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PubMed2001

Effects of substituent and temperature on enantioselectivity for lipase-catalyzed esterification of 2-(4-substituted phenoxy) propionic acids in organic solvents.

Substituent effects on the enantioselectivity for the lipase-catalyzed esterifications in organic solvents were studied by use of 2-(4-substituted phenoxy)propionic acids as the substrates with various substituents of H, F, Cl, CF(3), CH(3), CH(3)CH(2), and CH(3)O. The distinction in the behavior of their enantioselectivity was primarily responsible for the size effects of the substituents, although the substituents are far away from the stereocenter of the substrates. For the similar substituents in size, CH(3) and CF(3), however, their electronic effects played an important role in controlling the enantioselectivity. This variation of the enantioselectivity due to the electronic effects is also supported by the discussion based on the value of the Michaelis constant (K(m)) obtained. In addition, by raising the reaction temperature with enough water added to isopropyl ether as the reaction medium, the enantioselectivity is found to be dramatically enhanced for the substrate bearing CH(3)O group due to the strong electron-donating effect.

Candida↗
PubMed1983

Thermodynamics of distribution of p-substituted phenols between aqueous solution and organic solvents and phospholipid vesicles.

The distribution of p-substituted phenols between 0.15 M NaCl and a range of organic solvents (including 1-octanol) was examined over a range of temperatures. The thermodynamic parameters of transfer, delta G, delta H, and delta S, were determined and the values examined in the light of Hildebrand and Scott's solubility parameter theory, and the collision complexes between solute and organic solvent. Delta H of transfer was positive for nonpolar solvents and negative for 1-octanol; the transfer processes were entropy and enthalpy dominated, respectively. The distribution of the phenols into phospholipid vesicles was examined below the phase-transition temperature. Although delta G of transfer for vesicle-water systems was similar to that for octanol-water systems, the full thermodynamic analysis indicated that the two systems were dissimilar. The use of vesicle distribution data in structure-activity studies is discussed.

Phenols↗
PubMed2000

Effect of solvents on the photophysical properties of substituted imidazonaphthyridine derivatives.

The absorption and fluorescence characteristics of three substituted imidazonaphthyridine derivatives are studied in a series of organic solvents. The variation of Stokes shift with the polarity parameter of the solvent is studied and the excited state dipole moment of these derivatives is higher than the ground state dipole moment. The fluorescence lifetime profile shows single exponential decay in all the solvents. The fluorescence quantum yield, radiative and non-radiative rate constants are also calculated and these parameters show much variation in the change in substitution of these derivatives.

Fluorescence↗
PubMed2006

Nucleophilic group transfer reactivity for fibric acid derived drug molecules.

A novel group transfer reaction is reported in which a drug molecule undergoes a thermally induced 2-methyl-2-yl-propionic acid group transfer from one drug molecule to the carboxylic acid functional group of another. The resulting product, the 2-carboxy isopropyl ester of the parent compound, can itself participate in further reactions to yield a series of homologous products. The structural requirements and solvent dependence of this reactivity were investigated, and the resulting implications for the reaction mechanism were discussed. The experimental data is consistent with solvent-assisted nucleophilic substitution reaction mechanism, where the solvent is a small molecule or a second drug molecule. Hydrogen bonding appears to play an important role in both intramolecular activation of the leaving group, as well as intermolecular interaction with the attacking nucleophile. The reactivity is found to be intrinsic to the 2-arenoxy-2-methylpropionic acid structure, which is common to the extended class of fibrate PPAR drug molecules, suggesting that the potential for this reactivity exists for many of these drug molecules as well.

Chemical Phenomena↗
PubMed2005

Time-resolved infrared absorption studies of the solvent-dependent vibrational relaxation dynamics of chlorine dioxide.

