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Molecular Parameters (molecular + parameter)
Selected AbstractsRaman spectroscopy for spinline crystallinity measurements.JOURNAL OF APPLIED POLYMER SCIENCE, Issue 5 2008Abstract The original Doufas,McHugh two-phase microstructural/constitutive model for stress-induced crystallization is expanded to polyolefin systems and validated for its predictive capability of online Raman crystallinity and spinline tension data for two Dow homopolymer polypropylene resins. The material parameters,inputs to the model,are obtained from laboratory-scale material characterization data, that is, oscillatory dynamic shear, rheotens (melt extensional rheology), and differential scanning calorimetry data. The same set of two stress-induced crystallization material/molecular parameters are capable of predicting the crystallinity profiles along the spinline and fiber tension very well overall for a variety of industrial fabrication conditions. The model is capable of predicting the freeze point, which is shown, for the first time, to correlate very well with the measured stick point (i.e., the point in the spinline at which the fiber bundle converts from a solid-like state to a liquid-like state and sticks to a solid object such as a glass rod). The model quantitatively captures the effects of the take-up speed, throughput, and melt flow rate on the crystallization rate of polypropylene due to stress-induced crystallization effects. This validated modeling approach has been used to guide fiber spinning for rapid product development. The original Doufas,McHugh stress-induced crystallization model is shown to be numerically robust for the simulation of steady polypropylene melt spinning over a wide range of processing conditions without issues of discontinuities due to the onset of the two-phase constitutive formulation downstream of the die face, at which crystallization more realistically begins. Because of the capturing of the physics of polypropylene fiber spinning and the very good model predictive power, the approximations of the original Doufas,McHugh model are asserted to be reasonable. © 2008 Wiley Periodicals, Inc. J Appl Polym Sci, 2008 [source] Hypoxia-activated microglial mediators of neuronal survival are differentially regulated by tetracyclinesGLIA, Issue 8 2006Aaron Y. Lai Abstract The tetracycline derivatives minocycline (MINO) and doxycycline (DOXY) have been shown to be neuroprotective in in vivo and in vitro models of stroke. This neuroprotection is thought to be due to the suppression of microglial activation. However, the specific molecular parameters in microglia of the tetracyclines' effect are not understood. We subjected cultured rat microglial and neuronal cells to in vitro hypoxia and examined the effects of MINO and DOXY pre-treatments. Our data showed that MINO and DOXY protect against hypoxia-induced neuronal death by a mechanism dependent on regulation of microglial factors, but likely unrelated to regulation of microglial proliferation/viability. Both MINO and DOXY suppressed the hypoxic activation of ED-1, a marker for microglial activation. Morphological analyses of hypoxic microglia using the microglial marker Iba1 revealed that treatment with MINO and DOXY caused a higher percentage of microglia to remain in a non-activated state. MINO suppressed the hypoxic upregulation of pro-inflammatory agents nitric oxide (NO), interleukin-1 beta (IL-1,), and tumor necrosis factor alpha (TNF-,), while DOXY down-regulated only NO and IL-1,. In contrast, the hypoxic activation of pro-survival/neuroprotective microglial proteins, such as brain-derived neurotrophic factor (BDNF) and glial cell line-derived neurotrophic factor (GDNF), were unaffected by tetracycline treatments. Taken together, these results suggest that MINO and DOXY may provide neuroprotection against stroke by selectively down-regulating microglial toxic factors while maintaining functional pro-survival factors. © 2006 Wiley-Liss, Inc. [source] New aluminum-based ionic liquids: Synthesis, characterization, and theoretical studyHETEROATOM CHEMISTRY, Issue 7 2009Hossein Tavakol Synthesis, characterization, spectral and molecular parameters of some new room-temperature ionic liquids (tetraalkylammonium bromotrichloro aluminum [R4N]+[AlCl3Br],) have been studied in the present study. All synthesized ionic liquids were characterized by IR, 1H, 13C, and 81Br-NMR. In addition, synthesized structures were optimized at the B3LYP/LANL2DZ level of theory and then the structures, molecular specifications, and infrared spectra of these were extracted using