Atomistic Modeling of Silica Based Sol-Gel Processes

Density Functional Theory is used to study water, methanol, ethanol, TMOS, and TEOS molecules and the most important silica clusters participating in sol-gel processes. Calculated bond lengths, bond angles and electric dipole moments compare well with experimental data. The energy of these molecules is reported and used to discuss the energetics of the hydrolysis and condensation reactions. Molecular Dynamics is employed to simulate liquid water, methanol, ethanol, TMOS, TEOS and experimental sol-gel solutions. Calculated densities and enthalpies of vaporisation compare well with experimental data. Preliminary results are presented for MD simulations of sol-gel solutions.     

Sonoluminescence quenching of organic compounds in aqueous solution: frequency effects and implications for sonochemistry

Solute-induced quenching of sonoluminescence (SL) is reported for aqueous solutions of two homologous series of methyl esters and ketones using low (20 kHz) and high (515 kHz) ultrasound frequencies. SL data at 20 kHz from aqueous solutions containing alcohols and carboxylic acids are also presented to compare with previously published results at 515 kHz. In addition to supporting the previous findings on the existence of stable and transient bubbles at 515 and 20 kHz, respectively, the results suggest that the hydrogen-bonding characteristics of the solutes also play a major role in the extent of SL quenching. An increase in the SL intensity at low concentrations for most of the solutes suggests that these solutes increase the number of "active" bubbles by hindering the coalescence of bubbles. It is concluded that the effect of the solutes on the SL signal from aqueous solutions at both frequencies is primarily due to the balance of two factors, namely, the incorporation of solute within the bubble, leading to SL quenching, and the prevention of coalescence of the bubbles, leading to SL enhancement. At the higher frequency, SL quenching by the solutes is the main influence on the emission yield. However, at the lower frequency, hindrance to coalescence by the solutes dominates at lower concentrations and leads to SL enhancement. The implications of these results for optimizing conditions for aqueous sonochemical reactions are discussed.     

On the representation of electrostatic fields around ab initio charge distributions

Summary We compare two methods (Mulliken charges and a distributed multipole analysis, DMA) of representing an ab initio charge distribution for calculating the electrostatic field and potential outside the molecule, using pyrimidine and the RNA base uracil as examples. This is done using a 3-D graphical display of the electrostatic fields, which, when used with real-time rotation, zooming and clipping, has many advantages for qualitatively assessing the electrostatic interactions of a molecule. The errors involved in using Mulliken point charges may be of similar magnitude to the total electrostatic field in regions which are important in recognition processes. The DMA representation automatically includes the anisotropic electrostatic effects of non-spherical features in the charge distribution of each atom, and yet the displayed electrostatic fields around the atoms which have lone-pair density do not show marked anisotropy.     

HPLC of 9-fluorenylmethylchloroformate-polyamine derivatives with fluorescence detection

Summary There are a number of reagents available for fluorescent labelling of primary amines. These include dansyl chloride, o-phthalaldehyde, fluorescamine, and a new reagent, 9-fluorenylmethylchloroformate (FMOC), reported recently. This paper describes a reversed-phase HPLC procedure for the separation and fluorescence detection of polyamines following pre-column derivatization with FMOC. The polyamines studied by this method include putrescine, cadaverine, spermidine, and spermine. Experiments were carried out to determine maximum fluorescence excitation and emission wavelengths, optimum reaction pH, linear ranges, and minimum detection limits for each of the polyamines. The HPLC method includes a gradient program which provides complete separation from serum hydrolysate components and specificity for the four polyamines with detection limits ranging from 2 to 9 pg. This procedure was applied to hydrolyzed serum samples.     

Bridged to Fused Ring Interchange. Methodology for the Construction of Fused Cycloheptanes and Cyclooctanes. Total Syntheses of Ledol, Ledene, and Compressanolide

The type two intramolecular Diels-Alder reaction (T2IMDA) is an efficient method for the formation of medium rings. The methodology is particularly effective for the construction of seven- and eight-membered rings. A strategy for the synthesis of functionalized cycloheptanes and cyclooctanes has been developed that involves a bridged to fused ring interchange. The T2IMDA provides a synthesis for rigid bridged bicyclic molecules that can be stereoselectively elaborated before ozonolysis of the bridgehead double bond. Following oxidative cleavage, aldol condensation provides fused bicyclic ring systems that otherwise are difficult to synthesize. This methodology is amenable to the synthesis of terpene natural products. This is demonstrated here through total syntheses of (+/-)-ledol and (+/-)-ledene and a formal synthesis of (+/-)-compressanolide.     

