Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures

A Study of copper-compounds by x-Ray Absorption-spectroscopy

Chemical shifts, ΔE, of the K-absorption discontinuity in several compounds of copper possessing formal oxidation states between 0 and III have been measured. The shifts show a parabolic dependence on the formal oxidation state as well as on the effective atomic charge, q, on copper. Anomalous chemical shifts shown by some of the compounds are discussed in terms of the bonding in these compounds. The ΔE values have also been correlated with the core electron binding energies obtained from X-ray photoelectron spectroscopy.

Sequence Independent Recombination Triple Helices: A Molecular Dynamics Study

Recent experimental studies have shown that the Rec-A mediated homologous recombination reaction involves a triple helical intermediate, in which the third strand base forms hydrogen bonds with both the bases in the major groove of the Watson-Crick duplex. Such 'mixed' hydrogen bonds allow formation of sequence independent triplexes. DNA triple helices involving 'mixed' hydrogen bonds have been studied, using model building, molecular mechanics (MM) and molecular dynamics (MD). Models were built for a tripler comprising all four possible triplets viz., G.C*C, C.G*G, A.T*T and T.A*A. To check the stability of all the 'mixed' hydrogen bonds in such triplexes and the conformational preferences of such tripler structures, MD studies were carried out starting from two structures with 30 degrees and 36 degrees twist between the basepairs. It was observed that though the two triplexes converged towards a similar structure, the various hydrogen bonds between the WC duplex and the third strand showed differential stabilities. An MD simulation with restrained hydrogen bonds showed that the resulting structure was stable and remained close to the starting structure. These studies help us in defining stable hydrogen bond geometries involving the third strand and the WC duplex. It was observed that in the C.G*G triplets the N7 atom of the second strand is always involved in hydrogen bonding. In the G.C*C triplets, either N3 or O2 in the third strand cytosine can interchangeably act as a hydrogen bond acceptor.

Molecular Mechanics Studies of Homopolymeric and Mixed Sequence Py.Pu*Pu Triple Helices,

DNA triple helices containing two purine strands and one pyrimidine strand (C.G*G and T.A*A) have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that in the C.G*G case the structure with a parallel orientation of the third strand, resulting from Hoogsteen hydrogen bonds between the third strand and the Watson-Crick duplex, is energetically the most favourable while in the T.A*A case the antiparallel orientation of the third strand, resulting from reverse Hoogsteen hydrogen bonds, is energetically the most favourable. These studies when extended to the mixed sequence triplexes, in which the second strand is a mixture of G and A, correspondingly the third strand is a mixture of G and APT, show that though the parallel orientation is still energetically more favourable, the antiparallel orientation becomes energetically comparable with an increasing number of thymines in the third strand. Structurally, for the mixed triplexes containing G and T in the third strand, it is seen that the basepair non-isomorphism between the C.G*G and the T.A*T triplets can be overcome with some changes in the base pair parameters without much distortion of either the backbone or the hydrogen bonds.

Structural Polymorphism in d(T).d(A)*d(T) Triple Helices

DNA triple helices containing two thymine strands and one adenine strand have been studied, using model building followed by energy minimisation, for different orientations of the third strand resulting from variation in the hydrogen bonding between the Watson-Crick duplex and the third strand and the glycosidic torsion angle in the third strand. Our results show that the structure with a parallel orientation of the third strand, in which the third strand base forms Hoogsteen hydrogen bonds with the adenine base in the Watson-Crick duplex, is energetically the most favourable. An antiparallel orientation of the third strand is also possible, in which the third strand base hydrogen bonds to both the bases in the Watson-Crick duplex. This structure is energetically comparable to the parallel structure. For the parallel triplex a 200ps molecular dynamics simulation starting from two different starting structures indicates that at 300K significant structural heterogeneity exists in this tripler structure. The results are compared with existing structural data on this class of triplexes derived from theoretical and NMR techniques.

Conformational Polymorphism in Telomeric Structures: Loop Orientation and Interloop Pairing in d(G4TnG4),

Sequence repeats constituting the telomeric regions of chromosomes are known to adopt a variety of unusual structures, consisting of a G tetraplex stem and short stretches of thymines or thymines and adenines forming loops over the stem. Detailed model building and molecular mechanics studies have been carried out for these telomeric sequences to elucidate different types of loop orientations and possible conformations of thymines in the loop. The model building studies indicate that a minimum of two thymines have to be interspersed between guanine stretches to form folded-back structures with loops across adjacent strands in a G tetraplex (both over the small as well as large groove), while the minimum number of thymines required to build a loop across the diagonal strands in a G tetraplex is three. For two repeat sequences, these hairpins, resulting from different types of folding, can dimerize in three distinct ways-i.e., with loops across adjacent strands and on same side, with loops across adjacent strands and on opposite sides, and with loops across diagonal strands and on opposite sides-to form hairpin dimer structures. Energy minimization studies indicate that all possible hairpin dimers have very similar total energy values, though different structures are stabilized by different types of interactions. When the two loops are on the same side, in the hairpin dimer structures of d(G(4)T(n)G(4)), the thymines form favorably stacked tetrads in the loop region and there is interloop hydrogen bonding involving two hydrogen bonds for each thymine-thymine pair. Our molecular mechanics calculations on various folded-back as well as parallel tetraplex structures of these telomeric sequences provide a theoretical rationale for the experimentally observed feature that the presence of intervening thymine stretches stabilizes folded-back structures, while isolated stretches of guanines adopt a parallel tetraplex structure

