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  • 1990-1994  (1,001)
  • 1980-1984  (797)
  • Biochemistry  (1,150)
  • Gas chromatography
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  • 1
    Electronic Resource
    Electronic Resource
    Springer
    Comparative clinical pathology 4 (1994), S. 146-151 
    ISSN: 1433-2981
    Keywords: Biochemistry ; Development ; Haematology ; Koala
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Haematology and biochemistry of captive pouch young and back young koalas from 165 days to one year old were studied. Distinct changes with age were observed. Packed cell volume, haemoglobin, erythrocyte count, MCV and total plasma protein where lowest in the youngest animals less than 180 days old. Reticulocytes were highest in this age group. Haematological values differed from those of adult animals. Lymphocytosis occurred, especially between 210–330 days of age. Intense erythropoiesis was indicated by reticulocytosis and the presence of erythrocyte granular inclusions, anisocytosis and poikilocytosis on blood films, particularly up to 330 days of age. Microcytosis present on blood films throughout the study period could not be explained by iron deficiency.
    Type of Medium: Electronic Resource
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  • 2
    ISSN: 1432-2072
    Keywords: Risperidone ; Antipsychotics ; 5-HT2 antagonism ; D2 antagonism ; Pharmacology ; Receptor binding ; Biochemistry ; Review
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract This review reports on the pharmacodynamics of the new antipsychotic risperidone. The primary action of risperidone is serotonin 5-HT2 receptor blockade as shown by displacement of radioligand binding (Ki: 0.16 nM), activity on isolated tissues (EC50:0.5 nM), and antagonism of peripherally (ED50: 0.0011 mg/kg) and centrally (ED50:0.014 mg/kg) acting 5-HT2 receptor agonists in rats. Risperidone is at least as potent as the specific 5-HT2 receptor antagonist ritanserin in these tests. Risperidone is also a potent dopamine D2 receptor antagonist as indicated by displacement of radioligand binding (Ki: 1.4 nM), activity in isolated striatal slices (IC50: 0.89 nM), and antagonism of peripherally (ED50: 0.0057 mg/kg in dogs) and centrally acting D2 receptor agonists (ED50: 0.056–0.15 mg/kg in rats). Risperidone shows all effects common to D2 antagonists, including enhancement of prolactin release. However, some central effects such as catalepsy and blockade of motor activity occur at high doses only. Risperidone is 4–10 times less potent than haloperidol as a central D2 antagonist in rats and it differs from haloperidol by the following characteristics: predominant 5-HT2 antagonism; LSD antagonism; effects on sleep; smooth dose-response curves for D2 antagonism; synergism of combined 5-HT2/D2 antagonism; pronounced effects on amphetamine-induced oxygen consumption; increased social interaction; and pronounced effects on dopamine (DA) turnover. Risperidone displays similar activity at pre- and postsynaptic D2 receptors and at D2 receptors from various rat brain regions. The binding affinity for D4 and D3 receptors is 5 and 9 times weaker, respectively, than for D2 receptors; interaction with D1 receptors occurs only at very high concentrations. The pharmacological profile of risperidone includes interaction with histamine H1 and α-adrenergic receptors but the compound is devoid of significant interaction with cholinergic and a variety of other types of receptors. Risperidone has excellent oral activity, a rapid onset, and a 24-h duration of action. Its major metabolite, 9-hydroxyrisperidone, closely mimics risperidone in pharmacodynamics. Risperidone can be characterized as a potent D2 antagonist with predominant 5HT2 antagonistic activity and optimal pharmacokinetic properties.
    Type of Medium: Electronic Resource
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  • 3
    Electronic Resource
    Electronic Resource
    Springer
    Amino acids 6 (1994), S. 205-211 
    ISSN: 1438-2199
    Keywords: Amino acids ; Amino acid enantiomers ; Chiral analysis ; Chirasil-L-Val ; Gas chromatography ; Mass spectrometry ; Selected ion monitoring ; D-Serine ; D-Alanine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Summary The relative amounts of free D-amino acids (D-AA) in the urine of seven healthy volunteers (age 27 to 49 years) were determined using chiral phase (Chirasil-L-Val) capillary gas chromatography in conjunction with selected ion monitoring mass spectrometry. The absolute amounts of free D-AA were determined by pre-column derivatization of the amino acids witho-phthaldialdehyde andN-isobutyryl-L-cysteine followed by high-performance liquid chromatographic separation and fluorescence detection of the isoindol derivatives formed. The following most abundant D-AA were found (highest and lowest absolute and relative amounts): D-Ser (379.8 — 30.1µMol/L; 56.5 — 19.0%), D-Ala (53.8 — 7.6µMol/L; 19.6 — 5.7%), D-Thr (5.8 — 0.25µMol/L; 3.4 — 1.0%), D-Val (3.7 — 0µMol/L; 4.2 — 0%), and D-Phe (3.5 — 0.35µMol/L; 4.8 — 1.4%).
    Type of Medium: Electronic Resource
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  • 4
    ISSN: 1432-1459
    Keywords: PGAM deficiency ; Myopathy ; Biochemistry ; Muscle culture ; 31P-MR spectroscopy
    Source: Springer Online Journal Archives 1860-2000
    Topics: Medicine
    Notes: Abstract Muscle phosphoglycerate mutase (PGAM) deficiency has been so far identified in only six patients, five of these being African Americans. We report the results of clinical, morphological, biochemical, muscle culture and31P-MR spectroscopy studies in the first Caucasian patient with muscle PGAM deficiency. A 23-year-old man had a 10-year history of cramps after physical exertion with one episode of pigmenturia. Neurological examination and EMG study were normal. ECG and echocardiography revealed hypertrophy of the interventricular septum and slight dilatation of the left chambers of the heart. Muscle biopsy revealed increased glycogen content and some accumulation of mitochondria. Muscle PGAM activity was markedly decreased (6.5% and 9.7% of control value in two different biopsies). Citrate synthase and other mitochondrial respiratory chain enzyme activities were much higher than normal. In contrast to the marked decrease of PGAM activity observed in muscle biopsy, total enzyme activity in the patient's aneural muscle culture was normal, being represented exclusively by BB isoenzyme. The deficiency of PGAM-MM isoenzyme was reproduced in the patient's innervated muscle culture. Muscle31P-MR spectroscopy showed accumulation of phosphomonoesters only on fast “glycolytic” exercise. On “aerobic” exercise, Vmax, calculated from the work-energy cost transfer function, showed an increase consistent with the morphological and biochemical evidence of mitochondrial proliferation. This might represent a sort of compensatory aerobic effort in an attempt to restore muscle power.
    Type of Medium: Electronic Resource
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  • 5
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 38 (1994), S. 689-693 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Enantioselectivity ; GC-MS ; GC-GC-MS ; Pinus peuce ; Monoterpenes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Needles of the Macedonian Pine,Pinus peuce Griseb., a conifer growing in the Balkan mountains, were extracted by a Likens-Nickerson simultaneous distillation-solvent extraction device. The components of this essential oil were identified by the retention times obtained on two columns differing in polarity and by GC-MS. Because of the complex nature of such plant extracts, a multidimensional GC method for enantiomer analysis, using a non-chiral pre-column and a chiral main column has been developed. The enantiomeric ratios of five monoterpene hydrocarbons were estimated by GC-GC and GC-GC-MS.
    Type of Medium: Electronic Resource
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  • 6
    ISSN: 1612-1112
    Keywords: Column liquid chromatography ; Gas chromatography ; Particle beam MS detection ; Polycyclic aromatic metabolites ; Biodegradation in water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Two liquid chromatography-particle beam mass spectrometry (LC-PBMS) systems have been used for analysis of polycyclic aromatic hydrocarbon metabolites in water samples from a biological decomposition model experiment. The results were compared with those obtained by classical gas chromatography-mass spectrometry. Evaluation of spectral data indicated the presence of six main metabolites; 1H,3H-naphtho [1,8-cd]pyran-1,3-dione, 1-(hydroxymethyl)naphthalene, and 1,2-acenaphthenedione were identified by use of standard substances and spiking experiments. Enrichment of the investigated water samples with online pre-column (C18) concentration, freeze-drying, and solvent extraction led to similar results with only slight differences. The application of microbore separation columns proved to be a promising tool in particle beam LC-MS measurements.
    Type of Medium: Electronic Resource
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  • 7
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Porous polymer stationary phase ; Selectivity studies
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The behaviour of GC columns packed with the copolymer of methacrylic ester of p,p'-dihydroxydiphenylpropane diglicydyl ether and divinylbenzene was studied. Selectivity studies were made for three polymer samples of different molar ratio of monomers. To determine the selectivities of these copolymers retention indices for seven test compounds in comparison to those obtained on Porapak Q are calculated. Additionally, the efficiency of porous polymer purification was studied by a SFE-GC-MS technique.
    Type of Medium: Electronic Resource
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  • 8
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 39 (1994), S. 265-270 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Triglycerides ; Packed vs. capillary columns ; Milk fat
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Quantitative gas chromatography of triglycerides in conjunction with established triglyceride formulae can be used to determine various milk fat parameters. Since the evaluation of, for example, iodine number or content of non-milk fats (foreign fats) in milk fat requires only the separation of triglycerides by carbon number and since repeatabilities, especially of the highboiling triglycerides, have been less acceptable with capillary columns in the past, packed columns have been used exclusively. There is, however, an increasing demand for the use of capillary instead of packed columns and to that end the present investigation has been carried out. To achieve a suitable resolution, with this particularly exacting high-temperature application, a short 5 m capillary column of extreme temperature stability has been used. As well as modification of various analytical conditions different injection techniques have been investigated. On-column, PTV and split injection were compared with regard to repeatability. The cold-on-column injection technique was found to produce the best results, being comparable to the excellent precision of a packed column. Thus, a method is now available by means of which the determination of milk fat parameters by the triglyceride formulae, such as the amount of foreign fats in milk fat, can now be carried out with a standardized capillary column.
    Type of Medium: Electronic Resource
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  • 9
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Liquid modified adsorption capillary columns ; Polar compound analysis ; Aqueous solution analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The preparation of graphite layer open tubular (GLOT) columns is described together with their application to the analysis of priority pollutants and polar compounds such as alcohols, free carboxylic acids, aliphatic amines and phenols at the sub-nanogram level. A specific application of GLOT columns is for the direct analysis of aqueous solutions avoiding solvent extraction procedures. Several chromatograms of critical separations are reported together with calibration curves. A study of the reproducibility of column preparation is reported in terms of the standard deviation of the capacity ratio and of the minimum HETP obtained.
    Type of Medium: Electronic Resource
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  • 10
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 38 (1994), S. 679-688 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Stationary phases ; Phase constants ; Explanatory coefficients
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Explanatory phase coefficients according to Abraham et al. are calculated from McReynolds index differences and the phase constant B. The retention expression (log Vg)−A=BI/100 connects specific retention volumes and retention indices. McReynolds phase constants and Abrahams explanatory coefficients can be used with similar accuracy for the prediction of relative retention data and for the characterization of stationary phases in gas chromatography. The application of polarity constants for the characterization of stationary phases is discussed.
