Where is the sodium in self-assembled monolayers of single-stranded DNA?

Monolayers of single-stranded DNA (ssDNA) immobilized on surfaces form the basis of a number of important biotechnology applications, including DNA microarrays and biosensors. The organization of ssDNA as layer on a solid substrate allows one to investigate various properties of the DNA in a controlled manner and to use DNA for analytical applications as well as for exploring futuristic schemes for molecular electronics. It is commonly assumed that the adsorbed DNA layer contains some structural water and the cations. Here we show, based on XPS studies, that when monolayers of ssDNA are formed from sodium phosphate buffer and washed thoroughly, no Na+ signal is detected. A finite concentration of ions is observed when the DNA is made from a solution of Mg2+ ions, but it is still only a fifth of what it would be if all the phosphate ions were fully neutralized by the metal cations.     

Use of cluster expansion techniques in quantum chemistry. A linear response model for calculating energy differences

In this paper we have reviewed the theoretical framework of the coupled-cluster (cc) based linear response model as a tool for directly calculating energy differences of spectroscopic interest like excitation energy (ee), ionisation potential (ip) or electron affinity (ea). In this model, the ground state of a many-electron system is described as in a coupled cluster theory for closed shells. The electronic ground state is supposed to interact with an external photon field of frequencyw, and the poles of the linear response function as a function ofw furnish with the elementary excitations of the system. Depending on the general form of the coupling term chosen, appropriate difference energies like ee, ip or EA may be generated. Pertinent derivations of the general working equations are reviewed, and specific details as well as approximations for ee, ip or ea are indicated. It is shown that the theory bears a close resemblance to the equation of motion (eom) method but is superior to the latter in that the ground state correlation is taken to all orders and may be looked upon as essentially a variant of renormalisedtda. A perturbative analysis elucidating the underlying perturbative structure of the formulation is also given which reveals that the theory has a hybrid structure: the correlation terms are treated akin to an open shellmbpt, while the relaxation terms are treated akin to a Green function theory. A critique of the methodvis-a-vis other cc-based approaches for difference energies forms the concluding part of our review.     

Silicon clusters: chemistry and structure

The chemical reactions of size selected silicon cluster ions (containing up to 70 atoms) have been studied with a number of different reagents using injected ion drift tube techniques. Both kinetic and equilibrium measurements have been performed as a function of temperature, and the influence of cluster annealing on chemical reactivity explored. Unlike metal clusters, where bulk behavior appears to be approached with around 30 atoms, large silicon clusters (n up to 70) are much less reactive than bulk silicon surfaces. These results suggest that the clusters in the size range examined here are not small crystals of bulk silicon, but have compact, high coordination number structures with few dangling bonds.     

A high yielding, one-pot synthesis of O,S-dialkyl dithiocarbonates from alcohols using Mitsunobu’s reagent

A novel Mitsunobu-based protocol has been developed for the synthesis of O,S-dialkyl dithiocarbonates from a variety of primary, secondary and tertiary alcohols using carbon disulfide, in good to excellent yields. This protocol is mild and efficient compared to other reported methods.     

Enantiomeric separation and quantification of fluoxetine (Prozac) in human plasma by liquid chromatography/tandem mass spectrometry using liquid-liquid extraction in 96-well plate format

Fluoxetine (Prozac) is currently one of the widely prescribed selective serotonin reuptake inhibitors (SSRIs) for the treatment of depression. A high-throughput sample preparation procedure using liquid-liquid extraction (LLE) in a 96-well plate format in conjunction with liquid chromatography/tandem mass spectrometry (LC/MS/MS) was developed and validated for quantification of fluoxetine enantiomers in human plasma. After addition of internal standard and ammonium hydroxide, samples were extracted with ethyl acetate. The organic extract was evaporated to dryness and reconstituted in methanol. Where possible, sample transfer and LLE steps were automated using a Tomtec Quadra 96 workstation. Adequate separation of fluoxetine enantiomeric pairs (resolution of 1.17) was achieved on a vancomycin column eluted with methanol containing 0.075% (by weight) ammonium trifluoroacetate. A triple quadrupole mass spectrometer, operated in the multiple reaction monitoring mode at m/z 310-->44 for fluoxetine enantiomeric pairs and m/z 287-->241 for oxazepam (internal standard), was used. Analysis was performed in the positive ion mode using atmospheric pressure chemical ionization (APCI). The standard curve range was 2.0-1000 ng/mL for each fluoxetine enantiomer. The intra- and inter-day precision and accuracy of the quality control (QC) samples were <12.5% (CV) and <13.6% (CV), respectively, for each fluoxetine enantiomer; the correlation coefficient was >0.990. Method ruggedness was demonstrated by the reproducible performance of the assay during a three-day validation period.     

