Stereochemistry of 2'-5' linked nucleic acids: crystal and molecular structure of ammonium adenylyl-2',5'-adenosine tetrahydrate: a core fragment of 2'-5' oligo A's produced by interferon induced adenylate synthetase

The preponderance of 3'-5' phosphodiester links in nucleic acids is well known. Albeit less prevalent, the 2'-5' links are specifically utilised in the formation of 'lariat' in group II introns and in the msDNA-RNA junction in myxobacterium. As a sequel to our earlier study on cytidylyl-2',5'-adenosine we have now obtained the crystal structure of adenylyl-2',5'-adenosine (A2'p5'A) at atomic resolution. This dinucleoside monophosphate crystallizes in the orthorhombic space group P2(1)2(1)2(1) with a = 7.956(3) A, b = 12.212(3) A and c = 36.654(3) A. CuK alpha intensity data were collected on a diffractometer. The structure was sloved by direct methods and refined by full matrix least squares methods to R = 10.8%. The 2' terminal adenine is in the commonly observed anti (chi 2 = 161 degrees) conformation and the 5' terminal base has a syn (chi 1 = 55 degrees) conformation more often seen in purine nucleotides. A noteworthy feature of A2'p5'A is the intranucleotide hydrogen bond between N3 and O5' atoms of the 5' adenine base. The two furanose rings in A2'p5'A show different conformations - C2' endo, C3' endo puckering for the 5' and 2' ends respectively. In this structure too there is a stacking of the purine base on the ribose O4' just as in other 2'-5' dinucleoside structures, a feature characteristically seen in the left handed Z DNA. In having syn, anti conformation about the glycosyl bonds, C2' endo, C3' endo mixed sugar puckering and N3-O5' intramolecular hydrogen bond A2'p5'A resembles its 3'-5' analogue and several other 2'-5' dinucleoside monophosphate structures solved so far. Striking similarities between the 2'-5' dinucleoside monophosphate structures suggest that the conformation of the 5'-end nucleoside dictates the conformation of the 2' end nucleoside. Also, the 2'-5' dimers do not favour formation of miniature classical double helical structures like the 3'-5' dimers. It is conceivable, 2-5(A) could be using the stereochemical features of A2'p5'A which accounts for its higher activity.

Synthesis of Layered Perovskite Oxides, ACa2-xLaxNb3-xTix010 (A = K, Rb, Cs), and Characterization of New Solid Acids, HCa2-xLaxNb3-xTixOlo (0 < x d 2), Exhibiting Variable Bronsted Acidity?

Layered perovskite oxides of the formula ACa~,La,Nb3-,Ti,010 (A = K, Rb, Cs and 0 < x d 2) have been prepared. The members adopt the structures of the parent ACazNb3010. Interlayer alkali cations in the niobium-titanium oxide series can be ion-exchanged with Li+, Na+, NH4+, or H+ to give new derivatives. Intercalation of the protonated derivatives with organic bases reveals that the Bronsted acidity of the solid solution series, HC~ ~ , L ~ ,N~ ~ , T ~ ,dOep~eOnd, s on the titanium content. While the x = 1 member (HCaLaNbzTiOlo) is nearly as acidic as the parent HCazNb3010, the x = 2 member (HLazNbTizOlo) is a weak acid hardly intercalating organic bases with pKa - 11.3. The variation of acidity is probably due to an ordering of Nb/Ti atoms in the triple octahedral perovskite slabs, [Ca~,La,Nb~,Ti,0~0], such that protons are attached to NbO6 octahedra in the x = 1 member and to Ti06 octahedra in the x = 2 member.

Asymmetric Diels-Alder Reactions of Chiral Acrylates of Cholic Acid Derivatives

New steroid-based chiral auxiliaries 6, 9, and 12 have been synthesized from readily available cholic acid. These new chiral auxiliaries place the reactive and the shielding sites in a 1,5 relationship to each other. Diels-Alder reaction of cyclopentadiene with corresponding acrylate esters (7, 10, and 13) have been examined. Acrylates 7 and 10 yielded cycloadducts with 29-88% diastereomeric excess with excellent endo selectivity in the presence of an excess of Lewis acids such as AlCl3, BF3.OEt(2), FeCl3, SnCl4, TiCl4, and ZnCl2. Treatment of acrylate 7 with cyclopentadiene in the presence of BF3.OEt(2) at -80 degrees C gave the endo adduct (>99%) with 88% de. Lewis acid catalyzed and uncatalyzed reactions of acrylates 7 and 10 with cyclopentadiene yielded cycloadducts with opposite stereochemistry. The chiral auxiliary was recovered in a nondestructive manner only via iodolactonization. Acrylate ester of alcohol 12 did not show any selectivity in either catalyzed and uncatalyzed reactions with cyclopentadiene. The presence of a flat aromatic surface at C-7 of the steroid was found to be essential to effect high diastereoselection.

Bile acids in asymmetric synthesis and molecular recognition

This account summarizes the progress made in our laboratory towards the development of new uses of naturally occurring bile acids. Applications in Asymmetric Synthesis (intramolecular coupling, and intermolecular reactions) and Molecular Recognition are described with suitable examples.

