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  • Articles  (778)
  • Computational Chemistry and Molecular Modeling  (748)
  • kinetics
  • 1990-1994  (778)
  • Computer Science  (748)
  • Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics  (26)
  • Energy, Environment Protection, Nuclear Power Engineering  (4)
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  • Articles  (778)
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Biodegradation 4 (1993), S. 163-170 
    ISSN: 1572-9729
    Keywords: factorial analysis ; kinetics ; methane ; methanotrophs ; nutrients
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract The effect of different mineral nutrients on the kinetics of methane biodegradation by a mixed culture of methanotrophic bacteria was studied. The substrate factors examined were ammonia, iron, copper, manganese, phosphate, and sulphide. The presence of iron in the growth medium had a strong effect on the yield coefficient. Yield coefficients up to 0.49 mg protein per mg methane were observed when iron was added at concentrations of 0.10–5.0 mg/l. Iron addition also increased the maximum methane utilization rate. The same effect was observed after addition of ammonium to a medium where nitrate was the only nitrogen source. The observed Monod constant for methane utilization increased with increasing concentration of ammonia. This shows that ammonia is a weak competitive inhibitor as observed by other researchers. Relatively high levels of both ammonia (70 mg/l) and copper (300 µg/l) inhibited the methane degradation, probably due to the toxic effect of copper-amine complexes.
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  • 2
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 37 (1992), S. 65-80 
    ISSN: 1573-4889
    Keywords: internal oxidation ; kinetics ; alloys ; silver ; oxide particles ; coalescence
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Gravimetric measurements at low temperatures (〈600°C) and for dilute Ag-Mg alloys have given further information about the mechanism of oxide formation. This investigation shows that the fixation rate of oxygen is very high, which assumes the existence of species in an oxidized form, including one or two magnesium atoms called “elementary species” and denoted as MgO* and Mg2O*. When there are no free magnesium atoms, there is a coalescence process with the fixation of oxygen atoms or MgO* and Mg2O*: this process leads to the formation of the first “clusters” including an oxygen excess. At low temperatures, the thermal fluctuations do not permit significant changes. There is no significant increase in cluster size, but a rearrangement of these clusters toward a compact structure with the release of excess oxygen. Their size is less than 1 nm.
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 38 (1992), S. 89-98 
    ISSN: 1573-4889
    Keywords: kinetics ; oxidation ; zirconium hydride
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation kinetics of zirconium-hydride powders were studied in the temperature range of 298–1378 in air at atmospheric pressure. TG, DTA, DSC, x-ray analysis, and scanning electron microscopy were used. The results obtained are in accordance with the proposed pseudo-parabolic model of zirconium-hydride oxidation. This model includes the initial linear mode of oxide growth with oxygen diffusion through a non-solid film of ZrO2 of variable depth and a stationary diffusion process followed by oxide sintering. It has been established that the activation energy of the limiting stage of oxidation (238.3 kJ/mol) coincides with the activation energy of oxygen self-diffusion in monocline ZrO2.
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  • 4
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 33 (1990), S. 279-299 
    ISSN: 1573-4889
    Keywords: corrosion SO2 ; chromium ; manganese ; kinetics ; scale analysis ; phase diagram stability
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The corrosion of chromium and manganese by pure SO2 has been investigated in the temperature range 890–1350 K at SO2 pressure from 0.01–0.5 atm. Both metals oxidize according to a parabolic rate law, and the scales consist of an inner region containing a mixture of oxide and sulfide (Cr2O3+ CrS or MnO and MnS) and an outer region of oxide (Cr2O3 or MnO). These two metals have similar thermodynamic behavior, and the main mechanism of reaction is considered to be the direct reaction of the metal with SO2. The results also indicate that in the absence of trace amounts of oxygen, and at sufficiently low temperature (〈950 K), the formation of Mn3O4 does not occur only if a complete description of the atmosphere generated by a SO2-O2-S2 mixture was considered.
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  • 5
    ISSN: 1573-4889
    Keywords: nonisothermal oxidation ; kinetics ; iron ; iron-chromium alloys ; reactive-oxide coating
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The nonisothermal oxidation behavior of pure iron and a few iron-chromium alloys in dry air has been studied. The effects of a superficial coating of a reactive oxide, CeO2, on the oxidation behavior were studied. Linear heating rates of 3 K/min and 6 K/min were maintained up to a final temperature ranging from 1273–1473 K. Coatings were applied either from a slurry or an aqueous bath. The CeO2 coating has been found to be effective not only in decreasing the nonisothermal oxidation rate but also in improving the scale adherence. Moreover, the coated samples withstood a number of heating cycles without scale rupture. The mass gain of the samples as a function of temperature was recorded by means of a sensitive balance, and the scales have been characterized by SEM, EPMA, and x-ray diffraction analysis.
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  • 6
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 34 (1990), S. 473-496 
    ISSN: 1573-4889
    Keywords: Internal nitriding ; 310 stainless steel ; austenitic ; kinetics ; microhardness
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The internal-nitriding behavior in ammonia-hydrogen atmospheres of type-310 stainless steel and 310 to which either 2 wt.% Ti or 3 wt.% Al were added was studied over the range of 550–950°C. An Fe-24Cr binary alloy was included to assess the role of a BCC crystal structure vs the FCC crystal structure of 310 stainless steel. The BCC alloy exhibited the most rapid kinetics as expected. X-ray diffraction showed only the presence of CrN in all the alloys up to 735°C. At 850°C and above, both CrN and Cr2N were detected. The nonformation of TiN and AlN at lower temperatures is attributed to nucleation problems. Precipitates were extremely fine (unresolvable even at 20,000×) at 563°C and became much coarser with increasing temperature. The precipitate density, size, and shape varied across the internal-nitriding zone at the higher temperatures. External scaling was noted at 850°C and above, however, it was not a continuous film. The activation energy of internal nitriding from 563–735°C ranged from 3.8 kcal/mol for 310+2Ti to 18.2 kcal/mol for 310+3Al; from 850–950°C, the activation energy ranged from 44 (310+2Ti) to 56.6 kcal/mol (310+3Al). Microhardness profiles show that an intermediate zone exists between the nitride case and the base metal. The origin of this zone is discussed.
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  • 7
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 36 (1991), S. 439-464 
    ISSN: 1573-4889
    Keywords: V-A1 alloy ; Cr and Ti additions ; oxidation ; kinetics ; V2O5 ; Al2O3
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation behavior in air of pure vanadium, V-30Al, V-30Al-10Cr, and V-30Al-10Ti (weight percent) was investigated over the temperature range of 700–1000° C. The oxidation of pure vanadium was characterized by linear kinetics due to the formation of liquid V2O5 which dripped from the sample. The oxidation behavior of the alloys was characterized by linear and parabolic kinetics which combined to give an overall time dependence of 0.6–0.8. An empirical relationship of the form: ΔW/A=Bt + Ct1/2 + D was found to fit the data well, with the linear contribution suspected to be from V2O5 formation for V-30Al and V-30Al-10Cr, and a semi-liquid mixture of V2O5 and Al2O3 for V-30Al-10Ti. The parabolic term is presumed related to the formation of a solid mixture of V2O5 and Al2O3 for V-30Al and V-30Al-10Cr, and TiO2 for V-30Al-10Ti The addition of aluminum was found to reduce the oxidation rate of vanadium, but not to the extent predicted by the theory of competing oxide phases proposed by Wang, Gleeson, and Douglass. This was attributed to the formation of a liquid-oxide phase in the initial stages of exposure from which the alloys could not recover. Ternary additions of chromium and titanium were found to decrease the oxidation rate further, with chromium being the most effective. The oxide scales of the alloys were found to be highly porous at 900° C and 1000° C, due to the high vapor pressure of V2O5 above 800° C.
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 36 (1991), S. 143-156 
    ISSN: 1573-4889
    Keywords: plasma nitriding ; Fe-18Cr-9Ni ; CrN precipitates ; nitrogen diffusion ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract To clarify the mechanism of plasma nitriding, we examined the optical microstructure, the hardness, the precipitation, and the concentration of dissolved nitrogen in Fe-18Cr-9Ni nitrided using plasma in the range of 723–823 K. Compared with ammonia-gas nitriding, the features of plasma nitriding are the formation of small chromium-nitride precipitates (CrN), the absence of an externally nitrided layer, the high concentration of dissolved nitrogen, and the high hardness (HV=1200). The diffusion coefficient of nitrogen in the present alloy was determined using the growth rate of the internally nitrided layer, based on calculations used in internal oxidation. Plasma- and gas-nitriding were also compared with respect to the growth rate of the nitrided layer.
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  • 9
    ISSN: 1573-4889
    Keywords: niobium ; oxidation ; morphology ; kinetics ; stresses
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation of niobium at high temperature (900°C) leads to reaction products with “exotic” morphologies. Morphological and kinetics analysis have been undertaken with Nb platelets. A growth mechanism of the oxide at the edges of the platelet is proposed.
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 42 (1994), S. 223-237 
    ISSN: 1573-4889
    Keywords: kinetics ; scale ; oxidation ; zirconium ; purity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation kinetics of zirconium of different purities were studied over the temperature range of 600–1300°C (α- and β-phases). The structure of the oxidized specimens was examined. TGA, XRD, EPMA, SEM, metallographic analysis, and microhardness measurements were carried out. Impurity elements were found to increase the oxidation rate of technical zirconium. The mechanism of the effect of impurity elements on zirconium oxidation was shown to differ for the α- and β-phases. Activation energies were calculated for the parabolic and linear stages of oxidation.
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  • 11
    Electronic Resource
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    Oxidation of metals 42 (1994), S. 249-263 
    ISSN: 1573-4889
    Keywords: kinetics ; scale ; oxidation ; hafnium ; purity
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation kinetics of hafnium of different purities were studied in the temperature range of 800–1200°C. This paper concerns the structure studies of the oxidized samples. TGA, XRD, SEM methods, and microhardness measurements were used. Hafnium oxidation follows the parabolic rate law, changing with time to the linear one. Oxidation-reaction products are HfO2(moncl) and α-solid solution of oxygen in hafnium. Anomalous oxidation behavior of hafnium having a high impurity content was found in the range 800–950°C. Activation energies for the parabolic and linear oxidation stages were calculated.
