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PubMed2006

Synthesis, crystal structures, linear and nonlinear optical properties, and theoretical studies of (p-R-phenyl)-, (p-R-phenylethynyl)-, and (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes and related compounds.

The (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), (p-R-phenylethynyl)dimesitylboranes (R=Me(2)N, MeO, MeS, H), (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N, MeO, MeS, H, CN, NO(2)), (E)-[2-(2-thienyl)ethenyl]dimesitylborane, and (E)-[2-(o-carboranyl)ethenyl]dimesitylborane have been prepared through the reaction of the appropriate p-R-phenyl- and p-R-phenylethynyllithium reagents with dimesitylboron fluoride and by hydroboration of the appropriate p-R-phenylacetylene, 2-ethynylthiophene, and o-ethynylcarborane with dimesitylborane. Their UV/Vis absorption and emission spectra have been recorded in a range of solvents with the fluorescence maxima of the donor-substituted compounds in particular exhibiting large bathochromic shifts in highly polar solvents, indicative of charge transfer leading to large dipole moments in the excited state. The molecular structures of the (p-R-phenyl)dimesitylboranes (R=Me(2)N, MeO, MeS, Br, I), the (E)-[2-(p-R-phenyl)ethenyl]dimesitylboranes (R=Me(2)N, H(2)N MeO, MeS, H), (p-R-phenylethynyl)dimesitylborane (R=Me(2)N), and (E)-[2-(2-thienyl)ethenyl]dimesitylborane, which have been determined from single-crystal X-ray diffraction measurements, offer evidence of increased conjugation in the ground state with increased donor strength of the R substituent. Their first- and second-order molecular hyperpolarizabilities have been obtained from EFISH and THG measurements, the first-order hyperpolarizabilities being largest for the strongest R-substituent donors. AM1 calculations have been performed on these compounds, showing reasonable agreement with the experimentally obtained bond lengths and hyperpolarizabilities, as well as on several related hypothetical compounds containing multiple C==C bonds, most of which are proposed to have even larger hyperpolarizabilities.

Journal Article↗
PubMed2004

The interpretation of multiple-step transient-state kinetic isotope effects.

In contrast to steady-state kinetic isotope effects (KIEs), transient-state tKIEs are both time and signal dependent and therefore require a very different form of theory for their interpretation. We have previously provided such a theory for the case of single-step isotopic substitutions. No such properly derived theory applicable to the analysis of multiple-step isotopic substitutions required by transient-state solvent isotope effect studies has been available up to this time. Here, we set forth a more general form of that theory which is applicable to multiple-step substituted cases. We prove three theorems: 1. the observed transient-state KIE for any given reactive component in the reaction sequence evaluated at zero time (tKIE(0)) is in fact the arithmetic product of the intrinsic KIEs of all the steps that precede the formation of that component. 2. The observed tKIE(0) is completely independent of the intrinsic KIEs of any reverse step in the reaction. 3. The intrinsic KIE of any step may be obtained by dividing the value of the tKIE(0) for that step by the value of the tKIE(0) of the immediately preceding step in the reaction sequence.

Algorithms↗
PubMed1986

Mobile phase effects on the separations of substituted anilines with a beta-cyclodextrin-bonded column.

The capacity factors of several substituted anilines were measured on a beta-cyclodextrin (beta-CD)-bonded column with mobile phases varying from the classical, normal-phase condition, e.g. n-heptane-2-propanol, to the classical, reversed-phase condition, e.g. water-2-propanol. Different modifiers, such as acetonitrile, methanol, and tetrahydrofuran and a Partisil PXS-ODS column were also used for comparison. In general, it was found that the beta-CD column, having the ability to form inclusion complexes with certain substrates is better and more selective in the reversed-phase separation of many aromatic compounds than the Partisil PXS-ODS column. The normal-phase separation on beta-CD was even more efficient, owing to the presence of large number of hydroxy groups on the surface of beta-CD molecules and the more rapid mass transfer in the column. In the present case, alcohols were found to be better modifiers than aprotic solvents. The effects of organic solvents on both normal-and reversed-phase separations are also discussed. The minima observed for the log k' vs. percent organic solvent plots for a number of substituted anilines are reasoned to originate from solute-solvent competition, which interacts with the stationary phase, as well as from the "relative solubility" of solutes in the stationary and mobile phases.

