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.

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.

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.

Miscibility of Poly(aromatic acrylate)s and Methacrylates with Styrene/Acrylonitrile copolymers

Miscibilities of some poly[aromatic (meth)acrylatels namely, poly(pheny1 acrylate) (PPA), poly(pheny1 methacrylate) (PPMA), poly(benzy1 acrylate) (PBA), and poly(benzy1 methacrylate) (PBMAY polystyrene blends, have been studied through the so-called copolymer effect by incorporating acrylonitrile units in PS chains. In these systems, miscibility occurs on account of the strong repulsion between the acrylonitrile and styrene units in the copolymer. PBA and PBMA were blended with different styreneacrylonitrile (SAN) copolymers. A miscibility window has been identified for the latter system, and from these limits, the binary interaction energy density parameters (B,j.’sw) ere calculated. Using these values, the miscibilities in other homopolymer-copolymer and copolymer-copolymer systems containing benzyl methacrylate, acrylonitrile, and styrene monomer units have been predicted and subsequently verified experimentally. The miscibility window limits in poly[aromatic (meth)acrylate]s/SAN copolymer blends have been compared. PBA does not exhibit a miscibility window with SAN copolymers, which has been explained by the weak intramolecular hydrogen bonding in PBA. The miscibility window in the PBW SAN copolymer system, as observed by DSC, shows a considerable narrowing in nonradiative energy transfer (NRET) measurements, as this technique is more sensitive.

Miscibility of poly(aromatic acrylate)s and methacrylates with styrene/acrylonitrile copolymers

Miscibilities of some poly[aromatic (meth)crylate]s namely, poly(phenyl acrylate) (PPA, poly(phenyl methacrylate) (PPMA), poly(benzyl acrylate) (PBA), and poly(benzyl methacrylate) (PBMA)/polystyrene blends, have been studied through the so-called copolymer effect by incorporating acrylonitrile units in PS chains. In these systems, miscibility occurs on account of the strong repulsion between the acrylonitrile and styrene units in the copolymer. PBA and PBMA were blended with different styrene-acrylonitrile (SAN) copolymers. A miscibility window has been identified for the latter system, and from these limits, the binary interaction energy density parameters (Bij's) were calculated. Using these values, the miscibilities in other homopolymer-copolymer and copolymer-copolymer systems containing benzyl methacrylate, acrylonitrile, and styrene monomer units have been predicted and subsequently verified experimentally. The miscibility window limits in poly[aromatic (meth)acrylate]s/SAN copolymer blends have been compared. PBA does not exhibit a miscibility window with SAN copolymers, which has been explained by the weak intramolecular hydrogen bonding in PBA. The miscibility window in the PBMA/SAN copolymer system, as observed by DSC, shows a considerable narrowing in nonradiative energy transfer (NRET) measurements, as this technique is more sensitive.

Structure and stability of human telomeric sequence

Telomeric DNA of a variety of vertebrates including humans contains the tandem repeat d(TTAGGG)(n). We have investigated the structural properties of the human telomeric repeat oligonucleotide models d(T(2)AG(3))(4), d(G(3)T(2)A)(3)G(3), and d(G(3)T(2)AG(3)) using CD, gel electrophoresis, and chemical probing techniques. The sequences d(G(3)T(2)A)(3)G(3) and d(T(2)AG(3))(4) assume an antiparallel G quartet structure by intramolecular folding, while the sequence d(G(3)T(2)AG(3)) also adopts an antiparallel G quartet structure but by dimerization of hairpins. In all the above cases, adenines are in the loop. The TTA loops are oriented at the same end of the G tetrad stem in the case of hairpin dimer. Further, the oligonucleotide D(G(3)T(2)AG(3)) forms a higher order structure by the association of two hairpin dimers via stacking of G tetrad planes. Here we show that N-7 of adenine in the hairpin dimer is Hoogsteen hydrogen-bonded. The partial reactivity of loop adenines with DEPC in d(T(2)AG(3))(4) suggests that the intramolecular G quartet structure is highly polymorphic and structures with different loop orientations and topologies are formed in solution. Intra- and interloop hydrogen bonding schemes for the TTA loops are proposed to account for the observed diethyl pyrocarbonate reactivities of adenines. Sodium-induced G quartet structures differ from their potassium-induced counterparts not only in stability but also in loop conformation and interactions. Thus, the overall structure and stability of telomeric sequences are modulated by the cation present, loop sequence, and the number of G tracts, which might be important for the telomere function.

