Concentrated Ammonium Hydroxide Research Articles

In situ grafting of carboxylic acid-terminated hyperbranched poly(ether-ketone) to the surface of carbon nanotubes

Carboxylic acid-terminated hyperbranched poly(ether-ketone)s (HPEKs) were successfully grafted onto the surfaces of single-walled carbon nanotube (SWNT) and multi-walled carbon nanotube (MWNT) to afford HPEK- g-SWNT and HPEK- g-MWNT nanocomposites. They were prepared via in situ polymerization of 5-phenoxyisophthalic acid as an AB 2 monomer for the HPEK in the presence of SWNT or MWNT in polyphosphoric acid (PPA)/phosphorous pentoxide (P 2O 5) medium. The resultant nanocomposites were homogeneously dispersed in various common polar aprotic solvents as well as in concentrated ammonium hydroxide. The experimental results from Soxhlet extraction, solubility enhancement, elemental analysis (EA), thermogravimetric analysis (TGA), and scanning electron microscopy (SEM) provided clear evidences for grafting of hyperbranched polymers onto the surfaces of corresponding CNT's. Achieving enhanced solubility of CNT's in common organic solvents via the functionalization of CNT's is a key step for CNT's to be used in various application-specific purposes. The results could potentially envision to the area of CNT researches via the efficient introduction of three-dimensional globular dendritic macromolecules as increasing solubility, available multi-functionality, reactivity, processability, and also biocompatibility.

Restoration of engraved marks on steel surfaces by etching technique

It is known that restoration of erased engraved identification marks on the engine and the chassis of a car or on a firearm has low success rate. Unlike stamping, engraving on a metal surface leaves no pronounced, permanent subsurface deformation in the crystalline structure, also called dislocation that can be revealed by suitable methods. Hence, the current research work investigated whether metallographic reagents used in the restoration of stamp (compression) marks could be applied to recover engraved marks on steel surfaces and also to establish the sensitivity and effectiveness of some of these reagents for the restoration of the marks. Experiments were conducted by mechanically engraving alphanumeric characters on several steel plates using a computer controlled engraving machine called Gravograph. The markings were later erased from the above steel plates by removing the metal in stages of 0.01 mm through 0.04 mm below the bottom of the engraving. Several plates were thus prepared wherein each one had been abraded to a specific depth. Then eight metallographic reagents were tested on each one of the above erased plates using a swabbing technique. The results had shown that while most of the reagents were able to restore marks up to certain levels of erasure, the reagent 5 g copper sulphate, 60 ml water, 30 ml concentrated ammonium hydroxide and 60 ml concentrated hydrochloric acid restored marks erased to a depth of 0.04 mm below the engraving depth, thus presenting itself the most sensitive reagent. Quite significantly, the above reagent was also able to decipher successfully the original engraved marks that had been erased and engraved with a new number, or obliterated by centre punching. The results of this research work should benefit the forensic practitioners engaged in the serial number recovery on vehicles, firearms and other objects.

CHEMICAL AND ENZYMATIC SYNTHESIS OF 4′-THIO-β-D-ARABINOFURANOSYLCYTOSINE MONOPHOSPHATE AND TRIPHOSPHATE

N4-Acetyl-1-(2, 3-di-O-acetyl-4-thio-β-D-arabinofuranosyl)cytosine (2) was synthesized in three steps from 1-(4-thio-β-D-arabinofuranosyl)cytosine (1). The reaction of this partially blocked 4′-thio-ara-C derivative 2 with 2-chloro-4H-1,3,2-benzodioxaphosphorin-4-one gave the 5′-phosphitylate derivative 3, which on reaction with pyrophosphate gave the 5′-nucleosidylcyclotriphosphite 4. Product 4 was then oxidized with iodine/pyridine/water and deblocked with concentrated ammonium hydroxide to provide the desired 4′-thio-ara-C-5′-triphosphate 5. This triphosphate 5 was converted to 4′-thio-ara-C -5′-monophosphate 6 by treatment with snake venom phosphodiesterase I. The details of the synthesis, purification, and characterization of both nucleotides are described.

Oxathiaphospholane Approach to N‐ and O‐Phosphorothioylation of Amino Acids.

AbstractFor Abstract see ChemInform Abstract in Full Text.

A conformationally preorganized universal solid support for efficient oligonucleotide synthesis.

