bluuebunny/crossref_metadata_2025_split huggingface dataset:
An Atom Counting QSPR Protocol
Authors: Giri Santanab , Roy Dehesh R. , Van Damme Sofie , Bultinck Patrick , Subramanian Venkatesan , Chattaraj Pratim K. 
Published: October 2007

AbstractA simple descriptor, viz the number of carbon (NC)/non‐hydrogenic (NNH) atoms present in a molecule, is proposed for the development of useful Quantitative Structure–Property–Relationship (QSPR) models. This work is prompted by that of Randic and Basak (J. Chem. Inf. Comput. Sci. 2001, 41, 614–618) who have shown that this descriptor is superior to the simple connectivity index and is marginally worse than the variable connectivity index for analyzing the toxicity of aliphatic ethers. It is tested in the present work in models pertaining to the estimation of boiling point of alcohols, enthalpy of vaporization of Polychlorinated Biphenyls (PCBs), n‐octanol/water partition coefficient of PCBs and chloroanisoles, pKa values of carboxylic acids, phenols, alcohols, etc. High values of various regression coefficients (R2, $\rm{ R_{{\rm{CV}}}^2 }$, $\rm{ R_{{\rm{Ad}}}^2 }$) suggest the significance of this descriptor which further improves in the resulting two‐parameter QSPR models with electrophilicity or its local variant as an additional descriptor. Other statistical quantities are also analyzed for gaining additional insights into the proposed models. Although the atom number is not the best possible descriptor in a QSPR model in all cases, its simplicity provides it a special place in the development of those models. The present analysis extends the work of Randic and Basak by delineating the situations when NC/NNH performs well vis‐a‐vis the other descriptors.
Tayloring standard TDDFT approaches for computing UV/Vis transitions in thiocarbonyl chromophores
Authors: Preat Julien , Jacquemin Denis , Perpète Eric A. 
Published: October 2007

AbstractWe report the development of an accurate computational procedure for the calculation of the n → π* (λmax−1) and π → π* (λmax−2) transitions of a set of thiocarbonyl derivatives. To ensure converged results, all calculations are carried out using the 6‐311+G(2df,p) basis set for time‐dependent calculations, and the 6‐311G(2df,p) for the ground‐state geometrical optimization. Starting with two hybrids, PBE0 and B3LYP, the Hartree–Fock exchange percentage (α) used is optimized in order to reach excitation energies that fit experimental data. It turns out that BLYP(α) is the more adequate functional for calibration. For the n → π* excitation, the optimal α value lies in the 0.10–0.20 interval, whereas for the π → π* process setting α equal to 0.10 provides the most accurate results. The corresponding mean absolute errors (MAE) are limited to 17 nm for λmax−1, and to 10 nm for λmax−2, allowing a consistent and accurate prediction of both transitions. We also assess the merits of the ZINDO//AM1 scheme and it turns out that the semi‐empirical method only provides a poor prediction of the λmax of thiocarbonyl derivatives, especially for the n → π* transition. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Mercury telluride crystals encapsulated within single walled carbon nanotubes: A density functional study
Authors: Kuganathan Navaratnarajah , Green Jennifer C. 
Published: October 2007

AbstractThe structure and binding energies of mercury telluride crystals encapsulated within single walled carbon nanotubes (SWNTs) have been studied using density functional theory. The energies of three different pseudo one‐dimensional crystals of HgTe with 4:4, 3:3, and 2:2 coordination are compared. The initial structure for the 4:4 crystal was a 2 × 2 cubic motif derived from rock salt bulk structure, the 3:3 crystal corresponds to a novel structure found when HgTe was intercalated within SWNTs, and the 2:2 crystal is a chain motif derived from cinnabar (HgS) bulk structure. The isolated 3:3 crystal was found to be the most thermodynamically stable of the three structures. Calculations were performed on the 3:3 crystal inserted into three different SWNTs, (15, 0), (9, 9), and (17, 0), in order to investigate the perturbations on the molecular and electronic structure of the crystal and the SWNT, and the energy of formation of the HgTe@SWNT composites. The calculated structures are in good agreement with the experimental high resolution transmission electron microscopy images of the HgTe@SWNT composite. The calculated binding energies and density of states show that the interaction between nanotubes and the HgTe crystals is noncovalent. Since the energy difference of the “free” 4:4 and 3:3 structures is small and of the order of magnitude of the binding energies with the nanotubes, we carried out calculations on 4:4 HgTe structure inserted in to two different SWNTs, (15, 0) and (17, 0). The calculated binding energies show that, when the 4:4 structure is inserted into the smallest tube, the resultant composite has an energy comparable to the 3:3 structure, suggesting that this polymporph may also be found experimentally. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Theory of chemical bonds in metalloenzymes. VII. Hybrid‐density functional theory studies on the electronic structures of P450
Authors: Shoji Mitsuo , Isobe Hiroshi , Saito Toru , Yabushita Hirotaka , Koizumi Kenichi , Kitagawa Yasutaka , Yamanaka Shusuke , Kawakami Takashi , Okumura Mitsutaka , Hagiwara Masayuki , Yamaguchi Kizashi 
Published: October 2007

