Intermolecular Phenolic Hydroxy Methylation Occurring between Chiral N,N＇-Bis（2-hydroxyphenyl）-2,2-dimethyl-1,3-dioxolane-4,5-dicarbamide and Co-crystallized Methanol under Electron Impact Ionization Conditions

An intermolecular phenolic hydroxy methylation occurring between chiral N,N‘-bis(2-hydroxyphenyl)-2,2-dimethyl-1,3-dioxolane-4,5-dicarbamide and co-crystallized methanol under electron impact ionization conditions was observed. The result was confirmed by X-ray diffraction structural ananlysis of a co-crystalline of(R,R)-enantiomer and methanol.     

Synthesis of a DNA Promoter Segment Containing All Four Epigenetic Nucleosides: 5‐Methyl‐, 5‐Hydroxymethyl‐, 5‐Formyl‐, and 5‐Carboxy‐2′‐Deoxycytidine

A 5‐formyl‐2′‐deoxycytidine (fdC) phosphoramidite building block that enables the synthesis of fdC‐containing DNA with excellent purity and yield has been developed. In combination with phosphoramidites for 5‐methyl‐dC, 5‐hydroxymethyl‐dC, and carboxy‐dC, it was possible to prepare a segment of the OCT‐4 promoter that contains all four epigenetic bases. Because of the enormous interest in these new epigenetic bases, the ability to insert all four of them into DNA should be of great value for the scientific community.     

A new,validated HPLC‐MS/MS method for the simultaneous determination of the anti‐cancer agent capecitabine and its metabolites: 5′‐deoxy‐5‐fluorocytidine, 5′‐deoxy‐5‐fluorouridine, 5‐fluorouracil and 5‐fluorodihydrouracil,in human plasma

A rapid and selective liquid chromatography/tandem mass spectrometric method was developed for the simultaneous determination of capecitabine and its metabolites 5′‐deoxy‐5‐fluorocytidine (5′‐DFCR), 5′‐deoxy‐5‐fluorouracil (5′‐DFUR), 5‐fluorouracil (5‐FU) and dihydro‐5‐fluorouracil (FUH₂) in human plasma. A 200 μL human plasma aliquot was spiked with a mixture of internal standards fludarabine and 5‐chlorouracil. A single‐step protein precipitation method was employed using 10% (v/v) trichloroacetic acid in water to separate analytes from bio‐matrices. Volumes of 20 μL of the supernatant were directly injected onto the HPLC system. Separation was achieved on a 30 × 2.1 mm Hypercarb (porous graphitic carbon) column using a gradient by mixing 10 mm ammonium acetate and acetonitrile–2‐propanol–tetrahydrofuran (1 : 3 : 2.25, v/v/v). The detection was performed using a Finnigan TSQ Quantum Ultra equipped with the electrospray ion source operated in positive and negative mode. The assay quantifies a range from 10 to 1000 ng/mL for capecitabine, from 10 to 5000 ng/mL for 5′‐DFCR and 5′‐DFUR, and from 50 to 5000 ng/mL for 5‐FU and FUH₂ using a plasma sample of 200 μL. Correlation coefficients (r²) of the calibration curves in human plasma were better than 0.99 for all compounds. At all concentration levels, deviations of measured concentrations from nominal concentration were between ?4.41 and 3.65% with CV values less than 12.0% for capecitabine, between ?7.00 and 6.59% with CV values less than 13.0 for 5′‐DFUR, between ?3.25 and 4.11% with CV values less than 9.34% for 5′‐DFCR, between ?5.54 and 5.91% with CV values less than 9.69% for 5‐FU and between ?4.26 and 6.86% with CV values less than 14.9% for FUH₂. The described method was successfully applied for the evaluation of the pharmacokinetic profile of capecitabine and its metabolites in plasma of treated cancer patients. Copyright © 2009 John Wiley & Sons, Ltd.     

Determination of 5‐fluorocytosine, 5‐fluorouracil,and 5‐fluorouridine in hospital wastewater by liquid chromatography–mass spectrometry

Chemotherapeutics are pharmaceutical compounds the occurrence of which in the environment is of growing concern because of the increase in treatments against cancer diseases. They can reach the aquatic ecosystems after passing through wastewater treatment plants without complete removal. One of the most frequently used chemotherapeutics is 5‐fluorouracil which exhibits a strong cytostatic effect. In this paper, an analytical methodology was developed, validated, and applied to determine 5‐fluorouracil, its precursor, 5‐fluorocytosine, and its major active metabolite, 5‐fluorouridine, in hospital wastewater samples. Due to the expected low concentrations after dilution and interferences present in such a complex matrix, a very selective and sensitive detection method is required. Moreover, an extraction method must be implemented prior to the determination in order to purify the sample extract and preconcentrate the target analytes at micrograms per liter concentration levels. Solid‐phase extraction followed by liquid chromatography with tandem mass spectrometry was the combination of choice and all included parameters were studied. Under optimized conditions for wastewater samples analysis, recoveries from 63 to 108% were obtained, while intraday and interday relative standard deviations never exceeded 20 and 25%, respectively. Limits of detection between 61 and 620 ng/L were achieved. Finally, the optimized method was applied to samples from hospital wastewater effluents.     

