Cytosine to uracil conversion through hydrolytic deamination of cytidine monophosphate hydroxy‐alkylated on the amino group: a liquid chromatography – electrospray ionization – mass spectrometry investigation

A novel pathway for cytosine to uracil conversion performed in a micellar environment, leading to the generation of uridine monophosphate (UMP), was evidenced during the alkylation reaction of cytidine monophosphate (CMP) by dodecyl epoxide. Liquid chromatography‐electrospray ionization – ion trap ‐ mass spectrometry was used to separate and identify the reaction products and to follow their formation over time. The detection of hydroxy‐amino‐dodecane, concurrently with free UMP, in the reaction mixture suggested that, among the various alkyl‐derivatives formed, CMP alkylated on the amino group of cytosine could undergo tautomerization to an imine and hydrolytic deamination, generating UMP. Interestingly, no evidence for this peculiar conversion pathway was obtained when guanosine monophosphate (GMP), the complementary ribonucleotide of CMP, was also present in the reaction mixture, due to the fact that NH₂‐alkylated CMP was not formed in this case. The last finding emphasized the role played by CMP–GMP molecular interactions, mediated by a micellar environment, in hindering the alkylation reaction at the level of the cytosine amino group. Copyright © 2012 John Wiley & Sons, Ltd.     

2,2‐Bis(ethoxycarbonyl)vinyl (BECV) as a Versatile Amine Protecting Group for Selective Functional‐Group Transformations

A 2,2‐Bis(ethoxycarbonyl) vinyl‐ (BECV) group was used for the selective protection of amines at room temperature in the presence of potentially interfering functional groups such as OH, SH, COOH as well as other NH₂ groups. Several functional group transformations such as esterification, O‐alkylation, O‐acylation, N‐alkylation, N‐acylation, S‐alkylation can selectively be carried out in the presence of the BECV group. The selective deprotection of the BECV group was achieved in a short time using ethylenediamine at room temperature while several other functional groups such as benzoate, aliphatic esters, amides and ethers remain intact. The BECV group shows orthogonal stability against the common protecting groups such as Fmoc, Cbz and Boc.     

Visible‐Light‐Enabled Direct Decarboxylative N‐Alkylation

The development of efficient and selective C?N bond‐forming reactions from abundant feedstock chemicals remains a central theme in organic chemistry owing to the key roles of amines in synthesis, drug discovery, and materials science. Herein, we present a dual catalytic system for the N‐alkylation of diverse aromatic carbocyclic and heterocyclic amines directly with carboxylic acids, by‐passing their preactivation as redox‐active esters. The reaction, which is enabled by visible‐light‐driven, acridine‐catalyzed decarboxylation, provides access to N‐alkylated secondary and tertiary anilines and N‐heterocycles. Additional examples, including double alkylation, the installation of metabolically robust deuterated methyl groups, and tandem ring formation, further demonstrate the potential of the direct decarboxylative alkylation (DDA) reaction.     

Structural Characterization of N‐Alkylated Twisted Amides: Consequences for Amide Bond Resonance and N−C Cleavage

Herein, we describe the first structural characterization of N‐alkylated twisted amides prepared directly by N‐alkylation of the corresponding non‐planar lactams. This study provides the first experimental evidence that N‐alkylation results in a dramatic increase of non‐planarity around the amide N?C(O) bond. Moreover, we report a rare example of a molecular wire supported by the same amide C=O‐Ag bonds. Reactivity studies demonstrate rapid nucleophilic addition to the N?C(O) moiety of N‐alkylated amides, indicating the lack of n_N to π^*_C=O conjugation. Most crucially, we demonstrate that N‐alkylation activates the otherwise unreactive amide bond towards σ N?C cleavage by switchable coordination.     

Pd‐Catalyzed C−H Alkylation of Arenes Using PyrDipSi,a Transformable and Removable Silicon‐Tethered Directing Group

An efficient Pd‐catalyzed ortho‐C?H alkylation reaction of arenes using a transformable and removable Si‐tethered pyridyldiisopropylsilyl (PyrDipSi) directing group has been developed. In addition, the PyrDipSi directing group allows for an efficient sequential double‐fold C?H alkylation/oxygenation of arenes to produce meta‐alkylated phenols. This directing group can easily be removed or converted into valuable functionalities, such as aryl, iodo, boronic ester, or phenol.     

