR), and scanning electron microscopy (SEM-EDX). The structures of MS1-6 and MS7a are built up of inorganic-organic hybrid chains. These chains constructed from unusual four-membered rings, are formed by edge- and vertex-shared {LnO8} and {LiO4} polyhedra through oxygen atoms O3 (vertex) and O6-O7 (edge). Each chain is cross-linked to six neighboring chains through six terephthalate bridges. While, the structure of MS7b is constructed from double inorganic chains, and each chain is, in turn, related symmetrically to the adjacent one through the c glide plane. These chains are formed by infinitely alternating {LiO4} and {TbO8} polyhedra through (O2-O3) edges to create Tb–O–Li connectivity along the c-axis. Both MS1-6,7a and MS7b structures possess a 3D framework with 1D trigonal channels running along the a and c axes, containing water molecules and anhydrous, respectively. Topological studies revealed that MS1-6 and MS7a have a new 2-nodal 3,10-c net, while MS7b generates a 3D net with unusual β-Sn topology. The photoluminescence properties Eu- and Tb-doped compounds (MS5-6) are also investigated, exhibiting strong red and green light emissions, respectively, which are attributed to the efficient energy transfer process from the BDC ligand to Eu3+ and Tb3+.

Density functional theory study of α-Bromolauric acid adsorption on the α-quartz (1 0 1) surface

Adsorption mechanism of collector α-Bromolauric acid (CH3(CH2)9CHBrCOOH, α-BLA) on α-quartz (101) surface has been investigated by first-principles calculations based on density functional theory (DFT). The interaction energies of H2O molecule, calcium ions (Ca2+), hydroxyl ions (OH−), calcium hydroxyl ions (Ca(OH)+), and α-BLA− ions with α-quartz (101) surface were in the order of Ca(OH)+<Ca2+<OH−<H2O<α-BLA−. The results revealed that the collector α-BLA cannot adsorb on α-quartz (101) surface due to the hindrance of hydration shell of quartz surface, while Ca(OH)+ could repulse the hydration shell and consequently adsorb on quartz surface, which further leads to the adsorption of the collector α-BLA− anions on Ca(OH)+-activated quartz surface. Mulliken populations analysis of the external oxygen atom (O2) of quartz surface, calcium atom (Ca) of Ca(OH)+, and oxygen atom (O1) of collector α-BLA− (–OH group) shows that the electron transfer between the Ca–O1 and Ca–O2 atoms. The overlap area of electron density between Ca–O1 and Ca–O2 atoms indicates strong interactions among the three atoms of Ca, O1, and O2, suggesting that Ca(OH)+ ions act as a bridge between the α-quartz (101) surface and the α-BLA collector.

Powder X-ray diffraction of Metastudtite, (UO2)O2(H2O)2

There has been some confusion in the published literature concerning the structure of Metastudtite (UO2)O2(H2O)2 where differing unit cells and space groups have been cited for this compound. Owing to the absence of a refined structure for Metastudtite, Weck et al. (2012) have documented a first-principles study of Metastudtite using density functional theory (DFT). Their model presents the structure of Metastudtite as an orthorhombic (space group Pnma) structure with lattice parameters of a = 8.45, b = 8.72, and c = 6.75 Å. A Powder Diffraction File (PDF) database entry has been allocated for this hypothetical Metastudtite phase based on the DFT modeling (see 01-081-9033) and aforementioned Dalton Trans. manuscript. We have obtained phase pure powder X-ray diffraction data for Metastudtite and have confirmed the model of Weck et al. via Rietveld refinement (see Figure 1). Structural refinement of this powder diffraction dataset has yielded updated refined parameters. The new cell has been determined as a = 8.411(1), b = 8.744(1), and c = 6.505(1) Å; cell volume = 478.39 Å3. There are only subtle differences between the refined structure and that of the first-principles model derived from DFT. Notably, the b-axis is significantly contracted in the final refinement as compared with DFT. There were also subtle changes to the U1, O1, and O3 atom positions. Tabulated powder diffraction data (d's and I's) for the Metastudtite have been derived from the refined model and these new values can serve to augment the PDF entry 01-081-9033 with a more updated entry based on observed X-ray powder diffraction data.

