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  • 101
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Fire and Materials 21 (1997), S. 123-141 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The present study investigates the validity of a test method for smoldering cigarette ignition propensity of upholstery fabrics based on using ‘cotton duck’ fabrics, and proposed by NIST. A comparison was made between the ignition propensity of cigarettes as assessed by (1) a set of 500 upholstery fabrics (chosen at random among typical upholstery fabrics) and (2) a test method proposed by NIST (NIST 851), and based on ‘cotton duck’ fabrics. The set of 500 fabrics can be assumed to be a representative cross-section of the upholstery fabrics available in the early 1990s, while the ‘cotton duck’ fabrics are not typical upholstery fabrics, and it was unclear whether they would behave similarity or differently from upholstery fabrics. Of the 500 fabrics tested, only 145 fabrics were ignitable by cigarettes, all of them predominantly (or completely) cellulosic. This study found that the overall results obtained from the 500-upholstery fabric study correlate well with those of the ‘cotton duck’ study. Therefore, the ‘cotton ducks’ can be considered, as a whole, to behave similarly to the majority (estimated at perhaps 80%) of the upholstery fabrics available at the time of the study, and the test is valid. In this study it was also found that the ‘cotton duck’ test method correlated well with an earlier cigarette ignition test method, shown to be a good predictor of full-scale upholstered furniture cigarette ignition results, when using a set of five cigarettes. Finally, a fabric density threshold was found, above which the percentage of ignitions of cellulosic fabrics, the percentage of cellulosic fabrics that are ignitable and the flame spread rate of fabrics in a flaming ignition test are all unaffected. © 1997 John Wiley & Sons, Ltd.
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  • 102
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    New York, NY [u.a.] : Wiley-Blackwell
    Fire and Materials 21 (1997), S. 187-189 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The fire standard for aircraft interior panels has been compared to the corresponding marine standard with respect to smoke emission and heat release rate. This has been performed by testing an aircraft panel approved by the Federal Aviation Administration according to one of the International Maritime Organization standards for High-Speed Craft, according to the full-scale room fire test, ISO 9705. The test showed that even if the panel met the strict requirements of the Federal Aviation Administration it did not fulfil the apparently even stricter requirements of the International Maritime Organization. The panel failed on several accounts, including smoke production, heat release and structural integrity. © 1997 John Wiley & Sons, Ltd.
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  • 103
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The fire response of a potassium aluminosilicate (Geopolymer) matrix carbon fiber composite was measured and the results compared to organic matrix composites being used for transportation, military, and infrastructure applications. At irradiance levels of 50 kWm-2 typical of the heat flux in a well-developed fire, glass- or carbon-reinforced polyester, vinylester, epoxy, bismaleimde, cyanate ester, polyimide, phenolic, and engineering thermoplastic laminates ignited readily and released appreciable heat and smoke, while carbon-fiber reinforced Geopolymer composites did not ignite, burn, or release any smoke even after extended heat flux exposure. The Geopolymer matrix carbon fiber composite retains 67% of its original flexural strength after a simulated large fire exposure. © 1997 US Government
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  • 104
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    Fire and Materials 21 (1997), S. 191-194 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The study presented here was designed to provide information on the nature of fibres subjected to the action of raised temperature and on the possibility of determination of the incinerated material. X-ray powder diffraction was used as the most reliable method of identifying the composition of crystalline substances. The subject of study was natural and synthetic fibres, the most frequently used in Poland in recent years; for the simulation of phenomena caused by the action of raised temperature the fibres were incinerated in a muffle furnace. The samples of analyzed incinerated fibres were of different chemical species, and those differences were more evident for natural fibres, where from five to seven chemical species or minerals were detected. In specific forensic cases related to incinerated fibres FTIR, SEM/EDX, polarized light microscope and X-ray powder diffraction techniques should be used simultaneously to give full results. © 1997 John Wiley & Sons, Ltd.
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  • 105
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    Fire and Materials 21 (1997), S. 205-211 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The contrast attenuation coefficient characterizes smoke production properties of a material. These properties are closely connected with a contrast of luminance of a scene observed in a smoky medium, the range of visibility, and mass concentration in an environment volume. The range of visibility determines a person's chances of moving about in a fire zone. This paper presents considerations on conditions of visibility in smoky compartments, a method of the contrast attenuation measurement and test results for some materials. © 1997 John Wiley & Sons, Ltd.
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  • 106
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    Fire and Materials 21 (1997), S. 161-168 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A mathematical and computational model simulating the coupled heat and mass transfer and related processes in porous media exposed to elevated temperatures has been developed. Taking into account the conservation of mass, momentum and energy, and including the effects of evaporation and dehydration processes on the transport phenomena, a set of three coupled nonlinear differential equations is obtained. Siliceous aggregate concrete slabs subjected to the ASTM E119 standard fire exposure are modeled and validated against test data. Output depicts the coupled relationships between the material's temperature, moisture content, and pore pressure histories and distributions. © 1997 John Wiley & Sons, Ltd.
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  • 107
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    Fire and Materials 21 (1997), S. 235-244 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Application of zone model for studying atrium smoke-filling process was evaluated. The fire zone model FIRST was selected as the fire simulator. Studies were focused on the plume model, the geometry of the atria and the heat release rate of fires. Six plume models reported in the literature were reviewed. Their expressions on the velocity, temperature and mass flow were compared. Three halls of same volume but different shapes were taken as the samples. A small volume of 2000 m3 was used because a zone model should work in halls of this size. Numerical simulations of the fire environment in the atrium buildings with those six plume models were carried out using the zone model FIRST. A total number of 108 simulations were performed with nine sets of fires. © 1997 John Wiley & Sons, Ltd.
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  • 108
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    Fire and Materials 21 (1997), S. 169-177 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Dust explosion hazard exists in plants and facilities handling combustible dusts. The minimum ignition temperature of dust clouds is an important parameter requiring special attention to designing the explosion preventive measures. This paper presents a model developed for determining the minimum ignition temperature for an organic dust cloud, polyethylene, simulating the conditions in the Godbert-Greenwald furnace. The model correlates the particle size, as well as the dust concentration with the minimum ignition temperature. It is based on the two-stage oxidation mechanism involving devolatilization/decomposition of the solid particle and homogeneous oxidation of volatile combustible products. In the case of polyethylene, the main combustible gas responsible for ignition and flame propagation has been confirmed to be butylene. The results of the computations were compared with the experimental values and those predicted by Mitsui and Tanaka. The predicted values by the model developed are in close agreement with the experimental data which confirm the proposed ignition mechanism. The model can be used for the prediction of minimum ignition temperature of organic dusts having an autoignition mechanism similar to polyethylene dust. © 1997 John Wiley & Sons, Ltd.
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  • 109
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    Fire and Materials 21 (1997), S. 195-195 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 110
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 111
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    Fire and Materials 21 (1997), S. 199-204 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Small amounts of polytetrafluoroethylene (PTFE) are shown to modify the combustion behaviour of Acrylonitrile-Butadiene-Styrene terpolymers (ABS) fire retarded with a bromine/antimony synergistic system. PTFE makes ignition more difficult and decreases the rate of flame propagation in the early stage of combustion. The action of PTFE is shown to occur in the condensed phase by accumulation of fluorine in the residue of combustion and by reaction of PTFE with Sb2O3 to give volatile moieties. A catalytic action of fluorinated species formed in the presence of PTFE is suggested to take place on reactions of the bromine/antimony system increasing its effectiveness. © 1997 John Wiley & Sons Ltd.
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  • 112
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    Fire and Materials 21 (1997), S. 229-234 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper extends earlier work which explored the possibility of undertaking a life cycle analysis of flame-retardant cotton and polyester textiles and consequently enabled semi-quantitative estimations of their relative environmental impacts to be made. This model is extended to undertake full environmental audits of a range of flame-retardant textiles and requires full consideration of each stage from fibre/raw material production to eventual disposal. The need for comprehensive data at all stages, however, demonstrates that comparisons between competing products are neither simple nor, at present, possible. Thus an environmental rank value is given to each stage in the manufacturing process and product life of each flame retardant fibre and derived textile. Summation of rank values enables an overall environmental index to be defined which may be used to compare the environmental impact of each generic type of currently available flame retardant, single fibre-containing textile. The results show that each of the eleven generic fibres analysed yield environmental index values within a range 32-51% where 100% denotes the worst environmental position possible. This relatively low range of values suggests that current production and processes which attempt to maximize economic viability also tend to reduce environmental impact. © 1997 John Wiley & Sons Ltd.
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  • 113
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    Fire and Materials 21 (1997), S. 219-228 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: In accordance with the Montreal Protocol, production of all Halon fire suppressants ceased on 1 January 1994. FAR/JAR regulations require Halon 1211 or equivalent hand extinguishers to be installed on transport category aircraft. Although there is a Halon ’bank‘, a replacement agent will have to be found. The Aviation Authorities require that ’no loss of safety‘ should occur if a replacement agent is used. One proven benefit provided by Halon 1211 is the ability to extinguish hidden fires by a total flooding effect. Therefore, it is necessary to quantify the hidden fire-extinguishing ability exhibited by Halon 1211. Following an invitation for competitive tenders to develop a standard hidden fire test protocol, the Civil Aviation Authority (CAA) awarded a contract to Kidde International Research. After some range-finding work, a suitable test fixture was devised. This test fixture comprised arrays of four fires in two of five locations to establish in which regions an extinguishing concentration had been attained. A matrix of 10 tests ensured that each fire location was adequately represented. Tests have been carried out with hand extinguishers from four manufacturers. Results varied from 45% extinguishment to 60%, depending on the quantity of Halon contained in the extinguisher, and the discharge rate (a faster discharge rate creates more turbulence, aiding mixing and dispersion). In addition, tests were carried out using under- and over-filled extinguishers to examine the sensitivity of the test method. With the exception of one hand extinguisher, all results could be correlated to the mass and mass flow rate of agent used. This device extinguished a significantly higher percentage of fires than would be expected, based on its mass/mass flow rate characteristics. Limited testing was carried out with six Halon replacements: FM-200, FE-25, CEA-4.10, CEA-6.14, FE-36 and Triodide, using apparatus designed to give a constant discharge time (10±1 s). The results obtained appeared to be similar to Halon 1211 (50±5% extinguishment), provided the quantity of agent is scaled according to its n-heptane cupburner concentration. The two exceptions are agents with markedly different volatilities to Halon 1211 (b.p.-4°C): FE-25, b.p. -49° C, (65% extinguishment) and CEA-6.14, b.p.+58°C (35% extinguishment). Implications for the size and weight of a hand extinguisher, based on the results of these tests, are for the physically acting agents, a weight penalty of 1.4 to 2.6, and a volume penalty of 1.9 to 2.9. If Triodide is considered, there is a weight penalty of 1.06, and no volume penalty. However, it should be borne in mind that any hand extinguisher, before it is evaluated against hidden files, will have had to have passed the traditional ratings (currently UL 5B:C, BS 3A:34B) to be approved for aviation use. © 1997 John Wiley & Sons Ltd.