Substituent effects on the Bergman cyclization of (Z)‐1,5‐hexadiyne‐3‐enes: a systematic computational study

The effects of several substituents (? BH₂, ? BF₂, ? AlH₂, ? CH₃, ? C₆H₅, ? CN, ? COCH₃, ? CF₃, ? SiH₃, ? NH₂, ? NH₃⁺, ? NO₂, ? PH₂, ? OH, ? OH₂⁺, ? SH, ? F, ? Cl, ? Br) on the Bergman cyclization of (Z)‐1,5‐hexadiyne‐3‐ene (enediyne, 3 ) were investigated at the Becke–Lee–Yang–Parr (BLYP) density functional (DFT) level employing a 6‐31G* basis set. Some of the substituents (? NH₃⁺, ? NO₂, ? OH, ? OH₂⁺, ? F, ? Cl, ? Br) are able to lower the barrier (up to a minimum of 16.9 kcal mol^?1 for difluoro‐enediyne 7rr ) and the reaction enthalpy (the cyclization is predicted to be exergonic for ? OH₂⁺ and ? F) compared to the parent system giving rise to substituted 1,4‐dehydrobenzenes at physiological temperatures. © 2001 John Wiley & Sons, Inc. J Comput Chem 22: 1605–1614, 2001     

Quantification of peptides using N‐terminal isotope coding and C‐terminal derivatization for sensitive analysis by micro liquid chromatography‐tandem mass spectrometry

Stable isotope‐coding coupled with mass spectrometry is a popular method for quantitative proteomics and peptide quantification. However, the efficiency of the derivatization reaction at a particular functional group, especially in complex structures, can affect accuracy. Here, we present a dual functional‐group derivatization of bioactive peptides followed by micro liquid chromatography‐tandem mass spectrometry (LC‐MS/MS). By separating the sensitivity‐enhancement and isotope‐coding derivatization reactions, suitable chemistries can be chosen. The peptide amino groups were reductively alkylated with acetaldehyde or acetaldehyde‐d₄ to afford N‐alkylated products with different masses. This process is simple, quick and high‐yield, and accurate comparative analysis can be achieved for the mass‐differentiated peptides. Then, the carboxyl groups were derivatized with 1‐(2‐pyrimidinyl)piperazine to increase MS/MS sensitivity. Angiotensins I–IV, bradykinin and neurotensin were analyzed after online solid phase extraction by micro LC‐MS/MS. In all instances, a greater than 17‐fold increase in sensitivity was achieved, compared with the analyses of the underivatized peptides. Furthermore, the values obtained from the present method were in agreement with the result from isotope dilution quantification using isotopically labeled angiotensin I [Asp‐Arg‐(Val‐d₈)‐Tyr‐Ile‐His‐Pro‐(Phe‐d₈)‐His‐Leu]. Copyright © 2016 John Wiley & Sons, Ltd.     

CS‐Fe(II,III) complex as precursor for magnetite nanocrystal

Chitosan‐iron ions complex (CS‐Fe(II,III) complex) was used as precursor to synthesize magnetite nanocrystals and the mechanism was discussed. The magnetite nanocrystals have diameters of about 10 nm and clusters were formed due to slight aggregation of several magnetite nanocrystals. FT‐IR and X‐ray photoelectron spectrometer (XPS) investigations indicated that the Fe(II) and Fe(III) were chelated by ? NH₂ and ? OH groups of chitosan in CS‐Fe(II,III) complex, and the molar ratio of ? NH₂/Fe(II,III) was approximately 2. This chelation effect destroyed the hydrogen bonds of chitosan. In the following alkali treatment process, the chelated Fe(II) and Fe(III) provided nucleation site and formed the magnetite nanocrystals. After alkali treatment, the chelation effect between iron ions and ? NH₂ groups disappeared and some kind of weak interaction formed between magnetite and ? NH₂ groups. Moreover, the ? OH groups of chitosan have an interaction with the synthesized magnetite nanocrystals. Copyright © 2010 John Wiley & Sons, Ltd.     

Gas‐Phase Reaction of Monomethylhydrazine with Ozone: Kinetics and OH Radical Formation

The gas‐phase reaction of monomethylhydrazine (CH₃NH? NH₂; MMH) with ozone was investigated in a flow tube at atmospheric pressure and a temperature of 295 ± 2 K using N₂/O₂ mixtures (3–30 vol% O₂) as the carrier gas. Proton transfer reaction–mass spectrometry (PTR‐MS) and long‐path FT‐IR spectroscopy served as the main analytical techniques. The kinetics of the title reaction was investigated with a relative rate technique yielding k_MMH+O3 = (4.3 ± 1.0) × 10^?15 cm³ molecule^?1 s^?1. Methyldiazene (CH₃N?NH; MeDia) has been identified as the main product in this reaction system as a result of PTR‐MS analysis. The reactivity of MeDia toward ozone was estimated relative to the reaction of MMH with ozone resulting in k_MeDia+O3 = (2.7 ± 1.6) × 10^?15 cm³ molecule^?1 s^?1. OH radicals were followed indirectly by phenol formation from the reaction of OH radicals with benzene. Increasing OH radical yields with increasing MMH conversion have been observed pointing to the importance of secondary processes for OH radical generation. Generally, the detected OH radical yields were definitely smaller than thought so far. The results of this study do not support the mechanism of OH radical formation from the reaction of MMH with ozone as proposed in the literature.     

