BSDD-2.0: Biomolecules Segment Display Device - An updated web accessible computing resource

The existing internet computing resource, Biomolecules Segment Display Device (BSDD), has been updated with several additional useful features. An advanced option is provided to superpose the structural motifs obtained from a search on the Protein Data Bank (PDB) in order to see if the three-dimensional structures adopted by identical or similar sequence motifs are the same. Furthermore, the options to display structural aspects like inter- and intra-molecular interactions, ion-pairs, disulphide bonds, etc. have been provided.The updated resource is interfaced with an up-to-date copy of the public domain PDB as well as 25 and 90% non-redundant protein structures. Further, users can upload the three-dimensional atomic coordinates (PDB format) from the client machine. A free molecular graphics program, JMol, is interfaced with it to display the three-dimensional structures.

Advances in gene delivery through molecular design of cationic lipids

This feature article describes the recent developments in the design of cationic lipids and their applications in gene delivery. Various structure-activity investigations explaining the variations in gene transfection efficacies with respect to different molecular structures of the cationic lipids have been discussed. Gene transfer abilities are presented in relation to aggregation properties of different aqueous formulations such as cationic liposomes and surfactant aggregates from various amphiphiles and cationic lipids, as a function of their hydrophobic parts, linkers and head groups.

Oxidation of alkaline earth sulfides to sulfates: Thermodynamic aspects

The emf of the galvanic cell, Pt, Ni + NiO/(CaO) ZrO2/MS + MSO4, Ir, Pt, where M is calcium, strontium, or barium, has been measured in the temperature range 850 to 1100 K. From these measurements the Gibbs’ energy changes for the oxidation of sulfides of alkaline earth metals to their respective sulfates have been calculated. The results are compared with available thermodynamic data in the literature. The agreement varies from ±2 kJ for the strontium system to ±20 kJ in the case of barium. Trends in the stabilities of alkaline earth sulfates are discussed in relation to the properties of the cationic species involved.

Molecular analysis of inorganic nitrogen assimilation in yeasts

Assimilation of nitrate and various other inorganic nitrogen compounds by different yeasts was investigated. Nitrate, nitrite, hydroxylamine, hydrazine, ammonium sulphate, urea and L-asparagine were tested as sole sources of nitrogen for the growth of Candida albicans, C. pelliculosa, Debaryomyces hansenii, Saccharomyces cerevisiae, C. tropicalis, and C. utilis. Ammonium sulphate and L-asparagine supported the growth of all the yeasts tested except D. hansenii while hydroxylamine and hydrazine failed to support the growth of any. Nitrate and nitrite were assimilated only by C. utilis. Nitrate utilization by C. utilis was also accompanied by the enzymatic activities of NAD(P)H: nitrate oxidoreductase (EC 1.6.6.2) and NAD(P)H: nitrite oxidoreductase (EC 1.6.6.4), but not reduced methyl viologen-or FAD-nitrate oxidoreductases (EC 1.7.99.4). It is demonstrated here that nitrate and nitrite reductase activities are responsible for the ability of C. utilis to assimilate primary nitrogen.

Interaction of Metal Ions with 2'-Deoxyribonucleotides. Crystal and Molecular Structure of a Cobalt(l1) Complex with 2'-Deoxyinosine 5'-Monophosphate

The crystal structure of the cobalt( 11) complex with 2'-deoxyinosine 5'-monophosphate (5'- dlMP), [Co(5'-dlMP) (H,0),]-2H20, has been analysed by X-ray diffraction. The complex crystallizes in the space group P2,2,2, with a = 6.877(3), b = 10.904(2), c = 25.421 (6) A, and Z = 4. The structure was solved by the heavy-atom method and refined to an R value of 0.043 using 1 776 unique reflections. The cobalt ion binds only to the 6-oxopurine base of the nucleotide at the N(7) position, the octahedral co-ordination of the metal being completed by five water oxygens. The phosphate oxygens are involved in hydrogen bonding with the co-ordinated water molecules. The structure is closely similar to that of the corresponding ribonucleotide complex. The nucleotide has the energetically preferred conformation: an anti base, a C(3') -endo sugar pucker, and a gauche-gauche conformation about the C(4')-C( 5') bond. The significance of sugar puckering in the monomeric complexes of general formula [ M (5'-nucleotide) (H20),] is explained in terms of the structural requirements for metal-water-phosphate bridging interactions.

Steric Aspects Of The Oxidation Of Thioketones By Singlet Oxygen

Singlet oxygen oxidation of dialkyl thioketones yields the corresponding ketones and in some cases sulfoxides in varying amounts. Steric considerations on the reactive zwitterionic/diradical intermediates have been invoked to rationalise the product distribution.

