bluuebunny/crossref_metadata_2025_split huggingface dataset:
What stabilizes the 314‐helix in β3‐peptides? A conformational analysis using molecular simulation
Authors: Keller Bettina , Gattin Zrinka , van Gunsteren Wilfred F. 
Published: January 2010

Abstractβ‐Peptides are analogs of natural α‐peptides and form a variety of remarkably stable structures. Having an additional carbon atom in the backbone of each residue, their folded conformation is not only influenced by the side‐chain sequence but also and foremost by their substitution pattern. The precise mechanism by which the side chains interact with the backbone is, however, hitherto not completely known. To unravel the various effects by which the side chains influence the backbone conformation, we quantify to which extent the dihedral angles of a β3‐substited peptide with an additional methyl group on the central Cα‐atom can be regarded as independent degrees of freedom and analyze the distributions of these dihedral angles. We also selectively capture the steric effect of substituents on the Cα‐ and Cβ‐atoms of the central residue by alchemically changing them into dummy atoms, which have no nonbonded interactions. We find that the folded state of the β3‐peptide is primarily stabilized by a steric exclusion of large parts of the unfolded state (entropic effect) and only subsequently by mutual dependence of the ψ‐dihedral angles (enthalpic effect). The folded state of β‐peptides is stabilized by a different mechanism than that of α‐peptides. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Molecular dynamics study of interaction and substrate channeling between neuron‐specific enolase and B‐type phosphoglycerate mutase
Authors: Hakobyan Davit , Nazaryan Karen 
Published: January 2010

AbstractPhosphoglycerate mutase (PGM) and enolase are consecutive enzymes in the glycolytic pathway. We used molecular dynamics simulation to examine the interaction of human B‐type PGM (dPGM‐B) and neuron‐specific enolase (NSE). Specifically, we studied the interactions of 31 orientations of these enzymes by means of the effective energy function implicit solvation method. Interactions between active regions of the enzymes occurred preferentially, although the strongest interactions appeared to be between the back side of NSE and the active regions of dPGM‐B. Cleavage of 2PG from dPGM‐B was investigated, and the Ser14–Leu30 loop of dPGM‐B is suggested as a cleavage site and, likely, another entrance site of a ligand. Substrate channeling between the enzymes was observed when NSE with its active regions Leu11–Asn16, Arg49–Lys59, and Gly155–Ala158 covered the Ser14–Leu30 loop of dPGM‐B. Analyses of the results make us believe that the channeling between PGM and enolase “benefits” from weak interaction. The probability of formation of channeling favorable complex is estimated to be up to 5%, while functional interaction between NSE and dPGM‐B might be as high as 20%. NSE and dPGM‐B functional interaction seems not to be isotype specific. Proteins 2010. © 2010 Wiley‐Liss, Inc.
Stability of polar semiconductor heterostructures
Authors: Leitsmann R. , Bechstedt F. , Groiss H. , Schäffler F. 
Published: January 2010

AbstractIn the present paper we use an ab initio density functional theory approach to investigate the stability of differently terminated PbTe(rs)/CdTe(zb)(100) and ErAs(rs)/InGaAs2(zb)(100) heterostructures for different environmental conditions. While in PbTe/CdTesystems differently terminated interfaces are favored in ErAs/InGaAs2 heterostructure systems with two equivalent interface terminations are the most stable configuration. This behavior is the consequence of the less strong ionic character of InGaAs2 compared to CdTe (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Optical anisotropy of Si(111)‐(4 × 1)/(8 × 2)‐In nanowires calculated from first‐principles
Authors: Wippermann S. , Schmidt W. G. , Bechstedt F. , Chandola S. , Hinrichs K. , Gensch M. , Esser N. , Fleischer K. , McGilp J. F. 
Published: January 2010

