Effect of self-interaction error in the evaluation of the bond length alternation in trans-polyacetylene using density-functional theory

The calculation of the bond-length alternation (BLA) in trans-polyacetylene has been chosen as benchmark to emphasize the effect of the self-interaction error within density-functional theory (DFT). In particular, the BLA of increasingly long acetylene oligomers has been computed using the M?ller-Plesset wave-function method truncated at the second order and several DFT models. While local-density approximation (LDA) or generalized gradient corrected (GGA) functionals strongly underestimate the BLA, approaches including self-interaction corrections (SIC) provide significant improvements. Indeed, the simple averaged-density SIC scheme (ADSIC), recently proposed by Legrand et al. [J. Phys. B 35, 1115 (2002)], provides better results for the structure of large oligomers than the more complex approach of Krieger et al. [Phys. Rev. A 45, 101 (1992)]. The ADSIC method is particularly promising since both the exchange-correlation energy and potential are improved with respect to standard LDA/GGA using a physically appealing correction, through a different route than the more popular approach through the Hartree-Fock exchange inclusion within the hybrid functionals.     

Sample stacking of cationic and anionic analytes in capillary electrophoresis

The behavior of charged species along concentration boundaries in capillary zone electrophoresis (CZE) that was first described in detail by Everaerts et al. in 1979 assured the possibility of concentrating charged solutes inside the capillary. The concentration effect is based on the sudden change in analyte electrophoretic velocity brought about by the difference in the magnitude of the electric field. Furthermore, this on-line method could be the needed solution to the problem of low concentration sensitivity in CZE. Sample stacking, which is now its well known name, has then found valuable use in applying CZE in many fields, especially after the in-depth studies performed in the early 90s by Chien and Burgi. This article reviews the theory and methodological developments of sample stacking developed for charged analytes in CZE and also in electrokinetic chromatography. A table conveying the reported applications especially in the biomedical and environmental fields is given. On top of this, other on-line concentration methods for charged species, namely, sample self-stacking, acetonitrile stacking, sweeping, cation selective exhaustive injection-sweeping, and use of a pH junction, are briefly discussed.     

Synthesis of FDU-1 silica with narrow pore size distribution and tailorable pore entrance size in the presence of sodium chloride

Ordered silicas with large (9-15 nm), uniform, cagelike mesopores were synthesized under acidic aqueous conditions from tetraethyl orthosilicate in the presence of sodium chloride using poly(ethylene oxide)-poly(butylene oxide)-poly(ethylene oxide) triblock copolymer B50-6600 (EO39BO47EO39, Dow Chemicals) as a supramolecular template. Except for the use of NaCl in our case, the synthesis mixture composition was the same as that originally reported by Zhao et al. for the synthesis of FDU-1 silica, which was later shown to exhibit a cubic close-packed (Fm3m) structure with stacking faults related to the occurrence of hexagonal close-packed stacking sequences. The copolymer-templated silicas were formed at room temperature and in most cases were subjected to the hydrothermal treatment at 373 or 393 K. The calcined materials were characterized using small-angle X-ray scattering (SAXS) and nitrogen and argon adsorption at 77 K. SAXS patterns were generally similar to those reported for FDU-1 silica, indicating the cubic close-packed (Fm3m) structure, but the presence of stacking faults characteristic of a hexagonal close-packed structure cannot be precluded. The addition of the salt was found to significantly narrow the pore size distributions and to improve the uniformity of entrances to the cagelike mesopores, whereas the pore diameter, specific surface area, and pore volume were similar (in most cases slightly lower) to those for FDU-1 silicas obtained in the absence of NaCl. The materials synthesized in the presence of NaCl also appeared to have better resolved SAXS patterns. The feasibility of tailoring the pore cage diameter (from approximately 9.5 to 14.5 nm) and pore entrance diameter (from below 4 to approximately 8 nm) simply by adjusting the hydrothermal treatment temperature and time was demonstrated, indicating that these simple and convenient ways of structural design of cagelike mesopores are operative in the case of syntheses in the presence of inorganic salts.     