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  • 12
    Electronic Resource
    Electronic Resource
    Springer
    Oxidation of metals 35 (1991), S. 107-137 
    ISSN: 1573-4889
    Keywords: iron ; oxidation in CO2+CO mixtures ; kinetics ; reaction mechanisms
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Oxidation of high purity iron in CO 2 and CO2 + COmixtures at different total pressures (0.1–1 atm.) has been studied at 1000–1200°C. While paper I of this study emphasized studies of the relation between scale morphology and reaction kinetics, this paper focuses on the reaction mechanism during the initial oxidation involving growth of wüstite films and scales. The reaction behavior is analyzed in terms of coupled kinetics comprising a surface reaction and diffusional transport through the scale. A classical model derived by C. Wagner, based on the assumption that the properties and defect concentrations in the scale surface are exactly the same as in bulk wüstite equilibrated in CO 2 +CO mixtures, does not provide a satisfactory description of the reaction kinetics and the gas-pressure dependence of the surface reaction. As an alternative model, it is suggested that the gasous molecules/species interacts with the surface to form surface complexes, and that surface complexes withCO2 serve as preferred reaction sites for the surface reaction.
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  • 13
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    Oxidation of metals 33 (1990), S. 177-189 
    ISSN: 1573-4889
    Keywords: kinetics ; oxidation ; titanium hydride ; rutile
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The oxidation kinetics of titanium-hydride powders were studied in the temperature range of 298–1378 K in air at atmospheric pressure. DTA, DSC, X-ray analysis, and scanning electron microscopy were used. Oxidation was found to take place by TiHxOy oxyhydride phases formation. The oxidation reaction rate at temperatures above 870 K was limited by diffusion of oxygen atoms through a rutile scale formed on the surface. The activation energy and preexponential values of the Arrhenius equation for different interaction stages as well as transformation enthalpies were calculated.
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  • 14
    Electronic Resource
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    Springer
    Oxidation of metals 35 (1991), S. 397-404 
    ISSN: 1573-4889
    Keywords: copper alloys ; nitridation ; kinetics ; scale structure
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract One of the characteristic features of Mn-Cu binary alloys nitrided by gaseous nitrogen is that one of the two constitutive elements (Mn) can form nitrides, while the other one (Cu) does not give any stable compound with nitrogen. The only mixed manganese-copper nitride is the CuMn 3 N compound. The reaction kinetics with nitrogen are very slow and there is no internal nitriding. For alloys containing less than 20 at.% Mn, nitrogen reacts very little. The nitride scale formed on the alloys of greater Mn concentrations is a mixed nitride whose formula is Cu 1−x Mn 3+x N. The techniques of examination used are SEM, EMA, and GDS analysis.
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  • 15
    ISSN: 1573-4889
    Keywords: sulfidation ; Fe-Cr-Al alloys ; kinetics ; structures ; sulfide compositions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Sulfidation of an Fe-23.4Cr-18.6Al (at.%) alloy was investigated in H2S-H2 atmospheres, $$10^{ - 6} \leqslant {\text{P}}_{{\text{S}}_{\text{2}} } \leqslant 10^2 $$ Pa, at 973 K. It was found over this pressure range that sulfidation after an early transient period followed the parabolic rate law, being diffusion controlled. An investigation was carried out of the scales formed during early transient sulfidation over the sulfur pressure range $${\text{p}}_{{\text{S}}_{\text{2}} } = 10^{ - 6} - 10^{ - 2} $$ Pa. Fully developed scales were multilayered consisting of an inner compact layer of equiaxed grains, an intermediate layer of equiaxed and columnar grains exhibiting a small degree of porosity, and an outer porous layer of distinct plates and needles. The grains of the inner and intermediate layers contained quarternary sulfide phases. The following phases were identified: spinels (CrFe)Al2S4 and (FeAl)Cr2S4, hexagonal (FeCr)Al2S4, (CrAlFe)2S3, and (CrAlFe)5S6. The plates and needles were composed of hexagonal (FeCr)Al2S4 and (CrAlFe)2S3 at $${\text{p}}_{{\text{S}}_{\text{2}} } \geqslant 10^{ - 6} $$ and 10−5 Pa from which pyrrhotite, FeS, grew at $${\text{p}}_{{\text{S}}_{\text{2}} } \geqslant 10^{ - 4} $$ .
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  • 16
    ISSN: 1435-1536
    Keywords: Polystyrene seed ; poly(butyl acrylate-methacrylic acid) shell ; particle mophology ; location of carboxylic groups ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract Polystyrene (PS) (1)/Poly(n-butyl acrylate (BA)-methacrylic acid (MAA)) (2) structured particle latexes were prepared by emulsion polymerization using monodisperse polystyrene latex seed (118 nm) and different BA/MAA ratios. Three main aspects have been investigated: i) the polymerization kinetics; ii) the particle morphology as a function of reaction time; iii) the distribution of MAA units between the water phase and the polymer particles. The amount of MAA in the shell copolymer was found to be the main factor controlling the particle shape and morphology. The shape of the structured particles was, generally, non-spherical, and the shape irregularities increased as a particles was, generally, non-spherical, and the shape irregularities increased as a function of reaction time. At the beginning of the second stage reaction, new small particles were observed, which coalesced onto the PS seed as the polymerization proceeded. The distribution of the MAA groups in the latex particles and the serum was analyzed by alkali/back-acid titration, using ionic exchanged latexes. No MAA groups were detected in the latex serum. Due to the lowTg of the BA-MAA copolymers, alkali conductimetric titrations accounted for all the MAA groups on and within the polymer particles. Therefore, for these systems, this method is not only limited to a thin surface layer, as it is often assumed.
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  • 17
    ISSN: 1435-1536
    Keywords: Mn(III)-poly(ethylene glycol) ; acrylonitrile ; block copolymerization ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The kinetics and mechanism of thermal polymerization of acrylonitrile initiated by Mn(III) pyrophosphate — poly(ethylene glycol) (PEG, molecular weight 6000) redox system in aqueous sulfuric acid medium was studied in the temperature range 30–60°C. The overall rates of polymerization and the disappearance of Mn3+ were determined. The polymerization was initiated by the organic free radical produced from the Mn3+-PEG reaction and the termination was by the metal ions. The rate of polymerization of acrylonitrile was found to be directly proportional to the square of the monomer concentration and first power of PEG concentration, and inversely proportional to the concentration of Mn3+. The rate of manganic ion disappearance was found to be directly proportional to manganic ion concentration and PEG concentration, and independent of the monomer concentration. Based on these observations, a plausible reaction scheme was suggested and suitable kinetic expressions were evaluated.
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  • 18
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    Colloid & polymer science 268 (1990), S. 645-648 
    ISSN: 1435-1536
    Keywords: β-picolinium-p-chlorophenacylide ; α-α azobisisobutyronitrile ; N-vinyl pyrrolidone ; dilatometry ; retarder ; kinetics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract β-Picolinium-p-chlorophenacylide (β-PCFY) acts as a retarder for polymerization of N-vinyl pyrrolidone. The polymerization runs were carried out at 60°C using benzene as an inert solvent. The kinetic equation for the present system may be written asR p α[β-PCPY]−1.0 [AIBN]0.66[N-VP]1.0. The value of overall energy of activation for polymerization in presence and absence ofβ-PCPY was computed as 44.0 and 42.3 kJ mol−1, respectively. The inverse relationship ofR p and¯M v withβ-PCPY suggests thatβ-PCPY acts as a polymerization retarder. The retarding effect is also evidenced by higher initiator exponent value and higher value of energy of activation in presence of ylide. A mechanism is also proposed in which polymer propagating chain combines with one ylide component to give resonance stabilized radical.
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  • 19
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    Colloid & polymer science 270 (1992), S. 982-989 
    ISSN: 1435-1536
    Keywords: Ultrasonic relaxation ; kinetics ; hydrogen bonds ; counterion interactions ; polyelectrolytes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The ultrasonic absorption coefficient has been measured as a function of frequency between 5 MHz and 3.1 GHz for aqueous solutions of polyacrylic acid and of its sodium, potassium, and tetraethylammonium salts. Unlike an aqueous solution of propionic acid, all polymer solutions clearly exhibit excess absorption. Within the frequency range under consideration the excess absorption spectra can be analytically represented by two Debye-type relaxation terms. At 25°C the corresponding relaxation times adopt values between 3 and 12.4 ns, and between 0.12 and 0.22ns, respectively. The former process is discussed in accordance with previous models. The relaxation of the polyacrylic acid solutions is assumed to be related to the formation of hydrogen bonds of the polymeric molecules and that of the polyacrylate solutions may be due to interactions of counterions with chain segments. The latter process, the existence of which has been first proven in this study, is likely to reflect rotational motions of carboxyl groups.
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  • 20
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    Colloid & polymer science 270 (1992), S. 878-884 
    ISSN: 1435-1536
    Keywords: Adsorption-desorptionkinetics ; kinetics ; ionexchange ; lysozyme ; Sephadex C-25
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The ion-exchange reaction of lysozyme with carboxymethyl Sephadex C-25 was followed by conductivity change as a function of time just after the rapid mixing of the protein solution with the Sephadex suspension. A single relaxation process was observed; the conductivity increased exponentially with time in the 100 s scale. In this process, protons were released from the Sephadex C-25 in the same time scale. The relaxation process slowed down with an increase in the lysozyme concentration, but it quickened upon the addition of HCl. On the other hand, the ζ potential on the Sephadex C-25 surface changed from a negative value to a positive one with an increase in the amount of lysozyme adsorbed on the surface. On the basis of these data, the relaxation process was attributed to the ion-exchange reaction of lysozyme with several protons of carboxymethyl groups of the Sephadex.
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  • 21
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    Colloid & polymer science 272 (1994), S. 1-16 
    ISSN: 1435-1536
    Keywords: Polymer crystallization ; kinetics ; modeling ; POM ; PEEK
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics
    Notes: Abstract The isothermal crystallization of two engineering polymers — POM and PEEK — was studied, both theoretically and experimentally. The experiments were performed by means of differential scanning calorimetry (DSC) and polarized light optical microscopy (OM). Building on previously developed theoretical formalisms (Avrami/Evans, Hillier and Tobin), a new procedure is presented, based on Tobin's model coupled with a modification of Hillier's calculation technique, to accurately describe the kinetics and mechanism of the crystallization of polymers from quiescent melts. First, it is shown that Tobin's model alone, without modification, is more accurate than Avrami/Evans model to describe single-mechanism processes, for a wide range of materials and for longer crystallization times, despite having exactly the same nature and number of parameters (the kinetic, nucleation and growth rate-related, parameterK and the dimensionalityn). Then, Hillier's formalism is modified and combined with Tobin's model, to accurately predict the kinetics of dual mechanism crystallization processes; a clear contrast is drawn with Hillier's Avrami-based, original procedure which uses the same number and nature of parameters, but cannot adequately predict the experimental behavior. The parameter values predicted by the model(s) and procedure presented in this work are all given, are then physically interpreted and, in the case of POM, related to independent morphological observations by polarized light optical microscopy. They are also consistent with electron microscopy observations made by other authors on the detailed morphology of the spherulitic crystallization of polymers.
