bluuebunny/crossref_metadata_2025 huggingface dataset:
Structural and dynamical properties of the V3+ ion in dilute aqueous solution: An ab initio QM/MM molecular dynamics simulation
Authors: Kritayakornupong Chinapong
Published: April 2009

A hybrid ab initio QM/MM molecular dynamics simulation at the Hartree‐Fock level has been performed to investigate structural and dynamical parameters of the V3+ ion in dilute aqueous solution. A distorted octahedral structure with the average V3+‐O distance of 1.99 Å is evaluated from the QM/MM simulation, which is in good agreement with the X‐ray data. Several structural parameters such as angular distribution functions, θ‐ and tilt‐angle distributions have been determined to obtain the full description of the hydration structure of the hydrated V3+. The Jahn‐Teller distortions of the V3+ ion are pronounced in the QM/MM simulation. The mean residence time of 14.5 ps is estimated for the ligand exchange processes in the second hydration shell. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
A computational study of photochemical isomerization reactions of thiophenes
Authors: Su Ming‐Der
Published: April 2009

The mechanisms of the photochemical isomerization reactions were investigated theoretically using three model systems; 2‐methylthiophene, 2‐cyanothiophene, and 2‐phenylthiophene. The CASSCF (10‐electron/eight‐orbital active space) and MP2‐CAS methods were employed with the 6‐311(d) basis set. Three mechanisms, i.e., the internal cyclization‐isomerization route (path A), the zwitterion‐tricyclic route (path B), and the direct route (path C), have been used to explore the real photochemical reaction mechanism of these three model molecules. The structures of the conical intersections, which play a key role in such phototranspositions, were obtained. The intermediates and transition structures of the ground states were also calculated to assist in providing a qualitative explanation of the reaction pathways. Our model investigations suggest that the preferred reaction route is as follows: reactant → Franck‐Condon region → conical intersection → photoproduct. In particular, the conical intersection mechanism described in this work gives a better explanation than either the previously proposed internal cyclization‐isomerization (path A) or the zwitterion‐tricyclic pathway (path B) mechanisms, and is supported by the experimental observations. The results obtained allow a number of predictions to be made. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
Efficient extraction of free energy profiles from nonequilibrium experiments
Authors: Oberhofer Harald , Dellago Christoph
Published: April 2009

Hummer and Szabo recently presented a method based on the Jarzynski equality to calculate Helmholtz free energy profiles from nonequilibrium pathways obtained in simulations or experiments. In their approach, the free energy is reconstructed from weighted histograms. Here, we give a systematic derivation of the optimum weight, which—in principle—minimizes the statistical errors in the resulting free energy profiles. We then compare this optimum weight to Hummer and Szabo's original weight and several others by means of simulations of two one‐dimensional models, for which the free energy profile is analytically known. In addition, we carry out simulations of a deca‐alanine molecule pulled by a harmonic trap to assess the efficiency of the weights in a more realistic situation. In all cases, the weight of Hummer and Szabo performs very well leading to errors approximately equal to those obtained with a simplified version of the optimum weight. The performance of the optimum weight itself is unsatisfying due to statistical errors arising in the weight calculation. © 2009 Wiley Periodicals, Inc. J Comput Chem 2009
Paired orbitals for different spins equations
Authors: Zilberberg Igor , Ruzankin Sergey
Published: April 2009

Eigenvalue‐type equations for Löwdin–Amos–Hall spin‐paired (corresponding) orbitals are developed to provide an alternative to the standard spin‐polarized Hartree–Fock or Kohn–Sham equations in dealing with broken‐symmetry (BS) states. To derive paired orbitals for different spins (PODS) equations there has been applied Adams–Gilbert “localizing” operator approach. The PODS equations contain different operators for different spins the eigenvectors of which are paired orbitals associated with the same eigenvalue for each pair. Preliminary applications to simple systems show viability of this approach. Although the spectrum of possible applications of the PODS equations seems to be quite wide, they would be especially useful for obtaining and analyzing the Sz = 0 BS solutions for the systems with antiferromagnetic structure. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010
Optimized reuse and bioconversion from retentate of pre‐filtered palm oil mill effluent (POME) into microbial protease by Aspergillus terreus using response surface methodology
Authors: Wu Ta Yeong , Mohammad Abdul Wahab , Md. Jahim Jamaliah , Anuar Nurina
Published: April 2009

BACKGROUND: The membrane filtration process enables the treatment of wastewater, producing permeate which is less polluted. However, disposal is usually required for the retentate, which is produced as a concentrated constituent along with the permeate. In this study, the authors explored the possibility of reusing, rather than disposing of, the retentate of pre‐filtered palm oil mill effluent (POME) as a fermentation substrate in protease production by a wild type strain of Aspergillus terreus IMI 282743. In addition, the quantitative and interactive effects of the concentration factor for retentate, temperature, inoculum concentration, and fermentation time on the optimization of protease production were investigated using response surface methodology (RSM).

RESULTS: Using RSM, the optimum conditions were found to be a concentration factor of 7.27, temperature of 37.95 °C, inoculum concentration of 1.30% (v/v) and fermentation time of 3.83 days. The protease production was increased 4.37‐fold in comparison with the results obtained under non‐optimized conditions.

