Computer modeling studies on the binding of 2',5'-linked dinucleoside phosphates to ribonuclease T1-influence of subsite interactions on the substrate specificity

The modes of binding of Gp(2',5')A, Gp(2',5')C, Gp(2',5')G and Gp(2',5')U to RNase T1 have been determined by computer modelling studies. All these dinucleoside phosphates assume extended conformations in the active site leading to better interactions with the enzyme. The 5'-terminal guanine of all these ligands is placed in the primary base binding site of the enzyme in an orientation similar to that of 2'-GMP in the RNase T1-2'-GMP complex. The 2'-terminal purines are placed close to the hydrophobic pocket formed by the residues Gly71, Ser72, Pro73 and Gly74 which occur in a loop region. However, the orientation of the 2'-terminal pyrimidines is different from that of 2'-terminal purines. This perhaps explains the higher binding affinity of the 2',5'-linked guanine dinucleoside phosphates with 2'-terminal purines than those with 2'-terminal pyrimidines. A comparison of the binding of the guanine dinucleoside phosphates with 2',5'- and 3',5'-linkages suggests significant differences in the ribose pucker and hydrogen bonding interactions between the catalytic residues and the bound nucleoside phosphate implying that 2',5'-linked dinucleoside phosphates may not be the ideal ligands to probe the role of the catalytic amino acid residues. A change in the amino acid sequence in the surface loop region formed by the residues Gly71 to Gly74 drastically affects the conformation of the base binding subsite, and this may account for the inactivity of the enzyme with altered sequence i.e., with Pro, Gly and Ser at positions 71 to 73 respectively. These results thus suggest that in addition to recognition and catalytic sites, interactions at the loop regions which constitute the subsite for base binding are also crucial in determining the substrate specificity.

Regeneration of plantlets from leaf disc cultures of rosewood: control of leaf abscission and shoot tip necrosis

A method for mass production of rosewood (Dalbergia latifolia Roxb.) trees through leaf disc organogenesis was developed and standardized. Compact callus was initiated from mature leaf discs on Murashige and Skoog (MS) basal medium supplemented with 1.0 mg 1?1 2,4-dichlorophenoxy acetic acid (2,4-D), 5.0 mg 1?1 ?-naphthaleneacetic acid (NAA), 1.0 mg 1?1 6-benzylaminopurine (BAP) and 10% coconut water (CW). High frequency (15�20 shoots/g callus) regeneration of shoot bud differentiation was obtained on MS (3/4 reduced major elements) or Woody Plant Medium (WPM) or modified Woody Plant Medium (mWPM) supplemented with BAP (5.0 mg 1?1) and NAA (0.5 mg 1?1). Leaf abscission and shoot tip necrosis was controlled using mWPM. About 90% of the excised shoots were rooted in the mWPM supplemented with 2.0 mg 1?1 ?-indolebutyric acid (IBA) and 1.0 mg 1?1 caffeic acid. The in vitro-raised rooted plantlets were hardened for successful transplantation to soil. The transplanted plants were exposed to various humidity conditions and 80% transplant success was achieved. The in vitro-raised leaf-regenerated plants grew normally and vigorously in soil.

Specific-heat measurements during cooling through the glass-transition region

In this paper we report the measurements of specific heats of five glass formers as they are cooled through the glass-transition region. The measurements are compared with other specific-heat measurements such as adiabatic-calorimetry and ac-calorimetry measurements. The data are then analyzed using a model of enthalpy relaxation and nonequilibrium cooling, which can track the nonequilibrium relaxation time tau(S). The relevant parameters that describe tau(S) are obtained, allowing us to compare the enthalpy-relaxation times obtained from this method with other methods. We display the clear connection of the unrelaxed enthalpy with the nonequilibrium relaxation time and also show the role played by the delayed heat release from the unrelaxed enthalpy in the glass-transition region. We have also made certain definite observations regarding the equilibrium configurational specific heat and the Vogel-Fulcher law, which describes tau(S).