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  • 22
    ISSN: 1572-9729
    Keywords: cometabolism ; cosubstrate ; 4-chlorophenol ; inhibition ; kinetics ; modeling ; monooxygenase ; phenol ; substrate interactions
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Batch experiments on the simultaneous utilization of phenol (primary substrate) and 4-chlorophenol (cometabolic secondary substrate) demonstrated two critical substrate interactions. First, the cometabolic degradation of 4-chlorophenol was proportional to the rate of phenol oxidation, which provided the electrons for the initial monooxygenase reaction. Second, 4-chlorophenol inhibited the oxidation of the primary substrate, phenol. Modeling analyses of the degradation of phenol alone and of phenol and 4-chlorophenol together showed that the proportionality between phenol and 4-chlorophenol degradation rates averaged 0.1 mg 4-CP/mg phenol, which corresponds to 0.5% of the electrons generated by phenol oxidation being used as a cosubstrate for the monooxygenase reaction of 4-chlorophenol. In addition, modeling analyses suggest that 4-chlorophenol was a noncompetitive inhibitor of phenol oxidation for high phenol concentrations, but a competitive inhibitor for low phenol concentrations.
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  • 23
    ISSN: 1572-9729
    Keywords: 2,4-dichlorophenoxyacetic acid ; bacteria ; biodegradation ; kinetics ; kineralization ; xenobiotic
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Mineralization of 2,4-dichlorophenoxyacetic acid (2,4-D) by two Alcaligenes eutrophus strains and one Pseudomonas cepacia strain containing the 2,4-D degrading plasmids pJP4 or pRO101 (=pJP4::Tn1721) was tested in 50 g (wet wt) samples of non-sterile soil. Mineralization was measured as 14C-CO2evolved during degradation of uniformly-ring-labelled 14C-2,4-D. When the strains were inoculated to a level of approximately 108 CFU/g soil, between 20 and 45% of the added 2,4-D (0.05 ppm, 10 ppm or 500 ppm) was mineralized within 72 h. Mineralization of 0.05 ppm and 10 ppm, 2,4-D by the two A. eutrophus strains was identical and rapid whereas mineralization by P. cepacia DBO1(pRO101) occurred more slowly. In contrast, mineralization of 500 ppm 2,4-D by the two A. eutrophus strains was very slow whereas mineralization by P. cepacia DBO1 was more rapid. Comparison of 2,4-D mineralization at different levels of inoculation with P. cepacia DBO1(pRO101) (6×104, 6×106 and 1×108 CFU/g soil) revealed that the maximum mineralization rate was reached earlier with the high inoculation levels than with the low level. The kinetics of mineralization were evaluated by nonlinear regression analysis using five different models. The linear or the logarithmic form of a three-half-order model were found to be the most appropriate models for describing 2,4-D mineralization in soil. In the cases in which the logarithmic form of the three-half-order model was the most appropriate model we found, in accordance with the assumptions of the model, a significant growth of the inoculated strains.
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  • 24
    ISSN: 1572-9729
    Keywords: anaerobic fermentation ; olive mill waste ; kinetics ; support
    Source: Springer Online Journal Archives 1860-2000
    Topics: Biology , Energy, Environment Protection, Nuclear Power Engineering , Agriculture, Forestry, Horticulture, Fishery, Domestic Science, Nutrition
    Notes: Abstract Two materials of different structure, sepiolite and bentonite, evaluated as supports for the microorganisms effecting anaerobic fermentation, behaved differently towards condensation water from thermally concentrated olive mill wastewater from a kinetic point of view. Assuming the overall anaerobic digestion process to conform to first-order kinetics, the apparent kinetic constant for the digester including sepiolite as support was 1.12 day-1, while that of the digester using the bentonite support was 0.73 day-1. Thus, the apparent kinetic constant of the process was increased by 35% with the use of sepiolite. The yield coefficient, Yp/s, was 0.344 and 0.318 litres CH4 STP/g COD for the sepiolite and bentonite supports respectively.
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  • 25
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    Polymer International 34 (1994), S. 105-109 
    ISSN: 0959-8103
    Keywords: Zinc acrylate ; acrylonitrile ; As2S3-styrene complex ; copolymerization ; dilatometry ; kinetics ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Radical copolymerization of zinc acrylate (ZnA2) with acrylonitrile (AN), initiated by As2S3-styrene complex(I), in dimethyl Sulphoxide (DMSO) at 90 ± 0.1°C for 1.0h under inert atmosphere, yields non-alternating copolymers. The kinetic expression is Rp ∝ [I]0.33 [ZnA2]0.25 [AN]0.44, i.e. the system follows non-ideal kinetics, which is due to primary radical termination as well as degradative chain transfer reactions. The values for activation energy (E) and k2p/kt are 128kJ mol-1 and 8.57 × 10-7 litre mol-1 s-1, respectively. Thermal stability, solubility in different solvents, and IR and NMR spectra have been evaluated.
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  • 26
    ISSN: 0959-8103
    Keywords: cyclosilazanes ; polysilazanes ; cationic polymerization ; kinetics ; methyl triflate ; adiabatic calorimetric technique ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The ring-opening polymerization of hexamethylcyclodisilazane (D2NMe), initiated by methyl triflate in 1,2-dichloroethane, forms in the first, fast kinetic step both linear polymer and cyclic dimer (D4NMe). Subsequently a slow depolymerization process occurs leading to exclusively cyclotrisilazane (D3NMe). On the basis of kinetic measurements carried out using an adiabatic calorimetric technique and complementary experiments, mechanisms of both propagation, cyclization and back-biting reactions are proposed. The influence of the reaction temperature was also studied; it is demonstrated that, at low temperature, polymerization does not lead to cyclic oligomer formation. In such conditions, the polymerization presents a ‘living’ character.
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  • 27
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    Polymer International 34 (1994), S. 141-144 
    ISSN: 0959-8103
    Keywords: Iyotropic liquid crystalline polymer ; liquid crystalline phase transition ; kinetics ; Avrami equation ; depolarized light intensity technique ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The kinetics of liquid crystalline phase transition from the isotropic state to the anisotropic state, which is by analogy termed liquid crystallization, for poly(p-benzamide)(PBA)/H2SO4 and PBA/Nylon 6/H2SO4 systems was investigated by the depolarized light intensity (DLI) technique and polarized light microscopy (PLM). The experimental data were analysed using the Avrami equation. The n value, according to the Avrami equation, is about 1 for both PBA/H2SO4 and PBA/Nylon 6/H2SO4 systems, which suggests that the liquid crystallization of PBA/H2SO4 and PBA/Nylon 6/H2SO4 systems is a process of instantaneous nucleation with one-dimensional growth. The introduction of Nylon 6 into PBA/H2SO4 does not have any significant effect on the Avrami exponent n. The results also show that the Avrami exponent n and the half-time for the liquid crystallization are temperature dependent.
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  • 28
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    Polymer International 34 (1994), S. 279-287 
    ISSN: 0959-8103
    Keywords: aqueous medium ; redox initiator ; kinetics ; order of the reaction ; rate constant ; methyl cellosolve ; methyl methacrylate ; acrylonitrile ; overall energy of activation ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: Polymerizations of methyl methacrylate (MMA) and acrylonitrile (AN) were carried out in aqueous nitric acid at 30°C with the redox initiator system ammonium ceric nitrate-methyl cellosolve (MC). A short induction period was observed, as well as the attainment of a limiting conversion for polymerization reactions. The consumption of ceric ion was first order with respect to Ce(IV) concentration in the concentration range (0.5-3.0) × 10-3 M Ce(IV), and the point at higher concentration deviated from the graph. Plots of the inverse of the pseudo-first order rate constant for ceric ion consumption, [k′]-1, versus [MC]-1 gave straight lines with non-zero intercepts for both monomer systems, suggesting complex formation between Ce(IV) and MC. Complex formation between Ce(IV) and reducing agent was also detected by a shift in the absorption maximum of Ce(IV), using a Beckman spectrophotometer. The rates of polymerizations increased with increase in Ce(IV), MC and monomer concentrations; however, at higher concentration of AN (0.2187 M) a steep fall in Rp was observed for AN polymerization. The orders with respect to Ce(IV), MC and monomer for MMA polymerization were found to be 0.22, 0.35 and 1.73 respectively. The orders with respect to Ce(IV), MC and monomer for AN polymerization were found to be 0.56, 0.30 and 1.30 respectively. Maintaining constant nitrate ion in the reaction medium did not significantly change the rate of polymerization with [Ce(IV)], but a fall in RCe was observed. A kinetic scheme involving oxidation of MC by Ce(IV) via complex formation, whose decomposition gives rise to a primary radical, initiation, propagation, and termination of the polymeric radicals by bimolecular interaction, is proposed. An oxidative termination of primary radicals by Ce(IV) is also included.
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  • 29
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    Polymer International 35 (1994), S. 257-261 
    ISSN: 0959-8103
    Keywords: non-halo and halo polyesters ; nitroglycerine migration ; inhibitors ; kinetics ; diffusion ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The diffusion coefficients (D) of nitroglycerine (NG) migration through cured non-halo and halo polyesters have been calculated with the help of M∞ determined experimentally and Fick's Law. The calculated NG migrations at different time intervals compare very closely with the corresponding NG migrations determined experimentally. The concentration profiles at various locations in thin sheets of non-halo and halo polyesters have also been calculated.
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  • 30
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    Polymer International 33 (1994), S. 315-319 
    ISSN: 0959-8103
    Keywords: gelatin ; adsorption ; silica ; kinetics ; solid-liquid interface ; Chemistry ; Polymer and Materials Science
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Mechanical Engineering, Materials Science, Production Engineering, Mining and Metallurgy, Traffic Engineering, Precision Mechanics , Physics
    Notes: The kinetics of adsorption of gelatin from its aqueous solution on to silica has been studied at room temperature. The adsorption isotherms were found to be of the Langmuir type. From the adsorption isotherms, the adsorption coefficient, surface coverage and rate constants for adsorption and desorption were evaluated. The rate of adsorption was found to be maximum at the isoelectric point of gelatin and decreased with increase in pH of the adsorption medium. The increased ionic strength of the medium also caused an increase in the rate and amount of adsorption.
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  • 31
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    Journal of Computational Chemistry 11 (1990) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
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  • 32
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    Journal of Computational Chemistry 11 (1990), S. 1-18 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Counterpoise corrected ab initio calculations are reported for (H2O)2 and H2O-H2CO. Geometry searches were done in the moment-optimized basis DZP' at the SCF, MP2, and CEPA-1 levels of theory, followed by more accurate single-point calculations in basis ESPB, which includes bondfunctions to saturate the dispersion energy. The final equilibrium binding energies obtained are -4.7 ±0.3 kcal/mol for a near-linear (H2O)2 structure and -4.6 ±0.3 kcal/mol for a strongly bent HOH ‥ OCH2 structure. The energy difference between these systems is much smaller than in all previous ab initio work. Cyclic (C2h) and bifurcated (C2v) transition structures for (H2O)2 are located at 1.0 ±0.1 kcal/mol and 1.9 ±0.3 kcal/mol above the global minimum, respectively. A new partitioning scheme is presented that rigorously partitions the MP2 correlation interaction energy in intra and intermolecular (dispersion) contributions. These terms are large (up to 2 kcal/mol) but of opposite sign for most geometries studied and hence their overall effect upon the final structures is relatively small. The relative merits of the MP2 and CEPA-1 approaches are discussed are discussed and it is concluded that for economical reasons MP2 is to be preferred, especially for larger systems.