Ca(2+) -Induced Oxygen Generation by FeO4(2-) at pH 9-10.

Although FeO4(2-) (ferrate(IV)) is a very strong oxidant that readily oxidizes water in acidic medium, at pH 9-10 it is relatively stable (<2 % decomposition after 1 h at 298 K). However, FeO4(2-) is readily activated by Ca(2+) at pH 9-10 to generate O2. The reaction has the following rate law: d[O2]/dt=kCa [Ca(2+) ][FeO4(2-)](2). (18)O-labeling experiments show that both O atoms in O2 come from FeO4(2-). These results together with DFT calculations suggest that the function of Ca(2+) is to facilitate O-O coupling between two FeO4 (2-) ions by bridging them together. Similar activating effects are also observed with Mg(2+) and Sr(2+).

Ca2+‐Induced Oxygen Generation by FeO42− at pH 9–10

AbstractAlthough FeO42− (ferrate(IV)) is a very strong oxidant that readily oxidizes water in acidic medium, at pH 9–10 it is relatively stable (&lt;2 % decomposition after 1 h at 298 K). However, FeO42− is readily activated by Ca2+ at pH 9–10 to generate O2. The reaction has the following rate law: d[O2]/dt=kCa[Ca2+][FeO42−]2. 18O‐labeling experiments show that both O atoms in O2 come from FeO42−. These results together with DFT calculations suggest that the function of Ca2+ is to facilitate O–O coupling between two FeO42‐ions by bridging them together. Similar activating effects are also observed with Mg2+ and Sr2+.

Geometric and electronic structures of the synthetic Mn₄CaO₄ model compound mimicking the photosynthetic oxygen-evolving complex.

Water oxidation by photosystem II (PSII) converts light energy into chemical energy with the concomitant production of molecular oxygen, both of which are indispensable for sustaining life on Earth. This reaction is catalyzed by an oxygen-evolving complex (OEC) embedded in the huge PSII complex, and its mechanism remains elusive in spite of the extensive studies of the geometric and electronic structures. In order to elucidate the water-splitting mechanism, synthetic approaches have been extensively employed to mimic the native OEC. Very recently, a synthetic complex [Mn4CaO4(Bu(t)COO)8(py)(Bu(t)COOH)2] (1) closely mimicking the structure of the native OEC was obtained. In this study, we extensively examined the geometric, electronic and spin structures of 1 using the density functional theory method. Our results showed that the geometric structure of 1 can be accurately reproduced by theoretical calculations, and revealed many similarities in the ground valence and spin states between 1 and the native OEC. We also revealed two different valence states in the one-electron oxidized state of 1 (corresponding to the S2 state), which lie in the lower and higher ground spin states (S = 1/2 and S = 5/2), respectively. One remarkable difference between 1 and the native OEC is the presence of a non-negligible antiferromagnetic interaction between the Mn1 and Mn4 sites, which slightly influenced their ground spin structures (spin alignments). The major reason causing the difference can be attributed to the short Mn1-O5 and Mn1-Mn4 distances in 1. The introduction of the missing O4 atom and the reorientation of the Ca coordinating ligands improved the Mn1-O5 and Mn1-Mn4 distances comparable to the native OEC. These modifications will therefore be important for the synthesis of further advanced model complexes more closely mimicking the native OEC beyond 1.

Interaction of Cu(+) with cytosine and formation of i-motif-like C-M(+)-C complexes: alkali versus coinage metals.