We report a series of time-resolved infrared absorption studies on chlorine dioxide (OClO) dissolved in H2O, D2O, and acetonitrile. Following the photoexcitation at 401 nm, the evolution in optical density for frequencies corresponding to asymmetric stretch of OClO is measured with a time resolution of 120+/-50 fs. The experimentally determined optical-density evolution is compared with theoretical models of OClO vibrational relaxation derived from collisional models as well as classical molecular-dynamics (MD) studies. The vibrational relaxation rates in D2O are reduced by a factor of 3 relative to H2O consistent with the predictions of MD. This difference reflects modification of the frequency-dependent solvent-solute coupling accompanying isotopic substitution of the solvent. Also, the geminate-recombination quantum yield for the primary photofragments resulting in the reformation of ground-state OClO is reduced in D2O relative to H2O. It is proposed that this reduction reflects enhancement of the dissociation rate accompanying vibrational excitation along the asymmetric-stretch coordinate. In contrast to H2O and D2O, the vibrational-relaxation dynamics in acetonitrile are not well described by the theoretical models. Reproduction of the optical-density evolution in acetonitrile requires significant modification of the frequency-dependent solvent-solute coupling derived from MD. It is proposed that this modification reflects vibrational-energy transfer from the asymmetric stretch of OClO to the methyl rock of acetonitrile. In total, the results presented here provide a detailed description of the solvent-dependent geminate-recombination and vibrational-relaxation dynamics of OClO in solution.

Journal Article↗
PubMed2006

The W105G and W99G sorcin mutants demonstrate the role of the D helix in the Ca(2+)-dependent interaction with annexin VII and the cardiac ryanodine receptor.

Sorcin, a 21.6 kDa two-domain penta-EF-hand (PEF) protein, when activated by Ca(2+) binding, interacts with target proteins in a largely uncharacterized process. The two physiological EF-hands EF3 and EF2 do not belong to a structural pair but are connected by the D helix. To establish whether this helix is instrumental in sorcin activation, two D helix residues were mutated: W105, located near EF3 and involved in a network of interactions, and W99, located near EF2 and facing solvent, were substituted with glycine. Neither mutation alters calcium affinity. The interaction of the W105G and W99G mutants with annexin VII and the cardiac ryanodine receptor (RyR2), requiring the sorcin N-terminal and C-terminal domain, respectively, was studied. Surface plasmon resonance experiments show that binding of annexin VII to W99G occurs at the same Ca(2+) concentration as that of the wild type, whereas W105G requires a significantly higher Ca(2+) concentration. Ca(2+) spark activity of isolated heart cells monitors the sorcin-RyR2 interaction and is unaltered by W105G but is reduced equally by W99G and the wild type. Thus, substitution of W105, via disruption of the network of D helix interactions, affects the capacity of sorcin to recognize and interact with either target at physiological Ca(2+) concentrations, while mutation of solvent-facing W99 has little effect. The D helix appears to amplify the localized structural changes that occur at EF3 upon Ca(2+) binding and thereby trigger a structural rearrangement that enables interaction of sorcin with its molecular targets. The same activation process may apply to other PEF proteins in view of the D helix conservation.

Amino Acid Sequence↗
PubMed2002

Carbamoyl-phosphate synthetase. Creation of an escape route for ammonia.

Carbamoyl-phosphate synthetase catalyzes the production of carbamoyl phosphate through a reaction mechanism requiring one molecule of bicarbonate, two molecules of MgATP, and one molecule of glutamine. The enzyme from Escherichia coli is composed of two polypeptide chains. The smaller of these belongs to the Class I amidotransferase superfamily and contains all of the necessary amino acid side chains required for the hydrolysis of glutamine to glutamate and ammonia. Two homologous domains from the larger subunit adopt conformations that are characteristic for members of the ATP-grasp superfamily. Each of these ATP-grasp domains contains an active site responsible for binding one molecule of MgATP. High resolution x-ray crystallographic analyses have shown that, remarkably, the three active sites in the E. coli enzyme are connected by a molecular tunnel of approximately 100 A in total length. Here we describe the high resolution x-ray crystallographic structure of the G359F (small subunit) mutant protein of carbamoyl phosphate synthetase. This residue was initially targeted for study because it resides within the interior wall of the molecular tunnel leading from the active site of the small subunit to the first active site of the large subunit. It was anticipated that a mutation to the larger residue would "clog" the ammonia tunnel and impede the delivery of ammonia from its site of production to the site of utilization. In fact, the G359F substitution resulted in a complete change in the conformation of the loop delineated by Glu-355 to Ala-364, thereby providing an "escape" route for the ammonia intermediate directly to the bulk solvent. The substitution also effected the disposition of several key catalytic amino acid side chains in the small subunit active site.

