N-3-benzoyl-2 ',3 '-di-O-benzoyluridine

The structure of N-3-benzoyl-2',3'-di-O-benzoyluridine, C30H24N2O9, has two molecules in the asymmetric unit. The uracil bases of both the molecules are in the anti conformation with respect to the ribose moiety and the furanosyl rings adopt a C3'-endo conformation. The orientation about the C4'-C5' bond is gauche-gauche. The two crystallographically independent molecules are linked through several C-H ... O hydrogen bonds. The nucleoside molecules pack as columns along the a axis and these columns repeat along the c axis.

Drug-drug co-crystals: Temperature-dependent proton mobility in the molecular complex of isoniazid with 4-aminosalicylic acid

Two drug-drug co-crystals of the anti-tuberculosis drugs isoniazid (INH), pyrazinamide (PYR) and 4-aminosalicylic acid (PAS) are reported. The first is the 1 : 1 molecular complex of INH and PAS. The second is the monohydrate of the 1 : 1 complex of PYR and PAS. The crystal structures of both co-crystals are characterized by a number of hydrogen bonded synthons. Hydrogen bonding of the COOH center dot center dot center dot N-pyridine type is found in both cases. In the INH : PAS co-crystal, there are two symmetry independent COOH center dot center dot center dot center dot N-pyridine hydrogen bonds. In one of these, the H-atom is located on the carboxylic group and is indicative of a co-crystal. In the second case, partial proton transfer occurs across the hydrogen bond, and the extent of proton transfer depends on the temperature. This is more indicative of a salt. Drug-drug co-crystals may have some bearing in the treatment of tuberculosis.

4-Chlorobenzohydrazide

The crystal structure of the title compound, C7H7N2OCl, has been determined in the monoclinic space group P2(1)/c at room temperature. The structure is stabilized by intermolecular N-H...O and N-H...N hydrogen bonds.

A C-H center dot center dot center dot O hydrogen bond stabilized polypeptide chain reversal motif at the C terminus of helices in proteins

The serendipitous observation of a C-H...O hydrogen bond mediated polypeptide chain reversal in synthetic peptide helices has led to a search for the occurrence of a similar motif in protein structures. From a dataset of 634 proteins, 1304 helices terminating in a Schellman motif have been examined. The C-H...O interaction between the T - 4 (CH)-H-alpha and T + 1 C=O group (C...O 3.5 Angstrom) becomes possible only when the T + 1 residue adopts an extended beta conformation (T is defined as the helix terminating residue adopting an alpha(L) conformation). In all, 111 examples of this chain reversal motif have been identified and the compositional and conformational. preferences at positions T - 4, T, and T + 1 determined. A marked preference for residues like Set, Glu and Gln is observed at T - 4 position with the motif being further stabilized by the formation of a side-chain-backbone O...H-N hydrogen bond involving the side-chain of residue T - 4 and the N-H group of residue T + 3. In as many as 57 examples, the segment following the helix was extended with three to four successive residues in beta conformation. In a majority of these cases, the succeeding beta strand lies approximately antiparallel with the helix, suggesting that the backbone C-H...O interactions may provide a means of registering helices and strands in an antiparallel orientation. Two examples were identified in which extended registry was detected with two sets of C-H...O hydrogen bonds between (T - 4) (CH)-H-alpha...C=O (T + 1) and (T - 8) (CH)-H-alpha...C=O (T + 3). 0 2002 Published by Elsevier Science Ltd.