Molecular structure of a cyclic tetrapeptide disulfide. A novel 310 helical conformation with an S-S bridge

The crystal structure of the cyclic peptide disulfide Boc-Cys-Pro-Aib-Cys-NHMe has been determined by X-ray diffraction. The peptide crystallizes in the space group P212121, with A = 8.646(1), B = 18.462(2), C = 19.678(3)Å and Z = 4. The molecules adopt a highly folded compact conformation, stabilized by two intramolecular 4→ 1 hydrogen bonds between the Cys (1) and Pro (2) CO groups and the Cys (4) and methylamide NH groups, respectively. The backbone conformational angles for the peptide lie very close to those expected for a 310 helix. The S-S bridge adopts a right handed twist with a dihedral angle of 82°. The structure illustrates the role of stereochemically constrained residues, in generating novel peptide conformations. Aib, α-aminoisobutyric acid; Z, benzyloxycarbonyl; Boc, t-butyloxycarbonyl; OMe, methyl ester; OBz, benzyl ester; NHMe, N-methylamide; Tosyl, p-toluenesulfonyl.

Self-assembly of a Pd-II neutral molecular rectangle via a new organometallic Pd-2(II) molecular clip and oxygen donor linker

Two components self-assembly of a Pd-4 neutral molecular rectangle driven by Pd-O bond coordination has been achieved and this pi-electron rich rectangle shows fluorescence quenching in presence of nitroaromatics, which are the chemical signatures of many explosives.

Conformational Analysis and Electronic Structure of Monothiodiacetamide: Normal Coordinate Analysis and Molecular Orbital Study

The infrared spectra of monothiodiacetamide (MTDA, CHaCONHCSCH3) and its N-deuterated compound in solution, solid state and at low temperature are measured. Normal coordinate analysis for the planar vibrations of MTDAd o and -dl have been performed for the two most probable cis-trans-CONHCSor -CSNHCO-conformers using a simple Urey-Bradley force function. The conformation of MTDA derived from the vibrational spectra is supported by the all valence CNDO/2 molecular orbital method. The vibrational assignments and the electronic structure of MTDA are also given.

Crystal and molecular structures of alkali- and alkaline-earth-metal complexes of N,N-dimethylformamide

Structures of lithium, sodium, magnesium, and calcium complexes of NJ-dimethylformamide (DMF) have been investigated by X-ray crystallography. Complexes with the formulas LiCl.DMF.1/2H20, NaC104.2DMF, CaC12.2DMF.2H20, and Mg(C104)2.6DMF crystallized in space groups P2]/c, P2/c, Pi, and Ella, respectively, with the following cell dimensions: Li complex, a = 13.022 (7) A, b = 5.978 (4) A, c = 17.028 (10) A, = 105.48 (4)O, Z = 8; Na complex, a = 9.297 (4)A, b = 10.203 (3) A, c = 13.510 (6) A, /3 = 110.08 (4)O, Z = 4; Ca complex, a = 6.293 (4) A, b = 6.944 (2) A, c = 8.853(5) A, a = 110.15 (3)O, /3 = 105.60 (6)", y = 95.34 (5)", Z = 1; Mg complex, a = 20.686 (11) A, b = 10.962 (18) A,c = 14.885 (9) A, /3 = 91.45 (5)O, Z = 4. Lithium is tetrahedrally coordinated while the other three cations are octahedrally coordinated; the observed metal-oxygen distances are within the ranges generally found in oxygen donor complexes of these metals. The lithium and sodium complexes are polymeric, with the amide and the anion forming bridging groups between neighboring cations. The carbonyl distances become longer in the complexes accompanied by a proportionate decrease in the length of the central C-N bond of the amide; the N-C bond of the dimethylamino group also shows some changes in the complexes. The cations do not deviate significantly from the lone-pair direction of the amide carbonyl and remain in the amide plane. Infrared spectra of the complexes reflect the observed changes in the amide bond distances.

Molecular and crystal structure of deoxyguanosine 5'-phosphate

RECENT crystallographic studies of the dinucleosides ApU (ref. 1) and GpC (ref. 2) have given experimental proof for the base pairing arrangement proposed by Watson and Crick for the DNA double helix3. Another striking feature of this structure relates to the torsional angle about the C5'-C4' bond in the phosphate−sugar backbone chain. In the Crick and Watson model4, this conformation is gauche−trans (GT). Crystal structures of 5'-nucleotides, dinucleosides and dinucleotides so far studied, however, have shown only the gauche−gauche (GG) conformation about this bond. The GG conformer is also the only one found in the refined models of the proposed structure of the double helical nucleic acids and polynucleotides5−7. The only nucleotide with a GT conformation is 6-azauridine-5'-phosphate8 which is not a normal monomer unit of nucleic acids. It is also reported that 5'-dGMP assumes preferentially GT conformation in solution9.

Molecular motion in plastic crystals

Abstract is not available.