Why is indigo blue?

Although the color of indigo is strongly dependent on its environment, it is blue in most commonly encountered situations. Indigo's absorption at such long wavelengths for such a small molecule is unique, and I provide here an overview of the concepts advanced to account for this feature. A traditional valence-bond approach may be used to provide a reasonable qualitative explanation. A more rigorous, quantitative explanation is provided by molecular orbital methods of varying degrees of sophistication and several explanations have been proposed based on these models. Commonly, it is suggested that the important structural unit in determining color is based on the cross-conjugated “H-chromophore” concept. A second closely related explanation describes it as two symmetrically coupled merocyanine chains. Another proposal suggests that the basic chromophore may be interpreted as the aza analogue of two coupled anti aromatic-cyclopentadienyl ions. PiSYSTEM, a commercially available quantum mechanics program, has been used to provide a successful quantitative account of the colors of indigo and indirubin, a red isomer.     

Orbital shaker technology for the cultivation of mammalian cells in suspension

For large-scale applications in biotechnology, cultivation of mammalian cells in suspension is an essential prerequisite. Typically, suspension cultures are grown in glass spinner flasks filled to less than 50% of the nominal volume. We propose a superior system for suspension cultures of mammalian cells based on orbital shaker technology. We found that "square-shaped" bottles (square bottles) provide an inexpensive but efficient means to grow HEK-293 EBNA and CHO-DG44 cells to high density. Cultures in agitated 1-L square bottles exceeded the performance of cultures in spinner flasks, reaching densities up to 7 x 10(6) cells/mL for HEK-293 EBNA cells and 5 x 10(6) cells/mL for CHO-DG44 cells in comparison to (2.5-4) x 10(6) cells/mL for cultures of the same cells grown in spinner flasks. For 1-L square bottles, optimal cell growth and viability were observed with a filling volume of 30-40% of the nominal volume and an agitation speed of 130 rpm at a rotational diameter of 2.5 cm. Transient reporter gene expression following gene delivery by calcium phosphate-DNA co-precipitation was the same or slightly better for HEK-293 EBNA cells grown in square bottles as compared to spinner flasks. Reductions in cost, simplified handling, and better performance in cell growth and viability make the agitated square bottle a new and very promising tool for the cultivation of mammalian cells in suspension.     

Ion pair aggregates and reactions; experiment and theory

Two methods have been developed for determining the aggregation equilibrium constants of lithium enolates based on the change in UV-vis spectrum with concentration and the effect of aggregation on proton-transfer equilibria. Dimers and tetramers are common. Substitution α to the carbonyl group generally reduces aggregation. Kinetic studies show that S_N2 alkylations generally occur with the monomers, even in the presence of large amounts of aggregate. The qualitative chemistry is well modeled by ab initio computations at the HF level with modest basis sets; in these studies solvation is modeled by a combination of coordination of lithium cation with an ether oxygen and the electrostatic interaction of the resulting dipoles and quadrupoles with the solvent dielectric continuum. This review is based on the fifth annual Paul vR Schleyer Lecture presented at Professor Schleyer's 75th birthday symposium, Athens GA, Feb 26, 2005. Carbon Acidity 123. For no. 122 see Streitwieser A, Kaufman MJ, Bors DA, MacArthur CA, Murphy JT, Guibe F, Arkivoc (2005) (vi) 200–210Dedicated to Professor Dr. Paul von Ragué Schleyer on the occasion of his 75th birthday     

Density functional theoretical study of the structure, bonding and electrochemistry of N2S2 nitrosyl complexes of iron and cobalt

Density functional calculations are used to study the structure, bonding and properties of the N₂S₂ nitrosyl complexes (bme-pda)M(NO) and (bme-dach)M(NO) M = Fe, Co. The complexes studied in this work have been previously shown to exhibit unusual structural and electrochemical properties. Calculated optimal geometries and vibrational frequencies are compared to experimental data and found to be in excellent agreement. A very small energy barrier for rotation of the NO ligand relative to the S-donor atoms of the N₂S₂ ligand is calculated. The similarity in reduction potentials of Fe and Co complexes is investigated using molecular orbital analysis and calculation of absolute reduction potentials. It is concluded that reduction of the Fe complexes may produce triplet-state products. Such products are determined to be of lower energy than singlet-state products, and also consistent with the observed reduction potentials of the Fe and Co complexes.     