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  • 11
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 38 (1994), S. 304-312 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Electron capture detector ; Theoretical model of ECD
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This paper reports a theoretical model of the ECD detector. The model presented here can be used to examine the influence of pulse parameters on the current and signal characteristics of the detector. On the basis of this model it was found that a space charge is created in the detector when it is supplied with pulse voltage. Due to the electric potential generated by the space charge, in the time between the pulses the electrons and negative ions move towards the detector electrodes. The ionization current of the detector is the sum of the electron current flowing to the anode under the influence of the supplied pulse voltage and the current flowing under the space charge potential in the time between the pulses. It was also found that the detector signal is the sum of the differences between those two currents caused by introducing the sample molecules to the detector. The model was tested for a detector with different electrode configurations which worked at temperature of 300 K or 573 K and which was supplied with nitrogen or Ar+10% CH4 as the carrier gas.
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  • 12
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Curie-point pyrolysis ; Multivariate analysis ; Sodium dodecylbenzene sulfonate
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Multivariate analysis was used to develop a viable method for determination of sodium dodecylbenzene sulfonate (DBS) by Curie-point pyrolysis gas chromatography. The pyrograms obtained were normalized against a maximum peak area and peak height. Normalized values were used for Quantification IV, which is one of the multivariate analysis methods, to select useful values initially. Then cluster analysis was carried out using both the selected values and their deviations. This method corresponds to qualitative analysis and indicates which data-base is similar to the sample. On the basis of this data-base, calibration data-bases are chosen. Principal component analysis (PCA) was performed using the calibration data-base and a set of sample data simultaneously. The principal component scores and contribution coefficients obtained were used to construct a calibration curve from which the DBS content of the sample was calculated. The results are in fair agreement with theoretical values.
    Type of Medium: Electronic Resource
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  • 13
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Nitrogen phosphorus detection ; Atrazine and simazine ; Freeze-dried water analysis ; ELISA
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The determination of atrazine in freeze-dried water samples containing simazine, 0.6% glycine as stabilizer and other pesticides has been compared using three different techniques: (i) direct rapid-magnetic particlebased ELISA, (ii) dichloromethane liquid-liquid extraction (LLE) and Florisil column clean-up prior to ELISA determination and (iii) LLE, Florisil column clean-up and gas chroamtography with nitrogen phosphorus detection (GC-NPD). The methodology developed in this paper has shown the advantages of the introduction of a clean-up step prior to ELISA determination and its correlation with GC-NPD determinations. Atrazine could be determined at levels between 0.1 to 5 μg l−1 in water smaples using the different methods described in this paper. The crossreactivity problems found in the ELISA test associated with the presence of simazine are also discussed.
    Type of Medium: Electronic Resource
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  • 14
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 39 (1994), S. 210-215 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Correlation chromatography ; Concentration methods ; Polymer dynamic head-space sampling
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Gas chromatography has been used to study the kinetics of evolution of volatiles from polypropylene samples (at 70°C). Correlation chromatography (CC) and the trapping of volatiles on Tenax sorbents and activated charcoal were employed to improve the detector signal. As a reference, the kinetics of gas evolution was studied by making a series of direct single injections of polymer head-space gas on a GC column. The results of trapping differed from those obtained by single injection. However, the data from single injections and CC were in good agreement. The CC method was found to offer far more operator convenience for dynamic head-space analysis than sample trapping, being less subject to operator errors.
    Type of Medium: Electronic Resource
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  • 15
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 39 (1994), S. 294-298 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Preconcentration ; Thermal modulator ; Cross-correlation ; Trace analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The inside wall of an uncoated polyethylene capillary traps organic substances from a water sample pumped through it by a nitrogen gas stream. Heating the capillary in a chromatographic oven slowly releases the trapped organic substances from the wall. Nitrogen carrier gas transports sample substances released through a thermal desorption modulator and onto a chromatographic column. Pulsing the temperature of the modulator modulates the concentrations of sample components as they enter the column. Computing the cross correlation of the detector output signal against the applied modulation signal generates the chromatogram. Detection limits below 1 ppb are possible using a flame ionization detector. No sample pretreatment or cold trap is required.
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  • 16
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 39 (1994), S. 363-365 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Light hydrocarbons ; Stabilized crude oil ; Capillary guard column
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This paper reports a quick, and simple method for quantitative determination of C2 to C6 hydrocarbons in stabilized crude oil without using a back flush system. A mixture of crude oil and internal standard is injected into a GC equipped with a 6 meter length of fused silica capillary as a guard column. The light hydrocarbons are separated individually up to the last peak of the hexane group with the heavier components trapped in the guard column. The total analysis time for each sample is 15 minutes. The base line is table for up to 15 consecutive analyses. The guard column and the injector port are then reconditioned by simply heating them for one hour at 300 °C.
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  • 17
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Retention/structure and retention/temperature ; relationships ; Experimental design ; Enthalpy-entropy compensation ; para-Hydroxy benzoic esters
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary An experimental design has been used to study the effect of column temperature on the gas chromatographic retention of eightpara-hydroxy benzoic esters. A rapid procedure has been developed to reduce the number of experiments compared with traditional methods. Capacity factors were determined and the enthalpy and entropy of transfer from the mobile phase to the stationary phase, ΔHo and ΔSo, respectively, were calculated using the linear Van't Hoff equation (dependence of ln k′ on 1/T). A retention prediction system (RPS) for these compounds in GC was investigated. The molecular connectivity index was used to describe the quantitative structure relationships. Enthalpy — entropy compensation revealed that the mechanism was similar for all the compounds studied.
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  • 18
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Priority pollutants ; EPA methods ; Unleaded gasoline ; Volatile organochlorine compounds
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The complete separation of the sixty volatile organochlorine (VOC) priority pollutants has been achieved by coupling two different liquid-modified adsorption chromatography columns. Two temperature programs were used to obtain the complete separation in a relatively short analysis time. Detection was by FID alone
    Type of Medium: Electronic Resource
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  • 19
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 38 (1994), S. 93-97 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Retention index ; Adsorption effects ; Terpene alcohols ; Fused-silica capillary columns
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Retention indices of 6 selected hydroxy compounds (aliphatic and bicyclic alcohols, phenols) were determined on 2 HP-5 fused-silica, capillary columns with different film thicknesses (0.11 μm and 0.33 μm) at 8 different oven temperatures between 80 and 150°C. For some substances the I-T plot was found to show a minimum which cannot be explained by the common retention-index temperature-dependence in gas-liquid chromatography. This result is discussed in terms of adsorption at the liquid-solid interface of the capillary column.
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  • 20
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Stationary Phase and solute polarity ; Molecular structural coefficients ; Retention index ; Takács equation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Molecular structural coefficients, Sc, for one hundred solutes have been calculated by means of the Takács equation using retention data obtained with over fifty stationary phases, SP. Employing data of seven SP's (characterized in our laboratories) it was found that the variation of Sc with column temperature was linear for most solutes. With data of n-decane and the ten McReynolds probes on up to fifty SP's of polarity less than RP=72, at 120°C, it was found that the Sc of n-decane and cis-hydrindane decreased slightly with increasing SP polarity, while the Sc of non-alkanes remained constant or increased very little as the SP polarity increased. The points for n-decane fit well to a second order polynomial. Again using a temperature of 120°C, the increments of Sc for solutes belonging to an homologous series were correlated with the polarity of SP's. Reasonably straight lines were obtained for all the chemical functions studied, Sc increasing with increasing SP polarity.
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  • 21
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Stationary phase characterization ; Principal component analysis
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary In this study, several new stationary phases were characterized by principal component analysis. Fourteen new stationary phases, including substituted phenyl and oligoethyleneoxide functionalities on polysiloxane polymers, were tested and compared to three well known stationary phases. The main features of these phases were studied using a series of test solutes of varying chemical characteristics representing the data set for principal component analysis. Two principal compounds were found to account for 99.20% of the variance (the first accounted for 94.96% and the second for 4.24%). The data were represented as a two-dimensional map for visual representation of the characteristics of these stationary phases. The first principal component represented a selectivity based on polarity (r2=0.998), while the second showed Lewis acid-base characteristics of the phases. Polarizable and amphoteric characteristics of these phases also became evident using this evaluation method.
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  • 22
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Liquid-liquid extraction ; Supercritical fluid extraction ; Pesticides ; Freeze-dried water
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The stability of freeze-dried water samples spiked with eight agrochemicals (atrazine, simazine, linuron, carbaryl, propanil, fenitrothion, parathion and fenamiphos) were examined to evaluate their suitability as candidate reference materials for their determination in water samples. In addition, two different extraction procedures, liquid-liquid and supercritical fluid extraction, were compared for the isolation and trace enrichment of target analytes from freeze-dried water samples. Final analytical determinations were by gas chromatography-nitrogen phosphorus detection and electronic impact mass spectrometry, and by liquid chromatography-diode array detection. The whole methodology developed in this paper permitted the determination of pesticides spiked in water at levels varying from 0.03 to 6.9 μg L−1.
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  • 23
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 38 (1994), S. 624-628 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Ion-trap detection ; Nitriles ; Cerelas ; Perfluoroacylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Bromoxynil and ioxynil have been determined inplants and soil by gas chromatography. These herbicides are extracted from soil samples with methylene chloride at acidic pH. Plant samples are extracted with a basic acqueous solution and extracts purified by solvent partitioning. Herbicide residues are submitted to perfluoroacylation prior to GC separation. These compoiunds are determined by ion-trap detection with single ion monitoring; N-(3-chloro-4 methyl-phenyl_ perfluoropropyl amide is used as internal standard. The detection limit of the method is near 0.001 μg g−1 for the samples studied. The proposed methods are sensitive and reproducible enough to allow determination of these herbicides at residue levels in plants and soil.
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  • 24
    Electronic Resource
    Electronic Resource
    Springer
    Chromatographia 39 (1994), S. 11-14 
    ISSN: 1612-1112
    Keywords: Supercritical fluid extraction (SFE) ; Gas chromatography ; Pesticide residues ; Oxadixyl
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary This work describes the study of a degradation curve of Oxadixyl in field-treated potato and tomato samples. The residues were extracted using classical and supercritical fluid (SFE) extraction methods and analyzed by HRGC/ECD. The extraction techniques were compared and the results indicate the advantages of using SFE as an alternative method for pesticide analyses in these samples.
