Victor V Dotsenko1,2,3, Alexander V Bespalov1, Arthur S Vashurin3, Nicolai A Aksenov2, Inna V Aksenova2, Elena A Chigorina4,5, Sergey G Krivokolysko1. 1. Kuban State University, Department of Chemistry & High Technologies, 149 Stavropolskaya st., Krasnodar 350040, Russian Federation. 2. North Caucasus Federal University, Department of Organic Chemistry, 1 Pushkina st., Stavropol 355009, Russian Federation. 3. Ivanovo State University of Chemistry and Technology, Department of Inorganic Chemistry, 7 Sheremetievskiy Avenue, Ivanovo 153000, Russian Federation. 4. NRC "Kurchatov Institute", 1 Akademika Kurchatova pl., Moscow 123182, Russian Federation. 5. National Research Center "Kurchatov Institute"-IREA, 3 Bogorodsky Val, Moscow 107076, Russian Federation.
Abstract
trans-2-Amino-4-aryl-5-benzoyl-4,5-dihydrothiophene-3-carbonitriles were prepared either by the reaction of 3-aryl-2-cyanothioacrylamides with α-thiocyanatoacetophenone or by the Michael-type addition of cyanothioacetamide to α-bromochalcones followed by intramolecular cyclization. The mechanism of the first reaction was studied using high-level quantum chemical calculations. Density functional theory (DFT) studies were carried out to determine the mechanism of the first reaction. A new approach toward the construction of the thieno[2,3-d]pyrimidine core system was demonstrated by the reaction of the prepared dihydrothiophenes with HCHO and RNH2 under noncatalyzed Mannich conditions.
trans-2-Amino-4-aryl-5-benzoyl-4,5-dihydrothiophene-3-carbonitriles were prepared either by the reaction of 3-aryl-2-cyanothioacrylamides with α-thiocyanatoacetophenone or by the Michael-type addition of cyanothioacetamide to α-bromochalcones followed by intramolecular cyclization. The mechanism of the first reaction was studied using high-level quantum chemical calculations. Density functional theory (DFT) studies were carried out to determine the mechanism of the first reaction. A new approach toward the construction of the thieno[2,3-d]pyrimidine core system was demonstrated by the reaction of the prepared dihydrothiophenes with HCHO and RNH2 under noncatalyzed Mannich conditions.
2-Aminothiophenes
and related molecules are of particular interest,
especially within the realm of medicinal chemistry (for reviews, see
refs (1−7)). Many of the compounds based on the 2-aminothiophene structural
motif show a broad range of biological properties and were recognized
as potent pan-serotype dengue virus inhibitors,[8] antitubercular agents,[9−11] allosteric modulators
of the A1 adenosine receptor (A1R),[12] antiproliferative agents,[13,14] antimicrobials,[15] inhibitors of influenza virus polymerase,[16] GluR6-antagonists,[17] and protein-tyrosine phosphatase 1B (PTP1B) inhibitors[18] (Figure ). Some 2-aminothiophenes are traded drugs and were subjected
to extensive pharmacological studies. Among them, strontium ranelate
(Protelos/Osseor, useful for the treatment of osteoporosis,[19−25] as a dental pulp-like cell proliferation agent,[26] and as a radiopaque agent for calcium phosphate cement[27]), tinoridine (old but still useful anti-inflammatory
drug with a strong antiperoxidative and hepatoprotective activity),[28−30] and olanzapine[31−33] (Zyprexa, used to treat certain mental disorders
such as schizophrenia and bipolar disorder) should be noted (Figure ). In addition, the
2-aminothiophene motif is present in drugs and bioactive molecules
such as T-62 (a selective allosteric modulator of the adenosine A
receptor),[34] bentazepam (Tiadipona),[35] and brotizolam (Lendormin);[36−38] anxiolytic/anticonvulsant
agents and skeletal muscle relaxants; and the anticancer drug raltitrexed
(Tomudex)[39−41] (Figure ). 2-Aminothiophenes are able to act as starting points for
the synthesis of a variety of thiophene-containing heterocycles and
polycyclic hybrid molecules.[3−6,42] Moreover, as shown
recently, 2-aminothiophenes might find an application in the preparation
of functional materials such as electrochemically color switching
azomethines,[43−46] liquid crystalline materials,[47] oligothiophene-BODIPY
hybrids as NIR dyes,[48] organic photovoltaic
cells,[49] azodyes,[50] nonlinear optical materials,[51] and azomethine-bridged
polythiopheneferrocenes.[52]
Figure 1
Selected biologically
active 2-aminothiophenes.
Selected biologically
active 2-aminothiophenes.Such a diversity of available structures and applications is due
to the synthetic availability of 2-aminothiophenes. The most widely
used synthetic approach toward 2-aminothiophenes is based on the Gewald
reaction of methylene active nitriles with elemental sulfur and methylene
active ketones/aldehydes.[1−6] However, this approach provides an access to aromatic 2-aminothiophenes
only. Less is known on the chemistry of partially saturated analogs
such as 2-amino-4,5-dihydrothiophenes (ADHTs). In general, 2,3(4,5)-dihydrothiophenes
have a rich synthetic application, and dihydrothiophene ring systems
have been incorporated into a variety of biologically active molecules
(for reviews, see refs (53, 54)). For instance, ADHT 1 (Figure ) was reported as a moderately active microbicide
and fungicide,[55] ADHT-thiazoline hybrids 2 showed good anticancer activity against colon carcinoma
(HCT-116),[56] and benzofurane-ADHT hybrid 3 showed an antinociceptive effect.[57] Some esters of ADHT-3-carboxylic acids 4 were recognized
as specific inhibitors of malaria agent Plasmodium
falciparum dihydroorotate dehydrogenase.[58]
Figure 2
Biologically active compounds featuring an ADHT scaffold.
Biologically active compounds featuring an ADHT scaffold.However, the available methods for the synthesis
of ADHTs are somewhat
limited and the studies are somewhat hampered by the lack of common
practical procedures and by the narrow scope of useful substrates.
