Chalcogen functionalized pyrimidine synthesis by three-component free radical chalcogenation and pyrimidine ring construction

Jingfeng Ye a, Gengxin Li a, Changfeng Wan a and Jie-Ping Wan *ab
aJiangxi Province Key Laboratory of Natural and Biomimetic Drugs Research, College of Chemistry and Materials, Jiangxi Normal University, Nanchang 330022, China. E-mail: wanjieping@jxnu.edu.cn
bInternational Innovation Center for Forest Chemicals and Materials, Nanjing Forestry University, Nanjing 210037, China

Received 22nd August 2025 , Accepted 7th October 2025

First published on 8th October 2025


Abstract

A rather facile transition metal-free protocol for the synthesis of chalcogen functionalized pyrimidines has been established via three-component reactions of enaminones, disulfides/diselenide, and amidines/guanidine. The reactions proceed efficiently in the presence of I2/KOH and smoothly provide chalcogenated pyrimidines with a broad substrate scope. The reaction mechanism involves a key chalcogen (sulfur)-centered free radical, which has been verified by control experiments.


Introduction

The pyrimidine ring represents a fundamental heterocyclic moiety and is a key structural motif in a number of functional molecules, including pharmaceuticals, agrochemicals and natural products.1 For example (Scheme 1A), vitamin B1 exhibits notable anti-fungal and anti-inflammatory activities.2 Alamifovir, which features a sulfenylated pyrimidine backbone, is a clinical drug for the treatment of HBV.3 Recent research studies have also disclosed a wide range of additional bioactivities and functions of pyrimidine derivatives.4 Therefore, the synthesis of pyrimidines continues to attract extensive interest.5 For achieving the synthesis of pyrimidines from readily available materials, a plethora of methods have been investigated and established. Representative examples include the annulation of 1,3-dicarbonyl compounds6 or enals7 with amidines or related surrogates, the annulation of ketones with amines and C1 synthons,8 the annulation with organo cyanides,9 the Au-catalyzed annulation of alkynyl alcohols with 3-amino-benzo[d]isoxazoles,10 the annulation of amidines with alcohols11 or alkene building blocks,12 the transannulation reactions of chromones,13 and the cyclization of amidines with other less conventional partners,14 all of which have been demonstrated to be applicable tools for the synthesis of pyrimidines with diverse substructures.
image file: d5qo01206f-s1.tif
Scheme 1 Typical backgrounds.

Despite the notable advances in pyrimidine synthesis, challenges remain in this area, including the reliance on noble metal catalysts and the need for harsh conditions and oxidants. In particular, the synthesis of functionalized pyrimidines by combining ring construction and functional group installation remains rather challenging. For instance, although enaminones have been proven to be valuable building blocks for pyrimidine synthesis,15 the synthesis of functionalized pyrimidines, such as sulfur-group functionalized pyrimidines, has not been successful via one-step reactions. Instead, pre-functionalization of enaminones to enable C–H thiolation is required before pyrimidine annulation in known methods (Scheme 1B).16 In this context, developing new methods that enable cascade functionalization and pyrimidine ring formation via a one-step operation is highly desirable, as it would expand the structural diversity and application scope of pyrimidine scaffolds.17 Herein, we present a one-step protocol for the synthesis of 5-chalcogenated pyrimidines via three-component reactions of enaminones, amidine/guanidine salts and disulfides/diselenide. In the presence of KOH and molecular iodine, the products were synthesized efficiently with a broad substrate scope via a free radical pathway without using any transition metal reagent,18 exhibiting both novelty and sustainability and providing a facile route to access these S/Se-functionalized pyrimidines (Scheme 1C).

