Structure and dynamics of the solvation of bovine pancreatic trypsin inhibitor in explicit water: a comparative study of the effects of solvent and protein polarizability

To isolate the effects of the inclusion of polarizability in the force field model on the structure and dynamics of the solvating water in differing electrostatic environments of proteins, we present the results of molecular dynamics simulations of the bovine pancreatic trypsin inhibitor (BPTI) in water with force fields that explicitly include polarization for both the protein and the water. We use three model potentials for water and two model potentials for the protein. Two of the water models and one of the protein models are polarizable. A total of six systems were simulated representing all combinations of these polarizable and nonpolarizable protein and water force fields. We find that all six systems behave in a similar manner in regions of the protein that are weakly electrostatic (either hydrophobic or weakly hydrophilic). However, in the vicinity of regions of the protein with relatively strong electrostatic fields (near positively or negatively charged residues), we observe that the water structure and dynamics are dependent on both the model of the protein and the model of the water. We find that a large part of the dynamical dependence can be described by small changes in the local environments of each region that limit the local density of non-hydrogen-bonded waters, precisely the water molecules that facilitate the dynamical relaxation of the water-water hydrogen bonds. We introduce a simple method for rescaling for this effect. When this is done, we are able to effectively isolate the influence of polarizability on the dynamics. We find that the solvating water's relaxation is most affected when both the protein and the water models are polarizable. However, when only one model (or neither) is polarizable, the relaxation is similar regardless of the models used.     

Manipulating solute nucleophilicity with room temperature ionic liquids

In this work we report the effect of ionic liquids on a class of charge-neutral nucleophiles. We have studied the reactions of (n)butylamine, di-(n)butylamine, and tri-(n)butylamine with methyl p-nitrobenzenesulfonate in [bmpy][N(Tf)(2)], [bmpy][OTf], and [bmim][OTf] (bmpy = 1-butyl-1-methylpyrrolidinium; bmim = 1-butyl-3-methylimidazolium) and compared their reactivities, k(2), to those for the same reactions in the molecular solvents dichloromethane and acetonitrile. It was shown that all of the amines are more nucleophilic in the ionic liquids than in the molecular solvents studied in this work. Comparison is also made with the effect of ionic liquids on the reactivity of chloride ions, which are deactivated in ionic liquids. The Eyring activation parameters revealed that changes in the activation entropies are largely responsible for the effects seen. This can be explained in part by the differing hydrogen-bonding properties, as shown by the Kamlet-Taft solvent parameters, of each of these solvents and the formation of hydrogen bonds between the solvents and the nucleophiles.     

Investigations into the chromatographic behavior of a doxorubicin-peptide conjugate

HPLC impurity profile method development for a doxorubicin-heptapeptide conjugate included significant changes of the separation profile with diluent, eluent and pH. These separation variables were also temperature-dependent with a shift in retention from 35 to 45 degrees C. There was also a direct relationship of temperature with LC retention, and a pH minimum at 5.9. Atypical dependence of the impurity profile on diluent at a k' of 18 led to further investigation. A large change in retention by several minutes was a function of both the organic eluent composition and temperature between 15 and 30 degrees C. Several Van't Hoff temperature studies from 5 to 65 degrees C on several column types resulted in non-linear plots. Analysis of the molecular subunits suggested that the peptide portion of the analyte influenced the non-linear retention behavior. The stationary phase type was not a significant factor causing non-linearity. Circular dichroism-temperature studies indicated a notable transition in ellipticity for the amine regions (198-202 nm) that occurred between 39 and 44 degrees C. This transition temperature range coincided with the results of the Van't Hoff analysis, between 35 and 44 degrees C, to indicate that these effects were not primarily stationary phase induced.     