ADHTs can be prepared (Scheme ) by the reaction of γ-haloacetoacetic acid derivatives
with isothiocyanates,[58,59] treatment of Michael adducts
prepared from cyanoacetic esters and chalcone with elemental sulfur,[60] recyclization of thiiranes,[61,62] diastereoselective cycloadditions of aminothioisomünchnones
with chiral 1,2-diaza-1,3-butadienes,[63] condensation of S-acetylmercaptosuccinic anhydride
with methyl cyanoacetate,[64] reaction of
cyanothioacetamide with β-nitrostyrene,[65] reductive recyclization of functionalized thiazolidinones,[66] and cyclocondensation of benzoylpyruvate with
PhNCS[67] or β-ketothioamides with
oxalyl chloride.[68] Very recently, the organotin-catalyzed
reaction of arylmethylene malononitriles with α-mercaptoketones
was reported to produce ADHTs as a mixture of diastereomers.[69] Most of the reported procedures either require
the use of expensive/exotic reagents and harsh reaction conditions
or are accompanied by the formation of side products. The domino reaction
of 1,3-thiazolidinedione, active methylene nitriles, amines, and aromatic
aldehydes[70−75] demonstrates a common approach to functionalized ADHTs. Another
useful approach leading to trans-4,5-disubstituted
ADHT-3-carbonitriles is the reaction of 2-cyanothioacrylamide 5 with pyridinium[55,57,76,77] or sulfonium[76,78,79] ylides. However, the ylide method suffers
from some drawbacks such as the temperature-dependent cyclopropane
or pyridine byproduct formation,[80] elimination
of foul-smelling dimethyl sulfide, and relatively low atom economy.
Recent approaches consist of the Lewis acid catalyzed recyclizations
of donor–acceptor cyclopropanes upon treatment with NH4SCN,[81] thiourea,[82] or tetrathiomolybdates[83−85] (Scheme ). These reactions are also not free from
disadvantages such as long reaction times and difficult-to-obtain
starting materials and catalysts. Given the practical significance
of 2-aminothiophenes and ADHTs, the search for conceptually new rational
methodologies for their synthesis, as well as an extension of the
range, is of particular importance.
Scheme 1
The Reported Methods
for the Preparation of ADHTs
Earlier, we reported[86] the unusual synthesis
of highly functionalized ADHTs 6 as a mixture of trans
isomers based on the tertiary base catalyzed reaction of α-thiocyanato
acetophenone 7 with aldehydes and cyanothioacetamide 8 (or with 3-aryl-2-cyanothioacrylamides 5) (Scheme ).
Scheme 2
Different Approaches
toward the Synthesis of ADHTs 6
Despite the availability of the starting reagents and low-cost,
easy-to-handle synthesis, the reported procedures give only moderate
(up to 54%) yields. In addition, the reaction mechanism still remains
unclear. Herein, we report two modified superior procedures for the
synthesis of ADHTs 6 affording higher yields across the
range of substrates (Scheme ). Also, we present the detailed quantum-chemical study to
indicate the reaction mechanism. In addition, we also report the Mannich-type
double aminomethylation reactions of ADHTs 6, providing
an efficient approach to the synthesis of new functionalized thieno[2,3-d]pyrimidines 11.
Results and Discussion
To optimize the procedure for
the preparation of ADHTs 6, we used 2-chlorobenzaldehyde/furfural,
α-thiocyanatoacetophenone 7,[87] and cyanothioacetamide 8(88) as the model reagents and examined
the effect of catalyst and conditions (Scheme ). We found that the use of 10% aq KOH instead
of tertiary amines[86] dramatically shortened
the reaction time to within 1–2 min. However, it had no effect
on the yields as the target product 6a was isolated in
only a modest yield of 37% (Table , entry 1). Similarly, product 6b was
prepared in 37% yield from furfural (Scheme and Table , entry 5). The use of pre-prepared Knoevenagel products 5a,b had no advantages over the three-component approach since
the yields were only slightly improved (38–40%; Table , entries 7 and 13). Potassium
carbonate showed much better results as a catalyst to afford yields
of ADHTs 6a,b up to 70% (Table , entries 2, 3, 8, 9, 14, and 15).
Scheme 3
Synthesis
of ADHTs 6a–d
Table 1
Optimization of the Conditions for
the Synthesis of ADHTs 6a–d (Scheme )a
entry
reagents
conditions
product (yield,
%)
1
2-ClC6H4CHO, 7, 8
10% aq KOH, rt
6a (37)
2
2-ClC6H4CHO, 7, 8
10% aq K2CO3, 40–50
°C
6a (64)
3
2-ClC6H4CHO, 7, 8
10% aq K2CO3, rt
6a (60)
4
2-ClC6H4CHO, 7, 8
10% aqNa2CO3, 40–50
°C
6a (68)
5
furfural, 7, 8
10% aq KOH, rt
6b (37)
6
furfural, 7, 8
10% aqNa2CO3, 40–50 °C
6b (62)
7
5a, 7
10% aq KOH, rt
6a (38)
8
5a, 7
10% aq K2CO3, rt
6a (61)
9
5a, 7
10% aq K2CO3, 40–50 °C
6a (70)
10
5a, 7
10% aq K2CO3, reflux
6a (31)
11
5a, 7
10% aq Na2CO3, rt
6a (57)
12
5a, 7
10% aqNa2CO3, 40–50
°C
6a (74)
13
5b, 7
10% aq KOH, rt
6b (40)
14
5b, 7
10% aq K2CO3, rt
6b (56)
15
5b, 7
10% aq K2CO3, 40–50 °C
6b (62)
16
5b, 7
10% aq Na2CO3,
rt
6b (58)
17
5b, 7
10% aq Na2CO3, 40–50 °C
6b (63)
18
5c, 7
10% aq Na2CO3, 40–50 °C
6c (67)
19
2-C3H4S-CHO, 7, 8
10% aq Na2CO3, 40–50
°C
6c (69)
20
PhCHO, 7, 8
10% aq Na2CO3, 40–50 °C
6d (64)
Entries
1–6, 19, and 20:
molar ratio aldehyde/7/8 = 1:1:1, EtOH.
Entries 7–18: molar ratio 5/7 = 1:1,
EtOH.
Entries
1–6, 19, and 20:
molar ratio aldehyde/7/8 = 1:1:1, EtOH.