CONCLUSION: To a certain extent, protease production could be enhanced with an increase in concentration factor and temperature, and a decrease of inoculum concentration and fermentation time. Also, POME retentate was found to be a good substrate for protease production with high product activity and without nutrient supplementation. Copyright © 2009 Society of Chemical Industry
Kinetics of thermal inactivation of transglutaminase from a newly isolated Bacillus circulans BL32
Authors: de Souza Claucia Fernanda Volken , Faccin Débora Jung Luvizetto , Mertins Omar , Heck Júlio Xandro , da Silveira Nádya Pesce , Secchi Argimiro Resende , Ayub Marco Antônio Záchia
Published: April 2009

BACKGROUND: This paper describes the modeling of the kinetics of thermal inactivation of transglutaminase (TGase) from a newly isolated Bacillus circulans BL32, isolated from the Amazon environment. The purified enzyme was incubated at temperatures ranging from 30 to 70 °C and values of the thermodynamic inactivation parameters, such as activation energy (ΔE), activation enthalpy (ΔH), activation entropy (ΔS), and free energy (ΔG) for thermal inactivation, were calculated.

RESULTS: The kinetics of TGase thermo‐inactivation followed a Lumry–Eyring model. The enzyme was very stable up to 50 °C, with approximately 50% of activity remaining after heating for 12 h. It was completely inactivated by incubation at 70 °C for 2 min. ΔE for TGase was 350.5 kJ mol−1. ΔH and ΔS for thermo‐inactivation of the TGase were 347.8 kJ mol−1 and 744 J mol−1 K−1 at 50 °C, respectively. Dynamic light scattering measurements suggest that the thermal inactivation of this microbial TGase can be partially attributed to the formation of aggregates.

CONCLUSION: These results provide useful information about the thermal characteristics of the microbial TGase from B. circulans BL32 and indicate that this enzyme could be a good candidate for industrial applications. Copyright © 2009 Society of Chemical Industry
Simultaneous refolding, purification, and immobilization of recombinant Fibrobacter succinogenes 1,3‐1,4‐β‐D‐glucanase on artificial oil bodies
Authors: Zeng Yi‐Fang , Hung Ying‐Jing , Chen Ming‐Ju , Peng Chi‐Chung , Tzen Jason T. C. , Liu Je‐Ruei
Published: April 2009

BACKGROUND: 1,3‐1,4‐β‐D‐glucanase (1,3‐1,4‐β‐D‐glucan 4‐glucanohydrolase; EC 3.2.1.73) has been used in a range of industrial processes. As a biocatalyst, it is better to use immobilized enzymes than free enzymes, therefore, the immobilization of 1,3‐1,4‐β‐D‐glucanase was investigated.

RESULTS: A 1,3‐1,4‐β‐D‐glucanase gene from Fibrobacter succinogenes was overexpressed in Escherichia coli as a recombinant protein fused to the N terminus of oleosin, a unique structural protein of seed oil bodies. With the reconstitution of the artificial oil bodies (AOBs), refolding, purification, and immobilization of active 1,3‐1,4‐β‐D‐glucanase was accomplished simultaneously. Response surface modeling (RSM), with central composite design (CCD), and regression analysis were successfully applied to determine the optimal temperature and pH conditions of the AOB‐immobilized 1,3‐1,4‐β‐D‐glucanase. The optimal conditions for the highest immobilized 1,3‐1,4‐β‐D‐glucanase activity (7.1 IU mg−1 of total protein) were observed at 39 °C and pH 8.8. Furthermore, AOB‐immobilized 1,3‐1,4‐β‐D‐glucanase retained more than 70% of its initial activity after 120 min at 39 °C, and it was easily and simply recovered from the surface of the solution by brief centrifugation; it could be reused eight times while retaining more than 80% of its activity.

CONCLUSIONS: These results indicate that the AOB‐based system is a comparatively simple and effective method for simultaneous refolding, purification, and immobilization of 1,3‐1,4‐β‐D‐glucanase. Copyright © 2009 Society of Chemical Industry
Surface‐enhanced Raman scattering (SERS) spectra of chloramphenicol in Ag colloids prepared by microwave heating method
Authors: Si M. Z. , Kang Y. P. , Zhang Z. G.
Published: April 2009

Ag colloids were prepared by the microwave heating method. The UV‐visible spectrum and the transmission electron microscopy (TEM) were employed to characterize the Ag colloids. The surface‐enhanced Raman scattering (SERS) spectra of chloramphenicol (CAP) in Ag colloids were successfully recorded. The Raman spectra of CAP were recorded with good concordance comparing to the theoretical results calculated by the Gaussian'98 program. CAP molecules on the Ag surface are oriented tilted to the particle surface via C20‐O23, N‐O13, and N‐O23, which played an important role in the SERS effect. Copyright © 2009 John Wiley & Sons, Ltd.
Converting a tetrahedral mesh to a prism–tetrahedral hybrid mesh for FEM accuracy and efficiency
Authors: Yamakawa Soji , Shimada Kenji
Published: April 2009

