High-throughput purification of combinatorial libraries I: a high-throughput purification system using an accelerated retention window approach

We have developed a high-throughput purification system to purify combinatorial libraries at a 50-100-mg scale with a throughput of 250 samples/instrument/day. We applied an accelerated retention window method to shorten the purification time and targeted one fraction per injection to simplify data tracking, lower QC workload, and simplify the postpurification processing. First, we determined the accurate retention time and peak height for all compounds using an eight-channel parallel LC/UV/MS system, and calculated the specific preparative HPLC conditions for individual compounds. The preparative HPLC conditions include the compound-specific gradient segment for individual compounds with a fixed gradient slope and the compound-specific UV or ELSD threshold for triggering a fraction collection device. A unique solvent composition or solvent strength was programmed for each compound in the preparative HPLC in order to elute all compounds at the same target time. Considering the possible deviation of the predicted retention time, a 1-min window around the target time was set to collect peaks above a threshold based on UV or ELSD detection. Dual column preparative instruments were used to maximize throughput. We have purified more than 500 000 druglike compounds using this system in the past 3 years. We report various components of this high-throughput purification system and some of our purification results.     

Macrocyclization on the fullerene core: Direct regio- and diastereoselective multi-functionalization of [60]fullerene,and synthesis of fullerene-dendrimer derivatives

The macrocyclization between buckminsterfullerene, C₆₀, and bis-malonate derivatives in double Bingel reaction provides a versatile and simple method for the preparation of covalent bis-adducts of C₆₀ with high regio- and diastereoselectivity. A combination of spectral analysis, stereochemical considerations, and X-ray crystallography (Fig. 2) revealed that out of the possible in-in, in-out, and out-out stereoisomers, the reaction of bis-malonates linked by o-, m-, or p-xylylene tethers afforded only the out-out ones (Scheme 1). In contrast, the use of larger tethers derived from 1,10-phenanthroline also provided a first example, (±)- 19 (Scheme 2), of an in-out product. Starting from optically pure bis-malonate derivatives, the new bis-functionalization method permitted the diastereoselective preparation of optically active fullerene derivatives (Schemes 4 and 5) and, ultimately, the enantioselective preparation (enantiomeric excess ee > 97%) of optically active cis-3 bis-adducts whose chirality results exclusively from the addition pattern (Fig. 6). The macrocyclic fixation of a bis-malonate with an optically active, 9,9′-spirobi[9H-fluorene]-derived tether to C₆₀ under generation of 24 and ent- 24 with an achiral addition pattern (Scheme 4) was found to induce dramatic changes in the chiroptical properties of the tether chromophore such as strong enhancement and reversal of sign of the Cotton effects in the circular dichroism (CD) spectra (Figs. 4 and 5). By the same method, the functionafized bis-adducts 50 and 51 (Schemes 10 and 11) were prepared as initiator cores for the synthesis of the fullerene dendrimers 62 , 63 , and 66 (Schemes 12 and 13) by convergent growth. Finally, the new methodology was extended, to the regio- and diastereoselective construction of higher cyclopropanated adducts. Starting from mono-adduct 71 , a clipping reaction provided exclusively the all-cis-2 tris-adduct (±)- 72 (Scheme 14), whereas the similar reaction of bis-adduct 76 afforded the all-cis-2 tetrakis-adduct 77 (Scheme 15). Electrochemical investigations by steady-state voltammetry (Table 2) in CH₂Cl₂ (+0.1M Bu₄NPF₆) showed that all macroeyciic bis(methano)fullerenes underwent multiple reduction steps, and that regioisomerism was not much influencing the redox potentials, All cis-2 bis-adducts gave an instable dianion which decomposed during the electrochemical reduction. In CH₂Cl₂, the redox potential of the fullerene core in dendrimers 62, 63 , and 66 is not affected by differences in size and density of the surrounding poly(ether-amide) dendrons. The all-cis-2 tris- and tetrakis(meihano)fullercnes (±) -72 and 77 , respectively, are reduced at more negative potential than previously reported all-e tris- and tetrakis-adducts with methane bridges that are also located along an equatorial belt. This indicates a larger perturbation of the original fullerene π-chromophore and a larger raise in LUMO energy in the former derivatives.     