Direct analysis in real time mass spectrometry (DART‐MS) of highly non‐polar low molecular weight polyisobutylenes

Low molecular weight polyisobutylenes (PIB) with chlorine, olefin and succinic acid end‐groups were studied using direct analysis in real time mass spectrometry (DART‐MS). To facilitate the adduct ion formation under DART conditions, NH₄Cl as an auxiliary reagent was deposited onto the PIB surface. It was found that chlorinated adduct ions of olefin and chlorine telechelic PIBs, i.e. [M + Cl]^? up to m/z 1100, and the deprotonated polyisobutylene succinic acid [M? H]^? were formed as observed in the negative ion mode. In the positive ion mode formation of [M + NH₄]⁺, adduct ions were detected. In the tandem mass (MS/MS) spectra of [M + Cl]^?, product ions were absent, suggesting a simple dissociation of the precursor [M + Cl]^? into a Cl^? ion and a neutral M without fragmentation of the PIB backbones. However, structurally important product ions were produced from the corresponding [M + NH₄]⁺ ions, allowing us to obtain valuable information on the arm‐length distributions of the PIBs containing aromatic initiator moiety. In addition, a model was developed to interpret the oligomer distributions and the number average molecular weights observed in DART‐MS for PIBs and other polymers of low molecular weight. Copyright © 2015 John Wiley & Sons, Ltd.     

Detailed Studies of the Alkylation Sides of Pyridin‐2‐yl and 4,6‐Dimethylpyrimidin‐2‐yl‐cyanamides

Pyridin‐2‐yl‐ and 4,6‐dimethylpyrimidin‐2‐yl‐cyanamides entered into an alkylation reaction in the form of sodium salts. Pyridin‐2‐yl cyanamide 2 was alkylated at endo‐nitrogen atom of pyridine ring, while 4,6‐dimethylpyrimidin‐2‐yl cyanamide 1 was effectively alkylated at exo‐nitrogen atom of amino cyanamide group. The alkylation of cyanamides 1 and 2 with phenacylbromide gave the corresponding acetophenone derivatives. As a result of their intramolecular cyclization reactions 3‐(4,6‐dimethylpyrimidin‐2‐yl)‐5‐phenyloxazol‐2(3H )‐imine in the case of cyanamide 1 and 2‐amino‐3‐benzoylimidazo[1,2‐a ]pyridine in the case of cyanamide 2 were formed. The alkylated derivatives of pyridin‐2‐ylcyanamide 2 possess visible blue fluorescence with the main peak at 421 – 427 nm.     

4‐Vinyl­benzyl analogs of adenine and uracil: reactive monomers for nucleobase polymeric resins

The crystal structures of 9‐(4‐vinyl­benzyl)­adenine, C₁₄H₁₃N₅, and 1‐(4‐vinyl­benzyl)­uracil, C₁₃H₁₂N₂O₂, are composed of zigzag ribbon‐like structures that are stabilized by conventional (N—H?N‐type) hydrogen bonds for the former and conventional (N—H?O‐type) and non‐conventional (C—H?O‐type) hydrogen bonds for the latter; the hydrogen‐bonding patterns are represented by graph‐sets R(9) and R(8), respectively. The adenine and uracil moieties in these alkyl­ated derivatives are planar and are inclined at angles of 84.44 (4) and 79.07 (7)°, respectively, with respect to the phenyl rings.     

Gas‐phase intramolecular hydroxyl‐amino exchange of protonated arginine and verified by the synthetic intermediate compound

A new fragmentation process was proposed to interpret the characteristic product ion at m/z 130 of protonated arginine. The α‐amino group was dissociated from protonated arginine and then combined with the (M + H‐NH₃) fragment to form an ion‐neutral complex which further generated a hydroxyl‐amino exchange intermediate compound through an ion‐molecule reaction. This intermediate compound was synthesized from argininamide through a diazo reaction, and then the reaction mixture was analyzed using liquid chromatography combined with mass spectrometry (LC‐MS). The collision‐induced dissociation experiments under the same conditions revealed that this intermediate compound produced the characteristic product ion at m/z 130 as well as protonated arginine, and in addition, density functional theory calculations were performed to confirm simultaneous loss of NH₃ and CO from this intermediate to give the m/z 130 ion.     

