OligArch: A software tool to allow artificially expanded genetic information systems (AEGIS) to guide the autonomous self-assembly of long DNA constructs from multiple DNA single strands

• Kevin M. Bradley and
• Steven A. Benner

Beilstein J. Org. Chem. 2014, 10, 1826–1833, doi:10.3762/bjoc.10.192

• with unified entropy and enthalpy values from SantaLucia, et al. [14]. AEGIS bases B and P, both purines able to make 3 hydrogen bonds, are treated as G within Tm calculations, while S and Z, both pyrimidines able to form 3 hydrogen bonds, are treated as C. The exact Tm formula is: where R is the

• intermolecular hybridization, especially at low concentrations of oligonucleotide. Watson–Crick pairing rules follow two rules of complementarity: (a) size complementarity (large purines pair with small pyrimidines) and (b) hydrogen bonding complementarity (hydrogen bond acceptors, A, pair with hydrogen bond

Pyrene-modified PNAs: Stacking interactions and selective excimer emission in PNA₂DNA triplexes

• Alex Manicardi,
• Lucia Guidi,
• Alice Ghidini and
• Roberto Corradini

Beilstein J. Org. Chem. 2014, 10, 1495–1503, doi:10.3762/bjoc.10.154

• is formed, favoured by the prevalence of pyrimidines in the PNA [22][23]. The PNA2DNA triplex, in this sequence, is destabilized by the presence of a pyrimidine base (T) in the 5’-end of the DNA; thus this sequence represents a good model for evaluating the stabilization/destabilization effects due

• objective of stabilizing triplexes even in the presence of pyrimidines on the target sequence, while still maintaining and even increasing sequence selectivity. Moreover, for diagnostics, it is important that a very high and sequence-selective excimer to monomer ratio can be obtained, as with PNA2, upon

Use of activated enol ethers in the synthesis of pyrazoles: reactions with hydrazine and a study of pyrazole tautomerism

• Denisa Tarabová,
• Stanislava Šoralová,
• Martin Breza,
• Marek Fronc,
• Wolfgang Holzer and
• Viktor Milata

Beilstein J. Org. Chem. 2014, 10, 752–760, doi:10.3762/bjoc.10.70

• trifunctional electrophiles and are useful building blocks for the introduction of a three carbon fragment into the resulting molecule. Thus, the reaction of enol ethers with hydrazines produces pyrazoles, with amidines pyrimidines, with hydroxylamine isoxazoles, and with anilines quinolines/ones are formed [2

Copper–phenanthroline catalysts for regioselective synthesis of pyrrolo[3′,4′:3,4]pyrrolo[1,2-a]furoquinolines/phenanthrolines and of pyrrolo[1,2-a]phenanthrolines under mild conditions

• Rupankar Paira,
• Tarique Anwar,
• Maitreyee Banerjee,
• Yogesh P. Bharitkar,
• Shyamal Mondal,
• Sandip Kundu,
• Abhijit Hazra,
• Prakas R. Maulik and
• Nirup B. Mondal

Beilstein J. Org. Chem. 2014, 10, 692–700, doi:10.3762/bjoc.10.62

• summarized in Table 1, revealed the supremacy of copper catalysts in this particular reaction over the others; CuCl2 appeared to be the catalyst of choice (Table 1, entries 8–32). In order to explore the effect of ligands, a number of phosphines, bis-oxazocines, pyrazolyl-pyrimidines and phenanthroline

• , entries 21–28). Bis-oxazocines and pyrazolyl-pyrimidines on the other hand showed some promising results (Table 1, entries 29 and 30). However, both in terms of yield and cleaner reaction profile, 1,10-phenanthrolines (L1, L2) were identified as the best partners for CuCl2 (Table 1, entries 31 and 32

The Flögel-three-component reaction with dicarboxylic acids – an approach to bis(β-alkoxy-β-ketoenamides) for the synthesis of complex pyridine and pyrimidine derivatives