Entries 7–18: molar ratio 5/7 = 1:1,
EtOH.Finally, the best
yields (62–74%) were achieved when aq
Na2CO3 was taken as a catalyst and the reaction
was conducted at 40–50 °C (Table , entries 4, 6, 12, and 17–20). As
we found (see the discussion on the quantum-chemical calculations
of the mechanism below), one of the possible reaction pathways include
the Michael-type addition of phenacylthiocyanate 7 to
thioacrylamide 5 followed by the intramolecular SN2 substitution of the SCN group.Inspired by this, here
we proposed a new approach to ADHTs 6 based on the tandem
Michael addition–intramolecular
SN2 substitution of thioamide 8 to easily
available[89] α-bromochalcones 9a,d (Scheme ).
Scheme 4
Preparation of ADHTs 6 from α-Bromochalcones 9
Optimization of the reaction
of 8 with 9d showed that the yields of ADHTs 6 strongly depend on
the reaction conditions and the base used (Table ). The lowest yield of 6d was
observed when the mixture of thioamide 8 and bromochalcone 9d was treated with excessive Et3N at 25 °C
(Table , entry 1).
The best results were achieved when the reaction mixture was gently
refluxed with KOH (1 equiv) for 0.5 h (Table , entry 5). Compound 9a gave
similar results (Table , entry 6).
Table 2
The Reaction Conditions and the Yields
for the Synthesis of ADHTs 6a,d from α-Bromochalcones 9 and Cyanothioacetamide 8 (Scheme )
entry
reagentsa
conditions
product (yield,
%)
1
8, 9d
Et3N (1.5 equiv),
EtOH, rt, 6 days
6d (25)
2
8, 9d
Et3N 1.5 equiv,
EtOH, reflux
6d (46)
3
8, 9d
K2CO3, EtOH, 40–50 °C
6d (42)
4
8, 9d
Na2CO3, EtOH, 40–50
°C
6d (37)
5
8, 9d
KOH (1 equiv),
EtOH, reflux
6d (61)
6
8, 9a
KOH (1 equiv), EtOH, reflux
6a (57)
Molar ratio 8/9 = 1:1.
Molar ratio 8/9 = 1:1.
Quantum-Chemical
Calculations of the Mechanism of the Reaction
of 5 and 7
A quantum-chemical study
of possible mechanisms of the reaction between thioacrylamides 5 and α-thiocyanatoacetophenone 7 was performed
using the ORCA 5.0.1 software package.[90−92] The search for the transition
state, determination of reaction routes, and calculation of vibrational
frequencies and Gibbs free energy were performed using DFT and the
new Grimme composite approach r2SCAN-3c.[93] This approach is a combination of r2SCAN functional
with mTZVPP basis, including atom-pairwise dispersion correction based
on tight binding partial charges D4[94] and
geometrical counterpoise correction gCP.[95] The found geometry of transition states was confirmed by the presence
of an imaginary vibrational frequency corresponding to the reaction
coordinate. All the calculations were performed with the correction
for the influence of nonspecific solvation (EtOH) using the CPCM model.[96] We used the Gabedit 2.5 software[97] to generate the input files and the ChemCraft
1.8 software[98] to visualize the molecular
geometry and vibrational frequencies.At a first glance at the
overall reaction, it seems likely that the first step is the formation
of the Michael adducts 10 (Scheme ). However, further intramolecular cyclization
of the Michael adducts 10 can proceed by two different
mechanisms (Scheme , pathways A and B). In the first case (pathway A), one-step intramolecular
nucleophilic substitution of the thiocyanate group at the carbon atom
(C1) by the sulfur atom (S14) can occur. The literature data on the
nucleofugality of pseudohalide NCS– anion are rather
scarce, though some substitution reactions with thiocyanate as a leaving
group were reported.[99−106] It is likely that trans stereochemistry of the target ADHTs 6 should be determined at the formation of the Michael adducts 10 since bulky benzoyl and (het)aryl substituents would occupy
a sterically favorable trans relationship. Therefore, two enantiomeric
pairs of the Michael adducts 10A,10B and 10C,10D (Scheme ) with an anti-periplanar orientation of (het)aryl and benzoyl groups
appear to be the most stable.
Scheme 5
Possible Mechanisms of the Formation
and Stereochemistry of ADHTs 6
In the second case (pathway B), a four-stage process is assumed,
including the nucleophilic addition of the carbon atom (C3) to the
nitrile fragment (C6-N7) of the thiocyanate group followed by the
transfer of a proton from the nitrogen atom (N13) to the nitrogen
atom (N7) and by the elimination of HNCS and transfer of the second
proton from nitrogen atom (N13) to nitrogen atom (N7). Arguments in
favor of the pathway B involving the nucleophilic attack of a carbanion
on the carbon atom of the SCN group come from numerous examples of
the reactions of organic thiocyanates with active methylene compounds.[87,107]To determine the most plausible mechanism, a quantum-chemical
study
of the reaction trajectories was carried out. Molecular geometries
and Gibbs energies for intermediates and transition states were calculated.The optimized molecular structures of most stable conformations,
all transition states, and intermediates are shown in Figures –6, and the calculated
energy diagrams are shown in Figure . Since the starting anionic intermediate 10 contains two asymmetric carbon atoms (C1 and C2), it can exist as
four diastereomers or two enantiomeric pairs: R,S/S,R and S,S/R,R. Using S,S- and R,S-structures,
we have calculated possible reaction pathways for each diastereomeric
channel. A preliminary conformational analysis was performed for the
studied isomers, and the most stable conformations R1 (for the S,S-isomer) and R2 (for the R,S-isomer) were found (Figure ). It is noteworthy that the difference in
energy between the most stable conformations of these isomers is extremely
small (less than 1.5 kJ/mol; the R,S-isomer is more
stable).
Figure 3
The most stable conformations R1 (for the S,S-isomer) and R2 (for the R,S-isomer).
Geometry optimized at the r2SCAN-3c level.
Figure 6
The optimized molecular
structures of intermediates formed during
the thiophene ring formation through the addition–elimination
mechanism starting from S,S- (I1.1, I1.2, I1.3) and R,S-isomers
(I2.1, I2.2, I2.3) (geometry
optimized at the r2SCAN-3c level).
