bluuebunny/crossref_metadata_2025_split huggingface dataset:
Studies of Fe‐binding sites within multiwall carbon nanotubes using Mössbauer spectroscopy
Authors: Luberda‐Durnaś Katarzyna , Nieznalska Magdalena , Mazurkiewicz Marta , Małolepszy Artur , Khachataryan Gohar , Khachataryan Karen , Tomasik Piotr , Michalski Oskar , Matlak Krzysztof , Korecki Józef , Stobinski Leszek , Burda Květoslava 
Published: July 2011

AbstractThe potential applications of carbon nanotubes (CNTs) are strongly related to their physical and chemical properties. In this work, results of different methods for the oxidation of crude CNTs are reported. These methods changed Fe binding sites within multiwall carbon nanotubes (MWCNTs). Mössbauer spectroscopy was used to detect the chemical properties of the Fe‐phases in MWCNTs. Signals from the iron carbide Fe3C were the main components in the Mössbauer spectra of unmodified MWCNTs revealing magnetic ordering even at 300 K. In oxidized MWCNTs, the amount of Fe3C decreased and γ‐Fe and α‐Fe, ferrihydrates of iron oxides and different forms of goethite appeared. In MWCNTs oxidized with HClO4, a significant fraction (∼24%) of magnetically ordered Fe2O3 particles was detected. This study showed that traces of iron catalyst embedded in MWCNTs could be used as a sensitive probe to monitor various MWCNT modifications.
Al catalyzed growth of silicon nanowires and subsequent in situ dry etching of the catalyst for photovoltaic application
Authors: Kohen David , Tileli Vasiliki , Cayron Cyril , Faucherand Pascal , Morin Christine , Dufourcq Joël , Noël Sébastien , Levis Michel , Brioude Arnaud , Perraud Simon 
Published: July 2011

AbstractAluminum‐catalyzed epitaxial growth of silicon nanowire (SiNW) arrays was performed on Si wafer by chemical vapor deposition at 600 °C. The arrays showed a low optical total reflectance in the visible light spectrum, with a minimum of 2% around 450 nm wavelength. Following SiNW growth, dry etching of the Al catalyst was performed in situ using HCl chemistry at 600 °C. The effectiveness of aluminum etching was assessed by energy dispersive X‐ray spectroscopy, by high resolution transmission electron microscopy and by a controlled growth experiment. This SiNW array growth and subsequent catalyst dry etching opens up the possibility of an all in vacuum fabrication process of radial junction solar cells.Al catalyst dry etching following growth using HCl gas at 600 °C.magnified imageAl catalyst dry etching following growth using HCl gas at 600 °C.
Pentagonal puckering in a sheet of amorphous graphene
Authors: Li Y. , Inam F. , Kumar Avishek , Thorpe M. F. , Drabold D. A. 
Published: July 2011

AbstractOrdered graphene has been extensively studied. In this paper, we undertake a density functional study of topologically disordered analogs of graphene, in the form of a random network, consisting predominantly of hexagonal rings, but also including pentagons and heptagons. After some preliminaries with crystalline material, we relax various random network models and find that the presence of carbon pentagons induce local curvature, thus breaking the initial planar symmetry, in some analogy with the case of fullerenes. Using density functional theory to calculate the total energy, we find that while the planar state is locally stable, there is a puckered state that has lower energy. The scale of the puckering is consistent with that expected with local maxima and minima associated with pentagons surrounded by larger rings, forming local “buckyball domes”.
Density functional theory studies on structures and absorption spectra of [Au(tpy)Cl]2+ and its derivatives: Role of basis set, functional, solvent effect, and spin orbit effect
Authors: Li Haibin , Wu Shuixing , Liao Yi , Su Zhongmin , Kan Yuhe , Tang Xueling 
Published: July 2011

