Preprocessing of rotamers for protein design calculations

We have developed a process that significantly reduces the number of rotamers in computational protein design calculations. This process, which we call Vegas, results in dramatic computational performance increases when used with algorithms based on the dead-end elimination (DEE) theorem. Vegas estimates the energy of each rotamer at each position by fixing each rotamer in turn and utilizing various search algorithms to optimize the remaining positions. Algorithms used for this context specific optimization can include Monte Carlo, self-consistent mean field, and the evaluation of an expression that generates a lower bound energy for the fixed rotamer. Rotamers with energies above a user-defined cutoff value are eliminated. We found that using Vegas to preprocess rotamers significantly reduced the calculation time of subsequent DEE-based algorithms while retaining the global minimum energy conformation. For a full boundary design of a 51 amino acid fragment of engrailed homeodomain, the total calculation time was reduced by 12-fold.     

Steric Stabilization of Colloids by Poly(dimethylsiloxane) in Carbon Dioxide: Effect of Cosolvents

Steric stabilization and flocculation of colloids with surface-grafted poly(dimethylsiloxane) (PDMS) chains are examined in liquid and supercritical carbon dioxide with and without hexane as a cosolvent. Neither poly(methyl methacrylate) (PMMA) nor silica particles with grafted 10,000 g/mol PDMS could be stabilized in pure CO(2) at pressures up to 345 bar at 25 degrees C and 517 bar at 65 degrees C without stirring. The addition of 15 wt% hexane to CO(2) led to stable dispersions with sedimentation velocities of 0.2 mm/min for 1-2 μm PMMA particles. The critical flocculation pressure of the colloids in the hexane/CO(2) mixture, determined from turbidity versus time measurements, was found to be the same for silica and PMMA particles and was well above the upper critical solution pressure for the PDMS-CO(2) system. The addition of a nonreactive cosolvent, hexane, eliminates flocculation of PMMA particles synthesized through dispersion polymerization in CO(2) with PDMS-based surfactants. Copyright 2000 Academic Press.     

The dielectric constant and salt effects upon the acid hydrolysis of ethyl formate

The hydrolysis of ethyl formate catalysed by hydrochloric acid was studied at three temperatures in water-acetone media and in water media containing different concentrations of sodium nitrate. The effect of various ionic strengths and dielectric constants upon the rate of acid hydrolysis of ethyl formate is presented from the point of electrostatics and the results were compared to like effects upon the acid hydrolysis of ethyl acetate and methyl propionate. Neither the dielectric constant effect nor the salt effect lends itself readily to theoretical interpretation. It was assumed that a partial explanation of these anomalous results might be in the extrapolation of the acid radical to the simplest carboxylic acid. This suggestion was supported somewhat by the trends towards less adherance to the electrostatic theory at certain temperatures in the series methyl propionate, ethyl acetate and ethyl formate.     

Importance of dynamic surface tension to the residual water content of fabrics

At the end of the final spin cycle of the laundry process, the residual moisture content (RMC) of fabric is directly related to the dynamic surface tension of the residual water in the fabric. The LaPlace equation for capillary rise predicts that the capillary rise of solutions in a capillary is proportional to the surface tension at the air-liquid interface. If fabric can be considered to be a large ensemble of capillaries due to interfiber spacing, then the RMC of fabrics will be directly related to the surface tension of residual solution in the fabric. The use of a tailored rinse additive has the potential to decrease the surface tension of solution significantly, thus leading to a decrease in the residual water content of the fabric. It is expected that as the surfactant concentration increases the surface tension decreases. Hence, the RMC of fabrics must decrease with increasing surfactant concentration. However, a peak is observed in the RMC of fabrics before the critical micelle concentration (CMC) is reached. Prior to the CMC, it is proposed that a sudden adsorption of surfactant is occurring on the fabric surface leading to a decrease in bulk monomer concentration. The decrease in free monomer concentration should result in an increase in the equilibrium surface tension of the residual solution leading to a concomitant increase in RMC. Because the dynamic surface tension is measured on a short time scale (on the order of milliseconds), there will be less adsorption of monomer onto the newly created air-liquid interface of the bubbles during the measurement process. This decrease in adsorption should lead to a pronounced increase in the dynamic surface tension. This indeed was observed. The RMC correlates very well with the dynamic surface tension of the residual solution.     

Automated continuous-flow determinations of serum proteins by pulse polarography

A new flow-through cell is described for application of the dropping mercury electrode to the determination of serum proteins in an automated continuous-flow system. By using differential pulse polarography with short controlled drop times, it is possible to run a rapid automated system at sampling rates of up to 120 per hour with approximately +/- 1% precision and less than 3% carry-over. With the Brdicka reagent, hexa-amminecobalt(III) chloride, various serum proteins can be determined in the range 5-50 mug/ml. The method therefore offers a rapid and sensitive automated procedure for determination of serum proteins.     

Screening of urban aerosol particulate composites for selected metal distribution and their dependence on meteorological parameters

Local atmospheric aerosol particulate samples, collected as composites on daily 6-12 hour basis, at Quaid-i-Azam University campus, Islamabad, Pakistan, using high volume sampling technique, were analysed for Pb, Na, K, Fe, Mn, Cd, Cr, Ni, Zn and Co by FAAS method. The monitoring period ran from October, 2001 through March, 2002, with a total of 105 samples collected on cellulose filters, treated in part with the HNO3-based wet digestion method for metal quantification, and for particle size distribution separately. The metal content of the aerosols was examined in relation to dependence on meteorological parameters, such as temperature, relative humidity, wind speed, sun shine and pan evaporation. Statistical correlation analysis was conducted for multiple metal pairs in aerosols, and the data were examined in relation to meteorological parameters and relevant aerosol particle size fractions. The study revealed no viable strong correlation between the meteorological parameters and metal levels; in general, however, a significant positive correlation was found for temperature. A strong positive correlation was observed for PM<25 and PM2.5-10. For coarse particles (PM10-100 and PM>100), however, a negative correlation was observed. The levels of Na, K, Fe and Zn were found in the range of 1-5 microg/m3 while those for the rest of the metals in the sub microg/m3 range. Principal component analysis and cluster analysis were performed on dataset for source identification and appointment. Largest contribution (33%) was shown by the industrial emissions followed by traffic/road dust (16.7%).     