Results and discussion

Initially, the reaction of enaminone 1a, disulfide 2a and guanidine salt 3a was performed under different conditions for optimization (Table 1). It was first found that the presence of molecular iodine and K2CO3 in DMSO enabled the formation of product 4a in 43% yield upon heating at 80 °C (entry 1). Subsequent screening of reaction media showed that DMSO was most favourable (entries 2–4). While a base was indispensable, KOH was found to be capable of promoting the formation of 4a, resulting in a much higher yield (entries 5–8). Afterwards, the reaction was also performed in the presence of different iodine reagents, which implied that electrophilic iodine reagents were also suitable (entries 9–12). A loading of 50 mol% of iodine gave a further improved yield (entries 13 and 14), and increasing the loading of the base was also beneficial (entries 15 and 16). Altering the temperature, on the other hand, did not give a better result (entries 17 and 18). A parallel experiment using thiophenol as the alternative substrate to 2a gave product 4a with 88% yield (entry 19).
Table 1 Optimization of reaction conditionsa

image file: d5qo01206f-u1.tif

Entry Iodine source Base Solvent Yieldb (%)
a Conditions: 1a (0.2 mmol), 2a (0.12 mmol), 3a (0.4 mmol), iodine source (0.2 mmol), base (0.4 mmol), solvent (2 mL), stirred at 80 °C for 14 h. b Isolated yield. c I2 (0.06 mmol). d I2 (0.1 mmol). e Base (0.6 mmol). f Base (0.8 mmol). g At 60 °C. h At 100 °C. i PhSH (0.24 mmol) was used as an alternative to 2a.
1 I2 K2CO3 DMSO 43
2 I2 K2CO3 Dioxane 12
3 I2 K2CO3 DMF 40
4 I2 K2CO3 MeOH 35
5 I2 DMSO nr
6 I2 DABCO DMSO Trace
7 I2 KOH DMSO 64
8 I2 t BuOK DMSO 26
9 KOH DMSO nr
10 KI KOH DMSO nr
11 NIS KOH DMSO 12
12 PIDA KOH DMSO nr
13c I2 KOH DMSO 52
14d I2 KOH DMSO 75
15d,e I2 KOH DMSO 90
16d,f I2 KOH DMSO 85
17d,e,g I2 KOH DMSO 80
18d,e,h I2 KOH DMSO 84
19d,e,i I2 KOH DMSO 88


Following the results of the optimization experiments, the scope of the current method was examined. First, the scope of enaminones was investigated (Scheme 2). Enaminones with various functionalized benzoyl (4a–4l and 4v), heteroaroyl (4m–4o), and fused aroyl (4p and 4q) groups were all well tolerated. Substrates with strong electron-withdrawing groups on the aryl ring (4f, 4j and 4l) displayed lower reactivity, affording products in lower yields. Meanwhile, highly electron-rich arylated substrates also gave lower product yields, likely due to more number of side reactions (4m–4o and 4v). Notably, the extension of the method to the synthesis of 4-alkyl, 4-unsubstituted, and 4-vinyl pyrimidines could be efficiently achieved by using the corresponding enamine substrates. An even more significant fact was that the enaminones derived from functional molecules and natural products such as adamantine, α-ionone and pregnenolone were smoothly transformed into the pyrimidine derivatives 4w–4y. When an enaminone with a β-methyl group was used, the corresponding fully substituted pyrimidine 4z was obtained in 48% yield. The results in this section indicated the general application scope of enaminone substrates for the synthesis of the desired pyrimidines.


image file: d5qo01206f-s2.tif
Scheme 2 Scope of enaminones (a[thin space (1/6-em)]yield from a 5 mmol scale reaction).

Subsequently, the reactions of various disulfides and their chalcogen analogs, and the extension of the substrate scope from guanidine to amidines were investigated (Scheme 3). As expected, reactions using different diaryl disulfides afforded the corresponding products in good to excellent yields (4aa–4af). The pyridinylthiolated pyrimidine 4ag could be accessed in a moderate yield through the reaction with dipyridinyl disulfide. The electron-withdrawing nature of the aryl group in the disulfide reduced the efficiency of the corresponding product formation (4ag). Remarkably, the current method tolerated various dialkyl disulfides, affording the corresponding 5-alkylthiolated products 4ah–4aj in yields that were slightly lower than those obtained using equivalent thiophenols. A rather important point was that the 5-selenylated product 4ak could be synthesized via the reaction of diphenyl diselenide under the current conditions. Finally, amidines featuring alkyl or aryl groups at the C-site were proven to be practical substrates for the synthesis of 2-alkyl/aryl pyrimidines (4al and 4am). As an extended effort, reactions using an NH2-based enaminone and dibenzyl diselenide as substrates were conducted under the standard conditions. However, neither of the two substrates was compatible for the synthesis of the desired compound (Scheme 3).


image file: d5qo01206f-s3.tif
Scheme 3 Scope of disulfide/diselenide and amidine.