This paper presents a computational method for converting a tetrahedral mesh to a prism–tetrahedral hybrid mesh for improved solution accuracy and computational efficiency of finite element analysis. The proposed method performs this conversion by inserting layers of prism elements and deleting tetrahedral elements in sweepable sub‐domains, in which cross‐sections remain topologically identical and geometrically similar along a certain sweeping path. The total number of finite elements is reduced because roughly three tetrahedral elements are converted to one prism element. The solution accuracy of the finite element analysis improves since a prism element yields a more accurate solution than a tetrahedral element due to the presence of higher‐order terms in the shape function. Only previously known method for creating such a prism–tetrahedral hybrid mesh was to manually decompose a target volume into sweepable and non‐sweepable sub‐volumes and mesh each of the sub‐volumes separately. Unlike the previous method, the proposed method starts from a cross‐section of a tetrahedral mesh and replaces the tetrahedral elements with layers of prism elements until prescribed quality criteria can no longer be satisfied. A series of computational fluid dynamics simulations and structural analyses have been conducted, and the results verified a better performance of prism–tetrahedral hybrid mesh. Copyright © 2009 John Wiley & Sons, Ltd.
Discontinuous Galerkin finite volume element methods for second‐order linear elliptic problems
Authors: Kumar Sarvesh , Nataraj Neela , Pani Amiya K.
Published: April 2009

In this article, a one parameter family of discontinuous Galerkin finite volume element methods for approximating the solution of a class of second‐order linear elliptic problems is discussed. Optimal error estimates in L2 and broken H1‐ norms are derived. Numerical results confirm the theoretical order of convergences. © 2009 Wiley Periodicals, Inc. Numer Methods Partial Differential Eq, 2009
Paleopathology and health of native and introduced animals on Southern Peruvian and Bolivian Spanish Colonial sites
Authors: Defrance S. D.
Published: April 2009

Spanish colonial sites in southern Peru and Bolivia contain remains of native camelids and introduced bovids with examples of degenerative paleopathologies that are interpreted as reflecting changes in herd management, animal use and animal health following the Spanish conquest. The archaeological contexts include three Spanish colonial wineries from Moquegua in southern Peru and the nearby colonial village of Torata Alta where indigenous people were forced to resettle under Spanish control. Also from Peru is faunal material from the 14th to 16th century rural agropastoral village of Pillistay located near Camana. Animal remains with bone abnormalities are also present in residential, commercial and industrial sites associated with Spanish silver mining near Potosí, Bolivia at Tarapaya and Cruz Pampa. Eighteen pathological specimens are described including examples of degenerative changes to phalanges, vertebrae, tarsals, limb elements and ribs. Paleopathologies present include exostoses, osteophytes, porosity, grooving and eburnation. Examples of phalangeal exostoses on bovid phalanges indicate the use of these introduced animals as draught cattle. Exostoses on camelid first phalanges suggests their use as cargo animals as do thoracic vertebrae with severe cases of degenerative pathology. Introduced caprines contain few pathologies indicating their primary use as food animals. The bone abnormalities from colonial sites are more severe than those reported for prehispanic faunal assemblages. These data provide insights into the health and work behaviour of indigenous Andean camelids and introduced Eurasian animals following the Spanish conquest. Copyright © 2009 John Wiley & Sons, Ltd.
A supernumerary permanent mandibular premolar of wild boar (Sus scrofa L.) from the early medieval Novgorod, Russia
Authors: Zinoviev A. V.
Published: April 2009

The aim of this study was to investigate a unique case of polydonty in wild boar from the early medieval Novgorod (second half of 11th century AD). The only preserved distal part of the right mandibular branch shows a rotated transitional permanent extra premolar between P3 and P4. This abnormality has the potential to serve as a territorially‐based indicator of past wild boar populations. Copyright © 2009 John Wiley & Sons, Ltd.
Effect of cyclic acetals structure on efficiency of photoinitiation
Authors: Wang Kemin , Han Jing , Shi Suqing , Nie Jun
Published: April 2009

Cyclic acetals were proposed as free radical polymerization photoinitiators or co‐initiators. The photopolymerization kinetics was recorded by real‐time infrared spectroscopy (RTIR). 2‐proply‐1,3‐benzodioxole (PBDO) and 2‐hexyl‐1,3‐benzodioxole (HBDO) were efficient photoinitiators for the polymerization of 1,6‐hexanedioldiacrylate (HDDA). Polymerization occurred at the highest rate with 1,3‐benzodioxolane (BDO) as a co‐initiator. When 1.82 wt % benzophenone (BP) was used as a photoinitiator, the addition of PBDO increased the rate of polymerization (Rp) and the final double bond conversion (DCf) of HDDA, and an optimum cure rate (0.982 min−1) was obtained at 1.64 wt % of PBDO. Combination of p‐chlorobenzophenone (CBP) and PBDO had the highest initiating reactivity. Cyclic acetals were inefficient co‐initiators for isopropylthioxanthone (ITX). Copyright © 2009 John Wiley & Sons, Ltd.
Treatment of disseminated paraganglioma with gemcitabine and docetaxel
Authors: Mora Jaume , Cruz Ofelia , Parareda Andreu , Sola Teresa , de Torres Carmen
Published: April 2009

A male with metastatic paraganglioma received different chemotherapy regimens and 14 arterial embolizations with no or short‐lasting clinical benefit. He was started on gemcitabine and docetaxel and, after two cycles, remission of all clinical signs occurred over 2 months. A complete biochemical response was achieved and angiographic signs of portal hypertension disappeared. He received 18 cycles of therapy and no limiting side effects were observed. More than 2 years after gemcitabine and docetaxel treatment, the patient remains symptom free. Gemcitabine and docetaxel could be a potential therapeutic strategy for this patient. Pediatr Blood Cancer 2009;53:663–665. © 2009 Wiley‐Liss, Inc.
Ser/Thr/Tyr phosphoproteome analysis of pathogenic and non‐pathogenic Pseudomonas species
Authors: Ravichandran Ayshwarya , Sugiyama Naoyuki , Tomita Masaru , Swarup Sanjay , Ishihama Yasushi
Published: April 2009