热解过程中煤焦微晶结构变化及其对煤焦气化反应活性的影响

利用XRD技术考察了热解温度及升温速率对煤焦微晶结构的影响；使用Shi等的方法计算了煤焦微晶结构参数，获取了950℃～1400℃气化炉下煤焦微晶结构的特征及变化规律；结合热重分析得到了热解温度相关参数影响煤焦气化活性的机理。研究表明，热解温度升高，堆垛高度（Lc）明显增大而微晶尺寸（La）变化不大，说明煤焦基本晶格单元主要是进行纵向的接合缩聚，而晶格并没进行明显的内部生长，煤焦的微晶结构随热解温度的提高向有序化发展，但没达到石墨化的程度；慢速热解煤焦的气化反应活性明显低于相同温度下快速热解煤焦，慢速热解中，由于煤焦在高温下停留时间较长，而使煤焦微晶进行结构重整而变得更加有序，芳香单元失去边缘活性位，煤焦气化活性降低。     

On the condensation of salicylaldehyde with hydrazine

A simple procedure for preparing uncontaminated salicylaldehyde hydrazone is outlined. The condensation reaction of salicylaldehyde and hydrazine in 2:1 molar ratio usually gives initially a mixture of the three geometrical isomers of salicylaldazine: one isomer is bright yellow, another is cream, the third is light pink. The earlier reports of Feigl and of Terentev et al. on the use of salicylaldehyde in the detection of hydrazine have been found to be misleading and the later report of Jain et al. incomplete. A detailed account is now given and improved salicylaldehyde tests for hydrazine are recommended. The structure given by Jain et al. for the copper(II) complex of salicylaldehyde hydrazone is confirmed by means of infrared spectroscopy and microanalysis. Preliminary studies on the copper(II) complex of salicylaldazine are reported.     

Characterization of nucleobase-amino acid stacking interactions utilized by a DNA repair enzyme

The present work characterizes the gas-phase stacking interactions between four aromatic amino acid residues (histidine, phenylalanine, tyrosine, and tryptophan) and adenine or 3-methyladenine due to the proposed utilization of these interactions by enzymes that repair DNA alkylation damage. The MP2 potential energy surfaces of the stacked dimers are considered as a function of four variables (vertical displacement, angle of rotation, horizontal displacement, and tilt angle) using a variety of basis sets. It is found that the maximum stacking interaction energy decreases with the amino acid according to TRP > TYR approximately HIS > PHE for both nucleobases. However, the magnitude of the stacking interaction significantly increases upon alkylation (by 50-115%). Comparison of the stacking energies calculated using our surface scans to those estimated from experimental crystal structures indicates that the stacking interactions within the active site of 3-methyladenine DNA glycosylase can account for 65-75% of the maximum possible stacking interaction between the relevant molecules. The decrease in stacking in the crystal structure arises due to significant differences in the relative orientations of the nucleobase and amino acid. Nevertheless, alkylation is found to significantly increase the stacking energy when the crystal structure geometries are considered. Our calculations provide computational support for suggestions that alkylation enhances the stacking interactions within the active site of DNA repair enzymes, and they give a measure of the magnitude of this enhancement. Our results suggest that alkylation likely plays a more important role in substrate identification and removal than the nature of the aromatic amino acid that interacts with the substrate via stacking interactions.     

Trimethylsilylverbindungen der Vb-Elemente. VI. Synthese,Molekül- und Kristallstruktur des Tetrakis(trimethylsilyl)distibans im Vergleich mit Tetraphenyldistiban

Trimethylsilyl Derivatives of Vb-Elements. VI. Synthesis, Molecular and Crystal Structure of Tetrakis(trimethylsilyl)distibine Compared with Tetraphenyldistibine Tetrakis(trimethylsilyl)distibine already isolated by Breunig et al. [9] from cleavage reactions of tris(trimethylsilyl)stibine may also be obtained in high yields from lithium bis(trimethylsilyl)antimonide · 2THF and 1,2-dibromoethane in n-pentane. This compound intensely red in the solid state, but only slightly yellow in solution or in the melt crystallizes in the monoclinic space group P2₁/c with a = 680.6(1); b = 1672.8(2); c = 1190.0(1) pm; β = 119.01(5)°; Z = 2 at +20°C. An X-ray structure determination (R = 0.017) shows the bis(trimethylsilyl)-stibino groups to be arranged in a transoid position. Characteristic bond lengths and angles are: Sb? Sb 286.7(1); Sb? Si 259.4 pm; Si? Sb? Si 94.46(3); Sb? Sb? Si 98.68(3) and 94.43(3)°. As in similiar 2,2′,5,5′-tetramethyldistibolyl published recently by Ashe III et al. [8] this crystal structure, too, is characterized by a nearly linear sequence of Sb? Sb groups. Compared with the sum of van-der-Waals radii the intermolecular Sb-Sb contact in such a chain is shortened from 440 to 399 pm. This probably allows electronic interactions of unknown type responsible for the colour of the crystals. In keeping with this assumption an analogous formation of chains is not found in solid, only yellow tetraphenyldistibine 5 the structure of which has already been studied by Rehder et al. [44].     