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  • 25
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    Chromatographia 39 (1994), S. 706-712 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Short chain fatty acids ; Intestinal fluids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The quantification of short chain fatty acids in their free form, by gas chromatography, is the method of choice provided that the underivatized acids elute with good peak shape and reproducibility. In biological samples not only the highly polar acids themselves but also deposits of nonvolatile sample components may interact with the column or the packing material. As a result, the peak symmetry of the fatty acids and their reproducibility can become increasingly poor. Reduction of the nonvolatile matrix components by filtration of the sample has been examined in order to achieve direct analysis of the short chain fatty acids in intestinal samples by packed column GC. Membrane filter units (0.8 μm) allow a quick and simple filtration of the samples. This pretreatment reduces the peak tailing and the broadening of the peaks. The method, when applied to different intestinal samples, allowed the quantification of short chain fatty acids in hundreds of samples without derivatization. Good results are obtained at sample concentrations higher than 0.2 mmol l−1 for each acid.
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  • 26
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    Chromatographia 39 (1994), S. 224-227 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; C1−C4 alkyl tert-butyl ethers ; Retention index
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The separation of C1−C4 alkyl tert-butyl ethers with the general formula (CH3)3C−O−R (R-alkyl substituent) on fused-silica capillary columns coated with dimethylsilicone and cyanopropylmethylsilicone stationary phases was investigated. Retention indices were determined at two temperatures in order to understand their chromatographic behaviour. The respective standard deviations were 0.3 and 0.5 i.u.
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  • 27
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Organonitrogen pesticides ; Organophosphorus pesticides ; Apples ; Solvent extraction
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A gas chromatographic method employing a capillary column and a selective nitrogen/phosphorus detector (NPD) has been developed for the determination of organophosphorus (OP) and organonitrogen (NP) pesticides in horticultural samples (apples). The separation of sixteen pesticides and the internal standard was performed in thirteen minutes. The analytical characteristics of the method, including linear response ranges, detection limits, and reproducibility, have been studied using a 1∶1 mixture of ethyl acetate and xylene as extraction solvent. The possibility of mutual interference between pesticides has also been studied. A procedure for the quantitative extraction of the sixteen pesticides from apple samples has also been developed; for fifteen of the pesticides recoveries 〉85% were obtained after 90 minutes extraction. The effect of different solvents both on recovery and on the sensitivity of the subsequent chromatography were also investigated. It was found that the sensitivity required must be considered when the solvent for sample treatment is selected.
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  • 28
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    Chromatographia 39 (1994), S. 419-426 
    ISSN: 1612-1112
    Keywords: Column liquid chromatography ; Gas chromatography ; Chirasil-Val ; Amino acid enantiomers ; N-Isobutyryl-cysteine
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Free D-amino acids (D-AA) were detected as native constituents in juices of vegetables (cultivars of cabbage, tomato, carrot, garlic) and fruits (organes, clementine, grapefruit, lemon, apples, pear, grapes) using gas chromatography (GC) or high-performance liquid chromatography (LC). For investigation by GC, AA enantiomers were converted into theirN(O)-pentafluoropropionyl 2-propyl esters and resolved on a Chirasil-L-Val capillary column. For determination by LC, precolumn derivatization of AA enantiomers usingo-phthaldialdehyde together with the chiral thiolsN-isobutyryl-L-cysteine orN-isobutyryl-D-cysteine and fluorescence detection of the diastereomeric isoindole derivatives, resolvable on an octadecylsilyl stationary phase, were used. D-Ala (0.6–3.8%) was detected in all freshly pressed plant juices usually in the highest relative amounts. Other D-AA detected were D-Asx (0.1–1.9%), D-Glx (0–1.3%), D-Ser (0–1.7%), D-Arg (0.4–1.2%, in grapes, orange, grapefruit, and clementine) and D-Leu and D-Val (1% in cabbage). Absolute amounts of native D-AA were totally 28–57 μmol L−1 in fruit juices, 14.5 μmol L−1 in a tomato juice and 8.5 μmol L−1 in a carrot juice.
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  • 29
    ISSN: 0935-6304
    Keywords: Gas chromatography ; Atomic emission detection (AED) ; Programmed temperature vaporization (PTV) ; Nitro musks ; Human adipose tissue ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: Atomic emission detection (AED) has been successfully applied to the determination of nitro musks in the fat of human adipose tissue by gas chromatography at trace concentration levels. Element specific detection with the AED combined with a clean-up procedure for nonpolar substances makes target screening analysis for lipophilic nitro aromatic compounds possible for the first time. The lack of sensitivity, especially in the AED nitrogen and oxygen trace, was compensated by higher concentration of the extracts and injection of larger sample volumes performed by cold programmed temperature vaporization (PTV) in the solvent split mode. The combination of the superior quantification properties of the atomic emission detector with large sample volume introduction makes the quantification of nitro musks down to the ppb level possible. All five nitro musks investigated exhibit linear dynamic ranges going down close to instrumental limits of detection. Moreover, organochlorine compounds could be sensitively detected in the same sample extract by the AED chlorine trace without any interferences from coeluting matrix compounds.
    Additional Material: 7 Ill.
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  • 30
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    Journal of High Resolution Chromatography 17 (1994), S. 457-462 
    ISSN: 0935-6304
    Keywords: Gas chromatography ; Flame photometric detector ; Pyrolyzer ; Sulfur boiling point distribution ; Light cycle oils ; Exponential dilution flask ; Low sulfur diesel ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A method has been developed to determine the boiling point distribution of sulfur compounds in light cycle oils (LCO'S). The method chosen for this analysis was GC with a flame photometric detector (FPD) and pyrolyzer. Tests were carried out to evaluate the recovery efficiency, repeatability, and accuracy of the method. Repeatabilities within 2% were obtained. The recovery of benzothiophenes and dibenzothiophenes was close to 100%; this was important because these are the major sulfur components in LCO's. No hydrocarbon or solvent interferences were observed with the use of the pyrolyzer, even for a 95% solvent level. Comparison with results from other techniques showed that the method accurately determined the levels of sulfur compounds in the LCO boiling point range.
    Additional Material: 10 Ill.
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  • 31
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    Journal of High Resolution Chromatography 17 (1994), S. 411-414 
    ISSN: 0935-6304
    Keywords: Size exclusion chromatography ; Gas chromatography ; Coupled LC-GC ; Cleanup and analysis ; Automation ; Chemistry ; Analytical Chemistry and Spectroscopy
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology
    Notes: A fully automated on-line sample cleanup system based on the coupling of size exclusion chromatography to high resolution gas chromatography is described. The transfer technique employed is based on fully concurrent solvent evaporation using a loop-type interface, early vapor exit and co-solvent trapping. Optimization of the LC-GC transfer was done visually via an all-glass oven door. To circumvent the problem of mixing within the injection loop, an adaptation was made to the standard loop-type interface. The determination of a series of additives in a polymer matrix is presented as one example of the vast range of applications opened up by this technique.
    Additional Material: 6 Ill.
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  • 32
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    Chromatographia 38 (1994), S. 22-28 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Chiral separation ; Capillary column ; 2,6-Di-O-pentyl-3-O-propionyl-γ-cyclodextrin
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary 2,6-Di-O-pentyl-3-O-propionyl-γ-cyclodextrin has been synthesized and used for enantiomer separation in capillary gas chromatography. Experimental results showed that the stationary phase has good enantiomer selectivity toward amino acids, amines, alcohols, diols, epoxides, and lactones,etc. 2,6-Di-O-pentyl-3-O-propionyl-γ-cyclodextrin has good thermal stability: the highest recommended temperature isca 170°C.
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  • 33
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Pentachlorophenol residues ; Off-flavours ; Wines and corks ; Electrolytic conductivity detector/mass spectrometry ; detectors
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A gas chromatographic methodology with selective detection is presented for the analysis in wines and corks of pentachlorophenol residues, which are suspected to be the most likely precursors of some off-flavours described in several wine samples. After derivatisation, pentachlorophenol acetate residues were monitored by electrolytic conductivity detection and/or mass spectrometric detection in the selective ion mode at m/z 264 and 266. Recoveries varied from 80 to 96% for wine samples fortified with 5 to 100 μg l−1 and from 83 to 91% for corks (fortified at 25 to 100 μg kg−1). The proposed methodology allowed for a determination limit of μg l−1 for wine and 10 μg kg−1 for corks.
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  • 34
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    Chromatographia 38 (1994), S. 151-157 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; C5−C12 hydrocarbons in air ; Cryogenic focussing ; Thermal desorption
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A homemade cryogenic system derived from readily available material is described, illustrating its usage as an accessory for adsorption/thermal desorption chromatography. A small Chromsorb-W-HP packing (1 cm) was introduced into a deactivated precolumn as a cryofocussing, preconcentrating unit. This was able to retain the analyte which had been thermally desorpted from a Tenax TA sampling tube at a relatively higher temperature (−80°C∼−90°C), with the analyte also reinjected on the analytical column in a relatively narrow band. Average overall recoveries for 24 hydrocarbons tested were 97.5%. Cryofocussing enhanced sensitivity and improved resolution. Field studies at a petroleum industry site were carried out and the accessory proved to be useful for complex C5−C12 hydrocarbon analysis in ambient air.
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  • 35
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    Chromatographia 38 (1994), S. 595-598 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Chiral / enantiomeric separation ; Amphetamine ; Methamphetamine ; Cyclodextrin-derivatized phases
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Enantiomeric separation of amphetamine and methamphetamine as achiral derivatives on 2,6-di-O-pentyl-3-O-trifluoroacetyl-β-cyclodextrin, 2,6-di-O-pentyl-3-O-trifluoroacetyl-γ-cyclodextrin and 2,6-di-O-pentyl-3-O-propionyl-γ-cyclodextrin stationary phase in capillary gas chromatography is described. Trifluoroacetic anhydride and acetic anhydride were used as derivatizing reagents. Excellent precision was obtained for concentrations down to 0.1% / e.e. On 2,6-di-O-pentyl-3-O-propionyl-γ-cyclodextrin the elution order of R,S-amphetamine was reversed when the derivatizing reagent was changed but could not be reversed on any of the other phase types.
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  • 36
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Adsorption and partition columns in series ; Molecular sieves ; Isomers of benzene homologs
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The possibility of using short gas chromatographic columns packed with different molecular sieves (silicalite and aluminophosphates), showing definite selectivity to para-isomeric compounds, in series with columns containing a liquid stationary phase was investigated. The molecular sieves were of different origin, while 1,2,3-tris (2-cyanoethoxy)propane (TCEP) and polyethylene glycol adipate (PEGA) were used as the liquid stationary phase. Ortho-, meta- and para-isomers of xylene, chlorotoluene and dichlorobenzene were chromatographed on these columns. It is shown that the best separation is obtained on a combined column with silicalite containing pure silica gel as the molecular sieve, and 10% PEGA as the liquid phase. Molecular sieves of aluminophosphate origin show only weak selectivity toward the para isomers.
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  • 37
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    Chromatographia 39 (1994), S. 71-73 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Spectinomycin ; Silylation
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A gas chromatographic assay for spectinomycin hydrochloride is described. The method is based on that prescribed by the United States Pharmacopeia (USP XXII). The method involves silylation of spectinomycin hydrochloride; phenazone is used as an internal standard. Spectinomycin and phenazone have adequate stability under the prescribed conditions. The stationary phase is 3% OV-17 on Gaschrom Q 100–120 mesh. The selectivity of the proposed method is better than that of the GLC method described in the USP XXII.