Adenosine Triphosphate↗
PubMed2003

Facile Cu(OTf)2-catalyzed preparation of per-O-acetylated hexopyranoses with stoichiometric acetic anhydride and sequential one-pot anomeric substitution to thioglycosides under solvent-free conditions.

Solvent-free per-O-acetylation of hexoses with a stoichiometric amount of acetic anhydride employing 0.03 mol % Cu(OTf)2 proceeded in high yields (90-99%) at room temperature to give exclusively pyranosyl products as an anomeric mixture, the alpha/beta ratio of which was dependent on the temperature and amount of catalyst used. Sequential anomeric substitution with p-thiocresol in the presence of BF3.etherate gave the thioglycosides, isolated exclusively or predominantly as one anomer in 66-75% yields.

Acetic Anhydrides↗
PubMed1999

Absence of minor groove monovalent cations in the crosslinked dodecamer C-G-C-G-A-A-T-T-C-G-C-G.

The structure of a crosslinked B -DNA dodecamer of sequence C-G-C-G-A-A-T-T-C-G-C-G has been solved to a resolution of 1.43 A. The dithiobis-propane crosslink, -CH2-CH2-CH2-S-S-CH2-CH2-CH2-, bridges N7 atoms of adenine bases 6 and 18 in the two central base-pairs within the major groove. The crosslink is sufficiently long that no bending is induced in the helix, which is essentially isostructural with the native unlinked dodecamer at 1.9 A. A constellation of solvent peaks tentatively fitted as a spermine molecule in that earlier analysis is now seen at higher resolution to be a well-defined octahedral magnesium hexahydrate complex in the major groove. One end of the duplex curves around that complex to produce a roll-bend near base-pairs 3-5, and an overall bend in helix axis, as has long been noted. Two other magnesium complexes connect the helices and help to knit the crystal lattice together. No evidence exists for partial sodium or potassium ion substitution for solvent water molecules within the minor groove spine of hydration, as had been suggested previously: not coordination geometry and environment, nor B values, nor calculated valence values, nor difference map analyses. Indeed, the very numbers that have been claimed in support of partial substitution by sodium or potassium ions are reproduced with the present crystals, which by chemical analysis contains only one trace sodium ion per 160 bp, and one potassium ion per 41 bp. In contrast, our crystals contain one Mg2+ per base-pair, meaning that phosphate group charge neutrality is accomplished by divalent cations, not monovalent ions. Three of these magnesium cations per duplex are localized and visible in the X-ray analysis, and nine are disordered and invisible. Hence although binding of monovalent cations within the minor groove of A -tracts on occasion may be a consequence of groove narrowing, it cannot be the cause of that narrowing. Cations, contrary to what has been claimed, are not in charge.

Cations↗
PubMed2003

The solvent in CNBr cleavage reactions determines the fragmentation efficiency of ketosteroid isomerase fusion proteins used in the production of recombinant peptides.

Abnormal fragmentation during cyanogen bromide polypeptide cleavage rarely occurs, although parallel side reactions are known to typically accompany normal cleavage. We have observed that cyanogen bromide cleavage of highly hydrophobic fusion proteins utilized for production of recombinant peptides results in almost complete abolishment of the expected reaction products when the reaction is carried out in 70% trifluoroacetic acid. On the basis of mass spectrometric analysis of the reaction products, we have identified a number of fragments whose origin can be attributed to incomplete fragmentation of the fusion protein, and to unspecific degradation affecting the carrier protein. Substituting the solvent in the reaction media with 70% formic acid or with a matrix composed of 6M guanidinium hydrochloride in 0.1M HCl, however, was found to alleviate polypeptide cleavage. We have attributed the poor yields of the CNBr cleavage carried out in 70% TFA to the increased hydrophobicity of our particular fusion proteins, and to the poor solubilizing ability of this reaction medium. We propose the utilization of chaotropic agents in the presence of diluted acids as the preferred cyanogen bromide cleavage medium of fusion proteins in order to maximize cleavage efficiency of hydrophobic sequences and to prevent deleterious degradation and structural modifications of the target peptides.

Amino Acid Sequence↗
PubMed2004

Freeze-substitution and low-temperature embedding of dairy products for transmission electron microscopy.

