Lattice defects and magnetic ordering in plutonium oxides: a hybrid density-functional-theory study of strongly correlated materials

Experimental studies of actinide oxides are challenging, and conventional electronic structure calculations fail to qualitatively reproduce the scarce data. We employ a new generation of hybrid density functionals to model a defective plutonium dioxide lattice. The procedure is first tested against stoichiometric bulk PuO2 and Pu2O3, for which predictions agree well with experiment where known. The interstitial oxygen in PuO2.25 is found to be singly charged, consistent with experimental observations and contrary to the O2- previously proposed theoretically.     

Tautomers of cytosine and their excited electronic states: a matrix isolation spectroscopic and quantum chemical study

We have measured the IR and UV spectra of cytosine in a low-temperature argon matrix. An attempt was made to determine the tautomeric ratios existing in the matrix, making use of the matrix-isolation IR spectrum and computed IR intensities of the tautomers in a least squares fitting procedure. The mole fractions are about 0.22 for oxo(-amino) form, 0.26 and 0.44 for the two rotamers, respectively, of the hydroxy(-amino) form and 0.08 for the (oxo-)imino tautomer. These ratios were then used to simulate the matrix-isolation UV spectrum as a composite of the individual spectra, the latter calculated ab initio at high levels of electron correlation theory. The agreement between simulated and experimental UV spectra seems satisfactory. This indicates that, in contrast to the solid state and solution spectra described up to now by the oxo(-amino) form alone, the reproduction of the matrix-isolation UV spectrum needs at least the hydroxy(-amino) and oxo(-amino) forms, and probably also the (oxo-)imino form.     

Self-assembly of four new extended architectures based on reduced polyoxometalate clusters and cadmium complexes

Four new [P₄Mo₆] cluster-based extended structures containing cadmium complexes, [Cd₃(4,4′-Hbpy)₂(4,4′-bpy)₂(H₂O)₈][Cd(H₂PO₄)₂(HPO₄)₄(PO₄)₂(MoO₂)₁₂(OH)₆]·7H₂O 1, (4,4′-Hbpy)₂[Cd(4,4′-bpy)₃(H₂O)₃][Cd(4,4′-bpy)(H₂O)]₂[Cd(H₂PO₄)₂(HPO₄)₄ (PO₄)₂(MoO₂)₁₂(OH)₆]·H₂O 2, [Cd₄(phen)₂(H₂O)₄][Cd(phen)(H₂O)]₂[Cd(HPO₄)₄ (HPO₄)₄(MoO₂)₁₂(OH)₆]·5H₂O 3 and [Cd₄(2,2′-bpy)₂(H₂O)₄][Cd(2,2′-bpy)(H₂O)]₂ [Cd(HPO₄)₄(HPO₄)₄(MoO₂)₁₂(OH)₆]·3H₂O 4 (4,4′-bpy=4,4′-bpyridine, phen=1,10-phenanthroline, 2,2′-bpy=2,2′-bpyridine), have been synthesized and characterized by elemental analysis, IR, TG and single crystal X-ray diffraction. The structure of compound 1 is constructed from the Cd[P₄Mo₆]₂ dimers linked by [Cd₃(4,4′-Hbpy)₂(4,4′-bpy)₂(H₂O)₈] subunits to generate a plane layer. Compound 2 consists of the positive 2D sheets that constructed from Cd[P₄Mo₆]₂ dimers linked by [Cd(4,4′-bpy)(H₂O)] complexes, then the 2D sheets are further linked up together to form a 3D supramolecular framework via extensive hydrogen-bonding interactions among the [P₄Mo₆] clusters, free 4,4′-bpy molecules, dissociated [Cd(4,4′-bpy)₃(H₂O)₃]²⁺ complexes and water molecules. Compounds 3 and 4 show new 2D layered structure, with Cd[P₄Mo₆]₂ building blocks connected by tetra-nuclear [Cd₄{(phen)₂/(2,2′-bpy)₂}(H₂O)₄] clusters and [Cd(phen/2,2′-bpy)(H₂O)] complexes. The fluorescent activities of compounds 3 and 4 are reported.     

Characterization of Enediol-Containing Tautomers of L-Xylosone

ABSTRACT

Two interconvertible enediol group-containing reductones were produced nonenzymatically from L-xylosone in citrate-phosphate buffer (pH 6.0). These compounds were oxidized by ascorbate oxidase (E.C. 1.10.3.3.) and had ability to reduce 2.6-dichloroindophenol. GLC-MS analysis of trimethylsilylated L-xylosone indicates that it exists in several tautomeric forms including the enediol group-containing reductones which are L-glycero-2-pentenopyranose and L-glycero-2-pentenofuranose. The production rates of both reductones from L-xylosone were proportional to pH within a pH range 4 to 7, and above that pH range further degradation of the reductones occurred.     