Synthesis, spectral characterisation and single-crystal structure of a bicyclic tetraphosphapentazane tetraoxide, N5P4ET5O4(OC6H3Me2-2,6)2

Reaction of the bicyclic phosphazane N5P4Et5Cl2 with 2,6-dimethylphenol and subsequent oxidation of the product by aqueous hydrogen peroxide yields N5P4Et5O4(OC6H3Me2-2,6)2 in 85% yield. Its structure has been established by NMR spectroscopy and single-crystal X-ray diffraction. The compound crystallises in the monoclinic space group C2/c with a= 21.245(5), b= 10.879(2), c= 16.450(6)Å, ?= 123.94(2)°, Z= 4, R= 0.066. The structural features are compared with those of bicyclic ?5-phosphazenes of type N5P4R3(NR1R2)5(NHR3)(R1,R3= Me or Et, R2= H or Me). The observed conformation of the N3P3 rings in the present compound is mainly dictated by the maximisation of the stabilising influence of �negative hyperconjugative interactions� between the nitrogen lone pairs and the adjacent P�X ?* orbitals.

Synthesis, Reactivity, Structural Aspects, and Solution Dynamics of Cyclopalladated Compounds of N,N `,N `'-Tris(2-anisyl)guanidine

N,N',N `'-Tris(2-anisyl)guanidine, (ArNH)(2)C=NAr (Ar = 2-(MeO)C6H4), was cyclopallaclated with Pd(OC(O)R)(2) (R = Me, CF3) in toluene at 70 degrees C to afford palladacycles Pd{kappa(2)(C,N)-C6H3-(OMe)-3(NHC(NHAr)(=NAr))-2}(mu-OC(O)R)](2)(R = Me (1a) and CF3 (1b)) in 87% and 95% yield, respectively. Palladacycle 1a was subjected to a metathetical reaction with LiBr in aqueous ethanol at 78 degrees C to afford palladacycle Pd{kappa(2)(C,N)-C6H3(OMe)-3(NHC(NHAr)(=NAr))-2}(mu-Br)](2) (2) in 90% yield. Palladacycle 2 was subjected to a bridge-splitting reaction with Lewis bases in CH2Cl2 to afford the monomeric palladacycles Pd{kappa(2)(C,N)-C6H3(OMe)-3(NHC(NHAr)(=NAr))-2}Br(L)] (L = 2,6-Me2C5H3N (3a), 2,4-Me2C5H3N (3b), 3,5-Me2C5H3N (3c), XyNC (Xy = 2,6-Me2C6H3; 4a), (BuNC)-Bu-t (4b), and PPh3 (5)) in 87-95% yield. Palladacycle 2 upon reaction with 2 equiv of XyNC in CH2Cl2 afforded an unanticipated palladacycle, Pd{kappa(2)(C,N)-C(=NXy)(C6H3(OMe)-4)-2(N=C-(NH Ar)(2))-3} Br(CNXy)] (6) in 93% yield, and the driving force for the formation of 6 was ascribed to a ring contraction followed by amine-imine tautomerization. Palladacycles 1 a,b revealed a dimeric transoid in-in conformation with ``open book'' framework in the solid state. In solution, 1 a exhibited a fluxional behavior ascribed to the six-membered ``(C,N)Pd'' ring inversion and partly dissociates to the pincer type and kappa(2)-O,O'-OAc monomeric palladacycles by an anchimerically assisted acetate cleavage process as studied by variable-temperature H-1 NMR data. Palladacycles 3a,b revealed a unique trans configuration around the palladium with lutidine being placed trans to the Pd-C bond, whereas cis stereochemistry was observed between the Pd-C bond and the Lewis base in 4a (as determined by X-ray diffraction data) and 5 (as determined by P-31 and C-13 NMR data). The aforementioned stereochemical difference was explained by invoking relative hardness/softness of the donor atoms around the palladium center. In solution, palladacycles 3a-c exist as a mixture of two interconverting boat conformers via a planar intermediate without any bond breaking due to the six-membered ``(C,N)Pd'' ring inversion, whereas palladacycles 4a,b and 5 exist as a single isomer, as deduced from detailed H-1 NMR studies.

