The de novo design of median molecules within a property range of interest

Summary In this paper an application is presented of the median molecule workflow to the de novo design of novel molecular entities with a property profile of interest. Median molecules are structures that are optimised to be similar to a set of existing molecules of interest as an approach for lead exploration and hopping. An overview of this workflow is provided together with an example of an instance using the similarity to camphor and menthol as objectives. The methodology of the experiments is defined and the workflow is applied to designing novel molecules for two physical property datasets: mean molecular polarisability and aqueous solubility. This paper concludes with a discussion of the characteristics of this method.     

Rhodium and palladium β-diketonate determination with on-line supercritical fluid extraction-high performance liquid chromatography via solid phase extraction

 An on-line system of supercritical fluid extraction (SFE) and high performance liquid chromatography (HPLC) via solid phase extraction (SPE) is described for the determination of palladium and rhodium 2,2,6,6-tetramethyl-3,5-heptanedione-(thd) as well as rhodium-acetylacetonate-(acac) and benzylacetonate-(bzac) chelates. The chelates were extracted with supercritical CO₂ from sand and humic acid, concentrated on SPE cartridges and analysed with HPLC. Two cartridge materials were tested and compared to off-line trapping. The percentage of the breakthrough and cartridge retained material were measured in liquid dichloromethane. The SFE conditions could be optimized to separate metal chelates during the extraction. The supercritical fluid (SF) behaviour of different ligands on rhodium were investigated. Received: 19 July 1996/Revised: 11 December 1996/Accepted: 14 December 1996     

Arsenic Speciation in As(III)- and As(V)-Treated Soil Using XANES Spectroscopy

Arsenic (As) is a toxic trace element that occurs naturally in groundwater and soils. Understanding the reactions of arsenite (As(III)) and arsenate (As(V)) with soil and mineral surfaces is critical for predicting the fate and transport of As in the environment and developing better ways to remediate As-contaminated areas. This investigation uses X-ray absorption near edge spectroscopy (XANES) to evaluate the solid phase oxidation state and mineral surface binding sites in three agricultural soil samples from California, USA by fitting linear combinations of XANES spectra derived from several synthetic and well characterized As(III)- and As(V)-treated model compounds (Fe and Al metal hydroxides and aluminosilicate illite clay mineral). The results suggest that As(III) is either partially or completely oxidized to As(V) when reacted with soil in an aqueous, batch reaction. The As(III)-treated Aiken soil was composed of 60% As(III) attached to surfaces similar to lepidocrocite (γ-FeOOH)) and 40% As(V) attached to aluminosilicate (illite). The Fallbrook soil completely oxidized As(III) and the product was As(V) adsorbed on Al hydroxide (gibbsite, γ-Al(OH)₃) (62%), illite (16%), and lepidocrocite (γ-FeOOH) (22%). The reaction of As(III) with Wyo soil resulted in 42% As(III) adsorbed on surface similar to goethite and 58% As(V) adsorbed on lepidocrocite. Arsenic(V) adsorption on soil resulted in stable As(V) surface complexes that were well described by XANES spectra from As(V) adsorption complexes on gibbsite, illite, and lepidocrocite.     

Molecular conformation search by distance matrix perturbations

Three-dimensional molecular structure is fundamental in chemical function identification and computer-aided drug design. The enumeration of a small number of feasible conformations provides a rigorous way to determine the optimal or a few acceptable conformations. Our contribution concerns a heuristic enhancement of a method based on distance geometry, typically in relation with experiments of the NMR type. Distance geometry has been approached by different viewpoints; ours is expected to help in several subtasks arising in the process that determines 3D structure from distance information. More precisely, the input to our algorithm consists of a set of approximate distances of varying precision; some are specified by the covalent structure and others by Nuclear Magnetic Resonance (NMR) experiments (or X-ray crystallography which, however, requires crystallization). The output is a valid tertiary structure in a specified neighborhood of the input. Our approach should help in detecting outliers of the NMR experiments, and handles inputs with partial information. Moreover, our technique is able to bound the number of degrees of freedom of the conformation manifold. We have used numerical linear algebra algorithms for reasons of speed, and because they are well-implemented, fully documented and widely available. Our main tools include, besides distance matrices, structure-preserving matrix perturbations for minimizing singular values. Our MATLAB (or SCILAB) implementation is described and illustrated.AMS subject Classification: 92E10 Molecular structure, 92C40 Biochemistry, molecular biology, 65F15 Eigenvalues, eigenvectors, 15A18 Eigenvalues, singular values, and eigenvectors     

Interactions of diethylenetriaminepentaacetic acid (dtpa) and triethylenetetraaminehexaacetic acid (ttha) with major components of natural waters

The binding ability of diethylene triamine pentaacetate (dtpa(5-)) and triethylene tetraamine hexaacetate (ttha(6-)) ligands towards major components, H(+), Na(+), Mg(2+) and Ca(2+), of natural waters was studied in both single and mixed ionic media at different ionic strengths and at T=25 degrees C. Some measurements, performed in Mg(2+)-Ca(2+) mixtures, allowed us to find the formation of new mixed species MgCa(dtpa), MgCa(ttha) and MgCaH(ttha), here reported for the first time. All the complexes formed in the various systems were characterized in terms of both stoichiometry and stability, and an attempt was made to find general rules for the stability of mixed metal complexes in comparison with that of simple species. To obtain quantitative information on the complexing ability of dtpa and ttha in seawater, measurements have been carried out in artificial seawater ionic medium (Na(+), K(+), Ca(2+), Mg(2+), Cl(-) and SO(4)(2-)). Calculations, performed by considering the salt mixture as single salt BA, allowed us to find some quite stable B(i)H(j)L species. Under the natural seawater conditions [S(salinity)=35], we found for the most important species logbeta( B(dtpa))=9.64 and. Literature data comparison is also reported.     