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  • 38
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    Chromatographia 39 (1994), S. 645-648 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Headspace analysis ; Gonadotrophins ; Residual solvents
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A headspace, gas chromatographic method for determining residual solvents in pharmaceutical products such as the gonadotrophin powders, has been developed. The method allows the determination of residual solvents by transferring the samples directly into a vial contianing 10 mL 2M sodium chloride; the analysis is carried out by sampling the headspace and separating by capillary gas chromatography using a programmedtemperature vaporizer (PTV) injector. The procedure described is simple, sensitive and reproducible. The lower limit of detection is 20 ppb for ethyl alcohol, 8 ppb for acetone and 0.5 ppb for diethyl ether.
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  • 39
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Method validation ; Reggedness test ; Residual solvents
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Ruggedness testing is performed on a gas chromatographic method for the quantitative determination of residual solvents in steroids. Eight experimental variables or factors which were expected to influence the quantitative results were selected. These factors were divided into two independent groups, i.e. four factors related to the injection process and four factors related to separation and detection. In order to determine interaction between factors and quadratic effects, a central composite design was selected for the set-up of the experiments. Because in the method an internal standard is used, relative peak area was used as response. A deviation of up to 2.5% per factor for the quantitative results was regarded as acceptable. Other responses studied are related to the system suitability. Observed main, quadratic and interaction effects were translated into rugged intervals of the experimental variables by graphical presentation. It was found that besides main effects significant interaction effects were present, for example between the temperature of the injector and the split-flow. Interaction effects can easily result in the reduction of the rugged intervals by a factor of 2. The calculated rugged intervals were compared with the precision of the instrument or factor settings in order to estimate the ruggedness of the factors. Eventually, the maximum effect of the variation in the instrument settings on the quantitative results regarding the precision of the factor settings was found to be only 2.2%. Overall, the method proved to be rugged for most factors, except for the split-flow of the injector for which the method was only rugged to a limited extent.
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  • 40
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Correlation chromatography ; Simulation model ; Adsorption effects ; Separation improvement
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Experiments and simulations prove that correlation chromatography can greatly reduce the disadvantage of a non-linear response of the chromatographic column. A factor that has been accepted as being an important source of error in correlation or multiplex chromatography, has been shown not to be. Separations affected, improve dramatically when correlation chromatography is used, and a substantial amount of correlation noise only arises when there is a large difference in separation between a conventional chromatogram and a correlogram. A model has been developed for simulating these nonlinearities. It is shown that, especially for correlation chromatography, the simulation results match the practical measurements very well.
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  • 41
    ISSN: 1612-1112
    Keywords: Gas chromatography ; PTV injection system ; Aqueous samples ; Pesticides ; Breakthrough volumes
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A GC method is described for the determination of pollutants in aqueous samples by direct enrichment out of large sample volumes in a PTV injector. The vaporized water is eliminated through the split vent and the analytes are concentrated on an adsorbent inside the insert of the PTV. For the selection of suitable adsorbents, breakthrough volumes of selected pesticides and nitroaromatics on Tenax TA, Tenax GR, Chemipack C18 and graphitized carbon blacks have been determined by experiment. The determination of the breakthrough volumes was carried out directly in the PTV insert. Tenax TA proved to be the best sorbent with regard to the breakthrough volumes and its inertness to the analytes to be determined. As the result of the investigations, 500 μl of aqueous standard solutions of pesticides and nitroaromatics (concn.=0.02 ... 2 μg/l) were analyzed with an average relative standard deviation of 10%. The procedure was successfully applied for the analysis of real samples.
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  • 42
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Chiral phases ; Phenylalanine tetraamides ; Amino acids
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A wide series of L-phenylalanine tetraamide selectors (Phe-n-O-TA) have been synthesized and used as stationary phases for chiral resolution of D,L-amino acids by capillary gas chromatography. The influence of length and polarity of the oxaalkanoyl bridge spacing the diamide chains of the selectors and the effects of steric hindrance on separating power were investigated. The characteristics of the chiral columns and the separation factors of D,L-n-butyl-N-trifluoroacetyl amino esters are reported.
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  • 43
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Reversed-flow technique ; Absorption rate ; Air pollutants
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A simple chromatographic method is developed to determine the rate constant for expulsion of an air pollutant from water or its diffusion parameter in the liquid, the rate constant for chemical reaction of the pollutant with water, its mass transfer coefficient in the liquid, and the partition coefficient between liquid water and air. From these physicochemical parameters, the absorption rate by sea water and, therefore, the depletion rate of a polluting substance from the air can be calculated, together with the equilibrium state of this absorption. The method has been applied to nitrogen dioxide being absorbed by triple-distilled water and by sea water, at various temperatures. From the temperature variation of the reaction rate constant and of the partition coefficient, the activation energy for the reaction and the differential heat of solution were determined.
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  • 44
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    Chromatographia 38 (1994), S. 475-478 
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Phenolic acids ; Olive and elm tree tissues ; Soil phenolics
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary A method for the separation of phenolic acids along with shikimic and quinic acids by means of capillary gas chromatography is described and discussed. The method involves the previous derivatization of the acids to trimethylsilyl derivatives and it has been applied to the separation of acids extracted from olive leaves and roots, elm leaves and a soil A horizon. Quite good results were achieved both from qualitative and quantitative points of view. Qualitative differences have been pointed out in the phenolic acid composition of two olive cultivars and between leaves and roots of the same cultivar; also two elm species can be discriminated on the basis of the phenolic acid content.
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  • 45
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Morpholine ; Hydrazine ; Boiler feed water and steam condensates
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary Hydrazine, an oxygen scavenger in boiler water, was derivatised to the corresponding acetone azine and determined at the ng ml−1 level by gas chromatography. Morpholine, a corrosion inhibitor used in steam boilers, was estimated either directly (if 〉2.0 μg ml−1) or by quantitative preconcentration (0.1 ng – 2.0 μg ml−1). To obtain symmetrical peaks for these amines, the column packing was coated with KOH. Use of a nitrogen-specific detector improved accuracy of estimation of hydrazine and morpholine, giving a RSD of 1.9–3.6%. Chromatographic analysis of these amines in boiler feed water and steam condensate samples collected from boilers servicing a petroleum refinery is described. Environmental safety regulations calls for monitoring of hydrazine and the methods developed can easily be adapted for this purpose.
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  • 46
    ISSN: 1612-1112
    Keywords: Gas chromatography ; MSD, ECD and NPD ; Non-steroidal anti-inflammatory drugs (NSAIDs) ; Plasma samples
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The aim of this work was to compare the performance of the MSD, ECD and NPD systems when used for drug assay in biological fluids. As a practical test, six non steroidal anti-inflammatory drugs added to plasma samples were detected and quantified. The analyses were carried out after solvent extraction from an acidic medium and subsequent methylation. The linearity of response was tested for all the detection systems in the range of 1 to 25 ng/ml. Precision and accuracy were determined at 1, 5 and 10 ng/ml. The minimum quantifiable level for the six drugs was about 1 ng/ml with each of the three detection systems.
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  • 47
    ISSN: 1612-1112
    Keywords: Gas chromatography ; Enantiomer separation ; Permethylated cyclodextrin stationary phases ; Side-chain fluorinated alkylbenzenes ; Thermodynamic data
    Source: Springer Online Journal Archives 1860-2000
    Topics: Chemistry and Pharmacology
    Notes: Summary The separation of racemic side-chain fluorinated alkylbenzenes and bromofluorinated analogues by capillary gas chromatography using permethylated α, β and γ-cyclodextrins dissolved in polysiloxanes of different polarity as stationary phases is described. The influence of the achiral polysiloxane matrices on the separation of enantiomers is discussed in the light of the results obtained with the different phases. For a part of the tested compounds thermodynamic data are determined which describe the interaction of enantiomers with the stationary phase. The mechanism of separation is discussed on this basis and by comparison with data for structurally similar compounds.
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  • 48
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    Journal of Computational Chemistry 15 (1994), S. 12-22 
    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 suitability of the two most widely used strategies to compute semiempirical MEPs is examined. For this purpose, MEP minima, electrostatic charges, and dipoles for a large number of molecules were computed at the AM1, MNDO, and PM3 levels using both the NDDO strategy developed by Ferenczy, Reynolds, and Richards and our own quasi-ab initio method. Results demonstrate that the quasi-ab initio is preferred over the NDDO method for the computation of MEP minima. It is also found that the best set of semiempirical charges and dipoles are obtained using either the AM1 NDDO or the MNDO quasi-ab initio methods. In these two cases, the quality of the results is fully comparable with 6-31G* values. © 1994 by John Wiley & Sons, Inc.
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  • 49
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    Journal of Computational Chemistry 15 (1994), S. 54-60 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Explicitly correlated Gaussian functions have been used in variational calculations on the ground state of the helium atom. The major problem of this application, as well as in other applications of the explicitly correlated Gaussian functions to compute electronic energies of atoms and molecules, is the optimization of the nonlinear parameters involved in the variational wave function. An effective Newton-Raphson optimization procedure is proposed based on analytic first and second derivatives of the variational functional with respect to the Gaussian exponents. The algorithm of the method and its computational implementation is described. The application of the method to the helium atom shows that the Newton-Raphson procedure leads to a good convergence of the optimization process. © 1994 by John Wiley & Sons, Inc.
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  • 50
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    Journal of Computational Chemistry 15 (1994), S. 90-104 
    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 described various technical aspects in applying reaction field theories using continuum models to practical problems. It was investigated how solvent-dependent properties of solute molecules are influenced by the following factors: difference in quantum-chemical description of solute-solvent (continuum dielectric) interaction, difference in values of empirically determinable parameters such as atomic radii to define a size of a cavity created in a dielectric to accommodate a solute, and difference in the sophistication level of molecular orbital calculation, including electron correlation and different parameter sets (MNDO, AM1, and PM3). Through these investigations, the better parameter sets were found to evaluate accurately physicochemically important parameters such as hydration enthalpy. © 1994 by John Wiley & Sons, Inc.
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  • 51
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    Journal of Computational Chemistry 15 (1994), S. 132-143 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio MP2/6-31G*//MP2/6-31G* and semiempirical AM1 and PM3 calculations on a series of differently substituted α-oxo-ketenes are used to investigate E/Z-isomerism and rotational barriers in these molecules. Sterically crowded derivatives are found to exist solely as s-E conformers. The unusual stability of these derivatives thus can be attributed to their inability to adopt the s-Z conformation required for the normal α-oxo-ketene reactions. With respect to structures and energies, the PM3 method (especially in the case of highly crowded molecules) is found to be less reliable than AM1. Ab initio HF/3-21G and PM3 vibrational frequencies appear to be of sufficient accuracy for a distinction between s-Z and s-E conformers. In this respect, the AM1 method appears less reliable. © 1994 by John Wiley & Sons, Inc.