A novel, conformationally preorganized nonnucleosidic universal solid support for oligonucleotide synthesis was developed. The solid support featured two chemically equivalent hydroxy groups locked in syn-periplanar orientation and orthogonally protected with 4,4'-dimethoxytrityl and acetyl groups. The solid support was extensively tested in the preparation of oligonucleotides and their phosphorothioate analogues containing 2'-deoxy, 2'-O-methyl, and 2'-O-methoxyethylnucleoside residues at the 3'-terminus. Upon completion of oligonucleotide chain assembly, the support-bound oligonucleotide material was treated with concentrated ammonium hydroxide, which removed the O-acetyl protection. The deprotected hydroxy group then effected the transesterification of a phosphate linkage between the solid support and the 3'-terminal nucleoside residue to result in a facile release of the oligonucleotide to solution. The kinetics of the release process was studied in a continuous flow of concentrated aqueous ammonium hydroxide at a temperature of 300.15 K. Optimal conditions for the release of oligonucleotides depending on the chemistry of the backbone and 3'-terminal nucleoside residue were formulated.

Formation of Tungsten Oxide Defects during Tungsten CMP

Most tungsten chemical mechanical polishing (CMP) processes utilize a subsequent cleaning process referred to as post-CMP cleaning for removal of contaminated layers. Even after a proper post-CMP cleaning has treated polished wafers, several defects such as slurry particles, microscratches, and metallic impurities are still easily observable. In this study, a new kind of defect has been observed at the stage between overpolishing and post-CMP clean in the course of the tungsten CMP. The circular-shape defect was composed of very thin tungsten oxide, which could be removed by several treatments such as HF solution dipping, additional oxide CMP, and the treatment of concentrated ammonium hydroxide solution during poly(vinyl alcohol) brushing. Among them, the most available method without any further process issues was the use of concentrated ammonium hydroxide solution. © 2003 The Electrochemical Society. All rights reserved.

3‐(N‐tert‐Butylcarboxamido)‐1‐propyl and 4‐Oxopentyl Groups for Phosphate/Thiophosphate Protection in Oligodeoxyribonucleotide Synthesis

This unit provides procedures for the preparation of deoxyribonucleoside phosphoramidites and appropriate phosphordiamidite precursors with P(III) protecting groups different than the standard 2-cyanoethyl group. Specifically, these phosphoramidites are functionalized with the 3-(N-tert-butylcarboxamido)-1-propyl or 4-oxopentyl groups. The usefulness of these novel deoxyribonucleoside phosphoramidites in the solid-phase synthesis of a 20-mer DNA oligonucleotide and its phosphorothioated analog is demonstrated. It is also shown that removal of the 3-(N-tert-butylcarboxamido)-1-propyl phosphate/thiophosphate-protecting group from these oligonucleotides is rapidly effected under thermolytic conditions at neutral pH, whereas the 4-oxopentyl group is preferably removed by treatment with pressurized ammonia gas or concentrated ammonium hydroxide at ambient temperature. These detailed methods constitute an economical and alkylation-free approach to large-scale preparations of therapeutic oligonucleotides.

Oxathiaphospholane approach to N- and O-phosphorothioylation of amino acids.

A method of highly efficient synthesis of N- and O-phosphorothioylated amino acids was developed. N- and O-(2-Thiono-1,3,2-oxathiaphospholanyl)amino acid methyl esters (3) were prepared in high yields in reaction of amino acid methyl esters with 2-chloro-1,3,2-oxathiaphospholane in pyridine in the presence of elemental sulfur. Compounds 3 were converted in high yield into the corresponding methyl or benzyl phosphorothioamides 6 and 7 by DBU-assisted treatment with methanol or benzyl alcohol. When 3-hydroxypropionitrile was used instead of methanol or benzyl alcohol, the corresponding 2-cyanoethylphosphorothioamidates 4 were obtained in high yield, from which the 2-cyanoethyl group was removed with concentrated ammonium hydroxide. The oxathiaphospholane methodology was also applied for the phosphorylation of amino acids. Thus, 2-oxo-1,3,2-oxathiaphospholane derivatives 10 were prepared by oxidation of compounds 3 with SeO(2.) Compounds 10 were transformed into the corresponding phosphate diesters or amidoesters upon treatment with 3-hydroxypropionitrile in the presence of DBU. The DBU-assisted oxathiaphospholane ring-opening process in 3 and 10 did not cause any measurable C-racemization of phosphorothioylated/phosphorylated amino acids.

