Conformational preferences of 6-furfuryl amino purine and 6-benzyl amino purine

Conformational preferences of N⁶-furfurylamino purine (kinetin) and N⁶-benzyl amino purine (BAP ) have been investigated theoretically by the quantum chemical perturbative configuration interaction using localized orbitals method. The predicted most stable conformations for these molecules are quite similar. The N⁶ substituents in both these molecules are oriented toward N(1) and away from the imidazole moiety of the purine. The furfuryl ring in kinetin as well as the aromatic benzene ring in BAP are not coplanar with the purine ring. Comparison of these results with the preferred conformation of another compound N⁶-(Δ²-isopentenyl) adenine reveals striking similarity in the orientations of the N⁶ substituents in these cytokinin-active plant-growth-stimulating substances.     

Ultrasound-assisted rapid and efficient synthesis of propargylamines

Ultrasound was used for the addition of metal acetylides to in situ generated imines to generate propargylamines in good to excellent yields using copper iodide in water at ambient temperature. This process is an efficient alternative to traditional heated reactions. A variety of aldehydes and amines were used for this reaction.     

Organic Surface Modification of TEOS Based Silica Aerogels Synthesized by Co-Precursor and Derivatization Methods

The experimental results on the organic modification of tetraethoxysilane (TEOS) based silica aerogels synthesized by co-precursor and derivatization methods are reported and discussed. In order to obtain silica aerogels with better physicochemical properties in terms of higher hydrophobicity, optical transmission and thermal stability, eight organosilane compounds (hydrophobic reagents) of the type R _n SiX_4–n have been used. The molar ratio of tetraethoxysilane (TEOS), ethanol (EtOH), water (0.001 M oxalic acid catalyst) was kept constant at 1:5:7 respectively. The organically modified silica aerogels were produced by two different methods: (i) Co-precursor method and (ii) Derivatization method. In the former method, the molar ratio of hydrophobic reagent (HR) to TEOS was varied from 0.1 to 0.6. In the later method, derivatization of the wet gels was carried out using 20% hydrophobic reagent in methanol. The merits and demerits of both these methods have been presented. The organic surface modification of the aerogels was confirmed by the Fourier Transform Infrared (FTIR) spectroscopic studies and the contact angle measurements. In the co-precursor method, with the increase in hydrophobic reagent/TEOS molar ratio, the hydrophobicity increases ( = 136°) and the optical transmission decreases (5%), whereas in the derivatization method the optical transmission is very high (T 85%) but the hydrophobicity is low ( = 120°). The thermal stability of the hydrophobic aerogels (the temperature up to which the hydrophobicity is retained) was studied in the temperature range of 25–800°C. The aerogels based on the co-precursor method retained the hydrophobicity up to a temperature as high as 520°C and on the other hand, the derivatized aerogels are hydrophobic only up to a temperature of 285°C. For the first time, TEOS based hydrophobic silica aerogels have been obtained with negligible volume shrinkage using the trimethylethoxysilane (TMES) co-precursor. The aerogels were characterized by Fourier transform infrared spectroscopy (FTIR), optical transmittance, Scanning Electron Microscope (SEM), thermogravimetric (TG) and differential thermal (DT) analyses and the contact angle measurements.     

The compensation effect

This paper is a rebuttal to the paper of Zsakó and Somasekharan. It has been shown that the criticisms of Zsakó and Somasekharan are baseless. The procedure proposed earlier by Agrawal to distinguish between true and false compensation effect is reasonable and gives good results. To establish true c.e., it has been reaffirmed that bothT _iso and Ink _iso are prerequisite.The author would like to thank the reviewer for his constructive criticisms.     

Supported aqueous-phase enzymatic catalysis in organic media

The use of partially hydrated porous silica particles has been studied as a support for cofactor-dependent enzymatic catalysis in organic solvents. At an optimal pore hydration corresponding to 70% pore volume, horse liver alcohol dehydrogenase catalyzes the oxidation and reduction of alcohols and aldehydes, respectively, with rates sixfold higher than with nonporous glass beads as the enzymatic support and with cofactor recycling numbers in excess of 10⁵. Thus, supported aqueous-phase enzymatic catalysis makes highly effective use of the enzyme and cofactor by coimmobilization and by providing a high interfacial area for reactions in organic media.     

Oligodeoxynucleotides containing alpha-L-ribo configured LNA-type C-aryl nucleotides

Synthesis of 2[prime or minute]-O,4[prime or minute]-C-methylene-[small alpha]-l-ribofuranosyl derivatives containing phenyl and 1-pyrenyl aglycons, i.e., novel [small alpha]-l-ribo configured LNA-type C-aryl nucleosides, has been accomplished. Key synthetic steps included stereoselective Grignard reactions on tetrahydrofuran aldehyde, configurational inversion of the resulting alcohol into alcohol, and concomitant Mitsonobu cyclization furnishing the desired bicyclic furanosyl skeleton with a locked conformation. The phosphoramidite derivatives and were used for automated synthesis of 9-mer DNA and [small alpha]-L-LNA oligonucleotides containing the [small alpha]-L-LNA-type C-aryl monomers ([small alpha]L)Ph(L) and ([small alpha]L)Py(L) containing a phenyl and pyrenyl aglycon, respectively. Thermal denaturation studies showed universal base pairing behavior for the pyrenyl monomer ([small alpha]L)Py(L) when incorporated into a DNA or an [small alpha]-L-LNA oligonucleotide.     

