Interaction of metal ions with 6-oxopurine nucleotides. Part 1. X-Ray structures of ternary cobalt(III) complexes with inosine 5'-monophosphate or guanosine 5'-monophosphate

The crystal structures of two ternary metal nucleotide complexes of cobalt, [Co(en)2(H2O)2]-[Co(5?-IMP)2(H2O)4]Cl2·4H2O (1) and [Co(en)2(H2O)2][Co(5?-GMP)2(H2O)4]Cl2·4H2O (2), have been analysed by X-ray diffraction (en = ethylenediamine, 5?-IMP = inosine 5?-monophosphate, and 5?-GMP = guanosine 5?-monophosphate). Both complexes crystallize in the orthorhombic space group C2221 with a= 8.725(1), b= 25.891(5), c= 21.212(5)Å, Z= 4 for (1) and a= 8.733(2), b= 26.169(4), c= 21.288(4)Å, Z= 4 for (2). The structure of (1) was solved by the heavy-atom method, while that of (2) was deduced from (1). The structures were refined to R values of 0.09 and 0.10 for 1 546 and 1 572 reflections for (1) and (2) respectively. The two structures are isomorphous. A novel feature is that the chelate ligand en and the nucleotide are not co-ordinated to the same metal ion. One of the metal ions lying on the two-fold a axis is octahedrally co-ordinated by two chelating en molecules and two water oxygens, while the other on the two-fold b axis is octahedrally co-ordinated by two N(7) atoms of symmetry-related nucleotides in a cis position and four water oxygens. The conformations of the nucleotides are C(2?)-endo, anti, and gauche�gauche. In both (1) and (2) the charge-neutralising chloride ions are disordered in the vacant space between the molecules. These structures bear similarities to the mode of nucleotide co-ordination to PtII complexes of 6-oxopurine nucleotides, which are the proposed models for intrastrand cross-linking in DNA by a metal complex.

Stabilization of the bio-membrane by small molecules: interaction of trehalose with the phospholipid bilayer

Anhydrobiotic organisms undergo periods of acute dehydration during their life cycle. It is of interest to understand how the biomembrane remains intact through such stress. A disaccharide, trehalose, which is metabolised during anhydrobiosis is found to prevent disruption of model membrane systems. Molecular modelling techniques are used to investigate the possible mode of interaction of trehalose with a model monolayer. The objective is to maximise hydrogen bonding between the two systems. A phospholipid matrix consisting of 1,2-dimyristoyl-sn-glycero-3-phosphatidylcholine (DMPC) is chosen to represent the monolayer. The crystal structure of DMPC reveals that there are two distinct conformers designated as A and B. An expansion of the monolayer, coplanar with its surface, results in the trehalose molecule being accommodated in a pocket formed by four B conformers. One glucose ring of the sugar rests on the hydrophobic patch provided by the choline methyls of an A conformer. Five hydrogen bonds are formed involving the phosphate oxygens of three of the surrounding B conformers. The model will be discussed with reference to relevant experimental data on the interaction.

Structure of N2-carbamoyl-L-asparagine

CsH9N304, M r= 175.1, orthorhombic,P212~2 ~, a = 7.486 (1), b = 9.919 (2), c =20.279 (2) A, V= 1505.8 A 3, z = 8, D x = 1.54, D m = 1.60 Mg m -3, ~,(Cu Ka) = 1.5418 A, g = 1. I I mm -~, F(000) = 736, T = 300 K, final R = 0.032 for 1345 observed reflections. The two independent molecules in the asymmetric unit are related by a pseudo twofold axis, with the asparagine side chains having different conformations [X 2 being -132.1 (3) and 139.6 (2)°]. The crystal structure is stabilized by extensive hydrogen bonding, with a specific interaction between the carboxyl group of one molecule and the carbamoyl group of another forming hydrogen-bonded chains.

Electronic structure and conformational study of thiobiurets

Quantum mechanical calculations at all valence complete neglect of differential overlap (CNDO/2) and self-consistent charge extend Huckel (SCC-EH) and the Pi electron Pariser-Parr-Pople with limited configuration interaction (PPP-LCI) levels of approximation have been accomplished for monothiobiuret and dithiobiuret. From the calculated results, a discussion of the electronic structure, photoelectron and electronic spectra and the conformational stability are given. The electronic and1H nmr spectra are also reported. A trans-cis-CONHCS-structure is found to be the stable conformation for monothiobiuret consistent with other evidences.