Microscopic origin of the chirality driven morphologies of the amphiphilic monolayers and bilayers

It is widely known that the compressed monolayers and bilayers of chiral lipids or fatty acids form helical morphologies, while the corresponding racemic modification gives only flat platelets without twist. No molecular explanation of this phenomenon is yet available, although subtle interactions at the chiral centers have often been proposed as the driving force behind the morphology of the aggregate to form a particular shape. In the present study, the morphologies of the chiral amphiphilic assemblies have been predicted on the basis of an effective pair potential between the molecules, which depends on the relative sizes of the groups attached to the chiral centers, the orientation of the amphiphilic molecules and also on the distance between them. It is shown that fur a pair of same kind of enantiomers, the minimum energy conformation favours a twist angle between them. This twist between the neighbouring molecules gives rise to the helicity of the aggregate. The present theory also shows from the molecular considerations that for a pair of mirror-image isomers (i.e. the racemic modification) the minimum energy conformation corresponds to the zero angle between the molecules, thus giving rise to flat platelets as observed in experiments. Another fascinating aspect of such chirality driven helical structures is that the sense (or the handedness) of the helix is highly specific about the chirality of the monomer concerned. The molecular theory shows, for the first time, that the sense of the helical structures in many cases is determined by the sizes of the groups attached to the chiral centers and the effective potential between them. The predicted senses of the helical structures are in complete agreement with the experimental results.

Tropical deep convection, convective available potential energy and sea surface temperature

The convective available potential energy (CAFE) based on monthly mean sounding has been shown to be relevant to deep convection in the tropics. The variation of CAFE with SST has been found to be similar to the variation of the frequency of deep convection at one station each in the tropical Atlantic and W. Pacific oceans. This suggests a strong link between the frequency of tropical convection and CAFE. It has been shown that CAFE so derived can be interpreted as the work potential of the atmosphere above the boundary layer with ascent in the convective region and subsidence in the surrounding cloud-free region.

First-order hyperpolarizabilities and pKa of weak organic acids in protic solvents are lineraly related

Second-order nonlinearities (beta) of five weak organic acids in protic solvents have been measured by the double-quantum Rayleigh scattering (DRS) technique. beta is found to bear a linear relationship to the pK(a) of these compounds in those solvents. A direct implication of this observation is that the DRS technique can be used to determine the pK(a) of weak organic acids in any solvent.

Dissociation constants of weak organic acids in protic solvents obtained from their first hyperpolarizabilities in solution

The first hyperpolarizabilities (beta) of some weak aromatic organic acids have been measured in protic solvents by the hyper-Rayleigh scattering (HRS) technique at low concentrations. The measured hyperpolarizability (beta(m)) varies between the two extreme limits: the hyperpolarizability of the acid form (beta(HA)) at the lower side and that of the basic form (beta(A-)) at the higher side. The degree of dissociation (alpha) of the acid in a solvent is related to the measured hyperpolarizability, beta(m), by the following relationship: beta(m)(2)=(1-alpha)beta(HA)(2)+alpha beta(A-)(2). The calculated beta's including solvent effects in terms of an Onsager field do not reproduce the experimentally measured hyperpolarizabilities. Other solvent-induced effects like hydrogen bonding and van der Waals interactions seem to influence the first hyperpolarizability and, thus, indirectly the extent of dissociation of these weak acids in these protic solvents.

Microwave Assisted Synthesis and Antimicrobial Study of Schiff Base Vanadium(IV) Complexes of Phenyl Esters of Amino Acids

Schiff base vanadium(IV) complexes of phenyl esters of the two acidic amino acids, i.e., aspartic and glutamic acid, were synthesized. The phenyl esters of these amino acids were synthesized by conventional method whereas the Schiff base vanadium(IV) complexes were synthesized using microwave irradiation. The complexes were characterized by spectroscopic tools such as IR, 1H NMR, mass (ES), ESR, and UV visible spectroscopy. All the complexes were studied for antibacterial and antifungal activity and found to be moderately active.

A perspective of biological supramolecular electron transfer

Electron transfer is an essential activity in biological systems. The migrating electron originates from water-oxygen in photosynthesis and reverts to dioxygen in respiration. In this cycle two metal porphyrin complexes possessing circular conjugated system and macrocyclic pi-clouds, chlorophyll and hems, play a decisive role in mobilising electrons for travel over biological structures as extraneous electrons. Transport of electrons within proteins (as in cytochromes) and within DNA (during oxidative damage and repair) is known to occur. Initial evaluations did not favour formation of semiconducting pathways of delocalized electrons of the peptide bonds in proteins and of the bases in nucleic acids. Direct measurement of conductivity of bulk material and quantum chemical calculations of their polymeric structures also did not support electron transfer in both proteins and nucleic acids. New experimental approaches have revived interest in the process of charge transfer through DNA duplex. The fluorescence on photoexcitation of Ru-complex was found to be quenched by Rh-complex, when both were tethered to DNA and intercalated in the base stack. Similar experiments showed that damage to G-bases and repair of T-T dimers in DNA can occur by possible long range electron transfer through the base stack. The novelty of this phenomenon prompted the apt name, chemistry at a distance. Based on experiments with ruthenium modified proteins, intramolecular electron transfer in proteins is now proposed to use pathways that include C-C sigma-bonds and surprisingly hydrogen bonds which remained out of favour for a long time. In support of this, some experimental evidence is now available showing that hydrogen bond-bridges facilitate transfer of electrons between metal-porphyrin complexes. By molecular orbital calculations over 20 years ago. we found that "delocalization of an extraneous electron is pronounced when it enters low-lying virtual orbitals of the electronic structures of peptide units linked by hydrogen bonds". This review focuses on supramolecular electron transfer pathways that can emerge on interlinking by hydrogen bonds and metal coordination of some unnoticed structures with pi-clouds in proteins and nucleic acids, potentially useful in catalysis and energy missions.