Conformational analysis of gossypol and its derivatives by molecular mechanics

Conformations and inversion pathways leading to racemization of all the tautomers of gossypol, gossypolone, anhydrogossypol, and a diethylamine Schiff's base of gossypol were investigated with MM3(2000). All forms have hindered rotation because of clashes between the methyl carbon atom and oxygen-containing moieties ortho to the bond linking the two naphthalene rings. Inversion energies generally agree with available experimental data. Gossypol preferentially inverts in its dihemiacetal tautomeric form through the cis pathway (where similar groups clash). Gossypolone inverts more easily than gossypol, and preferentially through the trans pathway (where dissimilar groups clash) when one of its outer rings has an enol-keto group and the other has an aldehyde group. Anhydrogossypol racemizes through the cis pathway. The bridge bond and the ortho exo-cyclic bonds in all the structures bend from planarity, and the inner naphthalene rings pucker to accommodate the inversion. For gossypol, the transition is achieved through greater bending of the exo-cyclic bonds (up to 12°) and less distortion of the inner benzyl rings (q≤0.34 Å), (up to 12.7°) . For gossypolone the transition occurs with greater distortion of the inner benzyl rings (q≤0.63 Å) and less out-of-plane bending (up to 8.4°). By isolating individual clashes, their contribution to the overall barrier can be analyzed, as shown for the dialdehyde tautomer of gossypol.     

Cauchy sequences in quasi-pseudo-metric spaces

This paper considers the problem of defining Cauchy sequence and completeness in quasi-pseudo-metric spaces. The definitions proposed allow versions of such classical theorems as the Baire Category Theorem, the Contraction Principle and Cantor's characterization of completeness to be formulated in the quasi-pseudo-metric setting.     

A method for rapidly predicting drug tissue distribution using surfactant vesicle electrokinetic chromatography

Lung tissue distribution of an inhaled drug is important for its potency in the airways and with minimum systemic effects within its dose range. As the lung has the smallest diffusion distance of all the organs in the body and negligible diffusion delays, the characteristics of drug distribution in the lung will mainly depend on drug binding to both tissue and plasma protein. This research aims to develop and evaluate surfactant vesicle electrokinetic chromatography (SEKC) methods for high throughput profile prediction of tissue distribution for inhaled drugs. Several electrokinetic chromatography methods reported in the literature, as well as immobilised artificial membrane chromatography, were compared and evaluated in respect to chromatographic characteristics and statistical correlations. Among these methods, the docusate sodium salt (AOT) SEKC system showed good reproducibility, short run time, and the highest selectivity for alkylphenone test compounds. It also showed a significant statistical correlation between the retention of inhaled drugs and their in vivo volume of distribution at steady-state (V(ss)) in whole human body neglecting the plasma protein-binding differences. Stronger correlations were observed between the AOT SEKC retention of a series of basic drugs and their rat lung tissue-to-plasma water partitioning coefficient (K(pu)), which is affected only by drug binding to the tissue constituent. Further, on comparing correlations between AOT SEKC retention and K(pu) at various rat tissues, it was observed that the strongest correlation was with lung tissue distribution, while the weakest was with brain tissue distribution.     

A Gibbs free energy correlation for automated docking of carbohydrates

Thermodynamic information can be inferred from static atomic configurations. To model the thermodynamics of carbohydrate binding to proteins accurately, a large binding data set has been assembled from the literature. The data set contains information from 262 unique protein-carbohydrate crystal structures for which experimental binding information is known. Hydrogen atoms were added to the structures and training conformations were generated with the automated docking program AutoDock 3.06, resulting in a training set of 225,920 all-atom conformations. In all, 288 formulations of the AutoDock 3.0 free energy model were trained against the data set, testing each of four alternate methods of computing the van der Waals, solvation, and hydrogen-bonding energetic components. The van der Waals parameters from AutoDock 1 produced the lowest errors, and an entropic model derived from statistical mechanics produced the only models with five physically and statistically significant coefficients. Eight models predict the Gibbs free energy of binding with an error of less than 40% of the error of any similar models previously published.     