• Mrinal K. Bera,
• Moisés Domínguez,
• Paul Hommes and
• Hans-Ulrich Reissig

Beilstein J. Org. Chem. 2014, 10, 394–404, doi:10.3762/bjoc.10.37

• these enamides to 4-hydroxypyridine derivatives or to functionalized pyrimidines efficiently provided symmetrically and unsymmetrically substituted fairly complex (hetero)aromatic compounds containing up to six conjugated aryl and hetaryl groups. In addition, subsequent functionalizations of the

• . Keywords: alkoxyallenes; condensations; DFT calculations; β-ketoenamides; multi-component reactions; olefin metathesis; pyridines; pyrimidines; Introduction Multicomponent reactions (MCRs) generally allow a diversity-oriented fast and efficient access to complex synthetic intermediates and are thus

• that are remarkably versatile cyclization precursors for the synthesis of functionalized heterocycles such as 4-hydroxypyridines [38][39][40][41][42][43][44], furopyridines [45], 5-acetyloxazoles [46][47], pyrimidines [43][48][49] and their corresponding N-oxides [50] (Scheme 1). This approach

IBD-mediated oxidative cyclization of pyrimidinylhydrazones and concurrent Dimroth rearrangement: Synthesis of [1,2,4]triazolo[1,5-c]pyrimidine derivatives

• Caifei Tang,
• Zhiming Li and
• Quanrui Wang

Beilstein J. Org. Chem. 2013, 9, 2629–2634, doi:10.3762/bjoc.9.298

• derivatives 5a–o. These incipient products undergo feasible Dimroth rearrangement to furnish the isolated [1,2,4]triazolo[1,5-c]pyrimidines 6a–o in moderate to high yields. Keywords: cyclization; hydrazones; hypervalent iodine; oxidation; rearrangement; [1,2,4]triazolo[1,5-c]pyrimidines; Introduction The

• as selective antagonists for human A2A and A3 adenosine receptor sub-types which offer great promise in the treatment of Parkinson’s disease, or as Hsup90 modulators [8]. Clarkson and co-workers have prepared a range of benzothieno-fused 1,2,4-triazolo[4,3-c]pyrimidines and 1,2,4-triazolo[1,5-c

• ]pyrimidines by the oxidative cyclisation of benzothieno[2,3-d]pyrimidine hydrazones. The investigation has also suggested the important ability as inhibitors of Shiga toxin trafficking for protecting HeLa cells [9]. The wide range of biological activities shown by various triazolopyrimidines encouraged

Recent advances in transition metal-catalyzed Csp²-monofluoro-, difluoro-, perfluoromethylation and trifluoromethylthiolation

• Grégory Landelle,
• Armen Panossian,
• Sergiy Pazenok,
• Jean-Pierre Vors and
• Frédéric R. Leroux

Beilstein J. Org. Chem. 2013, 9, 2476–2536, doi:10.3762/bjoc.9.287

• [114] as well as of various arenes and heteroarenes (pyridines, pyrimidines, pyrazines, quinolines, pyrroles, thiophenes, furans, pyrazoles, imidazoles, thiazoles, oxazoles, thiadiazoles, triazoles) [115]. The yields were low to excellent, depending on the substrate (Scheme 12 and Figure 20). Iron(II

An overview of the synthetic routes to the best selling drugs containing 6-membered heterocycles

• Marcus Baumann and
• Ian R. Baxendale

Beilstein J. Org. Chem. 2013, 9, 2265–2319, doi:10.3762/bjoc.9.265

• Dihydropyridines and piperidines Pyrimidines and quinazolines Pyrazines and piperazines Pyridazines and perhydropyridazines Triazines and polyazacyclic systems Synthetic chemistry can rightfully be considered a prerequisite of our modern society [1]. This discipline supplies many valuable resources to our world

