Search

Abstract Background Even after years of exploration, the terrestrial origin of bio-molecules remains unsolved and controversial. Today, observation of amino acid composition in proteins has become an alternative way for a global understanding of the mystery encoded in whole genomes and seeking clues for the origin of amino acids. Results In this study, we statistically monitored the frequencies of 20 alpha-amino acids in 549 taxa from three kingdoms of life: archaebacteria, eubacteria, and eukaryotes. We found that the amino acids evolved independently in these three kingdoms; but, conserved linkages were observed in two groups of amino acids, (A, G, H, L, P, Q, R, and W) and (F, I, K, N, S, and Y). Moreover, the amino acids encoded by GC-poor codons (F, Y, N, K, I, and M) were found to "lose" their usage in the development from single cell eukaryotic organisms like S. cerevisiae to H. sapiens, while the amino acids encoded by GC-rich codons (P, A, G, and W) were found to gain usage. These findings further support the co-evolution hypothesis of amino acids and genetic codes. Conclusion We proposed a new chronological order of the appearance of amino acids (L, A, V/E/G, S, I, K, T, R/D, P, N, F, Q, Y, M, H, W, C). Two conserved evolutionary paths of amino acids were also suggested: A→G→R→P and K→Y.

The in vitro effects of individual brominated flame retardants (BFRs), selected metals, and their binary mixtures on ethoxyresorufin-O-deethylase (EROD) activity were evaluated using a plate-reader method. The BFRs, 2,2′,4,4′-tetrabromodiphenyl ether (BDE-47), decabromodiphenyl oxide (BDE-209), hexabromocyclododecane (HBCD), and tetrabromobisphenol A (TBBPA), were tested at doses ranging from 0.1 ng/L to 100 µg/L. Selected metals (Cu 2+ , Cd 2+ , Hg 2+ , and Zn 2+ ) were screened at doses of 0.1 mg/L to 50 mg/L. The activity of EROD was significantly induced by TBBPA, BDE-209, and Zn 2+ , while HBCD, Cu 2+ , Cd 2+ , and Hg 2+ decreased EROD activity. Moreover, following exposure to binary mixtures of metals and BFRs, the EROD activity dose-response curves were similar to those of the metals alone, indicating that EROD activity was governed by the metals. [ABSTRACT FROM AUTHOR]

The knowledge of accurate bond strengths is a fundamental basis for a proper analysis of chemical reaction mechanisms. Quantum chemical calculations at different levels of theory have been used to investigate heterolytic Feâ€'O and Feâ€'S bond energies of paraâ€substituted phenoxydicarbonyl( η5â€cyclopentadienyl) iron [ pâ€Gâ€C6H4O( η5â€C5H5)Fe(CO)2, abbreviated as pâ€Gâ€C6H4OFp ( 1), where G = NO2, CN, COMe, CO2Me, CF3, Br, Cl, F, H, Me, MeO, and NMe2] and paraâ€substituted benzenethiolatodicarbonyl( η5â€cyclopentadienyl) iron [ pâ€Gâ€C6H4S( η5â€C5H5)Fe(CO)2, abbreviated as pâ€Gâ€C6H4SFp ( 2)] complexes. The results show that BP86 and TPSSTPSS can provide the best price/performance ratio and more accurate predictions in the study of Î' Hhet(Feâ€'O)'s and Î' Hhet(Feâ€'S)'s. The excellent linear freeâ€energy relations [ r = 0.99 (g, 1a), 1.00 (g, 2b)] among the Î'Î' Hhet (Feâ€'O)'s and Î'p ka's of Oâ€'H bonds of pâ€Gâ€C6H4OH or Î'Î' Hhet(Feâ€S)'s and Î'p ka's of Sâ€'H bonds of pâ€Gâ€C6H4SH imply that the governing structural factors for these bond scissions are similar. And the linear correlations [ r = âˆ'0.99 (g, 1g), âˆ'0.98 (g, 2h)] among the Î'Î' Hhet (Feâ€O)'s or Î'Î' Hhet(Feâ€S)'s and the substituent σpâˆ' constants show that these correlations are in accordance with Hammett linear freeâ€energy relationships. The polar effects of these substituents and the basis set effects influence the accuracy of Î' Hhet(Feâ€'O)'s or Î' Hhet(Feâ€'S)'s. Î'Î' Hhet(Feâ€'O)'s(g) ( 1) and Î'Î' Hhet(Feâ€'S)'s(g)( 2) follow the Captoâ€dative principle. The substituent effects on the Feâ€'O bonds are much stronger than those on the less polar Feâ€'S bonds. Insight from this work may help the design of more effective catalytic processes. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