Protein phosphorylation on serine, threonine, and tyrosine is well established as a crucial regulatory posttranslational modification in eukaryotes. With the recent whole‐genome sequencing projects reporting the presence of serine/threonine kinases and two‐component proteins both in prokaryotes and eukaryotes, the importance of protein phosphorylation in archaea and bacteria is gaining acceptance. While conventional biochemical methods failed to obtain a snapshot of the bacterial phosphoproteomes, advances in MS methods have paved the way for in‐depth mapping of phosphorylation sites. Here, we present phosphoproteomes of two ecologically diverse non‐enteric Gram‐negative bacteria captured by a nanoLC‐MS‐based approach combined with a novel phosphoenrichment method. While the phosphoproteome data from the two species are not very similar, the results reflect high similarity to the previously published dataset in terms of the pathways the phosphoproteins belong to. This study additionally provides evidence to prior observations that protein phosphorylation is common in bacteria. Notably, phosphoproteins identified in Pseudomonas aeruginosa belong to motility, transport, and pathogenicity pathways that are critical for survival and virulence. We report, for the first time, that motility regulator A, probably acting via the novel secondary messenger cyclic diguanylate monophosphate, significantly affects protein phosphorylation in Pseudomonas putida.
Characteristics of Portuguese Public-Sector Project Managers: Toward Closing the Effectiveness Gap
Authors: Yasin Mahmoud M. , Gomes Carlos Ferreira , Miller Phillip E.
Published: April 2009

Using a sample of 102 Portuguese public-sector officials with project management experience, this study examines the characteristics of effective project managers in the Portuguese public sector. Factor-analysis procedures are used to identify the factors related to areas of knowledge relevant to effective project management. The results appear to stress the increasing importance of people, organizational, and leadership skills in the effective management of today's complex and dynamic projects.
A chimeric mechanism for polyvalent trans‐phosphorylation of PKA by PDK1
Authors: Romano Robert A. , Kannan Natarajan , Kornev Alexandr P. , Allison Craig J. , Taylor Susan S.
Published: April 2009

Phosphorylation on the activation loop of AGC kinases is typically mediated by PDK1. The precise mechanism for this in‐trans phosphorylation is unknown; however, docking of a hydrophobic (HF) motif in the C‐tail of the substrate kinase onto the N‐lobe of PDK1 is likely an essential step. Using a peptide array of PKA to identify other PDK1‐interacting sites, we discovered a second AGC‐conserved motif in the C‐tail that interacts with PDK1. Since this motif [FD(X)1‐2Y/F] lies in the active site tether region and in PKA contributes to ATP binding, we call it the Adenosine binding (Ade) motif. The Ade motif is conserved as a PDK1‐interacting site in Akt and PRK2, and we predict it will be a PDK1‐interacting site for most AGC kinases. In PKA, the HF motif is only recognized when the turn motif Ser338 is phosphorylated, possibly serving as a phosphorylation “switch” that regulates how the Ade and HF motifs interact with PDK1. These results demonstrate that the extended AGC C‐tail serves as a polyvalent element that trans‐regulates PDK1 for catalysis. Modeling of the PKA C‐tail onto PDK1 structure creates two chimeric sites; the ATP binding pocket, which is completed by the Ade motif, and the C‐helix, which is positioned by the HF motif. Together, they demonstrate substrate‐assisted catalysis involving two kinases that have co‐evolved as symbiotic partners. The highly regulated turn motifs are the most variable part of the AGC C‐tail. Elucidating the highly regulated cis and trans functions of the AGC tail is a significant future challenge.
Impact of missing data on type 1 error rates in non‐inferiority trials
Authors: Yoo Bongin
Published: April 2009

In this paper, a simulation study is conducted to systematically investigate the impact of different types of missing data on six different statistical analyses: four different likelihood‐based linear mixed effects models and analysis of covariance (ANCOVA) using two different data sets, in non‐inferiority trial settings for the analysis of longitudinal continuous data. ANCOVA is valid when the missing data are completely at random. Likelihood‐based linear mixed effects model approaches are valid when the missing data are at random. Pattern‐mixture model (PMM) was developed to incorporate non‐random missing mechanism. Our simulations suggest that two linear mixed effects models using unstructured covariance matrix for within‐subject correlation with no random effects or first‐order autoregressive covariance matrix for within‐subject correlation with random coefficient effects provide well control of type 1 error (T1E) rate when the missing data are completely at random or at random. ANCOVA using last observation carried forward imputed data set is the worst method in terms of bias and T1E rate. PMM does not show much improvement on controlling T1E rate compared with other linear mixed effects models when the missing data are not at random but is markedly inferior when the missing data are at random. Copyright © 2009 John Wiley & Sons, Ltd.
Requirements for packaging from an ageing consumer's perspective
Authors: Duizer L. M. , Robertson T. , Han J.
Published: April 2009