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  • 33
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    Journal of Computational Chemistry 11 (1990), S. 45-57 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A data compression method is presented that is generally applicable to first-order convergent iterative procedures that employ subspace expansions or extrapolations based on successive correction vectors. This method is based on the truncation of insignificant information in successive correction vectors. Although the correction vectors themselves may be severely truncated with the proposed approach, the final solution vector may be represented to arbitrary accuracy. A feature of the proposed method is that more slowly convergent iterative procedures allow the correction vectors to be more severely truncated without affecting the overall convergence rate. The method is implemented and applied to the iterative Davidson diagonalization method. If the compressed representation of the expansion vectors can be held in main computer memory, then a significant reduction in the I/O requirements is achieved.
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  • 34
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    Journal of Computational Chemistry 11 (1990), S. 67-75 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: By examining the displacement coordinate metric three modes of constrained optimization for large molecules and clusters are suggested. The first method corresponds to a conventional optimization using internal coordinates. The second mode has applications with respect to both internal and cartesian coordinates. The final mode is particularly interesting because it can result in computational savings. A mixture of both internal and cartesian coordinates is specified where these coordinates are usually a subset of the molecules or clusters total coordinate set. In the optimization only a subset of the energy derivatives need be evaluated reducing the computational effort associated with the gradient calculation.
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  • 35
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    Journal of Computational Chemistry 11 (1990), S. 82-87 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A finite-field method for the calculation of polarizabilities and hyperpolarizabilities is developed based on both an energy expansion and a dipole moment expansion. This procedure is implemented in the MOPAC semiempirical program. Values and components of the dipole moment (μ), polarizability (α), first hyperpolarizability (β), and second hyperpolarizability (γ) are calculated as an extension of the usual MOPAC run. Applications to benzene and substituted benzenes are shown as test cases utilizing both MNDO and AM1 Hamiltonians.
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  • 36
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    Journal of Computational Chemistry 11 (1990), S. 121-151 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A procedure has been developed for global energy minimization of surface loops of proteins in the presence of a fixed core. The ECEPP potential function has been modified to allow more accurate representations of hydrogen bond interactions and intrinsic torsional energies. A computationally efficient representation of hydration free energy has been introduced. A local minimization procedure has been developed that uses a cutoff distance, minimization with respect to subsets of degrees of freedom, analytical second derivatives, and distance constraints between rigid segments to achieve efficiency in applications to surface loops. Efficient procedures have been developed for deforming segments of the initial backbone structure and for removing overlaps. Global energy minimization of a surface loop is accomplished by generating a sequence (or a trajectory) of local minima, the component steps of which are generated by searching collections of local minima obtained by deforming seven-residue segments of the surface loop. The search at each component step consists of the following calculations: (1) A large collection of backbone structures is generated by deforming a seven-residue segment of the initial backbone structure. (2) A collection of low-energy backbone structures is generated by applying local energy minimization to the resulting collection of backbone structures (interactions involving side chains that will be searched in this component step are not included in the energy). (3) One low-energy side-chain structure is generated for each of the resulting low-energy backbone structures. (4) A collection of low-energy local minima is generated by applying local energy minimization to the resulting collection of structures. (5) The local minimum with the lowest energy is retained as the next point of the trajectory. Applications of our global search procedure to surface segments of bovine pancreatic trypsin inhibitor (BPTI) and bovine trypsin suggest that component-step searches are reasonably complete. The computational efficiency of component-step searches is such that trajectories consisting of about 10 component steps are feasible using an FPS-5200 array processor. Our procedure for global energy minimization of surface loops is being used to identify and correct problems with the potential function and to calculate protein structure using a combination of sequence homology and global energy minimization.
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  • 37
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    Journal of Computational Chemistry 11 (1990), S. 416-430 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A systematic analysis of the molecular electrostatic potential (MEP) is presented. This study has been performed with a twofold purpose: first, to study the MEP dependence with regard to the quality of the basis set used to compute the ab initio SCF wavefunction and second, to develop and to assess a new strategy for computing isoelectrostatic potential maps using the semiempirical MNDO wavefunction. The only differences between this procedure and the ab initio SCF MEP computation lie in the freezing of the inner electrons and in the origin of the first-order density matrix. The statistical analysis of MEPs computed for a large number of molecules from MNDO wavefunction and ab initio SCF wavefunctions obtained using STO-3G, 4-31G, 6-31G, 4-31G*, 6-31G*, and 6-31G** basis sets points out the ability of any wavefunction to reproduce the general topological characteristics of the MEP surfaces. Nevertheless, split-valence basis sets including polarization functions are necessary to obtain accurate MEP minimum energy values. MNDO wavefunction tends to overestimate the MEP minima depth by a constant factor and shows an excellent ability to reflect the relative variation of MEP minima energies derived from a rather sophisticated (6-31G*) basis set, lacking of the shortcomings detected in the semiempirical CNDO approximation.
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  • 38
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    Journal of Computational Chemistry 11 (1990), S. 487-492 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Expressions are derived for computing the kinetic energy of a peptide with fixed geometry, in terms of dihedral angles as generalized coordinates; other expressions required for the solution of Lagrange's equations are also presented. The peptide is regarded as held stationary at one end. We also outline the computations that are needed in calculating the components of the third derivative of a potential energy function that consists of a sum of pairwise interatomic interactions.
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  • 39
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    Journal of Computational Chemistry 11 (1990), S. 819-828 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Complexes of alkali and alkaline earth cations with organic compounds are modeled by describing ionligand interaction energies with pair potentials and intraligand as well as interligand energies with the MM2 potential. New pair potentials for the interaction of Li+, Na+, K+, Mg2+, and Ca2+ ions are derived on the basis of 30,000 ab initio interaction energy values with 70 selected model ligand molecules. Various problems of the combination of these two basically different potentials are discussed. An application for the K+ complex of 18-crown-6 is presented. For more flexible ligands the introduction of three-body correction terms of the pair potentials seems necessary.
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  • 40
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    Journal of Computational Chemistry 11 (1990), S. 924-929 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry, electronic structure, and photoelectron spectra of Sb2 and Sb4 have been investigated employing the LCGTO-MP-LSD method. For both molecules the geometrical and spectroscopic constants computed using the VWN potential are in very good agreement with the available experimental data. The HeI photoelectron spectra were computed with different potentials (Xα, GL, HL, BH, and VWN). The calculated spectra are in excellent agreement with the experimental ones and the use of the VWN potential gives the most accurate results. The reliable results for molecules complement those for the Sb atom and show that the proposed LSD Model Potential is able to give an accurate description of the structural and spectroscopic properties of the title molecules.
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  • 41
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    Journal of Computational Chemistry 11 (1990), S. 958-971 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Intermolecular potential functions have been developed for use in computer simulations of alkyl ethers. The simple OPLS model was adopted and parameterized to yield good descriptions of bimolecular and ion-molecule complexes as well as to reproduce experimental thermodynamic properties of liquid ethers. The principal testing featured Monte Carlo statistical mechanics simulations for liquid dimethyl ether (DME), ethyl methyl ether (EME), diethyl ether (DEE), and tetrahydrofuran (THF). Average errors of 1-3% are obtained for the computed densities and heats of vaporization including results for THF at pressures up to 5000 atm. The torsional motion about the central C—O bonds in EME and DEE was included in the simulations using rotational potential functions fit to results of molecular mechanics (MM2) calculations. The liquid-state environment is found to have negligible effect on the conformational equilibria.
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  • 42
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    Journal of Computational Chemistry 11 (1990), S. 972-977 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A quadrature-point-driven implementation of the standard Rys polynomial method for computing two-electron repulsion integrals of gaussian basis functions has been found to be both concise and openended with respect to the angular momentum of the gaussian functions (i.e., s,p,d,f,g,…). These are important features in certain applications, such as molecular properties and property gradients.
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  • 43
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    Journal of Computational Chemistry 11 (1990), S. 994-1002 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Free energy perturbation calculations were performed to determine the free energy of binding associated with the presence of perhaps an unusual hydroxyl group in the transition state analog of nebularine, an inhibitor of the enzyme adenosine deaminase. The presence of a single hydroxyl group in this inhibitor has been found to contribute -9.8 kcal/mol to the free energy of binding, with a 108-fold increase in the binding affinity by the enzyme. In this work, we calculate the difference in solvation free energy for the 1,6-dihydropurine complex versus that of the 6-hydroxyl-1,6-dihydropurine complex to determine if this marked increase in binding affinity is attributed to an unusually hydrophobic hydroxyl group. The calculated ΔG associated for the solvation free energy is -11.8 kcal/mol. This large change in the solvation free energy suggests that this hydroxyl is instead unusually hydrophilic and that the difference in free energy of interaction for the two inhibitors to the enzyme must be at least ca. 20 kcal/mol. Although the crystal structure for adenosine deaminase is currently not known, we attempt to mimic the nature of the active site by constructing models which simulate the enzyme-inhibitor complex. We present a first attempt at determining the change in free energy of binding for a system in which structural data for the enzyme is incomplete. To do this, we construct what we believe is a minimal model of the binding between adenosine deaminase and an inhibitor. The active site is simulated as a single charged carboxyl group which can form a hydrogen bond with the hydroxyl group of the analog. Two different carboxyl anion models are used. In the first model, the association is modeled between an acetic acid anion and the modified inhibitor. The second model consists of a hydrophobic amino acid pocket with an interior Glu residue in the active site. From these models we calculate the change in free energy of association and the overall change in free energy of binding. We calculate the free energies of interaction both in the absence and presence of water. We conclude from this that the presence of a single suitably placed-CO-2 group probably cannot explain the binding effect of the-OH group and that additional interactions will be found in the adenosine deaminase active site.
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  • 44
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    Journal of Computational Chemistry 11 (1990), S. 1029-1037 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Pseudopotentials and valence basis sets to be used in calculations for organometallic compounds of zinc and magnesium have been tested in calculations for the M(CH3)n (M = Zn, Mg; n = 1,2) molecules. Valence correlation effects are treated at the SDCI and CEPA levels. The capability of a polarization potential on zinc to account for the valence shell contracting effect of core valence correlation is studied. Properties considered are geometries, force constants, Mulliken populations, ionization potentials, atomization, and binding energies. Differences in bonding between the two dimethyl compounds are discussed.