Constructions of 2D-Metallamacrocycles Using Half-Sandwich Ru-2(II) Precursors: Synthesis, Molecular Structures, and Self-Selection for a Single Linkage Isomer

Coordination-driven self-assembly of oxalato-bridged half-sandwich p-cymene ruthenium complex Ru-2(mu-eta(4)-C2O4)(MeOH)(2)(eta(6)-p-cymene)(2)] (O3SCF3)(2) (1a) with several ditopic donors (L-a-L-d) in methanol affords a series of bi- and tetranuclear metallamacrocycles (2a and 3-5). Similarly, the combination of 2,5-dihydroxy-1,4-benzoquinonato (dhbq)-bridged binuclear complex Ru-2(mu-eta(4)-C6H2O4)(MeOH)(2)(eta(6)-p-cymene)(2)](O3SCF3)(2) (1b) with a flexible bidentate amide linker (L-a) in 1:1 molar ratio gave the corresponding tetranuclear complex 2b. All the macrocycles were isolated as their triflate salts in high yields and were fully characterized by various spectroscopic techniques. Finally, the molecular structures of all the assemblies were determined unambiguously by single-crystal X-diffraction analysis. Interestingly, the combination of acceptor 1a or 1b with an unsymmetrical linear ditopic donor L-a results in a self-sorted linkage isomeric (head-to-tail) macrocycle (2a or 2b) despite the possibility of formation of two different isomeric macrocycles (head-to-head or head-to-tail) due to different connectivity of the donor. Molecular structures of the complexes 2a and 2b showed tetranuclear rectangular geometry with dimensions of 5.51 angstrom x 13.29 angstrom for 2a and 7.91 angstrom x 13.46 angstrom for 2b. In both cases, two binuclear Ru-2(II) building blocks are connected by a mu-N-(4-pyridyl)isonicotinamide donor in a head-to-tail fashion. Surprisingly, the macrocycle 2a loses one counteranion and cocrystallizes with monodeprotonated 1,3,5-trihydroxybenzene via strong intermolecular pi-pi stacking and hydrogen bonding. The tweezer complex 3 showed strong fluorescence in solution, and it showed fluorescence sensing toward nitroaromatic compounds. A fluorescence study demonstrated a marked quenching of the initial fluorescence intensity of the macrocycle 3 upon gradual addition of trinitrotoluene and exhibits significant fluorescence quenching response only for nitroaromatic compounds compared to various other aromatic compounds tested.

Comparison of the miscibility strategies in poly(benzyl methacrylate)-polystyrene blends

Exothermic interactions like hydrogen bonding, ionic and charge transfer, etc., and ''copolymer effect'' are commonly used to induce miscibility in immiscible blends. The efficacy of these methods in promoting miscibility in poly(benzyl methacrylate) (PBMA)-polystyrene (PS) immiscible blends has been studied by suitably modifying the structure of the component polymers. It has been found that hydrogen bonding approach is most advantageous among these approaches as it involves the need for minimum interacting sites. It has also been shown that these results can be extended to the blends of poly(acrylate)s or poly(methacrylate)s with PS. (C) 1996 John Wiley & Sons, Inc.

4-Hydroxy-6-(4-methoxyphenyl)-4-phenyl-1,3-diazinane-2-thione

In the title compound, C17H18N2O2S, the 1,3-diazinane-2-thione ring system is not coplanar with the benzene ring and methoxyphenyl ring system, the dihedral angle between the planes being 65.58 (13) and 89.18 (10)degrees, respectively. The crystal structure is characterized by intermolecular O-H...S, N-H...S, N-H...O and C-H...S hydrogen bonding.

Modes of binding of 2'-AMP to RNase T1. A computer modeling study

The modes of binding of adenosine 2'-monophosphate (2'-AMP) to the enzyme ribonuclease (RNase) T1 were determined by computer modelling studies. The phosphate moiety of 2'-AMP binds at the primary phosphate binding site. However, adenine can occupy two distinct sites--(1) The primary base binding site where the guanine of 2'-GMP binds and (2) The subsite close to the N1 subsite for the base on the 3'-side of guanine in a guanyl dinucleotide. The minimum energy conformers corresponding to the two modes of binding of 2'-AMP to RNase T1 were found to be of nearly the same energy implying that in solution 2'-AMP binds to the enzyme in both modes. The conformation of the inhibitor and the predicted hydrogen bonding scheme for the RNase T1-2'-AMP complex in the second binding mode (S) agrees well with the reported x-ray crystallographic study. The existence of the first mode of binding explains the experimental observations that RNase T1 catalyses the hydrolysis of phosphodiester bonds adjacent to adenosine at high enzyme concentrations. A comparison of the interactions of 2'-AMP and 2'-GMP with RNase T1 reveals that Glu58 and Asn98 at the phosphate binding site and Glu46 at the base binding site preferentially stabilise the enzyme-2'-GMP complex.