Figure 7
Energy
diagrams of the proposed cyclization mechanisms: intramolecular
nucleophilic substitution of thiocyanate anion (S,S/R,R-diastereomeric channel, pathway A) or nucleophilic
addition at the SCN nitrile fragment with subsequent elimination of
thiocyanate anion (R,S/S,R-diastereomeric
channel, pathway B). The calculated Gibbs energies are given relative
to the energy of the most stable conformation of the S,S-isomer (R1).
The most stable conformations R1 (for the S,S-isomer) and R2 (for the R,S-isomer).
Geometry optimized at the r2SCAN-3c level.The optimized molecular structures of SN transition
states (TS) for S,S-(TS1c, TS1) and R,S-isomers (TS2c, TS2) (geometry optimized at the r2SCAN-3c
level).The optimized molecular structures of transition
states formed
during the thiophene ring formation through the addition–elimination
mechanism starting from S,S- (TS1.1, TS1.2, TS1.3, TS1.4) and R,S-isomers (TS2.1, TS2.2, TS2.3, TS2.4) (geometry optimized at the r2SCAN-3c level).The optimized molecular
structures of intermediates formed during
the thiophene ring formation through the addition–elimination
mechanism starting from S,S- (I1.1, I1.2, I1.3) and R,S-isomers
(I2.1, I2.2, I2.3) (geometry
optimized at the r2SCAN-3c level).Energy
diagrams of the proposed cyclization mechanisms: intramolecular
nucleophilic substitution of thiocyanate anion (S,S/R,R-diastereomeric channel, pathway A) or nucleophilic
addition at the SCN nitrile fragment with subsequent elimination of
thiocyanate anion (R,S/S,R-diastereomeric
channel, pathway B). The calculated Gibbs energies are given relative
to the energy of the most stable conformation of the S,S-isomer (R1).First, proper conformational changes of the intermediate 10 are required for successful intramolecular nucleophilic
substitution since S14, C1, and S4 atoms should occupy suitable relative
positions in the molecule to permit a nucleophilic attack. The rotation
barrier around the C1–C2 bond was calculated as 31.8 kJ/mol
for the S,S-isomer and 34.0 kJ/mol for the R,S-isomer. The transition states of the indicated conformational
changes (TS1c and TS2c) and the processes
of subsequent nucleophilic substitution (TS1 and TS2) are shown in Figure .
Figure 4
The optimized molecular structures of SN transition
states (TS) for S,S-(TS1c, TS1) and R,S-isomers (TS2c, TS2) (geometry optimized at the r2SCAN-3c
level).
As a result of calculations, it was found that
intramolecular nucleophilic
substitution (pathway A, Scheme ) can be realized successfully only in the S,S/R,R-diastereomeric channel. In the R,S-isomer, S14, C1, and S4 atoms cannot occupy a configuration
suitable for the SN2 process due to spatial difficulties
caused by the bulky benzoyl group that prevents the sulfur S14 from
approaching the C1 carbon from the rear side. Thereby, the process
of synchronous substitution is disrupted, which leads to a sharp increase
in the activation energy up to 298.8 kJ/mol. At the same time, the
calculated activation energy of nucleophilic substitution for the S,S-isomer is even slightly lower (27.9 kJ/mol) than that
of the previous conformational transition.As for the alternative
mechanism (pathway B, Scheme ), the entire process can be presented as
a sequence of the following four steps (the optimized molecular structures
of transition states are shown in Figure ):
Figure 5
The optimized molecular structures of transition
states formed
during the thiophene ring formation through the addition–elimination
mechanism starting from S,S- (TS1.1, TS1.2, TS1.3, TS1.4) and R,S-isomers (TS2.1, TS2.2, TS2.3, TS2.4) (geometry optimized at the r2SCAN-3c level).
Nucleophilic addition of C3 atom to
C6 atom of the SCN group through the formation of transition states TS1.1 (for the S,S-isomer) and TS2.1 (for the R,S-isomer), leading to the closure of
the thiophene ring and the formation of anionic intermediates I1.1 and I2.1. According to the calculated data,
the activation energy of this process is 54.5 kJ/mol for the S,S-isomer and 46.6 kJ/mol for the R,S-isomer. It should be noted that the process does not require preliminary
conformational changes and can be realized directly from the most
stable conformers R1 and R2.Transfer of H28 proton from N13 nitrogen
atom to N7 atom with the formation of transition states TS1.2 (for the S,S-isomer) and TS2.2 (for
the R,S-isomer) with the formation of intermediate
products I1.2 and I2.2.The elimination of HNCS with the cleavage
of the C3–C10 bond. This stage has the highest activation energy
(63.4 kJ/mol for the S,S-isomer and 77.2 kJ/mol for
the R,S-isomer) and therefore should be considered
as the rate-limiting step.Transfer of the second proton H29 from
N13 atom of the HNCS molecule to N7 atom with the formation of transition
states TS1.4 (for the S,S-isomer) and TS2.4 (for the R,S-isomer), leading to the
formation of final dihydrothiophenes 6.Overall, the reaction of thioacrylamides 5 with α-thiocyanatoacetophenone 7 can proceed
through the cyclization of the Michael adducts 10 by
two alternative pathways: intramolecular SN2 substitution
of the SCN group (pathway A, Scheme ) and nucleophilic addition/elimination of
HNCS sequence (pathway B, Scheme ). For S,S/R,R-diastereomers,
both variants are possible, but nucleophilic substitution (pathway
A) seems to be more likely due to the lower activation energy. Moreover,
from the stereochemical point of view, the intramolecular nucleophilic
substitution for the S,S-isomer should lead to the
formation of trans isomers of 6, while the realization
of the alternative addition–elimination process should give
only cis isomers that were not observed experimentally. In contrast,
the intramolecular SN2 reaction cannot be realized with R,S/S,R-diastereomers of 10 due to steric hindrance. Therefore, in this case, cyclization can
proceed only through the addition–elimination mechanism (pathway
B) with the formation of trans isomers of dihydrothiophenes 6. The calculations performed are thus consistent with the
experimental results pointing to the formation of trans isomers of
dihydrothiophenes 6.