The overall objective of this research was to explore ageing consumers' attitudes towards currently available food packaging in New Zealand. Ninety‐nine individuals (over the age of 60) in New Zealand were surveyed to determine packaging attributes of importance when selecting food products. This was followed with a focus group of 13 individuals to discuss improvements to packaging. Frequencies of responses were calculated for the survey data, and cross‐tabulations and chi‐square tests were used to determine the relationships between variables. Price, safety, size of packaging and ability to recycle were of most importance to these individuals. Problems encountered with food packaging included tight lids, small printing and spillage during opening. Of the types of package closures investigated, opening of packages, rather than resealing of packages proved problematic. Fifty percent or more of respondents indicated that peelable induction seals, lug closures and continuous thread closures were problems that occurred ‘very often’ or ‘frequently’. Sixty‐one percent of the participants surveyed had asked for assistance opening some types of packages, and this was particularly prevalent among individuals who had weakness in their arms, hands or wrists. Changes to package closures suggested during the focus groups included increasing the size of twist off caps, larger ring pulls on aluminium cans and including more sliding resealable closures on foil and plastic packaging. Larger printing on labels was also recommended by the participants. Copyright © 2008 John Wiley & Sons, Ltd.

This article was published online on 1st December 2008. An error was subsequently identified. This notice is included in the online and print versions to indicate that both were corrected on 19th March 2009.
Beyond QSAR: Lead Hopping to Different Structures
Authors: Martin Yvonne C. , Muchmore Steven
Published: April 2009

We investigated the ability of several computer programs to detect lead hops that had been reported to result from pharmacophore searching. None of the methods identified all of these lead hops and some were not found by any program. The methods that performed the best identified different lead hops. Hence, we have deployed a lead hopping application that uses belief theory to combine the results of ROCS, Daylight, and ECFP_6 similarities.
Calculations of D‐wave bound states and resonance states of the screened helium atom using correlated exponential wave functions
Authors: Kar Sabyasachi , Ho Y. K.
Published: April 2009

We have investigated the effects of screened Coulomb (Yukawa) potentials on the bound 1,3D states and the doubly excited 1,3 De resonance states of helium atom using highly correlated exponential basis functions. The Density of resonance states are calculated using stabilization method. Highly correlated exponential basis functions are used to consider the correlation effect between the charged particles. A total of 18 resonances (nine each for 1 De and 3 De states) below the n = 2 He + threshold has been calculated. For each spin states, this includes four members in the 2pnp series, three members in the 2snd series, and two members in 2pnf series. The resonance energies and widths for various screening parameters ranging from infinity to a small value for these 1,3 De resonance states are reported along with the bound‐excited 1s3d 1,3 D state energies. Overall behavior of the spectral profile of 1s3d 1D state of helium atom due to electron‐electron and electron‐nucleus screening are also presented. Accurate resonance energies and widths are also reported for He in vacuum. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
My association with Frank Harris: An arc of forty‐four years
Authors: Monkhorst Hendrik J.
Published: April 2009

My collaborations with Frank Harris are reviewed. Besides reminiscing commentary on our long association, I explain the essentials of a recent proposal by Frank and me for a correlated basis set to implement the Molecular Coupled Cluster method I published in 1987. Its use will require the accurate evaluation of integrals over fully correlated Gaussian‐type n body functions. This has been achieved for arbitrary n in a pair of publications. A third paper by Frank shows the way to include angular factors. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
General two‐electron exponential type orbital integrals in polyatomics without orbital translations
Authors: Hoggan Philip E.
Published: April 2009

This article advocates the use of atomic orbitals which have direct physical interpretation, i.e., hydrogen‐like orbitals. They are exponential type orbitals (ETOs). Convenient nodeless linear combinations are used, namely Slater type orbitals (STOs) (with a product of a single power of r and an exponential as radial factor). Until 2008, such orbital products on different atoms were difficult to manipulate for the evaluation of two‐electron integrals. The difficulty was mostly due to cumbersome orbital translations involving slowly convergent infinite sums. These are completely eliminated using Coulomb resolutions. They provide an excellent approximation that reduces these integrals to a sum of one‐electron overlap‐like integral products that each involve orbitals on at most two centers. Such two‐center integrals are separable in prolate spheroidal coordinates. They are thus readily evaluated. Only these integrals need to be re‐evaluated to change basis functions. The above is still valid or three‐center integrals. In four‐center integrals, the resolutions require translating one potential term per product. This is outlined here and detailed elsewhere. Numerical results are reported for the H2 dimer and CH3F molecule. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Bonding in titanocenyl complexes containing O,O′‐cyclic ligands
Authors: Conradie Jeanet
Published: April 2009

Density functional theory calculations show that the formal 16‐electron count of d0 [Cp2TiIV(O,O′‐BID)]0/1 complexes containing a O,O′‐chelated bidentate ligand O,O′‐BID of different ring size, is increased via Ti←O π bonding when both the O donor atoms carry a formal negative charge. The Ti←O π bonding occurs by symmetry lowering of the complex by either symmetrical (Cs) or unsymmetrical (C2) folding of the O,O′‐BID ligand round the O···O axis. An NBO analysis confirms the Ti←O π charge transfer via back‐bonding. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2010
Stueckelberg oscillations in the charge transfer into the n = 2 and n = 3 shells of He2 on collision with H
Authors: Stolterfoht N. , Cabrera‐Trujillo R. , Krstić P. S. , Öhrn Y. , Deumens E. , Sabin J. R.
Published: April 2009