Experimental and theoretical comparison of actinide and lanthanide bonding in M[N(EPR(2))(2)](3) complexes (M = U, Pu, La, Ce; E = S, Se, Te; R = Ph, iPr, H)

Treatment of M[N(SiMe3)2]3 (M = U, Pu (An); La, Ce (Ln)) with NH(EPPh2)2 and NH(EPiPr2)2 (E = S, Se), afforded the neutral complexes M[N(EPR2)2]3 (R = Ph, iPr). Tellurium donor complexes were synthesized by treatment of MI3(sol)4 (M = U, Pu; sol = py and M = La, Ce; sol = thf) with Na(tmeda)[N(TePiPr2)2]. The complexes have been structurally and spectroscopically characterized with concomitant computational modeling through density functional theory (DFT) calculations. The An-E bond lengths are shorter than the Ln-E bond lengths for metal ions of similar ionic radii, consistent with an increase in covalent interactions in the actinide bonding relative to the lanthanide bonding. In addition, the magnitude of the differences in the bonding is slightly greater with increasing softness of the chalcogen donor atom. The DFT calculations for the model systems correlate well with experimentally determined metrical parameters. They indicate that the enhanced covalency in the M-E bond as group 16 is descended arises mostly from increased metal d-orbital participation. Conversely, an increase in f-orbital participation is responsible for the enhancement of covalency in An-E bonds compared to Ln-E bonds. The fundamental and practical importance of such studies of the role of the valence d and f orbitals in the bonding of the f elements is emphasized.     

Gas phase spectra of all-benzenoid polycyclic aromatic hydrocarbons: triphenylene

The jet-cooled laser-induced fluorescence and dispersed fluorescence spectra of the S1(A1')<--S0(A1') transition of triphenylene are reported. The spectra exhibit false origins of e' symmetry which are modeled by performing calculations of Herzberg-Teller coupling using time-dependent density functional theory. It is found that this level of theory reproduces the main features of the observed spectra. The oscillator strength of the strongest band is calculated to be f=7x10(-4). From a combination of theory and the observed upper state lifetime of 41 ns, an estimate of the fluorescence yield is made of PhiF=0.084, in agreement with previous studies in the condensed phase.     

Development of an inverse heat conduction model and its application to determination of heat transfer coefficient during casting solidification

The interfacial heat transfer coefficient (IHTC) is required for the accurate simulation of heat transfer in castings especially for near net-shape processes. The large number of factors influencing heat transfer renders quantification by theoretical means a challenge. Likewise experimental methods applied directly to temperature data collected from castings are also a challenge to interpret because of the transient nature of many casting processes. Inverse methods offer a solution and have been applied successfully to predict the IHTC in many cases. However, most inverse approaches thus far focus on use of in-mold temperature data, which may be a challenge to obtain in cases where the molds are water-cooled. Methods based on temperature data from the casting have the potential to be used however; the latent heat released during the solidification of the molten metal complicates the associated IHTC calculations. Furthermore, there are limits on the maximum distance the thermocouples can be placed from the interface under analysis. An inverse conduction based method have been developed, verified and applied successfully to temperature data collected from within an aluminum casting in proximity to the mold. A modified specific heat method was used to account for latent heat evolution in which the rate of change of fraction solid with temperature was held constant. An analysis conducted with the inverse model suggests that the thermocouples must be placed no more than 2 mm from the interface. The IHTC values calculated for an aluminum alloy casting were shown to vary from 1,200 to 6,200 Wm^?2 K^?1. Additionally, the characteristics of the time-varying IHTC have also been discussed.     