New scaling algorithms for the assignment and minimum mean cycle problems

In this paper we suggest new scaling algorithms for the assignment and minimum mean cycle problems. Our assignment algorithm is based on applying scaling to a hybrid version of the recentauction algorithm of Bertsekas and the successive shortest path algorithm. The algorithm proceeds by relaxing the optimality conditions, and the amount of relaxation is successively reduced to zero. On a network with 2n nodes,m arcs, and integer arc costs bounded byC, the algorithm runs in O( m log(nC)) time and uses very simple data structures. This time bound is comparable to the time taken by Gabow and Tarjan's scaling algorithm, and is better than all other time bounds under thesimilarity assumption, i.e.,C = O(n ^k ) for somek. We next consider the minimum mean cycle problem. Themean cost of a cycle is defined as the cost of the cycle divided by the number of arcs it contains. Theminimum mean cycle problem is to identify a cycle whose mean cost is minimum. We show that by using ideas of the assignment algorithm in an approximate binary search procedure, the minimum mean cycle problem can also be solved in O( m lognC) time. Under the similarity assumption, this is the best available time bound to solve the minimum mean cycle problem.     

Multilabeled pyrene-functionalized 2'-amino-LNA probes for nucleic acid detection in homogeneous fluorescence assays

Homogeneous fluorescence assays for detection of nucleic acids are widely used in biological sciences. Typically, probes such as molecular beacons that rely on distance-dependent fluorescence quenching are used for such assays. Less attention has been devoted to tethering a single kind of fluorophores to oligonucleotides and exploiting hybridization-induced modulation of fluorescence intensity for nucleic acid detection. Herein, thermal denaturation experiments and fluorescence properties of oligodeoxyribonucleotides containing one or more 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA monomer(s) X are described. These pyrene-functionalized 2'-amino-LNAs display large increases in thermal stability against DNA/RNA complements with excellent Watson-Crick mismatch discrimination. Upon duplex formation of appropriately designed 2'-N-(pyren-1-yl)carbonyl-2'-amino-LNA probes and complementary DNA/RNA, intensive fluorescence emission with quantum yields between 0.28 and 0.99 are observed. Quantum yields of such magnitudes are unprecedented among pyrene-labeled oligonucleotides. Molecular modeling studies suggest that the dioxabicyclo[2.2.1]heptane skeleton and amide linkage of monomer X fix the orientation of the pyrene moiety in the minor groove of a nucleic acid duplex. Interactions between pyrene and nucleobases, which typically lead to quenching of fluorescence, are thereby reduced. Duplexes between multiple modified probes and DNA/RNA complements exhibit additive increases in fluorescence intensity, while the fluorescence of single stranded probes becomes increasingly quenched. Up to 69-fold increase in fluorescence intensity (measured at lambda(em) = 383 nm) is observed upon hybridization to DNA/RNA. The emission from duplexes of multiple modified probes and DNA/RNA at concentrations down to less than 500 nM can easily be seen by the naked eye using standard illumination intensities.     

Kinetics of aquation and base hydrolysis ofcis-(carboxylato) (ethylamine)bis(ethylenediamine)cobalt(III) ions

Summary The aquation ofcis-[Co(en)₂(NH₂Et)O₂CR]²⁺ [R=H or Me] is strongly acid-catalysed and the rate and activation parameters for this process are reported. No significant rate difference is observed in the spontaneous aquation path for the complexes. The acetato complex undergoes acid catalysed aquation at a rate comparable to the of the corresponding formato complex, in contrast with the relative basicities of the coordinated formate and acetate. This result is interpreted in terms of relative solvation effects of the initial and transition states of both complexes.The base hydrolysis of both complexes obeys overall second order kinetics in the 0.05[OH^–]_T 0.35 mol dm^–3 range (I=0.5 mol dm^–3). The formato complex reacts five times faster than its acetato analogue under comparable conditions, which is fully consistent with the dissociative mode of activation of the amido conjugate base involving Co–O bond heterolysis. A substantially large positive value for the activation entropy supports SN₁CB mechanism for base hydrolysis.     

New efficient total syntheses of derivatives of protoporphyrin-IX bearing deuteriated methyl groups

New total syntheses of hemins which are regioselectively deuteriated in the 1,5 (2), 5 (3) or 8 (4) methyl groups are described. Syntheses of hemins 2 and 3 follow the progression from pyrromethane 12 to t-butyl tripyrrene-carboxylate hydrobromide (17 and 30) and then to a,c-biladiene dihydrobromide (19 and 31), but for reasons of economy in use of labeled monopyrroles, the o,c-biladiene dihydrobromide 40 for hemin 4 is approached in an initially “clockwise” manner by synthesis of a benzyl tripyrrene-carboxylate hydrobromide 37 from the pyrromethane 5. Cyclization of the a,c-biladienes (19, 31, and 40) was accomplished by brief heating in dimethylformamide in the presence of copper(II) chloride.