Efficiency of the multicanonical simulation method as applied to peptides of increasing size: the heptapeptide deltorphin

The advantage of the multicanonical (MUCA) simulation method of Berg and coworkers over the conventional Metropolis method is in its ability to move a system effectively across energy barriers thereby providing results for a wide range of temperatures. However, a MUCA simulation is based on weights (related to the density of states) that should be determined prior to a production run and their calculation is not straightforward. To overcome this difficulty a procedure has been developed by Berg that calculates the MUCA weights automatically. In a previous article (Ya?ar et al. J Comput Chem 2000, 14, 1251-1261) we extended this procedure to continuous systems and applied it successfully to the small pentapeptide Leu-enkephalin. To investigate the performance of the automated MUCA procedure for larger peptides, we apply it here to deltorphin, a linear heptapeptide with bulky side chains (H-Tyr(1)-D-Met(2)-Phe(3)-His(4)-Leu(5)-Met(6)-Asp(7)-NH(2)). As for Leu-enkephalin, deltorphin is modeled in vacuum by the potential energy function ECEPP. MUCA is found to perform well. A weak second peak is seen for the specific heat, which is given a special attention. By minimizing the energy of structures along the trajectory it is found that MUCA provides a good conformational coverage of the low energy region of the molecule. These latter results are compared with conformational coverage obtained by the Monte Carlo minimization method of Li and Scheraga.     

A dielectric study of the amorphous fraction in oriented nylon 610

Since some dielectric loss peaks can be assigned to amorphous phase motions, it would appear that dielectric measurements should be a good probe to study the effects of macroscopic plastic deformation on the structure of the amorphous phase. We report here results of measurements of dielectric constant and loss in nylon 610 measured both parallel (∥) to and perpendicular (⊥) to the extrusion direction in specimens prepared by extrusion through a die at 160°. It is found that the intensity of the (∥) loss was nearly zero and the (⊥) loss intensity was greatly reduced compared to unoriented material. The other relaxation parameters (loss width and location) were largely unaffected. Since the amide dipole is nearly perpendicular to the chain axis and alternates in direction in the extended conformation, a considerable degree of chain alignment parallel to the draw direction is indicated. These results therefore show considerable permanent amorphous phase orientation even though the deformation was carried out 100° above its glass temperature.     

Exploring the thermodynamics of a two-dimensional Bose gas

Using in situ measurements on a quasi-two-dimensional, harmonically trapped (87)Rb gas, we infer various equations of state for the equivalent homogeneous fluid. From the dependence of the total atom number and the central density of our clouds with chemical potential and temperature, we obtain the equations of state for the pressure and the phase-space density. Then, using the approximate scale invariance of this 2D system, we determine the entropy per particle and find very low values (below 0.1k(B)) in the strongly degenerate regime. This shows that this gas can constitute an efficient coolant for other quantum fluids. We also explain how to disentangle the various contributions (kinetic, potential, interaction) to the energy of the trapped gas using a time-of-flight method, from which we infer the reduction of density fluctuations in a nonfully coherent cloud.     

Reaction of 2-imino-2H-chromene-3-carboxamide with some phosphorus esters: Synthesis of some novel chromenes containing phosphorus heterocycles and phosphonate groups and their antioxidant and cytotoxicity properties

Abstract

Novel chromenyl α-aminophosphonic acid 4 and dialkyl chromenyl phosphonate 6 have been obtained. In addition, some novel types of chromene fused with phosphorus heterocycles such as chromeno[4,3-c][1,2]azaphospholes 5 and 7, chromeno[2,3-d][1,3,2]diazaphosphinine 8 and 1,2-oxaphosphinino[3,4-c]pyridine 10 have been synthesized. The methodology depended on treatment of 2-imino-2H-chromene-3-carboxamide (1) with some phosphorus esters. The synthesized compounds were evaluated for antioxidant and cytotoxic activities. Among the synthesized compounds, compound 5 exhibited the most antioxidant activity with IC₅₀ = 2.8?μg/mL in comparison with ascorbic acid as standard antioxidant. Also, compound 5 had significant cytotoxic effects against four cancer cell lines. Its IC₅₀ values ranged between 4.96 and 7.44?μg/mL in comparison to doxorubicin (IC₅₀ = 0.426–0.493?μg/mL).     

