The hydrogen bonding properties of cytosine: a computational study of cytosine complexed with hydrogen fluoride, water, and ammonia

Density functional theory is used to study the hydrogen bonding pattern in cytosine, which does not contain alternating proton donor and acceptor sites and therefore is unique compared with the other pyrimidines. Complexes between various small molecules (HF, H(2)O, and NH(3)) and four main binding sites in (neutral and (N1) anionic) cytosine are considered. Two complexes (O2(N1) and N3(N4)) involve neighboring cytosine proton acceptor and donor sites, which leads to cooperative interactions and bidendate hydrogen bonds. The third (less stable) complex (N4) involves a single cytosine donor. The final (O2-N3) complex involves two cytosine proton acceptors, which leads to an anticooperative hydrogen bonding pattern for H(2)O and NH(3). On the neutral surface, the anticooperative O2-N3 complex is less stable than those involving bidentate hydrogen bonds, and the H(2)O complex cannot be characterized when diffuse functions are included in the (6-31G(d,p)) basis set. On the contrary, the anionic O2-N3 structure is the most stable complex, while the HF and H(2)O N3(N4) complexes cannot be characterized with diffuse functions. B3LYP and MP2 potential energy surface scans are used to consider the relationship between the water N3(N4) and O2-N3 complexes. These calculations reveal that diffuse functions reduce the conversion barrier between the two complexes on both the neutral and anionic surfaces, where the reduction leads to a (O2-N3) energy plateau on the neutral surface and complete (N3(N4)) complex destabilization on the anionic surface. From these complexes, the effects of hydrogen bonds on the (N1) acidity of cytosine are determined, and it is found that the trends in the effects of hydrogen bonds on the (N1) acidity are similar for all pyrimidines.     

The first example of regiospecific magnesium carbenoid 1,3-CH insertion: its mechanism and stereochemistry

Addition reaction of two geometrical isomers of 1-chlorovinyl p-tolyl sulfoxides, derived from unsymmetrical ketones and chloromethyl p-tolyl sulfoxide, with lithium enolate of tert-butyl acetate gave single isomers of the adduct, respectively. Treatment of each diastereomer with i-PrMgCl resulted in the formation of magnesium carbenoids. Highly regiospecific 1,3-CH insertion reaction was found to take place from the magnesium carbenoids to afford cyclopropanes in high yields. Stereochemistry of the adducts, reaction mechanism, and origin of the regiospecificity are discussed.     

A deterministic algorithm for constrained enumeration of transmembrane protein folds

A deterministic algorithm for enumeration of transmembrane protein folds is presented. Using a set of sparse pairwise atomic distance constraints (such as those obtained from chemical cross-linking, FRET, or dipolar EPR experiments), the algorithm performs an exhaustive search of secondary structure element packing conformations distributed throughout the entire conformational space. The end result is a set of distinct protein conformations, which can be scored and refined as part of a process designed for computational elucidation of transmembrane protein structures.     

Microchip electrophoretic protein separation using electroosmotic flow induced by dynamic sodium dodecyl sulfate-coating of uncoated plastic chips

Separation of sodium dodecyl sulfate (SDS)-protein complexes is difficult on plastic microchips due to protein adsorption onto the wall. In this paper, we elucidated the reasons for the difficulties in separating SDS-protein complexes on plastic microchips, and we then demonstrated an effective method for separating proteins using polymethyl methacrylate (PMMA) microchips. Separation difficulties were found to be dependent on adsorption of SDS onto the hydrophobic surface of the channel, by which cathodic electroosmotic flow (EOF; reversed flow) was generated. Our developed method effectively utilized the reversed flow from this cathodic EOF as a driving force for sample proteins using permanently uncoated but dynamic SDS-coated PMMA microchips. High-speed (6 s) separation of proteins and peptides up to 116 kDa was successfully achieved using this system.     