Aniline Compounds↗
PubMed2002

Browsing gene banks for Fe2S2 ferredoxins and structural modeling of 88 plant-type sequences: an analysis of fold and function.

One-hundred-and-seventy-nine sequences of Fe2S2 ferredoxins and ferredoxin precursors were identified in and retrieved from currently available protein and cDNA databases. On the basis of their cluster-binding patterns, these sequences were divided into three groups: those containing the CX4CX2CXnC pattern (plant-type ferredoxins), those with the CX5CX2CXnC pattern (adrenodoxins), and those with a different pattern. These three groups contain, respectively, 139, 36, and 4 sequences. After excluding ferredoxin precursors in the first group, two subgroups were identified, again based on their cluster-binding patterns: 88 sequences had the CX4CX2CX29C pattern, and 29 had the CX4CX2CXmC (m not equal 29) pattern. The structures of the 88 ferredoxins with the CX4CX2CX29C pattern were modeled based on the available experimental structures of nine proteins within this same group. The modeling procedure was tested by building structural models for the ferredoxins with known structures. The models resulted, on average, in being within 1 A of the backbone root-mean-square deviation from the corresponding experimental structures. In addition, these structural models were shown to be of high quality by using assessment procedures based on energetic and stereochemical parameters. Thus, these models formed a reliable structural database for this group of ferredoxins, which is meaningful within the framework of current structural genomics efforts. From the analysis of the structural database generated it was observed that the secondary structural elements and the overall three-dimensional structures are maintained throughout the superfamily. In particular, the residues in the hydrophobic core of the protein were found to be either absolutely conserved or conservatively substituted. In addition, certain solvent-accessible charged groups, as well as hydrophobic groups, were found to be conserved to the same degree as the core residues. The patterns of conservation of exposed residues identified the regions of the protein that are critical for its function in electron transfer. An extensive analysis of protein-protein interactions is now possible. Some conserved interactions between residues have been identified and related to structural and/or functional features. All this information could not be obtained from the analyses of the primary sequences alone. Finally, the analysis of the sequences of the related subgroup featuring the CX4CX2CXmC (m not equal 29) cluster-binding pattern in the light of the structural and functional insights provided by the inspection of the mentioned structural database affords some hints on the functional features of ferredoxins belonging to this subgroup.

Amino Acid Sequence↗
PubMed1986

Mutant forms of staphylococcal nuclease with altered patterns of guanidine hydrochloride and urea denaturation.

Eleven mutant forms of staphylococcal nuclease with one or more defined amino acid substitutions have been analyzed by solvent denaturation by using intrinsic fluorescence to follow the denaturation reaction. On the basis of patterns observed in the value of m--the rate of change of log Kapp (the apparent equilibrium constant between the native and denatured states) with denaturant concentration--these proteins can be grouped into two classes. For class I mutants, the value of m with guanidine hydrochloride is less than the wild-type value and is either constant or increases slightly with increasing denaturant; the value of m with urea is also less than wild type but shows a marked increase with increasing denaturant concentration, often approaching but never exceeding the wild-type value. For class II mutants, m is constant and is greater than wild type in both denaturants, with the increase being consistently larger in guanidine hydrochloride than in urea. When double or triple mutants are constructed from members of the same mutant class, the change in m is usually the sum of the changes produced by each mutation in isolation. One plausible explanation for these altered patterns of denaturation is that chain-chain or chain-solvent interactions in the denatured state have been modified--interactions which appear to involve hydrophobic groups.

Circular Dichroism↗
PubMed1976

The structure of two alanine containing ferrichromes: sequence determination by proton magnetic resonance.