AbstractFirst‐principles calculations of the anisotropic optical response of Si(111)‐(4 × 1)(8 × 2)‐In from the mid‐infrared to the visible region are compared with recent experimental data. The experimental data show that the anisotropic Drude tail of the (4 × 1) room‐temperature phase is replaced by two peaks at 0.50eV and 0.72eV after the phase transition to the low‐temperature (8 × 2) structure took place.The spectrum calculated from both intraband and interband transitions for the metallic zig‐zag chain model of the (4 × 1) phase accounts well for the room‐temperature data. The low‐temperature data are well explained on the basis of the semiconducting hexagon (8 × 2) model by interband transitions mainly from a region close the high‐symmetry line of the Brillouin zone (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
A hybrid approach to the surface biofunctionalization of nanostructured porous alumina
Authors: Silván Miguel Manso , González Ruy Sanz , Ruiz Josefa Predestinación García , Vélez Manuel Hernández 
Published: January 2010

AbstractThe application of nanostructured porous alumina templates as a solid support in biomedical assays requires a surface biofunctionalization process that has been addressed in this work by an hybrid aminopropyl‐triethoxysilane/tetraisopropyl‐orthotitanate (APTS/ TIPT) self assembled film. The nanostructured porous alumina templates are activated in a peroxide solution before immersion in the biofunctionalizing APTS/TIPT solution. The biofunctionalization process was followed up by UV‐vis spectroscopy, which confirmed the modification of the dielectric structure of the alumina surface. The influence of the biofunctionalization step in an immunological assay was carried out by fluorescence microscopy. Results confirm the gain in activity after the immobilization of an FITC labelled mouse Igg. Specific biological recognition in a bovine serum albumin (BSA)‐antiBSA assay is proved afterwards by shifts observed in the reflectance interferograms thus providing a fast biosensing transducer platform. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Kelvin‐probe studies of n‐conductive organic field‐effect transistors during operation
Authors: Lüttich Franziska , Lehmann Daniel , Graaf Harald , Zahn Dietrich R. T. , Borczyskowski Christian von 
Published: January 2010

AbstractWe report on our investigations of the structural and electronic properties of n‐conductive organic field‐effect transistors (OFETs). For this purpose we employed the atomic force microscopy (AFM) and Kelvin‐probe force microscopy (KPFM) in dual frequency mode. This study facilitates the determination of the local potential in the channel of active OFETs. We studied the influence of insulator treatment on the electrical potential and field distribution within the channel using a self‐assembled monolayer of N‐octadecyltrichlorosilane (OTS). For the investigated OFETs we used air‐stable and electron conducting N,N′‐bis(n‐octyl)‐dicyanoperylene‐3,4:9,10‐bis(dicarboximide) (PDI‐8CN2). It appears that the insulator treatment improves the performance even if the surface topography did not change. These results can lead to a better understanding of the charge transport and injection and pave the way towards the optimisation of the electronical properties of active organic devices (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Molecular and biomolecular interfaces to metal oxide semiconductors
Authors: Hamers Robert J. , Chambers Scott A. , Evans Paul G. , Franking Ryan , Gerbec Zachary , Gopalan Padma , Kim Heesuk , Landis Elizabeth C. , Li Bo , McCoy Michael W. , Ohsawa Takeo , Ruther Rose 
Published: January 2010

AbstractPrevious work has shown that organic alkenes will graft to covalent semiconductors such as diamond and silicon. Here, we demonstrate that organic alkenes can be grafted to the surfaces of metal oxide semiconductors, including TiO2 in nanocrystalline thin films and as single‐crystal anatase(001) epitaxial films grown on SrTiO3(001) substrates. The resulting layers can be used as a starting point for linking biomolecules such as DNA to metal oxide surfaces. Initial results are presented showing that this chemistry can also be applied to graft molecular layers to zirconium oxide thin films. (© 2010 WILEY‐VCH Verlag GmbH & Co. KGaA, Weinheim)
Graphical displays for clarifying how allocation ratio affects total sample size for the two sample logrank test
Authors: Saville Benjamin R. , Kim Yong S. , Koch Gary G. 
Published: January 2010

