Interruptions of (CG)n sequences by GG, TG and CA need not prevent B to Z transition in solution

Oligonucleotides containing alternating purines-pyrimidines with AT base pairs have been shown to exist in the Z-form preferably in solid state. We report that oligodeoxyribonucleotides with GG, TG and CA interruptions in their alternating CG sequences can undergo B to Z transition in solution in the absence of any chemical modification or topological constraint. The sequences, d(CGCGCGGCGCGC) and d(CGTGCGCACG) have been synthesised and shown to adopt Z- conformation in presence of millimolar concentrations of Ni2+ under low water activity conditions. Significance of GG, TG and CA interruptions in the B to Z transition is discussed.

Molecular conformation of alamethicin in dimethylsulfoxide solution A two-dimensional n.m.r. study

The solution conformation of alamethicin, a 20-residue antibiotic peptide, has been investigated using two-dimensional n.m.r. spectroscopy. Complete proton resonance assignments of this peptide have been carried out using COSY, SUPERCOSY, RELAY COSY and NOESY two-dimensional spectroscopies. Observation of a large number of nuclear Overhauser effects between sequential backbone amide protons, between backbone amide protons and CβH protons of preceding residues and extensive intramolecular hydrogen bonding patterns of NH protons has established that this polypeptide is in a largely helical conformation. This result is in conformity with earlier reported solid state X-ray results and a recent n.m.r. study in methanol solution (Esposito et al. (1987) Biochemistry26, 1043-1050) but is at variance with an earlier study which favored an extended conformation for the C-terminal half of alamethicin (Bannerjee et al.

Polypeptide models of collagen. II. Solution properties of (Pro-Gly-Phe)n

The conformation of (Pro-Gly-Phe)n in trifluoroethanol was investigated using CD, nmr and ir techniques. After making appropriate correction for the contribution of the phenylalanine chromophore to the observed CD spectra of the polytripeptide at several temperatures, it is found that (Pro-Gly-Phe)n can exist in a partially triple-helical conformation in this solvent a t low temperatures. The nmr and ir data support this conclusion. In conjunction with recent theoretical sutdies, our data offer an explanation for the preferential occurrence of the Phe residue in position 2 of the tripeptide sequence Gly-R2-R3, in collagen.

Steady compressible flow of granular materials through a wedge-shaped hopper: The smooth wall, radial gravity problem

A continuum model based on the critical state theory of soil mechanics is used to generate stress and density profiles, and to compute discharge velocities for the plane flow of cohesionless materials. Two types of yield loci are employed, namely, a yield locus with a corner, and a smooth yield locus. The yield locus with a corner leads to computational difficulties. For the smooth yield locus, results are found to be relatively insensitive to the shape of the yield locus, the location of the upper traction-free surface and the density specified on this surface. This insensitivity arises from the existence of asymptotic stress and density fields, to which the solution tends to converge on moving down the hopper. Numerical and approximate analytical solutions are obtained for these fields and the latter is used to derive an expression for the discharge velocity. This relation predicts discharge velocities to within 13% of the exact (numerical) values. While the assumption of incompressibility has been frequently used in the literature, it is shown here that in some cases, this leads to discharge velocities which are significantly higher than those obtained by the incorporation of density variation.

Polarization Caging in Diffusion-Controlled Electron Transfer Reactions in Solution

In some bimolecular diffusion-controlled electron transfer (ET) reactions such as ion recombination (IR), both solvent polarization relaxation and the mutual diffusion of the reacting ion pair may determine the rate and even the yield of the reaction. However, a full treatment with these two reaction coordinates is a challenging task and has been left mostly unsolved. In this work, we address this problem by developing a dynamic theory by combining the ideas from ET reaction literature and barrierless chemical reactions. Two-dimensional coupled Smoluchowski equations are employed to compute the time evolution of joint probability distribution for the reactant (P-(1)(X,R,t)) and the product (p((2))(X,R,t)), where X, as is usual in ET reactions, describes the solvent polarization coordinate and R is the distance between the reacting ion pair. The reaction is described by a reaction line (sink) which is a function of X and R obtained by imposing a condition of equal energy on the initial and final states of a reacting ion pair. The resulting two-dimensional coupled equations of motion have been solved numerically using an alternate direction implicit (ADI) scheme (Peaceman and Rachford, J. Soc. Ind. Appl. Math. 1955, 3, 28). The results reveal interesting interplay between polarization relaxation and translational dynamics. The following new results have been obtained. (i) For solvents with slow longitudinal polarization relaxation, the escape probability decreases drastically as the polarization relaxation time increases. We attribute this to caging by polarization of the surrounding solvent, As expected, for the solvents having fast polarization relaxation, the escape probability is independent of the polarization relaxation time. (ii) In the slow relaxation limit, there is a significant dependence of escape probability and average rate on the initial solvent polarization, again displaying the effects of polarization caging. Escape probability increases, and the average rate decreases on increasing the initial polarization. Again, in the fast polarization relaxation limit, there is no effect of initial polarization on the escape probability and the average rate of IR. (iii) For normal and barrierless regions the dependence of escape probability and the rate of IR on initial polarization is stronger than in the inverted region. (iv) Because of the involvement of dynamics along R coordinate, the asymmetrical parabolic (that is, non-Marcus) energy gap dependence of the rate is observed.