AbstractA first principle investigation has been carried out for intermediate states of the catalytic cycle of a cytochrome P450. To elucidate the whole catalytic cycle of P450, the electronic and geometrical structures are investigated not only at each ground state but also at low‐lying energy levels. Using the natural orbital analysis, the nature of chemical bonds and magnetic interactions are investigated. The ground state of the Compound 1 (cpd1) is calculated to be a doublet state, which is generated by the antiferromagnetic coupling between a triplet Fe(IV)O moiety and a doublet ligand radical. We found that an excited doublet state of the cpd1 is composed of a singlet Fe(IV)O and a doublet ligand radical. This excited state lies 20.8 kcal mol−1 above the ground spin state, which is a non‐negligible energy level as compared with the activation energy barrier of ΔE# = 26.6 kcal mol−1. The reaction path of the ground state of cpd1 is investigated on the basis of the model reaction: 3O(3p) + CH4. The computational results suggest that the reactions of P450 at the ground and excited states proceed through abstraction (3O‐model) and insertion (1O‐model) mechanisms, respectively. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Novel silicon nanorings: Persilacyclacenes at DFT
Authors: Kassaee M. Z. , Arefrad H. , Ghambarian M. 
Published: October 2007

AbstractStructures, energies, and aromatic characters are compared and contrasted for a series of [n]persilacyclacenes with n = 6–12: Si24H12, Si28H14, Si32H16, Si36H18, Si40H20, Si44H22, and Si48H24, respectively, at B3LYP levels (n, number of fused benzenoid rings). These are a brand of silicon nanorings that bear a resemblance to the shortest zig‐zag silicon nanotubes (SiNTs), henceforth referred to as SiNRs. The NBO results show nearly sp2‐hybridization for virtually all Si atoms of our SiNRs. This is in contrast to most reports where sp3‐hybridization is proposed for typical SiNTs. Comparison between the optimized SiNRs and their corresponding planar (polyacenic) forms shows longer bond lengths for the former, due to their curvatures. Except for sterically hindered Si24H12 (n = 6), all even SiNRs (n = 8, 10, and 12), are more aromatic than the odd ones (n = 7, 9, and 11). Such a higher aromaticity is witnessed inside, outside, and on the surface of the scrutinized SiNRs. Also, except for Si44H22 (n = 11), the energy gaps (ΔEHOMO−LUMO) for the odd set of SiNRs, as well as the even set, appear inversely proportional to their corresponding diameters, per se. Except for the sterically hindered SiNRs with n = 6 or 7, all the even SiNRs enjoy a higher stability (aromaticity) and conductivity for showing lower ΔEHOMO−LUMO than the odd ones. Evidently, the ideal diameter for persilacyclacenes (SiNRs) studied is from 0.92 to 1.42 nm, corresponding to n = 8–12, respectively. Higher than 1.42 nm causes structural disorders while lower than 0.92 brings about bond localization due to the high‐steric effects. © 2007 Wiley Periodicals, Inc. Int J Quantum Chem, 2008
Efficient identification and quantification of proteins using isotope‐coded 1‐(6‐methylnicotinoyloxy)succinimides by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry
Authors: Tsumoto Hiroki , Murata Chie , Miyata Naoki , Kohda Kohfuku , Taguchi Ryo 
Published: October 2007