Semi-empirical study of a reduced rubredoxin analogue

Molecular orbitals were determined for an analogue of reduced rubredoxin in an iterative extended Hückel (self-consistent charge) calculation. Zero field splittings and Mössbauer spectral parameters were then computed. The results are compared with available experimental data.     

Fluorene: An extended experimental thermodynamic study

This work reports new experimental thermodynamic results on fluorene. Vapor pressures of both crystalline and liquid phases were measured using a pressure gauge (capacitance diaphragm manometer) and Knudsen effusion methods over a wide temperature range (292.20 to 412.16) K yielding accurate determination of enthalpy and entropy of sublimation and of vaporization. The enthalpy of sublimation was also determined using Calvet microcalorimetry. The enthalpy of fusion was derived from vapor pressure results and from d.s.c. experiments. Static bomb calorimetry was used to determine the enthalpy of combustion of fluorene from which the standard enthalpy of formation in the crystalline phase was calculated. The enthalpy of formation in the gaseous phase was calculated combining the result derived for the crystalline phase with the enthalpy of sublimation.     

Tautomers of 4,5-dihydroxy-1,8-bis(dimethylamino)naphthalene and related boron compounds: A quantum-chemical study

The quantum-chemical method PBE0/cc-pV(D,T)Z was applied to determine structural parameters, relative energies, and dipole moments of the prototropic tautomers of 4,5-dihydroxy-1,8-bis(dimethylamino) naphthalene. According to the calculations, this compound can exist in the gas phase as low-polar molecules with one asymmetric intramolecular hydrogen bond. In a polarizable medium a pair of zwitter-ionic tautomers dominate of similar energy with two asymmetric intramolecular hydrogen bonds. These tautomers and a hypothetic heterocyclic analog containing a BH ₂ ⁺ group instead of a proton between the nitrogen atoms are characterized by a high value of dipole moment and first hyperpolarizability. Mutual transformation of enantiomers (mirror antipodes) when transferring a proton from the hydroxy group to a neighboring atom in the O-boron-containing zwitter-ion is an example of strictly degenerate prototropic tautomerism.     

Tautomers and topomers: challenging the uncertainties of direct physicochemical modeling

To address the goal of improved discovery decision making, the uncertainties of physicochemical modeling, as exemplified by tautomer identification, are contrasted with methods focused exclusively on the sole experimental system variable, the changes in ligand structures, as exemplified by topomers.     

Bioethanol combustion based on a reduced kinetic mechanism

Bioethanol is a fuel additive or a fuel substitute that has the benefit of being cleaner and price competitive with gasoline. Therefore, we develop a reduced kinetic mechanism capable of modeling the ethanol combustion and the generation of the combustion products $\text{H}_{2}\text{O},~\text{CO}_{2},~\text{CO},~ \text{H}_{2},~ \text{C}_{2}\text{H}_{4}$ and OH. Based on a mechanism composed by 372 reversible elementary reactions among 56 reactive species, we propose a reduction strategy to obtain an eight-step mechanism for the ethanol. The reduction strategy consists in estimating the order of magnitude of the reaction rate coefficients, defining the main chain, applying the steady-state and partial equilibrium hypotheses, and justifying the assumptions through an asymptotic analysis. The main advantage of the obtained reduced mechanism is the decrease of the work needed to solve the system of chemical equations proportionally to the number of elementary reactions present in the complete mechanism. Numerical tests are carried out for a jet diffusion flame of ethanol and the results compare well with available data in the literature.     

Unprecedented Role of Hydronaphthoquinone Tautomers in Biosynthesis

Quinones and hydroquinones are among the most common cellular cofactors, redox mediators, and natural products. Here, we report on the reduction of 2‐hydroxynaphthoquinones to the stable 1,4‐diketo tautomeric form of hydronaphthoquinones and their further reduction by fungal tetrahydroxynaphthalene reductase. The very high diastereomeric and enantiomeric excess, together with the high yield of cis‐3,4‐dihydroxy‐1‐tetralone, exclude an intermediary hydronaphthoquinone. Labeling experiments with NADPH and NADPD corroborated the formation of an unexpected 1,4‐diketo tautomeric form of 2‐hydroxyhydronaphthoquinone as a stable intermediate. Similar 1,4‐diketo tautomers of hydronaphthoquinones were established as products of the NADPH‐dependent enzymatic reduction of other 1,4‐naphthoquinones, and as substrates for different members of the superfamily of short‐chain dehydrogenases. We propose an essential role of hydroquinone diketo tautomers in biosynthesis and detoxification processes.     