The Watson-Crick structure of DNA is among the most well-known molecular structures of our time. However, alternative base-pairing motifs are also known to occur, often depending on base sequence, pH, or the presence of cations. Pairing of cytosine (C) bases induced by the sharing of a single proton (C-H(+)-C) may give rise to the so-called i-motif, which occurs primarily in expanded trinucleotide repeats and the telomeric region of DNA, particularly at low pH. At physiological pH, silver cations were recently found to stabilize C dimers in a C-Ag(+)-C structure analogous to the hemiprotonated C-dimer. Here we use infrared ion spectroscopy in combination with density functional theory calculations at the B3LYP/6-311G+(2df,2p) level to show that copper in the 1+ oxidation state induces an analogous formation of C-Cu(+)-C structures. In contrast to protons and these transition metal ions, alkali metal ions induce a different dimer structure, where each ligand coordinates the alkali metal ion in a bidentate fashion in which the N3 and O2 atoms of both cytosine ligands coordinate to the metal ion, sacrificing hydrogen-bonding interactions between the ligands for improved chelation of the metal cation.

Crystal and electronic structure of high temperature superconducting compound Y1−xCaxBa2Cu3Oy in the temperature interval 80–300 K

For Y1−хСахBa2Cu3Oy with varying oxygen and calcium content, the change of crystal structure at cooling from room temperature to 80 K has been investigated. The main change is associated with a shift of apical oxygen atoms. Using determined unit cell parameters as function of temperature, the coefficients of linear thermal expansion have been calculated as αX = 1/X·(dX/dT), where Х = a, b, c – unit cell dimensions. For the compound without calcium all αX values demonstrate anomalous behavior such as growing at cooling in temperature interval T1 ÷ T2 ∼ 150 ÷ 225 K. The calculation of electronic structure at temperatures above, below and within this interval shows the appearance of the electronic states density peak for Ba and O4 atoms. It is explained by the localization of charge carriers with the participation of the lattice distortion in a form of apical Cu–O bond compression. As the material Y0.9Са0.1Ba2Cu3Oy regardless of the oxygen content possess low and constant coefficient of thermal expansion along all crystallographic directions, that makes this material suitable for superconducting films and other composites.

Ab initio Studies of O2 Adsorption on (110) Nickel-Rich Pentlandite (Fe4Ni5S8) Mineral Surface

Ab initio density functional theory was used to investigate the adsorption of oxygen molecule on the nickel-rich pentlandite (110) surface, which is important for mineral extraction. The three most reactive adsorption sites: Fe-top, Ni-top, and fcc-hollow have been considered. Firstly, the non-adsorbed pentlandite surface reflects the Ni atoms relaxing inwards. Consequently, their electronic structure showed high Fe 3d-orbital contribution than the Ni 3d-orbitals at the EF (indicating that the Fe atoms are more reactive than Ni). Secondly, the O2-adsorbed surface predicted lowest adsorption energy for Fe-top (-1.902 eV), as a more spontaneous reaction is likely to occur than on fcc-hollow (-1.891 eV) and Ni-top (-0.040 eV) sites, suggesting Fe preferential oxidation. The density of states indicates that the O2 show prevalence of electrons in the πp* antibonding orbitals, and are reduced to zero states at the valence band on metal-bonded oxygen (O1). The πp* orbital is observed to reside just above the EF for Fe-top and fcc-hollow site, while on Ni-top is half-occupied for both metal-bonded oxygen (O1) and terminal oxygen (O2). Finally, the isosurface charge density difference showed electron (charge) depletion on Ni/Fe metals and accumulation on the O2 molecule. Bader analysis indicated that the oxidized Fe and Ni atoms adopt more positive charge, while O2 on Fe-top atoms possesses more negative charge than on Ni-top, resulting with O1 possessing a smaller charge than O2 atom.