Crystal and molecular structure of l-valyl-l-lysine hydrochloride

l-Valyl-l-lysine hydrochloride, C11N3O3H23 HCl, rystallizes in the monoclinic space group P2, with a = 5.438(5), b = 14.188(5), c = 9.521(5) Å, β= 95.38(2)° and Z = 2. The crystal structure, solved by direct methods, refined to R = 0.036, using full matrix least-squares method. The peptide exists in a zwitterionic form, with the N atom of the lysine side-chain protonated. The two γ-carbons of the valine side-chain have positional disorder, giving rise to two conformations, χ111= -67.3 and 65.9°, one of which (65.9°) is sterically less favourable and has been found to be less popular amongst residues branching at β-C. The lysine side-chain has the geometry of g− tgt, not seen in crystal structures of the dipeptides reported so far. Interestingly, χ32 (63.6°) of lysine side-chain has a gauche+ conformation unlike in most of the other tructures, where it is trans. The neighbouring peptide molecules are hydrogen bonded in a head-to-tail fashion, a rather uncommon interaction in lysine peptide structures. The structure shows considerable similarity with that of l-Lys-l-Val HO in conformational angles and H-bond interactions [4].

Frame Soil Interaction And Winkler Model

The Winkler spring model is the most convenient representation of soil support in the domain of linear elasticity for framed structure-soil interaction analyses. The closeness of the analytical results obtained using this model with those corresponding to the elastic half-space continuum has been investigated in the past for foundation beams. The findings, however, are not applicable to framed structures founded on beam or strip footings. Moreover, the past investigations employ the concept of characteristic length which does not adequately account for the stiffness contribution of the superstructure. A framed structure on beam foundation can be described parametrically by the ratios of stiffnesses of superstructure and foundation beams to that of soil. For a practical range of soil allowable pressures, the ranges of these relative stiffness ratios have been established. The present study examines the variation between interactive analyses based on Winkler springs with those using the half-space continuum over these ranges of relative stiffness ratios. The findings enable the analyst to undertake a Winkler spring-based-interaction analysis with knowledge of the likely variation of values with those derived for the more computation-intensive half-space continuum.

Octabromotetraphenylporphyrin and its metal derivatives: Electronic structure and electrochemical properties

The free-base octabromotetraphenylporphyrin (H2OBP) has been prepared by a novel bromination reaction of (meso-tetraphenylporphyrinato)copper(II). The metal [V(IV)O, Co(II), Ni(II), Cu(II), Zn(II), Pd(II), Ag(II), Pt(II)] derivatives exhibit interesting electronic spectral features and electrochemical redox properties. The electron-withdrawing bromine substituents at the pyrrole carbons in H2OBP and M(OBP) derivatives produce remarkable red shifts in the Soret (50 nm) and visible bands (100 nm) of the porphyrin. The low magnitude of protonation constants (pK3 = 2.6 and pK4 = 1.75) and the large red-shifted Soret and visible absorption bands make the octabromoporphyrin unique. The effect of electronegative bromine substituents at the peripheral positions of the porphyrin has been quantitatively analyzed by using the four-orbital approach of Gouterman. A comparison of MO parameters of MOBP derivatives with those of the meso-substituted tetraphenylporphyrin (M(TPP)) and unsubstituted porphine (M(P)) derivatives provides an explanation for the unusual spectral features. The configuration interaction matrix element of the M(OBP) derivatives is found to be the lowest among the known substituted porphyrins, indicating delocalization of ring charge caused by the increase in conjugation of p orbitals of the bromine onto the ring orbitals. The electron-transfer reactivities of the porphyrins have been dramatically altered by the peripheral bromine substituents, producing large anodic shifts in the ring and metal-centered redox potentials. The increase in anodic shift in the reduction potential of M(OBP)s relative to M(TPP)s is found to be large (550 mV) compared to the shift in the oxidation potential (300 mV). These shifts are interpreted in terms of the resonance and inductive interactions of the bromine substituents.

Steric and rotational constraints in the X-ray structure of the animalarial drug amodiaquine

In the crystal structure of the antimalarial drug amodiaquine, the bonds linking the quinoline and the phenyl groups show partial double-bond character. The partial double-bond character of the two exocyclic bonds, together with stereochemical constraints, reduce flexibility of the two ring systems of the molecule. The dihedral angle between the two ring planes is lowest compared to those in the antileukaemic drug amsacrine and its derivatives. CPK-modelling studies suggest the way amodiaquine can bind to DNA. Stacking interaction between the quinoline and phenyl groups of independent molecules and the hydrogen-bond network stabilize the crystal structure.

Crystal and molecular structure of putrescine DL- glutamic acid complex

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

The crystal and molecular structure of putrescine - di-glutamic acid complexes

The polyamines spermine, spermidine, putrescine, cadaverine, etc. have been implicated in a variety of cellular functions. However, details of their mode of interaction with other ubiquitous biomolecules is not known. We have solved a few structures of polyamine-amino acid complexes to understand the nature and mode of their interactions. Here we report the structure of a complex of putrescine with DL-glutamic acid. Comparison of the structure with the structure of putrescine-L-glutamic acid complex reveals the high degree of similarity in the mode of interaction in the two complexes. Despite the presence of a centre of symmetry in the present case, the arrangement of molecules is strikingly similar to the L-glutamic acid complex.