Furthermore, the synthetic applicability of the sulfenylated pyrimidines 4 was studied by carrying out different transformations on 4a (Scheme 4). Subjecting 4a to oxidation with mCPBA enabled the formation of the corresponding sulfinyl and sulfonyl pyrimidines 5 and 6 at room temperature via varying the oxidant loading and reaction time. In addition, treatment with NIS and NaNO2 in DMF led to the synthesis of 2-iodopyrimidine 7via a formal substitution. Finally, the reaction of benzyl chloride with 4a led to dibenzoyl protected amino pyrimidine 8 under air conditions, promoted by triethyl amine (Scheme 4).


image file: d5qo01206f-s4.tif
Scheme 4 Transformation of compound 4a.

Control experiments aimed at exploring the reaction mechanism were conducted from two different perspectives. The first involved a reaction sequence test. The pre-synthesized sulfenyl enaminone 9 was reacted with guanidine 3a, and pyridine 10 was reacted with disulfide 2a, both the reactions were performed under the standard conditions. The former afforded 4a in an excellent yield, and the latter did not give 4a, confirming that sulfenylation took place before pyrimidine ring formation (Scheme 5A). Later, the model reaction was performed in the presence of typical free radical trappers (FRTs) such as 2,2,6,6-tetramethylpiperidoxyl (TEMPO), butylated hydroxytoluene (BHT) and 1,1-diphenylethylene (DPE). While all these entries show evident inhibition of product formation, the free radical adduct 11 resulting from the reaction between the sulfur-centered radial and DPE was detected via GC-MS, confirming that the generation of the sulfur-centered radical was a key step in the reaction. Additionally, when the reaction was conducted in the presence of DPE without adding iodine, neither product 4a nor adduct 11 was formed, indicating that molecular iodine was crucial for free radical generation (Scheme 5B).


image file: d5qo01206f-s5.tif
Scheme 5 Control experiments.

Based on the insights from the control experiments, a possible reaction mechanism is proposed (Scheme 6). First, the typical reaction of disulfide with iodine takes place to afford phenyl hypoiodothioite A, which upon heating undergoes homolytic cleavage to afford the sulfur-centered free radical B and iodine radical. The addition of B to enaminone leads to intermediate C, which quickly couples with the iodine radical to provide intermediate D. The subsequent β-elimination of HI from D affords the sulfenyl enaminone 9. Meanwhile, the interaction of the base with the guanidine salt gives free guanidine E. Through a typical transamination between guanidine and the amino group in 9, intermediate G is formed, which undergoes intramolecular condensation to yield product 4via intermediate H.


image file: d5qo01206f-s6.tif
Scheme 6 The plausible reaction mechanism.

In summary, by using simple starting materials of enaminones, disulfides/diselenide, and guanidine/amidines, we have developed a facile three-component method for the synthesis of 5-chalcogenated pyrimidines featuring diverse substitutions in the heterocycle. Without employing any transition metal reagent, the reactions proceed via a free radical pathway, enabling the synthesis of the desired product with a broad substrate scope and generally satisfactory yield. This method could be useful for the synthesis of sulfenyl/selenyl pyrimidines and their derivatives due to the simple starting materials and operation.

Conflicts of interest

There are no conflicts to declare.

Data availability

The data supporting this article have been included as part of the supplementary information (SI). Supplementary information: general experimental information, synthetic procedures, characterization data and NMR spectra. See DOI: https://doi.org/10.1039/d5qo01206f.