Synthesis of New Furo[2,3‐d]pyrimidines and Pyrimido[4′,5′:4,5]furo[2,3‐d]pyrimidines

Sodium salt of 4‐hydroxy‐6‐methyl‐2‐phenylpyrimidine‐5‐carbonitrile ( 3 ) was subjected to alkylation with different a‐halo compounds, where the corresponding O‐alkylated products 4_a‐g were obtained. Ring closure of the O‐alkylated product 4_a‐c performed using sodium ethoxide in refluxing ethanol afforded furo[2,3‐d]pyrimidines 5_a‐c The latter compounds on reaction with a variety of reagents gave other new furopyrimidines as well as a number of furodipyrimidines.     

Synthesis,Water Adsorption,and Proton Conductivity of Solid‐Solution‐Type Metal–Organic Frameworks Al(OH)(bdc‐OH)x(bdc‐NH2)1−x

Mixed‐ligand metal–organic frameworks Al(bdc‐OH)_x(bdc‐NH₂)_1?x (H₂bdc‐NH₂=aminoterepthalic acid, H₂bdc‐OH=hydroxyterephthalic acid) were synthesized and their water adsorption behavior and proton conductivity were investigated. All obtained compounds were isostructural to MIL‐53 (MIL=Materials of Institut Lavoisier) according to XRD measurements under ambient humidity conditions, and were also found to be single phase across the whole mixing ratio from the XRD measurements under humidified conditions. This result clearly shows that all compounds are a solid‐solution‐type mixture of ligands. MIL‐53‐NH₂ adsorbs one water molecule per formula with humidification whereas MIL‐53‐OH adsorbs five water molecules. The mixing ratio of the ligands in Al(OH)(bdc‐OH)_x(bdc‐NH₂)_1?x affected the gate‐opening pressure for water adsorption and total water uptake. Proton conductivity of these compounds largely depends on the adsorbed amount of water, which indicates that the proton conductivity of these compounds depends strongly on the hydrogen‐bond network of the conducting media.     

NH3‐Driven Benzene C−H Activation with O2 that Opens a New Way for Selective Phenol Synthesis

Catalytic benzene C?H activation toward selective phenol synthesis with O₂ remains a stimulating challenge to be tackled. Phenol is currently produced industrially by the three‐steps cumene process in liquid phase, which is energy‐intensive and not environmentally friendly. Hence, there is a strong demand for an alternative gas‐phase single‐path reaction process. This account documents the pivotal confined single metal ion site platform with a sufficiently large coordination sphere in β zeolite pores, which promotes the unprecedented catalysis for the selective benzene hydroxylation with O₂ under coexisting NH₃ by the new inter‐ligand concerted mechanism. Among alkali and alkaline‐earth metal ions and transition and precious metal ions, single Cs⁺ and Rb⁺ sites with ion diameters >0.300 nm in the β pores exhibited good performances for the direct phenol synthesis in a gas‐phase single‐path reaction process. The single Cs⁺ and Rb⁺ sites that possess neither significant Lewis acidic?basic property nor redox property, cannot activate benzene, O₂, and NH₃, respectively, whereas when they coadsorbed together, the reaction of the inter‐coadsorbates on the single alkali‐metal ion site proceeds concertedly (the inter‐ligand concerted mechanism), bringing about the benzene C?H activation toward phenol synthesis. The NH₃‐driven benzene C?H activation with O₂ was compared to the switchover of the reaction pathways from the deep oxidation to selective oxidation of benzene by coexisting NH₃ on Pt₆ metallic cluster/β and Ni₄O₄ oxide cluster/β. The NH₃‐driven selective oxidation mechanism observed with the Cs⁺/β and Rb⁺/β differs from the traditional redox catalysis (Mars‐van Krevelen) mechanism, simple Langmuir‐Hinshelwood mechanism, and acid?base catalysis mechanism involving clearly defined interaction modes. The present catalysis concept opens a new way for catalytic selective oxidation processes involving direct phenol synthesis.     