The role of non-classical supramolecular interactions in the structures of 2-amino-4,6-dimethylpyridinium tetrahalocuprate (II) salts

The compounds [2-amino-4,6-dimethylpyridinium]₂CuCl₄ (1) and [2-amino-4,6-dimethylpyridinium]₂CuBr₄ (2) were prepared from acidic ethanolic media containing CuX₂ and [2-amino-4,6-dimethylpyridine] in the molar ratio 1:1. The compounds were characterized by IR and single-crystal X-ray diffraction and found to be isomorphous in the space group with V = 991.2(10) Å³ for (1) and 1059.26(12) Å³ for (2) . There is no significant difference in the non-classical N-H?X hydrogen bonding between (1) and (2). The anions show essentially the same extent of distortion from tetrahedral geometry with max./min. values for the X-Cu-X bond angles of 139.72(6)°/96.78(6)° for (1) and 139.43(4)°/96.64(3)° for (2). Each [CuX₄]²⁻ anion is hydrogen bonded nonsymmetrically to four cations. In this manner, ladder chains are formed that run along the b-axis, with planar cations falling parallel to the (2, 0, 1) plane. Weaker π-π interactions exist between cations from different chains with centroid to centroid distance of 4.07 Å in (1) and a long 4.594 Å in (2). The X-π electrostatic interactions are surprisingly stronger in (2) than in (1) with a Br to centroid of pyridinic ring distance of 3.890 Å compared with 3.996 Å for the chloride analogue.     

Stereoselective single-step synthesis and X-ray crystallographic investigation of acetylated aryl 1,2-trans glycopyranosides and aryl 1,2-cis C2-hydroxy-glycopyranosides

Reported is an attractive and environmentally friendly method for the synthesis of the title compounds in moderate yield using inexpensive 1,2,3,4,6-penta-O-acetyl-beta-D-gluco- and galactopyranoses as sugar donors, five different phenols as acceptors and H-beta zeolite as the catalyst. The yield (23-28%) of aryl 3,4,6-tri-O-acetyl-alpha-D-glycopyranosides obtained in this single-step procedure is considerably higher than that obtained using previously reported methods. Treatment of an orthoacetate, 3,4,6-tri-O-acetyl-[1,2-O-(1-p-fluorophenoxyethylidene)]-alpha-D-glucopyranose, with p-fluorophenol under the same solvent-free reaction conditions also led to the formation of the title compounds in similar yield and composition. X-ray crystallographic analysis of phenyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranoside and p-fluorophenyl 3,4,6-tri-O-acetyl-alpha-D-glucopyranoside showed that the molecular packing is stabilized by C-H...O, C-H...pi and C-H...F interactions, in addition to regular hydrogen bonding patterns.     

The Relativistic Quantum Defect Orbital Method and some of its Applications

Justification of a simple and reliable relativistic procedure for the prediction of a large body of transition probability data is made. The main features of the Relativistic Quantum Defect Orbital (RQDO) formalism are described, and several examples of the data yielded by this method are presented in tabular and graph forms.     

Kinematic data on primate head and neck posture: Implications for the evolution of basicranial flexion and an evaluation of registration planes used in paleoanthropology