The high-pressure electronic structure of the [Ni(ptdt)2] organic molecular conductor

The electronic structure of the single component molecular crystal [Ni(ptdt)(2)] (ptdt = propylenedithiotetrathiafulvalenedithiolate) is determined at ambient and high pressure using density functional theory. The electronic structure of this crystal is found to be of the "crossing bands" type with respect to the dispersion of the HOMO and LUMO, resulting in a small, non-zero density of states at the Fermi energy at ambient pressure, indicating that this crystal is a "poor quality" metal, and is consistent with the crystal's resistivity exhibiting a semiconductor-like temperature dependence. The ambient pressure band structure is found to be predominantly one-dimensional, reflecting enhanced intermolecular interactions along the [100] stacking direction. Our calculations indicate that the band structure becomes two-dimensional at high pressures and reveals the role of shortened intermolecular contacts in this phenomenon. The integrity of the molecular structure is found to be maintained up to at least 22 GPa. The electronic structure is found to exhibit a crossing bands nature up to 22 GPa, where enhanced intermolecular interactions increase the Brillouin zone centre HOMO-LUMO gap from 0.05 eV at ambient pressure to 0.15 eV at 22 GPa; this enhanced HOMO-LUMO interaction ensures that enhancement of a metallic state in this crystal cannot be simply achieved through the application of pressure, but rather requires some rearrangement of the molecular packing. Enhanced HOMO-LUMO interactions result in a small density of states at the Fermi energy for the high pressure window 19.8-22 GPa, and our calculations show that there is no change in the nature of the electronic structure at the Fermi energy for these pressures. We correspondingly find no evidence of an electronic semiconducting-metal insulator transition for these pressures, contrary to recent experimental evidence [Cui et al., J. Am. Chem. Soc. 131, 6358 (2009)].     

Structural and electronic property responses to the arsenic/phosphorus exchange in GC‐related DNA of the B‐form

The suggestion that phosphorus/arsenic replacement in DNA can play a role in living things has generated great controversy (Wolfe‐Simon et al., Science 2011, 332, 1163). Examined here theoretically are substitution effects on Watson–Crick base pairing and base stacking patterns in realistic DNA subunits. Using duplex DNA models deoxyguanylyl‐3′,5′‐deoxycytidine ([dGpdC]₂) and deoxycytidyly‐3′,5′‐deoxyguanosine ([dCpdG)]₂), this research reveals that the geometric variations caused by the As/P exchange are small and are limited to the phosphate/arsenate groups. As/P replacement leads to alterations of ～0.15 Å in P/As? O bond lengths and less than 1.5° variations in O? P/As? O angles. The Watson–Crick base pairing and base stacking patterns are independent of the As/P replacement. The vertical electron detachment energies are also largely unaffected. However, the electron capture ability of the DNA units is improved by the As substitution. The arsenate is found to be the main electron acceptor in As‐DNA. The results are relevant to the possible existence of viable As‐DNAs, at least in the guanine and cytosine (GC)‐related B‐form DNA. © 2012 Wiley Periodicals, Inc. J Comput Chem, 2012     

On the existence of ordered organic adlayers at the Cu(111)/electrolyte interface

We have reinvestigated the behavior of a Cu(111) electrode in pure and cinchonidine containing aqueous 0.1 M HClO4 solution by cyclic voltammetry (CV) and in situ electrochemical scanning tunneling microscopy (STM). In contrast to previous publications by Wan et al. (Langmuir 2000, 19, 1958-1962 and references cited therein) on Cu(111) in pure 0.1 M HClO4 which claimed an adsorbate-free Cu(111) surface in the entire potential range, we have found a highly ordered hexagonal adsorbate structure with a (4 x 4) unit cell, which is stable in the potential range from hydrogen evolution at -350 to -150 mV (RHE). The adsorbate-free (1 x 1) Cu(111) surface is only visible in a fairly small potential range from -150 to +50 mV. A disordered surface structure is formed at more positive potentials which is interpreted by adsorption of an oxygen-containing species. Furthermore, the formation of a highly ordered cinchonidine adlayer on Cu(111) in 0.1 M HClO4 as reported by Wan et al. (J. Am. Chem. Soc. 2002, 124, 14300-14301) could not be reproduced here. In fact, the similarity of all structures reported by Wan et al. for a great variety of different organic adlayers on Cu(111) in HClO4 solution including cinchonidine with the (4 x 4) superstructure found here already in pure HClO4 solution (i.e., without organic solute) casts serious doubts on the validity of those previous results by Wan et al. in general.     

