bluuebunny/crossref_metadata_2025_split huggingface dataset:
Laplacian‐based models for the exchange energy
Authors: Cancio A. C. , Wagner Chris E. , Wood Shaun A. 
Published: June 2012

AbstractRecent Quantum Monte Carlo data for the exchange‐correlation energy density of pseudopotential systems strongly suggest the value of using the Laplacian of the density as a variable for constructing first‐order corrections to the local density approximation of density functional theory. We report on an exchange functional built on these observations and extended to the all‐electron case. The model keeps the typical properties of constraint‐based generalized gradient approximations (GGAs) and also has a finite‐valued potential at the nucleus, unlike the GGA. Problems with oscillatory behavior in the potential due to higher order derivatives are controlled by a curvature minimization constraint. The results are tested against exact potentials for the He and Ne atom. A combination of gradient and Laplacian as suggested by a gradient expansion of the exchange hole gives the best overall results. © 2012 Wiley Periodicals, Inc.
The reduced density gradient in atoms
Authors: del Campo Jorge M. , Gázquez José L. , Alvarez‐Mendez Rodrigo J. , Vela Alberto 
Published: June 2012

AbstractA study of the reduced density gradient s together with the density of s, g(s), for atoms across the periodic table (Li through Xe), following the work of Zupan et al. (Int. J. Quantum Chem. 1997, 61, 835), is presented. The results indicate that the reduced density gradient has maxima and minima related with the shell structure, and that these critical points are associated to the maxima in g(s). The behavior of the critical points in s, of the maxima in g(s) and of the average s calculated through g(s) across the rows and the columns of the periodic table is analyzed. © 2012 Wiley Periodicals, Inc.
Electronic structures and molecular structures of polyynes
Authors: Imamura Akira , Aoki Yuriko 
Published: June 2012

AbstractRecently, many interesting materials made from carbon atoms have been discovered such as carbon nanotubes, fullerenes, and graphenes. In this article, we studied electronic structures and molecular structures of polyynes with sp2 carbons on both ends. Polyynes calculated were H2CCnCH2 with various number of n. These molecules have two π systems which are perpendicular to each other and these π systems have their tendency to make double bond nature by Peierls instability but for different alternating bonds. In other words, these two π systems are competing to form the double bond formations. The calculations were performed at Hartree–Fock level geometry optimization with 6‐31G, 6‐311G, and 6‐31G** basis sets. For CH2(C)2mCH2, we have found that there are two metastable structures, one of which is the bond‐alternating structure and another is nearly equi‐bond structure. The former has small highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap while the latter has relatively large gap although it is smaller in comparison with the value of polyyne with sp carbon atoms on both ends: H(C)2mH. The small highest occupied molecular orbital (HOMO)–lowest unoccupied molecular orbital (LUMO) gap in bond‐alternating structure is due to the fact that HOMO and MO's near to HOMO have relatively localized electronic distribution in both end regions, and thus, the weak interaction between the both regions leads to the small HOMO–LUMO gap. The stability is larger for the former especially in long polyynes. For CH2(C)2m+1CH2, we have found only one stable structure, that is, equi‐bond structure. This type of polyyne oligomers has two terminal CH2 groups which are perpendicular with each other. It is found that the longer the length of oligomer is, the smaller the HOMO–LUMO gap is as is usually expected. By summarizing these results, we proposed a design for a single‐chain electronically conductive polymers. © 2012 Wiley Periodicals, Inc.
Implementation of a variational code for the calculation of rate constants and application to barrierless dissociation and radical recombination reactions: CH3OH = CH3 + OH
Authors: de M. Oliveira Rodrigo C. , Bauerfeldt Glauco F. 
Published: June 2012