• carmegliptin as its HCl salt. 3. Pyrimidines and quinazolines Whilst pyridine rings and their partially or fully saturated derivatives are very frequent components of pharmaceutical species there are also a considerable number of compounds based on diazine and triazine ring systems. Amongst the diazines

• , pyrimidine-derived analogues (1,3-diazines) are the most common. Pyridazines (1,2-diazines) and pyrazines (1,4-diazines) are less prominent. The main reasons are most probably that pyrimidines are highly abundant in important biogenic molecules such as the ribonucleotides and that this heterocycle can be

One-step synthesis of pyridines and dihydropyridines in a continuous flow microwave reactor

• Mark C. Bagley,
• Vincenzo Fusillo,
• Robert L. Jenkins,
• M. Caterina Lubinu and
• Christopher Mason

Beilstein J. Org. Chem. 2013, 9, 1957–1968, doi:10.3762/bjoc.9.232

• that this cyclocondensation proceeds in a similar fashion and high efficiency under microwave irradiation [48], and that we have previously demonstrated that pyridines and pyrimidines can both be formed rapidly and efficiently from ethynyl ketones using microwave dielectric heating, the transfer of

The first example of the Fischer–Hepp type rearrangement in pyrimidines

• Inga Cikotiene,
• Mantas Jonusis and
• Virginija Jakubkiene

Beilstein J. Org. Chem. 2013, 9, 1819–1825, doi:10.3762/bjoc.9.212

• -pyrimidinediamines. It was found that the outcome of the reaction strongly depends on the structure of the pyrimidines. Activation of the pyrimidine ring by three groups with a positive mesomeric effect is crucial for the intramolecular nitroso group migration. Keywords: Fischer–Hepp rearrangement; nitrosation; 5

• -nitrosopyrimidines; nucleophilic substitution; pyrimidinediamines; Introduction The pyrimidine moiety is an important structural motif in natural products and therefore frequently used as a building block for pharmaceutical agents [1][2]. It is well-known that chemical properties of pyrimidines depend on the π

• rebuttal to the article about the electrophilic nitrosation of selected pyrimidines [15]. We showed that instead of the previously reported electrophilic attack of the C-5 by NO+, the secondary amino substituents in position 4 of the pyrimidine ring underwent N-nitrosation reactions (Scheme 2). We also

3-Pyridylnitrene, 2- and 4-pyrimidinylcarbenes, 3-quinolylnitrenes, and 4-quinazolinylcarbenes. Interconversion, ring expansion to diazacycloheptatetraenes, ring opening to nitrile ylides, and ring contraction to cyanopyrroles and cyanoindoles

• Curt Wentrup,
• Nguyen Mong Lan,
• Adelheid Lukosch,
• Pawel Bednarek and
• David Kvaskoff

Beilstein J. Org. Chem. 2013, 9, 743–753, doi:10.3762/bjoc.9.84

• 21 → 20, with free energies of activation of 18–22 kcal/mol in solution, has been demonstrated for 1,2,3-triazolo[1,5-a]pyrimidines [24] but not for 1,2,3-triazolo[1,5-c]pyrimidines [25][26]. However, 7-benzyl-3-ethoxycarbonyl-1,2,3-triazolo[1,5-c]pyrimidin-5-ol and its diazo valence tautomer, 6-(2

• -diazoethoxycarbonylmethylene)-2-(α-hydroxybenzyl)pyrimidin-4-(2H)-one, have been reported [27]. We find that FVT of the 4- and 2-(5-tetrazolyl)pyrimidines 22–24 also affords cyanopyrroles (Scheme 8). FVT of 2-(5-tetrazolyl)pyrimidine (22) affords a ca. 1:1 ratio of 2- and 3-cyanopyrroles (Scheme 8). The results of FVT of

Some aspects of radical chemistry in the assembly of complex molecular architectures