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  • 114
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    Fire and Materials 21 (1997), S. 253-257 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The theoretical bases for calculation of heat release rate during burning of conveyor belts in the fire-testing gallery has been presented. Taking as an example the results of measurements of oxygen, carbon dioxide and monoxide content in the products of combustion of conveyor belts during the testing of their flammability in the full-scale fire gallery, the possibility has been demonstrated for using the calculations of heat release rate in an assessment of conveyor belt flammability. The total quantity of heat released during the belt fire in the experimental gallery can provide the basis to develop a new method of testing as well as the criteria for assessment of fire resistance of the conveyor belts using oxygen consumption calorimetry. © 1997 John Wiley & Sons, Ltd.
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  • 115
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    Fire and Materials 21 (1997), S. 259-264 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This paper reports an analysis of data from a study conducted by the cigarette industry to determine whether the fabrics used in a measurement method for cigarette ignition propensity reasonably represent the ignition behaviour of actual upholstery fabrics. A ‘consistency score’ is defined to evaluate objectively the relative agreement of ignition test results on various test fabrics compared with the cotton duck fabrics used in the measurement method. Particular attention is paid to those cases where the cigarettes show statistically significant differences by the chi-squared test. This analysis finds that the aggregated set of 79 industry fabrics ranks the four test cigarettes in the same order as do the three cotton duck fabrics in the measurement method. Thus, to the extent that the industry set is representative of those fabrics used in upholstery, it would be proper to use the three test fabrics as surrogates for the purpose of determining the relative ignition propensity of a cigarette. The analysis does identify six to ten fabrics that would be expected to show persistent reversals compared to the aggregate ordering; however, three-fourths of the fabrics rank the cigarettes consistently with the cotton duck fabrics. © 1997 John Wiley & Sons, Ltd.
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  • 116
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    International Journal for Numerical and Analytical Methods in Geomechanics 21 (1997), S. 153-174 
    ISSN: 0363-9061
    Keywords: constitutive model ; hypoplasticity ; failure ; stability ; granular material ; Engineering ; Civil and Mechanical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Notes: Recent investigations on the hypoplastic constitutive model for granular materials show that the failure surface can be surpassed by some stress paths. This is contradictory to the conventional definition of failure surface in plasticity, according to which the stress is allowed to move on the failure surface but never across it. In the present paper, the interrelations among the different constitutive models are discussed with special reference to failure and stability. For the hypoplastic constitutive equation, the accessible stress states and the stable stress states are found to be enclosed by a bound surface and a stability surface in the stress space, respectively. Theoretical findings about the bound surface and the stability surface are verified qualitatively by presenting results of triaxial tests on dry sand. © 1997 by John Wiley & Sons, Ltd.
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  • 117
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    International Journal for Numerical and Analytical Methods in Geomechanics 21 (1997), S. 241-253 
    ISSN: 0363-9061
    Keywords: rockbolt ; Euler-Bernoulli ; beam-column ; roof-reinforcement ; stability ; pull-out ; Engineering ; Civil and Mechanical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Notes: A simple analytical procedure that applies classical beam-column theory for evaluating passive rockbolt roof reinforcement is presented in this paper. The analytical model is derived from first principles and is capable of modelling any number of reinforcing bolts. Each rockbolt is modelled as a linear spring and the model allows for non-uniform bolt spacing. In this study the rock beam is assumed to be isotropic and linearly elastic for the sake of simplicity. However, the analytical model can be extended to include anisotropic rockmass as well as inelastic material behaviour. The solution to the coupled set of governing equations is obtained by using a simple numerical solution procedure. The results from the analytical model indicate that the critical buckling load of a rock beam is strongly influenced by the ambient rock modulus. For salt-rock excavations the rock modulus typically declines with time due to various phenomena, and a diminished modulus could seriously compromise roof stability. The other main conclusion of this study is that rockbolts loose their effectiveness in restraining a roof beam once its critical buckling load is approached. In such a situation, increasing bolt stiffness does not improve its reinforcing action on a roof beam but it enhances the possibility of bolt failure due to anchor pull-out. © 1997 by John Wiley & Sons, Ltd. Int. J. Numer. Anal. Meth. Geomech., vol. 21, 241-253 (1997)
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  • 118
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    International Journal for Numerical and Analytical Methods in Geomechanics 21 (1997), S. 337-345 
    ISSN: 0363-9061
    Keywords: method of slices ; sands ; stability ; retaining walls ; passive pressure ; Engineering ; Civil and Mechanical Engineering
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Geosciences
    Notes: A method of slices satisfying all the conditions of statical equilibrium has been developed to deal with the problem of determination of passive earth pressure over a retaining wall in sand. A method similar to that of Morgenstern and Price, which was used to solve the stability of slopes, has been followed. The earth pressure coefficients with the proposed methodology have been computed for a vertical retaining wall for both positive and negative wall friction angle. Also examined is the variation of the interslice shear force between the retaining wall and the Rankine Passive boundary. Due to complete satisfaction of the equilibrium conditions, the method generates exactly the same earth pressure coefficients as computed by using Terzaghi's overall limit equilibrium approach. © 1997 by John Wiley & Sons, Ltd.
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  • 119
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    Fire and Materials 2 (1978) 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 120
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    Fire and Materials 2 (1978), S. 1-1 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 121
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    Fire and Materials 2 (1978), S. 2-6 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The Complexity of the behavior of smoke at fires can lead to great difficulties in obtaining measurements from instruments which are both reliable and correlatable with human observations. The first article in this two-part review considers the principal characteristics of smoke, the factors which influence its behaviour at fires, the basic theory of light transmission through smoke, and the behaviour of the eye in smoky conditions. This information will be used in the second article to assess the performance and limitations of various types of smoke measuring instruments.
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  • 122
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    Fire and Materials 2 (1978), S. 7-10 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: An attempt has been made to present toxicological results obtained by a biological evaluation method in a simple and comprehensive way. The calculation of a toxicity index which expresses mortality rates as a function of the very important time factor is proposed. Additionally it is shown how such an index could be used to rank a series of twenty materials according to their relative toxicity.
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  • 123
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    Fire and Materials 2 (1978), S. 11-17 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The small-scale smoke testing apparatus now proposed as a standard in France under the designation NF-T51-073 measures the total obscuration from a stream of smoke generated from a small sample. Although like other small-scale fire tests, it is not claimed to be of relevance to real fire situations, it is possible by varying the temperature over a wide range (200-900°C) to obtain a plot of specific optical density for various materials which broadly corresponds with general experience and certain other smoke tests. The plots show that nearly all flammable substances give a rapid rise in smoke opacity in the 350-500°C region above which there is always a steep drop sometimes to smoke densities of virtually zero. Apart from one or two synthetic materials which show a very low smoke density through-out, there is no general trend as between natural and synthetic substances. Oxygen depletion which often occurs in a real fire situation has some effect on the smoke density but it is not a major one. On the other hand, in some cases reheating the smoke can have quite a dramatic effect, due very probably to further pyrolysis and combustion.
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  • 124
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    Fire and Materials 2 (1978), S. 25-26 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The thermal degradation of untreated and wool treated by various flame retardants, using pyrolysis gas chromatography, has been studied. The concentration of CO, CO2 and benzene produced does not appear to be affected by the flame retardants studied. The latter slightly decreases the concentration of toluene produced while the HCN production depends on the chemical composition of the retardant and on the temperature of exposure.
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    Fire and Materials 2 (1978), S. 18-24 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A study was conducted of the smoke and flow field in a corridor subject to a room fire. The study was conducted using a scale model of roughly 0.35 m in height. The effect of corridor-exit doorway width was recorded while the room doorway and fire-room temperature were maintained constant. Smoke was generated from cotton wads soaked with titanium tetrachloride which produces white particles of titanium dioxide. By this means, the smoke layer resulting from the room fire and the corridor flow characteristics were visualized. The results show the lowering interface of the corridor smoke layer with decreasing corridor-exit door width. Also a four-layer horizontal counter-current flow pattern was displayed and shown to result from a restriction (e.g. soffit) at the corridor exit. The mixing of the incoming cold flow and exiting hot flow at the corridor exit was observed to be shedding vortices swept into the cold floor jet. Results based on velocity measurements and smoke observations are presented for the corridor smoke layer height and doorway neutral-plane heights. The limitations of current predictive models are demonstrated for layer-heights and flow rates for the room and corridor experiments.
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  • 126
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    Fire and Materials 2 (1978), S. 34-36 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Limiting Oxygen Indexes were determined for a polyester resin fire retarded with a number of different brominated hydrocarbons. It was found that up to a concentration of 28 phr bromine the values obtained were linearly related to the bromine concentration and independent of the carbon-bromine bond.