Catalytic CO Oxidation by O2 Mediated by Noble‐Metal‐Free Cluster Anions Cu2VO3–5−

Catalytic CO oxidation by molecular O₂ is an important model reaction in both the condensed phase and gas‐phase studies. Available gas‐phase studies indicate that noble metal is indispensable in catalytic CO oxidation by O₂ under thermal collision conditions. Herein, we identified the first example of noble‐metal‐free heteronuclear oxide cluster catalysts, the copper–vanadium bimetallic oxide clusters Cu₂VO_3–5^? for CO oxidation by O₂. The reactions were characterized by mass spectrometry, photoelectron spectroscopy, and density functional calculations. The dynamic nature of the Cu?Cu unit in terms of the electron storage and release is the driving force to promote CO oxidation and O₂ activation during the catalysis.     

Direct Sensing of 5‐Methylcytosine by Polymerase Chain Reaction

The epigenetic control of genes by the methylation of cytosine resulting in 5‐methylcytosine (5mC) has fundamental implications for human development and disease. Analysis of alterations in DNA methylation patterns is an emerging tool for cancer diagnostics and prognostics. Here we report that two thermostable DNA polymerases, namely the DNA polymerase KlenTaq derived from Thermus aquaticus and the KOD DNA polymerase from Thermococcus kodakaraensis, are able to extend 3′‐mismatched primer strands more efficiently from 5 mC than from unmethylated C. This feature was advanced by generating a DNA polymerase mutant with further improved 5mC/C discrimination properties and its successful application in a novel methylation‐specific PCR approach directly from untreated human genomic DNA.     

Study of the Reaction of 5‐Aryl‐7‐hydrazino‐2‐phenylpyra‐zolo[1,5‐c]pyrimidines with 1,3‐Dicarbonyl Compounds

A novel synthetic method for the preparation of 5‐aryl‐7‐(3,5‐dimethyl‐1H‐pyrazol‐1‐yl)‐2‐phenylpyrazolo[1,5‐c]‐pyrimidines and 1‐(5‐aryl‐2‐phenylpyrazolo[1,5‐c]pyrimidin‐7‐yl)‐3‐methyl‐1H‐pyrazol‐5‐ols is provided by condensative cyclization of 5‐aryl‐7‐hydrazino‐2‐phenylpyrazolo[1,5‐c]pyrimidines with 1,3‐dicarbonyl compounds. The study of the more reactive position for electrophilic substitusion reactions on such ring system was also achieved.     

Photofragmentation of 2‐Deoxy‐D‐Ribose Molecules in the Gas Phase

We have measured the synchrotron‐induced photofragmentation of isolated 2‐deoxy‐D ‐ribose molecules (C₅H₁₀O₄) at four photon energies, namely, 23.0, 15.7, 14.6, and 13.8 eV. At all photon energies above the molecule′s ionization threshold we observe the formation of a large variety of molecular cation fragments, including CH₃⁺, OH⁺, H₃O⁺, C₂H₃⁺, C₂H₄⁺, CH_xO⁺ (x=1,2,3), C₂H_xO⁺ (x=1–5), C₃H_xO⁺ (x=3–5), C₂H₄O₂⁺, C₃H_xO₂⁺ (x=1,2,4–6), C₄H₅O₂⁺, C₄H_xO₃⁺ (x=6,7), C₅H₇O₃⁺, and C₅H₈O₃⁺. The formation of these fragments shows a strong propensity of the DNA sugar to dissociate upon absorption of vacuum ultraviolet photons. The yields of particular fragments at various excitation photon energies in the range between 10 and 28 eV are also measured and their appearance thresholds determined. At all photon energies, the most intense relative yield is recorded for the m/q=57 fragment (C₃H₅O⁺), whereas a general intensity decrease is observed for all other fragments— relative to the m/q=57 fragment—with decreasing excitation energy. Thus, bond cleavage depends on the photon energy deposited in the molecule. All fragments up to m/q=75 are observed at all photon energies above their respective threshold values. Most notably, several fragmentation products, for example, CH₃⁺, H₃O⁺, C₂H₄⁺, CH₃O⁺, and C₂H₅O⁺, involve significant bond rearrangements and nuclear motion during the dissociation time. Multibond fragmentation of the sugar moiety in the sugar–phosphate backbone of DNA results in complex strand lesions and, most likely, in subsequent reactions of the neutral or charged fragments with the surrounding DNA molecules.     