Dairy products are comprised largely of fat, air and water, which makes it difficult to preserve their ultrastructure for electron microscopy. Keeping the samples frozen throughout fixation and embedding protects the structure and distribution of the components of emulsions and foams. Therefore, dairy products were freeze-substituted and embedded at low temperature (-20 degrees C) to prepare them for transmission electron microscopy. Whipped cream, ice cream mix and dairy/non-dairy mixed systems were frozen by plunging in propane, at its boiling point (-187 degrees C). Ice cream, because it is already frozen, was fractured into 1-mm3 pieces in liquid nitrogen and then added to frozen fixative (-196 degrees C). Fixative solution consisted of glutaraldehyde, osmium tetroxide and uranyl acetate dissolved in either methanol or acetone. When material was to be stained after sectioning the fixative was limited to glutaraldehyde in methanol. The temperature was increased step-wise from -80 to -20 degrees C. Solvent was replaced with resin; the polar resin Lowicryl HM4, the non-polar resin Lowicryl HM20, LR White and LR Gold were tested. Samples were embedded and polymerized at -20 degrees C using ultraviolet light to cross-link the resin. Methanol proved to be the most effective solvent for substituting the ice; the hydrophobic resin Lowicryl HM20 was the most effective resin for retaining fat structure following osmium fixation.

Journal Article↗
PubMed1988

Relaxometry of calf lens homogenates, including cross-relaxation by crystallin NH groups.

We studied the magnetic field dependence of the longitudinal relaxation rates of water protons (1/T1 nuclear magnetic relaxation dispersion (NMRD) profiles) in transparent homogenates of calf lens. The samples included nuclear homogenates with total (heterogeneous) crystallin contents between 34% (v/v) (native) and 14% (diluted) as well as cortical homogenate, 21% (native) and 34% (concentrated). The NMRD profiles had two components: a monotonic dispersive component (analogous to that of both globular protein solutions and diamagnetic tissue) and "14N quadrupolar peaks." 14N peaks have never been reported for protein solutions, only for tissues and dehydrated proteins. These peaks occur between 0.5 and 5 MHz proton Larmor frequency and arise from interactions of solvent water protons with NH moieties of proteins. The 14N peaks in lens cytoplasm are very large and may correlate with the crystallin structure and interactions required to maintain short-range order and lens transparency. The monotonic and 14N quadrupolar components were largest in concentrated samples, but with different concentration dependencies. The dispersive components of samples above approximately 19% protein concentration had a fixed functional form, the amplitude of which varied with protein volume fraction, f, by the multiplicative factor f/(1 - f), suggesting spatial organization and dynamics of the solute proteins that are relatively independent of water content. In contrast, at concentrations less than 19%, the NMRD profiles are concentration dependent, indicating a dependence of the orientational relaxation time of the proteins on protein-protein interactions seen previously in other globular proteins at these concentrations. The 14N peaks are not resolved below approximately 19% protein and increase linearly with incremental volume fraction at protein concentrations above 19%. In addition, the 14N peaks in nuclear homogenates are 50-100% larger than those of cortical homogenates at the same concentrations. Partial substitution of solvent D2O for H2O decreases the peak heights, indicating that an exchangeable proton mediates the interaction between solvent protons and protein 14N nuclei.

Animals↗
PubMed2006

Preparation of coal slurry with 2-propanol.

This study explored the feasibility of using waste organic solvents as substitutes for water to prepare coal slurries. The rheological properties of coal-2-propanol slurries were examined and compared with that of coal-water slurry (CWS). The good compatibility between coal particles and 2-propanol resulted in stable particle suspension in slurry which usually exhibit Newtonian behaviour. However, coal-2-propanol slurries usually shown higher viscosities comparing to CWSs at a fixed solid loading due to swelling of coal by 2-propanol. In addition, coal-2-propanol slurries demonstrated lower settling rates (higher stability) compared to CWSs presumably due to good compatibility between coal particles and 2-propanol. Finally, coal-2-propanol slurries formed bulky sediment with loose structure even coal particles suspended in 2-propanol were more stable than coal particles in CWSs.

2-Propanol↗
PubMed1995

Patterns of chemical use and exposure control in the Semiconductor Health Study.