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  • 127
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    Fire and Materials 2 (1978), S. 27-33 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Equations have been developed which give the time available for escape or rescue, i.e., the time interval between detection and blockage of the escape route by smoke, heat or toxic gases. Alternative assumptions are explored concerning exponential vs power law fire growth and an extended fire plume vs uniform filing of the building. The equations are developed in such a form that the threat variable by which the fire is detected is not necessarily the same threat variable which first blocks the escape route. A number of interesting results have been obtained, and numerical values of key parameters measured in various test fires at Factory Mutual Research are tabulated. It is shown that for many polymeric fuels smoke will block the escape route well before temperature or toxicity becomes excessive. In such cases, if the fire, assumed to be growing exponentially, is detected by its smoke, the detector being located in the escape route, then the escape time, surprisingly, is independent of the smokiness of the material as well as the size and shape of the building. It is determined only by the growth rate constant (doubling time) of the fire and the sensitivity of the detector.
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  • 128
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    Fire and Materials 2 (1978), S. v 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Fire and Materials 2 (1978), S. 37-38 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 130
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    Fire and Materials 2 (1978), S. v 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 131
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    Fire and Materials 2 (1978) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 132
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    Fire and Materials 2 (1978), S. 39-53 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A theoretical model of compartment fires in the post-flashover stage is presented. The model incorporates the stirred reactor assumption and window flow approximation of Kawagoe, but treats fuel burning rates and burning regimes in a theoretical manner. The resulting formulation preserves the important features of the fire behavior but is simple enough to permit use for building fire safety design purposes.
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  • 133
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    Fire and Materials 2 (1978), S. 54-62 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A simple analytical model has been developed to determine the time required for a room to fill with products of combustion from a small fire. The room is assumed to be closed except for small openings at either the floor or ceiling level and the assumption is made that the leak is large enough to allow the transient pressure term in the energy equation to be neglected. Products of combustion are assumed to occupy a layer next to the ceiling and the model predicts the growth of the thickness and the mean density of this layer as a function of time. The analysis shows that times required to fill a typical room are small. For example, a typical bedroom fills with products from a 20 kW fire in several minutes. The time required to fill a room and the mean density of ceiling layer are determined in terms of fire size, room geometry, leak position, fire elevation and geometry.
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  • 134
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    Fire and Materials 2 (1978), S. 63-67 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The influence of flame retardants and stabilizers on the thermooxidative and thermal stability of polyethylene systems has been investigated. In the present study 18 polymeric composites were prepared and their stabilities investigated by static and dynamic methods; their flammability parameters were also determined.
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    Fire and Materials 2 (1978), S. 68-79 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Relative toxicity test data on 270 materials are presented, based on test procedures developed at the University of San Francisco. The effects of chemical composition, using data on 13 types of synthetic polymers and eight types of fabrics, are discussed. Selected materials were evaluated using nine test conditions with the USF method, and using methods developed at the FAA Civil Aeromedical Institute, Douglas Aircraft Company and San Jose State University.
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    Fire and Materials 2 (1978), S. 84-84 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Fire and Materials 2 (1978), S. 84-84 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Fire and Materials 2 (1978), S. 80-83 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Further evidence has been obtained to suggest that the fire retardation efficiencies of several organo-bromine compounds, as measured by the limiting oxygen index method, are independent of the type of carbon-bromine bond, depending almost entirely upon the bromine concentration. Linear regression analysis has confirmed the linearity of the relationship between the limiting oxygen index method and the bromine concentration. The fire retardation efficiency (as measured by the limiting oxygen index method) of the organo-bromine compounds does, however, depend to a marked extent upon the substrate.
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  • 139
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    Fire and Materials 2 (1978) 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 140
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    Fire and Materials 2 (1978), S. 85-101 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: This is an extensive review of the work done on the effect of turbulence on combustion of gases.
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  • 141
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    Fire and Materials 2 (1978), S. 102-109 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: A limited review of the methods available for measuring smoke from burning materials has been carried out in order to define a method that could provide data for calculating smoke load. Results available in the literature have been expressed on a common basis and augmented by further experimental work carried out with a furnace similar to the National Bureau of Standards test furnace and a smoke-containment volume (13.4m3) closer to that used by the Fire Research Station test. Encouraging agreement between the data have been found for methods which allow smoke to become diluted and to accumulate. Agreement could be improved if an allowance was made for flaming being extinguished at different times in a test, dependent on thermal stress and oxygen concentration, even when a pilot light is present. To help express the results clearly, a new unit for smokiness is proposed - the obscura (ob) defined as 1 ob=1 dB light attenuation per metre of light path. The smoke-producing potential of different materials (Do) is then expressed in units of obscura - cubic metres per gram of volatiles produced during the fire condition (ob m3 g -1).
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  • 142
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    Fire and Materials 2 (1978), S. 110-116 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Characteristics of smoke particulates generated from a wood fire in a ventilated model tunnel were investigated using an in situ optical and a grid sampling technique. Volume-to-surface mean diameter and mass concentration of the smoke particles, and the transmission, optical density per unit length and particulate optical density of the smokeladen exhaust gas were obtained as a function of the burning process in the tunnel. It was found that high concentration of smoke (∼1 mg l-1) were rapidly generated as the fire changed from oxygen-rich to fuel-rich burning, resulting in fast obscuration of the passageway. The simultaneous generationof large amounts of smoke and high temperature carbon monoxide (∼8%) coupled with low transmission (∼1% though 0.5 m) represents and extremely hazardous situation in such a fire environment. Present measurements and others from current smoke testing chambers are compared and discussed.
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  • 143
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    Keywords: Chemistry ; Polymer and Materials Science
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    Notes: This communication presents a two zone flame model which allows computation of flame propagation velocity and average properties in the radical generation region and fuel attack region of the flame. The approach is computationally simpler than formal flame theory calculations; however, it provides only limited information since detailed structural information is sacrificed for computational simplicity. The zonal approach to flame structure is described and justification is provided for the various approximations which characterize the model. The model is largely a chemical one; however, the balance maintained between the radical molecule attack reaction and diffusional transport of radicals into the reaction region controls the propagation rate. The model was tested on five H2 + air flames, and the computed propagation velocities compared favorably with experimental values. HCL inhibition of the stoichiometric H2 + air flame was investigated, and the zonal approach was found suitable for studying flame inhibition.
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  • 144
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    Fire and Materials 2 (1978), S. 122-131 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Nitrogen-containing compounds such as hydrogen cyanide, acetonitrile, acrylonitrile, pyridine, benzonitrile, ammonia and methylamine, which are typical of the products likely to be encountered during the decomposition of nitrogen-containing polymers in fires, have been introduced into hydrogen and methane flames burning in oxygen-argon atmospheres. There is a complete conversion of fuel nitrogen in all cases to oxides of nitrogen and molecular nitrogen. The relative conversion to oxides of nitrogen (as NOx/N2) increases as the injection rate of nitrogen-containing fuels is decreased. The relative yields of oxides of nitrogen tend to be similar with methane and hydrogen premixed flames and markedly greater than observed with hydrogen diffusion flame. In all cases the yield of oxides of nitrogen-containing products such as hydrogen cyanide can also present a toxic risk during the burning of nitrogen-containing polymers, particularly when high temperature are involved. The combustion of these products in flame zones cannot be assumed to alleviate the additional toxic risk because of their conversion to oxides of nitrogen.
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  • 145
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    Fire and Materials 2 (1978), S. iii 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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    Fire and Materials 2 (1978), S. 132-135 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: The effect of halogen additives, containing bromine as one of the substituents (e.g. CF2CIBr, CF3Br), on the self-ignition of polypropylene has been investigated. These compounds appear to promote self-ignitionat low concentration and inhibit self-ignition at high concentration when introduced into the oxidant gas. The lability of bromine is thought to influence the limiting concentration above which these additives act as inhibitors. By comparison with other systems of oxidation the authors propose an explanation an explanation in which HBr and Br' radical species are the only active entities in all cases.
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    Fire and Materials 2 (1978) 
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    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
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  • 148
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    Notes: In order to evaluate the performance of the indices of toxicity which have been developed, thermal decomposition products of three polymers, polyvinylchloride, polychloroprene, and polycarbonate were tested for sensory irritation, physiological stress induction, and acute lethality. Each polymer has been contrasted with the same polymer containing 5% zinc ferrocyanide. The most irritating and the most stressful pyrolysis products were those from polyvinylchloride. The least irritation and stress were associated with polycarbonate decomposition products. The acute lethality for polychloroprene was higher than that of the other two polymers by a factor of 4. The addition of zinc ferrocyanide had a variable effect, depending on the polymer and the index of toxicity being evaluated. Sensory irritation was lessened by the presence of zinc ferrocyanide in polycarbonate. The sample weight required to cause death of 50% of the animals was reduced for the two hydrogen chloride-generating polymers, polyvinylchloride and polychloroprene. However, the acute lethality of polycarbonate did not change with addition of zinc ferrocyanide. By itself, zinc ferrocyanide decomposed very slowly during heating, caused almost no irritation or stress, and no deaths.
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    Fire and Materials 2 (1978), S. 141-153 
    ISSN: 0308-0501
    Keywords: Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Architecture, Civil Engineering, Surveying , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Various aspects of Pyrolysis gas toxicity studies at the University of San Francisco are discussed. Animal response data can be used to establish patterns which would help identify specific toxicants by their mode of action. Reference time-concentration curves for individual gaseous toxicants can be used to permit deduction of importance of these toxicants in complex mixtures of toxic gases. These techniques can be used to identify cause and mechanisms of toxicity without significant additional cost. The versatility and economy of the basic test permits rapid survey of test variables to identify potential problem situations.