Gaussian 03 program. Theoretical data show good agreement with the experimental results. © 2010 Wiley Periodicals, Inc. Heteroatom Chem 20:398,404, 2009; Published online in Wiley InterScience (www.interscience.wiley.com). DOI 10.1002/hc.20564 [source] Distinct CpG island methylation profiles and BRAF mutation status in serrated and adenomatous colorectal polypsINTERNATIONAL JOURNAL OF CANCER, Issue 11 2008Yong Ho Kim Abstract A subset of colorectal cancers with CpG island methylator phenotype-high (CIMP-H) is frequently associated with MSI and BRAF V600E mutation. Since limited data are available on different histological types of colorectal polyps, we compared the pattern and the frequency of promoter methylation, CIMP-H, MSI, KRAS and BRAF V600E mutations and the relationship among these molecular parameters and the clinicopathologic characteristics in 110 serrated polyps (48 hyperplastic polyps, 32 sessile serrated adenomas and 30 serrated adenomas) and 32 tubular adenomas using 7 commonly used tumor-associated gene loci. No significant difference in the frequency of overall methylation frequency (86% vs. 100%) and CIMP-H (39% vs. 28%) between serrated polyps and tubular adenomas was observed, but proximally located serrated polyps showed more frequent methylation at 5 of 7 loci examined, and were more likely to be CIMP-H (62% vs. 22%). MGMT methylation was more common in tubular adenomas while MLH1 and HIC1 were more frequently methylated in serrated polyps. BRAF mutation was frequently present in all types of serrated polyps (80%), but was absent in tubular adenomas and was not associated with CIMP or MSI status. These results show comparable frequencies of promoter methylation of tumor-associated genes and CIMP-H, but distinct differences in gene-specific or colonic site-specific methylation profiles occur in serrated polyps and tubular adenomas. BRAF mutation occurs independently of CIMP and MSI in all types of serrated polyps and may serve as a marker of serrated pathway of colorectal carcinogenesis. © 2008 Wiley-Liss, Inc. [source] Evaluation of data for atmospheric models: Master Equation/RRKM calculations on the combination reaction ClO + NO2 , ClONO2, a recurring issueINTERNATIONAL JOURNAL OF CHEMICAL KINETICS, Issue 9 2009David M. Golden Experimental data for the title reaction have been modeled using Master Equation/RRKM methods based on the Multiwell suite of programs. The starting point for the exercise was the empirical fitting provided by the NASA and IUPAC data evaluation panels, which represent the data in the experimental pressure ranges rather well. Despite the availability of quite reliable parameters for these calculations (molecular vibrational frequencies and a value of the bond dissociation energy of ClONO2, DH298(ClONO2) = 26.5 kcal mol,1, corresponding to ,H00 = 25.35 kcal mol,1 at 0 K) and use of RRKM/Master Equation methods, fitting calculations to the reported data was anything but straightforward. Using these molecular parameters resulted in a discrepancy between the calculations and the database of rate constants of a factor of ca 4 at, or close to, the low-pressure limit. © 2009 Wiley Periodicals, Inc. Int J Chem Kinet 41: 573,581, 2009 [source] Genetic and epigenetic aspects of bladder cancerJOURNAL OF CELLULAR BIOCHEMISTRY, Issue 1 2005Wun-Jae Kim Abstract Transitional cell carcinoma of the urinary bladder has a diverse collection of biologic and functional characteristics. This is reflected in differing clinical courses. The diagnosis of bladder cancer is based on the information provided by cystoscopy, the gold standard in combination with urinary cytology findings. Many tumor markers have been evaluated for detecting and monitoring the disease in serum, bladder washes, and urinary specimens. However, none of these biomarkers reported to date has shown sufficient sensitivity and specificity for the detection of the whole spectrum of bladder cancer diseases in routine clinical practice. The limited value of established prognostic markers requires the analysis of new molecular parameters of interest in predicting the prognosis of bladder cancer patients; in particular, the high-risk patient groups at risk of progression and recurrence. Over the past decade, there has been major progress elucidating of the molecular genetic and epigenetic changes leading to the development of transitional cell carcinoma. This review focuses on the recent advances of genetic and epigenetic aspects in bladder cancer, and emphasizes how molecular biology would be likely to affect the future therapies. © 2005 Wiley-Liss, Inc. [source] H-bond donor