AbstractWe describe a convenient and useful method for the identification and relative quantification of proteins using light and heavy reagents, 1‐(6‐methylnicotinoyloxy)succinimides (6‐CH3‐Nic‐NHS and 6‐CD3‐Nic‐NHS, respectively). This method is based on the chemical derivatization of amino groups of tryptic peptides with these reagents, i.e., the basic moiety of the reagents thus incorporated into both the N‐terminal amino group and the ε‐amino group of the lysine residue would improve the ionization efficiency of tryptic peptides. An increase in protein sequence coverage is achieved by derivatization with these reagents or by combination of mass values before and after derivatization. Since a combination of 6‐CH3‐Nic‐NHS and d3‐labeled reagent (6‐CD3‐Nic‐NHS) generates a 3 Da mass difference per reaction site, the d3‐labeled reagent shifts the mass values of d0‐labeled peptides according to the number of reactive amino groups in the peptides. In the case of tryptic peptides, the mass values of C‐terminal arginine and lysine peptides are shifted by 3 and 6 Da, respectively. Further, the 3 Da mass difference between 6‐CH3‐Nic‐NHS and 6‐CD3‐Nic‐NHS offers a means for the relative quantification of protein by matrix‐assisted laser desorption/ionization time‐of‐flight mass spectrometry. Copyright © 2007 John Wiley & Sons, Ltd.
Neutral loss analysis of amino acids by desorption electrospray ionization using an unmodified tandem quadrupole mass spectrometer
Authors: Corso Gaetano , Paglia Giuseppe , Garofalo Daniela , D'Apolito Oceania 
Published: October 2007

AbstractA new method to analyze free amino acids using desorption electrospray ionization (DESI) has been implemented. The method is based on the neutral loss mode determination of underivatized amino acids using a tandem quadrupole mass spectrometer equipped with an unmodified atmospheric interface. Qualitative and quantitative optimization of DESI parameters, including ESI voltage, solvent flow rate, angle of collection and incidence, gas flow and temperatures, was performed for amino acids detection. The parameters for DESI analysis were evaluated using a mixture of valine, leucine, methionine, phenylalanine and tyrosine standards. A few microliters of this mixture were deposited on a slide, dried and analyzed at a flow rate of 2 µL/min. The optimal ionization response was obtained using laboratory glass slides and an equivalent solution of water/methanol doped with 2% of formic acid. The method specificity was evaluated by comparing product ion spectra and neutral loss analysis of amino acids obtained either by DESI or by electrospray ionization flow injection analysis (ESI‐FIA). To evaluate the quantitative response on amino acids analyzed by DESI, calibration curves were performed on amino acid standard solutions spiked with a fixed amount of labelled amino acids. The method was also employed to analyze free amino acids from blood spots, after a rapid solvent extraction without other sample pretreatment, from positive and negative subjects. The method enables one to analyze biological samples and to discriminate healthy subjects from patients affected by inherited metabolic diseases. The intrinsic high‐throughput analysis of DESI represents an opportunity, because of its potential application in clinical chemistry, for the expanded screening of some inborn errors of metabolism. Copyright © 2007 John Wiley & Sons, Ltd.
Duality theory of the optimal two‐blockH∞problem
Authors: Djouadi S. M. , Birdwell J. D. 
Published: October 2007

AbstractThis paper provides the Banach duality theory structure of the optimal two‐blockH∞problem. Alignment conditions are obtained and show that the optimal solution is flat or allpass in general, and is unique in the single‐input single‐output case. The optimal solution is shown to satisfy an extremal identity, which gives a necessary and sufficient condition for a controller to be optimal. Moreover, nearly optimal control laws are shown to satisfy an approximate allpass condition. It is also proved that under specific conditions a Hankel–Toeplitz operator achieves its norm on the discrete spectrum, therefore generalizing a similar result obtained formerly for finite‐dimensional (rational) systems. The norm of this Hankel–Toeplitz operator corresponds to the optimal two‐blockH∞performance. The dual description leads naturally to a numerical solution based on convex programming for linear time‐invariant (possibly infinite‐dimensional) systems. Copyright © 2007 John Wiley & Sons, Ltd.
Estimating adult Chinook salmon exposure to dissolved gas supersaturation downstream of hydroelectric dams using telemetry and hydrodynamic models
Authors: Johnson Eric L. , Clabough Tami S. , Peery Christopher A. , Bennett David H. , Bjornn Theodore C. , Caudill Christopher C. , Richmond Marshall C. 
Published: October 2007