Enantioselective Copper‐Catalyzed Alkylation of Quinoline N‐Oxides with Vinylarenes

An asymmetric copper‐catalyzed alkylation of quinoline N ‐oxides with chiral Cu–alkyl species, generated by migratory insertion of a vinylarene into a chiral Cu−H complex, is reported. A variety of quinoline N ‐oxides and vinylarenes underwent this Cu‐catalyzed enantioselective alkylation reaction, affording the corresponding chiral alkylated N‐heteroarenes in high yield with high‐to‐excellent enantioselectivity. This enantioselective protocol represents the first general and practical approach to access a wide range of chiral alkylated quinolines.     

Theoretical study of the ring‐closing reaction of 5′‐AMP to cAMP and H2O in the gas phase

The ring‐closing reaction of 5′‐adenosine monophosphate (5′‐AMP) to generate cyclic 3′, 5′‐adenosine monophosphate (cAMP) and H₂O was theoretically investigated at the B3LYP/6‐31G**level. It was found that the ring‐closing reaction of 5′‐AMP may proceed in a synchronous way or in a stepwise way. For the latter, the reaction is a multichannel elimination reaction including inner H transfer. The potential energy surface of Path 3 is lowest in all the ring‐closing reaction paths. In addition, H shuttling reaction with the participation of a water molecule to act as a shuttle were also studied at the same level. The calculations indicate that the participation of a water molecule facilitates hydrogen transfer reaction. Our present calculations rationalized all the possible reaction channels. © 2005 Wiley Periodicals, Inc. Int J Quantum Chem, 2005     

Elucidation of artefacts in proton transfer reaction time‐of‐flight mass spectrometers

We present an effective procedure to differentiate instrumental artefacts, such as parasitic ions, memory effects, and real trace impurities contained in inert gases. Three different proton transfer reaction mass spectrometers were used in order to identify instrument‐specific parasitic ions. The methodology reveals new nitrogen‐ and metal‐containing ions that up to date have not been reported. The parasitic ion signal was dominated by [N₂]H⁺ and [NH₃]H⁺ rather than by the common ions NO⁺ and O₂⁺. Under dry conditions in a proton transfer reaction quadrupole interface time‐of‐flight mass spectrometer (PTR‐QiTOF), the ion abundances of [N₂]H⁺ were elevated compared with the signals in the presence of humidity. In contrast, the [NH₃]H⁺ ion did not show a clear humidity dependency. On the other hand, two PTR‐TOF1000 instruments showed no significant contribution of the [N₂]H⁺ ion, which supports the idea of [N₂]H⁺ formation in the quadrupole interface of the PTR‐QiTOF. Many new nitrogen‐containing ions were identified, and three different reaction sequences showing a similar reaction mechanism were established. Additionally, several metal‐containing ions, their oxides, and hydroxides were formed in the three PTR instruments. However, their relative ion abundancies were below 0.03% in all cases. Within the series of metal‐containing ions, the highest contribution under dry conditions was assigned to the [Fe(OH)₂]H⁺ ion. Only in one PTR‐TOF1000 the Fe⁺ ion appeared as dominant species compared with the [Fe(OH)₂]H⁺ ion. The present analysis and the resulting database can be used as a tool for the elucidation of artefacts in mass spectra and, especially in cases, where dilution with inert gases play a significant role, preventing misinterpretations.     

Multiple Decay Mechanisms and 2D‐UV Spectroscopic Fingerprints of Singlet Excited Solvated Adenine‐Uracil Monophosphate

The decay channels of singlet excited adenine uracil monophosphate (ApU) in water are studied with CASPT2//CASSCF:MM potential energy calculations and simulation of the 2D‐UV spectroscopic fingerprints with the aim of elucidating the role of the different electronic states of the stacked conformer in the excited state dynamics. The adenine ¹L_a state can decay without a barrier to a conical intersection with the ground state. In contrast, the adenine ¹L_b and uracil S(U) states have minima that are separated from the intersections by sizeable barriers. Depending on the backbone conformation, the CT state can undergo inter‐base hydrogen transfer and decay to the ground state through a conical intersection, or it can yield a long‐lived minimum stabilized by a hydrogen bond between the two ribose rings. This suggests that the ¹L_b, S(U) and CT states of the stacked conformer may all contribute to the experimental lifetimes of 18 and 240 ps. We have also simulated the time evolution of the 2D‐UV spectra and provide the specific fingerprint of each species in a recommended probe window between 25 000 and 38 000 cm^?1 in which decongested, clearly distinguishable spectra can be obtained. This is expected to allow the mechanistic scenarios to be discerned in the near future with the help of the corresponding experiments. Our results reveal the complexity of the photophysics of the relatively small ApU system, and the potential of 2D‐UV spectroscopy to disentangle the photophysics of multichromophoric systems.