• Béatrice Quiclet-Sire and
• Samir Z. Zard

Beilstein J. Org. Chem. 2013, 9, 557–576, doi:10.3762/bjoc.9.61

• . Synthesis of bicyclic cyclobutane motifs. Construction of the CD rings of steroids. Rapid assembly of polyquinanes. Formation of a polycyclic structure via an allene intermediate. A polycyclic structure via the alkylative Birch reduction. Synthesis of polycyclic pyrimidines and indoline structures

Diarylethene-modified nucleotides for switching optical properties in DNA

• Sebastian Barrois and
• Hans-Achim Wagenknecht

Beilstein J. Org. Chem. 2012, 8, 905–914, doi:10.3762/bjoc.8.103

• reactivity the 5-position of pyrimidines (U/T and C) and the 8-position of purines (A and G) are preferred as chromophore modification sites. The assumption, that these points of attachment allow the chromophores to point into the major groove is only partially true, if at all. In particular, large and

• base pairing. In the case of the pyrimidines the modification at position 5 should not significantly interfere with the preferred anti-conformation of the nucleosidic bond. Thus, the Watson–Crick base pairing of the corresponding modified oligonucleotides should be maintained. Over the past few years

Synthesis and characterization of Sant-75 derivatives as Hedgehog-pathway inhibitors

• Chao Che,
• Song Li,
• Bo Yang,
• Shengchang Xin,
• Zhixiong Yu,
• Taofeng Shao,
• Chuanye Tao,
• Shuo Lin and
• Zhen Yang

Beilstein J. Org. Chem. 2012, 8, 841–849, doi:10.3762/bjoc.8.94

• heterocycles (motif C) and the position of the nitrogen atom in pyridine. As shown in Scheme 6, para-substituted pyridine was first replaced with meta- and ortho-pyridine, and other heterocycles, including pyrimidines and five-membered heteroaryl rings, as well as nonaromatic heterocycles, such as morpholine

Chemistry of polyhalogenated nitrobutadienes, 10: Synthesis of highly functionalized heterocycles with a rigid 6-amino-3-azabicyclo[3.1.0]hexane moiety

• Viktor A. Zapol’skii,
• Jan C. Namyslo,
• Armin de Meijere and
• Dieter E. Kaufmann

Beilstein J. Org. Chem. 2012, 8, 621–628, doi:10.3762/bjoc.8.69

• substitution. Therefore, upon treatment with the azabicyclohexane 1 under mild conditions (methanol, rt) the enamine 24 was formed in 86% yield (Scheme 6). Similar pyrido[1,2-a]pyrimidines show antiviral [29], antithrombotic [30] and antibacterial [31][32][33][34] activities. Alternatively, conversion of bis

Synthesis, solid-state fluorescence properties, and computational analysis of novel 2-aminobenzo[4,5]thieno[3,2-d]pyrimidine 5,5-dioxides

• Kenichirou Yokota,
• Masayori Hagimori,
• Naoko Mizuyama,
• Yasuhisa Nishimura,
• Hiroshi Fujito,
• Yasuhiro Shigemitsu and
• Yoshinori Tominaga

Beilstein J. Org. Chem. 2012, 8, 266–274, doi:10.3762/bjoc.8.28

• the π–π-electron conjugated system in the sulfonyl group of benzothienopyrimidine 5,5-dioxide is stronger than that of the carbonyl group of the indeno pyrimidines. Benzo[4,5]thieno[3,2-d]pyrimidine derivative 6 and benzo[4,5]furo[3,2-d]pyrimidine derivative 7 showed different emission properties from

Regioselectivity in the multicomponent reaction of 5-aminopyrazoles, cyclic 1,3-diketones and dimethylformamide dimethylacetal under controlled microwave heating

• Kamal Usef Sadek,
• Ramadan Ahmed Mekheimer,
• Tahany Mahmoud Mohamed,
• Moustafa Sherief Moustafa and
• Mohamed Hilmy Elnagdi