Mass spectrometry characterization of 3‐OH butyrated β‐cyclodextrin

Oligo(3‐OH butyrate)‐β‐cyclodextrin esters (PHB‐CD) were obtained through ring opening of β‐butyrolactone (β‐BL) in the presence of β‐cyclodextrin (CD) and (‐)‐sparteine (SP) as nucleophilic activator. The resulted reaction mixture was first separated in two fractions and then investigated through a deep mass spectrometry (MS) study performed on a liquid chromatography‐electrospray ionization‐quadrupole time of flight (LC‐ESI‐QTOF) instrument. LC MS and tandem MS structural assignment of the reaction products was completed by NMR. The performed analysis revealed that poly(3‐OH butyrate) homopolymers (PHB) are formed together with the PHB‐CD products. Secondary reactions resulting in the formation of crotonates were also proved to occur. A comparison between MS and NMR results demonstrated that more than one PHB oligomer is attached to the CD in the PHB‐CD product. The tandem MS fragmentation studies validated the proposed structure of CD derivatives. © 2010 Wiley Periodicals, Inc. J Polym Sci Part A: Polym Chem, 2010     

A robust and rapid liquid chromatography tandem mass spectrometric method for the quantitative analysis of 5‐azacytidine

The DNA methyltransferase inhibitor 5‐azacytidine is being evaluated clinically as an oral formulation to treat various solid tumors. A sensitive, reliable method was developed to quantitate 5‐azacytidine using LC‐MS/MS to perform detailed pharmacokinetic studies. The drug of interest was extracted from plasma using Oasis MCX ion exchange solid‐phase extraction 96‐well plates. Chromatographic separation was achieved with a YMC J'sphere M80 C₁₈ column and isocratic elution with a methanol–water–formic acid (15:85:0.1, v/v/v) mobile phase over a 7 min total analytical run time. An AB Sciex 5500 triple quadrupole mass spectrometer operated in positive electrospray ionization mode was used for the detection of 5‐azacytidine. The assay range was 5–500 ng/mL and proved to be accurate (97.8–109.1%) and precise (CV ≤ 9.8%). Tetrahydrouridine was used to stabilize 5‐azacytidine in blood/plasma samples. With the addition of tetrahydrouridine, long‐term frozen plasma stability for 5‐azacytidine at ?70°C has been determined for at least 323 days. The method was applied for the measurement of total plasma concentrations of 5‐azacytidine in a cancer patient receiving a 300 mg oral daily dose. Copyright © 2015 John Wiley & Sons, Ltd.     

[N⋅⋅⋅I+⋅⋅⋅N] Halogen‐Bonded Dimeric Capsules from Tetrakis(3‐pyridyl)ethylene Cavitands

Two [N???I⁺???N] halogen‐bonded dimeric capsules using tetrakis(3‐pyridyl)ethylene cavitands with different lower rim alkyl chains are synthesized and analyzed in solution and the gas phase. These first examples of symmetrical dimeric capsules making use of the iodonium ion (I⁺) as the main connecting module are characterized by ¹H NMR spectroscopy, diffusion ordered NMR spectroscopy (DOSY), electrospray ionization mass spectrometry (ESI‐MS), and ion mobility‐mass spectrometry (TW‐IMS) experiments. The synthesis and effective halogen‐bonded dimerization proceeds through analogous dimeric capsules with [N???Ag⁺???N] binding motifs as the intermediates as evidenced by the X‐ray structures of (CH₂Cl₂)₂@[ 3 a ₂?Ag₄?(H₂O)₂?OTs₄] and (CH₂Cl₂)₂@[ 3 a ₂?Ag₄?(H₂O)₄?OTs₄], two structurally different capsules.     

Modified Nucleotides for Discrimination between Cytosine and the Epigenetic Marker 5‐Methylcytosine

5‐Methyl‐2′‐deoxycytosine, the most common epigenetic marker of DNA in eukaryotic cells, plays a key role in gene regulation and affects various cellular processes such as development and carcinogenesis. Therefore, the detection of 5mC can serve as an important biomarker for diagnostics. Here we describe that modified dGTP analogues as well as modified primers are able to sense the presence or absence of a single methylation of C, even though this modification does not interfere directly with Watson–Crick nucleobase pairing. By screening several modified nucleotide scaffolds, O⁶‐modified 2′‐deoxyguanosine analogues were identified as discriminating between C and 5mC. These modified nucleotides might find application in site‐specific 5mC detection, for example, through real‐time PCR approaches.     

Noble‐Metal‐Free Single‐Atom Catalysts CuAl4O7–9− for CO Oxidation by O2

The single copper atom doped clusters CuAl₄O_7–9^? can catalyze CO oxidation by O₂. The CuAl₄O_7–9^? clusters are the first group of experimentally identified noble‐metal free single atom catalysts for such a prototypical reaction. The reactions were characterized by mass spectrometry and density functional theory calculations. The CuAl₄O₉CO^? is much more reactive than CuAl₄O₉^? in the reaction with CO to generate CO₂. One adsorbed CO is crucial to stabilize Cu of CuAl₄O₉^? around +I oxidation state and promote the oxidation of another CO. The widely emphasized correlation between the catalytic reactivity of CO oxidation and Cu oxidation state can be understood at the strictly molecular level. The remarkable difference between Cu catalysis and noble‐metal catalysis was discussed.