CCDC 2473846 contains the supplementary crystallographic data for this paper.19

Acknowledgements

This work was supported by the National Natural Science Foundation of China (22561026 and 22161022).

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  17. During the preparation of our manuscript, Guo and Zheng et al. reported the synthesis of 5-sulfenylated/selenylated pyrimidines by enaminone-based three-component reactions employing thio/seleno-benzenesulfonates as the sulfenyl/selenyl source via a fully ionic cascade transformation: Z. Zhang, Y. Wang, X. Hua, C. Zheng, P. Chen, Y. Lin, X. Zhu, L. Zheng and W. Guo, One-pot three-component cascade strategy for the site-selective synthesis of 5-sulfenylated/selenylated 2,4-disubstituted pyrimidines, Org. Lett., 2025, 27, 7247–7252 CrossRef CAS.
  18. For selected recent works, see: (a) Z. Wang, L. Gan, Z. Song, Y. Liu and J.-P. Wan, tBuOK/TMSOK-mediated “alkyl halide to alkyl free radical” transformation for transition-metal-free benzoin α-C–H alkylation, Chin. J. Chem., 2024, 42, 3041–3046 CrossRef CAS; (b) C. Wang, Y. Liu and J.-P. Wan, Construction of fused oxacyclic compounds via dual α- and β-C–H functionalization and ring decomposition of cyclic ethers, Org. Lett., 2025, 27, 3983–3987 CrossRef CAS PubMed; (c) W.-T. Ouyang, J. Jiang, Y.-F. Jiang, T. Li, Y.-Y. Liu, H.-T. Ji, L.-J. Ou and W.-M. He, Sono-photocatalytic amination of quinoxalin-2(1H)-ones with aliphatic amines, Chin. Chem. Lett., 2024, 35, 110038 CrossRef CAS; (d) J.-Z. Li, L. Mei, X.-E. Cai, C.-C. Zhang, T.-T. Cao, X.-J. Huang, Y.-L. Liu and W.-T. Wei, Transition-metal-free radical cyclization of 2-arylbenzoimidazoles with unactivated alkanes via C(sp3)–H functionalizations in aqueous media, Adv. Synth. Catal., 2022, 364, 2080–2085 CrossRef CAS; (e) P. Xiang, K. Sun, S. Wang, X. Chen, L. Qu and B. Yu, Direct benzylation reactions from benzyl halides enabled by transition-metal-free photocatalysis, Chin. Chem. Lett., 2022, 33, 5074–5079 CrossRef CAS; (f) X. Wang, S. Guo, Y. Zhang, Z. Zhang, G. Zhang, Y. Ye and K. Sun, Metal-free organoselenium-enabled radical relay azidation-carbocyclization, Adv. Synth. Catal., 2021, 363, 3290–3296 CrossRef CAS; (g) G. Guo, X. Li, J. Ma, Y. Shi, J. Lv and D. Yang, Chin. Chem. Lett., 2024, 35, 110024 CrossRef CAS; (h) Y. Lv, J. Hao, J. Huang, L. Song, H. Yue, W. Wei and D. Yi, Metal-free visible-light-mediated aerobic nitrooxylation for the synthesis of nitrate esters with t-BuONO, Chem. Commun., 2024, 60, 9801–9804 RSC; (i) H. Guo, Y. Liu and J.-P. Wan, Electrochemical cascade pyrazole annulation and C–H halogenation for the synthesis of 4-halopyrazoles, Green Synth. Catal., 2025, 6, 206–210 CAS; (j) M. Cabrera-Afonso, A. Jaafar, C. Cristóbal, J. Adrio and M. Ribagorda, Visible-light-promoted synthesis of 1,6-imino alcohols by metal-free 1,2-carboimination of alkenes, Org. Lett., 2025, 27, 2346–2351 CrossRef CAS PubMed.
  19. CCDC 2473846: Experimental Crystal Structure Determination, 2025,  DOI:10.5517/ccdc.csd.cc2p17hh.

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