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  • 150
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    Journal of Computational Chemistry 18 (1997), S. 139-149 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new program for automatic resonance assignment of nuclear magnetic resonance (NMR) spectra of proteins, GARANT (General Algorithm for Resonance Assignment), is introduced. Three principal elements used in this approach are: (a) representation of resonance assignments as an optimal match of two graphs describing, respectively, peaks expected from combined knowledge of the primary structure and the magnetization transfer pathways in the spectra used, and experimentally observed peaks; (b) a scoring scheme able to distinguish between correct and incorrect resonance assignments; and (c) combination of an evolutionary algorithm with a local optimization routine. The score that evaluates the match of expected peaks to observed peaks relies on the agreement of the information available about these peaks, most prominently, but not exclusively, the chemical shifts. Tests show that the combination of an evolutionary algorithm and a local optimization routine yields results that are clearly superior to those obtained when using either of the two techniques separately in the search for the correct assignments. GARANT is laid out for assignment problems involving peaks observed in two- and three-dimensional homonuclear and heteronuclear NMR spectra of proteins. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 159-168 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A parallel implementation of the computation of RHF energy second derivatives with respect to the nuclear coordinates is described. The algorithm and organization of the code are described in detail on the most computationally demanding steps with special emphasis on the integral transformation code. Key features of the proposed algorithm are its large degree of concurrency, limited interprocessor communication, and critical memory needs distributed over the processors. The cpu times and computer and network resources used are reported and discussed for a few examples. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 198-210 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: All four possible Diels-Alder reactions between 2H-phosphole and phosphaethene were examined at various theoretical levels, including HF, MP4SDQ, CCSD(T), and CASSCF. MP2/6-31G* geometry optimizations could not be employed since the potential energy surface is qualitatively incorrect at this level of theory, due to the inherent underestimation of the activation energies (ameliorated at higher-order MP or coupled-cluster levels). Solvent effects were examined employing the Onsager, polarized continuum, and isodensity and surface polarized continuum models. At MP4SDQ/6-31G*//HF/6-31G* these reactions are exothermic by 34-38 kcal mol-1 and have very low activation energies, 5-7 kcal mol-1. The P—P/C—C regioisomer products are lower in energy than the C—P isomers and, within each pair, the exo isomer is lower in energy. At low computational levels the smallest activation energy is for the reaction leading to the C—P endo product. Larger basis sets, electron correlation, and solvent favor the transition state leading to the experimentally observed P—P/C—P endo isomer. The dimerization of phosphole is, therefore, kinetically controlled. Based on geometric and electron density analysis, the reactions are concerted and synchronous. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 9-19 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A G2 search of the triplet [H4, Si, P]+ potential energy surface (PES) was carried out, along with a study of a number of mechanisms for the reaction of the P+ (3P) ion with silane. The most stable isomer, which corresponds to the species resulting from transferring three hydrogen atoms from the silicon to the phosphorus atom, lies 67.3 kcal/mol below the reactants' level. The P+—SiH4 ion-molecule complex also has remarkable stability, 20.4 kcal/mol. Bond properties were calculated and are discussed for all the stable species found on the PES. Various exothermic reaction paths were also fully characterized. The abstractions of a hydrogen molecule and a hydrogen atom, yielding species with P—Si bonds, have comparable kinetic hindrance, although release of molecular hydrogen was found to be more exothermic. Finally, hydrogen and/or charge transfer reactions between P+ (3P) and silane are also discussed. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 449-462 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four commonly used molecular mechanics force fields, CHARMM22, OPLS, CVFF, and GROMOS87, are compared for their ability to reproduce experimental free energies of hydration (ΔGhydr) from molecular dynamics (MD) simulations for a set of small nonpolar and polar organic molecules: propane, cyclopropane, dimethylether, and acetone. ΔGhydr values were calculated by multiconfiguration thermodynamic integration for each of the different force fields with three different sets of partial atomic charges: full charges from an electrostatic potential fit (ESP), and ESP charges scaled by 0.8 and 0.6. All force fields, except for GROMOS87, give reasonable results for ΔGhydr · if partial atomic charges of appropriate magnitude are assigned. For GROMOS87, the agreement with experiment for hydrocarbons (propane and ethane) was improved considerably by modifying the repulsive part of the carbon-water oxygen Lennard-Jones potential. The small molecules studied are related to the chemical moieties constituting camphor (C10Hl6O). By invoking force-field transferability, we calculated the ΔGhydr for camphor. With the modified GROMOS force field, a ΔGhydr within 4 kJ/mol of the experimental value of -14.8 kJ/mol was obtained. Camphor is one of the largest molecules for which an absolute hydration free energy has been calculated by molecular simulation. The accuracy and reliability of the thermodynamic integration calculations were analyzed in detail and we found that, for ΔGhydr calculations for the set of small molecules in aqueous solution, molecular dynamics simulations of 0.8-1.0 ns in length give an upper statistical error bound of 1.5 kJ/mol, whereas shorter simulations of 0.25 nm in length given an upper statistical error bound of 3.5 kJ/mol. © 1997 by John Wiley & Sons, Inc.
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  • 155
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We describe the implementation of the cell multipole method (CMM) in a complete molecular dynamics (MD) simulation program (MPSim) for massively parallel supercomputers. Tests are made of how the program scales with size (linearly) and with number of CPUs (nearly linearly) in applications involving up to 107 particles and up to 500 CPUs. Applications include estimating the surface tension of Ar and calculating the structure of rhinovirus 14 without requiring icosahedral symmetry. © 1997 by John Wiley & Sons, Inc.
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  • 156
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    Journal of Computational Chemistry 18 (1997), S. 712-721 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; neolignans ; conformational analysis ; environment effect ; active conformation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational analysis of 20 neolignans was performed to determine the most probable conformer that may fit the receptor. The molecular mechanics method (MM2) was employed to construct conformational maps in both a vacuum and a biological environment. Boltzmann's distribution among several local minima was calculated. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 712-721, 1997
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  • 157
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    Journal of Computational Chemistry 18 (1997), S. 723-743 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A Monte Carlo docking procedure that combines random displacements of the substrate and protein side chains with minimization of the enzyme - substrate complex is described and applied to finding the binding mode of the blocked tetrapeptide N-acetyl-Leu-Pro-Phe-methylamide to the FK506 binding protein (FKBP). The tetrapeptide, an analog of the preferred FKBP substrate, and the FKBP binding site are flexible during the docking procedure. The twisted-imide transition-state form of the substrate is used during docking. The enzyme charges are scaled individually to account for solvent screening of specific binding site residues during the Monte Carlo sampling. To evaluate the relative binding free energies of the resulting structures, a rapid method for calculating polar and nonpolar solvation effects is introduced. Accurate electrostatic solute - solvent energies are calculated by solving the finite-difference linearized Poisson - Boltzmann equation; nonpolar contributions to the stability of the different conformers are estimated by the free energy of cavity formation, which is obtained from the molecular surface, and the solute - solvent van der Waals energy, which is calculated with a continuum approach. In the conformation of the enzyme - substrate complex with the lowest free energy, the tetrapeptide is bound as a type VIa proline turn with solvent accessible ends to permit longer polypeptide chains to act as substrates. Except for the imide carbonyl, which is involved in polar interactions with aromatic side chains of the FKBP binding site, all of the seven potential hydrogen bond donors or acceptors of the tetrapeptide are satisfied. The FKBP binding site has a similar conformation in the substrate complex as in the FKBP-FK506 cocrystal structure, except for the predicted reorientation of the Tyr 82 hydroxyl, which plays an important role in substrate binding. The present model for the FKBP - substrate complex is in agreement with the recently determined crystal structure of a cyclic peptide - FK506 hybrid bound to FKBP and supports the structure obtained previously by iterative model building. In addition, it is consistent with the observed effects of FKBP point mutations on the enzyme activity. The approach described here should be useful, in general, for the prediction of the structure of a molecule in solution or as part of a complex. It provides for the effective sampling of conformational space and for the inclusion of solvent effects. © 1997 by John Wiley & Sons, Inc.
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  • 158
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    Journal of Computational Chemistry 18 (1997), S. 796-811 
    ISSN: 0192-8651
    Keywords: DNA ; normal mode ; flexibility ; modeling ; DNA bending ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Normal mode calculations for two alternating sequence dodecamers in A, B, and Z conformations have been performed in dihedral angle space extended to endocyclic valence angles to account for sugar ring flexibility. Normal modes are analyzed in terms of helicoidal and backbone parameter variations with special attention being paid to global deformations of the double helix such as bending, twisting, or stretching. Results show that the allomorphic form of DNA has the largest influence on the flexibility of the sugar-phosphate backbone. Amplitudes of these vibrations follow the order: B 〉 Z 〉 A. In contrast, the amplitudes of helicoidal parameter variations are much more dependent on the base sequence. Global deformations of the double helix occur with characteristic times in the range of 1 to 10 ps and can be of mixed character, the strongest bending mode being at the same the time strongest stretching mode. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 796-811, 1997
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  • 159
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    Journal of Computational Chemistry 18 (1997), S. 381-392 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present the results of simulations of the structures and optical absorption spectra of Na atoms in solid and liquid Ar at its triple point, and in critical-point Ar fluid. The spectral simulations combine a classical Monte Carlo scheme for generating thermally accessible ground state configurations, along with a first-order perturbation theory treatment of the interactions between the excited Na*(3p 2P) atom and the surrounding Ar perturbers [Boatz and Fajardo, J. Chem. Phys., 101, 3472 (1994)]. These simulations predict a “triplet” (i.e., three peaks) absorption lineshape for Na atoms in solid and liquid Ar at its triple point, and an asymmetrical, blue degraded absorption band for Na atoms in critical Ar fluid. We also note and discuss the similarities between the simulated Na/Ar(1) lineshape and an experimental Li/Ar/Xe mixed host matrix spectrum, and the similarities between the simulated spectrum of Na atoms in critical point Ar fluid, and an experimental Li/H2 matrix absorption spectrum. © 1997 by John Wiley & Sons, Inc.