Sampling unfolding intermediates in calmodulin by single-molecule spectroscopy

We used single-pair fluorescence resonance energy transfer (spFRET) measurements to characterize denatured and partially denatured states of the multidomain calcium signaling protein calmodulin (CaM) in both its apo and Ca(2+)-bound forms. The results demonstrate the existence of an unfolding intermediate. A CaM mutant (CaM-T34C-T110C) was doubly labeled with fluorescent probes AlexaFlour 488 and Texas Red at opposing globular domains. Single-molecule distributions of the distance between fluorophores were obtained by spFRET at varying levels of the denaturant urea. Multiple conformational states of CaM were observed, and the amplitude of each conformation was dependent on urea concentration, with the amplitude of an extended conformation increasing upon denaturation. The distributions at intermediate urea concentrations could not be adequately described as a combination of native and denatured conformations, showing that CaM does not denature via a two-state process and demonstrating that at least one intermediate is present. The intermediate conformations formed upon addition of urea were different for Ca(2+)-CaM and apoCaM. An increase in the amplitude of a compact conformation in CaM was observed for apoCaM but not for Ca(2+)-CAM upon the addition of urea. The changes in the single-molecule distributions of CaM upon denaturation can be described by either a range of intermediate structures or by the presence of a single unfolding intermediate that grows in amplitude upon denaturation. A model for stepwise unfolding of CaM is suggested in which the domains of CaM unfold sequentially.     

Quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry: A study of ion suppression

The effect of coeluting matrix compounds on the quantitation of SR 27417 in human plasma using electrospray liquid chromatography-tandem mass spectrometry has been examined. During the method development stage of this assay, plasma samples spiked with the analyte at 100 pg/mL were extracted using three different procedures: a hexane liquid-liquid extraction, an ethyl acetate back-extraction, and a solid phase extraction. Ion intensity of the analyte was found to be related inversely to the percent ionization of coeluting matrix components as evidenced by full scan spectra. The ethyl acetate back-extraction, which contained the fewest coeluting components, resulted in the highest ion intensity for the analyte. An assay comparison was done by using the liquid-liquid hexane and the ethyl acetate back-extractions for sample preparation. Replicate 1-mL samples (n=5) at 11 concentrations from 5 to 2000 pg/mL were extracted and analyzed. The results for the ethyl acetate back-extracted samples were acceptable from 2000 to 5 pg/mL with accuracy ranging from ?11.6 to 2.61% of the nominal concentrations. In contrast, the hexane liquid-liquid method had poor accuracy and precision below 20 pg/mL. The difference is explained by suppression of analyte ion intensity. These results are consistent with the current theory of electrospray ionization.     

Design and Construction of a Pulsed Field-Gradient NMR Probe for a High-Field Superconducting Magnet

We describe the design and construction of a high-resolution pulsed field-gradient NMR probe for use in a high-field superconducting magnet. Overview and details of the design and construction of the probe case, rf circuitry, temperature control and shielded gradient coils for a heteronuclear probe suitable for a spectrometer (Bruker MSL-300) equipped with a wide bore (i.e., 89 mm) magnet (Oxford) are given. The interior of the probe is designed so mat it may be easily moved to variable height so as to accept easily various gradient coils. A design for a novel jig for the winding of saddle-geometry rf coils is given.     

Ionization of five aqueous fluorobenzoic acids: Conductance and thermodynamics

The three monofluorobenzoic acids together with 2,4-difluoro and 2,6-difluorobenzoic acids in aqueous solution are the subject of precision conductance measurements. The experimental data are analyzed to give ionization constants and limiting conductances at temperatures from 0 to 100°C. Walden products for the acid anions are derived from the limiting conductances while the ionization consatants are fitted by statistical methods to the function pK _a (m)=A+B/T+ C logT+DT. Only the 2,6- acid requires the fourth term of the function to fit the data to a precision of better than 0.03%. Mathematical analysis of the pK function gives the standard changes in enthalpy, entropy, and heat capacity. All the acids studied are more acidic than the parent, benzoic acid, as well as more acidic than the isoelectronic methylbenzoic acids. In general the increased acidity is tied to decreases in enthalpy while entropy changes on ionization differn little from those found for the parent acid.