Solid-phase synthesis and biochemical studies of O-boranophosphopeptides and O-dithiophosphopeptides.

Signal transduction cascades maintain control over important cellular processes such as cell growth and differentiation by orchestrating protein phosphorylation and dephosphorylation. Specific control of these processes in vivo and in vitro can be achieved with peptide analogues that mimic the binding properties of phosphoproteins. We present here the solid-phase synthesis of two novel classes of phosphopeptide mimetics, O-boranophosphopeptides and O-dithiophosphopeptides, derivatized on tyrosine, serine, and threonine. The use of H-phosphonate and H-phosphonothioate monoesters containing the base labile 9-fluorenemethyl protecting group was key to the synthesis of both phosphopeptide mimetics. O-Boranophosphopeptides were synthesized by condensing O-(9-fluorenemethyl)-H-phosphonate to the peptide hydroxylic component (tyr, ser, or thr) followed by oxidation with borane complexes. Similarly, the synthesis of O-dithiophosphopeptides used the O-(9-fluorenemethyl)-H-phosphonothioate synthon and oxidation with elemental sulfur. Base elimination of the Fmol protecting group and cleavage from the solid support with concentrated ammonium hydroxide afforded the boranophosphopeptide and dithiophosphopeptide target compounds. Ac-YIIPLPG-NH2, having either dithiophosphoryl tyrosine or boranophosphoryltyrosine but no sequence specificity for Yersinia protein tyrosine phosphatase (PTP), was found to competitively inhibit this enzyme with KI values of 430 +/- 50 and 670 +/- 50 microM, respectively. In addition, both phosphopeptide analogues were resistant toward Yersinia PTP enzymatic hydrolysis. Under conditions (pH 8.0) where the phosphopeptide was rapidly dephosphorylated, the boranophosphopeptide hydrolyzed slowly (t1/2 = 15 h) and the dithiophosphopeptide was completely stable over 24 h.

Ion chromatographic analysis of anions in ammonium hydroxide, hydrofluoric acid, and slurries, used in semiconductor processing

In this study, ion chromatography (IC) with suppressed conductivity detection was used for the determination of trace anions in 29% (w/w) ammonium hydroxide, 49% (w/w) hydrofluoric acid and slurries. For these samples, various sample pretreatment methods were applied to eliminate matrix interferences. For concentrated ammonium hydroxide, an on-line electrochemical neutralizer (SP10 AutoNeutralization module) was used to neutralize the base prior to the IC analysis. For concentrated hydrofluoric acid, a heart cutting technique with an ion-exclusion column was used to separate the anions of interest prior to an IC separation. A method was also developed to analyze chloride in silica slurries by IC.

The 4-oxopentyl group as a labile phosphate/thiophosphate protecting group for synthetic oligodeoxyribonucleotides

An efficient and economical method for the solid-phase synthesis of oligodeoxyribonucleotides and their phosphorothioate analogues is described. The method entails the use of the 4-oxopentyl group for phosphate/thiophosphate protection. Post-synthesis removal of the protecting group is easily and rapidly achieved under mild conditions at ambient temperature using either pressurized gaseous amines or concentrated ammonium hydroxide.

The 2-(N-formyl-N-methyl)aminoethyl group as a potential phosphate/thiophosphate protecting group in solid-phase oligodeoxyribonucleotide synthesis.

[reaction in text] The 2-(N-formyl-N-methyl)aminoethyl deoxyribonucleoside phosphoramidite 1 has been synthesized and used in the solid-phase synthesis of an octadecathymidylic acid as a cost-efficient monomer for potential application in the preparation of therapeutic oligonucleotides. The 2-(N-formyl-N-methyl)aminoethyl group can be cleaved from oligonucleotides according to a unique thermolytic cyclodeesterification process at pH 7.0. In addition to being cost-effective, the use of 1 simplifies oligonucleotide postsynthesis processing by eliminating the utilization of concentrated ammonium hydroxide in oligonucleotide deprotection.

2-Benzamidoethyl group--a novel type of phosphate protecting group for oligonucleotide synthesis.