Exact static polarizabilities of correlated finite model systems

A finite-field method for calculating exact polarizabilities of correlated conjugated model systems within the valence bond (VB) framework is presented. The correlations reduce the polarizabilities from their noninteracting values and extend the range of linearity to higher external fields. The large nonlinear polarizabilities observed in strongly correlated conjugated organic molecules cannot be directly attributed to electron correlations. The method described can be employed to calculate static polarizabilities for any desired state of a correlated system.

Thermodynamic partial properties of Na2O in Nasicon solid solution, Na1+xZr2SixP3-xO12

The thermodynamic activity of sodium oxide (Na2O) in the Nasicon solid solution series, Na1+xZr2SixO12, has been measured in the temperature range 700�1100 K using solid state galvanic cells: Pt|CO2 + O2|Na2CO3?Na1+xZr2SixP3-xO12?(Y2O3)ZrO2?In + In2O3|Ta, Pt for 1 = ? = 2.5, and Pt?CO2 + O2?Na2CO3?ß-alumina?Na1+xZr2SixP3-xO12?Ar + O2?Pt for x = 0, 0.5, 2.5, and 3. The former cell, where the Nasicon solid solution is used as an electrolyte along with yttria-stabilized zirconia, is well suited for Nasicon compositions with high ionic conductivity. In the latter cell, ß-alumina is used as an electrolyte and the Nasicon solid solution forms an electrode. The chemical potential of Na2O is found to increase monotonically with x at constant temperature. The partial entropy of Na2O decreases continuously with x. However, the partial enthalpy exhibits a maximum at x = 2. This suggests that the binding energy is minimum at the composition where ionic conductivity and cell volume have maximum values.

Uniformly valid analytical solution to the problem of a decaying shock wave

An explicit representation of an analytical solution to the problem of decay of a plane shock wave of arbitrary strength is proposed. The solution satisfies the basic equations exactly. The approximation lies in the (approximate) satisfaction of two of the Rankine-Hugoniot conditions. The error incurred is shown to be very small even for strong shocks. This solution analyses the interaction of a shock of arbitrary strength with a centred simple wave overtaking it, and describes a complete history of decay with a remarkable accuracy even for strong shocks. For a weak shock, the limiting law of motion obtained from the solution is shown to be in complete agreement with the Friedrichs theory. The propagation law of the non-uniform shock wave is determined, and the equations for shock and particle paths in the (x, t)-plane are obtained. The analytic solution presented here is uniformly valid for the entire flow field behind the decaying shock wave.

Theory of unitarity bounds and low-energy form factors

We present a general formalism for deriving bounds on the shape parameters of the weak and electromagnetic form factors using as input correlators calculated from perturbative QCD, and exploiting analyticity and unitarily. The values resulting from the symmetries of QCD at low energies or from lattice calculations at special points inside the analyticity domain can be included in an exact way. We write down the general solution of the corresponding Meiman problem for an arbitrary number of interior constraints and the integral equations that allow one to include the phase of the form factor along a part of the unitarity cut. A formalism that includes the phase and some information on the modulus along a part of the cut is also given. For illustration we present constraints on the slope and curvature of the K-l3 scalar form factor and discuss our findings in some detail. The techniques are useful for checking the consistency of various inputs and for controlling the parameterizations of the form factors entering precision predictions in flavor physics.

Stereochemistry of peptides containing 1-aminocyclopentane carboxylic acid (Acc5). Solution and solid state conformations of Boc-Acc5-Acc5-NHMe.

The conformational analysis of a protected homodipeptide of 1-aminocyclopentanecarboxylic acid (Acc5) has been carried out. 1H-nmr studies establish a ?-turn conformation for Boc-Acc5-Acc5-NHMe in chloroform and dimethylsulfoxide solutions involving the methylamide NH in an intramolecular hydrogen bond. Supportive evidence for the formation of an intramolecular hydrogen bond is obtained from ir studies. X-ray diffraction studies reveal a type III ?-turn conformation in the solid state stabilized by a 4 ? 1 hydrogen bond between the Boc CO and methylamide NH groups. The ?,? values for both Acc5 residues are close to those expected for an ideal 310-helical conformation (?? ± 60°, ?? ±30°).