Phase-transfer-catalyzed free-radical polymerization: Kinetics of polymerization of methyl methacrylate using ammonium peroxydisulfate/hexadecyl pyridinium chloride in ethyl acetate/water

The kinetics of phase-transfer-catalyzed free-radical polymerization of methyl methacrylate using the system ammonium peroxydisulfate/hexadecyl pyridinium chloride have been investigated in the temperature range of 50–60°C in ethyl acetate/water two-phase systems. The superior efficiency of the phase-transfer-catalyzed reaction in comparison with polymerization initiated by oil soluble initiators such as 2,2′-azobisisobutyronitrile and benzoylperoxide has been demonstrated. Rate of polymerization increased with increase in concentration of the quaternary salt but showed a tendency to level off at higher concentrations. Increase in the peroxydisulfate concentration also resulted in an increase in the rate at lower concentrations, but was found to decrease at higher concentrations. The order with respect to the monomer was found to be approximately unity. The title reaction has been found to be not truly phase-transfer catalyzed in character as claimed by previous workers. A suitable kinetic scheme has been proposed to account for the experimental data and its significance discussed.     

Reductive Amination of Aldehydes and Ketones with Sodium Triacetoxyborohydride. Studies on Direct and Indirect Reductive Amination Procedures(1)

Sodium triacetoxyborohydride is presented as a general reducing agent for the reductive amination of aldehydes and ketones. Procedures for using this mild and selective reagent have been developed for a wide variety of substrates. The scope of the reaction includes aliphatic acyclic and cyclic ketones, aliphatic and aromatic aldehydes, and primary and secondary amines including a variety of weakly basic and nonbasic amines. Limitations include reactions with aromatic and unsaturated ketones and some sterically hindered ketones and amines. 1,2-Dichloroethane (DCE) is the preferred reaction solvent, but reactions can also be carried out in tetrahydrofuran (THF) and occasionally in acetonitrile. Acetic acid may be used as catalyst with ketone reactions, but it is generally not needed with aldehydes. The procedure is carried out effectively in the presence of acid sensitive functional groups such as acetals and ketals; it can also be carried out in the presence of reducible functional groups such as C-C multiple bonds and cyano and nitro groups. Reactions are generally faster in DCE than in THF, and in both solvents, reactions are faster in the presence of AcOH. In comparison with other reductive amination procedures such as NaBH(3)CN/MeOH, borane-pyridine, and catalytic hydrogenation, NaBH(OAc)(3) gave consistently higher yields and fewer side products. In the reductive amination of some aldehydes with primary amines where dialkylation is a problem we adopted a stepwise procedure involving imine formation in MeOH followed by reduction with NaBH(4).     

Bifunctional Lewis acid-nucleophile-based asymmetric catalysis: mechanistic evidence for imine activation working in tandem with chiral enolate formation in the synthesis of beta-lactams

We report a mechanistically based study of bifunctional catalyst systems in which chiral nucleophiles work in conjunction with Lewis acids to produce beta-lactams in high chemical yield, diastereoselectivity, and enantioselectivity. Chiral cinchona alkaloid derivatives work best when paired with Lewis acids based on Al(III), Zn(II), Sc(III), and, most notably, In(III). Homogeneous bifunctional catalysts, in which the catalyst contains both Lewis acidic and Lewis basic sites, were also studied in detail. Mechanistic evidence allows us to conclude that the chiral nucleophiles form zwitterionic enolates that react with metal-coordinated imines. Alternative scenarios, which postulated metal-bound enolates, were disfavored on the basis of our observations.     

The potential of inductively coupled plasma-mass spectrometric detection for capillary electrophoretic analysis of pesticides

In this work, the potential of inductively coupled plasma-mass spectrometry (ICP-MS) coupled to capillary electrophoresis (CE) to determine organophosphorus pesticides (OPPs) is demonstrated. Element specific detection of (31)P with ICP-MS is performed for the detection of OPPs. Three common OPPs, including glyphosate, glufosinate, and aminomethylphosphonic acid (AMPA), were analyzed by CE-ICP-MS to demonstrate its applicability for the analysis of OPPs. The advantages of using ICP-MS with respect to other common detectors, such as flame photometric detection (FPD), for CE analysis of OPPs are shown. Additionally, different CE separation conditions were studied to achieve complete baseline separation of the pesticide compounds in short migration times. Two CE buffer systems were evaluated for the separation of OPPs using ICP-MS detection. A buffer solution containing 40 mmol.L(-1) ammonium acetate at pH 9.0 and an applied voltage of +20 kV were finally selected leading to a separation time of 10.0 min. Both migration time and area relative standard deviations (%RSD) were evaluated and their respective values were in the intervals of 1.1-3.3% and 2.7-5.3%. Detection limits obtained with the CE-ICP-MS system were in the range of 0.11-0.19 mg.L(-1) (as compound) yielding an enhancement of 130- to 230-fold with respect to FPD. The proposed methodology was finally applied for the determination of the OPPs mentioned above in natural river water samples.