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    Journal of Computational Chemistry 11 (1990), S. 1094-1100 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The acid-catalyzed hydrolysis mechanisms of maleamic (4-amino-4-oxo-2-butenoic) acids were studied using AM1 method. The reaction proceeded mainly in two steps: (1) nucleophilic attack of the undissociated carboxyl group on the adjacent aminocarbonyl carbon via a zwitterionic intermediate; and (2) the rate-determining proton transfer to form the zwitterionic tetrahedral intermediate. In each step, the hydration of water and hydronium ion molecules was important in stabilizing the polarized intermediates. The substituent effects at the amide moiety and the 2,3-positions of the maleamic acids were qualitatively estimated for each step.
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  • 46
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    Journal of Computational Chemistry 11 (1990) 
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 47
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    Journal of Computational Chemistry 11 (1990), S. 1139-1146 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A prescription for applying the method of molecular similarity calculations based on electrostatic potentials and fields is developed by consideration of a typical structure-activity series. Firm conclusions are drawn about the nature of the grid of points surrounding the molecules and about the choice of geometry, but options for point charges are less clearcut.
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  • 48
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    Journal of Computational Chemistry 11 (1990), S. 899-908 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An expanded form of the Wiener number is suggested for characterization of molecular graphs and structure-property correlations. The simple, computer-oriented method for counting of the novel index is briefly discussed.
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  • 49
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    Journal of Computational Chemistry 11 (1990), S. 1193-1205 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A common requirement in conformational analysis is the identification of a molecule's lowest energy conformations. The application of the A* algorithm to this problem is examined. The algorithm uses heuristic information about the problem domain to direct the search and has been implemented in a system for performing automated conformational analysis. The method is detailed and sample results presented. Some limitations of the approach are identified.
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  • 50
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    Journal of Computational Chemistry 11 (1990), S. 1009-1016 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Heats of formation and net atomic charges of some 120 structures involving substituted phenols, anilines, and benzoic acids and the corresponding anions were calculated by MNDO, AM1, and PM3 semiempirical methods. The gas phase acidities of substituted phenols and anilines and the net atomic charges on the anionic heteroatoms of the corresponding anions have been successfully correlated with σ- constants. Moreover, good correlations with σ were found for the charges on the acidic hydrogens of substituted phenols and anilines. In contrast, the gas phase acidities of substituted benzoic acids and the charges on the anionic oxygens of the corresponding anions are better correlated with Taft σ° constants. Comparisons of these results with experimental data and ab initio theoretical calculations indicate that AM1 and PM3 methods are much better than MNDO in predicting the acidity of aromatic compounds.
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  • 51
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    Journal of Computational Chemistry 11 (1990), S. 1038-1046 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We studied geometries and energies of complexes between water and neutral or protonated imidazole by ab initio molecular orbital calculations using the 4-31G basis set with and without the counterpoise correction. Positions of hydration sites and relative binding energies could be also estimated by using the electrostatic field map of imidazole as calculated by our bond increment method. The reliability of the calculations is confirmed by comparing the geometries of the imidazole-water complex to the experimental ones from the Cambridge Structural Database. These were obtained by X-ray diffraction studies on crystals with water bound to a molecule containing the imidazole fragment.
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  • 52
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    Journal of Computational Chemistry 11 (1990), S. 1061-1071 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A new method for the evaluation of metal complexes with molecular mechanics calculations is described. The method has been employed to determine the global minimum energy conformations of three seven-coordinate lanthanide complexes. The method searches the potential energy surface of the metal complexes for the global minimum structure using the recently reported Random Incremental Pulse Search (RIPS). The molecular mechanics calculations were performed using the MM2 metal-extended force field (MM2MX). This force field excludes 1-3 bending terms about the metal center and, instead, explicitly includes 1-3 nonbonded van der Waals interactions. This affords a model based mainly on steric interactions about the ligating atoms, and removes the necessity of specifying ligand-metal-ligand bond angles for seven-coordinate and higher metal complexes in which no preferred bond angle can be proficiently determined. The calculated minimum-energy structures were well known seven-coordinate conformations in all cases, and a comparison with X-ray crystallographic is presented.
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  • 53
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    Journal of Computational Chemistry 11 (1990), S. 1076-1079 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The method of approximation of the frozen molecular fragment (FMF) we derived has been applied to calculations of proton affinities. Results are in good agreement with experimental data and extended basis set calculations.
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  • 54
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    Journal of Computational Chemistry 11 (1990), S. 1087-1093 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Myelin basic protein (MBP) is the major extrinsic protein of the myelin sheath in the central nervous system. It is this protein that is destroyed in such demyelinating diseases as multiple sclerosis. We have examined the predicted structures of one segment of MBP using the molecular mechanics program ECEPP83 developed by Scheraga and co-workers as modified by Chuman, Momany, and Schafer. We have focused upon a segment, 87-118, containing the Pro-Pro-Pro sequence (residues 100-102), which has been predicted from standard algorithms to exist in a hairpin loop connecting anti-parallel beta-strands. Several local energy minima have been found and reported. Tripoline sequences are not rare in proteins, but their structure and function is still uncertain.
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  • 55
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    Journal of Computational Chemistry 11 (1990), S. 1101-1110 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Two new computational methods for the evaluation and partitioning of projected, planar, and averaged slab electron densities, implemented in the program PRODEN, are presented. The new algorithms for the projection, demarcation, and integration of electron densities are described and evaluated in terms of speed and numerical accuracy. Integrated Projected Populations are analyzed and some of the advantages and limitations of the methods are discussed.
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  • 56
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    Journal of Computational Chemistry 12 (1991), S. 175-179 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This is a study of the effect of data structures and algorithms on parallelism and vectorization for the molecular dynamics package GROMOS. About 80% of the computing time (for the GROMOS benchmark) is spent on the nonbonded interactions, and an important issue is the method that is used for finding all pairs of atoms (actually atom groups) which are within a given cutoff radius of each other. Favored by the authors of GROMOS is the use of the (Verlet) neighbor list with direct calculation of all distances. Substantial restructuring of their code for the nonbonded interactions has resulted in a speedup of a factor 6.9 for the eight-processor Alliant FX/8 through the use of concurrent subroutine calls. Vectorization gave a further improvement of 30%. However, the direct calculation of all distances does not scale up linearly with the number of atoms. (Nor would neighbor lists be needed if cutoffs were abandoned in favor of such techniques as the fast multipole method). Therefore an alternative GROMOS subroutine that implements the “gridcell plus linked list” approach without a neighbor list was also rewritten and tested. This resulted in the discovery of an apparent flaw in an early study of the relative merits of the two algorithms. It is observed that actually the neighbor list version of GROMOS is not much faster.
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  • 57
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Conformational energies of different conformers have been calculated for a series of molecules using various molecular mechanics and semiempirical methods. The quality of the force fields has also been tested by calculating barriers to rotation about carbon-carbon bonds. The molecular mechanics force fields used are MM2(85), Sybyl 5.1, Sybyl 5.21, and ChemX, ver. Jan 89. The semiempirical methods used are AM1 and PM3. Molecules with different functional groups, for which good experimental data exist, have been selected. The semiempirical methods generally calculate barriers to rotation which are lower than the experimentally determined. The conformational energies for hydrocarbons are reasonably well reproduced by all tested methods although MM2(85) gives the quantitatively best agreement with experiments. For compounds containing oxygen, nitrogen and halogens MM2(85) gives results which are in best agreement with the experimentally determined values.
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  • 58
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    Journal of Computational Chemistry 12 (1991), S. 147-166 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The modeling program AMBER 3.0 was used to study the conformations adopted by the C8-substituted guanosine adduct of the carcinogen N-2-acetylaminofluorene (AAF), called dGuo-AAF. This conformational study was extended to the hexamer d(CGCGCG)2 in the Z form, modified by AAF at guanine G4 with the carcinogen situated at the helix exterior in two different orientations (named ZAAF-5′ and ZAAF-3′). Considering the importance of electrostatic interactions in case of charged molecules like nucleic acids, minimization and molecular dynamics (MD) were performed using different electrostatic parameters (dielectric functions and scale factors). For that purpose, a subroutine allowing the use of a sigmoidal distance-dependent dielectric function εcal has been added to the program. For dGuo-AAF, the results show a great importance of the starting conformation and of the force field parameters on the minimization and MD behaviors. For the AAF-modified Z-DNA, the results display a pronouned dependence on the choice of the set of electrostatic parameters as well. With the distance-dependent dielectric function ε = r, the force field parameters favor the formation of intramolecular H bonds, which can lead to important distortions of Z-DNA. The use of ε = 4r or ε = εcal attenuates effectively such a tendency, except in full MD simulations. The dielectric function εcal is computing intense, but often similar results are obtained with ε = 4r, especially with the use of the BELLY option. AAF appears to prefer the ZAAF-5′ conformation, i.e., with the fluorene ring stacking on the sugar phosphate backbone of the following 5′ C-G bases. Such a conformation is further stabilized by an intramolecular hydrogen bond between the amino group of the 3′ cytosine and the carbonyl group of AAF. The fluorene ring, although mobile around its long axis, does not flip-flop between its two main orientations, ZAAF-5′ and ZAAF-3′. The presence of the AAF does not prevent the ZI to ZII transitions. Whatever the electrostatic parameters, the presence or absence of AAF, the cytosine sugars stay in the C2′-endo pucker domain. In unmodified Z-DNA, the guanine sugars stay in the C3′-endo region, except for the terminal guanines which transit to the C2′endo region. In modified Z-DNA, the sugar of the modified guanine behaves as a terminal guanine sugar.
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    Journal of Computational Chemistry 12 (1991), S. 690-696 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: This article presents theoretical calculations on bond energies for the first-row diatomics C2, CN, CO, CF, N2, NO, NF, O2, FO, and F2, which vary in bond order from one to three. The atomic-centered basis functions are systematically augmented with bond functions (BFs), which range in composition from (sp) to 2(spd), to determine the basis set which yields a dissociation energy closest to the experimental De. A strong correlation is found to exist between the bond order and the number of BFs required in the optimum basis set. Based on these results, we are able to predict the optimum composition of the BF basis which should be added to a DZP-quality AO basis set for a case in which only the bond order is known. These optimized BF basis sets are shown in the accompanying article to give more accurate potential curves than larger basis sets without bond functions.