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  • 160
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    Journal of Computational Chemistry 18 (1997), S. 403-415 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method has been developed for minimizing the energy of a polypeptide with rigid geometry while keeping all disulfide loops closed exactly. Exact closure of disulfide loops implies that some dihedral angles become implicit functions of the remaining dihedral angles in the polypeptide; the efficacy of the method is related to the manner in which the implicitly defined dihedral angles are chosen. The method has been used to find minimum-energy conformations of bovine pancreatic trypsin inhibitor, ribonuclease A, crambin, the defensin HNP3 dimer, and ω-conotoxin. For the first two proteins, the starting conformations for energy minimization had been derived previously from crystal structures using pseudopotentials to keep the disulfide loops almost closed. Starting conformations for the remaining three proteins were derived from their crystal or NMR structures by similar procedures. In all cases, the energy-minimized structures had a significantly and, in some cases, substantially, lower energy than the starting structures. The RMS deviations between the exactly closed energy- minimized structures and the crystal or NMR structures from which they were derived ranged from 0.9 Å to 1.9 Å, suggesting that the computed structures can serve as “regularized” native structures for these proteins. The energy of a ribonuclease derivative lacking the 65-72 disulfide bridge was minimized using the procedure; the result showed that this derivative has a low-energy structure with a conformation very close to that of native ribonuclease, and is consistent with its postulated role in the folding of ribonuclease. These results offer strong support for the validity of the rigid-geometry model in the studies of the conformational energy of proteins. © 1997 by John Wiley & Sons, Inc.
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  • 161
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational scheme is presented which combines quantum mechanical ab initio techniques with methods using analytical potential functions. The scheme is designed for use in structure optimizations and is also applicable to molecular dynamics simulations. The implementation covers both molecular and periodic systems. The problem of the link atoms is solved by a subtraction scheme which is easily implemented for any combination of methods. As a first application dense and microporous silica polymorphs are studied. The Hartree-Fock method is combined with both a force field and an ion pair shell model potential. Comparison is made with lattice energy minimizations which use the force field or the shell model potential alone as well as with free cluster optimizations and optimizations in which the outer part of the cluster is kept fixed. © 1997 by John Wiley & Sons, Inc.
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  • 162
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    Journal of Computational Chemistry 18 (1997), S. 489-500 
    ISSN: 0192-8651
    Keywords: benzofuroxan ; ortho-dinitrosobenzene ; nitrosobenzene ; vibrational spectra ; tautomerism ; density functional theory (DFT) ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular rearrangement of benzofuroxan was studied by comparing calculated and experimental IR spectra, the latter taken before and during the reaction. All calculations were performed at the B3-LYP/6-31G(d) density functional level with a further refinement of the computed force constants done by applying the scaled quantum mechanical force field (SQM) technique. Complete assignments for the IR spectra of benzofuroxan and nitrosobenzene are given. The agreement between computed and experimental spectra is excellent, but in benzofuroxan these spectra are very different from previously calculated data. The conformation of the ortho-dinitrosobenzene intermediate of this tautomeric reaction was identified by modeling a composite IR spectrum of four possible components. It shows good agreement with an experimental spectrum that was obtained after photolysing benzofuroxan in Xe matrix. Knowing the conformation of the intermediate provides insight into the reaction mechanism and allows inferences for the thermal reaction, which could not be clarified conclusively by energetic considerations only. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 489-500, 1997
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  • 163
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    Journal of Computational Chemistry 18 (1997), S. 533-551 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Allyl cation geometries optimized using an extended version of MMP2, newly parameterized for localized and delocalized classical cations, compare favorably with those obtained at the MP2(full) /6-31G* level. Hence, the force field should provide good starting structures for ab initio calculations. The π-electron densities obtained by these two very different methods are quite similar. The relative energies of various isomers at MP4/6-31G*//MP2(full)/6-31G* are reproduced well by the force-field calculations. The heats of formation calculated by MMP2, as well as those predicted from the ab initio data, agree with experimentally determined values. The force-field method provides interpretive capabilities. Energy differences between isomers can be separated into electronic and steric contributions, reasonable estimates of resonance energies are given, and nonbonded resonance energies in delocalized cations can be evaluated. The stabilizing 1-3 π-interactions in allyl cations are quite significant, but are reduced by alkyl groups hyperconjugatively and sterically. © 1997 by John Wiley & Sons, Inc.
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  • 164
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    Journal of Computational Chemistry 18 (1997), S. 569-583 
    ISSN: 0192-8651
    Keywords: fast multigrid boundary element method ; macromolecular electrostatic calculations ; poisson equation ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A fast multigrid boundary element (MBE) method for solving the Poisson equation for macromolecular electrostatic calculations in a solvent is developed. To convert the integral equation of the BE method into a numerical linear equation of low dimensions, the MBE method uses an adaptive tesselation of the molecular surface by BEs with nonregular size. The size of the BEs increases in three successive levels as the uniformity of the electrostatic field on the molecular surface increases. The MBE method provides a high degree of consistency, good accuracy, and stability when the sizes of the BEs are varied. The computational complexity of the unrestricted MBE method scales as O(Nat), where Nat is the number of atoms in the macromolecule. The MBE method is ideally suited for parallel computations and for an integrated algorithm for calculations of solvation free energy and free energy of ionization, which are coupled with the conformation of a solute molecule. The current version of the 3-level MBE method is used to calculate the free energy of transfer from a vacuum to an aqueous solution and the free energy of the equilibrium state of ionization of a 17-residue peptide in a given conformation at a given pH in ∼ 400 s of CPU time on one node of the IBM SP2 supercomputer. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 569-583, 1997
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  • 165
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    Journal of Computational Chemistry 18 (1997), S. 584-593 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A homomolecular differential bond separation reaction may be defined as the difference between the conventional bond separation reactions involving the unsaturated system and its saturated counterpart. Such a reaction is homomolecular in that the basic molecular structures involved are the same on both sides of the reaction. The type of homodesmotic reaction that also conserves structure in this way may be termed a homomolecular homodesmotic reaction. Both types of homomolecular reactions are readily related to hydrogenation reactions and, more importantly, to each other. Δ B(n), the energy of the homomolecular differential bond separation reaction involving a system with n double bonds, and H(n), the corresponding homomolecular homodesmotic reaction, are related by: $$\Delta B(n)-H(n)= n \cdot (h(1)-h(e))$$ where h(1) and h(e) are the hydrogenation energies of the system's monoene and of ethylene, respectively. Both types of reactions yield measures of cyclic conjugation energies that for certain classifications of molecules are simply related to each other. Consideration of extra conjugation in the monoenes allows a ready interpretation of those cases in which a simple classification is not obtained. Ab initio calculations illustrating these effects have been carried out on a variety of molecules including many five- and six-membered ring systems using second order Møller-Plesset and density functional approaches. © 1997 by John Wiley & Sons, Inc.
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  • 166
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    Journal of Computational Chemistry 18 (1997), S. 1-8 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The polarizable continuum model of Miertus et al. was implemented in the semiempirical molecular orbital method SINDO1. A fast and precise method for the calculation of solvation energies is achieved based on isodensity surfaces for the cavity surface and on approximated electrostatic potentials. The calculated solvation energies in water agree well with experimental and other calculated data. © 1997 by John Wiley & Sons, Inc.
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  • 167
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    Journal of Computational Chemistry 18 (1997), S. 28-44 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Force-field calculations are reported for large delocalized cations. The results for the geometries, heats of formation, and π-electron densities agree well with MP2(full)/6-31G* ab initio calculations. Both methods give similar results for the distortion of the carbon skeletons of unsubstituted cations by hyperconjugating methyl groups. Because of the SCF treatment of π-interactions, the MMP2 force-field technique enables calculations of resonance energies in delocalized cations. The additional resonance stabilization produced by extending conjugation is directly related to the π-charge on the carbon at which a vinyl group is substituted. The good agreement of MMP2 results for nonbonded resonance effects in large delocalized cationic π-systems with ab initio data suggests that MMP2 can be used to study the influence of these interactions in cationic π-systems too large to be calculated by correlated ab initio methods. © 1997 by John Wiley & Sons, Inc.
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  • 168
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    Journal of Computational Chemistry 18 (1997), S. 45-55 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry optimization using natural internal coordinates was applied for transition metal complexes. The original definitions were extended here for the skeletal degrees of freedom which are related to the translational and rotational displacements of the ηn-bonded ligands. We suggest definitions for skeletal coordinates of ηn-bonded small unsaturated rings and chains. The performance of geometry optimizations using the suggested coordinates were tested on various conformers of 14 complexes. Consideration was given to alternative representations of the skeletal internal coordinates, and the performance of optimization is compared. Using the skeletal internal coordinates presented here, most transition metal complexes were optimized between 10 and 20 geometry optimization cycles in spite of the usually poor starting geometry and crude approximation for the Hessian. We also optimized the geometry of some complexes in Cartesian coordinates using the Hessian from a parametrized redundant force field. We found that it took between two and three times as many iterations to reach convergence in Cartesian coordinates than using natural internal coordinates. © 1997 by John Wiley & Sons, Inc.
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  • 169
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    Journal of Computational Chemistry 18 (1997), S. 80-85 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method for generating a full backbone protein structure from the coordinates of α-carbons, is presented. The method extracts information from known protein structures to generate statistical positions for the reconstructed atoms. Tests on a set of proteins structures show the algorithm to be of comparable accuracy to existing procedures. However, the basic advantage of the presented method is its simplicity and speed. In a test run, the present program is shown to be much faster than existing database searching algorithms, and reconstructs about 8000 residues per second. Thus, it may be included as an independent procedure in protein folding algorithms to rapidly generate approximate coordinates of backbone atoms. © 1997 by John Wiley & Sons, Inc.