Electrochemical catalysis and corrosion of defective MoS2: Microscopic behaviors and density-functional-theory calculations

MoS₂ is an intriguing layered material widely used in catalysis, lubrication, optoelectronic devices and many other fields, where various structural defects (e.g., vacancies, edges, dopants) will be created in the synthesis and application processes. The promoting effect of defects on the electrochemical reactions, for example, oxygen reduction reaction (ORR) and hydrogen evolution reaction (HER), on MoS₂ has been intensively pursued for efficient catalysts, but should be avoided for durable and superior lubricants and optoelectronic devices working in many atmospheric/aqueous environments. Here, from the perspectives of density-functional-theory simulation, we review the contemporary research progresses on these electrochemical reactions and the underlying microscopic mechanisms of defective MoS₂, and finally project the future research trends and challenges on the electrochemical catalysis and corrosion of defective MoS₂.     

6-硫代黄嘌呤互变异构体的密度泛函理论计算

在密度泛函B3LYP/6-311G**水平下,对14种气相和水相中可能存在的6-硫代黄嘌呤异构体进行了几何构型的全自由度优化,并计算出它们的总能量、焓、熵、吉布斯自由能。Onsager反应场溶剂模型用于水相的计算.计算结果表明,6-硫代黄嘌呤在气相中和水相中主要以硫酮的形式存在.在气相和水相中,硫酮-N7(H)均比硫酮-N9(H)更稳定.计算结果同已有实验结果一致.6-硫代黄嘌呤异构化的熵效应小,对互变异构平衡几乎没有显著的影响,而焓变对互变异构产生了主要的影响.较详细地讨论了水溶剂化作用对异构体的能量、几何结构、电荷分布和偶极矩的影响.     

Effects of Zr doping on stoichiometric and reduced ceria: a first-principles study

The Zr doping in CeO(2) may change the reduction properties and therefore the redox properties of CeO(2). Using first-principles density functional theory with the inclusion of on-site Coulomb interaction for a 96-atom supercell, these effects are studied by comparing the differences in atomic structures, electronic structures, and reduction energies of the doped CeO(2) and those of the nondoped CeO(2). It is found that (1) Zr doping of the ceria structure results in important modifications involving nonequivalent O atoms; (2) the oxygen anions (still four-coordinated) next to the doping center show considerably lower reduction energies (by 0.6 eV) and larger displacements ("higher mobilities"); (3) an O vacancy is most easily created close to the Zr centers, therefore the Zr-doping centers might serve as nucleation centers for vacancy clustering; and (4) the electrons left by the released oxygen localize on two Ce cations neighboring the vacancy, which results in the reduction of two Ce(4+) ions.     

Protonated adenine: Tautomers,solvated clusters,and dissociation mechanisms

Ab initio and density functional theory calculations at the B3-MP2 and CCSD(T)/6-311 + G(3df,2p) levels of theory are reported that address the protonation of adenine in the gas phase, water clusters, and bulk aqueous solution. The calculations point to N-1-protonated adenine (1+) as the thermodynamically most stable cationic tautomer in the gas phase, water clusters, and bulk solution. This strongly indicates that electrospray ionization of adenine solutions produces tautomer 1+ with a specificity calculated as 97-90% in the 298-473 K temperature range. The mechanisms for elimination of hydrogen atoms and ammonia from 1+ have also been studied computationally. Ion 1+ is calculated to undergo fast migrations of protons among positions N-1, C-2, N-3, N-10, N-7, and C-8 that result in an exchange of five hydrogens before loss of a hydrogen atom forming adenine cation radical at 415 kJ mol(-1) dissociation threshold energy. The elimination of ammonia is found to be substantially endothermic requiring 376-380 kJ mol(-1) at the dissociation threshold and depending on the dissociation pathway. The overall dissociation is slowed by the involvement of ion-molecule complexes along the dissociation pathways. The competing isomerization of 1+ proceeds by a sequence of ring opening, internal rotations, imine flipping, ring closures, and proton migrations to effectively exchange the N-1 and N-10 atoms in 1+, so that either can be eliminated as ammonia. This mechanism explains the previous N-1/N-10 exchange upon collision-induced dissociation of protonated adenine.     

Substituent effects on the stability of extended benzylic carbocations: a computational study of conjugation

A set of design rules for the prediction of relative stabilities of methoxy substituted naphthyl methyl carbocations are presented based on a series of DFT calculations. The peri-effect, over-crowding, substitutions on the ring carrying the CH(2)(+) group and substitution on the opposite ring are the principal factors that influence the stability of the carbocations. All of these factors have to be taken simultaneously into account. The most pronounced destabilization occurs when the methyl part of the methoxy substituent lies out of the plane of the aromatic core because this causes the resonance stabilization of the carbocation to become hindered. The performance of the DFT-calculations was assessed on the results of a G3(MP2)//B3LYP calculation-a method that is known to predict energies to within chemical accuracy. These values were found to compare well with those obtained at the B3LYP/6-31G(d) level. Thus, a computationally inexpensive method such as the B3LYP/6-31G(d) might prove to be a powerful tool in the design of future complex extended aromatic systems.     