Biological water: Femtosecond dynamics of macromolecular hydration

The unique features of a macromolecule and water as a solvent make the issue of solvation unconventional, with questions about the static versus dynamic nature of hydration and the, physics of orientational and translational diffusion at the boundary. For proteins, the hydration shell that covers the surface is critical to the stability of its structure and function. Dynamically speaking, the residence time of water at the surface is a signature of its mobility and binding. With femtosecond time resolution it is possible to unravel the shortest residence times which are key for the description of the hydration layer, static or dynamic. In this article we review these issues guided by experimental studies, from this laboratory, of polar hydration dynamics at the surfaces of two proteins (Subtilisin Carlsberg (SC) and Monellin). The natural probe tryptophan amino acid was used for the interrogation of the dynamics, and for direct comparison we also studied the behavior in bulk water - a complete hydration in 1 ps. We develop a theoretical description of solvation and relate the theory to the experimental observations. In this - theoretical approach, we consider the dynamical equilibrium in the hydration shell, defining the rate processes for breaking and making the transient hydrogen bonds, and the effective friction in the layer which is defined by the translational and orientational motions of water molecules. The relationship between the residence time of water molecules and the observed slow component in solvation dynamics is a direct one. For the two proteins studied, we observed a "bimodal decay" for the hydration correlation function, with two primary relaxation times: ultrafast, typically 1 ps or less, and longer, typically 15-40 ps, and both are related to the residence time at the protein surface, depending on the binding energies. We end by making extensions to studies of the denatured state of the protein, random coils, and the biomimetic micelles, and conclude with our thoughts on the relevance of the dynamics of native structures to their functions.

Conformation and orientation of alkyl chains in the layered organic-inorganic hybrids: (CnH2n+1NH3)(2)PbI4 (n=12,16,18)

Layered organic inorganic hybrids based on perovskite-derived alkylammonium lead halides have been demonstrated as important new materials in the construction of molecular electronic devices. Typical of this class of materials are the single-perovskite slab lead iodides of the general formula (CnH2n+1NH3)(2)PbI4. While for small n, these compounds are amenable to single-crystal structure determination, the increasing degree of disorder in the long chain (n = 12,14...) compounds makes such an analysis difficult. In this study, we use powder X-ray diffraction, and vibrational and C-13 NMR spectroscopies to establish the conformation, orientation and organization of hydrocarbon chains in the series of layered alkylammonium lead iodides (CnH2n+1NH3)(2)PbI4 (n = 12,16,18). We find that the alkyl chains adopt a tilted bilayer arrangement, while the structure of the inorganic layer remains invariant with respect to the value of n. Conformation-sensitive methylene stretching modes in the infrared and Raman spectra, as well as the C-13 NMR spectra indicate that bonds in the methylene chain are in trans configuration. The skeletal modes of the alkyl chain in the Raman spectra establish that there is a high degree of all-trans conformational registry for the values of n studied here. From the orientation dependence of the infrared spectra of crystals of (CnH2n+1NH3)(2)PbI4 ( n = 12,16), we find that the molecular axis of the all-trans alkyl chains are tilted away from the interlayer normal by an angle of 55degrees. This value of this tilt angle is consistent with the dependence of the c lattice expansion as a function of n, as determined from powder X-ray diffraction.

Dehydrophenylalanine zippers: strong helix-helix clamping through a network of weak interactions

A decapeptide Boc-L-Ala-(DeltaPhe)(4)-L-Ala-(DeltaPhe)(3)-Gly-OMe (Peptide I) was synthesized to study the preferred screw sense of consecutive alpha,beta-dehydrophenylalanine (DeltaPhe) residues. Crystallographic and CD studies suggest that, despite the presence of two L-Ala residues in the sequence, the decapeptide does not have a preferred screw sense. The peptide crystallizes with two conformers per asymmetric unit, one of them a slightly distorted right-handed 3(10)-helix (X) and the other a left-handed 3(10)-helix (Y) with X and Y being antiparallel to each other. An unanticipated and interesting observation is that in the solid state, the two shape-complement molecules self-assemble and interact with an extensive network of C-H...O hydrogen bonds and pi-pi interactions, directed laterally to the helix axis with amazing regularity. Here, we present an atomic resolution picture of the weak interaction mediated mutual recognition of two secondary structural elements and its possible implication in understanding the specific folding of the hydrophobic core of globular proteins and exploitation in future work on de novo design.