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  • 170
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    Journal of Computational Chemistry 18 (1997), S. 115-125 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the molecular surface and the accessible surface lead to exactly the same results when calculating solvation free energies and transfer free energies, from methods using the surface tension as a parameter if the exact geometric curvature is used with the accessible surface. However, the use of the exact curvature is not necessarily the best approach chemically. Other modifications, including an approximate curvature improves the approach. Such modifications are difficult to include in methods in which the molecular surface rather than the accessible surface is used to calculate solvent effects. A modification of a Gaussian curvature term is necessary if dissociation is to be accounted for properly. The inclusion of a Gaussian curvature term, in addition to the usual mean curvature term, reconciles the difference in magnitude of the microscopic and macroscopic surface tension in the case of the accessible surface area. © 1997 by John Wiley & Sons, Inc.
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  • 171
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The five energetically lowest minima on the potential energy surface of N-acetyl-N′-methylalaninamide were optimized at the Becke3LYP/DZd level of theory to compare these density functional theory results with the literature findings at restricted Hartree-Fock/3-21G. While the relative energies are very similar, the amide moiety is predicted to be much more flexible at Becke3LYP/DZd. As a consequence, the three minima that favor a nonplanar amide group differ by up to 14° in their φ and ψ values between the two levels. To compare the change in the density functional NMR chemical shifts with respect to φ and ψ with experimental results, Becke3LYP/DZd was employed to optimize a structure for N-acetyl-N′-methylalaninamide at each 30° interval on the (φ, ψ) surface in the regions that correspond to the α helix and the β-pleated sheet and at each 60° interval elsewhere. The corresponding NMR chemical shielding surface was computed with the density functional program deMon. The resultant NMR chemical shielding surfaces for N and Cβ are in good agreement with the experiment, while the change in the NMR chemical shielding of C′ and Cα cannot be described only in terms of φ and ψ. The chemical shifts for those atoms also depend on the nonplanarity of the amide moiety. We evaluated this dependence for N-methylacetamide as a model system. Estimates of the parameters derived from N-methyl-acetamide allowed the NMR-shielding surfaces of C′ and Cα to be corrected for the nonplanar nitrogen influence. Although the effect is less pronounced with lower level theoretical geometries, due to the smaller degree of pyramidalization of the amide nitrogen, the (φ, ψ) NMR chemical shielding surfaces will need to be corrected. The agreement with the experiment was much better for the corrected surface of C′ when the nitrogen in the α helix had a nonplanar environment. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 211-220 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Test particle calculations are employed to derive van der Waals parameters for methane. It is shown that it is possible to derive these parameters completely based on ab initio calculations. The newly derived parameters are tested in molecular dynamics calculations of liquid methane and the results are compared with the results of existing force fields. It is shown that the newly derived parameters perform better in the prediction of the density, the heat of vaporization, and the self-diffusion coefficient of methane. Scaling of the parameters to account for systematic errors in the employed ab initio method does not generally improve the parameters with respect to the properties calculated. © 1997 by John Wiley & Sons, Inc.
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  • 173
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    Journal of Computational Chemistry 18 (1997), S. 221-239 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Empirical force field parameters for nicotinamide (NIC+) and 1,4-dihydronicotinamide (NICH) were developed for use in modeling of the coenzymes nicotinamide adenine dinucleotide (NAD+) and NAD hydride (NADH). The parametrization follows the methodology used in the development of the CHARMM22 all-hydrogen parameters for proteins, nucleic acids, and lipids. Parametrization of inorganic phosphate for use in adenosine di- and triphosphates (e.g., ADP and ATP) is also presented. While high level ab initio data, such as conformational energies, dipole moments, interactions with water, and vibrational frequencies, were adequately reproduced by the developed parameters, strong emphasis was placed on the successful reproduction of experimental geometries and crystal data. Results for molecular dynamics crystal simulations were in good agreement with available crystallographic data.Simulations of NAD+ in the enzyme alcohol dehydrogenase compared quite favorably with experimental geometries and protein matrix interactions. © 1997 by John Wiley & Sons, Inc.
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  • 174
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    Journal of Computational Chemistry 18 (1997), S. 260-267 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: It is shown that the claims that density functional theory (DFT) can handle orbitally degenerate states are ungrounded. The constraint search formulation of DFT allows one to determine a set of densities and eigenvalues for the degenerate term that, however, are neither observables, nor can they be used to solve the system of coupled equations for the nuclear motions to obtain observables, as in the wave function presentation. A striking example of the failure of the existing versions of DFT to describe degenerate states is provided by the Berry phase problem: the strong dependence of the results on the phase properties of the electronic wave function that are smeared out in the density formulation. The solution of the Jahn-Teller E-e problem illustrates these statements. For nondegenerate states with the full wave function taken in the adiabatic approximation as a product of the electronic and nuclear parts, the formulation of DFT is rigorous if and only if the dependence of the electronic wave function on nuclear coordinates is ignored. This lowers the accuracy of the results, in general, and may lead to erroneous presentation as in the case of molecular systems in strong magnetic fields. © 1997 by John Wiley & Sons, Inc.
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  • 175
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    Journal of Computational Chemistry 18 (1997), S. 290-299 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The development of a crystal indexing computer program using interplanar angles and lattice spacings is very useful, particularly in nanocrystal research by transmission electron microscopy. However, the indexing involves a large number of possible variables, which prohibits the use of simple mathematical techniques. This article is concerned with an application of a combinatorial optimization technique using the simulated annealing algorithm for solving the crystal indexing problem where traditional descent optimization cannot be used. We show that the program can unambiguously identify the Miller indices using a set of interplanar angles even for crystals with low symmetry elements. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 313-322 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present the theory and implementation of a new approach for studying solvent effects. The electronic structure of the solute, calculated at the ab initio level, is obtained in the presence of the surrounding medium. We employ a mean field theory in which the solvent response is described by means of point charges chosen in such a way that they reproduce the average value of the solvent electrostatic potential calculated from molecular dynamics data. In this way, the complete solvent potential can be introduced into the solute Hamiltonian without making use of a one-center multiple expansion of the solute-solvent potential. In the proposed method, only one quantum calculation has to be performed and a great number of configurations can easily be included making the calculation statistically significant. We show that, despite the large fluctuations in the solute charge distribution induced by the solvent, the proposed mean field theory adequately reproduces the energetics and properties of formamide and water molecules in aqueous solution. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 368-380 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A potential energy model is developed to study the intramolecular proton transfer in the enol form of acetylacetone. It makes use of the empirical valence bond approach developed by Warshel to combine standard molecular mechanics potentials for the reactant and product states to reproduce the interconversion between these two states. Most parameters have been fitted to reproduce the key features of an ab initio potential surface obtained from 4-31G* Hartree-Fock calculations. The partial charges have been fitted to reproduce the electrostatic potential surface of 6-31G* Hartree-Fock wave functions, subject to total charge and symmetry constraints, using a fitting procedure based on generalized inverses. The resulting potential energy function reproduces the features most important for proton transfer simulations, while being several orders of magnitude faster in evaluation time than ab initio energy calculations. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 393-402 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The thermal effect of a reaction makes the temperature inside the reaction system deviate from a prescribed heating program. To take into account the effect of such temperature deviations on kinetic evaluations, a computational method applicable to an arbitrary variation in temperature has been developed. The method combines the isoconversional principle of evaluating the activation energy with numerical integration of the equation, dα/dt = k[T(t)]f(α), over the actual variation of the temperature with the time, T(t). Details of the numerical algorithm are reported. A model example has been used to verify the reliability of this method as compared to an analogous method which does not account for the deviations of the temperature from a prescribed program. The method has been tested for tolerance for noise in the temperature. © 1997 by John Wiley & Sons, Inc.
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  • 179
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    Journal of Computational Chemistry 18 (1997), S. 430-448 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A massively parallel version of the configuration interaction (CI) section of the COLUMBUS multireference singles and doubles CI (MRCISD) program system is described. In an extension of our previous parallelization work, which was based on message passing, the global array (GA) toolkit has now been used. For each process, these tools permit asynchronous and efficient access to logical blocks of 1- and 2-dimensional (2-D) arrays physically distributed over the memory of all processors. The GAs are available on most of the major parallel computer systems enabling very convenient portability of our parallel program code. To demonstrate the features of the parallel COLUMBUS CI code, benchmark calculations on selected MRCI and SRCI test cases are reported for the CRAY T3D, Intel Paragon, and IBM SP2. Excellent scaling with the number of processors up to 256 processors (CRAY T3D) was observed. The CI section of a 19 million configuration MRCISD calculation was carried out within 20 min wall clock time on 256 processors of a CRAY T3D. Computations with 38 million configurations were performed recently; calculations up to about 100 million configurations seem possible within the near future. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 478-488 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The implementation of parallel molecular dynamics techniques is discussed in the context of the simulation of single-site anisotropic potentials. We describe the use of both replicated data and domain decomposition approaches to molecular dynamics and present results for systems of up to 65536 Gay-Berne molecules on a range of parallel computers (Transtech i860/XP Paramid, Intel iPSC/860 Hypercube, Cray T3D). We find that excellent parallel speed-ups are possible for both techniques, with the domain decomposition method found to be the most efficient for the largest systems studied. © 1997 by John Wiley & Sons, Inc.