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  • 52
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    Journal of Computational Chemistry 15 (1994), S. 155-161 
    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 described for refining the populations of a set of multiple-solution conformers using experimental nuclear Overhauser effects (nOes). The method is based upon representing the effective relaxation matrix for the set of interconverting proposed conformers as a linear combination of relaxation matrices (LCORMs) due to each conformer. The conformer population derivative of the nOe is derived from a Taylor series expression for the calculated nOe. This derivative may then be used in a standard nonlinear least-squares refinement procedure. The LCORM nOe procedure is tested using a monosaccharide system, 1-O-methyl-α-L-iduronate, that is known to exhibit conformational variability. The measured nOes for this system are used to refine the populations of a set of three static conformers, namely, the 1C4, 4C1, and 2S0 ring conformers. The populations thus derived are compared to those previously obtained using nuclear magnetic resonance proton-proton coupling constant information. Two possible extensions to the method are discussed: The first uses combined nOe and coupling constant data while the second removes the restrictions that the conformers used for fitting be rigid entities. © 1994 by John Wiley & Sons, Inc.
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  • 53
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    Journal of Computational Chemistry 15 (1994), S. 190-199 
    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 introduces a novel potential function that allows the use of topographical information in molecular modeling. Quantitative shape data are provided by techniques such as electron-microscopy-based three-dimensional image reconstruction for large macromolecular assemblies. Such data can provide important constraints for molecular mechanics. We represent topographical data by spherical harmonic surfaces, first used by Max and Getzoff21 for displaying molecular surfaces. A simple harmonic potential is used to constrain atoms within these spherical harmonic surfaces. This potential was implemented in the yammp molecular mechanics package.27 Implementation details and results of several test cases are discussed here. © 1994 by John Wiley & Sons, Inc.
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  • 54
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    Journal of Computational Chemistry 15 (1994), S. 249-249 
    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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  • 55
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    Journal of Computational Chemistry 15 (1994), S. 283-299 
    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 MM3 force field has been extended to cover alkyl radicals. Structures, conformational energies, vibrational spectra, and heats of formation have been well fit, mostly to ab initio data. © 1994 by John Wiley & Sons, Inc.
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  • 56
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    Journal of Computational Chemistry 15 (1994), S. 269-282 
    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 chemical computations on a subset of a large molecule can be performed, at the neglect of diatomic differential overlap (NDDO) level, without further approximation provided that the atomic orbitals of the frontier atoms are replaced by parametrized orthogonal hybrid orbitals. The electrostatic interaction with the rest of the molecule, treated classically by the usual molecular mechanical approximations, is included into the self-consistent field (SCF) equations. The first and second derivatives of energy are obtained analytically, allowing the search for energy minima and transition states as well as the resolution of Newton equations in molecular dynamics simulations. The local self-consistent field (LSCF) method based on these approximations is tested by studying the intramolecular proton transfer in a Gly-Arg-Glu-Gly model tetrapeptide, which reveals an excellent agreement between a computation performed on the whole molecule and the results obtained by the present method, especially if the quantum subsystem includes the side chains and the peptidic unit in between. The merits of the LSCF method are examplified by a study of proton transfer in the Asp69 - Arg71 salt bridge in dihydrofolate reductase. Simulations of large systems, involving local changes of electronic structure, are therefore possible at a good degree of approximation by introducing a quantum chemical part in molecular dynamics studies. This methodology is expected to be very useful for reactivity studies in biomolecules or at the surface of covalent solids. © 1994 by John Wiley & Sons, Inc.
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  • 57
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    Journal of Computational Chemistry 15 (1994), S. 333-345 
    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 alkyl boronic acid moiety is incorporated into many biologically interesting structures. To provide parameters for molecular mechanics and dynamics studies of compounds containing this group, we performed ab initio calculations at the 6-31G* level to obtain bond stretching, bending, and torsion constants. The hydrodynamic formulation of the time-dependent density functional theory was used to calculate the attractive part of van der Waals (VDW) 6-12 potential. The geometry of boronic acid moiety of the 6-31G* optimized methyl boronic acid was similar to that of the X-ray crystal structure of phenyl boronic acid. To test the reliability of nonbonded parameters, Monte Carlo free energy perturbation simulations and the thermodynamic cycle approach were used to estimate the differences in solvation free energy between alkyl alcohol and alkyl boronic acid, both in water and in chloroform. These free energy differences were also obtained experimentally by measuring the vapor-water and water-chloroform partition coefficients. The close agreement between experimental values and the results of our simulations suggests the reliability of new molecular mechanics force-field parameters for alkyl boronic acids. © 1994 by John Wiley & Sons, Inc.
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  • 58
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    Journal of Computational Chemistry 15 (1994) 
    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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  • 59
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    Journal of Computational Chemistry 15 (1994), S. 395-404 
    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 kinetics and thermodynamics of lactam/lactim tautomerization in 2-pyridone have been investigated, with special attention to direct and assisted proton transfer mechanisms in the ground and first excited electronic state. Specific interactions with a single water molecule strongly enhance the reaction rate and shift the equilibrium toward the lactam form. The effect of bulk solvent is comparatively negligible, although the lactam form is further stabilized. Electron excitation strongly destabilizes the saddle point for proton transfer and, especially, the lactim form with respect to the lactam species. As a consequence, the direct reaction barrier is increased, but the reverse barrier is lowered. Nonpotential energy effects are relatively small and do not modify the aforementioned general trends. © 1994 by John Wiley & Sons, Inc.
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  • 60
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    Journal of Computational Chemistry 15 (1994), S. 374-374 
    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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  • 61
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    Journal of Computational Chemistry 15 (1994), S. 377-384 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Theoretical and numerical results related to the calculation of multidimensional vibrational levels are presented. A description of the methodological details of a very general method (normal coordinates-finite elements, NC-FEM) is provided. Several representative three-dimensional (3D) systems (Henon-Heiles and Eckart potentials, and the H3+ molecule) are studied, and NC-FEM results are compared with those published by other authors. For the H3+, a vibrational Hamiltonian expressed in terms of the three internuclear distances is integrated, and the results obtained are compared with the experimental ones. © 1994 by John Wiley & Sons, Inc.
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  • 62
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    Journal of Computational Chemistry 15 (1994), S. 466-474 
    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 code has been written to perform relativistic Dirac-Fock self-consistent field (SCF) calculations on closed-shell molecules of any symmetry. The choice of the basis set allows us to work at different levels of approximation depending on the precision required. Calculations on the H2Po molecule show that accurate results on specific problems like geometry optimization can be obtained by evaluating the two-electron integrals on half the basis spinors. © 1994 by John Wiley & Sons, Inc.
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  • 63
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    Journal of Computational Chemistry 15 (1994), S. 455-465 
    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 molecular mechanics force field for studying some beta-lactams was developed from ab initio and experimental data. The optimized parameters allowed accurate calculation of the geometries of both the compounds on which the parametrization was based and others on which the validity of the predictions was checked. © 1994 by John Wiley & Sons, Inc.
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  • 64
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    Journal of Computational Chemistry 15 (1994) 
    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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  • 65
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    Journal of Computational Chemistry 15 (1994), S. 524-531 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Starting from the bond polarization theory (BPT), a new semiempirical method for the calculation of net atomic charges is developed. The bond polarization theory establishes a linear dependence of atomic charges from the bond polarization energy. This energy is calculated from the hybrid orbitals forming a bond and the point charges within the neighborhood. Empirical parameters are introduced for the polarity of an unpolarized bond and for the change of the atomic charge with σ- and π-bond polarization. Because these parameters are linear, they can be calibrated directly using net atomic charges from ab initio calculations. This procedure was performed using the charges from STO3G calculations on a set of 18 amino acids. Using the two parameters for CH, OH, σ-CO, and NH bonds and the three parameters for CC, CO, and CN bonds, the 350 ab initio charges can be reproduced with high accuracy by solving sets of linear equations for the charges. The calculation of charges for large molecular systems including all inter- and intramolecular mutual polarizations requires only a few seconds (up to 100 atoms) or minutes (700 atoms) on a PC. This procedure is well suited for the application in molecular mechanics or molecular dynamics programs to overcome the limitations of most force fields used up to now. One of the weakest points in these programs is the use of fixed or topological charges to define the electrostatic potential. As an application of the new method, we calculated the interaction energy of an ion with valinomycin. This ring molecule forms octahedral oxygen cages around ions like potassium and acts thereby as selective ion carrier. To accomplish this function, valinomycin has to strip off the hydratization spheres of the ions, and therefore its preference for certain types of ions could be deduced from the interaction energies. © 1994 by John Wiley & Sons, Inc.
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  • 66
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    Journal of Computational Chemistry 15 (1994), S. 488-506 
    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 efficient methodology, further referred to as ICM, for versatile modeling operations and global energy optimization on arbitrarily fixed multimolecular systems is described. It is aimed at protein structure prediction, homology modeling, molecular docking, nuclear magnetic resonance (NMR) structure determination, and protein design. The method uses and further develops a previously introduced approach to model biomolecular structures in which bond lengths, bond angles, and torsion angles are considered as independent variables, any subset of them being fixed. Here we simplify and generalize the basic description of the system, introduce the variable dihedral phase angle, and allow arbitrary connections of the molecules and conventional definition of the torsion angles. Algorithms for calculation of energy derivatives with respect to internal variables in the topological tree of the system and for rapid evaluation of accessible surface are presented. Multidimensional variable restraints are proposed to represent the statistical information about the torsion angle distributions in proteins. To incorporate complex energy terms as solvation energy and electrostatics into a structure prediction procedure, a “double-energy” Monte Carlo minimization procedure in which these terms are omitted during the minimization stage of the random step and included for the comparison with the previous conformation in a Markov chain is proposed and justified. The ICM method is applied successfully to a molecular docking problem. The procedure finds the correct parallel arrangement of two rigid helixes from a leucine zipper domain as the lowest-energy conformation (0.5 Å root mean square, rms, deviation from the native structure) starting from completely random configuration. Structures with antiparallel helixes or helixes staggered by one helix turn had energies higher by about 7 or 9 kcal/mol, respectively. Soft docking was also attempted. A docking procedure allowing side-chain flexibility also converged to the parallel configuration starting from the helixes optimized individually. To justdy an internal coordinate approach to the structure prediction as opposed to a Cartesian one, energy hypersurfaces around the native structure of the squash seeds trypsin inhibitor were studied. Torsion angle minimization from the optimal conformation randomly distorted up to the rms deviation of 2.2 Å or angular rms deviation of l0° restored the native conformation in most cases. In contrast, Cartesian coordinate minimization did not reach the minimum from deviations as small as 0.3 Å or 2°. We conclude that the most promising detailed approach to the protein-folding problem would consist of some coarse global sampling strategy combined with the local energy minimization in the torsion coordinate space. © 1994 by John Wiley & Sons, Inc.