A number of 5'-O-(4,4'-dimethoxytrityl)thymidine N,N-diisopropylamino phosphoramidites protected at P(III) with derivatives of 2-benzamidoethanol were synthesized and incorporated into synthetic oligonucleotides. Depending on substitution patterns at the alkyl chain, amido group, and phenyl ring, the time required for removal of these protecting groups using concentrated ammonium hydroxide varied from 48 h at 55 degrees C to 25 min at 25 degrees C. Of the 11 groups studied, 2-[N-isopropyl-N- (4-methoxybenzoyl)amino]ethyl- (H) and omega-(thionobenzoylamino)alkyl protections (I and K) were most easily removed. Derivatives of the 2-[N-methyl-N-benzoylamino]ethyl group (E-G) demonstrated moderate stability, but those of the 2-(N-benzoylamino)ethyl group (A-C) were the most stable. For the most reactive group, H, a phosphitylating reagent, bisamidite 60, was synthesized and used in the preparation of four deoxynucleoside phosphoramidites 28 and 65-67, plus the 2'-O-(2-methoxyethyl)-5-methyluridine phosphoramidite 68. All of these novel building blocks were successfully tested in the preparation of natural, 20-mer oligonucleotides and their phosphorothioate analogues. With the model phosphotriester 37, the mechanism of deprotection was studied and revealed, in the case of group H, a pH-independent formation of the 2-oxazolinium cation 47. Under aqueous conditions, 47 gave 54, which in turn was converted in the presence of ammonia to a number of identified products. It is important to note that none of the products formed was reactive toward the oligonucleotide backbone or nucleic bases. Thus, a general strategy for protection of internucleosidic phosphodiester groups is described, which may also find application in synthetic organic chemistry of phosphorus(III) and (V).

A facile synthesis of 2,7‐diazapyrene

Abstract2,7‐Diazapyrene is synthesized in three high‐yield steps from commercially available 1,4,5,8‐naphthalene tetracarboxylic dianhydride, which first reacts with concentrated ammonium hydroxide solution at room temperature to give 1,4,5,8‐naphthalenetetracarboxylic diimide (96%). The latter compound is subsequently reduced with borane in refluxing tetrahydrofuran to give 1,2,3,6,7,8‐hexahydro‐2,7‐diazapyrene (77%), which in turn is oxidized with manganese dioxide in refluxing benzene giving 2,7‐diazapyrene (71%).

Determination of α-Solanine and α-Chaconine in Potatoes by High-Performance Thin-Layer Chromatography/Densitometry

A high-performance thin-layer chromatographic (HPTLC) method was used to determine the glycoalkaloids alpha-solanine and alpha-chaconine in potatoes. Alpha-solanine and alpha-chaconine are extracted from dehydrated potatoes with boiling methanol-acetic acid (95 + 5, v/v). The analytes are separated on a Silica Gel 60 F254 HPTLC plate by a saturated mixture of dichloromethane-methanol-water-concentrated ammonium hydroxide (70 + 30 + 4 + 0.4, v/v), which is used for vertical development of the plate up to a distance of 85 mm. For visualization, the plate is dipped 3 times into a modified Carr-Price reagent, 20% (w/v) antimony(III) chloride in acetic acid-dichloromethane (1 + 3, v/v), and subsequently heated on a hot plate at 105 degrees C for 5 min. The glycoalkaloids all appear as red chromatographic zones on a colorless background. Densitometric quantification is performed at 507 nm by reflectance scanning. After determination of the appropriate response function, the proposed method was validated. Good results with respect to linearity, accuracy, and precision were obtained in the concentration range studied.

Microscale Synthesis of Hexaamminechromium(III) Nitrate Using Liquid Ammonia Generated in the Laboratory

The previously published synthesis of hexaamminechromium(III) nitrate using liquid ammonia as the solvent is an experiment that can be used in an advanced inorganic chemistry laboratory as an example of using a nonaqueous inorganic solvent in inorganic synthesis. Potential hazards are associated with the amount of liquid ammonia used in the experiment and the need to store this corrosive material (which is also expensive to purchase). These problems can be eliminated or reduced by performing this experiment on a microscale level and generating the small amount of ammonia needed directly in the laboratory at the time of the experiment. The ammonia is generated by heating concentrated ammonium hydroxide and condensing the ammonia vapors into the reaction vessel.

Allyl group as a protecting group for internucleotide phosphate and thiophosphate linkages in oligonucleotide synthesis: facile oxidation and deprotection conditions.