Cyclodextrin-based liquid chromatographic enantiomeric separation of chiral dihydrofurocoumarins, an emerging class of medicinal compounds

A set of 28 racemic dihydrofurocoumarins in which the stereogenic center is located in the furan ring have been synthesized. Currently no effective asymmetric synthesis of this class of compounds exists, although their enantiomers are produced biologically by certain plants. Their diverse medicinal properties are being investigated in several laboratories. The enantioselective separation of these dihydrofurocoumarins by three native and six derivatized cyclodextrins has been evaluated in the reversed-phase mode, the polar organic mode, and normal-phase mode. The hydroxypropyl-beta-cyclodextrin is the most effective chiral stationary phase (CSP) at separating the dihydrofurocoumarins into enantiomers, showing some enantioselectivity for 22 dihydrofurocoumarins, and baseline resolving 16 of the 28 compounds in the reversed-phase mode. The acetyl-beta-cyclodextrin and 2,3-dimethyl-beta-cyclodextrin also showed enantioselectivity for a large number (18 and 17, respectively) of dihydrofurocoumarins in the reversed-phase mode. The native cyclodextrins are ineffective and the aromatic derivatized beta-cyclodextrins are only marginally effective at separating the furocoumarin enantiomers in the reversed-phase mode. The polar organic mode and the normal-phase mode have also been evaluated with these CSPs, but no enantioseparations were observed.     

Effects of melt‐processing conditions on the quality of poly(ethylene terephthalate) montmorillonite clay nanocomposites

Organically modified montmorillonite was synthesized with a novel 1,2‐dimethyl‐3‐N‐alkyl imidazolium salt or a typical quaternary ammonium salt as a control. Poly(ethylene terephthalate) montmorillonite clay nanocomposites were compounded via melt‐blending in a corotating mini twin‐screw extruder operating at 285 °C. The nanocomposites were characterized with thermal analysis, X‐ray diffraction, and transmission electron microscopy to determine the extent of intercalation and/or exfoliation present in the system. Nanocomposites produced with N,N‐dimethyl‐N,N‐dioctadecylammonium treated montmorillonite (DMDODA‐MMT), which has a decomposition temperature of 250 °C, were black, brittle, and tarlike resulting from DMDODA degradation under the processing conditions. Nanocomposites compounded with 1,2‐dimethyl‐3‐N‐hexadecyl imidazolium treated MMT, which has a decomposition temperature of 350 °C, showed high levels of dispersion and delamination. © 2002 Wiley Periodicals, Inc. J Polym Sci Part B: Polym Phys 40: 2661–2666, 2002     

Measurement of the rate coefficient for collisional removal of O2(X3Sigma- g, upsilon=1) by O(3P)

We report a laboratory measurement of the rate coefficient for the collisional removal of O(2)(X(3)Sigma(g) (-),upsilon=1) by O((3)P) atoms. In the experiments, 266-nm laser light photodissociates ozone in a mixture of molecular oxygen and ozone. The photolysis step produces vibrationally excited O(2)(a(1)Delta(g)) that is rapidly converted to O(2)(X(3)Sigma(g) (-),upsilon=1-3) in a near-resonant electronic energy-transfer process with ground-state O(2). In parallel, a large amount of O((1)D) atoms is generated that promptly relaxes to O((3)P). Under the conditions of the experiments, only collisions with the photolytically produced O((3)P) atoms control the lifetime of O(2)(X(3)Sigma(g) (-),upsilon=1), because its removal by molecular oxygen at room temperature is extremely slow. Tunable 193-nm laser light monitors the temporal evolution of the O(2)(X(3)Sigma(g) (-),upsilon=1) population by detection of laser-induced fluorescence near 360 nm. The removal rate coefficient for O(2)(X(3)Sigma(g) (-),upsilon=1) by O((3)P) atoms is (3.2+/-1.0)x10(-12) cm(3) s(-1) (2sigma) at a temperature of 315+/-15 K (2sigma). This result is essential for the analysis and correct interpretation of the 6.3-mum H(2)O(nu(2)) band emission in the Earth's mesosphere and indicates that the deactivation of O(2)(X (3)Sigma(g) (-),upsilon=1) by O((3)P) atoms is significantly faster than the nominal values recently used in atmospheric models.     