Probabilities for charge transfer by He2+ impact on atomic H are calculated at low‐collision energies using an ab initio theory, which solves the time‐dependent Schrödinger equation. The charge transfer is interpreted in terms of radial and rotational couplings of molecular orbitals. Strong Stueckelberg oscillations for the charge transfer probability into the n = 2 shell of helium are observed over nearly the entire impact parameter range. The same oscillations are found for the charge transfer into the n = 3 shell in the impact parameter range from 2.5 a.u. upwards, whereas at impact parameters below 2.5 a.u. the oscillations disappear abruptly. This observation is associated with specific pathways along the potential curves, which are responsible for the charge transfer. Similarities with the interferences in Young's two‐slit experiment are pointed out. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
The highly unsaturated dimetal hexacarbonyls of manganese and rhenium: Alternatives to a formal metal–metal quintuple bond
Authors: Xu Bing , Li Qian‐Shu , Xie Yaoming , King R. Bruce , Schaefer Henry F.
Published: April 2009

The structures of M2(CO)6 (M = Mn, Re) are of interest since a formal metal–metal quintuple bond is required to give each metal atom the favored 18‐electron configuration, assuming that all six carbonyl groups are the usual two‐electron donors. However, density functional theory studies on these systems provide no evidence for such structures having the very short metal–metal distances required for formal metal–metal quintuple bonds. Instead, the lowest energy structures predicted for Mn2(CO)6 have geometries consistent with a formal MnMn triple bond and two four‐electron donor bridging carbonyl groups, which also lead to the favored 18‐electron configuration for each manganese atom. For Mn2(CO)6, there is a higher‐lying structure (6–9 kcal/mol above the global minimum) with a MnMn quadruple bond distance of ∼2.18 Å. Four‐electron donor bridging carbonyl groups appear to be less favorable in the low‐energy Re2(CO)6 structures. Thus, the lowest energy Re2(CO)6 structure by ∼12 kcal/mol has all terminal carbonyl groups and a ReRe distance of 2.55 Å thereby suggesting a formal triple bond and a 16‐electron configuration for both rhenium atoms. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Spectrum‐like graphical representation of RNA secondary structure
Authors: Randić Milan , Vračko Marjan , Novič Marjana , Plavšić Dejan
Published: April 2009

We consider graphical representation for RNA secondary structure by assigning four horizontal lines to the unpaired bases A, C, G, U and four horizontal lines to paired bases A′, C′, G′, U′. The RNA graphical representation based on eight equidistant horizontal lines can be viewed as natural extension of the earlier four‐line graphical representation of DNA (Randić et al., Chem Phys Lett, 2003, 371, 202) to RNA. Numerical characterization of RNA is based on 8 × 8 matrices recording the adjacency of the nucleotide bases in the primary sequence of RNA when RNA is read from 5′ to 3′. The approach is illustrated on a set of nine viral RNAs, reported in the literature. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
On the Brillouin‐zone integrations in second‐order many‐body perturbation calculations for extended systems of one‐dimensional periodicity
Authors: Shimazaki Tomomi , Hirata So
Published: April 2009

The validity and accuracy of various ways of drastically reducing the number of k‐points in the Brillouin zone integrations occurring in second‐order many‐body perturbation calculations of one‐dimensional solids has been investigated. The most promising approximation can recover correlation energies of polyethylene and polyacetylene within 1% of converged values at less than a tenth of usual computational cost. The quasi‐particle energy bands have also been reproduced quantitatively with the same approximation. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Polarizabilities and second hyperpolarizabilities of hydrogen chains using the spin‐component‐scaled Møller–Plesset second‐order method
Authors: Champagne Benoît , Kirtman Bernard
Published: April 2009

Static longitudinal polarizabilities (α) and second hyperpolarizabilities (γ) of model H2 chains have been calculated at different ab initio levels to address the performance of the recently proposed spin‐component‐scaled MP2 (SCS‐MP2) method (Grimme, J. Chem Phys 2003, 118, 9095). For both α and γ, the SCS‐MP2 method improves over the MP2 results in comparison with reference values evaluated at the CCSD(T) level. Differences from the reference are in the range of 4–6% for α and 1–4% for γ. In the case of γ, the SCS‐MP2 scheme improves not only over MP2 but also MP4 and CCSD. Further studies are needed on π‐conjugated systems to evaluate the generality of these results. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Dynamics for the dynamic Frank Harris: Exploring H+ + CF4 at Elab = 20 and 30 eV
Authors: Maiti Buddhadev , McLaurin Patrick M. , Sadeghi Raymond , Ajith Perera S. , Morales Jorge A.
Published: April 2009

The H+ + CF4 reaction at collision energies ELab = 20 and 30 eV is investigated with the electron nuclear dynamics (END) theory. The level of END herein employed prescribes a classical‐mechanics description for the nuclei and a single‐determinantal representation for the electrons. The results include visualizations of the simulated collisions, and calculations of various scattering properties. The present simulations always predict noncharge‐transfer scattering (NCTS) for H+ + CF4 and exclude charge‐transfer, dissociation, and rearrangement reactions. The predicted rainbow angles and the total NCTS differential cross sections agree satisfactorily with the available experimental results. The present results are compared with those of the previously simulated H+ + CH4. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
An SO(4) invariant Hamiltonian and the two‐body bound state. I: Coulomb interaction between two spinless particles
Authors: Huntington Lee M. J. , Nooijen Marcel
Published: April 2009