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  • 67
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    Journal of Computational Chemistry 15 (1994) 
    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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  • 68
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    Journal of Computational Chemistry 15 (1994), S. 627-632 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: An important area of research in computational biochemistry is the design of molecules for specific applications. The design of these molecules, which depends on the accurate determination of their three-dimensional structure, can be formulated as a global optimization problem. In this article, we present results from the application of a new conformation searching method based on direct search methods. We compare these results to some earlier results using genetic algorithms and simulated annealing. © 1994 by John Wiley & Sons, Inc.
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  • 69
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    Journal of Computational Chemistry 15 (1994), S. 719-732 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Traditional net atomic charge models were found unsatisfactory for representing the molecular electric potential (MEP) of n-alkanes ethane through decane in their van der Waals envelopes. The MEP of these molecules was calculated by ab initio methods. Mulliken atomic charges were erratic and gave root mean square (rms) relative errors of fit to the MEP ranging from 152 to 607% with the 6-31 + + g** basis set. Fitting the MEP with potential-derived net atomic charges (PD charges) gave errors ranging from 51 to 62% with the same basis set. The use of larger basis sets, inclusion of electron correlation, use of more MEP data points, or relaxation to optimal structural geometry did not improve significantly the representation of the MEP by net atomic charges. In many cases PD charges of hydrogen atoms were negative, and carbon atoms were positive. To improve the representation of the MEP of n-alkanes, augmentation of the model with nonatomic sites was investigated with the program PDM93. Models with additional charge sites located between hydrogens, on a line bisecting the CH2 group, achieved fits to the MEP with errors reduced to 8% or less, except for n-butane, where the fitting error was 16%. The PD models augmented with methylene bisector sites generally show positive hydrogen charges. They also show CH2 group charge alternation along the n-alkane chains. The augmented charge models were consistent with the observed quadrupole moment of ethane and gave satisfactory predictions for the crystal structures of pentane and octane. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 733-746 
    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 semiempirically parameterized version of the extended Hückel molecular orbital method has been combined with an efficient quasi-Newton Broyden-Fletcher-Goldfarb-Shannon (BFGS) optimization algorithm to obtain accurate geometries for compounds containing H, C, N, O, and F. The requirement of only one matrix diagonalization per energy evaluation makes the EHNDO (Extended Hückel Neglect of Differential Overlap) method faster than semiempirical Hartree-Fock NDDO methods such as MNDO, AM1, and PM3. Geometrical results for EHNDO appear to be as good as or better than results for the widely used AM1 technique, and geometry optimization for EHNDO also requires only a fraction of the time. © 1994 by John Wiley & Sons, Inc.
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  • 71
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    Journal of Computational Chemistry 15 (1994), S. 782-790 
    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 applied the FEM-MP2 method (an implementation of the p-version finite element technique within the framework of second-order Møller-Plesset perturbation theory, [J. Chem. Phys., 98, 5642 (1993), and references therein]) to calculate second-order correlation energies for the atoms Be, Ca, Sr, Ba, Yb, Cd, and Hg and thus to complete our studies on closed-shell elements. The FEM-MP2 method permits the use of virtual orbitals of very high angular momentum (lmax = 12) in combination with radial basis sets which are very close to completeness, in such a way that we are able to obtain results that could be the most accurate published so far and, in some cases, the only values available in the literature. We hope they may be useful as a reference for basis set saturation tests and for new methods to calculate correlation energies. © 1994 by John Wiley & Sons, Inc.
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  • 72
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    Journal of Computational Chemistry 15 (1994), S. 820-837 
    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 method is presented to reduce the memory requirement of normal mode analysis applied to systems containing two or more large proteins when these systems exhibit symmetry properties. We use a rigid geometry model (i.e., only the dihedral angles of the polypeptide chain are considered as variables). This model allows a reduction by a factor of 8 on average of the number of variables with a concomitant freezing of the high-frequency modes. The symmetry properties of the system are used to reduce further the number of variables that must be considered in the computation. Application of group theory leads to a factorization of the matrices of interest (the coefficient and the Hessian matrices) into independent blocks along the diagonal. The initial, reducible representation is thus transformed into a number of irreducible representations of smaller dimensions. In the case of the C2 symmetry group, the method leads to a reduction of the size of the matrices that must be manipulated during the computation (coefficient matrix, Hessian matrix, and eigenvectors matrix) by a factor of 256 compared with the usual normal mode analysis in Cartesian coordinate space. The method is particularly well adapted to the study of the dynamics of oligomeric proteins because these proteins often display symmetry properties (e.g., virus coat proteins, immunoglobulins, hemoglobin, etc.). In favorable cases, in conjunction with X-ray diffuse scattering data, the study of systems showing allosteric properties might be considered. © 1994 by John Wiley & Sons, Inc.
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  • 73
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    Journal of Computational Chemistry 15 (1994), S. 561-570 
    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 nuclear magnetic resonance (NMR), the four ring forms of psicose, α-and β-pyranose and α- and β-furanose, have almost equal concentrations in aqueous solution. Prediction of this equilibrium by molecular mechanics tests both the balance within the force field and the methods for including the many degrees of freedom in the system. For both the α- and β-furanoses, each of 410 different ring shapes was studied in combination with 37 combinations of staggered side-group orientations. Of these, 48 and 57 initial combinations of side-group orientations contributed to the α- and β-furanose energy surfaces. The pyranoses were analyzed in two steps. First, the 38 characteristic ring conformations were optimized with the 63 staggered side-group combinations. All combinations that gave the lowest energy at one or more of the 38 shapes (20 combinations for α-pyranose, 15 for β-pyranose) were then optimized with 4912 different ring forms. Ring conformations were generated by fixing nonadjacent ring atoms (two for furanose rings, three for pyranoses) at increments of 0.1 Å from the plane of the remaining three atoms. At a dielectric constant of 4.0, prediction was in fair agreement with the NMR results. Model northern and southern conformers contribute to the furanose equilibrium, and both chairs are important for α-psicopyranose. © 1994 by John Wiley & Sons, Inc.
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  • 74
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    Journal of Computational Chemistry 15 (1994), S. 588-595 
    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 genetic algorithm has been developed for molecular mechanics calculations. It has been proved to be a robust and efficient structure optimization technique. Because it uses randomly generated starting structures and stochastic operators, the resulting structures are not subjected to the chemist's bias. © 1994 by John Wiley & Sons, Inc.
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  • 75
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    Journal of Computational Chemistry 15 (1994), S. 644-652 
    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 studied the effect of excess charge on the bond strength in the silanes SiH4 and Si2H6 to assess whether charge trapping in a solid-state lattice might promote the technologically important photodegradation of amorphous silicon alloys (the Staebler-Wronski effect). The calculations indicate that both positive and negative charges reduce the strength of Si—H and Si—Si bonds considerably, to the point where they may be broken easily by visible or even infrared light. © 1994 by John Wiley & Sons, Inc.
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  • 76
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    Journal of Computational Chemistry 15 (1994), S. 596-626 
    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 effects of substituents (X) on the structures and stabilities of CH2X- anions for groups comprised of fourth- and fifth-period main group elements (X = K, CaH, GaH2, GeH3, AsH2, SeH, Br, Rb, SrH, InH2, SnH3, SbH2, TeH, and I) have been investigated by ab initio pseudopotential calculations. Full geometry optimizations have been carried out on the CH2X- anions and the corresponding neutral parent molecules, CH3X, at HF/DZP + and MP2/DZP + levels. Results for substituents from the second (X = Li—F) and third (X = Na—Cl) periods provide comparisons of substituent effects of the main group elements of the first four rows of the periodic table on methyl anions. Frequency calculations characterize the nature of stationary points and show pyramidal CH2X- anion structures to be the most stable unless π acceptor interactions (e.g., with BH2, AlH2, GaH2, and InH2 favor planar geometries. The CH2X- stabilization energies [at QCISD(T)/DZP + /MP2/DZP + + ZPE level for X = K—I and QCISD(T)/6-31 + G*/MP2/6-31 + G* + ZPE level] for X = Li—Cl) also show strong π-stabilizing effects for the same substituents. With the exception of CH3 and NH2, all substituents stabilize methyl anions, although the σ stabilization by OH and F is small. The SiH3—PH2—SH—Cl, GeH3—AsH2—SeH—Br, and SnH3—SbH2—TeH—I sets of substituents give stabilization energies between 19 and 30 kcal/mol. The stability of methyl anions substituted by the halogens and the chalcogens (X = OH, SH, SeH, and TeH) increases down a group in accord with the increasing substituent polarizability, while for π acceptors (BH2, AlH2, GaH2, and InH2) the stability decreases down a group in line with their π-accepting ability. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 633-643 
    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 is developed and applied to characterize the global shape of the hydrogen-bonded networks formed in solvent and solute-solvent clusters. The methodology combines elements of geometry and topology of molecular chains, and it provides a description of the compactness and complexity of the entanglements formed by the network of hydrogen bonds between solute and solvent molecules. This approach complements others in the literature, where the hydrogen bonding is described in terms of the spatial distribution of bonds, their energetics and lifetimes, or the length hydrogen-bonded walks in space. The results of the present technique do not depend too strongly on the details of the molecular geometry. Therefore, one can assess the extent to which large-scale architecture is modified by rearrangements in the nuclear configuration, information which is important in molecular dynamics when estimating the persistence of essential structural features along dynamic trajectories. In this article we discuss the methodology and illustrate its application to the study of water clusters and solvated clusters of acetic acid. Expected qualitative features in the change of shape descriptors in actual reorganizations of hydrogen-bonding patterns are discussed briefly. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 662-665 
    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 X-PLOR scheme for imitating the action of ribosomes in aiding synthesizing peptides to find their ultimate conformations is introduced. The scheme is tested with an example from the Delta-Sleep-Inducing-Peptide mutant family. © 1994 by John Wiley & Sons, Inc.
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    Journal of Computational Chemistry 15 (1994), S. 667-683 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: New atom- and group-based spherical-cutoff methods have been developed for the treatment of nonbonded interactions in molecular dynamics (MD) simulation. A new atom-based method, force switching, leaves short-range forces unaltered by adding a constant to the potential energy, switching forces smoothly to zero over a specified range. A simple improvement to group-based cutoffs is presented: Switched group-shifting shifts the group-group potential energy by a constant before being switched smoothly to zero. Also introduced are generalizations of atom-based force shifting, which adds a constant to the Coulomb force between two charges. These new approaches are compared to existing methods by evaluating the energy of a model hydrogen-bonding system consisting of two N-methyl acetamide molecules and by full MD simulation. Thirty-five 150 ps simulations of carboxymyoglobin (MbCO) hydrated by 350 water molecules indicate that the new methods and atom-based shifting are each able to approximate no-cutoff results when a cutoff at or beyond 12 Å is used. However, atom-based potential-energy switching and truncation unacceptably contaminate group-group electrostatic interactions. Group-based potential truncation should not be used in the presence of explicit water or other mobile electrostatic dipoles because energy is not a state function with this method, resulting in severe heating (about 4 K/ps in the simulations of hydrated MbCO). The distance-dependent dielectric (∊ ∝ r) is found to alter the temperature dependence of protein dynamics, suppressing anharmonic motion at high temperatures. Force switching and force shifting are the best atom-based spherical cutoffs, whereas switched group-shifting is the preferred group-based method. To achieve realistic simulations, increasing the cutoff distance from 7.5 to 12 Å or beyond is much more important than the differences among the three best cutoff methods. © 1994 by John Wiley & Sons, Inc.This article is a US Government work and, as such, is in the public domain in the United States of America.