Stereocontrolled synthesis of cis-dibenzoquinolizine chlorofumarates: curare-like agents of ultrashort duration

The quaternizations of dibenzoquinolizines 9 and 14 with 3-halo-1-propanols are highly cis-selective (94-100% cis), results consistent with the N-methylation of O-methylcapaurine (7b), but in contrast to the proposed trans-stereochemistry of dibenzo[a,h]quinolizine methiodide 10 and the analogous quaternizations of 1-benzyl- and 1-phenylisoquinoline congeners 5b and 5c. In this report, we describe stereoselective preparation of the unique cis-dibenzoquinolizinium propanols 15 and 16and their transformation into bis- and mixed-onium chlorofumarates 19, 20ab, and 26. Dibenzo[a,g]quinolizinium propanol 15 was prepared enantioselectively in three steps from dihydroisoquinoline 11. Asymmetric transfer hydrogenation of 11 in the presence of triethylamine/formic acid and Noyori's chiral ruthenium catalyst 12 produced R-(-)-5',8-dimethoxynorlaudanosine (13) in 98% yield and 87% ee. Pictet-Spengler cyclization of 13 in formalin/formic acid afforded the dibenzo[a,g]quinolizine 14 in 65% yield. Quaternization of 14 with 3-chloro-1-propanol under Finkelstein conditions generated cis-dibenzoquinolizinium propanol 15 in 85% yield with >94% cis-selectivity. The cis-dibenzo[a,h]quinolizinium propanol 16 was obtained as a single stereoisomer by reaction of the known tetramethoxyquinolizine 9 with neat 3-iodo-1-propanol. Bis-onium chlorofumarates 18 and 19 and the mixed-onium derivative 20ab were prepared by a pool synthesis procedure from (1R)-trans-6a, 16, and chlorofumaryl chloride (17). Mixed-onium alpha-chlorofumarate 26 was synthesized from (1S)-trans-6d, 15 and (+/-)-trans-2,3-dichlorosuccinic anhydride (22), employing a recently disclosed chlorofumarate mixed-diester synthesis. The title compounds (19, 20ab, and 26) displayed curare-like effects of ultrashort duration in rhesus monkeys.     

An interesting ring contraction of a class of bromohydrins and trans-dibromides

An efficient ring contraction of stereoisomeric 1,2-benzo-4-bromo-3-hydroxycyclohept-1-ene and their derivatives (1a-e) to (2a-c) is reported, and a probable mechanism for this ring contraction has been suggested.     

Floating spherical Gaussian orbital model study of average electric polarisabilities and magnetic susceptibilities: Some aliphatic hydrocarbons

Floating spherical Gaussian orbital model is used to discuss the average electric polarisabilities and magnetic susceptibilities of a series of hydrocarbons. It has been noticed that the core contributions are negligibly small and these quantities (average electric polarisabilities and magnetic susceptibilities) can be well estimated from contributions localised on bond Gaussians.     

o-hydroxylmethylphenylchalcogens: synthesis, intramolecular nonbonded chalcogen...OH interactions, and glutathione peroxidase-like activity

[Structure: see text]. The synthesis and characterization of a series of organochalcogen (Se, Te) compounds derived from benzyl alcohol 13 are described. The synthesis of the key precursor dichalcogenides 15, 22, and 29 was achieved by the ortho-lithiation route. Selenide 18 was obtained by the reaction of the dilithiated derivative 14 with Se(dtc)2. Oxidation of 15 and 22 with H2O2 afforded the corresponding cyclic ester derivatives 17 and 24, respectively. Oxidation of selenide 18 with H2O2 affords the spirocyclic compound 19. The presence of intramolecular interactions in dichalcogenides 15 and 22 has been proven by single-crystal X-ray studies. The cyclic compounds 17 and 19 have also been characterized by single-crystal X-ray studies. GP(X)-like antioxidant activity of selenium compounds has been evaluated by the coupled bioassay method. Density functional theory calculations at the mPW1PW91 level on ditelluride 22 have identified a fairly strong nonbonding interaction between the hydroxy oxygen and tellurium atom. The second-order perturbation energy obtained through NBO analysis conveys the involvement of n(O) --> sigma(Te-Te) orbital overlap in nonbonding interaction. Post wave function analysis with the Atoms in Molecules (AIM) method identified distinct bond critical point in 15 and 22 and also indicated that the nonbonding interaction is predominantly covalent. Comparison between diselenide 15 and ditelluride 22 using the extent of orbital interaction as well as the value of electron density at the bond critical points unequivocally established that a ditelluride could be a better acceptor in nonbonding interaction, when the hydroxy group acts as the donor.