We consider the nonrelativistic treatment of a hydrogenic atom in a four‐dimensional Euclidean space. The focus of this work is on the angular part of the problem, as this is potentially more generally applicable. Using a suitable coordinate system, the su(2)×su(2) structure of the so(4) Lie algebra is exploited. The hyperspherical harmonic solutions of the angular part of the problem are obtained in two ways: as solutions of a partial differential equation and by means of a ladder operator approach. The solutions of the radial equation and energy spectrum are determined and possible implications of the model are briefly discussed. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Chemical reactions in the gas phase and in condensed matter: From wavefunctions to density operators
Authors: Micha David A.
Published: April 2009

This contribution generalizes the treatment of chemical reactions in the gas phase based on the reaction channel decomposition of the wavefunction, by introducing a similar channel decomposition of the statistical density operator valid also for condensed phases such as liquid solutions and solid surfaces. Coupled equations for the channel components of the density operator are derived and a brief presentation is given of their partial Wigner transform, which leads to a general treatment for coupling quantum and classical variables. This provides a general approach for reactions involving electronically excited states in many‐atom systems. It is pointed out that reactions involving coupled quantal and classical variables can be correctly described provided (a) initial conditions for trajectories are generated from quantal distributions and (b) the bundle of trajectories for the whole initial classical phase space is propagated coupled to the quantal elements of the density matrix and used in the calculation of reaction flux averages. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Infinite‐order functional for nonlinear parameters optimization in explicitly correlated coupled cluster theory
Authors: Przybytek Michal , Jeziorski Bogumil , Szalewicz Krzysztof
Published: April 2009

Coupled cluster (CC) calculations with Gaussian geminals rely heavily on extensive optimizations of nonlinear parameters (exponents and positions) defining the geminal basis functions. As the CC method is not a variational theory, it provides no functional for such an optimization. The nonlinear parameters must therefore be supplied by some other theory, giving pair functions that can be expected to be close to those of the CC method. The conventional approach thus far was to use the second‐order many‐body perturbation theory with Møller–Plesset partition of the Hamiltonian (MP2) for this purpose and to minimize the corresponding Hylleraas‐type functional. We present a new functional, which goes beyond the second order, and can be applied in situations when the Møller–Plesset theory converges slowly. This functional does take a partial account of infinite‐order terms in the MP theory, but neglects the interpair coupling in the spirit of the independent electron pair approximation approach. The pair functions minimizing this new functional include the most important infinite‐order contributions from the point of view of the MP theory and are much closer to the CC pair functions than the first‐order ones. The nonlinear parameters obtained using this infinite‐order functional are then better suited for coupled cluster calculations than those obtained using the MP2 functional. The effectiveness of the new functional is demonstrated by performing coupled cluster doubles (CCD) calculations for the Be atom and Li− ion. The obtained energies are much better than those based on the MP2 optimizations and represent the most accurate CCD energies for these systems obtained thus far. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
An accurate few‐parameter ground state wave function for the lithium atom
Authors: Guevara Nicolais L. , Harris Frank E. , Turbiner Alexander V.
Published: April 2009

A simple, seven‐parameter trial function is proposed for a description of the ground state of the Lithium atom. It includes both spin functions. Inter‐electronic distances appear in exponential form as well as in a pre‐exponential factor, and the necessary energy matrix elements are evaluated by numerical integration in the space of the relative coordinates. Encouragingly accurate values of the energy and the cusp parameters as well as for some expectation values are obtained. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Quantum potential for diffraction and exchange effects
Authors: Dufty James , Dutta Sandipan , Bonitz Michael , Filinov Alexei
Published: April 2009

Semiclassical methods of statistical mechanics can incorporate essential quantum effects by using effective quantum potentials. An ideal Fermi gas interacting with an impurity is represented by a classical fluid with effective electron–electron and electron‐impurity quantum potentials. The electron‐impurity quantum potential is evaluated at weak coupling, leading to a generalization of the Kelbg potential to include both diffraction and degeneracy effects. The electron–electron quantum potential for exchange effects only is the same as that discussed earlier by others. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
Energy‐dependent scaling of the Dirac equation
Authors: Karwowski Jacek , Pestka Grzegorz
Published: April 2009

Using an energy‐dependent scaling, the Dirac Hamiltonian eigenvalue problem has been transformed to a Lévy–Leblond‐like equation. Its spectrum is bounded from below and the algebraic representation results in an algebraic eigenvalue problem for the large component of the Dirac wavefunction. © 2009 Wiley Periodicals, Inc. Int J Quantum Chem, 2009
A retention‐time‐shift‐tolerant background subtraction and noise reduction algorithm (BgS‐NoRA) for extraction of drug metabolites in liquid chromatography/mass spectrometry data from biological matrices
Authors: Zhu Peijuan , Ding Wei , Tong Wei , Ghosal Anima , Alton Kevin , Chowdhury Swapan
Published: April 2009