A convenient two-step synthesis of 6-methylenesubstituted-4-trichloromethyl-2-methylsulfanyl pyrimidines

This work reports a two-step synthetic strategy to obtain a series of 6-methylenesubstituted-4-trichloromethyl-2-methylsulfanylpyrimidines from the cyclization of 5-bromo-4-methoxy-1,1,1-trichloro-pent-3-en-2-ones with 2-methyl-2-pseudothiourea sulfate, followed by nucleophilic substitution of 6-bromomethyl-4-trichloromethyl-2-methylsulfanylpyrimidine with a series of nucleophiles. Alternative strategies to obtain 6-halomethyl-4-trichloro[fluoro]methyl-2-methylsulfanyl pyrimidines have been addressed.     

Electrostatics of phosphatidic acid monolayers: Insights from computer simulations

In this paper, we argue that many of the fascinating electrostatic effects that take place in amphiphilic systems are strongly related to the particular organization of the oxygen atoms within each individual molecule. In particular, we focus on two effects: charge inversion and dielectric overscreening. For that purpose, we present molecular dynamics simulations of phosphatidic acid (DMPA²⁻) in the presence of divalent counterions. Our results show that the many oxygens present in DMPA²⁻ cooperatively create strong binding sites for counterions, which in some cases lead to charge inversion. We also present an analysis of the role of interfacial water and relate our analysis to the phenomenon of dielectric overscreening. Several experimental implications are discussed in the conclusions.     

Improved separation of palladium species in biological matrices by using a combination of gel permeation chromatography and isotachophoresis

The binding of palladium to high-molecular-mass compounds in palladium-treated lettuce is investigated as an example for a biological matrix. The total palladium concentration in lettuce leaves is 10.3 ng/g wet weight. After homogenization, high-molecular-mass compounds (> 10 kDa) are isolated by ultrafiltration. For separation of these palladium species a combination of preparative gel permeation chromatography (GPC) and preparative isotachophoresis (ITP) is used. Palladium is determined in separated fractions by using a highly sensitive total reflection X-ray fluorescence (TXRF) method after preconcentration. After GPC separation, four main fractions of palladium species are collected, each containing palladium in ng quantities (3-10 ng). Two of these fractions are further separated by ITP, yielding at least three main peaks per GPC fraction, each containing palladium in the range of 0.3-3 ng. These palladium containing peaks are characterized by high-performance size exclusion chromatography (HPSEC) and capillary isotachophoresis (cITP) in parallel. HPSEC enables the estimation of the molecular mass of six main palladium peaks, covering a molecular mass range of 69-200 kDa. It is also shown that the estimation of molecular mass after separation is more reliable than the respective estimation directly in the first GPC run. However, cITP reveals that each of the separated peaks is still a mixture of at least five different compounds.     

Accurate ab initio determination of the van der Waals interaction in the X 2Σ+ ground state of LiHe

Accurate quantum-chemical ab initio calculations have been performed at the SCF and CEPA (coupled electron pair approximation) levels for the van der Waals interaction in the X ² Σ ⁺ ground state of LiHe. An extended basis set has been used and the counterpoise correction for the basis set superposition error (BSSE) has been applied. The calculated potential energy curve has a very shallow minimum at 11.56 a ₀ with a well depth of only 1.49 cm^?1. This is too small to allow for a bound vibrational level. The analysis of the results shows that the interaction mainly consists of the Pauli repulsion between Li(1s ²2s) and He (1s ²), which is decaying exponentially, and the attractive London dispersion energy. Van der Waals coefficients C₆, C₈, and C₁₀ have been determined by a least squares fit to the long-range part of the calculated potential curve.     

Ab initio calculations of small hydrides including electron correlation

Five different structures of CH₅ ⁺ and one structure of CH₅ ^– are calculated using a gaussian basis both in the SCF approximation and with the inclusion of electron correlation in the independent electron pair approximation (IEPA). While on SCF level the C _sstructure of CH₅ ⁺ has to lowest energy, the energy difference between the C _sand C _2vstructures becomes negligible if correlation is included. In contrast to this the approach of a proton to CH₄ at large and intermediate distances is most favorable towards a corner of the CH₄ tetrahedron which means a structure. The decomposition of CH₅ ⁺ into CH₃ ⁺ and H₂ requires 20kcal/mol on SCF level and 40 kcal/mol if correlation is included.     