Metal coordination confers an extraordinary structural stability to the ferrichromes which, independent of their variable amino acid composition, results in a basically unperturbed conformation for all the homologous peptides in the series. The proton magnetic resonance (pmr) characteristics for Al3+ analogues (alumichromes) reflect this conformational isomorphism in usual solvents so that single site substitutions are clearly recognized in the pmr spectra. Thus, the substitution of glycine by L-alanine or L-serine introduce new resonances characteristic of the sidechains and alter the pattern of the amide NH pmr region in that doublets substitute for glycyl triplets at the same site. Since for glycine- and L-serine containing alumichromes the resonances have already been identified, it is possible to unequivocally establish the primary structure of the two L-alanyl homologues ferrichrome C (see article) and sake colorant A (see article) on the basis of the comparative pmr spectra of their Al3+ analogues, namely, alumichrome C and alumisake. The resonance assignment, and hence the site occupancy, is substantiated by the temperature coefficients of the NH chemical shifts, rates of 1H-2H exchange and homonuclear proton spin decoupling experiments centered on the NH spectral region. Occupancy of site 1 by a glycine residue is observed for all known ferrichromes, which serves to conserve a "hairpin" turn. This method of obtaining sequence information should prove of general use for other systems of homologous polypeptides, provided their conformations are not affected by the residue substitutions.

Alanine↗
PubMed1988

Ultrastructure of matrix vesicles in chick growth plate as revealed by quick freezing and freeze substitution.

The ultrastructure of extracellular membrane-bound matrix vesicles (MVs), their biogenesis, and the surrounding matrix in chick tibial growth plate were studied after quick freezing and freeze substitution (FS) in an organic solvent. There were several notable differences in the ultrastructural preservation of cartilage when FS was used as compared with conventional fixation. The ultrastructural appearance of MVs after FS was extremely variable. Within the MVs, intravesicular filaments, amorphous material, and membrane-associated undercoat structures were observed. Intravesicular filaments, similar in diameter to microfilaments seen in the cytoplasm, were attached to the inside of MV membranes. This observation indicates the similarity of MV membranes and the plasma membrane. In some MVs in the proliferative zone an electron-dense material was present along the inner side of the MV membrane. In the prehypertrophic zone, crystalline material often appeared within the electron-dense material, which may be a precursor form of hydroxyapatite. The earliest crystals observed were in MVs but not in the extracellular matrix. Regarding MV formation, in addition to budding from cell surfaces and to cellular disintegration, this study also indicates that a sequential process of extrusion of preformed cytoplasmic structures may occur. Also, small MVs measuring 25-40 nm seem to arise from the disruption of large MVs. This is a previously unreported observation on MV biogenesis. FS preserves proteoglycans in the cartilage matrix as a fine, filamentous network. Initial extracellular calcification was not associated with this network.

Animals↗
PubMed1999

Carbonic anhydrase catalyzes cyanamide hydration to urea: is it mimicking the physiological reaction?

The interaction of human carbonic anhydrase (hCA) isozymes I and II with cyanamide, a linear molecule isoelectronic with the main physiological substrate of the enzyme, CO(2), was investigated through spectroscopic, kinetic, and X-ray crystallographic studies. We show here that cyanamide is hydrated to urea in the presence of CAs, and that it also acts as a weak non-competitive inhibitor (K(I)=61+/-3 mM and 238+/-9 mM for hCA II and hCA I, respectively) towards the esterasic activity of these enzymes, as tested with 4-nitrophenyl acetate. Changes in the spectrum of the Co(II)-hCA II derivative observed in the presence of cyanamide suggest that it likely binds the metal ion within the CA active site, adding to the coordination sphere, not substituting the metal-bound solvent molecule. It thereafter undergoes a nucleophilic attack from the metal-bound hydroxide ion, forming urea which remains bound to the metal, as observed in the X-ray crystal structure of hCA II soaked in cyanamide solutions for several hours. The urea molecule is directly coordinated to the active site Zn(II) ion through a protonated nitrogen atom. Several hydrogen bonds involving active site residues Thr199 and Thr200 as well as three water molecules (Wat99, Wat122, and Wat123) further stabilize the urea-hCA II adduct. Kinetic studies in solution further proved that urea acts as a tight binding inhibitor of the two isozymes hCA I and hCA II, with very slow binding kinetics (k(on) = 2.5 x 10(-5)s(-1)M(-1)). A mechanism to explain the hydration process of cyanamide by CAs, as well as the tight binding of urea in the active site, is also proposed based on the hypothesis that urea is deprotonated when bound to the enzyme. Cyanamide is thus the first true suicide substrate of this enzyme for which binding has been documented by means of X-ray crystallographic and spectroscopic studies.