Shear and dilatational relaxation mechanisms of globular and flexible proteins at the hexadecane/water interface

Proteins adsorbed at fluid/fluid interfaces influence many phenomena: food emulsion and foam stability (Murray et al. Langmuir 2002, 18, 9476 and Borbas et al. Colloids Surf., A 2003, 213, 93), two-phase enzyme catalysis (Cascao-Pereira et al. Biotechnol. Bioeng. 2003, 83, 498; 2002, 78, 595), human lung function (Lunkenheimer et al. Colloids Surf., A 1996, 114, 199; Wustneck et al.; and Banerjee et al. 2000, 15, 14), and cell membrane mechanical properties (Mohandas et al. 1994, 23, 787). Time scales important to these phenomena are broad, necessitating an understanding of the dynamics of biological macromolecules at interfaces. We utilize interfacial shear and dilatational deformations to study the rheology of a globular protein, lysozyme, and a disordered protein, beta-casein, at the hexadecane/water interface. Linear viscoelastic properties are measured using small amplitude oscillatory flow, stress relaxation after a sudden dilatational displacement, and shear creep response to probe the rheological response over broad experimental time scales. Our studies of lysozyme and beta-casein reveal that the interfacial dissipation mechanisms are strongly coupled to changes in the protein structure upon and after adsorption. For beta-casein, the interfacial response is fluidlike in shear deformation and is dominated by interfacial viscous dissipation, particularly at low frequencies. Conversely, the dilatational response of beta-casein is dominated by diffusion dissipation at low frequencies and viscous dissipation at higher frequencies (i.e., when the experimental time scale is faster than the characteristic time for diffusion). For lysozyme in shear deformation, the adsorbed protein layer is primarily elastic with only a weak frequency dependence. Similarly, the interfacial dilatational moduli change very little with frequency. In comparison to beta-casein, the frequency response of lysozyme does not change substantially after washing the protein from the bulk solution. Apparently, it is the irreversibly adsorbed fraction that dominates the dynamic rheological response for lysozyme. Using stress relaxation after a sudden dilatational displacement and shear creep response, the characteristic time of relaxation was found to be 1000 s in both modes of deformation. The very long relaxation time for lysozyme likely results from the formation of a glassy interfacial network. This network develops at high interfacial concentrations where the molecules are highly constrained because of conformation changes that prevent desorption.     

Structural study of the T#2-LixCoO2 (0.52 < x < or = 0.72) phase

The metastable O2-LiCoO(2) phase undergoes several reversible phase transitions upon lithium deintercalation. The first transition leads to an unusual oxygen stacking in such layered compounds. This stacking is found to be stable for 0.52 < x < or = 0.72 in Li(x)()CoO(2) and is called T(#)2. We studied this phase from a structural viewpoint using X-ray and neutron diffraction (ab initio method). The new stacking derives from the O2 one by gliding every second CoO(2) slab by (1/3, 1/6, 0). The lithium ions are found to occupy very distorted tetrahedral sites in this structure. We also discuss the possibility of this T(#)2 phase to exhibit stacking faults, whose amount depends on the method used to prepare this deintercalated phase.     

Designing novel nicotinic agonists by searching a database of molecular shapes

Summary We introduce an approach by which novel ligands can be designed for a receptor if a pharmacophore geometry has been established and the receptor-bound conformations of other ligands are known. We use the shape-matching method of Kuntz et al. [J. Mol. Biol., 161 (1982) 269–288] to search a database of molecular shapes for those molecules which can fit inside the combined volume of the known ligands and which have interatomic distances compatible with the pharmacophore geometry. Some of these molecules are then modified by interactive modeling techniques to better match the chemical properties of the known ligands. Our shape database (about 5000 candidate molecules) is derived from a subset of the Cambridge Crystallographic Database [Allen et al., Acta Crystallogr., Sect. B,35 (1979) 2331–2339]. We show, as an example, how several novel designs for nicotinic agonists can be derived by this approach, given a pharmacophore model derived from known agonists [Sheridan et al., J. Med. Chem., 29 (1986) 889–906]. This report complements our previous report [DesJarlais et al., J. Med. Chem., in press], which introduced a similar method for designing ligands when the structure of the receptor is known.     

Evaluation Of Some Methods For 17- Ketosteroids In Urine

Abstract

Three procedure for 17-ketosteroids are compared: The method of Callow et al., the method of Drekter et al. and the method of Corker et al. Good correlation has been found between results obtained by the methods of Callow and Corker. Analyses of single analytical steps showed that Drekter's method gives in some cases too high results because non-specific chromogens are included when readings are taken only at 520 nm. Of these three procedures that of Corker et al. is proposed as the method of choice.     