Kinematic data on primate head and neck posture were collected by filming 29 primate species during locomotion. These were used to test whether head and neck posture are significant influences on basicranial flexion and whether the Frankfurt plane can legitimately be employed in paleoanthropological studies. Three kinematic measurements were recorded as angles relative to the gravity vector, the inclination of the orbital plane, the inclination of the neck, and the inclination of the Frankfurt plane. A fourth kinematic measurement was calculated as the angle between the neck and the orbital plane (the head-neck angle [HNA]). The functional relationships of basicranial flexion were examined by calculating the correlations and partial correlations between HNA and craniometric measurements representing basicranial flexion, orbital kyphosis, and relative brain size (Ross and Ravosa [1993] Am. J. Phys. Anthropol. 91:305–324). Significant partial correlations were observed between relative brain size and basicranial flexion and between HNA and orbital kyphosis. This indicates that brain size, rather than head and neck posture, is the primary influence on flexion, while the degree of orbital kyphosis may act to reorient the visual field in response to variation in head and neck posture. Regarding registration planes, the Frankfurt plane was found to be horizontal in humans but inclined in all nonhuman primates. In contrast, nearly all primates (including humans) oriented their orbits such that they faced anteriorly and slightly inferiorly. These results suggest that for certain functional craniometric studies, the orbital plane may be a more suitable registration plane than Frankfurt “Horizontal.” Am J Phys Anthropol 108:205–222, 1999. © 1999 Wiley-Liss, Inc.     

Anisotropic intersubunit and inter-ring interactions revealed in the native bullet-shaped chaperonin complex from Thermus thermophilus

Background

The recent morphological studies on chaperonins have revealed that nearly equivalent amount of symmetric GroEL–(GroES)₂ (football-shaped) and asymmetric GroEL–GroES (bullet-shaped) complexes coexist during the chaperonin reaction cycle, which prompted us to reexamine the equatorial split observed for chaperonin from Thermus thermophilus by implementing semi-empirical molecular orbital (MO) calculations, since it is now believed that the symmetric formation is a precursor to the equatorial split.

Methods

Semi-empirical MO calculations were employed to investigate the intersubunit interactions within the bullet-shaped T. thermophilus chaperonin capturing the substrate of folding intermediates. Interaction energies between each cis-GroEL subunit and closely related remaining subunits in cis-GroEL ring, or in trans-GroEL ring across the equatorial plane, and further, interaction energies between each GroES subunit and adjacent subunits in the same GroES ring and in cis-GroEL ring were simulated.

Results

Anisotropic intensities and energy distribution of the subunits were revealed by the calculations, which are consistent with two conformations of the subunits forming cis-GroEL ring as revealed by X-ray crystal structure, and with an anisotropic critical binding site on cis-GroEL ring for chaperonin functioning.

Conclusions

This is the first application of semi-empirical MO calculations to the macromolecular complex of the native bullet-shaped chaperonin (GroEL–GroES–ADP homolog) from T. thermophilus.

General significance

The results also appear to support the occurrence of the equatorial split for T. thermophilus chaperonin observed via electron microscopy, but has not yet been fully observed for Escherichia coli GroEL–GroES system.     

The outcome of radiation therapy as a primary treatment in orbital lymphoma: a systematic review

BackgroundThe extranodal marginal-zone B-cell lymphomas of mucosa-associated lymphoid tissue (MALT) is the most common orbital and adnexal lymphomas. Radiotherapy is one of the most preferred treatment options for orbital lymphomas since they are localized and radiation sensitive. The objective of this study is to evaluate how radiation therapy affected the outcome of orbital MALT lymphoma.Materials and methodsPRISMA guideline was used to conduct this systematic review of electronic databases (PubMed, EMBASE and Cochrane Library), then we assessed the quality of evidence of each paper.ResultsTwenty-five studies were finally included. 94% studies were intended for definitive therapy and almost all of the studies used external radiation sources. The total doses given to the tumor bed ranged from 4 Gy to 55 Gy and were divided into three groups: ultra-low dose (4–6 Gy), standard-dose (24–30.6 Gy), and high-dose (> 30.6 Gy). 75–90% patients showed CR and local relapse was only reported at 3.5–5%. Higher 5-year PFS was reported in the patients group with lens shielding (90.1% vs. 82.1%) and an increase in Meiboscore after RT courses. Toxicities, including dry eye and cataract, were reported in several patients. Acute toxicities subsided gradually over a few months with artificial tears. The risk of early cataract formation increases in patients who received > 30 Gy and lower in the IMRT group.ConclusionRT is a successful primary definitive therapy for low-grade orbital MALT lymphoma, with a high survival rate, low recurrence rate, and typically acceptable toxicity.