The Noncatalyzed Aminomethylation
of ADHTs Leading to Thieno[2,3-d]pyrimidines
Thieno[2,3-d]pyrimidines
are purine bioisosteres coming to the
center of interest due to their high structural diversity and well-documented
spectrum of biological activity (for reviews, see refs (108−115)). Much less is known on the preparation and reactions of partially
saturated thieno[2,3-d]pyrimidines.[116−120] To study the reactivity of the prepared
ADHTs 6 under Mannich conditions, their behavior upon
treatment with a series of primary amines and HCHO was examined here.We found that ADHTs 6 react with RNH2 and
excessive HCHO resulted in double aminomethylation to afford new 2,3,4,4a,5,6-hexahydrothieno[2,3-d]pyrimidines 11 (Scheme ). To optimize the reaction conditions, p-toluidine
and ADHT 6b were chosen as model reagents. We found that
EtOH was a superior solvent compared to DMF, MeOH, or i-PrOH (Table , entries
1–2 and 4–5). This is probably connected with the better
solubility of either products or starting ADHTs 6 in
a solvent. However, the use of DMF or DMF–EtOH mixtures as
solvents is also effective in the case of less soluble ADHT 6a. Doubling the amount of the amine component did not affect
the yields of product 11e (Table , entry 3).
Scheme 6
The Aminomethylation
of ADHTS 6
Table 3
Optimization of the Conditions for
the Synthesis of Thienopyrimidines 11
entry
reagentsa
conditions
product (yield,
%)
1
6b, 4-MeC6H4NH2 (1.05
equiv)
EtOH, reflux
11e (69)
2
6b, 4-MeC6H4NH2 (1.05 equiv)
DMF, reflux
11e (44)
3
6b, 4-MeC6H4NH2 (2 equiv)
DMF, reflux
11e (43)
4
6b, 4-MeC6H4NH2 (1.05 equiv)
MeOH, reflux
11e (63)
5
6b, 4-MeC6H4NH2 (1.05 equiv)
i-PrOH,
reflux
11e (61)
At least 10-fold excess of aq 37%
HCHO used in each entry.
At least 10-fold excess of aq 37%
HCHO used in each entry.With the optimized conditions, good yields (60–86%) of new
2,3,4,4a,5,6-hexahydrothieno[2,3-d]pyrimidines 11a–l were achieved (Scheme and Figure ). Also,
when p-phenylenediamine was reacted with 2 equiv
of ADHT 6d and excessive HCHO, polycyclic compound 12 was isolated in 48% yield. It is noteworthy that the reaction
required no catalysts. It should be noted that ADHTs 6 play here an unusual role of 1,3-dinucleophilic β-enaminonitrile
species. In general, the Mannich-type reactions of β-enaminocarbonyls
and related enamines with HCHO and primary amines leading to tetrahydropyrimidines
are well known;[121−134] however, as far as we know, no cyclic enaminonitriles were reported
as substrates in the Mannich reaction prior to our studies.
Figure 8
The scope and
yields of products 11.
The scope and
yields of products 11.The structure of the products was supported by IR, 1H
NMR, 13C APT NMR, HPLC–MS, and elemental analysis.1H NMR spectra of compounds 11,12 revealed the
presence of signals of the =NCH2NCH2–
fragment: two doublets (or AB-quartet) of methylene protons C(4)H2 at δ 2.87–3.69 and δ 3.03–4.20
ppm (2J = 11.4–12.6 Hz) and two
doublets (or AB-quartet) of methylene protons C(2)H2 at
δ 4.05–4.79 ppm and δ 4.50–5.37 ppm (2J = 16.7–17.4 Hz). The doublet of
C(5)H was observed at δ 4.04–4.64 ppm, and C(6)H appeared
as doublet at δ 5.97–6.38 ppm (3J = 10.4–10.9 Hz). The IR spectra of compounds 11,12 revealed the absence of absorption bands of NH2 and conjugated
C≡N groups. Instead, a weak band appears at ν 2235–2245
cm–1 (nonconjugated C≡N). The absorption
bands corresponding to the vibrations of C=O and C=N
groups are found at ν 1680–1690 and 1647–1664
cm–1. In addition, the structure of compound 11l was confirmed by X-ray studies (Figure ).
Figure 9
The structure of compound 11l according
to X-ray data.
Thermal ellipsoids of nonhydrogen atoms are shown at the 30% probability
level.
The structure of compound 11l according
to X-ray data.
Thermal ellipsoids of nonhydrogen atoms are shown at the 30% probability
level.The independent part of the unit
cell contains two molecules of
compound 11l: A and B with
a close conformation. The tetrahydropyrimidine ring has a distorted half-chair conformation with an almost planar fragment C6-N2-C4-C3
(torsion angle 4.7(3)° in molecule 11l-A and 3.2(3)°
in molecule 11l-B). Atoms N1 and C5 deviate from this
plane by 0.243(4) and −0.516(4) Å (molecule 11l-A) and by 0.276(4) and −0.496(4) Å (molecule 11l-B). The tetrahydrothiophene ring is in the twist conformation
with the deviation of the C2 and C3 atoms from the plane of the rest
of the ring atoms by −0.469(4) and 0.250(4) Å (11l-A) and by −0.258(4) and 0.396(4) Å (11l-B). The nitrogen atom N1 has a pyramidal configuration; the sum of
the bond angles centered on the atom is 344.7° (11l-A) or 349.8° (11l-B). The substituents at C1, C2,
and N1 atoms have an equatorial orientation (torsion angles C4-S1-C1-C7
139.98(15)° (11l-A) and 131.00(15)° (11l-B), S1-C1-C2-C14 −172.61(14)° (11l-A) and −163.25(14)° (11l-B), and N2-C6-N1-C21
178.98(18)° (11l-A) and 169.30(17)° (11l-B)). The nitrile group is in the axial position (torsion
angle N2-C4-C3-C20–101.5(2)° (11l-A) and
−100.4(2)° (11l-B)). Molecules 11l-A and 11l-B differ in the orientation of the phenyl substituent
at the N1 atom, which is in the –ac conformation
in molecule 11l-A and in the –sc conformation in molecule 11l-B relative to the idealized
position of the lone pair (Lp) of electrons of the nitrogen atom (torsion
angle C22-C21-N2-Lp(N1) −122° (11l-A) and
−61° (11l-B)). The rotation of the substituent
is facilitated by the repulsion between hydrogen atoms in the ortho
positions (shortened intramolecular contacts H26...H6a 2.19 Å
(11l-A) and 2.23 Å (11l-B), and H22...H5a
2.17 Å (11l-A, 11l-B) (sum of van der
Waals radii 2.32 Å[135])). The molecule
also contains shortened intramolecular contacts between the hydrogen
atom at C1 and hydrogen atoms in the ortho positions of the phenyl
substituents at C2 and C7 (H1...H9 2.22 Å (11l-A) and 2.13 Å (11l-B), and H1...H15 2.29 Å