AbstractGas bubble disease (GBD) has been recognized as a potential problem for fishes in the Columbia River basin. GBD results from exposure to gas supersaturated water created by discharge over dam spillways. Spill creates a downstream plume of water with high total dissolved gas supersaturation (TDGS) that may be positioned along either shore or mid‐channel, depending on dam operations. We obtained spatial data on fish migration paths and migration depths for adult spring and summer Chinook salmon, Oncorhynchus tshawytscha, during 2000. Migration paths were compared to output from a two‐dimensional (2‐dimensional) hydrodynamic and dissolved gas model to estimate the potential for GBD expression and to test for behavioural avoidance of the high TDGS plume. We observed salmon swam sufficiently deep in the water column to receive complete hydrostatic compensation 95.9% of the time spent in the Bonneville Dam tailrace and 88.1% of the time in the Ice Harbor Dam tailrace. The majority of depth uncompensated exposure occurred at TDGS levels >115%. Adult Chinook salmon tended to migrate near the shoreline and they tended to remain in relatively deep water. Adults moved into the high dissolved‐gas plume as often as they moved out of it downstream of Bonneville Dam, providing no evidence that adults moved laterally to avoid areas with elevated dissolved gas levels. When water depths decreased due to reduced river discharge, adults tended to migrate in the deeper navigation channel downstream from Ice Harbor Dam. The strong influence of dam operations on the position of the high‐TDGS plume and shoreline‐orientation behaviours of adults suggest that exposure of adult salmonids to high‐TDGS conditions may be minimized using operational conditions that direct the spilled water mid‐channel. Our approach illustrates the potential for combined field and modelling efforts to estimate the fine‐scale environmental conditions encountered by fishes in natural and regulated rivers. Published in 2007 by John Wiley & Sons, Ltd.
Long‐term changes in macroinvertebrate communities of a heavy metal polluted stream: the river Nent (Cumbria, UK) after 28 years
Authors: Armitage Patrick D. , Bowes Michael J. , Vincent Helen M. 
Published: October 2007

AbstractThe macroinvertebrate fauna of the river Nent, a heavy metal polluted upland stream in northern England, first surveyed in 1976, was re‐examined in 2004 to assess long‐term changes in relation to activities in the catchment which have included, a river restoration project, works associated with the development of a mine heritage site and the removal of a chicken farm and more effective organic pollution control measures. The degree of change between years in total abundance, numbers of taxa and community composition varied considerably between sites. Two tributary sites showed marked changes between years due to a reduction in acidity in one and changed substratum in the other but in the main river no significant difference in total taxa and total abundance was observed between years, although seasonal differences were significant. Multivariate community analyses grouped 1976 samples with those taken in 2004 but revealed a clear separation between upper and lower Nent sites. This observed difference may be related to increased algal cover in the lower sites in conjunction with geomorphological features of the lower Nent. Environmental assessment methodology River Invertebrate Prediction and Classification System (RIVPACS) identified ‘sensitive’ faunal groups and indicated that the extensive impact of zinc pollution in the main river has remained practically the same between 1976 and 2004. This persistence of community structure despite the heavily disturbed nature of the river is attributed to relative constancy in instream habitat conditions. The recent activities in the catchment have had little effect on the overall controllers of faunal communities in this system, zinc concentrations and geomorphological characteristics of the stream. However, further disturbances involving movement of spoil heaps and channel alterations in the upper catchment may increase both sediment and heavy metal loadings to the river. Copyright © 2007 John Wiley & Sons, Ltd.
Thinking about systems: student and teacher conceptions of natural and social systems
Authors: Sweeney L. Booth , Sterman John D. 
Published: October 2007

AbstractMany in the system dynamics community argue that children are natural systems thinkers. Here we study how middle school students and teachers think about everyday settings involving feedback, stocks and flows, time delays and nonlinearities, prior to any formal training in these concepts. We develop instruments to elicit understanding of systems concepts and test them with students and teachers from two middle schools in the U.S.A. We find, with some exceptions, generally limited intuitive systems thinking abilities. “Open‐loop” or one‐way causal thinking is common. Explanations lack references to time horizons and time delays. Significant misconceptions of stock and flow structures appear regardless of age. Teachers generally outperformed students, although one‐quarter of the students performed at the median level for teachers. We discuss the nature of students' and teachers' intuitive models of dynamic systems, explore potential barriers to understanding dynamic systems, and discuss implications for effective teaching of systems concepts. Copyright © 2007 John Wiley & Sons, Ltd.
The history and conclusions of The Limits to Growth
Authors: Meadows Donella H. , Meadows Dennis 
Published: October 2007