Producing Glucose 6-Phosphate from Cellulosic Biomass: STRUCTURAL INSIGHTS INTO LEVOGLUCOSAN BIOCONVERSION

The most abundant carbohydrate product of cellulosic biomass pyrolysis is the anhydrosugar levoglucosan (1,6-anhydro-β-d-glucopyranose), which can be converted to glucose 6-phosphate by levoglucosan kinase (LGK). In addition to the canonical kinase phosphotransfer reaction, the conversion requires cleavage of the 1,6-anhydro ring to allow ATP-dependent phosphorylation of the sugar O6 atom. Using x-ray crystallography, we show that LGK binds two magnesium ions in the active site that are additionally coordinated with the nucleotide and water molecules to result in ideal octahedral coordination. To further verify the metal binding sites, we co-crystallized LGK in the presence of manganese instead of magnesium and solved the structure de novo using the anomalous signal from four manganese atoms in the dimeric structure. The first metal is required for catalysis, whereas our work suggests that the second is either required or significantly promotes the catalytic rate. Although the enzyme binds its sugar substrate in a similar orientation to the structurally related 1,6-anhydro-N-acetylmuramic acid kinase (AnmK), it forms markedly fewer bonding interactions with the substrate. In this orientation, the sugar is in an optimal position to couple phosphorylation with ring cleavage. We also observed a second alternate binding orientation for levoglucosan, and in these structures, ADP was found to bind with lower affinity. These combined observations provide an explanation for the high Km of LGK for levoglucosan. Greater knowledge of the factors that contribute to the catalytic efficiency of LGK can be used to improve applications of this enzyme for levoglucosan-derived biofuel production.

The photo-degradation of mesotrione, a triketone herbicide, in the presence of Cu II ions

The study focuses first on the complexation of CuII ions with mesotrione. Experimental absorption spectra combined with quantum chemical calculations highlight that CuII ions bind to the molecule in bidentate mode between O1 and O7 atoms. The calculated electronic transitions of the complex show that three of them are mostly ligand-to-ligand electron transfer while the lowest-energy one involves a ligand-to-metal charge transfer (LMCT). The second aim of this work is to explore the effect of CuII complexation on the photo-degradation of mesotrione. The kinetics and mechanisms of the reactions are proposed on the basis of the experimental results. The effect of different parameters such as the irradiation wavelength, the oxygen concentration and the pH of the mixture and also the production of reactive species such as hydroxyl radicals is investigated. The photochemical degradation of mesotrione in water arises from the triplet excited state of the molecule and results in a photo-hydrolysis process. For the complex, by exciting mainly in its LMCT absorption band, an electron transfer between copper and mesotrione probably occurs and the mechanism of mesotrione-CuII photo-degradation differs: in addition to the photo-hydrolysis route, a photo-cyclisation process takes place and the oxidation of the ligand is accompanied by the reduction of CuII ions.

Analysis of the Role of Peripheral Ligands Coordinated to Zn(II) in Enhancing the Energy Barrier in Luminescent Linear Trinuclear Zn-Dy-Zn Single-Molecule Magnets.