strength;JOURNAL OF COMPUTATIONAL CHEMISTRY, Issue 9 2009Abraham parameter; A quantum chemical model is introduced to predict the H-bond donor strength of monofunctional organic compounds from their ground-state electronic properties. The model covers OH, NH, and CH as H-bond donor sites and was calibrated with experimental values for the Abraham H-bond donor strength parameter A using the ab initio and density functional theory levels HF/6-31G** and B3LYP/6-31G**. Starting with the Morokuma analysis of hydrogen bonding, the electrostatic (ES), polarizability (PL), and charge transfer (CT) components were quantified employing local molecular parameters. With hydrogen net atomic charges calculated from both natural population analysis and the ES potential scheme, the ES term turned out to provide only marginal contributions to the Abraham parameter A, except for weak hydrogen bonds associated with acidic CH sites. Accordingly, A is governed by PL and CT contributions. The PL component was characterized through a new measure of the local molecular hardness at hydrogen, ,(H), which in turn was quantified through empirically defined site-specific effective donor and acceptor energies, EEocc and EEvac. The latter parameter was also used to address the CT contribution to A. With an initial training set of 77 compounds, HF/6-31G** yielded a squared correlation coefficient, r2, of 0.91. Essentially identical statistics were achieved for a separate test set of 429 compounds and for the recalibrated model when using all 506 compounds. B3LYP/6-31G** yielded slightly inferior statistics. The discussion includes subset statistics for compounds containing OH, NH, and active CH sites and a nonlinear model extension with slightly improved statistics (r2 = 0.92). © 2008 Wiley Periodicals, Inc. J Comput Chem 2009 [source] Asymmetrical flow field-flow fractionation coupled to multiangle laser light scattering detector: Optimization of crossflow rate, carrier characteristics, and injected mass in alginate separationJOURNAL OF SEPARATION SCIENCE, JSS, Issue 14 2007Enrica Alasonati Abstract The coupling of the flow field-flow fractionation (FlFFF) to differential refractive index (DRI) and multiangle laser light scattering (LS) detectors is a powerful tool for characterizing charged polysaccharides such as alginate. However, the correct interpretation of the experimental results and extrapolation of meaningful molecular parameters by using an analytical tool with such a level of complexity requires improvement of the knowledge of the alginate behavior in the channel and careful optimization of the operating conditions. Therefore, the influence of the critical operating parameters, such as crossflow rate, carrier composition and concentration, and sample load, on the alginate retention was carefully evaluated. Combined information obtained simultaneously by DRI and LS detectors over the wide range of the crossflow rate, carrier liquid concentration, and injected amount, allowed to set the appropriate combination of optimal parameters. It was found that the crossflow rate of 0.25 mL/min, carrier solution containing 5×10,2 mol/L ammonium or sodium chloride, and 50,100 ,g of injected sample mass were necessary to achieve complete separation and determination of the meaningful molecular characteristics. The values of the weight-average hydrodynamic radius (RHw), radius of gyration (RG), and molar mass (M), obtained under the optimal conditions were in good agreement to those found for alginates in the literature. [source] Crazing and Fracture in Polymers: Micro-Mechanisms and Effect of Molecular VariablesMACROMOLECULAR SYMPOSIA, Issue 1 2004H.H. Kausch Abstract The influence of the primary molecular parameters chain configuration, architecture and molecular weight (MW) on the mode of mechanical breakdown is discussed for two series of (amorphous) thermoplastic polymers, methyl methacrylate glutarimide copolymers and amorphous semi-aromatic polyamides. Structural and dynamic analyses and fracture mechanical methods applied to such adequately chemically modified (glassy) polymers permit us to show and to explain the effect of intrinsic variables on local molecular motions and on the competition between chain scission, disentanglement and segmental slip, which in turn determine the dominant mode of instability and plastic behaviour. Above a critical molecular weight, toughness depends most strongly on the entanglement density; a positive effect of the intensity of sub-Tg relaxations and in-chain cooperative motions on the toughness of these materials is clearly evident. [source] Computation and