AbstractHere, a new implementation for calculating canonical variational rate constants is introduced and tested against methanol dissociation rate constants and the (high pressure) radical recombination reaction, CH3 + OH → CH3OH. Reaction paths are described at the CASSCF level, with energy corrections at MRMP2. Molecular properties for both stationary and non‐stationary points along the reaction path are used for the calculation of rate constants. Different models for the low vibrational frequencies are discussed: harmonic oscillator and free rotor models. The CH3 + OH → CH3OH recombination rate constants are determined from dissociation rate constants and equilibrium constants. Our calculated rate constants agree with previously reported data for these reactions, suggesting the good performance of our implemented code in calculating canonical variational rate constants. The rate expressions are suggested: as: kdis (T) = 8.42 × 10+16 × e−96.18/RT and krec (T) = 2.05 × 10−10 × (T/298)−0.24 × e−0.30/RT, in units s−1 and cm3 molecule−1 s−1, respectively, and over the temperature range 300–2000 K, with activation energies in kcal/mol. © 2012 Wiley Periodicals, Inc.
Exploring the conformation, charge density distribution and the electrostatic properties of galanthamine molecule in the active site of AChE using DFT and AIM theory
Authors: Renuga Parameswari Azhagesan , Kumaradhas Poomani 
Published: June 2012

AbstractQuantum chemical calculations and charge density analysis were carried out to understand the geometry, charge density distribution and the electrostatic properties of isolated galanthamine molecule (form I) and for the same lifted out from the active site (form II) of AChE. The optimized geometry of isolated galanthamine was obtained from a hybrid density functional theory (B3LYP/6‐311G**) calculation. A docking analysis on galanthamine with AChE was performed, and the lowest docked energy structure was selected from the active site of AChE for the further study. A single point energy quantum chemical calculation (B3LYP/6‐311G**) was carried out for the lowest energy structure, which was lifted from the galanthamine–AChE complex from molecular docking analysis. The structural comparison between (I) and (II) helps to understand the conformational modification of the galanthamine molecule in the active site. When the molecule present in the active site, the molecular geometry is seen to be significantly altered, specifically, large changes were observed in the outer core of the molecule while the inner core geometry is intact. The bond topological and electrostatic properties of (I) and (II) were calculated. The dipole moment of the galanthamine molecule also increases from 2.09 to 2.67 D in the process. A large negative electrostatic potential region is found at the vicinity of oxygen and nitrogen atoms of the molecule, which predominantly involve strong hydrophobic and electrostatic interactions with the amino acid residues TRP84, PHE330, GLY118, TYR70, and SER122 present in the active site of AChE. © 2013 Wiley Periodicals, Inc.
The number of spanning trees in an (r, s)‐semiregular graph and its line graph
Authors: Bibak Khodakhast 
Published: June 2012

AbstractFor a graph G, a “spanning tree” in G is a tree that has the same vertex set as G. The number of spanning trees in a graph (network) G, denoted by t(G), is an important invariant of the graph (network) with lots of decisive applications in many disciplines. In the article by Sato (Discrete Math. 2007, 307, 237), the number of spanning trees in an (r, s)‐semiregular graph and its line graph are obtained. In this article, we give short proofs for the formulas without using zeta functions. Furthermore, by applying the formula that enumerates the number of spanning trees in the line graph of an (r, s)‐semiregular graph, we give a new proof of Cayley's Theorem. © 2013 Wiley Periodicals, Inc.
Insights for design of Trypanosoma cruzi GAPDH inhibitors: A QM/MM MD study of 1,3‐bisphospo‐D‐glyceric acid analogs
Authors: Araújo Silva José Rogério , Lameira Jerônimo , Alves Cláudio Nahum 
Published: June 2012

AbstractGlyceraldehyde‐3‐phosphate dehydrogenase (GAPDH) is a key‐enzyme for design of new drugs against Chagas disease. Herein, molecular inhibition mechanism of GAPDH involving 1,3‐bisphospho‐D‐glyceric acid (1,3‐BPGA) analogs were studied using the hybrid quantum mechanical/molecular mechanical (QM/MM) approach and molecular dynamic simulations. The analysis of the binding contribution of the individual residues shows that Lys209, Asp210, Arg212, Thr167, Thr197, Thr199, Ser224, Thr226, Ser247, Arg249, water molecules, and NAD+ are responsible for stabilization of the protein‐inhibitor complexes. The results obtained suggest that Arg249 plays an important role in the GAPDH‐inhibitor complex and might induce the compression of the 1,3‐BPGA analogs inside the active site of GAPDH. In addition, analysis of QM/MM molecular dynamics simulations have shown that the extended conformation 1,3‐BPGA analogs contribute to biological activity of these compounds. © 2012 Wiley Periodicals, Inc.
Electron detachment energies of aqueous and cluster halide anions from electron propagator calculations with the polarizable continuum model
Authors: Dolgounitcheva Olga , Zakrzewski Viatcheslav G. , Ortiz Joseph Vincent 
Published: June 2012