Carbonic Anhydrases↗
PubMed1996

Tolerance does not develop to the suppressant effects of (-)-norpseudoephedrine on ingestive behavior in the rat.

-(-)-Norpseudoephedrine (NPE), the enantiomer of cathine and a structural analog of phenylpropanolamine, shows anorectic and antidipsic effects that have been referred to its structural analogies with amphetamine. When amphetamine is chronically administered to rats, its anorectic effects fade out, water intake is progressively increased, and the diuretic response to the drug remains stable. Our previous studies show that chronic administration of NPE does not produce the typical amphetamine hyperdipsic response. In the present study, designed to obtain a more detailed picture of the ingestive and diuretic effects of chronic exposure to NPE, we evaluated the effects of 11 daily administrations of three doses of NPE (17, 32, and 56 mg/kg IP) on food and water intake, as well as on diuresis, in rats maintained in conditions of free access to food and water. Results show that all three doses inhibited food intake at 2 h, whereas only the highest dose inhibited food intake at 5 h. No differences between groups were detected at 24 h. These responses remained unchanged throughout the 11 days of treatment, and substitution of NPE with a solvent injection caused no rebound feeding. NPE treatment did not modify the ingestive response to a challenge injection of amphetamine, 0.56 and 1.0 mg/kg IP, given 1 day apart. Although NPE inhibited water intake throughout the experiment, it did so significantly only during the first 2 h postinjection. Urine output in the NPE-treated groups increased significantly on the first day only. These findings make it unlikely that the anorectic effects of NPE depend on an amphetamine-like mechanism of action. In addition, the short-lasting anorectic and antidipsic effects of NPE and the lack of tolerance to them raise the possibility of a therapeutic use of this drug as an adjuvant in the therapy of eating disorders characterized by binge episodes.

Amphetamine↗
PubMed2004

Effects of removal of the acetabular labrum in a sheep hip model.

OBJECTIVE: The aim of this study was to learn whether partial resection of the acetabular labrum would lead to degenerative arthritis in an ovine model. METHODS: A 2 cm segment of labrum was removed from one hip in 18 mature Swiss Alpine sheep and a sham procedure was performed on the opposite side. Animals were permitted ad lib activity until sacrifice at 6, 12 or 24 weeks. The hip joint was removed en bloc, and loaded with a force of one body weight, using a custom device designed to recreate a physiologic joint reaction force. While under load, the joint was plunge frozen, and then fixed by freeze substitution using aldehydes in methanol/acetone solvents. The entire joint was embedded in methacrylate and sectioned in a standardized frontal plane following the reaction force and including the femoral neck and the acetabular fossa. The sections were evaluated for concentricity and evidence of arthrosis. Six hip joints of three sheep with no surgical procedure were loaded with high or low loads and served as non-surgical controls. RESULTS: Degenerative changes were present in all surgical hips, but the changes were symmetrical and mild. In 16 of 18 hips, the labrum regenerated to the extent that dense fibrous scar extending from the surgically denuded origin filled the defect. CONCLUSION: Resection of the labrum does not cause rapid degeneration or altered stability of the sheep hip.

Acetabulum↗
PubMed1975

On the interaction of 3,4,5,6-tetrahydrouridine with human liver cytidine deaminase.

In contrast to the rapid inhibition of bacterial cytidine deaminase by 3,4,5,6-tetrahydrouridine, the onset of inhibition of the enzyme from human liver was found to be relatively slow. Inhibition was found to be reversible, and the corrected rate constants for binding (kon = 2.4 x 10(4) M-1 sec-1) and release (koff = 5.6 x 10(-4) sec-1) were in reasonable agreement with a Ki value (2.9 x 10(-8) M) measured separately under steady-state conditions, which was several orders of magnitude lower than estimates previously reported in the literature. Rates of binding and release of this potential transition state analogue were not appreciably affected by the substitution of deuterium oxide for solvent water. The slow onset of inhibition, which was also observed for cytidine deaminase from HeLa cells, suggests that structural reorganization precedes the formation of a stable enzyme-inhibitor complex. 6-Azacytidine, which favors a "high-anti" configuration at the glycosidic bond, was found to be active as a substrate for cytidine deaminase, with a turnover number exceeding that of cytidine. 2,2'-Anhydro-1-beta-D-arabinofuranosylcytosine, which is restricted to the "syn" configuration, was found to be without activity as a substrate or an inhibitor.