AbstractFor time‐to‐event data, the power of the two sample logrank test for the comparison of two treatment groups can be greatly influenced by the ratio of the number of patients in each of the treatment groups. Despite the possible loss of power, unequal allocations may be of interest due to a need to collect more data on one of the groups or to considerations related to the acceptability of the treatments to patients. Investigators pursuing such designs may be interested in the cost of the unbalanced design relative to a balanced design with respect to the total number of patients required for the study. We present graphical displays to illustrate the sample size adjustment factor, or ratio of the sample size required by an unequal allocation compared to the sample size required by a balanced allocation, for various survival rates, treatment hazards ratios, and sample size allocation ratios. These graphical displays conveniently summarize information in the literature and provide a useful tool for planning sample sizes for the two sample logrank test. Copyright © 2010 John Wiley & Sons, Ltd.
A DFT study of acetonitrile adsorption and decomposition on the TiO2 (110) surface
Authors: Zou Xiu‐Juan , Ding Kai Ning , Zhang Yong Fan , Li Jun Qian 
Published: January 2010

AbstractThe adsorption and decomposition of acetonitrile on the TiO2 (110) surface have been investigated with first principles calculations. Our results reveal that both CN and CC bonds of acetonitrile become weakened after adsorption. Acetonitrile behaves as an electron donor, and electrons transfer from acetonitrile to substrate is obvious. The reaction mechanism of further decomposition of acetonitrile on TiO2 (110) surface is also investigated, and the result shows that acetonitrile can decompose into CH3 and CN fragments and form OCH3 and NCO groups on the TiO2 (110) surface, which consists with the experimental results. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Theoretical investigation of solvent effects on tautomeric equilibrium of 2‐diazo‐4,6‐dinitrophenol
Authors: Liu Yan , Du Hongchen , Wang Guixiang , Gong Xuedong , Wang Lianjun , Xiao Heming 
Published: January 2010

AbstractThe density functional theory has been used to study the tautomeric equilibrium of 2‐diazo‐4,6‐dinitrophenol(DDNP) in the gas phase and in 14 solvents at the B3LYP/6‐31G* level. The solvent effects on the tautomeric equilibria were investigated by the self‐consistent reaction field theory (SCRF) based on conductor polarized continuum model (CPCM) in apolar and polar solvents and by the hybrid continuum‐discrete model in protic solvent, respectively. Solvent effects on the computed molecular properties, such as molecular geometries, dipole moments, ELUMO, EHOMO, total energies for DDNP tautomers and transition state, tautomerization energies and solvation energies have been found to be evident. The tautomeric equilibrium of DDNP is solvent‐dependent to a certain extent. The tautomer I (cyclic azoxy form) is preferred in the gas phase, while in nonpolar solvents tautomer I and II (quinold form) exist in comparable amounts, and in highly polar solvents, the tautomeric equilibrium is shifted in favor of the more polar tautomer II. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Theoretical study on the interaction of sulfur‐ and aminopyridine‐containing chelating resins with Hg(II) and Pb(II)
Authors: Niu Yuzhong , Feng Shengyu , Qu Rongjun , Ding Yunqiao , Wang Dengxu , Wang Yike 
Published: January 2010

AbstractThe geometries and energetics of complexes of Hg(II) and Pb(II) with sulfur‐ and aminopyridine‐containing chelating resin including crosslinked polystyrene immobilizing 2‐aminopyridine via sulfur‐containing (PVBS‐AP), sulfoxide‐containing (PVBSO‐AP), and sulfone‐containing (PVBSO2‐AP) spacer arms have been investigated theoretically, and thus interactions of the metal ions with chelating resins were evaluated. The results indicate that PVBS‐AP behaves as a tridentate ligand to coordinate with the metal ions by S and two N atoms to form chelating compounds with S atom playing a dominant role in the coordination, whereas PVBSO‐AP and PVBSO2‐AP interact with metal cations, respectively, in a tricoordinate manner by O and two N atoms forming chelating complexes. Furthermore, it is revealed that O and N2 atoms of PVBSO‐AP are the main contributor of coordination to Hg(II), whereas N2 atom of PVBSO2‐AP is mainly responsible for the coordination to Hg(II). For PVBSO‐AP‐Pb2+ and PVBSO2‐AP‐Pb2+ complex, the coordination is dominated by the synergetic effect of N1, N2, and O atoms. Natural bond orbital and second‐order perturbation analyses suggest that the charge transfer from the chelating resins to metal ions is mainly dominated by the interactions of lone pair of electrons of the donor atoms with the unoccupied orbitals of metal ions. Hg(II) complexes exhibit larger binding energies than the corresponding Pb(II) complexes, implying the chelating resins exhibit higher affinity toward Hg(II), which is consistent with the experimental results. Combined the theoretical and experimental results, further understanding of the structural information of the complexes and the coordination mechanism was achieved. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Computational study of FOX‐7 synthesis in a solvated reaction system
Authors: Liu Min‐Hsien , Cheng Ken‐Fa , Chen Cheng , Hong Yaw‐Sun 
Published: January 2010