Oxidation of nitrided si(100) by gaseous atomic and molecular oxygen

The nitridation of Si(100) by ammonia and the subsequent oxidation of the nitrided surface by both gaseous atomic and molecular oxygen was investigated under ultrahigh vacuum (UHV) conditions using X-ray photoelectron spectroscopy (XPS). Nitridation of Si(100) by the thermal decomposition of NH3 results in the formation of a subsurface nitride and a decrease in the concentration of surface dangling bond sites. On the basis of changes in the N1s spectra obtained after NH3 adsorption and decomposition, we estimate that the nitride resides about four to five layers below the vacuum-solid interface and that the concentration of surface dangling bonds after nitridation is only 59% of its value on Si(100)-(2 x 1). Oxidation of the nitrided surface is found to produce an oxide phase that remains in the outer layers of the solid and interacts only weakly with the underlying nitride for oxygen coverages up to 2.5 ML. Slight changes in the N1s spectra observed after oxidizing at 300 K are suggested to arise primarily from the introduction of strain within the nitride, and by the formation of a small amount of Si2=N-O species near the nitride-oxide interface. The nitrogen bonding environment changes negligibly after oxidizing at 800 K, which is indicative of greater phase separation at elevated surface temperature. Nitridation is also found to significantly reduce the reactivity of the Si(100) surface toward both atomic and molecular oxygen. A comparison of the oxygen uptake on the clean and nitrided surfaces shows quantitatively that the decrease in dangling bond concentration is responsible for the reduced activity of the nitrided surface toward oxidation, and therefore that dangling bonds are the initial adsorption site for both gaseous oxygen atoms and molecules. Increasing the surface temperature is found to promote the uptake of oxygen when O2 is used as the oxidant, but brings about only a small enhancement in the uptake of gaseous O-atoms. The different effects of surface temperature on the uptake of O versus O2 are interpreted in terms of the efficiency at which dangling bond pairs are regenerated on the surface at elevated temperature and the different site requirements for the adsorption of O and O2.     

On-line coupling of packed capillary electrochromatography with coordination ion spray-mass spectrometry for the separation of enantiomers

Pressure-supported packed capillary electrochromatography (CEC) and packed capillary high-performance liquid chromatography (pHPLC) have been coupled on-line to electrospray ionization-mass spectrometry (ESI-MS) and coordination ion spray-mass spectrometry (CIS-MS). Separation of enantiomers of barbiturates and chlorinated alkyl phenoxypropanoates were performed on a permethylated beta-cyclodextrin stationary phase by pressure-supported CEC. For on-line detection with ESI- and CIS-MS, a modified sheath-liquid interface was used. CIS-MS is a universal, novel ionization technique which improves the selectivity as well as the sensitivity. Charged complexes were formed through the addition of central complexing ions such as silver(I), cobalt(II), copper(II), and lithium(I) to the sheath flow. Advantages of CIS-MS detection compared to the ESI-MS mode are discussed. In the CIS-MS mode, increased sensitivity and high selectivity was attained through different possibilities of complexation. The superiority of pressure-supported CEC compared to pHPLC in the hyphenation with CIS-MS is demonstrated.     

Dual quartz crystal microbalance compensation using a submerged reference crystal. Effect of surface roughness and liquid properties

Absolute resonant frequency measurements were made on gold-coated AT-cut quartz crystals with one face in contact with a series of liquids. The effect of surface roughness and liquid properties (viscosity and density) was analyzed in terms of a “trapped liquid” model. In this model, liquid present in surface imperfections is viewed as rigidly coupled mass. In some of the literature this density-dependent, but not viscosity-dependent, term is viewed as being additive to the hydrodynamic shift seen for a smooth surface. Data obtained using 1 μm and 5 μm surface finish crystals are inconsistent with the predictions of the trapped liquid model. This suggests hydrodynamic coupling between liquid internal and external to the crevices. Despite the lack of a theoretical model for the liquid motion, it is possible to compensate for frequency variations resulting from changing liquid properties and for roughness effects by making direct measurements of the resonant frequency difference between two crystals exposed to the same solution. This novel procedure works to the extent that the two crystals have similar surface topographies. Compensation is excellent for 1 μm finish crystals and good for 5 μm finish crystals.