Azacitidine↗
PubMed1998

High-Pressure Oxygen-17 NMR Study of the Dihydroxo-Bridged Rhodium(III) Hydrolytic Dimer. Mechanistic Evidence for Limiting Dissociative Water Exchange Pathways.

Rate constants and activation parameters for water exchange on the Rh(III) hydrolytic dimer [(H(2)O)(4)Rh(&mgr;-OH)(2)Rh(H(2)O)(4)](4+) were determined using (17)O NMR spectroscopy as a function of temperature (308-323 K) and pressure (0.1-150 MPa). This represents the first variable-pressure (17)O NMR study conducted on a polynuclear metal aqua ion. Two pathways for water exchange with similar rates were found for H(2)O coordinated at positions cis (k(cis)) and trans (k(trans)) to the bridging OH groups on the Rh(III) centers. The bridging OH groups were not found to exchange with the bulk solvent, indicating that they are substitution inert on the time scale of these experiments. The kinetic parameters for water exchange on the fully protonated Rh(III) dimer at [H(+)] = 1.0 M and &mgr; = 2.0 M are as follows: k(trans)(298) = 8.5 x 10(-)(7) s(-)(1), DeltaH(trans) = 150 +/- 2 kJ mol(-)(1), DeltaS(trans) = +141 +/- 7 J K(-)(1) mol(-)(1), DeltaV(trans) = +8.5 +/- 0.8 cm(3) mol(-)(1) (+8.5 +/- 0.6 cm(3) mol(-)(1) at [H(+)] = 2.0 M and &mgr; = 3.0 M); k(cis)(298) = 5.4 x 10(-)(7) s(-)(1), DeltaH(cis) = 159 +/- 8 kJ mol(-)(1), DeltaS(cis) = +168 +/- 24 J K(-)(1) mol(-)(1), DeltaV(cis) = +10.1 +/- 0.3 cm(3) mol(-)(1) (+10.9 +/- 1.0 cm(3) mol(-)(1) at [H(+)] = 2.0 M and &mgr; = 3.0 M). In comparison to the water exchange for [Rh(H(2)O)(6)](3+), the introduction of bridging OH groups in the dimer was found to labilize the bound waters but not to the same extent as deprotonation of the monomer. Assuming an expansion of the ground-state partial molar volume of 3-5 cm(3) mol(-)(1) due to the labilizing effect of bridging OH groups in the dimer, the kinetic results suggest a limiting dissociative pathway, D, for water exchange in both the cis and trans positions. It is postulated that dissociation of a more labile trans water molecule in the Rh(III) dimer will lead to a five-coordinate intermediate which can undergo a rapid Berry pseudorotation to account for the similarity in rate and activation parameters for exchange of both cis and trans water molecules.

Journal Article↗
PubMed2002

Social isomers in encapsulation complexes.

We introduce here a new form of isomerism-social isomerism-that arises when two different guests are confined to a cylindrical host capsule. The isomerism deals with the orientationof one guest with respect to the other when they are in a container. Specifically, para-substituted toluenes coencapsulated with typical solvent molecules such as benzene, chloroform, and cyclohexane show two different isomeric arrangements that interconvert slowly on the NMR time scale. The dimensions of the capsule prevent the guests from squeezing past one another or tumbling freely.

Journal Article↗
PubMed2005

Dynamic nature of the transition state for the SN1 reaction mechanism of diphenylmethyl acetates.

Picosecond absorption spectroscopy is employed in the study of the reaction dynamics for the contact ion pairs produced upon the photolysis of a series of substituted diphenylmethyl acetates in the solvents acetonitrile, dimethyl sulfoxide, and 2,2,2-trifluoroethanol. From the temperature dependence of the rate constants, the activation parameters associated with covalent bond formation and diffusional separation to the solvent-separated ion pair are obtained. The activation parameters for bond formation are examined within the context of the Hynes theory for solvent dynamical effects on the passage through the transition state; deviations from the transition-state theory are found to be large. Factors that control nucleophilicity are discussed. Finally the validity of applying the Marcus equation to the SN1 reaction mechanism is addressed.