Density-matrix renormalization-group study of low-lying excitations of polyacene within a Pariser-Parr-Pople model

We have carried out symmetrized density-matrix renormalization-group calculations to study the nature of excited states of long polyacene oligomers within a Pariser-Parr-Pople Hamiltonian. We have used the C-2 symmetry, the electron-hole symmetry, and the spin parity of the system in our calculations. We find that there is a crossover in the lowest dipole forbidden two-photon state and the lowest dipole allowed excited state with size of the oligomer. In the long system limit, the two-photon state lies below the lowest dipole allowed excited state. The triplet state lies well below the two-photon state and energetically does not correspond to its description as being made up of two triplets. These results are in agreement with the general trends in linear conjugated polymers. However, unlike in linear polyenes wherein the two-photon state is a localized excitation, we find that in polyacenes, the two-photon excitation is spread out over the system. We have doped the systems with a hole and an electron and have calculated the charge excitation gap. Using the charge gap and the optical gap, we estimate the binding energy of the 1(1)B(-) exciton to be 2.09 eV. We have also studied doubly doped polyacenes and find that the bipolaron in these systems, to be composed of two separated polarons, as indicated by the calculated charge-density profile and charge-charge correlation function. We have studied bond orders in various states in order to get an idea of the excited state geometry of the system. We find that the ground state, the triplet state, the dipole allowed state, and the polaron excitations correspond to lengthening of the rung bonds in the interior of the oligomer while the two-photon excitation corresponds to the rung bond lengths having two maxima in the system.

Determination of the reactivity ratios for the oxidative copolymerizations of indene with methyl, ethyl and butyl acrylates

Full Paper: The copolyperoxides of various compositions of indene with methyl acrylate, ethyl acrylate and butyl acrylate have been synthesized by the free-radical-initiated oxidative copolymerization. The compositions of copolyperoxide obtained from H-1 and C-13 NMR spectra have been used to determine the reactivity ratios of the monomers. The copolyperoxides contain a greater proportion of the indene units in random placement. The NMR studies have shown irregularities in the copolyperoxide chain due to the cleavage reactions of the propagating peroxide radical. The thermal analysis by differential scanning calorimetry suggests alternating peroxide units in the copolyperoxide chain. From the activation energy for the thermal degradation, it was inferred that degradation occurs via the dissociation of the peroxide (O-O) bonds of the copolyperoxide chain. The flexibility of the polyperoxides in terms of glass transition temperature (T-g) has also been examined.

Electrochemical tuning and mechanical resilience of single-wall carbon nanotubes

Single-wall carbon nanotubes (SWNTs) are fascinating systems exhibiting many novel physical properties. In this paper, we give a brief review of the structural, electronic, vibrational, and mechanical properties of carbon nanotubes. In situ resonance Raman scattering of SWNTs investigated under electrochemical biasing demonstrates that the intensity of the radial breathing mode varies significantly in a nonmonotonic manner as a function of the cathodic bias voltage, but does not change appreciably under anodic bias. These results can be quantitatively understood in terms of the changes in the energy gaps between the 1 D van Hove singularities in the electron density of states, arising possibly due to the alterations in the overlap integral of pi bonds between the p-orbitals of the adjacent carbon atoms. In the second part of this paper, we review our high-pressure X-ray diffraction results, which show that the triangular lattice of the carbon nanotube bundles continues to persist up to similar to10 GPa. The lattice is seen to relax just before the phase transformation, which is observed at similar to10 GPa. Further, our results display the reversibility of the 2D lattice symmetry even after compression up to 13 GPa well beyond the 5 GPa value observed recently. These experimental results explicitly validate the predicted remarkable mechanical resilience of the nanotubes.

Hydrogen-bond dynamics near a micellar surface: Origin of the universal slow relaxation at complex aqueous interfaces

The dynamics of hydrogen bonds among water molecules themselves and with the polar head groups (PHG) at a micellar surface have been investigated by long molecular dynamics simulations. The lifetime of the hydrogen bond between a PHG and a water molecule is found to be much longer than that between any two water molecules, and is likely to be a general feature of hydrophilic surfaces of organized assemblies. Analyses of individual water trajectories suggest that water molecules can remain bound to the micellar surface for more than 100 ps. The activation energy for such a transition from the bound to a free state for the water molecules is estimated to be about 3.5 kcal/mol.