Viscoelastic measurements of single molecules on a millisecond time scale by magnetically driven oscillation of an atomic force microscope cantilever

The dynamical nature of biomolecular systems means that knowledge of their viscoelastic behavior is important in fully understanding function. The linear viscoelastic response can be derived from an analysis of Brownian motion. However, this is a slow measurement and technically demanding for many molecular systems of interest. To address this issue, we have developed a simple method for measuring the full linear viscoelastic response of single molecules based on magnetically driven oscillations of an atomic force microscope cantilever. The cantilever oscillation frequency is periodically swept through the system resonance in less than 200 ms allowing the power spectrum to be obtained rapidly and analyzed with a suitable model. The technique has been evaluated using dextran, a polysaccharide commonly used as a test system for single molecule mechanical manipulation experiments. The monomer stiffness and friction constants were compared with those derived from other methods. Excellent agreement is obtained indicating that the new method accurately and, most importantly, rapidly provides the viscoelastic response of a single molecule between the tip and substrate. The method will be a useful tool for studying systems that change their structure and dynamic response on a time scale of 100-200 ms, such as protein folding and unfolding under applied force.     

From cyclopentanone oximes to bis[1,2,3]dithiazolo-s-indacenes, cyclopenta[c][1,2]thiazine, pentathiepino-, tetrathiino-, and thienocyclopenta[1,2,3]dithiazoles as a rich source of new materials

[Structure: see text]. The 1,5- and 1,7-s-hydrindacenedione dioximes reacted with S2Cl2 and iBu3N to give the first examples of bis[1,2,3]dithiazolo-s-indacenes; one of them was a near-infrared dye. In contrast, the silylated bicyclo[3.3.0]octan-2,6-dione dioxime reacted with S2Cl2 and Et3N to give a bicyclic 4-cyanoethylcyclopenta[1,2,3]dithiazole or, after addition of Li2S, a tricyclic 4-cyanoethyl-5,6-pentathiepinocyclopenta[1,2,3]dithiazole, also obtained from 2-cyanoethylcyclopentanone oxime, S2Cl2, and Hünig's base. In related reactions, 2-oxocyclopentylpropionate oxime gave the expected cyclopenta[1,2,3]dithiazole, in addition to an unexpected cyclopenta[c][1,2]thiazine that showed a reversible reduction wave in its CV at -0.95 V. Ethyl 2-oxocyclopentanecarboxylate oxime reacted with S2Cl2, Hünig's base, and Li2S to give a 5,6-tetrathiinocyclopenta[1,2,3]dithiazole derivative. Cyclopentathiophen-4-one oximes reacted with S2Cl2 and iBu3N to give thienocyclopenta[1,2,3]dithiazoles that showed UV-vis spectral bands that depended on the positions of the ring fusion.     

Yield of I(2Psol:12) in the photodissociation of CH2I2

The production of I(²P_{$\text{1}\text{2}$}) in the photolysis of CH₂I₂ has been studied optoacoustically at excitation wavelengths between 365.5 and 247.5 nm. Bands found at 32200 and 47000 cm^?1 correlate with I(²P_{$\text{3}\text{2}$}) whilst those at 34700 and 40100 cm^?1, which correlate with I(²P_{$\text{1}\text{2}$}), give final ²P_{$\text{3}\text{2}$}/²P_{$\text{1}\text{2}$} ratios of 1.75 and 1.1, respectively, after curve crossing.     

The complete characterization of a rhodium Lewis acid-dipolarophile complex as an intermediate for the enantioselective catalytic 1,3-dipolar cycloaddition of C,N-diphenylnitrone to methacrolein

The 1,3-dipolar cycloaddition reaction of C,N-diphenylnitrone with methacrolein is efficiently catalyzed by the rhodium diphosphine compound (SRh,RC)-[(eta5-C5Me5)Rh(R-Prophos)(H2O)](SbF6)2 [R-Prophos = (R)-(+)-1,2-bis(diphenylphosphino)-propane, 1.SbF6]; the asymmetric catalytic process occurs with reversal of regioselectivity, perfect endo selectivity, and up to 92% ee. The complete (NMR and X-ray analysis) characterization of the involved intermediate (SRh,RC)-[(eta5-C5Me5)Rh(R-Prophos)(methacrolein)](SbF6)2 (7.SbF6) allows us to interpret the observed selectivity.