Acetates↗
PubMed2001

Remote substituent effects on the oxymercuration of 2-substituted norbornenes: an experimental and theoretical study.

The effect of a remote substituent on regioselectivity in the oxymercuration of 2-substituted norbornenes has been investigated experimentally and theoretically using density functional theory (DFT). Regioselectivities of 1:1 to 14:1 were observed with various 2-substituted norbornenes. Exo-2-substituted norbornenes always gave greater regioselectivities compared to the corresponding endo-2-substituted norbornenes. The effects of solvents on the regioselectivity have also been examined, and ethereal solvents were found to be the best choice giving the optimal yield and regioselectivity. The relative rate of oxymercuration was estimated by competition experiments. The least reactive substrate (X = OAc) gave the highest regioselectivity. According to DFT predictions, the increased difference between the reaction barriers that results in the greater regioselectivity is correlated directly with the larger polarity of the C=C double bond, which is attacked by the mercury and oxygen. A number of stable exo and endo conformers were predicted. All exo conformers show the same polarity of the double bond, while some endo conformers have a reversal of this polarity. All the conformers except those with the OAc substituent are very close in energy and thus should react. The existence of a mixture of endo conformers with the C=C double bond of opposite polarity clearly explains a decrease in regioselectivity for the endo species. The origin of the greatest regioselectivity for the OAc-2-norbornenes lies in the fact that the conformer with the largest polarity is notably lower in energy than others due to an internal C-H-O hydrogen bond.

Journal Article↗
PubMed2003

Photochemical generation of a primary vinyl cation from (E)-bromostyrene: mechanisms of formation and reaction.

The photochemistry of (E)-bromostyrene was investigated to determine the nature of the product-forming intermediates and to clarify the mechanism of formation of vinylic cations and vinylic radicals. Both a cation- and a radical-derived product are formed, and the ionic origin of the former product is demonstrated by significant scrambling of the label, starting from specifically deuterated (E)-bromostyrene. MO calculations show that the isolated incipient primary vinyl cation is not a metastable species, but that specific interaction with a counterion in combination with a polar environment makes it metastable. The effects of variation of the wavelength of irradiation, solvent polarity, temperature, and isotopic substitution all agree with a mechanism of direct heterolytic C-Br bond cleavage producing an ion pair followed by formation of a radical pair via electron transfer. The vinylic cation is proposed to stem directly from the indirectly populated lowest excited singlet state of bromostyrene with an energy of activation of 6.7 kcal/mol. Branching between proton loss and electron transfer in the resulting ion pair determines the ratio of cation- to radical-derived product. The E/Z-isomerization occurs in a separate process and does not involve C-Br bond cleavage.

Journal Article↗
PubMed1996

A novel method of preparing PLGA microcapsules utilizing methylethyl ketone.

PURPOSE: To substitute dichloromethane with a safer solvent, a solvent extraction process using methylethyl ketone (MEK) was developed to prepare poly(d,l-lactide-co-glycolide) microcapsules. METHODS: The MEK dispersed phase containing PLGA and progesterone was emulsified in the MEK-saturated aqueous phase (W1) to make a transient oil-in-water (O/W1) emulsion. It was then transferred to a sufficient amount of water (W2) so that MEK residing in polymeric droplets could be extracted effectively into the continuous phase. RESULTS: This solvent extraction process provided the encapsulation efficiency for progesterone ranging from 77 to 60%. The amount of MEK predissolved in W1, as well as the degree of progesterone payload, influenced the encapsulation efficiency. The leaching profile of MEK analyzed by GC substantiated that, upon dispersion of O/W1, to W2, MEK quickly diffused into the continuous phase. Such a rapid diffusion of MEK from and the ingression of water into polymeric droplets produced hollow microcapsules, as evidenced by their SEM micrographs. CONCLUSIONS: When solvent extraction/evaporation techniques are employed for preparing PLGA microcapsules, water-immiscibility of a dispersed phase is not an absolute prerequisite to the successful microencapsulation. Adjustment of an initial extraction rate of MEK and formation of a primary transient O/W1 emulsion are found to be very crucial not only for the success of microencapsulation but also for the determination of microcapsule morphology.

Butanones↗