analysis of 19F substituent chemical shifts of some bridgehead-substituted polycyclic alkyl fluoridesMAGNETIC RESONANCE IN CHEMISTRY, Issue 7 2003William Adcock Abstract The 19F NMR shieldings for several remotely substituted rigid polycyclic alkyl fluorides with common sets of substituents covering a wide range of electronic effects were calculated using the DFT-GIAO theoretical model. The level of theory, B3LYP/6,311+G(2d,p), was chosen based on trial calculations which gave good agreement with experimental values where known. The optimized geometries were used to obtain various molecular parameters (fluorine natural charges, electron occupancies on fluorine of lone pairs and of the CF bond, and hybridization states) by means of natural bond orbital (NBO) analysis which could help in understanding electronic transmission mechanisms underlying 19F substituent chemical shifts (SCS) in these systems. Linear regression analysis was employed to explore the relationship between the calculated 19F SCS and polar substituent constants and also the NBO derived molecular parameters. The 19F SCS are best described by an electronegativity parameter. The most pertinent molecular parameters appear to be the occupation number of the NBO p-type fluorine lone pair and the occupation number of the CF antibonding orbital. This trend suggests that in these types of rigid saturated systems hyperconjugative interactions play a key role in determining the 19F SCS. Electrostatic field effects appear to be relatively unimportant. Copyright © 2003 John Wiley & Sons, Ltd. [source] Rheological behavior of highly filled ethylene propylene diene rubber compoundsPOLYMER ENGINEERING & SCIENCE, Issue 5 2000M. G. Markovic The rheological behavior of highly filled ethylene propylene diene rubber (EPDM) compounds was studied with respect to the effect of curative system, grafted rubber, shear rate, temperature and die swell using a Monsanto Processability Tester (MPT) to gain an understanding of the molecular parameters that control the surface finish. All systems show pseudoplastic behavior. At a particular shear rate, shear viscosity increases with blend ratio. The dependence of flow behavior on extrusion velocity indicates a surface effect. The extrudate die swell and maximum recoverable deformation are related by a linear relationship, which is independent of sulfur/accelerator ratio, extrusion temperature and shear rates and blend ratio. The principal normal stress difference increases nonlinearly with shear stress. Activation energy decreases with shear rate in most cases. The faster relaxing system produces extrudate of better surface quality. [source] Mass spectrometric determination of the dissociation energy of Mn2F6(g)RAPID COMMUNICATIONS IN MASS SPECTROMETRY, Issue 16 2002Andrea Ciccioli The gaseous Mn2F6 molecule has been identified for the first time in the vapor produced by MnF3 vaporization and the MnF3(g) dimerization equilibrium studied by the Knudsen cell mass spectrometry technique in the 884,1015,K temperature range. The experimental vapor pressure data were treated by the second- and third-law procedures, and the enthalpy of Mn2F6(g) dissociation has been determined as: . Thermodynamic functions of gaseous MnF3 were calculated from geometrical and vibrational parameters taken from the literature. For gaseous Mn2F6, they were evaluated by comparison with molecular parameters of Co2F6(g). Copyright © 2002 John Wiley & Sons, Ltd. [source] From expert opinion to evidence-based: changes in the gold standard of primary brain tumour diagnosis,THE JOURNAL OF PATHOLOGY, Issue 1 2007JM Kros Abstract Since 1997, significant progress has been made in the WHO guidelines for the diagnosis of primary tumours of the central nervous system. A large group of international experts was involved in editing the content; consensus on definitions and classifications was sought; and updated findings of genomic investigations were included. Nevertheless, significant inter-observer variability still exists in the histopathological diagnosis of several tumour types. The challenge for the near future is to identify histological and genotypic characteristics with prognostic or predictive value. With that aim, testing histological or molecular parameters in prospective clinical studies is indicated. Copyright © 2007 Pathological Society of Great Britain and Ireland. Published by John Wiley & Sons, Ltd. [source] Banff '09 Meeting Report: Antibody Mediated Graft Deterioration and Implementation of Banff Working GroupsAMERICAN JOURNAL OF TRANSPLANTATION, Issue 3 2010B. Sis The 10th Banff Conference on Allograft