Beilstein J. Org. Chem. 2012, 8, 18–24, doi:10.3762/bjoc.8.3

• pyrazoloquinolinones (Hantzsch-type dihydropyridines). On the other hand, the use of sonication at room temperature under neutral conditions favours the formation of isomeric pyrazolo[5,1-b]quinazolin-8(4H)-ones (Biginelli-type dihydro-pyrimidines) [9]. Employing more nucleophilic bases to catalyse the reaction

Synthesis of diverse dihydropyrimidine-related scaffolds by fluorous benzaldehyde-based Biginelli reaction and post-condensation modifications

• Bruno Piqani and
• Wei Zhang

Beilstein J. Org. Chem. 2011, 7, 1294–1298, doi:10.3762/bjoc.7.150

• with four boronic acids yielded 5-biaryl-5H-thiazolo[3,2-a]pyrimidines 6a–h in 55–64% yields after F-SPE and flash chromatography purifications (Table 2). Dihydropyrimidinethione 4f was used for the Liebeskind–Srogl coupling reaction with a phenylboronic acid to convert to 2-aryl-1,6-dihydropyrimidine

Functionalization of heterocyclic compounds using polyfunctional magnesium and zinc reagents

• Paul Knochel,
• Matthias A. Schade,
• Sebastian Bernhardt,
• Georg Manolikakes,
• Albrecht Metzger,
• Fabian M. Piller,
• Christoph J. Rohbogner and
• Marc Mosrin

Beilstein J. Org. Chem. 2011, 7, 1261–1277, doi:10.3762/bjoc.7.147

• pyrimidines and purines are very important for the design of antiviral agents. The amination of this class of heterocycles is of particular importance. Recently, we developed an oxidative amination procedure for lithium derivatives using chloranil as oxidation agent [43]. We applied this procedure in the

• using TMPMgCl·LiCl (41) or TMP2Mg·2LiCl (129) The directed magnesiation of aromatic substrates using TMPMgCl·LiCl (41) constitutes an economical preparation of a range of functionalized arylmagnesium compounds [25][26]. Sensitive heterocycles such as pyrimidines can be readily magnesiated with

Synthesis, reactivity and biological activity of 5-alkoxymethyluracil analogues

• Lucie Brulikova and
• Jan Hlavac

Beilstein J. Org. Chem. 2011, 7, 678–698, doi:10.3762/bjoc.7.80

• efficient synthetic route for the preparation of ethoxy-substituted 5-(perfluoroalkyl)pyrimidines (Scheme 10) and investigated their regioselective transformations [18]. Some of these fluorine-containing pyrimidine analogues are potent antitumor and antiviral agents. The reported synthesis started with the

• treatment of 5-bromo-2,4-diethoxypyrimidine (65) with either perfluorobutyl or perfluorohexyl iodide in the presence of activated copper bronze in DMSO. This reaction afforded 5-(perfluoroalkyl)pyrimidines 66 and 67 in high yields. Subsequent acid hydrolysis of 66 and 67 provided 5-(perfluoroalkyl

• )pyrimidines 68 and 69. The latter readily underwent nucleophilic attack by alkoxide ions to yield alicyclic or cyclic acetals 70–73 and 74, respectively, depending on the alcohol used. Uridine and arabinofuranosyl analogues: 5-Substituted uracil nucleosides where the sugar component is ribose or arabinose

An overview of the key routes to the best selling 5-membered ring heterocyclic pharmaceuticals

• Marcus Baumann,
• Ian R. Baxendale,
• Steven V. Ley and
• Nikzad Nikbin

Beilstein J. Org. Chem. 2011, 7, 442–495, doi:10.3762/bjoc.7.57

C–C (alkynylation) vs C–O (ether) bond formation under Pd/C–Cu catalysis: synthesis and pharmacological evaluation of 4-alkynylthieno[2,3-d]pyrimidines