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    Journal of Computational Chemistry 12 (1991), S. 731-741 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The harmonic molecular force fields for the nucleic acid bases, cytosine, and guanine, that have been previously published by several investigators are tested by the calculation of the relative intensities of the in-plane modes in the ultraviolet resonance Raman (UVRR) effect from the two lowest lying absorption bands using a theoretical approach devised previously.1-3 Since only a fraction of the 2N - 3 in-plane vibrations of a molecule are active in the UVRR, the two criteria that are taken for the adjustment of the force constant are: (1) the closest possible agreement between the observed and calculated frequencies of the 2N - 3 in-plane vibrations, and (2) the closest possible agreement between the calculated and observed intensities of those few vibrations that are strongly active in the ultraviolet resonance Raman effect. In particular it is necessary that the force constants be adjusted to avoid the calculation of intense Raman lines with frequencies that are not observed in the UVRR spectrum. Using this criteria, a new force field has been developed that appears to give better agreement with the observed UVRR intensities than previously published ones. It is suggested that this calculation of the UVRR intensities can be used to refine molecular force fields in combination with other methods such as isotopic replacement currently in use to refine force constants.
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    Journal of Computational Chemistry 12 (1991), S. 839-843 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The calculated result obtained with MM2(87) for the rotation of the isopropyl group in 3-methyl-1-butene is not in agreement with experimental data. In order to reparametrize the Csp2-Csp3-Csp-Csp3 torsional angle, 3-methyl-1-butene and 1-butene have been studied by molecular mechanics (MM2(87)) and ab initio (MP2/6-31G* and MP3/6-31G*) calculations. The reparametrization of the torsional angle gives calculated results from MM2(87) in agreement with experimental data and ab initio calculations for both 3-methyl-1-butene and 1-butene. The calculated barriers for the rotation of alkyl groups in alkylbenzenes are improved with these new parameters.
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  • 62
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    Journal of Computational Chemistry 12 (1991), S. 880-884 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Vibrational spectra were obtained for the structurally similar compounds 2-methylbutyronitrile and 3-methyl-1-pentyne, and vibrational assignments were made with the aid of normal coordinate calculations. Molecular mechanics calculations were also made, and each compound was shown to exist as a mixture of three conformers, with the most stable conformer being the one with the two methyl groups trans to each other. Results of the calculations are given.
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  • 63
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    Journal of Computational Chemistry 12 (1991), S. 909-912 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite difference methods are becoming very popular for calculating electrostatic fields around molecules. Due to the large amount of computer memory required, grid spacings cannot be made extremely small in relation to the size of the van der Waals radii of the atoms. As a result, the calculations make a rather crude approximation to the molecular surface by defining grid line midpoints discontinuously as either interior or exterior. We present a method which “smoothes” the boundary, but more accurately models the potential from the analytic solution of the discontinuous dielectric problem and improves convergence in electrostatic energy calculations. In addition, a small improvement in convergence rate is observed.
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    Journal of Computational Chemistry 12 (1991), S. 868-871 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An algorithm is presented for calculating the solvent accessible surface area of proteins using a three-dimensional grid. Since it requires only calculations based on single atomic positions, the algorithm is easy to be vectorized. It has been implemented on ST100 and may also be implemented on supercomputers like the CRAY or the CYBER. Results on several proteins indicate that its deviation from that of the Shrake-Rupley algorithm is very small while the computation time is much reduced.
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    Journal of Computational Chemistry 12 (1991), S. 885-890 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The use of principal components as a basis for a graphical procedure to analyze polar tensor data is proposed. Molecular orbital and experimental polar tensor data for all possible sign combinations of the ∂p/∂Qj of CHCl3 and CDCl3 are represented graphically as principal component scores facilitating sign selection for the ∂p/∂Qj. The graphs are particularly useful in analyzing an apparent conflict in ∂p/∂Qj sign choices based on the isotopic invariance criterion and molecular orbital results for the A1 symmetry species of these molecules. The numerical impacts of individual sign ambiguities for the ∂p/∂Qj on the polar tensor data are measured by the variances associated with the principal components. Assuming the ∂p/∂Qj sign sets with indeterminate signs provide replicated results for the polar tensor elements, their errors are estimated and compared with errors obtained previously by propagating intensity uncertainties through the polar tensor equations.
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    Journal of Computational Chemistry 12 (1991), S. 913-917 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A novel method to calculate electrostatic charges is proposed. Partial charges are fitted to reproduce the electrostatic potential of a distributed multipole series without explicitly evaluating electrostatic potentials. The calculation is economical and results in charges reflecting the symmetry properties of charge centers and being independent of molecular orientation.
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    Journal of Computational Chemistry 12 (1991), S. 1129-1133 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: MM2-87 calculations have been performed on C60 (buckminsterfullerence; footballene) and C70 with full energy minimization. The steric energies for C60 and C70 were computed to be 179.9 and 177.9 kcal/mol, respectively. The heats of formation for C60 is found to be more stable than C60. The two bond lengths for C60 were computed to be 1.393 and 1.444 Å. Eight different bond lengths were found for C70 ranging from 1.386 to 1.452 Å. Bond angles, dihedral angles, and moments of inertia are also reported for the compounds.
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    Journal of Computational Chemistry 12 (1991), S. 1065-1076 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The Metropolis Monte Carlo method has been added to the program FANTOM for energy refinement of polypeptides and proteins using a Newton-Raphson minimizer in torsion angle space. With this extension, different strategies for global minimization of the semiempirical energy function ECEPP/2 by various temperature schedules and restriction of conformational space were tested for locating local minimum conformations with low energy of the pentapeptide Met-enkephalin. In total, 1881 conformations below -10 kcal/mol were found. These conformations could be represented by 77 nonidentical conformations which were analysed for their pattern of hydrogen bonds, types of tight turn, pairwise root-mean-square-deviation (rmsd), Zimmermann codes and side chain conformations. All low energy conformations below -10.4 kcal/mol show strong similarity to the global minimum conformation in the backbone structure.
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    Journal of Computational Chemistry 12 (1991) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 12 (1991), S. 1187-1197 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have developed a method for building up accurate electrostatic models for polypeptides, based on a distributed multipole representation of the SCF charge densities for the dipeptides (CH3.CO.NH.CHR.CO.NH.CH3) of the naturally occurring amino acids. It is based on the observation that each peptide residue has almost the correct formal charge (0, ±1). We find that the variations in the backbone charge distributions (excluding proline) with sidechain have a negligible effect on the predicted electrostatic potential around the residue. However changes in the atomic multipoles with the torsion angles (φ, ψ, χ) are more significant, and may need to be taken into account if electrostatic potential close to the residue is required to high accuracy. This type of DMA peptide library provides more accurate, more theoretically based, estimates of the electrostatic potential around polypeptides than current models.
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  • 71
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    Journal of Computational Chemistry 13 (1992), S. 478-491 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An extensive conformational analysis of 3′-azido-3′-deoxythymidine (AZT) was performed at the semiempirical AM1 level with full relaxation of all geometric parameters and careful consideration of furan puckering and the rotational states of the thymine - furan, furan - azide, furan - methylene, and methylene - hydroxyl bonds. The search located 70 conformers, 21 of which have relative energies within 2.5 kcal/mol of the global minimum. Several geometric features, including various forms of hydrogen bonding, within this selected lowenergy subset were examined in terms of their relative contributions to the conformational states of AZT. Hydrogen bonding of thymine's position 2 carbonyl oxygen atom to the hydroxymethyl group (O2—;HO), which until recently has not been mentioned in the literature, is observed in a few low-energy AM1 conformations; however, this form is less favored at the AM1 level than the usually depicted modes involving the thymine moiety with the oxygen atoms of the hydroxyl and furan groups (H6—;OH and H6—Ofur, as observed in the two crystallographically independent structures), as well as that involving the hydroxyl hydrogen and furan oxygen atoms (OH—Ofur, which also has not been mentioned for AZT in the literature until recently). The AM1-optimized geometries agree more closely with nuclear magnetic resonance data than with crystallographic structures and bear little resemblance to molecular mechanics results. The present study shows no evidence of a single dominant conformation or single structural parameter that determines AZT's conformational states. In contrast to our previous analogous study of cGMP, this computational study of AZT does not show strong evidence of a syn conformation with hydrogen bonding involving the base.
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The potential energy surfaces of four cyclic alkanes have been examined using molecular mechanics, semiempirical, and ab initio methods to determine if they produce mutually consistent results and investigate the source of any errors between the methods. The C5 — C8 cyclic alkanes were chosen since these structures present a finite set of conformations and transition-state geometries and are still within the computational time and memory limits of the quantum mechanical approaches. We also examined several conformations of 1,2-dideoxyribose to determine the effect of heteroatoms on the results for the 5-membered ring. The molecular mechanics and ab initio calculations are consistent in the relative energies and geometries determined for the conformers of all ring systems. While the semiempirical calculations yielded geometries consistent with the other methods (except for 5-membered rings), the relative energies often deviated substantially. A decomposition analysis of the semiempirical and molecular mechanics energies revealed that the disparities are mainly due to errors in the 1-center energies of the semiempirical calculations. The 2-center bonding and nonbonding energies followed reasonable trends for the conformers. The core-repulsion function, however, is suspected of producing anomalies. A minimum in the attractive Gaussian of this term at 2.1 Å for H—H interactions partly explains the propensity of the 5-membered rings to optimize to near planarity (decreasing 1,2-diaxial hydrogen distances to 2.3 Å) and the underestimation of the relative energy of the boat structure of cyclohexane.
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    Journal of Computational Chemistry 13 (1992), S. 585-594 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We have derived alternative expressions for computing the energies and forces associated with angle bending and torsional energy terms commonly used in molecular mechanics and molecular dynamics computer programs. Our expressions address the problems of singularities that are intrinsic in popular angle energy functions and that occur from other chain rule derivations of force expressions. Most chain rule derivations of expressions for Cartesian forces due to angle energies make use of relations such as \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial \cos \phi }}\frac{{\partial \cos \phi }}{{\partial x}} $$\end{document} where φ is a bond or torsion angle, E(φ) is energy, and ∂/∂x represents a derivative with respect to some Cartesian coordinate. This expression leads to singularities from the middle term, -1/sin φ, when φ is 0 or π. This is a problem that prevents the use of torsional energy expressions that have phase angles, φ°, other than 0 or π, such as in E(φ) = κ[1 + cos(nφ - phsi;°)]. Our derivations make use of a different, but equivalent, form of the chain rule: \documentclass{article}\pagestyle{empty}\begin{document}$$ \frac{{\partial E}}{{\partial x}} = \frac{{\partial E}}{{\partial \phi }}\frac{{\partial \phi }}{{\partial x}} $$\end{document} This form still possesses singularities for the bond angle forces since the last factor is undefined when φ is 0 or π. However, the alternate form may be used to great advantage for the torsional angle forces where no such problem arises. The new expressions are necessary if one desires the use of torsional energy expressions with general phase angles. Even for energy expressions in common use, i.e., with phase angles of 0 or π, our force expressions are as computationally efficient as the standard ones. The new expressions are applicable to all molecular simulations that employ restrained, or phase-shifted, torsional angle energy expressions.