Simulation of DNA electrophoresis through microstructures

The dependence of the mobility of DNA molecules through an hexagonal array of micropillars on their length and the applied electric field was investigated and it was found that mobility is a nonmonotonic function of their length. Results also revealed that the size dependence of the DNA mobility depends on the applied electric field and there is a crossover around E approximately 25 V/cm for the mobility of lambda-DNA and T4-DNA. These observations are explained in terms of the diffusion process inside the structure affected by the solvent and are modeled using the Langevin and its corresponding Fokker-Planck equations. The phenomenon is generalized under three regimes in a phase diagram relating the electric field and the DNA lengths. The model and the associated phase diagram described here provide an explanation for the conflicting results reported by previous authors (Han et al. on the one hand, and Duong et al. and Inatomi et al. on the other) about the dependence of mobility on the DNA size in lattices near or below the radius of gyration.     

Polymorphic phases of sp3-hybridized carbon under cold compression

It is well established that graphite can be transformed into superhard carbons under cold compression (Mao et al. Science 2003, 302, 425). However, structure of the superhard carbon is yet to be determined experimentally. We have performed an extensive structural search for the high-pressure crystalline phases of carbon using the evolutionary algorithm. Nine low-energy polymorphic structures of sp(3)-hybridized carbon result from the unbiased search. These new polymorphic carbon structures together with previously reported low-energy sp(3)-hybridized carbon structures (e.g., M-carbon, W-carbon, and Cco-C(8) or Z-carbon) can be classified into three groups on the basis of different ways of stacking two (or more) out of five (A-E) types of buckled graphene layers. Such a classification scheme points out a simple way to construct a variety of sp(3)-hybridized carbon allotropes via stacking buckled graphene layers in different combinations of the A-E types by design. Density-functional theory calculations indicate that, among the nine low-energy crystalline structures, seven are energetically more favorable than the previously reported most stable crystalline structure (i.e., Cco-C(8) or Z-carbon) in the pressure range 0-25 GPa. Moreover, several newly predicted polymorphic sp(3)-hybridized carbon structures possess elastic moduli and hardness close to those of the cubic diamond. In particular, Z-carbon-4 possesses the highest hardness (93.4) among all the low-energy sp(3)-hybridized carbon structures predicted today. The calculated electronic structures suggest that most polymorphic carbon structures are optically transparent. The simulated X-ray diffraction (XRD) spectra of a few polymorphic structures are in good agreement with the experimental spectrum, suggesting that samples from the cold-compressed graphite experiments may consist of multiple polymorphic phases of sp(3)-hybridized carbon.     

Local structure of Pt and Pd ions in Ce(1-x)TixO2: x-ray diffraction, x-ray photoelectron spectroscopy, and extended x-ray absorption fine structure

Ce(1-x-y)Ti(x)Pt(y)O(2-delta) (x=0.15; y=0.01) and Ce(1-x-y)Ti(x)Pd(y)O(2-delta) (x=0.25; y=0.02 and 0.05) are found to be good CO oxidation catalysts [T. Baidya et al., J. Phys. Chem. B 110, 5262 (2006); T. Baidya et al., J. Phys. Chem. C 111, 830 (2007)]. A detailed structural study of these compounds has been carried out by extended x-ray absorption fine structure along with x-ray diffraction and x-ray photoelectron spectroscopy. The gross cubic fluorite structure of CeO(2) is retained in the mixed oxides. Oxide ion sublattice around Ti as well as Pt and Pd ions is destabilized in the solid solution. Instead of ideal eight coordinations, Ti, Pd, and Pt ions have 4+3, 4+3, and 3+4 coordinations creating long and short bonds. The long Ti-O, Pd-O, and Pt-O bonds are approximately 2.47 A (2.63 A for Pt-O) which are much higher than average Ce-O bonds of 2.34 A.     

Theoretical studies of some nonbenzenoid hydrocarbons—IV : Pleiadiene and related compounds

Pleiadiene and other similar compounds have been studied by the semi-empirical SCFMO method of Pariser, Parr and Pople using the core resonance integral value developed by Lo and Whitehead, Dewar et al. and Yamaguchi et al. It has been found that π^*←π transitions predicted by the methods of Lo and Whiteheadand Dewar et al. suitable for the prediction of ground state properties are also in good agreement with experimental results where available and comparable to those predicted by the method of Yamaguchi et al. developed for the prediction of spectral transitions. The resonance stabilization of the molecules 3,4.5,7,8 and 9 have also been studied. It is found that ethylinic linkage across the naphthalene moity in pleiadiene increases the resonance energy of the final compound, in contrast to our previous observation, i.e. ethylinic linkage across the naphthalene moiety reduces the resonance energy of the final compound.