(11l-A) and 2.24 Å (11l-B)).Crystals of compound 11l consist of alternating layers
of molecules 11l-A and 11l-B parallel to
the plane (0 0 1). In this case, layers 11l-A and 11l-A have different structures. A common feature of molecules 11l-A and 11l-B is the formation of centrosymmetric
dimers due to hydrogen bonds between the carbonyl group and methylene
hydrogen atoms (C5-H5a...O1i [i: −x, 1 – y, 1 – z] (H...O
2.31 Å, C–H...O 152°) in layer A and
C6-H6b...O1ii [ii: 1 – x, 1 – y, −z] (H...O 2.45 Å, C–H...O
141°)). Also in layer A, molecules are linked by
hydrogen bonds C16-H16...N3ii [ii: 1 – x, −y, 1 – z] (H...N
2.58 Å, C–H...N 136°) and C–H...π contacts
C6-H6b...C11iii [iii: −1 + x, y, z] (H...C 2.89 Å, C–H...C
135°) and C12-H12...C16iv [iv: 1 – x, 1 – y, 1 – z] (H...C 2.89 Å, C–H...C 158°). In layer B, the molecules are linked by intermolecular hydrogen bonds C1-H1...N3v [v: 2 – x, 1 – y, −z] (H...N 2.53 Å, C–H...N
158°) and C9-H9...N3v (H...N 2.52 Å, C–H...N
157°) and C–H...π contacts C13-H13...C26ii (H...C 2.87 Å, C–H...C 179°), C26-H26...C10vi [vi: −1 + x, 1 + y, z] (H...C 2.87 Å, C–H...C 154°),
and C6-H6b...C24vii [vii: 1 – x, 2 – y, −z] (H...C
2.78 Å, C–H...C 133°).The copies of IR and
NMR spectra as well as LCMS and X-ray data
for new compounds are given in the Supporting Information.
Conclusions
In summary, we have optimized synthetic
procedures for the preparation
of highly functionalized, useful building blocks, trans-2-amino-4-aryl-5-benzoyl-4,5-dihydrothiophene-3-carbonitriles 6 (ADHTs), starting from easily available α-thiocyanatoacetophenone 7 and cyanothioacetamide 8. The reaction mechanism
was studied on the r2SCAN-3c level of theory. The reaction
of α-thiocyanatoacetophenone 7 with 3-aryl-2-cyanothioacrylamides 5 proceeds through the formation of the corresponding Michael
adduct that undergoes further cyclization. The cyclization can proceed
by two different mechanisms: by intramolecular SN2 substitution
of the SCN group (only for S,S/R,R-diastereomers of the Michael adduct 10) or through
intramolecular nucleophilic addition to the SCN carbon atom followed
by elimination of the HNCS molecule (only for S,R/R,S-diastereomers of the Michael adduct 10), as it was supported by quantum chemical calculations performed
on the r2SCAN-3c level of theory.In addition, a
new approach for the preparation of ADHTs 6 was developed,
starting from cyanothioacetamide 8 and available α-bromochalcones 9. We have also
demonstrated that a small library of new 2,3,4,4a,5,6-hexahydrothieno[2,3-d]pyrimidine-4a-carbonitriles 11 could be synthesized by noncatalyzed double Mannich-type
cyclization, starting from ADHTs 6, primary amines, and
aq HCHO. The work demonstrates a new approach to the formation of
pharmacologically interesting thieno[2,3-d]pyrimidines. The procedure
has certain advantages such as mild reaction conditions, short reaction
time, and a diversity of useful starting building blocks and provides
pure target products in good yields. All the reported procedures preclude
volatile, foul smelling, or toxic solvents or byproducts. The formation
of both starting ADHTs 6 and thieno[2,3-d]pyrimidines 11 proceeds in an atom-economical way with a broad substrate
scope under metal-free conditions.
Experimental Section
Solvents and starting reagents were purified according to common
procedures. Melting points were determined on a Kofler hot stage and
reported uncorrected. IR spectra were recorded on an IKS-29 spectrometer
in Nujol mulls or a Thermo Nicolet Avatar 370 FT-IR spectrometer in
KBr pellets. 1H and 13C NMR spectra were recorded
on a Bruker DRX-500 (500.13 MHz for 1H and 125.74 MHz for 13C) or Bruker DPX-400 (400.40 MHz for 1H) spectrometer
at room temperature in DMSO-d6. Chemical
shifts are given in parts per million (ppm) with reference to TMS
or to the residual solvent signals; coupling constants are given in
Hz; and multiplicities are given as s (singlet), d (doublet), dd (doublet
of doublets), m (multiplet), and br (broad). LC–MS data were
obtained using the LC–MS system consisting of the high-performance
liquid chromatograph Agilent 1100 equipped with diode-matrix and mass-selective
detector Agilent LC/MSD SL (APCI ionization in positive and negative
modes) and on a PE SCIEX API 150EX mass spectrometer following separation
on a Shimadzu LC-10 AD liquid chromatography system equipped with
a Shimadzu SP D-10AUV–vis detector (254 nm) and Sedex 75 ELSD
detector (ES-API ionization). The elemental analysis (C, H, N) was
performed using a Carlo Erba Strumentazione 1106 analyzer. The analytical
results were within ±0.4% of the theoretical values. Thin-layer
chromatography (TLC) was performed on Silufol UV-254 plates using
EtOAc, EtOAc–hexane, or acetone–hexane 1:1 mixture as
eluents; the spots were visualized with iodine vapors, UV light, or
KMnO4–H2SO4 solution. Cyanothioacetamide 8 was prepared by bubbling H2S gas through a malononitrile
solution in EtOH containing a catalytic amount of Et3N
at 10–15 °C for 6–8 h.[136] 3-Aryl-2-cyanothioacrylamides 5 were prepared by the
Knoevenagel condensation of cyanothioacetamide 8 with
aromatic aldehydes in the presence of catalytic amounts of Et3N (EtOH, 20 °C).[137] α-Bromochalcones 9a,d were prepared by dehydrobromination of the corresponding
chalcone dibromide.[138,139]α-Thiocyanatoacetophenone
7 was prepared as
follows: the mixture of α-bromoacetophenone (23.5 g, 0.118 mol)
and dry KSCN (12.6 g, 0.13 mol) in anhydrous acetone (70 mL) was boiled
under vigorous stirring for 1 h and evaporated to one-half of the
volume. The slurry obtained was cooled to 25 °C and treated with
50 mL of cold water. The precipitate formed was filtered off and washed
with water and twice with cold 40% aq EtOH to give 20.6 g (98.5%)
of thiocyanate 7 as colorless crystals, mp 74–75
°C [lit.:[140] 72.5–73.5 °C].