AbstractTo calibrate computational studies of photoelectron spectra of dissolved anions, the vertical electron detachment energies (VEDEs) of the fluoride and chloride anions in isolation and in the presence of six coordinated water molecules have been calculated with and without the polarizable continuum model (PCM) of solvation in water. Large shifts in VEDEs and important changes in coordination geometries about the chloride anion occur with the use of the PCM. Cluster and PCM calculations confirm previous, qualitative conclusions on Dyson orbitals corresponding to the lowest VEDEs of aqueous halide anions. For the fluoride case, Dyson orbitals for the lowest VEDEs are spread over water molecules, not the anion, but for the chloride case, the Dyson orbitals for the lowest VEDEs are localized on the anion. The partial third‐order (P3) and P3+ approximations of electron propagator theory provide a reliable means to calculating VEDEs with polarized atomic basis sets. © 2012 Wiley Periodicals, Inc.
Rung 3.5 density functionals: Another step on Jacob's ladder
Authors: Janesko Benjamin G. 
Published: June 2012

AbstractApplications of density functional theory (DFT) to computational chemistry and solid‐state physics rely on a “Jacob's Ladder” of progressively more complicated approximations to the many‐body exchange‐correlation (XC) density functional. Accurate, computationally tractable DFT calculations on large and periodic systems remain challenging for existing XC functionals. Simple XC functionals on the three lowest rungs of Jacob's Ladder are insufficiently accurate for many properties, while fourth‐rung hybrid functionals incorporating nonlocal information can be prohibitively expensive. This perspective presents our work toward a compromise, a new class of “Rung 3.5” functionals that incorporate a linear dependence on the nonlocal one‐particle density matrix. This work reviews these functionals' formal underpinning, numerical performance, and prospects for modeling solids and surfaces. © 2012 Wiley Periodicals, Inc.
DFT modeling of band shifts and widths in the absorption spectrum of a 9‐(diphenylamino)acridine/silica receptor center upon its interaction with gas‐phase NH3, C2H5OH, and (CH3)2CO molecules
Authors: Chashchikhin Vladimir , Rykova Elena , Scherbinin Andrei , Bagaturyants Alexander 
Published: June 2012

AbstractThe interaction of small analyte molecules (NH3, C2H5OH, and (CH3)2CO) in the gas phase with the 9‐(diphenylamino)acridine dye adsorbed on an amorphous silica surface is studied by density functional theory (DFT) calculations using the cluster approach. Two cluster models for the silica surface are considered: a small SiH3OH model and an extended Si10O11(OH)18 one, constructed using classical molecular dynamics simulations. The electronic absorption spectra of the adsorbed dye are calculated within the time‐dependent density functional theory (TDDFT) formalism and the effects of dye–analyte interactions are investigated. The spectral line broadening due to vibrations is estimated within the Pekar model. A computationally efficient procedure is proposed for the prediction of changes in the absorption spectra of organic dyes adsorbed on silica on their interaction with analytes. © 2012 Wiley Periodicals, Inc.
Optoelectronic properties of KDP by first principle calculations
Authors: Aliabad Hossein Asghar Rahnamaye , Fathabadi Marjan , Ahmad Iftikhar 
Published: June 2012

