Automated oligoribonucleotide synthesis on silica gel supports

The oligoribonucleotides (Ap)₇A, (CP)₇C, (Gp)₇G and (UP)₇U were prepared via an automated synthesizer using a silica gel support and the methyl dichlorophosphite procedure.     

Determination of ammonia based on the electro-oxidation of hydroquinone in dimethylformamide or in the room temperature ionic liquid, 1-ethyl-3-methylimidazolium bis(trifluoromethylsulfonyl)imide

The results detail a novel methodology for the electrochemical determination of ammonia based on its interaction with hydroquinone in DMF. It has been shown that ammonia reversibly removes protons from the hydroquinone molecules, thus facilitating the oxidative process with the emergence of a new wave at less positive potentials. The analytical utility of the proposed methodology has been examined with a linear range from 10 to 95 ppm and corresponding limit-of-detection of 4.2 ppm achievable. Finally, the response of hydroquinone in the presence of ammonia has been examined in the room temperature ionic liquid 1-ethyl-3-methylimidazolium bis(trifluormethylsulfonyl)imide, [EMIM][N(Tf)₂]. Analogous voltammetric waveshapes to that observed in DMF were obtained, thereby confirming the viability of the method in either DMF or [EMIM][N(Tf)₂] as solvent.     

Determination of the total nitrogen content of hard, semihard, and processed cheese by the Kjeldahl method: collaborative study

The objective of this collaborative study was to determine interlaboratory performance statistics for a modified and optimized version of AOAC Method 920.123 for the determination of the total nitrogen content of hard, semihard, and processed cheese by Kjeldahl analysis. Details included addressing the issues of material homogeneity, test portion size (1 g), quantitative transfer (weighing on to filter paper), ensuring system suitability (nitrogen recoveries), and using AOAC Method 991.20 as the basis for nitrogen analysis. Fifteen laboratories tested 18 pairs of blind duplicate cheese materials with a crude protein content between 18 and 36%. Materials represented hard, semihard, and processed commercial cheeses with a wide range of composition. Statistical performance parameters expressed as crude protein (nitrogen x 6.38), g/100 g, with invalid and outlier data removed were mean = 26.461, repeatability standard deviation (Sr) 0.111, reproducibility standard deviation (S(R)) = 0.153, repeatability relative standard deviation (RSDr) = 0.42%, reproducibility relative standard deviation (RSDR) = 0.58%, repeatability (r) = 0.312, and reproducibility (R) = 0.428. The interlaboratory study results were acceptable and comparable to those for the milk Kjeldahl nitrogen method on a relative nitrogen basis. The Study Directors recommend that this modified method for the determination of total nitrogen in hard, semihard, and processed cheese by Kjeldahl analysis be adopted First Action as an improved method to replace Method 920.123.     

Synthesis and solid-state structures of new cyclophane host molecules

Five new cyclophane host molecules (corrals) are prepared by linking together two α,α′-di(4-hydroxyphenyl)-1,4-diisopropylbenzene or α,α′-di(3,5-dimethyl-4-hydroxyphenyl)-1,4-diisopropylbenzene units with two permethylene spacers. Three small cyclophane hosts (boxes) are synthesized by cyclization of α,α′-di(4-hydroxyphenyl)-1,4-diisopropylbenzene with di(bromomethyl)benzene compounds. Solid-state structures of one corral and one box are reported.     

Substitution reactions of [Fe(4)S(4)Cl(4)](2-) with Bu(t)NC or Et(2)NCS(2)(-): trapping intermediates and detecting new pathways

Kinetic studies on the substitution reaction between [Fe(4)S(4)Cl(4)](2-) and Bu(t)NC or Et(2)NCS(2)(-) are reported. The binding of small molecules and ions to Fe-S clusters is a fundamental step in substitution reactions but can be difficult to follow directly because these reactions are rapid and often associated with small spectroscopic changes. A novel kinetic method is reported which allows the time course of molecule and ion binding to Fe-S clusters to be followed by monitoring the lability of the cluster. Using a stopped-flow, sequential-mix apparatus, [Fe(4)S(4)Cl(4)](2-) and L (L = Et(2)NCS(2)(-) or Bu(t)NC) are rapidly mixed, and after a known time (delta) the resulting solution is mixed with a solution of PhS(-). The thiolate substitutes for the chloro ligands on the cluster, in a reaction which is easy to follow because of the large change in the visible absorption spectrum. The rate of this substitution is extremely sensitive to whether L is bound to the cluster or not. By correlation of delta with the rate of the reaction with PhS(-), the time course of the reaction between [Fe(4)S(4)Cl(4)](2-) and L can be mapped out. In studies where L = Bu(t)NC this technique has allowed the detection of an intermediate ([Fe(4)S(4)Cl(4)(CNBu(t))](2-)) which cannot be detected spectrophotometrically. In further studies, the substitution reactions of [Fe(4)S(4)Cl(4)](2-) with PhS(-), Et(2)NCS(2)(-), or Bu(t)NC are all perturbed by the addition of Cl(-). In all cases a common pathway for substitution is evident, but with Et(2)NCS(2)(-) an additional, slower pathway becomes apparent under conditions where the common pathway is completely inhibited by Cl(-).     

