Crystal and molecular structure of [rac-1S,2S,-3S,4R]methyl 2-benzoyl-3,4-dimethyl-4-phenylcyclobutane-1-carboxylate,C21H22O3

The structure of the title compound C₂₁H₂₂O₃, was determined by X-rays.Minr=322.4, monoclinic, space groupP2₁/a,a=11.960(2),b=14.275(3),c=10.858(2) Å,=103.20(2)°,V _c =1804.8 ų,Z=4,D _x =1.223 Mg m^–3. CuK radiation (graphite crystal monochromator,=1.54184 Å),(CuK)=6.53 cm^–1,F(000)=688, T=290 K. Final conventionalR factor=0.050,R _w =0.069 for 1679 unique reflections and 284 variables. The structure was solved usingMultan.     

Magnetic properties of a basalt glass and glass-ceramics

Mössbauer, ESR and magnetization measurements have been carried out on a basalt glass heat-treated at different temperatures (600, 650, 700, 800 and 900°C for 8 h). The as-annealed glass and the above five samples showed two-doublet Mössbauer spectra, while the last two samples also showed a six line magnetic hyperfine pattern at 300 K. At 4 K, the last four samples showed magnetic hyperfine patterns, while the as-annealed glass showed that there was already short range magnetic ordering present. High field Mössbauer data at 4 K showed that the surface spins are canted. The minimum quadrupole splitting and the maximum isomer shift around 700°C are related to the improved symmetry of the magnetite lattice. ESR spectra showed paramagnetic resonances at g = 4.3 and g = 2.0 for the first two samples, while the last four samples showed superparamagnetic resonance centred around g = 2.0 at 300 K. At lower temperatures, the 650 and 700°C samples showed ferrimagnetic resonance. Magnetization curves against H/T superpose well both at 300 and 77 K, showing the typical superparamagnetic behaviour of the small magnetite particles. The saturation magnetization (at 270 K) showed a sharp change around 700°C, showing the formation of magnetite. The magnetic structure of the small magnetite particles are discussed in terms of the above results.     

Thickness of the hydration layer of a protein from molecular dynamics simulation

Water molecules around a protein exhibit slow dynamics with respect to that of pure bulk water. One important issue in protein hydration is the thickness of the hydration layer (i.e., the distance from the protein surface up to which the water dynamics is influenced by the protein). Estimation of thickness is crucial to understand better the properties of "biological water" and the role that it plays in guiding the protein's function. We have performed an atomistic molecular dynamics simulation of an aqueous solution of the protein villin headpiece subdomain or HP-36 to estimate the thickness of its hydration water. In particular, several dynamical properties of water around different segments (three alpha-helices) of the protein have been calculated by varying the thickness of the hydration layers. It is found that in general the influence of the helices on water properties extends beyond the first hydration layer. However, the heterogeneous nature of water among the first hydration layers of the three helices diminishes as the thickness is increased. It indicates that, for a small protein such as HP-36, the thickness of "biological water" is uniform for different segments of the protein.     

Helix forming tendency of valine substituted poly-alanine: a molecular dynamics investigation

In this study, classical molecular dynamics simulations have been carried out on the valine (guest) substituted poly alanine (host) using the host-guest peptide approach to understand the role of valine in the formation and stabilization of helix. Valine has been substituted in the host peptide starting from N terminal to C terminal. Various structural parameters have been obtained from the molecular dynamics simulation to understand the tolerance of helical motif to valine. Depending on the position of valine in the host peptide, it stabilizes (or destabilizes) the formation of the helical structure. The substitution of valine in the poly alanine at some positions has no effect on the helix formation (deformation). It is interesting to observe the coexistence of 3 10 and alpha-helix in the peptides due to the dynamical nature of the hydrogen bonding interaction and sterical interactions.     

A self-organizing algorithm for molecular alignment and pharmacophore development

We present a method for simultaneous three-dimensional (3D) structure generation and pharmacophore-based alignment using a self-organizing algorithm called Stochastic Proximity Embedding (SPE). Current flexible molecular alignment methods either start from a single low-energy structure for each molecule and tweak bonds or torsion angles, or choose from multiple conformations of each molecule. Methods that generate structures and align them iteratively (e.g., genetic algorithms) are often slow. In earlier work, we used SPE to generate good-quality 3D conformations by iteratively adjusting pairwise distances between atoms based on a set of geometric rules, and showed that it samples conformational space better and runs faster than earlier programs. In this work, we run SPE on the entire ensemble of molecules to be aligned. Additional information about which atoms or groups of atoms in each molecule correspond to points in the pharmacophore can come from an automatically generated hypothesis or be specified manually. We add distance terms to SPE to bring pharmacophore points from different molecules closer in space, and also to line up normal/direction vectors associated with these points. We also permit pharmacophore points to be constrained to lie near external coordinates from a binding site. The aligned 3D molecular structures are nearly correct if the pharmacophore hypothesis is chemically feasible; postprocessing by minimization of suitable distance and energy functions further improves the structures and weeds out infeasible hypotheses. The method can be used to test 3D pharmacophores for a diverse set of active ligands, starting from only a hypothesis about corresponding atoms or groups.     