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    Journal of Computational Chemistry 15 (1994), S. 704-718 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Molecular dynamics (MD) simulation and thermodynamic integration (TI) techniques have been used to study the relative free energies of the 8-methyl-N5-deazapterin and 8-methyl-pterin cations (N3 protonated) in aqueous solution. The MD simulations were performed at constant temperature and volume, and the mutations between the cations were carried out by changing the coupling parameter continuously and linearly with the MD simulation time (continuous coupling or slow growth method). The free energy changes have been calculated using both linear and nonlinear couplings of the potential energy functions. Free energy changes have also been computed using the perturbation method for comparison. After separation into electrostatic and van der Waals mutations, most (ca. 80%) of the total free energy change is found to be due to mutation of the electrostatic terms. The free energy change is found to be sensitive to the cutoff radii for interactions between solvent molecules, but rather insensitive to the cutoff radii for interactions between cation and solvent. The free energy changes have also been calculated using various cation and solvent models. Atomic charges for the cations were derived from the molecular electrostatic potential at the semiempirical AM1 and ab initio self-consistent field (SCF) (3-21G, 6-31G, 6-31G*, 6-311G**) levels using AM1 and 3-21G optimized geometries. The TIP3P and SPC models were adopted for the solvent. For the TIP3P solvent model, the order of the free energy change is 6-31G 〉 3-21G 〉 6-31G* ≈ 6-311G** 〉 AM1, where the difference between 6-31G and AM1 is approximately 1 kcal/mol. The free energies obtained using 3-21G optimized geometries are approximately 0.7 kcal/mol larger than those obtained using AM1 geometries for the cations. The free energy change computed using the TIP3P/6-311G* model is 0.3 kcal/mol larger than that obtained for the SPC/6-311G* model. © 1994 by John Wiley & Sons, Inc.
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  • 81
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    Journal of Computational Chemistry 15 (1994), S. 752-768 
    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 CFF931 all-atom force field for aromatic polyesters based on ab initio calculations is reported. The force field parameters are derived by fitting to quantum mechanical data which include total energies, first and second derivatives of the total energies, and electrostatic potentials. The valence parameters and the ab initio electrostatic potential (ESP) derived charges are then scaled to correct the systematic errors originating from the truncation of the basis functions and the neglect of electron correlation in the HF/6-31G* calculations. Based on the force field, molecular mechanics calculations are performed for homologues of poly(p-hydroxybenzoic acid) (PHBA) and poly(ethylene terephthalate) (PET). The force field results are compared with available experimental data and the ab initio results. © 1994 by John Wiley & Sons, Inc.
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  • 82
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    Journal of Computational Chemistry 15 (1994), S. 769-781 
    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 molecular dynamics (MD) simulation of 35,000 picoseconds (ps) has been carried out to study the conformational interconversions of 1,1-difluoro-4,4-dimethylcycloheptane at room temperature using the MM3 force field. The exchange between axial and equatorial fluorine atoms was the only conformational interconversion that occurred, and it took place via the process of pseudorotation. Ring inversions (twist-chair 〈 twist-boat 〈 twist-chair) were not observed. The axial-equatorial exchange of the two fluorine atoms took place five times during the MD trajectory of 35,000 ps. The two CH3 groups occupied symmetrical positions (exchangeable by a C2-like rotations, where C2-like means it would be C2 if the fluorines were not present) in the MM3 structures, and during most of the time of the MD trajectory. The methyls occasionally moved off the C2-like axis in the simulated process, mostly because the C2-like axis was momentarily moved so that it did not pass through the ring atom to which the two CH3 groups are bonded. A C2-like symmetry of the twist-chair conformation was maintained approximately during most of the MD simulation. The conformational geometry with the highest energy obtained during the axial-equatorial exchange process was found and used to locate the transition state. The energy barrier for this axial-equatorial exchange was calculated to be 4.7 kcal/mol, and it compares with the value (5.0 kcal/mol) determined by dynamic nuclear magnetic resonance (NMR). © 1994 by John Wiley & Sons, Inc.
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  • 83
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    Journal of Computational Chemistry 15 (1994), S. 838-846 
    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 detailed comparison has been made of the performance of molecular dynamics and hybrid Monte Carlo simulation algorithms for calculating thermodynamic properties of 2D Lennard-Jonesium. The hybrid Monte Carlo simulation required an order of magnitude fewer steps than the molecular dynamics simulation to calculate reproducible values of the specific heat. The ergodicity of the two algorithms was compared via the use of intermediate scattering functions. For classical systems the intermediate scattering functions should be real; however, a simple analysis demonstrates that this function will have a significant imaginary component when ergodicity breaks down. For q vectors near the zone boundary, the scattering functions are real for both algorithms. However, for q vectors near the zone center (i.e., harmonic, weakly coupled modes), the scattering function calculated via molecular dynamics had a significantly larger imaginary component than that calculated using hybrid Monte Carlo. Therefore, the hybrid Monte Carlo algorithm is more ergodic and samples phase space more efficiently than molecular dynamics for simulations of 2D Lennard-Jonesium. © 1994 by John Wiley & Sons, Inc.
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  • 84
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    Journal of Computational Chemistry 15 (1994), S. 847-857 
    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 AM1/MST strategy for the computation of hydrated neutral molecules has been optimized. For this purpose, we have systematically explored the best cavity definition, the most suitable strategy to compute the molecular electrostatic potential (MEP), and the use of MEP scaling factors to correct the semiempirical MEPs. As a result, we have developed an optimized version of the AM1/MST method, which allows us to reproduce well the experimental free energies of hydration (root mean square, rms, deviation in the range of 1 kcal/mol) as well as the water-induced dipoles computed at the 6-31G*/MST level (rms deviations in the range of 0.3 D). © 1994 by John Wiley & Sons, Inc.
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  • 85
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    Journal of Computational Chemistry 15 (1994), S. 866-874 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Based on results of electron diffraction, gas phase infrared spectroscopy (IR), and MP2/6-31 + G* ab initio calculations, a set of molecular mechanics (MM3) parameters was developed for molecules containing the N(sp3) - O(sp3) moiety. Using this set of parameters, MM3 is able to reproduce structures (bond lengths and bond angles) and vibrational spectra satisfactorily. © 1994 by John Wiley & Sons, Inc.
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  • 86
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    Journal of Computational Chemistry 15 (1994), S. 919-924 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: Ab initio calculations are used to test the ability of various representations to reproduce bond energies. It is found that expansion in 1/R, where R is the bond length, is remarkably efficient and is consistently better than the usual R expansion. A quadratic form in 1/R is better than a cubic representation in R and sometimes even as good as a quartic representation. A cubic function in 1/R is, in all cases studied, better performing than the quartic expansion in R. It is also found that parameters derived with the 1/R expansion are defined more sharply than those derived for the R expansion. It is suggested that the 1/R expansion may be computationally more efficient for simulations of large biomolecules and for constructions of reactive force fields than the standard bond functions. © 1994 by John Wiley & Sons, Inc.
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  • 87
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    Journal of Computational Chemistry 15 (1994), S. 947-962 
    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 studies the backbone influence on the side chains of N-methyl N′-acetyl amides (dipeptides) of alanine, valine, phenylalanine, leucine, isoleucine, glutamine, and lysine. Several local minima corresponding to protein φ, ψ, and χ values for each dipeptide are determined through optimization in the MM2 force field. These local minima are located in various regions on the Ramachandran map related to particular protein secondary structures. The dipeptide backbone influence on the side chain is explored via the sensitivity of the side chain torsion angles χ with respect to the backbone φ and ψ angles. Sensitivity coefficients are calculated, describing the χ response to an externally imposed change in φ or ψ. The χ response, which depends on the backbone conformation in a particular region, is induced primarily by the van der Waals and dipole interactions between the backbone and the side chain, which change with a deviation in φ or ψ. Various sensitivity trends are observed in the particular Ramachandran regions, revealing the subtle relationships between the dipeptide backbone and the side chain. © 1994 by John Wiley & Sons, Inc.
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  • 88
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    Journal of Computational Chemistry 15 (1994), S. 1053-1063 
    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 present potential energy surfaces for Rh—CO obtained from density functional theory for two electronic states of Rh—CO. We have performed local spin-density calculations including relativistic as well as gradient corrections. The construction of a reasonably accurate atom-atom potential for Rh—CO is not possible. We were much more successful in constructing the potential energy surfaces by representing the potential as a spherical expansion. The expansion coefficients, which are functions of the distance between the rhodium atom and the carbon monoxide center of mass, can be represented by Lennard-Jones, Buckingham, or Morse functions, with an error of the fit within 10 kJ/mol. The potential energy surfaces, using Morse functions, predict that the electronic ground state of Rh—CO is 2Σ+ or 2Δ. This is a linear structure with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.253 nm. The bonding energy is -184 kJ/mol. Further, Morse functions predict that the first exicted state is 4A′. This is a bent structure (∠Rh—CO = 14°) with an equilibrium distance of rhodium to the carbon monoxide center of mass of 0.298 nm. The bonding energy of this state is -60 kJ/mol. Both these predictions are in good agreement with the actual density functional calculations. We found 0.250 nm with -205 kJ/mol for 2Σ+ and 0.253 nm with -199 kJ/mol for 2Δ. For 4A′, we found 0.271 nm, ∠Rh—CO = 30°, with -63 kJ/mol. The larger deviation for 4A′ than for 2Σ+ or 2Δ is a consequence of the fact that the minimum for 4A′ is a very shallow well. © 1994 by John Wiley & Sons, Inc.
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  • 89
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    Journal of Computational Chemistry 15 (1994), S. 1105-1112 
    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 efficient algorithm for parallelization of a molecular mechanics program operating in the space of internal coordinates such as dihedral angles, bond angles, and bond lengths is described. The iterative procedure to calculate analytical energy derivatives with respect to the internal coordinates was modified to allow parallelization. Computationally intensive modules that calculate energy and its derivatives, solvent-accessible surface, electrostatic polarization energy and that update lists of interactions were parallelized with nearly 100% efficiency. The proposed strategy for the shared-memory computer architecture is easily scalable and requires minimum changes in a program code. The overall speedup for a realistic calculation minimizing the energy of a myoglobin reaches a factor of 3 for 4 processors. © 1994 by John Wiley & Sons, Inc.