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  • 181
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    Journal of Computational Chemistry 18 (1997), S. 522-532 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Interaction energies are a function of the molecular charge distribution. In previous work, we found that the set of atomic partial charges giving the best agreement with experimental vacuum dipole moments were from density functional theory calculations using an extended basis set. Extension of such computations to larger molecules requires an atomic partial charge calculation beyond present computational resources. A solution to this problem is the calculation of atomic partial charges for segments of the molecule and reassociation of such fragments to yield partial charges for the entire molecule. Various partitions and reassociation methods for five molecules relevant to HIV-1 protease inhibitors are examined. A useful method of reassociation is introduced in which atomic partial charges for a large molecule are computed by fitting to the combined electrostatic potential calculated from the fragment partial charges. As expected, the best sites for partitions are shown to be carbon - carbon rather than carbon - nitrogen bonds. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 562-568 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A number of cluster models used to study the interaction of NH3 and NH-4 with the Bronsted sites of the acidic zeolite, chabazite, are assessed by comparison with the results from full periodic Hartree-Fock calculations. Corrections to bare cluster models to take account of the electrostatic environment due to the periodic zeolite are found to agree well with periodic calculations, and appear to be more successful than a more sophisticated embedding procedure. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 594-599 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new algorithm is presented for the location of the global minimum of a multiple minima problem. It begins with a series of randomly placed probes in phase space, and then uses an iterative Gaussian redistribution of the worst probes into better regions of phase space until all probes converge to a single point. The method quickly converges, does not require derivatives, and is resistant to becoming trapped in local minima. Comparison of this algorithm with others using a standard test suite demonstrates that the number of function calls has been decreased conservatively by a factor of about three with the same degree of accuracy. A sample problem of a system of seven Lennard-Jones particles is presented as a concrete example. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 638-645 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this article a new method is described to superimpose molecules using a crystallographic Fourier transform approach. Superimposed molecules, among other purposes, serve as a basis for three-dimensional (3D) QSAR analyses in drug design and therefore an objective and reproducible method of molecule alignment is of major importance. Fourier data are generated for hypothetical crystals of cubic symmetry for the compounds under consideration. A Patterson-density-based similarity index is used to optimize rotational alignment of the molecules. After optimization of rotational orientation, an electron density derived similarity index is used to further optimize overlap of electron density as a function of translation of the molecules. Both similarity indices are maximized by a simple optimization routine, thus enabling automated superposition. The use of Fourier space offers several advantages. First, rotational and translational parameters can be optimized separately, thus providing a small parameter space. Second, a limited number of data already provide an adequate, continuous description of the electron (or Patterson) density distribution. Third, crystallography provides simple methods to calculate the Fourier transforms that are needed. The resolution of the Patterson (electron) density representation used for superposition can be varied in a straightforward manner. Results are shown for the superposition of two antiviral agents, 2rs1 and 2r04; the dihydrofolate reductase ligands, methotrexate and dihydrofolate; and a set of three ε-thrombin inhibitors. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 677-693 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Charge distributions of a protonated and unprotonated Schiff base model compound are determined using different quantum chemical methods. After fitting the model molecule onto the protonated retinal Schiff base in Bacteriorhodopsin, electrostatic interaction energies between the model molecule and protein are calculated. Interaction energies as well as the calculated pK1/2 values of the model molecule are shown to depend considerably on the chosen charge distribution. Electrostatic potential derived partial charges determined at different ab initio levels reveal interaction energies between the model molecule and nearby residues such as ARG-82, ASP-85, and ASP-212, which are relatively method independent. Consequently, such charge distributions also result in pK1/2 values for the model molecule that are very similar. Larger deviations in the electrostatic interaction energies, however, are found in the case of charge distributions derived according to the Mulliken population analysis. Nevertheless, some sets of Mulliken derived partial charges predicted pK1/2 values for the model molecule that are close to those determined with electrostatic potential derived partial charges. This agreement, however, is only achieved because the individual errors of the contributing terms are approximately compensated. The use of the extended atom model is shown to be problematic. Although potential derived charges can correctly describe electrostatic interaction energies, they fail to predict pK1/2 values. On the basis of the present investigation a new set of partial charges for the protonated and unprotonated retinal Schiff base is proposed to be used in molecular dynamics simulations and electrostatics calculations. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 702-711 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The typical shallowness of the potential surfaces of weakly bound clusters implies sizable ground-state vibrational excursions in the weak modes, a feature often complicated by considerable anharmonicity. The difficulties of vibrational analysis are exacerbated as the number of weak modes increases with the number of molecules in a cluster. Quantum Monte Carlo (QMC) approaches offer a general suitability to the problem of vibrational dynamics of weakly bound clusters in that they can fully account for anharmonicity and large amplitude motions. We report on the effectiveness and convergence behavior of diffusion quantum Monte Carlo for both energies and the key spectroscopic values of vibrationally averaged rotational constants. QMC involves recurring evaluations of the interaction potential, and we show how property-based, two-and three-body potentials (e.g., those involving intrinsic molecular tensor properties) may be carefully linked to the QMC propagation steps. © 1997 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 18 (1997), S. 757-774 
    ISSN: 0192-8651
    Keywords: O(SINGLE BOND)H ··· O hydrogen bond ; intermolecular perturbation theory ; crystal structures ; directionality ; esters ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An attractive way to study intermolecular hydrogen bonding is to combine analysis of experimental crystallographic data with ab initio - based energy calculations. Using the Cambridge Structural Database (CSD), a distributed multipole analysis (DMA)-based description of the electrostatic energy, and intermolecular perturbation theory (IMPT) calculations, hydrogen bonding between donor alkanol hydroxyl groups and oxygen acceptor atoms in ketone, ether, and ester functional groups is characterized. The presence and absence of lone pair directionality to carbonyl and ether or ester oxygens, respectively, can be explained in terms of favored electrostatic energies, the major attractive contribution in hydrogen bonding. A hydrogen bond in its optimum geometry is only slightly stronger when formed to a ketone group than to an ether group. Hydrogen bonds formed to carbonyl groups have similar properties in a ketone or ester, but the ester O2 differs from an ether oxygen due to various environmental effects rather than a change in its intrinsic properties. For (E)-ester oxygens, there are few hydrogen bonds found in the CSD because of the competition with the adjacent carbonyl group, but the interaction energies are similar to an ether. Hydrogen bonds to O2 of (Z)-esters are destabilized by the repulsive electrostatic interaction with the carbonyl group. The relative abundance of nonlinear hydrogen bonds found in the CSD can be explained by geometrical factors, and is also due to environmental effects producing slightly stronger intermolecular interaction energies for an off-linear geometry. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 757-774, 1997
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    Journal of Computational Chemistry 18 (1997), S. 826-846 
    ISSN: 0192-8651
    Keywords: molecular quantum similarity measures (MQSM) ; atomic shell approximation (ASA) ; global maximization ; molecular alignments ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A quantum similarity measure between two molecules is normally identified with the maximum value of the overlap of the corresponding molecular electron densities. The electron density overlap is a function of the mutual positioning of the compared molecules, requiring the measurement of similarity, a solution of a multiple-maxima problem. Collapsing the molecular electron densities into the nuclei provides the essential information toward a global maximization of the overlap similarity function, the maximization of which, in this limit case, appears to be related to the so-called assignment problem. Three levels of approach are then proposed for a global search scanning of the similarity function. In addition, atom - atom similarity Lorentzian potential functions are defined for a rapid completion of the function scanning. Performance is tested among these three levels of simplification and the Monte Carlo and simplex methods. Results reveal the present algorithms as accurate, rapid, and unbiased techniques for density-based molecular alignments. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 826-846, 1997
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    Journal of Computational Chemistry 18 (1997), S. 902-919 
    ISSN: 0192-8651
    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present a comparison of four free energy calculation methods: thermodynamic integration (TI); traditional free energy perturbation (FEP); Bennett's acceptance ratio method (IPS); and a method that is related to an implementation of the WHAM method (CRS). The theoretical bases of the methods are first described, then calculations of the solvation free energies of methane and ethane are performed to determine the magnitude of the errors for the different methods. We find that the methods give similar errors when many intermediate states (windows) are used, but the IPS and CRS methods give smaller errors than the TI and FEP methods when no intermediate states are used. We also present a new procedure (based on the CRS method) that uses coordinates from simulations of a set of solutes to calculate the salvation free energies of additional solutes for which no simulations were performed. Solvation free energies for nine solutes (methanol, dimethylether, methylamine, methylammonium, dimethylamine, fluoromethane, difluoromethane, trifluoromethane, and tetrafluoromethane) are estimated based only on simulations of set of small hydrophobic solutes (including methane, ethane, and propane). These estimates can be surprisingly accurate and appear to be useful for making rapid estimates of solvation free energies. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 902-919, 1997
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    Journal of Computational Chemistry 18 (1997), S. 955-969 
    ISSN: 0192-8651
    Keywords: electrostatic ; potential ; charge ; PRDDO ; PESP ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new approach for the calculation of electrostatic potential derived atomic charges is presented. Based on molecular orbital calculations in the PRDDO/M approximation, the new parametrized electrostatic potential (PESP) method is parametrized against ab initio MP2/6-31G** calculations. For a data set of 820 atoms in 145 molecules containing H, C, N. O, F, P, S, Cl, and Br (including hypervalent species), the PESP method achieves a mean absolute error of 0.037 e- with a correlation coefficient of 0.990. Unlike other approximate approaches, no scaling factor is required to improve the agreement between PESP charges and the underlying ab initio results. PESP calculations are an order of magnitude faster than the simplest ab initio calculation (STO-3G) on large molecules while achieving a level of accuracy that rivals much more elaborate ab initio methods. © 1997 by John Wiley & Sons, Inc. J Comput Chem 18: 955-969, 1997