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

Analysis of sequence dependent variations in secondary and tertiary structure of tRNA molecules

The double helical regions of the five tRNA(Phe) and two tRNA(Asp) crystal structures have been analyzed using the local basepair step parameters. The sequence dependent effects in the mini double helices of tRNA are very similar to those observed in the crystal structures of oligonucleotides in the A-form, the purine-pyrimidine and purine-purine steps have small roll angles when compared to the fiber models of A-DNA as well as A-RNA, while the pyrimidine-purine doublet steps have large roll angles. The orientation of the basepairs in the D-stem is unusual and invariant i.e. they are different from the other three stems but are very similar in all the five tRNA(Phe) crystal structures, presumably due to tertiary interaction of the Watson-Crick basepairs with other bases, with all bases being highly conserved. The origin of the differences between the tertiary structures of tRNA(Phe) and tRNA(Asp) from yeast has also been investigated. It is found that even though the angle between the acceptor arm and the D-stem is very similar in the two structures, the angle subtended by the acceptor arm and the anticodon arm is smaller in the tRNA(Phe) structure (by more than 10 degrees). This is due to differences in the orientation of the two mini helices constituting the anticodon arm, which are inclined to each other by approximately 25 degrees in tRNA(Phe) and 16 degrees in tRNA(Asp). In addition, the acceptor arm, the D-stem and the anticodon stem are nearly coplanar in tRNA(Phe), while in tRNA(Asp) the anticodon stem projects out of the plane defined by the acceptor arm and the anticodon stem. These two features together lead to a larger separation between the acceptor and anticodon ends in tRNA(Asp) and indicate that the junction between the D-stem and the anticodon stem is quite variable, with features characteristic of a ball-and-socket type joint and determined for each tRNA molecule by the base sequence at the junction.

Electronic absorption and emission spectroscopic investigations of the interaction of the fullerenes, C60 and C70, with amines and aromatic molecules

Electronic absorption spectroscopy and fluorescence spectroscopy have been used to investigate the interaction of the fullerenes C60 and C70 with diethylaniline, and with aromatic solvents such as benzene. C60 interacts weakly with aromatic amines in the ground state while C70 does not interact at all. Steady state fluorescence emission and lifetime measurements show that both C60 and C70 form excited state complexes (exciplexes) with the amines in non-aromatic solvents such as methylcyclohexane, but not in benzene. In benzene, only fluorescence quenching is observed due to the interaction between the π systems of the aromatic solvent and the fullerene in the ground state. This is also borne out by the systematic study of solvent effects on the absorption and emission spectra of the fullerenes.

Electronic structure of La1-xSrxFeO3

We have investigated the electronic structure of well-characterized samples of La1-xSrxFeO3 (x=0.0�0.4) by x-ray photoelectron spectroscopy (XPS), ultraviolet photoelectron spectroscopy, bremsstrahlung isochromat (BI) spectroscopy, and Auger electron spectroscopy. We find systematic behavior in the occupied and unoccupied density of states reflecting changes in the electronic structure on hole doping via Sr substitution as well as providing estimates for different interaction strengths. The spectral features, particularly of the unoccupied states obtained from BI spectra, indicate the probable reason for the absence of an insulator-metal transition in this series. Analysis of the Auger spectra provides the estimates of the on-site effective Coulomb interaction strengths in Fe 3d and O 2p states. The parameter values for the bare charge-transfer energy ? and the Fe 3d�O 2p hybridization strength t? for LaFeO3 are obtained from an analysis of the Fe 2p core-level XPS in terms of a model many-body calculation. We discuss the character of the ground state in LaFeO3 as well as the nature of the doped hole states in La1-xSrxFeO3, based on these parameter values.

Molecular structure of Lantadene-B&C, triterpenoids ofantana camara, red variety: Lantadene-B, 22β-angeloyloxy-3-oxoolean-12-en-28-oic acid; Lantadene-C, 22 β-(S)-2′-methyl butanoyloxy-3-oxoolean-12-en-28-oic acid

(I)Lantadene-B: C35H52O5,M r =552.80, MonoclinicC2,a=25.65(1),b=6.819(9),c=18.75(1) Å,beta=100.61(9),V=3223(5) Å3,Z=4,D x =1.14 g cm–3 CuKagr (lambda=1.5418A),mgr=5.5 cm–1,F(000)=1208,R=0.118,wR=0.132 for 1527 observed reflections withF o ge2sgr(F o ). (II)Lantadene-C: C35H54O5·CH3OH,Mr=586.85, Monoclinic,P21,a=9.822(3),b=10.909(3),c=16.120(8)Å,beta=99.82(4),V=1702(1)Å3,Z=2,D x =1.145 g cm–3, MoKagr (lambda=0.7107Å), mgr=0.708 cm–1 F(000)=644,R=0.098, wR=0.094 for 1073 observed reflections. The rings A, B, C, D, and E aretrans, trans, trans, cis fused and are in chair, chair, sofa, half-chair, chair conformations, respectively, in both the structures. In the unit cell the molecules are stabilized by O-HctdotO hydrogen bonds in both the structures, however an additional C-HctdotO interaction is observed in the case of Lantadene-C.