Molecular dynamics simulations of sliding in an Fe-Cu tribopair system

Experimental evidence suggests that high strain rates, stresses, strains and temperatures are experienced near sliding interfaces. The associated microstructural changes are due to several dynamic an interacting phenomena. 3D non-equilibrium molecular dynamics (MD) simulations of sliding were conducted with the aim of understanding the dynamic processes taking place in crystalline tribopairs, with a focus on plastic deformation and microstructural evolution. Embedded atom potentials were employed for simulating sliding of an Fe-Cu tribopair. Sliding velocity, crystal orientation and presence of lattice defects were some of the variables in these simulations. Extensive plastic deformation involving dislocation and twin activity, dynamic recrystallization, amorphization and/or nanocrystallization, mechanical mixing and material transfer were observed. Mechanical mixing in the vicinity of the sliding interface was observed even in the Fe-Cu system, which would cluster under equilibrium conditions, hinting at the ballistic nature of the process. Flow localization was observed at high velocities implying the possible role of adiabatic heating. The presence of preexisting defects (such as dislocations and interfaces) played a pivotal role in determining friction and microstructural evolution. The study also shed light on the relationship between adhesion and plastic deformation, and friction. Comparisons with experiments suggest that such simulations can indeed provide valuable insights that are difficult to obtain from experiments.

Molecular convergence of hexosamine biosynthetic pathway and ER stress leading to insulin resistance in L6 skeletal muscle cells

Augmentation of hexosamine biosynthetic pathway (HBP) and endoplasmic reticulum (ER) stress were independently related to be the underlying causes of insulin resistance. We hypothesized that there might be a molecular convergence of activated HBP and ER stress pathways leading to insulin resistance. Augmentation of HBP in L6 skeletal muscle cells either by pharmacological (glucosamine) or physiological (high-glucose) means, resulted in increased protein expression of ER chaperones (viz., Grp78, Calreticulin, and Calnexin), UDP-GlcNAc levels and impaired insulin-stimulated glucose uptake. Cells silenced for O-glycosyl transferase (OGT) showed improved insulin-stimulated glucose uptake (P < 0.05) but without any effect on ER chaperone upregulation. While cells treated with either glucosamine or high-glucose exhibited increased JNK activity, silencing of OGT resulted in inhibition of JNK and normalization of glucose uptake. Our study for the first time, demonstrates a molecular convergence of O-glycosylation processes and ER stress signals at the cross-road of insulin resistance in skeletal muscle.

Crystal and molecular structure of isogarcinol

The controversy with regard to the structures of the closely related polyisoprenylated phenolic compounds, garcinol, isogarcinol, camboginol, cambogin, xanthochymol and isoxanthochymol is cleared by X-ray crystallographic analysis of the naturally occurring isogarcinol. The unusual UV spectral characteristics of the chromophore of isogarcinol are discussed.

Molecular structure of Boc-Aib-Aib-Phe-Met-NH2·DMSO. A fragment of a biologically active enkephalin analogue

The tetrapeptide t-butyloxycarbonyl--aminoisobutyryl--aminoisobutyryl-L- phenylalanyl-L-methionyl amide crystallizes in the orthorhombic space group P212121 with a= 9.096, b= 18.067, c= 21.701 Å and Z= 4. The crystals contain one molecule of dimethyl sulphoxide (DMSO) associated with each peptide. The structure has been solved by direct methods and refined to an R value of 0.103 for 2 672 observed reflections. The peptide adopts a distorted 310 helical structure stabilized by two intramolecular 4 1 hydrogen bonds between the Boc CO and Aib(1) CO groups and the NH groups of Phe(3) and Met(4), respectively. A long hydrogen bond (N O = 3.35 Å) is also observed between Aib(2) CO and one of the terminal amide hydrogens. The DMSO molecule is strongly hydrogen bonded to the Aib(1) NH group. The solid-state conformation agrees well with proposals made on the basis of n.m.r. studies in solution.

A molecular dynamics investigation of the structure of PbO---PbF2 glasses*1

The structure of PbO---PbF2 glasses has been studied using molecular dynamics (MD). The existence of [OPb4] structural units is observed over the entire glass-forming range, in conformity with a model proposed earlier based on various structural investigations of this system. Various other features of the structural model are also supported by the MD calculations.

Soft Functional Materials Induced by Fibrillar Networks of Small Molecular Photochromic Gelators

Low-molecular-mass organogelators (LMOGs) based on photochromic molecules aggregate in selected solvents to form gels through various spatio-temporal interactions. The factors that control the mode of aggregation of the chromophoric core in the LMOGs during gelation, gelation-induced changes in fluorescence, the formation of stacked superstructures of extended pi-conjugated systems, and so forth are discussed with selected examples. Possible ways of generating various light-harvesting assemblies are proposed, and some unresolved questions, future challenges, and their possible solutions on this topic are presented.