• Dhilli Rao Gorja,
• K. Shiva Kumar,
• K. Mukkanti and
• Manojit Pal

Beilstein J. Org. Chem. 2011, 7, 338–345, doi:10.3762/bjoc.7.44

• /C–CuI–PPh3 catalytic system facilitated C–C bond formation between 4-chlorothieno[2,3-d]pyrimidines and terminal alkynes in methanol with high selectivity without generating any significant side products arising from C–O bond formation between the chloro compounds and methanol. A variety of novel 4

• -alkynylthieno[2,3- d]pyrimidines were prepared via alkynylation of 4-chlorothieno[2,3-d]pyrimidines in good to excellent yields. Some of the compounds synthesized were tested for cytotoxic activity in vitro. Keywords: catalysis; C–C bond; copper; palladium; thieno[2,3-d]pyrimidine; Introduction Alkynyl

• substituted pyrimidines are of considerable pharmacological interest because of their notable biological activities [1], in particular, adenosine kinase inhibitory activity in the treatment of pain and inflammatory diseases [2] and thymidylate synthase inhibitory properties in cancer therapy [3]. On the other

Approaches towards the synthesis of 5-aminopyrazoles

• Ranjana Aggarwal,
• Vinod Kumar,
• Rajiv Kumar and
• Shiv P. Singh

Beilstein J. Org. Chem. 2011, 7, 179–197, doi:10.3762/bjoc.7.25

• -dielectrophiles has been extensively used for the preparation of bicyclic nitrogen heterocycles, especially in the preparation of condensed heterocycles such as pyrazolo[3,4-d]pyrimidines, pyrazolo[3,4-b]pyridines, imidazopyrazoles etc. In view of significant interest in the synthesis of these heterocyclics, we

Synthesis of some novel hydrazono acyclic nucleoside analogues

• Mohammad N. Soltani Rad,
• Ali Khalafi-Nezhad and
• Somayeh Behrouz

Beilstein J. Org. Chem. 2010, 6, No. 49, doi:10.3762/bjoc.6.49

• ], hereby, we wish to report the synthesis of some novel hydrazono acyclic nucleosides having similar scaffolds to the miconazole framework. In these compounds, the nucleobases including pyrimidines, purines and other azole derivatives were substituted as heterocyclic cores and the ether bond in miconazole

• . This proved to be the case, and the corresponding ketones 1h–1o could not be obtained satisfactorily by this method. The main limitation of using the aforementioned pathway for purines and pyrimidines is their low solubility in acetonitrile, which results in low yields of the corresponding ketones 1h

Synthesis of some novel annulated pyrido[2,3-d]pyrimidines via stereoselective intramolecular hetero Diels–Alder reactions of 1-oxa-1,3-butadienes

• Mohit L. Deb and
• Pulak J. Bhuyan

Beilstein J. Org. Chem. 2010, 6, No. 11, doi:10.3762/bjoc.6.11

• Mohit L. Deb Pulak J. Bhuyan Medicinal Chemistry Division, North East Institute of Science & Technology, Jorhat 785006, Assam, India, Fax: 0376 2370011 10.3762/bjoc.6.11 Abstract Some novel annulated pyrido[2,3-d]pyrimidines 6 and 7 were synthesized stereoselectively by intramolecular hetero

• Diels–Alder reactions involving 1-oxa-1,3-butadienes. Keywords: β-halo aldehydes; hetero Diels–Alder reaction; 1-oxa-1,3-butadiene; pyrido[2,3-d]pyrimidines; uracil; Introduction The importance of uracil and its annulated derivatives is well recognized by synthetic as well as biological chemists [1][2

• ][3][4][5][6][7][8]. Pyrido[2,3-d]pyrimidines represent a broad class of annelated uracils which have received considerable attention over the past years due to their wide range of biological activities such as antibacterial [9][10], antitumor [11][12], cardiotonic [13][14], hepatoprotective [13