Three new Dy complexes have been prepared according to a complex-as-ligand strategy. Structural determinations indicate that the central Dy ion is surrounded by two LZn units (L(2-) is the di-deprotonated form of the N2 O2 compartmental N,N'-2,2-dimethylpropylenedi(3-methoxysalicylideneiminato) Schiff base. The Dy ions are nonacoordinate to eight oxygen atoms from the two L ligands and to a water molecule. The Zn ions are pentacoordinate in all cases, linked to the N2 O2 atoms from L, and the apical position of the Zn coordination sphere is occupied by a water molecule or bromide or chloride ions. These resulting complexes, formulated (LZnX)-Dy-(LZnX), are tricationic with X=H2 O and monocationic with X=Br or Cl. They behave as field-free single-molecule magnets (SMMs) with effective energy barriers (Ueff ) for the reversal of the magnetization of 96.9(6) K with τ0 =2.4×10(-7) s, 146.8(5) K with τ0 =9.2×10(-8) s, and 146.1(10) K with τ0 =9.9×10(-8) s for compounds with ZnOH2 , ZnBr, and ZnCl motifs, respectively. The Cole-Cole plots exhibit semicircular shapes with α parameters in the range of 0.19 to 0.29, which suggests multiple relaxation processes. Under a dc applied magnetic field of 1000 Oe, the quantum tunneling of magnetization (QTM) is partly or fully suppressed and the energy barriers increase to Ueff =128.6(5) K and τ0 =1.8×10(-8) s for 1, Ueff =214.7 K and τ0 =9.8×10(-9) s for 2, and Ueff =202.4 K and τ0 =1.5×10(-8) s for 3. The two pairs of largely negatively charged phenoxido oxygen atoms with short DyO bonds are positioned at opposite sides of the Dy(3+) ion, which thus creates a strong crystal field that stabilizes the axial MJ =±15/2 doublet as the ground Kramers doublet. Although the compound with the ZnOH2 motifs possesses the larger negative charges on the phenolate oxygen atoms, as confirmed by using DFT calculations, it exhibits the larger distortions of the DyO9 coordination polyhedron from ideal geometries and a smaller Ueff value. Ab initio calculations support the easy-axis anisotropy of the ground Kramers doublet and predict zero-field SMM behavior through Orbach and TA-QTM relaxations via the first excited Kramers doublet, which leads to large energy barriers. In accordance with the experimental results, ab initio calculations have also shown that, compared with water, the peripheral halide ligands coordinated to the Zn(2+) ions increase the barrier height when the distortions of the DyO9 have a negative effect. All the complexes exhibit metal-centered luminescence after excitation into the UV π-π* absorption band of ligand L(2-) at λ=335 nm, which results in the appearance of the characteristic Dy(III) ((4) F9/2 →(6) HJ/2 ; J=15/2, 13/2) emission bands in the visible region.

Novel Fluorescent Schiff Base Derivatives of 4‐Aminoantipyrine with Large Stokes Shifts and Dual Emission Properties: Crystal Structure, Molecular Interactions, Molecular Surfaces, Conformational and DFT Analyses

Two novel Schiff base analogs derived from 4‐aminoantipyrine, namely, (E)‐4‐(2‐nitrobenzylideneamino)‐1,5‐dimethyl‐2‐phenyl‐1H‐pyrazol‐3(2H)‐one (3a) and (E)‐4‐(4‐nitrobenzylideneamino)‐1,5‐dimethyl‐2‐phenyl‐1H‐pyrazol‐3(2H)‐one (3b), were synthesized using a mild and efficient method and characterized by FT‐IR, 1H NMR, mass spectrometry, and single‐crystal X‐ray diffraction studies. X‐ray analysis of a single crystal of 3a revealed an orthorhombic space group P2(1)2(1)2(1) structure, with an E‐configuration around the azomethine (C12N3) double bond. One unit cell was found to contain four molecules showing π−π and π−σ van der Waals stacking interactions. Plausible intermolecular interactions were analyzed using 3D Hirshfeld surfaces and the related 2D fingerprint plots. The optimized molecular structure, potential energy surface (PES) scan, vibrational frequencies, Mulliken charge distribution, molecular electrostatic potential (MEP) maps, frontier molecular orbitals (FMOs), and associated energies of 3a and 3b were calculated using density functional theory (DFT) calculations using the B3LYP method and the 6‐311G(d,p) basis set. PES scans showed that the conformational energy profiles of 3a and 3b were dissimilar around the torsion angles N3–C12–C13–C14/C18 and C12–N3–C3–C2/C1 due to substituent position effects on the benzylidene phenyl ring. Mulliken charge distribution analysis revealed that O1, N1, and N3 atoms of 3a and 3b could act as electron donors and coordinate with metals, while MEP analysis showed that O1, N3, and O2–O3 are the most suitable sites for electrophilic attack. Regarding drug–receptor interactions, molecular lipophilic potential (MLP) maps demonstrated that the benzylidene phenyl ring favors lipophilic contact and the pyrazolone ring hydrophilic contact. In addition, UV–vis and fluorescence spectroscopic experiments showed that both compounds have good absorbance and fluorescent properties and large Stokes shifts. Interestingly, both compounds showed dual emission in ethanol, acetone, and diethyl ether, possibly due to conformational isomerization induced by photoexcitation.