Metal-ligand bond enthalpy data can afford invaluable insights into important reaction patterns in organometallic chemistry and . In this paper, the Fe-O and Fe-S homolytic bond dissociation energies [Δ Hhomo(Fe-O)'s and Δ Hhomo(Fe-S)'s] of two series of para-substituted phenoxydicarbonyl( η5-cyclopentadienyl) iron [ p-G-C6H4OFp ( 1)] and (para-substituted benzenethiolato)dicarbonyl( η5-cyclopentadienyl) iron [ p-G-C6H4SFp ( 2)] were studied using Hartree-Fock and density functional theory (DFT) methods with large basis sets. In this study, Fp is ( η5-C5H5)Fe(CO)2, and G are NO2, CN, COMe, CO2Me, CF3, Br, Cl, F, H, Me, MeO, and NMe2. The results show that DFT methods can provide the best price/performance ratio and accurate predictions of Δ Hhomo(Fe-O)'s and Δ Hhomo(Fe-S)'s. The remote substituent effects on Δ Hhomo(Fe-O)'s and Δ Hhomo(Fe-S)'s [ΔΔ Hhomo(Fe-O)'s and ΔΔ Hhomo(Fe-S)'s] can also be satisfactorily predicted. The good correlations [ r = 0.98 (g, 1), 0.98 (g, 2)] of ΔΔ Hhomo(Fe-O)'s and ΔΔ Hhomo(Fe-S)'s in series 1 and 2 with the substituent σp+ constants imply that the para-substituent effects on Δ Hhomo(Fe-O)'s and Δ Hhomo(Fe-S)'s originate mainly from polar effects, but those on radical stability originate from both spin delocalization and polar effects. ΔΔ Hhomo(Fe-O)'s ( 1) and ΔΔ Hhomo(Fe-S)'s ( 2) conform to the captodative principle. Insight from this work may help the design of more effective catalytic processes. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]

By the B3P86/6-311G(3d,2p) method, remote substituent effects on trans-YCHCHCHF were investigated by examining their conformational stabilities, molecular geometries, and stereoelectronic interactions in this paper. The cis conformer is favored for YH, Cl, Me, Vinyl, CF, CN, CHO, and NO, whereas the gauche is favored for YOMe, OH. A correlation of Δ H with the substituent constants σ(Y) shows that the increasing electron-withdrawing ability of the substituent Y increases the relative stability of the cis conformer. It was found that the substituent effect on the molecule stabilization energies (relative to CHCHCHF) is more significant in the gauche conformers than in the cis conformers. In agreement, molecular structures of the gauche conformers were also observed to vary more significantly with the substitution than those of the cis conformers. By the second-order perturbation energy ( E(2)) in NBO analysis, it was found that the total C-C vicinal hyperconjugation is determinant in the enthalpy difference and consequently controls the conformational stability. Further analysis shows that the substituent effect on the C-C vicinal hyperconjugations is much higher in the gauche conformers than in the cis conformers. The highly sensitive π→σ* interaction to the substitution in the gauche conformers, is the leading factor in variation of molecular stability and geometry. Copyright © 2010 John Wiley & Sons, Ltd. In this paper, it was found that the conformational preference for the cis or gauche conformer in trans-YCH=CHCHF is highly related with the Y substitution. The substituent effect is transmitted through the double bond and influences the C−C vicinal hyperconjugations, which are the determinant factor for the conformational stability. [ABSTRACT FROM AUTHOR]