AbstractThe optoelectronic properties of KDP (KH2PO4), in orthorhombic and tetragonal phases, have been investigated by generalized gradient approximation (GGA) and mBJ‐GGA within density functional theory. The calculated fundamental indirect band gaps for orthorhombic and tetragonal KDPs are 2.83 and 4.35 eV, respectively. The calculated effective mass of electron, in this compound, is very close to the effective mass of carriers in a bilayer graphene. The electron density plots show that the covalent bonds between P and O within the PO4 tetrahedra are symmetric in tetragonal phase, whereas in the orthorhombic phase this symmetry breaks, which affects the covalent bonds among the tetrahedra. The comparison of the calculated optical spectra by GGA and mBJ‐GGA with the experimental results reveals that the optical dispersion spectra by mBJ‐GGA are in closer agreement with the experimental results. © 2012 Wiley Periodicals, Inc.
Stochastic stability and robust stabilization of semi‐Markov jump linear systems
Authors: Huang Ji , Shi Yang 
Published: June 2012

SUMMARYThe semi‐Markov jump linear system (S‐MJLS) is more general than the Markov jump linear system (MJLS) in modeling some practical systems. Unlike the constant transition rates in the MJLS, the transition rates of the S‐MJLS are time varying. This paper focuses on the robust stochastic stability condition and the robust control design problem for the S‐MJLS with norm‐bounded uncertainties. The infinitesimal generator for the constructed Lyapunov function is first derived. Numerically solvable sufficient conditions for the stochastic stability of S‐MJLSs are then established in terms of linear matrix inequalities. To reduce the conservativeness of the stability conditions, we propose to incorporate the upper and lower bounds of the transition rate and meanwhile apply a new partition scheme. The robust state feedback controller is accordingly developed. Simulation studies and comparisons demonstrate the effectiveness and advantages of the proposed methods. Copyright © 2012 John Wiley & Sons, Ltd.
The Effect of Some Fluids on Surface Oxidation and Amount of Released Iron of Stainless Steel Endodontic Files
Authors: Saghiri Mohammad Ali , García‐Godoy Franklin , Lotfi Mehrdad , Mehrvazfar Peyman , Aminsobhani Mohsen , Rezaie Samad , Asgar Kamal 
Published: June 2012

SummaryEndodontic files come in contact with blood, infected pulp tissue, and irrigating solutions during root canal therapy. Some instruments such as stereomicroscopy and scanning electron microscopy are used to observe corrosion of endodontic files which are complicated and dependent on preparation methods. Having knowledge of the corrosion and ion release of endodontic files can help in drawing firm deductions as to which files would perform better in the clinical scenario. Therefore, we have used energy dispersive X‐ray analysis and an atomic absorption spectrophotometer to track oxygen on the surface and iron in the exposed media to observe the oxidative rate of the media. In this study, corrosion by blood was higher than other biological fluids, but less than with sodium hypochlorite (NaOCl). Observations of energy dispersive X‐ray analysis and atomic absorption spectrophotometer results demonstrated that after exposure the amount of oxygen on the surface and surrounding areas increased. Therefore, the files should be rinsed as soon as possible during and after use to hinder the oxidation rate, but blood may produce a different behavior and it might be considered as a decreased risk of broken stainless steel files remaining in the root canal after treatment. SCANNING 34: 309‐315, 2012. © 2012 Wiley Periodicals, Inc.
Electron Beam Induced Growth of Silver Nanoparticles
Authors: Shi Guanghua , Bao Shengxiang , Lai Weiming , Rao Zhenzhen , Zhang Xiaowen , Wang Zuwen 
Published: July 2012

SummaryAn electron beam inducing method for sprouting large quantities of silver nanoparticles on the surface of silver chloride particles is reported. The electron beam driven process was characterized by time‐dependent scanning electron microscope (SEM) and energy dispersive spectrum (EDS), allowing for observing several key intermediates in and characteristics of the growth process. Theoretical calculation coupled with experimental observation demonstrated that the growth of silver nanoparticles was mostly related to the current density of electron beam. Decomposition of the silver chloride on the surface of sample was under electron beam irradiation resulted in silver nanoparticles and chlorine. This phenomenon could be useful in developing a novel mechanism for preparation of nanostructures and proposing a reference to avoid image distortion during the characterization of silver compounds under SEM. SCANNING 35: 69‐74, 2013. © 2012 Wiley Periodicals, Inc.
Sustainable Architecture, Design and Housing
Authors: Keitsch Martina 
Published: June 2012