Computer modelling studies of ribonuclease A-pyrimidine nucleotide complexes

Different modes of binding of pyrimidine monophosphates 2'-UMP, 3'-UMP, 2'-CMP and 3'-CMP to ribonuclease (RNase) A are studied by energy minimization in torsion angle and subsequently in Cartesian coordinate space. The results are analysed in the light of primary binding sites. The hydrogen bonding pattern brings out roles for amino acids such as Asn44 and Ser123 apart from the well known active site residues viz., His12,Lys41,Thr45 and His119. Amino acid segments 43-45 and 119-121 seem to be guiding the ligand binding by forming a pocket. Many of the active site charged residues display considerable movement upon nucleotide binding.

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.

Evaluation of interfacial frictional resistance

Three distinct mechanisms — sliding, bonding and bearing — for the mobilisation of interfacial friction have been identified. In the light of these mechanisms, the effect of variation in reinforcement parameters, such as extensibility, flexibility and hardness on mobilisation of interfacial friction, and the mechanisms themselves has been examined. The influence of boundary effects of apparatus on the interfacial friction has been discussed and a method of estimating the same in a pull-out box has been proposed.

Influence of Starch Polysaccharide on the Remolded Properties of 2 Indian clay Samples

The reported presence in marine clays and the recognized role of polysaccharide as a bonding agent provided the motivation to examine the role of starch polysaccharide in the remoulded properties of nonswelling (kaolinite) and swelling (bentonite) groups of clays. The starch polysaccharide belongs to a group of naturally occurring, large-sized organic molecules (termed polymers) and is built up by extensive repetition of simple chemical units called repeat units. The results of the study indicate that the impact of the starch polysaccharide on the remoulded properties of clays is dependent on the mineralogy of the clays. On addition to bentonite clay, the immensely large number of segments (repeat units) of the starch polysaccharide create several polymer segment - clay surface bonds that cause extensive aggregation of the bentonite units layers. The aggregation of the bentonite unit layers greatly curtails the available surface area of the clay mineral for diffuse ion layer formation. The reduction in diffuse ion layer thickness markedly lowers the consistency limits and vane shear strength of the bentonite clay. On addition to kaolinite, the numerous polymer segment - clay surface bonds enhance the tendency of the kaolinite particles to flocculate. The enhanced particle flocculation is responsible apparently for a small to moderate increase in the liquid limit and remoulded undrained strength of the nonswelling clay.

Role of molecular reorientation in the vitrification of molecular liquids: A Monte Carlo study of the liquid and glassy states of 2,2-dimethylbutane

The liquid and the glassy phases of 2,2-dimethylbutane have been investigated by isothermal isobaric ensemble Monte Carlo simulation. Thermodynamic Properties and radial distribution functions for both the liquid and the glass have been obtained. The radial distribution functions have been classified into three types based on the accessibility of the group. It has been shown that the structure of the Iiquid and the glass can be understood in terms of the above classification of the radial distribution functions. Molecular reorientation plays an important role in the structural rearrangement accompanying glass formation. As much as 35% of the contribution to the increase in the intermolecular interaction energy on vitrification is due to the reorientation of the neighbouring pairs of molecules. The observed changes in the dimerisation energy and the bonding energy distribution function are consistent with the observed structural changes.

Nano structured carbon nitrides prepared by chemical vapour deposition

Nanostructured carbon nitride films were prepared by pyrolysis assisted chemical vapour deposition(CVD). A two zone furnace with a temperature profile having a uniform temperature over a length of 20 cm length has been designed and developed. The precursor Azabenzimidazole was taken in a quartz tube and evaporated at 400 degrees C. The dense vapours enter the pyrolysis zone kept at a desired temperature and deposit on the quartz substrates. The FTIR spectrum of the prepared samples shows peaks at 1272 cm(-1) (C-N stretching) and 1600 cm(-1) (C=N) confirms the bonding of nitrogen with carbon. Raman D and G peaks, are observed at 1360 cm(-1) and 1576 cm(-1) respectively. XPS core level spectra of C 1s and N 1s show the formation of pi bonding between carbon and nitrogen atoms. The size of the nano crystals estimated from the SEM images and XRD is similar to 100 nm. In some regions of the sample a maximum of 57 atom % of nitrogen has been observed.