Information on chemical use and exposure control between 1986 and 1990 was collected from 14 companies participating in the Semiconductor Health Study. Questionnaires and site visits provided data used to develop exposure categories for three epidemiological studies: prospective, historical, and cross-sectional. Patterns of use of target chemicals were compiled for 82 silicon-wafer fabrication rooms (fabs), including 47 from which subjects were selected for study. Chemical use was examined by operation, year, and epidemiological component. Target agents for epidemiological analyses were present in more than 50% of fabs. Use of these agents was fairly constant from 1986 to 1990, except for a moderate increase in use of propylene glycol monomethyl ether acetate, a solvent being substituted for ethylene-based glycol ethers (EGE) in photoresists. The distribution of personal protective equipment, engineering controls, and other factors potentially affecting employee exposure was also examined. Controls designed to manage processes or high acute toxicity were present in most fabs; their prevalence remained unchanged from 1986 through 1990. Controls designed to reduce exposures to chemicals with low acute toxicity were less widely distributed; their prevalence increased moderately from 1986 to 1990.

Drug-Related Side Effects and Adverse Reactions↗
PubMed1992

Alpha-helix to random coil transitions: determination of peptide concentration from the CD at the isodichroic point.

A method is presented for determining the concentrations of peptides and proteins having isodichroic points near 203 nm. The existence of an isodichroic point for a given substance indicates a local two-state (alpha-helix, random coil) population. The mean residue ellipticity at the isodichroic point, [theta lambda i], is, of course, independent of helix content. For a wide variety of synthetic and natural peptides, including both single helices and coiled coils, it is shown that [theta lambda i] is also essentially independent of substance and of whether the transition is induced by temperature, ionic strength, pH, chain length changes, amino acid substitution, or solvent perturbation. Averaging [theta lambda i] values culled from various laboratories gives -151 +/- 16 (SD, 7 sources) deg.cm2.mmol-1. In our laboratory, nonpolymerizable rabbit alpha-tropomyosin and two alpha-tropomyosin subsequences yield -135 +/- 10 (SD, 190 values) deg.cm2.mmol-1. Thus, given [theta lambda i] for a peptide of known concentration, it is possible to estimate the concentration of any other peptide provided that it has an isodichroic point at which the ellipticity is accurately measurable. It is then possible to calculate [theta lambda] at any other wavelength for which theta is known. It is advisable to determine [theta lambda i] for the best known peptide in one's own laboratory, since it depends on absolute instrument and cell calibrations and an absolute concentration determination.

Amino Acid Sequence↗
PubMed1994

Determination of amino- and amide-15N glutamine enrichment with tertiary butyldimethylsilyl derivatives.

We have developed a simple and rapid method for the selective synthesis of tetra-tertiarybutyldimethylsilyl (TBDMS) glutamine, which allows the simultaneous quantitation of glutamine (2-15N) and (5-15N) isotopic enrichment by selected ion monitoring (SIM) gas chromatographic/mass spectrometric analysis. The tetra-TBDMS glutamine (4S-gln) has an electron impact mass fragment at m/z 258 that contains only the amino-N and larger fragments (e.g., at m/z 545) that have both nitrogens. Derivatization with acetonitrile (ACN) and N-methyl-N-(tert-butyldimethylsilyl)trifluoroacetamide yields primarily tri-TBDMS glutamine (3S-gln) and quantities of 4S-gln too small to allow accurate SIM and tracer/tracee ratio determinations. However, when N,N-dimethylformamide, a more polar aprotic solvent, was substituted for ACN and the sample was heated for 30 min at 125 degrees C, greater than 80% of derivatized glutamine appeared as 4S-gln. Derivatized plasma samples that had been mixed with amide- and/or amino-15N glutamine and analyzed by SIM demonstrated strong agreement (r > or = 0.998, p = 0.0001) between theoretical and observed enrichment values for the 4S-gln fragments at m/z 258 and 545. Deamidation of glutamine to glutamate is negligible during sample processing and analysis. This procedure will facilitate the investigation of the specific sources and fates of glutamine amide and amino nitrogen as well as stable isotope studies involving amino acid transamination, ammonia clearance, urea production and other areas of nitrogen metabolism.

Acetamides↗