Phylogenetic and experimental characterization of an acyl-ACP thioesterase family reveals significant diversity in enzymatic specificity and activity

Background

The inorganic (P_i) phosphate transporter (PiT) family comprises known and putative Na⁺- or H⁺-dependent P_i-transporting proteins with representatives from all kingdoms. The mammalian members are placed in the outer cell membranes and suggested to supply cells with P_i to maintain house-keeping functions. Alignment of protein sequences representing PiT family members from all kingdoms reveals the presence of conserved amino acids and that bacterial phosphate permeases and putative phosphate permeases from archaea lack substantial parts of the protein sequence when compared to the mammalian PiT family members. Besides being Na⁺-dependent P_i (NaP_i) transporters, the mammalian PiT paralogs, PiT1 and PiT2, also are receptors for gamma-retroviruses. We have here exploited the dual-function of PiT1 and PiT2 to study the structure-function relationship of PiT proteins.

Results

We show that the human PiT2 histidine, H₅₀₂, and the human PiT1 glutamate, E₇₀, - both conserved in eukaryotic PiT family members - are critical for P_i transport function. Noticeably, human PiT2 H₅₀₂ is located in the C-terminal PiT family signature sequence, and human PiT1 E₇₀ is located in ProDom domains characteristic for all PiT family members. A human PiT2 truncation mutant, which consists of the predicted 10 transmembrane (TM) domain backbone without a large intracellular domain (human PiT2ΔR₂₅₄-V₄₈₃), was found to be a fully functional P_i transporter. Further truncation of the human PiT2 protein by additional removal of two predicted TM domains together with the large intracellular domain created a mutant that resembles a bacterial phosphate permease and an archaeal putative phosphate permease. This human PiT2 truncation mutant (human PiT2ΔL₁₈₃-V₄₈₃) did also support P_i transport albeit at very low levels.

Conclusions

The results suggest that the overall structure of the P_i-transporting unit of the PiT family proteins has remained unchanged during evolution. Moreover, in combination, our studies of the gene structure of the human PiT1 and PiT2 genes (SLC20A1 and SLC20A2, respectively) and alignment of protein sequences of PiT family members from all kingdoms, along with the studies of the dual functions of the human PiT paralogs show that these proteins are excellent as models for studying the evolution of a protein's structure-function relationship.     

Synthesis and structural chemistry of alkali metal tris(HMDS) magnesiates containing chiral diamine donor ligands

Six alkali metal tris(HMDS) magnesiate complexes (HMDS, 1,1,1,3,3,3,-hexamethyldisilazide) containing chiral diamine ligands have been prepared and characterised in both the solid- and solution-state. Four of the complexes have a solvent-separated ion pair composition of the form [{M·(chiral diamine)(2)}(+){Mg(HMDS)(3)}(-)] [M = Li for 1 and 3, Na for 2 and 4; chiral diamine = (-)-sparteine for 1 and 2, (R,R)-TMCDA for 3 and 4, (where (R,R)-TMCDA is N,N,N',N'-(1R,2R)-tetramethylcyclohexane-1,2-diamine)] and two have a contacted ion pair composition of the form [{K·chiral diamine}(+){Mg(HMDS)(3)}(-)](n) [chiral diamine = (-)-sparteine for 5 and (R,R)-TMCDA for 6]. In the solid-state, complexes 1-4 are essentially isostructural, with the lithium or sodium cation sequestered by the respective chiral diamine and the previously reported anion consisting of three HMDS ligands coordinated to a magnesium centre. As such, complexes 1-4 are the first structurally characterised complexes in which the alkali metal is sequestered by two molecules of either of the chiral diamines (-)-sparteine (1 and 2) or (R,R)-TMCDA (3 and 4). In addition, complex 4 is a rare (R,R)-TMCDA adduct of sodium. In the solid state, complexes 5 and 6 exist as polymeric arrays of dimeric [{K·chiral diamine}(+){Mg(HMDS)(3)}(-)](2) subunits, with 5 adopting a two-dimensional net arrangement and 6 a linear arrangement. As such, complexes 5 and 6 appear to be the only structurally characterised complexes in which the chiral diamines (-)-sparteine (5) or (R,R)-TMCDA (6) have been incorporated within a polymeric framework. In addition, prior to this work, no (-)-sparteine or (R,R)-TMCDA adducts of potassium had been reported.