Formation of dimers that contain unbridged W(IV)/W(IV) double bonds

A tungsten neopentylidene complex has been found to decompose to yield a heterochiral dimer that contains a W=W double bond and no bridging ligands. Decompositions of related bisalkoxide complexes also yield compounds that contain an "unsupported" W=W double bond, while a sample of [Mo(NAr)(CH2-t-Bu)(OC6F5)]2 has been found to be a homochiral species related to [W(NAr)(CH2-t-Bu)(OC6F5)]2.     

Method Development for the Speciation of Chromium in River and Industrial Wastewater Using GFAAS

A simple, sensitive and inexpensive method for the speciation of Cr(VI) and Cr(III) in river and industrial wastewater was developed, optimized and validated. Samples were collected, filtered and then chromium species were determined in the filtrate. In the filtrate, total Cr was determined directly by Graphite Furnace Atomic Absorption Spectrometry (GFAAS). A portion of the filtered sample was buffered to pH 6.4, extracted with Amberlite LA-2/MIBK and finally Cr(VI) was determined in the organic extract and Cr(III) in the aqueous phase using GFAAS. The method was evaluated by analysis of the certified reference material, CRM 544, and good accuracy was obtained. The limit of detection for Cr(VI) and Cr(tot)/Cr(III) was found to be 0.30 and 0.08 µg L⁻¹, respectively, and a precision expressed as relative standard deviation of better than 11% was achieved for nine replicates. A number of water samples from the Tinishu Akaki River, Ethiopia, and wastewater samples from a chemical plant in Germany, were analysed. In addition to the GFAAS method, Cr(tot) was also determined using ICP-MS (in CRM 544, lyophilized water, and Tinishu Akaki River water samples) and Cr(tot) and Cr(VI) using UV-VIS spectrophotometry (in CRM 544 and industrial wastewater samples). Good agreement between the different methods was found.     

Effects of alkali metal halide salts on the hydrogen bond network of liquid water

Measurements of the oxygen K-edge X-ray absorption spectrum (XAS) of aqueous sodium halide solutions demonstrate that ions significantly perturb the electronic structure of adjacent water molecules. The addition of halide salts to water engenders an increase in the preedge intensity and a decrease in the postedge intensity of the XAS, analogous to those observed when increasing the temperature of pure water. The main-edge feature exhibits unique behavior and becomes more intense when salt is added. Density functional theory calculations of the XAS indicate that the observed red shift of the water transitions as a function of salt concentration arises from a strong, direct perturbation of the unoccupied molecular orbitals on water by anions, and does not require significant distortion of the hydrogen bond network beyond the first solvation shell. This contrasts the temperature-dependent spectral variations, which result primarily from intensity changes of specific transitions due to geometric rearrangement of the hydrogen bond network.     

Automated multi-attribute method sample preparation using high-throughput buffer exchange tips

Rationale

The multi-attribute method (MAM) has become a valuable mass spectrometry (MS)-based tool that can identify and quantify the site-specific product attributes and purity information for biotherapeutics such as monoclonal antibodies (mAbs) and fusion molecules in recent years. As we expand the use of the MAM at various stages of drug development, it is critical to enhance the sample preparation throughput without additional chemical modifications and variability.

Methods

In this study, a fully automated MAM sample preparation protocol is presented, where rapid desalting in less than 15 minutes is achieved using miniaturized size-exclusion chromatography columns in pipette tips on an automated liquid handler. The peptide samples were analyzed using an electrospray ionization (ESI) orbitrap mass spectrometer coupled to an ultra-high-performance liquid chromatography (UHPLC) system with a dual column switching system.

Results

No significant change was observed in product attributes and their quantities compared with manual, low-artifact sample preparation. The sample recovery using the buffer exchange tips was greatly enhanced over the manual spin cartridges while still demonstrating excellent reproducibility for a wide variety of starting sample concentrations. Unlike a plate desalting system, the individual columns provide flexibility in the number of samples prepared at a time and sample locations within plates.

Conclusions

This automated protocol enables the preparation of up to 96 samples with less “at-bench” time than the manual preparation of a smaller batch of samples, thereby greatly facilitating support of process development and the use of the MAM in quality control.

     

Theoretical Definition of a Functional Group and the Molecular Orbital Paradigm

It is the purpose of this review to demonstrate that the empirical classification of the observations of chemistry in terms of the properties assigned to functional groups is a consequence of and is predicted by physics. This is accomplished by showing that the atoms and functional groups of chemistry can be identified with bounded space-filling objects whose properties are defined by quantum mechanics. The quantum mechanical definition of a group is combined with a new pictorial representation of its form to obtain a unified picture which should make it eminently recognizable to chemists. This picture, when combined with the demonstrated ability of these groups to recover the measured properties of atoms in molecules, is offered as one which meets the expectations a chemist associates with the concept of a functional group. The manner in which this physical definition of a group differs fundamentally from models of functional groups based upon molecular orbital theory is discussed.