Tautomers and reference 3D-structures: the orphans of in silico drug design

The importance of calculating not only the correct tautomer, but also the correct protonation state and conformation in 3D modeling applications is emphasized. Above all, identifying and characterizing the most stable form of a ligand under physiological conditions is seen to be the key to successful 3D modeling. Modeling strategies that make use of the performance of modern hardware can employ physically more appropriate models than most currently in use and still be easily applicable to large numbers of compounds. Because the performance of quantitative structure–property relationships is likely to be limited by the available training and validation data, we must either find new sources of such data or resort to explicit modeling, which can partly be parameterized using definitive ab initio calculations for reference data such as gas-phase proton affinities.     

核酸碱基互变异构体的结构、稳定性及其物理化学性质

核酸碱基是DNA及RNA分子的重要组成部分, 在基因遗传信息的传递方面起着主导作用. 核酸碱基存在多种互变异构体, 它们在DNA及RNA分子中主要以最稳定的异构体形式存在, 但是在气相或凝聚相中也有少量的其他异构体形式存在. 核酸碱基的稀有互变异构体往往能够引起碱基对的错配对, 这可能会导致DNA及RNA分子形成不规则的结构, 并进一步导致DNA或RNA双螺旋的自发突变. 因此, 对核酸碱基的互变异构体进行系统的研究, 有助于人们深入认识DNA和RNA分子的结构和性质. 国际上有很多研究小组已经通过实验和理论对核酸碱基互变异构体的结构、相对能量及其性质进行了研究. 本文对文献中有关核酸碱基互变异构体的实验和理论研究进行了综述. 在对前人研究进行归纳总结的基础上, 我们利用密度泛函计算对核酸碱基的互变异构体进行了排序, 得到的最优异构体结构参数和相对能量与实验值相比较为一致. 此外, 因为核酸碱基的物理化学性质可以为生物、化学、材料等方面的研究提供重要的基础性信息, 因此我们还对它们的电子亲和能、电离能、质子亲和能等研究进行了总结.     

Lanthanide(III)/pyrimidine-4,6-dicarboxylate/oxalate extended frameworks: a detailed study based on the lanthanide contraction and temperature effects

Detailed structural, magnetic, and luminescence studies of six different crystalline phases obtained in the lanthanide/pyrimidine-4,6-dicarboxylate/oxalate system have been afforded: {[Ln(μ-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·3H(2)O}(n) (1-Ln), {[Ln(μ-pmdc)(μ-ox)(0.5)(H(2)O)(3)]·2H(2)O}(n) (2-Ln), {[Ln(μ(3)-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·~2.33H(2)O}(n) (3-Ln), {[Ln(2)(μ(3)-pmdc)(μ(4)-pmdc)(μ-ox)(H(2)O)(3)]·5H(2)O}(n) (4-Ln), {[Ln(μ(3)-pmdc)(μ-ox)(0.5)(H(2)O)(2)]·H(2)O}(n) (5-Ln), and [Ln(pmdc)(1.5)(H(2)O)(2.5)] (6-Ln). The slow generation of the oxalate (ox) anion, obtained from the in situ partial hydrothermal decomposition of the pyrimidine-4,6-dicarboxylate (pmdc) ligand, allows us to obtain good shaped single crystals, while direct addition of potassium oxalate provides the same compounds but as polycrystalline samples. The crystal structures of all compounds are based on the double chelation established by the pmdc and ox ligands to provide distorted 2D honeycomb layers that, in some cases, are fused together, leading to 3D systems, by replacing some of the coordinated water molecules that complete the coordination sphere of the lanthanide by uncoordinated carboxylate oxygen atoms of the pmdc. The presence of channels occupied by crystallization water molecules is also a common feature with the exception of compounds 5-Ln. It is worth noting that compounds 3-Ln present a commensurate crystal structure related to the partial occupancy of the crystallization water molecules placed within the channels. Topological analyses have been carried out, showing a previously nonregistered topology for compounds 4-Ln, named as jcr1. The crystal structures are strongly dependent on the lanthanide ion size and the temperature employed during the hydrothermal synthesis. The lanthanide contraction favors crystal structures involving sterically less hindranced coordination environments for the final members of the lanthanide series. Additionally, reinforcement of the entropic effects at high temperatures directs the crystallization process toward less hydrated crystal structures. The magnetic data of these compounds indicate that the exchange coupling between the lanthanide atoms is almost negligible, so the magnetic behavior is dominated by the spin-orbit coupling and the ligand field perturbation. The luminescence properties that exhibit the compounds containing Nd(III), Eu(III), and Tb(III) have been also characterized.