Kinetics of free radical polymerization—XXXI. Solvent effect on the polymerization rate of ethyl acrylate

The free radical polymerization of ethyl acrylate was investigated in benzene and dimethyl formamide solutions at 50°. The effects of initiator and monomer concentration were studied over a wide range. The overall rate of polymerization was proportional to (initiator concentration)^{$\text{1}\text{2}$} but not to the concentration of the monomer. We attempted to interpret this solvent effect on the basis of (i) the diffusion theory, (ii) the theory of charge transfer complexes and (iii) the theory of hot radicals. Our experimental results could only be explained quantitatively in terms of hot radicals.     

Comparison of the Temperature Effect on the π∗←n and π∗←π Electronic Transition Bands of NO<Subscript>3</Subscript><Superscript>−</Superscript>(aq)

The effect of temperature on the π∗←π transition band in the UV absorption spectrum of NO₃⁻(aq) centered at ≈200 nm was studied in the temperature range 10–70 ^∘C. The observed temperature independence of this band was in contrast to the significant influence of temperature on the nitrate π∗←n transition reported recently by us. However, taking into account the electronic states involved in both the transitions, it was concluded that this finding was in accordance with our previous assumption that interconversion between spectrally distinct (with respect to π∗←n band) nitrate species included the rupture/formation of hydrogen bond(s) in the hydration shell of the nitrate ion.     

Monodisperse chloromethyl-functionalized macroporous polymer particles by seeded polymerization in aqueous media

This study presents a method to produce monodisperse chloromethyl-functionalized macroporous poly(styrene-co-divinylbenzene) polymer particles by seeded polymerization in aqueous media. We observed that the molecular structure of polystyrene seed particles, the composition of the secondary monomer mixtures, and the type of solvents were very important factors that determine the morphology and porosity of the final particles. This study proposes that the molecular chemistry of polystyrene seed polymers, increasing molecular weight or crosslinking, is another factor that can control the porosity of the final particles. Also, the selection of a poor solvent was effective in forming the larger surface area. In this study, it was confirmed that the chloromethyl groups introduced on the surface of porous particles were quantified chemically and their effective incorporation had a close relationship with the surface area.     

Structural Changes of Cellulose Crystallites Induced by Mercerisation in Different Solvent Systems; Determined by Powder X-ray Diffraction Method

The completeness of mercerisation can be evaluated by investigating the changes in the crystalline regions of cellulose from cellulose I (C-I) to cellulose II (C-II) by the X-ray powder diffraction method. Mercerisation experiments in four different solution systems: ethanol/water, acetone, DMSO and xylene, are reported. Also the effect of some additives, external pressure, treatment time and alkalisation temperature were studied. In two-phase solvent systems, structural changes of cellulose crystallites depended primarily on the distribution and solubility of sodium hydroxide in the solvent phases. The sodium hydroxide concentration in the hydrophilic phase must exceed 7–8 w/w-% before complete crystal change from C-I to C-II can occur. The precipitation of sodium hydroxide due to high concentration prevents the successful use of one-phase ethanol/water system in slurry process. On the contrary, the 2-propanol/water/sodium hydroxide system separates into two layers; to the water-rich lower layer and the 2-propanol-rich upper layer, where the sodium hydroxide remains mainly in the water-rich lower layer. This prevents the precipitation of sodium hydroxide and promotes the alkalisation of cellulose. Ammonium chloride and ammonium hydroxide clearly had a positive effect by promoting the crystal changes, however, the urea concentration used in this study was obviously too small. In the advantageous two-phase 2-propanol/water systems, the alkalisation time was only 15 min when the treatment temperature was kept between 0 and 10 °C. Reduced external pressure was found to have a small but still detectable positive effect on cellulose alkalisation while over-pressure prevented crystal changes.     

Facile generation of platinum(IV) compounds with mixed labile moieties. Hydrogen peroxide oxidation of platinum(II) to platinum(IV) compounds

Hydrogen peroxide oxidation of platinum(II) compounds containing labile groups such as Cl, OH, and alkene moieties has been carried out and the products characterized. The reactions of [Pt^II (X)₂ (N–N)] (X = Cl, OH, X₂ = isopropylidenemalorate (ipm); N–N 2,2-dimethyl-1,3-propanediamine [(dmpda), N-isopropyl-1,3-propanediamine (ippda)] with hydrogen peroxide in an appropriate solvent at room temperature affords [Pt^IV (OH)(Y)(X)₂(N–N)] (Y = OH, OCH₃). The crystal structures of [Pt^IV(OH)(OCH₃)(Cl)₂(dmpda)]·2H₂O (P-1 bar, a = 6.339(2) Å , b = 9.861(1) Å, c = 11.561(1) Å, a = 92.078(9)°, β = 104.78(1)°, γ=100.54(1)°, V = 684.3(2) ų, Z = 2R = 0.0503) and [Pt^IV(OH)₂(ipm)(ippda)]·3H₂O (C 2/c, a = 27.275(6) Å, b=6.954(2) Å, c = 22.331(4) Å, β = 118.30(2)°, V = 3729(2) ų, Z = 8, R = 0.0345) have been solved and refined. The local geometry around the platinum(IV) atom approximates to a typical octahedral arrangement with two added groups (OH and OCH₃; OH and OH) in a transposition. The platinum(IV) compounds with potential labile moieties may be important intermediate species for further reactions.