Abstract In this work, a new approach for TMPyP [5,10,15,20-tetrakis (1-methylpyridinium-4-yl) porphyrin] and TMAPP [5,10,15,20-tetrakis (N,N,N-trimethyl-anilinium-4-yl) porphyrin] intercalation into a-phase of zirconium hydrogen phosphate (a-ZrP) was described: porphyrins were inserted through exchanging pre-intercalated alkylamine. Pre-intercalated n-butylamine (BA) could form either a mobile monolayer or a stable bilayer in a-ZrP. The exchange speed between porphyrins and BA in mobile monolayer is obviously faster than that in stable bilayer. Therefore mobility of spacers is one important intercalation factor. In addition, we investigated the interlayer state of TMPyP by XRD, visible spectrum, fluorescence spectrum and molecular modeling. The results collectively revealed that the porphyrin was orderly arranged with their planes inclined to the host lamella and was presented as monomer instead of aggregation in the gallery of a-ZrP. [ABSTRACT FROM AUTHOR]

Molecular modeling methods have been applied to the structural characterization of the interaction between chiral metal complexes [Co(phen)2dppz]3+ (where phen = 1, 10-phenanthroline, dppz = dipyrido[3,2-a: 2′, 3′ -c]phenazine) and the oligonucleotide (B-DNA fragment). The natures of two kinds of the binding modes, which are currently intense controversy, have been explored. Barton proposed that there is enantio-selective DNA binding by the octahedral complexes and intercalative access by these complexes from the major groove; but Norden suggested that both enantiomers bind extremely strongly to DNA from the minor groove without any noticeable enantio-selectivity. Our results support and extend structural models based upon Norden’s studies, and conflict with Barton’ model. [ABSTRACT FROM AUTHOR]

The knowledge of accurate bond strengths is a fundamental basis for a proper analysis of chemical reaction mechanisms. Quantum chemical calculations at different levels of theory have been used to investigate heterolytic Feâ€'O and Feâ€'S bond energies of paraâ€substituted phenoxydicarbonyl( η5â€cyclopentadienyl) iron [ pâ€Gâ€C6H4O( η5â€C5H5)Fe(CO)2, abbreviated as pâ€Gâ€C6H4OFp ( 1), where G = NO2, CN, COMe, CO2Me, CF3, Br, Cl, F, H, Me, MeO, and NMe2] and paraâ€substituted benzenethiolatodicarbonyl( η5â€cyclopentadienyl) iron [ pâ€Gâ€C6H4S( η5â€C5H5)Fe(CO)2, abbreviated as pâ€Gâ€C6H4SFp ( 2)] complexes. The results show that BP86 and TPSSTPSS can provide the best price/performance ratio and more accurate predictions in the study of Î' Hhet(Feâ€'O)'s and Î' Hhet(Feâ€'S)'s. The excellent linear freeâ€energy relations [ r = 0.99 (g, 1a), 1.00 (g, 2b)] among the Î'Î' Hhet (Feâ€'O)'s and Î'p ka's of Oâ€'H bonds of pâ€Gâ€C6H4OH or Î'Î' Hhet(Feâ€S)'s and Î'p ka's of Sâ€'H bonds of pâ€Gâ€C6H4SH imply that the governing structural factors for these bond scissions are similar. And the linear correlations [ r = âˆ'0.99 (g, 1g), âˆ'0.98 (g, 2h)] among the Î'Î' Hhet (Feâ€O)'s or Î'Î' Hhet(Feâ€S)'s and the substituent σpâˆ' constants show that these correlations are in accordance with Hammett linear freeâ€energy relationships. The polar effects of these substituents and the basis set effects influence the accuracy of Î' Hhet(Feâ€'O)'s or Î' Hhet(Feâ€'S)'s. Î'Î' Hhet(Feâ€'O)'s(g) ( 1) and Î'Î' Hhet(Feâ€'S)'s(g)( 2) follow the Captoâ€dative principle. The substituent effects on the Feâ€'O bonds are much stronger than those on the less polar Feâ€'S bonds. Insight from this work may help the design of more effective catalytic processes. Copyright © 2013 John Wiley & Sons, Ltd. [ABSTRACT FROM AUTHOR]