Byte structure variable length coding (BS-VLC): a new specific algorithm applied in the compression of trajectories generated by molecular dynamics

Molecular dynamics is a well-known technique very much used in the study of biomolecular systems. The trajectory files produced by molecular dynamics simulations are extensive, and the classical lossless algorithms give poor efficiencies in their compression. In this work, a new specific algorithm, named byte structure variable length coding (BS-VLC), is introduced. Trajectory files, obtained by molecular dynamics applied to trypsin and a trypsin:pancreatic trypsin inhibitor complex, were compressed using four classical lossless algorithms (Huffman, adaptive Huffman, LZW, and LZ77) as well as the BS-VLC algorithm. The results obtained show that BS-VLC nearly triplicates the compression efficiency of the best classical lossless algorithm, preserving a near lossless behavior. Compression efficiencies close to 50% can be obtained with a high degree of precision, and the maximum efficiency possible (75%), within this algorithm, can be performed with good precision.     

Gold adatoms and clusters on PPV: An ab initio investigation

We have performed an ab initio investigation of the energetic, structural, electronic, and vibrational properties of Au atoms and clusters adsorbed on poly-p-phenylene vinylene (PPV) chains, Au(n)/PPV (with n =?1, 2, 6, 7, 10, and 12). We find that the Au(n)/PPV systems are energetically stable by 0.5 eV, compared with the isolated systems, viz., PPV chain and Au(n) clusters, thus supporting the formation of Au(n)/PPV nanocomposites. Further support to the formation of Au(n)/PPV has been provided by examining the vibrational properties of pristine PPV and Au(n)/PPV systems. In agreement with experimental measurements, we find a reduction on the in-plane vibrational frequency of C-C bonds of Au(n)/PPV, when compared with the same vibrational modes of pristine PPV. The electronic properties of isolated Au(n) clusters are modified when adsorbed on PPV. The highest occupied states of Au(n)/PPV are mostly concentrated on the Au(n) cluster, while the lowest unoccupied states are mainly localized along the PPV chain. The HOMO-LUMO energy gap of the Au(n)/PPV systems are smaller than the energy gap of the isolated systems, Au(n) clusters, and pristime PPV chains.     

Enantioselective Iridium‐Catalyzed Allylation of Acetylenic Ketones via 2‐Propanol‐Mediated Reductive Coupling of Allyl Acetate: C14‐C23 of Pladienolide D

Highly enantioselective catalytic reductive coupling of allyl acetate with acetylenic ketones occurs in a chemoselective manner in the presence of aliphatic or aromatic ketones. This method was used to construct C14‐C23 of pladienolide D in half the steps previously required.     

On the accuracy of frozen density embedding calculations with hybrid and orbital-dependent functionals for non-bonded interaction energies

We analyze the accuracy of the frozen density embedding (FDE) method, with hybrid and orbital-dependent exchange-correlation functionals, for the calculation of the total interaction energies of weakly interacting systems. Our investigation is motivated by the fact that these approaches require, in addition to the non-additive kinetic energy approximation, also approximate non-additive exact-exchange energies. Despite this further approximation, we find that the hybrid/orbital-dependent FDE approaches can reproduce the total energies with the same accuracy (about 1 mHa) as the one of conventional semi-local functionals. In many cases, thanks to error cancellation effects, hybrid/orbital-dependent approaches yield even the smallest error. A detailed energy-decomposition investigation is presented. Finally, the Becke-exchange functional is found to reproduce accurately the non-additive exact-exchange energies also for non-equilibrium geometries. These performances are rationalized in terms of a reduced-gradient decomposition of the non-additive exchange energy.     

Mixed-Ligand Complex Formation Equilibria of Vanadium(III) with 2,2′-Bipyridine and the Amino Acids Glycine, Proline, α-Alanine and β-Alanine Studied in 3.0 mol?dm?3 KCl at 25 °C

We studied speciation of the mixed-ligand complex formation equilibria of vanadium(III) with both 2,2??-bipyridine (Bipy) and the amino acids glycine (HGly), proline (HPro), ??-alanine (H??Ala), and ??-alanine (H??Ala) by means of electromotive forces measurements emf(H) using 3.0?mol?dm^?3 KCl as the ionic medium at 25 °C. The experimental data were analyzed by means of the computational least-squares program LETAGROP, taking into account the hydrolysis of the vanadium(III) cation, the respective stability constants of the binary complexes, and the acid/base reactions of the ligands which were kept fixed during the analysis. In all four amino acid systems studied we observed the complexes [V₂O(Bipy)(B)]³⁺, [V₂O(Bipy)₂(B)₂]²⁺, [V(OH)(Bipy)(B)₂] and [V(OH)₂(Bipy)(B)], where B represents the deprotonated form of the amino acids studied in this work. The respective stability constants were determined and the species distribution diagrams as a function of pH are briefly discussed.     

Effects of irradiation on trans fatty acids formation in ground beef

In order to give the consumer the assurance that meat processed by irradiation is a safe product, a great deal of research has been developed in the world. The effect of irradiation on the hygienic quality of meat and meat products is considered as related to the control of meat-borne parasites of humans; elimination of pathogens from fresh meat and poultry; and elimination of pathogens from processed meat. Lipid oxidation and associated changes are the major causes of the quality deterioration of meat during storage. Irradiation of lipids induces the production of free radicals, which react with oxygen, leading to the formation of carbonyls, responsible for alterations in food nutritional and sensorial characteristics. Trans fatty acids are present in ground beef and can also be formed during its processing. Interestingly, the trans fatty acids, due to their chemical and physical characteristics, show more resistance to the oxidizing process. This property motivated us to investigate the level of the trans fatty acids, as well as the level of oxidation in irradiated ground beef. Irradiation of ground beef was performed by gamma rays from a ⁶⁰Co source. The applied radiation doses were 0; 1.0; 2.0; 3.0; 4.0; 5.0; 6.0; 7.0 and 8.0 kGy. Lipid peroxidation in terms of TBA number and carbonyl content was monitored during storage. The sample characteristics and trans fatty acids composition were measured, following irradiation and after 60 and 90 days of storage at –10°C.     