AbstractEthene and two kinds of nitrating reagents (HNO3 and N2O5) in a variety of solvents were included in respective molecular systems, and each underwent a two‐stage electrophilic and free radical nitro‐substitution reaction to obtain the corresponding nitroethene compounds. Subsequent halogenation (using Cl2 and Br2) and amination (using NH3) were then performed in solvents, also by electrophilic and radical substitution, to produce the desired 1,1‐diamino‐2,2‐dinitroethene (FOX‐7) derivatives. The reaction energy barrier in the nitration stage for obtaining each kind of mononitro ethene exhibited a stepwise decreasing trend when the reaction was carried out in H2O‐solvated and CH3OH‐solvated systems, no matter what nitrating agent was used. Related energy barrier data showed that the nitration reaction is more feasible in an H2O‐solvated than a CH3OH‐solvated system. The modeling results suggested that N2O5 is the better agent for nitration to proceed in water, bromine is suitable for halogenation, and the bromine derivatives are convenient for further amination in an H2O‐solvated system. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Critical investigation on the pseudobond approach for QM/MM and fragment‐based QM methods
Authors: Exner Thomas E. 
Published: January 2010

AbstractIn mixed quantum mechanical/molecular mechanical and fragment‐based quantum chemical calculations an accurate treatment of bonds, which are cut to build the fragments, is greatly desired so that the structural and electronic properties of the fragment resemble the properties of the original molecule as accurately as possible. Many different methods have been proposed in the literature to deal with bond fragmentation. One of these methods, the pseudobond approach of Zhang et al. (J Chem Phys, 1999, 110, 46), is analyzed in this work. Reparameterizations were conducted for different training sets and diviations in various molecular properties were used as the objective function of the optimazation process. Most of these parameterizations, including the original one, show good performance in reproducing the structures of five substituted ethane molecules and 17 amino acids, as well as in the energy calculation of an oligopeptide based on our fragment‐based quantum chemical approach: the field‐adapted adjustable density matrix assembler. Nevertheless, none of the parameterizations shows significant and consistent improvement over simple capping hydrogen atoms, despite the simplicity of that approach. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Theoretical study of third‐row transition metal monofluorides
Authors: Kalamse Vijayanand , Wadnerkar Nitin , Chaudhari Ajay 
Published: January 2010

AbstractThe 5d‐metal (excluding La) monofluorides were studied using second order Moller‐Plesset (MP2) perturbation theory. The basis set used was Stuttgart/Dresden (SDD) effective core potentials (ECPs). The ground state multiplicity for these dimers was obtained. The cation and anion of these dimers were also studied at the same level of theory. Relative stability, atomic charges, electron affinity, ionization potential, binding energy (BE), vibrational frequencies, and electronic configuration for these dimers were also obtained. The properties of the neutral dimers were compared with those of their anion and cation. The electronic states of each neutral dimer as well as its ions at their ground state were also defined. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
A DFT study of a novel oxime anticancer trans platinum complex: Monofunctional and bifunctional binding to purine bases
Authors: Xu Zhijuan , Zhou Lixin 
Published: January 2010