AbstractThe geometries of [Au(tpy)Cl]2+ (tpy = 2,2′:6′,2″‐terpyridine) and its derivatives (1–4) were optimized using relativistic density functional theory (DFT) at both scalar and two‐component spin orbit coupling (SOC) level of theory via zero order regular approximation (ZORA). The combination of OPTX exchange, PW91c correlation functional (denoted as OP91), all‐electron ZORA TZ2P basis set was found to be the optimal combination for geometry. The results reveal that both SOC and substituents have little effect on the geometry of complexes 1–4. Then, their absorption spectra were investigated by scalar relativistic time dependent DFT (TDDFT)/SAOP/TZ2P in vacuum, in CH2Cl2, CH3CN solvents by means of conductor like screening model. The calculations indicate that the nature of the low‐lying spin‐allowed excited states is gold‐perturbed intraligand transition, namely charge reorganization. This fact also demonstrates that the influence of the polarity of solvent on absorption spectra of 1–4 is negligible. The spin orbit TDDFT was also performed to get further insight into the effect of SOC on the absorption spectra. It is found that the SOC has little influence on the simulation of electronic spectrum of complexes 1–4 due to no significant involvement of d‐orbitals during electronic transition. Our conclusions are reliable and are in good agreement with the previous experimental results and theoretical investigations. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
An experimental and theoretical approach to the molecular structure of 3‐{[4‐(3‐Methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐ indol‐2‐one
Authors: Saraçoğlu Hanİfe , Cukurovali Alaaddin 
Published: July 2011

AbstractThe title molecule, 3‐{[4‐(3‐methyl‐3‐phenyl‐cyclobutyl)‐thiazol‐2‐yl]‐hydrazono}‐1,3‐dihydro‐indol‐2‐one (C22H20N4O1S1), was prepared and characterized by 1H NMR, 13C NMR, IR, UV–visible, and single‐crystal X‐ray diffraction. The compound crystallizes in the monoclinic space group P21 with a = 8.3401(5), b = 5.6976(3), c = 20.8155(14) Å, and β = 95.144(5)°. Molecular geometry from X‐ray experiment and vibrational frequencies of the title compound in the ground state has been calculated using the Hartree–Fock with 6‐31G(d, p) and density functional method (B3LYP) with 6‐31G(d, p) and 6‐311G(d, p) basis sets, and compared with the experimental data. The calculated results show that optimized geometries can well reproduce the crystal structural parameters, and the theoretical vibrational frequencies values show good agreement with experimental data. Density functional theory calculations of the title compound and thermodynamic properties were performed at B3LYP/6‐31G(d, p) level of theory. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
New graphical representation of a DNA sequence based on the ordered dinucleotides and its application to sequence analysis
Authors: Huang Yujuan , Wang Tianming 
Published: July 2011

AbstractGraphical representation of a DNA sequence is a powerful tool for basic biological research. Based on the ordered dinucleotides, we propose a novel three dimensional (3D) graphical representation without circuit or degeneracy. Simultaneously, we derive the projection curve of the 3D graph. These two curves have good visualization for longer DNA sequences. The utility of the proposed curves is illustrated by mutation analysis, similarity analysis, and evolutionary relationships of different species. The results indicate that our method is efficient and powerful. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Vibrational contribution to static and dynamic (Hyper)polarizabilities of zigzag BN nanotubes calculated by the finite field nuclear relaxation method
Authors: Ferrabone Matteo , Kirtman Bernard , Lacivita Valentina , Rérat Michel , Orlando Roberto , Dovesi Roberto 
Published: July 2011

AbstractThe vibrational contribution to static and dynamic (hyper)polarizabilities for the zigzag (n,0) family of BN nanotubes, with n ranging from (6,0) to (36,0), has been obtained. Calculations were done by the finite field nuclear relaxation (FF‐NR) method for periodic systems, newly implemented in the CRYSTAL code, using the Coupled Perturbed Kohn‐Sham (CPKS) scheme at the B3LYP/6‐31G* level for the required electronic properties. Both transverse and transverse‐longitudinal tensor components are determined by applying finite, i.e. static, fields in the transverse direction. The magnitude of the vibrational term increases with the radius of the nanotube as determined by the increase in the field‐induced geometric deformation. The resulting vibrational (hyper)polarizability varies from being dominant to negligible, when compared with the corresponding static electronic contribution. This depends upon the radius, as well as the property and the component, in a systematic manner. The extension to longitudinal components, not yet available, will be implemented next. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Double icosahedron‐based motif of Nin (n = 20−30)
Authors: Song Wei , Lu Wen‐Cai , Zang Qing‐Jun , Wang C. Z. , Ho K. M. 
Published: July 2011