AbstractIn this unpublished memoir, written in the early 1990s, the late Dana Meadows reflects on the history of The Limits to Growth, including its origins, conclusions, and the reactions it generated. This memoir had been condensed and edited by Dennis Meadows. Copyright © 2007 John Wiley & Sons, Ltd.
Making system dynamics useful: a personal memoir
Authors: Roberts Edward B. 
Published: October 2007

AbstractDuring the many years that I was a founding member of the MIT Industrial Dynamics (ID) Group, later system dynamics (SD), I focused on trying to apply SD concepts, tools and techniques to the real world and to having real impact. That orientation originated from listening to Jay Forrester as he related his personal history and communicated his personal values to our group and to me individually in his forceful and influential manner. Here I review that history and some lessons I learned. As this is a personal memoir I do not attempt to review the entire field, but concentrate entirely on my years of activity in the SD field from 1958 to 1993 and on the aspects most familiar to me, i.e., my own teaching and research and the work of Pugh–Roberts Associates, Inc. Copyright © 2007 John Wiley & Sons, Ltd.
Forecasting turning points in shipping freight rates: lessons from 30 years of practical effort
Authors: Randers Jørgen , Göluke Ulrich 
Published: October 2007

AbstractWe argue that it is possible to explain much of the history of the world's shipping markets since 1950 as the interaction of two balancing feedback loops: a capacity adjustment loop which creates a roughly 20‐year wave, and a capacity utilization adjustment loop which generates a roughly 4‐year cycle. We show how this insight has been used rather successfully since the early 1980s for practical forecasting of turning points in freight rates and the “sentiment” in the shipping market 1_4 years ahead of time. The basic mechanisms in the shipping system create a strong “deterministic backbone” which is visible through the exogenous noise, and hence predictable with useful precision. Our experience leads to a number of questions concerning system dynamics best practice for future research. Copyright © 2007 John Wiley & Sons, Ltd.
System dynamics applied to project management: a survey, assessment, and directions for future research
Authors: Lyneis James M. , Ford David N. 
Published: October 2007

AbstractOne of the most successful areas for the application of system dynamics has been project management. Measured in terms of new system dynamics theory, new and improved model structures, number of applications, number of practitioners, value of consulting revenues, and value to clients, “project dynamics” stands as an example of success in the field. This paper reviews the history of project management applications in the context of the underlying structures that create adverse dynamics and their application to specific areas of project management, synthesizes the policy messages, and provides directions for future research and writing. Copyright © 2007 John Wiley & Sons, Ltd.
System dynamics—the next fifty years
Authors: Forrester Jay W. 
Published: October 2007

AbstractFifty years after its creation, I review the current status of the field of system dynamics and assess prospects for the next fifty. I focus on the challenges the field must face if it is to realize its potential.The first 50 years of system dynamics have established an introduction to the field. We have shown the importance of achieving a better understanding of complex systems in nature and human affairs. Now, the field is on a plateau ready to launch the next great thrust forward.We can better understand the present status of system dynamics by comparison to professions that have developed earlier. We are now at about the same state of advancement that engineering was when MIT first opened its doors in 1865, or that medicine was in the late 1800s when the Johns Hopkins School of Medicine was established.We have as much to learn yet about high‐order nonlinear feedback structures around us as those earlier professions have already learned about their fields in the last 150 years. Now is the time to plan how the next 50 years can start to close this huge knowledge gap.Like those early days in more mature professions, we do not yet have universities devoted to 4‐year and 6‐year programs in system dynamics. Like the older professions at their beginning, we do not yet have the equivalent of programs in science and biology in kindergarten through 12th grade education to prepare students for more advanced study at the university level. Nevertheless, there has been major progress in system dynamics during the last 50 years just as there had been in those older professions before they became formalized in advanced educational programs and before they were publicly recognized. Copyright © 2007 Jay W. Forrester.