AbstractThe first and second substitution reactions binding of the anticancer drug trans‐[Pt((CH3)2CNOH)((CH3)2CHNH2)Cl2] to purine bases were studied computationally using a combination of density functional theory and isoelectric focusing polarized continuum model approach. Our calculations demonstrate that the trans monoaqua and diaqua reactant complexes (RCs) can generate either trans‐ or cis‐monoadducts via identical or very similar trans trigonal‐bipyramidal transition‐state structures. Furthermore, these monoadducts can subsequently close by coordination to the adjacent purine bases to form 1,2‐intrastrand Pt‐DNA adducts and eventually distort DNA in the same way as cisplatin. Thus, it is likely that the transplatin analogues have the same mechanism of anticancer activity as cisplatin. For the first substitutions, the activation free energies of monoaqua complexes are always lower than that of diaqua complexes. The lowest activation energy for monoaqua substitutions is 16.2 kcal/mol for guanine and 16.5 kcal/mol for adenine, whereas the lowest activation energy for diaqua substitutions is 17.1 kcal/mol for guanine and 25.9 kcal/mol for adenine. For the second substitutions, the lowest activation energy from trans‐monoadduct to trans‐diadduct is 19.1 kcal/mol for GG adduct and 20.7 kcal/mol for GA adduct, whereas the lowest activation energy from cis‐monoadduct to cis‐diadduct is 18.9 kcal/mol for GG adduct and 18.5 kcal/mol for GA adduct. In addition, the first and second substitutions prefer guanine over adenine, which is explained by the remarkable larger complexation energy for the initial RC in combination with lower activation energy for the guanine substitution. Overall, the hydrogen‐bonds play an important role in stabilizing these species of the first and second substitutions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem, 2011
Contractual and policy challenges to developing ecocities
Authors: Gunawansa Asanga 
Published: January 2010

AbstractDevelopment of ecocities is one of the recent responses to climate change. What is envisaged in such developments is the creation of cities that are responsive to the surrounding environment in terms of pollution control, sustainable land use, mitigation of climate change and adaptation to changing climate conditions. Development of such cities from scratch or the conversion of existing cities into ecocities will be no easy task. The enormous financial and technological resources required for such developments may lead governments to rely on private sector participation in the development and management process of such cities. This paper argues that the concept of developing ecocities requires not only the successful completion of a project, but also the long‐term maintenance of the sustainable features and their acceptance by the public. Thus, the paper points out that, in addition to the environmental sustainability concerns, the financial viability of the project, cultural considerations, community needs, capacity for future maintenance of the city and availability of a suitable regulatory and administrative framework for the administration of the city are important considerations. Further, the paper argues that the use of a traditional public–private‐partnership (PPP) model of project development may not be a suitable vehicle for developing ecocities. Copyright © 2010 John Wiley & Sons, Ltd and ERP Environment.
On Simon's two‐stage design for single‐arm phase IIA cancer clinical trials under Beta‐binomial distribution
Authors: Liu Junfeng , Lin Yong , Shih Weichung Joe 
Published: January 2010

AbstractSimon (Control. Clin. Trials 1989; 10:1–10)'s two‐stage design has been broadly applied to single‐arm phase IIA cancer clinical trials in order to minimize either the expected or the maximum sample size under the null hypothesis of drug inefficacy, i.e. when the pre‐specified amount of improvement in response rate (RR) is not expected to be observed. This paper studies a realistic scenario where the standard and experimental treatment RRs follow two continuous distributions (e.g. beta distribution) rather than two single values. The binomial probabilities in Simon's (Control. Clin. Trials 1989; 10:1–10) design are replaced by prior predictive Beta‐binomial probabilities that are the ratios of two beta functions and domain‐restricted RRs involve incomplete beta functions to induce the null hypothesis acceptance probability. We illustrate that Beta‐binomial mixture model based two‐stage design retains certain desirable properties for hypothesis testing purpose. However, numerical results show that such designs may not exist under certain hypothesis and error rate (type I and II) setups within maximal sample size ∼130. Furthermore, we give theoretical conditions for asymptotic two‐stage design non‐existence (sample size goes to infinity) in order to improve the efficiency of design search and to avoid needless searching. Copyright © 2010 John Wiley & Sons, Ltd.