Pathology was held in Banff, Canada from August 9 to 14, 2009. A total of 263 transplant clinicians, pathologists, surgeons, immunologists and researchers discussed several aspects of solid organ transplants with a special focus on antibody mediated graft injury. The willingness of the Banff process to adapt continuously in response to new research and improve potential weaknesses, led to the implementation of six working groups on the following areas: isolated v-lesion, fibrosis scoring, glomerular lesions, molecular pathology, polyomavirus nephropathy and quality assurance. Banff working groups will conduct multicenter trials to evaluate the clinical relevance, practical feasibility and reproducibility of potential changes to the Banff classification. There were also sessions on quality improvement in biopsy reading and utilization of virtual microscopy for maintaining competence in transplant biopsy interpretation. In addition, compelling molecular research data led to the discussion of incorporation of omics-technologies and discovery of new tissue markers with the goal of combining histopathology and molecular parameters within the Banff working classification in the near future. [source] Genetic diversity of dog breeds: within-breed diversity comparing genealogical and molecular dataANIMAL GENETICS, Issue 3 2009G. Leroy Summary The genetic diversity of 61 dog breeds raised in France was investigated. Genealogical analyses were performed on the pedigree file of the French kennel club. A total of 1514 dogs were also genotyped using 21 microsatellite markers. For animals born from 2001 to 2005, the average coefficient of inbreeding ranged from 0.2% to 8.8% and the effective number of ancestors ranged from 9 to 209, according to the breed. The mean value of heterozygosity was 0.62 over all breeds (range 0.37,0.77). At the breed level, few correlations were found between genealogical and molecular parameters. Kinship coefficients and individual similarity estimators were, however, significantly correlated, with the best mean correlation being found for the Lynch & Ritland estimator (r = 0.43). According to both approaches, it was concluded that special efforts should be made to maintain diversity for three breeds, namely the Berger des Pyrénées, Braque Saint-Germain and Bull Terrier. [source] Molecular Structure and QSAR Study on Antispasmodic Activity of some Xanthoxyline DerivativesARCHIV DER PHARMAZIE, Issue 5 2006Rodrigo dos Santos Abstract Semi-empirical molecular orbital calculations at AM1 level were done with the aim to investigate the structure-activity relationships of antispasmodic activities of ten 2-(X-benzyloxy)-4,6-dimethoxyacetophenones with X = H, 4,-F, 4,-NO2, 4,-CH3, 4,-Cl, 3,,4,-(CH3)2, 4,-OCH3, 4,-Br, 4,-OCH2C6H5, and 4,-C(CH3)3, against acetylcholine-induced contraction of the guinea pig ileum. The most significant quantum chemical descriptors for this series of compounds were the net atomic charges, nucleophilic and electrophilic frontier electron density, HOMO and LUMO orbitals, and reactivity indices. While no significant correlations were found employing molecular parameters such as heat of formation, dipole moment, molecular polarizability, and so on, good correlations were obtained using the reactivity indices of HOMO and LUMO orbitals at specific atoms of the molecules. These results indicate that the spatial distribution of HOMO and LUMO orbitals over these specific atoms play an important role for an increase of biological activity. [source] Molecular dynamics calculations on amylose fragments.BIOPOLYMERS, Issue 2 2002Abstract Molecular dynamics simulations (NPT ensembles, 1 atm) using the all atom force field AMB99C (F. A. Momany and J. L. Willett, Carbohydrate Research, Vol. 326, pp 194,209 and 210,226), are applied to a periodic cell containing ten maltodecaose fragments and TIP3P water molecules. Simulations were carried out at 25 K intervals over a range of temperatures above and below the expected glass transition temperature, Tg, for different water concentrations. The amorphous cell was constructed through successive dynamic equilibration steps at temperatures above Tg and the temperature lowered until several points of reduced slope (1/T vs volume) were obtained. This procedure was carried out at each hydration level. Each dynamics simulation was continued until the volume remained constant without up or down drift for at least the last 100 ps. For a given temperature, most simulations required 400,600 ps to reach an equilibrium state, but longer times were necessary as the amount of water in the cell was reduced. A total