Kinetics of thermal degradation of vinyl polyperoxides in solution

The thermal degradation of vinyl polyperoxides, poly(styrene peroxide, (PSP), poly(alpha-methylstyrene peroxide) (PAMSP) and poly(alpha-phenylstyrene pet-oxide) (PAPSP), was carried out at different temperatures in toluene. The time evolution of molecular weight distributions (MWDs) was determined by gel permeation chromatography (GPC). A continuous distribution model was used to evaluate the random chain degradation rate coefficients. The activation energies, determined from the temperature dependence of the rate coefficients, suggest that thermal degradation of polyperoxides is controlled by the dissociation of the O-O bonds in the backbone of the polymer chain. Among the three polyperoxides investigated, the thermal stability is the highest for PAPSP and the lowest for PAMSP. (C) 2002 Elsevier Science Ltd. All rights reserved.

On the importance of backbone loop and peptide flip in the Walker sequence in F-1-ATPase action

The Walker sequence, GXXXXGKT, present in all the six subunits of F-1-ATPase exists in a folded form, known as phosphate-binding loop (P-loop). Analysis of the Ramachandran angles showed only small RMS deviation between the nucleotide-bound and nucleotide-free forms. This indicated a good overlap of the backbone loops. The catalytic beta-subunits (chains D, E and F) showed significant changes in the Ramachandran angles and the side chain torsion angles, but not the structural alpha-subunits (chains A, B and C). Most striking among these are the changes associated with Val160 and Gly161 corresponding to a flip in the peptide unit between them when a nucleotide is bound (chains D or F compared to nucleotide-free chain E). The conformational analysis further revealed a hitherto unnoticed hydrogen bond between amide-N of the flipped Gly161 and terminal phosphate-O of the nucleotide. This assigns a role for this conserved amino acid, otherwise ignored, of making an unusual direct interaction between the peptide backbone of the enzyme protein and the incoming nucleotide substrate. Significance of this interaction is enhanced, as it is limited only to the catalytic subunits, and also likely to involve a mechanical rotation of bonds of the peptide unit. Hopefully this is part of the overall events that link the chemical hydrolysis of ATP with the mechanical rotation of this molecule, now famous as tiny molecular motor.

Reactivity ratios for the oxidative copolymerizations of indene with methyl methacrylate and methacrylonitrile

The copolyperoxides of indene with methyl methacrylate and methacrylonitrile have been synthesized by the free-radical-initiated oxidative copolymerization of indene and the monomers. The compositions of copolyperoxides, obtained from H-1 and C-13 NMR spectra, have been utilized to determine the reactivity ratios. The reactivity ratios indicate that the copolyperoxides contain a large proportion of the indene units in random placement. Thermal degradation studies of the copolyperoxides by differential scanning calorimetry and electron-impact mass spectroscopy support alternating peroxide units in the copolyperoxide chain. The energy of activation for thermal degradation suggests that the degradation is controlled by the dissociation of the peroxide (-O-O-) bonds in the copolyperoxide chain. The flexibility of copolyperoxide in terms of glass transition temperature (T-g) has also been examined. (C) 2002 Elsevier Science Ltd. All rights reserved.

Solid propellant binders

Solid, propellants are widely used in modern rockets and missiles. Although the history of solid rockets could be traced to the discovery of gunpowder over a thousand years ago, the technology could be perfected only by the later half of the 20(th) century. The failure of gunpowder rockets was largely due to the unknown consolidating technique of the powder composition. The emergence of large solid propellant motors had, to await the dawn of polymer. science and technology(S&T). Specific syntheses of functionally terminated polymers having cross-linking capability led to the emergence of casting technology of solid composite propellants. This review describes the various polymeric fuel/binder systems used or considered for use in solid,propellants. It includes a brief background, advantages, and shortcomings of the various systems, an account of the currently used binders and a critical survey of the advanced polymers envisaged for future usage. Special emphasis has been laid on recently synthesized polymers having N-N bonds in their structures, and-on the feasibility of developing smokeless propellants based on ammonium nitrate.