(Ba3MTiMO9)-Ti-III-O-V (M-III = Fe, Ga, Y, Lu, M-V = Nb, Ta, Sb) perovskite oxides Synthesis, structure and dielectric properties

We describe the synthesis structures and dielectric properties of new perovskite oxides of the formula (Ba3MTiMO9)-Ti-III-O-V for M-III = Fe Ga Y Lu and M-V = Nb Ta Sb While M-V = Nb and Ta oxides adopt disordered/partially ordered 3C perovskite structures where M-III/Ti/M-V metal-oxygen octahedra are corner connected the M-V = Sb oxides show a distinct preference for the 6H structure where Sb-V/Ti-IV metal-oxygen octahedra share a common face forming (Sb Ti)O-9 dimers that are corner-connected to the (MO6)-O-III octahedra The preference of antimony oxides (Sb-V 4d(10)) for the 6H structure which arises from a special Sb-V-O chemical bonding that tends to avoid linear Sb-O-Sb linkages unlike Nb-V/Ta-V d(0) atoms which prefer similar to 180 degrees Nb/Ta-O-Nb/Ta linkages - is consistent with the crystal chemistry of M-V-O oxides in general The dielectric properties reveal a significant difference among Mill members All the oxides with the 3C structure excepting those with Mill = Fe show a normal low loss dielectric behaviour with epsilon = 20-60 in the temperature range 50-400 degrees C the M-III = Fe members with this structure (M-V = Nb Ta) display a relaxor-like ferroelectric behaviour with large E values at frequencies <= 1 MHz (50-500 degrees C) (C) 2010 Elsevier Masson SAS All rights reserved

Theoretical and Computational Analysis of Static and Dynamic Anomalies in Water-DMSO Binary Mixture at Low DMSO Concentrations

Experiments have repeatedly observed both thermodynamic and dynamic anomalies in aqueous binary mixtures, surprisingly at low solute concentration. Examples of such binary mixtures include water-DMSO, water-ethanol, water-tertiary butyl alcohol (TBA), and water-dioxane, to name a few. The anomalies have often been attributed to the onset of a structural transition, whose nature, however, has been left rather unclear. Here we study the origin of such anomalies using large scale computer simulations and theoretical analysis in water-DMSO binary mixture. At very low DMSO concentration (below 10%), small aggregates of DMSO are solvated by water through the formation of DMSO-(H2O)(2) moieties. As the concentration is increased beyond 10-12% of DMSO, spanning clusters comprising the same moieties appear in the system. Those clusters are formed and stabilized not only through H-bonding but also through the association of CH3 groups of DMSO. We attribute the experimentally observed anomalies to a continuum percolation-like transition at DMSO concentration X-DMSO approximate to 12-15%. The largest cluster size of CH3-CH3 aggregation clearly indicates the formation of such percolating clusters. As a result, a significant slowing down is observed in the decay of associated rotational auto time correlation functions (of the S = O bond vector of DMSO and O-H bond vector of water). Markedly unusual behavior in the mean square fluctuation of total dipole moment again suggests a structural transition around the same concentration range. Furthermore, we map our findings to an interacting lattice model which substantiates the continuum percolation model as the reason for low concentration anomalies in binary mixtures where the solutes involved have both hydrophilic and hydrophobic moieties.

Lanthanide Luminescent Coordination Polymer Constructed from Unsymmetrical Dinuclear Building Blocks Based on 4-((1H-Benzod]imidazol-1-yl)methyl)benzoic Acid

Lanthanide coordination polymers of the general formula Ln(2)(L)(5)(NO3)(H2O)(4)](n) (Ln = Eu (1), Tb (2), Gd (3)) supported by a novel aromatic carboxylate ligand 4-((1H-benzod]imidazol-1-yl)methyl)benzoic acid (HL) have been synthesized, characterized, and their photoluminescence behavior is examined. The powder X-ray diffraction patterns of complexes 1-3 showed that 1-3 are isostructural; thus, 1 has been chosen as an example to discuss in detail about the molecular structure by single-crystal X-ray diffraction. Complex 1 is a one-dimensional (1D) helical chain-like coordination polymer consisting of unique unsymmetrical dinuclear lanthanide building blocks. The 1D chains are further linked by the significant intermolecular hydrogen-bonding interactions to form a two-dimensional supramolecular network. The Tb3+ complex exhibits bright green luminescence efficiency in the solid state with a quantum yield of 15%. On the other hand, poor luminescence efficiency has been noted for Eu3+-benzoate complex.