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  • 90
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    Journal of Computational Chemistry 15 (1994), S. 1437-1445 
    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 of alkenes from ab initio 6-31G* energies has been developed. For a group of 26 compounds, the root mean square (rms) error for the calculated heat of formation was 0.78 kcal/mol. Heats of formation have been predicted for an additional nine compounds for which the experimental values are either unknown or suspect. The heats of hydrogenation of barrelene and related compounds are discussed. © 1994 by John Wiley & Sons, Inc.
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  • 91
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    Journal of Computational Chemistry 15 (1994), S. 1127-1138 
    ISSN: 0192-8651
    Keywords: Computational Chemistry and Molecular Modeling ; Biochemistry
    Source: Wiley InterScience Backfile Collection 1832-2000
    Topics: Chemistry and Pharmacology , Computer Science
    Notes: To understand and calculate the interactions of a solute with a solvent, a good method of computing the molecular surface is needed. Three kinds of surfaces may be used: the van der Waals Surface, the Accessible Surface, and the Molecular Surface. The latter is redefined in this article as the Solvent-Excluding Surface. The new algorithm for computing the Solvent-Excluding Surface included in the GEPOL93 program is described. GEPOL93 follows the same concept as former versions of GEPOL but with a full new algorithm. Thus, it computes the Solvent-Excluding Surface by filling the spaces not accessible to the solvent with a set of new spheres. The computation is controlled by three parameters: the number of triangles per sphere, controlled by NDIV; the maximum overlap among the new spheres (OFAC); and the size of the smallest sphere that can be created (RMIN). The changes introduced for the computation of the ESURF make GEPOL93 not just a new version but a new program. An estimation is made of the error in the area and volume obtained in the function of the parameters. © 1994 by John Wiley & Sons, Inc.
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  • 92
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    Journal of Computational Chemistry 15 (1994), S. 1176-1185 
    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 the results of an extensive examination of the stable conformations of CH3CH2OCH2CH2OH at various levels of theory. In particular, 41 initial conformations are optimized using the MM2 force field in BIGSTRN-3; the MINDO/3, MNDO, and AM1 Hamiltonians in AMPAC 2.2; the PM3 Hamiltonian in MOPAC 7.0; and at the HF/STO-3G and HF/3-21G levels using Gaussian 92. The optimized HF/3-21G structures are reoptimized at the HF/6-31G(d) level, and the unique structures are optimized again at the MP2 = FULL/6-31G(d) level. In addition, single-point MP2/6-31G(d) calculations are performed using the HF/6-31G(d) geometries. The goal is to determine the relative accuracy of each method and discuss their strengths and weaknesses. © 1994 by John Wiley & Sons, Inc.
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  • 93
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    Journal of Computational Chemistry 15 (1994), S. 1199-1216 
    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 previously proposed method of modeling force field transition structures as the lowest energy structure on the seam of two intersecting potential energy surfaces is improved with respect to the force field expression and the efficiency of the optimization algorithm. Comparison with ab initio and experimental results show that the force field method may have the potential of achieving almost quantitative results. It appears that the results from transition state modeling are currently limited by the accuracy of the underlying force field. © 1994 by John Wiley & Sons, Inc.
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  • 94
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    Journal of Computational Chemistry 15 (1994), S. 1217-1227 
    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 report on an implementation of quantum mechanical density functional calculations carried out in a dielectric medium. The dielectric medium is introduced by integrating the solution of the Poisson-Boltzmann equations into the density functional calculation. The calculations are carried out for a simple amide in vacuum, in the field of an ion, and in the ion field in several dielectric environments. The environment was constructed to include a low dielectric interior embedded in a high dielectric continuum of dielectric 80 (corresponding to aqueous solution). The energies and electron densities of formamide in the ion field were calculated at various configurations in this system, including at the low dielectric-high dielectric interface. The systems were designed to simulate situations which are similar to those that occur in proteins (i.e., the protein constitutes the low dielectric medium surrounded by aqueous solution). The system mimics situations in which charges in such proteins located in various regions interact with other parts of the protein and with ligands which mainly bind to the surface. © 1994 by John Wiley & Sons, Inc.
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  • 95
    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 using molecular mechanics to calculate internal energies and the generalized Born/surface area (GB/SA) method for calculating solvation free energy has been compared with the corresponding terms obtained from ab initio quantum chemical calculations in the gas phase and the free energy perturbation method implemented in Monte Carlo (MC) simulations to study conformational equilibria in solution. 1,2-Ethanediol, 2-hydroxybenzoic acid, the neutral and protonated histamine, were considered in aqueous solution as systems capable of intramolecular hydrogen bonding. The molecular mechanics method with all atom and united atom models, using the AMBER* force field and the parameterization as implemented in the MacroModel modeling package and the GB/SA continuum solvation model, produces smaller separation in relative conformer free energies than does the ab initio + MC method in aqueous solution. The GB/SA relative solvation free energies using the charges from the AMBER* force fields were consistently smaller than the values obtained in Monte Carlo simulations. Using the charge sets from the Monte Carlo simulations and considering solute geometries with torsional angles fixed at the optimized ab initio values, the relative solvation free energies remained underestimated by up to 30% as compared to the Monte Carlo values. The AMBER*//GB/SA predicted most stable conformer for the 1,2-ethandiol system in aqueous solution is in contrast with the ab initio + MC finding and the available experimental results. For the histamine system predictions by only the united atom AMBER*//GB/SA model agree with those by ab initio + MC and with data derived from nuclear magnetic resonance (NMR) experiments. Differences in the two methods are considered mainly due to the application of torsional parameters and atomic charges developed in the AMBER* parameter set for monofunctional polar systems. New parameters seem to be needed for quantitative description of the in-solution conformational equilibria for organic compounds with a possible intramolecular hydrogen bond. © 1994 by John Wiley & Sons, Inc.
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  • 96
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    Journal of Computational Chemistry 15 (1994), S. 1278-1290 
    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-dimensional protein (ferritin) aggregates with a square lattice symmetry, which were formed within a thin liquid layer on a mercury surface, were studied by molecular dynamics (MD) simulation. For the simulation, the ferritin molecule was modeled by an assembly of 49 spheres, and the intermolecular interactions were given by simple formulae. During the simulation, molecules were confined within a layer, which corresponds to the thin liquid layer. An annealing MD simulation was done starting from a random molecular configuration within the layer, and aggregates with the square lattice symmetry were also obtained. To study the stability of aggregates, dissociation processes of the aggregates were analyzed using MD simulations at room temperature. Interactions between the nearest-neighbor molecules were regarded as bonds. Mean bond energies and correlation coefficients between the bond energies were calculated from the MD trajectories. A decay profile according to the dissociation was obtained, yielding a dissociation rate constant. Buried bonds were stronger than peripheral bonds. The larger the aggregate size, the stronger the bond for each of the buried and peripheral bonds. A simple theoretical account, which is applicable to a general bonded network, was introduced to analyze the dynamics of the aggregates. © 1994 by John Wiley & Sons, Inc.
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  • 97
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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 special-purpose computer GRAPE-2A accelerates the calculation of pairwise interactions in many-body systems. This computer is a back-end processor connected to a host computer through a Versa Module Europe (VME) bus. GRAPE-2A receives coordinates and other physical data for particles from the host and then calculates the pairwise interactions. The host then integrates an equation of motion by using these interactions. We did molecular dynamics simulations for two systems of liquid water: System 1 (1000 molecules), and System 2 (1728 molecules). The time spent for one step of molecular dynamics was 3.9 s (System l), and 10.2 s (System 2). The larger the molecular system, the higher the performance. The speed of GRAPE-2A did not depend on the formula describing the pairwise interaction. The cost performance was about 20 times better than that of the fastest workstations available today, and GRAPE-2A cost only $22,000. © 1994 by John Wiley & Sons, Inc.
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  • 98
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    Journal of Computational Chemistry 15 (1994), S. 28-43 
    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 fast multipole method proposed by Greengard and Rokhlin (GR) is applied to large biomacromolecular systems. In this method, the system is divided into a hierarchy of cells, and electric field exerted on a particle is decomposed into two parts. The first part is a rapidly varying field due to nearby cells, so that it needs rigorous pairwise calculations. The second part is a slowly varying local field due to distant cells; hence, it allows rapid calculations through a multipole expansion technique. In this work, two additional possibilities for improving the performance are numerically examined. The first is an improvement of the convergence of the expansion by increasing the number of nearby cells, without including higher-order multipole moments. The second is an acceleration of the calculations by the particle-particle and particle-mesh/multipole expansion (PPPM/MPE) method, which uses fast Fourier transform instead of the hierarchy. For this purpose, the PPPM/MPE method originally developed by the authors for a periodic system is extended to a nonperiodic isolated system. The advantages and disadvantages of the GR and PPPM/MPE methods are discussed for both periodic and isolated systems. It is numerically shown that these methods with reasonable costs can reduce the error in potential felt by each particle to 0.1-1 kcal/mol, much smaller than the 30-kcal/mol error involved in conventional simple truncations. © 1994 by John Wiley & Sons, Inc.
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  • 99
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    Journal of Computational Chemistry 15 (1994), S. 72-79 
    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 application of canonical numerical integrators to molecular dynamics simulations. Computer experiments are done to analyze the relative merits of using canonical integrators against their noncanonical counterparts. These experiments involve the study of the properties of liquid argon utilizing the Lennard-Jones interaction potential. To accomplish this comparative study of canonical and noncanonical integrators, we computed thermodynamic and structural quantities. Our results indicate that noncanonical methods, with one exception, fail miserably to conserve energy and as a consequence give poor estimates of the other quantities. Also, higher-order canonical methods may offer an advantage over the Störmer/Verlet method. © 1994 by John Wiley & Sons, Inc.
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  • 100
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    Journal of Computational Chemistry 15 (1994), S. 105-123 
    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 convergence behavior of free energy calculations has been explored in more detail than in any previously reported work, using a model system of two neon atoms in a periodic box of water. We find that for thermodynamic integration-type free energy calculations as much as a nanosecond or more molecular dynamics sampling is required to obtain a fully converged value for a single λ point of the integrand. The concept of “free energy derivatives” with respect to the individual parameters of the force field is introduced. This formalism allows the total convergence of the simulation to be deconvoluted into components. A determination of the statistical “sampling ratio” from these simulations indicates that for window-type free energy calculations carried out in a periodic waterbox of typical size at least 0.6 ps of sampling should be performed at each window (0.7 ps if constraint contributions to the free energy are being determined). General methods to estimate and reduce the error in thermodynamic integration and free energy perturbation calculations are discussed. We show that the difficulty in applying such methods is determining a reliable estimate of the correlation length from a short series of data. © 1994 by John Wiley & Sons, Inc.
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