Crystal structure of a daturalactone - a withanolide

The crystal structure of a daturalactone derivative has been determined by X-ray structural analysis. The compound crystallizes in orthorhomic space group P2(1)2(1)2(1) with cell parameters a = 15.141(1) angstrom, b = 18.425(1) angstrom, c = 19.251(2) angstrom. The structure was solved by direct methods and refined to R = 0.082. The asymmetric unit contains two non-equivalent molecules. Extensive hydrogen bonding is present. The conformations of the rings are A: a distorted half-chair, B: a perfect half-chair, C: a chair, D: an envelope-half chair and E: a twist boat. Ring junctions A/B, B/C, C/D are all trans fused. Methyl carbons C(18), C(19), C(27) and the lactone moiety is beta-oriented whereas the methyl carbons C(21) and C(28) are alpha-oriented.

Unsteady three-dimensional boundary layer flow due to a stretching surface

In this numerical study, the unsteady laminar incompressible boundary-layer flow over a continuously stretching surface has been investigated when the velocity of the stretching surface varies arbitrarily with time. Both the nodal and the saddle point regions of flow have been considered for the analysis. Also, constant wall temperature/concentration and constant heat/mass flux at the stretching surface have been taken into account. The quasilinearisation method with an implicit finite-difference scheme is used in the nodal point region (0 less-than-or-equal-to c less-than-or-equal-to 1) where c denotes the stretching ratio. This method fails in the saddle point region (-1 less-than-or-equal-to c less-than-or-equal-to 0) due to the occurrence of reverse flow in the y-component of velocity. In order to overcome this difficulty, the method of parametric differentiation with an implicit finite-difference scheme is used, where the values at c = 0 are taken as starting values. Results have been obtained for the stretching velocities which are accelerating and decelerating with time. Results show that the skin friction, the heat transfer and the mass transfer parameters respond significantly to the time dependent stretching velocities. Suction (A > 0) is found to be an important parameter in obtaining convergent solution in the case of the saddle point region of flow. The Prandtl number and the Schmidt number strongly affect the heat and mass transfer of the diffusing species, respectively.

Photochemical intramolecular gamma-hydrogen abstraction in a ketone and an alkene and the role of tunneling of hydrogen

Intramolecular gamma-hydrogen abstraction reactions were examined in pentane-2-one and 2-methyl-1-pentene in their lowest triplet states using the AM1 semi-empirical molecular orbital method with the complete geometry optimization in the unrestricted Hartree-Fock frame. The results reveal that the oxygen atom of the carbonyl group and the end carbon atom of the olefinic bond acquire high free valence and spin density indices in their respective lowest triplet states, leading to abstraction of hydrogen from the gamma-position relative to the carbonyl and olefinic bonds. The theoretical energy profiles fit with a polynomial and the probability of tunneling of hydrogen was estimated by the WKB (Wentzel, Kramer and Brillouin) method. The results, after thermal averaging of the rate constants, reveal that tunneling of hydrogen is significant at room temperature.

Realtime kinetic analysis of antigen-antibody interaction using solid phase binding: Transformation of hCG-monoclonal antibody complex

Kinetic constants of MAb-hCG interactions have been determined using solid phase binding of I-125[hCG] to immobilized MAb. While association has been shown to follow the expected pattern, dissociation consists of at least two reversible steps, one with a rate constant of 0.0025 min(-1), and a second with a rate constant of 0.00023 min(-1). Validity of affinity constant measurements in the light of the complex reaction kinetics is discussed, A comparison between the method of surface plasmon resonance technology (BIAcore) and solid phase binding (SPB) for determination of kinetic parameters shows that SPB provides not only a cost-effective approach for determination of realtime kinetic parameters of macromolecular ligand-ligate interaction but also a method with several advantages over the BIAcore system in investigating the mechanism of antigen-antibody interaction.