A retention‐time‐shift‐tolerant background subtraction and noise reduction algorithm (BgS‐NoRA) is implemented using the statistical programming language R to remove non‐drug‐related ion signals from accurate mass liquid chromatography/mass spectrometry (LC/MS) data. The background‐subtraction part of the algorithm is similar to a previously published procedure (Zhang H and Yang Y. J. Mass Spectrom. 2008, 43: 1181–1190). The noise reduction algorithm (NoRA) is an add‐on feature to help further clean up the residual matrix ion noises after background subtraction. It functions by removing ion signals that are not consistent across many adjacent scans. The effectiveness of BgS‐NoRA was examined in biological matrices by spiking blank plasma extract, bile and urine with diclofenac and ibuprofen that have been pre‐metabolized by microsomal incubation. Efficient removal of background ions permitted the detection of drug‐related ions in in vivo samples (plasma, bile, urine and feces) obtained from rats orally dosed with 14C‐loratadine with minimal interference. Results from these experiments demonstrate that BgS‐NoRA is more effective in removing analyte‐unrelated ions than background subtraction alone. NoRA is shown to be particularly effective in the early retention region for urine samples and middle retention region for bile samples, where the matrix ion signals still dominate the total ion chromatograms (TICs) after background subtraction. In most cases, the TICs after BgS‐NoRA are in excellent qualitative correlation to the radiochromatograms. BgS‐NoRA will be a very useful tool in metabolite detection and identification work, especially in first‐in‐human (FIH) studies and multiple dose toxicology studies where non‐radio‐labeled drugs are administered. Data from these types of studies are critical to meet the latest FDA guidance on Metabolite in Safety Testing (MIST). Copyright © 2009 John Wiley & Sons, Ltd.
Analysis of underivatized oligosaccharides by liquid chromatography/electrospray ionization tandem mass spectrometry with post‐column addition of formic acid
Authors: Verardo Giancarlo , Duse Irene , Callea Alessandro
Published: April 2009

Underivatized oligosaccharides were analyzed by electrospray ionization (ESI) using a linear ion trap mass spectrometer in the negative ion mode with post‐column addition of an aqueous solution of formic acid. Under these conditions all oligosaccharides showed the presence of the corresponding formate adduct [M + HCOO]− with high intensity and easy subsequent low‐energy collision‐induced dissociation (CID) fragmentation using successive MSn experiments. A careful examination of the mass spectra obtained from these MSn experiments pointed out some significant differences useful to identify and quantify the single components in mixtures of coeluted disaccharides. This new sensitive and rapid method was successfully applied to the quantification of oligosaccharides in some juices minimizing sample handling. Copyright © 2009 John Wiley & Sons, Ltd.
Autonomous robot navigation in outdoor cluttered pedestrian walkways
Authors: Morales Yoichi , Carballo Alexander , Takeuchi Eijiro , Aburadani Atsushi , Tsubouchi Takashi
Published: April 2009

This paper describes an implementation of a mobile robot system for autonomous navigation in outdoor concurred walkways. The task was to navigate through nonmodified pedestrian paths with people and bicycles passing by. The robot has multiple redundant sensors, which include wheel encoders, an inertial measurement unit, a differential global positioning system, and four laser scanner sensors. All the computation was done on a single laptop computer. A previously constructed map containing waypoints and landmarks for position correction is given to the robot. The robot system's perception, road extraction, and motion planning are detailed. The system was used and tested in a 1‐km autonomous robot navigation challenge held in the City of Tsukuba, Japan, named “Tsukuba Challenge 2007.” The proposed approach proved to be robust for outdoor navigation in cluttered and crowded walkways, first on campus paths and then running the challenge course multiple times between trials and the challenge final. The paper reports experimental results and overall performance of the system. Finally the lessons learned are discussed. The main contribution of this work is the report of a system integration approach for autonomous outdoor navigation and its evaluation. © 2009 Wiley Periodicals, Inc.
Microinvertebrate dynamics in riverine slackwater and mid‐channel habitats in relation to physico‐chemical parameters and food availability
Authors: Ning Nathan S. P. , Nielsen Daryl L. , Paul Warren L. , Hillman Terry J. , Suter Phil J.
Published: April 2009

Microinvertebrates play a critical role in riverine food webs, and recent studies have hypothesized that slackwaters, non‐flowing regions associated with the main channel, are important for their reproduction and recruitment. However, little is known regarding the population and community dynamics of microinvertebrate communities in slackwater regions, or how they compare with those in mid‐channel regions. This study examined microinvertebrate communities in the epibenthic and pelagic zones of slackwater and mid‐channel regions (i.e. four habitats) of an Australian floodplain river in relation to physico‐chemical parameters and food availability (as estimated by chlorophyll‐a concentration) between September 2005 and November 2006. Results from this study indicate that microinvertebrate abundance and diversity were greater in slackwater habitats than mid‐channel habitats overall, corresponding with the slower current velocities associated with the former. Nevertheless, communities in all four habitats were most abundant and diverse in late spring (coinciding with an increase in water temperature), and followed similar seasonal trajectories in terms of density, taxon richness and community structure. These findings support the view that slackwaters are important for in‐channel microinvertebrate production, and suggest that animals frequently disperse (either actively or passively) among slackwater and other main channel regions year round. Given the critical importance of microinvertebrates in riverine food webs, rivers should be managed with a view to maintaining a natural variety of accessible slackwater regions in order to support the production and survival of microinvertebrate communities. Copyright © 2009 John Wiley & Sons, Ltd.