[reaction: see text] The allyl group, which serves as a protecting group for an internucleotide bond for both phosphates and phosphorothioates, can be easily removed by good nucleophiles under weakly basic or neutral conditions. For a practical synthesis on solid support, camphorsulfonyloxaziridine was used as the oxidizing agent for synthesizing DNA, while the Beaucage reagent was used for preparing phosphorothioate oligomers. Both types of oligonucleotides were easily deprotected by concentrated ammonium hydroxide containing 2% mercaptoethanol.

Oligonucleotide synthesis on maleic anhydride copolymers covalently bound to silica spherical support and characterization of the obtained conjugates

A new route was proposed to make polymer-oligonucleotide conjugates of potential applications in diagnostics. It consisted in direct synthesis of oligonucleotides onto controlled pore glass surface grafted with poly(maleic anhydride-alt-methyl vinyl ether) (P[MAMVE]) or poly(maleic anhydride-alt-ethylene) (P[MAE]). The anhydride moieties were used for both the covalent coupling of the copolymer via ester bond and binding of 5′-dimethoxytrityl thymidine 3′-(6-aminohexyl phosphate) (I) initiator of oligodeoxynucleotide (ODN) synthesis via amide bond. The difference of stability between ester and amide links under basic treatment was used for the selective cleavage of (polymer-oligonucleotide) conjugates after DNA synthesis completion. We succeeded in grafting functionalized copolymer onto silica surface and Polythymidine 26-mer ODN was performed. After concentrated ammonium hydroxide treatment, conjugate crude materials were characterized by size exclusion chromatography coupled to multiangle laser light scattering detection. The number average molecular weight (Mn) for conjugate with P[MAMVE] was abnormally lower than expected and was assigned to polymer degradation using high pH conditions. Such a phenomenon did not occur with P[MAE]-polythymidine conjugate. However, in both cases, parasite ODN synthesis was also evidenced, which was attributed to thymidine phosphoramidite adsorption side reaction during DNA synthesis. © 1998 John Wiley & Sons, Inc. J Appl Polym Sci 70: 2487–2497, 1998

Common Stock Solutions, Buffers, and Media

This collection of recipes describes the preparation of buffers and reagents used in Current Protocols in Pharmacology for cell culture, manipulation of neural tissue, molecular biological methods, and neurophysiological/neurochemical measurements. RECIPES: Acid, concentrated stock solutions Ammonium hydroxide, concentrated stock solution EDTA (ethylenediaminetetraacetic acid), 0.5 M (pH 8.0) Ethidium bromide staining solution Fetal bovine serum (FBS) Gel loading buffer, 6× LB medium (Luria broth) and LB plates Potassium phosphate buffer, 0.1 M Sodium phosphate buffer, 0.1 M TE (Tris/EDTA) buffer Tris⋅Cl, 1 M.

Evaluation of 3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) as a new sulfurizing reagent in combination with labile exocyclic amino protecting groups for solid-phase oligonucleotide synthesis.

3-ethoxy-1,2,4-dithiazoline-5-one (EDITH) was recently introduced as an efficient sulfurizing reagent for solid-phase oligonucleotide synthesis. The successful syntheses were performed using standard base protecting groups (i.e. benzoyl for A and C, isobutyryl for G), which required deprotection in concentrated ammonium hydroxide at 55 degrees C for 15-18 h. We have explored the possibility of using EDITH in combination with fast deprotection chemistry(e.g. Expedite Chemistry using tert -butylphenoxy acetyl as a base protecting group). Surprisingly, poor synthesis performance was observed when syntheses were conducted with EDITH, Expedite Chemistry and standard synthesis cycle (i.e. Coupling-Thio-Cap). Potential G modification seemed to be the source of incompatibility since sequences containing no G or carrying isobutyryl- protected G residues could be synthesized with high efficiency. However, the deleterious G modification can be readily eliminated by inserting a capping step before the sulfurization reaction. Oligomers prepared with the Coupling-Cap-Thio-Cap cycle contained few phosphodiester contaminants as measured by31P-NMR, anion-exchange HPLC and MALDI-TOF mass spectrometry. In addition to reducing deprotection time, this new combination also provides a mild method for the preparation of certain phosphorothioate oligomers that may be sensitive to prolonged ammonia treatment (e.g. thioated RNAs).