Further studies on Norrish type II reactions including a reaction in the first excited singlet state and cyclization of 1:4 biradicals

The Norrish type II processes of methyl-2,2-dimethyl- cyclopropyl ketone, alpha-alkoxy acetones and alkyl pyruvates have been examined using the AM1 semi-empirical molecular orbital method with complete geometry optimization at the partial configuration interaction level in the restricted Hartree-Fock (RHF) frame. The results reveal that the methyl-substituted cyclopropyl ketone has a constrained geometry favourable for hydrogen abstraction from the gamma-position relative to the carbonyl group in the excited singlet state. The presence of the ether oxygen atom in the beta-position relative to the carbonyl group in alkoxy acetones and alkyl pyruvates leads to increased reactivity relative to alkyl monoketones and diketones respectively. The cyclization of 1:4 biradicals has been studied in the unrestricted Hartree-Fock (UHF) frame, and the results reveal that the 1:4 biradical derived from alkoxy acetones readily cyclizes to form oxetanols. On the other hand, in the 1:4 biradicals derived from methyl-substituted cyclopropyl ketone, the three-membered ring breaks readily to form an enol intermediate. Delocalization of an odd electron in 1:4 biradicals derived from alkyl pyruvates is thought to make cyclization difficult.

Thermo and photoluminescence properties of Eu3+ activated hexagonal, monoclinic and cubic gadolinium oxide nanorods

Different phases of Eu3+ activated gadolinium oxide (Gd (OH)(3), GdOOH and Gd2O3) nanorods have been prepared by the hydrothermal method with and without cityl trimethyl ammonium bromide (GAB) surfactant. Cubic Gd2O3:Eu (8 mol%) red phosphor has been prepared by the dehydration of corresponding hydroxide Gd(OH)(3):Eu after calcinations at 350 and 600 degrees C for 3 h, respectively. When Eu3+ ions were introduced into Gd(OH)(3), lattice sites which replace the original Gd3+ ions, a strong red emission centered at 613 nm has been observed upon UV illumination, due to the intrinsic Eu3+ transition between D-5(0) and F-7 configurations. Thermoluminescence glow curves of Gd (OH)(3): Eu and Gd2O3:Eu phosphors have been recorded by irradiating with gamma source ((CO)-C-60) in the dose range 10-60 Gy at a heating rate of 6.7 degrees C sec(-1). Well resolved glow peaks in the range 42-45, 67-76,95-103 and 102-125 degrees C were observed. When gamma-irradiation dose increased to 40 Gy, the glow peaks were reduced and with increase in gamma-dose (50 and 60 Gy) results the shift in first two glow peak temperatures at about 20 degrees C and a new shouldered peak at 86 degrees C was observed. It is observed that there is a shift in glow peak temperatures and variation in intensity, which is mainly attributed to different phases of gadolinium oxide. The trapping parameters namely activation energy (E), order of kinetics (b) and frequency factor were calculated using peak shape and the results are discussed. (C) 2010 Elsevier B.V. All rights reserved.

Organometallic chemistry of diphosphazanes. Rhodium(I) complexes of RN(PX2)2 (R = C6H5; X = OC6H5, OC6H4Br?p, R = CH3; X = OC6H5)

Reactions of [Rh(COD)Cl](2) with the ligand RN(PX(2))(2) (1: R=C6H5; X=OC6H5) give mono- or disubstituted complexes of the type [Rh-2(COD)Cl-2{eta(2)-C6H5N(P(OC6H5)(2))(2)}-] or [RhCl{eta(2)-C6H5N(P(OC6H5)(2))(2)}](2), depending on the reaction conditions. Reaction of 1 with [Rh(CO)(2)Cl](2) gives the symmetric binuclear complex, [Rh(CO)Cl{mu-C6H5N(P(OC6H5)(2))(2)}], whereas the same reaction with 2 (R=CH3; X=OC6H5) leads to the formation of an asymmetric complex of the type [Rh(CO)(mu-CO)Cl{mu-CH3N(P(OC6H5)(2))(2)}] containing both terminal and bridging CO groups. Interestingly the reaction of 3 (R=C6H5, X = OC6H4Br-p) with either [Rh(COD)Cl](2) or [Rh(CO)(2)Cl](2) leads only to the formation of the chlorine bridged binuclear complex, [RhCl{eta(2)-C6H5N(P(OC6H4Br-p)(2))(2)}](2). The structural elucidation of the complexes was carried out by elemental analyses, IR and P-31 NMR spectroscopic data.