Conformational preferences of α-functionalised keten-S,N-acetals: Potential role of SO and SS interactions in solution

PMR spectra of carbonyl compounds 2a-k reveal significant variations in the population of E and Z isomers on changing the solvent from CDCl3 to DMSO-d6. In non-polar media, the intramolecular N-H…. O hydrogen bonded form is exclusively observed. In DMSO-d6, the alternative Z form is also populated. A similar conformational switch is also noted in the corresponding thiones. Different interpretations are critically analysed. The most consistent explanation is suggested to involvean interplay of N-H….X hydrogen bonding and S…X attractive interaction (X = O,S) in these systems. Ab initio calculations support this interpretation.

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.

Mo3O5(OH)(2)(AsO4)2: A new solid with a structure related to beta VOPO4

Mo3O5(OH)(2)(AsO4)(2) was prepared at 100 degrees C from an aqueous solution of MoO3 containing arsenic and nitric acids. It crystallises in the monoclinic system, a = 13.024(1)Angstrom, b = 7.2974 (2) Angstrom, c = 13.281(1) Angstrom, beta = 121.124(8)degrees, Z = 4, space group C2/c. The structure was determined by Rietveld refinement from X-ray powder diffraction data. The three-dimensional structure is built up from MoO6 and MoO5OH octahedra and AsO4 tetrahedra sharing corners. The octahedra share two opposite vertices forming zigzag chains that run parallel to [10(1) over bar]. Each AsO4 tetrahedron is connected to four octahedra, two of which belong to the same chain, thus linking three chains. The resulting covalent framework is similar to that of beta VOPO4 in which one tetrahedral P site for every three is empty. The two protons are likely to be bonded to two (out of four) unshared oxygen atoms surrounding this empty site. All the Mo atoms are strongly off-centred in the octahedra; and the off-centring is disordered. The disorder is discussed in terms of Mo shifts perturbed by a disordered hydrogen bonding scheme.

A Change in the 3(10)- to alpha-Helical Transition Point in the Heptapeptides Containing Sulfur and Selenium

Crystal structures of three heptapeptides Boc-Ala-Leu-Aib-XXX-Ala-Leu-Aib-OMe (where XXX = methionine in peptide A, selenomethionine in peptide B, and S-benzyl cysteine in peptide C) reveal mixed 3(10)-/alpha-helical conformations with R factors of 6.94, 5.79, and 5.98, respectively. All the structures were solved in the P2(1)2(1)2(1) space group. 3(10)- to a-helical transitions are observed in all of these peptides. The helices begin as a 3(10)-helical segment at the N-terminus and then transit for peptides A and C at residue Aib(3) carbonyl (O(3)), while for peptide B the transition occurs at residue Leu(2) carbonyl oxygen (O(2)). There are water molecules associated in the crystal of each of these peptides and they form different types of hydrogen bonding patterns in each crystal. The observations suggest that 3(10)- to alpha-helical transition is sequence dependent in these short heptapeptide sequences.

Studies in crystal engineering: Crystal packing, topological photodimerization and structure-reactivity correlations in fluoro-substituted styrylcoumarins

In continuation of our studies on the influence of fluoro substitution on the solid state photobehaviour and packing pattern of styrylcoumarins, the results obtained for 4-(3-fluorostyryl)coumarin 1, 4-styryl-6-fluorocoumarin 2 and 4-styryl-7-fluorocoumarin 3 are presented. The configuration of the dimers was established on the basis of crystal packing of 1 and 2 (alpha-packed). A rationale for the significantly lower dimer yield in the crystal for 2 is proposed. In the observed centrosymmetric arrangement of the reactants the C=O ...pi (phenyl) contacts seem to provide additional attractive interactions. C-H ... O and C-H ... F hydrogen bonding seems to provide stability in these structures.