Molecular structures of (5656)macrotetracyclic 3d metal chelates formed in the M(II) ion–ethanedithioamide–formaldehyde systems according to the density functional theory method

The thermodynamic and geometric parameters of macrotetracyclic Mn(II), Fe(II), Co(II), Ni(II), Cu(II), and Zn(II) complexes with the (NNNN)-coordination of donor sites of the ligand formed upon complexation of the corresponding metal(II) hexacyanoferrates(II) with ethanedithioamide (NH2-C(=S)–C(=S)–NH2) and formaldehyde (H2C(=O)) in gelatin-immobilized matrices, as well as of the 14-membered macrocyclic ligand (chelant) forming these complexes, have been calculated by the OPBE/TZVP density functional theory (DFT) method with the use of the Gaussian 09 program package. The fiveand sixmembered chelate rings formed as a result of template “cross-link” are nonplanar. For the six-membered rings, the deviation from coplanarity is significantly more pronounced. In all complexes, the O1 and O2 oxygen atoms and both six-membered rings are located on different sides of the NNNN plane of the nitrogen donor atoms.

The catalytic mechanism and unique low pH optimum of Caldicellulosiruptor bescii family 3 pectate lyase.

The unique active site of the Caldicellulosiruptor bescii family 3 pectate lyase (PL3) enzyme has been thoroughly characterized using a series of point mutations, X-ray crystallography, pK(a) calculations and biochemical assays. The X-ray structures of seven PL3 active-site mutants, five of them in complex with intact trigalacturonic acid, were solved and characterized structurally, biochemically and computationally. The results confirmed that Lys108 is the catalytic base, but there is no clear candidate for the catalytic acid. However, the reaction mechanism can also be explained by an antiperiplanar trans-elimination reaction, in which Lys108 abstracts a proton from the C5 atom without the help of simultaneous proton donation by an acidic residue. An acidified water molecule completes the anti β-elimination reaction by protonating the O4 atom of the substrate. Both the C5 hydrogen and C4 hydroxyl groups of the substrate must be orientated in axial configurations, as for galacturonic acid, for this to be possible. The wild-type C. bescii PL3 displays a pH optimum that is lower than that of Bacillus subtilis PL1 according to activity measurements, indicating that C. bescii PL3 has acquired a lower pH optimum by utilizing lysine instead of arginine as the catalytic base, as well as by lowering the pK(a) of the catalytic base in a unique active-site environment.

Sensing mechanism of SnO2(1 1 0) surface to H2: Density functional theory calculations

Using density functional theory, we investigate the H2-sensing mechanism of SnO2(110) surfaces to understand the H2-sensing behaviors of SnO2 surfaces with different reduction degrees and their sensing mechanism at the atomic level. We found that oxygen concentration in the ambient atmosphere greatly affects the H2-sensing mechanism of SnO2 surface. At considerable high oxygen concentrations H2 interacts with oxygen species pre-adsorbed onto SnO2(110) surface, leading to electron release back to the semiconductor SnO2. When interacting with O2−, H2 gas dissociates with one H atom to form hydroxyl adsorbed onto Sn site and another H atom adsorbed onto the oxygen atom of pre-adsorbed O2−; when interacting with the O−, H2O molecule is formed in the production. At very low oxygen concentration, structural reconstruction is induced by the interaction between H2 and SnO2 sub-reduced surface with removed twofold-coordinated bridging oxygen rows, accompanying electron transfer from H2 to surface without H2O formation. The above-calculated results are consistent with the experimental observation.