Infrared spectra of 1.3-dithiole-2-thione and its selenium analogues ând frequency assignment and molecular force constants

Infrared spectra of 1,3-dithiole-2-thione (DTT) and its four selenium analogues have been studied in the region 4000 to 20 cm�1. Assignment of all the fundamental frequencies was made by noting the band shifts on progressive selenation. Normal coordinate analysis procedures have been applied for both in-plane and out-of-plane vibrations to help the assignments. The Urey�Bradley force function supplemented with valence force constants for the out-of-plane vibrations was employed for coordinate calculations. A correlation of the infrared assignments of DTT with its different selenium analogues is accomplished. Further, the infrared assignments are compared with those of trithiocarbonate ion and its selenium analogues and other structurally related heterocyclic molecules.

Singlet and triplet molecular interaction in excimers

A perturbative approach is developed to determine, term by term, the contributions of the various forces to the excimer potentials of the singlet and triplet excimers. The results show that the singlet excimer of naphthalene is more stable than the corresponding triplet excimer primarily due to large contributions of the exciton-resonance and the dispersion energy terms. The variation of the various terms with the conformations of the excimers suggests that the singlet and triplet excimers of naphthalene cannot have identical structure.

Molecular vibrations, electronic structure and conformation of diprotonated thiocarbohydrazide

The infrared spectra of diprotonated species of thiocarbohydrazide and its perdeuterated derivative have been examined in the crystalline state. A complete vibrational assignment with a full normal coordinate treatment based on a Urey—Bradley type intramolecular potential Function supplemented with a valence force function for the out of plane and torsional modes is proposed and the origin of the amide II band splittings is explained. A CNDO/2 study of diprotonated thiocarbohydrazide and its neutral molecule is undertaken and the changes in the molecular electronic structures and conformations consequent to protonation are determined and briefly discussed. The magnitude of the N—N+H3 torsional barrier is estimated to be 21 kJ mol− (5.0 kcal mol−1) whereas the barrier for the C—N group is found to be 92 kJ mol−1 (22.0 kcal mol−1).

Molecular-complexes of metallo tetraphenyl porphyrins with 2,4,5,7-tetranitro fluorenone

The interactions of mesotetraphenyl porphyrin and its metallo derivatives with 2,4,5,7-tetra nitrofluorenone have been studied using spectroscopic methods. The association constants (K) for 1:1 complexes in Ch2Cl2Cl2 follow the order Pd+2>Co+2> Cu+2>VO+2>Ni+2>Zn+2. The values of K are accounted in terms of stereochemistry of MTPPs and the electronic configuration of the metal ions. The magnitude and direction of the proton NMR shifts of the acceptor and donor in the complexes and their ESR parameter furnish information as to the possible structures of these complexes in solution.

Self-Assembly of Molecular Prisms via Pt-3 Organometallic Acceptors and a Pt-2 Organometallic Clip

The design and two-component [2 + 3] self-assembly of a series of new organometallic molecular prisms (3a-d) are described. Assemblies 3a,b incorporate 4,4',4'-tris[ethynyl-trans-Pt(PEt3)(2)]triphenylamine (1a) containing a Pt-ethynyl functionality as tritopic planar acceptor and organic ``clips'' 2a and 2b, respectively [where 2a = 1,3-bis(3-pyridyl)isophthalic amide; 2b= 1,3-bis(ethynyl-3-pyridyl)benzene]. In a complementary approach all organic tritopic planar donor ligand 2c [2c 4,4',4'-tris(4-pyridylethynyl)triphenylamine] was assembled with all organometallic ``clip'', 1,8-bis[{trans-Pt(PEt3) (2)(NO3)}ethynyl]anthracene (1b), to obtain prism 3c. A organometallic carbon-centered acceptor, 1,1,1- tris[4-{trans-Pt(PEt3)(2)(NO3)}ethynylphenyl]ethane (1c), has been prepared, and its prism derivative (3d) using an organic `clip'' is prepared. Assemblies (3a-d) were characterized by multinuclear NMR spectroscopy, electrospray ionization mass spectroscopy, and elemental analysis. 3a-d showed fluorescence behavior in solution, and quenching of fluorescence intensity (3a,3c-d) was noticed upon addition of TNT (2,4,6-trinitrotoluene), a common constituent of many commercial explosives. A thin film of the assembly 3d made by spin coating of a solution of 3 x 10(-5) M in DMF on it 1 cm(2) quartz plate showed fluorescence response to the vapor of TNT.

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.

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.