of more than 30 ns of simulations were required for the complete study. The Tg for each hydrated cell was taken as that point at which a discontinuity in slope of the volume (V), potential energy (PE), or density (,) vs 1/T was observed. The average calculated Tg values were 311, 337, 386, and 477 K for hydration levels of 15.8, 10, 5, and 1%, respectively, in generally good agreement with experimental values. The Tg for anhydrous amylose is above the decomposition temperature for carbohydrates and so cannot be easily measured. However, it has also been difficult to obtain a value of Tg for anhydrous amylose using simulation methods. Other molecular parameters such as end-to-end distances, mean square distributions, and pair distributions are discussed. Published 2002 John Wiley & Sons, Inc. Biopolymers 63: 99,110, 2002 [source] Theoretical Characterization of Charge Transport in One-Dimensional Collinear Arrays of Organic Conjugated MoleculesCHEMPHYSCHEM, Issue 5 2010Lucas Viani Abstract A great deal of interest has recently focused on host,guest systems consisting of one-dimensional collinear arrays of conjugated molecules encapsulated in the channels of organic or inorganic matrices. Such architectures allow for controlled charge and energy migration processes between the interacting guest molecules and are thus attractive in the field of organic electronics. In this context, we characterize here at a quantum-chemical level the molecular parameters governing charge transport in the hopping regime in 1D arrays built with different types of molecules. We investigate the influence of several parameters (such as the symmetry of the molecule, the presence of terminal substituents, and the molecular size) and define on that basis the molecular features required to maximize the charge carrier mobility within the channels. In particular, we demonstrate that a strong localization of the molecular orbitals in push,pull compounds is generally detrimental to the charge transport properties. [source] Enantioselectivity of the musk odor sensationCHIRALITY, Issue 8 2001Philip Kraft Abstract This brief review, the summary of a talk at the Symposium on Biological Chirality 2000 in Szeged, Hungary, illustrates what chiral recognition tells us about the molecular parameters of the musk odor sensation. While the enantioselectivity of odor perception is strong evidence for the key role of proteinogenic receptors in the molecular mechanism of olfaction, the quantitative and qualitative odor differences of enantiomers are often not very pronounced, as in the case of muscone (17/26). In those cases, however, where there is strong enantiodiscrimination, we find most intense musk odorants with very low odor thresholds, such as (,)-(12R)-12-methyl-9-oxa-14-tetradecanolide (35), (12R;9Z)-12-methyl-14-tetradec-9-enolide [(R)-Nirvanolide®, 38], and (,)-(4S;7R)-1,3,4,6,7,8-hexahydro-4,6,6,7,8,8-hexamethylcyclopenta[g]-2-benzopyran [(,)-(4S;7R)-Galaxolide®, 57], the latter being rather rigid. We thus can assume the geometry of the musk receptor to be fairly complementary to these compounds, which therefore can serve as templates for the design of new musk odorants. Chirality 13:388,394, 2001. © 2001 Wiley-Liss, Inc. [source] Substituent effects on the photofading of disperse azo dyes on poly(ethylene terephthalate) substrateCOLORATION TECHNOLOGY, Issue 3 2010Yasuyo Okada The relationships between the chemical structures and oxidative fading of the disperse azo dyes, p -nitrophenylazo- and benzothiazoleazo-anilines, on poly(ethylene terephthalate) substrate are discussed in terms of the parameters k0,i (rate constants of reaction towards 1O2) and fi (photosensitivity), the molecular parameters of molecular orbital theory and substituents in the diazo and coupling components, on the assumption that the initial rates of oxidative fading are proportional to the product of k0,i and fi. 2-Methoxy-5-acetylamino- N -substituted aniline couplers exhibited large fi values. 2-Chloro and 4-nitro substituents of aniline diazo components exhibited small fi values or high quantum yields of internal conversion, while 4-nitro substituent did not. A close correlation between N -substituents and light fastness, proposed by Müller and supplemented by Dawson, demonstrates the applicability of frontier orbital theory, through the highest occupied molecular orbital (HOMO) energy of the dyes, to the analysis of oxidative fading. Dyes with N -2-cyanoethyl substituents, which gave a lower HOMO energy, also exhibited superior light fastness compared with N -2-hydroxyethyl substituents. [source] | |||||||||||||||||||