4,6-Diacetylresorcinol in Heterocyclic Synthesis,Part I: Synthesis and Biological Evaluation of Some New Linearly and Angularly Substituted Pyrano[3,2-g] Chromenes via Vilsmeier–Haack Formylation of 4,6-Diacetylresorcinol,Its Schiff Bases,and Hydrazones

Application of Vilsmeier–Haack reaction on 4,6-diacetylresorcinol (1) led to the formation of 4,6-dioxo-4H,6H-pyrano[3,2-g]chromene-3,7-dicarboxaldehyde (2) in good yield. The dicarboxaldehyde 2 was condensed with some carbon and nitrogen nucleophiles. Some aliphatic and aromatic Schiff bases of 4,6-diacetylresorcinol (1) were subjected to Vilsmeier–Haack formylation reaction to afford 4,6-bis(alkyl/arylimino)-4H,6H-pyrano[3,2-g]chromene-3,7-dicarbaldehydes 10, 14, and 15. Also, treatment of some bis-hydrazones of 4,6-diacetylresorcinol 16–19 with Vilsmeier–Haack reagent afforded the corresponding 4,6-bis(4-formylpyrazol-3-yl)resorcinols 20 and 21, which underwent oxidation with iodine to yield the pyrano[3,2-g]chromeno[4,3-c:7,6-c]dipyrazole-4,8-diones 22 and 23, respectively. Most of the synthesized compounds revealed weak antimicrobial activities. It was noticed that the dicarboxaldehydes 2, 10, 14, and 15 exhibited moderate antibacterial activity against Gram-positive bacteria, yeast, and fungus.

[Supplementary materials are available for this article. Go to the publisher's online edition of Synthetic Communications® for the following free supplemental resource(s): Full experimental and spectral details.]     

Sparsity constrained deconvolution approaches for acoustic source mapping

Using microphone arrays for estimating source locations and strengths has become common practice in aeroacoustic applications. The classical delay-and-sum approach suffers from low resolution and high sidelobes and the resulting beamforming maps are difficult to interpret. The deconvolution approach for the mapping of acoustic sources (DAMAS) deconvolution algorithm recovers the actual source levels from the contaminated delay-and-sum results by defining an inverse problem that can be represented as a linear system of equations. In this paper, the deconvolution problem is carried onto the sparse signal representation area and a sparsity constrained deconvolution approach (SC-DAMAS) is presented for solving the DAMAS inverse problem. A sparsity preserving covariance matrix fitting approach (CMF) is also presented to overcome the drawbacks of the DAMAS inverse problem. The proposed algorithms are convex optimization problems. Our simulations show that CMF and SC-DAMAS outperform DAMAS and as the noise in the measurements increases, CMF works better than both DAMAS and SC-DAMAS. It is observed that the proposed algorithms converge faster than DAMAS. A modification to SC-DAMAS is also provided which makes it significantly faster than DAMAS and CMF. For the correlated source case, the CMF-C algorithm is proposed and compared with DAMAS-C. Improvements in performance are obtained similar to the uncorrelated case.     

Detection of bacteria using antimicrobial polymer derived via ring-opening metathesis (romp) pathway

There is growing interest in the detection of bacteria in consumables, for example, in the food and water sectors. In this study, the aim was to produce a polymer-based bacteria biosensor via ROMP (ring opening metathesis polymerization). In the first part of the study, block and random copolymers were synthesized, and their biocidal activities were tested on the glass surface. Interdigitated electrode arrays coated with the polymers possessing the highest activity were used to screen the affinity towards different bacterial strains by monitoring impedance variations in real-time. The polymer-coated electrode could detect gram-positive and gram-negative bacteria strains at a concentration of 10⁷ cfu/mL. The results show that ROMP-based polymer offers bacterial detection and can be used in developing biosensor devices for efficiently detecting pathogenic bacteria.