AbstractA genetic algorithm (GA) coupled with a tight‐binding (TB) interatomic potential was used to search for the low‐energy structures of the medium‐sized Nin (n = 20−30) clusters. The low‐energy candidate structures from the GA/TB search were further optimized by using the density functional theory calculations with the Perdew, Burke, and Ernzerhof exchange‐correlation energy functional. The obtained lowest‐energy structures of the medium‐sized Nin (n = 20−30) clusters are shown to exhibit double icosahedron‐based motif. The properties of the nickel clusters including binding energies, second differences in energy, and especially magnetic properties have also been studied. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Theoretical thermochemistry: Enthalpies of formation of a set of nitrogen‐containing compounds
Authors: He Xin , Zhang Jiaheng , Gao Haixiang 
Published: July 2011

AbstractGas‐phase standard state formation enthalpies of 63 nitrogen‐containing compounds (NCCs) were studied by computational methods. Gaussian‐n and complete basis set composite methods were applied. After the calculation of the set of NCCs, the results were analyzed in several ways. All the seven selected methods depicted various precisions in this work. According to the calculations and further data processing, G4 was proven to be appropriate and capable of formation enthalpy calculations on NCCs with a mean absolute deviation of 0.63 kcal/mol. Thus, G4 calculation may help us on choosing experimental values and conducting predictions. Isodesmic reactions using G4 methods are also conducted and further correction was given. The high accuracy of G4 method makes it reliable for calculating gas‐phase enthalpies of formations and allows them to serve as a valuable check on the accuracy of reported experimental data. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Structure‐Dependence of the magnetic moment in small palladium clusters: Surprising results from the M06‐L Meta‐GGA functional
Authors: Koitz Ralph , Soini Thomas M. , Genest Alexander , Trickey S. B. , Rösch Notker 
Published: July 2011

AbstractThe size‐ and structure‐dependence of the magnetic moment in Pdn clusters (n = 13, 19, 38) was studied with density functional theory. We compare the Becke‐Perdew gradient‐corrected exchange‐correlation functional with the parameterized meta‐generalized gradient approximation functional by Zhao and Truhlar (M06‐L). Although the former functional shows the expected quenching of the clusters' magnetic moment with increasing nuclearity, the latter one predicts a strongly increasing magnetic moment. In a series of fixed‐spin calculations with the two functionals at different geometries, we observe a strong dependence of the magnetic moment on the cluster structure, where the untypically long metal‐metal bonds predicted by the M06‐L functional are a dominant influence on the stability of the high‐spin cluster configurations. Furthermore, we observe differing behavior of the two functionals with respect to the magnetic moment as particular bonds in the cluster are strained, indicating that, in addition to the structural contribution, the description of exchange‐correlation energy in the M06‐L functional may intrinsically favor high magnetic moments in these Pd clusters. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Wigner crystallization of quadratically dispersing electrons in graphene
Authors: Iyakutti Kombiah , Surya Velappa Jayaraman , Rajeswarapalanichamy Ratnavelu , Kawazoe Yoshiyuki 
Published: July 2011

AbstractThe graphene surface with the unpaired π electrons presents an ideal two‐dimensional electron system. Although the effective massless Dirac fermions are important, they are not the only carriers that describe the quantum transport in graphene. Above zero energy, the current carrying carriers in graphene are the usual electrons. This electron density may vary depending on the surface defects and π–σ interaction, and this may lead to a possible Wigner crystallization on the surface of graphene. Calculations for nonmagnetic, ferromagnetic, and antiferromagnetic Wigner crystals are carried out based on the Koster–Kohn variational principle for direct calculation of Wannier functions. The effect of positive background due to the carbon ions is suitably treated. From our results, we find that Wigner crystallization is possible in grapheme, if we consider the electrons on the surface, which obey quadratic dispersion relation. The electron crystal with ferromagnetic phase and face centered square lattice structure has the lowest energy. © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Ab initio path integral simulation of AgOH(H2O)
Authors: Koizumi Akihito , Suzuki Kimichi , Shiga Motoyuki , Tachikawa Masanori 
Published: July 2011