ChemInform Abstract: Synthesis Based on Cyclohexadienes. Part 16. Synthesis of Methyl 2,7-Dimethyltricyclo (5.2.2.01,5)undec-5-ene-6-carboxylates

Synthesis of methyl 2, 7-dimethyltricyclo{5.2.2.0(1,5}undec-5-en-6-carboxylates, the tricyclic skeleton present in (+)-allo-cedrol (1) is described using the Diels-Alder strategy. Thus, Birch reduction of the aromatic acid 8 gives 5, the methyl ester of which is isomerised with DBU to a 1:1 mixture of the dienes 6 and 4. Cycloaddition of this mixture with 2-chloroacrylonitrile followed by hydrolysis yields the ketone 60 having the tricyclo{5.2.2.0(1.5)}undec-5-ene framework. Similar reaction with methyl vinyl ketone affords the regioisomeric adducts 61 and 62.

Mean-field theory of charge ordering and phase transitions in the colossal-magnetoresistive manganites

We study phase transitions in the colossal-magnetoresistive manganites by using a mean-field theory both at zero and non-zero temperatures. Our Hamiltonian includes double-exchange, superexchange, and Hubbard terms with on-site and nearest-neighbour Coulomb interaction, with the parameters estimated from earlier density-functional calculations. The phase diagrams show magnetic and charge-ordered (or charge-disordered) phases as a result of the competition between the double-exchange, superexchange, and Hubbard terms, the relative effects of which are sensitively dependent on parameters such as doping, bandwidth, and temperature. In accord with the experimental observations, several important features are reproduced from our model, namely, (i) a phase transition from an insulating, charge-ordered antiferromagnetic to a metallic, charge-disordered ferromagnetic state near dopant concentration x = 1/2, (ii) the reduction of the transition temperature TAF-->F by the application of a magnetic field, (iii) melting of the charge order by a magnetic field, and (iv) phase coexistence for certain values of temperature and doping. An important feature, not reproduced in our model, is the antiferromagnetism in the electron-doped systems, e.g., La1-xCaxMnO3 over the entire range of 0.5 less than or equal to x less than or equal to 1, and we suggest that a multi-band model which includes the unoccupied t(2g) orbitals might be an important ingredient for describing this feature.

Icosahedral quasicrystalline and hexagonal approximant phases in the Al-Mn-Be alloy system

We report the formation of a primitive icosahedral quasicrystal with increased stability in Al Mn-Be alloys close to the compound Al15Mn13Be2, by melt spinning and injection casting. The crystal structure of this compound was unknown. We show that in as-cast as well as heat treated condition the intermetallic phase H1 has a hexagonal structure with lattice parameters a = 1.2295 run and c = 2.4634 nm. The space group is P6(3)/mmc In the injection-cast samples, the quasicrystal coexists with another closely related hexagonal phase H2 with a = 1.2295 nm and c = 1.2317 nm with a possible space group of P6/mmm. This phase exhibits specific orientation relationships with the icosahedral quasicrystal given by [0001](hex)//2f(QC) and [01 (1) over bar0](hex)//5f(QC) where 2f(QC) and 5f(QC) represent twofold and fivefold axes respectively. Electron diffraction patterns from both phases exhibit a close resemblance to the quasicrystalline phase. It is shown that the H1 phase is closely related to mu-Al4Mn with the same e parameter while the a parameter is reduced by tau. Following Kreiner and Franzen, it is postulated that both structures (H1 and H2) can be understood by a simple hexagonal packing of I13 clusters.