Application of preparative high-speed counter-current chromatography for the separation of flavonoids from the leaves of Byrsonima crassa Niedenzu (IK)

The methanolic extract of the leaves of the medicinal plant Byrsonima crassa (Malpighiaceae) contain flavonoids with antioxidant activity. They were separated in a preparative scale using high-speed counter-current chromatography. The optimum solvent system used was composed of a mixture of ethyl acetate-n-propanol-water (140:8:80 (v/v/v)) and led to a successful separation between monoglucosilated flavonoids (quercetin-3-O-alpha-L-arabinoside, quercetin-3-O-beta-D-galactoside) and the biflavonoid amentoflavone in only 3.5 h. The purities of quercetin-3-O-alpha-L-arabinoside (95 mg), quercetin-3-O-beta-D-galactoside (16 mg) and the biflavonoid amentoflavone (114 mg) were all isolated at purity over 95%. Identification was performed by 1H NMR, 13C NMR and UV analyses.     

Theoretical study of the CO catalytic oxidation on Au/SAPO‐11 zeolite

Quantum chemistry calculations were carried out, using ONIOM2 methodology, to investigate the CO adsorption and oxidation on gold supported on Silicoaluminophospates (SAPO) molecular sieves Au/SAPO‐11 catalysts. Two models were studied, one containing one Au atom per site (Au? SAPO‐11), and the other with two Au atoms per site (Au₂? SAPO‐11). The results reveal that the CO adsorption and oxidation are exothermic on Au/SAPO11 with an ΔE of ?41.0 kcal/mol and ΔE = ?52.0 kcal/mol, for the adsorption and oxidation, respectively. On the Au₂? SAPO‐11 model, the CO adsorption and oxidation reaction occur, with a ΔE of ?29.7 kcal/mol and ?52 kcal/mol, respectively. According to our results, the oxidation reaction exhibits an Eley‐Rideal type mechanism with adsorbed CO. The theoretical calculations reveal that this type of material could be interesting to disperse Au and consequently to strengthen its catalytic use for different reactions. © 2010 Wiley Periodicals, Inc. Int J Quantum Chem 110:2573–2582, 2010     

Holo- and hemidirected lead(II) in the polymeric [Pb(4)(mu-3,4-TDTA)2(H2O)2]*4H2O complex. N,N,N',N'-tetraacetate ligands derived from o-phenylenediamines as sequestering agents for lead(II)

The coordinating ability of the ligands 3,4-toluenediamine-N,N,N',N'-tetraacetate (3,4-TDTA), o-phenylenediamine-N,N,N',N'-tetraacetate (o-PhDTA), and 4-chloro-1,2-phenylenediamine-N,N,N',N'-tetraacetate (4-Cl-o-PhDTA) (H4L acids) toward lead(II) is studied by potentiometry (25 degrees C, I = 0.5 mol x dm(-3) in NaClO4), UV-vis spectrophotometry, and 207Pb NMR spectrometry. The stability constants of the complex species formed were determined. X-ray diffraction structural analysis of the complex [Pb4(mu-3,4-TDTA)4(H2O)2]*4H2O (1) revealed that 1 has a 2-D structure. The layers are built up by the polymerization of centrosymmetric [Pb4L2(H2O)2] tetranuclear units. The neutral layers have the aromatic rings of the ligands pointing to the periphery, whereas the metallic ions are located in the central part of the layers. In compound 1, two types of six-coordinate lead(II) environments are produced. The Pb(1) is coordinated to two nitrogen atoms and four carboxylate oxygens from the ligand, whereas Pb(2) has an O6 trigonally distorted octahedral surrounding. The lead(II) ion is surrounded by five carboxylate oxygens and a water molecule. The carboxylate oxygens belong to four different ligands that are also joined to four other Pb(1) ions. The selective uptake of lead(II) was analyzed by means of chemical speciation diagrams as well as the so-called conditional or effective formation constants K(Pb)eff. The results indicate that, in competition with other ligands that are strong complexing agents for lead(II), our ligands are better sequestering agents in acidic media.     

Extraction and Characterization of Cellulose Nanowhiskers from Balsa Wood

Summary: In this study cellulose nanowhiskers were obtained from balsa wood. For this purpose, fibers of balsa wood were exposed to hydrolysis reactions for lignin and hemicellulose digestion and acquisition of nano-scale cellulose. Transmission electron microscopy (TEM) results demonstrated that the obtained cellulose nanocrystals had average length and thickness of 176 (±68 nm) and 7.5 (±2.9 nm), respectively. Infrared spectroscopy (FTIR) and wide angle x-ray diffraction (WAXD) showed that the process for extracting the nanowhiskers digested nearly all the lignin and hemicellulose from the balsa fiber and still preserved the aspect ratio and crystallinity satisfactory enough for future application as nanofillers in polymer nanocomposites. The thermogravimetric analysis (TGA) showed that the onset temperature of thermal degradation of the cellulose nanocrystals (226 °C) was higher than the onset temperature of the balsa fiber (215 °C), allowing its use in molding processes with polymers melts.