AbstractAb initio path integral molecular dynamics simulation of MOH(H2O) (M = Cu, Ag, and Au) clusters has been performed to analyze how the hydrogen‐bonded proton can be affected by the counter noble metal cation. The CuOH(H2O) cluster does not form hydrogen bonded structure even for the static equilibrium structures. Contrary to our previous article of hydrated alkali metal hydroxide clusters (Koizumi et al., J Chem Phys 2011, 134, 031101), proton transferred distribution was not observed because of the high potential barrier heights of MOH(H2O). © 2011 Wiley Periodicals, Inc. Int J Quantum Chem, 2012
Temperature Determination of Resonantly Excited Plasmonic Branched Gold Nanoparticles by X‐ray Absorption Spectroscopy
Authors: Van de Broek Bieke , Grandjean Didier , Trekker Jesse , Ye Jian , Verstreken Kris , Maes Guido , Borghs Gustaaf , Nikitenko Sergey , Lagae Liesbet , Bartic Carmen , Temst Kristiaan , Van Bael Margriet J. 
Published: July 2011

AbstractThe fields of bioscience and nanomedicine demand precise thermometry for nanoparticle heat characterization down to the nanoscale regime. Since current methods often use indirect and less accurate techniques to determine the nanoparticle temperature, there is a pressing need for a direct and reliable element‐specific method. In‐situ extended X‐ray absorption fine structure (EXAFS) spectroscopy is used to determine the thermo‐optical properties of plasmonic branched gold nanoparticles upon resonant laser illumination. With EXAFS, the direct determination of the nanoparticle temperature increase upon laser illumination is possible via the thermal influence on the gold lattice parameters. More specifically, using the change of the Debye–Waller term representing the lattice disorder, the temperature increase is selectively measured within the plasmonic branched nanoparticles upon resonant laser illumination. In addition, the signal intensity shows that the nanoparticle concentration in the beam more than doubles during laser illumination, thereby demonstrating that photothermal heating is a dynamic process. A comparable temperature increase is measured in the nanoparticle suspension using a thermocouple. This good correspondence between the temperature at the level of the nanoparticle and at the level of the suspension points to an efficient heat transfer between the nanoparticle and the surrounding medium, thus confirming the potential of branched gold nanoparticles for hyperthermia applications. This work demonstrates that X‐ray absorption spectroscopy‐based nanothermometry could be a valuable tool in the fast‐growing number of applications of plasmonic nanoparticles, particularly in life sciences and medicine.
Evolution of Langmuir Film of Nanoparticles Through Successive Compression Cycles
Authors: Kim Jin Young , Raja Shilpa , Stellacci Francesco 
Published: July 2011

AbstractThe success of nanoparticle‐based devices will need reliable fabrication methods for well‐defined, defect‐free self‐assembled structures of nanoparticles (NPs). NP self‐assembly is a process governed by an interplay between many inter‐particle interactions, such as core–core van der Waals and dipolar attractions, as well as interactions of the ligand shells, which, when generating an interpenetration, is called interdigitation. The result of this delicate balance between strong interactions is often kinetically hindered; hence, the reaching and recognition of an equilibrium structure becomes challenging. Here, a systematic study is presented that aims at approaching equilibrium 2D NP assemblies (i.e., NP monolayers) based on cyclic compression and relaxation in Langmuir NP monolayers. Cyclic isotherm curves are taken at various surface pressures together with a complete characterization of the corresponding structural evolution of the NP structures. Results are obtained through the analysis of the images, using in‐house software that enables the analysis and visualization of the degree of ligand interdigitation as well as the NPs short‐ and long‐range order. It is found that the initial structures obtained through Langmuir assembly can be quite far from equilibrium, mostly due to inhomogeneities in the ligand shell interdigitation and interaction. A few compression cycles render the whole assembly more homogeneous and significantly increases the long‐range order. Finally, this structural analysis shows that the ligand shell can act a buffer to the size polydispersity in the particle cores.
Clustering genes with expression and beyond
Authors: Shiga Motoki , Mamitsuka Hiroshi 
Published: July 2011

AbstractClustering over gene expression is now a popular computational analysis in biology. In general, the amount of expression can be measured by high‐throughput techniques over thousands of genes simultaneously. The expression dataset can be a large table (or matrix) with numerical values, each being specified by one gene and one sample, and needs computational methods to be analyzed. This review starts with surveying techniques of clustering genes by expression, classifying them into three types: hierarchical, partitional, and subspace clustering. Major methods of hierarchical and partitional clustering as well as a variety of algorithms for subspace clustering are extensively reviewed. Techniques for clustering over expression, however, are now well matured and their performance is limited due to the inevitable noisiness of the high‐throughput nature of expression data. We then extend the scope of this review further to clustering genes with recently emerging data, gene networks, and show graph partitioning approaches, such as spectral methods, for clustering genes by a network. Furthermore, advanced approaches of gene clustering now combine gene networks with expression. This setting corresponds to so‐called semi‐supervised clustering in machine learning, and approaches under this problem setting will be widely reviewed, classifying those approaches into three types. © 2011 John Wiley & Sons, Inc. WIREs Data Mining Knowl Discov 2011 1 496–511 DOI: 10.1002/widm.41This article is categorized under:

Algorithmic Development > Biological Data Mining
Application Areas > Science and Technology
Technologies > Machine Learning
Nanotechnology in interventional cardiology
Authors: Cyrus Tillmann , Wickline Samuel A. , Lanza Gregory M. 
Published: July 2011

AbstractHigh‐grade atherosclerotic stenoses are reduced to zero or minimal residual stenosis grades by a single or a series of balloon angioplasties. Currently, stents are implanted to prevent immediate vascular recoil and elution of an antimitotic drug from the stent struts minimizes restenosis. An unwanted side‐effect of this drug elution is delayed re‐endothelialization which requires treatment with two anti‐platelet drugs, in many cases for a minimum of 1 year to prevent acute in‐stent thrombosis. Advances in stent design and drug elution technology, now in its fourth generation, have not abated this issue. Nanotechnology‐based local drug delivery has the potential to achieve restenosis prevention while not impeding endothelial healing. Molecularly targeted drugs can be aimed to specifically bind to epitopes in the injured media and adventitia. Thus, endothelial healing may progress unhindered. To prevent restenosis, this technology may be used with bare metal or biodegradable stents. In this article novel nanoparticulate agents will be compared regarding their potential to deliver drugs to molecular targets within the vascular wall. Potential molecular targets, targeting mechanisms, drug‐delivery propensities, and biocompatibility will be reviewed. WIREs Nanomed Nanobiotechnol 2012, 4:82–95. doi: 10.1002/wnan.154This article is categorized under:

Therapeutic Approaches and Drug Discovery > Emerging Technologies
Diagnostic Tools > In Vivo Nanodiagnostics and Imaging
Therapeutic Approaches and Drug Discovery > Nanomedicine for Cardiovascular Disease
Clinical Significance of the B7‐H4 Coregulatory Molecule as a Novel Prognostic Marker in Gastric Cancer
Authors: Arigami Takaaki , Uenosono Yoshikazu , Ishigami Sumiya , Hagihara Takahiko , Haraguchi Naoto , Natsugoe Shoji 
Published: July 2011

AbstractBackgroundThe B7‐H4 coregulatory molecule is a member of the B7 family of molecules, which regulate the T‐cell‐mediated immune response through CD28 receptors. Recently, B7‐H4 has been reported to be a negative regulator of the immune response in patients with several malignant diseases. However, few reports have investigated the clinical significance of B7‐H4 expression in patients with gastric cancer. In the present study, we analyzed B7‐H4 expression and the relationship between its expression and clinicopathological factors including prognosis in gastric cancer.MethodsB7‐H4 expression in gastric cancer cell lines and clinical gastric cancer specimens was initially assessed with the reverse transcription‐polymerase chain reaction (RT‐PCR). Moreover, B7‐H4 and CD3 expression in 120 resected specimens from gastric cancer patients were evaluated by immunohistochemistry (IHC).ResultsB7‐H4 expression was identified in the gastric cancer cell lines and clinical tumor tissues by RT‐PCR. B7‐H4 expression was high in 25.8% (31/120) of resected tumor specimens. B7‐H4 expression significantly correlated with tumor stage (P = 0.04). The 5‐year survival rate was significantly lower in patients with high B7‐H4 expression than in those with low B7‐H4 expression (P = 0.001). Multivariate analysis demonstrated that B7‐H4 expression was an independent prognostic factor (P = 0.035). Immunohistochemical analysis of CD3 expression showed that B7‐H4 expression was inversely correlated with the number of tumor infiltrating T lymphocytes (P < 0.001).ConclusionsThe B7‐H4 coregulatory molecule is a novel prognostic marker related to the T‐cell‐mediated immune response, and its pathway may be a molecular target for controlling tumor progression in patients with gastric cancer.