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  • 74
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    Journal of Computational Chemistry 13 (1992), S. 622-632 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Atomic monopoles are routinely determined through a least squares fit to molecular electrostatic potentials. We report studies of the variation in atomic monopoles with variation in conformation for the zwitterionic polar head group of lecithins, a common class of lipid. The monopole of one atom, a relatively buried carbon, varied by 1.3 electron units between different conformers. “Exterior” atoms, as seen previously, showed smaller changes in charge and smaller estimated standard deviations. The total charge of local groups of atoms varied less than the charge of individual atoms, indicating that shifts in charge occurred mostly between neighboring atoms. This effect might be reflected in the high correlations seen between charges of many neighboring atoms. These correlations, while present for many logical groupings of atoms (such as within methylene and methyl groups), are curiously absent between some bonded atoms. Monopoles were fit to multiple conformations simultaneously to provide a charge set that could optimally reproduce the electrostatic potential of all the conformers as a means of generating monopoles for molecular dynamics simulations or other studies where conformation varies. In some cases, the charges on chemically equivalent atoms (e.g., the hydrogen atoms in a methyl group) were different by more than their estimated error of fit. These studies lead to the suggestion that a minimum error in reported charges is on the order of 10%. All conformations show that the positive charge of the trimethylalkyl ammonium group is carried by the methyl hydrogens; the total charge on the nine hydrogens is over 2 electron units, counterbalanced by negative monopoles on the carbons. The presence of this diffuse cloud of substantial charge would appear to be a disindicator of the use of a “united” atoms approach for these methyl groups. The effects of the charge variation on intermolecular interactions is also examined.
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  • 75
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    Journal of Computational Chemistry 13 (1992) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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  • 76
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    Journal of Computational Chemistry 13 (1992), S. 722-729 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An ab initio study of 3-chloro-, 3-hydroxy-, 3-mercapto-, and 3-amino-propanenitrile and 4-chloro-bu- tanenitrile was carried out at several levels of theory. The calculated stabilities and geometrical trends are interpreted in terms of the effects of intramolecular hydrogen bonds and anomeric interactions, and compared with available experimental data.
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  • 77
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    Journal of Computational Chemistry 13 (1992), S. 772-791 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Quantum mechanical (ab initio and semiempirical) and force field calculations are reported for representative torsion potentials in several tetrahydropyran derivatives. The overall agreement between the various methods is quite good except that the AMBER torsion profiles are sensitive to the choice of atomic point charges. Using electrostatic potential (ESP) derived atomic point charges determined with the STO-3G basis set we find that AMBER is able to match the best quantum mechanical results quite well. However, when the point charges are derived using the 6-31G* basis set we find that scaling the intramolecular electrostatic nonbond interactions is necessary. AM1 does not work very well for these compounds when compared to the ab initio methods and, therefore, should only be used in cases when ab initio calculations would be prohibitive. Based upon our results we feel that any force field that makes use of 6-31G* ESP derived atomic point charges will need to scale intramolecular interactions. Implications of scaling intramolecular interactions to the development of force fields based on 6-31G* ESP derived atomic point charges are discussed. © 1992 by John Wiley & Sons, Inc.
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  • 78
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    Journal of Computational Chemistry 13 (1992), S. 842-850 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The molecular electrostatic potential (MEP) distribution of anisole, chlorobenzene, and fluorobenzene obtained from STO-3G, 3-21G, and 6-31G* basis set ab initio and MNDO and AM1 semiempirical wave functions is investigated to explain the differences among the MEP features obtained for polychlorodibenzo-p-dioxins. The main topological features as well as the absoltue and relative minima location obtained from ab initio calculations are independent from the choice of the basis set. MNDO calculations are in good agreement with the ab initio ones in the case of anisole and fluorobenzene, while they incorrectly describe the MEP of chlorobenzene. The AM1 fails to localize the absolute minimum of fluorobenzene and does not find the minimum above the chlorobenzene chlorine atom. The poor agreement of both semiempirical methods with ab initio for any kind of chlorinated compounds is confirmed by results obtained for chloreothylene and chloroethane. We hypothesize that the main problem concerning these methods is that they freeze a too large amount of electrons in the atomic core of elements belonging to the second row, which makes for a wrong description of the core-valence electron interactions. Results obtained by modifying the AM1 parameters related to these interactions confirm our hypothesis. © 1992 by John Wiley & Sons, Inc.
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  • 79
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    Journal of Computational Chemistry 13 (1992), S. 874-882 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A numerical method for solving the approximate Schrödinger equation (SE) for a single internal motion is presented. In the SE the reduced moment of inertia I(φ) and potential energy V(φ) are expressed as functions of the torsional angle φ. Molecular examples include ethane, chloroethane, and 1,2-dichloroethane for which I(φ) and V(φ) have been derived from the HF/6-31G* optimized geometries and energies at φ increments of 30°. The resulting potential energy curves, energy levels, and wave functions are shown graphically. The calculated fundamental torsional frequencies are found to fall within 10 cm-1 of the experimental values. Approximations for the off-diagonal energy matrix elements, and numerical accuracy of torsional energy levels, are shown to be satisfactory. Attention is called to the computer programs developed for this work and their applications to torsional studies in relevant areas of spectroscopy, thermodynamics, and reaction rates. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 912-918 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The electronegativities () of some 36 atoms/groups (including some 6 ionic ones) X are calculated from the atomic charges in the corresponding methyl species CH3X that were obtained by applying Bader's theory of atoms in molecules. The numerical values of the for the various groups studied are reasonable and correlate linearly with the two existing experimental scales for group electronegativity, Inamoto's i scale and the 1JCC (ortho-ipso) coupling constants in the monosubstituted benzenes, to satisfactory extents. The relations between the values and some “critical properties” of the various CH3X molecules considered are also studied. It is suggested that in a molecule PX, rP/R where rP is the distance of Bader's critical point on the bond PX of length R from the atom P or the binding atom of the group P can be a very good measure of the electronegativity of the atom/group X. © 1992 by John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 13 (1992), S. 565-569 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Modifications to the distance geometry algorithm as embodied in the program DGEOM have been made to improve sampling capabilities. Specifically, torsion angle sampling replaces distance sampling for 1,4 atomic relationships and correlated distance sampling is disabled. The effects of these modifications are illustrated by comparing the different sets of conformations produced for butane. In addition, these changes are shown to increase the conformational sampling of two medium-sized rings, cycloheptadecane and caprylolactam. The current results for these molecules are compared to those of other conformational searching methods.
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    Journal of Computational Chemistry 13 (1992), S. 595-601 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A two-component Kramers' restricted Hartree-Fock method (KRHF) has been developed for the polyatomic molecules with closed shell configurations. The present KRHF program utilizes the relativistic effective core potentials with spin-orbit operators at the Hartree-Fock (HF) level and produces molecular spinors obeying the double group symmetry. The KRHF program enables the variational calculation of spin-orbit interactions at the HF level. KRHF calculations have been performed for the HX, X2, XY(X, Y = I, Br), and CH3I molecules. It is demonstrated that the orbital energies from KRHF calculations are useful for the interpretation of spin-orbit splittings in photoelectron spectra. In all molecules studied, bond lengths are only slightly expanded, harmonic vibrational frequencies are reduced, and bond energies are significantly decreased by the spin-orbit interactions.
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    Journal of Computational Chemistry 13 (1992), S. 614-621 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A computational chemistry study of the artificial redox enzyme synthesized by covalently attaching flavin to cyclodextrins explains some of its properties. Calculations indicate that the flavin moiety covalently attached to cyclodextrin is not within the cavity of cyclodextrin. This result is consistent with the UV-vis spectrum of the artificial enzyme. The calculations also indicate hydrogen bonds formed between the carbonyl groups of the catalytic functionality and the hydroxyl groups of cyclodextrin play a role in their most stable conformation. This explains the observed overall stability of these artificial enzymes compared to riboflavin. Electrostatic energies and solvation energies play a major role in the stability of the hosts and the orientation of guests included within the artificial enzymes. The rates of oxidation of various thiols catalyzed by the artificial enzyme can be explained by the relative distances between the sulfur atom of the substrates and C(4a) of the flavin moiety.
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    Journal of Computational Chemistry 13 (1992), S. 651-656 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The polynomial path is introduced for the calculation of liquid state free energies. The well-characterized SPC, TIP4P, and MCY water models were used to demonstrate its efficiency, as well as its range of applicability in conjunction with Monte Carlo computer simulations using thermodynamic integration based on Gaussian quadratures. The technique employed is compared with the slow-growth method (another variant of thermodynamic integration), the perturbation method, and the use of the grand-canonical ensemble.
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    Journal of Computational Chemistry 13 (1992), S. 675-680 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The free energy gradient or Hessian of a molecule interacting with a liquid represented by a dielectric continuum is derived in the self-consistent reaction field formalism. An ellipsoidal approximation of the cavity is proposed with an algorithm to automatically define the ellipsoid from the nuclear coordinates of the atoms. With this approximation, geometry optimization of the solvated molecule becomes very fast. This method has been implemented in some standard ab initio or semiempirical computational codes. As a first test of the method, full geometry optimization of formamide in a high dielectric constant medium reveals that the CPU time needed for one optimization cycle is less than 3% longer for a solvated species than for the corresponding free molecule.