Single-file diffusion through inhomogeneous nanopores

Strict one-dimensional diffusion, due to geometrical confinement in a nanopore, of an assembly of particles forbids overtaking by each other, giving rise to single-file diffusion (SFD). Smooth carbon nanotube is the epitome of SFD. However, natural nanoporous materials are far from smooth; morphologically, the nanopores' inner surface may provide an inhomogeneous environment for diffusion to occur, giving rise to subnormal diffusion even for an isolated particle diffusing through this fractal landscape. The realm of fractional diffusion (FD) falls under this paradigm. In order to understand the characteristics of SFD through inhomogeneous nanopores, here, we introduce a fractional SFD (FSFD) formalism that deals with a combination of these two phenomena, namely, SFD of particles, each of which are moving subdiffusively in one dimension. For an infinite system, we obtain the mean square displacement (MSD) of the combined entity and our analysis is based on FD equation for particles moving in concert where the single-file correlation is established through reflection principle. For a finite system, we calculate the transport probabilities based on continuous time random walk model. While both the diffusion mechanisms (SFD and FD) acting separately are responsible for slow dynamics at long times, their combined effect leads to ultraslow diffusion. For example, while the long time asymptote of MSD of SFD scales as sqr rt of t, that for FSFD is sqr rt of t(alpha), where alpha is the measure of the extent of inhomogeneity. These findings, which are believed to occur in a natural inhomogeneous nanopore, is also important for design and fabrication of nanofluidic devices through which the fluid delivery can be engineered.     

Photodissociation of noble metal-doped carbon clusters

Noble metal carbide cluster cations (MC(n)(+), M = Cu, Au) are produced by laser vaporization in a pulsed molecular beam and detected with time-of-flight mass spectrometry. Copper favors the formation of carbides with an odd number of carbon atoms, while gold shows marked drops in ion intensity after clusters with 3, 6, 9, and 12 carbons. These clusters are mass selected and photodissociated at 355 nm. Copper carbides with an odd number of carbons fragment by eliminating the metal from the cluster; for the small species it is eliminated as Cu(+) and for the larger species it is lost as neutral Cu. Copper carbides with an even number of carbons also lose the metal, but in addition to this they eliminate neutral C(3). This even-odd alternation, with the even clusters having mixed fragments, holds true for clusters as large as CuC(30)(+). No loss of C(2) is observed for even the largest clusters studied, indicating that fullerene formation does not occur. The gold carbide photodissociation data closely parallel that of copper, with even clusters losing primarily C(3) and odd ones losing gold. Comparisons to known carbon cluster ionization potentials give some insight into the structures of carbon photofragments. DFT calculations performed on CuC(3-11)(+) allow comparisons of the energetics of isomers likely present in our experiment, and metal-carbon dissociation energies help explain the even-odd alternation in the fragmentation channels. The simplest picture of these metal-doped carbides consistent with all the data is that the small species have linear chain structures with the metal attached at the end, whereas the larger species have cyclic structures with the metal attached externally to a single carbon.     

Influence of degree of intercalation on the crystal growth kinetics of poly[(butylene succinate)-co-adipate] nanocomposites

The influence of the degree of intercalation of polymer chains in the two dimensional silicate galleries on the crystallization behavior of poly[(butylene succinate)-co-adipate] (PBSA) is being reported on. The nanocomposites were prepared by melt-blending of PBSA and organically modified montmorillonite (OMMT) in a batch-mixer. Two different types of commercially available OMMTs, with different extents of miscibility of organic modifiers with PBSA, were used, leading to highly delaminated and stacked/intercalated nanocomposite structures as revealed by X-ray diffraction (XRD) patterns and transmission electron microscopy (TEM) observations. The non-isothermal crystallization behavior of PBSA and the nanocomposite samples were studied by differential scanning calorimetry (DSC). Crystal growth kinetics studies showed that when silicate layers are highly delaminated into the PBSA matrix, nucleation behaviors decreased significantly, relative to the stacked/intercalated silicate layers. These observations indicate that the overall crystal growth kinetics retard in delaminated nanocomposites, opposed to increasing in the case of stacked/intercalated nanocomposites. Polarized optical microscopy (POM) observations and light scattering studies indicate that PBSA spherulites are fairly large and more perfectly grown in the case of delaminated nanocomposites, relative to the pure PBSA matrix. The effect of high levels of dispersion of silicate layers in the PBSA matrix on cold crystallization behavior was also studied.     

Oximato-bridged copper(II) compounds: syntheses,molecular structures,magnetic, thermal and spectroscopic properties

Reaction of the Schiff base, 1-(4-methylimidazol-5-yl) phenylhydrazonopropane-2-one oxime (LH), with copper(II) perchlorate hexahydrate and copper(II) nitrate trihydrate in a 1 : 1 M proportion in methanol affords [Cu₂L₂(H₂O)(ClO₄)](ClO₄) (1) and [Cu₂L₂(H₂O)₂](NO₃)₂] (2) in moderate yields. Both 1 and 2 have been characterized by elemental analysis, ESI-MS, FT-IR, UV–vis absorption spectroscopy, EPR, electric conductivity, and magnetic susceptibility measurements. The X-ray crystal structures of 1·CH₃COCH₃ and 2 have been determined. Both compounds are dinuclear copper(II) complexes, with each copper μ₂-bridged by two oxime ligands in a μ₂-η¹,η² fashion. Variable temperature magnetic studies on 1 and 2 show that both compounds are dominated by an antiferromagnetic coupling through the oxime bridges.     

Synthesis of 3‐aminomethylidenechroman‐2‐carboxamides by a Sequential One‐pot Three Component Reaction and by Post‐Passerini Condensation Modification

3‐Arylaminomethylidenechroman‐2‐carboxamide has been synthesized by a one‐pot three component reaction among 3‐formylchromone, aromatic amine, and cyclohexyl isocyanide. 3‐(N‐alkylsubstitued/unsubstituted)aminomethylidenechroman‐2‐carboxamides were synthesized by heating Passerini products derived from chromone‐3‐carbaldehyde with different aliphatic primary amines. The products obtained from the reactions of aliphatic primary amines readily form chromeno[2,3‐c]pyrrole when heated in acetic acid. Bischromanones have also been synthesized using this methodology.