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    Journal of Computational Chemistry 18 (1997), S. 980-991 
    ISSN: 0192-8651
    Keywords: molecular electrostatic potential (MEP) ; density functional method (DFT) ; electrostatic potential (ESP) derived charges ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A systematic analysis was performed on the suitability of the molecular electrostatic potential (MEP) and MEP-derived properties determined by means of density functional (DFT) methods. Attention was paid to the electrostatic potential (ESP) derived charges, the ESP and exact quantum mechanical dipole moments, the depth of MEP minima, and the MEP distribution in layers around the molecule for a large series of molecules. The electrostatic properties were determined at either local or nonlocal DFT levels using different functionals. The results were compared with the values estimated from quantum mechanical calculations performed at Hartree-Fock, Møller-Plesset up to fourth order, and CIPSI levels. The suitability of the MEP-derived properties estimated from DFT methods is discussed for application in different areas of chemical interest. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 980-991, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1011-1022 
    ISSN: 0192-8651
    Keywords: line search minimization algorithm ; topography ; multidimensional potential energy surfaces ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The most robust numerical algorithms for unconstrained optimization that involve a line search are tested in the problem of locating stable structures and transition states of atomic microclusters. Specifically, the popular quenching technique is compared with conjugate gradient and variable metric algorithms in the Mg+Arn clusters. It is found that the variable metric method BFGS combined with an approximate line minimization routine is the most efficient, and it shows global convergence properties. This technique is applied to find a few hundred stationary points of Mg+Ar12 and to locate isomerization paths between the two most stable icosahedral structures found for Mg+Ar12. The latter correspond to a solvated and a nonsolvated ion, respectively. © 1997 John Wiley & Sons, Inc. J Comput Chem 18:1011-1022, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1056-1060 
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    Keywords: Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Following the publication of a comparison of several molecular mechanics methods [Gundertofte et al., J. Comput. Chem. 17, 429 (1996)], we have expanded the set of force fields tested by examining CHARMm 23.0 with its associated parameter set (version 22.0) relative to the gas-phase data used in the Gundertofte et al. study. CHARMm calculated rotational barriers and conformational energies within the same range of accuracy as the most accurate ones of the other force fields. The average absolute error was 0.64 kcal/mol, and 0.52 kcal/mol when the rotational barriers were excluded. © 1997 John Wiley & Sons, Inc. J Comput Chem 18: 1056-1060, 1997
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  • 194
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    Keywords: force field ; open-shell amino acids ; peptides ; glycine ; glycine radical ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Parameters suitable for extending the AMBER force field for nucleic acids and proteins to open-shell derivatives of amino acid residues are proposed and tested. Two new atom types (radical carbon [CE] and hydrogen directly bonded to it [HE]) are introduced, whose parameters have been determined by a best fitting of quantum-mechanical computations of the simplest analogue of glycine radical (GlyR) in a peptide. The new force field is able to fit the reference results concerning both the structural parameters and the relative stabilities of the different conformers. It has been next applied to a conformational study of the distortions induced by extraction of the glycine Hα atom in an initially helical structure of a dodecamer of alanine including a central glycine residue. Our results show that the helical structure corresponds to a local energy minimum, but deeper minima are found which correspond to a fully planar GlyR residue included in a distorted helical sequence.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1720-1728, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1773-1784 
    ISSN: 0192-8651
    Keywords: three-membered ring formation ; intramolecular nucleophilic substitution ; ab initio molecular orbital method ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Three-membered ring (3MR) forming processes of -X(SINGLE BOND)CH2(SINGLE BOND)CH2(SINGLE BOND)F and -CH2(SINGLE BOND)C((SINGLE BOND)Y)(SINGLE BOND)CH2(SINGLE BOND)F (X(DOUBLE BOND)CH2, O, or S and Y(DOUBLE BOND)0 or S) through a gas phase neighboring group mechanism (SNi) are studied theoretically using the ab initio molecular orbital method with the 6-31+G* basis set. When electron correlation effects are considered, the activation (ΔG≠) and reaction energies (ΔG0) are lowered by ca. 10 kcal mol-1, indicating the importance of the electron correlation effect in these reactions. The contribution of entropy of activation (-TΔS≠) at 298 K to ΔG≠ is very small, and the reactions are enthalpy controlled. The ΔG≠ and ΔG0 values for these ring closure processes largely depend on the stabilities of the reactants and the heteroatom acting as a nucleophilic center. The Bell-Evans-Polanyi principle applies well to all these reaction series.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1773-1784, 1997
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  • 196
    ISSN: 0192-8651
    Keywords: diborylmethane ; conrotation and disrotation ; 1,3 H exchange ; orbital deletion procedure ; gradient line reaction path ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The paths of correlated internal disrotation (barrier less than 0.4 kcal/mol) and conrotation (barrier around 1.9 kcal/mol) of the two BH2 groups in H2BCH2BH2 have been computed employing ab initio [MP2(full)/6-31G**] and density functional theory (Becke3LYP/6-311+G**) methods. Two B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative interactions stabilize the Cs symmetric H2BCH2BH2 isomer (1). The B(SINGLE BOND)C(DOTTED BOND)B(p) hyperconjugative stabilization, evaluated by homodesmotic reactions and using the orbital deletion procedure (which “deactivates” the “vacant” born p orbital), is less than 6 kcal/mol in diborylmethane. The B(SINGLE BOND)C(DOTTED BOND)B(p) stabilization is shown to be remarkably large in C4B6H10 (Td). At MP2(fu)/6-31G**, disproportionation into 1 and methane is only 5.6 kcal/mol exothermic. The 1,3 H exchange in diborylmethane is an asynchronous process and proceeds via a doubly bridged cyclic intermediate with 9.3 kcal/mol barrier. Structures with “planar tetracoordinate” carbon are stabilized considerably by BH2 substituents, but they are still high in energy.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1792-1803, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1827-1847 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; sulfides ; mercaptans ; vibrational spectra ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The MM4 force field has been extended to the title class of compounds. The vibrational spectra, structures, conformational equilibria, and heats of formation have been studied for 47 conformers of 29 compounds. In general, the properties may be calculated with accuracy that is competitive with that for hydrocarbons. The structures are better fit than previously because of the inclusion of a torsion-bend interaction term, which has its origin in the lone pair (Bohlmann) effect. Available experimental data do not suffice to yield detailed torsional potentials, or geometries as a function of torsion angle, and these quantities were determined by ab initio calculations at the MP2/6-31G* level. The rms error in the calculated frequencies of seven representative structures (with a total of 64 experimental and 96 ab initio frequencies) is 25 cm-1. The heats of formation for 23 compounds have a weighted rms error of 0.36 kcal/mol.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1827-1847, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1848-1862 
    ISSN: 0192-8651
    Keywords: molecular dynamics ; biomolecules ; electrostatics ; software ; reversible multiple time-step algorithms ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: In this study, we present a new molecular dynamics program for simulation of complex molecular systems. The program, named ORAC, combines state-of-the-art molecular dynamics (MD) algorithms with flexibility in handling different types and sizes of molecules. ORAC is intended for simulations of molecular systems and is specifically designed to treat biomolecules efficiently and effectively in solution or in a crystalline environment. Among its unique features are: (i) implementation of reversible and symplectic multiple time step algorithms (or r-RESPA, reversible reference system propagation algorithm) specifically designed and tuned for biological systems with periodic boundary conditions; (ii) availability for simulations with multiple or single time steps of standard Ewald or smooth particle mesh Ewald (SPME) for computation of electrostatic interactions; and (iii) possibility of simulating molecular systems in a variety of thermodynamic ensembles. We believe that the combination of these algorithms makes ORAC more advanced than other MD programs using standard simulation algorithms.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1848-1862, 1997
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    Journal of Computational Chemistry 18 (1997), S. 1760-1772 
    ISSN: 0192-8651
    Keywords: computer simulations ; wavepacket ; zero-point vibration ; activation energy ; reaction coordinate ; empirical valence bond ; Fourier transform ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We present results of mixed quantum-classical molecular dynamics simulations of the intramolecular proton transfer in acetylacetone. Simulations are performed starting from the reactant and transition state configurations with initial velocities at each configuration chosen from an ensemble at 300 K. The proton motion is treated quantum mechanically and the remaining degrees of freedom are treated classically. Two mixed quantum-classical molecular dynamics methods are implemented. In the first, a quantum-classical time-dependent self-consistent field method (QC/TDSCF), the time-dependent Schrödinger equation for the proton is solved using the split operator approach and a plane-wave basis. In the second, a mixed quantum-classical adiabatic method (QC/A), the instantaneous ground state wave function is calculated by solving the time-independent Schrödinger equation for the configurations of the classical particles by propagating in imaginary time using the split operator approach and the same plane-wave basis. A comparison of the two approaches with classical trajectories is presented. The QC/TDSCF and QC/A results are very similar for trajectories started from the reactant configuration. The two methods, however, yield somewhat different results when the trajectories are started from the transition state configuration. The proton wave function of the QC/A method adjusts instantaneously to the position of the classical particles, whereas the motion of the QC/TDSCF wavepacket more faithfully represents the true proton dynamics.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1760-1772, 1997
    Additional Material: 6 Ill.
    Type of Medium: Electronic Resource
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  • 200
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 18 (1997), S. 1804-1811 
    ISSN: 0192-8651
    Keywords: molecular mechanics ; geometric statement function method ; in-plane and out-of-plane bend ; improper torsion ; MM2, MM3, and MM4 force fields ; Chemistry ; Theoretical, Physical and Computational Chemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simple and very efficient formulas are presented for four-body out-of-plane bend (used in MM2 and MM3 force fields) and improper torsion (used in the MM4 force field) internal coordinates and their first and second derivatives. The use of a small set of bend and stretch intermediates allows for order of magnitude decreases in calculation time for potential energies and their first and second derivatives, which are required in molecular mechanics calculations. The formulas are eminently suitable for use in molecular simulations of systems with complicated bond networks.   © 1997 John Wiley & Sons, Inc.   J Comput Chem 18: 1804-1811, 1997
    Additional Material: 1 Ill.
    Type of Medium: Electronic Resource
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