Starburst dendrimer-supported pseudostationary phases for electrokinetic chromatography

Pseudo-stationary phases for electrokinetic chromatography were prepared by the alkylation of starburst dendrimers (SBDs). The SBD-supported pseudo-stationary phase with dodecyl groups showed higher efficiency than short-akyl derivatives, and maintained the hydrophobic property inthe presence of methanol. The dodecyl-modified SBD provided wide migration time windows ar high methanol content to effect the separation of sixteen aromatic hydrocarbons, the priority pollutants designated by EPA, in 65% methanol. The selectivity of polymer-supported pseudo-stationary phase can be varied simply by changing the length of the alkyl groups. The dodecyl SBD showed relatively similar selectivity as sodium dodecyl culfate micelle, whereas short alkyl derivatives showed preference towards rigid and planar compounds based on the rigid and planar compounds based on the rigid polymer backbones. The selectivity of SBD-supported pseudo-stationary phases was dominated by the chain length of the alkyl groups, with the minor effect of the structure of the core and the generation of SBD where alkyl groups were attached.     

Evaluation of postoperative hepatobiliary function by deconvolution analysis of hepatobiliary image data by 99mTc-N-pyridoxyl-5-methyltryptophan

Dynamic hepatobiliary image data were analyzed by the mathematical deconvolution to derive the transfer function (TF) which represents the impulse response function of the liver following direct bolus injection of a tracer into the liver. Biliary flow was evaluated by TF in patients with previous hepatobiliary surgery to detect abnormal flow causing problems such as cholangitis. Serial image data were collected for 60 min after intravenous injection of 37-75 MBq (1-2 mCi) of 99mTc-N-pyridoxyl-5-methyltryptophan (99mTc-PMT). TF was obtained by the matrix algorithm, using regional hepatogram as output and time-activity curve over the heart as input function. Minimum, mean and maximum transit time (Max. TT) were determined from TF. The functional image for each of the transit times was constructed by displaying the distribution of the values for matrix elements with a color scale. In this study, a critical Max. TT of 60 min was used to detect abnormal biliary flow. Of 30 cases, 9 positive cases were discriminated from 21 negative cases on the basis of the finding of presence or absence of areas with Max. TT of more than 60 min anywhere in the liver. Bowel activity overlapping the liver was excluded in the judgment. The validity of this method was evaluated in comparison with the clinical courses after surgery with (8 cases) or without (22 cases) problems. The results were sensitivity of 88%, specificity of 91%, accuracy of 90% and positive predictive value of 78%.(ABSTRACT TRUNCATED AT 250 WORDS)     

Study on Segmental Motion and Ion Binding in Polyelectrolyte Solutions by Ultrasonic Spectroscopy

The ultrasonic absorption spectra of aqueous solutions of polyacrylate (PA), polyphosphate (PP), and polystyrenesulfonate (PSS), neutralized by tetramethylammonium hydroxide (TMAOH), were measured. The effects of addition of tetramethylammonium chloride (TMACl) and sodium chloride (NaCl) to the polyelectrolyte solutions were investigated in the frequency range from 500 kHz to 100 MHz. Two ultrasonic relaxation processes due to the local segmental motions were observed. The relaxation frequency for TMAPP solution decreased as the ionic strength was increased by the addition of TMACl. For the other two polymer solutions, the ionic strength did not affect the relaxation spectra. The addition of NaCl led to an increase of the ultrasonic absorption, which was ascribed to ion binding. The ultrasonic absorption due to the ion binding was estimated by subtracting the contribution of the segmental motion from the measuring ultrasonic spectra. The volume changes accompanying the ion binding for polyacrylate and polyphosphate salts were estimated to be 5 and 8 cm³-mol^?1, respectively.     

Preconcentration of palladium(II) from water with thionalide loaded on silica gel

2-Mercapto-N-2-naphthylacetamide (thionalide) on silica gel is used for rapid preconcentration of μg l^?1 levels of palladium(II) from aqueous solution, followed by atomic absorption spectrometric measurement. In batch experiments, palladium was quantitatively retained on the gel from solutions 5 M in acid to pH 8; equilibrium was achieved within 10 s. The chelating capacity of the gel was 7.5 μmol Pd g^?1 at pH < 4. The effect of flow rate on retention was studied. Palladium retained on the column was completely eluted with 20 ml of 0.2 M thiourea in 0.1 M hydrochloric acid. The palladium concentration in sea water is shown to be < 0.3 μg l^?1.