General
Procedures for the Synthesis of 2-Amino-5-benzoyl-4-(het)aryl-4,5-dihydrothiophene-3-carbonitriles
(6)
A. KOH-Catalyzed Reaction of Aldehydes, Cyanothioacetamide 8, and Phenacyl Thiocyanate 7 (Table , Entries 1 and 5)
To a suspension of 0.5 g (5 mmol) of cyanothioacetamide 8 in 20 mL of EtOH, 5 mmol of the corresponding aldehyde and one drop
of 10% aq KOH were successively added with stirring. The mixture was
stirred for 0.5 h, and then 0.89 g (5 mmol) of α-thiocyanatoketone 7 and an excess (4 mL) of 10% aq KOH were added. The mixture
was stirred for 0.5 h, diluted with water (10 mL), and then kept for
0.5 h at 25 °C. The precipitate of dihydrothiophenes 6a or 6b was filtered off and purified by recrystallization
from EtOH–acetone.
B. KOH-Catalyzed Reaction of Thioacrylamides 5a,b and Phenacyl Thiocyanate 7 (Table , Entries 7 and 13)
To a suspension
of 2.5 mmol of α,β-unsaturated thioamide 5a,b (0.55 g of 5a or 0.45 g of 5b) and 0.44
g (2.5 mmol) of α-thiocyanatoketone 7 in 10 mL
of EtOH, an excess (2.0 mL) of 10% aq KOH was added dropwise with
vigorous stirring. The mixture immediately turned red, and the starting
reagents dissolved. The reaction mixture quickly turned yellow, and
a yellow solid precipitated within 30–60 s. The mixture was
stirred for 0.5 h, diluted with 5 mL of water, and then allowed to
stand for another 0.5 h. The precipitate was filtered off, washed
with water and cold EtOH, and recrystallized from EtOH–acetone.
The yields were 323 mg (38%, 6a) and 300 mg (40%, 6b).
C. Na2CO3-Catalyzed
Reaction of Thioacrylamides 5a–c and
Phenacyl Thiocyanate 7 (Table , Entries
12, 17, and 18)
To a suspension of 2.25 mmol of unsaturated
thioamides 5a–c and 400 mg (2.26
mmol) of α-thiocyanatoketone 7 in 10 mL of alcohol,
2.4 mL of 10% aq Na2CO3 solution was added with
stirring (Na2CO3 partially precipitated). The
reaction mixture was stirred under gentle heating (40–50 °C)
until the starting reagents had dissolved. The solution turned light
brown, and CO2 was evolved. The mixture was allowed to
cool to 25 °C and diluted with 3–4 mL of water (a yellow
solid precipitated). After 72 h, the precipitate was filtered off,
washed with water and cold EtOH, and purified (if appropriate) by
recrystallization from EtOH–acetone.
D. Na2CO3-Catalyzed Reaction of Aldehydes,
Cyanothioacetamide 8, and Phenacyl Thiocyanate 7 (Table ,
Entries 4, 6, 19, and 20)
To a suspension of 0.5 g (5 mmol)
of cyanothioacetamide 8 in 10 mL of EtOH, 5 mmol of the
corresponding aldehyde and one drop of 10% aq Na2CO3 were successively added with stirring. The mixture was stirred
for 0.5 h, and then 0.89 g (5 mmol) of α-thiocyanatoketone 7 and an excess (4 mL) of 10% aq Na2CO3 were added. The mixture was stirred for 0.5 h, diluted with water
(10 mL), and then kept for 0.5 h at 25 °C. The precipitate of
dihydrothiophenes 6a–d was filtered
off and purified (if appropriate) by recrystallization from EtOH–acetone.
E. Synthesis of ADHTs 6a,d from Cyanothioacetamide 8 and α-Bromochalcones 9a,d (Table , Entries 5 and 6)
The mixture of 400 mg (4.0 mmol) of cyanothioacetamide 8, 4.0 mmol of the corresponding α-bromochalcone 9a,d, and EtOH (20 mL) was treated with 2.4 mL (4 mmol) of 10% aq KOH.
The resulting red solution was slowly brought to reflux under vigorous
stirring and kept for 0.5 h. The mixture was cooled; after 24 h, the
precipitate was filtered off, washed with 50% EtOH and ether, and
purified by recrystallization from acetone/n-BuOH
(2:1) to give 6a,d as yellow crystalline solids.
Recrystallization from 1:2 n-BuOH/acetone
gave yellow crystals, mp 207–209 °C. IR (KBr, cm–1) νmax 3412, 3300, 3184 (NH2), 2201 (C≡N),
1670 (C=O).1H NMR (400 MHz, DMSO-d6) δ 4.75 (1H, d, 3J = 3.0 Hz, H-4), 5.21 (1H, d, 3J = 3.0
Hz, H-5), 7.13 (2H, br s, NH2), 7.27–7.32 (1H, m,
H–Ph), 7.37–7.38 (4H, m, H–Ph), 7.49–7.59
(2H, m, H-3, H-5 benzoyl), 7.62–7.66 (1H, m, H-4 benzoyl),
7.90 (2H, d, 3J = 7.5 Hz, H-2 and H-6
benzoyl).13C NMR (126 MHz, DMSO-d6) δ 50.8 (C-4), 56.0 (C-5), 70.9 (C-3), 118.2 (C≡N),
127.3 (C-4 Ph), 127.4 (C-3, C-5 Ph), 128.61 (C-2, C-6 Ph), 128.62
(C-3, C-5 benzoyl), 128.8 (C-2, C-6 benzoyl), 133.6 (C-4 benzoyl),
134.5 (C-1 benzoyl), 141.8 (C-1 Ph), 161.1 (C-2), 193.0 (C=O).