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    Journal of Computational Chemistry 13 (1992), S. 718-721 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The geometry of acryloyl fluoride was optimized completely at the RHF/6-31G* level of theory at 10 points on the theoretical potential energy curve for internal rotation. The energies obtained were used to determine a six term cosine expansion of the torsional potential energy function. This function was then refined using the experimental torsional transition frequencies in the s-trans and s-cis wells in conjunction with the geometrical parameters optimized at the RHF/6-31G* level. The effective potential function obtained is compared with previous results. The necessity of accounting for relaxation of the geometry upon internal rotation is stressed. © 1992 by John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 13 (1992), S. 768-771 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Finite-difference Poisson-Boltzmann (FDPB) methods allow a fast and accurate calculations of the reaction field (charge-solvent) energies for molecular systems. Unfortunately, the energy in the FDPB calculations includes the self-energies and the finite-difference approximation to the Coulombic energies as well as the reaction field energy. A second finite-difference calculation, in a uniform dielectric, is therefore necesssary to eliminate these contributions. In this article we describe a rapid and accurate method to calculate the self energy and finite-difference Coulombic energies in a uniform dielectric thus eliminating the need for a second finite-difference calculation. The computational savings for this method range from a factor of 4 for a typical protein to a factor of 103 for small molecules. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 793-798 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Simulation data from an off-lattice polymer model are compared with data from the Rouse model. The polymer model is built of sequentially connected rigid monomer units that represent the amide planes of a protein backbone. The time propagation of the dynamics of the polymer model is performed by a Monte Carlo method. The elementary Monte Carlo steps correspond to local confomational changes in a window of three consecutive monomer units. The time autocorrelation functions of end-to-end distances from segments within the linear chain molecule are considered in detail. Both models exhibit a stretched exponential decay pattern. A comparison of the data from the Rouse model and the computer simulation provide an estimate of the time unit of 15 ps for a full scan of the algorithm for local conformational changes along the chain. With a conservative estimate of the parameters governing the Rouse model this time unit is four orders of magnitude longer than the elementary time step of a conventional computer simulation of polymer dynamics based upon the classical equations of motion for all atoms. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 838-841 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A bond and group equivalent scheme that allows the calculation of heats of formation for carboxylic acids and esters from ab initio 6-31G* energies has been developed. For a group of 16 compounds, the rms error for the calculated heats of formation was 0.64 kcal/mol. Heats of formation have been predicted for an additional seven compounds for which the experimental values are either unknown or suspect. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 830-837 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A semi-empirical NDDO method, generalized from a similar scheme at the CNDO/2 level developed previously, is presented to treat very large molecules. The extended molecular system is divided into a relatively small subsystem where substantial chemical changes take place and an environment remaining more-or-less unperturbed during the process. Expanding the wave function on an atomic hybrid basis an SCF procedure is performed for the subsystem in the field of the iteratively determined electronic distribution of the environment. A computer program has been written for the IBM RISC System/6000 530 computer and several test calculations were done for a variety of large classical molecules, like substituted aliphatic hydrocarbons, water oligomers, and a heptapeptide. Protonation energies, proton transfer potential curves, rotational barriers, atomic net charges, and HOMO and LUMO energies, as computed by the exact version of the NDDO method, are fairly well reproduced by our approximation if the subsystem is appropriately defined. © 1992 by John Wiley & Sons, Inc.
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  • 91
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    Journal of Computational Chemistry 14 (1993) 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 14 (1993), S. 237-245 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The affinity of a ligand for a receptor is usually expressed in terms of the dissociation constant (Ki) of the drug-receptor complex, conveniently measured by the inhibition of radioligand binding. However, a ligand can be an antagonist, a partial agonist, or a full agonist, a property largely independent of its receptor affinity. This property can be quantitated as intrinsic activity (1A), which can range from 0 for a full antagonist to 1 for a full agonist. Although quantitative structure-activity relationship (QSAR) methods have been applied to the prediction of receptor affinity with considerable success, the prediction of IA, even qualitatively, has rarely been attempted. Because most traditional QSAR methods are limited to congeneric series, and there are often major structural differences between agonists and antagonists, this lack of success in predicting IA is understandable. To overcome this limitation, we used the method of comparative molecular field analysis (CoMFA), which, unlike traditional Hansch analysis, permits the inclusion of structurally dissimilar compounds in a single QSAR model. A structurally diverse set of 5-hydroxytryptamine1A (5-HT1A) receptor ligands, with literature IA data (determined by the inhibition of 5-HT sensitive forskolin-stimulated adenylate cyclase), was used to develop a 3-D QSAR model correlating intrinsic activity with molecular structure properties of 5HT1A receptor ligands. This CoMFA model had a crossvalidated r2 of 0.481, five components and final conventional r2 of 0.943. The receptor model suggests that agonist and antagonist ligands can share parts of a common binding site on the receptor, with a primary agonist binding region that is also occupied by antagonists and a secondary binding site accommodating the excess bulk present in the sidechains of many antagonists and partial agonists. The CoMFA steric field graph clearly shows that agonists tend to be “flatter” (more coplanar) than antagonists, consistent with the difference between the 5-HT1A agonist and antagonist pharmacophores proposed by Hibert and coworkers. The CoMFA electrostatic field graph suggests that, in the region surrounding the essential protonated aliphatic amino group, the positive molecular electrostatic potential may be weaker in antagonists as compared to agonists. Together, the steric and electrostatic maps suggest that in the secondary binding site region increased hydrophobic binding may enhance antagonist activity. These results demonstrate that CoMFA is capable of generating a statistically crossvalidated 3-D QSAR model that can successfully distinguish between agonist and antagonist 5-HT1A ligands. To the best of our knowledge, this is the first time this or any other QSAR method has been successfully applied to the correlation of structure with IA rather than potency or affinity. The analysis has suggested various structural features associated with agonist and antagonist behaviors of 5-HT1A ligands and thus should assist in the future design of drugs that act via 5-HT1A receptors. © 1993 John Wiley & Sons, Inc.
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  • 93
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    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Four semiempirical methods (AM1, MNDO, PM3, and MINDO/3) are used to calculate the deformation angles of [n]paracyclophanes and their Dewar benzene isomers for n = 3… 10. The results obtained by all these methods are in good agreement with data from X-ray studies. We have determined the strain energies that, in both series of compounds, are due to two components: (1) the strain energy of deformation of the cycle (aromatic or Dewar Benzene skeletons) and (2) the strain energy of the oligomethylene chain. In [6]paracyclophane, the strain energy [SEring(MNDO) ≍ 32.9 kcal/mol] almost compensates the resonance energy (Eresonance ≈ 36 kcal/mol) so that its chemical properties are closer to alkenes than to benzenic compounds. To better reproduce the enthalpy of the valence isomerization [n]Dewar bezene → [n]paracyclophane, which is poorly calculated with these methods, a correction is proposed and the reaction enthalpy of [6]paracyclophane is estimated to be about ΔHr ≈ 15 ± 15 kcal/mol. It is found that MNDO and MINDO/3 need the smallest corrections, but MNDO leads to better geometries than MINDO/3. In conclusion, MNDO seems to be the best technique for further studies of these compounds. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1089-1097 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Our recently proposed scheme for including aqueous solvation free energies in parameterized NDDO SCF models is extended to the Parameterized Model 3 semiempirical Hamiltonian. The solvation model takes accurate account of the hydrophobic effect for hydrocarbons, as well as electric polarization of the solvent, the free energy of cavitation, and dispersion interactions. Eight heteroatoms are included (along with H and C), and the new model is parameterized accurately for the water molecule itself, which allows meaningful treatments of specifically hydrogen bonded water molecules. The unphysical partial charges on nitrogen atoms predicted by the Parameterized Model 3 Hamiltonian limit the accuracy of the predicted solvation energies for some compounds containing nitrogen, but the model may be very useful for other systems, especially those for which PM3 is preferred over AM1 for the solute properties of the particular system under study. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1119-1124 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The particular expression that relates the first Mori coefficients of the solvent particles with the solute particles as a function of their masses m1 and m2 is generalized to the case of the solute particle also having a different volume. The resulting density relationship, in terms of the mass factor M(m2) and coupling constants CD, is also valid for the second Mori coefficients and for two- and three-dimensional system. © 1992 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 13 (1992), S. 1170-1170 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
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    Journal of Computational Chemistry 13 (1992), S. 1216-1233 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A distribution of conformations of heptaalanine is obtained using a new Monte Carlo (MC) method that grows the chain atom by atom. Resulting configurations are energy minimized and a detailed analysis is performed of the minimum-energy conformers using a method of classification that partitions φψ space. The MC-generated configurations are compared with those generated from high-temperature molecular dynamics (MD) simulations. It is found that the new method generates a wide distribution of low-energy conformers at least 10 times more quickly than the MD. An analysis of the generated energy minima demonstrates that they can be divided into clusters in the space defined by the five pairs of φ - ψ angles of the inner residues. The space occupied by the minima populating each cluster is restricted. © 1992 by John Wiley & Sons, Inc.
    Additional Material: 10 Ill.
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  • 98
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 30-36 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: We consider the tree search problem for the recurrence relation that appears in the evaluation of molecular integrals over Cartesian Gaussian basis functions. A systematic way of performing tree search is shown. By applying the result of tree searching to the LRL2 method of Lindh, Ryu, and Liu (LRL) (J. Chem. Phys., 95, 5889 1991), which is an auxiliary function-based method, we obtain significant reductions of the floating point operations (FLOPS) counts in the K4 region. The resulting FLOPS counts in the K4 region are comparable up to [dd|dd] angular momentum cases to the LRL1 method of LRL, currently the method requiring least FLOPS for [dd|dd] and higher angular momentum basis functions. For [ff|ff], [gg|gg], [hh|hh], and [ii|ii] cases, the required FLOPS are 24, 40, 51, and 59%, respectively, less than the LRL1 method in the K4 region. These are the best FLOPS counts available in the literature for high angular momentum cases. Also, there will be no overhead in either the K2 or K0 region in implementing the present scheme. This should lead to more efficient codes of integral evaluations for higher angular momentum cases than any other existing codes. © 1993 John Wiley & Sons, Inc.
    Additional Material: 8 Ill.
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  • 99
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 19-29 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: A method is proposed to perform computer simulations of protein dynamics in the long-time regime. The method is based upon a Monte Carlo technique. The only molecular degrees of freedom considered are bond rotations. All other degrees of freedom including the amide plane torsions are kept rigid. These constraints approximately account for all interactions related to chemical bonding. An individual Monte Carlo step adopts the Go and Scheraga algorithm where local conformational changes in a small window of the protein backbone are performed. By using correlated rotations, the conformation of residues outside the window remains invariant. To test the reliability of the method, the nonbonded interactions are turned off in the present application. Exact statistical averages are compared with values obtained from data of computer simulation involving 2 × 106 scans of the window along the protein backbone. Time is related to the number of scans of the window along the protein backbone. End-to-end distance autocorrelation functions decay to 1/e of its initial value in about 103-104 scans of the window algorithm. Time decay follows a stretched exponential Kohlrausch decay law. © 1993 John Wiley & Sons, Inc.
    Additional Material: 7 Ill.
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  • 100
    Electronic Resource
    Electronic Resource
    New York, NY [u.a.] : Wiley-Blackwell
    Journal of Computational Chemistry 14 (1993), S. 45-53 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: The antitumor drug cis-diamminedichloroplatinum(II) (cisplatin) binds preferentially to GpG and ApG sequences of DNA, forming N7,N7 intrastrand chelates. Molecular modeling of the intrastrand adducts have been handicapped, so far, by the lack of force-field data describing the Pt-guanine and Pt-adenine binding. We used ab initio calculations with relativistic pseudopotentials to evaluate three important parameters for the platinum-adenine model complex [Pt(NH3)3(Ade)]2+: (1) the force constant for the Pt—N7 bond bending out of the adenine plane; (2) the energy profile for the torsion about Pt—N7; (3) a set of fractional atomic charges that reproduce the ab initio potential for a number of space points placed around the adduct. A population analysis and comparative study on the tetrammine complex [Pt(NH3)4]2+ have shown that for platinum adenine is a better σ-donor than NH3, but its capacity as a π-acceptor is weak. © 1993 John Wiley & Sons, Inc.
    Additional Material: 6 Ill.
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