ABSTRACTThis editorial article for the special issue of Sustainable Development ‘Sustainable architecture, design and housing’ introduces the main topics and reviews the following nine articles. The aim of the special issue is to discuss key concepts, methods, applications and lessons learned in sustainable architecture, design and housing. Sustainable architecture challenges new and ingenious architectural design at various levels. Examples are the following. (1) Minimizing the negative environmental impact of buildings by enhancing efficiency and moderating the use of materials, energy and development space. (2) Developing measures to relate form and adapt the design to the site, the region and the climate. (3) Establishing a harmonious, long lasting relationship between the inhabitants and their surroundings by addressing the essence of good form‐giving (Abidin et al., ). In summary, sustainable architecture shall be well built, easy to use and beautiful. The selected articles highlight special aspects of sustainability in architecture, design and housing, either due to their novel theoretical contributions or in relation to tools, measurements and strategies. A main research objective on sustainable design is to promote understanding for the particular problems that architects and designers face and to discuss solutions to solve them. This can in turn also be described as the relevance of sustainable design research for the overarching sustainable development debate. Sustainable design is dynamic and comprises both normative, strategic, designerly and technical aspects (Cross, ). Three areas are thematically highlighted in this special issue.

Overarching conception of sustainable architecture and design and their impact on a sustainable development.
Methodologies and tools and their applications to sustainable design.
Policy and strategy development to assess and implement sustainable design. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment.
Sustainability from a Performance‐Oriented Architecture Perspective – Alternative Approaches to Questions regarding the Sustainability of the Built Environment
Authors: Hensel Michael U. 
Published: June 2012

ABSTRACTThis article introduces and discusses a series of alternative and interrelated concepts and approaches regarding questions of the sustainability of the built environment and architectural design. The need for this discussion arises from the realization that the majority of current approaches to questions of sustainability in architectural design tend to considerably stifle complexity in approach, problem analysis and definition. This development is characterized by isolated and partial aspects of environmental problems, instead of a more holistic systems approach, often present in the approaches of other disciplines or interdisciplinary efforts.The shortage of alternative approaches in architectural design requires a critical rethinking of the question of sustainability of the built environment and its relation to other domains in and outside the anthroposphere. To address this problem is the goal of this article. In doing so, it introduces and discusses concepts and approaches that are rooted in a systems approach and aims for more complex problem definitions, while taking longer‐term perspectives into consideration. This is done from a performance‐oriented architecture perspective, which operates on the dynamic interactions between local ecosystems (including humans), environment and the spatial–material organization complex of architecture. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment.
Innovative Foresights in Sustainable Design and Architecture – How to Promote Seemingly Impossible, but Still Crucial, Radical Changes
Authors: Edeholt Håkan 
Published: June 2012

ABSTRACTScientific warnings of an escalation of climate disaster become more severe by the day. Seemingly, the magnitude of the alarms increases at a pace that outcompetes the concerns it seems to generate in public policies and discourses. Are we perhaps, as some suggest, in the middle of a huge public denial? Why is this so? What could design and design research possibly do about it?This paper briefly discusses some characteristic features within the domains of society, science and design (including architecture) and how these three domains interrelate when it comes to the challenge of climate change and global sustainability. The intention is to create a creative analytical field of tensions, with complementary actors. The paper then especially focuses on possible contributions from the domain of design. One of the conclusions is that the challenge is so huge that we need to utilize a variety of professional domains of competence and that all should contribute where their involvement will make most difference. We therefore suggest that perhaps the most important contribution that design can make is to suggest new possible, preferable and radically different alternatives of living. Here the intention is to facilitate creative discourses rather than creating creative solutions that direct solve all the complex problems at hand.A master course in design, entitled ‘Shaping futures’, where students are required to come up with plausible scenarios that address possible climate changes, is used as an illustrative example. In order to address climate change the course joins the domains of foresight, innovation and design. The course reveals both opportunities for design work, and also areas where design as a discipline needs further development. Copyright © 2012 John Wiley & Sons, Ltd and ERP Environment.