LCMS (m/z, ES-API) 307.5 [M + H]+, 613.3 [2 M + 1]+, 919.3 [3 M + 1]+. Anal. Calcd for C18H14N2OS: C,
70.56; H, 4.61; N, 9.14. Found C, 70.60; H, 4.70; N, 9.08.General
Procedure for the Synthesis of 2,3,4,4a,5,6-Hexahydrothieno[2,3-d]pyrimidine-4a-carbonitriles
(11a–i)The corresponding ADHTs 6a-d (0.6–0.8
mmol) and a primary amine (1.05 equiv, 0.65–0.85 mmol) were
dissolved in EtOH (10–12 mL) (for less soluble ADHTs 6a,b, DMF (2 mL) or DMF–EtOH mixture (2 + 8 mL) is
also useful), and an excess (1.0 mL) of 37% aq HCHO was added to the
resulting solution. The reaction mixture was heated to reflux under
vigorous stirring for 2–3 min (in some cases, a colorless crystalline
solid started to separate). The reaction mixture was allowed to stand
for 24 h at 20 °C, and the crystals were filtered off, washed
with EtOH and hexane, and purified (if appropriate) by recrystallization
to give thieno[2,3-d]pyrimidines 11 as colorless crystals.
Single
crystals of 6-benzoyl-3,5-diphenyl-2,3,4,4a,5,6-hexahydrothieno[2,3-d]pyrimidine-4a-carbonitrile
C26H21N3OS (11l), M = 423.52, were prepared by recrystallization from EtOH/acetone
= 1:1. The crystals are triclinic at 298 K: a = 11.9327(7)
Å, b = 12.7829(6) Å, c = 16.4847(6) Å, α = 79.805(4)°, β = 88.022(4)°,
γ = 62.234(6)°, V = 2186.53(19) Å3, T = 839(2), space group P1 (no. 2), Z = 4, μ(Mo Kα) = 0.171 mm–1, dcalc = 1.29 g/cm3, F(000) = 888, 16,692 reflections measured,
9840 unique (Rint = 0.0200) that were
used in all calculations. The final wR2 was 0.1243 (all data), and R1 was 0.0582
(>2sigma(I)). The unit cell parameters and the
intensities
of 16,692 reflections were measured on an Xcalibur 3 diffractometer
(Mo Kα, graphite monochromator, CCD detector, ω-scanning,
2θmax 57.52°). The structure was solved by the direct method
with the SHELX-97 software package.[141] The
hydrogen atoms were placed geometrically and refined with a riding
model with Uiso = 1.2 Ueq for the
supporting atom. The structure was refined on F2
by the full-matrix least-squares method with an anisotropic approximation
for the nonhydrogen atoms to wR2 0.124 at 9840 reflections
(R1 0.058 at 6619 reflections with F > 4σ(F), S = 1.03). A
full
set of crystallographic data has been deposited in the Cambridge Crystallographic
Data Center (CCDC 1063909).
The mixture of ADHT 6d (151
mg, 0.49 mmol) and p-phenylenediamine (27 mg, 0.25
mmol) was dissolved in hot EtOH (10 mL). Then an excess (0.8 mL) of
37% aq HCHO was added, and the mixture was refluxed for 5 min under
vigorous stirring. The precipitate formed upon cooling was filtered
off after 4 h and triturated with boiling acetone for 2–3 min.
Beige powder, yield 90 mg (48%), mp 164–166 °C. IR (Nujol
mulls, cm–1) νmax 2245 (C≡N), 1685 (C=O), 1650 (C=N).1H NMR (400 MHz, DMSO-d6) δ 3.57
(4H, AB-q, 2J = 11.9 Hz, H-4, H-4′),
4.17 (2H, d, 3J = 10.6 Hz, H-5, H-5′),
4.61 (2H, d, 2J = 17.3 Hz, H-2, H-2′),
5.20 (2H, d, 2J = 17.3 Hz, H-2, H-2′),
6.26 (2H, d, 3J = 10.6 Hz, H-6, H-6′),
6.84 (4H, br s, 1,4-NC6H4N), 7.34–7.39
(6H, m, Ph), 7.56–7.63 (8H, m, Ph), 7.70–7.73 (2H, m,
H-4, H-4′ benzoyl), 8.09 (4H, d, 3J = 7.5 Hz, H-2, H-6, H-2′, H-6′ benzoyl). Due to the
poor solubility, the authors were unable to record 13C
NMR spectra of 12. LCMS (m/z, ES-API) 120.3 [H2C=NC6H4N + H]+, 426.8 [M + 2MeCN + 2H]+2, 451.0 [thienopyrimidine-3-yl-C6H4-N=CH2 + H]+, 768.8
[M + H]+. Anal. Calcd for C46H36N6O2S2: C, 71.85; H, 4.72;
N, 10.93. Found 71.74; H, 4.76; N, 11.00.
Authors: Daniel Collado; Juan Casado; Sandra Rodríguez González; Juan T López Navarrete; Rafael Suau; Ezequiel Perez-Inestrosa; Ted M Pappenfus; M Manuela M Raposo Journal: Chemistry Date: 2010-11-05 Impact factor: 5.236
Authors: Pierre J Meunier; Christian Roux; Ego Seeman; Sergio Ortolani; Janusz E Badurski; Tim D Spector; Jorge Cannata; Adam Balogh; Ernst-Martin Lemmel; Stig Pors-Nielsen; René Rizzoli; Harry K Genant; Jean-Yves Reginster Journal: N Engl J Med Date: 2004-01-29 Impact factor: 91.245
Authors: Regina Wilson; Pradeep Kumar; Vijay Parashar; Catherine Vilchèze; Romain Veyron-Churlet; Joel S Freundlich; S Whitney Barnes; John R Walker; Michael J Szymonifka; Emily Marchiano; Shubhada Shenai; Roberto Colangeli; William R Jacobs; Matthew B Neiditch; Laurent Kremer; David Alland Journal: Nat Chem Biol Date: 2013-06-16 Impact factor: 15.040